% Encoding: UTF-8
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@article{faucris.122342264,
author = {Schleyer, Paul and Kos, Alex and Clark, Timothy and et al.},
author_hint = {SCHLEYER PV, KAUFMANN E, KOS AJ, CLARK T, POPLE JA},
doi = {10.1002/anie.198601691},
faupublication = {yes},
journal = {Angewandte Chemie (International Edition in English)},
pages = {169-170},
peerreviewed = {unknown},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {1,2-{DILITHIOETHYLENE} {ISOMERS} {AND} {THEIR} {MECHANISMS} {OF} {INTERCONVERSION} - {AN} {ABINITIO} {STUDY}},
volume = {25},
year = {1986}
}
@article{faucris.122342704,
author = {Clark, Timothy},
doi = {10.1021/ja00256a042},
faupublication = {yes},
journal = {Journal of the American Chemical Society},
pages = {6838-6840},
peerreviewed = {Yes},
title = {1,3-{HYDROGEN} {SHIFTS} {IN} {OLEFIN} {RADICAL} {CATIONS} - {AN} {ABINITIO} {STUDY}},
volume = {109},
year = {1987}
}
@article{faucris.122343584,
abstract = {The crystal structures of three 1,5-doubly lithium bridged heteroatom-linked diaryl systems with sulfur (4), oxygen (5), and nitrogen (6) as flexible centers have been determined. All are monomers in the crystals. Each lithium bridges both deprotonated ortho carbons symmetrically. The coordination sphere of the metal is completed by the bidentate ligand tetramethylethylenediamine (TMEDA). The pi-system is coplanar in o,o'-bis(lithio.TMEDA)diphenyl thioether (4b), but the rings are tilted markedly in o,o'-bis(lithio.TMEDA)diphenyl ether (5b) and in 1,2'-bis(lithio.TMEDA)-N-phenylcarbazole (6b). The distance between the metalated carbons is responsible for the degree of twisting of the phenyl rings. The structural features of 4b and 6b are reproduced well by MNDO calculations (with ethylenediamine (EDA) (4a-6a) as a model for TMEDA), but less so for the oxygen derivative 5b. MNDO emphasizes the thermodynamic preference for double lithium bridging in o,o'-dilithiated diphenyl systems. The MNDO relative energies of 4a-6a agree well with ab initio results with regard to the stabilization effects of each of the three heteroatoms ortho to a negative charge. Gilman's claim that N-phenylcarbazole gave the o,o'-dilithiated-N-phenyl product could not be confirmed; instead, one of the adjacent sites on the carbazole ring is metalated. The principle of symmetrical doubly lithium bridging has been evaluated computationally (MNDO) for two aromatic systems dilithiated in the 1,4-positions. The symmetrically doubly bridged rotamer of o,o'-bis(lithio.EDA)biphenyl (9a')(with perfectly coplanar pi-systems) is 8.8 kcal/mol more stable than the isomer with perpendicular phenyl rings (9a''). Steric proximity of H8/H8' in doubly bridged 2,2'-bis(lithio-EDA)-1,1'-binaphthyl (10a') prevents coplanarity of the naphthyl moieties. A slight preference (0.7 kcal/mol) for the perpendicular conformation (10a'') results. While the pi-systems are not coplanar in 10a', this is compensated by the tilting of the naphthyl moieties. Thus, the distance between both anionic centers in 10a' is still appropriate for lithium double bridging. X-ray structures of 5b and 6b and the MNDO geometry of 10a emphasize the preference for symmetrical double lithium bridging, even if the pi-systems are twisted.},
author = {Hampel, Frank and Clark, Timothy and Kos, Alex and Schleyer, Paul and et al.},
author_hint = {KRANZ M, DIETRICH H, MAHDI W, MULLER G, HAMPEL F, CLARK T, HACKER R, NEUGEBAUER W, KOS AJ, SCHLEYER PV},
doi = {10.1021/ja00064a034},
faupublication = {yes},
journal = {Journal of the American Chemical Society},
pages = {4698-4704},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {1,5-{DILITHIATED} {ARENES} - {DOUBLE} {METAL} {BRIDGING} {VERIFIED} {BY} 3 {X}-{RAY} {STRUCTURES} {AND} {MNDO} {CALCULATIONS}},
volume = {115},
year = {1993}
}
@article{faucris.122344684,
abstract = {We present the results of a theoretical study and pur forward a novel mechanism for the photodegradation of the polymer poly (2,6-dimethyl-1,4-phenylene oxide) (PPE). The primary step is a 1,5-hydrogen transfer from the methyl group of one ring system to the ipso-carbon of the adjacent monomeric unit. Therefore, in contrast to other proposed mechanisms, the primary step is a result of the three-dimensional structure of PPE rather than a consequence of structural defects in the polymer chain or of impurities.},
author = {Schneider, Siegfried and Gedeck, Peter and Clark, Timothy and et al.},
author_hint = {Schneider S, Gedeck P, Harrer J, Richter F, Clark T},
doi = {10.1016/0009-2614(96)00584-2},
faupublication = {yes},
journal = {Chemical Physics Letters},
pages = {616-621},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {1,5-hydrogen transfer - {A} hitherto ignored decay channel in the photodegradation of poly(2,6-dimethyl-1,4-phenylene oxide)},
volume = {257},
year = {1996}
}
@article{faucris.206094581,
abstract = {The syntheses of five 1D coordination polymers containing the sawhorse-type unit [Ru-2(mu-OAc)(2)(CO)(4)] linked by various bridging N,N-donor ligands are reported. Various pi-conjugated linkers, such as trans-[1,2-bis(N-methyl)imidazol-2-yl]ethylene (trans-bie), pyrazine (pyz), 4,4-bipyridine (4,4-bipy) and 1,2-bis(4-pyridyl)ethylene (bpe) as well as the aliphatic linker 1,4-diazabicyclo[2.2.2]octane (DABCO), were applied in the syntheses. The formation of 1D coordination polymers was proven by crystal structure determinations of two of the polymeric materials. The geometries and electronic structures of all polymers were analysed further by CASSCF/CASPT2 and DFT calculations based on monomeric model compounds. Finally, first attempts regarding deposition of the 1D chain, the sawhorse fragment and/or the ligands on a highly ordered pyrolytic graphite surface, analysed by STM measurements, are also reported.},
author = {Fritsch, Nico and Wick, Christian and Waidmann, Thomas and Pflock, Stephan and Dral, Pavlo and Tucher, Johannes and Steiner, Christian and Shubina, Tatyana and Maier, Sabine and Clark, Timothy and Burzlaff, Nicolai},
doi = {10.1002/ejic.201701246},
faupublication = {yes},
journal = {European Journal of Inorganic Chemistry},
keywords = {Coordination polymers;Chain structures;Bridging ligands;N ligands;Ruthenium},
month = {Jan},
pages = {54-61},
peerreviewed = {Yes},
title = {{1D} {Chains} of {Diruthenium} {Tetracarbonyl} {Sawhorse} {Complexes}},
year = {2018}
}
@article{faucris.121589424,
abstract = {Ab initio (CCSD(T)/6-31+G*) calculations suggest that 1H-phosphiranes and 1H-phosphirenes invert their configuration at phosphorus by a rotation of the PX group (X = H, F, Cl, Br) above the C-2 moiety, rather than the more usual planar trigonal inversion pathway via a C-2v transition state.},
author = {Göller, Andreas H. and Clark, Timothy},
doi = {10.1039/a701788j},
faupublication = {yes},
journal = {Chemical Communications},
pages = {1033-1034},
peerreviewed = {Yes},
title = {{1H}-phosphiranes and -enes invert at phosphorus via a turnstile rotation},
year = {1997}
}
@article{faucris.122333024,
abstract = {A new method of comparison of protein sequences has been formulated. The sequence of amino acids is represented by a set of point masses in a 20D space. The distribution of points in the space is obtained by applying the method of a walk in the 20D space. Projections of the 20D representation into 2D or 3D spaces illustrate the distribution of particular amino acids along the sequence. 20D moments of inertia are proposed as new descriptors of protein sequences. (C) 2015 Elsevier Inc. All rights reserved.},
author = {Czerniecka, Agata and Bielinska-Waz, Dorota and Waz, Piotr and Clark, Timothy},
doi = {10.1016/j.ygeno.2015.12.003},
faupublication = {yes},
journal = {Genomics},
keywords = {Similarity/dissimilarity analysis of protein sequences;Descriptors;Alignment-free methods;Moments of inertia},
month = {Jan},
pages = {16-23},
peerreviewed = {Yes},
title = {{20D}-dynamic representation of protein sequences},
volume = {107},
year = {2016}
}
@article{faucris.213293312,
abstract = {The electronic coupling as well as the attenuation factor (\textgreekb), which depends primarily on the nature of the molecular bridge and is used as a benchmark to test the molecular wire behavior, have been determined in a systematic study carried out on a series of ZnP/C60 conjugates connected through a [2,2$\prime$]paracyclophane$-$oligophenylenevinylene (pCp-oPPV). The convergent synthesis involves a series of Horner$-$Emmons olefination reactions or double palladium-catalized Heck-type reactions. ZnP$-$pCp$-$C60 conjugates were finally obtained by the 1,3-dipolar cycloaddition reaction of the in situ-generated azomethyne ylide containing the ZnP$-$pCp moiety to the [60]fullerene using Prato conditions. Experimental (UV$-$vis, fluorescence, transient absorption spectroscopy, and solution electrochemistry) and theoretical studies revealed that the pCps act as molecular junctions. If hole transfer is assumed to be the dominant charge transfer (CT) mechanism, CT is facilitated in one direction (from C60 to ZnP via pCp) but disfavored in the other direction (from ZnP to C60 via pCp).},
author = {Molina-Ontoria, Agustin and Wielopolski, Mateusz and Gebhardt, Julian and Gouloumis, Andreas and Clark, Timothy and Guldi, Dirk Michael and Martin, Nazario},
doi = {10.1021/ja109745a},
faupublication = {yes},
journal = {Journal of the American Chemical Society},
note = {EAM Import::2019-03-13},
pages = {2370-2373},
peerreviewed = {Yes},
title = {[2,2]{Paracyclophane}-{Based} π-{Conjugated} {Molecular} {Wires} {Reveal} {Molecular}-{Junction} {Behavior}},
volume = {133},
year = {2011}
}
@article{faucris.122347104,
abstract = {A new 'dynamic' 2D-graphical representation of DNA sequences is presented. The model is based on 2D-plots that have been used before and are easy to visualize, but it removes many degeneracies present in the previous approaches. The moments of inertia of the 'dynamic' graphs are proposed as a new kind of descriptor for DNA sequences. (C) 2007 Elsevier B.V. All rights reserved.},
author = {Clark, Timothy and et al.},
author_hint = {Bielinska-Waz D, Clark T, Waz P, Nowak W, Nandy A},
doi = {10.1016/j.cplett.2007.05.050},
faupublication = {yes},
journal = {Chemical Physics Letters},
pages = {140-144},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{2D}-dynamic representation of {DNA} sequences},
volume = {442},
year = {2007}
}
@article{faucris.109338504,
author = {Beck, Bernd and Clark, Timothy and Horn, Anselm and et al.},
author_hint = {Beck B, Clark T, Horn A, Carpenter J},
faupublication = {yes},
journal = {ACS National Meeting Book of Abstracts},
pages = {U701-U701},
peerreviewed = {unknown},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{3D} information-rich databases derived from quantum mechanical calculations},
volume = {217},
year = {1999}
}
@article{faucris.122349744,
abstract = {Current 3D-QSAR methods such as CoMFA or CoMSIA make use of classical force-field approaches for calculating molecular fields. Thus, they can not adequately account for noncovalent interactions involving halogen atoms like halogen bonds or halogen-pi interactions. These deficiencies in the underlying force fields result from the lack of treatment of the anisotropy of the electron density distribution of those atoms, known as the "sigma-hole", although recent developments have begun to take specific interactions such as halogen bonding into account. We have now replaced classical force field derived molecular fields by local properties such as the local ionization energy, local electron affinity, or local polarizability, calculated using quantum-mechanical (QM) techniques that do not suffer from the above limitation for 3D-QSAR We first investigate the characteristics of QM-based local property fields to show that they are suitable for statistical analyses after suitable pretreatment. We then analyze these property fields with partial least-squares (PLS) regression to predict biological affinities of two data sets comprising factor Xa and GABA-A/benzodiazepine receptor ligands. While the resulting models perform equally well or even slightly better in terms of consistency and predictivity than the classical CoMFA fields, the most important aspect of these augmented field-types is that the chemical interpretation of resulting QM-based property field models reveals unique SAR trends driven by electrostatic and polarizability effects, which cannot be extracted directly from CoMFA electrostatic maps. Within the factor Xa set, the interaction of chlorine and bromine atoms with a tyrosine side chain in the protease Si pocket are correctly predicted. Within the GABA-A/benzodiazepine ligand data set, PLS models of high predictivity resulted for our QM-based property fields, providing novel insights into key features of the SAR for two receptor subtypes and cross-receptor selectivity of the ligands. The detailed interpretation of regression models derived using improved QM-derived property fields thus provides a significant advantage by revealing chemically meaningful correlations with biological activity and helps in understanding novel structure-activity relationship features. This will allow such knowledge to be used to design novel molecules on the basis of interactions additional to steric and hydrogen-bonding features.},
author = {Güssregen, Stefan and Matter, Hans and Hessler, Gerhard and Müller, Marco and Schmidt, Friedemann and Clark, Timothy},
doi = {10.1021/ci300253z},
faupublication = {yes},
journal = {Journal of Chemical Information and Modeling},
pages = {2441-2453},
peerreviewed = {Yes},
title = {{3D}-{QSAR} {Based} on {Quantum}-{Chemical} {Molecular} {Fields}: {Toward} an {Improved} {Description} of {Halogen} {Interactions}},
volume = {52},
year = {2012}
}
@article{faucris.122350624,
author = {Hennemann, Matthias and Clark, Timothy and Lanig, Harald},
faupublication = {yes},
journal = {ACS National Meeting Book of Abstracts},
pages = {U682-U683},
peerreviewed = {unknown},
title = {{3D}-{QSAR} {OF} {D4}-antagonists based on full conformational searches and quantum mechanically derived descriptors},
volume = {217},
year = {1999}
}
@article{faucris.121611204,
author = {Clark, Timothy},
doi = {10.1002/jcc.540020307},
faupublication = {yes},
journal = {Journal of Computational Chemistry},
month = {Jan},
pages = {261-265},
peerreviewed = {Yes},
title = {3 {ELECTRON} {BONDS} .1. {THE} {H2SSH2}+ {RADICAL} {CATION}},
volume = {2},
year = {1981}
}
@article{faucris.116496864,
author = {Clark, Timothy},
doi = {10.1002/jcc.540030116},
faupublication = {yes},
journal = {Journal of Computational Chemistry},
month = {Jan},
pages = {112-116},
peerreviewed = {Yes},
title = {3-{ELECTRON} {BONDS} .2. {SS} {AND} {SCL} 3-{ELECTRON} {BONDS}},
volume = {3},
year = {1982}
}
@article{faucris.116864264,
author = {Clark, Timothy},
doi = {10.1002/jcc.540040316},
faupublication = {yes},
journal = {Journal of Computational Chemistry},
month = {Jan},
pages = {404-409},
peerreviewed = {Yes},
title = {3-{ELECTRON} {BONDS} .3. {PHOSPHORUS} {AND} {CHLORINE} {SIGMA}-{STAR} {RADICAL} {CATIONS}},
volume = {4},
year = {1983}
}
@article{faucris.121177584,
author = {Clark, Timothy and et al.},
author_hint = {NELSEN SF, CUNKLE GT, EVANS DH, HALLER KJ, KAFTORY M, KIRSTE B, KURRECK H, CLARK T},
doi = {10.1021/ja00299a013},
faupublication = {yes},
journal = {Journal of the American Chemical Society},
month = {Jan},
pages = {3829-3839},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {8,8'-{BI}(8-{AZABICYCLO}[3.2.1]{OCTANE}) {AND} {ITS} {OXIDIZED} {FORMS}},
volume = {107},
year = {1985}
}
@book{faucris.122351504,
abstract = {The use of ab initio molecular orbital theory to treat electron-transfer catalysis by metal ions and closely related subjects is described. The theoretical principles involved in ''hole-catalysis'' (acceleration of a reaction by one-electron oxidation) are first examined using the norbornadiene/quadricyclane radical cation rearrangement as an example. The theoretical techniques necessary to obtain reliable results for radical and radical ion systems are also discussed. Examples of calculational studies on hole-catalyzed cycloadditions, sigmatropic rearrangements and electrocyclic reactions are given. The basic principles governing the energetics of electron-transfer between metal ions and organic substrates are described. Finally, calculational examples of electron-transfer catalysis by metal ions are treated. The examples include 1,3-hydrogen shifts, cyclopropane ring-opening, ethylene dimerization, C-C bond activation, and cycloalkane and oxirane ring-opening.},
address = {Heidelberg},
author = {Clark, Timothy},
doi = {10.1007/3-540-60110-4{\_}1},
editor = {J. Mattay},
faupublication = {yes},
month = {Jan},
pages = {1-24},
peerreviewed = {unknown},
publisher = {Springer Verlag Kg},
series = {Topics in Current Chemistry, Vol. 77 Electron Transfer II},
title = {{Ab} initio calculations on electron-transfer catalysis by metal ions},
volume = {177},
year = {1996}
}
@article{faucris.122351944,
author = {Clark, Timothy and et al.},
author_hint = {CLARK T, ILLING G},
doi = {10.1021/ja00238a006},
faupublication = {yes},
journal = {Journal of the American Chemical Society},
pages = {1013-1020},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{ABINITIO} {LOCALIZED} {ELECTRON} {CALCULATIONS} {ON} {SOLVATED} {ELECTRON} {STRUCTURES}},
volume = {109},
year = {1987}
}
@article{faucris.122352384,
abstract = {The one-electron reduction of ethylene by alkali-metal atoms (Li, Na, K, Rb) has been investigated using ab initio molecular orbital theory. The gas-phase behavior of the metals is dominated by the electrostatic ion-pair energy in the M+:C2H4.- products. Lithium the smallest of the alkali metals, therefore gives the least endothermic reaction energy (M. + C2H4 --> M+:C2H4.-) in the gas phase. Self-consistent reaction field (SCRF) theory has been used to investigate the effect of solvent on the electron transfer reactions. The solvent effect is small for M = Li, but larger for the heavier metals, so that rubidium becomes comparable to lithium in polar solvents. The activation energy for the electron transfer reaction itself has been estimated for lithium using a linear synchronous transit between the reactant and product geometries.},
author = {Hänsele, Elke and Clark, Timothy},
doi = {10.1524/zpch.1991.171.Part{\_}1.021},
faupublication = {yes},
journal = {Zeitschrift für Physikalische Chemie-International Journal of Research in Physical Chemistry & Chemical Physics},
keywords = {ELECTRON TRANSFER;ABINITIO MO THEORY;SCRF THEORY;ALKALI METAL REDUCTION},
month = {Jan},
pages = {21-31},
peerreviewed = {Yes},
title = {{ABINITIO} {SIMULATION} {OF} {ELECTRON}-{TRANSFER} {REACTIONS} - {THE} {REACTION} {OF} {ALKALI}-{METAL} {ATOMS} {WITH} {ETHYLENE}},
volume = {171},
year = {1991}
}
@article{faucris.122698884,
author = {Clark, Timothy and Jemmis, Eluvathingal D. and Schleyer, Paul and et al.},
author_hint = {CLARK T, JEMMIS ED, SCHLEYER PV, BINKLEY JS, POPLE JA},
doi = {10.1016/S0022-328X(00)85542-4},
faupublication = {yes},
journal = {Journal of Organometallic Chemistry},
month = {Jan},
pages = {1-6},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{ABINITIO} {STRUCTURES} {OF} {ALLYL}-{LITHIUM}},
volume = {150},
year = {1978}
}
@article{faucris.115071924,
abstract = {The thrust of this work is to integrate small and uniformly sized carbon nanodots (CNDs) with single-walled carbon nanotubes (SWCNT) of different diameters as electron donors and electron acceptors, respectively, and to test their synergetic interactions in terms of optoelectronic devices. CNDs (denoted pCNDs, where p indicates pressure) were prepared by pressure-controlled microwave decomposition of citric acid and urea. pCNDs were immobilized on single-walled carbon nanotubes by wrapping the latter with poly(4-vinylbenzyl trimethylamine) (PVBTA), which features positively charged ammonium groups in the backbone. Negatively charged surface groups on the CNDs lead to attractive electrostatic interactions. Ground state interactions between the CNDs and SWCNTs were confirmed by a full-fledged photophysical investigation based on steady-state and time-resolved techniques. As a complement, charge injection into the SWCNTs upon photoexcitation was investigated by ultra-short time-resolved spectroscopy.},
author = {Strauß, Volker and Margraf, Johannes and Clark, Timothy and Guldi, Dirk Michael},
doi = {10.1039/c5sc02728d},
faupublication = {yes},
journal = {Chemical Science},
month = {Jan},
pages = {6878-6885},
peerreviewed = {Yes},
title = {{A} carbon-carbon hybrid - immobilizing carbon nanodots onto carbon nanotubes},
volume = {6},
year = {2015}
}
@article{faucris.122353924,
author = {Hänsele, Elke and Clark, Timothy and et al.},
author_hint = {HOFMANN H, HANSELE E, CLARK T},
doi = {10.1002/jcc.540111005},
faupublication = {yes},
journal = {Journal of Computational Chemistry},
pages = {1147-1150},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{A} {CAUTIONARY} {NOTE} {ON} {THE} {USE} {OF} {THE} {FROZEN}-{CORE} {APPROXIMATION} {FOR} {CORRELATION}-{ENERGY} {CALCULATIONS} {INVOLVING} {ALKALI}-{METALS}},
volume = {11},
year = {1990}
}
@article{faucris.208728632,
abstract = {The self-assembly of molecular building blocks is a promising route to low-cost nanoelectronic devices. It would be very appealing to use computer-aided design to identify suitable molecules. However, molecular self-assembly is guided by weak interactions, such as dispersion, which have long been notoriously difficult to describe with quantum chemical methods. In recent years, several viable techniques have emerged, ranging from empirical dispersion corrections for DFT to fast perturbation and coupled-cluster theories. In this work, we test these methods for the dimer of the prototypical building block for nanoelectronics, C-60-fullerene. Benchmark quality data is obtained from DFT-based symmetry adapted perturbation theory (SAPT), the adiabatic-connection fluctuation dissipation (ACFD) theorem using an adiabatic LDA kernel, and domain-based local pair natural orbital (DLPNO) coupled-pair and coupled-cluster methods. These benchmarks are used to evaluate economical dispersion-corrected DFT methods, double-hybrid DFT functionals, and second-order Moller-Plesset theory. Furthermore, we provide analytical fits to the benchmark interaction curves, which can be used for a coarse-grain description of fullerene self-assembly. These analytical expressions differ significantly from those reported previously based on bulk data.},
author = {Sharapa, Dmitry and Margraf, Johannes T. and Heßelmann, Andreas and Clark, Timothy},
doi = {10.1021/acs.jctc.6b00869},
faupublication = {yes},
journal = {Journal of Chemical Theory and Computation},
month = {Jan},
pages = {274-285},
peerreviewed = {Yes},
title = {{Accurate} {Intermolecular} {Potential} for the {C}-60 {Dimer}: {The} {Performance} of {Different} {Levels} of {Quantum} {Theory}},
volume = {13},
year = {2017}
}
@article{faucris.122354364,
abstract = {The variational method for the calculation of the electronic polarizability of molecules within the NDDO-based semiempirical MO methods MNDO, AM1, and PM3 was parametrized to improve its accuracy. A training set of 156 compounds was used to fit 34 parameters simultaneously for 12 elements using a simplex optimization. The resulting parameters were tested for a test set of 83 molecules and the calculated polarizabilities compared with the experimental data. For AM1, the RMS deviation between experimental and calculated polarizabilities was reduced from 2.99 (using the original variational treatment) to 0.70 Angstrom(3) for the test set and from 2.81 to 0.40 Angstrom(3) for the training set. MNDO and PM3 gave similar improvements. (C) 1999 John Wiley & Sons, Inc. Int J Quant Chem 75: 17-31, 1999.},
author = {Schürer, Gudrun and Gedeck, Peter and Gottschalk, Maik and Clark, Timothy},
doi = {10.1002/(SICI)1097-461X(1999)75:1<17::AID-QUA3>3.3.CO;2-I},
faupublication = {yes},
journal = {International Journal of Quantum Chemistry},
keywords = {polarizability;MNDO;AM1;PM3;NDDO},
pages = {17-31},
peerreviewed = {Yes},
title = {{Accurate} parametrized variational calculations of the molecular electronic polarizability by {NDDO}-based methods},
volume = {75},
year = {1999}
}
@article{faucris.240047598,
abstract = {We report on a combined activation mechanism for a class B G-protein-coupled receptor (GPCR), the glucagon receptor. By computing the conformational free-energy landscape associated with the activation of the receptor-agonist complex and comparing it with that obtained with the ternary complex (receptor-agonist-G protein) we show that the agonist stabilizes the receptor in a preactivated complex, which is then fully activated upon binding of the G protein. The proposed mechanism contrasts with the generally assumed GPCR activation mechanism, which proceeds through an opening of the intracellular region allosterically elicited by the binding of the agonist. The mechanism found here is consistent with electron cryo-microscopy structural data and might be general for class B GPCRs. It also helps us to understand the mode of action of the numerous allosteric antagonists of this important drug target.},
author = {Mattedi, Giulio and Acosta-Gutiérrez, Silvia and Clark, Timothy and Gervasio, Francesco Luigi},
doi = {10.1073/pnas.1921851117},
faupublication = {yes},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
keywords = {activation; enhanced sampling; glucagon receptor; GPCR},
note = {CRIS-Team Scopus Importer:2020-07-03},
peerreviewed = {Yes},
title = {{A} combined activation mechanism for the glucagon receptor},
year = {2020}
}
@article{faucris.122355244,
abstract = {A back-propagation artificial neural net has been trained to estimate C-13 chemical shifts from the results of AM1 and PM3 semiempirical MO calculations. The input descriptors include the atom-centered monopole, dipole and quadrupole moments derived from the natural atomic orbital/point charge (NAO/PC) model, the four highest bond orders to the carbon atom being considered and the elements to which these bonds are made. The resulting net estimates the chemical shifts of a test set of 156 chemical shifts with a standard deviation of less than 7 ppm from the experimental values for AMI and slightly more for PM3.},
author = {Clark, Timothy and Rauhut, Guntram and Breindl, Andreas},
doi = {10.1007/s008940050004},
faupublication = {yes},
journal = {Journal of Molecular Modeling},
keywords = {C-13 chemical shift;semiempirical MO;AM1;PM3;neural Net},
month = {Jan},
pages = {22-35},
peerreviewed = {Yes},
title = {{A} combined semiempirical {MO} neural net technique for estimating {C}-13 chemical shifts},
volume = {1},
year = {1995}
}
@article{faucris.122322904,
abstract = {hERG blockade is one of the major toxicological problems in lead structure optimization. Reliable ligand-based in silica models for predicting hERG blockade therefore have considerable potential for saving time and money, as patch-clamp measurements are very expensive and no crystal structures of the hERG-encoded channel are available. Herein we present a predictive QSAR model for hERG blockade that differentiates between specific and nonspecific binding. Specific binders are identified by preliminary pharmacophore scanning. In addition to descriptor-based models for the compounds selected as hitting one of two different pharmocophores, we also use a model for nonspecific binding that reproduces blocking properties of molecules that do not fit either of the two pharmacophores. PLS and SVR models based on interpretable quantum mechanically derived descriptors on a literature dataset of 773 molecules reach overall R-2 values between 0.60 and 0.70 for independent validation sets and R-2 values between 0.39 and 0.76 after partitioning according to the pharmacophore search for the test sets. Our findings suggest that hERG blockade may occur through different types of binding, so that several different models may be necessary to assess hERG toxicity.},
author = {Kramer, Christian and Beck, Bernd and Kriegl, Jan M. and Clark, Timothy},
doi = {10.1002/cmdc.200700221},
faupublication = {yes},
journal = {ChemMedChem},
keywords = {hERG;ion channels;semi-empirical calculations;structure-activity relationships;toxicology},
pages = {254-265},
peerreviewed = {Yes},
title = {{A} composite model for {hERG} blockade},
volume = {3},
year = {2008}
}
@article{faucris.121594924,
abstract = {Herein, we describe a new dataset of kinetic aqueous solubilities determined by nephelometry for 711 druglike compounds. The solubilities are reported in twelve classes ranging from < 2 mu g mL(-1) to > 250 mu g mL(-1). The measurements were designed to provide the appropriate data for applications in the early phases of drug discovery. Three class classification models (insoluble, moderately soluble, soluble) were built using the random forest algorithm and their performance for this dataset was analyzed.},
author = {Kramer, Christian and Heinisch, Tilmann and Fligge, Thilo and Beck, Bernd and Clark, Timothy},
doi = {10.1002/cmdc.200900205},
faupublication = {yes},
journal = {ChemMedChem},
keywords = {chemoinformatics;datasets;drug discovery;nephelometry;solubility},
pages = {1529-1536},
peerreviewed = {Yes},
title = {{A} {Consistent} {Dataset} of {Kinetic} {Solubilities} for {Early}-{Phase} {Drug} {Discovery}},
volume = {4},
year = {2009}
}
@article{faucris.313778180,
abstract = {We use enhanced-sampling simulations with an effective collective variable to study the activation of the β2-adrenergic receptor in the presence of ligands with different efficacy. The free-energy profiles are computed for the ligand-free (apo) receptor and binary (apo-receptor + G-protein α-subunit and receptor + ligand) and ternary complexes. The results are not only compatible with available experiments but also allow unprecedented structural insight into the nature of GPCR conformations along the activation pathway and their role in the activation mechanism. In particular, the simulations reveal an unexpected mode of action of partial agonists such as salmeterol and salbutamol that arises already in the binary complex without the G-protein. Specific differences in the polar interactions with residues in TM5, which are required to stabilize an optimal TM6 conformation that facilitates G-protein binding and receptor activation, play a major role in differentiating them from full agonists.},
author = {Calderón Reyes, Jacqueline and Ibrahim, Passainte and Gobbo, Dorothea and Gervasio, Francesco Luigi and Clark, Timothy},
doi = {10.1021/acs.jcim.3c00805},
faupublication = {yes},
journal = {Journal of Chemical Information and Modeling},
note = {CRIS-Team Scopus Importer:2023-11-10},
pages = {6332-6343},
peerreviewed = {Yes},
title = {{Activation}/{Deactivation} {Free}-{Energy} {Profiles} for the β2-{Adrenergic} {Receptor}: {Ligand} {Modes} of {Action}},
volume = {63},
year = {2023}
}
@article{faucris.117829844,
abstract = {Partial agonists exhibit a submaximal capacity to enhance the coupling of one receptor to an intracellular binding partner. Although a multitude of studies have reported different ligand-specific conformations for a given receptor, little is known about the mechanism by which different receptor conformations are connected to the capacity to activate the coupling to G-proteins. We have now performed molecular-dynamics simulations employing our recently described active-state homology model of the dopamine D2 receptor-Gαi protein-complex coupled to the partial agonists aripiprazole and FAUC350, in order to understand the structural determinants of partial agonism better. We have compared our findings with our model of the D2R-Gαi-complex in the presence of the full agonist dopamine. The two partial agonists are capable of inducing different conformations of important structural motifs, including the extracellular loop regions, the binding pocket and, in particular, intracellular G-protein-binding domains. As G-protein-coupling to certain intracellular epitopes of the receptor is considered the key step of allosterically triggered nucleotide-exchange, it is tempting to assume that impaired coupling between the receptor and the G-protein caused by distinct ligand-specific conformations is a major determinant of partial agonist efficacy. © 2014 Kling et al.},
author = {Kling, Ralf and Tschammer, Nuska and Lanig, Harald and Clark, Timothy and Gmeiner, Peter},
doi = {10.1371/journal.pone.0100069},
faupublication = {yes},
journal = {PLoS ONE},
note = {UnivIS-Import:2015-03-09:Pub.2014.nat.dchph.lphch.active},
peerreviewed = {Yes},
title = {{Active}-{State} {Model} of a {Dopamine} {D2} {Receptor} - {Gαi} {Complex} {Stabilized} by {Aripiprazole}-{Type} {Partial} {Agonists}},
url = {http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0100069},
volume = {9},
year = {2014}
}
@article{faucris.114142424,
abstract = {Based on the recently described crystal structure of the β adrenergic receptor - G-protein complex, we report the first molecular-dynamics simulations of ternary GPCR complexes designed to identify the selectivity determinants for receptor-G-protein binding. Long-term molecular dynamics simulations of agonist-bound β2AR-Gα and D2R-Gα complexes embedded in a hydrated bilayer environment and computational alanine-scanning mutagenesis identified distinct residues of the N-terminal region of intracellular loop 3 to be crucial for coupling selectivity. Within the G-protein, specific amino acids of the α5-helix, the C-terminus of the Gα-subunit and the regions around αN-β1 and α4-β6 were found to determine receptor recognition. Knowledge of these determinants of receptor-G-protein binding selectivity is essential for designing drugs that target specific receptor/G-protein combinations. © 2013 Kling et al.},
author = {Kling, Ralf and Lanig, Harald and Clark, Timothy and Gmeiner, Peter},
doi = {10.1371/journal.pone.0067244},
faupublication = {yes},
journal = {PLoS ONE},
peerreviewed = {Yes},
title = {{Active}-{State} {Models} of {Ternary} {GPCR} {Complexes}: {Determinants} of {Selective} {Receptor}-{G}-{Protein} {Coupling}},
volume = {8},
year = {2013}
}
@article{faucris.122355684,
abstract = {A method for the calculation of atomic polarizabilities based on the variational method for the calculation of the electronic polarizability in terms of the neglect of differential diatomic overlap (NDDO) approximation is presented. The resulting atomic polarizability tensors are additive. Calculation of an extended test set of 294 molecules gave an root-mean-square (rms) deviation between calculated and experimental mean polarizabilities of 0.68 Angstrom(3) (AM1). Comparison with the empirical atomic hybrid polarizability (AHP) parameters as defined by Miller gave good agreement. (C) 2000 John Wiley & Sons, Inc.},
author = {Martin, Bodo and Gedeck, Peter and Clark, Timothy},
doi = {10.1002/(SICI)1097-461X(2000)77:1<473::AID-QUA47>3.0.CO;2-4},
faupublication = {yes},
journal = {International Journal of Quantum Chemistry},
keywords = {atomic polarizability;group polarizability;AM1;MNDO;PM3},
pages = {473-497},
peerreviewed = {Yes},
title = {{Additive} {NDDO}-based atomic polarizability model},
volume = {77},
year = {2000}
}
@article{faucris.119328264,
abstract = {VESPA, an improved semiempirical method for the calculation of electrostatic potential-derived atomic charges has been tested. It is shown that this approach is even less dependent upon molecular orientation than ''high density'' CHELPG ab initio ESP-derived charges. The conformational dependence of VESPA charges has been investigated for rotation around the C-N bond in formamide and 11 different conformers of glycerolphosphorylcholine. The results obtained are compared to the corresponding ab initio values. Finally, VESPA is used to calculate electrostatic potential-derived charges for bioorganic molecules. We discuss the abilities and the limitations of ESP charges in this area.},
author = {Beck, Bernd and Clark, Timothy and Glen, Robert},
doi = {10.1007/s008940050014},
faupublication = {yes},
journal = {Journal of Molecular Modeling},
keywords = {computational chemistry;potential-derived charges;orientational and conformational dependence},
month = {Jan},
pages = {176-187},
peerreviewed = {Yes},
title = {{A} detailed study of {VESPA} electrostatic potential-derived atomic charges},
volume = {1},
year = {1995}
}
@article{faucris.116866024,
abstract = {The aminopeptidase of Aeromonas proteolytica (AAP) belongs to the group of metallo-hydrolases that require two divalent cations for full activity. Such binuclear metal centers are found in several aminopeptidases, raising the question whether a common mechanism, at least partly, is likely. We have used a quantum mechanical/molecular mechanical (QM/MM) approach to investigate the reaction mechanism of AAP. Among several possibilities, one reaction path was found to be clearly the most favorable. Beside the chemical transformation steps, effects of the enzyme environment and the influence of the solvent on the catalytic reaction were included in the study. The results are in good agreement with experimental studies and correspond to a high degree to our previous QM/MM calculations on the reaction mechanism of the related binuclear bovine lens leucine aminopeptidase (blLAP), which, although related to the AAP, has different Zn2+-coordination spheres and a different catalytic residue. The mechanisms of the two enzymes as suggested in the literature differ on the mode of coordination of the nucleophile and the identity of the general base. However, the results of this and our previous work on blLAP allow us to identify a common mechanism for the two enzymes. This mechanism is probably quite general for binuclear zinc enzymes.},
author = {Schürer, Gudrun and Lanig, Harald and Clark, Timothy},
doi = {10.1021/bi0340191},
faupublication = {yes},
journal = {Biochemistry},
pages = {5414-5427},
peerreviewed = {Yes},
title = {{Aeromonas} proteolytica aminopeptidase: {An} investigation of the mode of action using a quantum mechanical/molecular mechanical approach},
volume = {43},
year = {2004}
}
@article{faucris.208726162,
abstract = {A dispersion correction is introduced and tested for MNDO. The shift in electron density caused by the interaction between oscillating dipoles in the London picture of dispersion is mimicked by adding a small r(-7)-dependent attractive nucleus-electron potential to the core Hamiltonian. This potential results in a shift in electron density similar to that used by Feynman to explain dispersion. The resulting parameterized self-consistent and inherently multicenter treatment (MNDO-F) gives good results for CHNO compounds that do not exhibit hydrogen bonds, which MNDO cannot reproduce. This Feynman dispersion correction is also applicable to Hartree-Fock and density functional theory.},
author = {Kriebel, Maximilian and Weber, Konstantin and Clark, Timothy},
doi = {10.1007/s00894-018-3874-6},
faupublication = {yes},
journal = {Journal of Molecular Modeling},
keywords = {Dispersion correction;MNDO;Feynman dispersion;MNDO-F},
peerreviewed = {Yes},
title = {{A} {Feynman} dispersion correction: a proof of principle for {MNDO}},
volume = {24},
year = {2018}
}
@article{faucris.208735205,
abstract = {Prolyl hydroxylation domain enzymes (PHD) catalyze the hydroxylation of the transcription factor Hypoxia Inducible Factor (HIF) and serve as cellular oxygen sensors. HIF and the PHD enzymes regulate numerous potentially tissue protective target genes which can adapt cells to metabolic and ischemic stress. We describe a fluorescent PHD inhibitor (1-chloro-4-hydroxybenzo[g]isoquinoline-3-carbonyl)-glycine which is suited to fluorescent based detection assays and for monitoring PHD inhibitors in biological systems. In cell based assays, application of the fluorescent PHD inhibitor allowed co-localization with a cellular PHD enzyme and led to live cell imaging of processes involved in cellular oxygen sensing.},
author = {Mayer, Marleen and Fey, Kerstin and Heinze, Eva and Wick, Christian and Abboud, Martine I. and Yeh, Tzu Lan and Tumber, Anthony and Orth, Nicole and Schley, Gunnar and Buchholz, Björn and Clark, Timothy and Schofield, Christopher J. and Willam, Carsten and Burzlaff, Nicolai},
doi = {10.1002/cmdc.201800483},
faupublication = {yes},
journal = {ChemMedChem},
keywords = {fluorescence microscopy;HIF system;hypoxia;oxygen sensing;PHD inhibitors},
pages = {94-99},
peerreviewed = {Yes},
title = {{A} {Fluorescent} {Benzo}[g]isoquinoline-based {HIF} {Prolyl} {Hydroxylase} {Inhibitor} for {Cellular} {Imaging}.},
volume = {14},
year = {2018}
}
@article{faucris.121015444,
abstract = {Degenerate 1,3-BR2-shifts in allylboranes (R = alkyl) are shown by ab initio molecular orbital theory to proceed through a nonplanar transition structure with C(s) symmetry. The MP2/6-31G*//6-31G* + ZPE barrier of 9.2 kcal/mol for dimethylallylborane agrees with experimental values. However, the corresponding bridged structure (2) is the most stable form of the parent allylborane, CH2=CHCH2BH2 at MP2/6-31G*//MP2/6-31G* + ZPE. The unsymmetrical open conformation (1), which prefers C1 symmetry, is only 0.1 kcal/mol higher in energy. Other structures on the C3BH7 potential energy surface are also comparable in energy. Like the isoelectronic cyclobutyl cation (bicyclobutonium ion), the four-membered boron heterocycle boretane (3a) prefers a nonplanar structure (C(s) symmetry). Another small ring isomer, cyclopropylborane with a bisected geometry, 4a, is only 1.2 kcal/mol higher in energy than 1. The calculated (IGLO) chemical shifts of the isomers are discussed. The boron nucleus in the symmetrically bridged allylborane 2 is calculated to be strongly shielded (-49 ppm), whereas borons incorporated in small ring systems are predicted to be deshielded (e.g, 93 ppm for 5 and 97 ppm for planar 3b). The rotation barriers in vinylborane and dimethylvinylborane are 6.9 and 4.0 kcal/mol, respectively.},
author = {Schleyer, Paul and Clark, Timothy and et al.},
author_hint = {BUHL M, SCHLEYER PV, IBRAHIM MA, CLARK T},
doi = {10.1021/ja00007a018},
faupublication = {yes},
journal = {Journal of the American Chemical Society},
pages = {2466-2471},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{ALLYLBORANE} {AND} {ITS} {ISOMERS} - {AN} {ABINITIO} {STUDY} {OF} {THE} {C3BH7} {POTENTIAL}-{ENERGY} {SURFACE}, {THE} {BARRIER} {TO} 1,3-{SHIFTS} {IN} {ALLYLBORANES}, {AND} {NONCLASSICAL} {BORACYCLOBUTANE}, {CYCLOPROPYLBORANE}, {AND} {VINYLBORANE} {STRUCTURES}},
volume = {113},
year = {1991}
}
@article{faucris.122358764,
author = {Clark, Timothy and Schleyer, Paul and et al.},
author_hint = {CLARK T, ROHDE C, SCHLEYER PV},
doi = {10.1021/om50004a015},
faupublication = {yes},
journal = {Organometallics},
month = {Jan},
pages = {1344-1351},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{ALLYLLITHIUM}, {ALLYLSODIUM}, {AND} {ALLYLMAGNESIUM} {HYDRIDE} - {GEOMETRIES} {AND} {BONDING} - {A} {COMPARATIVE} {ABINITIO} {STUDY}},
volume = {2},
year = {1983}
}
@article{faucris.272553046,
abstract = {We used a systematic approach to shed light on the inherent differences in perylenes, namely monoimides versus diimides, including coplanarity and dipole moment, and their impact on singlet fission (SF) by designing, synthesizing, and probing a full fledged series of phenylene- and naphthalene-linked dimers. Next to changing the functionality of the perylene core, we probed the effect of the spacers and their varying degrees of rotational freedom, molecular electrostatic potentials, and intramolecular interactions on the SF-mechanism and -efficiencies. An arsenal of spectroscopic techniques revealed that for perylene-monoimides, a strong charge-transfer mixing with the singlet and triplet excited states restricts SF and yields low triplet quantum yields. This is accompanied by an up-conversion channel that includes geminate triplet-triplet recombination. Using perylene-diimides alters the SF-mechanism by populating a charge-separated-state intermediate, which either favors or shuts-down SF. Napthylene-spacers bring about higher triplet quantum yields and overall better SF-performance for all perylene-monoimides and perylene-diimides. The key to better SF-performance is rotational freedom because it facilitates the overall excited-state polarization and amplifies intramolecular interactions between chromophores.},
author = {Papadopoulos, Ilias and Gutierrez-Moreno, David and Bo, Yifan and Casillas, Ruben and Greißel, Phillip and Clark, Timothy and Fernandez-Lazaro, Fernando and Guldi, Dirk Michael},
doi = {10.1039/d1nr08523a},
faupublication = {yes},
journal = {Nanoscale},
note = {CRIS-Team WoS Importer:2022-04-08},
pages = {5194-5203},
peerreviewed = {Yes},
title = {{Altering} singlet fission pathways in perylene-dimers; perylene-diimide versus perylene-monoimide},
volume = {14},
year = {2022}
}
@article{faucris.122358104,
author = {Clark, Timothy and Chandrasekhar, Jayaraman and Schleyer, Paul and et al.},
author_hint = {ANDRADE JG, CLARK T, CHANDRASEKHAR J, SCHLEYER PV},
doi = {10.1016/S0040-4039(01)81798-6},
faupublication = {yes},
journal = {Tetrahedron Letters},
month = {Jan},
pages = {2957-2960},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{ALTERNATIVE} {MECHANISMS} {FOR} {CYANIDE} {ANION}-{EXCHANGE} {WITH} {ACETONITRILE}},
volume = {22},
year = {1981}
}
@article{faucris.122878624,
author = {Clark, Timothy},
faupublication = {yes},
journal = {ACS National Meeting Book of Abstracts},
pages = {114-114},
peerreviewed = {unknown},
title = {{AM1}*and beyond: {Aspects} of modern semiempirical methods},
volume = {232},
year = {2006}
}
@article{faucris.122362944,
abstract = {The effect of substituents on the stability of Ph(n)C(+) H(2-n)X (n = 0-2) carbocations, X = F, OH, OCH3, NH2, CH3, C6H5, CH=CH2, C=CK, CN, CHO, COOK, and NO2, has been studied with AM1 and PM3 semiempirical molecular orbital theories both in the gas phase and in solution. The results indicate that the amino group gives the most stabilization by pi-electron donation, whereas the nitro group is most destabilizing because of its strong sigma- and pi-accepting nature. Carbocation substituent stabilization energies decrease with increasing number of phenyl rings directly attached to the cation center. Electron-withdrawing substituents, (CN, CKO, and COOH) destabilize the cation center to a lesser extent than might be expected because they act as pi-electron donors when directly attached to a cation center. On going from the gas phase to solution, the stabilization energies of primary carbocations decrease, whereas for tertiary cations they increase. The secondary carbocations are of intermediate behavior.},
author = {Clark, Timothy and et al.},
author_hint = {ELNAHAS AM, CLARK T},
doi = {10.1021/jo00129a049},
faupublication = {yes},
journal = {Journal of Organic Chemistry},
pages = {8023-8027},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{AM1} {AND} {PM3} {CALCULATIONS} {ON} {THE} {EFFECT} {OF} {SUBSTITUENTS} {ON} {THE} {STABILITIES} {OF} {CARBOCATIONS} {IN} {THE} {GAS}-{PHASE} {AND} {IN} {SOLUTION}},
volume = {60},
year = {1995}
}
@article{faucris.122360744,
abstract = {Our extension of the AM1 semiempirical molecular orbital technique, AM1*, has been parameterized for the elements Al, Si, Ti and Zr. The basis sets for all four metals contain a set of d-orbitals. Thus, AM1* parameters are now available for H, C, N, O and F (which use the original AM1 parameters), Al, Si, P, S, Cl, Ti, Mo and Zr. Special attention was paid to reproducing homolytic and heterolytic bond-dissociation energies correctly. Such bond-energy data help to avoid eccentricities in the parameterization caused by inaccurate experimental heats of formation. The performance and typical errors of AM1* for the newly parameterized elements are discussed. Generally, the new method performs less well than established techniques for heats of formation but considerably better for the heats of reaction.},
author = {Winget, Paul and Clark, Timothy},
doi = {10.1007/s00894-005-0236-y},
faupublication = {yes},
journal = {Journal of Molecular Modeling},
keywords = {AM1*;parameterization;aluminum;silicon;titanium;zirconium;semiempirical MO-theory},
pages = {439-456},
peerreviewed = {Yes},
title = {{AM1}*parameters for aluminum, silicon, titanium and zirconium},
volume = {11},
year = {2005}
}
@article{faucris.107274024,
abstract = {Our extension of the AM1 semiempirical molecular orbital technique, AM1*, has been parameterized for the elements Br and I. The basis sets for both halogens contain a set of d-orbitals as polarization functions. AM1* performs as well as other MNDO-like methods that use dorbitals in the basis, and better than those that rely on an sp-basis. Thus, AM1* parameters are now available for H, C, N, O and F (which use the original AM1 parameters), Al, Si, P, S, Cl, Ti, Cu, Zn, Br, Zr, Mo and I.},
author = {Kayi, Hakan and Clark, Timothy},
doi = {10.1007/s00894-008-0419-4},
faupublication = {yes},
journal = {Journal of Molecular Modeling},
pages = {295--308},
peerreviewed = {Yes},
title = {{AM1}* parameters for bromine and iodine},
volume = {15},
year = {2009}
}
@article{faucris.107275124,
abstract = {We report the parameterization of AM1* for the elements Co and Ni. The basis sets for both metals contain one set each of s-, p- and d-orbitals. AM1* parameters are now available for H, C, N, O and F (which use the original AM1 parameters), Al, Si, P, S, Cl, Ti, V, Cr, Co, Ni, Cu, Zn, Br, Zr, Mo and I. The performance and typical errors of AM1* are discussed for Co and Ni and compared with available NDDO Hamiltonians.},
author = {Kayi, Hakan and Clark, Timothy},
doi = {10.1007/s00894-009-0503-4},
faupublication = {yes},
journal = {Journal of Molecular Modeling},
pages = {29--47},
peerreviewed = {Yes},
title = {{AM1}* parameters for cobalt and nickel},
volume = {16},
year = {2010}
}
@article{faucris.122362064,
abstract = {Our extension of the AM1 semiempirical molecular orbital technique, AM1*, has been parameterized for the elements Cu and Zn. The basis sets for both metals contain a set of d-orbitals. The zinc parameterization uses a filled d-shell to give 12 valence electrons. Thus, AM1* parameters are now available for H, C, N, O and F (which use the original AM1 parameters), Al, Si, P, S, Cl, Ti, Cu, Zn, Zr and Mo. The performance and typical errors of AM1* are discussed for the newly parameterized elements.},
author = {Kayi, Hakan and Clark, Timothy},
doi = {10.1007/s00894-007-0214-7},
faupublication = {yes},
journal = {Journal of Molecular Modeling},
keywords = {AM1*;copper parameters;semiempirical MO-theory;zinc parameters},
pages = {965-979},
peerreviewed = {Yes},
title = {{AM1}*parameters for copper and zinc},
volume = {13},
year = {2007}
}
@article{faucris.107276664,
abstract = {We report the parameterization of AM1* for the elements manganese and iron. The basis sets for both metals contain one set each of s-, p- and d-orbitals. AM1* parameters are now available for H, C, N, O and F (which use the original AM1 parameters), Al, Si, P, S, Cl, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Br, Zr, Mo, I and Au. The performance and typical errors of AM1* are discussed for Mn and Fe, and are compared with available NDDO Hamiltonians.},
author = {Kayi, Hakan and Clark, Timothy},
doi = {10.1007/s00894-009-0614-y},
faupublication = {yes},
journal = {Journal of Molecular Modeling},
pages = {1109--1126},
peerreviewed = {Yes},
title = {{AM1}* parameters for manganese and iron},
volume = {16},
year = {2010}
}
@article{faucris.120935364,
abstract = {0.1,0.1,0.1We report the parameterization of AM1* for the elements palladium and silver. The basis sets for both metals contain one set each of 0.1,0.1,0.1s0.1,0.1,0.1-, 0.1,0.1,0.1p0.1,0.1,0.1- and 0.1,0.1,0.1d0.1,0.1,0.1-orbitals. AM1* parameters are now available for H, C, N, O and F (which use the original AM1 parameters), Al, Si, P, S, Cl, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Br, Zr, Mo, Pd, Ag, I and Au. The performance and typical errors of AM1* are discussed for Pd and Ag and compared with the PM6 Hamiltonian.},
author = {Kayi, Hakan and Clark, Timothy},
doi = {10.1007/s00894-010-0940-0},
faupublication = {yes},
journal = {Journal of Molecular Modeling},
pages = {2585--2600},
peerreviewed = {Yes},
title = {{AM1}* parameters for palladium and silver},
volume = {17},
year = {2011}
}
@article{faucris.116869544,
abstract = {An extension of the AM1 semiempirical molecular orbital technique, AM1*, is introduced. AM1* uses AM1 parameters and theory unchanged for the elements H, C, N, O and F. The elements P, S and Cl have been reparameterized using an additional set of d orbitals in the basis set and with two-center core-core parameters, rather than the Gaussian functions used to modify the core-core potential in AM1. Voityuk and Rosch's AM1(d) parameters have been adopted unchanged for AM1* with the exception that new core-core parameters are defined for Mo-P, Mo-S and Mo-Cl interactions. Thus, AM1* gives identical results to AM1 for compounds with only H, C, N, O, and F, AM1(d) for compounds containing Mo, H, C, N, O and F only, but differs for molybdenum compounds containing P, S or Cl. The performance and typical errors of AM1* are discussed.},
author = {Winget, Paul and Horn, Anselm and Martin, Bodo and Clark, Timothy and et al.},
author_hint = {Winget P, Horn AHC, Selcuki C, Martin B, Clark T},
doi = {10.1007/s00894-003-0156-7},
faupublication = {yes},
journal = {Journal of Molecular Modeling},
keywords = {semiempirical parameterization;AM1;NDDO},
pages = {408-414},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{AM1}*parameters for phosphorus, sulfur and chlorine},
volume = {9},
year = {2003}
}
@article{faucris.107274464,
abstract = {Our extension of the AM1 semiempirical molecular orbital technique, AM1*, has been parameterized for the elements V and Cr. The basis sets for both metals contain one set each of s-, p- and d-orbitals. AM1* parameters are now available for H, C, N, O and F (which use the original AM1 parameters), Al, Si, P, S, Cl, Ti, V, Cr, Cu, Zn, Br, Zr, Mo and I. The performance and typical errors of AM1* are discussed for V and Cr and compared with available NDDO Hamiltonians.},
author = {Kayi, Hakan and Clark, Timothy},
doi = {10.1007/s00894-009-0489-y},
faupublication = {yes},
journal = {Journal of Molecular Modeling},
pages = {1253--1269},
peerreviewed = {Yes},
title = {{AM1}* parameters for vanadium and chromium},
volume = {15},
year = {2009}
}
@article{faucris.121003344,
abstract = {Bicycles made in crystals: The phosphorus atoms of the: π ligand 1,3-diphosphete turn out to be ambiphilic centers with pronounced intramolecular reactivity. This property results in a temperature-dependent bond formation in [(2,4-di-tBu-1,3-diphosphete)3Mo], which is found to be a topotactic reaction in the single crystal (see scheme). This new reactivity principle can be used to explain a series of complex interligand bond-formation reactions of phosphorus heterocycles.},
author = {Clark, Timothy and Toepffer, Christian and Heinemann, Frank Wilhelm and Hennemann, Matthias and Zenneck, Ulrich and et al.},
author_hint = {Clark Tim, Toepffer Christian, Heinemann Frank Wilhelm, Hennemann Matthias, Kummer Susanne, Pritzkow Hans, Zenneck Ulrich},
doi = {10.1002/1521-3773(20021104)41:21<4047::AID-ANIE4047>3.0.CO;2-4},
faupublication = {yes},
journal = {Angewandte Chemie International Edition},
keywords = {DFT calculations; Molybdenum; P ligands; Phosphorus heterocycles; Pi interactions; Solid-state reactions},
note = {UnivIS-Import:2015-04-14:Pub.2002.forsch.sonder.sfb583.ambiph},
pages = {4047-4052},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{Ambiphilicity}: {A} {Characteristic} {Reactivity} {Principle} of {Pi}-{Bound} {Phosphorus} {Heterocycles}},
volume = {41},
year = {2002}
}
@article{faucris.121153164,
abstract = {Systematic access to metal-functionalized polyoxometalates has thus far been limited to lacunary tungsten oxide and molybdenum oxide clusters. The first controlled, stepwise bottom-up assembly route to metal-functionalized molecular vanadium oxides is now presented. A di-vacant vanadate cluster with two metal binding sites, (DMA)(2)[V12O32Cl](3-) (DMA= dimethylammonium) is formed spontaneously in solution and characterized by single-crystal X-ray diffraction, ESI mass spectrometry, V-51 NMR spectroscopy, and elemental analyses. In the cluster, the metal binding sites are selectively blocked by hydrogen-bonded DMA placeholder cations. Reaction of the cluster with transition metals TM (Fe3+, Co2+, Cu2+, Zn2+) gives access to mono-functionalized vanadate clusters (DMA)[{TM(L)}V12O32Cl](n-) (L= ligand). Metal binding is accomplished by significant distortions of the vanadium oxide framework reminiscent of a pincer movement. Cluster stability under technologically relevant conditions in the solid-state and solution is demonstrated.},
author = {Kastner, Katharina and Margraf, Johannes and Clark, Timothy and Streb, Carsten},
doi = {10.1002/chem.201403592},
faupublication = {yes},
journal = {Chemistry - A European Journal},
keywords = {functionalization;metal oxide clusters;polyoxometalates;polyoxovanadates;self-assembly},
pages = {12269-12273},
peerreviewed = {Yes},
title = {{A} {Molecular} {Placeholder} {Strategy} {To} {Access} a {Family} of {Transition}-{Metal}-{Functionalized} {Vanadium} {Oxide} {Clusters}},
volume = {20},
year = {2014}
}
@article{faucris.115072364,
abstract = {The first highly water-soluble perylene-calix[4]arene hybrid with the calixarene scaffold acting as a structure-determining central platform is presented. In this tetrahedrally shaped amphiphilic architecture the hydrophilic and hydrophobic subunits are oriented at the opposite side of the calixarene platform. The hydrophobic part contains the two perylene diimide moieties, which enable strong pi-pi interactions in self-assembly processes. Two hydrophilic Newkome-type dendrons provide sufficient water solubility at slightly basic conditions. The tetrahedrally shaped amphiphile displays an unprecedented aggregation behavior down to concentrations as low as 10(-7) mol L-1. The intriguing self-assembly process of the compound in water as well as under changed polarity conditions, achieved by addition of THF, could be monitored by the complemented use of cryogenic transmission electron microscopy (cryo-TEM), UV-vis spectroscopy, and fluorescence spectroscopy. Molecular-dynamics and molecular modeling simulations helped in understanding the interplay of supramolecular and optical behavior.},
author = {Rodler, Fabian and Schade, Boris and Jaeger, Christof M. and Backes, Susanne and Hampel, Frank and Boettcher, Christoph and Clark, Timothy and Hirsch, Andreas},
doi = {10.1021/ja512048t},
faupublication = {yes},
journal = {Journal of the American Chemical Society},
pages = {3308-3317},
peerreviewed = {Yes},
title = {{Amphiphilic} {Perylene}-{Calix}[4]arene {Hybrids}: {Synthesis} and {Tunable} {Self}-{Assembly}},
volume = {137},
year = {2015}
}
@article{faucris.115050584,
abstract = {We have developed a multi-agent quantum Monte Carlo model to describe the spatial dynamics of multiple majority charge carriers during conduction of electric current in the channel of organic fieldeffect transistors. The charge carriers are treated by a neglect of diatomic differential overlap Hamiltonian using a lattice of hydrogen-like basis functions. The local ionization energy and local electron affinity defined previously map the bulk structure of the transistor channel to external potentials for the simulations of electron- and hole-conduction, respectively. The model is designed without a specific charge-transport mechanism like hopping- or band-transport in mind and does not arbitrarily localize charge. An electrode model allows dynamic injection and depletion of charge carriers according to source-drain voltage. The field-effect is modeled by using the source-gate voltage in a Metropolis-like acceptance criterion. Although the current cannot be calculated because the simulations have no time axis, using the number of Monte Carlo moves as pseudo-time gives results that resemble experimental I/V curves. (C) 2015 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution 3.0 Unported License.},
author = {Bauer, Thilo and Jäger, Christof and Jordan, Meredith J. T. and Clark, Timothy},
doi = {10.1063/1.4927397},
faupublication = {yes},
journal = {Journal of Chemical Physics},
peerreviewed = {Yes},
title = {{A} multi-agent quantum {Monte} {Carlo} model for charge transport: {Application} to organic field-effect transistors},
volume = {143},
year = {2015}
}
@article{faucris.109321564,
abstract = {Density functional theory (DFT) and ab initio (CBS-RAD) calculations have been used to investigate a series of "radical clock" reactions. The calculated activation energies suggest that the barriers for these radical rearrangements are determined almost exclusively by the enthalpy effect with no evidence of significant polar effects. The ring-closure reactions to cyclopentylmethyl radical derivatives and the ring opening of cyclopropylmethyl radicals give different correlations between the calculated heat of reaction and barrier, but the two types of reaction are internally consistent.},
author = {Jäger, Christof and Hennemann, Matthias and Mieszala, Andrzej and Clark, Timothy},
doi = {10.1021/jo702421m},
faupublication = {yes},
journal = {Journal of Organic Chemistry},
pages = {1536-1545},
peerreviewed = {Yes},
title = {{An} ab initio and density functional theory study of radical-clock reactions},
volume = {73},
year = {2008}
}
@article{faucris.122363384,
abstract = {Bond dissociation and formation in diatomic molecules are analyzed in terms of the reaction force F(R) and the reaction force constant kappa(R). These were determined for a group of 13 molecules from their extended-Rydberg potential energy functions V(R), which are of near-experimental quality. From F(R) and kappa(R) comes a two-stage description of dissociation/formation. In dissociation, the first stage involves stretching of the bond, which is opposed by an increasingly negative retarding force F(R). This reaches a minimum and then begins to weaken in the second stage, which is the transition from stretched molecule to free atoms. Bond formation begins with the reverse transition, driven by a positive F(R) which reaches a maximum for the stretched molecule and then becomes a decreasing restoring force. In the stages in which the system is a stretched molecule, kappa(R) is positive with its maximum at the equilibrium bond length; it is zero at the minimum or maximum of F(R), and negative throughout the transition stages, going through a minimum. kappa(R) < 0 has been found to characterize the transition portion of a reaction. This description of dissociation/formation is reinforced by computed B3LYP and Hartree-Fock force constants at different atom separations for the singlet molecules. Hartree-Fock wave function stability assessments suggest that, for the single-bonded singlet molecules, the onset of electron unpairing in dissociation comes in the neighborhood of the F(R) minimum.},
author = {Murray, Jane S. and Toro-Labbe, Alejandro and Clark, Timothy and Politzer, Peter},
doi = {10.1007/s00894-008-0400-2},
faupublication = {yes},
journal = {Journal of Molecular Modeling},
keywords = {Diatomic molecule dissociation/formation;Extended-Rydberg potential energy function;Position-dependent reaction force constant;Reaction force;Wave function stability},
pages = {701-706},
peerreviewed = {Yes},
title = {{Analysis} of diatomic bond dissociation and formation in terms of the reaction force and the position-dependent reaction force constant},
volume = {15},
year = {2009}
}
@article{faucris.116872404,
abstract = {A fully analytical description of molecular shape, as defined by the shrink-wrap isodensity or solvent-excluded surfaces and local properties related to Coulomb, donor/acceptor, and polarizability (dispersion) interactions is described. The molecular surface and four local properties adequate for describing intermolecular interactions (the molecular electrostatic potential and the local ionization energy, electron affinity, and polarizability) are fitted to spherical-harmonic expansions, which provide a compact and information-rich description of the properties of the static molecule. The resolution of the description can be varied from isotropic to near atomistic detail by adjusting the order of the individual spherical-harmonic expansions. Examples are given to illustrate the effect of truncating the different spherical-harmonic approximations.},
author = {Lin, Jr-Hung and Clark, Timothy},
doi = {10.1021/ci050059v},
faupublication = {yes},
journal = {Journal of Chemical Information and Modeling},
pages = {1010-1016},
peerreviewed = {Yes},
title = {{An} analytical, variable resolution, complete description of static molecules and their intermolecular binding properties},
volume = {45},
year = {2005}
}
@article{faucris.122368224,
author = {Clark, Timothy and et al.},
author_hint = {REED AE, CLARK T},
doi = {10.1039/dc9888500365},
faupublication = {yes},
journal = {Faraday Discussions},
month = {Jan},
pages = {365-372},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{A} {NATURAL} {BOND} {ORBITAL} {ANALYSIS} {OF} {THE} {BONDING} {IN} {SOLVATED} {ELECTRONS} {WITHIN} {A} {LOCALIZED} {ELECTRON} {MODEL}},
volume = {85},
year = {1988}
}
@article{faucris.122369104,
abstract = {Photolysis of alpha,alpha'-dilithio-alpha,alpha'-bis(trimethylsilyl)-o-xylene leads to an ESR spectrum assigned to the alpha,alpha'-bis(trimethylsilyl)-o-quinodimethane radical anion, the first representative of this class of radical anions to have been observed in solution.},
author = {Clark, Timothy and Schleyer, Paul and et al.},
author_hint = {LORENZ M, CLARK T, SCHLEYER PV, NEUBAUER K, GRAMPP G},
doi = {10.1039/c39920000719},
faupublication = {yes},
journal = {Journal of the Chemical Society - Series Chemical Communications},
pages = {719-721},
peerreviewed = {unknown},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{AN} {AUTHENTIC} {ORTHO}-{QUINODIMETHANE} {RADICAL}-{ANION}},
year = {1992}
}
@article{faucris.208728900,
abstract = {A generally applicable metadynamics scheme for predicting the free energy profile of ligand binding to G-protein-coupled receptors (GPCRs) is described. A common and effective collective variable (CV) has been defined using the ideally placed and highly conserved Trp6.48 as a reference point for ligand GPCR distance measurement and the common orientation of GPCRs in the cell membrane. Using this single CV together with well-tempered multiple-walker metadynamics with a funnel-like boundary allows an efficient exploration of the entire ligand binding path from the extracellular medium to the orthosteric binding site, including vestibule and intermediate sites. The protocol can be used with X-ray structures or high-quality homology models (based on a high-quality template and after thorough refinement) for the receptor and is universally applicable to agonists, antagonists, and partial and reverse agonists. The root-mean-square error (RMSE) in predicted binding free energies for 12 diverse ligands in five receptors (a total of 23 data points) is surprisingly small (less than 1 kcal mol(-1)). The RMSEs for simulations that use receptor X-ray structures and homology models are very similar.},
author = {Saleh, Noureldin and Ibrahim, Passainte and Saladino, Giorgio and Gervasio, Francesco Luigi and Clark, Timothy},
doi = {10.1021/acs.jcim.6b00772},
faupublication = {yes},
journal = {Journal of Chemical Information and Modeling},
pages = {1210-1217},
peerreviewed = {Yes},
title = {{An} {Efficient} {Metadynamics}-{Based} {Protocol} {To} {Model} the {Binding} {Affinity} and the {Transition} {State} {Ensemble} of {G}-{Protein}-{Coupled} {Receptor} {Ligands}},
volume = {57},
year = {2017}
}
@article{faucris.261570741,
abstract = {We report the synthesis of a unique cubic metal-organic framework (MOF), Fe-HHTP-MOF, comprising hexahydroxytriphenylene (HHTP) supertetrahedral units and Fe-III ions, arranged in a diamond topology. The MOF is synthesized under solvothermal conditions, yielding a highly crystalline, deep black powder, with crystallites of 300-500 nm size and tetrahedral morphology. Nitrogen sorption analysis indicates a highly porous material with a surface area exceeding 1400 m(2) g(-1). Furthermore, Fe-HHTP-MOF shows broadband absorption from 475 up to 1900 nm with excellent absorption capability of 98.5 % of the incoming light over the visible spectral region. Electrical conductivity measurements of pressed pellets reveal a high intrinsic electrical conductivity of up to 10(-3) S cm(-1). Quantum mechanical calculations predict Fe-HHTP-MOF to be an efficient electron conductor, exhibiting continuous charge-carrier pathways throughout the structure.},
author = {Mahringer, Andre and Doeblinger, Markus and Hennemann, Matthias and Gruber, Christoph and Fehn, Dominik and Scheurle, Patricia I. and Hosseini, Pouya and Santourian, Irina and Schirmacher, Alfred and Rotter, Julian M. and Wittstock, Gunther and Meyer, Karsten and Clark, Timothy and Bein, Thomas and Medina, Dana D.},
doi = {10.1002/anie.202102670},
faupublication = {yes},
journal = {Angewandte Chemie International Edition},
note = {CRIS-Team WoS Importer:2021-07-16},
peerreviewed = {Yes},
title = {{An} {Electrically} {Conducting} {Three}-{Dimensional} {Iron}-{Catecholate} {Porous} {Framework}},
year = {2021}
}
@article{faucris.119328704,
abstract = {A new empirical force field method for localized and delocalized carbocations is described. Additional geometry parameters for carbocations were added to Allinger's MMP2 molecular mechanics program, which can treat delocalized pi-systems. The effect of hyperconjugation in carbocations is introduced via a quantum chemical term into force field calculations for the first time. The calculated heats of formation are in excellent agreement with a wide range of experimental data; the largest deviations are about 3.5 kcal/mol. The calculated structures agree very well with those computed at correlated ab initio levels (MP2(full)/6-31G*). The relative energies and geometries of different conformations of representative carbocations also were in good agreement with MP4/6-31G*//MP2(full)/6-31G* results. (C) 1996 by John Wiley & Sons, Inc.},
author = {Clark, Timothy and Schleyer, Paul and et al.},
author_hint = {Reindl B, Clark T, Schleyer PV},
doi = {10.1002/(SICI)1096-987X(199609)17:12<1406::AID-JCC3>3.3.CO;2-P},
faupublication = {yes},
journal = {Journal of Computational Chemistry},
pages = {1406-1430},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{A} new method for empirical force field calculations on localized and delocalized carbocations},
volume = {17},
year = {1996}
}
@article{faucris.107244764,
abstract = {We describe an improved force field parameter set for the generalized AMBER force field (GAFF) for urea. Quantum chemical computations were used to obtain geometrical and energetic parameters of urea dimers and larger oligomers using AM1 semiempirical MO theory, density functional theory at the B3LYP/6-31G(d,p) level, MP2 and CCSD ab initio calculations with the 6-311++G (d,p), aug-cc-pVDZ, aug-cc-pVTZ, and aug-cc-pVQZ basis sets, and with the CBS-QB3 and CBS-APNO complete basis set methods. Seven different urea dimer structures were optimized at the MP2/aug-cc-pVDZ level to obtain accurate interaction energies. Atomic partial charges were calculated at the MP2/aug-cc-pVDZ level with the restrained electrostatic potential (RESP) fitting approach. The interaction energies computed with these new RESP charges in the force field are consistent with those obtained from CCSD and MP2 calculations. The linear dimer structure calculated using the force field with modified geometrical parameters and the new RESP charge set agrees well with available experimental data.},
author = {Özpinar, Gül and Peukert, Wolfgang and Clark, Timothy},
doi = {10.1007/s00894-010-0650-7},
faupublication = {yes},
journal = {Journal of Molecular Modeling},
pages = {1427--1440},
peerreviewed = {Yes},
title = {{An} improved generalized {AMBER} force field ({GAFF}) for urea},
volume = {16},
year = {2010}
}
@misc{faucris.120254464,
author = {Clark, Timothy},
faupublication = {yes},
peerreviewed = {automatic},
title = {{Anonymous} sd (.asd) files.},
year = {2005}
}
@article{faucris.119330244,
abstract = {A numerical self-consistent reaction field (SCRF) technique for the calculation of solvent effects within the parametrized NDDO-based semiempirical molecular orbital methods has been developed and extended to excited states. The method uses Tomasi's treatment of the reaction field within an arbitrarily (van der Waals) shaped cavity. The dispersion contribution has been included via an oscillating dipole model. The model can treat both bathochromic and hypsochromic shifts for organic dyes successfully. Dispersion is found to be very important for some dyes, but to play almost no role for others.},
author = {Rauhut, Guntram and Clark, Timothy and et al.},
author_hint = {RAUHUT G, CLARK T, STEINKE T},
doi = {10.1021/ja00073a036},
faupublication = {yes},
journal = {Journal of the American Chemical Society},
pages = {9174-9181},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{A} {NUMERICAL} {SELF}-{CONSISTENT} {REACTION} {FIELD} ({SCRF}) {MODEL} {FOR} {GROUND} {AND} {EXCITED}-{STATES} {IN} {NDDO}-{BASED} {METHODS}},
volume = {115},
year = {1993}
}
@article{faucris.108710184,
abstract = {Three new unsymmetrical anthracenyl-pentacene derivatives have been synthesized, characterized using X-ray crystallography, and used as semiconductors in OTFTs. For one derivative, ambipolar charge carrier transport was observed with a hole mobility of 0.2 cm V s and an electron mobility of 0.03 cm V s. © 2013 The Royal Society of Chemistry.},
author = {Tykwinski, Rik and Etschel, Sebastian and Halik, Marcus and Jäger, Christof and Clark, Timothy and Margraf, Johannes and Waterloo, Andreas and Hampel, Frank and Yousefi Amin, Atefeh},
doi = {10.1039/c3cc43270j},
faupublication = {yes},
journal = {Chemical Communications},
pages = {6725-6727},
peerreviewed = {Yes},
title = {{An} unsymmetrical pentacene derivative with ambipolar behavior in organic thin-film transistors},
url = {http://pubs.rsc.org/en/content/articlelanding/2013/cc/c3cc43270j#!divAbstract},
volume = {49},
year = {2013}
}
@article{faucris.208735469,
abstract = {Since quantum mechanical calculations do not typically lend themselves to chemical interpretation, analyses of bonding interactions depend largely upon models (the octet rule, resonance theory, charge transfer, etc.). This sometimes leads to a blurring of the distinction between mathematical modelling and physical reality. The issue of polarization vs. charge transfer is an example; energy decomposition analysis is another. The Hellmann-Feynman theorem at least partially bridges the gap between quantum mechanics and conceptual chemistry. It proceeds rigorously from the Schrödinger equation to demonstrating that the forces exerted upon the nuclei in molecules, complexes, etc., are entirely classically coulombic attractions with the electrons and repulsions with the other nuclei. In this paper, we discuss these issues in the context of noncovalent interactions. These can be fully explained in coulombic terms, electrostatics and polarization (which include electronic correlation and dispersion).},
author = {Clark, Timothy and Murray, Jane S. and Politzer, Peter},
doi = {10.1039/c8cp06786d},
faupublication = {yes},
journal = {Physical Chemistry Chemical Physics},
peerreviewed = {Yes},
title = {{A} perspective on quantum mechanics and chemical concepts in describing noncovalent interactions.},
year = {2018}
}
@article{faucris.115074564,
abstract = {Unsymmetrical subphthalocyanine fused dimers have been prepared from appropriate ortho-dinitrile SubPc precursors. In particular, either electron-donating or electron-accepting substituents have been introduced on each SubPc constituent unit, resulting in unprecedented push-pull pi-extended curved aromatic macrocycles. From fluorescence experiments in solvents of different polarity we conclude a dual fluorescence, namely a delocalized singlet excited state (1.73 eV) and a polarized charge transfer state (<1.7 eV). Pump probe experiments corroborate the dual nature of the fluorescence. On one hand, the delocalized singlet excited state gives rise to a several nanosecond lasting intersystem crossing yielding the corresponding triplet excited state. On the other hand, the polarized charge transfer state deactivates within a few picosesonds. Visualization of the charge transfer state was accomplished by means of molecular modeling with a slight polarization of the HOMO towards the electron donor and of the LUMO towards the electron acceptor.},
