Journal of Computational Chemistry, Volume 25

Volume 25, Number 1, 15 January 2004

• Sandeep Patel, Charles L. Brooks III:
  CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations. 1-16
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• Stewart A. Adcock:
  Peptide backbone reconstruction using dead-end elimination and a knowledge-based forcefield. 16-27
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• Nandou Lu, David A. Kofke, Thomas B. Woolf:
  Improving the efficiency and reliability of free energy perturbation calculations using overlap sampling methods. 28-40
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• Luc Claes, Jean-Pierre François, Michael S. Deleuze:
  Theoretical study of the internal conversion of sulfoxide precursors of poly-isothianaphthene and related polymers. 40-50
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• Haruhiko Fukaya, Taizo Ono:
  DFT-GIAO calculations of 19F NMR chemical shifts for perfluoro compounds. 51-60
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• Michael J. McQuaid, Huai Sun, David Rigby:
  Development and validation of COMPASS force field parameters for molecules with aliphatic azide chains. 61-71
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• Li Sheng, Ze-Sheng Li, Jing-Yao Liu, Jing-Fa Xiao, Chia-Chung Sun:
  Ab initio direct dynamics studies on the reaction of H atom with CH3CH2Cl. 72-82
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• Manuel Piacenza, Stefan Grimme:
  Systematic quantum chemical study of DNA-base tautomers. 83-99
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• Ricard Casadesús, Miquel Moreno, Àngels González-Lafont, José M. Lluch, Matthew P. Repasky:
  Testing electronic structure methods for describing intermolecular H · · · H interactions in supramolecular chemistry. 99-105
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• Takao Motoki, Akinobu Shiga:
  New reaction simulator LUMMOX and its application for prediction of catalytic activities. 106-111
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• Martin Preuss, Wolf G. Schmidt, Kaori Seino, Jürgen Furthmüller, Friedhelm Bechstedt:
  Ground- and excited-state properties of DNA base molecules from plane-wave calculations using ultrasoft pseudopotentials. 112-122
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• Juha Linnanto, Jouko Korppi-Tommola:
  Semiempirical PM5 molecular orbital study on chlorophylls and bacteriochlorophylls: Comparison of semiempirical, ab initio, and density functional results. 123-138
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• Ivan Tubert-Brohman, Cristiano Ruch Werneck Guimarães, Matthew P. Repasky, William L. Jorgensen:
  Extension of the PDDG/PM3 and PDDG/MNDO semiempirical molecular orbital methods to the halogens. 138-150
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• Bülent Balta, Viktorya Aviyente:
  Solvent effects on glycine. I. A supermolecule modeling of tautomerization via intramolecular proton transfer - Erratum. 151
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Volume 25, Number 2, 30 January 2004

• Xavier Gironés, Ramon Carbó-Dorca:
  TGSA-Flex: Extending the capabilities of the Topo-Geometrical superposition algorithm to handle flexible molecules. 153-159
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• Nohad Gresh, Gen-Bin Shi:
  Conformation-dependent intermolecular interaction energies of the triphosphate anion with divalent metal cations. Application to the ATP-binding site of a binuclear bacterial enzyme. A parallel quantum chemical and polarizable molecular mechanics investigation. 160-168
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• Ho-Jin Lee, Jong Hyun Kim, Hee Jung Jung, Kun-Young Kim, Eun-Jung Kim, Young-Sang Choi, Chang-Ju Yoon:
  Computational study of conformational preferences of thioamide-containing azaglycine peptides. 169-178
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• Ayako Nakata, T. Baba, H. Takahashi, Hiromi Nakai:
  Theoretical study on the excited states of psoralen compounds bonded to a thymine residue. 179-188
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• Célia Fonseca Guerra, Jan-Willem Handgraaf, Evert Jan Baerends, F. Matthias Bickelhaupt:
  Voronoi deformation density (VDD) charges: Assessment of the Mulliken, Bader, Hirshfeld, Weinhold, and VDD methods for charge analysis. 189-210
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• Thomas S. Hofer, Hung T. Tran, Christian F. Schwenk, Bernd M. Rode:
  Characterization of dynamics and reactivities of solvated ions by ab initio simulations. 211-217
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• Yue Zhang, Shaowen Zhang, Qian Shu Li:
  A dual-level ab initio and hybrid density functional theory dynamics study on the unimolecular decomposition reaction C2H5O CH2O + CH3. 218-226
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• Susana Pereira, Pedro Alexandrino Fernandes, Maria João Ramos:
  Theoretical study of ribonucleotide reductase mechanism-based inhibition by 2-azido-2-deoxyribonucleoside 5-diphosphates. 227-237
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• Holger Gohlke, David A. Case:
  Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf. 238-250
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• Qian-Shu Li, Chao Yang Wang:
  Direct dynamic study on the hydrogen abstraction reaction CH3CN + OH CH2CN + H2O. 251-257
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• Zheng-Wang Qu, Hui Zhu, Ze-Sheng Li, Xing-Kang Zhang, Qi-Yuan Zhang:
  Density functional investigation of reaction of borohydride cation BH2+ with propylene. 258-264
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• Michael Feig, Alexey Onufriev, Michael S. Lee, Wonpil Im, David A. Case, Charles L. Brooks III:
  Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures. 265-284
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• Tamás Beke, Imre G. Csizmadia, András Perczel:
  On the flexibility of -peptides. 285-307
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• Jean-Philip Piquemal, Benjamin Williams-Hubbard, Natalie Fey, Robert J. Deeth, Nohad Gresh, Claude Giessner-Prettre:
  Inclusion of the ligand field contribution in a polarizable molecular mechanics: SIBFA-LF. 308
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• Yi-Gui Wang, Chérif F. Matta, Nick Henry Werstiuk:
  Comparison of localization and delocalization indices obtained with Hartree-Fock and conventional correlated methods: Effect of Coulomb correlation. 309-459
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Volume 25, Number 3, February 2004

