Journal 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)L_n]^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
  
• S. 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
  
• S. Jalili, M. 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 Ca₂O_X 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 ùA" 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 ³J_HH 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
  
• K. Vanommeslaeghe, E. Hatcher, C. Acharya, S. Kundu, S. Zhong, J. Shim, E. Darian, O. Guvench, P. Lopes, I. Vorobyov, A. 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 M. 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 Sn_n (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-Dock^LHM: 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 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, Yu Zong 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 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, A. Sayede, M. Springborg:
  Relaxed energetic maps of kappa-carrabiose: A DFT study. 1312-1320
  

• J. J. Borrás-Almenar, S. Cardona-Serra, J. M. Clemente-Juan, E. Coronado, A. V. Palii, B. 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, Jiang-Ning 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
  
• J. 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 Sanchez-Garcia, 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, M. T. Hyvönen, A. 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, Z. F. 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, Yu-Dong 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 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, Yan-Ping 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 Co^I, Rh^I, and Ir^I 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 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
  
• P. González-Navarrete, L. Gracia, M. Calatayud, J. 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 C_3v C₆₀F₁₈ and D_3d C₆₀Cl₃₀. 2650-2657
  

• Mihaly Mezei:
  Simulaid: A simulation facilitator and analysis program. 2658-2668
  
• Oscar Bertran, S. 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 R. Caffarena, Tirso Pons, Pedro G. Pascutti:
  New parameterization approaches of the LIE method to improve free energy calculations of PlmII-Inhibitors complexes. 2723-2734
  
• Marcos Mandado, M. Natália D. S. 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 [Ru_nAu_m]^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
  

Last update Wed Feb 15 05:37:00 2012 CET by the DBLP Team — Data released under the ODC-BY 1.0 license — See also our legal information page