author = {Zango, German and Zirzlmeier, Johannes and Claessens, Christian G. and Clark, Timothy and Victoria Martinez-Diaz, M. and Guldi, Dirk Michael and Torres, Tomas},
doi = {10.1039/c5sc01709b},
faupublication = {yes},
journal = {Chemical Science},
month = {Jan},
pages = {5571-5577},
peerreviewed = {Yes},
title = {{A} push-pull unsymmetrical subphthalocyanine dimer},
volume = {6},
year = {2015}
}
@article{faucris.109342684,
abstract = {Descriptors derived from semiempirical (AM1) molecular orbital calculations have been used to construct a quantitative structure-property relationship (QSPR) for the thermodynamic hydrogen-bond basicity, pK(HB), of a series of six-membered aromatic nitrogen-heterocycles. The resulting model uses four-descriptors (the Coulson charge on the nitrogen atom, the energy of the localized nitrogen lone-pair orbital, the p-orbital contribution to this MO and an accessibility angle). The model gives r(cv)(2)=0.95 for 51 compounds with a standard deviation between calculation and experiment of 0.13 log units.},
author = {Hennemann, Matthias and Clark, Timothy},
doi = {10.1007/s00894-002-0075-z},
faupublication = {yes},
journal = {Journal of Molecular Modeling},
keywords = {pK(HB);hydrogen bonding;QSPR;AM1},
month = {Jan},
pages = {95-101},
peerreviewed = {Yes},
title = {{A} {QSPR}-approach to the estimation of the {pK}({HB}) of six-membered nitrogen-heterocycles using quantum mechanically derived descriptors},
volume = {8},
year = {2002}
}
@article{faucris.123725624,
abstract = {We present QSPR models for normal boiling points employing a neural network approach and descriptors calculated using semiempirical MO theory (AM1 and PM3). These models are based on a data set of 6000 compounds with widely varying functionality and should therefore be applicable to a diverse range of systems. We include cross-validation by simultaneously training 10 different networks, each with different training and test sets. The predicted boiling point is given by the mean of the 10 results, and the individual error of each compound is related to the standard deviation of these predictions. For our best model we find that the standard deviation of the training error is 16.5 K for 6000 compounds and the correlation coefficient (R-2) between our prediction and experiment is 0.96. We also examine the effect of different conformations and tautomerism on our calculated results. Large deviations between our predictions and experiment can generally be explained by experimental errors or problems with the semiempirical methods.},
author = {Beck, Bernd and Clark, Timothy and et al.},
author_hint = {Chalk AJ, Beck B, Clark T},
doi = {10.1021/ci0004614},
faupublication = {yes},
journal = {Journal of Chemical Information and Computer Sciences},
pages = {457-462},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{A} quantum mechanical/neural net model for boiling points with error estimation},
volume = {41},
year = {2001}
}
@article{faucris.122373504,
author = {Clark, Timothy and et al.},
author_hint = {Lawes DJ, Darwish TA, Clark T, Harper JB, Ball GE},
doi = {10.1002/anie.200600313},
faupublication = {yes},
journal = {Angewandte Chemie International Edition},
keywords = {ab initio calculations;alkane ligands;C-H activation;hyperconjugation;NMR spectroscopy},
month = {Jan},
pages = {4486-4490},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{A} rhenium-cyclohexane complex with preferential binding of axial {C}-{H} bonds: {A} probe into the relative ability of {C}-{H}, {C}-{D}, and {C}-{C} bonds as hyperconjugative electron donors?},
volume = {45},
year = {2006}
}
@article{faucris.211140226,
author = {Schreck, Maximilian H. and Röhr, Merle I.S. and Clark, Timothy and Stepanenko, Vladimir and Würthner, Frank and Lambert, Christoph},
doi = {10.1002/chem.201805685},
faupublication = {yes},
journal = {Chemistry - A European Journal},
keywords = {exchange narrowing; exciton coupling; dyes/pigments; noncovalent interactions; self-assembly},
peerreviewed = {Yes},
title = {{A} {Self}-{Assembled} {Unit} {Comprising} 12 {Squaraine} {Dyes} {Built} {Up} from {Two} {Star}-{Shaped} {Hexasquarainyl}-{Benzene} {Molecules}},
year = {2019}
}
@article{faucris.116874384,
abstract = {An intermolecular hybrid semiempirical MO/molecular mechanics technique is described. The model allows polarisation of the quantum mechanical molecule(s), but not of the molecular mechanics part and is shown to be relatively insensitive to the size of the molecular mechanics environment. It has been validated by comparison of calculated and experimental absorption energies of small organic molecules in various zeolites. This validation gives us confidence that the method is also appropriate for experimentally less well characterised problems, such as solvation or ligand/enzyme complexation.},
author = {Clark, Timothy and Alex, Alexander and Beck, Bernd and Gedeck, Peter and Lanig, Harald},
doi = {10.1007/s008940050100},
faupublication = {yes},
journal = {Journal of Molecular Modeling},
keywords = {AM1;semiempirical MO;hybrid method;QM/MM;zeolites;absorption energies},
month = {Jan},
pages = {1-7},
peerreviewed = {Yes},
title = {{A} semiempirical {QM}/{MM} implementation and its application to the absorption of organic molecules in zeolites},
volume = {5},
year = {1999}
}
@article{faucris.289305418,
abstract = {A modified neglect of differential overlap has been parameterized specifically for water and its oligomers with the addition of polarization functions on both hydrogen and oxygen, Feynman dispersion, and a slight modification of the treatment of the hydrogen nucleus. The results show that it is possible to easily obtain good geometries and energies for hydrogen-bonded water aggregates. Data from the Benchmark Energy and Geometry Database water-cluster database were used to parameterize the new Hamiltonian for water clusters from the dimer to the decamer using MP2/aug-cc-pVDZ optimized geometries and CCSD(T)/CBS oligomerization energies. Seventy five oligomerization and rearrangement energies derived from the parameterization data are reproduced with a root mean-square error (RMSE) of 0.79 kcal mol(-1) and the geometries of 38 oligomers with an RMSE of 0.17 angstrom. Interestingly, the Feynman dispersion term adopts a role different from that intended and tunes the atomic polarizability. The implications of these results in terms of future dedicated neglect of diatomic differential overlap Hamiltonians and those that use force-field-like atom types are discussed.},
author = {Hennemann, Matthias and Clark, Timothy},
doi = {10.1063/5.0132863},
faupublication = {yes},
journal = {Journal of Chemical Physics},
month = {Jan},
note = {CRIS-Team WoS Importer:2023-02-17},
peerreviewed = {Yes},
title = {{A} specific {MNDO} parameterization for water},
volume = {158},
year = {2023}
}
@article{faucris.122376584,
abstract = {The performance of computationally accessible levels of calculation for the transition states of organocatalytic reaction has been assessed. Reference post-Hartree-Fock single point energy calculations were used as standards for the gas-phase Born-Oppenheimer relative energies of pairs of alternative transition states that lead to the two product enantiomers. We show that semiempirical methods cannot even be relied on to yield qualitatively correct results. The geometries (optimized, for instance, with DFT) have a large impact on the results of high-level post-HF calculations, so that it is essential to use an adequate DFT technique and basis set. DFT can yield quantitatively correct results that are consistent with post-HF calculations if functionals that consider dispersion are used. Geometries for large systems show larger errors than those for smaller ones but are treated better by functionals such as M06-2X and w97Bxd that include dispersion implicitly or explicitly. Local correlation techniques introduce errors of comparable magnitude to those given by different levels of geometry optimization. We recommend RICC2/TZVP//M06-2X/TZVP, RI-MP2/TZVP//M06-2X/TZVP, and M06-2X/TZVP//M06-2X/TZVP calculations in that order, depending on the size of the system.},
author = {Schenker, Sebastian and Schneider, Christopher and Tsogoeva, Svetlana and Clark, Timothy},
doi = {10.1021/ct2002013},
faupublication = {yes},
journal = {Journal of Chemical Theory and Computation},
pages = {3586-3595},
peerreviewed = {Yes},
title = {{Assessment} of {Popular} {DFT} and {Semiempirical} {Molecular} {Orbital} {Techniques} for {Calculating} {Relative} {Transition} {State} {Energies} and {Kinetic} {Product} {Distributions} in {Enantioselective} {Organocatalytic} {Reactions}},
volume = {7},
year = {2011}
}
@article{faucris.109343344,
abstract = {Log P-OW, the negative logarithm of the octanol-water partition coefficient, is omnipresent in computational drug design. Here, we present a surface-integral model for calculating log P-OW. The model is based on local properties calculated using AM1 semiempirical molecular orbital theory. These are the molecular electrostatic potential (MEP), local ionization energy (IEL), local electron affinity (EA(L)), local hardness (HARD), local polarizability (POL), and the local field normal to the surface (FN). We have developed a new scheme to calculate a local hydrophobicity based on binning the range of local surface properties instead of using polynomial expansions of the base terms. The model has been trained using similar to 9500 compounds available from the literature. It was validated oil similar to 1350 compounds froth the literature and all in-house validation set of 768 compounds from Boehringer-Ingelheim. The model performs similarly to or slightly better than the best commercially available models. We also introduce a model based purely on conformationally rigid compounds that performs well for flexible compounds if the Boltzmann weighted predictions for the different conformers are used. This is the first 3D QSPR model based on such a large databasis that is able to benefit from using conformational ensembles.},
author = {Kramer, Christian and Beck, Bernd and Clark, Timothy},
doi = {10.1021/ci900431f},
faupublication = {yes},
journal = {Journal of Chemical Information and Modeling},
pages = {429-436},
peerreviewed = {Yes},
title = {{A} {Surface}-{Integral} {Model} for {Log} {P}-{OW}},
volume = {50},
year = {2010}
}
@article{faucris.124062224,
author = {Clark, Timothy and Schleyer, Paul and et al.},
author_hint = {SHAIK S, BERNARDI F, CLARK T, NGUYEN MT, OLIVUCCI, TRUHLAR DG, BORDEN WT, BUTLER LJ, SCHLEYER PV, KARADAKOV PB, HOUK KN, GERRATT J, ROBB MA, STONE AJ, WILLIAMS F, KARPLUS M, BALLY, WILSON, MICHL J, WALSH, TOMASI J, BERTRAN J},
faupublication = {yes},
journal = {Journal of the Chemical Society, Faraday Transactions},
pages = {1669-1680},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{A} {SYMPOSIUM} {ON} {POTENTIAL}-{ENERGY} {SURFACES} {AND} {ORGANIC}-{REACTION} {PATHS} {WAS} {HELD} {AT} {THE} {UNIVERSITY}-{OF}-{OXFORD} {ON} {THE} {15TH}, {16TH} {AND} {17TH} {DECEMBER} 1993 - {GENERAL} {DISCUSSION}},
volume = {90},
year = {1994}
}
@article{faucris.122708784,
abstract = {We present a temperature-dependent model for vapor pressure based on a feed-forward neural net and descriptors calculated using AM1 semiempirical MO-theory. This model is based on a set of 7681 measurements at various temperatures performed on 2349 molecules. We employ a 10-fold cross-validation scheme that allows us to estimate errors for individual predictions. For the training set we find a standard deviation of the error s = 0.322 and a correlation coefficient (R-2) of 0.976. The corresponding values for the validation set are s = 0.326 and R-2 = 0.976. We thoroughly investigate the temperature-dependence of our predictions to ensure that our model behaves in a physically reasonable manner. As a further test of temperature-dependence, we also examine the accuracy of our vapor pressure model in predicting the related physical properties, the boiling point, and the enthalpy of vaporization.},
author = {Beck, Bernd and Clark, Timothy and et al.},
author_hint = {Chalk AJ, Beck B, Clark T},
doi = {10.1021/ci0103222},
faupublication = {yes},
journal = {Journal of Chemical Information and Computer Sciences},
pages = {1053-1059},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{A} temperature-dependent quantum mechanical/neural net model for vapor pressure},
volume = {41},
year = {2001}
}
@article{faucris.118722824,
abstract = {Molecular-dynamics (MD) simulations of urea crystals of different shapes (cubic, rectangular prismatic, and sheet) have been performed using our previously published force field for urea. This force field has been validated by calculating values for the cohesive energy, sublimation temperature, and melting point from the MD data. The cohesive energies computed from simulations of cubic and rectangular prismatic urea crystals in vacuo at 300 K agreed very well with the experimental sublimation enthalpies reported at 298 K. We also found very good agreement between the melting points as observed experimentally and from simulations. Annealing the crystals just below the melting point leads to reconstruction to form crystal faces that are consistent with experimental observations. The simulations reveal a melting mechanism that involves surface (corner/edge) melting well below the melting point, and rotational disordering of the urea molecules in the corner/edge regions of the crystal, which then facilitates the translational motion of these molecules.},
author = {Ozpinar, Gul Altinbas and Beierlein, Frank and Peukert, Wolfgang and Zahn, Dirk and Clark, Timothy},
doi = {10.1007/s00894-011-1336-5},
faupublication = {yes},
journal = {Journal of Molecular Modeling},
pages = {3455--3466},
peerreviewed = {Yes},
title = {{A} test of improved force field parameters for urea: molecular-dynamics simulations of urea crystals},
volume = {18},
year = {2012}
}
@article{faucris.116875704,
author = {Clark, Timothy and Schleyer, Paul and et al.},
author_hint = {CRANS D, CLARK T, SCHLEYER PV},
doi = {10.1016/S0040-4039(00)78744-2},
faupublication = {yes},
journal = {Tetrahedron Letters},
month = {Jan},
pages = {3681-3684},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{A} {THEORETICAL} {EVALUATION} {OF} {THE} {SYNERGETIC} {CAPTO}-{DATIVE} {STABILIZATION} {OF} {FREE}-{RADICALS}},
volume = {21},
year = {1980}
}
@article{faucris.208724296,
abstract = {Molecular-dynamics simulations with metadynamics enhanced sampling reveal three distinct binding sites for arginine vasopressin (AVP) within its V-2-receptor (V2R). Two of these, the vestibule and intermediate sites, block (antagonize) the receptor, and the third is the orthosteric activation (agonist) site. The contacts found for the orthosteric site satisfy all the requirements deduced from mutagenesis experiments. Metadynamics simulations for V2R and its V1aR-analog give an excellent correlation with experimental binding free energies by assuming that the most stable binding site in the simulations corresponds to the experimental binding free energy in each case. The resulting three-site mechanism separates agonists from antagonists and explains subtype selectivity.},
author = {Saleh, Noureldin and Saladino, Giorgio and Gervasio, Francesco L. and Haensele, Elke and Banting, Lee and Whitley, David C. and Santos, Jana Sopkova-De Oliveira and Bureau, Ronan and Clark, Timothy},
doi = {10.1002/anie.201602729},
faupublication = {yes},
journal = {Angewandte Chemie International Edition},
keywords = {G-protein coupled receptors;hormones;metadynamics;molecular dynamics;receptors},
pages = {8008-8012},
peerreviewed = {Yes},
title = {{A} {Three}-{Site} {Mechanism} for {Agonist}/{Antagonist} {Selective} {Binding} to {Vasopressin} {Receptors}},
volume = {55},
year = {2016}
}
@article{faucris.115075444,
abstract = {We present an atomistic model of a full KRT35/KRT85 dimer, a fundamental building block of human hair. For both monomers initial structures were generated using empirical tools based on homology considerations, followed by the formulation of a naive dimer model from docking the monomers in vacuum. Relaxation in aqueous solution was then explored from molecular dynamics simulation. Driven by hydrophobic segregation and protein-protein hydrogen bonding relaxation dynamics result in a folded dimer arrangement which shows a striking encounter of cystein groups. Our simulations hence suggests that (i) cystein groups in the coil regions of keratin are well suited to establish disulfide bonds between the two monomers that constitute the dimer, and (ii) the particularly large number of cystein groups in the head and tail regions promotes the connection of dimers to establish meso- to macroscale fibers. Moreover, we show the molecular mechanisms of elastic and plastic deformation under tensile load. Upon elongation beyond the elastic regime, unfolding was identified as the exposure of hydrophobic moieties and the breaking of protein-protein hydrogen bonds. Therein, the step-wise character of the series of unfolding events leads to a broad regime of constant force in response to further elongation.},
author = {Duchstein, Patrick and Clark, Timothy and Zahn, Dirk},
doi = {10.1039/c5cp02676h},
faupublication = {yes},
journal = {Physical Chemistry Chemical Physics},
month = {Jan},
pages = {21880-21884},
peerreviewed = {Yes},
title = {{Atomistic} modeling of a {KRT35}/{KRT85} keratin dimer: folding in aqueous solution and unfolding under tensile load},
volume = {17},
year = {2015}
}
@article{faucris.208729167,
abstract = {The aggregation and the photophysics of a water soluble perylenediimide (PDI) derivative that features two bromine substituents in the bay positions has been probed. Non-fluorescent aggregates were found to be present at concentrations of 1.0 x 10(-5) M. In situ small-angle X-ray scattering (SAXS) measurements and complementary molecular modeling showed the presence of PDI aggregates. In their singlet excited states, the PDI aggregates are characterized by distinct transient fingerprints and rapid deactivation, as revealed by pump-probe experiments on the femto-, pico-, nano-, and microsecond timescales. The product of this deactivation is a PDI triplet excited state. The efficiency of the triplet formation depends on the concentration, and hence on the degree of aggregation. Notably, for PDI concentrations in the range of the critical micelle concentration, the efficiency of intersystem crossing is close to zero. In short, we have demonstrated, for the first time, aggregation-induced formation of triplet excited states for PDI derivatives.},
author = {Dirian, Konstantin and Bauroth, Stefan and Roth, Alexandra Marina and Syrgiannis, Zois and Rigodanza, F. and Burian, Max and Amenitsch, H. and Sharapa, Dmitry and Prato, M. and Clark, Timothy and Guldi, Dirk Michael},
doi = {10.1039/c7nr07870f},
faupublication = {yes},
journal = {Nanoscale},
pages = {2317-2326},
peerreviewed = {Yes},
title = {{A} water-soluble, bay-functionalized perylenediimide derivative - correlating aggregation and excited state dynamics},
volume = {10},
year = {2018}
}
@article{faucris.122745744,
abstract = {Three different indicators of aromatic electron delocalization have been investigated computationally for 1,2-(3), 1,4- (4), and 1,3-azaborine (5), all of which are experimentally unknown as unsubstituted compounds. MP2/6-31G* optimizations show a varying but considerable degree of electron delocalization. The calculated order of stability (3 much greater than 4 > 5) resolves the contradictions of former reports. In contrast to the noncorrelated level, consideration of electron correlation significantly lowers the relative energy of the 1,3-isomer, for which not even substituted derivatives are known. Natural bond orbital (NBO) analyses confirm the expected Lewis structures of the 1,2- and 1,4-isomers but offer an interesting description of the intricate pi-system of 1,3-azaborine. Isodesmic equations reveal a resonance energy for 4 similar to stable Huckel aromatics and a somewhat smaller effect for 3, whereas a hyperhomodesmotic equation assigns half the resonance energy of benzene to 4. Basic differences in the sigma framework of the azaborines are considered to be responsible for the stability of 3. Computational results are supported by comparison of the scarce NMR data with chemical shifts calculated by the individual gauge localized orbitals (IGLO) method.},
author = {Clark, Timothy and et al.},
author_hint = {KRANZ M, CLARK T},
doi = {10.1021/jo00046a035},
faupublication = {yes},
journal = {Journal of Organic Chemistry},
pages = {5492-5500},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{AZABORINES} - {AN} {ABINITIO} {STUDY}},
volume = {57},
year = {1992}
}
@article{faucris.120253144,
abstract = {A "frozen" electron donor-acceptor array that bears porphyrin and fullerene units covalently linked through the ortho position of a phenyl ring and the nitrogen of a pyrrolidine ring, respectively, is reported. Electrochemical and photophysical features suggest that the chosen linkage supports both through-space and through-bond interactions. In particular, it has been found that the porphyrin singlet excited state decays within a few picoseconds by means of a photoinduced electron transfer to give the rapid formation of a long-lived charge-separated state. Density functional theory (DFT) calculations show HOMO and LUMO to be localized on the electron-donating porphyrin and the electron-accepting fullerene moiety, respectively, at this level of theory. More specifically, semiempirical molecular orbital (MO) configuration interaction (CI) and unrestricted natural orbital (UNO)-CI methods shed light on the nature of the charge-transfer states and emphasize the importance of the close proximity of donor and acceptor for effective electron transfer. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.},
author = {Ciammaichella, Alina and Dral, Pavlo and Clark, Timothy and Tagliatesta, Pietro and Sekita, Michael and Guldi, Dirk Michael},
doi = {10.1002/chem.201202245},
faupublication = {yes},
journal = {Chemistry - A European Journal},
pages = {14008-14016},
peerreviewed = {Yes},
title = {{A} π-stacked porphyrin-fullerene electron donor-acceptor conjugate that features a surprising frozen geometry},
volume = {18},
year = {2012}
}
@article{faucris.228299768,
abstract = {Histamine H-4 receptor (H4R) orthologues are G-protein-coupled receptors (GPCRs) that exhibit species-dependent basal activity. In contrast to the basally inactive mouse H4R (mH(4)R), human H4R (hH(4)R) shows a high degree of basal activity. We have performed long-timescale molecular dynamics simulations and rigidity analyses on wild-type hH(4)R, the experimentally characterized hH(4)R variants S179M, F169V, F169V+S179M, F168A, and on mH(4)R to investigate the molecular nature of the differential basal activity. H4R variant-dependent differences between essential motifs of GPCR activation and structural stabilities correlate with experimentally determined basal activities and provide a molecular explanation for the differences in basal activation. Strikingly, during the MD simulations, F169(45.55) dips into the orthosteric binding pocket only in the case of hH(4)R, thus adopting the role of an agonist and contributing to the stabilization of the active state. The results shed new light on the molecular mechanism of basal H4R activation that are of importance for other GPCRs.},
author = {Wifling, David and Pfleger, Christopher and Kaindl, Jonas and Ibrahim, Passainte and Kling, Ralf and Buschauert, Armin and Gohlke, Holger and Clark, Timothy},
doi = {10.1002/chem.201902801},
faupublication = {yes},
journal = {Chemistry - A European Journal},
note = {CRIS-Team WoS Importer:2019-10-25},
peerreviewed = {Yes},
title = {{Basal} {Histamine} {H}-4 {Receptor} {Activation}: {Agonist} {Mimicry} by the {Diphenylalanine} {Motif}},
year = {2019}
}
@misc{faucris.121489984,
author = {King, William and Clark, Timothy},
faupublication = {yes},
peerreviewed = {automatic},
title = {beta-lactamase, a semiempirical study and novel mechanism.},
year = {2001}
}
@article{faucris.122377024,
author = {Clark, Timothy and Kos, Alex and Schleyer, Paul and Bickelhaupt, Friedrich and et al.},
author_hint = {CLARK T, KOS AJ, SCHLEYER PV, COFINO WP, DEWOLF WH, BICKELHAUPT F},
doi = {10.1039/C39830000685},
faupublication = {yes},
journal = {Journal of the Chemical Society - Series Chemical Communications},
month = {Jan},
pages = {685-687},
peerreviewed = {unknown},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{BETA}-{SUBSTITUTED} {CYCLOPROPYL} {RADICALS}},
year = {1983}
}
@article{faucris.208726429,
abstract = {The melanocortin-4 receptor (MC4R) is a potential drug target for treatment of obesity, anxiety, depression, and sexual dysfunction. Crystal structures for MC4R are not yet available, which has hindered successful structure-based drug design. Using microsecond-scale molecular-dynamics simulations, we have investigated selective binding of the non-peptide antagonist MCL0129 to a homology model of human MC4R (hMC4R). This approach revealed that, at the end of a multi-step binding process, MCL0129 spontaneously adopts a binding mode in which it blocks the agonistic-binding site. This binding mode was confirmed in subsequent metadynamics simulations, which gave an affinity for human hMC4R that matches the experimentally determined value. Extending our simulations of MCL0129 binding to hMC1R and hMC3R, we find that receptor subtype selectivity for hMC4R depends on few amino acids located in various structural elements of the receptor. These insights may support rational drug design targeting the melanocortin systems.},
author = {Saleh, Noureldin and Kleinau, Gunnar and Heyder, Nicolas and Clark, Timothy and Hildebrand, Peter W. and Scheerer, Patrick},
doi = {10.3389/fphar.2018.00560},
faupublication = {yes},
journal = {Frontiers in Pharmacology},
keywords = {MC4R;melanocortin-4 receptor;melanocortin-receptors;ligand binding;ligand selectivity;molecular dynamics},
peerreviewed = {unknown},
title = {{Binding}, {Thermodynamics}, and {Selectivity} of a {Non}-peptide {Antagonist} to the {Melanocortin}-4 {Receptor}},
volume = {9},
year = {2018}
}
@article{faucris.213303984,
abstract = {A series of ZnP-pCp-oPPV-C60 conjugates covalently connected through [2,2$\prime$]-paracyclophane-oligophenylenevinylene (pCp-oPPV) bridges containing one, two, and three [2,2$\prime$]-paracyclophanes (pCps) has been prepared in multistep synthetic procedures involving Horner--Wadsworth--Emmons olefination reactions and/or Heck type Pd-catalyzed reactions. Molecular modeling suggests that charge transfer is effectively mediated by the pCp-oPPVs through a predominant hole-transfer mechanism. Photophysical investigation supports molecular modeling and reveals two major trends. On one hand, C60 excitation of 1, 2, and 3 leads exclusively to charge transfer between pCp and C60 to afford a ZnP-(pCp-oPPV)•+-C60•-- radical ion pair state without giving rise to a subsequent charge shift to yield the ZnP•+-pCp-oPPV-C60•-- radical ion pair state. On the other hand, ZnP excitation of 1, 2, and 3 results in a rather slow charge transfer between ZnP and C60, after which the ZnP•+-pCp-oPPV-C60•-- radical ion pair state evolves. In temperature-dependent ZnP fluorescence experiments, which were performed in the temperature range from 273 to 338 K, two domains are discernible: low and high temperature behaviors. In the low temperature range (i.e., below 30 °C) the rate constants do not change, suggesting that a superexchange mechanism is the modus operandi. In the high temperature range (i.e., >30 °C) the rate constants increase. Moreover, we find rather strong distance dependence for 1 and 2 and weak distance dependence for 2 and 3. A damping factor of 0.145 Å--1 is derived for the former pair and 0.012 Å--1 for the latter.},
author = {Wielopolski, Mateusz and Molina-Ontoria, Agustin and Schubert, Christina and Margraf, Johannes and Krokos, Evangelos and Kirschner, Johannes and Gouloumis, Andreas and Clark, Timothy and Guldi, Dirk Michael and Martin, Nazario},
doi = {10.1021/ja401239r},
faupublication = {yes},
journal = {Journal of the American Chemical Society},
note = {EAM Import::2019-03-13},
pages = {10372-10381},
peerreviewed = {Yes},
title = {{Blending} {Through}-{Space} and {Through}-{Bond} π-π-{Coupling} in [2,2']-{Paracyclophane}-oligophenylenevinylene {Molecular} {Wires}},
volume = {135},
year = {2013}
}
@misc{faucris.122425204,
author = {Clark, Timothy},
faupublication = {yes},
peerreviewed = {automatic},
title = {{BONDING} {PRINCIPLES} {IN} {RADICAL} {REACTIONS}},
year = {1986}
}
@article{faucris.122409364,
author = {Clark, Timothy and Schleyer, Paul and et al.},
author_hint = {RAUSCHER G, CLARK T, POPPINGER D, SCHLEYER PV},
doi = {10.1002/anie.197802762},
faupublication = {yes},
journal = {Angewandte Chemie (International Edition in English)},
month = {Jan},
pages = {276-278},
peerreviewed = {unknown},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{C4LI4}, {TETRALITHIOTETRAHEDRANE}},
volume = {17},
year = {1978}
}
@article{faucris.208724566,
abstract = {Arginine vasopressin (AVP) has been suggested by molecular-dynamics (MD) simulations to exist as a mixture of conformations in solution. The H-1 and C-13 NMR chemical shifts of AVP in solution have been calculated for this conformational ensemble of ring conformations (identified from a 23 mu is molecular-dynamics simulation). The relative free energies of these conformations were calculated using classical metadynamics simulations in explicit water. Chemical shifts for representative conformations were calculated using density-functional theory. Comparison with experiment and analysis of the results suggests that the H-1 chemical shifts are most useful for assigning equilibrium concentrations of the conformations in this case. C-13 chemical shifts distinguish less clearly between conformations, and the distances calculated from the nuclear Overhauser effect do not allow the conformations to be assigned clearly. The H-1 chemical shifts can be reproduced with a standard error of less than 0.24 ppm (<2.2 ppm for C-13). The combined experimental and theoretical results suggest that AVP exists in an equilibrium of approximately 70% saddlelike and 30% clinched open conformations. Both newly introduced statistical metrics designed to judge the significance of the results and Smith and Goodman's DP4 probabilities are presented.},
author = {Hänsele, Elke and Saleh, Noureldin and Read, Christopher M. and Banting, Lee and Whitley, David C. and Clark, Timothy},
doi = {10.1021/acs.jcim.6b00344},
faupublication = {yes},
journal = {Journal of Chemical Information and Modeling},
pages = {1798-1807},
peerreviewed = {Yes},
title = {{Can} {Simulations} and {Modeling} {Decipher} {NMR} {Data} for {Conformational} {Equilibria}? {Arginine}-{Vasopressin}},
volume = {56},
year = {2016}
}
@article{faucris.123915044,
author = {Clark, Timothy},
faupublication = {yes},
journal = {ACS National Meeting Book of Abstracts},
peerreviewed = {unknown},
title = {{Can} simulations lead experiment?},
volume = {239},
year = {2010}
}
@article{faucris.123416524,
author = {Clark, Timothy},
doi = {10.1021/ci00068a005},
faupublication = {yes},
journal = {Journal of Chemical Information and Computer Sciences},
pages = {373-376},
peerreviewed = {Yes},
title = {{CAN} {WE} {PREDICT} {REACTIVITY} {USING} {MO} {CALCULATIONS}},
volume = {30},
year = {1990}
}
@article{faucris.123035044,
author = {Clark, Timothy and Schleyer, Paul},
doi = {10.1021/ja00520a036},
faupublication = {yes},
journal = {Journal of the American Chemical Society},
month = {Jan},
pages = {7747-7748},
peerreviewed = {Yes},
title = {{CARBENOID}, {CCL3LI}, {ESCHEWS} {TETRAHEDRAL} {STRUCTURES}},
volume = {101},
year = {1979}
}
@article{faucris.122382744,
author = {Clark, Timothy and et al.},
author_hint = {WILHELM D, CLARK T, COURTNEIDGE JL, DAVIES AG},
doi = {10.1039/C39830000213},
faupublication = {yes},
journal = {Journal of the Chemical Society - Series Chemical Communications},
month = {Jan},
pages = {213-214},
peerreviewed = {unknown},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{CARBON} {METAL} {BOND} {HOMOLYSIS} {IN} 1,2-{DIMETALLO}-{ORGANIC} {COMPOUNDS}},
year = {1983}
}
@article{faucris.216798796,
abstract = {ConspectusIn recent years, carbon nanodots (CNDs) have emerged as an environmentally friendly, biocompatible, and inexpensive class of material, whose features sparked interest for a wide range of applications. Most notable is their photoactivity, as exemplified by their strong luminescence. Consequently, CNDs are currently being investigated as active components in photocatalysis, sensing, and optoelectronics. Charge-transfer interactions are common to all these areas. It is therefore essential to be able to fine-tune both the electronic structure of CNDs and the electronic communication in CND-based functional materials.The complex, but not completely deciphered, structure of CNDs necessitates, however, a multifaceted strategy to investigate their fundamental electronic structure and to establish structure-property relationships. Such investigations require a combination of spectroscopic methods, such as ultrafast transient absorption and fluorescence up-conversion techniques, electrochemistry, and modeling of CNDs, both in the absence and presence of other photoactive materials. Only a sound understanding of the dynamics of charge transfer, charge shift, charge transport, etc., with and without light makes much-needed improvements in, for example, photocatalytic processes, in which CNDs are used as either photosensitizers or catalytic centers, possible.This Account addresses the structural, photophysical, and electrochemical properties of CNDs, in general, and the charge-transfer chemistry of CNDs, in particular. Pressure-synthesized CNDs (pCNDs), for which citric acid and urea are used as inexpensive and biobased precursor materials, lie at the center of attention. A simple microwave-assisted thermolytic reaction, performed in sealed vessels, yields pCNDs with a fairly homogeneous size distribution of ∼1-2 nm. The narrow and excitation-independent photoluminescence of pCNDs contrasts with that seen in CNDs synthesized by other techniques, making pCNDs optimal for in-depth physicochemical analyses. The atomistic and electronic structures of CNDs were also analyzed by quantum chemical modeling approaches that led to a range of possible structures, ranging from heavily functionalized, graphene-like structures to disordered amorphous particles containing small sp
2
domains.Both the electron-accepting and -donating performances of CNDs make the charge-transfer chemistry of CNDs rather versatile. Both covalent and noncovalent synthetic approaches have been explored, resulting in architectures of various sizes. CNDs, for example, have been combined with molecular materials ranging from electron-donating porphyrins and extended tetrathiafulvalenes to electron-accepting perylendiimides, or nanocarbon materials such as polymer-wrapped single-walled carbon nanotubes. In every case, charge-separated states formed as part of the reaction cascades initiated by photoexcitation. Charge-transfer assemblies including CNDs have also played a role in technological applications: for example, a proof-of-concept dye-sensitized solar cell was designed and tested, in which CNDs were adsorbed on the surface of mesoporous anatase TiO
2
. The wide range of reported electron-donor-acceptor systems documents the versatility of CNDs as molecular building blocks, whose electronic properties are tunable for the needs of emerging technologies.},
author = {Margraf, Johannes T. and Strauss, Volker and Clark, Timothy and Guldi, Dirk Michael and Cadranel, Alejandro},
doi = {10.1021/acs.accounts.8b00673},
faupublication = {yes},
journal = {Accounts of Chemical Research},
note = {CRIS-Team Scopus Importer:2019-05-02},
pages = {955-963},
peerreviewed = {Yes},
title = {{Carbon} {Nanodots} for {Charge}-{Transfer} {Processes}},
volume = {52},
year = {2019}
}
@article{faucris.115053444,
abstract = {We describe the formation of charge-transfer complexes that feature electron-donating carbon nanodots (CND) and electron-accepting perylenediimides (PDI). The functionalities of PDIs have been selected to complement those of CNDs in terms of electrostatic and -stacking interactions based on oppositely charged ionic head groups and extended -systems, respectively. Importantly, the contributions from electrostatic interactions were confirmed in reference experiments, in which stronger interactions were found for PDIs that feature positively rather than negatively charged head groups. The electronic interactions between the components in the ground and excited state were characterized in complementary absorption and fluorescence titration assays that suggest charge-transfer interactions in both states with binding constants on the order of 8x10(4)M(-1) (25Lg(-1)). Selective excitation of the two components in ultrafast pump probe experiments gave a 210ps lived charge-separated state.},
author = {Strauß, Volker and Margraf, Johannes and Dirian, Konstantin and Syrgiannis, Zois and Prato, Maurizio and Wessendorf, Cordula and Hirsch, Andreas and Clark, Timothy and Guldi, Dirk Michael},
doi = {10.1002/anie.201502482},
faupublication = {yes},
journal = {Angewandte Chemie International Edition},
keywords = {carbon nanodots;charge transfer;donor-acceptor compounds;perylenediimides;transient absorption},
pages = {8292-8297},
peerreviewed = {Yes},
title = {{Carbon} {Nanodots}: {Supramolecular} {Electron} {Donor}-{Acceptor} {Hybrids} {Featuring} {Perylenediimides}},
volume = {54},
year = {2015}
}
@article{faucris.107257524,
abstract = {We report the characterization of carbon nanodots (CNDs) synthesized under mild and controlled conditions, that is, in a microwave reactor. The CNDs thus synthesized exhibit homogeneous and narrowly dispersed optical properties. They are thus well suited as a testbed for studies of the photophysics of carbon-based nanoscopic emitters. In addition to steady-state investigations, time-correlated single-photon counting, fluorescence up-conversion, and transient pump probe absorption spectroscopy were used to elucidate the excited-state dynamics. Moreover, quenching the CND-based emission with electron donors or acceptors helped shed light on the nature of individual states. Density functional theory and semiempirical configuration-interaction calculations on model systems helped understand the fundamental structure-property relationships for this novel type of material.},
author = {Strauß, Volker and Margraf, Johannes and Dolle, Christian and Butz, Benjamin and Nacken, Thomas and Walter, Johannes and Bauer, Walter and Peukert, Wolfgang and Spiecker, Erdmann and Clark, Timothy and Guldi, Dirk Michael},
doi = {10.1021/ja510183c},
faupublication = {yes},
journal = {Journal of the American Chemical Society},
pages = {17308--17316},
peerreviewed = {Yes},
title = {{Carbon} {Nanodots}: {Toward} a {Comprehensive} {Understanding} of {Their} {Photoluminescence}},
volume = {136},
year = {2014}
}
@article{faucris.213259947,
abstract = {We report a combined experimental and computational study of the whey protein \textgreekb-lactoglobulin (BLG) in different electrolyte solutions. Vibrational sum-frequency generation (SFG) and ellipsometry were used to investigate the molecular structure of BLG modified air-water interfaces as a function of LiCl, NaCl, and KCl concentrations. Molecular dynamics (MD) simulations and thermodynamic integration provided details of the ion pairing of protein surface residues with alkali-metal cations. Our results at pH 6.2 indicate that BLG at the air-water interface forms mono- and bilayers preferably at low and high ionic strength, respectively. Results from SFG spectroscopy and ellipsometry are consistent with intimate ion pairing of alkali-metal cations with aspartate and glutamate carboxylates, which is shown to be more effective for smaller cations (Li(+) and Na(+)). MD simulations show not only carboxylate-alkali-metal ion pairs but also ion multiplets with the alkali-metal ion in a bridging position between two or more carboxylates. Consequently, alkali-metal cations can bridge carboxylates not only within a monomer but also between monomers, thus providing an important dimerization mechanism between hydrophilic surface patches.},
author = {Beierlein, Frank and Clark, Timothy and Braunschweig, Björn and Engelhardt, Kathrin and Glas, Lena and Peukert, Wolfgang},
doi = {10.1021/acs.jpcb.5b01944},
faupublication = {yes},
journal = {Journal of Physical Chemistry B},
keywords = {electrolyte; solution; molecular; dynamics; surface;},
note = {EAM Import::2019-03-13},
pages = {5505-5517},
peerreviewed = {Yes},
title = {{Carboxylate} {Ion} {Pairing} with {Alkali}-{Metal} {Ions} for β-{Lactoglobulin} and {Its} {Role} on {Aggregation} and {Interfacial} {Adsorption}},
volume = {119},
year = {2015}
}
@article{faucris.122383624,
author = {Clark, Timothy},
doi = {10.1021/ja00184a071},
faupublication = {yes},
journal = {Journal of the American Chemical Society},
month = {Jan},
pages = {761-763},
peerreviewed = {Yes},
title = {{CATALYSIS} {OF} {CLOSED}-{SHELL} {REACTIONS} {BY} {COMPLEXATION} {WITH} {METAL} {RADICAL} {CATIONS}},
volume = {111},
year = {1989}
}
@article{faucris.121196944,
abstract = {The 2s + 2s cycloaddition of ethylene, a forbidden Woodward-Hoffmann type closed-shell reaction, is illustrated by ab initio calculations to be catalyzed by complexation with Be.+. The reaction path calculated proceeds via a metallacyclopentane radical cation intermediate and two successive 1,2-hydrogen shifts to form the isomeric butenes. The possible reaction to cyclobutane by formation of a second carbon-carbon bond from the metallacyclopentane has also been examined. The complexed dimerization reaction is found to be exothermic for all products (26.3 kcal mol-1 for 1-butene, 27.9 kcal mol-1 for cis-2-butene, 29.5 kcal mol-1 for trans-2-butene, and 21.3 kcal mol-1 for cyclobutane) with no point on any of the reaction paths higher in energy than the starting point, Be.+ + 2C2H4. Remarkable parallels to transition-metal-catalyzed dimerizations are found.},
author = {Alex, Alexander and Clark, Timothy},
doi = {10.1021/ja00028a016},
faupublication = {yes},
journal = {Journal of the American Chemical Society},
month = {Jan},
pages = {506-510},
peerreviewed = {Yes},
title = {{CATALYSIS} {OF} {ETHYLENE} {DIMERIZATION} {BY} {COMPLEXATION} {WITH} {METAL} {RADICAL} {CATIONS} - {AN} {ABINITIO} {STUDY}},
volume = {114},
year = {1992}
}
@article{faucris.122388904,
abstract = {Ab anti and density-functional theory (DFT) calculations have been used to investigate the model rearrangements of quadricyclane to norbornadiene catalysed by single CuSO4 and SnCl2 molecules. The isolated reactions with the two molecular catalysts proceed via electron-transfer catalysis in which the hydrocarbon is oxidised, in contrast to systems investigated previously in which the substrate was reduced. The even-electron SnCl2-catalysed reaction shows singlet-triplet two-state reactivity. Solvation by a single methanol molecule changes the mechanism of the rearrangement to a classical Lewis acid-base process.},
author = {Shubina, Tatyana E. and Clark, Timothy},
doi = {10.1515/znb-2010-0319},
faupublication = {yes},
journal = {Zeitschrift für Naturforschung Section B-A Journal of Chemical Sciences},
keywords = {Ab initio Calculations;Density Functional Calculations;Electron Transfer;Catalysis;Rearrangement},
pages = {347-356},
peerreviewed = {Yes},
title = {{Catalysis} of the {Quadricyclane} to {Norbornadiene} {Rearrangement} by {SnCl2} and {CuSO4}},
volume = {65},
year = {2010}
}
@article{faucris.122393084,
abstract = {The ring opening and isomerization of cyclopropane are shown by ab initio calculations to be catalyzed by complexation with Be.+. The reactions proceed via a common metallacyclobutane radical cation intermediate formed in a reaction that is endothermic by 12.3 kcal mol-1 relative to the cyclopropane-Be.+ complex. From this intermediate, three alternative reaction paths were examined, two isomerizations to give a propene-Be.+ complex and a C-C bond cleavage forming a carbene-ethylene-Be.+ species. These reactions are found to be exothermic by 5.4 and 5.2 kcal mol-1 relative to the cyclopropane-Be.+ complex, respectively. The isomerization of cyclopropane to give propene is calculated to be exothermic by 8.0 kcal mol-1 (exptl 7.9 kcal mol-1). Remarkable parallels to transition-metal catalyzed reactions were found for all the reactions examined.},
author = {Alex, Alexander and Clark, Timothy},
doi = {10.1021/ja00053a028},
faupublication = {yes},
journal = {Journal of the American Chemical Society},
pages = {10897-10902},
peerreviewed = {Yes},
title = {{CATALYSIS} {OF} {THE} {RING}-{OPENING} {AND} {ISOMERIZATION} {OF} {CYCLOPROPANE} {BY} {COMPLEXATION} {WITH} {METAL} {RADICAL} {CATIONS} - {AN} {ABINITIO} {STUDY}},
volume = {114},
year = {1992}
}
@article{faucris.119330904,
abstract = {Reaction of(2-bromophenylethynyl)trimethylsilane 1 with trimethyl berate yielded the alkynearyl-boronic acid 2, which was coupled in situ with the bromoallenes 3 to give enyne-allenes 4. The intermediates 4 underwent a spontaneous cation-mediated C-2-C-7 cycloaromatization with a concomitant 1,2-shift of the trimethylsilyl group to give the naphthalene derivatives 5. Besides 5, yne-allenes 10 were isolated by chromatography of the crude reaction products. A key step in the formation of 10 is the hydrolysis of the aryl boronic acid 2, which led to phenylethynyltrimethylsilane 8. Under the reaction conditions used, the TMS group of 8 was subsequently removed to give phenylacetylene 9, which further reacted with the bromoallenes 3 to furnish the yne-allenes 10.},
author = {Saalfrank, Rolf W. and Haubner, Martin and Deutscher, Christian and Bauer, Walter and Clark, Timothy},
faupublication = {yes},
journal = {Journal of Organic Chemistry},
pages = {6166-6168},
peerreviewed = {Yes},
title = {{Cation}-mediated, substituent-controlled, {C}-2-{C}-7 cycloaromatization of an enyne-allene},
volume = {64},
year = {1999}
}
@article{faucris.122341604,
author = {Clark, Timothy and Schleyer, Paul and et al.},
author_hint = {ROHDE C, CLARK T, KAUFMANN E, SCHLEYER PV},
doi = {10.1039/C39820000882},
faupublication = {yes},
journal = {Journal of the Chemical Society - Series Chemical Communications},
month = {Jan},
pages = {882-884},
peerreviewed = {unknown},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {({CH2LIF})2 - {THE} {EFFECTS} {OF} {DIMERIZATION} {ON} {THE} {STRUCTURE} {AND} {DISSOCIATION}-{ENERGY} {OF} {CARBENOIDS}},
year = {1982}
}
@article{faucris.121944064,
author = {Clark, Timothy and Schindler, Thorsten},
faupublication = {yes},
journal = {ACS National Meeting Book of Abstracts},
pages = {U283-U283},
peerreviewed = {unknown},
title = {{Charge} carriers in polythiophenes.},
volume = {220},
year = {2000}
}
@article{faucris.208729435,
abstract = {The synthesis of a series of new electron donor bridge acceptor (D-B-A) conjugates (18-20) comprising electron-donating zinc(II) porphyrins (ZnPs) and electron-accepting fullerenes (C(60)s) connected through various co-oligonier bridges containing both dibenzothiophene-S,S-dioxide and fluorene units is reported. Detailed investigations using cyclic voltarnmetry, absorption, fluorescence, and femto/nanosecond transient absorption spectroscopy in.combination with quantum,chemical calculations have enabled us to develop a detailed mechanistic view of the charge-transfer processes that follow photoexcitation of ZnP, the bridge, or C-60. Variations in the dynamics of charge separation, charge recombination, and charge transfer gating are primarily consequences of the electronic properties of the co-oligomer bridges, including their electron affinity and the energy levels of the excited states. In particular, placing one dibenothiophene-S,S-dioxide building block at the center of the molecular bridge flanked by two fluorene building blocks, as in 20, favors hole rather than electron transfer between the remote electron donors and acceptors, as demonstrated by exciting C-60 rather than ZnP. In 18 and 19, in which one dibenzothiophene-S,S-dioxide and one throrene building block constitute the molecular bridge, photoexcitation of either ZnP or C-60 results in both hole and electron transfer. Dibenzothiophene-S,S-dioxide is thug shown to be an excellent building block for probing how subtle structural and electronic variations in the bridge affect unidirectional charge transport in D-B-A conjugates. The experimental results are supported by computational calculations.},
author = {Yzambart, Gilles and Zieleniewska, Anna and Bauroth, Stefan and Clark, Timothy and Bryce, Martin R. and Guldi, Dirk Michael},
doi = {10.1021/acs.jpcc.7b03889},
faupublication = {yes},
journal = {Journal of Physical Chemistry C},
pages = {13557-13569},
peerreviewed = {Yes},
title = {{Charge}-{Gating} {Dibenzothiophene}-{S},{S}-dioxide {Bridges} in {Electron} {Donor}-{Bridge}-{Acceptor} {Conjugates}},
volume = {121},
year = {2017}
}
@article{faucris.116876364,
author = {Clark, Timothy},
faupublication = {yes},
journal = {ACS National Meeting Book of Abstracts},
pages = {U278-U278},
peerreviewed = {unknown},
title = {{Charge} transport in conducting polymers.},
volume = {222},
year = {2001}
}
@article{faucris.208729703,
abstract = {An additional charge carrier described as its wave function is propagated in imaginary time using stepwise matrix multiplication and a correction to ensure that the simulation is norm-conserving. The propagation Hamilton operator uses the local ionization energy of a rubrene single crystal, calculated with semiempirical molecular orbital theory, as an external potential for holes to model the interaction with the underlying molecular structure. Virtual electrodes are modeled by setting the potentials in the appropriate areas to constant values with the difference corresponding to the source-drain voltage. Although imaginary time cannot be interpreted directly as time, the simulated gate-dependent imaginary transfer rate is in acceptable qualitative agreement with the experimentally measured gate-dependent hole-transfer rate through a rubrene single crystal.},
author = {Kriebel, Maximilian and Sharapa, Dmitry and Clark, Timothy},
doi = {10.1021/acs.jctc.7b00568},
faupublication = {yes},
journal = {Journal of Chemical Theory and Computation},
pages = {6308-6316},
peerreviewed = {Yes},
title = {{Charge} {Transport} in {Organic} {Materials}: {Norm}-{Conserving} {Imaginary} {Time} {Propagation} with {Local} {Ionization} {Energy} as the {External} {Potential}},
volume = {13},
year = {2017}
}
@book{faucris.107535824,
author = {Wielopolski, Mateusz and Guldi, Dirk Michael and Clark, Timothy and Martín, Nazario},
doi = {10.1002/9783527633074.ch6},
faupublication = {yes},
pages = {157-187},
publisher = {Wiley-VCH Verlag GmbH & Co. KGaA},
title = {{Charge} {Transport} through {Molecules}: {Organic} {Nanocables} for {Molecular} {Electronics}},
year = {2011}
}
@incollection{faucris.118244104,
address = {Singapur},
author = {Hirsch, Andreas and Mauser, Harald and Clark, Timothy},
booktitle = {Molecular Nanostructures},
editor = {Hans Kuzmany, Jörg Fink, Michael Mehring, Siegmar Roth},
faupublication = {yes},
pages = {55-60},
peerreviewed = {Yes},
publisher = {World Scientific Publishing Company},
title = {{Chemical} {Faraday} {Cages}: {The} {Inert} {Inner} {Surfaces} of {Strongly} {Bent} sp2-{Carbon} {Networks} and {Fullerenes}},
url = {http://www.worldscientific.com/worldscibooks/10.1142/3592},
year = {1998}
}
@article{faucris.116880324,
author = {Clark, Timothy},
doi = {10.1021/ja00520a035},
faupublication = {yes},
journal = {Journal of the American Chemical Society},
month = {Jan},
pages = {7746-7747},
peerreviewed = {Yes},
title = {{CHEMICAL} {GENERATION} {OF} {EXCITED}-{STATE} {RADICALS} - {SUCCINIMIDOYL}},
volume = {101},
year = {1979}
}
@article{faucris.121597784,
author = {Clark, Timothy},
faupublication = {yes},
journal = {ACS National Meeting Book of Abstracts},
pages = {U396-U396},
peerreviewed = {unknown},
title = {{Chemiinformatics} with quantum mechanics.},
volume = {222},
year = {2001}
}
@article{faucris.110122364,
abstract = {Do the chemical properties of the surface of a carbon sheet depend on its shape? This question addresses a criterion for chemical behaviour that has hardly been investigated previously. The current neglect of this question may be due to the fact that suitable model systems with easily distinguishable graphitic surfaces were essentially unknown until the discovery [1] and synthesis [2,3,4] of fullerenes, nanotubes and other related forms of carbon. In this study, we present the first systematic comparison of the chemical behaviour of the convex outer and the concave inner surfaces of C-60 by analysing the results of semiempirical and DFT calculations on exohedral and endohedral complexes with H- and F-atoms as well as with the methyl radical. We show that such extremely reactive species are trapped by the extraordinary inert inner surface of C-60 and do not undergo chemical reactions.},
author = {Mauser, Harald and van Eikema Hommes, Nico and Hirsch, Andreas and Clark, Timothy},
doi = {10.1007/s008940050059},
faupublication = {yes},
journal = {Journal of Molecular Modeling},
month = {Jan},
pages = {415-422},
peerreviewed = {Yes},
title = {{Chemistry} of {Convex} versus {Concave} {Carbon}: {The} {Reactive} {Exterior} and the {Inert} {Interior} of {C60}},
volume = {3},
year = {1997}
}
@article{faucris.205128276,
abstract = {A novel concept for constructing optimized ZnO-based photoanodes as integrative components of dye-sensitized solar cells (DSSCs) is realized by deploying differently sized nanoparticles, ranging from 2 to 10 nm, together with commercially available 20 nm nanoparticles. The 2 nm nanoparticles were used to construct an efficient buffer layer for transparent electrodes based on 10 nm nanoparticles, resulting in a relative increase of device efficiency from 1.8 to 3.0% for devices without and with a buffer layer, respectively. A mixture of 10 and 20 nm nanoparticles was optimized to maximize the diffuse reflection and to minimize the charge transport resistance in a light-scattering layer. This optimization resulted in a homogenous layer of more than 15 mm that provided a device efficiency of 3.3%. The buffer layer, transparent electrode, and light-scattering electrode, were then combined to give an overall efficiency of around 5%. Thus, this work demonstrates that varying the electrode architecture with nanoparticles of different diameters is a powerful strategy for improving the overall efficiency of ZnO-based DSSCs.},
author = {Pfau, Markus and Kunzmann, Andreas and Segets, Doris and Peukert, Wolfgang and Wallace, Gordon G. and Officer, David L. and Clark, Timothy and Costa, Ruben Dario and Guldi, Dirk Michael},
doi = {10.1039/c6ta11012f},
faupublication = {yes},
journal = {Journal of Materials Chemistry A},
pages = {7516-7522},
peerreviewed = {Yes},
title = {{Choosing} the right nanoparticle size-designing novel {ZnO} electrode architectures for efficient dye-sensitized solar cells},
volume = {5},
year = {2017}
}
@article{faucris.227513448,
abstract = {A tetrameric pentacene, PT, has been used to explore the effects of exciton delocalization on singlet fission (SF). For the first time, triplet decorrelation through intramolecular triplet diffusion was observed following SF. Transient absorption spectroscopy was used to examine different decorrelation mechanisms (triplet diffusion versus structural changes) for PT and its dimeric equivalent PD on the basis of the rate and activation barrier of the decorrelation step. Charge-separation experiments using tetracyano-p-quinodimethane (TCNQ) to quench triplet excitons formed through SF demonstrate that enhanced intersystem crossing, that is, spin catalysis, is a widely underestimated obstacle to quantitative harvesting of the SF products. The importance of spatial separation of the decorrelated triplet states is emphasized, and independent proof that the decorrelated triplet pair state consists of two (T-1) states per molecule is provided.},
author = {Hetzer, Constantin and Basel, Bettina and Kopp, Sebastian M. and Hampel, Frank and White, Fraser J. and Clark, Timothy and Guldi, Dirk Michael and Tykwinski, Rik R.},
doi = {10.1002/anie.201907221},
faupublication = {yes},
journal = {Angewandte Chemie International Edition},
note = {CRIS-Team WoS Importer:2019-10-04},
peerreviewed = {Yes},
title = {{Chromophore} {Multiplication} {To} {Enable} {Exciton} {Delocalization} and {Triplet} {Diffusion} {Following} {Singlet} {Fission} in {Tetrameric} {Pentacene}},
year = {2019}
}
@article{faucris.109346644,
abstract = {Density functional theory (DFT) calculations on iron(II) (FeP) and cobalt(II) (CoP) porphyrins with nitric oxide (NO) and carbon monoxide (CO) as axial ligands have been performed using BLYP, B3LYP, OLYP, B3PW91, and M06L functionals with double-and triple-xi basis sets. Optimized geometries and binding energies were found to depend very strongly on the functional and basis set used. MP2 fails completely to describe geometries and binding energies of FeP-CO, CoP-CO, and CoP-NO complexes, but performs relatively well for the FeP-NO complex. The calculated binding energies range from -4.5 to -19.6 kcal mol(-1) for CoP-CO, +4.0 to -29.1 kcal mol(-1) for FeP-CO, +7.6 to -41.1 kcal mol(-1) for FeP-NO, and -2.2 to -36.7 kcal mol(-1) for CoP-NO. B3PW91/6-311+G(d,p) and OLYP/6-311+G(d,p) perform better than the other functional/basis set combinations in reproducing the available experimental data. A complete active space self-consistent field/complete active space with second-order perturbation theory (CASSCF/CASPT2) analysis of the CO and NO interactions with FeP and CoP can be interpreted either in terms of sigma-donation/pi-back-donation mechanism (FeP-CO and CoP-CO) or sigma bond formation between the 3d(z2) orbital of metal and the pi* orbital of NO.},
author = {Shubina, Tatyana and Clark, Timothy},
doi = {10.1080/00958972.2010.503346},
faupublication = {yes},
journal = {Journal of Coordination Chemistry},
keywords = {Metalloporphyrins;Nitric oxide;Carbon monoxide;DFT;MP2},
month = {Jan},
pages = {2854-2867},
peerreviewed = {Yes},
title = {{CO} and {NO} complexes of {Fe}({II}) and {Co}({II}) porphyrins},
volume = {63},
year = {2010}
}
@article{faucris.122394624,
abstract = {The crystal structure of an unusual 1 : 1 molecular complex between benzene and acetylene, two very small and apolar molecules, has been determined by X-ray-analysis of crystals grown by first mixing the two liquids under conditions of low temperature and high pressure in a capillary, followed by repeated zone melting to form crystals directly on the goniometer head of a diffractometer. Each acetylene molecule is clamped between two parallel benzene rings, with its molecular axis apparently perpendicular to the benzene planes. Closer inspection of thermal-motion data from the diffraction experiment suggests that the acetylene molecule undergoes a wobbling, or precession, motion between the two rings so that it is perpendicular to them only in a time-averaged sense. The results of quantum-chemical calculations on isolated molecular dimers and trimers support this conclusion. In addition, the calculation of separate coulombic, dispersion, polarization and repulsion contributions to intermolecular bonding reveals that the C-H ... pi-bond interaction between acetylene and benzene in a T-shaped dimer consists of a mixture of coulombic and polarization interactions. In the benzene-acetylene cocrystal, its magnitude is quantitatively comparable with that of other dispersive interactions. 5.4 ns Molecular-dynamics simulations of the liquid mixture reveal that the two components are persistently miscible, a possible key to the formation of the cocrystal. No structure is, however, observed in the solution during the relatively short simulation time.},
author = {Clark, Timothy and et al.},
author_hint = {Boese R, Clark T, Gavezzotti A},
doi = {10.1002/hlca.200390095},
faupublication = {yes},
journal = {Helvetica Chimica Acta},
month = {Jan},
pages = {1085-1100},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{Cocrystallization} with acetylene. {The} 1 : 1 complex with benzene: {Crystal} growth, x-ray diffraction and molecular simulations},
volume = {86},
year = {2003}
}
@article{faucris.116831044,
author = {Bai, Yun and Flechtner, Ken and Marbach, Hubertus and Buchner, Florian and Hieringer, Wolfgang and Görling, Andreas and Shubina, Tatyana and Clark, Timothy and Steinrück, Hans-Peter and Gottfried, Michael},
faupublication = {yes},
journal = {ACS National Meeting Book of Abstracts},
peerreviewed = {unknown},
title = {{COLL} 106-{Surface} chemistry with metalloporphyrins and metallophthalocyanines: {Formation}, structure, and reactivity},
volume = {236},
year = {2008}
}
@article{faucris.228842573,
abstract = {A study on electron transfer in three electron donoracceptor complexes is reported. These architectures consist of a zinc phthalocyanine (ZnPc) as the excitedstate electron donor and a fullerene (C-60) as the groundstate electron acceptor. These complexes are brought together by axial coordination at ZnPc. The key variable in our design is the length of the molecular spacer, namely, oligopphenylenevinylenes. The lack of appreciable groundstate interactions is in accordance with strong excitedstate interactions, as inferred from the quenching of ZnPc centered fluorescence and the presence of a shortlived fluorescence component. Fullfledged femtosecond and nanosecond transient absorption spectroscopy assays corroborated that the ZnPc C-+(60) chargeseparated state formation comes at the expense of excitedstate interactions following ZnPc photoexcitation. At a first glance, the ZnPc C-+(60) charge separated state lifetime increased from 0.4 to 86.6 ns as the electron donoracceptor separation increased from 8.8 to 29.1 angstrom. A closer look at the kinetics revealed that the changes in chargeseparated state lifetime are tied to a decrease in the electronic coupling element from 132 to 1.2 cm(1), an increase in the reorganization energy of charge transfer from 0.43 to 0.63 eV, and a large attenuation factor of 0.27 angstrom(1).},
author = {Krug, Marcel and Stangel, Christina and Zieleniewska, Anna and Clark, Timothy and Torres, Tomas and Coutsolelos, Athanassios G. and Guldi, Dirk Michael},
doi = {10.1002/cphc.201900780},
faupublication = {yes},
journal = {ChemPhysChem},
note = {CRIS-Team WoS Importer:2019-11-08},
peerreviewed = {Yes},
title = {{Combining} {Zinc} {Phthalocyanines}, {Oligo}(p-{Phenylenevinylenes}), and {Fullerenes} to {Impact} {Reorganization} {Energies} and {Attenuation} {Factors}},
year = {2019}
}
@article{faucris.122233584,
abstract = {Residue Arg(3.50) belongs to the highly conserved DRY-motif of class A GPCRs, which is located at the bottom of TM3. On the one hand, Arg(3.50) has been reported to help stabilize the inactive state of GPCRs, but on the other hand has also been shown to be crucial for stabilizing active receptor conformations and mediating receptor-G protein coupling. The combined results of these studies suggest that the exact function of Arg(3.50) is likely to be receptor-dependent and must be characterized independently for every GPCR. Consequently, we now present comparative molecular-dynamics simulations that use our recently described inactive-state and Ga-bound active-state homology models of the dopamine D2 receptor (D2R), which are either bound to dopamine or ligand-free, performed to identify the function of Arg132(3.50) in D2R. Our results are consistent with a dynamic model of D2R activation in which Arg132(3.50) adopts a dual role, both by stabilizing the inactive-state receptor conformation and enhancing dopamine-dependent D2R-G protein coupling.},
author = {Kling, Ralf and Clark, Timothy and Gmeiner, Peter},
doi = {10.1371/journal.pone.0146612},
faupublication = {yes},
journal = {PLoS ONE},
month = {Jan},
peerreviewed = {Yes},
title = {{Comparative} {MD} {Simulations} {Indicate} a {Dual} {Role} for {Arg132}(3.50) in {Dopamine}-{Dependent} {D2R} {Activation}},
volume = {11},
year = {2016}
}
@article{faucris.261340684,
abstract = {The course of the Barton-Kellogg (BK) reaction for alkyl- and aryl-substituted substrates has been investigated at the DLPNO-CCSD(T)/def2-TZVPP//omega B97X-D/def2-TZVPP level of theory, with results compared to available experimental kinetic data. Through comparison with the unsubstituted parent system, the preference for the formation of 1,3,4-dihydrothia-diazole over the isomeric 1,2,3-dihydrothia-diazole was observed to result from reduced steric repulsion in the relevant transition-state structure. Nitrogen extrusion [retro-(3 + 2)-cycloaddition] from the intermediate dihydrothiadiazole was found to be the rate-determining step. The barrier for this process was, however, significantly lower for aromatic substrates, which is consistent with the difficulty in isolating aryl-substituted dihydrothiadiazoles. The electronic structure of the transient thiocarbonyl ylide was also investigated, highlighting the contradictory results from wave-function theory- and density functional theory-based methods. Correlation of unrestricted natural orbital eigenvalues with previous experimental models suggested that the dipole intermediates possess low diradical character and are therefore considered to be closed-shell species. Exergonic conrotatory electrocyclization of the dipole led to sterically congested thiirane products, even for very bulky systems (di-t-butyl). These results complement the recent work of Mloston et al. Finally, DLPNO-CCSD(T)//omega B97X-D was found to be a reliable method for estimating the feasibility of the BK reaction, which should assist experimentalists in the selection of viable substrates.},
author = {Burns, Jed M. and Clark, Timothy and Williams, Craig M.},
doi = {10.1021/acs.joc.1c00506},
faupublication = {yes},
journal = {Journal of Organic Chemistry},
note = {CRIS-Team WoS Importer:2021-07-09},
pages = {7515-7528},
peerreviewed = {Yes},
title = {{Comprehensive} {Computational} {Investigation} of the {Barton}-{Kellogg} {Reaction} for {Both} {Alkyl} and {Aryl} {Systems}},
volume = {86},
year = {2021}
}
@book{faucris.121598444,
abstract = {Enzymes play a key role in modern pharmaceutical research because they represent targets for the design of new drugs. In addition to the classical approach of inhibiting an enzyme by blocking its binding site with an inhibitor, the level of gene expression is now moving into the focus of interest. An important system for the investigation of mechanisms of transcriptional control is the Tet repressor/tet operator (TetR/tetO) system. We employ a combined classical/quantum mechanical approach to model the structure and the spectroscopic properties of the TetR-tetracycline complex. As our methods are based on semiempirical molecular orbital theory, we have also developed a parallel pseudodiagonalization technique for the major computational step in such calculations. The parallel pseudodiagonalizer gives acceptable performance for up to about eight processors.},
author = {Beierlein, Frank and Clark, Timothy},
doi = {10.1007/3-540-26657-7{\_}22},
faupublication = {yes},
keywords = {molecular dynamics;configuration interaction;AM1;MD/Cl;parallelization;pseudodiagonalization;parallel computing},
month = {Jan},
pages = {245-259},
peerreviewed = {unknown},
title = {{Computer} simulations of enzyme reaction mechanisms: {Simulation} of protein spectra},
year = {2004}
}
@article{faucris.119286464,
author = {Clark, Timothy},
doi = {10.1039/dc9847800203},
faupublication = {yes},
journal = {Faraday Discussions},
month = {Jan},
pages = {203-212},
peerreviewed = {unknown},
title = {{CONDENSED}-{PHASE} {RADICAL}-{ANIONS}},
volume = {78},
year = {1984}
}
@article{faucris.122396164,
author = {Clark, Timothy},
faupublication = {yes},
journal = {Chemistry in Britain},
month = {Jan},
pages = {891-891},
peerreviewed = {No},
title = {{CONFERENCE} {LABELING}},
volume = {20},
year = {1984}
}
@article{faucris.115589144,
author = {Lanig, Harald and Clark, Timothy and Gottschalk, Maik and Schneider, Siegfried},
doi = {10.1007/s008940050104},
faupublication = {yes},
journal = {Journal of Molecular Modeling},
note = {UnivIS-Import:2015-03-05:Pub.1999.nat.dchph.lpc1.confor},
pages = {46-62},
peerreviewed = {Yes},
title = {{Conformational} {Analysis} of {Tetracycline} using {Molecular} {Mechanical} and {Semiempirical} {MO}-{Calculations}},
volume = {5},
year = {1999}
}
@article{faucris.121600424,
abstract = {Electron donor-acceptor systems, in which phenothiazine is tethered to pyrene by means of a phenyl bridge, exhibit a dual emission in moderately and very polar solvents. Employing steady-state and time-resolved fluorescence spectroscopy, we were able to provide evidence that the "blue" and "red" emission bands originate from different conformers. The ground-state geometry of the majority species is identical to that found in the crystalline state (the quasi-equatorial conformer). This conformation executes a fast electron-transfer process accompanied by significant structural relaxation. Consequently, its fluorescence exhibits a large solvatochromic shift typical for charge-transfer states. The photophysical properties of the minority species (the quasi-axial conformer) vary significantly with the substitution pattern of the bridging phenyl ring. In part, this difference is related to the orientational factor, K, governing the rate of energy transfer between the pyrene and phenothiazine moieties. In the para-substituted derivative, fluorescence emission from both the excited phenylpyrene and the phenylphenothiazine subsystem can be observed. In the meta-substituted derivative, fluorescence originates mainly from the primarily absorbing phenylpyrene subsystem. In nonpolar solvent (cyclohexane), the nature of the fluorescing state differs for the para- and meta-substituted compounds. Whereas in the former, the fluorescence originates from the locally excited phenothiazine, it is governed by emission from a structurally modified CT state in the latter derivative. Semiempirical (AM1/CI) molecular orbital calculations with a continuum solvent treatment have been used to investigate the different states involved and provide explanations for the observed results. The calculations reveal the existence of an intermediately populated CT state in which the negative charge is partly localized in the bridge as well as in the pyrene acceptor.},
author = {Kurzawa, Jana and Acar, Nursel and Schneider, Siegfried and Daub, Jörg and Clark, Timothy and et al.},
author_hint = {Stockmann A, Kurzawa J, Fritz N, Acar N, Schneider S, Daub J, Engl R, Clark T},
doi = {10.1021/jp0142987},
faupublication = {yes},
journal = {Journal of Physical Chemistry A},
pages = {7958-7970},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{Conformational} control of photoinduced charge separation within phenothiazine-pyrene dyads},
volume = {106},
year = {2002}
}
@article{faucris.122396384,
author = {Clark, Timothy and Schleyer, Paul},
faupublication = {yes},
journal = {Journal of Computational Chemistry},
month = {Jan},
pages = {20-29},
peerreviewed = {Yes},
title = {{CONFORMATIONAL} {PREFERENCES} {OF} 34 {VALENCE} {ELECTRON} {A2X4} {MOLECULES} - {AN} {ABINITIO} {STUDY} {OF} {B2F4}, {B2CL4}, {N2O4}, {AND} {C2O4}(2-)},
volume = {2},
year = {1981}
}
@article{faucris.208729970,
abstract = {Conformation and dynamics of the vasoconstrictive peptides human urotensin II (UII) and urotensin related peptide (URP) have been investigated by both unrestrained and enhanced-sampling molecular-dynamics (MD) simulations and NMR spectroscopy. These peptides are natural ligands of the G-protein coupled urotensin II receptor (UTR) and have been linked to mammalian pathophysiology. U11 and URP cannot be characterized by a single structure but exist as an equilibrium of two main classes of ring conformations, open and folded, with rapidly interchanging subtypes. The open states are characterized by turns of various types centered at (KY9)-Y-8 or (FW7)-W-6 predominantly with no or only sparsely populated transannular hydrogen bonds. The folded conformations show multiple turns stabilized by highly populated transannular hydrogen bonds comprising centers (FWK8)-W-6-K-7 or (WKY9)-K-7-Y-8. Some of these conformations have not been characterized previously. The equilibrium populations that are experimentally difficult to access were estimated by replica-exchange MD simulations and validated by comparison of experimental NMR data with chemical shifts calculated with density-functional theory. UII exhibits approximately 72% open:28% folded conformations in aqueous solution. URP shows very similar ring conformations as TM but differs in an open folded equilibrium shifted further toward open conformations (86:14) possibly arising from the absence of folded N-terminal tail-ring interaction. The results suggest that the different biological effects of Ull and URP are not caused by differences in ring conformations but rather by different interactions with UTR.},
author = {Haensele, Elke and Mele, Nawel and Miljak, Marija and Read, Christopher M. and Whitley, David C. and Banting, Lee and Delepee, Carla and Santos, Jana Sopkova-De Oliveira and Lepailleur, Alban and Bureau, Ronan and Essex, Jonathan W. and Clark, Timothy},
doi = {10.1021/acs.jcim.6b00706},
faupublication = {yes},
journal = {Journal of Chemical Information and Modeling},
pages = {298-310},
peerreviewed = {Yes},
title = {{Conformation} and {Dynamics} of {Human} {Urotensin} {II} and {Urotensin} {Related} {Peptide} in {Aqueous} {Solution}},
volume = {57},
year = {2017}
}
@article{faucris.122397484,
abstract = {Quantitative structure property relationships for predicting the water octanol partition coefficient, logP(OW), are reported. The models are based on local properties calculated at the standard isodensity surface using semiempirical molecular orbital theory and use descriptors obtained as the areas of the surface found in each bin in a predefined binning scheme. The effect of conformation is taken into account but was found to have little effect on the predictive power of the models. A detailed error analysis suggests that the accuracy of the models is limited by that of the experimental data and that the best possible performance is approximately +/- 0.5 log units. The models yield a local hydrophobicity function at the surface of the molecules.},
author = {Mühlbacher, Markus and El Kerdawy, Ahmed and Kramer, Christian and Hudson, Brian and Clark, Timothy},
doi = {10.1021/ci200276v},
faupublication = {yes},
journal = {Journal of Chemical Information and Modeling},
pages = {2408-2416},
peerreviewed = {Yes},
title = {{Conformation}-{Dependent} {QSPR} {Models}: {logP}({OW})},
volume = {51},
year = {2011}
}
@article{faucris.121602404,
abstract = {H-1 NMR spectroscopic studies established the presence of a chair conformation for endo-3-methyl-6-morpholino-3-azabicyclo[3.1.0]hexane derivatives 8a and b. This was additionally confirmed by an X-ray structural analysis of 8b. The diastereomers 10a,b and the N-demethyl-endo-morpholino compounds 9a,b, however, were found to prefer a boat conformation. The correlation between dihedral angles and ring buckle of 3-azabicyclo[3.1.0]hexane 4 was determined by MNDOC semiempirical calculations. Further structural information about this bicyclic system was obtained by HF/6-31 G* calculations for the 3-azabicyclo[3.1.0]hexane parent compounds 4 and 5.},
author = {Clark, Timothy and et al.},
author_hint = {TETZLAFF C, BUTZ V, VILSMAIER E, WAGEMANN R, MAAS G, VONONCIUL AR, CLARK T},
doi = {10.1039/p29930001901},
faupublication = {yes},
journal = {Journal of the Chemical Society, Perkin Transactions 2},
pages = {1901-1905},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{CONFORMATION} {OF} 6-{MORPHOLINO}-3-{AZABICYCLO}[3.1.0]{HEXANE} {DERIVATIVES}},
year = {1993}
}
@article{faucris.122398804,
abstract = {Ab initio and density functional theory (DFT) calculations have been used to investigate the conformations and tautomeric forms of neutral anhydrotetracycline in aqueous solution.},
author = {Meindl, Kathrin and Clark, Timothy},
