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
  
• 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
  
• Y. C. Zhou, Michael Feig, G. W. 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
  
• D. 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 M_iX_i 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. N. 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, F. 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, 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
  
• 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
  
• P. 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
  
• 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
  
• 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 D. S. 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, B. 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, F. 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)CH_3-nCl_n (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. Perpéte, 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
  
• Christina L. Vizcarra, Naigong Zhang, Shannon A. Marshall, Ned S. Wingreen, Chen Zeng, Stephen L. Mayo:
  An improved pairwise decomposable finite-difference Poisson-Boltzmann method for computational protein design. 1153-1162
  
• Elad Project, Esther Nachliel, Menachem Gutman:
  Parameterization of Ca⁺²-protein interactions for molecular dynamics simulations. 1163-1169
  
• Hui Zhang, Guiling Zhang, Jing-Yao Liu, Bo Liu, Xiaoyang Yu, Ze-Sheng Li:
  Theoretical study on the OH + CH₃NHC(O)OCH₃ reaction. 1170-1176
  
• Oliver J. Clarke, Martin J. Parker:
  Time-averaged predictions of folded and misfolded peptides using a reduced physicochemical model. 1177-1185
  

Volume 29, Number 8, June 2008

• Seiken Tokura, Takeshi Sato, Takao Tsuneda, Takahito Nakajima, Kimihiko Hirao:
  A dual-level state-specific time-dependent density-functional theory. 1187-1197
  
• Viktor Bezugly, Pawel Wielgus, Frank R. Wagner, Miroslav Kohout, Yuri Grin:
  Electron localizability indicators ELI and ELIA: The case of highly correlated wavefunctions for the argon atom. 1198-1207
  
• Seung Kyu Min, Eun Cheol Lee, Han Myoung Lee, Dong Young Kim, Dongwook Kim, Kwang S. Kim:
  Complete basis set limit of Ab initio binding energies and geometrical parameters for various typical types of complexes. 1208-1221
  
• Yong Wu, Lu Jin, Ying Xue, Daiqian Xie, Chan Kyung Kim, Yong Guo, Guosen Yan:
  Theoretical study on the hydrolysis mechanism of N, N-dimethyl-N'-(2-oxo-1, 2-dihydro-pyrimidinyl)formamidine: Water-assisted mechanism and cluster-continuum model. 1222-1232
  
• Francisco Rodríguez-Ropero, David Zanuy, Carlos Alemán:
  Molecular dynamics of a calix[4]arene-containing polymer in dichloromethane solution: Ability of the solvent molecules to fill the cavity of the macrocycle. 1233-1241
  
• Alexander G. Donchev, Nikolay G. Galkin, Alexey A. Illarionov, Oleg V. Khoruzhii, Michael A. Olevanov, Vladimir D. Ozrin, Leonid B. Pereyaslavets, Vladimir I. Tarasov:
  Assessment of performance of the general purpose polarizable force field QMPFF3 in condensed phase. 1242-1249
  
• Yong Wu, Ying Xue, Chan Kyung Kim:
  Computational studies on the dimers and the thermal dimerization of norbornadiene. 1250-1258
  
• Ying Xiong, Hai-Ting Lu, Chang-Guo Zhan:
  Dynamic structures of phosphodiesterase-5 active site by combined molecular dynamics simulations and hybrid quantum mechanical/molecular mechanical calculations. 1259-1267
  
• Chen Levi, Jan M. L. Martin, Ilana Bar:
  Fundamental vibrational frequencies and dominant resonances in methylamine isotopologues by ab initio and density functional theory methods. 1268-1276
  
• Maciej Haranczyk, John D. Holliday, Peter Willett, Maciej Gutowski:
  Structure and singly occupied molecular orbital analysis of anionic tautomers of guanine. 1277-1291
  
• Qi Dai, Tian-Ming Wang:
  Use of statistical measures for analyzing RNA secondary structures. 1292-1305
  
• Wai-Leung Yim, Thorsten Klüner:
  Atoms-in-molecules analysis for planewave DFT calculations - A numerical approach on a successively interpolated charge density grid. 1306-1315
  
• Ryangguk Kim, Jeffrey Skolnick:
  Assessment of programs for ligand binding affinity prediction. 1316-1331
  