• Vladimir Pelmenschikov, Kyung-Bin Cho, Per E. M. Siegbahn:
  Class I ribonucleotide reductase revisited: The effect of removing a proton on Glu441. 311-321
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• Jennifer I. Chavez, Maira M. Carrillo, Kyle A. Beran:
  Isomers of C20: An energy profile III. 322-327
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• Robert J. Harrison:
  Krylov subspace accelerated inexact Newton method for linear and nonlinear equations. 328-334
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• Jií Kolafa:
  Time-reversible always stable predictor-corrector method for molecular dynamics of polarizable molecules. 335-342
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• Vinzenz Bachler:
  A simple computational scheme for obtaining localized bonding schemes and their weights from a CASSCF wave function. 343-367
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• A. N. Artemyev, Eduardo V. Ludeña, Valentin V. Karasiev, Antonio J. Hernández:
  A finite B-spline basis set for accurate diatomic molecule calculations. 368-374
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• Luca Frediani, Roberto Cammi, Christian Silvio Pomelli, Jacopo Tomasi, Kenneth Ruud:
  New developments in the symmetry-adapted algorithm of the Polarizable Continuum Model. 375-385
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• Ivan Infante, Lucas Visscher:
  QM/MM study of aqueous solvation of the uranyl fluoride [UO2F42-] complex. 386-392
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• Serena Donnini, André H. Juffer:
  Calculation of affinities of peptides for proteins. 393-411
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• Marco Cecchini, Peter Kolb, Nicolas Majeux, Amedeo Caflisch:
  Automated docking of highly flexible ligands by genetic algorithms: A critical assessment. 412-422
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• Li Sheng, Ze-Sheng Li, Jing-Yao Liu, Jing-Fa Xiao, Chia-Chung Sun:
  Theoretical study on the rate constants for the C2H5 + HBr C2H6 + Br reaction. 423-428
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• Rachel Crespo-Otero, Luis A. Montero, Giselle Rosquete, J. Alexander Padrón-García, Raúl H. González-Jonte:
  Theoretical model of internal rotation in monosubstituted derivatives of furfural. 429-438
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• Xavier Fradera, Miquel Solà:
  Second-order atomic Fukui indices from the electron-pair density in the framework of the atoms in molecules theory. 439-446
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• Shingo Urata, Seiji Tsuzuki, Akira Takada, Masuhiro Mikami, Tadafumi Uchimaru, Akira Sekiya:
  Analysis of the intermolecular interactions between CH3OCH3, CF3OCH3, CF3OCF3, and CH2F2, CHF3. 447-459
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• Ayako Nakata, T. Baba, H. Takahashi, Hiromi Nakai:
  Theoretical study on the excited states of psoralen compounds bonded to a thymine residue. 309
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Volume 25, Number 4, March 2004