doi = {10.1021/jp0451039},
faupublication = {yes},
journal = {Journal of Physical Chemistry B},
pages = {4279-4284},
peerreviewed = {Yes},
title = {{Conformations} and tautomers of 5a,6-anhydrotetracycline},
volume = {109},
year = {2005}
}
@article{faucris.121796444,
abstract = {Density functional theory (DFT) has been used to investigate the conformations and tautomeric forms of neutral tetracycline in aqueous solution. The results suggest that the extended conformation is 3-3.5 kcal mol(-1) more stable than the twisted one for equivalent tautomers and that as many as six different tautomeric forms lie within 10 kcal mol(-1) of the most stable one. The energetic preference for the extended conformation is a solvent effect. Calculated infrared, NMR, and UV/vis spectra are used to suggest ways of differentiating between tautomers. and conformations experimentally. It is shown that the (13)C chemical shifts of C4a, C5, and C6 can be used to distinguish between the twisted and extended conformations.},
author = {Othersen, Olaf and Beierlein, Frank and Lanig, Harald and Clark, Timothy},
doi = {10.1021/jp0364506},
faupublication = {yes},
journal = {Journal of Physical Chemistry B},
pages = {13743-13749},
peerreviewed = {Yes},
title = {{Conformations} and tautomers of tetracycline},
volume = {107},
year = {2003}
}
@article{faucris.124081584,
abstract = {A series of electron donor-acceptor arrays containing π-conjugated oligofluorenes (oFL) of variable length between a zinc porphyrin (ZnP) as electron donor and fullerene (C ) as electron acceptor have been prepared by following a convergent synthesis. The electronic interactions between the electroactive species were determined by cyclic voltammetry, UV-visible, fluorescence, and femto/nanosecond transient absorption spectroscopy. Our studies clearly confirm that, although the C units are connected to the ZnP donor through π-conjugated oFL frameworks, no significant electronic interactions prevail in the ground state. Theoretical calculations predict that a long-range electron transfer occurs primarily due to a maximized π-conjugated pathway from the donor to the acceptor. Photoexcitation of ZnP-oFL -C results in transient absorption maxima at 715 and 1010 nm, which are unambiguously attributed to the photolytically generated radical ion pair state, [ZnP - oFL -C ], with lifetimes in the microsecond time regime. Temperature-dependent photophysical experiments have shown that the charge-transfer mechanism is controllable by temperature. Both charge separation and charge recombination processes give rise to a molecular wire behavior of the oFL moiety with an attenuation factor (β) of 0.097 Å . The correlation β to the connection pattern between the ZnP donor and the oFL linker revealed that even small alterations of the linker π-electron system break the homogeneous π-conjugation pattern, leading to higher values of β. © 2010 American Chemical Society.},
author = {Wielopolski, Mateusz and De Miguel Rojas, Gustavo and Van Der Pol, Cornelia and Brinkhaus, Linda and Katsukis, Georgios and Bryce, Martin and Clark, Timothy and Guldi, Dirk Michael},
doi = {10.1021/nn1013758},
faupublication = {yes},
journal = {Acs Nano},
pages = {6449-6462},
peerreviewed = {Yes},
title = {{Control} over charge transfer through molecular wires by temperature and chemical structure modifications},
volume = {4},
year = {2010}
}
@article{faucris.124187624,
abstract = {The Hellmann-Feynman theorem assures us that the forces felt by the nuclei in a molecule or complex are purely classically electrostatic. Nevertheless, it is often claimed (incorrectly) that electrostatic considerations are not sufficient to explain noncovalent interactions. Such assertions arise largely from neglecting the polarization that is inherently part of the electrostatic interaction, and must be taken into account. Accordingly, we now outline the requirements for a correct electrostatic treatment and discuss the difference between physical observables and quantities that arise from mathematical models. Polarization and donor-acceptor charge transfer are shown to be equivalent for weak interactions. However, polarization is a physical observable while charge transfer, in this context, is mathematical modelling. We also discuss some popular schemes for analyzing noncovalent interactions. (C) 2014 John Wiley & Sons, Ltd.},
author = {Clark, Timothy and Politzer, Peter and Murray, Jane S.},
doi = {10.1002/wcms.1210},
faupublication = {yes},
journal = {Wiley Interdisciplinary Reviews: Computational Molecular Science},
pages = {169-177},
peerreviewed = {unknown},
title = {{Correct} electrostatic treatment of noncovalent interactions: the importance of polarization},
volume = {5},
year = {2015}
}
@article{faucris.224368017,
abstract = {A small coding error in the development version of EMPIRE led to some inconsistencies in the above article. They are corrected in this erratum.},
author = {Kriebel, Maximilian and Heßelmann, Andreas and Hennemann, Matthias and Clark, Timothy},
doi = {10.1007/s00894-019-4142-0},
faupublication = {yes},
journal = {Journal of Molecular Modeling},
note = {CRIS-Team Scopus Importer:2019-08-13},
peerreviewed = {Yes},
title = {{Correction} to: {The} {Feynman} dispersion correction for {MNDO} extended to {F}, {Cl}, {Br} and {I} ({Journal} of {Molecular} {Modeling}, (2019), 25, 6, (156), 10.1007/s00894-019-4038-z)},
volume = {25},
year = {2019}
}
@article{faucris.120273604,
abstract = {We show by molecular-dynamics (MD) simulations and cryotransmission electron microscopy (cryo-TEM) experiments that the size and form of structurally persistent micelles formed by the T-shaped amphiphile 1 are controlled by the counterions. The two techniques reveal that the micelles are specifically stabilized by sodium counterions relative to po-tassium ions. Both the simulations and the cryo-TEM experiments suggest that the micelles are stabilized by strongly conserved hydrated contact ion pairs with sodium counterions but not with potassium ions. We suggest that the TEM is observing local high density due to hydrated carboxylate/sodium ion pairs at the surface of the micelle. A high concentration of such structures is found in MD simulations with sodium counterions, but not with potassium. © 2009 Wiley-VCH Verlag GmbH & Co. KGaA.},
author = {Jäger, Christof and Hirsch, Andreas and Schade, Boris and Böttcher, Christoph and Clark, Timothy},
doi = {10.1002/chem.200900885},
faupublication = {yes},
journal = {Chemistry - A European Journal},
pages = {8586-8592},
peerreviewed = {Yes},
title = {{Counterions} control the self-assembly of structurally persistent micelles: {Theoretical} prediction and experimental observation of stabilization by sodium ions},
volume = {15},
year = {2009}
}
@article{faucris.115064664,
abstract = {Ab initio and DFT calculations are used to investigate the structure, electronic properties, spectra and reactivity of cubic C-8, which is predicted to be aromatic according to Hirsch's rule. Although highly strained and with a small amount of diradical character, the carbon cube represents a surprisingly deep minimum and should therefore be observable as an isolated molecule. It is, however, predicted to be very reactive, both with itself and triplet oxygen. Calculated IR, Raman, and UV/Vis spectra are provided to aid identification of cubic C-8 should it be synthesized.},
author = {Sharapa, Dmitry and Hirsch, Andreas and Meyer, Bernd and Clark, Timothy},
doi = {10.1002/cphc.201500230},
faupublication = {yes},
journal = {ChemPhysChem},
keywords = {ab initio calculations;carbon allotropes;cubic C-8;density functional calculations;superdense carbon},
pages = {2165-2171},
peerreviewed = {Yes},
title = {{Cubic} {C}-8: {An} {Observable} {Allotrope} of {Carbon}?},
volume = {16},
year = {2015}
}
@article{faucris.121201784,
abstract = {CypScore is an in silico approach for predicting the likely sites of cytochrome P450-mediated metabolism of druglike organic molecules. It consists of multiple models for the most important P450 oxidation reactions such as aliphatic hydroxylation, N-dealkylation, O-clealkylation, aromatic hydroxylation, double-bond oxidation, N-oxidation, and S-oxidation. Each of these models is based on atomic reactivity descriptors derived from surface-based properties calculated with ParaSurf (TM) and based on AMI semiempirical molecular orbital theory. The models were trained with data derived from Bayer Schering Pharma's in-house MajorMetabolite Database with more than 2300 transformations and more than 800 molecules collected from the primary literature. The models have been balanced to allow the treatment of relative intramolecular, intra-chemotype, and inter-chemotype reactivities of the labile sites toward oxidation. The models were evaluated with promising hit rates on three public datasets of varying quality in the annotation of the experimental positions. For 39 well-characterized compounds from 14 in-house lead optimization programs, we could detect at least one major metabolite for the three highest-ranked positions in 87% of the compounds and overall more than 62% of all major metabolites, with promising true-to false-positive ratios of 0.9.},
author = {Hennemann, Matthias and Friedl, Arno and Lobell, Mario and Keldenich, Jörg and Hillisch, Alexander and Clark, Timothy and Göller, Andreas H.},
doi = {10.1002/cmdc.200800384},
faupublication = {yes},
journal = {ChemMedChem},
keywords = {AM1;cytochromes;metabolism;semiempirical calculations;surface properties},
pages = {657-669},
peerreviewed = {Yes},
title = {{CypScore}: {Quantitative} {Prediction} of {Reactivity} toward {Cytochrornes} {P450} {Based} on {Semiempirical} {Molecular} {Orbital} {Theory}},
volume = {4},
year = {2009}
}
@article{faucris.215880367,
abstract = {Singlet fission (SF) allows two charges to be generated from the absorption of a single photon and is, therefore, potentially transformative toward improving solar energy conversion. Key to the present study of SF is the design of pentacene dimers featuring a xanthene linker that strictly places two pentacene chromophores in a rigid arrangement and, in turn, enforces efficient, intramolecular pi-overlap that mimics interactions typically found in condensed state (e.g., solids, films, etc.). Inter-chromophore communication ensures Davydov splitting, which plays an unprecedented role toward achieving SF in pentacene dimers. Transient absorption measurements document that intramolecular SF evolves upon excitation into the lower Davydov bands to form a correlated triplet pair at cryogenic temperature. At room temperature, the two spin-correlated triplets, one per pentacene moiety within the dimers, are electronically coupled to an excimer state. The presented results are transferable to a broad range of acene morphologies including aggregates, crystals, and films.},
author = {Basel, Bettina and Hetzer, Constantin and Zirzlmeier, Johannes and Thiel, Dominik and Guldi, Rebecca and Hampel, Frank and Kahnt, Axel and Clark, Timothy and Guldi, Dirk Michael and Tykwinski, Rik R.},
doi = {10.1039/c9sc00384c},
faupublication = {yes},
journal = {Chemical Science},
note = {CRIS-Team WoS Importer:2019-04-12},
pages = {3854-3863},
peerreviewed = {Yes},
title = {{Davydov} splitting and singlet fission in excitonically coupled pentacene dimers},
volume = {10},
year = {2019}
}
@article{faucris.121277464,
abstract = {We have realized for the first time a series of truly water-soluble and tightly coupled porphyrin/C electron-donor-acceptor conjugates in which the charge separation and charge recombination dynamics are controlled by modifying the nature of the dendrimer and/or the choice of the central metal atom. © 2010 Wiley-VCH Verlag GmbH & Co. KGaA. Weinheim.},
author = {Ruppert, Michaela and Spänig, Fabian and Wielopolski, Mateusz and Jäger, Christof and Bauer, Walter and Clark, Timothy and Hirsch, Andreas and Guldi, Dirk Michael},
doi = {10.1002/chem.201000760},
faupublication = {yes},
journal = {Chemistry - A European Journal},
pages = {10797-10807},
peerreviewed = {Yes},
title = {{Dendronizing} and metalating trans-2 {C60} tetraaryl porphyrins - {A} versatile approach toward water-soluble donor-acceptor conjugates},
volume = {16},
year = {2010}
}
@article{faucris.116880764,
abstract = {We have investigated techniques for distinguishing between drugs and nondrugs using a set of molecular descriptors derived from semiempirical molecular orbital (AM1) calculations. The "drug" data set of 2105 compounds was derived from the World Drug Index (WDI) using a procedure designed to select real drugs. The "nondrug" data set was the Maybridge database. We have first investigated the dimensionality of physical properties space based on a set of 26 descriptors that we have used successfully to build absorption, distribution, metabolism, and excretion-related quantitative structure-property relationship models. We discuss the general nature of the descriptors for physical property space and the ability of these descriptors to distinguish between drugs and nondrugs. The third most significant principal component of this set of descriptors serves as a useful numerical index of drug-likeness, but no others are able to distinguish between drugs and nondrugs. We have therefore extended our set of descriptors to a total of 66 and have used recursive partitioning to identify the descriptors that can distinguish between drugs and nondrugs. This procedure pointed to two of the descriptors that play an important role in the principal component found above and one more from the set of 40 extra descriptors. These three descriptors were then used to train a Kohonen artificial neural net for the entire Maybridge data set. Projecting the drug database onto the map obtained resulted in a clear distinction not only between drugs and nondrugs but also, for instance, between hormones and other drugs. Projection of 42 131 compounds from the WDI onto the Kohonen map also revealed pronounced clustering in the regions of the map assigned as druglike.},
author = {Brüstle, Matthias and Beck, Bernd and Schindler, Thorsten and King, William and Clark, Timothy and et al.},
author_hint = {Brustle M, Beck B, Schindler T, King W, Mitchell T, Clark T},
doi = {10.1021/jm011027b},
faupublication = {yes},
journal = {Journal of Medicinal Chemistry},
pages = {3345-3355},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{Descriptors}, physical properties, and drug-likeness},
volume = {45},
year = {2002}
}
@article{faucris.122399684,
author = {Clark, Timothy and Chandrasekhar, Jayaraman and Schleyer, Paul and et al.},
author_hint = {CLARK T, CHANDRASEKHAR J, SCHLEYER PV, SAUNDERS M},
doi = {10.1039/C39800000265},
faupublication = {yes},
journal = {Journal of the Chemical Society - Series Chemical Communications},
month = {Jan},
pages = {265-266},
peerreviewed = {unknown},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{DEUTERIUM}-{ISOTOPE} {EFFECT} {ON} {THE} {ESR}-{SPECTRUM} {OF} {ANNULENE} {RADICALS} - {A} {REAPPRAISAL}},
year = {1980}
}
@article{faucris.109616804,
abstract = {Synthesis, biological investigations and molecular docking studies of nonantibiotic and nontetracyclic inducers that feature a minimal key motif of the natural lead tetracycline are presented. The diarylpropane-1,3-dione motif was identified as the minimal substructure responsible for TetR induction by tetracyclines. The first nontetracyclic surrogates of the natural tetracyclines displayed significant inducing effects for TetR(BD)-S135L, whereby the chlorohydroxyphenyl-substituted β-diketone 31 displayed the highest activity. Interestingly, antibiotic activity could not be detected for 31. Homology modeling based on the X-ray structure of 7-chlorotetracycline bound to TetR indicated analogous binding modes for the natural inducer and the synthetic diarylpropane-1,3-dione derivatives. © 2009 Wiley-VCH Verlag GmbH & Co. KGaA.},
author = {Kormann, Christian and Pimenta, Irina and Löber, Stefan and Wimmer, Cornelius and Lanig, Harald and Clark, Timothy and Hillen, Wolfgang and Gmeiner, Peter},
doi = {10.1002/cbic.200900564},
faupublication = {yes},
journal = {ChemBioChem},
pages = {2924-2933},
peerreviewed = {Yes},
title = {{Diarylpropane}-1,3-dione derivatives as {TetR}-inducing tetracycline mimetics: {Synthesis} and biological investigations},
volume = {10},
year = {2009}
}
@article{faucris.253934723,
abstract = {The family of human muscarinic acetylcholine receptors (MRs) is characterized by a high sequence homology among the five subtypes (M1R-M5R), being the reason for a lack of subtype selective MR ligands. In continuation of our work on dualsteric dibenzodiazepinone-type M2R antagonists, a series of M2R ligands containing a dibenzodiazepinone pharmacophore linked to small basic peptides was synthesized (64 compounds). The linker moiety was varied with respect to length, number of basic nitrogens (0–2) and flexibility. Besides proteinogenic basic amino acids (Lys, Arg), shorter homologues of Lys and Arg, containing three and two methylene groups, respectively, as well as D-configured amino acids were incorporated. The type of linker had a marked impact on M2R affinity and also effected M2R selectivity. In contrast, the structure of the basic peptide rather determined M2R selectivity than M2R affinity. For example, the most M2R selective compound (UR-CG188, 89) with picomolar M2R affinity (pKi 9.60), exhibited a higher M2R selectivity (ratio of Ki M1R/M2R/M3R/M4R/M5R: 110:1:5200:55:2300) compared to the vast majority of reported M2R preferring MR ligands. For selected ligands, M2R antagonism was confirmed in a M2R miniG protein recruitment assay.},
author = {Weinhart, Corinna G. and Wifling, David and Schmidt, Maximilian and Neu, Eduard and Höring, Carina and Clark, Timothy and Gmeiner, Peter and Keller, Max},
doi = {10.1016/j.ejmech.2021.113159},
faupublication = {yes},
journal = {European Journal of Medicinal Chemistry},
keywords = {Basic amino acid; Dibenzodiazepinone derivative; Induced-fit docking; M2R antagonist; M2R selectivity; MR subtype selectivity; Muscarinic acetylcholine receptors; Peptide},
note = {CRIS-Team Scopus Importer:2021-04-02},
peerreviewed = {Yes},
title = {{Dibenzodiazepinone}-type muscarinic receptor antagonists conjugated to basic peptides: {Impact} of the linker moiety and unnatural amino acids on {M2R} selectivity},
volume = {213},
year = {2021}
}
@article{faucris.208730237,
abstract = {Protein nanobodies have been used successfully as surrogates for unstable G-proteins in order to crystallize G-protein-coupled receptors (GPCRs) in their active states. We used molecular dynamics (MD) simulations, including meta-dynamics enhanced sampling, to investigate the similarities and differences between GPCR-agonist ternary complexes with the alpha-subunits of the appropriate G-proteins and those with the protein nanobodies (intracellular binding partners, IBPs) used for crystallization. In two of the three receptors considered, the agonist-binding mode differs significantly between the two alternative ternary complexes. The ternary-complex model of GPCR activation entails enhancement of ligand binding by bound IBPs: Our results show that IBP-specific changes can alter the agonist binding modes and thus also the criteria for designing GPCR agonists.},
author = {Saleh, Noureldin and Ibrahim, Passainte and Clark, Timothy},
doi = {10.1002/anie.201702468},
faupublication = {yes},
journal = {Angewandte Chemie International Edition},
keywords = {allosterism;G-protein-coupled receptors;ligand binding;molecular dynamics;transmembrane receptors},
pages = {9008-9012},
peerreviewed = {Yes},
title = {{Differences} between {G}-{Protein}-{Stabilized} {Agonist}-{GPCR} {Complexes} and their {Nanobody}-{Stabilized} {Equivalents}},
volume = {56},
year = {2017}
}
@article{faucris.109348404,
author = {Clark, Timothy and et al.},
author_hint = {LENDVAI T, FRIEDL T, BUTENSCHON H, CLARK T, DEMEIJERE A},
doi = {10.1002/anie.198607191},
faupublication = {yes},
journal = {Angewandte Chemie (International Edition in English)},
pages = {719-720},
peerreviewed = {unknown},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{DIHYDROACEPENTALENEDIIDE}, {THE} {DIANION} {OF} {ACEPENTALENE}},
volume = {25},
year = {1986}
}
@article{faucris.116887804,
author = {Clark, Timothy and Kos, Alex and Schleyer, Paul and et al.},
author_hint = {WILHELM D, DIETRICH H, CLARK T, MAHDI W, KOS AJ, SCHLEYER PV},
doi = {10.1021/ja00335a088},
faupublication = {yes},
journal = {Journal of the American Chemical Society},
month = {Jan},
pages = {7279-7280},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{DILITHIUM} {TRIBENZYLIDENEMETHANE}-{2TMEDA} - {THE} {1ST} {X}-{RAY} {STRUCTURE} {OF} {A} {Y}-{CONJUGATED} {TRIMETHYLENEMETHANE} {DIANION} {DERIVATIVE}},
volume = {106},
year = {1984}
}
@article{faucris.116888464,
author = {Clark, Timothy and Schleyer, Paul and et al.},
author_hint = {KAUFMANN E, CLARK T, SCHLEYER PV},
doi = {10.1021/ja00318a061},
faupublication = {yes},
journal = {Journal of the American Chemical Society},
month = {Jan},
pages = {1856-1858},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{DIMERIZATION} {ENERGIES} {OF} {LITHIUM} {COMPOUNDS} {WITH} {1ST}-{ROW} {SUBSTITUENTS}},
volume = {106},
year = {1984}
}
@article{faucris.121989824,
abstract = {Long lived: Carbonyloxyl radicals (RCO2.) are reactive intermediates that play key roles in initiating polymerization reactions. This reactivity also makes their direct observation difficult. For the first time a persistent organic RCO2. radical is detected in the gas phase, its extraordinary longevity is attributed to the high barrier towards fragmentation owing to the endothermicity of the decarboxylation products.},
author = {Poad, Berwyck L. J. and Kirk, Benjamin B. and Hettiarachchi, Pramesh I. and Trevitt, Adam J. and Blanksby, Stephen J. and Clark, Timothy},
doi = {10.1002/anie.201304316},
faupublication = {yes},
journal = {Angewandte Chemie International Edition},
pages = {9301--9304},
peerreviewed = {Yes},
title = {{Direct} {Detection} of a {Persistent} {Carbonyloxyl} {Radical} in the {Gas} {Phase}},
volume = {52},
year = {2013}
}
@article{faucris.208730505,
abstract = {Charge-carrier transport in oriented COF thin films is an important factor for realizing COF-based optoelectronic devices. We describe how highly oriented electron-donating benzodithiophene BDT-COF thin fihns serve as a model system for a directed charge-transport study. Oriented BDT-COF films were deposited on different electrodes with excellent control over film roughness and topology, allowing for high-quality electrode COF interfaces suitable for device fabrication. Hole only devices were constructed to study the columnar hole mobility of the BDT-COF films. The transport measurements reveal a clear dependency of the measured hole mobilities on the BDT-COF film thickness, where thinner films showed about two orders of magnitude higher mobilities than thicker ones. Transport measurements under illumination yielded an order of magnitude higher mobility than in the dark. In-plane electrical conductivity values of up to 5 X 10(-7) S cm(-1) were obtained for the oriented films. Impedance measurements of the hole-only devices provided further electrical description of the oriented BDT-COF films in terms of capacitance, recombination resistance, and dielectric constant. An exceptionally low dielectric constant value of approximately 1.7 was estimated for the BDT-COF films, a further indication of their highly porous nature. DFT and molecular-dynamics simulations were carried out to gain further insights into the relationships between the COF layer interactions, electronic structure, and the potential device performance.},
author = {Medina, Dana D. and Petrus, Michiel L. and Jumabekov, Askhat N. and Margraf, Johannes and Weinberger, Simon and Rotter, Julian M. and Clark, Timothy and Bein, Thomas},
doi = {10.1021/acsnano.6b07692},
faupublication = {yes},
journal = {Acs Nano},
keywords = {covalent organic frameworks;thin films;charge transport;hole mobility;electrical conductivity;impedance spectroscopy},
pages = {2706-2713},
peerreviewed = {Yes},
title = {{Directional} {Charge}-{Carrier} {Transport} in {Oriented} {Benzodithiophene} {Covalent} {Organic} {Framework} {Thin} {Films}},
volume = {11},
year = {2017}
}
@article{faucris.120350384,
abstract = {The interaction energies between an argon atom and the dihalogens Br , BrCl, and BrF have been investigated using frozen core CCSD(T)(fc)/aug-cc-pVQZ calculations as reference values for other levels of theory. The potential-energy hypersurfaces show two types of minima: (1) collinear with the dihalogen bond and (2) in a bridging position. The former represent the most stable minima for these systems, and their binding energies decrease in the order Br > Cl > F. Isotropic atom-atom potentials cannot reproduce this binding pattern. Of the other levels of theory, CCSD(T)(fc)/aug-cc-pVTZ reproduces the reference data very well, as does MP2(fc)/aug-cc-pVDZ, which performs better than MP2 with the larger basis sets (aug-cc-pVQZ and aug-cc-pvTZ). B3LYP-D3 and M06-2X reproduce the binding patterns moderately well despite the former using an isotropic dispersion potential correction. B3LYP-D3(bj) performs even better. The success of the B3LYP-D3 methods is because polar flattening of the halogens allows the argon atom to approach more closely in the direction collinear with the bond, so that the sum of dispersion potential and repulsion is still negative at shorter distances than normally possible and the minimum is deeper at the van der Waals distance. Core polarization functions in the basis set and including the core orbitals in the CCSD(T)(full) calculations lead to a uniform decrease of approximately 20% in the magnitudes of the calculated interaction energies. The EXXRPA+@EXX (exact exchange random phase approximation) orbital-dependent density functional also gives interaction energies that correlate well with the highest level of theory but are approximately 10% low. The newly developed EXXRPA+@dRPA functional represents a systematic improvement on EXXRPA+@EXX. © 2013 American Chemical Society.},
author = {Elkerdawy, Ahmed and Murray, Jane S. and Politzer, Peter and Bleiziffer, Patrick and Heßelmann, Andreas and Görling, Andreas and Clark, Timothy},
doi = {10.1021/ct400185f},
faupublication = {yes},
journal = {Journal of Chemical Theory and Computation},
pages = {2264-2275},
peerreviewed = {Yes},
title = {{Directional} noncovalent interactions: {Repulsion} and dispersion},
volume = {9},
year = {2013}
}
@article{faucris.122401004,
abstract = {The prototypical directional weak interactions, hydrogen bonding and sigma-hole bonding (including the special case of halogen bonding) are reviewed in a united picture that depends on the anisotropic nature of the molecular electrostatic potential around the donor atom. Qualitative descriptions of the effects that lead to these anisotropic distributions are given and examples of the importance of sigma-hole bonding in crystal engineering and biological systems are discussed.},
author = {Murray, Jane S. and Riley, Kevin E. and Politzer, Peter and Clark, Timothy},
doi = {10.1071/CH10259},
faupublication = {yes},
journal = {Australian Journal of Chemistry},
month = {Jan},
pages = {1598-1607},
peerreviewed = {Yes},
title = {{Directional} {Weak} {Intermolecular} {Interactions}: sigma-{Hole} {Bonding}},
volume = {63},
year = {2010}
}
@article{faucris.208726695,
abstract = {High-level ab initio calculations on the complexes between noble gas atoms (He, Ne, Ar, Kr, and Xe) and dihalogen molecules (F-2, Cl-2, Br-2, and I-2) reveal trends, both in interaction energies and the energy difference between the linear and T-shaped structures, that can be explained well in terms of dispersion interactions enhanced by polar flattening of the halogens. The partial discrepancies with experimental findings are discussed.},
author = {Legon, Anthony C. and Sharapa, Dmitry and Clark, Timothy},
doi = {10.1007/s00894-018-3711-y},
faupublication = {yes},
journal = {Journal of Molecular Modeling},
keywords = {Polar flattening;Dispersion;Van der Waals complexes;Coupled cluster calculations},
peerreviewed = {Yes},
title = {{Dispersion} and polar flattening: noble gas-halogen complexes},
volume = {24},
year = {2018}
}
@article{faucris.122401444,
abstract = {We introduce an additional term to treat dispersion in NDDO-based semiempirical molecular orbital techniques. The dispersion energy is calculated using additive "atomic orbital" polarizability tensors determined with our modified version of Rivail's variational technique. Frequency-dependent polarizabilities can be obtained using Pade approximants, which proved more reliable than the Unsold approximation or a Taylor-series approach. Dispersion energies are best calculated using the Slater-Kirkwood modification of the London formula, although they can also be obtained using the Casimir-Polder approach with frequency-dependent polarizabitities. A test parameterization using MNDO as the semiempirical technique indicated that weak interactions can be reproduced satisfactorily.},
author = {Martin, Bodo and Clark, Timothy},
doi = {10.1002/qua.20856},
faupublication = {yes},
journal = {International Journal of Quantum Chemistry},
keywords = {dispersion;AMI;semiempirical MO theory;NDDO;polarizability},
pages = {1208-1216},
peerreviewed = {Yes},
title = {{Dispersion} treatment for {NDDO}-based semiempirical {MO} techniques},
volume = {106},
year = {2006}
}
@article{faucris.122402104,
author = {Clark, Timothy},
doi = {10.1039/c39840000093},
faupublication = {yes},
journal = {Journal of the Chemical Society - Series Chemical Communications},
month = {Jan},
pages = {93-94},
peerreviewed = {unknown},
title = {{DISSOCIATIVE} {ELECTRON}-{CAPTURE} {BY} {CHLOROMETHANE} {IN} {CONDENSED} {PHASES}},
year = {1984}
}
@article{faucris.122418604,
abstract = {We propose the statistical moments of mass-density distributions (created for two orthogonal directions) as new descriptors of DNA sequences. The distributions are derived using a 2D-dynamic representation technique proposed in our previous paper in which the sequence is coded by a set of point masses properly distributed in 2D-space. (c) 2007 Elsevier B.V. All rights reserved.},
author = {Bielinska-Waz, Dorota Joanna and Nowak, Wieslaw and Waz, Piotr and Clark, Timothy and et al.},
author_hint = {Bielinska-Waz D, Nowak W, Waz P, Nandy A, Clark T},
doi = {10.1016/j.cplett.2007.06.088},
faupublication = {yes},
journal = {Chemical Physics Letters},
pages = {408-413},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{Distribution} moments of {2D}-graphs as descriptors of {DNA} sequences},
volume = {443},
year = {2007}
}
@article{faucris.107109684,
abstract = {Extensive molecular-dynamics (MD) simulations have been used to investigate DNA-dye and DNA-photosensitizer conjugates, which act as reactants in templated reactions leading to the generation of fluorescent products in the presence of specific desoxyribonucleic acid sequences (targets). Such reactions are potentially suitable for detecting target nucleic acids in live cells by fluorescence microscopy or flow cytometry. The simulations show how the attached dyes/photosensitizers influence DNA structure and reveal the relative orientations of the chromophores with respect to each other. Our results will help to optimize the reactants for the templated reactions, especially length and structure of the spacers used to link reporter dyes or photosensitizers to the oligonucleotides responsible for target recognition. Furthermore, we demonstrate that the structural ensembles obtained from the simulations can be used to calculate steady-state UV-vis absorption and emission spectra. We also show how important quantities describing the quenching of the reporter dye via fluorescence resonance energy transfer (FRET) can be calculated from the simulation data, and we compare these for different relative chromophore geometries.},
author = {Beierlein, Frank and Paradas Palomo, Miguel and Sharapa, Dmitry and Zozulia, Oleksii and Mokhir, Andriy and Clark, Timothy},
doi = {10.1371/journal.pone.0160229},
faupublication = {yes},
journal = {Plos One},
pages = {e0160229},
peerreviewed = {unknown},
title = {{DNA}-{Dye}-{Conjugates}: {Conformations} and {Spectra} of {Fluorescence} {Probes}},
volume = {11},
year = {2016}
}
@article{faucris.115952804,
abstract = {Ab initio molecular orbital and density functional calculations at the CBS-RAD(QCISD,B3-LYP) level for Li + and at B3LYP for Na +, K +, Cu +, and Ag + reveal that the barrier to ring-closure of the 1 -hexen-6-yl ("Δ(5)-hexenyl") radical to the cyclopentylmethyl radical, a so-called radical clock reaction, is decreased very significantly by complexation of the double bond to metal cations. This barrier lowering should occur on complexation with many metal ions, as shown by calculations on all of the monovalent ions listed above. Additional density functional calculations including explicit solvation of the model system complexed to the lithium ion with tetrahydrofuran suggest that the effect found is not limited to the gas phase but may also be significant in experimental radical clock reactions in solution, even for lithium.},
author = {Horn, Anselm and Clark, Timothy},
doi = {10.1021/ja020954k},
faupublication = {yes},
journal = {Journal of the American Chemical Society},
note = {UnivIS-Import:2015-03-09:Pub.2003.forsch.sonder.sfb583.doesme},
pages = {2809-2816},
peerreviewed = {Yes},
title = {{Does} {Metal} {Ion} {Complexation} {Make} {Radical} {Clocks} {Run} {Fast}?},
year = {2003}
}
@article{faucris.107265884,
abstract = {Density functional theory (DFT) and semiempirical UHF natural orbital configuration interaction (UNO-CI) calculations are used to investigate the effect of heteroatom substitution at the central position of a model polycyclic aromatic hydrocarbon. The effects of the substitution on structure, strain, electronic and spectral properties, and aromaticity of the compounds are discussed.},
author = {Dral, Pavlo and Kivala, Milan and Clark, Timothy},
doi = {10.1021/jo3018395},
faupublication = {yes},
journal = {Journal of Organic Chemistry},
pages = {1894--1902},
peerreviewed = {Yes},
title = {{Doped} polycyclic aromatic hydrocarbons as building blocks for nanoelectronics: a theoretical study},
volume = {78},
year = {2013}
}
@article{faucris.122402764,
author = {Clark, Timothy and Schleyer, Paul and et al.},
author_hint = {WILHELM D, CLARK T, SCHLEYER PV, DIETRICH H, MAHDI W},
doi = {10.1016/0022-328X(85)87074-1},
faupublication = {yes},
journal = {Journal of Organometallic Chemistry},
month = {Jan},
pages = {C6-C10},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{DOUBLE} {LITHIUM} {BRIDGING} - {THE} {STRUCTURE} {OF} 1,4-{DILITHIO}-1,4-{DIPHENYL}-{CIS}-2-{BUTENE}},
volume = {280},
year = {1985}
}
@article{faucris.124146924,
author = {Kirschner, Johannes and Wang, Zhenxing and Eigler, Siegfried and Steinrück, Hans-Peter and Jäger, Christof and Clark, Timothy and Hirsch, Andreas and Halik, Marcus},
doi = {10.1039/C4NR02527J},
faupublication = {yes},
journal = {Nanoscale},
pages = {11344-11350},
peerreviewed = {Yes},
title = {{Driving} forces for the self-assembly of graphene oxide on organic monolayers},
url = {http://pubs.rsc.org/en/content/articlelanding/2014/nr/c4nr02527j#!divAbstract},
volume = {6},
year = {2014}
}
@article{faucris.312971237,
abstract = {Through comprehensive photo-assays, this study investigates the reaction coordinate governing the interconversion between quadricyclane (QC) and norbornadiene (NBD) upon photo-irradiation up to a wavelength of 550 nm. To harness this spectroscopic range for energy release, we link the NBD-core with a highly electron-accepting perylenediimide (PDI) with broad absorption, achieving strong electronic coupling between them. We detail the successful synthesis and present extensive DFT calculations to determine the amount of stored energy. By means of transient absorption spectroscopy, an oxidative electron transfer is observed during the QC-to-NBD isomerization following the initial PDI photoexcitation. This charge-separated state is key to triggering the back-isomerization with visible light excitation.},
author = {Zika, Wiebke and Leng, Andreas and Weiß, René and Pinter, Simone and Schüßlbauer, Christoph and Clark, Timothy and Hirsch, Andreas and Guldi, Dirk Michael},
doi = {10.1039/d3sc03679k},
faupublication = {yes},
journal = {Chemical Science},
note = {CRIS-Team Scopus Importer:2023-10-20},
peerreviewed = {Yes},
title = {{Driving} the quadricyclane-to-norbornadiene isomerization by charge separation with perylenediimide as electron acceptor},
year = {2023}
}
@article{faucris.122336324,
abstract = {A series of density functional/basis set combinations and second-order Moller-Plesset calculations have been used to test their ability to reproduce the trends observed experimentally for the strengths of hydrogen-bond acceptors in order to identify computationally efficient techniques for routine use in the computational drug-design process. The effects of functionals, basis sets, counterpoise corrections, and constraints on the optimized geometries were tested and analyzed, and recommendations (M06-2X/cc-pVDZ and X3LYP/cc-pVDZ with single-point counterpoise corrections or X3LYP/aug-cc-pVDZ without counterpoise) were made for suitable moderately high-throughput techniques.},
author = {El Kerdawy, Ahmed and Tautermann, Christofer S. and Clark, Timothy and Fox, Thomas},
doi = {10.1021/ci4006222},
faupublication = {yes},
journal = {Journal of Chemical Information and Modeling},
pages = {3262-3272},
peerreviewed = {Yes},
title = {{Economical} and {Accurate} {Protocol} for {Calculating} {Hydrogen}-{Bond}-{Acceptor} {Strengths}},
volume = {53},
year = {2013}
}
@article{faucris.121946044,
author = {Clark, Timothy},
faupublication = {yes},
journal = {Journal of Molecular Modeling},
pages = {1-1},
peerreviewed = {Yes},
title = {{Editorial} 2003},
volume = {9},
year = {2003}
}
@article{faucris.122404084,
author = {Schleyer, Paul and Clark, Timothy and et al.},
author_hint = {SCHLEYER PV, WURTHWEIN EU, KAUFMANN E, CLARK T, POPLE JA},
doi = {10.1021/ja00356a045},
faupublication = {yes},
journal = {Journal of the American Chemical Society},
month = {Jan},
pages = {5930-5932},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{EFFECTIVELY} {HYPERVALENT} {MOLECULES} .2. {CLI5}, {CLI6}, {AND} {THE} {RELATED} {EFFECTIVELY} {HYPERVALENT} {1ST}-{ROW} {MOLECULES}, {CLI5}-{NHN} {AND} {CLI6}-{NHN}},
volume = {105},
year = {1983}
}
@article{faucris.112660284,
abstract = {Self-assembled monolayer field-effect transistors (SAMFETs) are not only a promising type of organic electronic device but also allow detailed analyses of structure-property correlations. The influence of the morphology on the charge transport is particularly pronounced, due to the confined monolayer of 2D-\textgreekp-stacked organic semiconductor molecules. The morphology, in turn, is governed by relatively weak van-der-Waals interactions and is thus prone to dynamic structural fluctuations. Accordingly, combining electronic and physical characterization and time-averaged X-ray analyses with the dynamic information available at atomic resolution from simulations allows us to characterize self-assembled monolayer (SAM) based devices in great detail. For this purpose, we have constructed transistors based on SAMs of two molecules that consist of the organic p-type semiconductor benzothieno[3,2-b][1]benzothiophene (BTBT), linked to a C11 or C12 alkylphosphonic acid. Both molecules form ordered SAMs; however, our experiments show that the size of the crystalline domains and the charge-transport properties vary considerably in the two systems. These findings were confirmed by molecular dynamics (MD) simulations and semiempirical molecular-orbital electronic-structure calculations, performed on snapshots from the MD simulations at different times, revealing, in atomistic detail, how the charge transport in organic semiconductors is influenced and limited by dynamic disorder.},
author = {Schmaltz, Thomas and Gothe, Bastian and Krause, Andreas and Leitherer, Susanne and Steinrück, Hans-Georg and Thoss, Michael and Clark, Timothy and Halik, Marcus},
doi = {10.1021/acsnano.7b02394},
faupublication = {yes},
journal = {Acs Nano},
peerreviewed = {Yes},
title = {{Effect} of {Structure} and {Disorder} on the {Charge} {Transport} in {Defined} {Self}-{Assembled} {Monolayers} of {Organic} {Semiconductors}},
url = {https://pubs.acs.org/doi/abs/10.1021/acsnano.7b02394},
year = {2017}
}
@article{faucris.121603944,
abstract = {The electron transfer kinetics of the donor bridge-acceptor (D-B-A) compounds investigated is governed by three different effects: polarity of the solvent, change of conformation (especially rotation of the single bond of the vinylnaphthalene moiety) and the p-character of the bridge (bicyclooctane, norbornane, stellane). The expected increase of the rate of electron back transfer with increasing p-character of the bridge orbitals is only clearly seen in medium and very polar solvents (methylene chloride and acetonitrile). In less polar solvent (2-methyl-THF) the temperature dependence of the charge-transfer (CT) fluorescence of the system with the bicyclooctane bridge points to the existence of two emitting CT conformers. Semiempirical MO calculations with configuration interaction reveal that 2 or even 3 (norbornane bridge) local minima exist on the energy surface of the CT state. They differ mainly in the angle of rotation of the single bond mentioned above, but also by deformation of the bridge structure. In non-polar solvent (methylcyclohexane) the fluorescence behaviour becomes even more complex because emission from the CT state(s) and from the locally excited state overlap. The analysis points to an equilibrium between different rotamers on the energy surface of the lowest locally excited state, on the one hand, and of the CT state, on the other hand. Investigations of the compound with the stellane bridge are hampered by significant photodegradation in methylcyclohexane solution.},
author = {Kurzawa, Jana and Schneider, Siegfried and Clark, Timothy and et al.},
author_hint = {Kurzawa J, Schneider S, Buber J, Gleiter R, Clark T},
doi = {10.1039/b316157a},
faupublication = {yes},
journal = {Physical Chemistry Chemical Physics},
pages = {3811-3823},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{Effect} of through bond coupling and conformation on the photophysical properties of sigma-bridged systems comprising a vinylnaphthalene donor and a dicyanovinyl acceptor},
volume = {6},
year = {2004}
}
@article{faucris.121604384,
author = {Kos, Alex and Clark, Timothy and Schleyer, Paul and et al.},
author_hint = {BUDZELAAR PHM, KOS AJ, CLARK T, SCHLEYER PV},
doi = {10.1021/om00122a001},
faupublication = {yes},
journal = {Organometallics},
month = {Jan},
pages = {429-437},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{EFFECTS} {OF} {BORON} {SUBSTITUENTS} {IN} {BORIRENES}, {BORIRANES}, {AND} {BORANES} - {THE} {ENERGIES} {OF} {B}-{X} {BONDS}},
volume = {4},
year = {1985}
}
@article{faucris.122404964,
author = {Spitznagel, Günther W. and Clark, Timothy and Schleyer, Paul and Hehre, Warren},
doi = {10.1002/jcc.540080807},
faupublication = {yes},
journal = {Journal of Computational Chemistry},
pages = {1109-1116},
peerreviewed = {Yes},
title = {{EFFICIENT} {DIFFUSE} {FUNCTION}-{AUGMENTED} {BASIS}-{SETS} {FOR} {ANION} {CALCULATION} .4. {AN} {EVALUATION} {OF} {THE} {PERFORMANCE} {OF} {DIFFUSE} {FUNCTION}-{AUGMENTED} {BASIS}-{SETS} {FOR} {2ND}-{ROW} {ELEMENTS}, {NA}-{CL}},
volume = {8},
year = {1987}
}
@article{faucris.119331784,
author = {Clark, Timothy and Schleyer, Paul and et al.},
author_hint = {CLARK T, CHANDRASEKHAR J, SPITZNAGEL GW, SCHLEYER PV},
doi = {10.1002/jcc.540040303},
faupublication = {yes},
journal = {Journal of Computational Chemistry},
month = {Jan},
pages = {294-301},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{EFFICIENT} {DIFFUSE} {FUNCTION}-{AUGMENTED} {BASIS} {SETS} {FOR} {ANION} {CALCULATIONS}. {III}. {THE} 3-21+{G} {BASIS} {SET} {FOR} {FIRST}-{ROW} {ELEMENTS}, {LI}-{F}},
volume = {4},
year = {1983}
}
@article{faucris.121604824,
author = {Clark, Timothy},
faupublication = {yes},
journal = {ACS National Meeting Book of Abstracts},
peerreviewed = {unknown},
title = {{Electronic} properties and intermolecular binding in drug-like molecules},
volume = {238},
year = {2009}
}
@article{faucris.116888904,
abstract = {AM1 and HF/6-31G* molecular orbital calculations have been used to investigate the electron self-exchange reactions between a series of substituted 1,4-diaminobenzenes and their radical cations. Comparisons with known experimental data and the results of the ab initio calculations suggest that AM1 performs well for this problem. The internal reorganization energy, lambda(i), has been estimated from the differences between the vertical and adiabatic ionization potentials of the neutral compounds and the corresponding electron affinities of the radical cations and is found to be significantly larger than previous estimates. Direct CI calculations of lambda for the radical cation/neutral molecule complex reveal that stabilization of the ground state (complexation) and the corresponding destabilization of the first excited state increase lambda further. There is, however, a large zero-point energy contribution that lowers the classical electron-transfer activation energy significantly. The calculated thermodynamics of the classical activation process are in good agreement with experiment.},
author = {Rauhut, Guntram and Clark, Timothy},
doi = {10.1021/ja00073a031},
faupublication = {yes},
journal = {Journal of the American Chemical Society},
pages = {9127-9135},
peerreviewed = {Yes},
title = {{ELECTRON}-{TRANSFER} {REACTIONS} - {AM1} {AND} {AB}-{INITIO} {STUDIES} {ON} {SELF}-{EXCHANGE} {IN} {P}-{DIAMINOBENZENE} {SYSTEMS}},
volume = {115},
year = {1993}
}
@article{faucris.122408924,
abstract = {The optical spectrum of 2,7-dinitronaphthalene radical anion generated by Na(Hg) reduction in acetonitrile containing a large excess of cryptand[2.2.2] exhibits a Hush-type intervalence charge-transfer band at 1070 nm, estimated to correspond to an off-diagonal matrix coupling element of 310 cm(-1). The interpolated rate constant for intramolecular electron transfer at 293 K measured by ESR between 225 and 320 K for this solution is 3.1(+/-0.2) x 10(9) s(-1). Rate constants estimated in two ways from the optical parameters using the Marcus-Hush assumption that the diabatic surfaces should be parabolae are 1.0 and 0.11 x 10(9) s(-1), and those using diabatic surfaces that fit the observed charge-transfer band are 9.6 and 3.4 x 10(9) s(-1), when used with an electron-transfer distance on the adiabatic surfaces of 6.42 A. Similar measurements and comparisons were also carried out using dimethylformamide and butyronitrile as solvents. The success of simple, classical two-state Marcus-Hush theory precludes an electron-hopping mechanism. UHF calculations predict a planar unsymmetrical gas-phase structure for 1,3-dinitrobenzene radical anion but give serious spin contamination. Semiempirical AM1 calculations using singles excitation configuration interaction with an active space of 70 orbitals and the COSMO solvent model also give a planar unsymmetrical structure. These calculations make the internal vibrational component of the reorganization energy nearly constant, and much smaller than the solvent reorganizational component, and predict the transition energy to lie between that observed in acetonitrile (9360 cm(-1)) and those observed in dimethylformamide (8100 cm(-1)) and butyronitrile (8040 cm(-1)).},
author = {Clark, Timothy and et al.},
author_hint = {Nelsen SF, Weaver MN, Konradsson AE, Telo JP, Clark T},
doi = {10.1021/ja046566v},
faupublication = {yes},
journal = {Journal of the American Chemical Society},
pages = {15431-15438},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{Electron} transfer within 2,7-dinitronaphthalene radical anion},
volume = {126},
year = {2004}
}
@article{faucris.119366104,
abstract = {We present high resolution oxygen K near-edge x-ray absorption spectra of the acenaphthenequinone (ANQ) derivative 3,8-dibromo-5,6-dichloro-ANQ (Br Cl-ANQ). The spectral features exhibit an almost identical vibronic fine structure compared to that shown by ANQ. The unequal distances of the vibronic levels as derived from the least-squares fit analysis of the vibronic progressions allows us to determine the anharmonicity of the excited state potentials involved. We conclude that a single vibrational progression couples to the resonant excitation of O 1s core electrons preferentially. Comparison of the two ANQ derivatives gives a clear indication that the vibronic mode corresponds to a C=O stretching mode, rather than coupling to a C-H mode as suggested previously. These conclusions are supported by density functional theory calculations. © 2011 American Institute of Physics.},
author = {Schmidt, Norman Anja and Clark, Timothy and Urquhart, Stephen G. and Fink, Rainer},
doi = {10.1063/1.3646732},
faupublication = {yes},
journal = {Journal of Chemical Physics},
peerreviewed = {Yes},
title = {{Electron}-vibron coupling in halogenated acenaphthenequinone upon {O} {K}-edge soft x-ray absorption},
volume = {135},
year = {2011}
}
@article{faucris.109356544,
author = {Clark, Timothy and Weiß, Robert},
doi = {10.1021/jo01298a010},
faupublication = {yes},
journal = {Journal of Organic Chemistry},
month = {Jan},
pages = {1790-1794},
peerreviewed = {Yes},
title = {{ELECTROPHILIC} {AROMATIC}-{SUBSTITUTION} {IN} {CYCLOPROPENIUM} {IONS}},
volume = {45},
year = {1980}
}
@article{faucris.116894184,
abstract = {UMP4SDTQ/6-31G*//6-31G* calculations indicate that complexation of the oxidant with alkali metal cations provides both a strong catalysis of the forward reaction and a thermodynamic stabilization of the products in hydrogen atom abstraction reactions of triplet dioxygen and the hydroperoxy radical with methane, which was used as a model carbon-centered hydrogen atom donor. This effect, which is expected to be general for metal monocations, is based on purely electrostatic interactions, as is shown by the dependence of the calculated activation and reaction energies on the ionic radius of the metal and on the polarization of the O-3(2) and by model calculations using only 1 s orbital as the basis set for Li+.},
author = {Clark, Timothy and et al.},
author_hint = {HOFMANN H, CLARK T},
doi = {10.1021/ja00007a011},
faupublication = {yes},
journal = {Journal of the American Chemical Society},
pages = {2422-2425},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{ELECTROSTATIC} {CATALYSIS} {OF} {OXIDATION} {REACTIONS} {BY} {METAL}-{CATIONS} - {AN} {ABINITIO} {STUDY}},
volume = {113},
year = {1991}
}
@article{faucris.107267644,
abstract = {No abstract available},
author = {Hennemann, Matthias and Clark, Timothy},
doi = {10.1007/s00894-014-2331-4},
faupublication = {yes},
journal = {Journal of Molecular Modeling},
pages = {2331},
peerreviewed = {Yes},
title = {{EMPIRE}: a highly parallel semiempirical molecular orbital program: 1: self-consistent field calculations},
volume = {20},
year = {2014}
}
@article{faucris.118793444,
abstract = {No abstract available for this article},
author = {Margraf, Johannes and Hennemann, Matthias and Meyer, Bernd and Clark, Timothy},
doi = {10.1007/s00894-015-2692-3},
faupublication = {yes},
journal = {Journal of Molecular Modeling},
peerreviewed = {Yes},
title = {{EMPIRE}: a highly parallel semiempirical molecular orbital program: 2: periodic boundary conditions},
volume = {21},
year = {2015}
}
@article{faucris.234055125,
abstract = {Direct NDDO-based Born-Oppenheimer molecular dynamics (MD) have been implemented in the semiempirical molecular orbital program EMPIRE. Fully quantum mechanical MD simulations on unprecedented time and length scales are possible, since the calculation of self-consistent wavefunctions and gradients is performed in a massively parallel manner. MD simulations can be performed in the NVE and NVT ensembles, using either deterministic (Berendsen) or stochastic (Langevin) thermostats. Furthermore, dynamics for condensed-phase systems can be performed under periodic boundary conditions. We show three exemplary applications: the dynamics of molecular reorganization upon ionization, long timescale dynamics of an endohedral fullerene, and calculation of the vibrational spectrum of a nanoparticle consisting of more than eight hundred atoms. Graphical AbstractA snapshot from an MNDO-H simulation of NH4+@C60 at 4000 K shortly before a proton crosses the fullerene wall to give NH3@C60H+.},
author = {Margraf, Johannes T. and Hennemann, Matthias and Clark, Timothy},
doi = {10.1007/s00894-020-4293-z},
faupublication = {yes},
journal = {Journal of Molecular Modeling},
keywords = {Born-Oppenheimer molecular dynamics; EMPIRE; Massively parallel; Semiempirical MO theory},
note = {CRIS-Team Scopus Importer:2020-02-11},
pages = {43-},
peerreviewed = {Yes},
title = {{EMPIRE}: a highly parallel semiempirical molecular orbital program: 3: {Born}-{Oppenheimer} molecular dynamics},
volume = {26},
year = {2020}
}
@article{faucris.122410024,
abstract = {Allyl cation geometries optimized using an extended version of MMP2, newly parameterized for localized and delocalized classical cations, compare favorably with those obtained at the MP2(full)/6-31G* level. Hence, the force field should provide good starting structures for ab initio calculations. The pi-electron densities obtained by these two very different methods are quite similar. The relative energies of various isomers at MP4/6-31G*//MP2(full)/6-31G* are reproduced well by the force-field calculations. The heats of formation calculated by MMP2, as well as those predicted from the ab initio-data, agree with experimentally determined values. The force-field method provides interpretive capabilities. Energy differences between isomers can be separated into electronic and steric contributions, reasonable estimates of resonance energies are given, and nonbonded resonance energies in delocalized cations can be evaluated. The stabilizing 1-3 pi-interactions in allyl cations are quite significant, but are reduced by alkyl, groups hyperconjugatively and sterically. (C) 1997 by John Wiley & Sons, Inc.},
author = {Clark, Timothy and Schleyer, Paul and et al.},
author_hint = {Reindl B, Clark T, Schleyer PV},
doi = {10.1002/(SICI)1096-987X(199703)18:4<533::AID-JCC7>3.0.CO;2-U},
faupublication = {yes},
journal = {Journal of Computational Chemistry},
month = {Jan},
pages = {28-44},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{Empirical} force-field and ab initio calculations on delocalized open chain cations},
volume = {18},
year = {1997}
}
@book{faucris.118191524,
address = {Chichester},
editor = {Schleyer, Paul and Allinger, Norman L. and Clark, Timothy and Gasteiger, Johann and Kollman, Peter and Schaefer III, Henry F. and Schreiner, Peter R.},
faupublication = {yes},
isbn = {0-471-96588-X},
note = {UnivIS-Import:2015-05-08:Pub.1998.nat.dchph.lthch.relati{\_}0},
publisher = {Wiley},
title = {{Encyclopedia} of {Computationsl} {Chemistry}},
year = {1998}
}
@article{faucris.249345649,
abstract = {The rising demand for clean water for a growing and increasingly urban global population is one of the most urgent issues of our time. Here, we introduce the synthesis of a unique nanoscale architecture of pillar-like Co-CAT-1 metal-organic framework (MOF) crystallites on gold-coated woven stainless steel meshes with large, 50 mu m apertures. These nanostructured mesh surfaces feature superhydrophilic and underwater superoleophobic wetting properties, allowing for gravity-driven, highly efficient oil-water separation featuring water fluxes of up to nearly one million L m(-2) h(-1). Water physisorption experiments reveal the hydrophilic nature of Co-CAT-1 with a total water vapor uptake at room temperature of 470 cm(3) g(-1). Semiempirical molecular orbital calculations shed light on water affinity of the inner and outer pore surfaces. The MOF-based membranes enable high separation efficiencies for a number of liquids tested, including the notorious water pollutant, crude oil, affording chemical oxygen demand (COD) concentrations below 25 mg L-1 of the effluent. Our results demonstrate the great impact of suitable nanoscale surface architectures as a means of encoding on-surface extreme wetting properties, yielding energy-efficient water-selective large-aperture membranes.},
author = {Maehringer, Andre and Hennemann, Matthias and Clark, Timothy and Bein, Thomas and Medina, Dana D.},
doi = {10.1002/anie.202012428},
faupublication = {yes},
journal = {Angewandte Chemie International Edition},
month = {Jan},
note = {CRIS-Team WoS Importer:2021-02-12},
peerreviewed = {Yes},
title = {{Energy} {Efficient} {Ultrahigh} {Flux} {Separation} of {Oily} {Pollutants} from {Water} with {Superhydrophilic} {Nanoscale} {Metal}-{Organic} {Framework} {Architectures}},
year = {2021}
}
@article{faucris.208735733,
abstract = {The potential of covalent organic frameworks (COFs) for realizing porous, crystalline networks with tailored combinations of functional building blocks has attracted considerable scientific interest in the fields of gas storage, photocatalysis, and optoelectronics. Porphyrins are widely studied in biology and chemistry and constitute promising building blocks in the field of electroactive materials, but they reveal challenges regarding crystalline packing when introduced into COF structures due to their nonplanar configuration and strong electrostatic interactions between the heterocyclic porphyrin centers. A series of porphyrin-containing imine-linked COFs with linear bridges derived from terephthalaldehyde, 2,5-dimethoxybenzene-1,4-dicarboxaldehyde, 4,4'-biphenyldicarboxaldehyde and thieno[3,2- b]thiophene-2,5-dicarboxaldehyde, were synthesized, and their structural and optical properties were examined. By combining X-ray diffraction analysis with density-functional theory (DFT) calculations on multiple length scales, we were able to elucidate the crystal structure of the newly synthesized porphyrin-based COF containing thieno[3,2- b]thiophene-2,5-dicarboxaldehyde as linear bridge. Upon COF crystallization, the porphyrin nodes lose their 4-fold rotational symmetry, leading to the formation of extended slipped J-aggregate stacks. Steady-state and time-resolved optical spectroscopy techniques confirm the realization of the first porphyrin J-aggregates on a > 50 nm length scale with strongly red-shifted Q-bands and increased absorption strength. Using the COF as a structural template, we were thus able to force the porphyrins into a covalently embedded J-aggregate arrangement. This approach could be transferred to other chromophores; hence, these COFs are promising model systems for applications in photocatalysis and solar light harvesting, as well as for potential applications in medicine and biology.},
author = {Keller, Niklas and Calik, Mona and Sharapa, Dmitry and Soni, Himadriben and Zehetmaier, Peter M. and Rager, Sabrina and Auras, Florian and Jakowetz, Andreas C. and Görling, Andreas and Clark, Timothy and Bein, Thomas},
doi = {10.1021/jacs.8b08088},
faupublication = {yes},
journal = {Journal of the American Chemical Society},
pages = {16544},
peerreviewed = {Yes},
title = {{Enforcing} {Extended} {Porphyrin} {J}-{Aggregate} {Stacking} in {Covalent} {Organic} {Frameworks}.},
volume = {140},
year = {2018}
}
@article{faucris.122414644,
abstract = {In a feasibility study, a single conformation 3D version of the Maybridge database (53 471 compounds) has been produced using geometries optimized with AM1 semiempirical MO-theory. The database entries include full electrostatic information within the NAO-PC model and can be used to generate spectroscopic and physical properties using established QSPR models. The data were generated from the original database using custom cleanup software to remove database inconsistencies and, for instance, to isolate the "interesting" ion of ion pairs, 2D to 3D conversion using CORINA and subsequent geometry optimization using VAMP. The complete geometry optimization run was carried out in less than 15 h elapsed time on a Silicon Graphics Origin 2000 with 126 processors. The total failure rate for the structure cleanup, 2D to 3D conversion, and geometry optimization steps was around 1%.},
author = {Beck, Bernd and Horn, Anselm and Clark, Timothy and et al.},
author_hint = {Beck B, Horn A, Carpenter JE, Clark T},
doi = {10.1021/ci9801318},
faupublication = {yes},
journal = {Journal of Chemical Information and Computer Sciences},
pages = {1214-1217},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{Enhanced} {3D}-databases: {A} fully electrostatic database of {AM1}-optimized structures},
volume = {38},
year = {1998}
}
@article{faucris.122415524,
author = {Clark, Timothy and et al.},
author_hint = {VONONCIUL A, CLARK T},
doi = {10.1039/c39890001082},
faupublication = {yes},
journal = {Journal of the Chemical Society - Series Chemical Communications},
pages = {1082-1084},
peerreviewed = {unknown},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{ENHANCED} {HYPERCONJUGATION} {AND} {FACILE} 1,2-{HALOGEN} {SHIFTS} {IN} {METAL} {CATION} {COMPLEXES} {OF} 2-{HALOGENOALKYL} {RADICALS} - {AN} {ABINITIO} {STUDY}},
year = {1989}
}
@article{faucris.116896824,
abstract = {We have Calculated the geometries, energies, and normal vibrations of 845 compounds containing the elements H, C, N, O, R Al, Si, R S, and Cl using hybrid density functional theory in order to investigate the accuracy of atom-additive schemes for predicting enthalpies of formation at 298 K. The results give a more realistic estimate of the accuracy of density functional calculations than some overoptimistic earlier correlations. We have also calculated atom-additive schemes for the zero-point energies and enthalpic corrections to the energies. Remarkably, it is not important to include the vibrational or rotational contributions, which can be estimated well within a purely Born-Oppenheimer regression model. (C) 2004 Wiley Periodicals, Inc.},
author = {Winget, Paul and Clark, Timothy},
doi = {10.1002/jcc.10398},
faupublication = {yes},
journal = {Journal of Computational Chemistry},
keywords = {B3LYP;enthalpies of formulation},
pages = {725-733},
peerreviewed = {Yes},
title = {{Enthalpies} of formation from {B3LYP} calculations},
volume = {25},
year = {2004}
}
@article{faucris.116845784,
author = {Yalalov, Denis A. and Tsogoeva, Svetlana and Shubina, Tatyana and Martynova, Irina M. and Clark, Timothy},
doi = {10.1002/anie.200800849},
faupublication = {yes},
journal = {Angewandte Chemie International Edition},
keywords = {asymmetric catalysis;density functional calculations;Mannich-type reactions;thioureas;transition states},
month = {Jan},
pages = {6624-6628},
peerreviewed = {Yes},
title = {{Evidence} for an enol mechanism in a highly enantioselective {Mannich}-{Type} reaction catalyzed by primary amine-thiourea},
volume = {47},
year = {2008}
}
@article{faucris.208726961,
abstract = {Singlet fission (SF) is a process that converts one singlet excited state into two triplet states. The mechanism of SF is still not well understood. Here, we report on the use of a combination of transient absorption and electron paramagnetic resonance spectroscopies in conjunction with theoretical calculations to probe SF in a pentacene dimer linked by a non-conjugated, 1,4-diethynylbicyclo[2.2.2]octane spacer. Next to observing the key intermediates in solution-based SF, including the formation and decay of a quintet state that precedes formation of the pentacene triplet excitons, we demonstrate that the coupling is sufficiently weak that SF is essentially inoperative in non-polar media. Transitioning to a polar medium, however, amplifies the coupling strength such that SF becomes operative and supports long triplet lifetimes. Our results offer strong evidence for a charge-transfer mediation and, in turn, provide a solid framework for decoding the complete mechanism of SF in systems beyond pentacene.},
author = {Basel, Bettina and Zirzlmeier, Johannes and Hetzer, Constantin and Seelam, Rajagopala Reddy and Phelan, Brian T. and Krzyaniak, Matthew D. and Volland, Michel and Brana Coto, Pedro and Young, Ryan M. and Clark, Timothy and Thoss, Michael and Tykwinski, Rik and Wasielewski, Michael R. and Guldi, Dirk Michael},
doi = {10.1016/j.chempr.2018.04.006},
faupublication = {yes},
journal = {Chem},
pages = {1092-1111},
peerreviewed = {Yes},
title = {{Evidence} for {Charge}-{Transfer} {Mediation} in the {Primary} {Events} of {Singlet} {Fission} in a {Weakly} {Coupled} {Pentacene} {Dimer}},
volume = {4},
year = {2018}
}
@article{faucris.110981684,
author = {Clark, Timothy and Bleisteiner, Bernd and Schneider, Siegfried},
doi = {10.1007/s00894-002-0077-x},
faupublication = {yes},
journal = {Journal of Molecular Modeling},
note = {UnivIS-Import:2015-03-09:Pub.2002.nat.dchph.lpc1.excite},
pages = {87-94},
peerreviewed = {Yes},
title = {{Excited} state conformational dynamics of semiflexibly bridged electron donor-acceptor systems: a semiempirical {CI}-study including solvent effects},
volume = {8},
year = {2002}
}
@article{faucris.116837424,
abstract = {The gas phase anion proton affinities of the periodinane anions IBX(-) and IBA(-) were examined using mass spectrometry-based experiments, and estimated as 1300 +/- 25 and 1390 +/- 10 kJ mol(-1), respectively. The experimental results were supported by theoretical calculations, which yielded proton affinities of 1336 and 1392 kJ mol(-1) for IBX(-) and IBA(-) respectively, at the B3LYP/aug-cc-PVDZ level of theory.},
author = {Waters, Tom and Boulton, Jack and Clark, Timothy and Gallen, Michael J. and Williams, Craig M. and O'Hair, Richard A. J.},
doi = {10.1039/b803452d},
faupublication = {yes},
journal = {Organic & Biomolecular Chemistry},
month = {Jan},
pages = {2530-2533},
peerreviewed = {Yes},
title = {{Experimental} determination of the gas phase proton affinities of the conjugate base anions of 2-iodoxybenzoic acid ({IBX}) and 2-iodosobenzoic acid ({IBA})},
volume = {6},
year = {2008}
}
@article{faucris.229591248,
abstract = {The interactions between a wide variety of molecules having σ-holes or Ï-holes and several nitrogen bases have been analyzed computationally. The σ- A nd Ï-hole atoms span groups III-VII of the periodic table. The interaction energies range from quite weak, typical of non-covalent bonding, to unusually strong: From-4.6 to-22.0 kcal/mol for σ-hole bonding and from-4.0 to-42.4 kcal/mol for Ï-hole bonding. The markedly greater strengths of some bonds does not imply that any new factors or types of bonding are involved; they simply reflect higher degrees of the polarization that is part of any Coulombic interaction. To explain the stronger bonding, this polarization must be explicitly taken into account. We show that the interaction energies can be related quite well to (a) the maximum positive electrostatic potentials associated with the σ-or Ï-holes on their molecular surfaces, (b) the polarizabilities of the nitrogen bases, and especially (c) the polarizing electric fields of the σ-or Ï-hole molecules at the positions of the nitrogens. ©},
author = {Politzer, Peter and Murray, Jane S. and Clark, Timothy},
doi = {10.1021/acs.jpca.9b08750},
faupublication = {yes},
journal = {Journal of Physical Chemistry A},
note = {CRIS-Team Scopus Importer:2019-11-22},
peerreviewed = {Yes},
title = {{Explicit} inclusion of polarizing electric fields in σ- {A} nd {Ï}-hole interactions},
year = {2019}
}
@article{faucris.277341824,
abstract = {We report the fully fledged photophysical characterization of isomerically pure, empty-caged, tubular fullerenes D5h-C90 and D5d-C100 and compare their key properties. In particular, the focus was on cage sizes between 60 and 150 carbon atoms with D3, D3d/h, and D5d/h symmetry. The optical band gap of D5d-C100 is 1.65 eV, which is larger than 1.37 eV of D5h-C90. In stark contrast to the nonluminescent D5h-C90, D5d-C100 luminesces at room temperature. Transient absorption spectroscopy shows that photoexcited D5d-C100 is subject to a slow intersystem crossing that generates a triplet excited state. In contrast, a fast, nonradiative internal conversion governs the deactivation of D5h-C90: In this case, exploring the corresponding triplet excited state required triplet-triplet sensitization experiments with anthracene. Density functional theory calculations revealed the electronic structure of the fullertubes, and calculations are consistent with our experimental findings. The calculated band gap systematically decreases with the number of carbon atoms within the D3 and D3d/h series. In contrast, an oscillating behavior is noted within the series of D5d/h fullertubes. Finally, photoexcited D5d-C100 was found to undergo hole transfer with electron-donating triethylamines readily but not electron transfer with electron-accepting methyl viologens.},
author = {Schüßlbauer, Christoph and Krug, Marcel and Ullrich, Tobias and Franklin, Hannah M. and Stevenson, Steven and Clark, Timothy and Guldi, Dirk Michael},
doi = {10.1021/jacs.2c02442},
faupublication = {yes},
journal = {Journal of the American Chemical Society},
note = {CRIS-Team Scopus Importer:2022-07-01},
pages = {10825-10829},
peerreviewed = {Yes},
title = {{Exploring} the {Threshold} between {Fullerenes} and {Nanotubes}: {Characterizing} {Isomerically} {Pure}, {Empty}-{Caged}, and {Tubular} {Fullerenes} {D5h}-{C90} and {D5d}-{C100}},
volume = {144},
year = {2022}
}
@article{faucris.316773703,
abstract = {A metadynamics protocol is presented to characterize the binding and unbinding of peptide ligands to class A G-protein-coupled receptors (GPCRs). The protocol expands on the one previously presented for binding and unbinding small-molecule ligands to class A GPCRs and accounts for the more demanding nature of the peptide binding-unbinding process. It applies to almost all class A GPCRs. Exemplary simulations are described for subtypes Y1R, Y2R, and Y4R of the neuropeptide Y receptor family, vasopressin binding to the vasopressin V2 receptor (V2R), and oxytocin binding to the oxytocin receptor (OTR). Binding free energies and the positions of alternative binding sites are presented and, where possible, compared with the experiment.},
author = {Calderón, Jacqueline C. and Plut, Eva and Keller, Max and Cabrele, Chiara and Reiser, Oliver and Gervasio, Francesco L. and Clark, Timothy},
doi = {10.1021/acs.jcim.3c01574},
faupublication = {yes},
journal = {Journal of Chemical Information and Modeling},
month = {Jan},
note = {CRIS-Team Scopus Importer:2024-01-19},
pages = {205-218},
peerreviewed = {Yes},
title = {{Extended} {Metadynamics} {Protocol} for {Binding}/{Unbinding} {Free} {Energies} of {Peptide} {Ligands} to {Class} {A} {G}-{Protein}-{Coupled} {Receptors}},
volume = {64},
year = {2024}
}
@article{faucris.124067064,
author = {Clark, Timothy and et al.},
author_hint = {BRIX B, CLARK T},
doi = {10.1021/jo00249a047},
faupublication = {yes},
journal = {Journal of Organic Chemistry},
pages = {3365-3366},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{FACILE} {CONVERSION} {OF} {CHLOROMETHYLATED} {POLYSTYRENE} {TO} {THE} {LITHIUM} {OR} {POTASSIUM} {DERIVATIVES}},
volume = {53},
year = {1988}
}
@article{faucris.120498444,
abstract = {Oxalate decarboxylase (OxDC) catalyzes the Mn-dependent conversion of the oxalate monoanion into CO2 and formate. Many questions remain about the catalytic mechanism of OxDC although it has been proposed that the reaction proceeds via substrate-based radical intermediates. Using coupled cluster theory combined with implicit solvation models we have examined the effects of radical formation on the structure and reactivity of oxalic acid-derived radicals in aqueous solution. Our results show that the calculated solution-phase free-energy barrier for C-C bond cleavage to form CO2 is decreased from 34.2 kcal/mol for oxalic acid to only 9.3 kcal/mol and a maximum of 3.5 kcal/mol for the cationic and neutral oxalic acid-derived radicals, respectively. These studies also show that the C-C s bonding orbital of the radical cation contains only a single electron, giving rise to an elongated C-C bond distance of 1.7 angstrom; a similar lengthening of the C-C bond is not observed for the neutral radical. This study provides new chemical insights into the structure and stability of plausible intermediates in the catalytic mechanism of OxDC, and suggests that removal of an electron to form a radical (with or without the concomitant loss of a proton) may be a general strategy for cleaving the unreactive C-C bonds between adjacent sp(2)-hybridized carbon atoms.},
author = {Molt, Robert W. and Lecher, Alison M. and Clark, Timothy and Bartlett, Rodney J. and Richards, Nigel G. J.},
doi = {10.1021/ja510666r},
faupublication = {yes},
journal = {Journal of the American Chemical Society},
pages = {3248-3252},
peerreviewed = {Yes},
title = {{Facile} {C}-sp(2)-{C}-sp(2) {Bond} {Cleavage} in {Oxalic} {Acid}-{Derived} {Radicals}},
volume = {137},
year = {2015}
}
@article{faucris.109357204,
author = {Herz, Thomas and Gedeck, Peter and Clark, Timothy},
doi = {10.1021/ja9836500},
faupublication = {yes},
journal = {Journal of the American Chemical Society},
pages = {1379-1380},
peerreviewed = {Yes},
title = {{Fast} long-range adiabatic electron transfer in a model polyglycine alpha-helix},
volume = {121},
year = {1999}
}
@article{faucris.121987624,
abstract = {The erosion resistance of materials against partial discharges (PD) is a useful first indicator of their suitability for use as high voltage insulators. Epoxy resin-based composites loaded with different concentrations of silica nanoparticles were exposed to high voltage stress via an IEC(b) electrode. Laser scanning analysis was used to investigate the eroded volume and the erosion depth. The aged samples were investigated by transmission electron microscopy (TEM) analysis and scanning transmission electron microscopy (STEM), which show the formation of a protective layer of partially fused nanoparticles. The results suggest that improved erosion resistance against PD using the IEC(b) electrode is caused by the in situ formation of a protective layer consisting of sintered nanoparticles.},
author = {Meichsner, Christian and Clark, Timothy and Groeppel, Peter and Winter, Benjamin and Butz, Benjamin and Spiecker, Erdmann},
doi = {10.1109/TDEI.2012.6215081},
faupublication = {yes},
journal = {IEEE Transactions on Dielectrics and Electrical Insulation},
pages = {786--792},
peerreviewed = {Yes},
title = {{Formation} of a protective layer during {IEC}(b) test of epoxy resin loaded with silica nanoparticles},
volume = {19},
year = {2012}
}
@article{faucris.107243884,
abstract = {Because of discrepancies in the available experimental data, an extensive theoretical investigation of the formation of the Vilsmeier-Haack (VH) complex has been carried out. The barriers to complex formation calculated using eight different density functional methods (BLYP, B2-PLYP, B3LYP, B3PW91, MPW1K, M06-2X, and PBE1PBE), MP2, and extrapolation techniques (CBS-QB3, G3B3) with several basis sets (6 − 31 + G**, 6 − 311++G**, 6 − 311 + (3df,2p), aug-cc-pVDZ, and aug-cc-pVTZ) were compared with experimental data. For the overall reaction, MP2/aug-cc-pVDZ and M06-2X/6−31 + G(d,p) perform best compared to the CBS techniques. The results help clarify some open mechanistic questions.},
author = {Ozpinar, Gul Altinbas and Kaufmann, Dieter E. and Clark, Timothy},
doi = {10.1007/s00894-010-0941-z},
faupublication = {yes},
journal = {Journal of Molecular Modeling},
pages = {3209--3217},
peerreviewed = {Yes},
title = {{Formation} of the {Vilsmeier}-{Haack} complex: the performance of different levels of theory},
volume = {17},
year = {2011}
}
@article{faucris.208725372,
author = {Lohse, Maria S. and Rotter, Julian M. and Margraf, Johannes and Werner, Veronika and Becker, Matthias and Herbert, Simon and Knochel, Paul and Clark, Timothy and Bein, Thomas and Medina, Dana D.},
doi = {10.1039/c6ce00193a},
faupublication = {yes},
journal = {Crystengcomm},
pages = {4295-4302},
peerreviewed = {Yes},
title = {{From} benzodithiophene to diethoxy-benzodithiophene covalent organic frameworks-structural investigations},
volume = {18},
year = {2016}
}
@article{faucris.107256424,