• Olexander Yakovenko, Alexander A. Oliferenko, Volodymyr G. Bdzhola, Vladimir A. Palyulin, Nikolai S. Zefirov:
  Kirchhoff atomic charges fitted to multipole moments: Implementation for a virtual screening system. 1332-1343
  
• József Csontos, Nicholas Y. Palermo, Richard F. Murphy, Sándor Lovas:
  Calculation of weakly polar interaction energies in polypeptides using density functional and local Møller-Plesset perturbation theory. 1344-1352
  

Volume 29, Number 9, 15 July 2008

• Sophie Barbe, Marc Le Bret:
  Ab initio determination of the flexibility of 2'-aminoribonucleosides and 2'-aminoarabinonucleosides inserted in duplexes. 1353-1363
  
• Yi-yuan Chiu, Jenn-kang Hwang, Jinn-moon Yang:
  Soft energy function and generic evolutionary method for discriminating native from nonnative protein conformations. 1364-1373
  
• Villö K. Pálfi, András Perczel:
  How stable is a collagen triple helix? An ab initio study on various collagen and beta-sheet forming sequences. 1374-1386
  
• Robert Ponec, György Lendvay, Joaquin Chaves:
  Structure and bonding in binuclear metal carbonyls from the analysis of domain averaged Fermi holes. I. Fe₂(CO)₉ and Co₂(CO)₈. 1387-1398
  
• Hajime Hirao:
  A reactive bond orbital investigation of the Diels-Alder reaction between 1, 3-butadiene and ethylene: Energy decomposition, state correlation diagram, and electron density analyses. 1399-1407
  
• Pablo Echenique, José Luis Alonso:
  Efficient model chemistries for peptides. I. General framework and a study of the heterolevel approximation in RHF and MP2 with Pople split-valence basis sets. 1408-1422
  
• Xueye Wang, Hengliang Wang, Yuanqiang Tan:
  DFT study of the cryptand and benzocryptand and their complexes with alkali metal cations: Li⁺, Na⁺, K⁺. 1423-1428
  
• Karine Voltz, Joanna Trylska, Valentina Tozzini, Vandana Kurkal-Siebert, Jörg Langowski, Jeremy C. Smith:
  Coarse-grained force field for the nucleosome from self-consistent multiscaling. 1429-1439
  
• Julien Pilmé, Jean-Philip Piquemal:
  Advancing beyond charge analysis using the electronic localization function: Chemically intuitive distribution of electrostatic moments. 1440-1449
  
• Mauro Ferrero, Michel Rérat, Roberto Orlando, Roberto Dovesi:
  The calculation of static polarizabilities of 1-3D periodic compounds. the implementation in the crystal code. 1450-1459
  
• Piotr Rotkiewicz, Jeffrey Skolnick:
  Fast procedure for reconstruction of full-atom protein models from reduced representations. 1460-1465
  
• József Csontos, Péter Kálmán, Gyula Tasi, Miklós Kálmán, Richard F. Murphy, Sándor Lovas:
  The effect of electron correlation on the conformational space of melatonin. 1466-1471
  
• Laurence Leherte, Daniel P. Vercauteren:
  Collective motions of rigid fragments in protein structures from smoothed electron density distributions. 1472-1489
  
• Asit K. Chandra, Salma Parveen, Subojit Das, Thérèse Zeegers-Huyskens:
  Blue shifts of the C-H stretching vibrations in hydrogen-bonded and protonated trimethylamine. Effect of hyperconjugation on bond properties. 1490-1496
  
• Matthew A. Addicoat, Mark A. Buntine, Brian Yates, Gregory F. Metha:
  Associative versus dissociative binding of CO to 4d transition metal trimers: A density functional study. 1497-1506
  
• Riccardo Chelli, Victor V. Volkov, Roberto Righini:
  Retrieval of spectral and dynamic properties from two-dimensional infrared pump-probe experiments. 1507-1516
  
• Qi Liu, Victor Olman, Huiqing Liu, Xiuzi Ye, Shilun Qiu, Ying Xu:
  RNACluster: An integrated tool for RNA secondary structure comparison and clustering. 1517-1526
  