• Yi Ren, San-Yan Chu:
  Modified Gaussian-2 level investigation of the identity ion-pair SN2 reactions of lithium halide and methyl halide with inversion and retention mechanisms. 461-471
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• Lingchun Song, Wei Wu, Qianer Zhang, Sason Shaik:
  A practical valence bond method: A configuration interaction method approach with perturbation theoretic facility. 472-478
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• Emilio Gallicchio, Ronald M. Levy:
  AGBNP: An analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling. 479-499
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• Xiang-Yuan Li, Ke-Xiang Fu:
  Continuous medium theory for nonequilibrium solvation: I. How to correctly evaluate solvation free energy of nonequilibrium. 500-509
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• Evangelos A. Coutsias, Chaok Seok, Matthew P. Jacobson, Ken A. Dill:
  A kinematic view of loop closure. 510-528
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• Mitsunori Ikeguchi:
  Partial rigid-body dynamics in NPT, NPAT and NPT ensembles for proteins and membranes. 529-541
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• Michael J. Liddell, Davor Margetic, Anthony S. Mitchell, Ronald N. Warrener:
  An AM1 semiempirical study of host-guest complexation in hemicarcerand complexes. 542-557
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• Li Wang, Jing-Yao Liu, Ze-Sheng Li, Chia-Chung Sun:
  Direct ab initio dynamics studies on the hydrogen-abstraction reactions of OH radicals with HOX (X = F, Cl, and Br). 558-564
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• S. Banu Ozkan, Hagai Meirovitch:
  Conformational search of peptides and proteins: Monte Carlo minimization with an adaptive bias method applied to the heptapeptide deltorphin. 565-572
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• Francisco Corzana, Mohammed S. Motawia, Catherine Hervé du Penhoat, Serge Pérez, Sarah M. Tschampel, Robert J. Woods, Søren Balling Engelsen:
  A hydration study of (1->4) and (1->6) linked alpha-glucans by comparative 10 ns molecular dynamics simulations and 500-MHz NMR. 573-586
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• Johannes Neugebauer, Markus Reiher:
  Vibrational center-ligand couplings in transition metal complexes. 587-597
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• Shinichi Yamabe, Noriko Tsuchida:
  A computational study of the role of hydrogen bonds in SN1 and E1 reactions. 598-608
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• Maxim Totrov:
  Accurate and efficient generalized born model based on solvent accessibility: Derivation and application for LogP octanol/water prediction and flexible peptide docking. 609-619
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Volume 25, Number 5, 15 April 2004

• Martin Saunders:
  Stochastic search for isomers on a quantum mechanical surface. 621-626
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• Richard I. Maurer, Christopher A. Reynolds:
  A multilayered approach to approximating solute polarization. 627-631
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• Zheng Yuan, John S. Mattick, Rohan D. Teasdale:
  SVMtm: Support vector machines to predict transmembrane segments. 632-636
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• John Cullen:
  Performance of the Harris functional for extended basis sets at the Hartree-Fock and density functional levels. 637-648
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• Siân T. Howard, Colin D. Abernethy:
  Intramolecular CHCcarbene hydrogen bonds and competing interactions in monoprotonated tripodal carbenes. 649-659
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• Ali Khalaf Al-Matar, David A. Rockstraw:
  A generating equation for mixing rules and two new mixing rules for interatomic potential energy parameters. 660-668
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• Fan Wang, Lemin Li:
  Numerical examination of performance of some exchange-correlation functionals for molecules containing heavy elements. 669-677
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• Michael Patra, Mikko Karttunen:
  Systematic comparison of force fields for microscopic simulations of NaCl in aqueous solutions: Diffusion, free energy of hydration, and structural properties. 678-689
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• Bülent Balta, Viktorya Aviyente:
  Solvent effects on glycine II. Water-assisted tautomerization. 690-703
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• Piotr Zarzycki, Robert Charmas, Pawel Szabelski:
  Study of proton adsorption at heterogeneous oxide/electrolyte interface. Prediction of the surface potential using Monte Carlo simulations and 1-pK approach. 704-711
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• Eran Eyal, Rafael Najmanovich, Brendan J. McConkey, Marvin Edelman, Vladimir Sobolev:
  Importance of solvent accessibility and contact surfaces in modeling side-chain conformations in proteins. 712-724
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• Paul Winget, Timothy Clark:
  Enthalpies of formation from B3LYP calculations. 725-733
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• D. B. Chesnut, L. D. Quin:
  Nature of bonding in the sulfuryl group. 734-738
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• Kazuhiro Ishida:
  Accurate and fast algorithm of the molecular incomplete gamma function with a complex argument. 739-748
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• Harry A. Stern:
  Simple algorithm for isothermal-isobaric molecular dynamics. 749-761
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• M. Michael Gromiha, Shandar Ahmad, Makiko Suwa:
  Neural network-based prediction of transmembrane -strand segments in outer membrane proteins. 762-767
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• M. K. Shukla, Jerzy Leszczynski:
  TDDFT investigation on nucleic acid bases: Comparison with experiments and standard approach. 768-778
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Volume 25, Number 6, 30 April 2004

