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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
- Najeh Rekik, 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, Yuzong 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 - Maria Safi, Ryan H. Lilien:
Restricted dead-end elimination: Protein redesign with a bounded number of residue mutations. 1207-1215 - Hao Wu, Alana Canfield, Jhashanath Adhikari, Shuanghong Huo:
Quantum mechanical studies on model alpha-pleated sheets. 1216-1223 - Kenneth W. Borrelli, Benjamin P. Cossins, Victor Guallar:
Exploring hierarchical refinement techniques for induced fit docking with protein and ligand flexibility. 1224-1235 - Gráinne Black, John M. Simmie:
Barrier heights for H-atom abstraction by HO.2 from n-butanol - A simple yet exacting test for model chemistries? 1236-1248 - Xue-Gang Yang, Wei Lv, Yuzong Chen, Ying Xue:
In silico prediction and screening of gamma-secretase inhibitors by molecular descriptors and machine learning methods. 1249-1258 - Ahmed Mehdi, Legesse Adane, Dhilon S. Patel, Prasad V. Bharatam:
Electronic structure and reactivity of guanylthiourea: A quantum chemical study. 1259-1267 - Peter K. Eastman, Vijay S. Pande:
Efficient nonbonded interactions for molecular dynamics on a graphics processing unit. 1268-1272 - Anne Lopes, Marcel Schmidt am Busch, Thomas Simonson:
Computational design of protein-ligand binding: Modifying the specificity of asparaginyl-tRNA synthetase. 1273-1286 - Norio Takenaka, Yoshiyuki Koyano, Yukinori Nakagawa, Masataka Nagaoka:
An optimum strategy for solution chemistry using semiempirical molecular orbital method: Importance of description of charge distribution. 1287-1296 - Chérif F. Matta:
How dependent are molecular and atomic properties on the electronic structure method? Comparison of Hartree-Fock, DFT, and MP2 on a biologically relevant set of molecules. 1297-1311 - N. Yousfi, Majda Sekkal-Rahal, Adlane Sayede, Michael Springborg:
Relaxed energetic maps of kappa-carrabiose: A DFT study. 1312-1320
- J. J. Borrás-Almenar, Salvador Cardona-Serra, Juan M. Clemente-Juan, Eugenio Coronado, Andrew V. Palii, Boris S. Tsukerblat:
MVPACK: A package to calculate energy levels and magnetic properties of high nuclearity mixed valence clusters. 1321-1332 - Andrzej J. Rzepiela, Lars V. Schäfer, Nicolae Goga, H. Jelger Risselada, Alex H. de Vries, Siewert J. Marrink:
Reconstruction of atomistic details from coarse-grained structures. 1333-1343
Volume 31, Number 7, May 2010
- Trevor M. Cickovski, Santanu Chatterjee, Jacob Wenger, Christopher R. Sweet, Jesús A. Izaguirre:
MDLab: A molecular dynamics simulation prototyping environment. 1345-1356 - Hisashi Okumura, Emilio Gallicchio, Ronald M. Levy:
Conformational populations of ligand-sized molecules by replica exchange molecular dynamics and temperature reweighting. 1357-1367 - Changjun Chen, Yi Xiao:
Accurate free energy calculation along optimized paths. 1368-1375 - Na Qi, Rong-Zhen Liao, Jian-Guo Yu, Ruo-Zhuang Liu:
DFT study of the asymmetric nitroaldol (Henry) reaction catalyzed by a dinuclear Zn complex. 1376-1384 - Tianshu Chu:
Quantum mechanics and quasiclassical study of the H/D+FO -> OH/OD+F, HF/DF+O reactions: Chemical stereodynamics. 1385-1396 - Wen-Zuo Li, Jian-Bo Cheng, Qing-Zhong Li, Bao-An Gong, Jia-Zhong Sun:
Theoretical study on HBO+ and HOB+ cations using multiconfiguration second-order perturbation theory. 1397-1401 - Edyta Malolepsza, Birgit Strodel, Mey Khalili, Semen Trygubenko, Szilard N. Fejer, David J. Wales:
Symmetrization of the AMBER and CHARMM force fields. 1402-1409 - Xiao-Nan Jiang, Chang-Liang Sun, Chang-Sheng Wang:
A scheme for rapid prediction of cooperativity in hydrogen bond chains of formamides, acetamides, and N-methylformamides. 1410-1420 - Yena Qu, Kehe Su, Xin Wang, Yan Liu, Qingfeng Zeng, Laifei Cheng, Litong Zhang:
Reaction pathways of propene pyrolysis. 1421-1442 - Amir Abbas Rafati, Sayed Majid Hashemianzadeh, Zabiollah Bolboli Nojini, Negin Naghshineh:
Canonical Monte Carlo simulation of adsorption of O2 and N2 mixture on single walled carbon nanotube at different temperatures and pressures. 1443-1449 - Rungtiwa Chidthong, Supa Hannongbua:
Excited state properties, fluorescence energies, and lifetimes of a poly(fluorene-phenylene), based on TD-DFT investigation. 1450-1457 - Xiaoyan Zheng, Xueye Wang, Shanfeng Yi, Nuanqing Wang, Yueming Peng:
Density functional theory study of calix[4]arene-N-azacrown-5, calix[4]arene-N-phenyl-azacrown-5, and their complexes with alkali-metal cations: Na+, K+, and Rb+. 1458-1468 - Ville Weijo, Maharavo Randrianarivony, Helmut Harbrecht, Luca Frediani:
Wavelet formulation of the polarizable continuum model. 1469-1477 - Lin Zhu, Jie Yang, Jiangning Song, Kuo-Chen Chou, Hong-Bin Shen:
Improving the accuracy of predicting disulfide connectivity by feature selection. 1478-1485 - Lj. Miljacic, D. E. Ellis:
Radial-template approach for accurate density representation in computational quantum theory. 1486-1494 - Jorge M. C. Marques, A. A. C. C. Pais, P. E. Abreu:
Generation and characterization of low-energy structures in atomic clusters. 1495-1503 - Viktor Bezugly, Pawel Wielgus, Miroslav Kohout, Frank R. Wagner:
Electron localizability indicators ELI-D and ELIA for highly correlated wavefunctions of homonuclear dimers. I. Li2, Be2, B2, and C2. 1504-1519 - Yizhen Tang, Jingyu Sun, Xiujuan Jia, Hao Sun, Xiumei Pan, Rongshun Wang:
Mechanistic and kinetic investigations of N2H4 + OH reaction. 1520-1527 - Thomas A. Manz, David S. Sholl:
A dimensionless reaction coordinate for quantifying the lateness of transition states. 1528-1541 - Artur Gertych, Jacek Koput:
Ab initio prediction of the structure and vibration-rotation spectroscopic properties of Na2OH and K2OH. 1542-1549 - Alexey Aleksandrov, Thomas Simonson:
A molecular mechanics model for imatinib and imatinib: kinase binding. 1550-1560
- Pu Liu, Dimitris K. Agrafiotis, Douglas L. Theobald:
Fast determination of the optimal rotational matrix for macromolecular superpositions. 1561-1563 - Hendrik Heinz:
Computational screening of biomolecular adsorption and self-assembly on nanoscale surfaces. 1564-1568
Volume 31, Number 8, June 2010
- Clara D. Christ, Alan E. Mark, Wilfred F. van Gunsteren:
Basic ingredients of free energy calculations: A review. 1569-1582 - Asbjørn Holt, Jonas Boström, Gunnar Karlström, Roland Lindh:
A NEMO potential that includes the dipole-quadrupole and quadrupole-quadrupole polarizability. 1583-1591 - Ying Xiong, Junjun Liu, Guangfu Yang, Chang-Guo Zhan:
Computational determination of fundamental pathway and activation barriers for acetohydroxyacid synthase-catalyzed condensation reactions of alpha-keto acids. 1592-1602 - Elsa Sánchez-García, Markus Doerr, Walter Thiel:
QM/MM study of the absorption spectra of DsRed.M1 chromophores. 1603-1612 - Michael Wessel, Richard Dronskowski:
A first-principles study on the existence and structures of the lighter alkaline-earth pernitrides. 1613-1617 - Xian-Yong Pang, Bin Xing, Li-Qin Xue, Gui-Chang Wang:
Selective oxidation of styrene on an oxygen-adsorbed Cu(111): A comparison with Au(111). 1618-1624 - Stephen D. Bond, Jehanzeb Hameed Chaudhry, Eric C. Cyr, Luke N. Olson:
A first-order system least-squares finite element method for the Poisson-Boltzmann equation. 1625-1635 - Nathan Schmid, Mathias Bötschi, Wilfred F. van Gunsteren:
A GPU solvent-solvent interaction calculation accelerator for biomolecular simulations using the GROMOS software. 1636-1643 - Maciej Maciejczyk, Aleksandar Spasic, Adam Liwo, Harold A. Scheraga:
Coarse-grained model of nucleic acid bases. 1644-1655 - Nitin Wadnerkar, Vijayanand Kalamse, Ajay Chaudhari:
Hydrogen uptake capacity of C2H4Sc and its ions: A density functional study. 1656-1661 - Qing-Zhong Li, Xu Dong, Bo Jing, Wen-Zuo Li, Jian-Bo Cheng, Bao-An Gong, Zhi-Wu Yu:
A new unconventional halogen bond C-X--H-M between HCCX (X = Cl and Br) and HMH (M = Be and Mg): An ab initio study. 1662-1669 - G. Cilpa, Marja T. Hyvönen, Artturi Koivuniemi, M.-L. Riekkola:
Atomistic insight into chondroitin-6-sulfate glycosaminoglycan chain through quantum mechanics calculations and molecular dynamics simulation. 1670-1680 - J. W. Liu, Zhifeng Liu:
Thermal dissociation of tripropylamine as the first step in the growth of carbon nanotubes inside AlPO4-5 channels. 1681-1688 - Jun Wang, Ray Luo:
Assessment of linear finite-difference Poisson-Boltzmann solvers. 1689-1698 - Hiroshi Takeuchi:
Global minimum geometries of acetylene clusters (HCCH)n with n <= 55 obtained by a heuristic method combined with geometrical perturbations. 1699-1706 - Polina Georgieva, Fahmi Himo:
Quantum chemical modeling of enzymatic reactions: The case of histone lysine methyltransferase. 1707-1714 - Li-Hua Gan, Jian-Qiang Zhao, Qun Hui:
Nonclassical fullerenes with a heptagon violating the pentagon adjacency penalty rule. 1715-1721 - J. Santeri Puranen, Mikko J. Vainio, Mark S. Johnson:
Accurate conformation-dependent molecular electrostatic potentials for high-throughput in silico drug discovery. 1722-1732 - Marcin Makowski, Jacek Korchowiec, Feng Long Gu, Yuriko Aoki:
Describing electron correlation effects in the framework of the elongation method - Elongation-MP2: Formalism, implementation and efficiency. 1733-1740 - Julien Preat, Francisco Rodríguez-Ropero, Juan Torras, Oscar Bertran, David Zanuy, Carlos Alemán:
Parameterization of the torsional potential for calix[4]arene-substituted poly(thiophene)s. 1741-1751 - Yibo Lei, Bingbing Suo, Yusheng Dou, Yubin Wang, Zhenyi Wen:
New implementations of MRCI in semiempirical frameworks. 1752-1758 - Guang-Yue Li, Guang-Jiu Zhao, Yu-Hui Liu, Ke-Li Han, Guo-Zhong He:
TD-DFT study on the sensing mechanism of a fluorescent chemosensor for fluoride: Excited-state proton transfer. 1759-1765 - Lei Chen, Ziliang Qian, Kaiyan Feng, Yudong Cai:
Prediction of interactiveness between small molecules and enzymes by combining gene ontology and compound similarity. 1766-1776 - Anna Maria Ferrari, Bartolomeo Civalleri, Roberto Dovesi:
Ab initio periodic study of the conformational behavior of glycine helical homopeptides. 1777-1784 - Chinapong Kritayakornupong, Viwat Vchirawongkwin, Bernd M. Rode:
An ab initio quantum mechanical charge field molecular dynamics simulation of a dilute aqueous HCl solution. 1785-1792
- W. H. E. Schwarz:
Book review: The Periodic Table: Its Story and Its Significance. 1793-1794
Volume 31, Number 9, July 2010
- Weiyu Song, Jing Wang, Jian Meng, Zhijian Wu:
Half metallic properties of LaSrVMoO6. 1795-1798 - Sergei Grudinin, Stephane Redon:
Practical modeling of molecular systems with symmetries. 1799-1814 - Santanab Giri, Debesh Ranjan Roy, Soma Duley, Arindam Chakraborty, Ramakrishnan Parthasarathi, Munusamy Elango, Ramadoss Vijayaraj, Venkatesan Subramanian, Rafael Islas, Gabriel Merino, Pratim Kumar Chattaraj:
Bonding, aromaticity, and structure of trigonal dianion metal clusters. 1815-1821 - Chunzhi Ai, Yan Li, Yonghua Wang, Wei Li, Peipei Dong, Guangbo Ge, Ling Yang:
Investigation of binding features: Effects on the interaction between CYP2A6 and inhibitors. 1822-1831 - Milan Randic, Tomaz Pisanski, Marjana Novic, Dejan Plavsic:
Novel graph distance matrix. 1832-1841 - Benjamí Martorell, Anna Clotet, Jordi Fraxedas:
A first principle study of the structural, vibrational and electronic properties of tetrathiafulvalene adsorbed on Ag(110) and Au(110) surfaces. 1842-1852 - Timm Lankau, Chin-Hui Yu:
A model study of the efficiency of the Asp-His-Ser triad. 1853-1859 - Richard P. Muller, Ann E. Mattsson, Curtis L. Janssen:
Calculation of chemical reaction energies using the AM05 density functional. 1860-1863 - Elad Project, Esther Nachliel, Menachem Gutman:
Force field-dependant structural divergence revealed during long time simulations of Calbindin d9k. 1864-1872 - Janne Pesonen, Krister O. E. Henriksson:
Polymer conformations in internal (polyspherical) coordinates. 1873-1881 - Krister O. E. Henriksson, Janne Pesonen:
Polymer dynamics in torsion space. 1882-1888 - Roman Affentranger, Xavier Daura:
Polypeptide folding on a conformational-space network: Dependence of network topology on the structural discretization procedure. 1889-1903 - Erjun Zhao, Jinping Wang, Jian Meng, Zhijian Wu:
Phase stability and mechanical properties of rhenium borides by first-principles calculations. 1904-1910 - Jan Fuhrmann, Alexander Rurainski, Hans-Peter Lenhof, Dirk Neumann:
A new Lamarckian genetic algorithm for flexible ligand-receptor docking. 1911-1918 - Tim Geppert, Ewgenij Proschak, Gisbert Schneider:
Protein-protein docking by shape-complementarity and property matching. 1919-1928 - Efrat Noy, Amiram Goldblum:
Flexible protein-protein docking based on Best-First search algorithm. 1929-1943
Volume 31, Number 10, July 2010
- Potjaman Poolmee, Supa Hannongbua:
Investigation of excited-state properties of fluorene-thiophene oligomers by the SAC-CI theoretical approach. 1945-1955 - Jingheng Wu, Juan Mei, Sixiang Wen, Siyan Liao, Jincan Chen, Yong Shen:
A self-adaptive genetic algorithm-artificial neural network algorithm with leave-one-out cross validation for descriptor selection in QSAR study. 1956-1968 - John T. Tsalavoutis, Michael P. Sigalas:
Density functional investigation and bonding analysis of pentacoordinated iron complexes with mixed cyano and carbonyl ligands. 1969-1978 - Suchaya Pongsai:
Combination of the Metropolis Monte Carlo and Lattice Statics method for geometry optimization of H-(Al)-ZSM-5. 1979-1985 - Júlio C. S. da Silva, Roberta P. Dias, Wagner B. De Almeida, Willian R. Rocha:
DFT study of the full catalytic cycle for the propene hydroformylation catalyzed by a heterobimetallic HPt(SnCl3)(PH3)2 model catalyst. 1986-2000 - Prasenjit Seal:
Carbondioxide rare-gas systems: Sensitivity of basis sets and double-hybrid density functionals. 2001-2007 - Philip Brown, Christopher J. Woods, Simon McIntosh-Smith, Frederick R. Manby:
A massively multicore parallelization of the Kohn-Sham energy gradients. 2008-2013 - Huameng Li, Chenglong Li:
Multiple ligand simultaneous docking: Orchestrated dancing of ligands in binding sites of protein. 2014-2022 - Cui-Yu Niu, Jiao Jiao, Bin Xing, Gui-Chang Wang, Xian-He Bu:
Reaction mechanism of methanol decomposition on Pt-based model catalysts: A theoretical study. 2023-2037 - Zheng-Wang Qu, Hui Zhu:
Do anionic titanium dioxide nano-clusters reach bulk band gap? A density functional theory study. 2038-2045 - Hasan Pasalic, Adélia J. A. Aquino, Daniel Tunega, Georg Haberhauer, Martin H. Gerzabek, Herbert C. Georg, Tatiane F. Moraes, Kaline Coutinho, Sylvio Canuto, Hans Lischka:
Thermodynamic stability of hydrogen-bonded systems in polar and nonpolar environments. 2046-2055 - Shu-Hui Yin, Yufang Liu, Wei Zhang, Ming-Xing Guo, Peng Song:
Time-dependent density functional theory study on the hydrogen bonding-induced twisted intramolecular charge-transfer excited states of 2-(4'-N, N-dimethylaminophenyl)imidazo[4, 5-b]pyridine. 2056-2062 - Xiao Zhu, Peter H. Koenig, Michael Hoffmann, Arun Yethiraj, Qiang Cui:
Establishing effective simulation protocols for beta- and alpha/beta-peptides. III. Molecular mechanical model for acyclic beta-amino acids. 2063-2077 - Károly Németh, Matt Challacombe, Michel Van Veenendaal:
The choice of internal coordinates in complex chemical systems. 2078-2086
Volume 31, Number 11, August 2010
- Udo Schnupf, Julious L. Willett, Frank A. Momany:
27 ps DFT molecular dynamics simulation of alpha-maltose: A reduced basis set study. 2087-2097 - Li-Dong Gong, Zhong-Zhi Yang:
Investigation of the molecular surface area and volume: Defined and calculated by the molecular face theory. 2098-2108 - Xun Li, Yan Li, Tiejun Cheng, Zhihai Liu, Renxiao Wang:
Evaluation of the performance of four molecular docking programs on a diverse set of protein-ligand complexes. 2109-2125 - Jia-Feng Yu, Xiao Sun:
Reannotation of protein-coding genes based on an improved graphical representation of DNA sequence. 2126-2135 - Ping-An He, Yanping Zhang, Yu-Hua Yao, Yi-Fa Tang, Xu-Ying Nan:
The graphical representation of protein sequences based on the physicochemical properties and its applications. 2136-2142 - Xiaoyan Zheng, Xueye Wang, Keqi Shen, Nuanqing Wang, Yueming Peng:
Molecular design of a "molecular syringe" mimic for metal cations using a 1, 3-alternate calix[4]arene cavity. 2143-2156 - Rui Wang, Ce Hao, Peng Li, Ning-Ning Wei, Jingwen Chen, Jieshan Qiu:
Time-dependent density functional theory study on the electronic excited-state hydrogen-bonding dynamics of 4-aminophthalimide (4AP) in aqueous solution: 4AP and 4AP-(H2O)1, 2 clusters. 2157-2163 - Xiangqian Hu, Hao Hu, David N. Beratan, Weitao Yang:
A gradient-directed Monte Carlo approach for protein design. 2164-2168 - Maarten G. Wolf, Martin Hoefling, Camilo Aponte-Santamaría, Helmut Grubmüller, Gerrit Groenhof:
g_membed: Efficient insertion of a membrane protein into an equilibrated lipid bilayer with minimal perturbation. 2169-2174 - Yuko Ito, Mitsunori Ikeguchi:
Structural fluctuation and concerted motions in F1-ATPase: A molecular dynamics study. 2175-2185 - Kenta Hongo, Ryo Maezono, Kenichi Miura:
Random number generators tested on quantum Monte Carlo simulations. 2186-2194 - Ramon Carbó-Dorca, Luz Dary Mercado:
Commentaries on quantum similarity (1): Density gradient quantum similarity. 2195-2212 - Jakub Kaminský, Ivan Raich, Katerina Tomcáková, Petr Bour:
Conformational behavior of simple furanosides studied by optical rotation. 2213-2224 - Hajime Muta, Noriaki Hirayama:
Alpha sphere filter method: Application of pseudomolecular descriptors in virtual screening of 2D chemical structures. 2225-2232
Volume 31, Number 12, September 2010
- Bisheng Tan, Rufang Peng, Hongbo Li, Bo Jin, Shijin Chu, Xinping Long:
Theoretical investigation of an energetic fullerene derivative. 2233-2237 - Xian-Hui Wu, Guo-Lin Zou, Jun-Min Quan, Yun-Dong Wu:
A theoretical study on the catalytic mechanism of Mus musculus adenosine deaminase. 2238-2247 - Yong Wu, Lu Jin, Ying Xue, Ik-Mo Lee, Chan Kyung Kim:
Mechanisms of norbornadiene dimerization to Binor-S using cationic CoI, RhI, and IrI catalysts. 2248-2257 - Chin-Hung Lai, Pi-Tai Chou:
A computational study on the capability of borane-cyclic boryl anion adducts to act as hydrogen atom donors. 2258-2262 - Xiujuan Jia, You-Jun Liu, Jingyu Sun, Hao Sun, Fang Wang, Zhongmin Su, Xiumei Pan, Rongshun Wang:
Computational studies on the mechanism and kinetics of Cl reaction with C2H5I. 2263-2272 - Viktor Bezugly, Pawel Wielgus, Miroslav Kohout, Frank R. Wagner:
Electron localizability indicators ELI-D and ELIA for highly correlated wavefunctions of homonuclear dimers. II. N2, O2, F2, and Ne2. 2273-2285 - Stijn Fias, Sofie Van Damme, Patrick Bultinck:
Multidimensionality of delocalization indices and nucleus-independent chemical shifts in polycyclic aromatic hydrocarbons II: Proof of further nonlocality. 2286-2293 - Milan Oncák, Detlef Schröder, Petr Slavícek:
Theoretical study of the microhydration of mononuclear and dinuclear uranium(VI) species derived from solvolysis of uranyl nitrate in water. 2294-2306 - Benjamin Waldher, Jadwiga Kuta, Samuel Chen, Neil J. Henson, Aurora E. Clark:
ForceFit: A code to fit classical force fields to quantum mechanical potential energy surfaces. 2307-2316 - Hisashi Ishida:
Branch migration of Holliday junction in RuvA tetramer complex studied by umbrella sampling simulation using a path-search algorithm. 2317-2329 - Xiao Zhu, Alexander D. MacKerell Jr.:
Polarizable empirical force field for sulfur-containing compounds based on the classical Drude oscillator model. 2330-2341 - Shuchi Nagar, Achintya Saha:
Modeling of diarylalkyl-imidazole and diarylalkyl-triazole derivatives as potent aromatase inhibitors for treatment of hormone-dependent cancer. 2342-2353 - Vali Zare-shahabadi, Fatemeh Abbasitabar:
Application of ant colony optimization in development of models for prediction of anti-HIV-1 activity of HEPT derivatives. 2354-2362
- Peng Tao, H. Bernhard Schlegel:
A toolkit to assist ONIOM calculations. 2363-2369
Volume 31, Number 13, October 2010
- Sadegh Salehzadeh, Mehdi Bayat:
Theoretical studies on the structure and protonation of Cu(II) complexes of a series of tripodal aliphatic tetraamines: Good correlations with the experimental data. 2371-2380 - Hiroaki Umeda, Yuichi Inadomi, Toshio Watanabe, Toru Yagi, Takayoshi Ishimoto, Tsutomu Ikegami, Hiroto Tadano, Tetsuya Sakurai, Umpei Nagashima:
Parallel Fock matrix construction with distributed shared memory model for the FMO-MO method. 2381-2388 - David Casanova, Pere Alemany, Santiago Alvarez:
Symmetry measures of the electron density. 2389-2404 - Anuja P. Rahalkar, Michio Katouda, Shridhar R. Gadre, Shigeru Nagase:
Molecular tailoring approach in conjunction with MP2 and Ri-MP2 codes: A comparison with fragment molecular orbital method. 2405-2418 - Zhixiong Lin, Haiyan Liu, Wilfred F. van Gunsteren:
Using one-step perturbation to predict the effect of changing force-field parameters on the simulated folding equilibrium of a beta-peptide in solution. 2419-2427 - Gregory Scott, Martin Gruebele:
Solving the low dimensional Smoluchowski equation with a singular value basis set. 2428-2433 - Cédric Grauffel, Roland H. Stote, Annick Dejaegere:
Force field parameters for the simulation of modified histone tails. 2434-2451 - Ramon Carbó-Dorca, Emili Besalú:
Communications on quantum similarity (2): A geometric discussion on holographic electron density theorem and confined quantum similarity measures. 2452-2462 - Santhosh Kannan Venkatesan, Anil Kumar Shukla, Vikash Kumar Dubey:
Molecular docking studies of selected tricyclic and quinone derivatives on trypanothione reductase of Leishmania infantum. 2463-2475 - Bulumoni Kalita, Ramesh C. Deka:
Adsorption of CO on oxygen preadsorbed neutral and charged gas phase Pd4 clusters: A density functional study. 2476-2482 - Kiyull Yang, Young Hee Park, Soo Gyeong Cho, Hai Whang Lee, Chan Kyung Kim, Hyun-Joo Koo:
Theoretical studies on the formation mechanism and explosive performance of nitro-substituted 1, 3, 5-triazines. 2483-2492 - Patricio González-Navarrete, Lourdes Gracia, Monica Calatayud, Juan Andrés:
Density functional theory study of the oxidation of methanol to formaldehyde on a hydrated vanadia cluster. 2493-2501 - Xuewei Jiang, Changjun Chen, Yi Xiao:
Improvements of network approach for analysis of the folding free-energy surface of peptides and proteins. 2502-2509 - Antoni Aguilar-Mogas, Xavier Giménez, Josep Maria Bofill:
Implementation of an algorithm based on the Runge-Kutta-Fehlberg technique and the potential energy as a reaction coordinate to locate intrinsic reaction paths. 2510-2525
- Wolfgang Quapp, Josep Maria Bofill:
A comment to the nudged elastic band method. 2526-2531
Volume 31, Number 14, November 2010
- Haiying Liu, Xiaohua Chen, Yuxiang Bu:
Redox-induced configuration conversion for thioacetamide dimer can function as a molecular switch. 2533-2539 - Jianwen A. Feng, Garland R. Marshall:
SKATE: A docking program that decouples systematic sampling from scoring. 2540-2554 - Slawomir Berski, Zdzislaw Latajka, Agnieszka J. Gordon:
Ab Initio and Quantum Chemical Topology studies on the isomerization of HONO to HNO2. Effect of the basis set in QCT. 2555-2567 - Kathrin Götz, Florian Meier, Carlo Gatti, Asbjörn M. Burow, Marek Sierka, Joachim Sauer, Martin Kaupp:
Modeling environmental effects on charge density distributions in polar organometallics: Validation of embedded cluster models for the methyl lithium crystal. 2568-2576 - Jianguo Qian, Fuji Zhang:
Counting the cyclocized polyphenacenes. 2577-2584 - Cun-Xi Liu, Hai-Xia Wang, Ze-Rong Li, Chong-Wen Zhou, Hanbing Rao, Xiang-Yuan Li:
Accurate prediction of enthalpies of formation for a large set of organic compounds. 2585-2592 - Per Larsson, Erik Lindahl:
A high-performance parallel-generalized born implementation enabled by tabulated interaction rescaling. 2593-2600 - Ramin M. Abolfath, Thomas Brabec:
DNA-backbone radio resistivity induced by spin blockade effect. 2601-2606 - Fahrettin Gogtas, Rukiye Tutuk, Mustafa Kurban:
Time-dependent quantum study of H(2S) + FO(2Pi) -> OH(2Pi) + F(2P) reaction on the 13A' and 13A" states. 2607-2611 - Alice Borghini, Paolo Crotti, Daniele Pietra, Lucilla Favero, Anna Maria Bianucci:
Chemical reactivity predictions: Use of data mining techniques for analyzing regioselective azidolysis of epoxides. 2612-2619 - Jörg Von Appen, Bernhard Eck, Richard Dronskowski:
A density-functional study of the phase diagram of cementite-type (Fe, Mn)3C at absolute zero temperature. 2620-2627 - Yoshiyuki Koyano, Norio Takenaka, Yukinori Nakagawa, Masataka Nagaoka:
An optimum strategy for solution chemistry using semiempirical molecular orbital method. II. Primary importance of reproducing electrostatic interaction in the QM/MM framework. 2628-2641 - Esteban Vöhringer-Martinez, Alejandro Toro-Labbé:
The role of water in the proton transfer reaction mechanism in tryptophan. 2642-2649 - Shu-Wei Tang, Jing-Dong Feng, Yong-Qing Qiu, Hao Sun, Feng-Di Wang, Ying-Fei Chang, Rongshun Wang:
Electronic structures and nonlinear optical properties of highly deformed halofullerenes C3v C60F18 and D3d C60Cl30. 2650-2657
- Mihaly Mezei:
Simulaid: A simulation facilitator and analysis program. 2658-2668 - Oscar Bertran, Samuel B. Trickey, Juan Torras:
Incorporation of deMon2k as a new parallel quantum mechanical code for the PUPIL system. 2669-2676
Volume 31, Number 15, November 2010
- Christopher J. R. Illingworth, Paul D. Scott, Kevin E. B. Parkes, Christopher R. Snell, Matthew P. Campbell, Christopher A. Reynolds:
Connectivity and binding-site recognition: Applications relevant to drug design. 2677-2688 - Sree V. Chintapalli, Boon K. Yew, Christopher J. R. Illingworth, Graham J. G. Upton, Philip J. Reeves, Kevin E. B. Parkes, Christopher R. Snell, Christopher A. Reynolds:
Closed loop folding units from structural alignments: Experimental foldons revisited. 2689-2701 - Dennis M. Elking, Lalith E. Perera, Robert E. Duke, Thomas A. Darden, Lee G. Pedersen:
Atomic forces for geometry-dependent point multipole and Gaussian multipole models. 2702-2713 - Katsumi Murata, Naoya Nagata, Isao Nakanishi, Kazuo Kitaura:
SDOVS: A solvent dipole ordering-based method for virtual screening. 2714-2722 - Pedro A. Valiente, Alejandro Gil L., Paulo R. Batista, Ernesto Raúl Caffarena, Tirso Pons, Pedro Geraldo Pascutti:
New parameterization approaches of the LIE method to improve free energy calculations of PlmII-Inhibitors complexes. 2723-2734 - Marcos Mandado, M. Natália Dias Soeiro Cordeiro:
On the stability of metal-aminoacid complexes in water based on water-ligand exchange reactions and electronic properties: Detailed study on iron-glycine hexacoordinated complexes. 2735-2745 - Eri Sano, Weihua Li, Hitomi Yuki, Xinli Liu, Tomomi Furihata, Kaoru Kobayashi, Kan Chiba, Saburo Neya, Tyuji Hoshino:
Mechanism of the decrease in catalytic activity of human cytochrome P450 2C9 polymorphic variants investigated by computational analysis. 2746-2758 - Tzong-Yi Lee, Justin Bo-Kai Hsu, Feng-Mao Lin, Wen-Chi Chang, Po-Chiang Hsu, Hsien-Da Huang:
N-Ace: Using solvent accessibility and physicochemical properties to identify protein N-acetylation sites. 2759-2771 - Hao Zhang, Yun-Hong Zhang:
Ab initio investigation on the ion-associated species and process in Mg(NO3)2 solution. 2772-2782 - Juan Du, Lili Xi, Beilei Lei, Jing Lu, Jiazhong Li, Huanxiang Liu, Xiaojun Yao:
Structure-based quantitative structure-activity relationship studies of checkpoint kinase 1 inhibitors. 2783-2793 - Hui Zhang, Guiling Zhang, Jing-Yao Liu, Miao Sun, Bo Liu, Ze-Sheng Li:
Theoretical studies on the reactions CH3SCH3 with OH, CF3, and CH3 radicals. 2794-2803 - Q. I. Liang Lu, Li Li Chen, Jian Guo Wan, Guang Hou Wang:
First principles studies on the interaction of O2 with X@Al12 (X = Al-, P+, C, Si) clusters. 2804-2809 - Volker Hähnke, Matthias Rupp, Mireille Krier, Friedrich Rippmann, Gisbert Schneider:
Pharmacophore alignment search tool: Influence of canonical atom labeling on similarity searching. 2810-2826
Volume 31, Number 16, December 2010
- Emilia L. Wu:
Coriolis coupling and nonadiabaticity in chemical reaction dynamics. 2827-2835 - Dimitrios N. Garbounis, Athanassios C. Tsipis, Constantinos A. Tsipis:
Structural, electronic, bonding, magnetic, and optical properties of bimetallic [RunAum]0/+ (n + m <= 3) clusters. 2836-2852 - Ning-Ning Wei, Ce Hao, Zhilong Xiu, Jingwen Chen, Jieshan Qiu:
Time-dependent density functional theory study on excited-state dihydrogen bonding O-H***H-Ge of the dihydrogen-bonded phenol-triethylgermanium complex. 2853-2858 - Huan Rui, Wonpil Im:
Protegrin-1 orientation and physicochemical properties in membrane bilayers studied by potential of mean force calculations. 2859-2867 - Bernhard Knapp, Nadja Lederer, Ulrich Omasits, Wolfgang Schreiner:
vmdICE: A plug-in for rapid evaluation of molecular dynamics simulations using VMD. 2868-2873 - Neetha Mohan, Kunduchi P. Vijayalakshmi, Nobuaki Koga, Cherumuttathu H. Suresh:
Comparison of aromatic NH***pi, OH***pi, and CH***pi interactions of alanine using MP2, CCSD, and DFT methods. 2874-2882 - Erjun Zhao, Jinping Wang, Zhijian Wu:
Structural stability and phase transition in OsC and RuC. 2883-2888 - Stewart N. Weiss, Lulu Huang, Lou Massa:
A generalized higher order kernel energy approximation method. 2889-2899 - Seungsoo Hahn, Orr Ashenberg, Gevorg Grigoryan, Amy E. Keating:
Identifying and reducing error in cluster-expansion approximations of protein energies. 2900-2914 - Young Kee Kang, Byung Jin Byun:
Assessment of density functionals with long-range and/or empirical dispersion corrections for conformational energy calculations of peptides. 2915-2923 - Shinji Aono, Shigeki Kato:
Proton transfer in phenol-amine complexes: Phenol electronic effects on free energy profile in solution. 2924-2931 - Benedict M. Sattelle, Andrew Almond:
Less is more when simulating unsulfated glycosaminoglycan 3D-structure: Comparison of GLYCAM06/TIP3P, PM3-CARB1/TIP3P, and SCC-DFTB-D/TIP3P predictions with experiment. 2932-2947 - Anik Sen, Bishwajit Ganguly:
What is the minimum number of water molecules required to dissolve a potassium chloride molecule? 2948-2954 - Maria L. Sushko, Peter V. Sushko, Igor V. Abarenkov, Alexander L. Shluger:
QM/MM method for metal-organic interfaces. 2955-2966
- Claudia Steffen, Klaus Thomas, Uwe Huniar, Arnim Hellweg, Oliver Rubner, Alexander Schroer:
TmoleX - A graphical user interface for TURBOMOLE. 2967-2970
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