Volume 29, Number 10, 30 July 2008

• Ivelin Georgiev, Ryan H. Lilien, Bruce Randall Donald:
  The minimized dead-end elimination criterion and its application to protein redesign in a hybrid scoring and search algorithm for computing partition functions over molecular ensembles. 1527-1542
  
• Ferran Feixas, Eduard Matito, Jordi Poater, Miquel Solà:
  On the performance of some aromaticity indices: A critical assessment using a test set. 1543-1554
  
• Yutaka Imamura, Hiromi Nakai:
  Energy density analysis for second-order Møller-Plesset perturbation theory and coupled-cluster theory with singles and doubles: Application to C₂H₄-CH₄ complexes. 1555-1563
  
• Juan Torras, Gustavo de M. Seabra, Erik Deumens, Samuel B. Trickey, Adrian E. Roitberg:
  A versatile AMBER-Gaussian QM/MM interface through PUPIL. 1564-1573
  
• Michal Brylinski, Jeffrey Skolnick:
  Q-Dock: Low-resolution flexible ligand docking with pocket-specific threading restraints. 1574-1588
  
• L. A. Zotti, G. Teobaldi, K. Palotás, W. Ji, H.-J. Gao, W. A. Hofer:
  Adsorption of benzene, fluorobenzene and meta-di-fluorobenzene on Cu(110): A computational study. 1589-1595
  
• Ke Chen, Lukasz A. Kurgan, Jishou Ruan:
  Prediction of protein structural class using novel evolutionary collocation-based sequence representation. 1596-1604
  
• Vladimir Hnizdo, Jun Tan, Benjamin J. Killian, Michael K. Gilson:
  Efficient calculation of configurational entropy from molecular simulations by combining the mutual-information expansion and nearest-neighbor methods. 1605-1614
  
• Pawel Szabelski:
  Spontaneous segregation on a hybrid chiral surface. 1615-1625
  
• Jong Chan Kim, Kyoung Hoon Kim, Jaehoon Jung, Young-Kyu Han:
  Reaction mechanisms of dissociative chemisorption of HI, I₂, and CH₃I on a magic cluster Al^-₁₃. 1626-1631
  
• Yu-Hua Yao, Qi Dai, Xu-Ying Nan, Ping-An He, Zuo-Ming Nie, Song-Ping Zhou, Yao-Zhou Zhang:
  Analysis of similarity/dissimilarity of DNA sequences based on a class of 2D graphical representation. 1632-1639
  
• Thenmalarchelvi Rathinavelan, Wonpil Im:
  A novel strategy to determine protein structures using exclusively residual dipolar coupling. 1640-1649
  
• Qingxu Li, Yuanping Yi, Zhigang Shuai:
  Local approach to coupled cluster evaluation of polarizabilities for long conjugated molecules. 1650-1655
  
• F. Iori, Stefano Corni:
  Including image charge effects in the molecular dynamics simulations of molecules on metal surfaces. 1656-1666
  
• Xiao-Jing Liu, Chuan-Lu Yang, Xiang Zhang, Ke-Li Han, Zi-Chao Tang:
  Theoretical study on the structure and formation mechanism of [C₆H₅M_m]^- (M-Ag, Au; m = 1-3). 1667-1674
  
• Liang-Tsung Huang, M. Michael Gromiha:
  Analysis and prediction of protein folding rates using quadratic response surface models. 1675-1683
  
• David de Sancho, Antonio Rey:
  Energy minimizations with a combination of two knowledge-based potentials for protein folding. 1684-1692
  
• Paul Labute:
  The generalized Born/volume integral implicit solvent model: Estimation of the free energy of hydration using London dispersion instead of atomic surface area. 1693-1698
  

Volume 29, Number 11, August 2008

• Nitin S. Sapre, Nilanjana Pancholi, Swagata Gupta, Neelima Sapre:
  Computational modeling of tetrahydroimidazo-[4, 5, 1-jk][1, 4]-benzodiazepinone derivatives: An atomistic drug design approach using Kier-Hall electrotopological state (E-state) indices. 1699-1706
  
• Michel Masella, Daniel Borgis, Philippe Cuniasse:
  Combining a polarizable force-field and a coarse-grained polarizable solvent model: Application to long dynamics simulations of bovine pancreatic trypsin inhibitor. 1707-1724
  