• Matthias Keil, Thomas E. Exner, Jürgen Brickmann:
  Pattern recognition strategies for molecular surfaces: III. Binding site prediction with a neural network. 779-789
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• David Curcó, Carlos Alemán:
  Performance of SuSi: A method for generating atomistic models of amorphous polymers based on a random search of energy minima. 790-798
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• Rochus Schmid:
  Car-Parrinello simulations with a real space method. 799-812
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• Jun Zeng, Daiqian Xie:
  Hydrogen bonding and solvent effects on the lowest 1(n, *) excitations of triazines in water. 813-822
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• Nohad Gresh, Sherif A. Kafafi, Jean-François Truchon, Dennis R. Salahub:
  Intramolecular interaction energies in model alanine and glycine tetrapeptides. Evaluation of anisotropy, polarization, and correlation effects. A parallel ab initio HF/MP2, DFT, and polarizable molecular mechanics study. 823-834
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• Xiang-Yuan Li, Ke-Xiang Fu, Quan Zhu, Min-Hua Shan:
  Continuous medium theory for nonequilibrium solvation: II. Interaction energy between solute charge and reaction field and single-sphere model for spectral shift. 835-842
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• Jinn-Moon Yang:
  Development and evaluation of a generic evolutionary method for protein-ligand docking. 843-857
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• Ricardo L. Mancera, Per Källblad, Nikolay P. Todorov:
  Ligand-protein docking using a quantum stochastic tunneling optimization method. 858-864
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• Yang Zhang, Jeffrey Skolnick:
  SPICKER: A clustering approach to identify near-native protein folds. 865-871
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• Dmitri G. Fedorov, Ryan M. Olson, Kazuo Kitaura, Mark S. Gordon, Shiro Koseki:
  A new hierarchical parallelization scheme: Generalized distributed data interface (GDDI), and an application to the fragment molecular orbital method (FMO). 872-880
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• Feng Yang, Zhen-Dong Wang, Yun-Ping Huang:
  Modification of the Wiener index 4. 881-887
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• Fabien Pascale, C. M. Zicovich-Wilson, F. López Gejo, Bartolomeo Civalleri, Roberto Orlando, Roberto Dovesi:
  The calculation of the vibrational frequencies of crystalline compounds and its implementation in the CRYSTAL code. 888-897
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Volume 25, Number 7, May 2004

• Harold Basch, Mark A. Ratner:
  Reduced basis set for the gold atom in cluster complexes. 899-906
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• Yi Zhao, Wenguo Xu, Qian-Shu Li, Yaoming Xie, Henry F. Schaefer III:
  The arsenic clusters Asn (n = 1-5) and their anions: Structures, thermochemistry, and electron affinities. 907-920
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• Anatoliy Volkov, Philip Coppens:
  Calculation of electrostatic interaction energies in molecular dimers from atomic multipole moments obtained by different methods of electron density partitioning. 921-934
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• Alexander H. Boschitsch, Marcia O. Fenley:
  Hybrid boundary element and finite difference method for solving the nonlinear Poisson-Boltzmann equation. 935-955
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• Juan Cortés, Thierry Siméon, Magali Remaud-Siméon, Vinh Tran:
  Geometric algorithms for the conformational analysis of long protein loops. 956-967
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• Xiaoping Han, Yue Zhang, Huibin Xu:
  First-principles pair potentials across the metal-ceramic interface. 968-973
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• Massimiliano Aschi, Costantino Zazza, Riccardo Spezia, Cecilia Bossa, Alfredo Di Nola, Maurizio Paci, Andrea Amadei:
  Conformational fluctuations and electronic properties in myoglobin. 974-984
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• Arnaud Blondel:
  Ensemble variance in free energy calculations by thermodynamic integration: Theory, optimal Alchemical path, and practical solutions. 985-993
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• Mihai V. Putz, Nino Russo, Emilia Sicilia:
  On the applicability of the HSAB principle through the use of improved computational schemes for chemical hardness evaluation. 994-1003
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Volume 25, Number 8, June 2004

