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ORCIDJournal of Computational Chemistry, Volume 30
Volume 30, Number 1, 15 January 2009
- Gernot Frenking, Charles L. Brooks III, Shigeyoshi Sakaki:
Editors' note. 1 - Vincenzo Barone, Mirco Zerbetto, Antonino Polimeno:
Hydrodynamic modeling of diffusion tensor properties of flexible molecules. 2-13 - Olga Yuzlenko, Katarzyna Kiec-Kononowicz
:
Molecular modeling of A1 and A2A adenosine receptors: Comparison of rhodopsin- and beta2-adrenergic-based homology models through the docking studies. 14-32 - Bing Niu, Lin Lu, Liang Liu, Tian Hong Gu, Kai-Yan Feng, Wen-Cong Lu, Yu-Dong Cai:
HIV-1 protease cleavage site prediction based on amino acid property. 33-39 - Yuto Komeiji, Takeshi Ishikawa, Yuji Mochizuki, Hiroshi Yamataka, Tatsuya Nakano:
Fragment Molecular Orbital method-based Molecular Dynamics (FMO-MD) as a simulator for chemical reactions in explicit solvation. 40-50 - Bryan M. Wong:
Noncovalent interactions in supramolecular complexes: A study on corannulene and the double concave buckycatcher. 51-56 - Matthew A. Addicoat, Gregory F. Metha:
Kick: Constraining a stochastic search procedure with molecular fragments. 57-64 - Lukás Bucinský, Stanislav Biskupic, Michal Ilcin, Vladimír Lukes, Viliam Laurinc:
On relativistic effects in ground state potential curves of Zn2, Cd2, and Hg2 dimers. A CCSD(T) study. 65-74 - Daniel Escudero, Antonio Frontera, David Quiñonero, Pere M. Deyà:
Interplay between anion-pi and hydrogen bonding interactions. 75-82 - Wissam Helal, Stefano Evangelisti, Thierry Leininger, Daniel Maynau:
Ab-initio multireference study of an organic mixed-valence Spiro molecular system. 83-92 - Weiyang Chen, Bo Liao, Wen Zhu, Hao Liu, Qingguang Zeng:
An ant colony pairwise alignment based on the dot plots. 93-97 - Ángel Martín Pendás, M. A. Blanco, Evelio Francisco:
Steric repulsions, rotation barriers, and stereoelectronic effects: A real space perspective. 98-109 - Gota Kikugawa, Rossen Apostolov, Narutoshi Kamiya, Makoto Taiji, Ryutaro Himeno, Haruki Nakamura, Yasushige Yonezawa:
Application of MDGRAPE-3, a special purpose board for molecular dynamics simulations, to periodic biomolecular systems. 110-118 - A. S. Zyubin, A. M. Mebel, Michitoshi Hayashi, Huan-Cheng Chang, S. H. Lin:
Quantum chemical modeling of photoadsorption properties of the nitrogen-vacancy point defect in diamond. 119-131 - Michael D. Altman, Jaydeep P. Bardhan, Jacob K. White, Bruce Tidor:
Accurate solution of multi-region continuum biomolecule electrostatic problems using the linearized Poisson-Boltzmann equation with curved boundary elements. 132-153 - Nikolaj Otte, Marco Bocola, Walter Thiel:
Force-field parameters for the simulation of tetrahedral intermediates of serine hydrolases. 154-162 - Ke Chen, Yingfu Jiang, Li Du, Lukasz A. Kurgan:
Prediction of integral membrane protein type by collocated hydrophobic amino acid pairs. 163-172
Volume 30, Number 2, 30 January 2009
- Juan Manuel Ramírez-Anguita, Àngels González-Lafont, José M. Lluch:
Formation pathways of DMSO from DMS-OH in the presence of O2 and NOx: A theoretical study. 173-182 - Wen Lai Huang, Qingshan Zhu:
DFT calculations on the electronic structures of BiOX (X = F, Cl, Br, I) photocatalysts with and without semicore Bi 5d states. 183-190 - Dmitri V. Sakharov, Carmay Lim:
Force fields including charge transfer and local polarization effects: Application to proteins containing multi/heavy metal ions. 191-202 - Artur Galstyan, Ernst-Walter Knapp:
Accurate redox potentials of mononuclear iron, manganese, and nickel model complexes. 203-211 - Chris Oostenbrink:
Efficient free energy calculations on small molecule host-guest systems - A combined linear interaction energy/one-step perturbation approach. 212-221 - Anmin Zheng, Shang-Bin Liu, Feng Deng:
13C shielding tensors of crystalline amino acids and peptides: Theoretical predictions based on periodic structure models. 222-235 - Hui Zhang, Guiling Zhang, Jing-Yao Liu, Miao Sun, Bo Liu, Ze-Sheng Li:
Theoretical study on the reaction of SiH(CH3)3 with SiH3 radical. 236-242 - Alexey Aleksandrov, Thomas Simonson:
Molecular mechanics models for tetracycline analogs. 243-255 - Xiaolei Zhu, Luhua Lai:
A novel method for enzyme design. 256-267 - Edgar Luttmann, Daniel L. Ensign, Vaidyanathan Vishal, Mike Houston, Noam Rimon, Jeppe Øland, Guha Jayachandran, Mark S. Friedrichs, Vijay S. Pande:
Accelerating molecular dynamic simulation on the cell processor and Playstation 3. 268-274 - Albert Poater, Ana Gallegos Saliner, Ramon Carbó-Dorca, Jordi Poater, Miquel Solà, Luigi Cavallo, Andrew P. Worth:
Modeling the structure-property relationships of nanoneedles: A journey toward nanomedicine. 275-284 - Chao Deng, Xiao-Peng Wu, Xiao-Ming Sun, Yi Ren, Ying-Hong Sheng:
Neutral hydrolyses of carbon disulfide: An ab initio study of water catalysis. 285-294 - Qishi Du, Ri-Bo Huang, Yu-Tuo Wei, Zong-Wen Pang, Li-Qin Du, Kuo-Chen Chou:
Fragment-based quantitative structure-activity relationship (FB-QSAR) for fragment-based drug design. 295-304
- Li-Ping Ju, Ke-Li Han, John Z. H. Zhang:
Global dynamics and transition state theories: Comparative study of reaction rate constants for gas-phase chemical reactions. 305-316 - Jon Baker, Krzysztof Wolinski, Massimo Malagoli, Don Kinghorn, Pawel Wolinski, Gábor Magyarfalvi, Svein Saebo, Tomasz Janowski, Peter Pulay:
Quantum chemistry in parallel with PQS. 317-335
Volume 30, Number 3, February 2009
- Edmond P. F. Lee, Daniel K. W. Mok, Foo-Tim Chau, John M. Dyke:
A combined ab initio and Franck-Condon factor simulation study on the photodetachment spectrum of ScO2-. 337-345 - Ján Busa, Shura Hayryan, Chin-Kun Hu, Jaroslav Skrivánek, Ming-Chya Wu:
Enveloping triangulation method for detecting internal cavities in proteins and algorithm for computing their surface areas and volumes. 346-357 - Yi Ren, Hiroshi Yamataka:
Does alpha-effect exist in E2 reactions? A G2(+) investigation. 358-365 - Ivo Cacelli, Carlo Federico Lami, Giacomo Prampolini:
Force-field modeling through quantum mechanical calculations: Molecular dynamics simulations of a nematogenic molecule in its condensed phases. 366-378 - António J. C. Varandas:
Møller-Plesset perturbation energies and distances for HeC20 extrapolated to the complete basis set limit. 379-388 - Al Mokhtar Lamsabhi, Otilia Mó, Soledad Gutiérrez-Oliva, Patricia Pérez, Alejandro Toro-Labbé, Manuel Yáñez:
The mechanism of double proton transfer in dimers of uracil and 2-thiouracil - The reaction force perspective. 389-398 - Lingchun Song, Jinshuai Song, Yirong Mo, Wei Wu:
An efficient algorithm for energy gradients and orbital optimization in valence bond theory. 399-406 - Wan-Chun Cheng, Soonmin Jang, Chen-Chang Wu, Ren-Jie Lin, Hsiu-Feng Lu, Feng-Yin Li:
Site specificity of the alphaC-H bond dissociation energy for a naturally occurring beta-hairpin peptide - An ab initio study. 407-414 - C. Mediavilla, José Tortajada, V. G. Baonza:
Modeling high pressure reactivity in unsaturated systems: Application to dimethylacetylene. 415-422 - Yinglong Miao, Peter J. Ortoleva:
Molecular dynamics/order parameter extrapolation for bionanosystem simulations. 423-437 - Li-Qin Xue, Xian-Yong Pang, Gui-Chang Wang:
Selective oxidation of styrene on an oxygen-adsorbed Au(111): A density functional theory study. 438-446 - Maik Goette, Helmut Grubmüller:
Accuracy and convergence of free energy differences calculated from nonequilibrium switching processes. 447-456 - Loukas Petridis, Jeremy C. Smith:
A molecular mechanics force field for lignin. 457-467 - Cristopher Camacho, Henryk A. Witek, Shigeyoshi Yamamoto:
Intruder states in multireference perturbation theory: The ground state of manganese dimer. 468-478 - Stephan Frickenhaus, Srinivasaraghavan Kannan, Martin Zacharias:
Efficient evaluation of sampling quality of molecular dynamics simulations by clustering of dihedral torsion angles and Sammon mapping. 479-492 - Hao Zhang, Yun-Hong Zhang, Feng Wang:
Theoretical understanding on the v1-SO42- band perturbed by the formation of magnesium sulfate ion pairs. 493-503
Volume 30, Number 4, March 2009
- Rong Wang, Jian-Sheng Wang, Gui-Rong Liu, Jongyoon Han, Yuzong Chen:
Simulation of DNA electrophoresis in systems of large number of solvent particles by coarse-grained hybrid molecular dynamics approach. 505-513 - Daan P. Geerke, Sandra Luber, Koni H. Marti, Wilfred F. van Gunsteren:
On the direct calculation of the free energy of quantization for molecular systems in the condensed phase. 514-523 - Wenli Zou, Wenjian Liu:
Comprehensive ab initio calculation and simulation on the low-lying electronic states of TlX (X = F, Cl, Br, I, and At). 524-539 - Katalin E. Kövér, Tamás Beke, András Lipták, András Perczel:
Combined NMR three-bond scalar coupling measurements and QM calculations to calculate OH-rotamer equilibrium of polyalcohols. 540-550 - Inmaculada García Cuesta, Alfredo M. J. Sánchez De Merás, Stefano Pelloni, Paolo Lazzeretti:
Understanding the ring current effects on magnetic shielding of hydrogen and carbon nuclei in naphthalene and anthracene. 551-564 - Lei Yang, Jing-Yao Liu, Su-Qin Wan, Ze-Sheng Li:
Theoretical studies of the reactions of CF3CHCLOCHF2/CF3CHFOCHF2 with OH radical and Cl atom and their product radicals with OH. 565-580 - Darren J. Simpson, Thomas Bredow, Andrea R. Gerson:
MSINDO study of acid promoted dissolution of planar MgO and NiO surfaces. 581-588 - Wenbo Yu, Lei Liang, Zijing Lin, Sanliang Ling, Maciej Haranczyk, Maciej Gutowski:
Comparison of some representative density functional theory and wave function theory methods for the studies of amino acids. 589-600 - Keith T. Butler, F. Javier Luque, Xavier Barril:
Toward accurate relative energy predictions of the bioactive conformation of drugs. 601-610 - Li Wang, Jing-Yao Liu, Hong Gao, Su-Qin Wan, Ze-Sheng Li:
Dual-level direct dynamics studies for the reactions of OH radical with bromine-substituted ethanes. 611-620 - Oliver J. Clarke, Martin J. Parker:
Identification of amyloidogenic peptide sequences using a coarse-grained physicochemical model. 621-630 - Zunnan Huang, Chung F. Wong:
Conformational selection of protein kinase A revealed by flexible-ligand flexible-protein docking. 631-644 - Zanxia Cao, Zhixiong Lin, Jun Wang, Haiyan Liu:
Refining the description of peptide backbone conformations improves protein simulations using the GROMOS 53A6 force field. 645-660
- V. Ganesh:
MeTA studio: A cross platform, programmable IDE for computational chemist. 661-672
Volume 30, Number 5, 15 April 2009
- Andreas Vitalis, Rohit V. Pappu:
ABSINTH: A new continuum solvation model for simulations of polypeptides in aqueous solutions. 673-699 - Pei-Kun Yang, Carmay Lim:
Strategies to model the near-solute solvent molecular density/polarization. 700-709 - Alexandra T. P. Carvalho, Pedro Alexandrino Fernandes, Marcel Swart, Joost N. P. Van Stralen, Friedrich Matthias Bickelhaupt, Maria João Ramos:
Role of the variable active site residues in the function of thioredoxin family oxidoreductases. 710-724 - Yun-Xiang Lu, Jian-Wei Zou, Ji-Cai Fan, Wen-Na Zhao, Yong-Jun Jiang, Qing-Sen Yu:
Ab initio calculations on halogen-bonded complexes and comparison with density functional methods. 725-732 - Jeffrey S. Tan, Stephan X. M. Boerrigter, Raymond P. Scaringe, Kenneth R. Morris:
Application of error-ranked singular value decomposition for the determination of potential-derived atomic-centered point charges. 733-742 - Lonnie D. Crosby, Shawn M. Kathmann, Theresa L. Windus:
Implementation of dynamical nucleation theory with quantum potentials. 743-749 - Pär Söderhjelm, Ulf Ryde:
Conformational dependence of charges in protein simulations. 750-760 - Volker Hähnke, Bettina Hofmann, Tomislav Grgat, Ewgenij Proschak, Dieter Steinhilber, Gisbert Schneider:
PhAST: Pharmacophore alignment search tool. 761-771 - Yingfu Jiang, Paul Iglinski, Lukasz A. Kurgan:
Prediction of protein folding rates from primary sequences using hybrid sequence representation. 772-783 - Victor M. Anisimov, Vladislav L. Bugaenko:
QM/QM docking method based on the variational finite localized molecular orbital approximation. 784-798 - Frank Eckert, Ivo Leito, Ivari Kaljurand, Agnes Kütt, Andreas Klamt, Michael Diedenhofen:
Prediction of acidity in acetonitrile solution with COSMO-RS. 799-810 - Grzegorz Mazur, Radoslaw Wlodarczyk:
Application of the dressed time-dependent density functional theory for the excited states of linear polyenes. 811-817 - Loriano Storchi, Giuseppe Vitillaro, Francesco Tarantelli:
Implementation and use of a direct, partially integral-driven non-Dyson propagator method for molecular ionization. 818-825 - Hiroaki Umeda, Yuichi Inadomi, Hiroaki Honda, Umpei Nagashima:
Parallel Fock matrix construction program for molecular orbital calculation - Specific computer with a hierarchical network. 826-831 - Sandro Chiodo, Nino Russo:
One-electron spin-orbit contribution by effective nuclear charges. 832-839
Volume 30, Number 6, 30 April 2009
- Hua Zhu, Daiqian Xie:
N2O in small para-hydrogen clusters: Structures and energetics. 841-846 - Hua-Qing Yang, Song Qin, Chang-Wei Hu:
Theoretical study on the gas-phase reaction mechanism between nickel monoxide and methane for syngas production. 847-863 - Mark S. Friedrichs, Peter K. Eastman, Vaidyanathan Vishal, Mike Houston, Scott LeGrand, Adam L. Beberg, Daniel L. Ensign, Christopher M. Bruns, Vijay S. Pande:
Accelerating molecular dynamic simulation on graphics processing units. 864-872 - Gwonchan Yoon, Hyeong-Jin Park, Sungsoo Na, Kilho Eom:
Mesoscopic model for mechanical characterization of biological protein materials. 873-880 - Jason Martin, Jon Baker, Peter Pulay:
Comments on the molecular geometry of ferrocene: The dangers of using quantum chemistry programs as black boxes. 881-883 - Jorge A. Vila, Héctor A. Baldoni, Harold A. Scheraga:
Performance of density functional models to reproduce observed 13Calpha chemical shifts of proteins in solution. 884-892 - T. R. Walsh, T. Liang:
A multipole-based water potential with implicit polarization for biomolecular simulations. 893-899 - Shuyan Li, Lili Xi, Chengqi Wang, Jiazhong Li, Beilei Lei, Huanxiang Liu, Xiaojun Yao:
A novel method for protein-ligand binding affinity prediction and the related descriptors exploration. 900-909 - Amanda M. Salisburg, Ashley L. Deline, Katrina W. Lexa, George C. Shields, Karl N. Kirschner:
Ramachandran-type plots for glycosidic linkages: Examples from molecular dynamic simulations using the Glycam06 force field. 910-921 - Nitin S. Sapre, Swagata Gupta, Nilanjana Pancholi, Neelima Sapre:
A group center overlap based approach for "3D QSAR" studies on TIBO derivatives. 922-933 - Vincenzo Barone, Maurizio Casarin, Daniel Forrer, Michele Pavone, Mauro Sambi, Andrea Vittadini:
Role and effective treatment of dispersive forces in materials: Polyethylene and graphite crystals as test cases. 934-939 - Peng Zhou, Feifei Tian, Zhicai Shang:
2D depiction of nonbonding interactions for protein complexes. 940-951 - Yi Luo, Satoshi Maeda, Koichi Ohno:
Automated exploration of stable isomers of H+(H2O)n (n = 5-7) via ab initio calculations: An application of the anharmonic downward distortion following algorithm. 952-961 - Hajime Okamoto, Tetsuo Yamada, Shuichiro Kihara, Kazumasa Takechi, Hiroyuki Takagi, Kyozaburo Takeda:
Conformational transitions of cyclic D, L-peptides. 962-973 - Emanuel H. Rubensson, Elias Rudberg, Pawel Salek:
Truncation of small matrix elements based on the Euclidean norm for blocked data structures. 974-977 - Guohua Gao, Xiang Xu, Hong Seok Kang:
A theoretical study on fullerene-dizincocene hybrids. 978-982 - Jakub Kaminský, Jirí Sebek, Petr Bour:
Molecular dynamics with restrictions derived from optical spectra. 983-991 - Sarah Remmert, Carol A. Parish:
Energetic analyses of chair and boat conformations of maleimide substituted cyclohexane derivatives. 992-998 - Ilya V. Loksha, James R. Maiolo III, Cheng W. Hong, Albert H. Ng, Christopher D. Snow:
SHARPEN - Systematic Hierarchical Algorithms for Rotamers and Proteins on an Extended Network. 999-1005
Volume 30, Number 7, May 2009
- Cun-Xi Liu, Ze-Rong Li, Chong-Wen Zhou, Xiang-Yuan Li:
Accurate prediction of thermodynamic properties of alkyl peroxides by combining density functional theory calculation with least-square calibration. 1007-1015 - James S. Wright, Hooman Shadnia, Leonid L. Chepelev:
Stability of carbon-centered radicals: Effect of functional groups on the energetics of addition of molecular oxygen. 1016-1026 - Erika Ivonne López-Martínez, Luz María Rodríguez-Valdez, Norma Flores-Holguín, Alfredo Márquez-Lucero, Daniel Glossman-Mitnik:
Theoretical study of electronic properties of organic photovoltaic materials. 1027-1037 - Shunzhou Wan, Peter V. Coveney:
A comparative study of the COX-1 and COX-2 isozymes bound to lipid membranes. 1038-1050 - Lixin Zhan, Jeff Z. Y. Chen, Wing-Ki Liu:
Comparison of predicted native structures of Met-enkephalin based on various accessible-surface-area solvent models. 1051-1058 - Xavier Periole, Lucy R. Allen, Kamil Tamiola, Alan E. Mark, Emanuele Paci:
Probing the free energy landscape of the FBP28WW domain using multiple techniques. 1059-1068 - Stanislav Böhm, Otto Exner:
Interaction of two functional groups through the benzene ring: Theory and experiment. 1069-1074 - Miguel Angelo Fonseca de Souza, Elizete Ventura, Regiane C. M. U. Araújo, Mozart N. Ramos, Silmar Andrade do Monte:
CASSCF and multireference CI with singles and doubles study of low-lying valence and Rydberg states of 2H-tetrazole. 1075-1081 - Juan I. Rodríguez, Andreas M. Köster, Paul W. Ayers, Ana Santos-Valle, Alberto Vela, Gabriel Merino:
An efficient grid-based scheme to compute QTAIM atomic properties without explicit calculation of zero-flux surfaces. 1082-1092 - Heiko Jacobsen:
Chemical bonding in view of electron charge density and kinetic energy density descriptors. 1093-1102 - Jin Wang, Jin Huai Liu:
Novel bi-transition metallic encapsulated naphthalene-like Si20 prismatic cage: A DFT investigation. 1103-1110 - Laura R. Hofto, Caroline E. Lee, Mauricio Cafiero:
The importance of aromatic-type interactions in serotonin synthesis: Protein-ligand interactions in tryptophan hydroxylase and aromatic amino acid decarboxylase. 1111-1115 - Young Kee Kang, Nam Sook Kang:
Conformational preferences of N-methoxycarbonyl proline dipeptide. 1116-1127 - Hong-Liang Xu, Fang-Fang Wang, Zhi-Ru Li, Bing-Qiang Wang, Di Wu, Wei Chen, Guang-Tao Yu, Feng Long Gu, Yuriko Aoki:
The nitrogen edge-doped effect on the static first hyperpolarizability of the supershort single-walled carbon nanotube. 1128-1134 - Ji-Lai Li, Cai-Yun Geng, Yuxiang Bu, Xu-Ri Huang, Chia-Chung Sun:
Conformational transition pathway in the allosteric process of calcium-induced recoverin: Molecular dynamics simulations. 1135-1145 - Ramon Carbó-Dorca, Ana Gallegos, Ángel J. Sánchez:
Notes on quantitative structure-properties relationships (QSPR) (1): A discussion on a QSPR dimensionality paradox (QSPR DP) and its quantum resolution. 1146-1159 - Daniel Seeliger, Bert L. de Groot:
tCONCOORD-GUI: Visually supported conformational sampling of bioactive molecules. 1160-1166 - Ritwik Kavathekar, Subodh Khire, V. Ganesh, Anuja P. Rahalkar, Shridhar R. Gadre:
WebMTA: A web-interface for ab initio geometry optimization of large molecules using molecular tailoring approach. 1167-1173 - Zuzana Jirousková, Radka Svobodová Vareková, Jakub Vanek, Jaroslav Koca:
Software news and updates electronegativity equalization method: Parameterization and validation for organic molecules using the Merz-Kollman-Singh charge distribution scheme. 1174-1178
Volume 30, Number 8, June 2009
- Ahmed Dkhissi, Jean Marie Ducéré, Ralf Blossey, Claude Pouchan:
Can the hybrid meta GGA and DFT-D methods describe the stacking interactions in conjugated polymers? 1179-1184 - K. S. Kang, James W. Davenport, James Glimm, David E. Keyes, Michael McGuigan:
Linear augmented Slater-type orbital method for free standing clusters. 1185-1193 - Oana Cramariuc, Terttu I. Hukka, Tapio T. Rantala, Helge Lemmetyinen:
Ab initio description of photoabsorption and electron transfer in a doubly-linked porphyrin-fullerene dyad. 1194-1201 - Xue-Gang Yang, Duan Chen, Min Wang, Ying Xue, Yuzong Chen:
Prediction of antibacterial compounds by machine learning approaches. 1202-1211 - M. Fernanda Rey-Stolle, Marta Enciso, Antonio Rey:
Topology-based models and NMR structures in protein folding simulations. 1212-1219 - Pedro A. Derosa:
A combined semiempirical-DFT study of oligomers within the finite-chain approximation, evolution from oligomers to polymers. 1220-1228 - Miguel Arenas, M. Carmen Villaverde, Fredy Sussman:
Prediction and analysis of binding affinities for chemically diverse HIV-1 PR inhibitors by the modified SAFE_p approach. 1229-1240 - Aneta Jezierska, Jaroslaw J. Panek:
Investigations of an O-H * * * S hydrogen bond via Car-Parrinello and path integral molecular dynamics. 1241-1250 - Yan Zhang, Chang-Sheng Wang:
Estimation on the intramolecular 10-membered ring N-H***O-C hydrogen-bonding energies in glycine and alanine peptides. 1251-1260 - Vincent Liégeois, Benoît Champagne:
Vibrational Raman optical activity of pi-conjugated helical systems: Hexahelicene and heterohelicenes. 1261-1278 - Lin Jin, Yi-Hong Ding:
Stability of N42--based sandwich-like energetic complexes [N4TiN4]2-: Effect of spins and counterions. 1279-1289 - Michael Gilleßen, Richard Dronskowski:
A combinatorial study of full Heusler alloys by first-principles computational methods. 1290-1299 - Michael Devereux, Paul L. A. Popelier, Iain M. McLay:
Toward an ab initio fragment database for bioisosterism: Dependence of QCT properties on level of theory, conformation, and chemical environment. 1300-1318 - Celestino Angeli:
On the nature of the pi -> pi* ionic excited states: The V state of ethene as a prototype. 1319-1333 - Jinhyuk Lee, Sihyun Ham, Wonpil Im:
Beta-hairpin restraint potentials for calculations of potentials of mean force as a function of beta-hairpin tilt, rotation, and distance. 1334-1343 - Jian-Ding Qiu, San-Hua Luo, Jian-Hua Huang, Ru-Ping Liang:
Using support vector machines for prediction of protein structural classes based on discrete wavelet transform. 1344-1350 - Yasuomi Kiyota, Jun-Ya Hasegawa, Kazuhiro Fujimoto, Ben Swerts, Hiroshi Nakatsuji:
A multicore QM/MM approach for the geometry optimization of chromophore aggregate in protein. 1351-1359
Volume 30, Number 9, 15 July 2009
- Liuming Yan, Changle Shao, Xiaobo Ji:
Evaluation of electroosmotic drag coefficient of water in hydrated sodium perfluorosulfonate electrolyte polymer. 1361-1370 - Jan Fuhrmann, Alexander Rurainski, Hans-Peter Lenhof, Dirk Neumann:
A new method for the gradient-based optimization of molecular complexes. 1371-1378 - Anatoliy Volkov, Tibor Koritsanszky, Michal Chodkiewicz, Harry F. King:
On the basis-set dependence of local and integrated electron density properties: Application of a new computer program for quantum-chemical density analysis. 1379-1391 - Cherumuttathu H. Suresh, Neetha Mohan, K. Periya Vijayalakshmi, Renjumon George, Janice M. Mathew:
Typical aromatic noncovalent interactions in proteins: A theoretical study using phenylalanine. 1392-1404 - Arghya Barman, Woody Taves, Rajeev Prabhakar:
Insights into the mechanism of methionine oxidation catalyzed by metal (Cu2+, Zn2+, and Fe3+) - Amyloid beta (Abeta) peptide complexes: A computational study. 1405-1413 - Xuan Xiao, Pu Wang, Kuo-Chen Chou:
GPCR-CA: A cellular automaton image approach for predicting G-protein-coupled receptor functional classes. 1414-1423 - Jianming Wu, Xin Xu:
Accurate prediction of heats of formation by a combined method of B3LYP and neural network correction. 1424-1444 - Sándor Kristyán:
Interesting properties of Thomas-Fermi kinetic and Parr electron-electron-repulsion DFT energy functional generated compact one-electron density approximation for ground-state electronic energy of molecular systems. 1445-1453 - Johannes Schwöbel, Ralf-Uwe Ebert, Ralph Kühne, Gerrit Schüürmann:
Modeling the H bond donor strength of -OH, -NH, and -CH sites by local molecular parameters. 1454-1464 - Federico Iori, Rosa Di Felice, E. Molinari, Stefano Corni:
GolP: An atomistic force-field to describe the interaction of proteins with Au(111) surfaces in water. 1465-1476 - Juan Manuel Ramírez-Anguita, Àngels González-Lafont, José M. Lluch:
Formation pathways of DMSO2 in the addition channel of the OH-initiated DMS oxidation: A theoretical study. 1477-1489 - Lennart Nilsson:
Efficient table lookup without inverse square roots for calculation of pair wise atomic interactions in classical simulations. 1490-1498 - Alexander Rurainski, Andreas Hildebrandt, Hans-Peter Lenhof:
A consensus line search algorithm for molecular potential energy functions. 1499-1509 - Riccardo Concu, Gianni Podda, Eugenio Uriarte, Humberto González Díaz:
Computational chemistry study of 3D-structure-function relationships for enzymes based on Markov models for protein electrostatic, HINT, and van der Waals potentials. 1510-1520 - Meiyan Wang, Lin Cheng, Bo Hong, Zhijian Wu:
Reaction mechanism of palladium-catalyzed silastannation of allenes by density functional theory. 1521-1531 - Dray-Ming Shien, Tzong-Yi Lee, Wen-Chi Chang, Justin Bo-Kai Hsu, Jorng-Tzong Horng, Po-Chiang Hsu, Ting-Yuan Wang, Hsien-Da Huang:
Incorporating structural characteristics for identification of protein methylation sites. 1532-1543
Volume 30, Number 10, 30 July 2009
- Bernard R. Brooks, Charles L. Brooks III, Alexander D. MacKerell Jr., Lennart Nilsson, Robert J. Petrella, Benoît Roux, Y. Won, G. Archontis, Christian Bartels, Stefan Boresch, Amedeo Caflisch, Leo S. D. Caves, Qiang Cui, Aaron R. Dinner, Michael Feig, S. Fischer, Jiali Gao, Milan Hodoscek, Wonpil Im, Krzysztof Kuczera, Themis Lazaridis, J. Ma, Victor Ovchinnikov, Emanuele Paci, Richard W. Pastor, C. B. Post, J. Z. Pu, Michael Schaefer, Bruce Tidor, Richard M. Venable, H. Lee Woodcock III, X. Wu, W. Yang, Darrin M. York, Martin Karplus:
CHARMM: The biomolecular simulation program. 1545-1614
Volume 30, Number 11, August 2009
- Massimiliano Bonomi, Alessandro Barducci, Michele Parrinello:
Reconstructing the equilibrium Boltzmann distribution from well-tempered metadynamics. 1615-1621 - Wonpil Im, Jinhyuk Lee, Taehoon Kim, Huan Rui:
Novel free energy calculations to explore mechanisms and energetics of membrane protein structure and function. 1622-1633 - Edina Rosta, H. Lee Woodcock III, Bernard R. Brooks, Gerhard Hummer:
Artificial reaction coordinate "tunneling" in free-energy calculations: The catalytic reaction of RNase H. 1634-1641 - Jan H. Meinke, Ulrich H. E. Hansmann:
Free-energy-driven folding and thermodynamics of the 67-residue protein GS-alpha3W - A large-scale Monte Carlo study. 1642-1648 - Mengen Chen, Wei Yang:
On-the-path random walk sampling for efficient optimization of minimum free-energy path. 1649-1653 - Payel Das, Jingyuan Li, Ajay K. Royyuru, Ruhong Zhou:
Free energy simulations reveal a double mutant avian H5N1 virus hemagglutinin with altered receptor binding specificity. 1654-1663 - Clara D. Christ, Wilfred F. van Gunsteren:
Comparison of three enveloping distribution sampling Hamiltonians for the estimation of multiple free energy differences from a single simulation. 1664-1679 - Xin Zhang, Artem B. Mamonov, Daniel M. Zuckerman:
Absolute free energies estimated by combining precalculated molecular fragment libraries. 1680-1691
- Jennifer L. Knight, Charles L. Brooks III:
lambda-Dynamics free energy simulation methods. 1692-1700 - Dian Jiao, Jiajing Zhang, Robert E. Duke, Guohui Li, Michael J. Schnieders, Pengyu Y. Ren:
Trypsin-ligand binding free energies from explicit and implicit solvent simulations with polarizable potential. 1701-1711 - Gerhard König, Stefan Bruckner, Stefan Boresch:
Unorthodox uses of Bennett's acceptance ratio method. 1712-1718 - Mikolai Fajer, Robert V. Swift, James Andrew McCammon:
Using multistate free energy techniques to improve the efficiency of replica exchange accelerated molecular dynamics. 1719-1725 - Harald Oberhofer, Christoph Dellago:
Efficient extraction of free energy profiles from nonequilibrium experiments. 1726-1736 - Eric Vanden-Eijnden:
Some recent techniques for free energy calculations. 1737-1747
Volume 30, Number 12, September 2009
- Sofie Van Damme, Patrick Bultinck:
Conceptual DFT properties-based 3D QSAR: Analysis of inhibitors of the nicotine metabolizing CYP2A6 enzyme. 1749-1757 - Zdenek Futera, Julia Klenko, Judit E. Sponer, Jirí Sponer, Jaroslav V. Burda:
Interactions of the "piano-stool" [ruthenium(II) (eta6-arene)(en)CL]+ complexes with water and nucleobases; ab initio and DFT study. 1758-1770 - Adrià Gil, Mariona Sodupe, Juan Bertrán:
Influence of ionization on the conformational preferences of peptide models. Ramachandran surfaces of N-formyl-glycine amide and N-formyl-alanine amide radical cations. 1771-1784 - Guo-Xu Zhang, Ying Xie, Haitao Yu, Hong-Gang Fu:
First-principles calculations of the stability and electronic properties of the PbTiO3 (110) polar surface. 1785-1798 - Séverine Queyroy, Haruki Nakamura, Ikuo Fukuda:
Numerical examination of the extended phase-space volume-preserving integrator by the Nosé-Hoover molecular dynamics equations. 1799-1815 - Xinli Song, Jicun Li, Hua Hou, Baoshan Wang:
Extensive theoretical studies of a new energetic material: Tetrazino-tetrazine-tetraoxide (TTTO). 1816-1820 - Pedro E. M. Lopes, Guillaume Lamoureux, Alexander D. MacKerell Jr.:
Polarizable empirical force field for nitrogen-containing heteroaromatic compounds based on the classical Drude oscillator. 1821-1838 - Shih-Wei Chao, Arvin Huang-Te Li, Sheng D. Chao:
Molecular dynamics simulations of fluid methane properties using ab initio intermolecular interaction potentials. 1839-1849 - Shun Sakuraba, Akio Kitao:
Multiple Markov transition matrix method: Obtaining the stationary probability distribution from multiple simulations. 1850-1858 - Kai Lüder, Lennart Lindfors, Jan Westergren, Sture Nordholm, Rasmus A. X. Persson, Mikaela Pedersen:
In silico prediction of drug solubility: 4. Will simple potentials suffice? 1859-1871 - Ujjal Das, Krishnan Raghavachari:
Predicting PH vibrations of gas phase molecules and surface-adsorbed species using bond length-frequency correlations. 1872-1881 - Wen Lai Huang:
Electronic structures and optical properties of BiOX (X = F, Cl, Br, I) via DFT calculations. 1882-1891 - Huaiyong Li, Siyuan Zhang, Shihong Zhou, Xueqiang Cao:
Investigation of chemical bond characteristics, thermal expansion coefficients and bulk moduli of alpha-R2MoO6 and R2Mo2O7 (R = rare earths) by using a dielectric chemical bond method. 1892-1898 - Max K. Leong, Yen-Ming Chen, Tzu-Hsien Chen:
Prediction of human cytochrome P450 2B6-substrate interactions using hierarchical support vector regression approach. 1899-1909 - Robert Grybos, Lubomir Benco, Tomás Bucko, Jürgen Hafner:
Interaction of NO molecules with Pd clusters: Ab initio density-functional study. 1910-1922 - Eun-Jong Hong, Shaun M. Lippow, Bruce Tidor, Tomás Lozano-Pérez:
Rotamer optimization for protein design through MAP estimation and problem-size reduction. 1923-1945 - Frederik J. Tielens:
Exploring the reactivity of framework vanadium, niobium, and tantalum sites in zeolitic materials using DFT reactivity descriptors. 1946-1951
- William J. Allen, Justin A. Lemkul, David R. Bevan:
GridMAT-MD: A grid-based membrane analysis tool for use with molecular dynamics. 1952-1958
Volume 30, Number 13, October 2009
- Shuang Chen, Jing Ma:
Charge transport in stacking metal and metal-free phthalocyanine iodides. Effects of packing, dopants, external electric field, central metals, core modification, and substitutions. 1959-1972 - Seonah Kim, Anita M. Orendt, Marta B. Ferraro, Julio C. Facelli:
Crystal structure prediction of flexible molecules using parallel genetic algorithms with a standard force field. 1973-1985 - Junmeng Cai, Siyu Chen:
A new iterative linear integral isoconversional method for the determination of the activation energy varying with the conversion degree. 1986-1991 - Xia Wu, Wensheng Cai, Xueguang Shao:
Optimization of bimetallic Cu-Au and Ag-Au clusters by using a modified adaptive immune optimization algorithm. 1992-2000 - Bahram Hemmateenejad, Ahmad R. Mehdipour, Ramin Miri, Mojtaba Shamsipur:
Application of MOLMAP approach for QSAR modeling of various biological activities using substituent electronic descriptors. 2001-2009 - Konrad H. Marti, Markus Reiher:
Haptic quantum chemistry. 2010-2020 - Aurélien Grosdidier, Vincent Zoete, Olivier Michielin:
Blind docking of 260 protein-ligand complexes with EADock 2.0. 2021-2030 - Weiyang Chen, Bo Liao, Wen Zhu, Xuyu Xiang:
Multiple sequence alignment algorithm based on a dispersion graph and ant colony algorithm. 2031-2038 - Michio Iwaoka, Naoki Kimura, Daisuke Yosida, Toshiya Minezaki:
The SAAP force field: Development of the single amino acid potentials for 20 proteinogenic amino acids and Monte Carlo molecular simulation for short peptides. 2039-2055 - Jian Lin, Kechen Wu, Mingxin Zhang:
A new hybrid DFT approach to electronic excitation and first hyperpolarizabilities of transition metal complexes. 2056-2063 - Brecht M. R. Donckels, Dirk J. W. De Pauw, Peter A. Vanrolleghem, Bernard De Baets:
A kernel-based method to determine optimal sampling times for the simultaneous estimation of the parameters of rival mathematical models. 2064-2077 - Mario Piris, Jesus M. Ugalde:
Iterative diagonalization for orbital optimization in natural orbital functional theory. 2078-2086 - Vinzenz Bachler:
Time-dependent density functional calculations on the electronic spectra of the neutral nickel complex [Ni(LISQ)2] (LISQ = 3, 5-di-tert-butyl-o-diiminobenzosemiquinonate(1-)) and its monoanion and dication. 2087-2098 - Ramon Carbó-Dorca, Ana Gallegos Saliner:
Notes on quantitative structure-properties relationships (QSPR) part 2: The role of the number of atoms as a molecular descriptor. 2099-2104 - Wenbo Yu, Xuee Xu, Hongbao Li, Rui Pang, Kun Fang, Zijing Lin:
Extensive conformational searches of 13 representative dipeptides and an efficient method for dipeptide structure determinations based on amino acid conformers. 2105-2121 - Yang Wang:
Perfect planar tetracoordinate carbon in neutral unsaturated hydrocarbon cages: A new strategy utilizing three-dimensional electron delocalization. 2122-2126 - Yi He, Yi Xiao, Adam Liwo, Harold A. Scheraga:
Exploring the parameter space of the coarse-grained UNRES force field by random search: Selecting a transferable medium-resolution force field. 2127-2135 - Yongqi Huang, Huifang Li, Yuxiang Bu:
Molecular dynamics simulation exploration of cooperative migration mechanism of calcium ions in sarcoplasmic reticulum Ca2+-ATPase. 2136-2145 - Nigel J. Brookes, David C. Graham, Gemma Christian, Robert Stranger, Brian F. Yates:
The influence of peripheral ligand bulk on nitrogen activation by three-coordinate molybdenum complexes - A theoretical study using the ONIOM method. 2146-2156
- Leandro Martínez, Ricardo Andrade, Ernesto G. Birgin, José Mario Martínez:
PACKMOL: A package for building initial configurations for molecular dynamics simulations. 2157-2164
Volume 30, Number 14, 15 November 2009
- Zhigang Zhou, Yanli Wang, Stephen H. Bryant:
Computational analysis of the cathepsin B inhibitors activities through LR-MMPBSA binding affinity calculation based on docked complex. 2165-2175 - Shih-I Lu:
Gibbs energy of activation for thermal isomerization of (1Z)-acetaldehyde hydrazone and (1Z)-acetaldehyde N, N-dimethylhydrazone by Gaussian-4 theory and CCSD(T)/CBS computations. 2176-2180 - Gab-Yong Lee:
Substituent effect on electron affinity, gas-phase basicity, and structure of monosubstituted propynyl radicals and their anions: A theoretical study. 2181-2186 - C. David Sherrill, Bobby G. Sumpter, Mutasem O. Sinnokrot, Michael S. Marshall, Edward G. Hohenstein, Ross C. Walker, Ian R. Gould:
Assessment of standard force field models against high-quality ab initio potential curves for prototypes of pi-pi, CH/pi, and SH/pi interactions. 2187-2193 - Hong-Xia Liu, Ying Wang, Lei Yang, Jing-Yao Liu, Hong Gao, Ze-Sheng Li, Chia-Chung Sun:
CH3NHNH2 + OH reaction: Mechanism and dynamics studies. 2194-2204 - Bo Liao, Weiyang Chen, Xingming Sun, Wen Zhu:
A binary coding method of RNA secondary structure and its application. 2205-2212 - Masanori Miura, Yuriko Aoki:
Ab initio theory for treating local electron excitations in molecules and its performance for computing optical properties. 2213-2230 - Yifan Song, Junjun Mao, Marilyn R. Gunner:
MCCE2: Improving protein pKa calculations with extensive side chain rotamer sampling. 2231-2247 - Lei Chen, Lin Lu, Kairui Feng, Wenjin Li, Jie Song, Lulu Zheng, Youlang Yuan, Zhenbing Zeng, Kai-Yan Feng, Wen-Cong Lu, Yudong Cai:
Multiple classifier integration for the prediction of protein structural classes. 2248-2254 - Chenggang Zhou, Jinping Wu, Liang Chen, Yang Wang, Hansong Cheng, Robert C. Forrey:
Force field for copper clusters and nanoparticles. 2255-2266 - Yumi N. Imai, Yoshihisa Inoue, Isao Nakanishi, Kazuo Kitaura:
Amide-pi interactions between formamide and benzene. 2267-2276 - Dongsheng Zou, Zhongshi He, Jingyuan He:
beta-Hairpin prediction with quadratic discriminant analysis using diversity measure. 2277-2284 - Matthias Rupp, Petra Schneider, Gisbert Schneider:
Distance phenomena in high-dimensional chemical descriptor spaces: Consequences for similarity-based approaches. 2285-2296 - Conrad Shyu, F. Marty Ytreberg:
Reducing the bias and uncertainty of free energy estimates by using regression to fit thermodynamic integration data. 2297-2304 - Ute F. Röhrig, Aurélien Grosdidier, Vincent Zoete, Olivier Michielin:
Docking to heme proteins. 2305-2315 - Pablo Rivero, Christoph Loschen, Ibério de Pinho Ribeiro Moreira, Francesc Illas:
Performance of plane-wave-based LDA+U and GGA+U approaches to describe magnetic coupling in molecular systems. 2316-2326 - Mikaël Kepenekian, Vincent Robert, Boris Le Guennic, Coen de Graaf:
Energetics of [Fe(NCH)6]2+ via CASPT2 calculations: A spin-crossover perspective. 2327-2333 - Wei Kan, Hua Zhong, Haitao Yu:
Theoretical prediction regarding structural and thermodynamical characteristics of stable CH3PO2 isomers and unimolecular decomposition mechanisms of species CH3P(=O)2, CH3O-P=O, and CH2=P(=O)OH. 2334-2350 - Tetsu Narumi, Kenji Yasuoka, Makoto Taiji, Siegfried Höfinger:
Current performance gains from utilizing the GPU or the ASIC MDGRAPE-3 within an enhanced Poisson Boltzmann approach. 2351-2357 - Erjun Zhao, Bo Hong, Jian Meng, Zhijian Wu:
First principles investigation on the ultra-incompressible and hard TaN. 2358-2363
- Adam Górecki, Marcin Szypowski, Maciej Dlugosz, Joanna Trylska:
RedMD - Reduced molecular dynamics package. 2364-2373
Volume 30, Number 15, 30 November 2009
- Olivier Delalande, Nicolas Férey, Gilles Grasseau, Marc Baaden:
Complex molecular assemblies at hand via interactive simulations. 2375-2387 - Xin Zhang, Ruibo Wu, Lingchun Song, Yuchun Lin, Menghai Lin, Zexing Cao, Wei Wu, Yirong Mo:
Molecular dynamics simulations of the detoxification of paraoxon catalyzed by phosphotriesterase. 2388-2401 - James R. Apgar, Seungsoo Hahn, Gevorg Grigoryan, Amy E. Keating:
Cluster expansion models for flexible-backbone protein energetics. 2402-2413 - Gergely Gidofalvi, Ron L. Shepard:
Computation of determinant expansion coefficients within the graphically contracted function method. 2414-2419 - Luis Fernández Pacios, Víctor M. Campos, Irene Merino, Luis Gómez:
Structures and thermodynamics of biphenyl dihydrodiol stereoisomers and their metabolites in the enzymatic degradation of arene xenobiotics. 2420-2432 - Hsin-Tsung Chen, Jee-Gong Chang, Hui-Lung Chen, Shin-Pon Ju:
Identifying the O2 diffusion and reduction mechanisms on CeO2 electrolyte in solid oxide fuel cells: A DFT + U study. 2433-2442 - Jacopo Sgrignani, Claudia Bonaccini, Giovanni Grazioso, Matteo Chioccioli, Andrea Cavalli, Paola Gratteri:
Insights into docking and scoring neuronal alpha4beta2 nicotinic receptor agonists using molecular dynamics simulations and QM/MM calculations. 2443-2454 - Hassan Golmohammadi:
Prediction of octanol-water partition coefficients of organic compounds by multiple linear regression, partial least squares, and artificial neural network. 2455-2465 - Nuno M. F. S. A. Cerqueira, P. J. Gonzalez, C. D. Brondino, Maria João Romão, C. C. Romão, Isabel Moura, José J. G. Moura:
The effect of the sixth sulfur ligand in the catalytic mechanism of periplasmic nitrate reductase. 2466-2484 - Aimee Gotway Bailey, C. P. Lowe:
MILCH SHAKE: An efficient method for constraint dynamics applied to alkanes. 2485-2493 - Jagdish Chandra Patra, Onkar Singh:
Artificial neural networks-based approach to design ARIs using QSAR for diabetes mellitus. 2494-2508 - Lu Wang, Jijun Zhao, Zhen Zhou, S. B. Zhang, Zhongfang Chen:
First-principles study of molecular hydrogen dissociation on doped Al12X (X = B, Al, C, Si, P, Mg, and Ca) clusters. 2509-2514 - Jacek Korchowiec, Jakub Lewandowski, Marcin Makowski, Feng Long Gu, Yuriko Aoki:
Elongation cutoff technique armed with quantum fast multipole method for linear scaling. 2515-2525 - Wen-Chi Chang, Tzong-Yi Lee, Dray-Ming Shien, Justin Bo-Kai Hsu, Jorng-Tzong Horng, Po-Chiang Hsu, Ting-Yuan Wang, Hsien-Da Huang, Rong-Long Pan:
Incorporating support vector machine for identifying protein tyrosine sulfation sites. 2526-2537 - Oscar Gálvez, Pedro C. Gómez, Luis Fernández Pacios:
Characterization of two types of intermolecular interactions on halogen monoxide monohydrates. 2538-2549 - Terutaka Yoshizawa, Masahiko Hada:
Relativistic and electron-correlation effects on magnetizabilities investigated by the Douglas-Kroll-Hess method and the second-order Møller-Plesset perturbation theory. 2550-2566 - Chang-Liang Sun, Xiao-Nan Jiang, Chang-Sheng Wang:
An analytic potential energy function for the amide-amide and amide-water intermolecular hydrogen bonds in peptides. 2567-2575
- Andrey A. Toropov, Alla P. Toropova, Emilio Benfenati, Alberto Manganaro:
QSPR modeling of enthalpies of formation for organometallic compounds by SMART-based optimal descriptors. 2576-2582
Volume 30, Number 16, December 2009
- Ayako Nakata, Takao Tsuneda, Kimihiko Hirao:
Modified regional self-interaction corrected time-dependent density functional theory for core excited-state calculations. 2583-2593 - Takeshi Ishikawa, Takakazu Ishikura, Kazuo Kuwata:
Theoretical study of the prion protein based on the fragment molecular orbital method. 2594-2601 - Satoshi Omori, Sotaro Fuchigami, Mitsunori Ikeguchi, Akinori Kidera:
Linear response theory in dihedral angle space for protein structural change upon ligand binding. 2602-2608 - Art E. Cho, David Rinaldo:
Extension of QM/MM docking and its applications to metalloproteins. 2609-2616 - Yin Wei, Bandaru Sateesh, Boris Maryasin, G. Narahari Sastry, Hendrik Zipse:
The performance of computational techniques in locating the charge separated intermediates in organocatalytic transformations. 2617-2624 - Takashi Nakamura, Azusa Yamaguchi, Hirotaka Kondo, Hirofumi Watanabe, Tatsuo Kurihara, Nobuyoshi Esaki, Shuichi Hirono, Shigenori Tanaka:
Roles of K151 and D180 in L-2-haloacid dehalogenase from Pseudomonas sp. YL: Analysis by molecular dynamics and ab initio fragment molecular orbital calculations. 2625-2634 - Mehdi Bagheri Hamaneh, Matthias Buck:
Refinement of the primary hydration shell model for molecular dynamics simulations of large proteins. 2635-2644 - Robert A. Evarestov, M. V. Losev:
All-electron LCAO calculations of the LiF crystal phonon spectrum: Influence of the basis set, the exchange-correlation functional, and the supercell size. 2645-2655 - Minoru Saito, Isao Okazaki:
Force-field parameters of the Psi and Phi around glycosidic bonds to oxygen and sulfur atoms. 2656-2665 - Thomas Sandberg, Matti Hotokka:
Conformational analysis of hydroxymatairesinol in aqueous solution with molecular dynamics. 2666-2673 - Xiaoyan Zheng, Xueye Wang, Shanfeng Yi, Nuanqing Wang, Yueming Peng:
DFT study of the carbon- and nitrogen-pivot lariat crown ethers and their complexes with alkali metal cations: Na+, K+. 2674-2683 - Wen Lai Huang:
First-principles calculations on the energetics, electronic structures and magnetism of SrFeO2. 2684-2693 - Xiaohua Chen, Dianxiang Xing, Liang Zhang, Robert I. Cukier, Yuxiang Bu:
Effect of metal ions on radical type and proton-coupled electron transfer channel: sigma-Radical vs pi-radical and sigma-channel vs pi-channel in the imide units. 2694-2705 - Han Zheng, Shenglong Wang, Yingkai Zhang:
Increasing the time step with mass scaling in Born-Oppenheimer ab initio QM/MM molecular dynamics simulations. 2706-2711 - Indrani Mitra, Kunal Roy, Achintya Saha:
QSAR of antilipid peroxidative activity of substituted benzodioxoles using chemometric tools. 2712-2722 - Yufang Liu, Junxia Ding, Ruiqiong Liu, Deheng Shi, Jinfeng Sun:
Time-dependent density functional theory study on the electronic excited-state geometric structure, infrared spectra, and hydrogen bonding of a doubly hydrogen-bonded complex. 2723-2727 - Akifumi Oda, Noriyuki Yamaotsu, Shuichi Hirono:
Evaluation of the searching abilities of HBOP and HBSITE for binding pocket detection. 2728-2737 - Peng Zhou, Jianwei Zou, Feifei Tian, Zhicai Shang:
Geometric similarity between protein-RNA interfaces. 2738-2751 - Sérgio Filipe Sousa, Emanuela S. Carvalho, Diana M. Ferreira, Isabel S. Tavares, Pedro Alexandrino Fernandes, Maria João Ramos, José A. N. F. Gomes:
Comparative analysis of the performance of commonly available density functionals in the determination of geometrical parameters for zinc complexes. 2752-2763 - J. Oscar C. Jiménez-Halla, Eduard Matito, Lluís Blancafort, Juvencio Robles, Miquel Solà:
Tuning aromaticity in trigonal alkaline earth metal clusters and their alkali metal salts. 2764-2776 - Chinapong Kritayakornupong:
Structural and dynamical properties of the V3+ ion in dilute aqueous solution: An ab initio QM/MM molecular dynamics simulation. 2777-2783
- Friedrich Matthias Bickelhaupt:
A chemist's guide to valence bond theory. 2784
- Garrett M. Morris, Ruth Huey, William Lindstrom, Michel F. Sanner, Richard K. Belew, David S. Goodsell, Arthur J. Olson:
AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. 2785-2791
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