• Laban Bondesson, Elias Rudberg, Yi Luo, Pawel Salek:
  Basis set dependence of solute-solvent interaction energy of benzene in water: A HF/DFT study. 1725-1732
  
• Alexander G. Donchev:
  Nonadditive effects in ternary H₂-cation-PAH systems. 1733-1739
  
• Luca Monticelli, Eric J. Sorin, D. Peter Tieleman, Vijay S. Pande, Giorgio Colombo:
  Molecular simulation of multistate peptide dynamics: A comparison between microsecond timescale sampling and multiple shorter trajectories. 1740-1752
  
• Max W. Chang, Richard K. Belew, Kate S. Carroll, Arthur J. Olson, David S. Goodsell:
  Empirical entropic contributions in computational docking: Evaluation in APS reductase complexes. 1753-1761
  
• Naigong Zhang, Chen Zeng:
  Reference energy extremal optimization: A stochastic search algorithm applied to computational protein design. 1762-1771
  
• Xueguang Shao, Xiaoli Yang, Wensheng Cai:
  A dynamic lattice searching method with interior operation for unbiased optimization of large Lennard-Jones clusters. 1772-1779
  
• Tian Zhang, Haoping Zheng, Shu Yan:
  The equivalent potential of water for electronic structure of aspartic acid. 1780-1787
  
• Siamkhanthang Neihsial, Richard H. Duncan Lyngdoh:
  Novel H-bonded base dimers as repeat units for information-bearing self-associative duplexes: A B3LYP/6-31G* search. 1788-1797
  
• Ying Zhang, Xin Xu, Yijing Yan:
  Systematic investigation on the geometric dependence of the calculated nuclear magnetic shielding constants. 1798-1807
  
• K. Periya Vijayalakshmi, Cherumuttathu H. Suresh:
  Theoretical studies on the carcinogenicity of polycyclic aromatic hydrocarbons. 1808-1817
  
• Chan Kyung Kim, Soo Gyeong Cho, Chang Kon Kim, Hyung-Yeon Park, Hui Zhang, Hai Whang Lee:
  Prediction of densities for solid energetic molecules with molecular surface electrostatic potentials. 1818-1824
  
• M. Y. Wang, L. Cheng, Z. J. Wu:
  Density functional study on the reaction mechanism of palladium-catalyzed addition of cyanoboranes to alkynes. 1825-1839
  
• Cherumuttathu H. Suresh, Aswathy Mary Vargheese, K. Periya Vijayalakshmi, Neetha Mohan, Nobuaki Koga:
  Role of structural water molecule in HIV protease-inhibitor complexes: A QM/MM study. 1840-1849
  
• Ning He, Hong-Bin Xie, Yi-Hong Ding:
  Structures and stability of lithium monosilicide clusters SiLi_n (n = 4-16): What is the maximum number, magic number, and core number for lithium coordination to silicon? 1850-1858
  
• Sunhwan Jo, Taehoon Kim, Vidyashankara G. Iyer, Wonpil Im:
  CHARMM-GUI: A web-based graphical user interface for CHARMM. 1859-1865
  

Volume 29, Number 12, September 2008

• Xiuzhen Hu, Qianzhong Li:
  Using support vector machine to predict beta- and gamma-turns in proteins. 1867-1875
  
• Witold Dyrka, Andy T. Augousti, Malgorzata Kotulska:
  Ion flux through membrane channels - An enhanced algorithm for the Poisson-Nernst-Planck model. 1876-1888
  
• Fahrettin Gogtas:
  Time-dependent quantum study of the kinetics of the H(²S) + FO(²II) -> OH(²II) + F(²P) reaction. 1889-1894
  
• Timothy J. Giese, Darrin M. York:
  Extension of adaptive tree code and fast multipole methods to high angular momentum particle charge densities. 1895-1904
  
• Asbjørn Holt, Gunnar Karlström:
  Induction correction model for rotation of two or three dihedral angles. 1905-1911
  
• Keiko Shinoda, Wataru Shinoda, Masuhiro Mikami:
  Efficient free energy calculation of water across lipid membranes. 1912-1918
  
• Rong-Zhen Liao, Wan-Jian Ding, Jian-Guo Yu, Wei-Hai Fang, Ruo-Zhuang Liu:
  Theoretical studies on pyridoxal 5'-phosphate-dependent transamination of alpha-amino acids. 1919-1929
  
