Stop the war!Остановите войну!
for scientists:
default search action
Google
Google Scholar
Semantic Scholar
Internet Archive Scholar
CiteSeerX
ORCIDJournal of Computational Chemistry, Volume 31
Volume 31, Number 1, 15 January 2010
- Halvor S. Hansen, Philippe H. Hünenberger
:
Using the local elevation method to construct optimized umbrella sampling potentials: Calculation of the relative free energies and interconversion barriers of glucopyranose ring conformers in water. 1-23
- Lili Xi, Juan Du, Shuyan Li, Jiazhong Li, Huanxiang Liu, Xiaojun Yao:
A combined molecular modeling study on gelatinases and their potent inhibitors. 24-42 - Ming-Der Su:
A computational study of photochemical isomerization reactions of thiophenes. 43-56 - In-Ho Lee, Seung-Yeon Kim, Jooyoung Lee:
Dynamic folding pathway models of the villin headpiece subdomain (HP-36) structure. 57-65 - Reza Sharifi Sedeh, Mark Bathe, Klaus-Jürgen Bathe:
The subspace iteration method in protein normal mode analysis. 66-74 - Tamar Ansbacher, Hemant Kumar Srivastava, Jan M. L. Martin, Avital Shurki:
Can DFT methods correctly and efficiently predict the coordination number of copper(I) complexes? A case study. 75-83 - Igor Zilberberg, Sergey Ruzankin:
Paired orbitals for different spins equations. 84-89 - Maja Parac, Markus Doerr, Christel M. Marian, Walter Thiel:
QM/MM calculation of solvent effects on absorption spectra of guanine. 90-106 - Hajime Torii, Masaki Yoshida:
Properties of halogen atoms for representing intermolecular electrostatic interactions related to halogen bonding and their substituent effects. 107-116 - Imran S. Haque, Vijay S. Pande:
PAPER - Accelerating parallel evaluations of ROCS. 117-132 - Evgeny B. Krissinel:
Crystal contacts as nature's docking solutions. 133-143 - Roman I. Zubatyuk, Leonid Gorb, Oleg V. Shishkin, Mo Qasim, Jerzy Leszczynski:
Exploration of density functional methods for one-electron reduction potential of nitrobenzenes. 144-150 - Traci Strohecker, Herschel Rabitz:
Quantum control implemented as combinatorial optimization. 151-153 - Bong Hyun Boo, Suk Im, Sungyul Lee:
Ab initio and DFT studies of the thermal rearrangement of trimethylsilyl(methyl)silylene: Remarkable rearrangements of silicon intermediates. 154-163 - Francisco J. Prado-Prado, Florencio M. Ubeira, Fernanda Borges, Humberto González Díaz:
Unified QSAR & network-based computational chemistry approach to antimicrobials. II. Multiple distance and triadic census analysis of antiparasitic drugs complex networks. 164-173 - Alfonso T. García-Sosa, Csaba Hetényi, Uko Maran:
Drug efficiency indices for improvement of molecular docking scoring functions. 174-184 - Marie-Céline van Severen, Christophe Gourlaouen, Olivier Parisel:
Application of the topological analysis of the electronic localization function to archetypical [Pb(II)Ln]p complexes: The bonding of Pb2+ revisited. 185-194 - Yin-Feng Wang, Zhi-Ru Li, Di Wu, Chia-Chung Sun, Feng Long Gu:
Excess electron is trapped in a large single molecular cage C60F60. 195-203 - Alexey K. Shaytan, Victor A. Ivanov, Konstantin V. Shaitan, Alexei R. Khokhlov:
Free energy profiles of amino acid side chain analogs near water-vapor interface obtained via MD simulations. 204-216 - Yu-Yen Ou, Shu-An Chen, M. Michael Gromiha:
Prediction of membrane spanning segments and topology in beta-barrel membrane proteins at better accuracy. 217-223