abstract = {Density functional theory calculations indicate that van der Waals fullerene dimers and larger oligomers can form interstitial electron traps in which the electrons are even more strongly bound than in isolated fullerene radical anions. The fullerenes behave like \"super atoms\", and the interstitial electron traps represent one-electron intermolecular σ-bonds. Spectroelectrochemical measurements on a bis-fullerene-substituted peptide provide experimental support. The proposed deep electron traps are relevant for all organic electronics applications in which non-covalently linked fullerenes in van der Waals contact with one another serve as n-type semiconductors.},
author = {Shubina, Tatyana and Sharapa, Dmitry and Schubert, Christina and Zahn, Dirk and Halik, Marcus and Keller, Paul A. and Pyne, Stephen G. and Jennepalli, Sreenu and Guldi, Dirk Michael and Clark, Timothy},
doi = {10.1021/ja505949m},
faupublication = {yes},
journal = {Journal of the American Chemical Society},
pages = {10890–10893},
peerreviewed = {Yes},
title = {{Fullerene} {Van} der {Waals} {Oligomers} as {Electron} {Traps}},
url = {http://pubs.acs.org/doi/full/10.1021/ja505949m},
volume = {136},
year = {2014}
}
@article{faucris.304453730,
abstract = {We present a generally applicable metadynamics protocol for characterizing the activation free-energy profiles of class A G-protein coupled receptors and a proof-of-principle study for the 5HT1A-receptor. The almost universal A100 activation index, which depends on five inter-helix distances, is used as the single collective variable in well-tempered multiple-walker metadynamics simulations. Here, we show free-energy profiles for the serotonin receptor as binary (apo-receptor + G-protein-α-subunit and receptor + ligand) and ternary complexes with two prototypical orthosteric ligands: the full agonist serotonin and the partial agonist aripiprazole. Our results are not only compatible with previously reported experimental and computational data, but they also allow differences between active and inactive conformations to be determined in unprecedented atomic detail, and with respect to the so-called microswitches that have been suggested as determinants of activation, giving insight into their role in the activation mechanism.},
author = {Calderón Reyes, Jacqueline and Ibrahim, Passainte and Gobbo, Dorothea and Gervasio, Francesco Luigi and Clark, Timothy},
doi = {10.1021/acs.jcim.3c00208},
faupublication = {yes},
journal = {Journal of Chemical Information and Modeling},
note = {CRIS-Team Scopus Importer:2023-06-02},
pages = {3105-3117},
peerreviewed = {Yes},
title = {{General} {Metadynamics} {Protocol} {To} {Simulate} {Activation}/{Deactivation} of {Class} {A} {GPCRs}: {Proof} of {Principle} for the {Serotonin} {Receptor}},
volume = {63},
year = {2023}
}
@article{faucris.122418164,
author = {Apeloig, Yitzhak and Clark, Timothy and Kos, Alex and Jemmis, Eluvathingal D. and Schleyer, Paul},
doi = {10.1002/ijch.198000051},
faupublication = {yes},
journal = {Israel Journal of Chemistry},
month = {Jan},
pages = {43-50},
peerreviewed = {Yes},
title = {{GEOMETRIES} {AND} {ENERGIES} {OF} {DILITHIOETHYLENE} {ISOMERS} {AND} {OF} {VINYL} {LITHIUM} - {AN} {ABINITIO} {STUDY}},
volume = {20},
year = {1980}
}
@article{faucris.208730774,
abstract = {Molecular-dynamics (MD) simulations are playing an increasingly important role in research into the modes of action of G-protein coupled receptors (GPCRs). In this field, MD simulations are unusually important as, because of the difficult experimental situation, they often offer the only opportunity to determine structural and mechanistic features in atomistic detail. Modern combinations of soft-and hardware have made MD simulations a powerful tool in GPCR research. This is important because GPCRs are targeted by approximately half of the drugs on the market, so that computer-aided drug design plays a major role in GPCR research.},
author = {Clark, Timothy},
doi = {10.3762/bjoc.13.106},
faupublication = {yes},
journal = {Beilstein Journal of Organic Chemistry},
keywords = {computer-aided drug design;GPCR;metadynamicxs;molecular dynamics},
pages = {1071-1078},
peerreviewed = {Yes},
title = {{G}-{Protein} coupled receptors: answers from simulations},
volume = {13},
year = {2017}
}
@article{faucris.116900784,
abstract = {Ground-state tautomerism and rotational isomerization in 4,5-dimethyl-2-(2-hydroxyphenyl)imidazole in the gas phase and in solution have been investigated by means of quantum mechanical calculations, NMR and steady-state fluorescence spectroscopy. In the gas phase, the cis-enol form is the most stable species, followed by the trans-enol and the keto forms. Several theoretical approaches were employed to characterize the electronic structure of the different isomers in the gas phase at the RB3LYP/6-31 + G* level of theory. The observed behavior could be rationalized according to the different weights of the resonance and the hydrogen-bond energies in the overall energy of each isomer. The hydroxyphenyl rings of the trans-enol and the cis-enol forms exhibit a nearly aromatic structure, whereas the electronic structure of the keto-form shows a higher degree of localization. In turn, it was found that the intramolecular hydrogen bond shows similar strength in the cis-enol and keto-forms, whereas this interaction is very weak in the trans-enol form. Polar solute-solvent non-specific interactions were modeled through the Onsager, SCI-PCM and COSMO methods based on ab initio and semiempirical Hamiltonians. In solution, the keto-form is stabilized by its much greater solute-solvent electrostatic interaction through its dipolar term and the aromatization of its phenyl ring. The trans-enol form is mainly stabilized by electrostatic interactions through higher multipolar terms than dipolar and specific solute-solvent interactions through the lone pair of the imidazole N-3.},
author = {Clark, Timothy and et al.},
author_hint = {Perez-Lustres JL, Brauer M, Mosquera M, Clark T},
faupublication = {yes},
journal = {Physical Chemistry Chemical Physics},
month = {Jan},
pages = {3569-3579},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{Ground}-state tautomerism and rotational isomerization in 4,5-dimethyl-2-(2-hydroxyphenyl)imidazole in the gas phase and in polar solvents: a theoretical study of the aromaticity, intramolecular hydrogen-bond strength and differential solute-solvent interactions},
volume = {3},
year = {2001}
}
@article{faucris.122336764,
abstract = {A sigma-hole bond is a noncovalent interaction between a covalently-bonded atom of Groups IV-VII and a negative site, e.g. a lone pair of a Lewis base or an anion. It involves a region of positive electrostatic potential, labeled a sigma-hole, on the extension of one of the covalent bonds to the atom. The sigma-hole is due to the anisotropy of the atom's charge distribution. Halogen bonding is a subset of sigma-hole interactions. Their features and properties can be fully explained in terms of electrostatics and polarization plus dispersion. The strengths of the interactions generally correlate well with the magnitudes of the positive and negative electrostatic potentials of the sigma-hole and the negative site. In certain instances, however, polarizabilities must be taken into account explicitly, as the polarization of the negative site reaches a level that can be viewed as a degree of dative sharing (coordinate covalence). In the gas phase, sigma-hole interactions with neutral bases are often thermodynamically unfavorable due to the relatively large entropy loss upon complex formation.},
author = {Politzer, Peter and Murray, Jane S. and Clark, Timothy},
doi = {10.1039/c3cp00054k},
faupublication = {yes},
journal = {Physical Chemistry Chemical Physics},
month = {Jan},
pages = {11178-11189},
peerreviewed = {Yes},
title = {{Halogen} bonding and other sigma-hole interactions: a perspective},
volume = {15},
year = {2013}
}
@article{faucris.122419704,
abstract = {A halogen bond is a highly directional, electrostatically-driven noncovalent interaction between a region of positive electrostatic potential on the outer side of the halogen X in a molecule R-X and a negative site B, such as a lone pair of a Lewis base or the pi-electrons of an unsaturated system. The positive region on X corresponds to the electronically-depleted outer lobe of the half-filled p-type orbital of X that is involved in forming the covalent bond to R. This depletion is labeled a sigma-hole. The resulting positive electrostatic potential is along the extension of the R-X bond, which accounts for the directionality of halogen bonding. Positive sigma-holes can also be found on covalently-bonded Group IV-VI atoms, which can similarly interact electrostatically with negative sites. Since positive sigma-holes often exist in conjunction with negative potentials on other portions of the atom's surface, such atoms can interact electrostatically with both nucleophiles and electrophiles, as has been observed in surveys of crystallographic structures. Experimental as well as computational studies indicate that halogen and other sigma-hole interactions can be competitive with hydrogen bonding, which itself can be viewed as a subset of sigma-hole bonding.},
author = {Politzer, Peter and Murray, Jane S. and Clark, Timothy},
doi = {10.1039/c004189k},
faupublication = {yes},
journal = {Physical Chemistry Chemical Physics},
month = {Jan},
pages = {7748-7757},
peerreviewed = {Yes},
title = {{Halogen} bonding: an electrostatically-driven highly directional noncovalent interaction},
volume = {12},
year = {2010}
}
@article{faucris.116901224,
abstract = {Halogen bonding refers to the non-covalent interactions of halogen atoms X in some molecules, RX, with negative sites on others. It can be explained by the presence of a region of positive electrostatic potential, the sigma-hole, on the outermost portion of the halogen's surface, centered on the R-X axis. We have carried out a natural bond order B3LYP analysis of the molecules CF3X, with X = F, Cl, Br and I. It shows that the Cl, Br and I atoms in these molecules closely approximate the s(2)p(x)(2)p(y)(2)p(z)(1) configuration, where the z-axis is along the R-X bond. The three unshared pairs of electrons produce a belt of negative electrostatic potential around the central part of X, leaving the outermost region positive, the sigma-hole. This is not found in the case of fluorine, for which the combination of its high electronegativity plus significant sp-hybridization causes an influx of electronic charge that neutralizes the sigma-hole. These factors become progressively less important in proceeding to Cl, Br and I, and their effects are also counteracted by the presence of electron-withdrawing substituents in the remainder of the molecule. Thus a sigma-hole is observed for the Cl in CF3Cl, but not in CH3Cl.},
author = {Clark, Timothy and Hennemann, Matthias and Murray, Jane S. and Politzer, Peter},
doi = {10.1007/s00894-006-0130-2},
faupublication = {yes},
journal = {Journal of Molecular Modeling},
keywords = {Halogen bonding;Sigma-hole;Electrostatic potential;DFT},
pages = {291-296},
peerreviewed = {Yes},
title = {{Halogen} bonding: the sigma-hole},
volume = {13},
year = {2007}
}
@article{faucris.208731041,
abstract = {The models behind simple bonding theory and the origins of some components often proposed to be involved in weak intermolecular bonds are described with special reference to sigma-hole bonding, of which halogen bonds are a subset. A protocol for the analysis of weak intermolecular interactions is proposed on the basis of sound physical principles. This protocol uses three different levels of interaction; "permanent" Coulomb interactions between unperturbed monomers, relaxed Coulomb interactions and dispersion. Of the three, only dispersion is not a real, measurable quantity. It is, however, included in order to describe interactions that cannot be treated entirely by the first two levels.},
author = {Clark, Timothy},
doi = {10.1039/c7fd00058h},
faupublication = {yes},
journal = {Faraday Discussions},
pages = {9-27},
peerreviewed = {unknown},
title = {{Halogen} bonds and sigma-holes},
volume = {203},
year = {2017}
}
@article{faucris.116902764,
abstract = {The mechanism of the photodehydrodimerization of 2,5-dihydrofuran (2,5-DHF) by suspended zinc sulfide powders was investigated through emission, inhibition, adsorption, and quantum yield studies. Zinc and cadmium ions influenced the emission intensity only marginally hut strongly inhibited the reaction, so the photoreactive surface sites were not identical with the emitting states. which had lifetimes in the 0.1-24 ns range. Adsorption isotherms for these metal ions and 2,5-DHF in aqueous solution indicated the presence of mono- and multilayer adsorption. Zn2+ and Cd2+ were both adsorbed physically and by metal sulfide precipitatation, hut in the case of Cd2+ a lattice exchange mechanism with ZnS afforded CdS and dissolved zinc ions also, C-13 NMR spectra and the good agreement between the calculated number of zinc sites and the measured amount of 2,5-DHF in the saturated solvent-solute surface monolayer indicated that 2,5-DHF was adsorbed perpendicular to the: surface at all the available zinc sites,The true adsorption constant (170 +/- 30 L mol(-1)) was consistent with the pseudo-constant (260+/-50 L mol(-1)) obtained from the concentration dependence of the reaction rate, C-13 NMR signals of the alpha-carbon atoms of 2,5-DHF and THP adsorbed onto ZnS from the gas phase were downfield shifted by 1.5 and 8.7 ppm as compared to those of the free substrates. respectively. The downfield shift of the olefinic signals was about 0.4 ppm. it is postulated that a dissociative electron transfer from adsorbed 2,5-DHF to the reactive hole afforded a proton and the dihydrofuryrl radical. The corresponding C-H bond dissociation energies were calculated by ab initio methods for various substrates. As expected, the apparent quantum yield of various substrates increased linearly with decreasing C-H bond dissociation energy. Tnc: intermediate dihydrofuryl radical dimerized to the products in the adsorbed state, as indicated bit the linear increase of the square root of the reaction rate with increasing 2,5-DHF surface concentration and by competition experiments with THF/?5-DHF mixtures. The reaction inhibition by Zn2+ and Cd2+ could be analyzed in terms of the Stern-Volmer model only when the surface concentration was considered. Inhibition by Cd2+ is about three times faster than inhibition by Zn2+, in which case no zinc metal was observed.},
author = {Roth, Henryette and Clark, Timothy and Kisch, Horst and et al.},
author_hint = {Horner G, Johne P, Kunneth R, Twardzik G, Roth H, Clark T, Kisch H},
doi = {10.1002/(SICI)1521-3765(19990104)5:1<208::AID-CHEM208>3.0.CO;2-0},
faupublication = {yes},
journal = {Chemistry - A European Journal},
keywords = {ab initio calculations;C-C coupling;photochemistry;surface chemistry;zinc sulfide},
month = {Jan},
pages = {208-217},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{Heterogeneous} photocatalysis, part {XIX} - {Semiconductor} type {A} photocatalysis: {Role} of substrate adsorption and the nature of photoreactive surface sites in zinc sulfide catalyzed {C}-{C} coupling reactions},
volume = {5},
year = {1999}
}
@article{faucris.106884844,
author = {Holzwarth, Johannes and Amsharov, Konstantin and Sharapa, Dmitry and Reger, David and Roshchyna, Kateryna and Lungerich, Dominik and Jux, Norbert and Hauke, Frank and Clark, Timothy and Hirsch, Andreas},
doi = {10.1002/anie.201706437},
faupublication = {yes},
journal = {Angewandte Chemie International Edition},
keywords = {alkylation; density-functional calculations; graphene; radicals; reaction mechanisms},
pages = {12184-12190},
peerreviewed = {Yes},
title = {{Highly} {Regioselective} {Alkylation} of {Hexabenzocoronenes}: {Fundamental} {Insights} into the {Covalent} {Chemistry} of {Graphene}},
volume = {56},
year = {2017}
}
@article{faucris.122422344,
abstract = {A computer-assisted method for the generation of pseudoreceptor models is presented together with two practical applications. From a three-dimensional alignment of known histamine H-4 receptor ligands, a pseudoreceptor model of the putative ligand binding site was constructed and used for virtual screening of a large collection of commercially available compounds. Two bioactive chemotypes were retrieved, demonstrating the general applicability of the approach. The pseudoreceptor model was also used to find the putative ligand binding pocket within the transmembrane receptor domain. For each frame of a molecular dynamics simulation of a homology-based H-4 receptor model, we automatically extracted potential ligand binding pockets and used their. compatibility with the pseudoreceptor as a selection criterion. The best-matching pocket fits perfectly with existing mutation data and previously published hypotheses suggesting Glu182(5.46) as the preferred binding partner of a positively charged moiety of H-4 receptor ligands. This new pseudoreceptor approach has demonstrated its suitability for both structure-based prioritization of protein receptor models, and ligand-based virtual screening with the aim to perform scaffold hopping.},
author = {Tanrikulu, Yusuf and Proschak, Ewgenij and Werner, Tim and Geppert, Tim and Todoroff, Nickolay and Klenner, Alexander and Kottke, Tim and Sander, Kerstin and Schneider, Erich and Seifert, Roland and Stark, Holger and Clark, Timothy and Schneider, Gisbert},
doi = {10.1002/cmdc.200800443},
faupublication = {yes},
journal = {ChemMedChem},
keywords = {drug design;GPCR;homology models;molecular dynamics;virtual screening},
pages = {820-827},
peerreviewed = {Yes},
title = {{Homology} {Model} {Adjustment} and {Ligand} {Screening} with a {Pseudoreceptor} of the {Human} {Histamine} {H}-4 {Receptor}},
volume = {4},
year = {2009}
}
@article{faucris.291581119,
abstract = {Context: Just how much effort and detail should we invest in analyzing interactions of the order of 5 kcal mol−1? This comment attempts to provide a conciliatory overview of what is often a contentious field and to pose some questions that I hope will eventually lead at least to some consensus. Methods: This is an opinion article without calculations or data.},
author = {Clark, Timothy},
doi = {10.1007/s00894-023-05460-4},
faupublication = {yes},
journal = {Journal of Molecular Modeling},
keywords = {Bonding analysis; Charge transfer; Covalent; Polarization},
note = {CRIS-Team Scopus Importer:2023-03-10},
peerreviewed = {Yes},
title = {{How} deeply should we analyze non-covalent interactions?},
volume = {29},
year = {2023}
}
@article{faucris.122423884,
abstract = {The binding of anhydrotetracycline (atc) in wild-type TetR( D), TetR( B), and four single tryptophan mutants of TetR( B) was investigated by UV/vis absorption, steady-state, and time-resolved fluorescence spectroscopy. From absorption titration experiments with Mg2+, we conclude that binding of one [atc-Mg](+) complex in the homodimer causes changes in the protein conformation around the second binding pocket. In the presence or absence of Mg2+, several different groups of atc-protein arrangements must exist, each with a characteristic atc fluorescence decay time. Taking into account the results of molecular dynamics ( MD) simulations, we propose as one possible origin for such a differentiation the extent of hydrogen bonding between atc and the surrounding amino acids. Binding of Mg2+ should change the arrangement of the surrounding amino acids such that some of the excited atc molecules do not undergo the relaxation processes typical for free atc. The MD simulations also show that the pattern of intra- and intermolecular hydrogen bonding in the two monomeric units is not correlated, thereby leading to different fluorescence kinetics for atc in the two monomeric units. Furthermore, it is suggested that hydrogen bonding between Arg104 and O10 of anhydrotetracycline could regulate the relaxation processes of excited anhydrotetracyclin},
author = {Leypold, Clemens and Marian, Dan-Thomas and Roman, Ciprian and Schneider, Siegfried and Schubert, Peter and Scholz, Oliver and Hillen, Wolfgang and Clark, Timothy and Lanig, Harald},
doi = {10.1039/b303431n},
faupublication = {yes},
journal = {Photochemical & Photobiological Sciences},
month = {Jan},
pages = {109-119},
peerreviewed = {Yes},
title = {{How} does {Mg2}+ affect the binding of anhydrotetracycline in the {TetR} protein?},
volume = {3},
year = {2004}
}
@article{faucris.240781905,
abstract = {Red-emissive pi-expanded diketopyrrolopyrroles (DPPs) with fluorescence reaching lambda=750 nm can be easily synthesized by a three-step strategy involving the preparation of diketopyrrolopyrrole followed by N-arylation and subsequent intramolecular palladium-catalyzed direct arylation. Comprehensive spectroscopic assays combined with first-principles calculations corroborated that both N-arylated and fused DPPs reach a locally excited (S-1) state after excitation, followed by internal conversion to states with solvent and structural relaxation, before eventually undergoing intersystem crossing. Only the structurally relaxed state is fluorescent, with lifetimes in the range of several nanoseconds and tens of picoseconds in nonpolar and polar solvents, respectively. The lifetimes correlate with the fluorescence quantum yields, which range from 6 % to 88 % in nonpolar solvents and from 0.4 % and 3.2 % in polar solvents. A very inefficient (T-1) population is responsible for fluorescence quantum yields as high as 88 % for the fully fused DPP in polar solvents.},
author = {Skonieczny, Kamil and Papadopoulos, Ilias and Thiel, Dominik and Gutkowski, Krzysztof and Haines, Philipp and McCosker, Patrick Michael and Laurent, Adele D. and Keller, Paul A. and Clark, Timothy and Jacquemin, Denis and Guldi, Dirk Michael and Gryko, Daniel T.},
doi = {10.1002/anie.202005244},
faupublication = {yes},
journal = {Angewandte Chemie International Edition},
note = {CRIS-Team WoS Importer:2020-07-24},
peerreviewed = {Yes},
title = {{How} {To} {Make} {Nitroaromatic} {Compounds} {Glow}: {Next}-{Generation} {Large} {X}-{Shaped}, {Centrosymmetric} {Diketopyrrolopyrroles}},
year = {2020}
}
@article{faucris.124067944,
author = {Clark, Timothy and Schürer, Gudrun and King, William},
faupublication = {yes},
journal = {ACS National Meeting Book of Abstracts},
pages = {U158-U158},
peerreviewed = {unknown},
title = {{Hybrid} {QM}/{MM} simulations of enzyme reaction mechanisms.},
volume = {220},
year = {2000}
}
@article{faucris.119333324,
abstract = {Details of the hydration and water exchange mechanism of Zn2+ have been studied using density functional calculations with a variety of different basis sets. The computed structures and hydration energies for complexes of the type [Zn(H2O)(n)](2+) with n = 1-6 are in good agreement with previous results obtained from ab initio calculations and self-consistent reaction field methods. Extension of our investigations to the second coordination (first solvation) sphere and thus to complexes of the general type [Zn(H2O)(n)](2+). mH(2)O with n = 5 and m = 1, 2 and n = 6 and m = 1 reveals two types of complexes having either one or two hydrogen bonds between first and second sphere water molecules. The water exchange mechanism of [Zn(H2O)(6)](2+) is analyzed on the basis of the structures and energies of these complexes. Within the variations due to the different basis sets employed, the Zn-O bond length for water molecules in the first coordination sphere is between 2.0 and 2.1 Angstrom, water molecules in the second coordination sphere between 3.6 and 4.1 Angstrom and at the frontier of both spheres between 2.7 and 3.0 Angstrom. Within the limitations of the present model, in which bulk water, counterions, and more than one exchanging water molecule have not been considered, a limiting dissociative (D) mechanism for the water exchange reaction on [Zn(H2O)(6)](2+) is suggested. On the basis of the most reliable structures (i.e., those that could be verified with all levels of theory), the energy of activation for the water exchange is between 4.2 and 4.6 kcal/mol, depending on the basis set employed. A transition state for the interchange mechanism could not be localized. All optimizations invariably led to transition state structures that indicate a limiting D mechanism.},
author = {Hartmann, Michael and Clark, Timothy and van Eldik, Rudi},
doi = {10.1021/ja970483f},
faupublication = {yes},
journal = {Journal of the American Chemical Society},
pages = {7843-7850},
peerreviewed = {Yes},
title = {{Hydration} and water exchange of zinc({II}) ions. {Application} of density functional theory},
volume = {119},
year = {1997}
}
@article{faucris.122424324,
author = {Clark, Timothy and Schleyer, Paul},
doi = {10.1016/S0022-328X(00)84876-7},
faupublication = {yes},
journal = {Journal of Organometallic Chemistry},
month = {Jan},
pages = {191-202},
peerreviewed = {Yes},
title = {{HYDROBORATION} - {ABINITIO} {STUDY} {OF} {REACTION} {OF} {BH3} {WITH} {ETHYLENE}},
volume = {156},
year = {1978}
}
@article{faucris.307849341,
abstract = {Activation of the µ-opioid receptor (µOR) by food components could lead to reward effects or to the modulation of motor functions in the gastrointestinal tract. In an unbiased search for novel µOR agonists in food, a three-step virtual-screening process selected 22 promising candidates with potential to interact with the µOR. Radioligand binding studies showed that ten of these substances indeed bind to the receptor. Functional assays identified kukoamine A as a full agonist (EC50 = 5.6 µM) and kukoamine B as a partial agonist (EC50 = 8.7 µM) to µOR. After extraction, both kukoamines were analyzed by LC–MS/MS in potato, tomato, pepper, and eggplant. Depending on the potato variety, up to 16 µg of kukoamine A and 157 µg of kukoamine B per gram dry weight could be determined in the whole tuber, mainly concentrated in the potato peel. Cooking did not influence the kukoamine contents.},
author = {Saller, Julia and List, Carina and Hübner, Harald and Gmeiner, Peter and Clark, Timothy and Pischetsrieder, Monika},
doi = {10.1016/j.foodchem.2023.136637},
faupublication = {yes},
journal = {Food Chemistry},
keywords = {Bioactive food compound; Kukoamine; Potato; Solanaceous plant; Virtual screening; µ-Opioid receptor},
note = {CRIS-Team Scopus Importer:2023-07-21},
peerreviewed = {Yes},
title = {{Identification} and quantification of kukoamine {A} and kukoamine {B} as novel μ-opioid receptor agonists in potato and other solanaceous plants},
volume = {427},
year = {2023}
}
@article{faucris.123950244,
abstract = {The dopamine D2 receptor (D2R) is involved in food reward and compulsive food intake. The present study developed a virtual screening (VS) method to identify food components, which may modulate D2R signalling. In contrast to their common applications in drug discovery, VS methods are rarely applied for the discovery of bioactive food compounds. Here, databases were created that exclusively contain substances occurring in food and natural sources (about 13,000 different compounds in total) as the basis for combined pharmacophore searching, hit-list clustering and molecular docking into D2R homology models. From 17 compounds finally tested in radioligand assays to determine their binding affinities, seven were classified as hits (hit rate = 41%). Functional properties of the five most active compounds were further examined in β-arrestin recruitment and cAMP inhibition experiments. D2R-promoted G-protein activation was observed for hordenine, a constituent of barley and beer, with approximately identical ligand efficacy as dopamine (76%) and a Ki value of 13 μM. Moreover, hordenine antagonised D2-mediated β-arrestin recruitment indicating functional selectivity. Application of our databases provides new perspectives for the discovery of bioactive food constituents using VS methods. Based on its presence in beer, we suggest that hordenine significantly contributes to mood-elevating effects of beer.},
author = {Sommer, Thomas and Hübner, Harald and El Kerdawy, Ahmed and Gmeiner, Peter and Pischetsrieder, Monika and Clark, Timothy},
doi = {10.1038/srep44201},
faupublication = {yes},
journal = {Scientific Reports},
pages = {44201},
peerreviewed = {Yes},
title = {{Identification} of the {Beer} {Component} {Hordenine} as {Food}-{Derived} {Dopamine} {D2} {Receptor} {Agonist} by {Virtual} {Screening} a {3D} {Compound} {Database}.},
url = {http://rdcu.be/pX4k},
volume = {7},
year = {2017}
}
@article{faucris.208724834,
abstract = {The chemokine receptor CXCR3 is a G protein-coupled receptor that conveys extracellular signals into cells by changing its conformation upon ligand binding. We previously hypothesized that small-molecule allosteric CXCR3-agonists do not bind to the same allosteric binding pocket as 8-azaquinazolinone-based negative allosteric modulators. We have now performed molecular-dynamics (MD) simulations with metadynamics enhanced sampling on the CXCR3 system to refine structures and binding modes and to predict the CXCR3-binding affinities of the biased allosteric agonist FAUC1036 and the negative allosteric modulator RAMX3. We have identified two distinct binding sites; a shallow and a second deeper pocket to which the biased allosteric agonist FAUC1036 and negative allosteric modulator RAMX3 bind, respectively.},
author = {Milanos, Lampros and Saleh, Noureldin and Kling, Ralf and Kaindl, Jonas and Tschammer, Nuska and Clark, Timothy},
doi = {10.1002/anie.201607831},
faupublication = {yes},
journal = {Angewandte Chemie International Edition},
keywords = {allosterism;membrane proteins;molecular dynamics;protein structures;signal transduction},
pages = {15277-15281},
peerreviewed = {Yes},
title = {{Identification} of {Two} {Distinct} {Sites} for {Antagonist} and {Biased} {Agonist} {Binding} to the {Human} {Chemokine} {Receptor} {CXCR3}},
volume = {55},
year = {2016}
}
@article{faucris.121040964,
author = {Clark, Timothy},
faupublication = {yes},
journal = {ACS National Meeting Book of Abstracts},
pages = {124-COMP},
peerreviewed = {unknown},
title = {{IMPROVING} {NUMERICAL} {SCRF} {TECHNIQUES} {FOR} {GROUND} {AND} {EXCITED}-{STATES}},
volume = {210},
year = {1995}
}
@article{faucris.107615684,
abstract = {A three-pronged approach has been used to design rational improvements in self-assembled monolayer field-effect transistors: classical molecular dynamics (MD) simulations to investigate atomistic structure, large-scale quantum mechanical (QM) calculations for electronic properties, and device fabrication and characterization as the ultimate goal. The MD simulations reveal the effect of using two-component monolayers to achieve intact dielectric insulating layers and a well-defined semiconductor channel. The QM calculations identify improved conduction paths in the monolayers that consist of an optimum mixing ratio of the components. These results have been used both to confirm the predictions of the calculations and to optimize real devices. Monolayers were characterized with X-ray reflectivity measurements and by electronic characterization of complete devices. © 2013 American Chemical Society.},
author = {Jäger, Christof and Schmaltz, Thomas and Novak, Michael and Khassanov, Artöm and Vorobiev, Alexei and Hennemann, Matthias and Krause, Andreas and Dietrich, Hanno and Zahn, Dirk and Hirsch, Andreas and Halik, Marcus and Clark, Timothy},
doi = {10.1021/ja401320n},
faupublication = {yes},
journal = {Journal of the American Chemical Society},
pages = {4893-4900},
peerreviewed = {Yes},
title = {{Improving} the {Charge} {Transport} in {Self}-{Assembled} {Monolayer} {Field}-{Effect} {Transistors}: {From} {Theory} to {Devices}},
volume = {135},
year = {2013}
}
@article{faucris.118500844,
abstract = {A combination of in situ vibrational sum-frequency generation (SFG) spectroscopy and molecular-dynamics (MD) simulations has allowed us to study the effects of indentation of self-assembled octadecylphosphonic acid (ODPA) monolayers on α-Al2O3(0001). Stress-induced changes in the vibrational signatures of C-H stretching vibrations in SFG spectra and the results of MD simulations provide clear evidence for an increase in gauche-defect density in the monolayer as a response to indentation. A stress-dependent analysis indicates that the defect density reaches saturation at approximately 155 MPa. After stress is released, the MD simulations show an almost instantaneous healing of pressure-induced defects in good agreement with experimental results. The lateral extent of the contact areas was studied with colocalized SFG spectroscopy and compared to theoretical predictions for pressure gradients from Hertzian contact theory. SFG experiments reveal a gradual increase in gauche-defect density with pressure before saturation close to the contact center. Furthermore, our MD simulations show a spatial anisotropy of pressure-induced effects within ODPA domains: molecules tilted in the direction of the pressure gradient increase in tilt angle while those on the opposite side form gauche-defects.},
author = {Meltzer, Christian and Paul, Jonas and Dietrich, Hanno and Jäger, Christof and Clark, Timothy and Zahn, Dirk and Braunschweig, Björn and Peukert, Wolfgang},
doi = {10.1021/ja5048076},
faupublication = {yes},
journal = {Journal of the American Chemical Society},
keywords = {spectroscopy; monolayer; self-assembly;},
pages = {10718--10727},
peerreviewed = {Yes},
title = {{Indentation} and {Self}-{Healing} {Mechanisms} of a {Self}-{Assembled} {Monolayer}-{A} {Combined} {Experimental} and {Modeling} {Study}},
volume = {136},
year = {2014}
}
@article{faucris.116908704,
abstract = {Extensive molecular-dynamics simulations show that the distance between the centers of gravity of the two equivalent helices 3 in the DNA-binding heads of the dimer of the tetracycline-repressor protein (TetR) cairn be used as a retiable diagnostic of induction. This is not, however, true for X-ray structures, but only for molecular-dynamics simulations. This is suggested to be because TetR is inherently flexible along the coordinate of the allosteric change (as is always likely to be the case for allosteric proteins), so that crystal-packing forces can determine the conformation of the protein. However, the time scale of the allosteric rearrangement in the absence of DNA-complexation is found to be of the order of tens of nanoseconds, so hat rearrangement can be observed reproducibly in 100 ns simulations. Metastable (pie-equilibrium) conformations of TetR have been observed for up to 60 ns. The likely equilibrium processes and key features of the TetR system are discussed. Proteins 2009; 77:857-866. (C) 2009 Wiley-Liss, Inc.},
author = {Haberl, Florian and Lanig, Harald and Clark, Timothy},
doi = {10.1002/prot.22505},
faupublication = {yes},
journal = {Proteins-Structure Function and Bioinformatics},
keywords = {molecular dynamics;signal transduction;tetracycline repressor},
pages = {857-866},
peerreviewed = {Yes},
title = {{Induction} of the tetracycline repressor: {Characterization} by molecular-dynamics simulations},
volume = {77},
year = {2009}
}
@article{faucris.112775124,
abstract = {The influence of electron attachment on the stability of the mono-and dihydrogenated buckminsterfullerene C was studied using density functional theory and semiempirical molecular orbital techniques. We have also assessed the reliability of computationally accessible methods that are important for investigating the reactivity of graphenic species and surfaces in general. The B3LYP and M06L functionals with the 6-311+G(d,p) basis set and MNDO/c are found to be the best methods for describing the electron affinities of C and C H . It is shown that simple frontier molecular orbital analyses at both the AM1 and B3LYP/6-31G(d) levels are useful for predicting the most favourable position of protonation of C H , that is, formation of the kinetically controlled product 1,9-dihydro[60]fullerene, which is also the thermodynamically controlled product, in agreement with experimental and previous theoretical studies. We have shown that reduction of exo-and endo-C H makes them more stable in contrast to the reduction of the exo,exo-1,9-C H , reduced forms of which decompose more readily, in agreement with experimental electrochemical studies. However, most other dihydro[60]fullerenes are stabilized by reduction and the regioselectivity of addition is predicted to decrease as the less stable isomers are stabilized more by the addition of electrons than the two most stable ones (1,9 and 1,7). Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.},
author = {Dral, Pavlo and Shubina, Tatyana and Hirsch, Andreas and Clark, Timothy},
doi = {10.1002/cphc.201100529},
faupublication = {yes},
journal = {ChemPhysChem},
pages = {2581-2589},
peerreviewed = {Yes},
title = {{Influence} of {Electron} {Doping} on the {Hydrogenation} of {Fullerene} {C60}: {A} {Theoretical} {Investigation}},
volume = {12},
year = {2011}
}
@article{faucris.230922128,
abstract = {The process of singlet fission (SF) produces two triplet excited states (T1 + T1) from one singlet excited exciton (S1) and a molecule in its ground state (S0). It, thus, possesses the potential to boost the solar cell efficiency above the thermodynamic Shockley-Queisser limit of 33%. A key intermediate in the SF mechanism is the singlet correlated triplet pair state 1(T1T1). This state is of great relevance, as its formation is spin-allowed and, therefore, very fast and efficient. Three fundamentally different pathways to formation of 1(T1T1) have been documented so far. The factors that influence which mechanism is associated with which chromophore, however, remain largely unknown. In order to harvest both triplet excitons independently, a decorrelation of the correlated triplet pair state to two individual triplets is required. This second step of the SF process implies a change in the total spin quantum number. In the case of a dimer, this is usually only possible if the coupling between the two pentacenes is sufficiently weak. In this study, we present two platinum-bridged pentacene dimers in which the pentacenes are coupled strongly, so that spin-decorrelation yielding (T1 + T1) was initially expected to be outcompeted by triplet-triplet annihilation (TTA) to the ground state. Both platinum-bridged pentacene dimers undergo quantitative formation of the (T1T1) state on a picosecond timescale that is unaffected by the internal heavy-atom effect of the platinum. Instead of TTA of (T1T1) to the ground state, the internal heavy-atom effect allows for 1(T1T1)-3(T1T1) and 1(T1T1)-5(T1T1) mixing and, thus, triggers subsequent TTA to the (T1S0) state and minor formation of (T1 + T1). A combination of transient absorption and transient IR spectroscopy is applied to investigate the mechanism of the (T1T1) formation in both dimers. Using a combination of experiment and quantum chemical calculations, we are able to observe a transition from the CT-mediated to the direct SF mechanism and identify relevant factors that influence the mechanism that dominates SF in pentacene. Moreover, a combination of time-resolved optical and electron paramagnetic resonance spectroscopic data allows us to develop a kinetic model that describes the effect of enhanced spin-orbit couplings on the correlated triplet pair state.},
author = {Basel, Bettina and Young, Ryan M. and Krzyaniak, Matthew D. and Papadopoulos, Ilias and Hetzer, Constantin and Gao, Yueze and La Porte, Nathan T. and Phelan, Brian T. and Clark, Timothy and Tykwinski, Rik R. and Wasielewski, Michael R. and Guldi, Dirk Michael},
doi = {10.1039/c9sc04410h},
faupublication = {yes},
journal = {Chemical Science},
note = {CRIS-Team Scopus Importer:2019-12-31},
pages = {11130-11140},
peerreviewed = {Yes},
title = {{Influence} of the heavy-atom effect on singlet fission: {A} study of platinum-bridged pentacene dimers},
volume = {10},
year = {2019}
}
@article{faucris.121699644,
abstract = {A 4.1 mu s molecular dynamics simulation of the NR4A1 (hNur77) apo-protein has been undertaken and a previously undetected druggable pocket has become apparent that is located remotely from the 'traditional' nuclear receptor ligand-binding site. A NR4A1/bisindole ligand complex at this novel site has been found to be stable over 1 mu s of simulation and to result in an interesting conformational transmission to a remote loop that has the capacity to communicate with a NBRE within a RXR-alpha/NR4A1 heterodimer. Several features of the simulations undertaken indicate how NR4A1 can be affected by alternate-site modulators.},
author = {Lanig, Harald and Reisen, Felix and Whitley, David and Schneider, Gisbert and Banting, Lee and Clark, Timothy},
doi = {10.1371/journal.pone.0135246},
faupublication = {yes},
journal = {PLoS ONE},
peerreviewed = {Yes},
title = {{In} {Silico} {Adoption} of an {Orphan} {Nuclear} {Receptor} {NR4A1}},
volume = {10},
year = {2015}
}
@article{faucris.116911564,
abstract = {We present an artificial neural network (ANN) model for the prediction of solubility of organic compounds in buffer at pH 6.5, thus mimicking the medium in the human gastrointestinal tract. The model was derived from consistently performed solubility measurements of about 5000 compounds. Semiempirical VAMP/AM1 quantum-chemical wave function derived, HQSAR-derived logP. and topology-based descriptors were employed after preselection of significant contributors by statistical and data mining approaches. Ten ANNs were trained each with 90% as a training set and 10% as a test set, and deterministic analysis of prediction quality was used in an iterative manner to optimize ANN architecture and descriptor space, based on Corina 3D molecular structure and AM1/COSMO single point wave function. In production mode, a mean prediction value of the 10 ANNs is created, as is a standard deviation based quality parameter. The productive ANN based on Corina geometries and AM1/COSMO wave function gives an of 0.50 and a root-mean-square error of 0.71 log units, with 87 and 96% of the compounds having an error of less than I and 1.5 log units, respectively. The model is able to predict permanently charged species, e.g. zwitterions or quaternary amines, and problematic structures such as tautomers and unresolved diastereomers almost as well as neutral compounds.},
author = {Göller, Andreas H. and Hennemann, Matthias and Keldenich, Jörg and Clark, Timothy},
doi = {10.1021/ci0503210},
faupublication = {yes},
journal = {Journal of Chemical Information and Modeling},
pages = {648-658},
peerreviewed = {Yes},
title = {{In} silico prediction of buffer solubility based on quantum-mechanical and {HQSAR}- and topology-based descriptors},
volume = {46},
year = {2006}
}
@article{faucris.122430704,
abstract = {Insolubility is a crucial issue in drug design because insoluble compounds are often measured to be inactive although they might be active if they were soluble. We provide and analyze various insolubility classification models based on a recently published data set and compounds measured in-house at Boehringer-Ingelheim. The 2D descriptor sets from pharmacophore fingerprints and MOE and the 3D descriptor sets from ParaSurf and VolSurf were examined in conjunction with support vector machines, Bayesian regularized neural networks, and random forests. We introduce a classifier-fusion strategy, called metaclassifier, which improves upon the best single prediction and at the same time avoids descriptor selection, a potential source of overfitting. The metaclassifier strategy is compared to the simpler fusion strategies of maximum vote and highest probability picking. A prediction accuracy of 72.6% on a three class model is achieved with the metaclassifier, with nearly perfect separation of soluble and insoluble compounds and prediction as good as our calculated maximum possible agreement with experiment.},
author = {Kramer, Christian and Beck, Bernd and Clark, Timothy},
doi = {10.1021/ci900377e},
faupublication = {yes},
journal = {Journal of Chemical Information and Modeling},
pages = {404-414},
peerreviewed = {Yes},
title = {{Insolubility} {Classification} with {Accurate} {Prediction} {Probabilities} {Using} a {MetaClassifier}},
volume = {50},
year = {2010}
}
@article{faucris.118735804,
abstract = {In the current work, we have explored a novel synthetic route towards metalated porphycenes and their use in p-type NiO-based dye-sensitized solar cells. Particular emphasis is placed on the influence that the relative positioning of the anchoring group exerts on the DSSC performance.},
author = {Feihl, Sebastian and Costa, Ruben D. and Brenner, Wolfgang and Margraf, Johannes and Casillas Pacheco, Ruben and Langmar, Oliver and Browa, Anne and Shubina, Tatyana and Jux, Norbert and Guldi, Dirk Michael and Clark, Timothy},
doi = {10.1039/c4cc04523h},
faupublication = {yes},
journal = {Chemical Communications},
pages = {11339--11342},
peerreviewed = {Yes},
title = {{Integrating} metalloporphycenes into p-type {NiO}-based dye-sensitized solar cells},
volume = {50},
year = {2014}
}
@article{faucris.216807482,
abstract = {The noncovalent interactions of the CH
3
•
, Cl
•
, CF
3
•
, and C(CH
3
)
3
•
radicals with CF
3
X molecules (X = Cl, Br, I) have been investigated using CCSD(T)/aug-cc-pVTZ energy calculations on MP2/aug-cc-pVTZ-optimized geometries. The electrophilic chlorine atom prefers to complex with the equatorial belt of the heavier halogen X, whereas the nucleophilic radicals CH
3
•
and C(CH
3
)
3
•
coordinate preferentially with the σ-hole of X to give C
3v
complexes. Complexation energies are generally small, ranging up to 5 kcal mol
-1
for CF
3
I with either the chlorine atom or the
t
Bu radical. Within the continuum from pure one-electron (SOMO-LUMO) to pure three-electron (SOMO-HOMO) bonds, the results can be interpreted in terms of predominantly one-electron bonds for nucleophilic radicals but closer to three-electron bonds for the chlorine atom. The trifluoromethyl radical binds very weakly via interhalogen interactions; the carbon radical center plays no role in the bonding.},
author = {Clark, Timothy},
doi = {10.1021/acs.jpca.9b01133},
faupublication = {yes},
journal = {Journal of Physical Chemistry A},
note = {CRIS-Team Scopus Importer:2019-05-02},
pages = {3326-3333},
peerreviewed = {Yes},
title = {{Interaction} of {Radicals} with σ-{Holes}},
volume = {123},
year = {2019}
}
@article{faucris.275322895,
abstract = {We address the long-standing controversy as to the physical origin of covalent bonding, whether it involves a lowering of the potential energy or a lowering of the kinetic energy. We conclude that both of these do occur and contribute to the formation of the bond. The analysis is in terms of the virial theorem and the variations in the potential energy and the kinetic energy as the atoms approach each other. At large separations, the change in kinetic energy relative to the separated atoms is negative and stabilizing, while the corresponding potential energy change is positive and destabilizing. However, as the atoms approach their equilibrium separation, these rapidly reverse; the kinetic energy increases and the potential energy decreases, so that at equilibrium the net kinetic energy is positive and the net potential energy negative. At equilibrium, the bonding is due solely to the potential energy and is electrostatic.},
author = {Clark, Timothy and Politzer, Peter and Murray, Jane S.},
doi = {10.1039/d2cp01529c},
faupublication = {yes},
journal = {Physical Chemistry Chemical Physics},
note = {CRIS-Team WoS Importer:2022-05-20},
peerreviewed = {Yes},
title = {{Interpreting} the variations in the kinetic and potential energies in the formation of a covalent bond},
year = {2022}
}
@article{faucris.124025264,
abstract = {Experimental and theoretical evidence is presented for a novel metal-dependent intramolecular reactivity of π-bonded, unsaturated P-heterocycles like 1,3-diphosphete and 1,3,5-triphosphinine. The nucleophilic attack of a P lone pair of 1,3-diphosphete toward a neighboring ligand leads to new bicyclic ligands with unique structural features. A metal-initiated intramolecular hydrogen transfer and C-C bond formation are observed for (1,3,5-triphosphinine)(COD)Fe to result in the formation of [(CO)5Cr(4,5,6-trihydro-1,3,5-triphosphinine)(trihydropentalene) Fe].},
author = {Clark, Timothy and Binger, Paul and Heinemann, Frank Wilhelm and Hennemann, Matthias and Pritzkow, Hans and Toepffer, Christian and Zenneck, Ulrich},
doi = {10.1080/10426500212211},
faupublication = {yes},
journal = {Phosphorus Sulfur and Silicon and the Related Elements},
keywords = {DFT calculations; Iron; Molybdenum; P-heterocycles, π-complexes},
note = {UnivIS-Import:2015-04-14:Pub.2002.forsch.sonder.sfb583.intram},
pages = {1523-1527},
peerreviewed = {Yes},
title = {{Intramolecular} {Reactivity} of {Pi}-{Coordinated} {P}-{Heterocycles}: {How} to {Form} {Five}-{Membered} {Rings} out of {Phosphaalkynes}},
volume = {177},
year = {2002}
}
@article{faucris.318756257,
abstract = {Triplet dynamics in singlet fission depend strongly on the strength of the electronic coupling. Covalent systems in solution offer precise control over such couplings. Nonetheless, efficient free triplet generation remains elusive in most systems, as the intermediate triplet pair 1(T1T1) is prone to triplet-triplet annihilation due to its spatial confinement. In the solid state, entropically driven triplet diffusion assists in the spatial separation of triplets, resulting in higher yields of free triplets. Control over electronic coupling in the solid state is, however, challenging given its sensitivity to molecular packing. We have thus developed a hexameric system (HexPnc) to enable solid-state-like triplet diffusion at the molecular scale. This system is realized by covalently tethering three pentacene dimers to a central subphthalocyanine scaffold. Transient absorption spectroscopy, complemented by theoretical structural optimizations and steady-state spectroscopy, reveals that triplet diffusion is indeed facilitated due to intramolecular cluster formation. The yield of free triplets in HexPnc is increased by a factor of up to 14 compared to the corresponding dimeric reference (DiPnc). Thus, HexPnc establishes crucial design aspects for achieving efficient triplet dissociation in strongly coupled systems by providing avenues for diffusive separation of 1(T1T1), while, concomitantly, retaining strong interchromophore coupling which preserves rapid formation of 1(T1T1).},
author = {Greißel, Phillip and Thiel, Dominik and Gotfredsen, Henrik and Chen, Lan and Krug, Marcel and Papadopoulos, Ilias and Miskolzie, Mark and Torres, Tomás and Clark, Timothy and Brøndsted Nielsen, Mogens and Tykwinski, Rik R. and Guldi, Dirk Michael},
doi = {10.1002/anie.202315064},
faupublication = {yes},
journal = {Angewandte Chemie International Edition},
keywords = {Oligoacene; Photoenergy Conversion; Singlet Fission; Triplet Dissociation; Ultrafast Spectroscopy},
note = {CRIS-Team Scopus Importer:2024-02-23},
peerreviewed = {Yes},
title = {{Intramolecular} {Triplet} {Diffusion} {Facilitates} {Triplet} {Dissociation} in a {Pentacene} {Hexamer}},
volume = {63},
year = {2024}
}
@article{faucris.208731309,
abstract = {Signalling by G-protein coupled receptors usually occurs via ternary complexes formed under cooperative binding between the receptor, a ligand and an intracellular binding partner (a G-protein or beta-arrestin). While a global rational for allosteric effects in ternary complexes would be of great help in designing ligands with specific effects, the paucity of structural data for ternary complexes with beta-arrestin, together with the intrinsic difficulty of characterizing the dynamics involved in the allosteric coupling, have hindered the efforts to devise such a model. Here we have used enhanced-sampling atomistic molecular-dynamics simulations to investigate the dynamics and complex formation mechanisms of both beta-arrestin- and G(s)-complexes with the beta 2-adrenergic receptor (ADRB2) in its apo-form and in the presence of four small ligands that exert different allosteric effects. Our results suggest that the structure and dynamics of arrestin-ADRB2 complexes depend strongly on the nature of the small ligands. The complexes exhibit a variety of different coupling orientations in terms of the depth of the finger loop in the receptor and activation states of ADRB2. The simulations also allow us to characterize the cooperativity between the ligand and intracellular binding partner (IBP). Based on the complete and consistent results, we propose an experimentally testable extended ternary complex model, where direction of the cooperative effect between ligand and IBP (positive or negative) and its magnitude are predicted to be a characteristic of the ligand signaling bias. This paves the avenue to the rational design of ligands with specific functional effects.},
author = {Saleh, Noureldin and Saladino, Giorgio and Gervasio, Francesco Luigi and Clark, Timothy},
doi = {10.1039/c6sc04647a},
faupublication = {yes},
journal = {Chemical Science},
pages = {4019-4026},
peerreviewed = {Yes},
title = {{Investigating} allosteric effects on the functional dynamics of beta 2-adrenergic ternary complexes with enhanced-sampling simulations},
volume = {8},
year = {2017}
}
@incollection{faucris.116915084,
abstract = {In recent years, the earlier view of proteins as relatively rigid structures has been replaced by a dynamic model in which the internal motions and resulting conformational changes play an essential role in their function. In this context, molecular dynamics (MD) simulations have become an important computational tool for understanding the physical basis of the structure and function of biological macromolecules. Also in the process of finding new drugs MD simulations play an important role. Our workgroup uses molecular dynamics simulations to study proteins of biological and medical relevance, e.g. signal transduction proteins or human integrin complexes. The general aim of these investigations is to find possible new lead structures or drugs and also to understand the basic and essential mechanisms behind the mode of action of our target systems. In MD simulation, the problem size is fixed and a large number of iterations must be executed, so the MD simulation suites have to scale to hundreds or thousands CPUs to get detailed view inside biomolecular systems. The used programs AMBER and GROMACS scale well up to 64 or 32 CPUs, respectively. A typical run for about 100 ns simulation time consumes 5500 up to 21000 CPU hour},
address = {Berlin},
author = {Haberl, Florian and Othersen, Olaf and Seidel, Ute and Lanig, Harald and Clark, Timothy},
booktitle = {High Performance Computing in Science and Engineering},
doi = {10.1007/978-3-540-69182-2{\_}12},
faupublication = {yes},
month = {Jan},
pages = {153-164},
peerreviewed = {unknown},
publisher = {Springer},
title = {{Investigating} {Protein}-{Protein} and {Protein}-{Ligand} {Interactions} by {Molecular} {Dynamics} {Simulations}},
year = {2008}
}
@article{faucris.116916624,
abstract = {Irradiation of CdS powder suspended in ethereal solutions of organolithium compounds, RLi, yields elemental Cd and the photooxidation products R-R. The mechanism is shown to be a radical one, the products R-R at least partly resulting from intraaggregate dimerization of radicals R(.) if the parent RLi is aggregated. Free solution-phase radicals have not been detected. The configuration of a benzyl anion adsorbate has been investigated using AM1 semiempirical molecular orbital calculations on a ZnS model surface. These suggest that eta(1)- and eta(7)-bound species compete with each other. A comparison of the reactivity of PhCH(2)Li and two alkyl-substituted, sterically hindered derivatives shows that the substituted benzylic species, which are eta(1)-bound, react faster than PhCH(2)Li. We therefore propose that PhCH(2)Li prefers a eta(7) configuration on the active CdS surface.},
author = {Clark, Timothy and et al.},
author_hint = {LORENZ M, CLARK T},
doi = {10.1021/om00005a064},
faupublication = {yes},
journal = {Organometallics},
pages = {2570-2574},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{INVESTIGATION} {OF} {ORGANOLITHIUM} {DIMERIZATION} {ON} {IRRADIATED} {CDS} {POWDER}},
volume = {14},
year = {1995}
}
@article{faucris.122436204,
author = {Hartmann, Michael and Clark, Timothy and van Eldik, Rudi},
doi = {10.1007/s0089460020358},
faupublication = {yes},
journal = {Journal of Molecular Modeling},
month = {Jan},
pages = {358-361},
peerreviewed = {Yes},
title = {{Investigation} of the uncatalyzed hydration of {CO2} and first approximations to the active site of carbonic anhydrase - {A} combined {Ab} initio and {DFT} study},
volume = {2},
year = {1996}
}
@article{faucris.109371504,
abstract = {The bicyclo[2.2.2]oct-2-ene radical cation (1(.+)) exhibits matrix ESR spectra that have two very different types of gamma-exo hydrogens (those hydrogens formally in a W-plan with the alkene pi bond), a(2H) about 16.9 G and a(2H) about 1.9 G, instead of the four equivalent hydrogens as would be the case in an untwisted C-2 structure. Moreover, deuterium substitution showed that the vinyl ESR splitting is not resolved (and under about 3.5 G); this is also a result of the twist. Enantiomerization of the C-2 structures is rapid on the ESR timescale above 110 K (barrier estimated at 2.0 kcal mol(-1)). Density functional theory calculations estimate the twist angle at the double bond to be 11-12 degrees and the barrier as 1.2-2.0 kcal mol(-1). Single-configuration restricted Hartree-Fock (RHF) calculations at all levels that were tried give untwisted C-2 structures for 1(.+), while RHF calculations that include configuration interactions (CI) demonstrate that this system undergoes twisting because of a pseudo Jahn-Teller effect (PJTE). Significantly, twisting does not occur until the sigma-orbital of the predicted symmetry is included in the CI active space. UHF calculations at all levels that include electron correlation (even semiempirical) predict twisting at the alkene pi bond because they allow the filled a and the P hole of the SOMO to have different geometries. The 2,3-dimethylbicyclo[2.2.2]oct-2-ene radical cation (2(.+)) is twisted significantly less than 1(.+), but has a similar temperature for maximum line broadening. Neither the 2,3-dioxabicyclo[2.2.2]octane radical cation (3(.+)) nor its 2,3dimethyl-2,3-diaza analogue (5(.+)) shows any evidence of twisting. Calculations show that the orbital energy gap between the SOMO and PJTE-active orbitals for 3(.+) is too large for sigificant PJTE stabilization to occur.},
author = {Clark, Timothy and et al.},
author_hint = {Nelsen SF, Reinhardt LA, Tran HQ, Clark T, Chen GF, Pappas RS, Williams F},
doi = {10.1002/1521-3765(20020301)8:5<1074::AID-CHEM1074>3.0.CO;2-K},
faupublication = {yes},
journal = {Chemistry - A European Journal},
keywords = {density functional calculations;EPR spectroscopy;matrix isolation;pseudo Jahn-Teller distortion;radical ions},
pages = {1074-1081},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{Ionized} bicyclo[2.2.2]oct-2-ene: {A} twisted olefinic radical cation showing vibronic coupling},
volume = {8},
year = {2002}
}
@article{faucris.109371724,
author = {Clark, Timothy and Schleyer, Paul},
doi = {10.1016/S0040-4039(01)86762-9},
faupublication = {yes},
journal = {Tetrahedron Letters},
month = {Jan},
pages = {4963-4966},
peerreviewed = {Yes},
title = {{ISOMERIC} {STRUCTURES} {OF} {THE} {CARBENOID}, {CHF2LI}},
year = {1979}
}
@article{faucris.109373704,
abstract = {Semiempirical (PM3) molecular orbital calculations on the mechanism of reoxidation of PQQ by triplet dioxygen suggest that the reaction can proceed purely by hydrogen-atom-transfer steps that are catalysed by the electrostatic effect of a coordinated calcium ion, rather than by an electron-transfer mechanism.},
author = {Schürer, Gudrun and Clark, Timothy},
doi = {10.1039/A707780G},
faupublication = {yes},
journal = {Chemical Communications},
month = {Jan},
pages = {257-258},
peerreviewed = {Yes},
title = {{Is} the calcium-ion catalysis of biological reoxidation of reduced {PQQ} purely electrostatic?},
year = {1998}
}
@article{faucris.281402650,
author = {Clark, Timothy},
doi = {10.1007/s00894-022-05191-y},
faupublication = {yes},
journal = {Journal of Molecular Modeling},
note = {CRIS-Team Scopus Importer:2022-09-09},
peerreviewed = {Yes},
title = {{Journal} of molecular modeling conversations},
volume = {28},
year = {2022}
}
@article{faucris.122437744,
abstract = {The semi-empirical molecular orbital method AM1 has been used as a tool for the prediction of radical intermediates and crosslink structures that may be of importance in the direct laser excitation of siloxanes. Special emphasis was put on configuration interaction (CI) in order to calculate energies and geometries of excited triplet states as well as potential curves of triplet reactions. Heats of formation of intermediates and reaction enthalpies of monomolecular fragmentation reactions of T1 excited states of 2-phenyl-1,1,1,2,3,3,3-heptamethyltrisiloxane and octamethyltrisiloxane were calculated. In the former case bimolecular reactions were also considered. Dissociation of a methyl group was found to be the most probable monomolecular fragmentation. Consecutive reactions of the silyl radical formed lead to crosslink structures like Si-CH2-Si and Si-C6H4-Si. Biphenyl- and phenylcyclohexadienyls are the most probable crosslink structures of bimolecular reactions with phenyl exciplexes as intermediates. Experimental evidence is given for these crosslink structures.},
author = {Clark, Timothy and et al.},
author_hint = {ROTH W, LORENZ M, CLARK T},
doi = {10.1002/apmc.1994.052150110},
faupublication = {yes},
journal = {Angewandte Makromolekulare Chemie},
pages = {121-128},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{LASER}-{INDUCED} {CROSS}-{LINKING} {OF} {SILOXANES} - {A} {SEMIEMPIRICAL} {MOLECULAR}-{ORBITAL} {STUDY}},
volume = {215},
year = {1994}
}
@article{faucris.116917724,
author = {Clark, Timothy and Chandrasekhar, Jayaraman and Schleyer, Paul},
doi = {10.1039/C39800000672},
faupublication = {yes},
journal = {Journal of the Chemical Society - Series Chemical Communications},
month = {Jan},
pages = {672-673},
peerreviewed = {unknown},
title = {{LI}-7-{C}-13-{NMR} {COUPLING}-{CONSTANTS} {AND} {THE} {NATURE} {OF} {THE} {CARBON}-{LITHIUM} {BOND} - {INDO} {MO} {CALCULATIONS}},
year = {1980}
}
@article{faucris.109382504,
abstract = {Density-functional theory (DFT) and ab initio (QCISD and CBS-RAD) calculations suggest that complexation of "naked" lithium cations to olefins favors the addition of alkyl radicals to the double bond over abstraction of an allyllic hydrogen atom. Thus, "naked" lithium cations in nonpolar solvents can catalyze the radical polymerization of olefins by favoring the chain-lengthening reaction over the competing hydrogenatom extraction, which is competitive in the absence of metal ions. One putative initiation reaction, addition of triplet dioxygen to the double bond, is thermoneutral and has a very low barrier when the oxygen molecule is complexed to a lithium cation. An alternative process, abstraction of an allyllic hydrogen atom to generate the allyl and hydroperoxy radicals, is also strongly favored by complexation of the oxygen to the lithium cation but is less favorable than addition. These results support Michl's recent interpretation of experimentally observed alkene polymerization in the presence of lithium salts of hydrophobic carborane anions.},
author = {Clark, Timothy},
doi = {10.1021/ja063204+},
faupublication = {yes},
journal = {Journal of the American Chemical Society},
keywords = {\},
pages = {11278-11285},
peerreviewed = {Yes},
title = {{Lithium} cation as radical-polymerization catalyst},
volume = {128},
year = {2006}
}
@article{faucris.122438404,
author = {Clark, Timothy and et al.},
author_hint = {HOFMANN H, CLARK T},
faupublication = {yes},
journal = {Angewandte Chemie International Edition},
pages = {648-650},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{LITHIUM}-{ION}-{CATALYZED} {EPOXIDATION} {BY} {TRIPLET} {DIOXYGEN} - {AN} {ABINITIO} {STUDY}},
volume = {29},
year = {1990}
}
@article{faucris.122439504,
abstract = {Expressions for the local electron affinity, electronegativity and hardness are derived in analogy to the local ionization energy introduced by Sjoberg, Murray and Politzer. The local polarizability is also defined based on an additive atomic orbital polarizability model that uses Rivail's variational technique. The characteristics of these local properties at molecular surfaces and their relevance to electrophilic aromatic substitution, to S(N)2 reactivity and to the nucleophilicity of enolate ions are discussed.},
author = {Ehresmann, Bernd and Martin, Bodo and Horn, Anselm and Clark, Timothy},
doi = {10.1007/s00894-003-0153-x},
faupublication = {yes},
journal = {Journal of Molecular Modeling},
keywords = {surface properties;AM1;local ionization energy;local electron affinity;local hardness},
pages = {342-347},
peerreviewed = {Yes},
title = {{Local} molecular properties and their use in predicting reactivity},
volume = {9},
year = {2003}
}
@article{faucris.115081824,
abstract = {The Hellmann-Feynman theorem provides a straightforward interpretation of noncovalent bonding in terms of Coulombic interactions, which encompass polarization (and accordingly include dispersion). Exchange, Pauli repulsion, orbitals, etc., are part of the mathematics of obtaining the system's wave function and subsequently its electronic density. They do not correspond to physical forces. Charge transfer, in the context of noncovalent interactions, is equivalent to polarization. The key point is that mathematical models must not be confused with physical reality.},
author = {Politzer, Peter and Murray, Jane S. and Clark, Timothy},
doi = {10.1007/s00894-015-2585-5},
faupublication = {yes},
journal = {Journal of Molecular Modeling},
keywords = {Noncovalent interactions;Hellmann-Feynman theorem;Electrostatic potential;Polarization;Charge transfer;Dispersion;sigma-hole interactions;Halogen bonding;Hydrogen bonding},
peerreviewed = {Yes},
title = {{Mathematical} modeling and physical reality in noncovalent interactions},
volume = {21},
year = {2015}
}
@article{faucris.116927844,
author = {Clark, Timothy and et al.},
author_hint = {CLARK T, HASEGAWA A, SYMONS MCR},
doi = {10.1016/0009-2614(85)80129-9},
faupublication = {yes},
journal = {Chemical Physics Letters},
month = {Jan},
pages = {79-82},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{MATRIX} {INTERACTIONS} {FOR} {RADICAL} {CATIONS} - {THEORETICAL} {AND} {EXPERIMENTAL} {RESULTS} {FOR} {THE} {TRICHLOROFLUOROMETHANE} {MATRIX} {ILLUSTRATED} {BY} {F}-19 {COUPLING} {FOR} {ME2SE}+ {RADICAL} {CATIONS}},
volume = {116},
year = {1985}
}
@misc{faucris.120465664,
author = {Beierlein, Frank and Lanig, Harald and Othersen, Olaf and Schneider, Siegfried and Clark, Timothy},
faupublication = {yes},
peerreviewed = {automatic},
title = {{MD}/{CI}-approach simulating {FRET} in proteins.},
year = {2004}
}
@article{faucris.121608784,
author = {Clark, Timothy and et al.},
author_hint = {NELSEN SF, CUNKLE GT, EVANS DH, CLARK T},
doi = {10.1021/ja00356a043},
faupublication = {yes},
journal = {Journal of the American Chemical Society},
month = {Jan},
pages = {5928-5929},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{MEASUREMENT} {OF} {THE} {ROTATIONAL} {BARRIER} {OF} {A} {TETRAALKYLHYDRAZINE} {RADICAL} {CATION}},
volume = {105},
year = {1983}
}
@article{faucris.116934664,
author = {Clark, Timothy and Schleyer, Paul and et al.},
author_hint = {CLARK T, WILHELM D, SCHLEYER PV},
doi = {10.1039/C39830000606},
faupublication = {yes},
journal = {Journal of the Chemical Society - Series Chemical Communications},
month = {Jan},
pages = {606-608},
peerreviewed = {unknown},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{MECHANISM} {OF} {HYDROBORATION} {IN} {ETHER} {SOLVENTS} - {A} {MODEL} {ABINITIO} {STUDY}},
year = {1983}
}
@article{faucris.119333544,
author = {Anders, Ernst and Clark, Timothy and et al.},
author_hint = {ANDERS E, CLARK T, GASSNER T},
doi = {10.1002/chin.198629087},
faupublication = {yes},
journal = {Chemische Berichte},
pages = {1350-1360},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{MECHANISTIC} {STUDIES} {ON} {THE} {DEPHOSPHORYLATING} {YLIDE}-{DIKETONE} {REARRANGEMENT} {OF} [({ARYLCARBONYLOXY}){ALKYLIDENE}]{PHOSPHORANES}},
volume = {119},
year = {1986}
}
@article{faucris.208731577,
abstract = {We report the synthesis of a full-fledged family of covalent electron donor-acceptor(1)-acceptor(2) conjugates and their charge-transfer characterization by means of advanced photophysical assays. By virtue of variable excited state energies and electron donor strengths, either Zn(II)Porphyrins or Zn(II)Phthalocyanines were linked to different electron-transport chains featuring pairs of electron accepting fullerenes, that is, C-60 and C-70. In this way, a fine-tuned redox gradient is established to power a unidirectional, long-range charge transport from the excited-state electron donor via a transient C-60(center dot-) toward C-70(center dot-). This strategy helps minimize energy losses in the reductive, short-range charge shift from C-60 to C-70. At the forefront of our investigations are excited-state dynamics deduced from femtosecond transient absorption spectroscopic measurements and subsequent computational deconvolution of the transient absorption spectra. These provide evidence for cascades of short-range charge-transfer processes, including reductive charge shift reactions between the two electron-accepting fullerenes, and for kinetics that are influenced by the nature and length of the respective spacer. Of key importance is the postulate of a mediating state in the charge-shift reaction at weak electronic couplings. Our results point to an intimate relationship between triplet-triplet energy transfer and charge transfer.},
author = {Wolf, Maximilian and Villegas, Carmen and Trukhina, Olga and Delgado, Juan Luis and Torres, Tomas and Martin, Nazario and Clark, Timothy and Guldi, Dirk Michael},
doi = {10.1021/jacs.7b08670},
faupublication = {yes},
journal = {Journal of the American Chemical Society},
pages = {17474-17483},
peerreviewed = {Yes},
title = {{Mediating} {Reductive} {Charge} {Shift} {Reactions} in {Electron} {Transport} {Chains}},
volume = {139},
year = {2017}
}
@article{faucris.217948048,
abstract = {Recent developments in metadynamics simulation techniques for ligand binding to Class A GPCRs are described and the results obtained elucidated. The computational protocol makes good use of modern massively parallel hardware, making simulations of the binding/unbinding process routine. The simulations reveal unprecedented details of the ligand-binding pathways, including multiple binding sites in many cases. Free energies of binding are reproduced very well and the simulations allow prediction of the efficacy (agonist, antagonist etc.)of ligands.},
author = {Ibrahim, Passainte and Clark, Timothy},
doi = {10.1016/j.sbi.2019.04.002},
faupublication = {yes},
journal = {Current Opinion in Structural Biology},
note = {CRIS-Team Scopus Importer:2019-05-21},
pages = {129-137},
peerreviewed = {Yes},
title = {{Metadynamics} simulations of ligand binding to {GPCRs}},
volume = {55},
year = {2019}
}
@article{faucris.121135124,
author = {Clark, Timothy},
doi = {10.1039/c39810000515},
faupublication = {yes},
journal = {Journal of the Chemical Society - Series Chemical Communications},
month = {Jan},
pages = {515-516},
peerreviewed = {unknown},
title = {{METHYL} {AND} {SILYL} {HALIDE} {RADICAL}-{ANIONS} - {AN} {ABINITIO} {STUDY}},
year = {1981}
}
@article{faucris.123427964,
author = {Clark, Timothy and Schleyer, Paul},
doi = {10.1039/c39760000798},
faupublication = {yes},
journal = {Journal of the Chemical Society - Series Chemical Communications},
month = {Jan},
pages = {798-799},
peerreviewed = {unknown},
title = {{METHYLENECYCLOHEPTATRIENYL} {DIANION}},
year = {1976}
}
@article{faucris.120268324,
abstract = {In this report, we investigate the impact of the molecular dipole moment and redox active head groups (C ) in pure and mixed self-assembled monolayers (SAMs), which serve as an ultra-thin hybrid dielectric layer in low-voltage operating organic thin-film transistors. We show that the dipole of the SAM-forming molecules affects the threshold voltage, while the concentration of redox-active C moieties determines the hysteresis in devices with α,α′-dihexyl-sexithiophene and pentacene as organic semiconductors. © 2012 American Institute of Physics.},
author = {Jedaa, Abdesselam and Salinas Batallas, Michael and Jäger, Christof and Clark, Timothy and Ebel, Alexander and Hirsch, Andreas and Halik, Marcus},
doi = {10.1063/1.3682301},
faupublication = {yes},
journal = {Applied Physics Letters},
pages = {63302},
peerreviewed = {Yes},
title = {{Mixed} self-assembled monolayer of molecules with dipolar and acceptor character-{Influence} on hysteresis and threshold voltage in organic thin-film transistors},
url = {http://scitation.aip.org/content/aip/journal/apl/100/6/10.1063/1.3682301},
volume = {100},
year = {2012}
}
@article{faucris.119984744,
abstract = {The peroxy radical complexed to a lithium cation has been used to model electrostatic catalysis in the oxidation of methane to methanol and the epoxidation of ethylene in nb initio molecular orbital calculations. Both reactions are found to proceed in two steps. The first steps of both reactions, hydrogen abstraction from methane and addition to ethylene, respectively, are conventional and enjoy both a kinetic and a thermodynamic advantage from complexation to the metal cation. The second step is in each case the cleavage of the O-O bond of the peroxide formed, This type of reaction is found to be remarkably facile in metal ion complexed peroxides and proceeds by a classical backside attack mechanism. For both reactions investigated, the metal ion complexation provides considerable assistance for the forward reaction. Analogies to iron-catalyzed biological oxidations are drawn, and suggestions of possible consequences for their reaction mechanisms are made.},
author = {Clark, Timothy and et al.},
author_hint = {CLARK T, HOFMANN H},
doi = {10.1021/j100102a054},
faupublication = {yes},
journal = {Journal of Physical Chemistry},
pages = {13797-13803},
peerreviewed = {unknown},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{MODEL} {AB}-{INITIO} {STUDIES} {ON} {METHANE} {OXIDATION} {AND} {ETHYLENE} {EPOXIDATION} {BY} {THE} {PEROXY} {RADICAL} {COMPLEXED} {TO} {THE} {LITHIUM} {CATION} - {ARE} {PEROXY} {RADICAL} {COMPLEXES} {ACTIVE} {INTERMEDIATES} {IN} {BIOLOGICAL} {OXIDATIONS}},
volume = {98},
year = {1994}
}
@article{faucris.117935004,
abstract = {We have investigated the conductance properties of C60-containing self-assembled monolayers (SAMs), which are used in organic field-effect transistors, employing a combination of molecular-dynamics simulations, semiempirical electronic structure calculations, and Landauer transport theory. The results reveal the close relation between the transport characteristics and the structural and electronic properties of the SAM. Furthermore, both local pathways of charge transport in the SAMs and the influence of structural fluctuations are analyzed.},
author = {Leitherer, Susanne and Jäger, Christof and Halik, Marcus and Clark, Timothy and Thoss, Michael},
doi = {10.1063/1.4876035},
faupublication = {yes},
journal = {Journal of Chemical Physics},
note = {UnivIS-Import:2015-04-14:Pub.2014.nat.dphy.ITP.ppem.modeli},
pages = {204702},
peerreviewed = {Yes},
title = {{Modeling} charge transport in {C60}-based self-assembled monolayers for applications in field-effect transistors},
url = {http://scitation.aip.org/content/aip/journal/jcp/140/20/10.1063/1.4876035},
volume = {140},
year = {2014}
}
@article{faucris.240998302,