• Daisuke Katagiri, Hideyoshi Fuji, Saburo Neya, Tyuji Hoshino:
  Ab initio protein structure prediction with force field parameters derived from water-phase quantum chemical calculation. 1930-1944
  
• Pankaj R. Daga, Robert J. Doerksen:
  Stereoelectronic properties of spiroquinazolinones in differential PDE7 inhibitory activity. 1945-1954
  
• Anna Marabotti, Francesca Spyrakis, Angelo M. Facchiano, Pietro Cozzini, Saverio Alberti, Glen E. Kellogg, Andrea Mozzarelli:
  Energy-based prediction of amino acid-nucleotide base recognition. 1955-1969
  
• Magdalena Gruziel, Pawel Grochowski, Joanna Trylska:
  The Poisson-Boltzmann model for tRNA: Assessment of the calculation set-up and ionic concentration cutoff. 1970-1981
  
• Inés Corral, Leticia González:
  Theoretical investigation of anthracene-9, 10-endoperoxide vertical singlet and triplet excitation spectra. 1982-1991
  
• Amit Mor, Guy Ziv, Yaakov Levy:
  Simulations of proteins with inhomogeneous degrees of freedom: The effect of thermostats. 1992-1998
  
• István Komáromi, Michael C. Owen, Richard F. Murphy, Sándor Lovas:
  Development of glycyl radical parameters for the OPLS-AA/L force field. 1999-2009
  
• Guang-Jiu Zhao, Ke-Li Han:
  Time-dependent density functional theory study on hydrogen-bonded intramolecular charge-transfer excited state of 4-dimethylamino-benzonitrile in methanol. 2010-2017
  
• Xuan Xiao, Wei-Zhong Lin, Kuo-Chen Chou:
  Using grey dynamic modeling and pseudo amino acid composition to predict protein structural classes. 2018-2024
  
• Hujun Xie, Ruibo Wu, Fei Xia, Zexing Cao:
  Effects of electron attachment on C_5'-O_5' and C_1'-N₁ bond cleavages of pyrimidine nucleotides: A theoretical study. 2025-2032
  
• Asbjørn Holt, Gunnar Karlström:
  Inclusion of the quadrupole moment when describing polarization. The effect of the dipole-quadrupole polarizability. 2033-2038
  

Volume 29, Number 13, October 2008

• Richard Dronskowski, Gernot Frenking:
  Foreword. 2039-2043
  
• Jürgen Hafner:
  Ab-initio simulations of materials using VASP: Density-functional theory and beyond. 2044-2078
  
• Robert A. Evarestov, Andrei V. Bandura, M. V. Losev, E. A. Kotomin, Yu. F. Zhukovskii, D. Bocharov:
  A first-principles DFT study of UN bulk and (001) surface: Comparative LCAO and PW calculations. 2079-2087
  
• Torsten Kerber, Marek Sierka, Joachim Sauer:
  Application of semiempirical long-range dispersion corrections to periodic systems in density functional theory. 2088-2097
  
• Michael J. Gillan, Dario Alfè, Stefano de Gironcoli, Frederick R. Manby:
  High-precision calculation of Hartree-Fock energy of crystals. 2098-2106
  
• Elena Voloshina, Beate Paulus:
  Cohesive properties of CeN and LaN from first principles. 2107-2112
  
• Cesare Pisani, Lorenzo Maschio, Silvia Casassa, Migen Halo, Martin Schütz, Denis Usvyat:
  Periodic local MP2 method for the study of electronic correlation in crystals: Theory and preliminary applications. 2113-2124
  
• Sheng-Qing Xia, Svilen Bobev:
  Are Ba₁₁Cd₆Sb₁₂ and Sr₁₁Cd₆Sb₁₂ Zintl phases or not? A density-functional theory study. 2125-2133
  
• Jianxiao Xu, Holger Kleinke:
  Unusual Sb-Sb bonding in high temperature thermoelectric materials. 2134-2143
  
• Pere Alemany, Miquel Llunell, Enric Canadell:
  Roles of cations, electronegativity difference, and anionic interlayer interactions in the metallic versus nonmetallic character of Zintl phases related to arsenic. 2144-2153
  