- Francesco Aquilante, Luca De Vico, Nicolas Ferré, Giovanni Ghigo, Per-Åke Malmqvist, Pavel Neogrády, Thomas Bondo Pedersen, Michal Pitonák, Markus Reiher, Björn Roos, Luis Serrano-Andrés, Miroslav Urban, Valera Veryazov, Roland Lindh:
MOLCAS 7: The Next Generation. 224-247
Volume 31, Number 2, 30 January 2010
- Viwat Vchirawongkwin, Andreas B. Pribil, Bernd M. Rode:
Ab Initio quantum mechanical charge field study of hydrated bicarbonate ion: Structural and dynamical properties. 249-257 - Hsin-Tsung Chen, Jee-Gong Chang, Shin-Pon Ju, Hui-Lung Chen:
First-principle calculations on CO oxidation catalyzed by a gold nanoparticle. 258-265 - Priyanka Prakash, Ramasubbu Sankararamakrishnan:
Force field dependence of phospholipid headgroup and acyl chain properties: Comparative molecular dynamics simulations of DMPC bilayers. 266-277 - Syed Sikander Azam, Len Herald V. Lim, Thomas S. Hofer, Bernhard R. Randolf, Bernd M. Rode:
Hydrated germanium (II): Irregular structural and dynamical properties revealed by a quantum mechanical charge field molecular dynamics study. 278-285 - Seifollah Jalili, Mojdeh Akhavan:
Molecular dynamics simulation study of association in trifluoroethanol/water mixtures. 286-294 - Lionello Pogliani:
Model of twelve properties of a set of organic solvents with graph-theoretical and/or experimental parameters. 295-307 - Johan Strümpfer, Kevin J. Naidoo:
Computing free energy hypersurfaces for anisotropic intermolecular associations. 308-316 - Irina S. Moreira, Pedro Alexandrino Fernandes, Maria João Ramos:
Protein-protein docking dealing with the unknown. 317-342 - Carlo Canepa:
A stationary-wave model of enzyme catalysis. 343-350 - Qi Dai, Xiao-Qing Liu, Lihua Li, Yuhua Yao, Bin Han, Lei Zhu:
Using Gaussian model to improve biological sequence comparison. 351-361 - Bin Li, Tian-Shu Chu, Ke-Li Han:
Non-Born-Oppenheimer dynamics calculations using the coherent switching with decay of mixing method. 362-370 - Zhongqiao Hu, Jianwen Jiang:
Assessment of biomolecular force fields for molecular dynamics simulations in a protein crystal. 371-380 - Andrey A. Toropov, Alla P. Toropova, Emilio Benfenati, Danuta Leszczynska, Jerzy Leszczynski:
SMILES-based optimal descriptors: QSAR analysis of fullerene-based HIV-1 PR inhibitors by means of balance of correlations. 381-392 - Shihai Yan, Sunwoo Kang, Tomoyuki Hayashi, Shaul Mukamel, Jin Yong Lee:
Computational studies on electron and proton transfer in phenol-imidazole-base triads. 393-402 - Hui Zhang, Guiling Zhang, Jing-Yao Liu, Miao Sun, Bo Liu, Ze-Sheng Li:
Theoretical study and rate constants calculation for the reactions of SiH3 radical with SiH3CH3 and SiH2(CH3)2. 403-411 - Christos Christodouleas, Demetrios Xenides, Theodore E. Simos:
Trends of the bonding effect on the performance of DFT methods in electric properties calculations: A pattern recognition and metric space approach on some XY2 (X = O, S and Y = H, O, F, S, Cl) molecules. 412-420 - Alexander V. Larin, G. M. Zhidomirov, D. N. Trubnikov, Daniel P. Vercauteren:
Ion-exchanged binuclear Ca2OX clusters, X = 1-4, as active sites of selective oxidation over MOR and FAU zeolites. 421-430 - Athanassios C. Tsipis, Ioannis G. Depastas, Efstathios E. Karagiannis, Constantinos A. Tsipis:
