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ORCIDJournal of Computational Chemistry, Volume 29
Volume 29, Number 1, January 2008
- Tanja Van Mourik:
Comment on "Aromatic-Backbone Interactions in Model alpha-Helical Peptides" [Palermo et al., J Comput Chem 2007, 28, 1208]. 1-3 - József Csontos, Nicholas Y. Palermo, Richard F. Murphy, Sándor Lovas:
Reply to "Comment on Aromatic-Backbone Interactions in Model alpha-Helical Peptides". 4-7 - Michael T. Feldmann, Julian C. Cummings, David R. Kent IV, Richard P. Muller, William A. Goddard III:
Manager-worker-based model for the parallelization of quantum Monte Carlo on heterogeneous and homogeneous networks. 8-16 - Kun Song, Viktor Hornak, Carlos De Los Santos, Arthur P. Grollman, Carlos Simmerling:
Molecular mechanics parameters for the FapydG DNA lesion. 17-23 - Lula Rosso, Ian R. Gould
:
Structure and dynamics of phospholipid bilayers using recently developed general all-atom force fields. 24-37 - Katrin Spiegel, Alessandra Magistrato, Patrick Maurer, Paolo Ruggerone, Ursula Rothlisberger, Paolo Carloni, Jan Reedijk, Michael L. Klein:
Parameterization of azole-bridged dinuclear platinum anticancer drugs via a QM/MM force matching procedure. 38-49 - R. James Milgram, Guanfeng Liu, Jean-Claude Latombe:
On the structure of the inverse kinematics map of a fragment of protein backbone. 50-68 - Francisco Rodríguez-Ropero, Jordi Casanovas, Carlos Alemán:
Ab initio calculations on pi-stacked thiophene dimer, trimer, and tetramer: Structure, interaction energy, cooperative effects, and intermolecular electronic parameters. 69-78 - Evgenii V. Kovalyov, Vladimir Elokhin, Aleksandr V. Myshlyavtsev:
Stochastic simulation of physicochemical processes performance over supported metal nanoparticles. 79-86 - Yongcheng Zhou, Michael Feig, Guo-Wei Wei:
Highly accurate biomolecular electrostatics in continuum dielectric environments. 87-97 - N. R. Jena, P. S. Kushwaha, P. C. Mishra:
Reaction of hypochlorous acid with imidazole: Formation of 2-chloro- and 2-oxoimidazoles. 98-107 - Ewgenij Proschak, Matthias Rupp, Swetlana Derksen, Gisbert Schneider:
Shapelets: Possibilities and limitations of shape-based virtual screening. 108-114 - Chinapong Kritayakornupong:
The Jahn-Teller effect of the Cr2+ ion in aqueous solution: Ab initio QM/MM molecular dynamics simulations. 115-121 - Matej Praprotnik, Stanko Hocevar, Milan Hodoscek, Matej Penca, Dusanka Janezic:
New all-atom force field for molecular dynamics simulation of an AlPO4-34 molecular sieve. 122-129 - Alexander V. Larin, D. N. Trubnikov, Daniel P. Vercauteren:
Electric field convergence versus atomic basis sets in all-siliceous zeolites. 130-138 - Ignacio Fdez. Galván, Martin J. Field:
Improving the efficiency of the NEB reaction path finding algorithm. 139-143
- Josep M. Porta, Lluís Ros, Federico Thomas, Francesc Corcho, Josep Cantó, Juan Jesús Pérez:
Complete maps of molecular-loop conformational spaces. 144-155
Volume 29, Number 2, January 2008
- Markus Christen, Wilfred F. van Gunsteren:
On searching in, sampling of, and dynamically moving through conformational space of biomolecular systems: A review. 157-166 - Florian Weigend:
Hartree-Fock exchange fitting basis sets for H to Rn. 167-175 - Weihua Zhu, Heming Xiao:
Ab initio study of electronic structure and optical properties of heavy-metal azides: TlN3, AgN3, and CuN3. 176-184 - Nathan E. Schultz, Yan Zhao, Donald G. Truhlar:
Benchmarking approximate density functional theory for s/d excitation energies in 3d transition metal cations. 185-189 - Mark Pinsky, David Casanova, Pere Alemany, Santiago Alvarez, David Avnir, Chaim Dryzun, Ziv Kizner, Alexander Sterkin:
Symmetry operation measures. 190-197 - Jian-Yi Ma, Jing-Bo Wang, Xiang-Yuan Li, Yao Huang, Quan Zhu, Ke-Xiang Fu:
A study on orientation and absorption spectrum of interfacial molecules by using continuum model. 198-210 - Qishi Du, Ri-Bo Huang, Yu-Tuo Wei, Li-Qin Du, Kuo-Chen Chou:
Multiple field three dimensional quantitative structure-activity relationship (MF-3D-QSAR). 211-219 - Dmitry N. Tarasov, R. P. Tiger:
Numerical computations of molecular reactions in associated systems caused by the formation of fractal structures. 220-224 - Yasuji Inada, Hideo Orita:
Efficiency of numerical basis sets for predicting the binding energies of hydrogen bonded complexes: Evidence of small basis set superposition error compared to Gaussian basis sets. 225-232 - Milan Oncák, Martin Srnec:
Electronic structure and physical properties of MiXi clusters (M = B, Al; X = N, P; i = 1, 2, 3): Ab initio study. 233-246 - Jing Yang, Qian Shu Li, Shaowen Zhang:
Direct dynamics study on the reaction of acetaldehyde with ozone. 247-255 - Kun Liu, Wensheng Bian:
Extensive theoretical study on the low-lying electronic states of silicon monofluoride cation including spin-orbit coupling. 256-265 - Bahram Hemmateenejad, Afshan Mohajeri:
Application of quantum topological molecular similarity descriptors in QSPR study of the O-methylation of substituted phenols. 266-274 - Yun Ding, Ye Mei, John Z. H. Zhang, Fu-Ming Tao:
Efficient bond function basis set for pi-pi interaction energies. 275-279 - Miguel A. Zamora, Fernando D. Suvire, Ricardo D. Enriz:
Ring inversion in 1, 4, 7 cyclononatriene and analogues: Ab initio and DFT calculations and topological analysis. 280-290 - Yin Wei, T. Singer, H. Mayr, G. Narahari Sastry, Hendrik Zipse:
Assessment of theoretical methods for the calculation of methyl cation affinities. 291-297 - Sean A. C. McDowell:
A comparative study of some red- and blue-shifted linear H-bonded complexes of N2. 298-305
- Mohamed Zerara:
pyVib, a computer program for the analysis of infrared and Raman optical activity. 306-311 - Willem-Jan Van Zeist, Célia Fonseca Guerra, Friedrich Matthias Bickelhaupt:
PyFrag - Streamlining your reaction path analysis. 312-315
Volume 29, Number 3, February 2008
- Yoanna María Alvarez-Ginarte, Yovani Marrero-Ponce, José Alberto Ruiz-García, Luis Alberto Montero-Cabrera, José Manuel García de la Vega, Pedro Noheda Marin, Rachel Crespo-Otero, Francisco Torrens Zaragoza, Ramón García-Domenech:
Applying pattern recognition methods plus quantum and physico-chemical molecular descriptors to analyze the anabolic activity of structurally diverse steroids. 317-333 - Koji Yasuda:
Two-electron integral evaluation on the graphics processor unit. 334-342 - Arvids Stashans, Gaston Chamba, Henry Pinto:
Electronic structure, chemical bonding, and geometry of pure and Sr-doped CaCO3. 343-349 - Ruibo Wu, Zexing Cao:
QM/MM study of catalytic methyl transfer by the N5-glutamine SAM-dependent methyltransferase and its inhibition by the nitrogen analogue of coenzyme. 350-357 - Stijn Fias, Sofie Van Damme, Patrick Bultinck:
Multidimensionality of delocalization indices and nucleus independent chemical shifts in polycyclic aromatic hydrocarbons. 358-366 - Norberto Castillo, Katherine N. Robertson, S. C. Choi, Russell J. Boyd, Osvald Knop:
Bond length and the electron density at the bond critical point: X-X, Z-Z, and C-Z bonds (X = Li-F, Z = Na-Cl). 367-379 - Peter W. Bates, Guo-Wei Wei, Shan Zhao:
Minimal molecular surfaces and their applications. 380-391 - Daniel Norberg, Nessima Salhi-Benachenhou:
McLafferty rearrangement of the radical cations of butanal and 3-fluorobutanal: A theoretical investigation of the concerted and stepwise mechanisms. 392-406 - Sebastian Schlund, Robert Müller, Carsten Graßmann, Bernd Engels:
Conformational analysis of arginine in gas phase - A strategy for scanning the potential energy surface effectively. 407-415 - Gilles Frison, Gilles Ohanessian:
A comparative study of semiempirical, ab initio, and DFT methods in evaluating metal-ligand bond strength, proton affinity, and interactions between first and second shell ligands in Zn-biomimetic complexes. 416-433 - Bin Gao, Jun Jiang, Kai Liu, Ziyu Wu, Wei Lu, Yi Luo:
An efficient first-principle approach for electronic structures calculations of nanomaterials. 434-444 - Richard J. Wheatley:
Time-dependent coupled-cluster calculations of polarizabilities and dispersion energy coefficients. 445-450 - Manuel Piacenza, Fabio Della Sala, Eduardo Fabiano, T. Maiolo, Giuseppe Gigli:
Torsional effects on excitation energies of thiophene derivatives induced by beta-substituents: Comparison between time-dependent density functional theory and approximated coupled cluster approaches. 451-457 - Toshiaki Matsubara, Michel Dupuis, Misako Aida:
An insight into the environmental effects of the pocket of the active site of the enzyme. Ab initio ONIOM-molecular dynamics (MD) study on cytosine deaminase. 458-465 - Chao Deng, Qiang-Gen Li, Yi Ren, Ning-Bew Wong, San-Yan Chu, Hua-Jie Zhu:
A comprehensive theoretical study on the hydrolysis of carbonyl sulfide in the neutral water. 466-480 - Bryan M. Wong, Maria M. Fadri, Sumathy Raman:
Thermodynamic calculations for molecules with asymmetric internal rotors. II. Application to the 1, 2-dihaloethanes. 481-487
- V. Ganesh, Ritwik Kavathekar, Anuja P. Rahalkar, Shridhar R. Gadre:
WebProp: Web interface for ab initio calculation of molecular one-electron properties. 488-495
Volume 29, Number 4, March 2007
- John Cullen:
An approximate diatomics in molecules formulation of generalized valence bond theory. 497-504 - Xiao-Wei Fan, Xue-Hai Ju:
Theoretical studies on four-membered ring compounds with NF2, ONO2, N3, and NO2 groups. 505-513 - Jiali Gao, Kin-Yiu Wong, Dan Thomas Major:
Combined QM/MM and path integral simulations of kinetic isotope effects in the proton transfer reaction between nitroethane and acetate ion in water. 514-522 - José-Vicente Pitarch Ruiz, José Sánchez-Marín, A. M. Velasco:
Full configuration interaction calculation of the low lying valence and Rydberg states of BeH. 523-532 - Maykel Cruz-Monteagudo, M. Natália Dias Soeiro Cordeiro, Fernanda Borges:
Computational chemistry approach for the early detection of drug-induced idiosyncratic liver toxicity. 533-549 - Lei Yang, Jing-Yao Liu, Li Wang, Hong-Qing He, Ying Wang, Ze-Sheng Li:
Theoretical study of the reactions CF3CH2OCHF2 + OH/Cl and its product radicals and parent ether(CH3CH2OCH3) with OH. 550-561 - Joseph P. Kenny, Curtis L. Janssen, Edward F. Valeev, Theresa L. Windus:
Components for integral evaluation in quantum chemistry. 562-577 - Flavio Forti, Xavier Barril, F. Javier Luque, Modesto Orozco:
Extension of the MST continuum solvation model to the RM1 semiempirical hamiltonian. 578-587 - M. Leonor Contreras, José Alvarez, D. Guajardo, Roberto Rozas:
Understanding topological symmetry: A heuristic approach to its determination. 588-600 - Aibing Liu, Steven J. Stuart:
Empirical bond-order potential for hydrocarbons: Adaptive treatment of van der Waals interactions. 601-611 - Yasushi Honda, Atsushi Kurihara, Masahiko Hada, Hiroshi Nakatsuji:
Excitation and circular dichroism spectra of (-)-(3aS, 7aS)-2-chalcogena-trans-hydrindans(Ch = S, Se, Te): SAC and SAC-CI calculations. 612-621 - Karl Nicholas Kirschner, Austin B. Yongye, Sarah M. Tschampel, Jorge González-Outeiriño, Charlisa R. Daniels, Bethany Lachele Foley, Robert J. Woods:
GLYCAM06: A generalizable biomolecular force field. Carbohydrates. 622-655 - Humberto González Díaz, Francisco J. Prado-Prado:
Unified QSAR and network-based computational chemistry approach to antimicrobials, part 1: Multispecies activity models for antifungals. 656-667 - Wei Yang, Hugh Nymeyer, Huan-Xiang Zhou, Bernd A. Berg, Rafael Brüschweiler:
Quantitative computer simulations of biomolecules: A snapshot. 668-672
Volume 29, Number 5, 15 April 2008
- Kitiyaporn Wittayanarakul, Supot Hannongbua, Michael Feig:
Accurate prediction of protonation state as a prerequisite for reliable MM-PB(GB)SA binding free energy calculations of HIV-1 protease inhibitors. 673-685 - Cai-Yun Geng, Ji-Lai Li, Xu-Ri Huang, Hui-Ling Liu, Zhuo Li, Chia-Chung Sun:
Theoretical elucidation of the rhodium-catalyzed [4 + 2] annulation reactions. 686-693 - Alex Robertson, Edgar Luttmann, Vijay S. Pande:
Effects of long-range electrostatic forces on simulated protein folding kinetics. 694-700 - Urs Haberthür, Amedeo Caflisch:
FACTS: Fast analytical continuum treatment of solvation. 701-715 - R. C. Binning Jr., Daniel E. Bacelo:
High-spin versus broken symmetry - Effect of DFT spin density representation on the geometries of three diiron (III) model compounds. 716-723 - Marcel Swart, Friedrich Matthias Bickelhaupt:
QUILD: QUantum-regions interconnected by local descriptions. 724-734 - Yutaka Imamura, Hiroyoshi Kiryu, Hiromi Nakai:
Colle-Salvetti-type correction for electron-nucleus correlation in the nuclear orbital plus molecular orbital theory. 735-740 - Robert M. Whitnell, Dow P. Hurst, Patricia H. Reggio, Frank Guarnieri:
Conformational memories with variable bond angles. 741-752 - Mikael P. Johansson, Ville R. I. Kaila, Liisa Laakkonen:
Charge parameterization of the metal centers in cytochrome c oxidase. 753-767 - Svetlana Stepanenko, Bernd Engels:
New Tabu Search based global optimization methods outline of algorithms and study of efficiency. 768-780 - Zhen Zhou, Jijun Zhao, Paul von Ragué Schleyer, Zhongfang Chen:
Insertion of C50 into single-walled carbon nanotubes: Selectivity in interwall spacing and C50 isomers. 781-787 - Emilio Gallicchio, Ronald M. Levy, Manish Parashar:
Asynchronous replica exchange for molecular simulations. 788-794 - Matteo Masetti, Andrea Cavalli, Maurizio Recanatini:
Modeling the hERG potassium channel in a phospholipid bilayer: Molecular dynamics and drug docking studies. 795-808 - Yue-meng Ji, Xiao-lei Zhao, Jing-Yao Liu, Ying Wang, Ze-Sheng Li:
Theoretical dynamic studies on the reactions of CH3C(O)CH3-nCln (n = 0-3) with the chlorine atom. 809-819 - Mark A. Olson, Michael Feig, Charles L. Brooks III:
Prediction of protein loop conformations using multiscale modeling methods with physical energy scoring functions. 820-831 - Mahmoud Mirzaei, Nasser L. Hadipour:
A computational NQR study on the hydrogen-bonded lattice of cytosine-5-acetic acid. 832-838
- Noel M. O'Boyle, Adam L. Tenderholt, Karol M. Langner:
cclib: A library for package-independent computational chemistry algorithms. 839-845
Volume 29, Number 6, 30 April 2008
- Rainer Grohmann, Torsten Schindler:
Toward robust QSPR models: Synergistic utilization of robust regression and variable elimination. 847-860 - Haydée Valdés, Vojtech Klusák, Michal Pitonák, Otto Exner, Ivo Starý, Pavel Hobza, Lubomír Rulísek:
Evaluation of the intramolecular basis set superposition error in the calculations of larger molecules: [n]helicenes and Phe-Gly-Phe tripeptide. 861-870 - Tatsuhiko Miyata, Fumio Hirata:
Combination of molecular dynamics method and 3D-RISM theory for conformational sampling of large flexible molecules in solution. 871-882 - Huancong Shi, David C. Roettger, Allan L. L. East:
Photochemistry studied with ab initio orbital-correlation and state-correlation plots: Classic cyclobutene ring opening, and the reaction of N2 with photoexcited O2. 883-891 - Fabienne Bessac, Feliu Maseras:
DFT modeling of reactivity in an ionic liquid: How many ion pairs? 892-899 - Kalju Kahn, Iiris Kahn:
Improved efficiency of focal point conformational analysis with truncated correlation consistent basis sets. 900-911 - Sandro Chiodo, Nino Russo:
Determination of spin-orbit coupling contributions in the framework of density functional theory. 912-920 - Denis Jacquemin, Eric A. Perpète, Ilaria Ciofini, Carlo Adamo:
Revisiting the relationship between the bond length alternation and the first hyperpolarizability with range-separated hybrid functionals. 921-925 - C. H. Mak:
RNA conformational sampling. I. Single-nucleotide loop closure. 926-933 - Stefan Duret, Ahmed Bouferguene, Hassan Safouhi:
Strategies for an efficient implementation of the Gauss-Bessel quadrature for the evaluation of multicenter integral over STFs. 934-944 - Lívia B. Pártay, György Hantal, Pál Jedlovszky, Árpád Vincze, George Horvai:
A new method for determining the interfacial molecules and characterizing the surface roughness in computer simulations. Application to the liquid-vapor interface of water. 945-956 - Fabrizio Santoro, Vincenzo Barone, Roberto Improta:
Can TD-DFT calculations accurately describe the excited states behavior of stacked nucleobases? The cytosine dimer as a test case. 957-964 - Deepak Bandyopadhyay, Dimitris K. Agrafiotis:
A self-organizing algorithm for molecular alignment and pharmacophore development. 965-982 - Alicia M. Davis, Gary Joanis, Lorena Tribe:
Molecular modeling of polymer-clay nanocomposite precursors: Lysine in montmorillonite interlayers. 983-987 - Grzegorz Mazur:
An improved SCPF scheme for polarization energy calculations. 988-993 - Núria Queralt, David Taratiel, Coen de Graaf, Rosa Caballol, Renzo Cimiraglia, Celestino Angeli:
On the applicability of multireference second-order perturbation theory to study weak magnetic coupling in molecular complexes. 994-1003 - Sabine Schweizer, Jörg Kussmann, Bernd Doser, Christian Ochsenfeld:
Linear-scaling Cholesky decomposition. 1004-1010 - Christoph R. Jacob, Johannes Neugebauer, Lucas Visscher:
A flexible implementation of frozen-density embedding for use in multilevel simulations. 1011-1018
Volume 29, Number 7, May 2008
- Ross C. Walker, Michael F. Crowley, David A. Case:
The implementation of a fast and accurate QM/MM potential method in Amber. 1019-1031 - Sunil Patil, R. C. Aiyer, K. C. Sharma:
Globally convergent computation of chemical equilibrium composition. 1032-1036 - Mette Alstrup Lie, Birgit Schiøtt:
A DFT study of solvation effects on the tautomeric equilibrium and catalytic ylide generation of thiamin models. 1037-1047 - Sven Lammers, Stephan Lutz, Markus Meuwly:
Reactive force fields for proton transfer dynamics. 1048-1063 - Miquel Torrent-Sucarrat, Pedro Salvador, Miquel Solà, Paul Geerlings:
The hardness kernel as the basis for global and local reactivity indices. 1064-1072 - Woo Youn Kim, Kwang S. Kim:
Carbon nanotube, graphene, nanowire, and molecule-based electron and spin transport phenomena using the nonequilibrium Green's function method at the level of first principles theory. 1073-1083 - Asbjørn Holt, Gunnar Karlström:
An intramolecular induction correction model of the molecular dipole moment. 1084-1091 - Marcel Schmidt am Busch, Anne Lopes, David Mignon, Thomas Simonson:
Computational protein design: Software implementation, parameter optimization, and performance of a simple model. 1092-1102 - Udo Schnupf, Julious L. Willett, Wayne B. Bosma, Frank A. Momany:
DFT conformational studies of alpha-maltotriose. 1103-1112 - Ninad V. Prabhu, Manoranjan Panda, Qingyi Yang, Kim A. Sharp:
Explicit ion, implicit water solvation for molecular dynamics of nucleic acids and highly charged molecules. 1113-1130 - Anthony D. Hill, Peter J. Reilly:
A Gibbs free energy correlation for automated docking of carbohydrates. 1131-1141 - Yang Zhong, G. Lee Warren, Sandeep Patel:
Thermodynamic and structural properties of methanol-water solutions using nonadditive interaction models. 1142-1152