• Changhoon Lee, Myung-Hwan Whangbo, Jürgen Köhler:
  Analysis of electronic structures and chemical bonding of metal-rich compounds. I. Density functional study of Pt metal, LiPt₂, LiPt, and Li₂Pt. 2154-2160
  
• Alexey I. Baranov, Miroslav Kohout:
  Electron localizability for hexagonal element structures. 2161-2171
  
• Dong-Kyun Seo, Sang-Hwan Kim:
  Nature of Stoner condition for metallic ferromagnetism. 2172-2176
  
• German D. Samolyuk, Gordon J. Miller:
  Relation between chemical bonding and exchange coupling approaches to the description of ordering in itinerant magnets. 2177-2186
  
• Dadi Dai, Hongjun Xiang, Myung-Hwan Whangbo:
  Effects of spin-orbit coupling on magnetic properties of discrete and extended magnetic systems. 2187-2209
  
• Daniel Fritsch, Klaus Koepernik, Manuel Richter, Helmut Eschrig:
  Transition metal dimers as potential molecular magnets: A challenge to computational chemistry. 2210-2219
  
• Anderì L. Tchougréeff, Richard Dronskowski:
  A computational study of the crystal and electronic structure of the room temperature organometallic ferromagnet V(TCNE)₂. 2220-2233
  
• C. Richard A. Catlow, Samuel A. French, Alexey A. Sokol, Abdullah A. Al-Sunaidi, Scott M. Woodley:
  Zinc oxide: A case study in contemporary computational solid state chemistry. 2234-2249
  
• Karl Jug, Viatcheslav A. Tikhomirov:
  Influence of intrinsic defects on the properties of zinc oxide. 2250-2254
  
• Atsushi Togo, Peter Kroll:
  First-principles lattice dynamics calculations of the phase boundary between beta-Si₃N₄ and gamma-Si₃N₄ at elevated temperatures and pressures. 2255-2259
  
• Holger Wolff, Richard Dronskowski:
  First-principles and molecular-dynamics study of structure and bonding in perovskite-type oxynitrides ABO₂N (A = Ca, Sr, Ba; B = Ta, Nb). 2260-2267
  
• Claudio M. Zicovich-Wilson, F. J. Torres, Fabien Pascale, L. Valenzano, Roberto Orlando, Roberto Dovesi:
  Ab initio simulation of the IR spectra of pyrope, grossular, and andradite. 2268-2278
  
• Jerome Cuny, Sabri Messaoudi, Veronique Alonzo, Eric Furet, Jean-François Halet, Eric Le Fur, Sharon E. Ashbrook, Chris J. Pickard, Regis Gautier, Laurent Le Polles:
  DFT calculations of quadrupolar solid-state NMR properties: Some examples in solid-state inorganic chemistry. 2279-2287
  
• Lindsay E. Roy, Tomasz Durakiewicz, Richard L. Martin, Juan E. Peralta, Gustavo E. Scuseria, Cliff G. Olson, John J. Joyce, Ela Guziewicz:
  Dispersion in the Mott insulator UO₂: A comparison of photoemission spectroscopy and screened hybrid density functional theory. 2288-2294
  
• Florian Janetzko, Thomas Bredow, Gerald Geudtner, Andreas M. Köster:
  Boron-doped diamond: Investigation of the stability of surface-doping versus bulk-doping using cyclic cluster model calculations. 2295-2301
  
• Ilka Hegemann, Andreas Schwaebe, Karin Fink:
  Adsorption of single Cu atoms at differently stabilized polar ZnO surfaces: An ab initio study. 2302-2310
  

Volume 29, Number 14, 15 November 2008

• Takashi Tsuchimochi, Masato Kobayashi, Ayako Nakata, Yutaka Imamura, Hiromi Nakai:
  Application of the Sakurai-Sugiura projection method to core-excited-state calculation by time-dependent density functional theory. 2311-2316
  
• Masato Morita, Satoshi Yabushita:
  Photoionization cross sections with optimized orbital exponents within the complex basis function method. 2317-2329
  
• Andreas B. Pribil, Thomas S. Hofer, Bernhard R. Randolf, Bernd M. Rode:
  Structure and dynamics of phosphate ion in aqueous solution: An ab initio QMCF MD study. 2330-2334
  