abstract = {The way chemists represent chemical structures as two-dimensional sketches made up of atoms and bonds, simplifying the complex three-dimensional molecules comprising nuclei and electrons of the quantum mechanical description, is the everyday language of chemistry. This language uses models, particularly of bonding, that are not contained in the quantum mechanical description of chemical systems, but has been used to derive machine-readable formats for storing and manipulating chemical structures in digital computers. This language is fuzzy and varies from chemist to chemist but has been astonishingly successful and perhaps contributes with its fuzziness to the success of chemistry. It is this creative imagination of chemical structures that has been fundamental to the cognition of chemistry and has allowed thought experiments to take place. Within the everyday language, the model nature of these concepts is not always clear to practicing chemists, so that controversial discussions about the merits of alternative models often arise. However, the extensive use of artificial intelligence (AI) and machine learning (ML) in chemistry, with the aim of being able to make reliable predictions, will require that these models be extended to cover all relevant properties and characteristics of chemical systems. This, in turn, imposes conditions such as completeness, compactness, computational efficiency and nonredundancy on the extensions to the almost universal Lewis and VSEPR bonding models. Thus, AI and ML are likely to be important in rationalizing, extending and standardizing chemical bonding models. This will not affect the everyday language of chemistry but may help to understand the unique basis of chemical language.},
author = {Clark, Timothy and Hicks, Martin G.},
doi = {10.3762/bjoc.16.137},
faupublication = {yes},
journal = {Beilstein Journal of Organic Chemistry},
note = {CRIS-Team WoS Importer:2020-07-31},
pages = {1649-1661},
peerreviewed = {Yes},
title = {{Models} of necessity},
volume = {16},
year = {2020}
}
@article{faucris.116940164,
abstract = {Calculations of optimized force field (MMP2 extended to carbocations) and ab initio (MP2/6-31G*) geometries as well as pi-electron densities of various benzyl and cyclic delocalized cations agree well. The MMP2 heats of formation reproduce the available experimental values. MMP2 pi-resonance energies are consistent with those obtained by isodesmic equations from experimental and ab initio data. When carbon pi-charges are lower than 0.2, the influence of phenyl substituents is attenuated. Thus, the triphenylmethyl cation resonance stabilization value (-41.6 kcal/mol average for each phenyl ring) is much less than that of the benzyl cation (-76.4 kcal/mol) and the benzhydryl cation (average stabilization value of -51.4 kcal/mol). MMP2 aromatic stabilization energy estimates of the benzyl and tropylium cations as well as benzene agree well with the assessments of aromaticity by the nucleus independent chemical shift (NICS) criterion, which is based on the magnetic shieldings computed at ring centers. The MMP2 method allows quantitative evaluations of homoconjugative interactions. The stabilization in the homotropylium cation due to 1,7 homoconjugative overlap is estimated to be quite appreciable, -13.4 kcal/mol.},
author = {Clark, Timothy and Schleyer, Paul and et al.},
author_hint = {Reindl B, Clark T, Schleyer PV},
doi = {10.1021/jp981406p},
faupublication = {yes},
journal = {Journal of Physical Chemistry A},
pages = {8953-8963},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{Modern} molecular mechanics and ab initio calculations on benzylic and cyclic delocalized cations},
volume = {102},
year = {1998}
}
@article{faucris.246709420,
abstract = {In contrast to previous work, the synergy between panchromatic absorption and molecular singlet fission (SF) is exploited to optimize solar energy conversion through evaluation of the distance dependence of intramolecular Forster Resonance Energy Transfer (i-FRET) in a series of subphthalocyanines (SubPcs) linked to pentacene dimers (Pnc(2)s). To provide control over i-FRET, the molecular spacer rather than the energy donating SubPc is tailored in the corresponding SubPc-Pnc(2) conjugates in terms of length (i.e., the number of aryl units) and flexibility (i.e., presence or absence of a CH2 group). AM1-CIS calculations support the experiments, which underline the importance of the molecular spacer to impact not only the i-FRET dynamics, but also the dynamics of intramolecular singlet fission (i-SF). For example, an additional phenyl group slows down both i-FRET and i-SF by a factor of similar to 3.8 and similar to 1.6, respectively, by a quinone-like conjugation pattern that affords a pentacene acceptor orbital that is fairly delocalized over both pentacenes and the bridging phenyl.},
author = {Zirzlmeier, Johannes and Lavarda, Giulia and Gotfredsen, Henrik and Papadopoulos, Ilias and Chen, Lan and Clark, Timothy and Tykwinski, Rik R. and Torres, Tomas and Guldi, Dirk Michael},
doi = {10.1039/d0nr06285e},
faupublication = {yes},
journal = {Nanoscale},
note = {CRIS-Team WoS Importer:2020-12-11},
pages = {23061-23068},
peerreviewed = {Yes},
title = {{Modulating} the dynamics of {Forster} resonance energy transfer and singlet fission by variable molecular spacers},
volume = {12},
year = {2020}
}
@article{faucris.116846004,
abstract = {Covalent organic frameworks (COFs) formed by connecting multidentate organic building blocks through covalent bonds provide a platform for designing multifunctional porous materials with atomic precision. As they are promising materials for applications in optoelectronics, they would benefit from a maximum degree of long-range order within the framework, which has remained a major challenge. We have developed a synthetic concept to allow consecutive COF sheets to lock in position during crystal growth, and thus minimize the occurrence of stacking faults and dislocations. Hereby, the three-dimensional conformation of propeller-shaped molecular building units was used to generate well-defined periodic docking sites, which guided the attachment of successive building blocks that, in turn, promoted long-range order during COF formation. This approach enables us to achieve a very high crystallinity for a series of COFs that comprise tri- and tetradentate central building blocks. We expect this strategy to be transferable to a broad range of customized COFs.},
author = {Ascherl, Laura and Sick, Torben and Margraf, Johannes and Lapidus, Saul H. and Calik, Mona and Hettstedt, Christina and Karaghiosoff, Konstantin and Doeblinger, Markus and Clark, Timothy and Chapman, Karena W. and Auras, Florian and Bein, Thomas},
doi = {10.1038/NCHEM.2444},
faupublication = {yes},
journal = {Nature Chemistry},
pages = {310-316},
peerreviewed = {Yes},
title = {{Molecular} docking sites designed for the generation of highly crystalline covalent organic frameworks},
volume = {8},
year = {2016}
}
@article{faucris.119333984,
abstract = {Molecular-dynamics simulations have been used to investigate the mechanism of induction of a mutant (revTetR) of the tetracycline repressor protein (TetR) that shows the reverse phenotype (i.e., it is induced in the absence of tetracyclines and not in their presence). Low-frequency, normal-mode analyses demonstrate that the reverse phenotype is reproduced by the simulations on the basis of criteria established for wild-type TetR. The reverse phenotype is caused by the fact that the DNA-binding heads in revTetR are closer than the ideal distance needed for DNA-binding when no inducer is present. This distance increases on binding an inducer. Whereas this distance increase makes the interhead distance too large in wild-type TetR, it increases to the ideal value in revTetR. Thus, the mechanism of induction is the same for the two proteins, but the consequences are reversed because of the smaller interhead distance in revTetR when no inducer is present.},
author = {Seidel, Ute and Othersen, Olaf and Lanig, Harald and Beierlein, Frank and Clark, Timothy},
doi = {10.1021/jp0674468},
faupublication = {yes},
journal = {Journal of Physical Chemistry B},
pages = {6006-6014},
peerreviewed = {Yes},
title = {{Molecular} {Dynamics} {Characterization} of the {Structures} and {Induction} {Mechanisms} of a {Reverse} {Phenotype} of the {Tetracycline} {Receptor}},
volume = {111},
year = {2007}
}
@article{faucris.109383384,
abstract = {Inhibitory glycine receptors mediate rapid synaptic inhibition in mammalian spinal cord and brainstem. The previously identified hyperekplexia mutation GLRA I(P250T), located within the intracellular TM1-2 loop of the GlyR alpha1 subunit, results in altered receptor activation and desensitization. Here, elementary steps of ion channel function of alpha1(250) mutants were resolved and shown to correlate with hydropathy and molar volume of residue alpha1 (250). Single-channel recordings and rapid activation kinetic studies using laser pulse photolysis showed reduced conductance but similar open probability of alpha1 (P250T) mutant channels. Molecular dynamics simulation of a helix-turn-helix motif representing the intracellular TM1-2 domain revealed alterations in backbone conformation, indicating an increased flexibility in these mutants that paralleled changes in elementary steps of channel function. Thus, the architecture of the TM1-2 loop is a critical determinant of ion channel conductance and receptor desensitization.},
author = {Breitinger, Hans-Georg Albrecht and Lanig, Harald and Breitinger, Ulrike and Clark, Timothy and et al.},
author_hint = {Breitinger HG, Lanig H, Vohwinkel C, Grewer C, Breitinger U, Clark T, Becker CM},
doi = {10.1016/j.chembiol.2004.07.008},
faupublication = {yes},
journal = {Chemistry & Biology},
pages = {1339-1350},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{Molecular} dynamics simulation links conformation of a pore-flanking region to hyperekplexia-related dysfunction of the inhibitory glycine receptor},
volume = {11},
year = {2004}
}
@article{faucris.118725244,
abstract = {Modern spectroscopic techniques such as time-resolved second harmonic generation spectroscopy allow molecules to be examined selectively directly at phase interfaces. Two-phase systems formed by glycerol/water and alkane layers have previously been studied by time-resolved second harmonic generation spectroscopic measurements. In this molecular-dynamics study, a triphenylmethane dye was inserted at the glycerol/water-alkane interface and was used as a probe for local properties such as viscosity. We now show how extensive simulations over a wide range of concentrations can be used to obtain a detailed view of the molecular structure at the glycerol/water-alkane interface. Glycerol is accumulated in a double layer adjacent to the alkane interface, which results in increased viscosity of the glycerol/water phase in the direct vicinity of the interface. We also show that conformational ensembles created by classical molecular-dynamics simulations can serve as input for QM/MM calculations, yielding further information such as transition dipoles, which can be compared with spectroscopic measurements.},
author = {Beierlein, Frank and Krause, Andreas and Jäger, Christof and Fita, Piotr and Vauthey, Eric and Clark, Timothy},
doi = {10.1021/la4021355},
faupublication = {yes},
journal = {Langmuir},
pages = {11898--11907},
peerreviewed = {unknown},
title = {{Molecular} {Dynamics} {Simulations} of {Liquid} {Phase} {Interfaces}: {Understanding} the {Structure} of the {Glycerol}/{Water}–{Dodecane} {System}},
volume = {29},
year = {2013}
}
@article{faucris.109625164,
abstract = {G-protein-coupled receptors have extraordinary therapeutic potential as targets for a broad spectrum of diseases. Understanding their function at the molecular level is therefore essential. A variety of crystal structures have made the investigation of the inactive receptor state possible. Recently released X-ray structures of opsin and the β -adrenergic receptor (β AR) have provided insight into the active receptor state. In addition, we have contributed to the crystal structure of an irreversible agonist-β adrenoceptor complex. These extensive studies and biophysical investigations have revealed that agonist binding leads to a low-affinity conformation of the active state that is suggested to facilitate G-protein binding. The high-affinity receptor state, which promotes signal transduction, is only formed in the presence of both agonist and G-protein. Despite numerous crystal structures, it is not yet clear how ligands tune receptor dynamics and G-protein binding. We have now used molecular dynamics simulations to elucidate the distinct impact of agonist and inverse agonist on receptor conformation and G-protein binding by investigating the influence of the ligands on the structure and dynamics of a complex composed of β AR and the C-terminal end of the Gα subunit (GαCT). The simulations clearly showed that the agonist isoprenaline and the inverse agonist carazolol influence the ligand-binding site and the interaction between β AR and GαCT differently. Isoprenaline induced an inward motion of helix 5, whereas carazolol blocked the rearrangement of the extracellular part of the receptor. Moreover, in the presence of isoprenaline, β AR and GαCT form a stable interaction that is destabilized by carazolol. © 2011 Elsevier Ltd. All rights reserved.},
author = {Goetz, Angela and Lanig, Harald and Gmeiner, Peter and Clark, Timothy},
doi = {10.1016/j.jmb.2011.10.015},
faupublication = {yes},
journal = {Journal of Molecular Biology},
pages = {611-623},
peerreviewed = {Yes},
title = {{Molecular} dynamics simulations of the effect of the {G}-protein and diffusible ligands on the β2-adrenergic receptor},
volume = {414},
year = {2011}
}
@article{faucris.122448084,
abstract = {Molecular dynamics simulations on the tetracycline-repressor (TetR) protein, both in the absence of an inducer and complexed with the inducers tetracycline and 5a,6-anhydrotetracycline, show significant differences in the structures and dynamics of the induced and non-induced forms of the protein. C-alpha-density-difference plots, low-frequency normal vibrations and inter-residue interaction energies all point to a common mechanism of induction. The inducer displaces Asp156 from the magnesium ion in the binding pocket, leading to a short cascade of rearrangements of salt bridges that results in the allosteric change. The increased flexibility of the induced form of the protein is suggested to contribute to the decrease in binding affinity to DNA on induction. (c) 2006 Elsevier Ltd. All rights reserved.},
author = {Lanig, Harald and Othersen, Olaf and Beierlein, Frank and Seidel, Ute and Clark, Timothy},
doi = {10.1016/j.jmb.2006.04.014},
faupublication = {yes},
journal = {Journal of Molecular Biology},
keywords = {tetracycline repressor;molecular dynamics;signal transduction;essential dynamics;low frequency modes},
pages = {1125-1136},
peerreviewed = {Yes},
title = {{Molecular} dynamics simulations of the tetracycline-repressor protein: {The} mechanism of induction},
volume = {359},
year = {2006}
}
@article{faucris.208734884,
author = {Brox, Regine and Milanos, Lampros and Saleh, Noureldin and Baumeister, Paul and Buschauer, Armin and Hofmann, Dagmar and Heinrich, Markus and Clark, Timothy and Tschammer, Nuska},
doi = {10.1124/mol.117.110296},
faupublication = {yes},
journal = {Molecular Pharmacology},
pages = {309-322},
peerreviewed = {Yes},
title = {{Molecular} mechanisms of biased and probe-dependent signaling at {CXC}-motif chemokine receptor {CXCR3} induced by negative allosteric modulators},
volume = {93},
year = {2018}
}
@article{faucris.111043724,
abstract = {An overview of recent molecular orbital theory and density functional theory studies on water exchange reactions of metal ions and complexes in solution is presented. The different theoretical techniques used are reviewed and representative examples are discussed. The mechanistic insight gained is discussed in reference to available experimental data and the predictive nature of the applied techniques is highlighted. © 2002 Elsevier Science B.V. All rights reserved.},
author = {van Eldik, Rudi and Clark, Timothy and Hanauer, Hans},
doi = {10.1016/S0010-8545(02)00296-5},
faupublication = {yes},
journal = {Coordination Chemistry Reviews},
keywords = {DFT studies; Molecular orbital; Water exchange mechanisms},
note = {UnivIS-Import:2015-03-09:Pub.2003.forsch.sonder.sfb583.molecu},
pages = {233-253},
peerreviewed = {Yes},
title = {{Molecular} orbital and {DFT} studies on water exchange mechanisms of metal ions},
year = {2003}
}
@article{faucris.116940384,
abstract = {Our previous AM1 semiempirical molecular orbital studies on the electron self-exchange reaction between p-diaminobenzene (PPD) and its radical cation have been extended to include dynamics calculations of the inner-sphere vibrational frequency, nu1, and a configuration interaction (CI) study of the distance dependence of the transfer-integral, V12. These and our previous results for the reorganization energy, lambda, and the classical activation barrier to electron transfer have been used to calculate a unimolecular gas-phase rate constant, k(et), of (3-7) x 10(10) s-1, compared with an experimental value in acetonitrile of 2 x 10(8) s-1. The solvent is thus suggested to lower k(et) by a factor of 150-350 for this reaction.},
author = {Rauhut, Guntram and Clark, Timothy},
doi = {10.1039/ft9949001783},
faupublication = {yes},
journal = {Journal of the Chemical Society, Faraday Transactions},
pages = {1783-1788},
peerreviewed = {Yes},
title = {{MOLECULAR}-{ORBITAL} {STUDIES} {OF} {ELECTRON}-{TRANSFER} {REACTIONS}},
volume = {90},
year = {1994}
}
@article{faucris.121232364,
abstract = {Semiempirical (AM1) molecular orbital theory has been used to investigate the oxidation of alcohols at the active site of liver alcohol dehydrogenase (LADH). The model active site consists of a zinc dication coordinated to two methyl-mercaptans (Cys-46, Cys-176), an imidazole (His-67), and a water. An imidazole (His-51) hydrogen bonded to a hydroxy-acetate (Ser-48) forms the remote base. AMI calculations that address the two distinct steps in the catalytic mechanism of ethanol oxidation by LADH are reported. These two steps are: (1) the deprotonation of ethanol by imidazole (His-51) via hydrogen-bonded hydroxy-acetate (Ser-48), creating a proton relay system; and (2) the rate-limiting hydride transfer step from ethanol C1 to nicotinamide adenine dinucleotide (NAD+), leading to product formation. Detailed calculations have been used to resolve the unsolved problems of mechanisms that have been suggested on the basis of kinetic data and crystal structures of several LADH complexes. We investigated two possible mechanisms for the deprotonation of ethanol, by zinc-bound OH and by direct deprotonation of zinc-bound ethanol by imidazole via hydroxy-acetate (Ser-48). Our calculations show that there is no need for LADH to activate a water molecule at the active site as in many other zinc enzymes. This result agrees with experimental evidence. Our calculations also indicate that substrates are bound in an inner-sphere-pentacoordinated complex to the active site zinc ion. In this case, spectroscopic investigations agree with our results but crystallographic data do not. The highest activation energy is found for the hydride transfer, in agreement with the experiment. Finally, we proposed an alternative mechanism for the mode of action of LADH based upon our results.},
author = {Clark, Timothy and et al.},
author_hint = {VONONCIUL AR, CLARK T},
doi = {10.1002/jcc.540140403},
faupublication = {yes},
journal = {Journal of Computational Chemistry},
pages = {392-400},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{MOLECULAR}-{ORBITAL} {STUDIES} {OF} {ENZYME} {MECHANISMS} .2. {CATALYTIC}-{OXIDATION} {OF} {ALCOHOLS} {BY} {LIVER} {ALCOHOL}-{DEHYDROGENASE}},
volume = {14},
year = {1993}
}
@misc{faucris.110516604,
author = {Clark, Timothy},
faupublication = {yes},
peerreviewed = {automatic},
title = {{Molecular} surfaces, {QSAR}, {QSPR} and reactivity},
year = {2007}
}
@article{faucris.213080057,
abstract = {In this review we highlight recent progress in the field of photochemically and thermally induced electron transport through molecular bridges as integrative parts of electron donor-bridge-acceptor conjugates. The major emphasis is hereby on the design and the modular composition of the bridges. To this end, we will demonstrate that control over attenuation factors and reorganization energies, on one hand, as well as electronic and electron-vibration couplings, on the other hand, enables tuning electron transport over distances as short as 3.5 Å and as large as 50 Å by up to nine orders of magnitude. In terms of electron transport, the maximum extreme is given by carbon-bridged oligo-p-phenylenevinylenes of different lengths, while a zinc tetraphenylporphyrin free base tetraphenylporphyrin dyad constitutes the minimum extreme.},
author = {Schubert, Christina and Margraf, Johannes and Clark, Timothy and Guldi, Dirk Michael},
doi = {10.1039/c4cs00262h},
faupublication = {yes},
journal = {Chemical Society Reviews},
note = {EAM Import::2019-03-12},
pages = {988-998},
peerreviewed = {Yes},
title = {{Molecular} wires - impact of π-conjugation and implementation of molecular bottlenecks},
volume = {44},
year = {2015}
}
@article{faucris.119346084,
abstract = {In recent decades, new less-invasive, nonlinear optical methods have been proposed and optimized for monitoring fast physiological processes in biological cells. One of these methods allows the action potential (AP) in cardiomyocytes or neurons to be monitored by means of second-harmonic generation (SHG). We now present the first, to our knowledge, simulations of the dependency of the intensity of the second harmonic (/SHG) on variations of the transmembrane potential (TMP) in a cardiomyocyte during an action potential (AP). For this, an amphiphilic potential-sensitive styryl dye molecule with nonlinear optical properties was embedded in a dipalmitoylphosphatidylcholine (DPPC) bilayer, replacing one of the phospholipid molecules. External electrical fields with different strengths were applied across the membrane to simulate the AP of a heart-muscle cell. We used a combined classical/quantum mechanical approach to model the structure and the spectroscopic properties of the embedded chromophore. Two 10 ns molecular dynamics (MD) simulations provided input geometries for semiempirical molecular orbital (QM/MM) single-point configuration interaction (CI) calculations, which were used to calculate the wavelengths and oscillator strengths of electronic transitions in the di-8-ANEPPS dye molecule. The results were then used in a sum-over-states treatment to calculate the second-order hyperpolarizability. The square of the hyperpolarizability scales with the intensity of the second harmonic, which is used to monitor the action potentials of cardiomyocytes experimentally. Thus, we computed changes in the intensity of the second harmonic (ΔI ) as function of TMP changes. Our results agree well with experimental measurements. © 2008 American Chemical Society.},
author = {Rusu, Catalin Florin and Lanig, Harald and Othersen, Olaf and Kryschi, Carola and Clark, Timothy},
doi = {10.1021/jp075372+},
faupublication = {yes},
journal = {Journal of Physical Chemistry B},
pages = {2445-2455},
peerreviewed = {Yes},
title = {{Monitoring} biological membrane-potential changes: {A} {CI} {QM}/{MM} study},
volume = {112},
year = {2008}
}
@article{faucris.106987364,
abstract = {Ab initio and semiempirical (AM1) molecular orbital theory has been used to model the cleavage of formamide at the active site of carboxypeptidase A. The model active site consists of a zinc dication coordinated to two imidazoles, an acetate, a water with a hydrogen-bonded formate, and a formamide molecule as model substrate. AM1 has been compared with ab initio theory for the coordination of water and formamide to Zn++ and found to give excellent energetic results. The course of the amide cleavage was therefore calculated with AM1. The first step of the reaction is the dissociation of the zine-coordinated water to give an active ZnOH+ species. The remote formate acts as proton acceptor. This process has an activation energy of only 4.6 kcal mol-1. The next and rate-determining step is the concerted addition of the ZnOH+ moiety to the formamide C=O bond. The Zn-0 distance in the transition state is more than 3 angstrom. In four further steps, the amide nitrogen is protonated and the C-N bond cleaved. The net activation energy for the entire process is 15.5 kcal mol-1 relative to the active site model and 19.6 kcal mol-1 relative to the most stable point on the calculated reaction profile.},
author = {Alex, Alexander and Clark, Timothy},
doi = {10.1002/jcc.540130605},
faupublication = {yes},
journal = {Journal of Computational Chemistry},
pages = {704-717},
peerreviewed = {Yes},
title = {{MO}-{STUDIES} {OF} {ENZYME} {REACTION}-{MECHANISMS} .1. {MODEL} {MOLECULAR}-{ORBITAL} {STUDY} {OF} {THE} {CLEAVAGE} {OF} {PEPTIDES} {BY} {CARBOXYPEPTIDASE}-{A}},
volume = {13},
year = {1992}
}
@article{faucris.121147884,
abstract = {The natural atomic orbital/point charge (NAO-PC) model based upon the AM1 wave function has been developed to calculate molecular electrostatic potentials (MEPs). Up to nine point charges (including the core charge) are used to represent heavy atoms. The positions and magnitudes of the eight charges that represent the atomic electron cloud are calculated from the natural atomic orbitals (NAOs) and their occupations. Each hybrid NAO is represented by two point charges situated at the centroid of each lobe. The positions of the centroids and the magnitudes of the charges were obtained by numerical integration of the Slater-type hybrids and the results used to set up polynomials and look-up tables that replace the integration step in the actual MEP calculation. The MEPs calculated using this method are found to be in better agreement with those obtained using RHF/6-31G* than those obtained from the AM1 wave function using Coulson charges or with MOPAC-ESP. The MEP calculations are extremely fast and have, for instance, been incorporated into an interactive graphics package.},
author = {Rauhut, Guntram and Clark, Timothy},
doi = {10.1002/jcc.540140502},
faupublication = {yes},
journal = {Journal of Computational Chemistry},
pages = {503-509},
peerreviewed = {Yes},
title = {{MULTICENTER} {POINT}-{CHARGE} {MODEL} {FOR} {HIGH}-{QUALITY} {MOLECULAR} {ELECTROSTATIC} {POTENTIALS} {FROM} {AM1} {CALCULATIONS}},
volume = {14},
year = {1993}
}
@article{faucris.208731846,
abstract = {The cannabinoid CB1 receptor (CB1R) is an abundant metabotropic G-protein-coupled receptor that has been difficult to address therapeutically because of CNS side effects exerted by orthosteric drug candidates. Recent efforts have focused on developing allosteric modulators that target CB1R. Compounds from the recently discovered class of mixed agonistic and positive allosteric modulators (Ago-PAMs) based on 2-phenylindoles have shown promising functional and binding properties as CB1R ligands. Here, we identify binding modes of both the CP55,940 agonist and GAT228, a 2-phenylindole allosteric modulator, by using our metadynamics simulation protocol, and quantify their affinity and cooperativity by atomistic simulations. We demonstrate the involvement of multiple adjunct binding sites in the Ago-PAM characteristics of the 2-phenylindole modulators and explain their ability to compete with orthosteric agonists at higher concentrations. We validate these results experimentally by showing the contribution of multiple sites on the allosteric binding of ZCZ011, another homologous member of the class, together with the orthosteric agonist.},
author = {Saleh, Noureldin and Hucke, Oliver and Kramer, Gert and Schmidt, Esther and Montel, Florian and Lipinski, Radoslaw and Ferger, Boris and Clark, Timothy and Hildebrand, Peter W. and Tautermann, Christofer S.},
doi = {10.1002/anie.201708764},
faupublication = {yes},
journal = {Angewandte Chemie International Edition},
keywords = {allostery;cannabinoid receptors;G-protein-coupled receptors;metadynamics},
pages = {2580-2585},
peerreviewed = {Yes},
title = {{Multiple} {Binding} {Sites} {Contribute} to the {Mechanism} of {Mixed} {Agonistic} and {Positive} {Allosteric} {Modulators} of the {Cannabinoid} {CB1} {Receptor}},
volume = {57},
year = {2018}
}
@article{faucris.122335004,
abstract = {The synthesis and structural characterization of new coordination polymers with the N,N-donor ligand trans-1,2-bis(N-methylimidazol-2-yl)ethylene (trans-bie) are reported. It was found that the acetate-bridged paddlewheel metal(II) complexes [M-2(O2CCH3)(4)(trans-bie)]n with M = Rh, Ru, Mo, and Cr are linked by the trans-bie ligand to give a one-dimensional alternating chain. The metal-metal multiple bonds were analyzed with density functional theory and CASSCF/CASPT2 calculations (bond orders: Rh, 0.8; Ru, 1.7; Mo, 3.3).},
author = {Fritsch, Nico and Wick, Christian and Waidmann, Thomas and Dral, Pavlo and Tucher, Johannes and Heinemann, Frank Wilhelm and Shubina, Tatyana and Clark, Timothy and Burzlaff, Nicolai},
doi = {10.1021/ic501435a},
faupublication = {yes},
journal = {Inorganic Chemistry},
pages = {12305-12314},
peerreviewed = {Yes},
title = {{Multiply} {Bonded} {Metal}({II}) {Acetate} ({Rhodium}, {Ruthenium}, and {Molybdenum}) {Complexes} with the trans-1,2-{Bis}({N}-methylimidazol-2-yl)ethylene {Ligand}},
volume = {53},
year = {2014}
}
@article{faucris.122449404,
abstract = {We report an implementation of an atomic multipole model (up to quadrupole) for calculating the electrostatic properties of molecules based on electron densities derived from MNDO-like NDDO-based semiempirical MO calculations with minimal s, p, d valence basis sets. The results were validated by a comparison of the calculated values of the molecular electrostatic potential with those obtained from fine grain numerical integrations (both with AM1*), B3LYP/6-31G(d) and MP2/6-31G(d). The DFT and ab initio potentials can be reproduced remarkably well (mean unsigned error < 2 kcal mol(-1) e(-1)) using simple linear regression equations to correct the AM1* (multipole) results.},
author = {Horn, Anselm and Lin, Jr-Hung and Clark, Timothy},
doi = {10.1007/s00214-005-0657-9},
faupublication = {yes},
journal = {Theoretical Chemistry Accounts},
pages = {159-168},
peerreviewed = {Yes},
title = {{Multipole} electrostatic model for {MNDO}-like techniques with minimal valence spd-basis sets},
volume = {114},
year = {2005}
}
@article{faucris.116941264,
author = {Horn, Anselm and Lin, Jr-Hung and Clark, Timothy},
doi = {10.1007/s00214-006-0167-4},
faupublication = {yes},
journal = {Theoretical Chemistry Accounts},
pages = {461-465},
peerreviewed = {Yes},
title = {{Multipole} electrostatic model for {MNDO}-like techniques with minimal valence spd-basis sets (vol 114, pg 159, 2005)},
volume = {117},
year = {2007}
}
@article{faucris.122451824,
abstract = {The recently introduced multipole approach for computing the molecular electrostatic potential (MEP) within the semiempirical neglect of diatomic differential overlap (NDDO) framework [Horn AHC, Lin Jr-H., Clark T (2005) Theor Chem Acc 114:159-168] has been used to obtain atomic charges of nearly ab initio quality by scaling the semiempirical MEP. The parameterization set comprised a total of 797 compounds and included not only the newly parameterized AM1* elements Al, Si, P, S, Cl, Ti, Zr, and Mo but also the standard AM1 elements H, C, N, O and F. For comparison, the ZDO-approximated MEP was also calculated analytically in the spd-basis. For the AM1*-optimized structures, single-point calculations at the B3LYP, HF and MP2 levels with the 6-31G(d) and LanL2DZP basis sets were performed to obtain the MEP. The regression analysis of all 12 combinations of semiempirical and ab initio MEP data yielded correlation coefficients of at least 0.99 in all cases. Scaling the analytical and multipole-derived semiempirical MEP by the regression coefficients yielded mean unsigned errors below 2.6 and 1.9 kcal mol(-1), respectively. Subsequently, for 22 drug molecules from the World Drug Index, atomic charges were computed according to the RESP procedure using XX/6-31G(d) (XX=B3LYP, HF, MP2) and scaled AM1* multipole MEP; the correlation coefficients obtained are 0.83, 0.85 and 0.83, respectively. Figure: Schematic representation of the atomic charge generation: The molecular electrostatic potential (MEP) is calculated using the AM1* Hamiltonian; then the semiempirical MEP is scaled to DFT or ab initio level, and atomic charges are generated subsequently by the restraint electrostatic potential (RESP) fit method.},
author = {Horn, Anselm and Clark, Timothy},
doi = {10.1007/s00894-006-0137-8},
faupublication = {yes},
journal = {Journal of Molecular Modeling},
keywords = {AM1*;semiempirical MO theory;atomic charges;molecular electrostatic potential;multipole},
pages = {381-392},
peerreviewed = {Yes},
title = {{Multipole} electrostatic potential derived atomic charges in {NDDO}-methods with spd-basis sets},
volume = {13},
year = {2007}
}
@article{faucris.116942144,
author = {Anders, Ernst and Boldt, Hans-Günter and Clark, Timothy and Gassner, Thomas and et al.},
author_hint = {ANDERS E, BOLDT HG, CLARK T, FUCHS R, GASSNER T},
doi = {10.1002/chin.198616143},
faupublication = {yes},
journal = {Chemische Berichte},
month = {Jan},
pages = {279-296},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{N}-[1-({ACYLOXY}){ALKYL}]{HETEROARYLIUM} {SALTS} {IN} {SYNTHESIS} .3. {INTRAMOLECULAR} {ORTHO}-{ACYLATION} {OF} {SOME} {N}-{HETEROAROMATIC} {RING}-{SYSTEMS}},
volume = {119},
year = {1986}
}
@article{faucris.122452264,
author = {Anders, Ernst and Clark, Timothy and et al.},
author_hint = {ANDERS E, CLARK T, STANKOWIAK A, BOLDT HG, FUCHS R},
faupublication = {yes},
journal = {Bulletin des Sociétés Chimiques Belges},
month = {Jan},
pages = {485-494},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{N}-(1-{ACYLOXYALKYL}){HETEROARYLLIUM} {SALTS} .4. {CONFORMATION}-{CONTROLLED} {DEPROTONATION}},
volume = {94},
year = {1985}
}
@article{faucris.121614284,
abstract = {The nature of the interaction of paramagnetic atoms A (=N-4,P-4,O-3,S-3) with pi systems and C-60 in the A...C6H6 complexes and endohedral fullerenes (A@C-60) has been investigated employing second-order Moller-Plesset perturbation level of theory and density functional theory calculations. The coupled cluster theory with single and double excitations, and with perturbed triplet excitations have also been carried out for the A...C6H6 complexes. The calculated geometries indicate that the paramagnetic N and P atoms lie on the C-6 axis of benzene in the A...C6H6 complex and at the center of the C-60 cage in A@C-60. On the other hand, the O and S atoms are slightly shifted towards the C-C bond of benzene in the A...C6H6 complex. A comparison of the calculated binding energies (BEs) of these paramagnetic complexes and the corresponding rare gas complexes like He...C6H6 and He@C-60 indicate that the BEs of the former are much larger than those of the latter. For both the rare gas and paramagnetic atom complexes dispersive interactions dominate the BEs. The energy barriers of the penetration of the O atom through a [6,6] bond are lower than the penetration of the helium atom and higher than the penetration of a N atom. (C) 2002 American Institute of Physics.},
author = {Clark, Timothy and et al.},
author_hint = {Park JM, Tarakeshwar P, Kim KS, Clark T},
doi = {10.1063/1.1479135},
faupublication = {yes},
journal = {Journal of Chemical Physics},
pages = {10684-10691},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{Nature} of the interaction of paramagnetic atoms ({A}={N}-4,{P}-4,{O}-3,{S}-3) with pi systems and {C}-60: {A} theoretical investigation of {A} center dot center dot center dot {C6H6} and endohedral fullerenes {A}@{C}-60},
volume = {116},
year = {2002}
}
@article{faucris.122455344,
abstract = {NDDO-based (AM1) configuration interaction (CI) calculations have been used to calculate the wavelength and oscillator strengths of electronic absorptions in organic molecules and the results used in a sum-over-states treatment to calculate second-order-hyperpolarizabilities. The results for both spectra and hyperpolarizabilities are of acceptable quality as long as a suitable CI-expansion is used. We have found that using an active space of eight electrons in eight orbitals and including all single and pair-double excitations in the CI leads to results that agree well with experiment and that do not change significantly with increasing active space for most organic molecules. Calculated second-order hyperpolarizabilities using this type of CI within a sum-over-states calculation appear to be of useful accuracy.},
author = {Clark, Timothy and Chandrasekhar, Jayaraman},
doi = {10.1002/ijch.199300050},
faupublication = {yes},
journal = {Israel Journal of Chemistry},
month = {Jan},
pages = {435-448},
peerreviewed = {Yes},
title = {{NDDO}-{BASED} {CI} {METHODS} {FOR} {THE} {PREDICTION} {OF} {ELECTRONIC}-{SPECTRA} {AND} {SUM}-{OVER}-{STATES} {MOLECULAR} {HYPERPOLARIZATION}},
volume = {33},
year = {1993}
}
@article{faucris.121234784,
abstract = {SERS spectra of eight benzodiazepine drugs were recorded with an FT-NIR Raman spectrometer employing AuFONs (gold films over nanospheres) as SERS-active substrates. A tentative assignment of the vibrational bands was made by comparison with the Raman spectra of crystalline reference samples and the results of density functional theory (DFT) calculations. It is concluded that the bands observed in the SERS spectra are almost exclusively due to vibrations located on rings a and b of the benzodiazepine moiety. The latter should be adsorbed with the molecular plane essentially orthogonal to the metal surface. However, different adsorption geometries are postulated for derivatives containing NH or NCH3 groups. It is demonstrated that a few hundred nanograms of analyte per well are sufficient to record spectra that allow identification and discrimination of the drugs. Such amounts can be collected at the output of an HPLC instrument employed for separating these drugs from blood serum. Copyright (C) 2004 John Wiley Sons, Ltd.},
author = {Schneider, Siegfried and Hennemann, Matthias and Clark, Timothy and et al.},
author_hint = {Trachta G, Schwarze B, Brehm G, Schneider S, Hennemann M, Clark T},
doi = {10.1002/jrs.1154},
faupublication = {yes},
journal = {Journal of Raman Spectroscopy},
keywords = {surface-enhanced Raman scattering;gold films over nanospheres;benzodiazepine drugs;high-performance liquid chromatography;high-throughput analysis},
pages = {368-383},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{Near}-infrared {Fourier} transform surface-enhanced {Raman} scattering spectroscopy of 1,4-benzodiazepine drugs employing gold films over nanospheres},
volume = {35},
year = {2004}
}
@article{faucris.116943464,
abstract = {We have used density-functional theory to investigate the neighboring-group stabilization of iodine, arsenic, and phosphorus-centered oxyanion moieties in species such as deprotonated 2-iodoxybenzoic acid (IBX) and its analogs. The magnitudes of different stabilizing effects and further candidates for analogous stabilization are analyzed.},
author = {O'Hair, Richard A. J. and Williams, Craig M. and Clark, Timothy},
doi = {10.1007/s00894-009-0567-1},
faupublication = {yes},
journal = {Journal of Molecular Modeling},
keywords = {Density functional theory;sigma-Hole;IBA;IBS;IBX;2-iodoxybenzoic},
pages = {559-565},
peerreviewed = {Yes},
title = {{Neighboring} group stabilization by sigma-holes},
volume = {16},
year = {2010}
}
@article{faucris.119334204,
author = {Schleyer, Paul and Clark, Timothy and Boche, Gernot and et al.},
author_hint = {DIETRICH H, MAHDI W, SCHLEYER PV, NEUGEBAUER W, CLARK T, WILHELM D, BOCHE G, ETZRODT H},
doi = {10.1107/S0108767384091315},
faupublication = {yes},
journal = {Acta Crystallographica Section A},
month = {Jan},
pages = {C292-C292},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{NEW} {LITHIUM} {ORGANIC} {STRUCTURES} {AND} {THEIR} {INTERPRETATION}},
volume = {40},
year = {1984}
}
@article{faucris.121615164,
abstract = {New molecular descriptors based on statistical descriptions of the local ionization potential, local electron affinity, and the local polarizability at the surface of the molecule are proposed. The significance of these descriptors has been tested by calculating them for the Maybridge database in addition to our set of 26 descriptors reported previously. The new descriptors show little correlation with those already in use. Furthermore, the principal components of the extended set of descriptors for the Maybridge data show that especially the descriptors based on the local electron affinity extend the variance in our set of descriptors, which we have previously shown to be relevant to physical properties. The first nine principal components are shown to be most significant. As an example of the usefulness of the new descriptors, we have set up a QSPR model for boiling points using both the old and new descriptors.},
author = {Ehresmann, Bernd and Alex, Alexander and Clark, Timothy and et al.},
author_hint = {Ehresmann B, de Groot MJ, Alex A, Clark T},
doi = {10.1021/ci034215e},
faupublication = {yes},
journal = {Journal of Chemical Information and Computer Sciences},
pages = {658-668},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{New} molecular descriptors based on local properties at the molecular surface and a boiling-point model derived from them},
volume = {44},
year = {2004}
}
@article{faucris.122458204,
abstract = {Two quasi-multipole electrostatic models for molecular charge distributions are presented. They assign arrays of point charges to nonhydrogen atoms on the basis of hybrid orbitals or localised molecular orbitals. When used with common semiempirical MO-techniques, they reproduce natural atomic orbital derived point charge (NAO-PC) and ab initio molecular potentials well. The localised orbital technique (LMO-PC) is intuitively more attractive than the hybrid orbital-point charge (HO-PC) method, although the former is more CPU-intensive.},
author = {Gedeck, Peter and Schindler, Thorsten and Alex, Alexander and Clark, Timothy},
doi = {10.1007/s0089400060452},
faupublication = {yes},
journal = {Journal of Molecular Modeling},
keywords = {molecular electrostatic potential;AM1;PM3;MNDO;point charge model},
month = {Jan},
pages = {452-466},
peerreviewed = {Yes},
title = {{New} multicentre point charge models for molecular electrostatic potentials from semiempirical {MO}-calculations},
volume = {6},
year = {2000}
}
@article{faucris.122459524,
abstract = {The structure of the 1,4-azaborinine ring in the title compound, a representative of a novel class of potentially aromatic compounds that are isoelectronic with arenes, confirms conclusions of earlier ab initio calculations that cyclic conjugation in 1,4-azaborinines is interrupted by the boron atom.},
author = {Hampel, Frank and Clark, Timothy and et al.},
author_hint = {KRANZ M, HAMPEL F, CLARK T},
doi = {10.1039/c39920001247},
faupublication = {yes},
journal = {Journal of the Chemical Society - Series Chemical Communications},
pages = {1247-1248},
peerreviewed = {unknown},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{N}-{METHYL}-{B}-{MESITYLDIBENZO}-1,4-{AZABORININE} - {THE} {1ST} {EXPERIMENTAL} {STRUCTURE} {OF} {A} 1,4-{AZABORININE} {DERIVATIVE}},
year = {1992}
}
@article{faucris.120124884,
abstract = {Density functional and molecular orbital theory calculations on models for cobalamin suggest that NO binds similarly to the Co(II) and Co(III) oxidation states. However, Co(III) can bind water far more strongly than Co(II) as a sixth ligand, so that the competition between water and NO complexation strongly favors water for Co(III) in the gas phase. Although the Co(II) oxidation state is found to bind water slightly more strongly than NO in the gas phase, the inclusion of solvation effects via the polarizeable continuum model makes NO binding more favorable. Thus, the experimentally observed ability of cob(II)alamin to bind NO in aqueous solution is the result of its weak complexation with water and the relatively poor solvation of NO. Calculated vibrational frequencies support the interpretation of the cob(II)alamin-NO complex as being cob(III)alamin-NO-, although the DFT calculations underestimate the degree of charge transfer in comparison to Hartree-Fock calculations.},
author = {van Eldik, Rudi and Clark, Timothy and et al.},
author_hint = {van Eldik Rudi, Selcuki Cenk, Clark Tim},
doi = {10.1021/ic0347945},
faupublication = {yes},
journal = {Inorganic Chemistry},
note = {UnivIS-Import:2015-03-09:Pub.2004.forsch.sonder.sfb583.nobind},
pages = {2828},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{NO} {Binding} to {Cobalamin}: {Influence} of the {Metal} {Oxidation} {State}},
year = {2004}
}
@article{faucris.266778101,
abstract = {The family of neuropeptide Y (NPY) receptors comprises four subtypes (Y1R, Y2R, Y4R, Y5R), which are addressed by at least three endogenous peptides, i.e., NPY, peptide YY, and pancreatic polypeptide (PP), the latter showing a preference for Y4R. A series of cyclic oligopeptidic Y4R ligands were prepared by applying a novel approach, i.e., N-terminus to arginine side-chain cyclization. Most peptides acted as Y4R partial agonists, showing up to 60-fold higher Y4R affinity compared to the linear precursor peptides. Two cyclic hexapeptides (18, 24) showed higher Y4R potency (Ca2+ aequorin assay) and, with pKi values >10, also higher Y4R affinity compared to human pancreatic polypeptide (hPP). Compounds such as 18 and 24, exhibiting considerably lower molecular weight and considerably more pronounced Y4R selectivity than PP and previously described dimeric peptidic ligands with high Y4R affinity, represent promising leads for the preparation of labeled tool compounds and might support the development of drug-like Y4R ligands.},
author = {Konieczny, Adam and Conrad, Marcus and Ertl, Fabian J. and Gleixner, Jakob and Gattor, Albert O. and Grätz, Lukas and Schmidt, Maximilian F. and Neu, Eduard and Horn, Anselm and Wifling, David and Gmeiner, Peter and Clark, Timothy and Sticht, Heinrich and Keller, Max},
doi = {10.1021/acs.jmedchem.1c01574},
faupublication = {yes},
journal = {Journal of Medicinal Chemistry},
note = {CRIS-Team Scopus Importer:2021-12-03},
pages = {16746-16769},
peerreviewed = {Yes},
title = {{N}-{Terminus} to {Arginine} {Side}-{Chain} {Cyclization} of {Linear} {Peptidic} {Neuropeptide} y {Y4Receptor} {Ligands} {Results} in {Picomolar} {Binding} {Constants}},
volume = {64},
year = {2021}
}
@article{faucris.109041504,
author = {Clark, Timothy},
faupublication = {yes},
journal = {ACS National Meeting Book of Abstracts},
pages = {U297-U297},
peerreviewed = {unknown},
title = {{Numerical} drug-fitness index.},
volume = {220},
year = {2000}
}
@misc{faucris.117129584,
author = {Clark, Timothy},
faupublication = {yes},
peerreviewed = {automatic},
title = {{Objective} models for ligand binding characteristics from quantum mechanics},
year = {2013}
}
@article{faucris.108891684,
author = {Clark, Timothy},
faupublication = {yes},
journal = {ACS National Meeting Book of Abstracts},
pages = {U801-U802},
peerreviewed = {unknown},
title = {{Odd}-electron bonds and electron transfer in model systems},
volume = {229},
year = {2005}
}
@article{faucris.209916664,
abstract = {The history and theory of one- and three-electron bonds are presented and discussed. It is shown that the dependence of the odd-electron bond energy on the difference in ionization potentials of the bonding partners must be corrected to include the ion-pairing energy for neutral odd-electron bonded complexes.},
author = {Clark, Timothy},
doi = {10.1002/cphc.201700417},
faupublication = {yes},
journal = {ChemPhysChem},
keywords = {abinitio calculations;bond theory;odd-electron bonds;radical reactions;reactive intermediates},
pages = {2766-2771},
peerreviewed = {Yes},
title = {{Odd}-{Electron} {Bonds}},
volume = {18},
year = {2017}
}
@article{faucris.109392624,
author = {Clark, Timothy},
doi = {10.1021/ja00214a003},
faupublication = {yes},
journal = {Journal of the American Chemical Society},
pages = {1672-1678},
peerreviewed = {Yes},
title = {{ODD}-{ELECTRON} {DELTA}-{BONDS}},
volume = {110},
year = {1988}
}
@article{faucris.116946764,
author = {Clark, Timothy and et al.},
author_hint = {Gallen MJ, Goummont R, Clark T, Terrier F, Williams CM},
doi = {10.1002/anie.200504156},
faupublication = {yes},
journal = {Angewandte Chemie International Edition},
keywords = {acidity;density functional calculations;o-iodoxybenzoic acid;oxidation;proton affinity},
month = {Jan},
pages = {2929-2934},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {o-iodoxybenzoic acid ({IBX}): {pK}(a) and proton-affinity analysis},
volume = {45},
year = {2006}
}
@article{faucris.208727217,
abstract = {Bond critical points (BCPs) in the quantum theory of atoms in molecules (QTAIM) are shown to be a consequence of the molecular topology, symmetry, and the Poincar,-Hopf relationship, which defines the numbers of critical points of different types in a scalar field. BCPs can be induced by a polarizing field or by addition of a single non-bonded atom to a molecule. BCPs and their associated bond paths are therefore suggested not to be a suitable means of identifying chemical bonds, or even attractive intermolecular interactions.},
author = {Wick, Christian and Clark, Timothy},
doi = {10.1007/s00894-018-3684-x},
faupublication = {yes},
journal = {Journal of Molecular Modeling},
keywords = {QTAIM;Bond critical points},
peerreviewed = {Yes},
title = {{On} bond-critical points in {QTAIM} and weak interactions},
volume = {24},
year = {2018}
}
@article{faucris.115084464,
abstract = {The design, synthesis, and electronic properties of a new series of D-pi-A conjugates consisting of free base (H2P) and zinc porphyrins (ZnP) as electron donors and a fullerene (C-60) as electron acceptor, in which the two electroactive entities are covalently linked through pyridine-vinylene spacers of different lengths, are described. Electronic interactions in the ground state were characterized by electrochemical and absorption measurements, which were further supported with theoretical calculations. Most importantly, charge-transfer bands were observed in the absorption spectra, indicating a strong push-pull behavior. In the excited states, electronic interactions were detected by selective photoexcitation under steady-state conditions, by time-resolved fluorescence investigations, and by pump probe experiments on the femto-, pico-, and nanosecond time scales. Porphyrin fluorescence is quenched for the different D-pi-A conjugates, from which we conclude that the deactivation mechanisms of the excited singlet states are based on photoinduced energy-and/or electron transfer processes between H2P/ZnP and C-60, mediated through the molecular spacers. The fluorescence intensity decreases and the fluorescence lifetimes shorten as the spacer length decreases and as the spacer substitution changes. With the help of transient absorption spectroscopy, the formation of charge-separated states involving oxidized H2P/ZnP and reduced C-60 was confirmed. Lifetimes of the corresponding charge-separated states, which ranged from similar to 400 picoseconds to 165 nanoseconds, depend on the spacer length, the spacer substitution, and the solvent polarity. Interestingly, D-pi-A conjugates containing the longest linkers did not necessarily exhibit the longest charge-separated state lifetimes. The distances between the electron donors and the acceptors were calculated by molecular modelling. The longest charge-separated state lifetime corresponded to the D-p-A conjugate with the longest electron donor-acceptor distance. Likewise, EPR measurements in frozen media revealed charge separated states in all the D-p-A conjugates investigated. A sharp peak with g values similar to 2.000 was assigned to reduced C-60, while a broader, less intense signal (g similar to 2.003) was assigned to oxidized H2P/ZnP. On-off switching of the formation and decay of the charge-separated states was detected by EPR at 77 K by repeatedly turning the irradiation source on and off.},
author = {Kirner, Sabrina and Arteaga, Danny and Henkel, Christian and Margrat, Johannes T. and Alegret, Nuria and Ohkubo, Kei and Insuasty, Braulio and Ortiz, Alejandro and Martin, Nazario and Echegoyen, Luis and Fukuzumi, Shunichi and Clark, Timothy and Guldi, Dirk Michael},
doi = {10.1039/c5sc02051d},
faupublication = {yes},
journal = {Chemical Science},
month = {Jan},
pages = {5994-6007},
peerreviewed = {Yes},
title = {{On}-off switch of charge-separated states of pyridine-vinylene-linked porphyrin-{C}-60 conjugates detected by {EPR}},
volume = {6},
year = {2015}
}
@article{faucris.122463704,
abstract = {The variation in the band gap of a (Gly)(30) alpha-helix with position in the peptide sequence has been investigated using AM1 semiempirical molecular orbital (MO) theory within an extensive singles configuration interaction (CI) treatment. The dipole-charge interaction along the length of the helix results in the highest local electron affinity near the N-terminus and the lowest local ionization potential near the C-terminus. The calculations suggest that the band gap, measured as the difference between the local ionization potential and electron affinity decreases from the C-terminus to the N-terminus for the model (Gly)(30) alpha-helix in vacuo. (C) 2000 John Wiley & Sons, Inc.},
author = {Herz, Thomas and Otto, Peter and Clark, Timothy},
doi = {10.1002/1097-461X(2000)79:2<120::AID-QUA7>3.0.CO;2-1},
faupublication = {yes},
journal = {International Journal of Quantum Chemistry},
keywords = {AM1;peptide;alpha-helix;band gap;semiconductor},
pages = {120-124},
peerreviewed = {Yes},
title = {{On} the band gap in peptide alpha-helices},
volume = {79},
year = {2000}
}
@article{faucris.106195584,
abstract = {Ab initio (UHF/6-31G*) and density functional (Becke3LYP/D95*) calculations have been used to investigate the structures and stabilities of the radical cations of the DNA bases and base pairs. The calculated structures of the base pairs show excellent agreement with crystallographic data. The most easily oxidizable base, guanine, forms a particularly stable radical cation base pair with cytosine, so that the calculated adiabatic ionization potential for the guanine-cytosine hydrogen-bonded complex is about 0.75 eV lower than that of guanine itself. UBecke3LYP/D95*//UHF/6-31G* calculations show that the shift of the central hydrogen-bended proton at N1 of guanine to N3 of cytosine is only slightly endothermic (+1.6 kcal mol(-1)). The product of the corresponding proton shift in the adenine-thymine system is unfavorable by +14.1 kcal mol(-1). These results suggest that the guanine-cytosine radical cation represents even more of a thermodynamic sink in oxidized DNA than might be concluded from the ionization potentials of the individual bases, and that it enjoys about 7.3 kcal mol(-1) extra stabilization from the central low-barrier hydrogen bond.},
author = {Clark, Timothy and et al.},
author_hint = {Hutter M, Clark T},
doi = {10.1021/ja953370+},
faupublication = {yes},
journal = {Journal of the American Chemical Society},
pages = {7574-7577},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{On} the enhanced stability of the guanine-cytosine base-pair radical cation},
volume = {118},
year = {1996}
}
@article{faucris.208732118,
abstract = {We propose a new approach to the synthesis of AH(x)(SIC)fullerene structures via reactions through the fullerene wall. To investigate the feasibility of the approach, the step-by-step hydrogenation of the template endofullerene N(SIC)C-60 up to NH4(SIC)C-60 has been studied using DFT and MP2 calculations. Protonation of the endohedral guest through the fullerene wall is competitive with escape of the guest, whereas reaction with a hydrogen atom is less favorable. Each protonation step is highly exothermic, so that less active acids can also protonate the guest with less accumulation of energy. The final product, NH4(SIC)C-60 is a novel concentric ion pair NH4 vertical bar(SIC)C-60(center dot)-in which the charge-centers of the two ions coincide.},
author = {Dral, Pavlo and Clark, Timothy},
doi = {10.1039/c7cp02865b},
faupublication = {yes},
journal = {Physical Chemistry Chemical Physics},
pages = {17199-17209},
peerreviewed = {Yes},
title = {{On} the feasibility of reactions through the fullerene wall: a theoretical study of {NHx}({SIC}){C}-60},
volume = {19},
year = {2017}
}
@article{faucris.116951384,
author = {Schleyer, Paul and Dieter, Wilhelm and Clark, Timothy},
faupublication = {yes},
journal = {Journal of Organometallic Chemistry},
month = {Jan},
pages = {C17-C20},
peerreviewed = {Yes},
title = {{ON} {THE} {NATURE} {OF} {THE} {CYCLOHEPTATRIENYL} {TRIANION} - {THE} {DECISIVE} {IMPORTANCE} {OF} {COUNTERION} {STABILIZATION} {IN} {POLYMETALLATED} {CARBANION} {SYSTEMS}},
volume = {281},
year = {1985}
}
@article{faucris.122464364,
author = {Schötz, Karl and Clark, Timothy and Schleyer, Paul and et al.},
author_hint = {SCHOTZ K, CLARK T, SCHALLER H, SCHLEYER PV},
doi = {10.1021/jo00178a041},
faupublication = {yes},
journal = {Journal of Organic Chemistry},
month = {Jan},
pages = {733-735},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{ON} {THE} {STABILITY} {OF} {TRIMETHYLENEMETHANE} {DICATIONS}},
volume = {49},
year = {1984}
}
@article{faucris.120303964,
abstract = {The synthesis, isolation, and spectroscopic characterization of the bisimino[60]fullerenes C(NCOOR), (1a: R = Et, 1b. R = tBu) with a cis-1 addition pattern as well as of their regioisomeric analogues 2-7 with different addition patterns are described. Whereas compounds 2-7 are typical fulleroaziridines and obey the rule of the minimization of [5,6] double bonds, the cis-1 isomers 1a and 1b represent the first examples of fullerene derivatives with open transannular [6,6] bonds. Characteristic features within the fullerene framework of these valence isomers VI are the presence of a doubly bridged open 14-membered ring with a phenanthrene perimeter as well as of an 8-membered 1,4-diazocine heterocycle. Moreover, it is shown that, by transforming cis-1-C60(NCOOtBu)2 (1b) into cis-1-C6O(NH)2 (1c), the fullerene cage can be closed in an intraring 2π → 2σ isomerization to valence isomer V. These are the first chemical modifications of the fullerene core that allow the synthesis of both open and closed valence isomers with the same addition pattern. Density-functional as well as AM1 calculations corroborate the experimental findings that it depends on the addition pattern as well as on the nature of the addends whether or not the transannular [6,6] bonds are closed. Only in the cis-1 adducts C60(NR) that prefer planar imino bridges (e.g., carbamates or amides) are the open forms VI more stable than the closed isomers V. © VCH Verlagsgesellschaft mbH. 1996.},
author = {Schick, Georg and Hirsch, Andreas and Mauser, Harald and Clark, Timothy},
doi = {10.1002/chem.19960020807},
faupublication = {yes},
journal = {Chemistry - A European Journal},
keywords = {clusters;fullerenes;nitrenes;regioselectivity;valence isomerization},
pages = {935-943},
peerreviewed = {Yes},
title = {{Opening} and closure of the fullerene cage in cis-1-bisimino adducts of {C60}: {The} influence of the addition pattern and the addend},
volume = {2},
year = {1996}
}
@article{faucris.227317147,
abstract = {The effect of extending the O-H bond length(s) in water on the hydrogen-bonding strength has been investigated using static ab initio molecular orbital calculations. The "polar flattening" effect that causes a slight sigma-hole to form on hydrogen atoms is strengthened when the bond is stretched, so that the sigma-hole becomes more positive and hydrogen bonding stronger. In opposition to this electronic effect, path-integral ab initio molecular-dynamics simulations show that the nuclear quantum effect weakens the hydrogen bond in the water dimer. Thus, static electronic effects strengthen the hydrogen bond in H2O relative to D2O, whereas nuclear quantum effects weaken it. These quantum fluctuations are stronger for the water dimer than in bulk water.},
author = {Clark, Timothy and Heske, Julian and Kühne, Thomas D.},
doi = {10.1002/cphc.201900839},
faupublication = {yes},
journal = {ChemPhysChem},
note = {CRIS-Team WoS Importer:2019-10-01},
peerreviewed = {Yes},
title = {{Opposing} {Electronic} and {Nuclear} {Quantum} {Effects} on {Hydrogen} {Bonds} in {H2O} and {D2O}},
year = {2019}
}
@article{faucris.109394604,
author = {Clark, Timothy and et al.},
author_hint = {CLARK T, TEASLEY MF, NELSEN SF, WYNBERG H},
doi = {10.1021/ja00253a025},
faupublication = {yes},
journal = {Journal of the American Chemical Society},
pages = {5719-5724},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{OPTICAL}-{ABSORPTION} {SPECTRA} {OF} {TETRAALKYL} {OLEFIN} {CATION} {RADICALS}},
volume = {109},
year = {1987}
}
@article{faucris.116954244,
abstract = {The halogen atoms in the 1-chloro-1H-phosphirenes, 5a-c, are easily substituted on reaction with organolithium and Grignard reagents, 14a-p, with formation of the corresponding O-, N-, C-, Si-, and Ge-substituted 1H-phosphirenes, 15a-t. Cl/H exchange reactions also occur on reaction with lithium metal hydrides (5a --> 17). Furthermore, substitution reactions are also realized with the alkali metal berates, 18a-g (--> 19a-g); the same is true for reactions with trimethylsilyl cyanide and azide (--> 22a-d). Some of the substitution products have been characterized in the form of their metal complexes, 16, 23, 24, and 25.},
author = {Göller, Andreas H. and Clark, Timothy and et al.},
author_hint = {Heydt H, Ehle M, Haber S, Hoffmann J, Wagner O, Goller A, Clark T, Regitz M},
doi = {10.1002/cber.19971300607},
faupublication = {yes},
journal = {Chemische Berichte},
keywords = {phosphorus heterocycles;1H-phosphirenes;nucleophilic substitution reactions at 1H-phosphirenes;metal-complexation of functionalized 1H-phosphirenes;carbonyl complexes},
pages = {711-723},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{Organophosphorus} compounds .118. {Reactions} of 1-chloro-{1H}-phosphirenes with nucleophiles},
volume = {130},
year = {1997}
}
@article{faucris.121854744,
abstract = {The 1H-phosphirenes 9a-g were alkylated by the trifluoromethanesulfonate esters 10a,b to furnish the stable phosphirenium salts 11a-i. The phosphirenium salts 14 bearing two identical exocyclic substituents at phosphorus were obtained by reactions of the silyl-substituted 1H-phosphirene 12 with a twofold molar amount of the esters 10a,b. As examples for the reactivity, the salts 11b,d were subjected to hydrolysis (--> 15a,b) and 11c to methanolysis (--> 16).},
author = {Göller, Andreas H. and Clark, Timothy and et al.},
author_hint = {Heydt H, Hoffmann J, Goller A, Clark T, Regitz M},
doi = {10.1055/s-1998-2010},
faupublication = {yes},
journal = {Synthesis-Stuttgart},
keywords = {alkylation;1H-phosphirenes;phosphirenium cations;triflates},
pages = {175-180},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{Organophosphorus} compounds; 122. {Alkylation} of {1H}-phosphirenes with triflates - {Synthesis} of lambda(5)sigma(4)-{1H}-phosphirenium cations},
year = {1998}
}
@article{faucris.281412748,
abstract = {The synthesis of covalent organic frameworks (COFs) based on a novel thiophene-extended benzotrithiophene (BTT) building block is described, which in combination with triazine-based amines (1,3,5-triazine-2,4,6-triyl)trianiline (TTA) or (1,3,5-triazine-2,4,6-triyl)tris(([1,1´-biphenyl]-4-amine)) (TTTBA)) affords crystalline, and porous imine-linked COFs, BTT TTA and BTT TTTBA, with surface areas as high as 932 and 1200 m2 g−1, respectively. Oriented thin films are grown successfully on different substrates, as indicated by grazing incidence diffraction (GID). Room-temperature in-plane electrical conductivity of up to 10−4 S m−1 is measured for both COFs. Temperature-dependent electrical conductivity measurements indicate activation energies of ≈123.3 meV for BTT TTA and ≈137.5 meV for BTT TTTBA and trap-dominated charge transport via a hopping mechanism for both COFs. Moreover, conductive atomic force microscopy reveals directional and defect-dominated charge transport in the oriented BTT COF films with a strong preference for the in-plane direction within the molecular 2D-planes. Quantum mechanical calculations predict BTT TTTBA to conduct holes and electrons effectively in both in-plane and out-of-plane directions. In-plane, charge carrier transport is of hopping character where the triazine cores represent the barrier. Out-of-plane, a continuous charge-carrier pathway is calculated that is hampered by an imposed structural defect simulated by a rotated molecular COF layer.},
author = {Frey, Laura and Poehls, Jonas Fredrik and Hennemann, Matthias and Maehringer, Andre and Reuter, Stephan and Clark, Timothy and Weitz, Ralf Thomas and Medina, Dana Dina},
doi = {10.1002/adfm.202205949},
faupublication = {yes},
journal = {Advanced Functional Materials},
keywords = {benzotrithiophene; covalent organic frameworks; electrical conductivity; thin films},
note = {CRIS-Team Scopus Importer:2022-09-09},
peerreviewed = {Yes},
title = {{Oriented} {Thiophene}-{Extended} {Benzotrithiophene} {Covalent} {Organic} {Framework} {Thin} {Films}: {Directional} {Electrical} {Conductivity}},
year = {2022}
}
@article{faucris.122468104,
abstract = {The oxidation of E-1,2-di-tert-butyl-1,2-dimesityl disilene (1) in benzene by gaseous dioxygen to give 2 and 3 has been studied at various temperatures and with rapid or slow addition of oxygen. The effect of various additives (amines, phosphines, THF) on the product distribution was also investigated. Ab initio MO calculations were carried out on the oxidation of H2Si=SiH2 with triplet oxygen. These led to a proposed reaction mechanism for the oxidation of 1, in which the initial intermediate is a disileneperoxy biradical 6', which can close to give 2 or react with another molecule of disilene to give ultimately 3.},
author = {Clark, Timothy and et al.},
author_hint = {MCKILLOP KL, WEST R, CLARK T, HOFMANN H},
doi = {10.1515/znb-1994-1219},
faupublication = {yes},
journal = {Zeitschrift für Naturforschung Section B-A Journal of Chemical Sciences},
keywords = {DISILENES},
pages = {1737-1742},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{OXIDATION} {OF} {DISILENES} - {EXPERIMENTAL} {AND} {THEORETICAL}-{STUDIES}},
volume = {49},
year = {1994}
}
@article{faucris.118767704,
author = {Zenneck, Ulrich and Clark, Timothy and Elvers, Achim and Heinemann, Frank Wilhelm and Hennemann, Matthias and Zeller, Matthias},
faupublication = {yes},
journal = {Angewandte Chemie},
note = {UnivIS-Import:2017-11-07:Pub.2000.nat.dchph.paoc22.p{\_}6{\_}an},
pages = {2174-2178},
peerreviewed = {Yes},
title = {{P{\_}6{\_}} and {P{\_}3{\_}} {Cymantrene}: {Consequences} of the {Inclusion} of {Phosphorus} {Atoms} in {Mn}-{Coordinated} {Cyclopentadienyl} {Ligands}},
volume = {112},
year = {2000}
}
@article{faucris.116955124,
author = {Clark, Timothy and Hennemann, Matthias and Zenneck, Ulrich and et al.},
author_hint = {Clark T, Elvers A, Heinemann FW, Hennemann M, Zeller M, Zenneck U},
doi = {10.1002/1521-3773(20000616)39:12<2087::AID-ANIE2087>3.0.CO;2-B},
faupublication = {yes},
journal = {Angewandte Chemie International Edition},
keywords = {arene complexes;density functional calculations;EPR spectroscopy;manganese;phosphorus heterocycles},
month = {Jan},
pages = {2087-+},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{P}-6 manganocene and {P}-3 cymantrene: {Consequences} of the inclusion of phosphorus atoms in {Mn}-coordinated cyclopentadienyl ligands},
volume = {39},
year = {2000}
}
@article{faucris.110332024,
author = {Clark, Timothy and Elvers, Achim and Heinemann, Frank Wilhelm and Hennemann, Matthias and Zeller, Matthias and Zenneck, Ulrich},
faupublication = {yes},
journal = {Angewandte Chemie-International Edition},
pages = {2087-2091},
peerreviewed = {unknown},
title = {{P}(6) {Manganocene} and {P}(3) {Cymantrene}: {Consequences} of the {Inclusion} of {Phosphorus} {Atoms} in {Mn}-{Coordinated} {Cyclopentadienyl} {Ligands} {This} work was supported by the {Deutsche} {Forschungsgemeinschaft} and the {Fonds} der {Chemischen} {Industrie}. {A}.{E}., {M}.{H}., and {M}.{Z}. thank the {DFG}-{Graduiertenkolleg} ("{Phosphorchemie} als {Bindeglied} verschiedener chemischer {Disziplinen}" of the {University} of {Kaiserslautern}) and {M}.{Z}. also thanks the {Studienstiftung} des {Deutschen} {Volkes} for fellowships.},
volume = {39},
year = {2000}
}
@article{faucris.240981854,
abstract = {Here, we present a novel butadiyne-linked HBC-ethynyl-porphyrin dimer, which exhibits in the ground state strong absorption cross sections throughout the UV and visible ranges of the solar spectrum. In short, a unidirectional flow of excited state energy from the HBC termini to the (metallo)porphyrin focal points enables concentrating light at the latter. Control over excitonic interactions within, for example, the electron-donating porphyrin dimers was realized by complexation of bidentate ligands to set up panchromatic absorption that extends all the way into the near-infrared range. The bidentate binding motif was then exploited to create a supramolecular electron donor-acceptor assembly based on a HBC-ethynyl-porphyrin dimer and an electron accepting bis(aminoalkyl)-substituted fullerene. Of great relevance is the fact that charge separation from the photoexcited HBC-ethynyl-porphyrin dimer to the bis(aminoalkyl)-substituted fullerene is activated not only upon photoexciting the HBCs in the UV as well as the (metallo)porphyrins in the visible but also in the NIR. Implicit is the synergetic interplay of energy and charge transfer in a photosynthetic mimicking manner. The dimer and bis-HBC-ethynyl-porphyrin monomers, which serve as references, were probed by means of steady-state as well as time-resolved optical spectroscopies, including global target analyses of the time-resolved transient absorption data.},
author = {Wolf, Maximilian and Lungerich, Dominik and Bauroth, Stefan and Popp, Maximilian and Platzer, Benedikt and Clark, Timothy and Anderson, Harry L. and Jux, Norbert and Guldi, Dirk Michael},
doi = {10.1039/d0sc02028a},
faupublication = {yes},
journal = {Chemical Science},
note = {CRIS-Team Scopus Importer:2020-07-31},
pages = {7123-7132},
peerreviewed = {Yes},
title = {{Panchromatic} light funneling through the synergy in hexabenzocoronene-(metallo)porphyrin-fullerene assemblies to realize the separation of charges},
volume = {11},
year = {2020}
}
@article{faucris.122325104,
abstract = {A frequent task in computer-aided drug design is to identify novel chemotypes similar in activity but structurally different to a given reference structure. Here we report the development of a novel method for atom-independent similarity comparison of molecular fragments (substructures of drug-like molecules). The fragments are characterized by their local surface properties coded in the form of 3D pharmacophores. As surface properties, we used the electrostatic potential (MEP), the local ionization energy (IEL), local electron affinity (EA(L)) and local polarizability (POL) calculated on isodensity surfaces. A molecular fragment can then be represented by a minimal set of extremes for each surface property. We defined a tolerance sphere for each of these extremes, thus allowing us to assess the similarity of fragments in an analogous manner to classical pharmacophore comparison. As a first application of this method we focused on comparing rigid fragments suitable for scaffold hopping. A retrospective analysis of successful scaffold hopping reported for Factor Xa inhibitors [Wood MR et al (2006) J Med Chem 49:1231] showed that our method performs well where atom-based similarity metrics fail.},
author = {Jakobi, Arjen-Joachim and Mauser, Harald and Clark, Timothy},
doi = {10.1007/s00894-008-0302-3},
faupublication = {yes},
journal = {Journal of Molecular Modeling},
keywords = {fragment;molecular surface;similarity searching;scaffold hopping;pharmacophore matching},
pages = {547-558},
peerreviewed = {Yes},
title = {{ParaFrag} - an approach for surface-based similarity comparison of molecular fragments},
volume = {14},
year = {2008}
}
@article{faucris.119335084,
author = {Clark, Timothy},
doi = {10.1007/s00894-006-0119-x},
faupublication = {yes},
journal = {Journal of Molecular Modeling},
pages = {529-529},
peerreviewed = {Yes},
title = {{Paul} von {Rague} {Schleyer} 75th birthday festschrift},
volume = {12},
year = {2006}
}
@article{faucris.217463655,
abstract = {Surpassing the Shockley–Queisser limit, which places an upper bound on solar conversion efficiency for a single p–n junction solar cell at slightly more than 30%, is one of the grand challenges in the field of solar-energy research. Singlet fission (SF)in molecular acenes, the molecular analog of multiple exciton generation (MEG), has the potential to initiate a game-changing advance in solar-energy conversion. SF allows singlet-excited states (S
1
)to be down-converted into twice as many triplet-excited states (T
1
).},
author = {Basel, Bettina and Papadopoulos, Ilias and Thiel, Dominik and Casillas, Ruben and Zirzlmeier, Johannes and Clark, Timothy and Guldi, Dirk Michael and Tykwinski, Rik R.},
doi = {10.1016/j.trechm.2019.02.002},
faupublication = {yes},
journal = {Trends in Chemistry},
keywords = {interfacial electron transfer; pentacenes; singlet fission; solar energy; time-resolved spectroscopy; triplet},
note = {CRIS-Team Scopus Importer:2019-05-14},
pages = {11-21},
peerreviewed = {Yes},
title = {{Pentacenes}: {A} {Molecular} {Ruler} for {Singlet} {Fission}},
volume = {1},
year = {2019}
}
@article{faucris.240982609,
abstract = {Triplet-excited-state energies of perylene-monoimides (PMIs) lie in the range 1.12 eV ± 2 meV when compared to singlet-excited-state energies of about 2.39 eV ± 2 meV; therefore, the corresponding naphthalene-linked PMI-Dimer was investigated as a novel singlet-fission (SF) material. Ultrafast transient absorption measurements demonstrated the (S1S0)-to-1(T1T1) transformation and the involvement of a mediating step in the overall 1(T1T1) formation. The intermediate is a charge-transfer state that links the initial (S1S0) with the final 1(T1T1), and imposes charge-transfer character on both, which are thus denoted (S1S0)CT and 1(T1T1)CT. At room temperature, the decorrelation and stability of 1(T1T1)CT is affected by the geminate triplet-triplet recombination (G-TTR) of the two triplets. Independent confirmation for G-TTR to afford up-converted (S1S0)UC in fsTA and nsTA measurements with PMI-Dimer, came from probing PMI-Monomer (T1)s in triplet-triplet annihilation up-conversion (TTA-UC). The G-TTR channel, active in the PMI-Dimer at room temperature, is suppressed by working at either low temperatures (∼140 K) or in polar solvents (benzonitrile): Both scenarios assist in stabilizing (T1T1)CT. As a consequence, the triplet quantum yields are 4.2% and 14.9% at room temperature and 140 K, respectively, in 2-methyltetrahydrofuran.},
author = {Papadopoulos, Ilias and Gutiérrez-Moreno, David and McCosker, Patrick Michael and Casillas, Ruben and Keller, Paul A. and Sastre-Santos, Ángela and Clark, Timothy and Fernández-Lázaro, Fernando and Guldi, Dirk Michael},
doi = {10.1021/acs.jpca.0c04091},
faupublication = {yes},
journal = {Journal of Physical Chemistry A},
note = {CRIS-Team Scopus Importer:2020-07-31},
pages = {5727-5736},
peerreviewed = {Yes},
title = {{Perylene}-{Monoimides}: {Singlet} {Fission} {Down}-{Conversion} {Competes} with {Up}-{Conversion} by {Geminate} {Triplet}-{Triplet} {Recombination}},
volume = {124},
year = {2020}
}
@article{faucris.109395704,
abstract = {Electron donor-acceptor systems with phenothiazine linked directly to pyrene exhibit a dual emission in moderately and very polar solvents. Steady state and time-resolved fluorescence spectroscopy provide evidence that the "blue" and "red" emission bands originate from different species. Fluorescence excitation spectra show a similar appearance when the emission is monitored either in the red or blue spectral range, but they are slightly shifted against each other. This suggests that different isomers exist with a distinctly different photophysical behavior. Semiempirical (AM1/CI) molecular orbital calculations with a continuum solvent treatment have been used to establish the geometry of the two nearly isoenergetic stereoisomers and to calculate the properties of their excited Franck-Condon states. Geometry optimization of various excited states provides evidence for different internal relaxation coordinates for the phenothiazine-localized S-1 state and the charge transfer state S-6, on one hand, and the pyrene-localized S-2 (S-3) state, on the other hand. The relaxed geometries in the excited states of both isomers represent mirror images with identical properties. The different photophysical behavior of the two isomers is most likely caused by the different potential energy curves, or more precisely speaking, by different location and/or heights of the barrier along the reaction coordinates from the locally excited to the geometry-relaxed CT states.},
