Journal 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
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• József Csontos, Nicholas Y. Palermo, Richard F. Murphy, Sándor Lovas:
  Reply to "Comment on Aromatic-Backbone Interactions in Model alpha-Helical Peptides". 4-7
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• 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
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• Kun Song, Viktor Hornak, Carlos De Los Santos, Arthur P. Grollman, Carlos Simmerling:
  Molecular mechanics parameters for the FapydG DNA lesion. 17-23
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• Lula Rosso, Ian R. Gould:
  Structure and dynamics of phospholipid bilayers using recently developed general all-atom force fields. 24-37
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• 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
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• R. James Milgram, Guanfeng Liu, Jean-Claude Latombe:
  On the structure of the inverse kinematics map of a fragment of protein backbone. 50-68
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• 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
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• Evgenii V. Kovalyov, Vladimir Elokhin, Aleksandr V. Myshlyavtsev:
  Stochastic simulation of physicochemical processes performance over supported metal nanoparticles. 79-86
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• Y. C. Zhou, Michael Feig, G. W. Wei:
  Highly accurate biomolecular electrostatics in continuum dielectric environments. 87-97
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• N. R. Jena, P. S. Kushwaha, P. C. Mishra:
  Reaction of hypochlorous acid with imidazole: Formation of 2-chloro- and 2-oxoimidazoles. 98-107
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• Ewgenij Proschak, Matthias Rupp, Swetlana Derksen, Gisbert Schneider:
  Shapelets: Possibilities and limitations of shape-based virtual screening. 108-114
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• Chinapong Kritayakornupong:
  The Jahn-Teller effect of the Cr²⁺ ion in aqueous solution: Ab initio QM/MM molecular dynamics simulations. 115-121
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• 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
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• A. V. Larin, D. N. Trubnikov, Daniel P. Vercauteren:
  Electric field convergence versus atomic basis sets in all-siliceous zeolites. 130-138
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• Ignacio Fdez. Galván, Martin J. Field:
  Improving the efficiency of the NEB reaction path finding algorithm. 139-143
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• Josep M. Porta, Lluís Ros, Federico Thomas, Francesc Corcho, Josep Cantó, Juan Jesús Pérez:
  Complete maps of molecular-loop conformational spaces. 144-155
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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
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• Florian Weigend:
  Hartree-Fock exchange fitting basis sets for H to Rn. 167-175
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• Weihua Zhu, Heming Xiao:
  Ab initio study of electronic structure and optical properties of heavy-metal azides: TlN₃, AgN₃, and CuN₃. 176-184
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• 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
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• Mark Pinsky, David Casanova, Pere Alemany, Santiago Alvarez, David Avnir, Chaim Dryzun, Ziv Kizner, Alexander Sterkin:
  Symmetry operation measures. 190-197
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• 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
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• 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
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• D. N. Tarasov, R. P. Tiger:
  Numerical computations of molecular reactions in associated systems caused by the formation of fractal structures. 220-224
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• 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
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• Milan Oncák, Martin Srnec:
  Electronic structure and physical properties of M_iX_i clusters (M = B, Al; X = N, P; i = 1, 2, 3): Ab initio study. 233-246
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• Jing Yang, Qian Shu Li, Shaowen Zhang:
  Direct dynamics study on the reaction of acetaldehyde with ozone. 247-255
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• Kun Liu, Wensheng Bian:
  Extensive theoretical study on the low-lying electronic states of silicon monofluoride cation including spin-orbit coupling. 256-265
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• Bahram Hemmateenejad, Afshan Mohajeri:
  Application of quantum topological molecular similarity descriptors in QSPR study of the O-methylation of substituted phenols. 266-274
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• Yun Ding, Ye Mei, John Z. H. Zhang, Fu-Ming Tao:
  Efficient bond function basis set for pi-pi interaction energies. 275-279
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• 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
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• Y. Wei, T. Singer, H. Mayr, G. N. Sastry, H. Zipse:
  Assessment of theoretical methods for the calculation of methyl cation affinities. 291-297
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• Sean A. C. McDowell:
  A comparative study of some red- and blue-shifted linear H-bonded complexes of N₂. 298-305
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• Mohamed Zerara:
  pyVib, a computer program for the analysis of infrared and Raman optical activity. 306-311
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• Willem-Jan Van Zeist, Célia Fonseca Guerra, F. Matthias Bickelhaupt:
  PyFrag - Streamlining your reaction path analysis. 312-315
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Volume 29, Number 3, February 2008

• Yoanna María Alvarez-Ginarte, Yovani Marrero-Ponce, José Alberto Ruiz-García, Luis Alberto Montero-Cabrera, Jose 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
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• Koji Yasuda:
  Two-electron integral evaluation on the graphics processor unit. 334-342
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• Arvids Stashans, Gaston Chamba, Henry Pinto:
  Electronic structure, chemical bonding, and geometry of pure and Sr-doped CaCO₃. 343-349
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• 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
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• Stijn Fias, Sofie Van Damme, Patrick Bultinck:
  Multidimensionality of delocalization indices and nucleus independent chemical shifts in polycyclic aromatic hydrocarbons. 358-366
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• 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
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• P. W. Bates, G. W. Wei, Shan Zhao:
  Minimal molecular surfaces and their applications. 380-391
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• 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
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• 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
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• 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
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• 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
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• Richard J. Wheatley:
  Time-dependent coupled-cluster calculations of polarizabilities and dispersion energy coefficients. 445-450
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• M. Piacenza, F. Della Sala, E. Fabiano, T. Maiolo, G. 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
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• 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
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• 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
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• 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
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• V. Ganesh, Ritwik Kavathekar, Anuja Rahalkar, Shridhar R. Gadre:
  WebProp: Web interface for ab initio calculation of molecular one-electron properties. 488-495
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Volume 29, Number 4, March 2007

• John Cullen:
  An approximate diatomics in molecules formulation of generalized valence bond theory. 497-504
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• Xiao-Wei Fan, Xue-Hai Ju:
  Theoretical studies on four-membered ring compounds with NF₂, ONO₂, N₃, and NO₂ groups. 505-513
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• Jiali Gao, Kin-Yiu Wong, Dan T. 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
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• 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
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• Maykel Cruz-Monteagudo, M. Natália D. S. Cordeiro, Fernanda Borges:
  Computational chemistry approach for the early detection of drug-induced idiosyncratic liver toxicity. 533-549
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• 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
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• Joseph P. Kenny, Curtis L. Janssen, Edward F. Valeev, Theresa L. Windus:
  Components for integral evaluation in quantum chemistry. 562-577
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• Flavio Forti, Xavier Barril, F. Javier Luque, Modesto Orozco:
  Extension of the MST continuum solvation model to the RM1 semiempirical hamiltonian. 578-587
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• M. Leonor Contreras, J. Alvarez, D. Guajardo, Roberto Rozas:
  Understanding topological symmetry: A heuristic approach to its determination. 588-600
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• Aibing Liu, Steven J. Stuart:
  Empirical bond-order potential for hydrocarbons: Adaptive treatment of van der Waals interactions. 601-611
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• 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
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• Karl Nicholas Kirschner, Austin B. Yongye, Sarah M. Tschampel, Jorge González-Outeiriño, Charlisa R. Daniels, B. Lachele Foley, Robert J. Woods:
  GLYCAM06: A generalizable biomolecular force field. Carbohydrates. 622-655
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• 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
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• Wei Yang, Hugh Nymeyer, Huan-Xiang Zhou, Bernd Berg, Rafael Brüschweiler:
  Quantitative computer simulations of biomolecules: A snapshot. 668-672
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