• Daniel R. Fisher, David R. Kent IV, Michael T. Feldmann, William A. Goddard III:
  An optimized initialization algorithm to ensure accuracy in quantum Monte Carlo calculations. 2335-2343
  
• Alexander V. Larin, I. K. Sakodynskaya, D. N. Trubnikov:
  Convergence of electric field and electric field gradient versus atomic basis sets in all-siliceous and Mg substituted phillipsites. 2344-2358
  
• Carl-Johan Högberg, Alexei M. Nikitin, Alexander Lyubartsev:
  Modification of the CHARMM force field for DMPC lipid bilayer. 2359-2369
  
• Zdenek Chval, Miroslav Sip, Jaroslav V. Burda:
  The trans effect in square-planar platinum(II) complexes - A density functional study. 2370-2381
  
• Paraskevas A. Karipidis, Constantinos A. Tsipis:
  The dramatic effect of NH₃ co-ligation on the FE⁺-assisted activation of carbon dioxide in the gas phase: From bare metal ions to complexes. 2382-2396
  
• Lula Rosso, Antony D. Gee, Ian R. Gould:
  Ab initio computational study of positron emission tomography ligands interacting with lipid molecule for the prediction of nonspecific binding. 2397-2405
  
• Gennady N. Chuev, Maxim V. Fedorov, Sandro Chiodo, Nino Russo, Emilia Sicilia:
  Hydration of ionic species studied by the reference interaction site model with a repulsive bridge correction. 2406-2415
  
• Jens Krüger, Wolfgang B. Fischer:
  Exploring the conformational space of Vpu from HIV-1: A versatile adaptable protein. 2416-2424
  
• Karmen Condic-Jurkic, V. Tamara Perchyonok, Hendrik Zipse, David M. Smith:
  On the modeling of arginine-bound carboxylates: A case study with Pyruvate Formate-Lyase. 2425-2433
  
• G. G. Camiletti, S. F. Machado, F. E. Jorge:
  Gaussian basis set of double zeta quality for atoms K through Kr: Application in DFT calculations of molecular properties. 2434-2444
  
• Maykel Cruz-Monteagudo, Fernanda Borges, M. Natália D. S. Cordeiro:
  Desirability-based multiobjective optimization for global QSAR studies: Application to the design of novel NSAIDs with improved analgesic, antiinflammatory, and ulcerogenic profiles. 2445-2459
  
• Carmen Herrmann, Johannes Neugebauer, Markus Reiher:
  QM/MM vibrational mode tracking. 2460-2470
  
• Masato Morita, Satoshi Yabushita:
  Photoionization cross sections of H₂⁺ and H₂ with complex Gaussian-type basis functions optimized for the frequency-dependent polarizabilities. 2471-2478
  
• Jinwoo Lee, Keehyoung Joo, Seung-Yeon Kim, Jooyoung Lee:
  Re-examination of structure optimization of off-lattice protein AB models by conformational space annealing. 2479-2484
  

• Asbjørn Holt, Gunnar Karlström:
  Inclusion of the quadrupole moment when describing polarization. The effect of the dipole-quadrupole polarizability. 2485-2486
  

Volume 29, Number 15, 30 November 2008

• Chin-Hung Lai, Ming-Der Su:
  Theoretical characterizations of HAsXH (X = N, P, As, Sb, and Bi) isomers in the singlet and triplet states. 2487-2499
  
• Juan A. Castillo-Garit, Yovani Marrero-Ponce, Francisco Torrens, Ramón García-Domenech, Vicente Romero-Zaldivar:
  Bond-based 3D-chiral linear indices: Theory and QSAR applications to central chirality codification. 2500-2512
  
• Yajun Liu, Hongyan Xiao, Mengtao Sun, Weihai Fang:
  Spin-orbit Ab initio investigation of the photodissociation of dibromomethane in the gas and solution phases. 2513-2519
  
• Wei Shi, Edward J. Maginn:
  Improvement in molecule exchange efficiency in Gibbs ensemble Monte Carlo: Development and implementation of the continuous fractional component move. 2520-2530
  
• Hirotaka Ode, Yuri Matsuo, Saburo Neya, Tyuji Hoshino:
  Force field parameters for rotation around chi torsion axis in nucleic acids. 2531-2542
  