author = {Acar, Nursel and Kurzawa, Jana and Schneider, Siegfried and Clark, Timothy and et al.},
author_hint = {Acar N, Kurzawa J, Fritz N, Stockmann A, Roman C, Schneider S, Clark T},
doi = {10.1021/jp036250u},
faupublication = {yes},
journal = {Journal of Physical Chemistry A},
pages = {9530-9541},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{Phenothiazine}-pyrene dyads: {Photoinduced} charge separation and structural relaxation in the {CT} state},
volume = {107},
year = {2003}
}
@article{faucris.107231124,
abstract = {We report a computational study on the chemical bonding of phosphonates and carboxylates to aluminum oxide surfaces and how the binding properties are related to the amount of water in the experimental environment. Two different surface structures were used in the calculations in order to model representative adsorption sites for the phosphonates and carboxylates and to account for the amorphous nature of the hydroxylated AlOx films in experiment. For the phosphonates, we find that the thermodynamically preferred binding mode changes between mono-, bi-, and tridentate depending on the surface structure and the amount of residual water. For the carboxylates, on the other hand, monodentate adsorption is always lower in energy at all experimental conditions. Phosphonates are more strongly bound to aluminum oxide than carboxylates, so that carboxylates can be replaced easily by phosphonates. The theoretical findings are consistent with those obtained in adsorption, desorption, and exchange reactions of n-alkyl phosphonic and carboxylic acids on AlOx surfaces. The results provide an atomistic understanding of the adsorption and help to optimize experimental conditions for self-assembly of organic films on aluminum oxide surfaces.},
author = {Bauer, Thilo and Schmaltz, Thomas and Lenz, Thomas and Halik, Marcus and Meyer, Bernd and Clark, Timothy},
doi = {10.1021/am4008374},
faupublication = {yes},
journal = {ACS Applied Materials and Interfaces},
pages = {6073--6080},
peerreviewed = {unknown},
title = {{Phosphonate}- and {Carboxylate}-{Based} {Self}-{Assembled} {Monolayers} for {Organic} {Devices}: {A} {Theoretical} {Study} of {Surface} {Binding} on {Aluminum} {Oxide} with {Experimental} {Support}},
url = {http://pubs.acs.org/doi/abs/10.1021/am4008374},
volume = {5},
year = {2013}
}
@article{faucris.237476859,
abstract = {The development of new chromophoric receptors capable of binding curved carbon nanostructures is central to the quest for improved fullerene-based organic photovoltaics. We herein report the synthesis and characterization of a subphthalocyanine-based multicomponent ensemble consisting of two electron-rich SubPc-monomers rigidly attached to the convex surface of an electron-poor SubPc-dimer. Such a unique configuration, especially in terms of the two SubPc-monomers, together with the overall stiffness of the linker, endows the multicomponent system with a well-defined tweezer-like topology to efficiently embrace a fullerene in its inner cavity. The formation of a 1 : 1 complex was demonstrated in a variety of titration studies with either C60 or C70. In solution, the underlying association constants were of the order of 105 M-1. Detailed physicochemical experiments revealed a complex scenario of energy- and electron-transfer processes upon photoexcitation in the absence and presence of fullerenes. The close proximity of the fullerenes to the electron-rich SubPcs enables a charge shift from the initially formed reduced SubPc-dimer to either C60 to C70.},
author = {Zango, Germán and Krug, Marcel and Krishna, Swathi and Mariñas, Víctor and Clark, Timothy and Martinez-Diaz, M. Victoria and Guldi, Dirk Michael and Torres, Tomás},
doi = {10.1039/d0sc00059k},
faupublication = {yes},
journal = {Chemical Science},
note = {CRIS-Team Scopus Importer:2020-04-17},
pages = {3448-3459},
peerreviewed = {Yes},
title = {{Photoactive} preorganized subphthalocyanine-based molecular tweezers for selective complexation of fullerenes},
volume = {11},
year = {2020}
}
@article{faucris.122544884,
author = {Clark, Timothy and Schneider, Siegfried},
faupublication = {yes},
journal = {ACS National Meeting Book of Abstracts},
pages = {U1028-U1028},
peerreviewed = {unknown},
title = {{Photochemistry} in solution with semiempirical {Cl}},
volume = {227},
year = {2004}
}
@article{faucris.208732387,
abstract = {The concepts of polarization (induction), charge transfer and covalent bonding contributions are discussed in terms of weak interactions. They are shown to be different incarnations of the same phenomenon, so that using polarization to describe them is most consistent as it is the only real, measurable and uniquely defined quantity of the three. Dispersion is discussed as a form of polarization within the Feynman description. Model calculations are described.},
author = {Clark, Timothy},
doi = {10.1007/s00894-017-3473-y},
faupublication = {yes},
journal = {Journal of Molecular Modeling},
keywords = {Bonding theory;Hydrogen bonds;Halogen bonds;Polarization;Charge transfer},
peerreviewed = {Yes},
title = {{Polarization}, donor-acceptor interactions, and covalent contributions in weak interactions: a clarification},
volume = {23},
year = {2017}
}
@article{faucris.212762996,
abstract = {The strong collinear polarizability of the A--H bond in A--H$·$$·$$·$B hydrogen bonds is shown to lead to an enhanced \textgreeks-hole on the donor hydrogen atom and hence to stronger hydrogen bonding. This effect helps to explain the directionality of hydrogen bonds, the well known cooperative effect in hydrogen bonding, and the occurrence of blue-shifting. The latter results when significant additional electron density is shifted into the A--H bonding region by the polarization effect. The shift in the A--H stretching frequency is shown to depend essentially linearly on the calculated atomic charge on the donor hydrogen for all donors in which A belongs to the same row of the periodic table. A further result of the polarization effect, which is also expected for other \textgreeks-hole bonds, is that the strength of the non-covalent interaction depends strongly on external electric fields.},
author = {Hennemann, Matthias and Murray, Jane S. and Politzer, Peter and Riley, Kevin E. and Clark, Timothy},
doi = {10.1007/s00894-011-1263-5},
faupublication = {yes},
journal = {Journal of Molecular Modeling},
note = {EAM Import::2019-03-08},
pages = {2461-2469},
peerreviewed = {Yes},
title = {{Polarization}-induced \textgreeks-holes and hydrogen bonding},
volume = {18},
year = {2012}
}
@article{faucris.121249964,
abstract = {The conductivity of bulk polysilanes is reported to occur via the migration of holes. Since there is considerable sigma delocalization along the backbone of polysilanes these materials can be considered as a one-dimensional molecular wire, the backbone being the wire and the alkyl side groups acting as the insulator. Here, quantum mechanical calculations on the polysilane model compound Si-17(CH3)(36) aimed at elucidation of the electronic properties related to electrical conductance are presented.},
author = {Clark, Timothy and et al.},
author_hint = {GROPPEL M, ROTH W, CLARK T},
faupublication = {yes},
journal = {Advanced Materials},
pages = {927-&},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{POLARON} {MIGRATION} {IN} {DOPED} {POLYSILANES} - {AM1} {CALCULATIONS} {ON} {THE} {RADICAL}-{CATION} {SI}-17({CH3})(36)(+)},
volume = {7},
year = {1995}
}
@article{faucris.208732653,
abstract = {We report on a series of electron donor-acceptor conjugates incorporating a Zn-II-porphyrin-based electron donor and a variety of non-conjugated rigid linkers connecting to push-pull chromophores as electron acceptors. The electron acceptors comprize multicyanobutadienes or extended tetracyanoquinodimethane analogues with first reduction potentials ranging from -1.67 to -0.23V vs. Fc(+)/Fc in CH2Cl2, which are accessible through a final-step cycloaddition-retroelectrocyclization (CA-RE) reaction. Characterization of the conjugates includes electrochemistry, spectroelectrochemistry, DFT calculations, and photophysical measurements in a range of solvents. The collected data allows for the construction of multiple Marcus curves that consider electron-acceptor strength, linker length, and solvent, with data points extending well into the inverted region. The enhancement of electron-vibration couplings, resulting from the rigid spacers and, in particular, multicyano-groups in the conformationally highly fixed push-pull acceptor chromophores affects the charge-recombination kinetics in the inverted region drastically.},
author = {Reekie, Tristan A. and Sekita, Michael and Urner, Lorenz M. and Bauroth, Stefan and Ruhlmann, Laurent and Gisselbrecht, Jean-Paul and Boudon, Corinne and Trapp, Nils and Clark, Timothy and Guldi, Dirk Michael and Diederich, Francois},
doi = {10.1002/chem.201700043},
faupublication = {yes},
journal = {Chemistry - A European Journal},
keywords = {donor-acceptor systems;electron transfer;Marcus theory;photochemistry;porphyrinoids},
pages = {6357-6369},
peerreviewed = {Yes},
title = {{Porphyrin} {Donor} and {Tunable} {Push}-{Pull} {Acceptor} {ConjugatesExperimental} {Investigation} of {Marcus} {Theory}},
volume = {23},
year = {2017}
}
@article{faucris.124080044,
abstract = {A series of donor-acceptor arrays (exTTF-oPPE-C ) containing π-conjugated oligo(phenyleneethynylene) wires (oPPE) of different length between π-extended tetrathiafulvalene (exTTF) as electron donor and fullerene (C ) as electron acceptor has been prepared by following a convergent synthesis. The key reaction in these approaches is the bromo-iodo selectivity of the Hagihara-Sonogashira reaction and the deprotecting of acetylenes with different silyl groups to afford the corresponding donor-acceptor conjugates in moderate yields. The electronic interactions between the three electroactive species were determined by using UV-visible spectroscopy and cyclic voltammetry. Our studies clearly confirm that, although the C units are connected to the exTTF donor through π-conjugated oPPE frameworks, no significant electronic interactions are observed in the ground state. Theoretical calculations predict how a simple exchange from C=C double bonds (i.e., oligo(p-phenylenevinylene) to C≡C triple bonds (i.e., oPPE) in the electron donor-acceptor conjugates considerably alters long-range electron transfer. Photoexcitation of exTTF-oPPE-C leads to the following features: a transient photoproduct with maxima at 660 and 1000 nm, which are unambiguously attributed to the photolytically generated radical-ion-pair state, [exTTF -oPPE- C ]. Both charge-separation and charge-recombination processes give rise to a molecular-wire behaviour of the oPPE moiety with an attenuation factor (β) of (0.2 ±0.05) Å . © 2008 Wiley-VCH Verlag GmbH & Co. KGaA.},
author = {Wielopolski, Mateusz and Atienza, Carmen and Clark, Timothy and Guldi, Dirk Michael and Martín, Nazario},
doi = {10.1002/chem.200800159},
faupublication = {yes},
journal = {Chemistry - A European Journal},
pages = {6379-6390},
peerreviewed = {Yes},
title = {p-{Phenyleneethynylene} molecular wires: influence of structure on photoinduced electron-transfer properties.},
volume = {14},
year = {2008}
}
@article{faucris.107552984,
abstract = {A new series of donor-bridge-acceptor (D-B-A) compounds consisting of π-conjugated oligofluorene (oFL) bridges between a ferrocene (Fc) electron-donor and a fullerene (C) electron-acceptor have been synthesized. In addition to varying the length of the bridge (i.e., mono- and bi-fluorene derivatives), four different ways of linking ferrocene to the bridge have been examined. The Fc moiety is linked to oFL: 1) directly without any spacer, 2) by an ethynyl linkage, 3) by a vinylene linkage, and 4) by a p-phenylene unit. The electronic interactions between the electroactive species have been characterized by cyclic voltammetry, absorption, fluorescence, and transient absorption spectroscopy in combination with quantum chemical calculations. The calculations reveal exceptionally close energy-matching between the Fc and the oFL units, which results in strong electronic-coupling. Hence, intramolecular charge-transfer may easily occur upon exciting either the oFLs or Fcs. Photoexcitation of Fc-oFL-C conjugates results in transient radical-ion-pair states. The mode of linkage of the Fc and FL bridge has a profound effect on the photophysical properties. Whereas intramolecular charge-separation is found to occur rather independently of the distance, the linker between Fc and oFL acts (at least in oFL) as a bottleneck and significantly impacts the intramolecular charge-separation rates, resulting in beta values between β 0.08 and 0.19 Å. In contrast, charge recombination depends strongly on the electron-donor-acceptor distance, but not at all on the linker. A value of β (0.35±0.01 Å) was found for all the systems studied. Oligofluorenes prove, therefore, to be excellent bridges for probing how small structural variations affect charge transport in D-B-A systems. Finely tuned transfer: Chemical modification of the oligo-fluorene linkers between Fc and C units enables fine-tuning of photoinduced charge-transfer processes in new donor-bridge-acceptor conjugates (see illustration). Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.},
author = {Schubert, Christina and Wielopolski, Mateusz and Mewes, Lars-Hendrik and De Miguel Rojas, Gustavo and Van Der Pol, Cornelia and Moss, Kathryn C. and Bryce, Martin and Moser, Jacques E. and Guldi, Dirk Michael and Clark, Timothy},
doi = {10.1002/chem.201204055},
faupublication = {yes},
journal = {Chemistry - A European Journal},
pages = {7575-7586},
peerreviewed = {Yes},
title = {{Precise} control of intramolecular charge-transport: {The} interplay of distance and conformational effects},
volume = {19},
year = {2013}
}
@article{faucris.121990924,
abstract = {Thermodynamically rigorous free energy methods in principle allow the exact computation of binding free energies in biological systems. Here, we use thermodynamic integration together with molecular dynamics simulations of a DNA-protein complex to compute relative binding free energies of a series of mutants of a protein-binding DNA operator sequence. A guanine-cytosine basepair that interacts strongly with the DNA-binding protein is mutated into adenine-thymine, cytosine-guanine, and thymine-adenine. It is shown that basepair mutations can be performed using a conservative protocol that gives error estimates of 10\% of the change in free energy of binding. Despite the high CPU-time requirements, this work opens the exciting opportunity of being able to perform basepair scans to investigate protein-DNA binding specificity in great detail computationally.},
author = {Beierlein, Frank and Kneale, G. Geoff and Clark, Timothy},
doi = {10.1016/j.bpj.2011.07.003},
faupublication = {yes},
journal = {Biophysical Journal},
pages = {1130--1138},
peerreviewed = {Yes},
title = {{Predicting} the {Effects} of {Basepair} {Mutations} in {DNA}-{Protein} {Complexes} by {Thermodynamic} {Integration}},
volume = {101},
year = {2011}
}
@article{faucris.116956884,
abstract = {Feed-forward artificial neural nets have been used to recognize H-bond donor and acceptor sites on drug-like molecules based on local properties (electron density, molecular electrostatic potential and local ionization energy, electron affinity, and polarizability) calculated at grid points around the molecule. Interaction energies for training were obtained from B97-D and omega 1397X-D/aug-cc-pVDZ: density-functional theory calculations on a series of model central molecules and H-bond acceptor and donor probes constrained to the grid points used for training. The resulting models provide maps of both classical and unusual H- and halogen-bonding sites. Note that these reactions result even though only classical H-bond donors and acceptors were used as probes around the central molecules. Some examples demonstrate the ability of the models to take the electronics of the central molecule into consideration and to provide semiquantitative estimates of interaction energies at low computational cost.},
author = {El Kerdawy, Ahmed and Wick, Christian and Hennemann, Matthias and Clark, Timothy},
doi = {10.1021/ci300095x},
faupublication = {yes},
journal = {Journal of Chemical Information and Modeling},
pages = {1061-1071},
peerreviewed = {Yes},
title = {{Predicting} the {Sites} and {Energies} of {Noncovalent} {Intermolecular} {Interactions} {Using} {Local} {Properties}},
volume = {52},
year = {2012}
}
@article{faucris.122474704,
abstract = {A back-propagation artificial neural net has been trained to estimate logP values of a large range of organic molecules from the results of AM1 and PM3 semiempirical MO calculations. The input descriptors include molecular properties such as electrostatic potentials, total dipole moments, mean polarizabilities, surfaces, volumes and charges derived from semiempirical calculated gas phase geometries. These properties can be related to the molecule's solubility in hydrophilic or lipophilic media. The input descriptors were selected with the help of a multiple linear regression analysis. The resulting net estimates the logP values of 105 organic compounds with a standard deviation of 0.53 units from the experimental logP values for AM1 and 0.67 units in the case of PM3.},
author = {Breindl, Andreas and Beck, Bernd and Clark, Timothy and Glen, Robert},
doi = {10.1007/s008940050027},
faupublication = {yes},
journal = {Journal of Molecular Modeling},
keywords = {partition coefficient;logP;AM1;PM3;QSAR;neural net},
month = {Jan},
pages = {142-155},
peerreviewed = {Yes},
title = {{Prediction} of the n-octanol/water partition coefficient, {logP}, using a combination of semiempirical {MO}-calculations and a neural network},
volume = {3},
year = {1997}
}
@article{faucris.250578478,
abstract = {Three linear dimers with two redox-active planarized triphenylamines were synthesized and their structures verified by X-ray crystallography. Their radical cations, which exhibit electron self-exchange between the two redox centers, are of great interest. This process was thoroughly investigated by means of electron paramagnetic resonance spectroscopy, absorption spectroscopy, and (time-dependent) density functional theory calculations. A comparison of the key parameters of electron transfer with non-planarized nitrogen-centered building blocks emphasizes the impact of using redox centers with low internal reorganization energies. However, the distance-dependence attenuation factor of the super-exchange mechanisms remains similar.},
author = {Krug, Marcel and Fröhlich, Nina and Fehn, Dominik and Vogel, Alexander and Rominger, Frank and Meyer, Karsten and Clark, Timothy and Kivala, Milan and Guldi, Dirk Michael},
doi = {10.1002/anie.202014567},
faupublication = {yes},
journal = {Angewandte Chemie International Edition},
note = {CRIS-Team WoS Importer:2021-02-26},
peerreviewed = {Yes},
title = {{Pre}-{Planarized} {Triphenylamine}-{Based} {Linear} {Mixed}-{Valence} {Charge}-{Transfer} {Systems}},
year = {2021}
}
@article{faucris.108387004,
abstract = {The direct metalation of tetraphenylporphyrin with bare metal atoms (Co and Zn) was studied with X-ray photoelectron spectroscopy, scanning tunneling microscopy, and temperature-programmed reaction measurements on ordered monolayer films of the molecules adsorbed on a Ag(111) surface. The mechanism of this novel type of surface reaction was investigated using density functional theory (DFT) calculations for the related gas-phase reactions of the unsubstituted porphyrin with the metals Fe, Co, Ni, Cu, and Zn. The reaction starts with the formation of an initial complex, in which the metal atom is coordinated by the intact unreduced porphyrin. This complex resembles the sitting-atop complex proposed for porphyrin metalation with metal ions in solution. In two subsequent steps, the pyrrolic hydrogen atoms are transferred to the metal atom, forming H , which is eventually released. The activation barriers of the H-transfer steps vary for the different metal atoms. DFT calculations suggest that metalations with Fe, Co, and Ni show two-state reactivity, while those with Cu and Zn proceed on a single potential energy surface. For metalation with Zn, we calculated a barrier of the first hydrogen transfer step of 32.6 kcal mol , in good agreement with the overall experimental activation energy of 31 kcal mol . © 2007 American Chemical Society.},
author = {Shubina, Tatyana and Marbach, Hubertus and Flechtner, Ken and Kretschmann, Andreas and Jux, Norbert and Buchner, Florian and Steinrück, Hans-Peter and Clark, Timothy and Gottfried, Michael},
doi = {10.1021/ja072360t},
faupublication = {yes},
journal = {Journal of the American Chemical Society},
pages = {9476-9483},
peerreviewed = {Yes},
title = {{Principle} and mechanism of direct porphyrin metalation: {Joint} experimental and theoretical investigation},
volume = {129},
year = {2007}
}
@article{faucris.121270424,
abstract = {Rigid electron donor-acceptor conjugates (1-3) that combine π-extended benzodifurans as electron donors and C molecules as electron acceptors with different linkers have been synthesized and investigated with respect to intramolecular charge-transfer events. Electrochemistry, fluorescence, and transient absorption measurements revealed tunable and structure-dependent charge-transfer processes in the ground and excited states. Our experimental findings are underpinned by density-functional theory calculations. Dumbbell arrays: A benzodifuran (BDF) donor is for the first time fused to two C molecules by different linkers to form triads 1-3 (see figure). Their redox behavior, absorption, fluorescence emission, and photoinduced intramolecular charge-transfer events have been investigated experimentally and theoretically. The lifetime of the resulting charge-separated state varies distinctly with the polarity of the solvents and the distance between the BDF and C units. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.},
author = {Li, Hui and Schubert, Christina and Dral, Pavlo and Costa, Ruben Dario and La Rosa, Andrea and Thüring, Jürg and Liu, Shi-Xia and Yi, Chenyi and Filippone, Salvatore and Martín, Nazario and Decurtins, Silvio and Clark, Timothy and Guldi, Dirk Michael},
doi = {10.1002/cphc.201300378},
faupublication = {yes},
journal = {ChemPhysChem},
pages = {2910-2919},
peerreviewed = {Yes},
title = {{Probing} charge transfer in benzodifuran-{C60} dumbbell-type electron donor-acceptor conjugates: {Ground}- and excited-state assays},
volume = {14},
year = {2013}
}
@article{faucris.121223784,
author = {Clark, Timothy and Winget, Paul and Horn, Anselm and Martin, Bodo and et al.},
author_hint = {Clark T, Winget P, Selcuki C, Horn A, Martin B},
faupublication = {yes},
journal = {ACS National Meeting Book of Abstracts},
pages = {U500-U500},
peerreviewed = {unknown},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{Progress} towards a "next generation" {NDDO}-based semiempirical technique.},
volume = {224},
year = {2002}
}
@article{faucris.230328377,
abstract = {Charge transport in two zinc metal-organic frameworks (MOFs) has been investigated using periodic semiempirical molecular orbital calculations with the AM1∗ Hamiltonian. Restricted Hartree-Fock calculations underestimate the band gap using Koopmans theorem (ca. 2 eV compared to the experimental value of 2.8 eV). However, it almost doubles when the constraint on the wave function to remain spin-restricted is removed and the energies of the UHF Natural Orbitals are used. Charge-transport simulations using propagation of the electron- or hole-density in imaginary time allow charge-transport paths and mechanisms to be determined. The calculated relative mobilities in the directions of the three crystal axes agree with experimental expectations, but the absolute values are not reliable using the current technique. Hole-mobility along the crystal c-axis (along the metal stacks) is found to be 13 times higher in the zinc MOF with anthracene linker (Zn-ANMOF-74) than in the other directions, whereas the factor is far smaller (1.7) for electron mobility. Directional preferences are far less distinct in the equivalent structure with phenyl linkers (Zn-MOF-74). The imaginary-time simulation technique does not give quantitative mobilities. The simulations reveal a change in mechanism between the different directions: Coherent polaron migration is observed along the stacks but tunneling hops between them.},
author = {Kriebel, Maximilian and Hennemann, Matthias and Beierlein, Frank and Medina, Dana D. and Bein, Thomas and Clark, Timothy},
doi = {10.1021/acs.jcim.9b00461},
faupublication = {yes},
journal = {Journal of Chemical Information and Modeling},
note = {CRIS-Team Scopus Importer:2019-12-10},
peerreviewed = {Yes},
title = {{Propagation} of {Holes} and {Electrons} in {Metal}-{Organic} {Frameworks}},
year = {2019}
}
@article{faucris.121254144,
author = {Clark, Timothy and Schleyer, Paul and et al.},
author_hint = {CLARK T, SCHLEYER PV, POPLE JA},
doi = {10.1039/c39780000137},
faupublication = {yes},
journal = {Journal of the Chemical Society - Series Chemical Communications},
month = {Jan},
pages = {137-138},
peerreviewed = {unknown},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{PROPOSAL} {FOR} {MECHANISM} {OF} {INVERSION} {OF} {ALKYL}-{LITHIUMS}},
year = {1978}
}
@article{faucris.115066864,
abstract = {The performance of nanocomposites for improved resistance to electrical discharges has resulted in increased interest in nano-loaded thermosetting resins. First assessments of the performance of new systems can be obtained by a plate-electrode construction according to IEC(b). Epoxy resins loaded with different amounts of spherical alumina particles were tested following this procedure and parameters such as erosion depth and standardized volume analyzed. Transmission electron microscopy (TEM) and a three-dimensional (3D) reconstruction using electron tomography were used to determine the particle size distribution. TEM analysis after preparation of the eroded samples indicates the advantages and disadvantages of using alumina nanoparticles to improve the erosion resistance and showed a novel effect of the surface-grafted polysiloxanes. A comparison with conventional nano-silica-loaded resins reveals that the lower sintering tendency of Al2O3 is important.},
author = {Meichsner, Christian and Clark, Timothy and Groeppel, Peter and Winter, Benjamin and Butz, Benjamin and Spiecker, Erdmann},
doi = {10.1109/TDEI.2015.004939},
faupublication = {yes},
journal = {IEEE Transactions on Dielectrics and Electrical Insulation},
keywords = {Alumina;epoxy resin;erosion resistance;nanoparticles;transmission electron microscopy;electron tomography},
pages = {2944-2950},
peerreviewed = {Yes},
title = {{Protective} {Layer} of {Al2O3} {Nanocomposites} and {Surface} {Composition} after {Electrical} {Stress}},
volume = {22},
year = {2015}
}
@article{faucris.122475364,
author = {Clark, Timothy and et al.},
author_hint = {CLARK T, SYMONS MCR},
doi = {10.1039/C39860000096},
faupublication = {yes},
journal = {Journal of the Chemical Society - Series Chemical Communications},
month = {Jan},
pages = {96-98},
peerreviewed = {unknown},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{PROTONATED} {BETA}-{HALOGENOETHYL} {RADICALS}},
year = {1986}
}
@article{faucris.119335524,
author = {Lanig, Harald and Clark, Timothy},
faupublication = {yes},
journal = {Journal of Molecular Graphics & Modelling},
pages = {272-272},
peerreviewed = {Yes},
title = {{QM}/{MM} calculations on the dimerization of vancomycin},
volume = {16},
year = {1998}
}
@article{faucris.123435444,
author = {Clark, Timothy},
faupublication = {yes},
journal = {ACS National Meeting Book of Abstracts},
pages = {U415-U415},
peerreviewed = {unknown},
title = {{QM}/{MM} studies on bovine lens leucyl aminopeptidase.},
volume = {222},
year = {2001}
}
@article{faucris.116959084,
abstract = {QSPR models for logP and vapor pressures of organic compounds based on neural net interpretation of descriptors derived from quantum mechanical (semiempirical MO; AM1) calculations are presented. The models are cross-validated by dividing the compound set into several equal portions and training several individual multilayer feedforward neural nets (trained by the back-propagation of errors algorithm), each with a different portion as test set. The results of these nets are combined to give a mean predicted property value and a standard deviation. The performance of two models, for logP and the vapor pressure at room temperature, is analyzed, and the reliability of the predictions is tested.},
author = {Beck, Bernd and Breindl, Andreas and Clark, Timothy},
doi = {10.1021/ci990131n},
faupublication = {yes},
journal = {Journal of Chemical Information and Computer Sciences},
pages = {1046-1051},
peerreviewed = {Yes},
title = {{QM}/{NN} {QSPR} models with error estimation: {Vapor} pressure and {LogP}},
volume = {40},
year = {2000}
}
@misc{faucris.122331044,
author = {Clark, Timothy and Gedeck, Peter and Lanig, Harald and Beck, Bernd},
faupublication = {yes},
peerreviewed = {automatic},
title = {{QM} (semiempirical {MO}) {MM} binding studies.},
year = {1997}
}
@article{faucris.124185204,
abstract = {The use of descriptors based on local properties calculated at the molecular surface for QSPR models is discussed. It is suggested that descriptors should be related to the physical theory of intermolecular interactions and the relationship between established surface-based descriptors and the fundamental types of intermolecular interaction is discussed. Descriptors based on local properties that do not encode the chemical constitution of the molecule directly are likely to provide less local QSPR models and favor scaffold hopping. The major disadvantage for surface-based descriptors is that they are difficult to interpret in the sense of relating predictions to the chemical composition of the molecule. This disadvantage must be alleviated by suitable model-interrogation techniques. (C) 2004 Elsevier Inc. All rights reserved.},
author = {Clark, Timothy},
doi = {10.1016/j.jmgm.2004.03.012},
faupublication = {yes},
journal = {Journal of Molecular Graphics & Modelling},
keywords = {QSPR;QSAR;descriptors},
pages = {519-525},
peerreviewed = {Yes},
title = {{QSAR} and {QSPR} based solely on surface properties?},
volume = {22},
year = {2004}
}
@article{faucris.122331484,
abstract = {A novel way of describing molecules in terms of their surfaces and local properties at the surfaces is described. The use of these surfaces and properties to explain chemical reactivity and model simple molecular properties has already been demonstrated. This study reports an examination of the use of these descriptions of molecules to model a simple chemical interaction (complex formation) and a diverse set of mutagens. Both of these systems have been modelled successfully and the results are discussed.},
author = {Livingstone, D. J. and Clark, Timothy and Ford, M. G. and Hudson, B. D. and Whitley, D. C.},
doi = {10.1080/10629360802085041},
faupublication = {yes},
journal = {Sar and Qsar in Environmental Research},
keywords = {spherical harmonic expansions;surface properties;charge-transfer complexes;mutagenicity;chemical reactivity;3-D QSAR},
month = {Jan},
pages = {285-302},
peerreviewed = {Yes},
title = {{QSAR} studies using the parashift system},
volume = {19},
year = {2008}
}
@inproceedings{faucris.109404944,
abstract = {Semiempirical molecular orbital calculations are fast and accurate enough to be used for complete databases of several hundred thousand compounds. They provide detailed information about the electrostatic and polarizability properties of the molecules that in turn allow us to construct reliable models for physical properties and biological activity because these rely on being able to describe the intermolecular interactions well. In this paper, techniques are described in which the electrostatic and polarizability data calculated from semiempirical MO-theory are used to construct an index of drug-fitness and for quantitative structure-activity relationship techniques that are suitable for high quality quantitative high throughput virtual screening on large databases.},
address = {Barcelona},
author = {Clark, Timothy},
editor = {H.D. Höltje and W. Sippl},
faupublication = {yes},
month = {Jan},
pages = {29-40},
peerreviewed = {unknown},
publisher = {Prous Science},
title = {{Quantum} cheminformatics: {An} oxymoron? {Part} {II}},
year = {2001}
}
@article{faucris.121229944,
abstract = {We have investigated the role of linker molecules in quantum-dot-sensitized solar cells (QDSSCs) using density-functional theory (DFT) and experiments. Linkers not only govern the number of attached QDs but also influence charge separation, recombination, and transport. Understanding their behavior is therefore not straightforward. DFT calculations show that mercaptopropionic acid (MPA) and cysteine (Cys) exhibit characteristic binding configurations on TiO2 surfaces. This information is used to optimize the cell assembly process, yielding Cys-based cells that significantly outperform MPA cells, and reach power conversion efficiencies (PCE) as high as 2.7% under AM 1.5 illumination. Importantly, the structural information from theory also helps understand the cause for this improved performance.},
author = {Margraf, Johannes and Ruland, Andres and Sgobba, Vito and Guldi, Dirk Michael and Clark, Timothy},
doi = {10.1021/la3047609},
faupublication = {yes},
journal = {Langmuir},
pages = {2434-2438},
peerreviewed = {Yes},
title = {{Quantum}-dot-sensitized solar cells: {Understanding} linker molecules through theory and experiment},
volume = {29},
year = {2013}
}
@article{faucris.106808944,
author = {Hennemann, Matthias and Clark, Timothy},
faupublication = {yes},
journal = {ACS National Meeting Book of Abstracts},
pages = {U683-U683},
peerreviewed = {unknown},
title = {{Quantum} mechanical estimation of {pK}(hb)},
volume = {217},
year = {1999}
}
@article{faucris.109407804,
abstract = {A combined quantum mechanical/molecular mechanical (QM/MM) docking approach for the investigation of protein-inhibitor complexes is presented. Starting points for QM/MM optimizations are generated with AutoDock. The subsequent semiempirical AM1 QM/MM optimization of the complex obtained by the docking procedure gives a more detailed description of the binding mode and the electronic properties of the ligand. As we use a flexible protein environment in the QM/MM optimizations, we are able to simulate limited structural changes of the enzyme upon binding a ligand, even within a simple geometry optimization. The method was validated using a set of structurally known protein-inhibitor complexes, whose crystallographic data were taken from the Protein Data Bank. In addition to protein structures taken directly from complexes with the inhibitors, structures of uncomplexed HIV-1-protease and thrombin were also used successfully for QM/MM docking experiments. By comparing the resulting structures with those obtained using protein structures from protein-inhibitor complexes, we find that the method is able to simulate the effect of the induced fit when a simple optimization is adequate to reproduce the protein movement. Describing the ligand quantum mechanically gives a detailed view of its electronic properties, for example its polarization within the active site of the enzyme. This study suggests strongly that a QM/MM molecular dynamics approach will be able to simulate the induced fit in general cases.},
author = {Beierlein, Frank and Lanig, Harald and Schürer, Gudrun and Horn, Anselm and Clark, Timothy},
doi = {10.1080/0026897031000092940},
faupublication = {yes},
journal = {Molecular Physics},
pages = {2469-2480},
peerreviewed = {Yes},
title = {{Quantum} mechanical/molecular mechanical ({QM}/{MM}) docking: an evaluation for known test systems},
volume = {101},
year = {2003}
}
@misc{faucris.122478664,
author = {Horn, Anselm and Beierlein, Frank and Lanig, Harald and Schürer, Gudrun and Clark, Timothy},
faupublication = {yes},
peerreviewed = {automatic},
title = {{Quantum} mechanical/molecular mechanical ({QM}/{MM}) docking: {A} new protocol and its evaluation for known test systems.},
year = {2004}
}
@article{faucris.122339184,
abstract = {We have used a set of four local properties based on semiempirical molecular orbital calculations (electron density (p), hydrogen bond donor field (HDF), hydrogen bond acceptor field (HAF), and molecular lipophilicity potential (MLP)) for 3D-QSAR studies to overcome the limitations of the current force field-based molecular interaction fields (MIFs). These properties can be calculated rapidly and are thus amenable to high-throughput industrial applications. Their statistical performance was compared with that of conventional 3D-QSAR approaches using nine data sets (angiotensin converting enzyme inhibitors (ACE), acetylcholinesterase inhibitors (AchE), benzodiazepine receptor ligands (BZR), cyclooxygenase-2 inhibitors (COX2), dihydrofolate reductase inhibitors (DHFR), glycogen phosphorylase b inhibitors (GPB), thermolysin inhibitors (THER), thrombin inhibitors (THR), and serine protease factor Xa inhibitors (fXa)). The 3D-QSAR models generated were tested thoroughly for robustness and predictive ability. The average performance of the quantum mechanical molecular interaction field (QM-MIF) models for the nine data sets is better than that of the conventional force field-based MIFs. In the individual data sets, the QM-MIF models always perform better than, or as well as, the conventional approaches. It is particularly encouraging that the relative performance of the QM-MIF models improves in the external validation. In addition, the models generated showed statistical stability with respect to model building procedure variations such as grid spacing size and grid orientation. QM-MIF contour maps reproduce the features important for ligand binding for the example data set (factor Xa inhibitors), demonstrating the intuitive chemical interpretability of QM-MIFs.},
author = {El Kerdawy, Ahmed and Güssregen, Stefan and Matter, Hans and Hennemann, Matthias and Clark, Timothy},
doi = {10.1021/ci400181b},
faupublication = {yes},
journal = {Journal of Chemical Information and Modeling},
pages = {1486-1502},
peerreviewed = {Yes},
title = {{Quantum} {Mechanics}-{Based} {Properties} for {3D}-{QSAR}},
volume = {53},
year = {2013}
}
@book{faucris.123509364,
author = {Clark, Timothy},
doi = {10.1002/9783527618279.ch35},
faupublication = {yes},
isbn = {9783527306800},
pages = {947-975},
peerreviewed = {unknown},
publisher = {Wiley Blackwell},
title = {{Quantum} {Mechanics}},
volume = {3},
year = {2008}
}
@article{faucris.119335964,
abstract = {Some of the essential features, strengths and weaknesses of semiempirical MO theory are discussed and suggestions made as to the role of this type of theory in the future and likely development directions. The impact of theories with an empirical component on computational chemistry is discussed. (C) 2000 Elsevier Science B.V. AU rights reserved.},
author = {Clark, Timothy},
doi = {10.1016/S0166-1280(00)00581-9},
faupublication = {yes},
journal = {Journal of Molecular Structure-Theochem},
keywords = {semiempirical MO-theory;linear scaling;QM/MM;polarizability;NDDO;MNDO;AM1;PM3},
pages = {1-10},
peerreviewed = {Yes},
title = {{Quo} {Vadis} semiempirical {MO}-theory?},
volume = {530},
year = {2000}
}
@article{faucris.109408904,
author = {Clark, Timothy},
doi = {10.1039/C39860001774},
faupublication = {yes},
journal = {Journal of the Chemical Society - Series Chemical Communications},
pages = {1774-1776},
peerreviewed = {unknown},
title = {{RADICAL}-{ADDITION} {TO} {ALKENE} {METAL} {CATION} {COMPLEXES}},
year = {1986}
}
@article{faucris.116962384,
author = {Clark, Timothy and Schleyer, Paul and et al.},
author_hint = {WILHELM D, CLARK T, SCHLEYER PV},
doi = {10.1039/C39830000211},
faupublication = {yes},
journal = {Journal of the Chemical Society - Series Chemical Communications},
month = {Jan},
pages = {211-213},
peerreviewed = {unknown},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{RADICAL}-{ANION} {REACTIONS} {IN} {NORMAL}-{BUTYL}-{LITHIUM}-{POTASSIUM} {TERT}-{PENTYL} {OXIDE} {MIXTURES}},
year = {1983}
}
@article{faucris.208732913,
abstract = {The radical arylation of anilines and pyrroles can be achieved under transition-metal- and catalyst-free conditions by using aryldiazotates in strongly alkaline aqueous solutions. The aryldiazotates act as protected diazonium ions, which do not undergo azo coupling with electron-rich aromatic substrates, but can still serve as an aryl radical source at slightly elevated temperatures. Based on an improved preparation of aryldiazotates in aqueous solution, homolytic aromatic substitutions of anilines and pyrroles were conducted with good overall yields and high regioselectivity. Moreover, DFT calculations provided further mechanistic insights.},
author = {Hofmann, Josefa and Gans, Eva and Clark, Timothy and Heinrich, Markus},
doi = {10.1002/chem.201701429},
faupublication = {yes},
journal = {Chemistry - A European Journal},
pages = {9647-9656},
peerreviewed = {Yes},
title = {{Radical} {Arylation} of {Anilines} and {Pyrroles} via {Aryldiazotates}},
volume = {23},
year = {2017}
}
@article{faucris.116964804,
author = {Clark, Timothy and Schleyer, Paul and et al.},
author_hint = {WILHELM D, CLARK T, SCHLEYER PV, COURTNEIDGE JL, DAVIES AG},
doi = {10.1021/ja00314a020},
faupublication = {yes},
journal = {Journal of the American Chemical Society},
month = {Jan},
pages = {361-367},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{REACTIONS} {OF} {POLYANIONS} {DERIVED} {FROM} {ALKYLBENZENES}},
volume = {106},
year = {1984}
}
@article{faucris.116967444,
abstract = {Potentially synthetically useful reactions of the dilithium salts of the title dianions have been investigated, Electrophilic quenching with a variety of reagents usually leads to the expected products in good yield. Quenching the diphenylacetone dianion with 1 equiv of trimethylchlorosilane, however, gives a good yield of 1,3-diphenylallene obtained by formal elimination of a trimethylsiloxy anion from an intermediate monoquenched monoanion salt. NMR studies, however, do not reveal the intermediacy of the 1,3-diphenyl-2-(trimethylsiloxy)allyl anion but rather suggest that the initial reaction site is at carbon, rather than oxygen, Oxidation of the dianions leads either to ring closure or dimerization for the tribenzylidenemethane dianion and to dimerization for the diphenylacetone dianion. The dimerization reactions are stereospecific, both with respect to the two new stereocenters produced and for the double bonds of the bis-silyl enol ether products if the dimeric bis-enolate dianion products are quenched with trimethylchlorosilane.},
author = {Mauser, Harald and Clark, Timothy and et al.},
author_hint = {Witt O, Mauser H, Friedl T, Wilhelm D, Clark T},
doi = {10.1021/jo971113c},
faupublication = {yes},
journal = {Journal of Organic Chemistry},
pages = {959-967},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{Reactions} of the lithium salts of the tribenzylidenemethane dianion, diphenylacetone dianion, and related compounds},
volume = {63},
year = {1998}
}
@book{faucris.116967884,
abstract = {The mechanisms of direct porphyrin metalation was investigated using density functional theory (DFT) calculations for the gas-phase reactions of the unsubstituted porphyrin with the metals Fe, Co, Ni, Cu and Zn. The related reaction of tetraphenylporphyrin with bare metal atoms (Co and Zn) was studied with X-ray photoelectron spectroscopy, scanning tunneling microscopy, and temperature-programmed reaction measurements on ordered monolayer films of the molecules adsorbed on a Ag(111) surface. DFT calculations suggest that metalations with Fe, Co and Ni show two-state reactivity, while those with Cu and Zn proceed on a single potential energy surface. For metalation with Zn, we calculated a barrier of the first hydrogen transfer step of 32.6 kcal mol(-1), in a good agreement with the overall experimental activation energy of 31 kcal mol(-1).},
author = {Shubina, Tatyana and Clark, Timothy},
doi = {10.1007/978-3-540-69182-2{\_}16},
faupublication = {yes},
month = {Jan},
pages = {201-212},
peerreviewed = {unknown},
title = {{Redox} {Catalysis} and {Reactivity} of {Metalloporphyrines}},
year = {2009}
}
@article{faucris.234648936,
abstract = {Convergent and convenient regioselective synthesis of novel thiazolo[2,3-a]pyrimidine derivatives was accomplished using the one-pot reaction of 6-ethylthiouracil, bromoacetic acid, anhydrous sodium acetate, acetic anhydride, acetic acid and suitable aldehyde. X-ray crystallographic study reveals the presence of the Z configuration of only one regioisomer confirmed by computational studies as being the most likely isomer present.},
author = {Fares, Mohamed and McCosker, Patrick M. and Alsherbiny, Muhammad A. and Willis, Anthony C. and Clark, Timothy and Neyts, Johan and Jochmans, Dirk and Keller, Paul A.},
doi = {10.1039/d0ra00257g},
faupublication = {yes},
journal = {RSC Advances},
note = {CRIS-Team Scopus Importer:2020-02-21},
pages = {5191-5195},
peerreviewed = {Yes},
title = {{Regioselective} convergent synthesis of 2-arylidene thiazolo[3,2-: {A}] pyrimidines as potential anti-chikungunya agents},
volume = {10},
year = {2020}
}
@article{faucris.109424744,
author = {Clark, Timothy and Schleyer, Paul and et al.},
author_hint = {NEUGEBAUER W, CLARK T, SCHLEYER PV},
doi = {10.1002/cber.19831161003},
faupublication = {yes},
journal = {Chemische Berichte},
month = {Jan},
pages = {3283-3292},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{REGIOSELECTIVE} {METALATION} {OF} {AROMATIC}-{COMPOUNDS} .2. {SECOND} {METALATION} {OF} 1-{LITHIONAPHTHALENE} {AND} 9-{LITHIOANTHRACENE}},
volume = {116},
year = {1983}
}
@article{faucris.114631044,
abstract = {Linear regression formulae are given for converting H-1 and C-13 magnetic shielding constants calculated at common ab initio and density functional theory levels of calculation into chemical shifts relative to tetramethylsilane. Accuracies of roughly +/- 2.2 ppm (C-13) and +/- 0.15 ppm (H-1) or better are found for the training set for most levels. The highest level calculations do not always give better results than economical standard calculations.},
author = {van Eikema Hommes, Nico and Clark, Timothy},
doi = {10.1007/s00894-004-0223-8},
faupublication = {yes},
journal = {Journal of Molecular Modeling},
keywords = {NMR chemical shifts;density functional calculations;linear regression formulae},
pages = {175-185},
peerreviewed = {Yes},
title = {{Regression} formulae for ab initio and density functional calculated chemical shifts},
volume = {11},
year = {2005}
}
@article{faucris.116969864,
author = {Clark, Timothy and Schleyer, Paul and et al.},
author_hint = {SCHOTZ K, CLARK T, SCHLEYER PV},
doi = {10.1021/ja00213a011},
faupublication = {yes},
journal = {Journal of the American Chemical Society},
pages = {1394-1405},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{RELATIVE} {INEFFECTIVENESS} {OF} {LONGICYCLIC} 3-{RIBBON} {INTERACTIONS} {IN} {DICATIONS} - {REARRANGEMENT} {PRODUCTS} {OF} {BENZOBARRELENE} {DICATIONS} - {AN} {MNDO} {AND} {EXPERIMENTAL}-{STUDY}},
volume = {110},
year = {1988}
}
@article{faucris.116972504,
author = {Clark, Timothy and Schleyer, Paul and et al.},
author_hint = {BUDZELAAR PHM, KROGHJESPERSEN K, CLARK T, SCHLEYER PV},
doi = {10.1021/ja00295a033},
faupublication = {yes},
journal = {Journal of the American Chemical Society},
month = {Jan},
pages = {2773-2779},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{REMARKABLE} {STRUCTURES} {OF} {C2B2H4} {ISOMERS}},
volume = {107},
year = {1985}
}
@article{faucris.245134260,
abstract = {There are notably few literature reports of electron donor-acceptor oligoynes, even though they offer unique opportunities for studying charge transport through "all-carbon" molecular bridges. In this context, the current study focuses on a series of carbazole-(C≡C)n-2,5-diphenyl-1,3,4-oxadiazoles (n = 1-4) as conjugated π-systems in general and explores their photophysical properties in particular. Contrary to the behavior of typical electron donor-acceptor systems, for these oligoynes, the rates of charge recombination after photoexcitation increase with increasing electron donor-acceptor distance. To elucidate this unusual performance, we conducted detailed photophysical and time-dependent density functional theory investigations. Significant delocalization of the molecular orbitals along the bridge indicates that the bridging states come into resonance with either the electron donor or acceptor, thereby accelerating the charge transfer. Moreover, the calculated bond lengths reveal a reduction in bond-length alternation upon photoexcitation, indicating significant cumulenic character of the bridge in the excited state. In short, strong vibronic coupling between the electron-donating N-arylcarbazoles and the electron-accepting 1,3,4-oxadiazoles accelerates the charge recombination as the oligoyne becomes longer.},
author = {Zieleniewska, Anna and Zhao, Xiaotao and Bauroth, Stefan and Wang, Changsheng and Batsanov, Andrei S. and Krick Calderon, Christina and Kahnt, Axel and Clark, Timothy and Bryce, Martin R. and Guldi, Dirk Michael},
doi = {10.1021/jacs.0c04003},
faupublication = {yes},
journal = {Journal of the American Chemical Society},
note = {CRIS-Team Scopus Importer:2020-11-13},
pages = {18769-18781},
peerreviewed = {Yes},
title = {{Resonance}-{Enhanced} {Charge} {Delocalization} in {Carbazole}-{Oligoyne}-{Oxadiazole} {Conjugates}},
volume = {142},
year = {2020}
}
@article{faucris.119337944,
author = {Clark, Timothy and Schleyer, Paul and et al.},
author_hint = {WILHELM D, CLARK T, SCHLEYER PV, DAVIES AG},
doi = {10.1039/C39840000558},
faupublication = {yes},
journal = {Journal of the Chemical Society - Series Chemical Communications},
month = {Jan},
pages = {558-559},
peerreviewed = {unknown},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{RING}-{OPENING} {OF} {A} {BICYCLO}[3.3.0]{OCTADIENEDIYL} {DIANION}},
year = {1984}
}
@article{faucris.122872024,
abstract = {The reaction of diphenyltin dichloride with enantiopure Grignard reagents prepared in situ leads to diphenyltin chlorides 7a-e, which contain chiral organyl substituents. The 2-bornyl derivative 7a forms a mixture of exo and endo isomers and the (-)-menthyl derivative 7b yields a mixture of epimers, whereas the cis- and trans-myrtanyl complexes 7c and 7d and the m-(2-bornyl-2-ene)phenyl species 7e form only one enantiomer as the tin atom is separated from the next stereogenic centre by a methylene or m-phenylene group. The target chirally modified 1-(triorganylstannyl)-1,2,4-triphospholes 2a-e are accessible from 7a-e by treatment of the latter with the salt (3,5-di-tert-butyl-1,2,4-triphospholyl)-sodium (Na5) in good yield. As for 7c-e, complexes 2c-e exhibit enantiopure organyl tin substituents that combine with the planar chiral 1,2,4-triphosphole moiety to form diastereomers. X-ray diffraction studies on crystalline phases of 2a,b,d and 7b,c confirm the stereochemical interpretations of their spectroscopic data with the help of absolute structure parameter determinations. Dynamic NMR spectroscopy experiments with these compounds demonstrate for the first time a facile stannyl group shift between the two adjacent P atoms (P1 and P2) of the heterocycles that includes ring in-version through a planar transition state (T(i)). In line with the NMR spectroscopic results for 2a-e, density functional calculations with the simplified model compound (trimethylstannyl)-1,2,4-triphosphole (9) point to 1-(trimethylstannyl)-1, 2,4-triphosphole (9a) as the global energetic minimum for 9 and an almost isoenergetic 1,2-shift and ring inversion as the main epimerisation processes of the two enantiomers of 9a. ((C) Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008).},
author = {Hofmann, Martin and Clark, Timothy and Heinemann, Frank Wilhelm and Zenneck, Ulrich},
doi = {10.1002/ejic.200701321},
faupublication = {yes},
journal = {European Journal of Inorganic Chemistry},
keywords = {phosphorus heterocycles;tin;stereochemistry;molecular dynamics;density functional calculations},
pages = {2225-2237},
peerreviewed = {Yes},
title = {{Rock} around the ring: {An} experimental and theoretical study of the molecular dynamics of stannyltriphospholes with chiral tin substituents},
year = {2008}
}
@article{faucris.121158884,
abstract = {A classical point-charge self-consistent polarization model has been used to investigate the role of polarization in the CF3Cl:OH2 complex. The polarised electron densities of the monomers component are shown to be a good representation of the electron densities of complexes, especially CF3Cl. The point-charge model overestimates the polarization of the water molecule, which is likely because exchange repulsion is unaccounted for in the classical model calculations.},
author = {Clark, Timothy and Murray, Jane S. and Politzer, Peter},
doi = {10.1071/CH13531},
faupublication = {yes},
journal = {Australian Journal of Chemistry},
month = {Jan},
pages = {451-456},
peerreviewed = {Yes},
title = {{Role} of {Polarization} in {Halogen} {Bonds}},
volume = {67},
year = {2014}
}
@article{faucris.122483504,
abstract = {The activation energies for rotation about the sigma-bonds of 1,1'-binaphthyl (1) and 2,2'-dibromo-l,l'-binaphthyl (2) have been computed with MNDO, AM1, and PM3 and of 2,2'-dilithio-l,l'-binaphthyl (3).2EDA (ethylenediamine) (3a) with MNDO. All methods find that 1 should racemize preferably through the anti path, in agreement with previous force field calculations. The PM3 rotational barrier for 1 (23.1 kcal/mol) matches the experimental value (22.5 kcal/mol) best; the ground-state bond lengths correspond well with the X-ray data. We developed a procedure which evaluates the distortion and the steric repulsion effects in the transition structures roughly. In 1, distortion effects (e.g., ring deformation) account for about 2/3 of the activation energy. On the basis of the rotational behavior of 1, previous authors have only considered the anti racemization mechanism to be viable for 2,2'-dimethyl-l,l'-binaphthyl (4). In contrast, we found that in 2 (methyl is about the same size as bromine) the syn pathway is favored substantially over the anti route by 15.1 (MNDO), 20.6 (AM1), and 26.3 (PM3) kcal/mol. For 2, PM3 again yields the lowest rotational barrier (30.3 kcal/mol) but the AM1 value (38.4 kcal/mol) is in better agreement with an earlier estimate for 4 (37-40 kcal/mol). The transition structures (TS) related to 2 are even more strongly dominated (75-93 %) by distortion effects than those for l. Two energetically almost degenerate energy minima are computed with MNDO for 3a: one with the lithiums symmetrically doubly bridging the markedly twisted naphthyl rings (twist angle: 42.5-degrees) and the other with each lithium closely coordinated to the contiguous pi-system (twist angle: 122.0-degrees). Despite the size of the Li.ethylenediamine 2,2'-substituents in 3a, the anti racemization pathway is preferred by 6.4 kcal/mol with an unusually close Li ... H contact (1.79 angstrom). However, the syn-TS is 6.3 kcal/mol lower in energy with Li.EDA (3a) instead of hydrogens (1) in the 2,2'-positions. Thus, the syn-TS of 3a profits from electrostatic stabilization through lithium double bridging. Upon further rotation, the lithium atoms swap their counterions. To correct for the known overestimation of the Li-C bond strength by MNDO, we compared its performance on a model system (1,4-dilithio-1,3-butadiene (6)) with the MP2/6-31G*//6-31G* results. Deviations between the semiempirical and the ab initio geometries of four isomers of 6 suggest that the magnitude of the MNDO overestimation are 8 kcal/mol for Li-C and 4 kcal/mol for Li-H interactions. When these corrections are applied, the activation energy of 3a (anti-TS: 22.1 kcal/mol) should be close to the experimental estimate for 2,2'-dilithio-l,l'-binaphthyl (3) in solution (18.4 kcal/mol).},
author = {Clark, Timothy and Schleyer, Paul and et al.},
author_hint = {KRANZ M, CLARK T, SCHLEYER PV},
doi = {10.1021/jo00064a018},
faupublication = {yes},
journal = {Journal of Organic Chemistry},
pages = {3317-3325},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{ROTATIONAL} {BARRIERS} {OF} 1,1'-{BINAPHTHYLS} - {A} {COMPUTATIONAL} {STUDY}},
volume = {58},
year = {1993}
}
@article{faucris.116974044,
abstract = {We present modeling results on the metabolism of alkanes by cytochrome P450 using the semiempirical method SAM1. For our model system consisting of unsubstituted porphyrin, iron, and methylthiolate, the structures for the complexes in all possible spin-states throughout the reaction cycle were calculated and extensive conformational searches were performed. These enable us to discuss the changes in relative energies, atomic charges and structures for each reaction step. The reaction cascade is exothermic for all steps except the last, the substrate oxidation, which has been suggested to be rate-limiting from experimental evidence. The oxygen-oxygen bond is elongated step-by-step and the atomic charge on the iron-bound oxygen analogously reduced. The porphyrin nitrogens act as a charge buffer, whereas iron becomes progressively more positive. Dioxygen is transformed to the singlet by end-on coordination to iron(II). The addition of two protons gives a concerted dissociation of water instead of the unfavorable water-oxide-complex. Thus, our results are in full agreement with experimental data and support the accepted mode of action of P450 enzymes. (C) 2001 Elsevier Science B.V. All rights reserved.},
author = {Göller, Andreas H. and Clark, Timothy},
doi = {10.1016/S0166-1280(00)00810-1},
faupublication = {yes},
journal = {Journal of Molecular Structure-Theochem},
keywords = {cytochrome P450;enzyme catalysis;molecular modelling;protein structures;semiempirical calculations},
pages = {263-281},
peerreviewed = {Yes},
title = {{SAM1} semiempirical calculations on the mechanism of cytochrome {P450} metabolism},
volume = {541},
year = {2001}
}
@article{faucris.111617044,
abstract = {A combination of structures, energies, and spectral data calculated using density functional theory (DFT) with experimental NMR data has been used to assign conformational equilibria for tetracycline and 5a,6anhydrotetracycline in water at pH 1, 7, and 10 and in chloroform (5a,6-anhydrotetracycline) and methanol (tetracycline). The results suggest that tetracycline always prefers the extended conformation but that 5a,6anhydrotetracycline exists in water as a mixture of the two conformers and in chloroform exclusively in the twisted conformation. The conformational equilibria are also shown to be pH dependent. © 2006 American Chemical Society.},
author = {Othersen, Olaf and Waibel, Reiner and Lanig, Harald and Gmeiner, Peter and Clark, Timothy},
doi = {10.1021/jp064457s},
faupublication = {yes},
journal = {Journal of Physical Chemistry B},
note = {UnivIS-Import:2015-03-09:Pub.2006.nat.dchph.lphch.adirec},
pages = {24766-24774},
peerreviewed = {Yes},
title = {{SCRF}-{DFT} and {NMR} {Comparison} of {Tetracycline} and 5a,6-{Anhydrotetracycline} in {Solution}},
url = {http://pubs.acs.org/doi/abs/10.1021/jp064457s},
volume = {110},
year = {2006}
}
@article{faucris.109434204,
abstract = {Density functional theory calculations have been performed for the water exchange mechanism of aquated Al(III). The effect of pH was considered by studying the exchange processes for [Al(H2O)(6)](3+) and its conjugated base, [Al(H2O)(5)OH](2+). Both complexes were found to exchange water in a dissociative way with activation energies (E-A) of 15.9 and 10.2 kcal/mol, respectively. The influence of solvent molecules on the gas-phase cluster model was considered by the addition of up to four water molecules to the model system. The stabilizing effect of the solvent on the transition state decreases E-A to 8.6 (hexa-aqua complex) and 7.6 (monohydroxo complex) kcal/mol, whereas E-A for all hydroxo species is consistently significantly lower than those for the related aqua systems, which indicates a much faster water exchange rate. For the hydroxo complex, all calculated five-coordinate intermediates, nH(2)O center dot[Al(H2O)(4)(OH)](2+) (n = 1, 2, 3, 4, 5), are more stable than the corresponding six-coordinate reactants. Our results therefore suggest the presence of a stable five-coordinate species of aquated Al(III), namely, the [Al(H2O)(4)(OH)](2+) complex.},
author = {Hanauer, Hans and Puchta, Ralph and Clark, Timothy and van Eldik, Rudi},
doi = {10.1021/ic061284c},
faupublication = {yes},
journal = {Inorganic Chemistry},
pages = {1112-1122},
peerreviewed = {Yes},
title = {{Searching} for stable, five-coordinate aquated {Al}({III}) species. {Water} exchange mechanism and effect of {pH}},
volume = {46},
year = {2007}
}
@article{faucris.120270304,
abstract = {A combined study using cryo-TEM experiments and molecular dynamics simulations reveals remarkable details of the factors that affect the self-organization of specifically designed T-shaped amphiphilic dendrimers upon treatment of an aqueous solution with ultrasound under a layer of hexane. This treatment leads to dodecameric, structured micelles rather than the heptameric ones observed without hexane. Three-dimensional reconstruction of the cryo-TEM images provides very detailed structures of the micelles, and molecular dynamics simulations suggest that approximately 36 hexane molecules are needed to stabilize the dodecameric micelles. Sodium counterions are found to exert a significant stabilizing effect that results in an apparent attraction between the highly negatively charged polycarboxylate headgroups. DFT calculations support the observation that the formation of ion multiplets is especially crucial for this stabilizing counterion effect, which reduces headgroup repulsion. This and the increased hydrophobic stabilization that results from the hexane-enlarged core of the micelle lead to stable dodecameric micelles. The specific effects found for sodium counterions are largely absent for potassium. © 2009 American Chemical Society.},
author = {Jäger, Christof and Hirsch, Andreas and Schade, Boris and Ludwig, Kai and Böttcher, Christoph and Clark, Timothy},
doi = {10.1021/la9038123},
faupublication = {yes},
journal = {Langmuir},
pages = {10460-10466},
peerreviewed = {Yes},
title = {{Self}-assembly of structurally persistent micelles is controlled by specific-ion effects and hydrophobic guests},
volume = {26},
year = {2010}
}
@article{faucris.121273724,
abstract = {The synthesis of a new series of electron donor-acceptor conjugates (5, 10, 13, and 16) in which the electron acceptor - C - and the electron donor - π-extended tetrathiafulvalene (exTTF) - are bridged by means of m-phenyleneethynylene spacers of variable length is reported. The unexpected self-association of these hybrids was first detected to occur in the gas phase by means of MALDI-TOF spectrometry and subsequently corroborated in solution by utilizing concentration-dependent and variable-temperature H NMR experiments. Furthermore, the ability of these new conjugates to form wirelike structures upon deposition onto a mica surface has been demonstrated by AFM spectroscopy. In light of their photoactivity and redoxactivity, 5, 10, 13, and 16 were probed in concentration-dependent photophysical experiments. Importantly, absorption and fluorescence revealed subtle dissimilarities for the association constants, that is, a dependence on the length of the m-phenylene spacers. The binding strength is in 5 greatly reduced when compared with those in 10, 13, and 16. Not only that, the spacer length also plays a decisive role in governing excited-state interactions in the corresponding electron donor-acceptor conjugates (5, 10, 13, and 16). To this end, 5, in which the photo- and electroactive constituents are bridged by just one aromatic ring, displayssexclusively and independent of the concentration (10 to 10 M) - efficient intramolecular electron transfer events on the basis of a "through-bond" mechanism. On the contrary, the lack of conjugation throughout the bridges in 10 (two m-phenyleneethynylene rings), 13 (three m-phenyleneethynylene rings), and 16 (four m-phenyleneethynylene rings) favors at low concentration (10 M) "through space" intramolecular electron transfer events. These are, however, quite ineffective and, in turn, lead to excited-state deactivations that are at high concentrations (10 M) dominated by intracomplex electron transfer events, namely, between exTTF of one molecule and C of another molecule, and that stabilize the resulting radical ion pair state with lifetimes reaching 4.0 μs. © 2009 American Chemical Society.},
author = {Molina-Ontoria, Agustin and Fernandez, Gustavo and Wielopolski, Mateusz and Atienza, Carmen and Sanchez, Luis and Gouloumis, Andreas and Clark, Timothy and Martin, Nazario and Guldi, Dirk Michael},
doi = {10.1021/ja9024269},
faupublication = {yes},
journal = {Journal of the American Chemical Society},
pages = {12218-12229},
peerreviewed = {Yes},
title = {{Self}-association and electron transfer in donor-acceptor dyads connected by meta-substituted oligomers},
volume = {131},
year = {2009}
}
@article{faucris.121990484,
abstract = {Proteins in the gas phase present an extreme (and unrealistic) challenge for self-consistent-field iteration schemes because their ionized groups are very strong electron donors or acceptors, depending on their formal charge. This means that gas-phase proteins have a very small band gap but that their frontier orbitals are localized compared to “normal” conjugated semiconductors. The frontier orbitals are thus likely to be separated in space so that they are close to, but not quite, orthogonal during the SCF iterations. We report full SCF calculations using the massively parallel EMPIRE code and linear scaling localized-molecular-orbital (LMO) calculations using Mopac2009. The LMO procedure can lead to artificially over-polarized wavefunctions in gas-phase proteins. The full SCF iteration procedure can be very slow to converge because many cycles are needed to overcome the over-polarization by inductive charge shifts. Example molecules have been constructed to demonstrate this behavior. The two approaches give identical results if solvent effects are included.},
author = {Wick, Christian and Hennemann, Matthias and Stewart, James J. P. and Clark, Timothy},
doi = {10.1007/s00894-014-2159-y},
faupublication = {yes},
journal = {Journal of Molecular Modeling},
pages = {2159},
peerreviewed = {Yes},
title = {{Self}-consistent field convergence for proteins: a comparison of full and localized-molecular-orbital schemes},
volume = {20},
year = {2014}
}
@incollection{faucris.110980364,
address = {Dordrecht},
author = {Clark, Timothy and Gedeck, Peter and Lanig, Harald and Schürer, Gudrun},
booktitle = {Molecular Modeling and Dynamics of Bioinorganic Systems},
doi = {10.1007/978-94-011-5171-9{\_}14},
editor = {L. Banci, P. Comba},
faupublication = {yes},
month = {Jan},
pages = {307-317},
peerreviewed = {Yes},
publisher = {Kluwer Academic Publishers},
series = {NATO ASI Series},
title = {{Semi}-empirical {MO} calculations on enzyme reaction mechanisms},
volume = {41},
year = {1997}
}
@article{faucris.109435084,
author = {Clark, Timothy},
faupublication = {yes},
journal = {ACS National Meeting Book of Abstracts},
pages = {U413-U413},
peerreviewed = {unknown},
title = {{Semiempirical} molecular dynamics.},
volume = {222},
year = {2001}
}
@article{faucris.116974264,
author = {Clark, Timothy},
doi = {10.1007/978-94-011-1974-0{\_}21},
faupublication = {yes},
journal = {Representation Theories and Algebraic Geometry},
month = {Jan},
pages = {369-380},
peerreviewed = {unknown},
title = {{SEMIEMPIRICAL} {MOLECULAR}-{ORBITAL} {THEORY} - {FACTS}, {MYTHS} {AND} {LEGENDS}},
volume = {406},
year = {1993}
}
@article{faucris.124020204,
author = {Clark, Timothy},
faupublication = {yes},
journal = {Journal of Molecular Graphics & Modelling},
pages = {275-275},
peerreviewed = {Yes},
title = {{Semiempirical} {QM}/{MM} techniques},
volume = {16},
year = {1998}
}
@article{faucris.107263684,
abstract = {Unrestricted Natural Orbital–Complete Active Space Configuration Interaction, abbreviated as UNO–CAS, has been implemented for NDDO-based semiempirical molecular-orbital (MO) theory. A computationally more economic technique, UNO–CIS, in which we use a configuration interaction (CI) calculation with only single excitations (CIS) to calculate excited states, has also been implemented and tested. The class of techniques in which unrestricted natural orbitals (UNOs) are used as the reference for CI calculations is denoted UNO–CI. Semiempirical UNO–CI gives good results for the optical band gaps of organic semiconductors such as polyynes and polyacenes, which are promising materials for nanoelectronics. The results of these semiempirical UNO–CI techniques are generally in better agreement with experiment than those obtained with the corresponding conventional semiempirical CI methods and comparable to or better than those obtained with far more computationally expensive methods such as time-dependent density-functional theory. We also show that symmetry breaking in semiempirical UHF calculations is very useful for predicting the diradical character of organic compounds in the singlet spin state.},
author = {Dral, Pavlo O. and Clark, Timothy},
doi = {10.1021/jp204939x},
faupublication = {yes},
journal = {Journal of Physical Chemistry A},
pages = {11303--11312},
peerreviewed = {Yes},
title = {{Semiempirical} {UNO}–{CAS} and {UNO}–{CI}: {Method} and {Applications} in {Nanoelectronics}},
volume = {115},
year = {2011}
}
@article{faucris.301469272,
abstract = {The goal of harnessing the theoretical potential of singlet fission (SF), a process in which one singlet excited state is split into two triplet excited states, has become a central challenge in solar energy research. Covalently linked dimers provide crucial models for understanding the role of chromophore arrangement and coupling in SF. Sensitizers can be integrated into these systems to expand the absorption bandwidth through which SF can be accessed. Here, we define the role of the sensitizer-chromophore geometry in a sensitized SF model system. To this end, two conjugates have been synthesized consisting of a pentacene dimer (SF motif) connected via a rigid alkynyl bridge to a subphthalocyanine (the sensitizer motif) in either an axial or a peripheral arrangement. Steady-state and time-resolved photophysical measurements are used to confirm that both conjugates operate as per design, displaying near unity energy transfer efficiencies and high triplet quantum yields from SF. Decisively, energy transfer between the subphthalocyanine and pentacene dimer occurs ca. 26 times faster in the peripheral conjugate, even though the two chromophores are ca. 3 angstrom farther apart than in the axial conjugate. Following a theoretical evaluation of the dipolar coupling, Vdip2, and the orientation factor, kappa 2, of both the axial (Vdip2 = 140 cm-2; kappa 2 = 0.08) and the peripheral (Vdip2 = 724 cm-2; kappa 2 = 1.46) arrangements, we establish that this rate acceleration is due to a more favorable (nearly co-planar) relative orientation of the transition dipole moments of the subphthalocyanine and pentacenes in the peripheral constellation.},
author = {Gotfredsen, Henrik and Thiel, Dominik and Greißel, Phillip and Chen, Lan and Krug, Marcel and Papadopoulos, Ilias and Ferguson, Michael J. and Nielsen, Mogens Brøndsted and Torres, Tomas and Clark, Timothy and Guldi, Dirk Michael and Tykwinski, Rik R.},
doi = {10.1021/jacs.2c13353},
faupublication = {yes},
journal = {Journal of the American Chemical Society},
note = {CRIS-Team WoS Importer:2023-05-19},
pages = {9548-9563},
peerreviewed = {Yes},
title = {{Sensitized} {Singlet} {Fission} in {Rigidly} {Linked} {Axial} and {Peripheral} {Pentacene}-{Subphthalocyanine} {Conjugates}},
volume = {145},
year = {2023}
}
@misc{faucris.120331244,
author = {Clark, Timothy},
faupublication = {yes},
peerreviewed = {automatic},
title = {{Shannon} entropy as a local surface property},
year = {2005}
}
@article{faucris.119340804,
abstract = {Multiple linear regression is a major tool in computational chemistry. Although it has been used for more than 30 years, it has only recently been noted within the cheminformatics community that the standard F-values used to assess the significance of the resulting models are inappropriate in situations where the variables included in a model are chosen from a large pool of descriptors, due to an effect known in the statistical literature as selection bias. We have used Monte Carlo simulations to estimate the critical F-values for many combinations of sample size (n), model size (p), and descriptor pool size (k), using stepwise regression, one of the methods most commonly used to derive linear models from large sets of molecular descriptors. The values of n, p, and k represent cases appropriate to contemporary cheminformatics data sets. A formula for general n, p, and k values has been developed from the numerical estimates that approximates the critical stepwise F-values at 90%, 95%. and 99% significance levels. This approximation reproduces both the original simulated values and an interpolation test set (within the range of the training values) with an R(2) value greater than 0.995. For an extrapolation test set of cases outside the range of the training set, the approximation produced an R(2) above 0.93.},
author = {Kramer, Christian and Tautermann, Christofer S. and Livingstone, David J. and Salt, David W. and Whitley, David C. and Beck, Bernd and Clark, Timothy},
doi = {10.1021/ci800318q},
faupublication = {yes},
journal = {Journal of Chemical Information and Modeling},
month = {Jan},
pages = {28-34},
peerreviewed = {Yes},
title = {{Sharpening} the {Toolbox} of {Computational} {Chemistry}: {A} {New} {Approximation} of {Critical} {F}-{Values} for {Multiple} {Linear} {Regression}},
volume = {49},
year = {2009}
}
@article{faucris.116975804,
abstract = {The geometrical changes in bond lengths and angles, which correlate with substituent electronegativities, are discussed for the different ring systems. The relative stabilities of unsaturated and saturated rings are compared using isodesmic ring-opening reactions and homodesmic substituent-exchange reactions. sigma*-Aromaticity, a hyperconjugative effect found in the disubstituted rings, causes lowering of ring strain energies for the unsaturated rings and preference of unsaturated rings over saturated ones for the more electronegative substituents. For the mono-substituted pi-aromatic silacyclopropenes and cyclopropenes, a destabilization by more electronegative ligands is found. For the neutral rings monosubstituted at main group V atoms like the 1H-phosphirenes and also the isoelectronic negatively charged rings with main group IV atoms like the silacyclopropenium anions, no correlation of stabilization energies or geometrical changes with ligand electronegativity is found.},
author = {Göller, Andreas H. and Clark, Timothy},
doi = {10.1007/PL00010724},
faupublication = {yes},
journal = {Journal of Molecular Modeling},
keywords = {sigma*-aromaticity;hyperconjugation;ab initio calculations;phosphorus rings;weak interactions},
month = {Jan},
pages = {133-149},
peerreviewed = {Yes},
title = {sigma*-aromaticity in three-membered rings},
volume = {6},
year = {2000}
}
@article{faucris.109436184,
abstract = {The influence of the electronegativity of the ligands Y (F, Cl, Br, I, OH, NH2, CH3, H) on the strength of the sigma*-aromatic effect in gem-disubstituted 1H-Phosphirenium cations and substituted 3-silacyclopropenes has been investigated with ab initio theory. Phosphorus and silicon provide a low lying p-type sigma*-orbital antibonding to the ligands Y. This interacts with the ring double bond analogously to a third p-orbital in a 2 pi Huckel system. These systems have bean compared to the analogous saturated rings. Calculations at the RHF/6-31G* and MP4/6-31+G* levels, NBO analyses of the effect of the ligands Y and comparisons of the relative stabilities of the saturated and unsaturated compounds suggest a weak but significant sigma*-aromatic effect dependent on the electronegativity of Y.},