Diagnosis of magnetoresponsive aromatic and antiaromatic zones in three-membered rings of d- and f-block elements. 431-446 - Tsutomu Ikegami, Toyokazu Ishida, Dmitri G. Fedorov, Kazuo Kitaura, Yuichi Inadomi, Hiroaki Umeda, Mitsuo Yokokawa, Satoshi Sekiguchi:
Fragment molecular orbital study of the electronic excitations in the photosynthetic reaction center of Blastochloris viridis. 447-454
- Oleg Trott, Arthur J. Olson:
AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. 455-461
Volume 31, Number 3, February 2010
- Rekik Najeh, Ghalla Houcine, Henryk T. Flakus, Magdalena Jablonska, Oujia Brahim:
Experimental and theoretical study of the polarized infrared spectra of the hydrogen bond in 3-thiophenic acid crystal. 463-475 - Daniel K. W. Mok, Foo-Tim Chau, Edmond P. F. Lee, John M. Dyke:
High-level ab initio calculations on HGeCl and the equilibrium geometry of the Ã1A" state derived from Franck-Condon analysis of the single-vibronic-level emission spectra of HGeCl and DGeCl. 476-491 - Peng Cui, Jian Wu, Guiqing Zhang, Russell J. Boyd:
A simple representation of energy matrix elements in terms of symmetry-invariant bases. 492-496 - Masahiro Sekiya, Takeshi Noro, Toshikatsu Koga, Shiro L. Saito:
Relativistic correlating basis sets for 57La and 89Ac. 497-499 - Mohamad Akbar Ali, B. Rajakumar:
Rate coefficients for the reaction of OH with CF3CH2CH3 (HFC-263fb) between 200 and 400 K: Ab initio, DFT, and transition state theory calculations. 500-509 - Yue-meng Ji, Fenglei Cao, Hui Gao, Xiangzhi Li, Cunyuan Zhao, Chengyong Su, Jing-Yao Liu, Ze-Sheng Li:
On the kinetic mechanism of the hydrogen abstraction reactions of the hydroxyl radical with CH3CF2Cl and CH3CFCl2: A dual level direct dynamics study. 510-519 - Jesús Gálvez, Antonio Guirado:
A theoretical study of topomerization of imine systems: Inversion, rotation or mixed mechanisms? 520-531 - Yong Zhang, Wenhua Xu, Qiming Sun, Wenli Zou, Wenjian Liu:
Excited states of OsO4: A comprehensive time-dependent relativistic density functional theory study. 532-551 - Angelika Baranowska, Andrzej J. Sadlej:
Polarized basis sets for accurate calculations of static and dynamic electric properties of molecules. 552-560 - Pieter M. S. Hendrickx, Francisco Corzana, Stefaan Depraetere, Dirk A. Tourwé, Koen Augustyns, José C. Martins:
The use of time-averaged 3JHH restrained molecular dynamics (tar-MD) simulations for the conformational analysis of five-membered ring systems: Methodology and applications. 561-572 - Wolfgang Quapp, Alraune Zech:
Transition state theory with Tsallis statistics. 573-585 - Feng Fan, Jiagao Cheng, Zhong Li, Xiaoyong Xu, Xuhong Qian:
Novel dimer based descriptors with solvational computation for QSAR study of oxadiazoylbenzoyl-ureas as novel insect-growth regulators. 586-591 - Dong-Sheng Cao, Yi-Zeng Liang, Qing-Song Xu, Hong-Dong Li, Xian Chen:
A new strategy of outlier detection for QSAR/QSPR. 592-602 - Youn Jo Ko, Won Ho Jo:
Chloride ion conduction without water coordination in the pore of ClC protein. 603-611 - Michael Gilleßen, Richard Dronskowski:
A combinatorial study of inverse Heusler alloys by first-principles computational methods. 612-619 - Jory Z. Ruscio, Nicolas L. Fawzi, Teresa Head-Gordon:
How hot? Systematic convergence of the replica exchange method using multiple reservoirs. 620-627 - Tao Liu, Bao-Hui Xia, Qing-Chuan Zheng, Xin Zhou, Qing-Jiang Pan, Hong-Xing Zhang:
DFT/TD-DFT investigation on Ir(III) complexes with N-heterocyclic carbene ligands: Geometries, electronic structures, absorption, and phosphorescence properties. 628-638 - T. G. A. Youngs:
Aten - An application for the creation, editing, and visualization of coordinates for glasses, liquids, crystals, and molecules. 639-648
- Thierry Schüpbach, Vincent Zoete, Brice Tsakam-Sotché, Olivier Michielin:
Fourier transform convolution integrals applied to generalized Born molecular volume. 649-659
- Udo Feldkamp:
CANADA: Designing nucleic acid sequences for nanobiotechnology applications. 660-663
Volume 31, Number 4, March 2010
- Sebastian Schlund, Eline M. Basílio Janke, Klaus Weisz, Bernd Engels:
Predicting the tautomeric equilibrium of acetylacetone in solution. I. The right answer for the wrong reason? 665-670 - Kenno Vanommeslaeghe, Elizabeth Hatcher, Chayan Acharya, Sibsankar Kundu, Shijun Zhong, Jihyun Shim, Eva Darian, Olgun Guvench, Pedro E. M. Lopes, Igor Vorobyov, Alexander D. MacKerell Jr.:
CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields. 671-690 - Ramu Anandakrishnan, Alexey Onufriev:
An N log N approximation based on the natural organization of biomolecules for speeding up the computation of long range interactions. 691-706 - Santiago Vilar, Joel Karpiak, Stefano Costanzi:
Ligand and structure-based models for the prediction of ligand-receptor affinities and virtual screenings: Development and application to the beta2-adrenergic receptor. 707-720 - Selina C. Wang, Peter A. Beal, Dean J. Tantillo:
Covalent hydration energies for purine analogs by quantum chemical methods. 721-725 - Julien Maupetit, Philippe Derreumaux, Pierre Tufféry:
A fast method for large-scale De Novo peptide and miniprotein structure prediction. 726-738 - Nilesh R. Tawari, Mariam S. Degani:
Pharmacophore mapping and electronic feature analysis for a series of nitroaromatic compounds with antitubercular activity. 739-751 - Hanbing Rao, Ze-Rong Li, Xiang-Yuan Li, Xiao Hua Ma, Choong Yong Ung, Hu Li, Xianghui Liu, Yu Zong Chen:
Identification of small molecule aggregators from large compound libraries by support vector machines. 752-763 - Villö K. Pálfi, András Perczel:
Stability of the hydration layer of tropocollagen: A QM study. 764-777 - Hui Li, Dmitri G. Fedorov, Takeshi Nagata, Kazuo Kitaura, Jan H. Jensen, Mark S. Gordon:
Energy gradients in combined fragment molecular orbital and polarizable continuum model (FMO/PCM) calculation. 778-790 - Katsumi Murata, Naoya Nagata, Isao Nakanishi, Kazuo Kitaura:
Ligand shape emerges in solvent dipole ordering region at ligand binding site of protein. 791-796 - Giulio Rastelli, Alberto Del Rio, Gianluca Degliesposti, Miriam Sgobba:
Fast and accurate predictions of binding free energies using MM-PBSA and MM-GBSA. 797-810 - Jean-François Truchon, Anthony Nicholls, J. Andrew Grant, Radu I. Iftimie, Benoît Roux, Christopher I. Bayly:
Using electronic polarization from the internal continuum (EPIC) for intermolecular interactions. 811-824 - Laibin Zhang, Huifang Li, Ji-Lai Li, Xiaohua Chen, Yuxiang Bu:
Absorption and fluorescence emission spectroscopic characters of naphtho-homologated yy-DNA bases and effect of methanol solution and base pairing. 825-836 - Samuel Genheden, Ulf Ryde:
How to obtain statistically converged MM/GBSA results. 837-846 - Ling Wang, Boris Stumm, Volkhard Helms:
Graph-theoretical identification of dissociation pathways on free energy landscapes of biomolecular interaction. 847-854 - Yves Noel, Philippe D'Arco, Raffaella Demichelis, Claudio Marcelo Zicovich-Wilson, Roberto Dovesi:
On the use of symmetry in the ab initio quantum mechanical simulation of nanotubes and related materials. 855-862 - Guang-Tao Yu, Wei Chen, Feng Long Gu, Yuriko Aoki:
Theoretical study on nonlinear optical properties of the Li+[calix[4]pyrrole]Li-dimer, trimer and its polymer with diffuse excess electrons. 863-870 - Xiaoyan Zheng, Xueye Wang, Shanfeng Yi, Nuanqing Wang, Yueming Peng:
Density functional theory study of the free and tetraprotonated spheroidal macrotricyclic ligands and the complexes with halide anions: F-, Cl-, Br-. 871-881 - Alejandro Speck Planche, Marcus Tulius Scotti, Vicente de Paulo Emerenciano, América García López, Enrique Molina Pérez, Eugenio Uriarte:
Designing novel antitrypanosomal agents from a mixed graph-theoretical substructural approach. 882-894
- Michael Springborg:
Book review. 895-896
Volume 31, Number 5, 15 April 2010
- Hwanho Choi, Hongsuk Kang, Hwangseo Park:
New angle-dependent potential energy function for backbone-backbone hydrogen bond in protein-protein interactions. 897-903 - Benjamin D. Allen, Stephen L. Mayo:
An efficient algorithm for multistate protein design based on FASTER. 904-916 - Mercedes Alonso, Bernardo Herradón:
A universal scale of aromaticity for pi-organic compounds. 917-928 - Behnam Assadollahzadeh, Sascha Schäfer, Peter Schwerdtfeger:
Electronic properties for small tin clusters Snn (n <= 20) from density functional theory and the convergence toward the solid state. 929-937 - Chao Gao, Hua-Qing Yang, Jian Xu, Song Qin, Chang-Wei Hu:
Theoretical study on the gas-phase reaction mechanism between rhodium monoxide and methane for methanol production. 938-953 - Yu Takano, Haruki Nakamura:
Electronic structures of heme a of cytochrome c oxidase in the redox states - Charge density migration to the propionate groups of heme a. 954-962 - Richard Kramer Campen, James D. Kubicki:
Interaction energy and the shift in OH stretch frequency on hydrogen bonding for the H2O -> H2O, CH3OH -> H2O, and H2O -> CH3OH dimers. 963-972 - Jiazhong Li, Shuyan Li, Beilei Lei, Huanxiang Liu, Xiaojun Yao, Mancang Liu, Paola Gramatica:
A new strategy to improve the predictive ability of the local lazy regression and its application to the QSAR study of melanin-concentrating hormone receptor 1 antagonists. 973-985 - Zheng Guo Huang, Lei Yu, Yu Mei Dai:
An ab initio potential energy surface and vibrational energy levels of ZnH2. 986-993 - An Ghysels, Veronique Van Speybroeck, Ewald Pauwels, Saron Catak, Bernard R. Brooks, Dimitri Van Neck, Michel Waroquier:
Comparative study of various normal mode analysis techniques based on partial Hessians. 994-1007 - Jason P. Holland, Jennifer C. Green:
Evaluation of exchange-correlation functionals for time-dependent density functional theory calculations on metal complexes. 1008-1014 - Bogdan Lev, Rui Zhang, Aurélien de la Lande, Dennis R. Salahub, Sergei Yu Noskov:
The QM-MM interface for CHARMM-deMon. 1015-1023 - Karmen Condic-Jurkic, Hendrik Zipse, David M. Smith:
A compound QM/MM procedure: Comparative performance on a pyruvate formate-lyase model system. 1024-1035 - Chang-Sheng Wang, Chang-Liang Sun:
Investigation on the individual contributions of N-H***O=C and C-H***O=C interactions to the binding energies of beta-sheet models. 1036-1044 - Yu-Hua Yao, Qi Dai, Ling Li, Xu-Ying Nan, Ping-An He, Yao-Zhou Zhang:
Similarity/dissimilarity studies of protein sequences based on a new 2D graphical representation. 1045-1052 - Vincent Tognetti, Pascal Le Floch, Carlo Adamo:
How the choice of a computational model could rule the chemical interpretation: The Ni(II) catalyzed ethylene dimerization as a case study. 1053-1062 - Noel Ferro, Thomas Bredow:
Assessment of quantum-chemical methods for electronic properties and geometry of signaling biomolecules. 1063-1079 - Yury N. Vorobjev:
Blind docking method combining search of low-resolution binding sites with ligand pose refinement by molecular dynamics-based global optimization. 1080-1092 - Michal Brylinski, Jeffrey Skolnick:
Q-DockLHM: Low-resolution refinement for ligand comparative modeling. 1093-1105
- Simone Marsili, Giorgio Federico Signorini, Riccardo Chelli, Massimo Marchi, Piero Procacci:
ORAC: A molecular dynamics simulation program to explore free energy surfaces in biomolecular systems at the atomistic level. 1106-1116
Volume 31, Number 6, 30 April 2010
- David Poger, Wilfred F. van Gunsteren, Alan E. Mark:
A new force field for simulating phosphatidylcholine bilayers. 1117-1125 - Jingyu Sun, Yizhen Tang, Hao Sun, Xiujuan Jia, Xiumei Pan, Rongshun Wang:
Theoretical and kinetic study of the H + C2H5CN reaction. 1126-1134 - Jens Kleesiek, Andrew E. Torda:
RNA secondary structure prediction using a self-consistent mean field approach. 1135-1142 - Urszula Kozlowska, Adam Liwo, Harold A. Scheraga:
Determination of side-chain-rotamer and side-chain and backbone virtual-bond-stretching potentials of mean force from AM1 energy surfaces of terminally-blocked amino-acid residues, for coarse-grained simulations of protein structure and folding. I. The method. 1143-1153 - Urszula Kozlowska, Gia G. Maisuradze, Adam Liwo, Harold A. Scheraga:
Determination of side-chain-rotamer and side-chain and backbone virtual-bond-stretching potentials of mean force from AM1 energy surfaces of terminally-blocked amino-acid residues, for coarse-grained simulations of protein structure and folding. II. Results, comparison with statistical potentials, and implementation in the UNRES force field. 1154-1167 - Ryota Jono, Yuusuke Watanabe, Kentaro Shimizu, Tohru Terada:
Multicanonical ab inito QM/MM molecular dynamics simulation of a peptide in an aqueous environment. 1168-1175 - Angelika Baranowska, Krzysztof Z. Laczkowski, Andrzej J. Sadlej:
Model studies of the optical rotation, and theoretical determination of its sign for beta-pinene and trans-pinane. 1176-1181 - K. Senthil Kumar, Archita Patnaik:
Intramolecular electronic communication in a dimethylaminoazobenzene-fullerene C60 dyad: An experimental and TD-DFT study. 1182-1194 - Len Herald V. Lim, Andreas B. Pribil, Andreas E. Ellmerer, Bernhard R. Randolf, Bernd M. Rode:
Temperature dependence of structure and dynamics of the hydrated Ca2+ ion according to ab initio quantum mechanical charge field and classical molecular dynamics. 1195-1200 - Xiaoqi Zheng, Chun Li, Jun Wang:
An information-theoretic approach to the prediction of protein structural class. 1201-1206