• Olgun Guvench, Shannon N. Greene, Ganesh Kamath, John W. Brady, Richard M. Venable, Richard W. Pastor, Alexander D. MacKerell Jr.:
  Additive empirical force field for hexopyranose monosaccharides. 2543-2564
  
• Natércia F. Brás, Sara A. Moura-Tamames, Pedro Alexandrino Fernandes, Maria João Ramos:
  Mechanistic studies on the formation of glycosidase-substrate and glycosidase-inhibitor covalent intermediates. 2565-2574
  
• Gernot Kieseritzky, Ernst-Walter Knapp:
  Improved pK_a prediction: Combining empirical and semimicroscopic methods. 2575-2581
  
• P. Poulain, A. Saladin, B. Hartmann, C. Prévost:
  Insights on protein-DNA recognition by coarse grain modelling. 2582-2592
  
• Giovanni Grazioso, Andrea Cavalli, Marco De Amici, Maurizio Recanatini, Carlo De Micheli:
  Alpha7 nicotinic acetylcholine receptor agonists: Prediction of their binding affinity through a molecular mechanics Poisson-Boltzmann surface area approach. 2593-2602
  
• Jakob Schluttig, Michael Bachmann, Wolfhard Janke:
  Comparative molecular dynamics and Monte Carlo study of statistical properties for coarse-grained heteropolymers. 2603-2612
  

Volume 29, Number 16, December 2008

• Santiago Vilar, Humberto González Díaz, Lourdes Santana, Eugenio Uriarte:
  QSAR model for alignment-free prediction of human breast cancer biomarkers based on electrostatic potentials of protein pseudofolding HP-lattice networks. 2613-2622
  
• Yan-Hong Cui, Wei-Quan Tian, Ji-Kang Feng, De-Li Chen:
  Structures, stabilities, electronic, and optical properties of C₆₄ fullerene isomers, anions (C₆₄^2- and C₆₄^4-), metallofullerene Sc₂@C₆₄, and Sc₂C₂@C₆₄. 2623-2630
  
• Lili Sun, Shuwei Tang, Yingfei Chang, Zhanliang Wang, Rongshun Wang:
  Searching for stable hept-C₆₂X₂ (X = F, Cl, and Br): Structures and stabilities of heptagon-containing C₆₂ halogenated derivatives. 2631-2635
  
• Jiazhong Li, Beilei Lei, Huanxiang Liu, Shuyan Li, Xiaojun Yao, Mancang Liu, Paola Gramatica:
  QSAR study of malonyl-CoA decarboxylase inhibitors using GA-MLR and a new strategy of consensus modeling. 2636-2647
  
• Guoming Liang, Xiaoguang Bao, Jiande Gu:
  The possibility of the decomposition of 2'-deoxyribose moiety of thymidine induced by the low energy electron attachment. 2648-2655
  
• Tomonaga Ozawa, Kosuke Okazaki:
  CH/pi hydrogen bonds determine the selectivity of the Src homology 2 domain to tyrosine phosphotyrosyl peptides: An ab initio fragment molecular orbital study. 2656-2666
  
• Mahito Chiba, Dmitri G. Fedorov, Kazuo Kitaura:
  Polarizable continuum model with the fragment molecular orbital-based time-dependent density functional theory. 2667-2676
  
• Karolina Kisowska, Slawomir Berski, Zdzislaw Latajka:
  The structure and chemical bonding in the N₂-CuX and N₂***XCu (X = F, Cl, Br) systems studied by means of the molecular orbital and Quantum Chemical Topology methods. 2677-2692
  
• Valery Andrushchenko, Petr Bour:
  Circular dichroism enhancement in large DNA aggregates simulated by a generalized oscillator model. 2693-2703
  
• María Suárez, Pablo Tortosa, Javier Carrera, Alfonso Jaramillo:
  Pareto optimization in computational protein design with multiple objectives. 2704-2711
  
• Mark Pinsky, Chaim Dryzun, David Casanova, Pere Alemany, David Avnir:
  Analytical methods for calculating Continuous Symmetry Measures and the Chirality Measure. 2712-2721
  
• Norbert Flocke, Victor Lotrich:
  Efficient electronic integrals and their generalized derivatives for object oriented implementations of electronic structure calculations. 2722-2736
  

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