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Journal of Computational Chemistry, Volume 32
Volume 32, Number 1, January 2011
- Subrata Mahanta, Bijan Kumar Paul, Rupashree Balia Singh, Nikhil Guchhait:
Inequivalence of substitution pairs in hydroxynaphthaldehyde: A theoretical measurement by intramolecular hydrogen bond strength, aromaticity, and excited-state intramolecular proton transfer reaction. 1-14 - Qiang Hao, Andrew C. Simmonett, Yukio Yamaguchi, De-Cai Fang, Henry F. Schaefer III:
From acetylene complexes to vinylidene structures: The GeC2H2 system. 15-22 - Oz Sharabi, Chen Yanover, Ayelet Dekel, Julia M. Shifman:
Optimizing energy functions for protein-protein interface design. 23-32 - Yongbing Zhao, Jing-Fa Xiao:
Homology modeling and molecular dynamics simulation studies of human type 1 3beta-hydroxysteroid dehydrogenase: Toward the understanding of cofactor specificity. 33-42 - Jon Baker, Krzysztof Wolinski:
Isomerization of stilbene using enforced geometry optimization. 43-53 - Eric J. Bylaska, Kiril Tsemekhman, Scott B. Baden, John H. Weare, Hannes Jónsson:
Parallel implementation of gamma-point pseudopotential plane-wave DFT with exact exchange. 54-69 - Shih-Hau Chiu, Chien-Chi Chen, Gwo-Fang Yuan, Thy-Hou Lin:
Deriving the phylogenetic information from some physicochemical properties of protein sequences computed. 70-80 - Annalisa Bordogna, Alessandro Pandini, Laura Bonati:
Predicting the accuracy of protein-ligand docking on homology models. 81-98 - Andrei M. Tokmachev, Richard Dronskowski:
Hydrogen-bond networks in finite ice nanotubes. 99-105 - Guillaume Launay, Thomas Simonson:
A large decoy set of protein-protein complexes produced by flexible docking. 106-120 - Mohammad Alaghemandi, Joachim Schulte, Frédéric Leroy, Florian Müller-Plathe, Michael C. Böhm:
Correlation between thermal conductivity and bond length alternation in carbon nanotubes: A combined reverse nonequilibrium molecular dynamics - Crystal orbital analysis. 121-133 - Conrad Shyu, F. Marty Ytreberg:
Accurate estimation of solvation free energy using polynomial fitting techniques. 134-141 - Qingyong Meng, Ming-Bao Huang:
A CAS study on S-loss and O-loss dissociation mechanisms of the SO2+ ion in the C, D, and E states. 142-151 - Chaoyang Zhang:
Shape and size effects in pi-pi interactions: Face-to-face dimers. 152-160 - Jae In Kim, Sungsoo Na, Kilho Eom:
Domain decomposition-based structural condensation of large protein structures for understanding their conformational dynamics. 161-169
- Joseph N. Zadeh, Conrad Steenberg, Justin S. Bois, Brian R. Wolfe, Marshall B. Pierce, Asif R. Khan, Robert M. Dirks, Niles A. Pierce:
NUPACK: Analysis and design of nucleic acid systems. 170-173 - Abdul-Rahman Allouche:
Gabedit - A graphical user interface for computational chemistry softwares. 174-182
- Gerald R. Kneller:
Comment on "Fast determination of the optimal rotational matrix for macromolecular superpositions" [J. Comp. Chem. 31 1561 (2010)]. 183-184
- Pu Liu, Dimitris K. Agrafiotis, Douglas L. Theobald:
Rapid communication reply to comment on: "Fast determination of the optimal rotational matrix for macromolecular superpositions". 185-186
Volume 32, Number 2, January 2011
- Samuel Genheden, Ulf Ryde:
A comparison of different initialization protocols to obtain statistically independent molecular dynamics simulations. 187-195 - Juan R. Perilla, Oliver Beckstein, Elizabeth J. Denning, Thomas B. Woolf:
Computing ensembles of transitions from stable states: Dynamic importance sampling. 196-209 - John W. Raymond, Daniel D. Holsworth, Mehran Jalaie:
The flexible alignment of molecular structures using simulated annealing with weighted Lagrangian multipliers. 210-217 - Wen-Zhi Yao, Da-Zhi Li, Si-Dian Li:
Bridging gold: B-Au-B three-center-two-electron bonds in electron-deficient B2Aun-/0 (n = 1, 3, 5) and mixed analogues. 218-225 - Kathy L. Phillips, Stanley I. Sandler, Pei C. Chiu:
A method to calculate the one-electron reduction potentials for nitroaromatic compounds based on gas-phase quantum mechanics. 226-239 - Blandine Courcot, Adam J. Bridgeman:
Optimization of a molecular mechanics force field for polyoxometalates based on a genetic algorithm. 240-247 - Peng Bao, Zhong-Heng Yu:
New procedure to evaluate aromaticity at the density functional theory, Hartree-Fock, and post-self-consistent field levels. 248-259 - Suyong Re, Takashi Imai, Jaewoon Jung, Seiichiro Ten-no, Yuji Sugita:
Geometrically associative yet electronically dissociative character in the transition state of enzymatic reversible phosphorylation. 260-270 - Dongsheng Zou, Zhongshi He, Jingyuan He, Yuxian Xia:
Supersecondary structure prediction using Chou's pseudo amino acid composition. 271-278 - Massimiliano Bartolomei, Estela Carmona-Novillo, Marta I. Hernández, José Campos-Martínez, Ramón Hernández-Lamoneda:
Long-range interaction for dimers of atmospheric interest: dispersion, induction and electrostatic contributions for O2-O2, N2-N2 and O2-N2. 279-290 - Alberto Otero-de-la-Roza, Víctor Luaña:
A fast and accurate algorithm for QTAIM integration in solids. 291-305 - Daniel Tunega, Ali Zaoui:
Understanding of bonding and mechanical characteristics of cementitious mineral tobermorite from first principles. 306-314 - Carmen Jiménez Calzado, Antonio Monari, Stefano Evangelisti:
Heisenberg behavior of some carbon-beryllium compounds: How well truncated-CI approaches work. 315-324 - Uttam Sinha Mahapatra, Sudip Chattopadhyay, Rajat K. Chaudhuri:
Second-order state-specific multireference Møller Plesset perturbation theory: Application to energy surfaces of diimide, ethylene, butadiene, and cyclobutadiene. 325-337 - Shu-Ling Chen, Dong-Xia Zhao, Zhong-Zhi Yang:
An estimation method of binding free energy in terms of ABEEMsigmapi/MM and continuum electrostatics fused into LIE method. 338-348 - Chewook Lee, Sihyun Ham:
Characterizing amyloid-beta protein misfolding from molecular dynamics simulations with explicit water. 349-355 - Lukás Bucinský, Stanislav Biskupic, Michal Ilcin, Vladimír Lukes, Viliam Laurinc:
Relativistic effects in HgHe and HgXe CCSD(T) ground state potential curves. Low-density viscosity simulations of Hg: Xe mixture. 356-367
- Richard Lonsdale, Jeremy N. Harvey, Frederick R. Manby, Adrian J. Mulholland:
Comment on "A stationary-wave model of enzyme catalysis" by Carlo Canepa. 368-369 - Carlo Canepa:
Reply to the comment on "A stationary-wave model of enzyme catalysis". 370-371
- J. Oscar C. Jiménez-Halla, Eduard Matito, Lluís Blancafort, Juvencio Robles, Miquel Solà:
Erratum: Tuning aromaticity in trigonal alkaline earth metal clusters and their alkali metal salts. 372-373
Volume 32, Number 3, February 2011
- Brad A. Bauer, Joseph E. Davis, Michela Taufer, Sandeep Patel:
Molecular dynamics simulations of aqueous ions at the liquid-vapor interface accelerated using graphics processors. 375-385 - Wouter Heyndrickx, Pedro Salvador, Patrick Bultinck, Miquel Solà, Eduard Matito:
Performance of 3D-space-based atoms-in-molecules methods for electronic delocalization aromaticity indices. 386-395 - Artem B. Mamonov, Xin Zhang, Daniel M. Zuckerman:
Rapid sampling of all-atom peptides using a library-based polymer-growth approach. 396-405 - Yuan Miao, Xueye Wang, Xin Jin, Ling Yi, Cuihuan Ren:
Density functional theory study of a molecular allosteric switch for 2, 2'-bipyridyl-3, 3'-15-crown-5. 406-415 - Bo Yang, Yanyan Zhu, Yan Wang, Guangju Chen:
Interaction identification of Zif268 and TATAZF proteins with GC-/AT-rich DNA sequence: A theoretical study. 416-428 - Matthew A. Addicoat, Gregory F. Metha, Tak W. Kee:
Density functional theory investigation of Cu(I)- and Cu(II)-curcumin complexes. 429-438 - Joseph N. Zadeh, Brian R. Wolfe, Niles A. Pierce:
Nucleic acid sequence design via efficient ensemble defect optimization. 439-452 - Omololu Akin-Ojo, Feng Wang:
The quest for the best nonpolarizable water model from the adaptive force matching method. 453-462 - Ahmed Mutanabbi Abdula, Reema Abu Khalaf, Mohammad S. Mubarak, Mutasem O. Taha:
Discovery of new beta-D-galactosidase inhibitors via pharmacophore modeling and QSAR analysis followed by in silico screening. 463-482 - Burak Alakent, Sena Baskan, Pemra Doruker:
Effect of ligand binding on the intraminimum dynamics of proteins. 483-496 - Andrés Jaramillo-Botero, Julius Su, Qi An, William A. Goddard III:
Large-scale, long-term nonadiabatic electron molecular dynamics for describing material properties and phenomena in extreme environments. 497-512 - Timothy H. Click, Aibing Liu, George A. Kaminski:
Quality of random number generators significantly affects results of Monte Carlo simulations for organic and biological systems. 513-524 - Aravindhan Ganesan, Feng Wang, Chantal T. Falzon:
Intramolecular interactions of L-phenylalanine: Valence ionization spectra and orbital momentum distributions of its fragment molecules. 525-535 - Dorota Latek, Andrzej Kolinski:
CABS-NMR - De novo tool for rapid global fold determination from chemical shifts, residual dipolar couplings and sparse methyl-methyl noes. 536-544
- Wenwei Zhao, Yihong Ding, Qiying Xia:
Time-dependent density functional theory study on the absorption spectrum of Coumarin 102 and its hydrogen-bonded complexes. 545-553
Volume 32, Number 4, March 2011
- Jagdish Chandra Patra, Boon H. Chua:
Artificial neural network-based drug design for diabetes mellitus using flavonoids. 555-567 - Dariusz Plewczynski, Michal Lazniewski, Marcin von Grotthuss, Leszek Rychlewski, Krzysztof Ginalski:
VoteDock: Consensus docking method for prediction of protein-ligand interactions. 568-581 - Ramon Carbó-Dorca, Emili Besalú, Luz Dary Mercado:
Communications on quantum similarity, part 3: A geometric-quantum similarity molecular superposition algorithm. 582-599 - Christian C. Gruber, Jürgen Pleiss:
Systematic benchmarking of large molecular dynamics simulations employing GROMACS on massive multiprocessing facilities. 600-606 - David Curcó, David Zanuy, Ruth Nussinov, Carlos Alemán:
A simulation strategy for the atomistic modeling of flexible molecules covalently tethered to rigid surfaces: Application to peptides. 607-619 - Athanassios C. Tsipis, Alexandros V. Stalikas:
Structural, electronic, and magnetoresponsive properties of triangular lanthanide clusters and their free-standing nitrides. 620-638 - Arthur N. Mayeno, Jonathan L. Robinson, Brad Reisfeld:
Rapid estimation of activation enthalpies for cytochrome-P450-mediated hydroxylations. 639-657 - Shu-Wei Tang, Jing-Dong Feng, Yong-Qing Qiu, Hao Sun, Feng-Di Wang, Zhongmin Su, Ying-Fei Chang, Rongshun Wang:
Thermochemical stabilities, electronic structures, and optical properties of C56X10 (X = H, F, and Cl) fullerene compounds. 658-667 - Guang-Yue Li, Guang-Jiu Zhao, Ke-Li Han, Guo-Zhong He:
A TD-DFT study on the cyanide-chemosensing mechanism of 8-formyl-7-hydroxycoumarin. 668-674 - Chun Li, Hong Ma, Yang Zhou, Xiaolei Wang, Xiaoqi Zheng:
Similarity analysis of DNA sequences based on the weighted pseudo-entropy. 675-680 - Juan M. Ruiz, R. Joshua Mulder, Célia Fonseca Guerra, Friedrich Matthias Bickelhaupt:
Steric effects on alkyl cation affinities of maingroup-element hydrides. 681-688 - T. Zoboki, I. Mayer:
Extremely localized nonorthogonal orbitals by the pairing theorem. 689-695 - Zahid Rashid, Joop H. van Lenthe:
Generation of Kekulé valence structures and the corresponding valence bond wave function. 696-708 - Matthew S. Lin, Teresa Head-Gordon:
Reliable protein structure refinement using a physical energy function. 709-717 - Andrzej T. Kowal:
Ab initio molecular geometry and anharmonic vibrational spectra of thiourea and thiourea-d4. 718-729 - Shih-I Lu:
Computational study of static first hyperpolarizability of donor-acceptor substituted (E)-benzaldehyde phenylhydrazone. 730-736 - Zongling Ding, Jun Jiang, Huaizhong Xing, Haibo Shu, Ruibin Dong, Xiaoshuang Chen, Wei Lu:
Transport properties of graphene nanoribbon-based molecular devices. 737-741
- Dariusz Plewczynski, Michal Lazniewski, Rafal Augustyniak, Krzysztof Ginalski:
Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database. 742-755
- Duan Chen, Zhan Chen, Changjun Chen, Weihua Geng, Guo-Wei Wei:
MIBPB: A software package for electrostatic analysis. 756-770
Volume 32, Number 5, April 2011
- Chang-Bin Shao, Lin Jin, Yi-Hong Ding:
A theoretical survey on the structures, energetics, and isomerization pathways of the B5O radical. 771-777 - Kenji Hori, Toru Yamaguchi, Keita Uezu, Michinori Sumimoto:
A free-energy perturbation method based on Monte Carlo simulations using quantum mechanical calculations (QM/MC/FEP method): Application to highly solvent-dependent reactions. 778-786 - Pralay Mitra, Debnath Pal:
Using correlated parameters for improved ranking of protein-protein docking decoys. 787-796 - Hossein Farrokhpour, Zainab Mombeini, Mansoor Namazian, Michelle L. Coote:
Intermolecular potential energy surface for CS2 dimer. 797-809 - Kay Hamacher:
Efficient quantification of the importance of contacts for the dynamical stability of proteins. 810-815 - Adam D. Swetnam, Michael P. Allen:
Improving the Wang-Landau algorithm for polymers and proteins. 816-821 - Eric A. C. Bushnell, Edvin Erdtman, Jorge Llano, Leif A. Eriksson, James W. Gauld:
The first branching point in porphyrin biosynthesis: A systematic docking, molecular dynamics and quantum mechanical/molecular mechanical study of substrate binding and mechanism of uroporphyrinogen-III decarboxylase. 822-834 - C. Weng, J. Kouvetakis, A. V. G. Chizmeshya:
A novel predictive model for formation enthalpies of Si and Ge hydrides with propane- and butane-like structures. 835-853 - Ramkumar Rajamani, Yen-Lin Lin, Jiali Gao:
The opsin shift and mechanism of spectral tuning in rhodopsin. 854-865 - Tingjun Hou, Junmei Wang, Youyong Li, Wei Wang:
Assessing the performance of the molecular mechanics/Poisson Boltzmann surface area and molecular mechanics/generalized Born surface area methods. II. The accuracy of ranking poses generated from docking. 866-877 - Bin Lin, B. Montgomery Pettitt:
Electrostatic solvation free energy of amino acid side chain analogs: Implications for the validity of electrostatic linear response in water. 878-885 - Syed Tarique Moin, Thomas S. Hofer, Bernhard R. Randolf, Bernd M. Rode:
Structure and dynamics of methanol in water: A quantum mechanical charge field molecular dynamics study. 886-892 - Goutam Mukherjee, Niladri Patra, Poranjyoti Barua, Bhyravabhotla Jayaram:
A fast empirical GAFF compatible partial atomic charge assignment scheme for modeling interactions of small molecules with biomolecular targets. 893-907 - Heribert Reis, Oleksandr Loboda, Aggelos Avramopoulos, Manthos G. Papadopoulos, Bernard Kirtman, Josep M. Luis, Robert Zalesny:
Electronic and vibrational linear and nonlinear polarizabilities of Li@C60 and [Li@C60]+. 908-914 - J. M. Villalba, A. J. Barbero, R. Diaz-Sierra, Enrique Arribas, M. J. Garcia-Meseguer, Francisco García-Sevilla, Manuela García-Moreno, J. A. Vidal De Labra, Ramón Varón:
Computerized evaluation of mean residence times in multicompartmental linear system and pharmacokinetics. 915-931 - Takuya Okamoto, Kenta Yamada, Yoshiyuki Koyano, Toshio Asada, Nobuaki Koga, Masataka Nagaoka:
A minimal implementation of the AMBER-GAUSSIAN interface for ab initio QM/MM-MD simulation. 932-942 - Gui-Xiang Wang, Xue-Dong Gong, Yan Liu, Hong-Chen Du, Xiao-Juan Xu, He-Ming Xiao:
Looking for high energy density compounds applicable for propellant among the derivatives of dpo with --n3, --ono2, and --nno2 groups. 943-952 - Yang Li, Xiao-Nan Jiang, Chang-Sheng Wang:
Rapid evaluation of the binding energies in hydrogen-bonded amide-thymine and amide-uracil dimers in gas phase. 953-966 - Yue Shi, Chuanjie Wu, Jay W. Ponder, Pengyu Y. Ren:
Multipole electrostatics in hydration free energy calculations. 967-977
- Andreas Uhe, Sebastian Kozuch, Sason Shaik:
Automatic analysis of computed catalytic cycles. 978-985
Volume 32, Number 6, April 2011
- Jie Luo, Xiujuan Jia, Yang Gao, Guicai Song, Yanbo Yu, Rongshun Wang, Xiumei Pan:
Theoretical study on the kinetics of OH radical reactions with CH3OOH and CH3CH2OOH. 987-997 - Halvor S. Hansen, Philippe H. Hünenberger:
A reoptimized GROMOS force field for hexopyranose-based carbohydrates accounting for the relative free energies of ring conformers, anomers, epimers, hydroxymethyl rotamers, and glycosidic linkage conformers. 998-1032 - Xiao-Na Li, Zhi-Jian Wu, Xi-Yan Li, Hong-Jie Zhang, Xiao-Juan Liu:
Theoretical study on phosphorescence efficiency and color tuning from orange to blue-green of Ir(III) complexes based on substituted 2-phenylimidazo[1, 2-a]pyridine ligand. 1033-1042 - Ivan I. Vorontsov, Osamu Miyashita:
Crystal molecular dynamics simulations to speed up MM/PB(GB)SA evaluation of binding free energies of di-mannose deoxy analogs with P51G-m4-Cyanovirin-N. 1043-1053 - Piotr De Silva, Jacek Korchowiec:
Energy partitioning scheme based on self-consistent method for subsystems: Populational space approach. 1054-1064 - Wen-Fei Huang, P. Raghunath, M. C. Lin:
Computational study on the reactions of H2O2 on TiO2 anatase (101) and rutile (110) surfaces. 1065-1081 - Gerhard König, Stefan Boresch:
Non-Boltzmann sampling and Bennett's acceptance ratio method: How to profit from bending the rules. 1082-1090 - Xianfeng Li, Robert A. Latour:
The temperature intervals with global exchange of replicas empirical accelerated sampling method: Parameter sensitivity and extension to a complex molecular system. 1091-1100 - Jee-Gong Chang, Hsin-Tsung Chen, Shin-Pon Ju, Ching-Sheng Chang, Meng-Hsiung Weng:
Adsorption and dissociation of NH3 on clean and hydroxylated TiO2 rutile (110) surfaces: A computational study. 1101-1112 - Francesco Rao:
Protein inherent structures by different minimization strategies. 1113-1116 - Marcel Swart, Miquel Solà, Friedrich Matthias Bickelhaupt:
Inter- and intramolecular dispersion interactions. 1117-1127 - Adam Tuer, Serguei Krouglov, Richard Cisek, Danielle Tokarz, Virginijus Barzda:
Three-dimensional visualization of the first hyperpolarizability tensor. 1128-1134 - Steven Lettieri, Artem B. Mamonov, Daniel M. Zuckerman:
Extending fragment-based free energy calculations with library monte carlo simulation: Annealing in interaction space. 1135-1143 - Jhon Zapata-Rivera, Rosa Caballol, Carmen Jiménez Calzado:
Electronic structure and relative stability of 1: 1 Cu-O2 adducts from difference-dedicated configuration interaction calculations. 1144-1158 - Huifang Li, Laibin Zhang, Li Han, Wenming Sun, Yuxiang Bu:
Internucleotide J-couplings and chemical shifts of the N---H···N hydrogen-bonds in the radiation-damaged guanine-cytosine base pairs. 1159-1169 - Meiyan Wang, Lin Cheng, Jinping Wang, Zhijian Wu:
Mechanism of methylacetylene bisselenation catalyzed by palladium complex from density functional study. 1170-1177
- Aurélien de la Lande, Dennis R. Salahub, Jacques Maddaluno, Anthony Scemama, Julien Pilmé, Olivier Parisel, Helene Gerard, Michel Caffarel, Jean-Philip Piquemal:
Spin-driven activation of dioxygen in various metalloenzymes and their inspired models. 1178-1182
- Michele Seeber, Angelo Felline, Francesco Raimondi, Stefanie Muff, Ran Friedman, Francesco Rao, Amedeo Caflisch, Francesca Fanelli:
Wordom: A user-friendly program for the analysis of molecular structures, trajectories, and free energy surfaces. 1183-1194 - Christoph Van Wüllen:
Shared-memory parallelization of the TURBOMOLE programs AOFORCE, ESCF, and EGRAD: How to quickly parallelize legacy code. 1195-1201