author = {Göller, Andreas H. and Clark, Timothy and et al.},
author_hint = {Goller A, Heydt H, Clark T},
doi = {10.1021/jo960387h},
faupublication = {yes},
journal = {Journal of Organic Chemistry},
pages = {5840-5846},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {sigma*-aromaticity of substituted {1H}-phosphirenium cations and substituted silacyclopropenes},
volume = {61},
year = {1996}
}
@book{faucris.115088424,
abstract = {The anisotropic electronic densities of covalently-bonded Group IV-VII atoms frequently give rise to regions of positive electrostatic potential on the extensions of covalent bonds to these atoms. Through such positive "sigma-holes," the atoms can interact attractively and highly directionally with negative sites such as the lone pairs of Lewis bases, anions, pi electrons, etc. In the case of Group VII this is called " halogen bonding." Hydrogen bonding can be viewed as a less directional subset of sigma-hole interactions. Since positive sigma-holes often exist in conjunction with regions of negative potential, the atoms can also interact favorably with positive sites. In accordance with the Hellmann-Feynman theorem, all of these interactions are purely Coulombic in nature (which encompasses polarization and dispersion). The strength of sigma-hole bonding increases with the magnitudes of the potentials of the positive sigma-hole and the negative site; their polarizabilities must sometimes also be taken explicitly into account.},
author = {Politzer, Peter and Murray, Jane S. and Clark, Timothy},
doi = {10.1007/128{\_}2014{\_}568},
faupublication = {yes},
keywords = {Coulombic interactions;Halogen bonding;sigma-Hole bonding},
month = {Jan},
pages = {19-42},
peerreviewed = {unknown},
publisher = {Springer Verlag Kg},
title = {sigma-{Hole} {Bonding}: {A} {Physical} {Interpretation}},
volume = {358},
year = {2015}
}
@article{faucris.121621764,
abstract = {It has been observed both experimentally and computationally that some divalently- bonded Group VI atoms interact in a noncovalent but highly directional manner with nucleophiles. We show that this can readily be explained in terms of regions of positive electrostatic potential on the outer surfaces of such atoms, these regions being located along the extensions of their existing covalent bonds. These positive regions can interact attractively with the lone pairs of nucleophiles. The existence of such a positive region is attributed to the presence of a "sigma-hole." This term designates the electron- deficient outer lobe of a half- filled p bonding orbital on the Group VI atom. The positive regions become stronger as the electronegativity of the atom decreases and its polarizability increases, and as the groups to which it is covalently bonded become more electron- withdrawing. We demonstrate computationally that the s- hole concept and the outer regions of positive electrostatic potential account for the existence, directionalities and strengths of the observed noncovalent interactions.},
author = {Clark, Timothy and et al.},
author_hint = {Murray JS, Lane P, Clark T, Politzer P},
doi = {10.1007/s00894-007-0225-4},
faupublication = {yes},
journal = {Journal of Molecular Modeling},
keywords = {directional noncovalent interactions;electrostatic potentials;group VI atoms;sigma-hole bonding},
pages = {1033-1038},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {sigma-hole bonding: molecules containing group {VI} atoms},
volume = {13},
year = {2007}
}
@article{faucris.116859864,
abstract = {sigma-Holes are regions of positive molecular electrostatic potential collinear with and opposite to covalent bonds to atoms of Groups IV-VII. They are responsible for many noncovalent bonding interactions, such as halogen bonding. sigma-Holes make 'negatively charged' atoms act as if they were 'positively charged'. The existence of sigma-hole bonding emphasizes what has been called 'the fallacy of net atomic charges', which means that many covalently bonded atoms cannot be represented adequately by a single charge because they look negative from some directions and positive from others. Hydrogen bonding can also be regarded as a special case of sigma-hole bonding, although in this case the origin of the sigma-hole is rationalized differently than in the heavier elements. Phenomena such as the directionality of hydrogen bonds and 'blue-shifted' hydrogen bonds can be explained very simply using the sigma-hole concept. (C) 2012 John Wiley & Sons, Ltd. How to cite this article: WIREs Comput Mol Sci 2013, 3:13-20 doi: 10.1002/wcms.1113},
author = {Clark, Timothy},
doi = {10.1002/wcms.1113},
faupublication = {yes},
journal = {Wiley Interdisciplinary Reviews: Computational Molecular Science},
month = {Jan},
pages = {13-20},
peerreviewed = {unknown},
title = {sigma-{Holes}},
volume = {3},
year = {2013}
}
@article{faucris.116977344,
abstract = {A first and fairly mild metal-free catalytic route was developed for the [3+2] cycloadditions of different N-acylhydrazones to cyclopentadiene, providing the synthetically and biologically important five-membered cyclic compounds pyrazolidines. The reaction was successfully conducted in high yields (up to 99%) with high diastereoselectivities (up to 98: 2 dr) by using catalytic amounts of TMSOTf (trimethylsilyl triflate) as a readily available Lewis acidic catalyst. The experimental findings were supported by DFT calculations of the reaction mechanism. The theoretical and experimental diastereomeric excess values show good agreement, rendering the computations an efficient tool for predicting the selectivities in these and related reactions.},
author = {Zamfir, Alexandru and Schenker, Sebastian and Bauer, Walter and Clark, Timothy and Tsogoeva, Svetlana},
doi = {10.1002/ejoc.201100206},
faupublication = {yes},
journal = {European Journal of Organic Chemistry},
keywords = {Cycloaddition;Lewis acids;Nitrogen heterocycles;Hydrazones;Silicon;Density functional calculations},
pages = {3706-3709},
peerreviewed = {Yes},
title = {{Silicon} {Lewis} {Acid} {Catalyzed} [3+2] {Cycloaddition} {Reactions} of {Hydrazones}/{Cyclopentadiene}: {Mild} {Access} to {Pyrazolidine} {Derivatives}},
year = {2011}
}
@article{faucris.116979984,
author = {Clark, Timothy},
doi = {10.1039/p29820001267},
faupublication = {yes},
journal = {Journal of the Chemical Society, Perkin Transactions 2},
month = {Jan},
pages = {1267-1271},
peerreviewed = {Yes},
title = {{SILYL} {HALIDE} {RADICAL}-{ANIONS}},
year = {1982}
}
@article{faucris.119341684,
abstract = {Similarity studies of DNA sequences using 2D-dynamic graphs are performed. The orientation of the graphs in 2D-space is proposed as a descriptor. Mass overlaps and comparison of the positions of the graphs are proposed as similarity measures of pairs of sequences. (C) 2007 Elsevier B.V. All rights reserved.},
author = {Bielinska-Waz, Dorota Joanna and Waz, Piotr and Clark, Timothy},
doi = {10.1016/j.cplett.2007.07.044},
faupublication = {yes},
journal = {Chemical Physics Letters},
pages = {68-73},
peerreviewed = {Yes},
title = {{Similarity} studies of {DNA} sequences using genetic methods},
volume = {445},
year = {2007}
}
@article{faucris.208737028,
abstract = {Systems in which movements occur on two significantly different time domains, such as organic electronic components with flexible molecules, require different simulation techniques for the two time scales. In the case of molecular electronics, charge transport is complicated by the several different mechanisms (and theoretical models) that apply in different cases. We cannot yet combine time scales of molecular and electronic movement in simulations of real systems. This review describes our progress towards this goal.},
author = {Clark, Timothy},
doi = {10.1016/j.pisc.2015.06.003},
faupublication = {yes},
journal = {Perspectives in Science},
pages = {58-65},
peerreviewed = {Yes},
title = {{Simulating} charge transport in flexible systems},
volume = {6},
year = {2015}
}
@article{faucris.122492744,
abstract = {We present a computational model study designed to simulate the results of time-resolved fluorescence spectra of tryptophan in proteins. In such measurements, the occurrence of more than one fluorescence lifetime is generally attributed to the existence of several tryptophan rotamers and/or structural conformations of the protein structure. The protein system we chose for this initial study is the tetracycline repressor (TetR), an interesting model system for the investigation of the mechanisms of transcriptional regulation. Fluorescence resonance energy transfer (FRET) from tryptophan to tetracycline is frequently observed in complexes of the TetR with the antibiotic tetracycline. We use a combined classical/quantum mechanical approach to model the structure and the spectroscopic properties of the TetR-tetracycline complex. A classical molecular dynamics simulation provides input geometries for semiempirical quantum mechanical/molecular mechanical (OM/MM) single-point configuration interaction (CI) calculations, which are used to calculate tryptophan vertical absorption and fluorescence energies and intensities as well as relative FRET rate constants. These rate constants together with the Einstein coefficients for spontaneous emission and an assumed rate for nonradiative deactivation allow us to simulate fluorescence decay curves with and without FRET and for the entire ensemble as well as for individual rotamers. Our results indicate that the classical "rotamer model", used to explain the multiexponential fluorescence-decay curves of time-resolved tryptophan emission spectra, can be extended to systems with FRET acceptors present in the protein matrix but that the interpretation of the fitted lifetimes is different to that usually used.},
author = {Beierlein, Frank and Othersen, Olaf and Lanig, Harald and Schneider, Siegfried and Clark, Timothy},
doi = {10.1021/ja058414l},
faupublication = {yes},
journal = {Journal of the American Chemical Society},
pages = {5142-5152},
peerreviewed = {Yes},
title = {{Simulating} {FRET} from tryptophan: {Is} the rotamer model correct?},
volume = {128},
year = {2006}
}
@misc{faucris.107261264,
abstract = {A combination of classical molecular dynamics simulations and very large scale semiempirical molecular orbital calculations has been used to simulate field-effect transistors in which both the dielectric layer and the semiconductor are incorporated in a self-assembled monolayer of suitable functionalized alkylphosphonic acids. In such simulations, both the dynamics of the flexible organic molecules and the electronic properties of the molecular aggregates must be taken into account. First steps towards realistic simulations of such devices are described.},
author = {Clark, Timothy and Halik, Marcus and Hennemann, Matthias and Jäger, Christof},
faupublication = {yes},
peerreviewed = {automatic},
title = {{Simulating} ’{Soft}’ {Electronic} {Devices}},
url = {http://www.beilstein-institut.de/en/symposia/proceedings/bozen-2012},
year = {2013}
}
@article{faucris.208733171,
abstract = {In weakly interacting organic semiconductors, static disorder and dynamic disorder often have an important impact on transport properties. Describing charge transport in these systems requires an approach that correctly takes structural and electronic fluctuations into account. Here, we present a multiscale method based on a combination of molecular-dynamics simulations, electronic-structure calculations, and a transport theory that uses time-dependent nonequilibrium Green's functions. We apply the methodology to investigate charge transport in C-60-containing self-assembled monolayers, which are used in organic field-effect transistors.},
author = {Leitherer, Susanne and Jager, C. M. and Krause, Andreas and Halik, Marcus and Clark, Timothy and Thoss, Michael},
doi = {10.1103/PhysRevMaterials.1.064601},
faupublication = {yes},
journal = {Physical Review Materials},
peerreviewed = {Yes},
title = {{Simulation} of charge transport in organic semiconductors: {A} time-dependent multiscale method based on nonequilibrium {Green}'s functions},
volume = {1},
year = {2017}
}
@article{faucris.230333929,
abstract = {Singlet fission has emerged as a promising strategy to avoid the loss of extra energy through thermalization in solar cells. A family of dimers consisting of nitrogen-doped pyrene-fused acenes that undergo singlet fission with triplet quantum yields as high as 125 % are presented. They provide new perspectives for nitrogenated polycyclic aromatic hydrocarbons and for the design of new materials for singlet fission.},
author = {Mora-Fuentes, Juan P. and Papadopoulos, Ilias and Thiel, Dominik and Alvarez-Boto, Roberto and Cortizo-Lacalle, Diego and Clark, Timothy and Melle-Franco, Manuel and Guldi, Dirk Michael and Mateo-Alonso, Aurelio},
doi = {10.1002/anie.201911529},
faupublication = {yes},
journal = {Angewandte Chemie International Edition},
note = {CRIS-Team WoS Importer:2019-12-10},
peerreviewed = {Yes},
title = {{Singlet} {Fission} in {Pyrene}-{Fused} {Azaacene} {Dimers}},
year = {2019}
}
@article{faucris.228443641,
abstract = {We present atomic scale models of differently sized eumelanin nanoaggregates from molecular dynamics simulations combined with a simulated annealing procedure. The analysis reveals the formation of secondary structures due to π-stacking on one hand, but on the other hand a broad distribution of stack geometries in terms of stack size, horizontal displacement angles, and relative torsion angles. The displacement angle distribution, which is a measure of the occurrence of zigzag and linear stacking motives, respectively, strongly depends on the aggregate size - and is hence controlled by the interplay of surface and bulk energy terms. Semiempirical spectra calculations of small stacks (up to five protomolecules) reveal a strong dependence on the precise stack structure and allow for a direct structure-property correlation. The observed spectral shifts result in an overall spectral broadening and, hence, further support the geometric disorder model, which complements the chemical disorder model in the interpretation of eumelanin's monotonically increasing broad-band absorption.},
author = {Träg, Johannes and Duchstein, Patrick and Hennemann, Matthias and Clark, Timothy and Guldi, Dirk Michael and Zahn, Dirk},
doi = {10.1021/acs.jpca.9b08722},
faupublication = {yes},
journal = {Journal of Physical Chemistry A},
note = {CRIS-Team Scopus Importer:2019-10-29},
peerreviewed = {Yes},
title = {{Size}-{Dependent} {Local} {Ordering} in {Melanin} {Aggregates} and {Its} {Implication} on {Optical} {Properties}},
year = {2019}
}
@article{faucris.120270524,
abstract = {Not only the self-aggregation of dendritic polycarboxylates intostructurally persistent micelles, but also that of the micelles themselves into superlatticesis controlled by alkali-metalcounterions and shows a pronounced sodium effect. Our combined experimental and computational work has revealed the formation of superlattices for the first time. The behavior of a variety of amphiphilic carboxylates and the different effects of the alkali cations Li, Na, and K have been investigated by conductivity measurements, cryogenic transmission electron microscopy (cryo-TEM), and molecular-dynamics (MD) simulations. Together, these show that sodium salts of the amphiphiles give the most stable micelles, followed by lithium and potassium. Our results suggest that ion multiplets in bridging positions, rather than contact ion pairs, are responsible for the enhanced stability and the formation of hexagonally ordered superlattices with sodium counter ions. Potassium ions do not form such ion multiplets and cannot therefore induce aggregation of the micelles. This sodium effect has far-reaching consequences for a large number of biological and technical systems and sheds new light on the origin of specific-ion effects. © 2010 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.},
author = {Rosenlehner, Karin and Schade, Boris and Böttcher, Christoph and Jäger, Christof and Clark, Timothy and Heinemann, Frank Wilhelm and Hirsch, Andreas},
doi = {10.1002/chem.201001150},
faupublication = {yes},
journal = {Chemistry - A European Journal},
pages = {9544-9554},
peerreviewed = {Yes},
title = {{Sodium} effect on self-organization of amphiphilic carboxylates: {Formation} of structured micelles and superlattices},
volume = {16},
year = {2010}
}
@article{faucris.268131817,
abstract = {We describe for the first time the full reaction coordinate regarding the photoisomerization of red-absorbing norbornadienes (NBDs) to quadricyclanes (QCs). Our studies go beyond steady-state investigations by using an arsenal of time-resolved techniques. Importantly, the red absorption of NBDs is made possible by a different charge-transfer character; adjusting its strength enables control over the photoreversibility of the rearrangement. In the case of strong charge-transfer character (a weakly electron-withdrawing ester and a strongly electron-donating dimethylaniline), photoirradiation with visible light into the delocalized charge-transfer absorption of NBD affords QC reversibly. In stark contrast, UV photoirradiation into the NBD localized excited state leads to a photoinduced degradation and cannot be back-isomerized to NBD under any circumstances. If the charge-transfer character is weak (a weakly electron-withdrawing ester and a weakly electron-donating phenyl), reversibility is seen independently of the photoirradiation light.},
author = {Alex, Wiebke and Lorenz, Patrick and Henkel, Christian and Clark, Timothy and Hirsch, Andreas and Guldi, Dirk Michael},
doi = {10.1021/jacs.1c04322},
faupublication = {yes},
journal = {Journal of the American Chemical Society},
note = {CRIS-Team WoS Importer:2022-01-14},
peerreviewed = {Yes},
title = {{Solar} {Energy} {Storage}: {Competition} between {Delocalized} {Charge} {Transfer} and {Localized} {Excited} {States} in the {Norbornadiene} to {Quadricyclane} {Photoisomerization}},
year = {2021}
}
@article{faucris.293243447,
author = {Alex, Wiebke and Lorenz, Patrick and Henkel, Christian and Clark, Timothy and Hirsch, Andreas and Guldi, Dirk Michael},
doi = {10.1021/jacs.1c04322},
faupublication = {yes},
journal = {Journal of the American Chemical Society},
pages = {153-162},
peerreviewed = {Yes},
title = {{Solar} {Energy} {Storage}: {Competition} between {Delocalized} {Charge} {Transfer} and {Localized} {Excited} {States} in the {Norbornadiene} to {Quadricyclane} {Photoisomerization}},
volume = {199},
year = {2022}
}
@article{faucris.115828724,
abstract = {The source of the effect of N-alkylation on the redox properties of Ni(II/I) and Cr(III/II) cyclam complexes has been investigated using DFT calculations. The structures of the anhydrous and hydrated complexes were optimized in the gas phase, and single point calculations were performed in a polarized continuum. The main results are the following: the decrease in outer sphere solvation upon N-alkylation is the major source of the relative stabilization of the lower oxidation state complexes by the tertiary amine ligands; tertiary amine nitrogen donors are stronger σ-donors than the secondary amines, as predicted from the inductive effect of alkyls; steric strain elongates the metal-nitrogen bonds in the tertiary complexes and decreases the ligand strain energies; and the site of water binding to the complexes differs because of their different electronic structures (i.e., in the Ni complexes, the water molecules bind to the M-N-H sites, whereas in the Cr complexes they bind to the central metal cation). Outer sphere hydrogen bonding of water to the ligands in the coordination sphere lowers the ionization potentials by charge delocalization.},
author = {Clark, Timothy and Hennemann, Matthias and van Eldik, Rudi and et al.},
author_hint = {Clark Tim, Hennemann Matthias, van Eldik Rudi, Meyerstein Dan},
doi = {10.1021/ic0113193},
faupublication = {yes},
journal = {Inorganic Chemistry},
note = {UnivIS-Import:2015-03-09:Pub.2002.forsch.sonder.sfb583.solvat},
pages = {2927-2935},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{Solvation} {Largely} {Accounts} for the {Effect} of {N}-{Alkylation} on the {Properties} of {Nickel}({II}/{I}) and {Chromium}({III}/{II}) {Cyclam} {Complexes}},
volume = {11},
year = {2002}
}
@article{faucris.243613370,
abstract = {Three diketopyrrolopyrrole (DPP) dimers, linked via different dithienylphenylene spacers, ortho-DPP (o-DPP), meta-DPP (m-DPP), and para-DPP (p-DPP), are synthesized, characterized, and probed in light of intramolecular singlet fission (i-SF). Importantly, the corresponding DPP reference (DPP-Ref) singlet and triplet excited state energies of 2.22 and 1.04 eV, respectively, suggest that i-SF is thermodynamically feasible. The investigations focus on the impact of the relative positioning of the DPPs, and give compelling evidence that solvent polarity and/or spatial overlap govern i-SF dynamics and efficiencies. Polar solvents make the involvement of an intermediate charge transfer (CT) state possible, followed by the population of 1(T1T1) and subsequently (T1 + T1), while spatial overlap drives the mutual interactions between the DPPs. In o-DPP, the correct balance between polar solvents and spatial overlap leads to the highest triplet quantum yield (TQY) of 40%. Notable is the superimposition of CT and triplet excited states, preventing an accurate TQY determination. For m-DPP, poorer spatial overlap correlates with weaker CT character and manifests in a TQY of 11%. Strong CT character acts as a trap and prevents i-SF, as found with p-DPP. The DPP separation is decisive, enabling a symmetry-breaking charge-separated state rather than CT formation, shutting down the formation 1(T1T1).},
author = {Papadopoulos, Ilias and Álvaro-Martins, Maria João and Molina, Desiré and McCosker, Patrick Michael and Keller, Paul A. and Clark, Timothy and Sastre-Santos, Ángela and Guldi, Dirk Michael},
doi = {10.1002/aenm.202001496},
faupublication = {yes},
journal = {Advanced Energy Materials},
keywords = {charge transfer states; diketopyrrolopyrrole dimers; intramolecular singlet fission},
note = {CRIS-Team Scopus Importer:2020-10-09},
peerreviewed = {Yes},
title = {{Solvent}-{Dependent} {Singlet} {Fission} in {Diketopyrrolopyrrole} {Dimers}: {A} {Mediating} {Charge} {Transfer} versus a {Trapping} {Symmetry}-{Breaking} {Charge} {Separation}},
year = {2020}
}
@article{faucris.116982404,
author = {Beck, Bernd and Clark, Timothy},
doi = {10.1007/0-306-46857-3{\_}8},
faupublication = {yes},
journal = {Perspectives in Drug Discovery and Design},
month = {Jan},
pages = {131-159},
peerreviewed = {Yes},
title = {{Some} biological applications of semiempirical {MO} theory},
volume = {9-11},
year = {1998}
}
@article{faucris.109441904,
author = {Clark, Timothy and et al.},
author_hint = {ALDER RW, PETTS JC, CLARK T},
doi = {10.1016/S0040-4039(00)98558-7},
faupublication = {yes},
journal = {Tetrahedron Letters},
month = {Jan},
pages = {1585-1588},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{SOME} {CYCLIC} {C9H6} {ISOMERS} {AND} {THEIR} {POTENTIAL} {TREFOIL} {AROMATICITY}},
volume = {26},
year = {1985}
}
@article{faucris.117437364,
author = {Maia de Pádua, Rodrigo and Meitinger, Nadine and Hennemann, Matthias and Schebitz, Pia and Waibel, Reiner and Löber, Stefan and Gmeiner, Peter and Clark, Timothy and Kreis, Wolfgang},
doi = {10.1016/j.tet.2016.06.024},
faupublication = {yes},
journal = {Tetrahedron},
pages = {4556-4563},
peerreviewed = {Yes},
title = {{Spontaneous} butenolide ring formation of pregnane-21-{O}-malonyl hemiesters under mild reaction conditions is facilitated by the 14β-hydroxy group present in all natural cardenolides},
volume = {72},
year = {2016}
}
@incollection{faucris.110124124,
address = {Woodbury, New York},
author = {Mauser, Harald and Clark, Timothy and Hirsch, Andreas},
booktitle = {AIP Conference Proceedings - Volume 442},
doi = {10.1063/1.56508},
editor = {Kuzmany, J. Fink, M. Mehring, S. Roth},
faupublication = {yes},
pages = {392-367},
peerreviewed = {unknown},
publisher = {AIP Publishing LLC},
title = {{Stabilisation} of atomic elements inside {C60}},
year = {1998}
}
@article{faucris.208733426,
abstract = {Electrospray ionisation of N-heterotriangulenes (i.e., dimethyl-methylene-bridged triphenylamines) with up to three pyridyl groups at their periphery, produces the true radical cation ([M](+center dot)) and the protonated molecule ([M+H](+)) simultaneously. These ions are studied as model systems to illustrate the stability alternation of odd-versus even-electron ions in energy-dependent collision-induced dissociation (CID) experiments. All ions show the same fragmentation pattern, the consecutive loss of three methyl radicals ((CH3)-C-center dot) from the dimethylmethylene bridges of the central triangulene core. [M](+center dot) ions dissociate at much lower collision energies than their [M+H](+) counterparts. The radical cation forms a singlet fragment with an extended aromatic system that is energetically favoured. Ab initio and density functional theory calculations support this interpretation and allow the assignment of the electronic structure of the fragment ions. Consecutive collision-induced dissociations provide a better match with theory when studied with an ion trap, rather than a linear quadrupole. This is attributed to the resonant nature of the excitation of intermediate ions.},
author = {Hitzenberger, Jakob and Dral, Pavlo O. and Meinhardt, Ute and Clark, Timothy and Thiel, Walter and Kivala, Milan and Drewello, Thomas},
doi = {10.1002/cplu.201600416},
faupublication = {yes},
journal = {ChemPlusChem},
keywords = {ab initio calculations;collision-induced dissociation;density functional calculations;electrospray ionisation;mass spectrometry;N-heterotriangulenes},
pages = {204-211},
peerreviewed = {unknown},
title = {{Stability} of {Odd}- {Versus} {Even}-{Electron} {Gas}-{Phase} ({Quasi}){Molecular} {Ions} {Derived} from {Pyridine}-{Substituted} {N}-{Heterotriangulenes}},
volume = {82},
year = {2017}
}
@article{faucris.120967484,
author = {Mauser, Harald and Hirsch, Andreas and van Eikema Hommes, Nico and Clark, Timothy and Pietzak, Björn and Weidinger, Alois and Dunsch, Lothar},
doi = {10.1002/anie.199728351},
faupublication = {yes},
journal = {Angewandte Chemie (International Edition in English)},
month = {Jan},
pages = {2835-2838},
peerreviewed = {Yes},
title = {{Stabilization} of {Atomic} {Nitrogen} {Inside} {C60}},
volume = {36},
year = {1997}
}
@article{faucris.123324344,
author = {Clark, Timothy and Schleyer, Paul and et al.},
author_hint = {CLARK T, KORNER H, SCHLEYER PV},
doi = {10.1016/S0040-4039(00)71461-4},
faupublication = {yes},
journal = {Tetrahedron Letters},
month = {Jan},
pages = {743-746},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{STABILIZATION} {OF} {METHYL} {ANIONS} {BY} {1ST} {ROW} {SUBSTITUENTS}},
volume = {21},
year = {1980}
}
@article{faucris.119343444,
author = {Spitznagel, Günther W. and Clark, Timothy and Chandrasekhar, Jayaraman and Schleyer, Paul},
doi = {10.1002/jcc.540030311},
faupublication = {yes},
journal = {Journal of Computational Chemistry},
month = {Jan},
pages = {363-371},
peerreviewed = {Yes},
title = {{STABILIZATION} {OF} {METHYL} {ANIONS} {BY} {1ST}-{ROW} {SUBSTITUENTS} - {THE} {SUPERIORITY} {OF} {DIFFUSE} {FUNCTION}-{AUGMENTED} {BASIS}-{SETS} {FOR} {ANION} {CALCULATIONS}},
volume = {3},
year = {1982}
}
@article{faucris.116983284,
author = {Clark, Timothy and Schleyer, Paul},
doi = {10.1016/S0040-4039(01)86671-5},
faupublication = {yes},
journal = {Tetrahedron Letters},
month = {Jan},
pages = {4641-4644},
peerreviewed = {Yes},
title = {{STABILIZATION} {OF} {METHYL} {CATIONS} {BY} {2ND} {ROW} {SUBSTITUENTS}},
year = {1979}
}
@article{faucris.122339624,
abstract = {We introduce spectral density distribution moments as molecular descriptors. We demonstrate that these descriptors correctly represent the molecular structure. To prove the correctness of the new descriptors, we consider the IR spectra of 76 chloronaphthalenes. We show that the consecutive substitutions of the hydrogen atoms by the chlorine atoms are reflected by a regular behavior of the descriptors and, consequently, that the descriptors may be used to construct classification diagrams. The diagrams allow for a clear distinction between the compounds containing different numbers of the substituents. In the diagrams, symbols corresponding to the isomers with a given number of chlorine atoms nearly overlap and form clusters. The clusters corresponding to different numbers of chlorine atoms are well separated and distributed in a regular way. The same kind of analysis we also use as a tool for checking the correctness of the calculated spectra.},
author = {Bielinska-Waz, Dorota and Waz, Piotr and Clark, Timothy and Puzyn, Tomasz and Peplowski, Lukasz and Nowak, Wieslaw},
doi = {10.1007/s10910-012-0117-4},
faupublication = {yes},
journal = {Journal of Mathematical Chemistry},
keywords = {Statistical spectroscopy;Descriptors;Molecular similarity;DFT methods},
pages = {857-867},
peerreviewed = {Yes},
title = {{Statistical} properties of spectra of chloronaphthalenes},
volume = {51},
year = {2013}
}
@article{faucris.123941444,
abstract = {Although general interest in radical arylation reactions has grown rapidly in recent years, poor regioselectivities and the need to use a large excess of the radical-accepting arene have hindered their application to substituted benzenes. We now describe experimental and computational investigations into the substituent effects that lead to regioselective addition based on the recent discovery of anilines as outstanding substrates for radical arylations.},
author = {Hofmann, Josefa and Clark, Timothy and Heinrich, Markus},
doi = {10.1021/acs.joc.6b01840},
faupublication = {yes},
journal = {Journal of Organic Chemistry},
pages = {9785-9791},
peerreviewed = {Yes},
title = {{Strongly} {Directing} {Substituents} in the {Radical} {Arylation} of {Substituted} {Benzenes}},
volume = {81},
year = {2016}
}
@article{faucris.122495384,
author = {Clark, Timothy and Schleyer, Paul},
faupublication = {yes},
journal = {Nouveau Journal de Chimie - New Journal of Chemistry},
month = {Jan},
pages = {665-666},
peerreviewed = {unknown},
title = {{STRUCTURAL} {ANALOGY} {BETWEEN} {FLY}-{OVER} {BRIDGE} {METAL}-{COMPLEXES} {AND} {ORGANIC} {DICATIONS} - {COMMENT}},
volume = {2},
year = {1978}
}
@article{faucris.120306164,
abstract = {Thin films of self-assembled supramolecular grid structures were prepared by electrochemical deposition. The surface structure of the films was determined by electrochemical in-situ scanning tunneling microscopy (STM), revealing ordered monolayers of the grid molecules on a Au(111) surface. The electronic structure of the films was studied by photoelectron spectroscopy. The thin films show semiconducting behavior with an insulating gap of ca. 2.5 eV. The size of insulating gap can be reduced to 0.5 eV by doping the films with additional Cd ions, which is in agreement with molecular orbital calculations. Additionally, conductivity measurements were performed. By doping of the thin films, their conductivity could be increased by several orders of magnitude. This is due to additional electronic states in the insulating HOMO-LUMO gap, which is confirmed by UPS measurements.},
author = {Hassmann, Jörg and Hahn, C. Y. and Waldmann, Oliver and Volz, Eduard and Schleemilch, H-J. and Hallschmid, Nikolaus and Müller, Paul and Hanan, Garry Shawn and Volkmer, Dirk and Schubert, Ulrich S. and Lehn, Jean-Marie and Mauser, Harald and Hirsch, Andreas and Clark, Timothy},
faupublication = {yes},
journal = {Materials Research Society Symposium - Proceedings},
pages = {447-452},
peerreviewed = {Yes},
title = {{Structural} and electronic properties of self-assembled supramolecular grid structures: {Doping} of supramolecular thin films},
url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-17144462000&origin=inward},
volume = {488},
year = {1998}
}
@article{faucris.122495604,
abstract = {The binding motif ( pharmacophore) for induction and the changes in the structure of the binding site that accompany induction have been determined from molecular-dynamics simulations on the tetracycline-repressor signal-transduction protein. The changes and the induction mechanism are discussed and compared with conclusions drawn from earlier X-ray structures. The differences in inducer strength of tetracycline and 5a, 6-anhydrotetracycline are discussed with respect to their interaction in the MD simulations.},
author = {Lanig, Harald and Othersen, Olaf and Seidel, Ute and Beierlein, Frank and Exner, Thomas and Clark, Timothy},
doi = {10.1021/jm060289g},
faupublication = {yes},
journal = {Journal of Medicinal Chemistry},
pages = {3444-3447},
peerreviewed = {Yes},
title = {{Structural} changes and binding characteristics of the tetracycline-repressor binding site on induction},
volume = {49},
year = {2006}
}
@article{faucris.109667624,
abstract = {We describe computational studies of the mode of action of the prolyl hydroxylase domain containing protein (PHD2). Long-term molecular dynamics (MD) simulations were performed to investigate the rigidity of the crystallographically observed conformations of PHD2 in solution. We also describe the influence of the C-terminal oxygen-dependent degradation domain (CODD) of hypoxia inducible factor 1α (HIF-1α) on the overall behaviour of the protein, including the effect of the natural ligand 2-oxoglutarate (2OG) and an isoquinoline inhibitor. To study the geometry of the 2-His-1-carboxylate facial triad and its dependency on the protein environment, we performed DFT calculations on model systems and compared them with quantum mechanics/molecular mechanics (QM/MM) gas-phase energy minimisations, which allowed us to treat the whole protein. The combination of these methods provides insight into the behaviour of the 2-His-1-carboxylate facial triad with 2OG and an inhibitor of PHD2 on the atomistic scale. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.},
author = {Wick, Christian and Lanig, Harald and Jäger, Christof and Burzlaff, Nicolai and Clark, Timothy},
doi = {10.1002/ejic.201200391},
faupublication = {yes},
journal = {European Journal of Inorganic Chemistry},
pages = {4973-4985},
peerreviewed = {Yes},
title = {{Structural} insight into the prolyl hydroxylase {PHD2}: {A} molecular dynamics and {DFT} study},
year = {2012}
}
@article{faucris.117830064,
abstract = {Subtype-selective agonists of the neurotensin receptor NTS2 represent a promising option for the treatment of neuropathic pain, as NTS2 is involved in the mediation of m-opioid-independent anti-nociceptive effects. Based on the crystal structure of the subtype NTS1 and previous structure-activity relationships (SARs) indicating a potential role for the sub-pocket around Tyr11 of NT(8-13) in subtype-specific ligand recognition, we have developed new NTS2-selective ligands. Starting from NT(8-13), we replaced the tyrosine unit by β2-amino acids (type 1), by heterocyclic tyrosine bioisosteres (type 2) and peptoid analogues (type 3). We were able to evolve an asymmetric synthesis of a 5-substituted azaindolylalanine and its application as a bioisostere of tyrosine capable of enhancing NTS2 selectivity. The S-configured test compound 2a, [(S)-3-(pyrazolo[1,5-α]pyridine-5-yl)-propionyl11]NT(8-13), exhibits substantial NTS2 affinity (4.8 nm) and has a nearly 30-fold NTS2 selectivity over NTS1. The (R)-epimer 2b showed lower NTS2 affinity but more than 600-fold selectivity over NTS1.},
author = {Schaab, Carolin and Kling, Ralf and Einsiedel, Jürgen and Hübner, Harald and Clark, Timothy and Seebach, Dieter and Gmeiner, Peter},
doi = {10.1002/open.201402031},
faupublication = {yes},
journal = {ChemistryOpen},
note = {UnivIS-Import:2015-03-09:Pub.2014.nat.dchph.lphch.struct},
pages = {206-218},
peerreviewed = {Yes},
title = {{Structure}-{Based} {Evolution} of {Subtype}-{Selective} {Neurotensin} {Receptor} {Ligands}},
volume = {3},
year = {2014}
}
@article{faucris.123751144,
abstract = {Crystal structures of G protein-coupled receptor (GPCR) ligand complexes allow a rational design of novel molecular probes and drugs. Here we report the structure-guided design, chemical synthesis and biological investigations of bivalent ligands for dopamine D-2 receptor/neurotensin NTS1 receptor (D2R/NTS1R) heterodimers. The compounds of types 1-3 consist of three different D2R pharmacophores bound to an affinity-generating lipophilic appendage, a polyethylene glycol-based linker and the NTS1R agonist NT(8-13). The bivalent ligands show binding affinity in the picomolar range for cells coexpressing both GPCRs and unprecedented selectivity (up to three orders of magnitude), compared with cells that only express D(2)Rs. A functional switch is observed for the bivalent ligands 3b,c inhibiting cAMP formation in cells singly expressing D(2)Rs but stimulating cAMP accumulation in D2R/NTS1R-coexpressing cells. Moreover, the newly synthesized bivalent ligands show a strong, predominantly NTS1R-mediated beta-arrestin-2 recruitment at the D2R/NTS1R-coexpressing cells.},
author = {Hübner, Harald and Schellhorn, Tamara and Gienger, Marie and Schaab, Carolin and Kaindl, Jonas and Leeb, Laurin and Clark, Timothy and Möller, Dorothee and Gmeiner, Peter},
doi = {10.1038/ncomms12298},
faupublication = {yes},
journal = {Nature Communications},
pages = {12298},
peerreviewed = {Yes},
title = {{Structure}-guided development of heterodimer-selective {GPCR} ligands},
volume = {7},
year = {2016}
}
@article{faucris.116991644,
author = {Schleyer, Paul and Clark, Timothy and Kos, Alex and Spitznagel, Günther W. and et al.},
author_hint = {KANETI J, SCHLEYER PV, CLARK T, KOS AJ, SPITZNAGEL GW, ANDRADE JG, MOFFAT JB},
doi = {10.1021/ja00267a018},
faupublication = {yes},
journal = {Journal of the American Chemical Society},
pages = {1481-1492},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{STRUCTURES} {AND} {ENERGIES} {OF} {THE} {LITHIUM}, {SODIUM}, {AND} {MAGNESIUM} {DERIVATIVES} {OF} {THE} {ANIONS} {CH2CN}- {AND} {CH2NC}- - {SOLVATION} {AND} {AGGREGATION} {OF} {THE} {LITHIUM} {SPECIES}},
volume = {108},
year = {1986}
}
@article{faucris.123439844,
author = {Schleyer, Paul and Clark, Timothy and Kos, Alex and Spitznagel, Günther W. and et al.},
author_hint = {SCHLEYER PV, CLARK T, KOS AJ, SPITZNAGEL GW, ROHDE C, ARAD D, HOUK KN, RONDAN NG},
doi = {10.1021/ja00334a001},
faupublication = {yes},
journal = {Journal of the American Chemical Society},
month = {Jan},
pages = {6468-6475},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{STRUCTURES} {AND} {STABILITIES} {OF} {ALPHA}-{HETERO}-{SUBSTITUTED} {ORGANO}-{LITHIUM} {AND} {ORGANOSODIUM} {COMPOUNDS} - {ENERGETIC} {UNIMPORTANCE} {OF} {2ND}-{ROW} {D}-{ORBITAL} {EFFECTS}},
volume = {106},
year = {1984}
}
@article{faucris.122496264,
author = {Clark, Timothy and Schleyer, Paul and et al.},
author_hint = {CLARK T, SCHLEYER PV, HOUK KN, RONDAN NG},
doi = {10.1039/C39810000579},
faupublication = {yes},
journal = {Journal of the Chemical Society - Series Chemical Communications},
month = {Jan},
pages = {579-581},
peerreviewed = {unknown},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{STRUCTURES} {OF} {ALPHA}-{LITHIOMETHANOL} {AND} {ALPHA}-{LITHIOMETHYLAMINE} - {AN} {ABINITIO} {STUDY}},
year = {1981}
}
@article{faucris.120128404,
abstract = {We report experimental and theoretical studies on the structure and properties of carbonato and bicarbonato complexes of bis(1,10-phenanthroline)zinc(II). The complex [Zn(phen)2-O2CO] has been synthesized and DFT calculations have been performed based upon its X-ray structure. The carbonate ligand coordinates in a bidentate binding mode to the metal centre with Zn-O distances of 2.130 and 2.092 Å in the X-ray structure and 2.027 Å for both distances in the calculated gas-phase structure. Because of the fundamental role of (bicarbonato)ZnII complexes, especially in different carbonic anhydrases, the structures and properties of the experimentally unknown bicarbonato complexes of this kind were investigated using DFT with different basis sets up to the Ahlrichs triple zeta basis set with additional polarization functions. The bidentate bicarbonato complex [Zn(phen)2O2C(OH)]+ was found to be about 8.2 kcal·mol-1 (SHAsvp), 6.4 kcal·mol-1 (Ahlrichs triple zeta with polarization functions) and 3.5 kcal·mol-1 (Ahlrichs triple zeta) more stable than the quasi-monodentate bicarbonato complex [Zn(phen)20(OH)CO]+. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2003).},
author = {Hanauer, Hans and Liehr, Günter and Clark, Timothy and van Eldik, Rudi and et al.},
author_hint = {Erras-Hanauer Hans, Mao Zong-Wan, Liehr Günter, Clark Tim, van Eldik Rudi},
doi = {10.1002/ejic.200390204},
faupublication = {yes},
journal = {European Journal of Inorganic Chemistry},
keywords = {Bicarbonate complexes; Carbonate complexes; Density functional calculations; Zinc},
note = {UnivIS-Import:2015-03-09:Pub.2003.forsch.sonder.sfb583.struct},
pages = {1562-1569},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{Structures} of {Carbonato} and {Bicarbonato} {Complexes} of {Bis}(1,10-phenanthroline){Zinc}({II}): {Experiment} and {Theory}},
year = {2003}
}
@article{faucris.108907524,
author = {Clark, Timothy and Schleyer, Paul},
doi = {10.1039/c39790000883},
faupublication = {yes},
journal = {Journal of the Chemical Society - Series Chemical Communications},
month = {Jan},
pages = {883-884},
peerreviewed = {unknown},
title = {{STRUCTURES} {OF} {THE} {CARBENOID} {CH2FLI} - {ABINITIO} {MO} {CALCULATIONS}},
year = {1979}
}
@misc{faucris.122498464,
author = {Schürer, Gudrun and Clark, Timothy},
faupublication = {yes},
peerreviewed = {automatic},
title = {{Study} of the reaction mechanism of bovine lens leucine aminopeptidase using semiempirical methods.},
year = {2001}
}
@article{faucris.116996044,
author = {Clark, Timothy and Spitznagel, Günther W. and Schleyer, Paul and et al.},
author_hint = {CLARK T, SPITZNAGEL GW, KLOSE R, SCHLEYER PV},
doi = {10.1021/ja00328a020},
faupublication = {yes},
journal = {Journal of the American Chemical Society},
month = {Jan},
pages = {4412-4419},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{SUBSTITUENT} {EFFECTS} {ON} {THE} {GEOMETRIES} {AND} {ENERGIES} {OF} {CYCLOPROPANES} {AND} {THE} {CORRESPONDING} 2-{PROPYL} {DERIVATIVES}},
volume = {106},
year = {1984}
}
@article{faucris.109449824,
abstract = {Surface-integral models based on AMI semiempirical molecular orbital calculations are presented for the free energies of solvation in water, n-octanol, and chloroform and for the enthalpy of solvation in water. A parametrized function of four local properties calculated at the isodensity surface (the molecular electrostatic potential, local ionization energy, electron affinity, and polarizability) is integrated over the triangulated surface area to obtain the target quantity. The resulting models give results only slightly less accurate than those reported for parametrized generalized Born/polar surface area models despite relying only on gas-phase calculations. The water and octanol free-energy models were validated by calculating the water-octanol partition coefficient for a test set of organic compounds with moderate success. The models lead to a local solvation energy, which can be projected onto the molecular isodensity surface and provides insight into "hot" areas for solvation in water or the other solvents.},
author = {Ehresmann, Bernd and Clark, Timothy and et al.},
author_hint = {Ehresmann B, de Groot MJ, Clark T},
doi = {10.1021/ci050025n},
faupublication = {yes},
journal = {Journal of Chemical Information and Modeling},
pages = {1053-1060},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{Surface}-integral {QSPR} models: {Local} energy properties},
volume = {45},
year = {2005}
}
@article{faucris.224992977,
abstract = {Two-dimensional covalent organic frameworks (2D COFs) attract great interest owing to their well-defined pore structure, thermal stability, high surface area, and permanent porosity. In combination with a tunable chemical pore environment, COFs are intriguing candidates for molecular sieving based on selective host-guest interactions. Herein, we report on 2D COF structures capable of reversibly switching between a highly correlated crystalline, porous and a poorly correlated, nonporous state by exposure to external stimuli. To identify COF structures with such dynamic response, we systematically studied the structural properties of a family of two-dimensional imine COFs comprising tris(4-aminophenyl)benzene (TAPB) and a variety of dialdehyde linear building blocks including terephthalaldehyde (TA) and dialdehydes of thienothiophene (TT), benzodithiophene (BDT), dimethoxybenzodithiophene (BDT-OMe), diethoxybenzodithiophene (BDT-OEt), dipropoxybenzodithiophene (BDT-OPr), and pyrene (Pyrene-2,7). TAPB-COFs consisting of linear building blocks with enlarged π-systems or alkoxy functionalities showed significant stability toward exposure to external stimuli such as solvents or solvent vapors. In contrast, TAPB-COFs containing unsubstituted linear building blocks instantly responded to exposure to these external stimuli by a drastic reduction in COF layer correlation, long-range order, and porosity. To reverse the process we developed an activation procedure in supercritical carbon dioxide (scCO2) as a highly efficient means to revert fragile nonporous and amorphous COF polymers into highly crystalline and open porous frameworks. Strikingly, the framework structure of TAPB-COFs responds dynamically to such chemical stimuli, demonstrating that their porosity and crystallinity can be reversibly controlled by alternating steps of solvent stimuli and scCO2 activation.},
author = {Sick, Torben and Rotter, Julian M. and Reuter, Stephan and Kandambeth, Sharath and Bach, Nicolai N. and Döblinger, Markus and Merz, Julia and Clark, Timothy and Marder, Todd B. and Bein, Thomas and Medina, Dana D.},
doi = {10.1021/jacs.9b02800},
faupublication = {yes},
journal = {Journal of the American Chemical Society},
note = {CRIS-Team Scopus Importer:2019-08-23},
peerreviewed = {Yes},
title = {{Switching} on and off {Interlayer} {Correlations} and {Porosity} in {2D} {Covalent} {Organic} {Frameworks}},
year = {2019}
}
@article{faucris.208725102,
abstract = {Covalent organic frameworks (COFs), formed by reversible condensation of rigid organic building blocks, are crystalline and porous materials of great potential for catalysis and organic electronics. Particularly with a view of organic electronics, achieving a maximum degree of crystallinity and large domain sizes while allowing for a tightly pi-stacked topology would be highly desirable. We present a design concept that uses the 3D geometry of the building blocks to generate a lattice of uniquely defined docking sites for the attachment of consecutive layers, thus allowing us to achieve a greatly improved degree of order within a given average number of attachment and detachment cycles during COF growth. Synchronization of the molecular geometry across several hundred nanometers promotes the growth of highly crystalline frameworks with unprecedented Spectroscopic data indicate considerable delocalization of excitations along the pi-stacked columns and the feasibility of donor-acceptor excitations across the imine bonds. The frameworks developed in this study can serve as a blueprint for the design of a broad range of tailor-made 2D COFs with extended pi-conjugated building blocks for applications in photocatalysis and optoelectronics.},
author = {Auras, Florian and Ascherl, Laura and Haldmioun, Amir H. and Margraf, Johannes and Hanusch, Fabian C. and Reuter, Stephan and Bessinger, Derya and Doeblinger, Markus and Hettstedt, Christina and Karaghiosoff, Konstantin and Herbert, Simon and Knochel, Paul and Clark, Timothy and Bein, Thomas},
doi = {10.1021/jacs.6b09787},
faupublication = {yes},
journal = {Journal of the American Chemical Society},
pages = {16703-16710},
peerreviewed = {Yes},
title = {{Synchronized} {Offset} {Stacking}: {A} {Concept} for {Growing} {Large}-{Domain} and {Highly} {Crystalline} {2D} {Covalent} {Organic} {Frameworks}},
volume = {138},
year = {2016}
}
@article{faucris.242409962,
author = {Anaya-Plaza, Eduardo and Joseph, Jan and Bauroth, Stefan and Wagner, Maximilian and Dolle, Christian and Sekita, Michael and Gröhn, Franziska and Spiecker, Erdmann and Clark, Timothy and de la Escosura, Andrés and Guldi, Dirk Michael and Torres, Tomás},
doi = {10.1002/ange.202006014},
faupublication = {yes},
journal = {Angewandte Chemie},
note = {CRIS-Team Scopus Importer:2020-09-11},
peerreviewed = {Yes},
title = {{Synergie} von elektrostatischen und π-π-{Wechselwirkungen} für die {Verwirklichung} von künstlichen photosynthetischen {Modellsystemen} auf {Nano}-{Ebene}},
year = {2020}
}
@article{faucris.242410199,
abstract = {In the scientific race to build up photoactive electron donor-acceptor systems with increasing efficiencies, little is known about the interplay of their building blocks when integrated into supramolecular nanoscale arrays, particularly in aqueous environments. Here, we describe an aqueous donor-acceptor ensemble whose emergence as a nanoscale material renders it remarkably stable and efficient. We have focused on a tetracationic zinc phthalocyanine (ZnPc) featuring pyrenes, which shows an unprecedented mode of aggregation, driven by subtle cooperation between electrostatic and π–π interactions. Our studies demonstrate monocrystalline growth in solution and a symmetry-breaking intermolecular charge transfer between adjacent ZnPcs upon photoexcitation. Immobilizing a negatively charged fullerene (C60) as electron acceptor onto the monocrystalline ZnPc assemblies was found to enhance the overall stability, and to suppress the energy-wasting charge recombination found in the absence of C60. Overall, the resulting artificial photosynthetic model system exhibits a high degree of preorganization, which facilitates efficient charge separation and subsequent charge transport.},
author = {Anaya-Plaza, Eduardo and Joseph, Jan and Bauroth, Stefan and Wagner, Maximilian and Dolle, Christian and Sekita, Michael and Gröhn, Franziska and Spiecker, Erdmann and Clark, Timothy and de la Escosura, Andrés and Guldi, Dirk Michael and Torres, Tomás},
doi = {10.1002/anie.202006014},
faupublication = {yes},
journal = {Angewandte Chemie International Edition},
keywords = {artificial photosynthesis; fullerenes; nanoscale self-assembly; phthalocyanines},
note = {CRIS-Team Scopus Importer:2020-09-11},
peerreviewed = {Yes},
title = {{Synergy} of {Electrostatic} and π–π {Interactions} in the {Realization} of {Nanoscale} {Artificial} {Photosynthetic} {Model} {Systems}},
year = {2020}
}
@article{faucris.228700194,
abstract = {The design and synthesis of functionalized isoindigo compounds by reaction of isoindigo with (S)-glycidyl tosylate, epibromohydrin, 2-(bromomethyl)-1-(arylsulfonyl)aziridine, and 2-(bromomethyl)-1-(alkylsulfonyl)aziridine in the presence of MeONa proceed under mild conditions in moderate yields. (3Z,3′Z)-3,3′-(Ethane-1,2-diylidene)bis(1-(oxiran-2-ylmethyl)indolin-2-one), with an extended central olefin π-conjugated moiety was also reacted with methyl-oxiranes to give the corresponding N.N″-disubstituted derivative. Calculations with DFT and TD-DFT of hypothetical isoindigo-thiophene DA molecules with various electron withdrawing substituents, including aziridine, oxirane, nitrile, carbonyl, and sulfonate, indicated that the proximity and strength of the functional group have a significant effect on the HOMO, LUMO, vertical excitation energy and oscillator strength of the π-π∗ transitions.},
author = {Khalili, Gholamhossein and McCosker, Patrick M. and Clark, Timothy and Keller, Paul A.},
doi = {10.3390/molecules24203649},
faupublication = {yes},
journal = {Molecules},
keywords = {Density functional theory; Donor-acceptor functionalization; Isoindigo alkylation; Organic semiconductor; Time dependent density functional theory},
note = {CRIS-Team Scopus Importer:2019-11-05},
peerreviewed = {Yes},
title = {{Synthesis} and density functional theory studies of azirinyl and oxiranyl functionalized isoindigo and ({3Z},3′{Z})-3,3′-(ethane-1,2-diylidene)bis(indolin-2-one) derivatives},
volume = {24},
year = {2019}
}
@article{faucris.121144364,
abstract = {A new guanidine-thiourea organocatalyst has been developed and applied as bifunctional organocatalyst in the Michael addition reaction of diethyl malonate to trans-β-nitrostyrene. Extensive DFT calculations, including solvent effects and dispersion corrections, as well as ab initio calculations provide a plausible description of the reaction mechanism.},
author = {Shubina, Tatyana and Freund, Matthias and Schenker, Sebastian and Clark, Timothy and Tsogoeva, Svetlana},
doi = {10.3762/bjoc.8.168},
faupublication = {yes},
journal = {Beilstein Journal of Organic Chemistry},
pages = {1485-1498},
peerreviewed = {Yes},
title = {{Synthesis} and evaluation of new guanidine-thiourea organocatalyst for the nitro-{Michael} reaction: {Theoretical} studies on mechanism and enantioselectivity},
volume = {8},
year = {2012}
}
@article{faucris.116846664,
abstract = {Despite of a remarkable ring strain hitherto unknown dibenzo[c,e][1,2]diazocines 3 could be prepared from readily available azo compounds 4 under mild Ullmann-type reaction conditions. The obtained stereoisomers of the new heterocycles 3 were structurally assigned by 2D NMR experiments and DFT calculations. (C) 2014 Elsevier Ltd. All rights reserved.},
author = {Nokubi, Tomomi and Kindt, Stephanie and Clark, Timothy and Kamimura, Akio and Heinrich, Markus},
doi = {10.1016/j.tetlet.2014.11.064},
faupublication = {yes},
journal = {Tetrahedron Letters},
keywords = {Radical reactions;Azo compounds;Ullmann coupling;Diazocines;Heterocycles},
month = {Jan},
pages = {316-320},
peerreviewed = {Yes},
title = {{Synthesis} of dibenzo[c,e][1,2]diazocines-a new group of eight-membered cyclic azo compounds},
volume = {56},
year = {2015}
}
@article{faucris.122500444,
abstract = {AM1 semiempirical molecular orbital calculations have been used to probe the complexation sites for naked and hydrated magnesium ions to the different conformations and protonation states of tetracycline. The calculations reveal a wealth of possible magnesium complexation sites within a small energy range, but also indicate that magnesium complexation does not change the conformational behavior of tetracycline significantly. A hitherto unknown solvated conformation is suggested for deprotonated tetracycline.},
author = {Othersen, Olaf and Lanig, Harald and Clark, Timothy},
doi = {10.1021/jm034199c},
faupublication = {yes},
journal = {Journal of Medicinal Chemistry},
pages = {5571-5574},
peerreviewed = {Yes},
title = {{Systematic} surface scan of the most favorable interaction sites of magnesium ions with tetracycline},
volume = {46},
year = {2003}
}
@article{faucris.237816345,
abstract = {Evolution has yielded biopolymers that are constructed from exactly four building blocks and are able to support Darwinian evolution. Synthetic biology aims to extend this alphabet, and we recently showed that 8-letter (hachimoji) DNA can support rule-based information encoding. One source of replicative error in non-natural DNA-like systems, however, is the occurrence of alternative tautomeric forms, which pair differently. Unfortunately, little is known about how structural modifications impact free-energy differences between tautomers of the non-natural nucleobases used in the hachimoji expanded genetic alphabet. Determining experimental tautomer ratios is technically difficult, and so, strategies for improving hachimoji DNA replication efficiency will benefit from accurate computational predictions of equilibrium tautomeric ratios. We now report that high-level quantum-chemical calculations in aqueous solution by the embedded cluster reference interaction site model, benchmarked against free-energy molecular simulations for solvation thermodynamics, provide useful quantitative information on the tautomer ratios of both Watson-Crick and hachimoji nucleobases. In agreement with previous computational studies, all four Watson-Crick nucleobases adopt essentially only one tautomer in water. This is not the case, however, for non-natural nucleobases and their analogues. For example, although the enols of isoguanine and a series of related purines are not populated in water, these heterocycles possess N1-H and N3-H keto tautomers that are similar in energy, thereby adversely impacting accurate nucleobase pairing. These robust computational strategies offer a firm basis for improving experimental measurements of tautomeric ratios, which are currently limited to studying molecules that exist only as two tautomers in solution.},
author = {Eberlein, Lukas and Beierlein, Frank and van Eikema Hommes, Nico and Radadiya, Ashish and Heil, Jochen and Benner, Steven A. and Clark, Timothy and Kast, Stefan M. and Richards, Nigel G.J.},
doi = {10.1021/acs.jctc.9b01079},
faupublication = {yes},
journal = {Journal of Chemical Theory and Computation},
note = {CRIS-Team Scopus Importer:2020-04-28},
pages = {2766-2777},
peerreviewed = {Yes},
title = {{Tautomeric} {Equilibria} of {Nucleobases} in the {Hachimoji} {Expanded} {Genetic} {Alphabet}},
volume = {16},
year = {2020}
}
@article{faucris.117001984,
abstract = {The importance of calculating not only the correct tautomer, but also the correct protonation state and conformation in 3D modeling applications is emphasized. Above all, identifying and characterizing the most stable form of a ligand under physiological conditions is seen to be the key to successful 3D modeling. Modeling strategies that make use of the performance of modern hardware can employ physically more appropriate models than most currently in use and still be easily applicable to large numbers of compounds. Because the performance of quantitative structure-property relationships is likely to be limited by the available training and validation data, we must either find new sources of such data or resort to explicit modeling, which can partly be parameterized using definitive ab initio calculations for reference data such as gas-phase proton affinities.},
author = {Clark, Timothy},
doi = {10.1007/s10822-010-9342-8},
faupublication = {yes},
journal = {Journal of Computer-Aided Molecular Design},
keywords = {Tautomers;QSPR;Force fields;pK(a)},
pages = {605-611},
peerreviewed = {Yes},
title = {{Tautomers} and reference {3D}-structures: the orphans of in silico drug design},
volume = {24},
year = {2010}
}
@article{faucris.115070384,
abstract = {A combined experimental and theoretical study shows that the photooxidative activity of two isostructural metal oxide clusters depends on their internal templates. To this end, two halide-templated bismuth vanadium oxide clusters [X(Bi(dmso)(3))(2)V12O33](-) (X=Cl-, Br-) are reported and fully characterized. The two clusters show similar absorption features and illustrate that bismuth incorporation results in increased visible-light absorption. Significantly higher photooxidative activity is observed for the bromide-templated cluster compared with the chloride-templated one. Detailed photophysical assays and complementary DFT calculations suggest that the more efficient triplet excited state formation in the Br--containing cluster is the decisive step in the photocatalysis and is due to the heavy-atom effect of the bromide. This concept can therefore open new pathways towards the optimization of photocatalytic activity in metal oxide clusters.},
author = {Tucher, Johannes and Peuntinger, Katrin and Margraf, Johannes and Clark, Timothy and Guldi, Dirk Michael and Streb, Carsten},
doi = {10.1002/chem.201501129},
faupublication = {yes},
journal = {Chemistry - A European Journal},
keywords = {density functional calculations;metal oxide;polyoxometalate;self-assembly;template},
pages = {8716-8719},
peerreviewed = {Yes},
title = {{Template}-{Dependent} {Photochemical} {Reactivity} of {Molecular} {Metal} {Oxides}},
volume = {21},
year = {2015}
}
@article{faucris.311728621,
abstract = {Photon energy conversion can be accomplished in many different ways, including the two opposing manners, down-conversion (i.e., singlet fission, SF) and up-conversion (i.e., triplet-triplet annihilation up-conversion, TTA-UC). Both processes have the potential to help overcome the detailed balance limit of single-junction solar cells. Tetracene, in which the energies of the lowest singlet excited state and twice the triplet excited state are comparable, exhibits both down- and up-conversion. Here, we have designed meta-diethynylphenylene- and 1,3-diethynyladamantyl-linked tetracene dimers, which feature different electronic coupling, to characterize the interplay between intramolecular SF (intra-SF) and intramolecular TTA-UC (intra-TTA-UC) via steady-state and time-resolved absorption and fluorescence spectroscopy. Furthermore, we have used Pd-phthalocyanine as a sensitizer to enable intra-TTA-UC in the two dimers via indirect photoexcitation in the near-infrared part of the solar spectrum. The work is rounded off by temperature-dependent measurements, which outline key aspects of how thermal effects impact intra-SF and intra-TTA-UC in different dimers.},
author = {Bo, Yifan and Hou, Yuxuan and Thiel, Dominik and Weiß, René and Clark, Timothy and Ferguson, Michael J. and Tykwinski, Rik R. and Guldi, Dirk Michael},
doi = {10.1021/jacs.3c02417},
faupublication = {yes},
journal = {Journal of the American Chemical Society},
note = {CRIS-Team Scopus Importer:2023-10-06},
pages = {18260-18275},
peerreviewed = {Yes},
title = {{Tetracene} {Dimers}: {A} {Platform} for {Intramolecular} {Down}- and {Up}-conversion},
volume = {145},
year = {2023}
}
@article{faucris.119344324,
author = {Weiß, Robert and Clark, Timothy and et al.},
author_hint = {WEISS R, WOLF H, SCHUBERT U, CLARK T},
doi = {10.1021/ja00410a027},
faupublication = {yes},
journal = {Journal of the American Chemical Society},
month = {Jan},
pages = {6142-6147},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{THE} {1ST} {BIS} {GEM} {DONOR}-{ACCEPTOR} {SUBSTITUTED} {ALLENE} - {SYNTHESIS}, {GEOMETRY}, {AND} {ELECTRONIC}-{STRUCTURE}},
volume = {103},
year = {1981}
}
@article{faucris.109451584,
author = {Kos, Alex and Clark, Timothy and Schleyer, Paul},
faupublication = {yes},
journal = {Angewandte Chemie International Edition},
month = {Jan},
pages = {620-621},
peerreviewed = {Yes},
title = {{THE} {ABINITIO} {CALCULATION} {OF} {THE} {STRUCTURE} {OF} 1,3-{DILITHIOACETONE}},
volume = {23},
year = {1984}
}
@article{faucris.117008804,
abstract = {It is a well-established concept that the C-N bond cleavage of carboxamide functions is facilitated by the coordination of a metal ion to the carbonyl oxygen atom. In contrast, the alternative C-N bond activation by coordination of a neutral tertiary carboxamide nitrogen atom has not been studied. We present the first results on the effect of nitrogen pyramidalization in N-coordinated metal complexes on the methanolysis of tertiary carboxamide groups. An analysis of the reactions products obtained from the methanol cleavage of [(N-Acyl-bpa)Cu](2+) (bpa = N,N-bispicolylamine) complexes is presented together with experimental and high-level theoretically calculated structures. The strong effect of different anions on the amide pyramidalization and subsequent C-N-bond cleavage is evaluated. We show that dichloro complexes [(N-Acyl-bpa)CuCl2] have much less activated amide groups than the corresponding triflate species. They should therefore be less reactive. However, [(N-Acyl-bpa)CuCl2] complexes dissociate in solution to give cationic monochloro complexes [(N-Acyl-bpa)Cu(S)Cl](+) (S = solvent molecule). Theoretical calculations show that the amide pyramidalization in the monochloro complexes is equal to that in the corresponding CF3SO3- salts. Consequently, chloro and triflato complexes are cleaved with similar rates and efficiencies. Parallels to and differences in the reactivity of purely organic distorted amides are discussed.},
author = {Hampel, Frank and Clark, Timothy and Alsfasser, Ralf and et al.},
author_hint = {Niklas N, Heinemann FW, Hampel F, Clark T, Alsfasser R},
doi = {10.1021/ic0496774},
faupublication = {yes},
journal = {Inorganic Chemistry},
pages = {4663-4673},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{The} activation of tertiary carboxamides in metal complexes: {An} experimental and theoretical study on the methanolysis of acylated bispicolylamine copper({II}) complexes},
volume = {43},
year = {2004}
}
@article{faucris.251071727,
abstract = {The synthesis of structurally diverse heterocycles for chemical space exploration was achieved via the cascade reactions of indigo with propargylic electrophiles. New pyrazinodiindolodione, naphthyridinedione, azepinodiindolone, oxazinoindolone and pyrrolodione products were prepared in one pot reactions by varying the leaving group (-Cl, -Br, -OMs, -OTs) or propargyl terminal functionality (-H, -Me, -Ph, -Ar). Mechanistic and density functional theory studies revealed that the unsaturated propargyl moiety can behave as an electrophile when aromatic terminal substitutions are made, and therefore competes with leaving group substitution for new outcomes. Selected products from the cascade reactions were investigated for their absorption and fluorescence properties, including transient absorption spectroscopy. This revealed polarity dependent excited state relaxation pathways, fluorescence, and triplet formation, thus highlighting these reactions as a means to access diverse functional materials rapidly.},
author = {Mccosker, Patrick M. and Butler, Nicholas M. and Shakoori, Alireza and Volland, Michel and Perry, Matthew J. and Mullen, Jesse W. and Willis, Anthony C. and Clark, Timothy and Bremner, John B. and Guldi, Dirk Michael and Keller, Paul A.},
doi = {10.1002/chem.202003662},
faupublication = {yes},
journal = {Chemistry - A European Journal},
note = {CRIS-Team WoS Importer:2021-03-05},
peerreviewed = {Yes},
title = {{The} {Cascade} {Reactions} of {Indigo} with {Propargyl} {Substrates} for {Heterocyclic} and {Photophysical} {Diversity}},
year = {2021}
}
@article{faucris.107006064,
author = {Schürer, Gudrun and Lanig, Harald and Clark, Timothy},
faupublication = {yes},
journal = {Journal of Molecular Graphics & Modelling},
pages = {278-278},
peerreviewed = {Yes},
title = {{The} catalytic mechanism of phospholipase {A2}: {Semiempirical} calculations including the protein environment by a {QM}/{MM} approach},
volume = {16},
year = {1998}
}
@incollection{faucris.208603016,
author = {Lanig, Harald and Clark, Timothy},
booktitle = {Systems Chemistry - Proceedings of the International Beilstein Workshop 2008},
editor = {M. G. Hicks, C. Kettner},
faupublication = {yes},
peerreviewed = {Yes},
title = {{The} {Chemistry} of {Signal} {Transduction} in the {TetR} {System}},
year = {2008}
}
@article{faucris.281402399,
author = {Clark, Timothy and Brinck, Tore},
doi = {10.1007/s00894-022-05192-x},
faupublication = {yes},
journal = {Journal of Molecular Modeling},
note = {CRIS-Team Scopus Importer:2022-09-09},
peerreviewed = {Yes},
title = {{The} {Conversation} on {Non}-{Covalent} {Interactions}: an introduction},
volume = {28},
year = {2022}
}
@article{faucris.208727483,
abstract = {Contrary to recent reports, the sigma-hole interaction energies of complexes between the carbon tetrahalides CX3I (X = F, Cl, Br, I) and halide anions Y- (Y = F, Cl, Br, I) are described very well by the simple Coulombic sigma-hole concept if it is applied properly. There is no need to invoke charge transfer, which in any case is not uniquely distinguishable from polarization.},
author = {Clark, Timothy and Heßelmann, Andreas},
doi = {10.1039/c8cp03079k},
faupublication = {yes},
journal = {Physical Chemistry Chemical Physics},
pages = {22849-22855},
peerreviewed = {Yes},
title = {{The} coulombic sigma-hole model describes bonding in {CX3I} center dot center dot center dot {Y}- complexes completely},
volume = {20},
year = {2018}
}
@article{faucris.116840724,
abstract = {Density-functional theory (DFT) and QCISD(T) calculations have been used to investigate the mechanism of cyclodimerisation and cyclotrimerisation of acetylene at a cyclopentadienyl-Col centre. In contrast to earlier investigations, we find that the most favourable mechanism for the formation of benzene involves the insertion of an acetylene molecule into a Co-C bond of the well known cobaltacyclopentadienyl intermediate. The product of this reaction then undergoes very facile ring-closure to benzene. This mechanism is found to be more favourable than the concerted Diels-Alder path, which is the highest in energy of the three mechanisms considered. The remaining reaction path involves initial addition of an acetylene molecule to the cyclopentadienyl ligand followed by rearrangement to give a 1,3,5-hexatrien-1-ylcyclopentane ligand system, which cleaves to give benzene and cyclopentadienyl ligands. Spin crossovers between the singlet and triplet states are found for the ring-closure of the cobaltacyclopentadienyl intermediate to give a cyclobutadiene complex and for the concerted Diels-Alder process. These spin crossovers and the reaction mechanisms in general are rationalised in terms of the concept of electron-transfer catalysis. ((C) Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008).},
author = {Xu, Rong and Winget, Paul and Clark, Timothy},
doi = {10.1002/ejic.200800077},
faupublication = {yes},
journal = {European Journal of Inorganic Chemistry},
keywords = {ab initio calculations;DFT calculations;transition states;electron transfer;electron-transfer catalysis},
pages = {2874-2883},
peerreviewed = {Yes},
title = {{The} cyclooligomerisation of acetylene at metal centres},
year = {2008}
}
@article{faucris.261851266,
abstract = {The deprotection of chiral 1,2-bis(tosylamides) to their corresponding 1,2-diamines is mostly unsuccessful under standard conditions. In a new methodology, the use of Mg/MeOH with sufficient steric additions allows the facile synthesis of 1,2-diamines in 78-98% yields. These results are rationalized using density functional theory and the examination of inner and outer-sphere reduction mechanisms.},
author = {Gaston, Jayden J. and Tague, Andrew J. and Smyth, Jamie E. and Butler, Nicholas M. and Willis, Anthony C. and van Eikema Hommes, Nico and Yu, Haibo and Clark, Timothy and Keller, Paul A.},
doi = {10.1021/acs.joc.1c00359},
faupublication = {yes},
journal = {Journal of Organic Chemistry},
note = {CRIS-Team WoS Importer:2021-07-23},
pages = {9163-9180},
peerreviewed = {Yes},
title = {{The} {Detosylation} of {Chiral} 1,2-{Bis}(tosylamides)},
volume = {86},
year = {2021}
}
@article{faucris.117010344,
author = {Clark, Timothy},
doi = {10.1021/ja00295a005},
faupublication = {yes},
journal = {Journal of the American Chemical Society},
month = {Jan},
pages = {2597-2599},
peerreviewed = {Yes},
title = {{THE} {DIPHOSPHINE} {RADICAL} {CATION} ({P2H4}+.)},
volume = {107},
year = {1985}
}
@article{faucris.121454564,
abstract = {Density-functional theory (DFT) and ab initio calculations have been used to investigate the effect of a complexed lithium cation on the radical-clock rearrangement of the 2-norcaranyl radical to the 3-cyclohexenylmethyl radical. As found earlier for ring-closing radical clocks, complexation with a metal ion leads to it significant lowering of the barrier to rearrangement. DFT calculations on a model for the norcaranyl clock in cytochrome P450 confirm the two-state reactivity proposal of Shaik et al. and indicate that the porphyrin exerts little or no electrostatic effect on the rearrangement barrier.},
author = {Jäger, Christof and Hennemann, Matthias and Clark, Timothy},
doi = {10.1002/chem.200801076},
faupublication = {yes},
journal = {Chemistry - A European Journal},
keywords = {ab initio calculations;density functional calculations;radical clocks;radicals;rearrangement},
month = {Jan},
pages = {2425-2433},
peerreviewed = {Yes},
title = {{The} {Effect} of a {Complexed} {Lithium} {Cation} on a {Norcarane}-{Based} {Radical} {Clock}},
volume = {15},
year = {2009}
}
@article{faucris.109454004,
author = {Clark, Timothy},
faupublication = {yes},
journal = {ACS National Meeting Book of Abstracts},
pages = {U506-U506},
peerreviewed = {unknown},
title = {{The} effect of metal ions on organic reactivity.},
volume = {215},
year = {1998}
}
@article{faucris.107258844,
abstract = {We have studied hydrogen-passivated amorphous carbon nanostructures with semiempirical molecular orbital theory in order to provide an understanding of the factors that affect their electronic properties. Amorphous structures were first constructed using periodic calculations in a melt/quench protocol. Pure periodic amorphous carbon structures and their counterparts doped with nitrogen and/or oxygen feature large electronic band gaps. Surprisingly, descriptors such as the elemental composition and the number of sp3-atoms only influence the electronic structure weakly. Instead, the exact topology of the sp2-network in terms of effective conjugation defines the band gap. Amorphous carbon nanodots of different structures and sizes were cut out of the periodic structures. Our calculations predict the occurrence of localized electronic surface states, which give rise to interesting effects such as amphoteric reactivity and predicted optical band gaps in the near-UV/visible range. Optical and electronic gaps display a dependence on particle size similar to that of inorganic colloidal quantum dots.},
author = {Margraf, Johannes and Strauß, Volker and Guldi, Dirk Michael and Clark, Timothy},
doi = {10.1021/jp510620j},
faupublication = {yes},
journal = {Journal of Physical Chemistry B},
pages = {7258-7265},
peerreviewed = {Yes},
title = {{The} {Electronic} {Structure} of {Amorphous} {Carbon} {Nanodots}},
volume = {119},
year = {2015}
}
@article{faucris.122508364,
author = {Clark, Timothy and et al.},
author_hint = {CLARK T, COURTNEIDGE JL, DAVIES AG, SCHOTZ K},
doi = {10.1039/C39860000547},
faupublication = {yes},
journal = {Journal of the Chemical Society - Series Chemical Communications},
pages = {547-548},
peerreviewed = {unknown},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{THE} {ELECTRON}-{SPIN}-{RESONANCE} {SPECTRA} {AND} {SPIN} {DISTRIBUTIONS} {OF} {BENZOBARRELENE} {RADICAL} {CATIONS}},
year = {1986}
}
@article{faucris.122509024,
author = {Clark, Timothy and et al.},
author_hint = {COURTNEIDGE JL, DAVIES AG, CLARK T, WILHELM D},
doi = {10.1039/p29840001197},
faupublication = {yes},
journal = {Journal of the Chemical Society, Perkin Transactions 2},
month = {Jan},
pages = {1197-1200},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{THE} {ELECTRON}-{SPIN} {RESONANCE}-{SPECTRUM} {OF} {THE} {BIPHENYL} {RADICAL} {CATION}},
year = {1984}
}
@article{faucris.117012984,
abstract = {Ab initio calculations ( coupled cluster with single and double excitations; CCSD) have been used to investigate the model redox systems ethylene: M( 0) ( M = Li, Na, K, Rb, Cs) and ethylene: M( I) ( M = Be, Mg, Ca, Sr, Ba, Zn, Cd, Hg). Within C-2v symmetry, the ground ((2)A(1)) states correspond to the charge distribution given in the title. The lowest (B-2(2)) excited states correspond, somewhat counter intuitively, to the ethylene (center dot-)/M(II) ion pair: These trends can be rationalized on the basis of simple electrostatic and configuration-mixing arguments that lead to two simple equations for predicting the electron-transfer energies for oxidation or reduction of the ethylene. The electron-transfer energies to the B-2(2) ion pairs are dominated by the electrostatic ion-pairing energies.},
author = {Alex, Alexander and Hänsele, Elke and Clark, Timothy},
doi = {10.1007/s00894-005-0029-3},
faupublication = {yes},
journal = {Journal of Molecular Modeling},
keywords = {electron transfer;ab initio;CCSD(T);ethylene},
pages = {621-629},
peerreviewed = {Yes},
title = {{The} ethylene/metal(0) and ethylene/metal({I}) redox system: model ab initio calculations},
volume = {12},
year = {2006}
}
@article{faucris.218975108,
abstract = {
The recently introduced “Feynman” dispersion correction for MNDO (MNDO-F) has been extended to include the elements fluorine, chlorine, bromine and iodine and the original parameterization for hydrogen, carbon, nitrogen and oxygen improved by allowing individual damping radii for the elements. MNDO-F gives a root-mean-square deviation to reference interaction energies of 0.35 kcal mol
−1
for the complete parameterization dataset of H, C, N, O, F, Cl, Br and I containing compounds. [Figure not available: see fulltext.].
},
author = {Kriebel, Maximilian and Heßelmann, Andreas and Hennemann, Matthias and Clark, Timothy},
doi = {10.1007/s00894-019-4038-z},
faupublication = {yes},
journal = {Journal of Molecular Modeling},
keywords = {Feynman dispersion; Halogens; MNDO-F; Semiempirical MO-theory},
note = {CRIS-Team Scopus Importer:2019-05-28},
peerreviewed = {Yes},
title = {{The} {Feynman} dispersion correction for {MNDO} extended to {F}, {Cl}, {Br} and {I}},
volume = {25},
year = {2019}
}
@article{faucris.109461484,
abstract = {The formation of an endo-complex between p-allylcalix[4]arene and t-butylamine was described by Gutsche in 1985. However, for a comparable system, it has been shown using NOE methods that the amine does not reside inside the calix. Instead, an exo-calix complex is formed. A reevaluation suggests that the previous conclusion is an artifact due to improper NMR-data processing. DFT (RB3LYP/6-31G(d)) calculations confirm the higher stability of the exo-complex over its endo-counterpart.},
author = {Puchta, Ralph and Clark, Timothy and Bauer, Walter},
doi = {10.1007/s00894-005-0079-6},
faupublication = {yes},
journal = {Journal of Molecular Modeling},
keywords = {DPFGSE-NOE;nuclear Overhauser effect;field gradient;calixarene;amine;endo-complex;exo-complex},
pages = {739-747},
peerreviewed = {Yes},
title = {{The} formation of endo-complexes between calixarenes and amines - a reinvestigation},
volume = {12},
year = {2006}
}
@article{faucris.208733696,
abstract = {A neglect of diatomic differential overlap (NDDO) Hamiltonian has been parametrized as an electronic component of a polarizable force field. Coulomb and exchange potentials derived directly from the NDDO Hamiltonian in principle can be used with classical potentials; thus forming the basis for a new generation of efficiently applicable multipolar polarizable force fields. The new hpCADD Hamiltonian uses force-field-like atom types and reproduces the, electrostatic properties (dipole moment, molecular electrostatic potential) and Koopmans theorem ionization potentials closely, as demonstrated fora large training set and an independent test set of small molecules. The Hamiltonian is not intended to reproduce geometries or total energies. ell, as these will be controlled by the Classical force-field potentials. In order to establish the hpCADD Hamiltonian as an electronic component in force-field-based. calculations, we tested its performance in combination with the 3D reference interaction site model (3D RISM) for aqueous solutions. Comparison of the resulting solvation free energies for the training and test Sets to atomic charges derived from standard procedures, exact solute-solvent electrostatics-based on high-level quantum-chemical reference data, and established semiempirical Hamiltonians demonstrates the advantages of the hpCADD parametrization.},
author = {Thomas, Heike Bettina and Hennemann, Matthias and Kibies, Patrick and Hoffgaard, Franziska and Guessregen, Stefan and Hessler, Gerhard and Kast, Stefan M. and Clark, Timothy},
doi = {10.1021/acs.jcim.7b00080},
faupublication = {yes},
journal = {Journal of Chemical Information and Modeling},
pages = {1907-1922},
peerreviewed = {Yes},
title = {{The} {hpCADD} {NDDO} {Hamiltonian}: {Parametrization}},
volume = {57},
year = {2017}
}
@article{faucris.121629464,
abstract = {The approach of CO2 to a series of active site model complexes of human carbonic anhydrase II (HCAII) and its catalytic hydration to bicarbonate anion have been investigated using semiempirical MO theory (AM1). The results show that direct nucleophilic attack of zinc-bound hydroxide to the substrate carbon occurs in each model system. Further rearrangement of the bicarbonate complex thus formed via a rotation-like movement of the bicarbonate ligand can only be found in active site model systems that include at least one additional water molecule. Further refinement of the model complex by adding a methanol molecule to mimic Thr-199 makes this process almost activationless. The formation of the final bicarbonate complex by an internal (intramolecular) proton transfer is only possible in the simplest of all model systems, namely {[Im(3)Zn(OH)](+). CO2}. The energy of activation for this process, however, is 36.8 kcal.mol(-1) and thus too high for enzymatic catalysis. Therefore, we conclude that within the limitations of the model systems presented and the level of theory employed, the overall mechanism for the formation of the bicarbonate complex comprises an initial direct nucleophilic attack of zinc-bound hydroxide to carbon dioxide followed by a rotation-like rearrangement of the bicarbonate ligand via a penta-coordinate Zn2+ transition state structure, including the participation of an extra active site water molecule.},
author = {Hartmann, Michael and Merz, Kenneth M. and van Eldik, Rudi and Clark, Timothy},
doi = {10.1007/s008940050094},
faupublication = {yes},
journal = {Journal of Molecular Modeling},
keywords = {human carbonic anhydrase II;semiempirical MO theory;AMl;enzyme catalysis},
month = {Jan},
pages = {355-365},
peerreviewed = {Yes},
title = {{The} important role of active site water in the catalytic mechanism of human carbonic anhydrase {II} - {A} semiempirical {MO} approach to the hydration of {CO2}},
volume = {4},
year = {1998}
}
@article{faucris.117014524,
author = {Schleyer, Paul and Kos, Alex and Clark, Timothy and Boche, Gernot and et al.},
author_hint = {SCHLEYER PV, KOS AJ, WILHELM D, CLARK T, BOCHE G, DECHER G, ETZRODT H, DIETRICH H, MAHDI W},
faupublication = {yes},
journal = {Journal of the Chemical Society - Series Chemical Communications},
month = {Jan},
pages = {1495-1496},
peerreviewed = {unknown},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{THE} {INFLUENCE} {OF} {CARBANION} {ORBITAL} {ORIENTATION} {AND} {CHARGE}-{DISTRIBUTION} {ON} {THE} {STRUCTURES} {OF} {POLYLITHIUM} {COMPOUNDS}},
year = {1984}
}
@article{faucris.122513204,
abstract = {The structures and molecular properties of 95 aromatic and heteroaromatic ligands previously tested as reversible inhibitors of chymotrypsin catalysis have been calculated using AM1. The properties obtained have been used as input for multiple linear regression analysis and as descriptors for a back-propagation neural network to predict the binding affinity of alpha-chymotrypsin inhibitors. Using polarizability, molecular shape, electrostatic similarity, dipole moment, ClogP, and the diagonalized quadrupole moments of the ligands, correlation coefficients between calculated and experimental affinities of 0.96 for the training set and 0.89 for the test set were obtained using a neural network. The performance of the multiple linear regression was significantly worse, although useful QSARs were also obtained.},
author = {Beck, Bernd and Glen, Robert and Clark, Timothy},
doi = {10.1016/S0263-7855(96)00041-0},
faupublication = {yes},
journal = {Journal of Molecular Graphics},
keywords = {alpha-chymotrypsin;computational chemistry;QSAR;neural networks},
pages = {130-&},
peerreviewed = {unknown},
title = {{The} inhibition of alpha-chymotrypsin predicted using theoretically derived molecular properties},
volume = {14},
year = {1996}
}
@article{faucris.106480704,
author = {Clark, Timothy and Schleyer, Paul},
doi = {10.1016/S0022-328X(00)81063-3},
faupublication = {yes},
journal = {Journal of Organometallic Chemistry},
month = {Jan},
pages = {347-353},
peerreviewed = {Yes},
title = {{THE} {ISOMERIC} {STRUCTURES} {OF} {SIH2LIF}},
volume = {191},
year = {1980}
}
@article{faucris.122515404,
abstract = {The experience of publishing the first fully electronic chemistry journal has exploded many of the myths and legends of the Internet. Tim Clark, editor of the Journal of Molecular Modeling, describes the aims and ideas behind the journal and considers its acceptance among computational chemists at universities and in industry. He briefly outlines how typically ''electronic'' features can be more fully exploited and concludes that we are at the beginning of an exciting new phase of scientific publishing.},
author = {Clark, Timothy},
doi = {10.1002/adma.19960081002},
faupublication = {yes},
journal = {Advanced Materials},
pages = {787-&},
peerreviewed = {Yes},
title = {{The} journal of molecular modeling: {Electronic} chemistry publishing},
volume = {8},
year = {1996}
}
@article{faucris.121631224,
abstract = {Experience shows that electronic journals are accepted as long as the quality of the published material is up to the standards of printed journals. Therefore, the aim of an electronic journal is primarily to be a serious scientific publication, and only secondarily an electronic publication. The Journal of Molecular Modeling, published for the first time in 1995, is the first fully electronic journal in chemistry. The aim of the journal is to provide high-quality science and take advantage of the electronic format. From the beginning, the journal was designed as trilogy of on-line, CD-ROM, and printed versions, which guarantees longevity of the published research data, allows access to articles and supplementary material without depending on the Internet, and allows the reader to leaf through the journal in the classical fashion. However, this does not mean that the Journal of Molecular Modeling will always be published in a conservative 'book-like' format. The goal is to find the electronic format that most appeals to readers without sacrificing the scientific quality of the journal. Scientific journals are steadily developing towards active and interactive publications.},
author = {Clark, Timothy and Roth, Henryette},
faupublication = {yes},
journal = {Chimia},
pages = {664-667},
peerreviewed = {Yes},
title = {{The} {Journal} of {Molecular} {Modeling}: {Impact}, expectations and experience},
volume = {52},
year = {1998}
}
@article{faucris.107261044,
abstract = {A technique known as intensity filtering is introduced to select valence-like virtual orbitals for calculating the local electron affinity, EAL. Intensity filtering allows EAL to be calculated using semiempirical molecular orbital techniques that include polarisation functions. Without intensity filtering, such techniques yield spurious EAL values that are dominated by the polarisation functions. As intensity filtering should also be applicable for ab initio or density functional theory calculations with large basis sets, it also makes EAL available for these techniques.},
author = {Clark, Timothy},
doi = {10.1007/s00894-009-0607-x},
faupublication = {yes},
journal = {Journal of Molecular Modeling},
pages = {1231--1238},
peerreviewed = {Yes},
title = {{The} local electron affinity for non-minimal basis sets},
volume = {16},
year = {2010}
}
@article{faucris.122515624,
author = {Bauer, Walter and Clark, Timothy and Schleyer, Paul},
doi = {10.1021/ja00238a002},
faupublication = {yes},
journal = {Journal of the American Chemical Society},
pages = {970-977},
peerreviewed = {Yes},
title = {{THE} {MECHANISM} {OF} {DIRECTED} {2ND} {LITHIATIONS} - {DETECTION} {OF} {SHORT} {PROTON}-{LITHIUM} {SEPARATIONS} {BY} {6LI}-{1H} {HOESY}},
volume = {109},
year = {1987}
}
@article{faucris.123442484,
author = {Clark, Timothy and Schleyer, Paul and et al.},
author_hint = {WILHELM D, CLARK T, FRIEDL T, SCHLEYER PV},
doi = {10.1002/cber.19831160232},
faupublication = {yes},
journal = {Chemische Berichte},
month = {Jan},
pages = {751-760},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{THE} {METALLATION}-{ELIMINATION} {REACTION} .2. {MONOCYCLIC} {ANIONS} {AND} {POLYANIONS}},
volume = {116},
year = {1983}
}
@article{faucris.117018044,
author = {Clark, Timothy and Schleyer, Paul and et al.},
author_hint = {WILHELM D, CLARK T, SCHLEYER PV},
doi = {10.1016/S0040-4039(00)88351-3},
faupublication = {yes},
journal = {Tetrahedron Letters},
month = {Jan},
pages = {4077-4078},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{THE} {METALLATION}-{ELIMINATION} {REACTION} .3. {POLYMETHYLENEBIPHENYL} {POLYANIONS} {BY} {METALLATION}-{ELIMINATION}},
volume = {23},
year = {1982}
}
@article{faucris.117029264,
abstract = {Phospholipase A(2) is a calcium-dependent enzyme involved in inflammatory processes by releasing arachidonic acid from the sn-2 position of phosphatidyl-cholines. The catalyzed reaction is an ester hydrolysis that takes place in two proton transfer steps via an intermediate. Two mechanisms, which differ mainly in the rate-limiting step, have been proposed in the literature. The reaction has been calculated semiempirically (PM3) for a protein fragment containing the active site (156 atoms). To take long-range electrostatic interactions of the protein bulk with the active site into account, a classical-mechanical protein environment has been provided by a rigid point-charge array with associated van der Waals potentials. In this way a model system has been built that simulates the natural situation in an enzyme more realistically than a pure model of the active site. A comparison between the relative energy paths obtained by calculating the reaction in the isolated active site and within the classical mechanical environment shows that the long-range interactions have a strong influence on the mechanism. While the calculations of the smaller system indicate that the first reaction step, the formation of the intermediate, is rate-limiting, the calculations including the protein environment show that the decomposition of the intermediate is probably rate-limiting. The results clearly show that the protein environment cannot be disregarded during quantum-mechanical calculations of enzyme mechanisms.},
author = {Schürer, Gudrun and Lanig, Harald and Clark, Timothy and Lanig, Harald},
doi = {10.1021/jp993330i},
faupublication = {yes},
journal = {Journal of Physical Chemistry B},
pages = {1349-1361},
peerreviewed = {Yes},
title = {{The} mode of action of phospholipase {A}(2): {Semiempirical} {MO} calculations including the protein environment},
volume = {104},
year = {2000}
}
@article{faucris.107243004,
abstract = {We report on a combined experimental and computational study on self-assembled monolayers (SAMs). The dielectric properties of SAMs based on n-alkyl phosphonic acids in large area thin film devices (organic field-effect transistors with good hole mobilities up to 0.3 cm² V−1 s−1 at −1 V and capacitors) depend on their chain length, but not consistently to theoretical pictures of tunneling through saturated n-alkanes. An unexpected saturation of current density with increasing chain length was obtained in devices, what impact on the leakage current in transistors and current density in capacitors. This is attributed to different self-assembled monolayer morphology ranging from an amorphous state for short alkyl chains to a quasi-crystalline state for longer alkyl chains. Molecular dynamics (MD) simulations provide a deeper insight into the nature of the three-dimensional intermolecular interactions and support the proposed SAM morphology. The change in morphology leads to a reduced effective SAM thickness in devices, which could be described by a Simmons approach quantitatively. The morphological aspect of self-assembled molecules is of enormous importance beyond the applications of SAMs in low-voltage, high mobility organic transistors because of it’s relevance for the hole field of molecular scale electronics. It demonstrates that even small changes in the molecular design can change the molecular interactions and monolayer assembly.},
author = {Novak, Michael and Jäger, Christof and Rumpel, Armin and Kropp, Henning and Peukert, Wolfgang and Clark, Timothy and Halik, Marcus},
doi = {10.1016/j.orgel.2010.05.009},
faupublication = {yes},
journal = {Organic Electronics},
pages = {1476-1482},
peerreviewed = {Yes},
title = {{The} morphology of integrated self-assembled monolayers and their impact on devices – {A} computational and experimental approach},
url = {http://www.sciencedirect.com/science/article/pii/S1566119910001692},
volume = {11},
year = {2010}
}
@article{faucris.123507604,
author = {Schleyer, Paul and Clark, Timothy},
faupublication = {yes},
journal = {Journal of the Chemical Society - Series Chemical Communications},
pages = {1371-1373},
peerreviewed = {unknown},
title = {{THE} {MOST} {STABLE} {SIH3LI} {STRUCTURE} {IS} {INVERTED}},
year = {1986}
}
@article{faucris.119344984,
abstract = {The natural atomic orbital/point (NAG-PC) model originally developed to calculate molecular electrostatic potentials (MEPs) and multiple moments based on the AM1 wave function has been extended to PM3. As for AM1, NAO-PC/PMS reproduces dipole moments calculated by the standard PM3 method very well. There is also a surprisingly good correlation between experimental and calculated quadrupole moments. The MEPs calculated using PM3/NAO-PC are found to be in better agreement with those given by RHF/6-31G* than those obtained from the PM3 wave function using Coulson charges. On the other hand, the NAG-PC model is often slightly worse then the method implemented in MOPAC-ESP. The MEPs calculated using our model based on the PM3 wave function are often in better agreement with those given by RHF/6-31G* than those obtain with AM1. (C) 1994 by John Wiley and Sons, Inc.},
author = {Beck, Bernd and Rauhut, Guntram and Clark, Timothy},
doi = {10.1002/jcc.540151003},
faupublication = {yes},
journal = {Journal of Computational Chemistry},
pages = {1064-1073},
peerreviewed = {Yes},
title = {{THE} {NATURAL} {ATOMIC} {ORBITAL} {POINT}-{CHARGE} {MODEL} {FOR} {PM3} - {MULTIPOLE} {MOMENTS} {AND} {MOLECULAR} {ELECTROSTATIC} {POTENTIALS}},
volume = {15},
year = {1994}
}
@article{faucris.123325664,
author = {Clark, Timothy and Schleyer, Paul and et al.},
author_hint = {WILHELM D, CLARK T, SCHLEYER PV, COURTNEIDGE JL, DAVIES AG},
doi = {10.1016/0022-328X(84)80513-6},
faupublication = {yes},
journal = {Journal of Organometallic Chemistry},
month = {Jan},
pages = {C1-C3},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{THE} {NATURE} {OF} {THE} {COUNTERION} {IN} {BUTYLLITHIUM} {POTASSIUM} {TERT}-{ALKOXIDE} {REACTION} {MIXTURES} - {AN} {ELECTRON}-{SPIN}-{RESONANCE} {STUDY}},
volume = {273},
year = {1984}
}
@article{faucris.120400104,
abstract = {We present a series of non-stoichiometric cadmium sulfide quantum-dot (QD) models. Using density functional theory (DFT) and semi-empirical molecular orbital (MO) calculations, we explore the ligand binding and exchange chemistry of these models. Their surface morphology allows for these processes to be rationalized on the atomic scale. This is corroborated by ultraviolet-visible (UV-vis), infrared (IR), and inductively coupled plasma-optical emission spectroscopy (ICP-OES). © 2013 American Chemical Society.},
author = {Margraf, Johannes and Ruland Palaia, Andres and Sgobba, Vito and Guldi, Dirk Michael and Clark, Timothy},
doi = {10.1021/la403633e},
faupublication = {yes},
journal = {Langmuir},
pages = {15450-15456},
peerreviewed = {Yes},
title = {{Theoretical} and experimental insights into the surface chemistry of semiconductor quantum dots},
volume = {29},
year = {2013}
}
@article{faucris.117029924,
author = {Schleyer, Paul and Clark, Timothy and et al.},
author_hint = {LUKE BT, POPLE JA, SCHLEYER PV, CLARK T},
doi = {10.1016/0009-2614(83)87382-5},
faupublication = {yes},
journal = {Chemical Physics Letters},
month = {Jan},
pages = {148-154},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{THEORETICAL}-{STUDY} {OF} {THE} {CARBENOID} {CH2FLI} - {STRUCTURES} {AND} {ENERGIES} {OF} {THE} {STABLE} {CONFIGURATIONS} {AND} {TRANSITION}-{STATES}},
volume = {102},
year = {1983}
}
@article{faucris.121634744,
abstract = {The complexes [Zn(H2O)(5)](2+). 2H(2)O and [Zn(H2O)(4)](2+). 2H(2)O turnend out to be the most stable zinc complexes with seven and six water molecules, respectively. This implies that a heptacoordinated zinc(II) complex, where all water molecules are located in the co-ordination sphere, should be energetically highly unfavorable and that [Zn(H2O)(6)](2+) can quite readily push two coordinated water molecules into the solvation sphere. For the pentaqua complex [Zn(H2O)(5)](2+) only one water molecule is easily lost to the solvation sphere, which makes the [Zn(H2O)(4)](2+). H2O complex the most favorable in order to consider the limiting dissociative and associative water exchange process of hexacoordinated zinc(II). The dehydration and hydration energies using the most stable zinc(II) complexes [Zn(H2O)(4)](2+). 2H(2)O, [Zn(H2O)(5)](2+). 2H(2)O and [Zn(H2O)(4)](2+). H2O were calculated to be 24.1 and -21.0 kcal/mol, respectively.},
author = {Hartmann, Michael and Clark, Timothy and van Eldik, Rudi},
doi = {10.1007/s0089460020354.894},
faupublication = {yes},
journal = {Journal of Molecular Modeling},
keywords = {ab initio;DFT;zinc complexes;hydration energies},
month = {Jan},
pages = {354-357},
peerreviewed = {Yes},
title = {{Theoretical} study of the water exchange reaction on divalent zinc ion using density functional theory},
volume = {2},
year = {1996}
}
@article{faucris.117030144,
author = {Clark, Timothy},
doi = {10.1039/c39840000666},
faupublication = {yes},
journal = {Journal of the Chemical Society - Series Chemical Communications},
month = {Jan},
pages = {666-667},
peerreviewed = {unknown},
title = {{THE} {OXIRANE} {RADICAL} {CATION}},
year = {1984}
}
@article{faucris.117036524,
author = {Clark, Timothy and et al.},
author_hint = {WILHELM D, COURTNEIDGE JL, CLARK T, DAVIES AG},
doi = {10.1039/c39840000810},
faupublication = {yes},
journal = {Journal of the Chemical Society - Series Chemical Communications},
month = {Jan},
pages = {810-811},
peerreviewed = {unknown},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{THE} {PENTALENE} {RADICAL}-{ANION}},
year = {1984}
}
@article{faucris.122518484,
abstract = {In this contribution we show that photodegradation of two model compounds, 2,6-dimethyl-diphenylether (DMDPE) and 4-(2',6'-dimethylphenoxy)-2,6-dimethylphenol (DIMEOH), takes place also in low temperature, oxygen-free solutions. Therefore, mechanisms must exist which start the degradation of these model compounds as well as of the polymer even in the absence of oxygen. Based on quantum-chemical model calculations it is suggested that 1,5-hydrogen transfer is a hitherto ignored decay channel in the photodegradation of PPE.},
author = {Schneider, Siegfried and Gedeck, Peter and Clark, Timothy and et al.},
author_hint = {Schneider S, Gedeck P, Harrer J, Richter F, Clark T},
faupublication = {yes},
journal = {Journal of information recording},
keywords = {PPE;poly(2,6-dimethyl-1,4-phenylene oxide) photodegradation;1,5-hydrogen transfer;UV-ois;quantum-chemical calculation},
month = {Jan},
pages = {521-529},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{The} photodegradation of poly(2,6-dimethyl-1,4-phenylene oxide) - {Experimental} and theoretical studies on model compounds},
volume = {22},
year = {1996}
}
@article{faucris.262182370,
abstract = {It follows from the Schrodinger equation that the forces operating within molecules and molecular complexes are Coulombic, which necessarily entails both electrostatics and polarization. A common and important class of molecular complexes is due to pi-holes. These are molecular regions of low electronic density that are perpendicular to planar portions of the molecular frameworks. pi-Holes often have positive electrostatic potentials associated with them, which result in mutually polarizing attractive forces with negative sites such as lone pairs, pi electrons or anions. In many molecules, pi-holes correspond to a flattening of the electronic density surface but in benzene derivatives and in polyazines the pi-holes are craters above and below the rings. The interaction energies of pi-hole complexes can be expressed quite well in terms of regression relationships that account for both the electrostatics and the polarization. There is a marked gradation in the interaction energies, from quite weak (about -2 kcal mol(-1)) to relatively strong (about -40 kcal mol(-1)). Gradations are also evident in the ratios of the intermolecular separations to the sums of the respective van der Waals radii and in the gradual transition of the pi-hole atoms from trigonal to quasi-tetrahedral configurations. These trends are consistent with the concept that chemical interactions form a continuum, from very weak to very strong.},
author = {Politzer, Peter and Murray, Jane S. and Clark, Timothy},
doi = {10.1039/d1cp02602j},
faupublication = {yes},
journal = {Physical Chemistry Chemical Physics},
note = {CRIS-Team WoS Importer:2021-07-30},
peerreviewed = {Yes},
title = {{The} pi-hole revisited},
year = {2021}
}
@article{faucris.109470724,
abstract = {Ab initio and density functional theory have been used to investigate the title reaction. The principles governing radical electrocyclic reactions are summarized and applied to the quadricyclane to norbornadiene radical cation rearrangement. The simple qualitative picture given by this interpretation is then compared with the detailed results of the calculations. In general, the qualitative theories proposed by Bischof and Haselbach provide an excellent conceptual framework for this and other radical electrocyclic reactions. The performance of the different levels of theory is compared and the density functional methods found to underestimate the energy gained from the pseudo-Jahn-Teller distortion away from a symmetrical transition state. Simple BLYP theory fails completely to reproduce this effect and Becke3LYP gives only a small distortion energy. Our best estimate of the activation energy for the rearrangement is less than or equal to 10 kcal mol(-1), in agreement with recent calculations by Each rr al. This value is about twice as high as the current experimental estimate.},
author = {Clark, Timothy},
doi = {10.3891/acta.chem.scand.51-0646},
faupublication = {yes},
journal = {Acta Chemica Scandinavica},
pages = {646-652},
peerreviewed = {Yes},
title = {{The} quadricyclane to norbornadiene radical cation rearrangement: {An} ab initio and density functional study},
volume = {51},
year = {1997}
}
@article{faucris.122519584,
abstract = {We present a quantum mechanical/molecular mechanical (QM/MM) study using the AMI Hamiltonian and a flexible MM part on the mode of action of the bovine lens leucine aminopeptidase (blLAP), a cytosolic exopeptidase that catalyzes the cleavage of the N-terminal amide bond of peptides. The reaction mechanism of this ubiquitous enzyme has not yet been clarified completely, although some suggestions based on crystallographic data have been made. One path of the several possibilities investigated was found to be clearly the most favorable and in good agreement with experimental results. Besides the elucidation of the functional roles of active-site residues, an estimation of the environment effects is given.},
author = {Schürer, Gudrun and Horn, Anselm and Gedeck, Peter and Clark, Timothy},
doi = {10.1021/jp025575s},
faupublication = {yes},
journal = {Journal of Physical Chemistry B},
pages = {8815-8830},
peerreviewed = {Yes},
title = {{The} reaction mechanism of bovine lens leucine aminopeptidase},
volume = {106},
year = {2002}
}
@article{faucris.117036964,
author = {Clark, Timothy and et al.},
author_hint = {CLARK T, ILLING G},
doi = {10.1039/c39850000529},
faupublication = {yes},
journal = {Journal of the Chemical Society - Series Chemical Communications},
month = {Jan},
pages = {529-530},
peerreviewed = {unknown},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{THE} {REDUCTION} {OF} {CHLOROALKANES} {BY} {ALKALI}-{METALS} - {A} {MODEL} {ABINITIO} {STUDY}},
year = {1985}
}
@article{faucris.119347404,
author = {Schleyer, Paul and Chandrasekhar, Jayaraman and Kos, Alex and Clark, Timothy and Spitznagel, Günther W.},
faupublication = {yes},
journal = {Journal of the Chemical Society - Series Chemical Communications},
month = {Jan},
pages = {882-884},
peerreviewed = {unknown},
title = {{THE} {RELATIONSHIP} {BETWEEN} {THE} {ENERGIES} {OF} {CARBANIONS}, {R}-, {AND} {THEIR} {LITHIATED} {COUNTERPARTS}, {RLI} - {AN} {ABINITIO} {STUDY}},
year = {1981}
}
@article{faucris.120272504,
abstract = {We report a quantitative study that describes and correlates the threshold voltage of low-voltage organic field-effect transistors with the molecular structure of self-assembled monolayer dielectrics. We have observed that the component of the dipole moment of such self-assembled molecules perpendicular to the surface correlates linearly with the threshold voltage shift in devices. The model was validated using three different organic semiconductors (pentacene, α,α′-dihexylsexithiophene, and fullerene-C ) on six different self-assembled monolayers. The correlation found can help optimize future devices, by tuning the dipole moments of the molecules that constitute the self-assembled monolayer. © 2012 American Chemical Society.},
author = {Salinas Batallas, Michael and Jäger, Christof and Yousefi Amin, Atefeh and Dral, Pavlo and Meyer-Friedrichsen, Timo and Hirsch, Andreas and Clark, Timothy and Halik, Marcus},
doi = {10.1021/ja303807u},
faupublication = {yes},
journal = {Journal of the American Chemical Society},
pages = {12648-12652},
peerreviewed = {Yes},
title = {{The} relationship between threshold voltage and dipolar character of self-assembled monolayers in organic thin-film transistors},
volume = {134},
year = {2012}
}
@article{faucris.115092384,
abstract = {The thermochromic and solvatochromic properties of Lindqvist metal oxide clusters [VxM6-xO19](n-) (x = 0, 1, 2, M = Mo, W) are reported. The cluster anions show pronounced changes of their electronic structure depending on their chemical environment (e.g. solvent polarity, temperature). These are rationalized using experimental and theoretical methods. A combined density functional theory and V-51-NMR study suggests that temperature-dependent changes in the structural dynamics of the metal oxide framework are the underlying cause for the observed thermochromism. The results might open new avenues for the design of molecular optical sensors.},
author = {Herrmann, Sven and Margraf, Johannes and Clark, Timothy and Streb, Carsten},
doi = {10.1039/c5cc05730b},
faupublication = {yes},
journal = {Chemical Communications},
month = {Jan},
pages = {13702-13705},
peerreviewed = {Yes},
title = {{Thermochromic} and solvatochromic properties of {Lindqvist} polyoxometalates},
volume = {51},
year = {2015}
}
@article{faucris.208727751,
abstract = {It is shown that the interactions of dihalogen molecules XY with halide anions Z(-) to form trihalide anions (XYZ)(-) can be satisfactorily described as Coulombic, involving the sigma-holes on the atoms Y, but only if polarization is taken into account. We have approximated the polarizing effect of the halide anion Z(-) by means of a unit negative point charge. The CCSD/aug-cc-pVTZ computed interaction energies Delta E correlate well with the most positive electrostatic potentials associated with the induced sigma-holes over a Delta E range of -12 to -63 kcal mol(-1). The (XYZ)(-) anions are more stable when the central atom is the largest, as has been observed, because the central atom is then the most polarizable, making the electrostatic potential associated with its sigma-hole more positive.},
author = {Clark, Timothy and Murray, Jane S. and Politzer, Peter},
doi = {10.1002/cphc.201800750},
faupublication = {yes},
journal = {ChemPhysChem},
keywords = {trihalide anions;Coulombic interactions;sigma-holes;polarization;electrostatic potentials},
pages = {3044-3049},
peerreviewed = {Yes},
title = {{The} sigma-{Hole} {Coulombic} {Interpretation} of {Trihalide} {Anion} {Formation}},
volume = {19},
year = {2018}
}
@article{faucris.208733963,
abstract = {A covalently-bonded atom typically has a region of lower electronic density, a "sigma-hole,'' on the side of the atom opposite to the bond, along its extension. There is frequently a positive electrostatic potential associated with this region, through which the atom can interact attractively but noncovalently with negative sites. This positive potential reflects not only the lower electronic density of the sigma-hole but also contributions from other portions of the molecule. These can significantly influence both the value and also the angular position of the positive potential, causing it to deviate from the extension of the covalent bond. We have surveyed these effects, and their consequences for the directionalities of subsequent noncovalent intermolecular interactions, for atoms of Groups IV-VII. The overall trends are that larger deviations of the positive potential result in less linear intermolecular interactions, while smaller deviations lead to more linear interactions. We find that the deviations of the positive potentials and the nonlinearities of the noncovalent interactions tend to be greatest for atoms of Groups V and VI. We also present arguments supporting the use of the 0.001 a. u. contour of the electronic density as the molecular surface on which to compute the electrostatic potential.},
author = {Politzer, Peter and Murray, Jane S. and Clark, Timothy and Resnati, Giuseppe},
doi = {10.1039/c7cp06793c},
faupublication = {yes},
journal = {Physical Chemistry Chemical Physics},
pages = {32166-32178},
peerreviewed = {Yes},
title = {{The} sigma-hole revisited},
volume = {19},
year = {2017}
}
@article{faucris.109471384,
author = {Hänsele, Elke and Clark, Timothy and et al.},
author_hint = {STEINKE T, HANSELE E, CLARK T},
doi = {10.1021/ja00207a021},
faupublication = {yes},
journal = {Journal of the American Chemical Society},
pages = {9107-9109},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{THE} {SOLVENT} {EFFECT} {ON} {THE} {ELECTRONIC} {NATURE} {OF} 1,3-{DIPOLES} - {AN} {ABINITIO} {SCRF} {STUDY}},
volume = {111},
year = {1989}
}
@article{faucris.117037184,
author = {Clark, Timothy and Schleyer, Paul and et al.},
author_hint = {WILHELM D, CLARK T, SCHLEYER PV},
doi = {10.1016/S0040-4039(00)88243-X},
faupublication = {yes},
journal = {Tetrahedron Letters},
month = {Jan},
pages = {3985-3988},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{THE} {STEREOCHEMISTRY} {OF} {THE} {DIBENZYLIDENE} - {ETHYLENE} {DIANION}},
volume = {24},
year = {1983}
}
@article{faucris.117039164,
abstract = {Structural studies of fullerene-like Si-60 and Ge-60 cages using ab initio methods were augmented by density functional tight-binding molecular dynamics (DFTB-MD) simulations of finite temperature effects. Neither the perfect I-h symmetry nor the distorted T-h structures are true minima. The energies of both are high relative to distorted, lower symmetry minima, C-i and T, respectively, which still preserve C-60-type connectivity. Both Si-60 and Ge-60 favor C-i symmetry cages in which Si and Ge vertexes exhibit either near-trigonal or pyramidal geometries. These structural variations imply significant reactivity differences between different positions. The small magnetic shielding effects (NICS) indicate that aromaticity is not important in these systems. The inorganic fullerene cages have lower stabilities compared with their carbon analogs. Si-60 is stable towards spontaneous disintegration up to 700 K according to DFTB-MD simulations, and thus has potential for experimental observation. In contrast, Ge-60 preserves its cage structure only up to 200 K. (C) 2003 Wiley Periodicals, Inc.},
author = {Chen, Zhongfang and Jiao, Haijun and Horn, Anselm and Clark, Timothy and Thiel, Walfried and Schleyer, Paul and et al.},
author_hint = {Chen ZF, Jiao HJ, Seifert G, Horn AHC, Yu DK, Clark T, Thiel W, Schleyer PV},
doi = {10.1002/jcc.10266},
faupublication = {yes},
journal = {Journal of Computational Chemistry},
keywords = {inorganic fullerenes;Si-60;Ge-60;DFT;DFTB},
pages = {948-953},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{The} structure and stability of {Si}-60 and {Ge}-60 cages: {A} computational study},
volume = {24},
year = {2003}
}
@article{faucris.119348504,
abstract = {Semiempirical molecular orbital theory has been used for a systematic scan of the binding positions for a Mg2+ ion with 5a,6-anhydrotetracycline taking both conformational flexibility and possible different tautomeric forms into account. The magnesium ion has been calculated alone and with four or five complexed water molecules in order to simulate the experimental situation more closely. The results are analyzed by comparing the behavior of the title compound with that of tetracycline itself and possible causes for the stronger induction of the Tetracycline Receptor (TetR) by 5a,6-anhydrotetracycline than by tetracycline are considered.},
author = {Othersen, Olaf and Lanig, Harald and Clark, Timothy},
doi = {10.1007/s00894-005-0055-1},
faupublication = {yes},
journal = {Journal of Molecular Modeling},
keywords = {AM1;5a,6-anhydrotetracycline;conformational analysis;magnesium interactions},
pages = {953-963},
peerreviewed = {Yes},
title = {{The} structure of 5a,6-anhydrotetracycline and its {Mg2}+ complexes in aqueous solution},
volume = {12},
year = {2006}
}
@article{faucris.119349384,
author = {Clark, Timothy and Schleyer, Paul and et al.},
author_hint = {STEZOWSKI JJ, HOIER H, WILHELM D, CLARK T, SCHLEYER PV},
doi = {10.1039/C39850001263},
faupublication = {yes},
journal = {Journal of the Chemical Society - Series Chemical Communications},
month = {Jan},
pages = {1263-1264},
peerreviewed = {unknown},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{THE} {STRUCTURE} {OF} {AN} {AROMATIC} 10-{PI} {ELECTRON} {DIANION} - {DILITHIUM} {PENTALENIDE}},
year = {1985}
}
@article{faucris.117040484,
author = {Clark, Timothy and Schleyer, Paul and Boche, Gernot and et al.},
author_hint = {WILHELM D, CLARK T, SCHLEYER PV, BUCKL K, BOCHE G},
doi = {10.1002/cber.19831160441},
faupublication = {yes},
journal = {Chemische Berichte},
month = {Jan},
pages = {1669-1673},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{THE} {TRIBENZYLIDENEMETHANE} {DIANION}},
volume = {116},
year = {1983}
}
@article{faucris.122526844,
author = {Clark, Timothy and Beck, Bernd and Breindl, Andreas and Hennemann, Matthias},
faupublication = {yes},
journal = {ACS National Meeting Book of Abstracts},
pages = {U706-U707},
peerreviewed = {unknown},
title = {{The} use of quantum mechanics for {QSPR} and {QSAR} models with error estimation},
volume = {217},
year = {1999}
}
@article{faucris.122530364,
abstract = {We discuss problems and features of current semiempirical molecular orbital techniques and test some of the approximations and assumptions used. Prerequisites for a ''next generation'' technique include orthogonalization corrections, effective core potentials and an implicit dispersion term. However, validation of experimental parameterization data using density functional theory or the Gaussian 2 approach reveals significant errors in some cases. Developers of future methods will need to validate all their parameterization data and may no longer be able to parameterize for heats of formation at 298 K, but may need to use Born-Oppenheimer binding energies. We also suggest that there is no inherent reason that semiempirical techniques should not reproduce hydrogen bonding and show that the Gaussian potentials added to the core-core terms in AM1 and the PMn methods actually weaken hydrogen bonding, rather than strengthening it.},
author = {Winget, Paul and Horn, Anselm and Martin, Bodo and Clark, Timothy and et al.},
author_hint = {Winget P, Selcuki C, Horn AHC, Martin B, Clark T},
doi = {10.1007/s00214-003-0454-2},
faupublication = {yes},
journal = {Theoretical Chemistry Accounts},
keywords = {molecular orbital theory;modified neglect of differential overlap;MNDO/d;AM1;PM3},
pages = {254-266},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{Towards} a ''next generation'' neglect of diatomic differential overlap based semiempirical molecular orbital technique},
volume = {110},
year = {2003}
}
@article{faucris.117041364,
author = {Schleyer, Paul and Clark, Timothy and et al.},
author_hint = {HOUK KN, RONDAN NG, SCHLEYER PV, KAUFMANN E, CLARK T},
doi = {10.1021/ja00295a053},
faupublication = {yes},
journal = {Journal of the American Chemical Society},
month = {Jan},
pages = {2821-2823},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{TRANSITION} {STRUCTURES} {FOR} {ADDITIONS} {OF} {LIH} {AND} {MELI} {TO} {ETHYLENE} {AND} {ACETYLENE}},
volume = {107},
year = {1985}
}
@article{faucris.112215004,
abstract = {Aromatic triazoles have been frequently used as π-conjugated linkers in intramolecular electron transfer processes. To gain a deeper understanding of the electron-mediating function of triazoles, we have synthesized a family of new triazole-based electron donor-acceptor conjugates. We have connected zinc(II)porphyrins and fullerenes through a central triazole moiety-(ZnP-Tri-C )-each with a single change in their connection through the linker. An extensive photophysical and computational investigation reveals that the electron transfer dynamics-charge separation and charge recombination-in the different ZnP-Tri-C conjugates reflect a significant influence of the connectivity at the triazole linker. Except for the m4m-ZnP-Tri-C 17, the conjugates exhibit through-bond photoinduced electron transfer with varying rate constants. Since the through-bond distance is nearly the same for all the synthesized ZnP-Tri-C conjugates, the variation in charge separation and charge recombination dynamics is mainly associated with the electronic properties of the conjugates, including orbital energies, electron affinity, and the energies of the excited states. The changes of the electronic couplings are, in turn, a consequence of the different connectivity patterns at the triazole moieties. © 2011 American Chemical Society.},
author = {De Miguel Rojas, Gustavo and Wielopolski, Mateusz and Schuster, David I. and Fazio, Michael A. and Lee, Olivia P. and Haley, Christopher K. and Ortiz, Angy L. and Echegoyen, Luis and Clark, Timothy and Guldi, Dirk Michael},
doi = {10.1021/ja202485s},
faupublication = {yes},
journal = {Journal of the American Chemical Society},
pages = {13036-13054},
peerreviewed = {Yes},
title = {{Triazole} bridges as versatile linkers in electron donor-acceptor conjugates},
volume = {133},
year = {2011}
}
@article{faucris.208734230,
abstract = {The traditional "F-delta" picture of fluorine suggests that it can only interact with electrophilic centers such as backbone-carbonyl carbon atoms or hydrogen-bond donors in proteins. We show that this view, which neglects polarization, is incomplete and the trifluoromethyl groups can act both as electrophiles and nucleophiles to form noncovalent interactions. The underlying polarization mechanism is based on the anomeric effect and is only fully operative if the geometry is allowed to relax. MP2/aug-cc-pVDZ calculations on model systems demonstrate the effect of the unusual group polarizability of trifluorometh-yl. A survey of the Protein Databank reveals more than 600 weak interactions involving a trifluorotoluene moiety. The unique combination of the anomeric effect and the group-polarization process associated with it in CF3 allows its most negative molecular electrostatic potential (MEP) on the surface in contact with a nucleophile to become zero, so that the area of positive MEP on the backside of the carbon atom becomes dominant. However, the reverse polarization is also facile, so that CF3 can also act as an H-bond acceptor for cations such as the guanidinium group of arginine.},
author = {Esterhuysen, Catharine and Heßelmann, Andreas and Clark, Timothy},
doi = {10.1002/cphc.201700027},
faupublication = {yes},
journal = {ChemPhysChem},
keywords = {ab initio calculations;drug discovery;molecular electrostatic potential;molecular recognition;PDB analysis},
pages = {772-784},
peerreviewed = {Yes},
title = {{Trifluoromethyl}: {An} {Amphiphilic} {Noncovalent} {Bonding} {Partner}},
volume = {18},
year = {2017}
}
@article{faucris.117041584,
author = {Bestmann, Hans-Jürgen and Frank, Wilhelm and Moll, Claus and Pohlschmidt, Andreas and Clark, Timothy and Göller, Andreas H.},
doi = {10.1002/(SICI)1521-3773(19980216)37:3<338::AID-ANIE338>3.0.CO;2-5},
faupublication = {yes},
journal = {Angewandte Chemie International Edition},
keywords = {ab initio calculations;betaines;isoelectronic analogues;ylides},
pages = {338-342},
peerreviewed = {Yes},
title = {{Triphenylphosphonioacetylide}: {A} species isoelectronic with isocyanides},
volume = {37},
year = {1998}
}
@article{faucris.221122951,
abstract = {The current work focuses on self-assembled nano-architectures in which metal-ligand coordination between a zinc tetraphenyl-porphyrin (ZnP) and a zinc tetrakis(4-((1,3-dithiol-2-ylidene)methyl)phenyl)-porphyrin (ZnP-TDP), as electron donors, and functionalized fullerenes (C60) featuring different conjugated pyridine substituents as electron acceptors have been designed and investigated. Stoichiometric ratios and binding constants were derived from absorption and fluorescence measurements. Important insight into the free-energy change of charge separation and recombination was obtained from differential pulse voltammetry studies. Compelling evidence for energy transfer, charge separation and recombination was obtained from femtosecond and nanosecond transient-absorption measurements in a wide temperature range. Intramolecular energy transfer is found to take place from TDP to ZnP followed by intramolecular charge transfer from ZnP to C60. Semiempirical and density-functional theory calculations were used to help understand the excited-state deactivation mechanisms.},
author = {Wang, Bingzhe and Bauroth, Stefan and Saha, Avishek and Chen, Muqing and Clark, Timothy and Lu, Xing and Guldi, Dirk Michael},
doi = {10.1039/c9nr02824b},
faupublication = {yes},
journal = {Nanoscale},
note = {CRIS-Team Scopus Importer:2019-06-21},
pages = {10782-10790},
peerreviewed = {Yes},
title = {{Tuning} electron transfer in supramolecular nano-architectures made of fullerenes and porphyrins},
volume = {11},
year = {2019}
}
@article{faucris.107510304,
abstract = {Weak wire-like behavior - with a damping factor (β) of 0.2 ± 0.05 Å - has been found in a series of C -wire- exTTF systems (i.e., p-phenyleneethynylene): these results contrast with previous observations involving p-phenylenevinylene systems. © The Royal Society of Chemistry 2006.},
author = {Atienza, Carmen and Martín, Nazario and Wielopolski, Mateusz and Haworth, Naomi and Clark, Timothy and Guldi, Dirk Michael},
doi = {10.1039/b603149h},
faupublication = {yes},
journal = {Chemical Communications},
pages = {3202-3204},
peerreviewed = {Yes},
title = {{Tuning} electron transfer through p-phenyleneethynylene molecular wires},
year = {2006}
}
@article{faucris.208728021,
abstract = {Different water-soluble perylenediimides (PDIs) have been used to individualize and stabilize single-walled carbon nanotubes (SWCNTs) in aqueous media. A key feature of the PDIs is that they can be substituted at the bay positions via the addition of two and/or four bromines. This enables control over structural and electronic PDI characteristics, which prompted us to conduct comparative assays with focus on SWCNTs' chirality and charge transfer. Electrochemical, microscopic, and spectroscopic experiments were used to investigate the SWCNT chiral selectivity of PDIs, on the one hand, and charge-transfer reactions between SWCNTs and PDIs, on the other hand.},
author = {Münich, Peter Wilhelm and Schierl, Christoph and Dirian, Konstantin and Volland, Michel and Bauroth, Stefan and Wibmer, Leonie and Syrgiannis, Zois and Clark, Timothy and Prato, Maurizio and Guldi, Dirk Michael},
doi = {10.1021/jacs.8b00452},
faupublication = {yes},
journal = {Journal of the American Chemical Society},
pages = {5427-5433},
peerreviewed = {Yes},
title = {{Tuning} the {Carbon} {Nanotube} {Selectivity}: {Optimizing} {Reduction} {Potentials} and {Distortion} {Angles} in {Perylenediimides}},
volume = {140},
year = {2018}
}
@article{faucris.115093704,
abstract = {Oligo(p-phenylenevinylene) (oPPV) wires of various lengths featuring pyridyls at one terminal and C-60 moieties at the other, have been used as molecular building blocks in combination with porphyrins to construct a novel class of electron donor-acceptor architectures. These architectures, which are based on non-covalent, directional interactions between the zinc centers of the porphyrins and the pyridyls, have been characterized by nuclear magnetic resonance spectroscopy and mass spectrometry. Complementary physico-chemical assays focused on the interactions between electron donors and acceptors in the ground and excited states. No appreciable electron interactions were noted in the ground state, which was being probed by electrochemistry, absorption spectroscopy, etc.; the electron acceptors are sufficiently decoupled from the electron donors. In the excited state, a different picture evolved. In particular, steady-state and time-resolved fluorescence and transient absorption measurements revealed substantial electron donor-acceptor interactions. These led, upon photoexcitation of the porphyrins, to tunable intramolecular electron-transfer processes, that is, the oxidation of porphyrin and the reduction of C-60. In this regard, the largest impact stems from a rather strong distance dependence of the total reorganization energy in stark contrast to the distance independence seen for covalently linked conjugates.},
author = {Stangel, Christina and Schubert, Christina and Kuhri, Susanne and Rotas, Georgios and Margraf, Johannes and Regulska, Elzbieta and Clark, Timothy and Torres, Tomas and Tagmatarchis, Nikos and Coutsolelos, Athanassios G. and Guldi, Dirk Michael},
doi = {10.1039/c4nr05165c},
faupublication = {yes},
journal = {Nanoscale},
month = {Jan},
pages = {2597-2608},
peerreviewed = {Yes},
title = {{Tuning} the reorganization energy of electron transfer in supramolecular ensembles - metalloporphyrin, oligophenylenevinylenes, and fullerene - and the impact on electron transfer kinetics},
volume = {7},
year = {2015}
}
@article{faucris.122534324,
author = {Clark, Timothy and et al.},
author_hint = {CLARK T, NELSEN SF},
doi = {10.1021/ja00211a028},
faupublication = {yes},
journal = {Journal of the American Chemical Society},
pages = {868-870},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{TWISTING} {IN} {ALKYL}-{SUBSTITUTED} {OLEFIN} {CATION} {RADICALS}},
volume = {110},
year = {1988}
}
@article{faucris.290177365,
abstract = {We investigate the gas-phase chemistry of noncovalent complexes of [10]cycloparaphenylene ([10]CPP) with C60 and C70 by means of atmospheric pressure photoionization and electrospray ionization mass spectrometry. The literature-known [1 : 1] complexes, namely [10]CPP⊃C60 and [10]CPP⊃C70, are observed as radical cations and anions. Their stability and charge distribution are studied using energy-resolved collision-induced dissociation (ER-CID). These measurements reveal that complexes with a C70 core exhibit a greater stability and, on the other hand, that the radical cations are more stable than the respective radical anions. Regarding the charge distribution, in anionic complexes charges are exclusively located on C60 or C70, while the charges reside on [10]CPP in the case of cationic complexes. [2 : 1] complexes of the ([10]CPP2⊃C60/70)+⋅/−⋅ type are observed for the first time as isolated solitary gas-phase species. Here, C60-based [2 : 1] complexes are less stable than the respective C70 analogues. By virtue of the high stability of cationic [1 : 1] complexes, [2 : 1] complexes show a strongly reduced stability of the radical cations. DFT analyses of the minimum geometries as well as molecular dynamics calculations support the experimental data. Furthermore, our novel gas-phase [2 : 1] complexes are also found in 1,2-dichlorobenzene. Insights into the thermodynamic parameters of the binding process as well as the species distribution are derived from isothermal titration calorimetry (ITC) measurements.},
author = {Freiberger, Markus and Minameyer, Martin and Solymosi, Iris and Frühwald, Stefan and Krug, Marcel and Xu, Youzhi and Hirsch, Andreas and Clark, Timothy and Guldi, Dirk Michael and von Delius, Max and Amsharov, Konstantin and Görling, Andreas and Perez-Ojeda Rodriguez, Maria Eugenia and Drewello, Thomas},
doi = {10.1002/chem.202203734},
faupublication = {yes},
journal = {Chemistry - A European Journal},
keywords = {cycloparaphenylenes; fullerenes; host-guest systems; polycyclic aromatic hydrocarbons; supramolecular chemistry},
note = {CRIS-Team Scopus Importer:2023-03-07},
peerreviewed = {Yes},
title = {{Two} {Rings} {Around} {One} {Ball}: {Stability} and {Charge} {Localization} of [1 : 1] and [2 : 1] {Complex} {Ions} of [10]{CPP} and {C60}/70[*]},
volume = {29},
year = {2022}
}
@article{faucris.238120646,
abstract = {We probed a series of multicomponent electron donor2-donor1-acceptor1 conjugates both experimentally and computationally. The conjugates are based on the light harvester and primary electron-donor zinc-porphyrin (ZnP, donor1) to whose β positions a secondary electron-donor ferrocene (Fc, donor2) and the primary electron-acceptor C60-fullerene (C60, acceptor1) are attached. Linking all of them via p-phenylene-acetylene/acetylene bridges of different lengths to gain full control over shuttling electrons and holes between C60, ZnP, and Fc is novel. Different charge-separation, charge-transfer, and charge-recombination routes have been demonstrated, both by transient absorption spectroscopy measurements on the femto, pico-, nano-, and microsecond time scales and by multiwavelength and target analyses. The molecular wire-like nature of the p-phenylene-acetylene bridges as a function of C60-ZnP and ZnP-Fc distances is decisive in the context of generating distant and long-lived C60 â¢--ZnP-Fcâ¢+ charge-separated states. For the first time, we confirm the presence of two adjacent charge-transfer states, a C60-ZnPâ¢--Fcâ¢+ intermediate in addition to C60 â¢--ZnPâ¢+-Fc, en route to the distant C60 â¢--ZnP-Fcâ¢+ charge-separated state. Our studies demonstrate how the interplay of changes in the reorganization energy and the damping factor of the molecular bridges, in addition to variation in the solvent polarity, affect the outcome of the charge-transfer and corresponding rate constants. The different regions of the Marcus parabola are highly relevant in this matter: The charge recombination of, for example, the adjacent C60 â¢--ZnPâ¢+-Fc charge-separated state is located in the inverted region, while that of the distant C60 â¢--ZnP-Fcâ¢+ charge-separated state lies in the normal region. Here, the larger reorganization energy of Fc relative to ZnP makes the difference.},
author = {Kaur, Ramandeep and Possanza, Fabio and Limosani, Francesca and Bauroth, Stefan and Zanoni, Robertino and Clark, Timothy and Arrigoni, Giorgio and Tagliatesta, Pietro and Guldi, Dirk Michael},
doi = {10.1021/jacs.0c01452},
faupublication = {yes},
journal = {Journal of the American Chemical Society},
note = {CRIS-Team Scopus Importer:2020-05-08},
peerreviewed = {Yes},
title = {{Understanding} and {Controlling} {Short}- {A} nd {Long}-{Range} {Electron}/{Charge}-{Transfer} {Processes} in {Electron} {Donor}-{Acceptor} {Conjugates}},
year = {2020}
}
@article{faucris.122534764,
abstract = {Acyl anion equivalents (umpolung) are the practitioner's first choice en route to 1,3-hydroxy keto compounds from epoxides. Why? This investigation evaluates computationally and experimentally the reactivity of a near comprehensive range of acyl anion equivalents using epoxide ring opening as a test vehicle. Reactivity understanding, reactivity order, surprise failures in performance, along with unprecedented, but far from superior, reactivity of TosMIC is presented for the first time.},
author = {Eger, Wilhelm A. and Grange, Rebecca L. and Schill, Heiko and Goumont, Regis and Clark, Timothy and Williams, Craig M.},
doi = {10.1002/ejoc.201001680},
faupublication = {yes},
journal = {European Journal of Organic Chemistry},
keywords = {Umpolung;Epoxides;Acyl anion equivalent;Carbonyl equivalent},
pages = {2548-2553},
peerreviewed = {Yes},
title = {{Understanding} the {Reactivity} of {Acyl} {Anion} {Equivalents}: {The} {Epoxide} {Ring} {Opening} {Case}},
year = {2011}
}
@article{faucris.289272943,
abstract = {Carbon nanodots (CNDs) synthesized from citric acid and formyl derivatives, that is, formamide, urea, or N-methylformamide, stand out through their broad-range visible-light absorbance and extraordinary photostability. Despite their potential, their use has thus far been limited to imaging research. This work has now investigated the link between CNDs’ photochemical properties and their chemical structure. Electron-rich, yellow carbon nanodots (yCNDs) are obtained with in situ addition of NaOH during the synthesis, whereas otherwise electron-poor, red carbon nanodots (rCNDs) are obtained. These properties originate from the reduced and oxidized dimer of citrazinic acid within the matrix of yCNDs and rCNDs, respectively. Remarkably, yCNDs deposited on TiO2 give a 30% higher photocurrent density of 0.7 mA cm−2 at +0.3 V versus Ag/AgCl under Xe-lamp irradiation (450 nm long-pass filter, 100 mW cm−2) than rCNDs. The difference in overall photoelectric performance is due to fundamentally different charge-transfer mechanisms. These depend on either the electron-accepting or the electron-donating nature of the CNDs, as is evident from photoelectrochemical tests with TiO2 and NiO and time-resolved spectroscopic measurements.},
author = {Reva, Yana and Jana, Bikash and Langford, Daniel and Kinzelmann, Marina and Bo, Yifan and Schol, Peter and Scharl, Tobias and Zhao, Xinyi and Crisp, Ryan and Drewello, Thomas and Clark, Timothy and Cadranel, Alejandro and Guldi, Dirk Michael},
doi = {10.1002/smll.202207238},
faupublication = {yes},
journal = {Small},
keywords = {carbon nanodots; excited state; photoelectrochemistry; semiconductors; time-resolved spectroscopy},
note = {Created from Fastlane, Scopus look-up},
peerreviewed = {Yes},
title = {{Understanding} the {Visible} {Absorption} of {Electron} {Accepting} and {Donating} {CNDs}},
year = {2023}
}
@article{faucris.208734499,
abstract = {When molecular dimers, crystalline films or molecular aggregates absorb a photon to produce a singlet exciton, spin-allowed singlet fission may produce two triplet excitons that can be used to generate two electron-hole pairs, leading to a predicted similar to 50% enhancement in maximum solar cell performance. The singlet fission mechanism is still not well understood. Here we report on the use of time-resolved optical and electron paramagnetic resonance spectroscopy to probe singlet fission in a pentacene dimer linked by a non-conjugated spacer. We observe the key intermediates in the singlet fission process, including the formation and decay of a quintet state that precedes formation of the pentacene triplet excitons. Using these combined data, we develop a single kinetic model that describes the data over seven temporal orders of magnitude both at room and cryogenic temperatures.},
author = {Basel, Bettina and Zirzlmeier, Johannes and Hetzer, Constantin and Phelan, Brian T. and Krzyaniak, Matthew D. and Seelam, Rajagopala Reddy and Brana Coto, Pedro and Horwitz, Noah E. and Young, Ryan M. and White, Fraser J. and Hampel, Frank and Clark, Timothy and Thoss, Michael and Tykwinski, Rik and Wasielewski, Michael R. and Guldi, Dirk Michael},
doi = {10.1038/ncomms15171},
faupublication = {yes},
journal = {Nature Communications},
peerreviewed = {Yes},
title = {{Unified} model for singlet fission within a non-conjugated covalent pentacene dimer},
volume = {8},
year = {2017}
}
@article{faucris.227309612,
abstract = {An index of the activation of Class A G-protein-coupled receptors (GPCRs) has been trained using interhelix distances from a series of microsecond molecular-dynamics simulations and tested for 268 published X-ray structures. In a three-class model that includes intermediate structures, 63% of the active structures are classified in agreement with the experimental assignment, 81% of the intermediate structures, and 89% of the inactives. An alternative two-state model classifies 94% of the actives and 99% of the inactives correctly. The intermediate structures are distributed 2:1 between actives and inactives. X-ray structures with protein nanobodies give good agreement between the assigned activation state and the predictions of the model, whereby many active nanobody structures are predicted to be weakly active. The five interhelix Cα-Cα distances that occur in the model relate clearly to the established activation mechanism. The model is available as a Python script or via an interactive web page. It can thus be used to classify both experimental and computational GPCR structures.},
author = {Ibrahim, Passainte and Wifling, David and Clark, Timothy},
doi = {10.1021/acs.jcim.9b00604},
faupublication = {yes},
journal = {Journal of Chemical Information and Modeling},
note = {CRIS-Team Scopus Importer:2019-10-01},
pages = {3938-3945},
peerreviewed = {Yes},
title = {{Universal} {Activation} {Index} for {Class} {A} {GPCRs}},
volume = {59},
year = {2019}
}
@article{faucris.117044224,
abstract = {2,4,6-Tri-tert-butyl-1,3,5-triphosphinine (7) was combined with 1,5-COD or 2,4-di-tertbutyl-1,3-diphosphete to form iron pi-complexes. The ligands of highly reactive [(2,4-di-tert-butyl-1,3-diphosphete)(2,4,6-tri-tert-butyl-1,3,5-triphosphinine)Fe] (8) are formed by cyclooligomerization of tert-butylphosphaalkyne (3) under the influence of the iron atom. 8 rearranges spontaneously to yield penta-tert-butyl-pentaphosphaferrocene (9) as the isolable product. An intramolecular electron transfer product [(1,5-COD)(eta(6)-1,3,5-triphosphacyclohexa-2,5-dine-1,4-diyl)Fe((2+))] (12) is obtained with 1,5-COD. Addition of [(CO)(5)Cr(THF)] initiates an interligand hydrogen transfer to form [(eta(5)-trihydropentalenyl)Fe(mu,1-3-eta-4,5,6-trihydro-1,3,5-triphosphinine)Cr(CO)(5)] (13) Extensive DFT calculations of isolated and reactive species, and several possible intermediates agree with the experimental observations and revealed for the first time a possible reaction sequence, which allows a low-activated exchange of ring elements between the ligands of sandwich complex 8 to form 9. The process is based on the specific combination of the metal and its heterocyclic pi-ligands. Both, singlet and triplet spin states play an important role in the process. (C) 2010 Academie des sciences. Published by Elsevier Masson SAS. All rights reserved.},
author = {Eggers, Karin and Heinemann, Frank Wilhelm and Hennemann, Matthias and Clark, Timothy and Binger, Paul and Zenneck, Ulrich},
doi = {10.1016/j.crci.2010.05.023},
faupublication = {yes},
journal = {Comptes Rendus Chimie},
keywords = {Phosphorus;Iron;pi-Complexes;Rearrangement;Density functional calculations},
pages = {1203-1212},
peerreviewed = {Yes},
title = {{Unprecedented} triphosphinine iron interactions: {Intramolecular} electron transfer, reactivity round a corner, and a low-activated ring element exchange reaction},
volume = {13},
year = {2010}
}
@article{faucris.208725669,
abstract = {We discuss the use of carbon nanodots (CNDs) as sensitizers in mesoscopic solar cells. The CNDs are synthesized using a one-step, bottom-up microwave approach with citric acid, urea, and formic acid as precursors in aqueous media. Their light-harvesting capabilities can be tuned by adjusting the synthetic parameters. Comprehensive spectroscopic and theoretical studies allow us to rationalize the nature of their absorption features. Promising power conversion efficiencies (\textgreekh) of 0.24% can be achieved from these cheap and eco-friendly sensitizers by optimizing the solar-cell assembly process. Interestingly, we found that extending the light absorption towards longer wavelengths does not necessarily improve the performance of the solar cells, since the longer-wavelength absorption features hardly contribute to the cells' photo-action spectra, so that the overall power conversion efficiency is actually worse. The origin of the lower performance is corroborated in transient absorption spectroscopy and photovoltage decay measurements. Our work points, on one hand, to the limits of as-synthesized CNDs as photosensitizers and, on the other hand, to possible improvements.},
author = {Margraf, Johannes and Lodermeyer, Fabian and Strauß, Volker and Haines, Philipp and Walter, Johannes and Peukert, Wolfgang and Costa, Ruben Dario and Clark, Timothy and Guldi, Dirk Michael},
doi = {10.1039/c6nh00010j},
faupublication = {yes},
journal = {Nanoscale Horizons},
pages = {220-226},
peerreviewed = {unknown},
title = {{Using} carbon nanodots as inexpensive and environmentally friendly sensitizers in mesoscopic solar cells},
volume = {1},
year = {2016}
}
@misc{faucris.119350924,
author = {Gedeck, Peter and Martin, Bodo and Schindler, Thorsten and Clark, Timothy},
faupublication = {yes},
peerreviewed = {automatic},
title = {{Using} quantum chemistry to calculate atomic and group descriptors for {QSAR} and {QSPR}.},
year = {2000}
}
@article{faucris.109475344,
abstract = {Ligand-based virtual screening (VS) techniques have become well established in the drug discovery process. However, despite their relative success, there still exists the problem of how to define the initial query compounds and which of their conformations should be used. Here, we propose a novel shape plus surface property approach using multiple local spherical harmonic (SH) functions. We also investigate the use of shape-based and shape plus property-based consensus SH queries calculated in several different ways. The utility of these approaches is compared using the 40 pharmaceutically relevant targets of the DUD database. Our results show that using a combination of SH-based properties often gives better VS performance than using simple shape-based queries. Shape-based consensus queries also perform well, but we find that explicit 3D shape-property conformations should be retained for highly flexible ligands.},
author = {Perez-Nueno, Violeta I. and Venkatraman, Vishwesh and Mavridis, Lazaros and Clark, Timothy and Ritchie, David W.},
doi = {10.1002/minf.201000149},
faupublication = {yes},
journal = {Molecular Informatics},
keywords = {Spherical harmonics;Consensus properties;Genetic algorithm;Virtual screening;Difficult targets;P38;FXA;PPAR-gamma},
pages = {151-159},
peerreviewed = {Yes},
title = {{Using} {Spherical} {Harmonic} {Surface} {Property} {Representations} for {Ligand}-{Based} {Virtual} {Screening}},
volume = {30},
year = {2011}
}
@article{faucris.216834139,
abstract = {
We have designed and used four different spacers, denoted A-D, to connect two pentacenes and to probe the impact of intramolecular forces on the modulation of pentacene-pentacene interactions and, in turn, on the key steps in singlet fission (SF), that is, the
1
(S
1
S
0
)-to-
1
(T
1
T
1
) as well as
1
(T
1
T
1
)-to-
5
(T
1
T
1
) transitions by means of transient absorption and electron paramagnetic resonance measurements. In terms of the
1
(S
1
S
0
)-to-
1
(T
1
T
1
) transition, a superexchange mechanism, that is, coupling to a higher-lying CT state to generate a virtual intermediate, enables rapid SF in A-D. Sizeable electronic coupling in A and B opens, on one hand, an additional pathway, that is, the population of a real intermediate, and changes, on the other hand, the mechanism to that of hopping. In turn, A and B feature much higher
1
(T
1
T
1
) quantum yields than C and D, with a maximum value of 162% for A. In terms of the
1
(T
1
T
1
)-to-
5
(T
1
T
1
) transition, the sizable electronic coupling in A and B is counterproductive, and C and D give rise to higher
5
(T
1
T
1
)-to-(T
1
+ T
1
) quantum yields than A and B, with a maximum value of 85% for D.
},
author = {Papadopoulos, Ilias and Zirzlmeier, Johannes and Hetzer, Constantin and Bae, Youn J. and Krzyaniak, Matthew D. and Wasielewski, Michael R. and Clark, Timothy and Tykwinski, Rik and Guldi, Dirk Michael},
doi = {10.1021/jacs.8b09510},
faupublication = {yes},
journal = {Journal of the American Chemical Society},
note = {CRIS-Team Scopus Importer:2019-05-02},
pages = {6191-6203},
peerreviewed = {Yes},
title = {{Varying} the {Interpentacene} {Electronic} {Coupling} to {Tune} {Singlet} {Fission}},
volume = {141},
year = {2019}
}
@article{faucris.117049064,
author = {Clark, Timothy and Hennemann, Matthias and Martin, Bodo},
faupublication = {yes},
journal = {ACS National Meeting Book of Abstracts},
pages = {U565-U565},
peerreviewed = {unknown},
title = {{Vector} and tensor pharmacophores from quantum mechanical calculations},
volume = {217},
year = {1999}
}
@article{faucris.122542904,
abstract = {An improved semiempirical method for computing electrostatic potential-derived atomic charges is described. It includes a very fast algorithm for the generation of the grid points around the molecule and the calculation of the electrostatic potential at these points. The dependency of the atomic paint charges obtained on the number of grid points used in the fitting procedure is examined. For ''buried'' atoms a high density grid is necessary. It is possible to obtain 6-31G*-quality atom-centered point charges, even for phosphorus compounds, using AM1 or PM3. This approach can therefore be recommended for general use in QSAR or molecular mechanics for any organic and bioorganic system up to about 200 atoms. (C) 1997 by John Wiley & Sons, Inc.},
author = {Beck, Bernd and Clark, Timothy and Glen, Robert},
doi = {10.1002/(SICI)1096-987X(19970430)18:6<744::AID-JCC2>3.0.CO;2-S},
faupublication = {yes},
journal = {Journal of Computational Chemistry},
keywords = {computational chemistry;semiempirical MO methods;ESP atomic charges;QSAR},
pages = {744-756},
peerreviewed = {Yes},
title = {{VESPA}: {A} new, fast approach to electrostatic potential-derived atomic charges from semiempirical methods},
volume = {18},
year = {1997}
}
@article{faucris.120819424,
abstract = {Rigid and soluble electron donor-acceptor conjugates (3 and 11) that combine π-extended tetrathiafulvalene (exTTF) as an electron donor and C as an electron acceptor have been synthesized using oligo-vinylfluorene (oFV) linkers to connect the electroactive entities. Fluorescence and transient absorption measurements confirm that light-induced excitation induces charge-transfer reactions over distances of 28 in THF. The incorporation of vinylene spacers into oligofluorene molecular wires has been shown both experimentally and theoretically to improve the charge-transfer features significantly to give a β value of 0.075 ± 0.001 . Enhanced π-conjugation caused by higher orbital overlap is responsible for this trend. © 2011 The Royal Society of Chemistry.},
author = {Wielopolski, Mateusz and Santos, José and Illescas, Beatriz M. and Ortiz, Alejandro and Insuasty, Braulio and Bauer, Thilo and Clark, Timothy and Guldi, Dirk Michael and Martín, Nazario},
doi = {10.1039/c0ee00499e},
faupublication = {yes},
journal = {Energy and Environmental Science},
pages = {765-771},
peerreviewed = {Yes},
title = {{Vinyl} spacers - {Tuning} electron transfer through fluorene-based molecular wires},
volume = {4},
year = {2011}
}
@article{faucris.117045764,
abstract = {The structure and water exchange mechanism of hexahydrated Ti(III), its hydrolysis, and the water exchange mechanism of analogous hydroxo-aqua complexes have been studied using density functional theory (DFT) calculations. Isolated metal-aqua and metal-hydroxo clusters corresponding to the gas-phase (T = 0 K) were used to approximate the model reactions. The structure of [Ti(H2O)(6)](3+) was found to have C-i symmetry and Ti-O bond lengths of 2.094 Angstrom. The water exchange reaction of this complex follows an (almost) limiting A mechanism with an energy of activation of 15.8 kcal mol(-1). The hydrolysis of hexahydrated Ti(III) was modeled by an in vacuo proton-transfer process between water molecules of the first and second coordination spheres of [Ti(H2O)(6)](3+).H2O. This process was found to be activationless and leads to the unusually stable dication:cation pair [Ti(H2O)(5)(OH)](2+).H3O+, which is lower in energy than the reactant by 4.5 kcal mol(-1). Only a weak structural influence, indicated by a slight increase in the mean value of the Ti-O bond lengths of water molecules in the first coordination sphere, is observed when the hydroxo ligand is formed. The water exchange reactions of the corresponding hydroxo-aqua complexes [Ti(H2O)(5)(OH)](2+) and [Ti(H2O)(5)(OH)](2+).H2O, respectively, were found to proceed via limiting D mechanisms. The energies of activation for the exchange of the water molecule in the trans-position to the hydroxo ligand were calculated to be only 9.8 and 7.2 kcal mol(-1), respectively. This, however, implies that the apparently weak influence of coordinated hydroxide still results in a significant reduction in the energy barrier for the water exchange reaction and also leads to a complete changeover in the preferred exchange pathway from A to D.},
author = {Hartmann, Michael and Clark, Timothy and van Eldik, Rudi},
doi = {10.1021/jp9918508},
faupublication = {yes},
journal = {Journal of Physical Chemistry A},
pages = {9899-9905},
peerreviewed = {Yes},
title = {{Water} exchange reactions and hydrolysis of hydrated titanium({III}) ions. {A} density functional theory study},
volume = {103},
year = {1999}
}
@article{faucris.122545104,
author = {Clark, Timothy and Kramer, Christian},
faupublication = {yes},
journal = {ACS National Meeting Book of Abstracts},
peerreviewed = {unknown},
title = {{What} does {logP} really mean?},
volume = {239},
year = {2010}
}
@inproceedings{faucris.265167519,
address = {WASHINGTON},
author = {Clark, Timothy and Ibrahim, Passainte},
booktitle = {ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY},
faupublication = {yes},
note = {CRIS-Team WoS Importer:2021-10-18},
peerreviewed = {unknown},
publisher = {AMER CHEMICAL SOC},
title = {{What} molecular dynamics simulations tell us about {GPCRs}},
venue = {San Diego, CA},
year = {2019}
}
@article{faucris.109476444,
author = {Winget, Paul and Clark, Timothy},
faupublication = {yes},
journal = {ACS National Meeting Book of Abstracts},
pages = {U903-U903},
peerreviewed = {unknown},
title = {{Where} good methods go bad: {Correcting} systematic errors in current semiempirical methods.},
volume = {227},
year = {2004}
}
@article{faucris.109327944,
abstract = {We have carried out B3PW91 and MP2-FC computational studies of dimethyl sulfoxide, (CH(3))(2)SO, and dimethyl sulfone, (CH(3))(2)SO(2). The objective was to establish quantitatively the basis for their high polarities and boiling points, and their strong solvent powers for a variety of solutes. Natural bond order analyses show that the sulfur-oxygen linkages are not double bonds, as widely believed, but rather are coordinate covalent single S(+) -> O(-) bonds. The calculated electrostatic potentials on the molecular surfaces reveal several strongly positive and negative sites (the former including sigma-holes on the sulfurs) through which a variety of simultaneous intermolecular electrostatic interactions can occur. A series of examples is given. In terms of these features the striking properties of dimethyl sulfoxide and dimethyl sulfone, their large dipole moments and dielectric constants, their high boiling points and why they are such good solvents, can readily be understood.},
author = {Clark, Timothy and Murray, Jane S. and Lane, Pat and Politzer, Peter},
doi = {10.1007/s00894-008-0279-y},
faupublication = {yes},
journal = {Journal of Molecular Modeling},
keywords = {dimethyl sulfoxide;dimethyl sulfone;electrostatic potentials;sigma-hole bonding;noncovalent interactions},
pages = {689-697},
peerreviewed = {Yes},
title = {{Why} are dimethyl sulfoxide and dimethyl sulfone such good solvents?},
volume = {14},
year = {2008}
}
@article{faucris.121726264,
abstract = {Density functional theory and ab initio molecular orbital calculations show that the observed inability of cationic hydridoiridium(III) complexes with beta-aminophosphane ligands to catalyse the direct hydrogenation of carbonyl compounds with dihydrogen ("H-2-hydrogenation") in contrast to their ruthenium(II) equivalents is due to the inability of H-2 to displace a coordinated solvent molecule from an intermediate hydrido complex.},
author = {Puchta, Ralph and Dahlenburg, Lutz and Clark, Timothy},
doi = {10.1002/chem.200701921},
faupublication = {yes},
journal = {Chemistry - A European Journal},
keywords = {ab initio calculations;density functional calculations;hydrogenation;iridium;solvent effects},
month = {Jan},
pages = {8898-8903},
peerreviewed = {Yes},
title = {{Why} do cationic hydridoiridium({III}) complexes with β-aminophosphane ligands favour the transfer hydrogenation of ketones over the direct "{H2}-hydrogenation"? - {A} computational approach},
volume = {14},
year = {2008}
}
@article{faucris.109477764,
author = {Clark, Timothy and Schleyer, Paul and et al.},
author_hint = {WILHELM D, CLARK T, SCHLEYER PV},
doi = {10.1039/P29840000915},
faupublication = {yes},
journal = {Journal of the Chemical Society, Perkin Transactions 2},
month = {Jan},
pages = {915-920},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{Y}-{CONJUGATED} {DIANIONS} - {A} {COMPARISON} {BETWEEN} {THE} 1,1-{DIBENZYLETHYLENE} {AND} {DIPHENYLACETONE}-{DERIVED} {DIANIONS}},
year = {1984}
}
@article{faucris.109478644,
author = {Clark, Timothy and Schleyer, Paul and et al.},
author_hint = {CLARK T, WILHELM D, SCHLEYER PV},
doi = {10.1016/S0040-4039(00)87665-0},
faupublication = {yes},
journal = {Tetrahedron Letters},
month = {Jan},
pages = {3547-3550},
peerreviewed = {Yes},
support_note = {Author relations incomplete. You may find additional data in field 'author{\_}hint'},
title = {{Y} {VS} {CYCLIC} {DELOCALIZATION} {IN} {SMALL} {RING} {DICATIONS} {AND} {DIANIONS} - {THE} {DOMINANCE} {OF} {CHARGE} {REPULSION} {OVER} {HUCKEL} {AROMATICITY}},
volume = {23},
year = {1982}
}
@article{faucris.213416274,
abstract = {A positive \textgreekp-hole is a region of positive electrostatic potential that is perpendicular to a portion of a molecular framework. It is the counterpart of a \textgreeks-hole, which is along the extension of a covalent bond to an atom. Both \textgreeks-holes and \textgreekp-holes become more positive (a) in going from the lighter to the heavier atoms in a given Group of the periodic table, and (b) as the remainder of the molecule is more electronwithdrawing. Positive \textgreeks- and \textgreekp-holes can interact in a highly directional manner with negative sites, e.g., the lone pairs of Lewis bases. In this work, the complexes of 13 \textgreekp-holecontaining molecules with the nitrogen lone pairs of HCN and NH3 have been characterized computationally using the MP2, M06-2X and B3PW91 procedures. While the electrostatic interaction is a major driving force in \textgreekp-hole bonding, a gradation is found from weakly noncovalent to considerably stronger with possible indications of some degree of coordinate covalency.},
author = {Murray, Jane S. and Lane, Pat and Clark, Timothy and Riley, Kevin E. and Politzer, Peter},
doi = {10.1007/s00894-011-1089-1},
faupublication = {yes},
journal = {Journal of Molecular Modeling},
note = {EAM Import::2019-03-14},
pages = {541-548},
peerreviewed = {Yes},
title = {σ-{Holes}, π-{Holes} and {Electrostatically}-{Driven} {Interactions}},
volume = {18},
year = {2012}
}