• Olgun Guvench, Charles L. Brooks III:
  Efficient approximate all-atom solvent accessible surface area method parameterized for folded and denatured protein conformations. 1005-1014
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• Nathalie Basdevant, Daniel Borgis, Tap Ha-Duong:
  A semi-implicit solvent model for the simulation of peptides and proteins. 1015-1029
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• Delano P. Chong, Erik Van Lenthe, Stan J. A. van Gisbergen, Evert Jan Baerends:
  Even-tempered slater-type orbitals revisited: From hydrogen to krypton. 1030-1036
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• Henk Bekker, Jur P. van den Berg, Tsjerk A. Wassenaar:
  A method to obtain a near-minimal-volume molecular simulation of a macromolecule, using periodic boundary conditions and rotational constraints. 1037-1046
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• Anil Kumar, Michaela Knapp-Mohammady, P. C. Mishra, Sándor Suhai:
  A theoretical study of structures and electron affinities of radical anions of guanine-cytosine, adenine-thymine, and hypoxanthine-cytosine base pairs. 1047-1059
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• Arturo Robertazzi, James A. Platts:
  Hydrogen bonding, solvation, and hydrolysis of cisplatin: A theoretical study. 1060-1067
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• Abdallah Sayyed-Ahmad, Kagan Tuncay, Peter J. Ortoleva:
  Efficient solution technique for solving the Poisson-Boltzmann equation. 1068-1074
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• Leslaw K. Bieniasz:
  Improving the accuracy of the spatial discretization in finite-difference electrochemical kinetic simulations, by means of the extended Numerov method. 1075-1083
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• András Perczel, Péter Hudáky, Anna K. Füzéry, Imre G. Csizmadia:
  Stability issues of covalently and noncovalently bonded peptide subunits. 1084-1100
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• Zlatko Vasilkoski, David L. Weaver:
  Diffusion-collision model algorithms for protein folding kinetics. 1101-1107
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Volume 25, Number 9, 15 July 2004

• Publisher's note: Sir John A. Pople, 1925-2004. 1108
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• J. Ulises Reveles, Andreas M. Köster:
  Geometry optimization in density functional methods. 1109-1116
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• Andy Becue, Nathalie Meurice:
  Evaluation of the protein solvent-accessible surface using reduced representations in terms of critical points of the electron density. 1117-1126
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• Kenneth B. Wiberg, Yi-Gui Wang:
  Conformational energies for 2-substituted butanes. 1127-1132
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• Ming Lei, Maria I. Zavodszky, Leslie A. Kuhn, M. F. Thorpe:
  Sampling protein conformations and pathways. 1133-1148
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• Genyuan Li, Jacqueline Schoendorf, Tak-San Ho, Herschel Rabitz:
  Multicut-HDMR with an application to an ionospheric model. 1149-1156
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• Junmei Wang, Romain M. Wolf, James W. Caldwell, Peter A. Kollman, David A. Case:
  Development and testing of a general amber force field. 1157-1174
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• Hiroaki Umeda, Shiro Koseki, Umpei Nagashima:
  Improvement of parallelization performance of GAMESS: Global sum and (semi-)direct integral calculation in multireference perturbation calculation. 1175-1183
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• Jia-Xu Zhang, Jing-Yao Liu, Ze-Sheng Li, Chia-Chung Sun:
  Theoretical study on the mechanism of the 1CHCl + NO2 reactions. 1184-1190
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• Sergio Aragon:
  A precise boundary element method for macromolecular transport properties. 1191-1205
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• Christopher C. Lovallo, Mariusz Klobukowski:
  Improved model core potentials for the second- and third-row transition metals. 1206-1213
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Volume 25, Number 10, 30 July 2004

• Delia Soto-Castro, Patricia Guadarrama:
  Macrocyclic vs. dendrimeric effect. A DFT study. 1215-1226
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• Ignacio Fdez. Galván, M. E. Martín, M. A. Aguilar:
  A new method to locate saddle points for reactions in solution by using the free-energy gradient method and the mean field approximation. 1227-1233
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• David Muñoz, Coen de Graaf, Francesc Illas:
  Putting error bars on the Ab Initio theoretical estimates of the magnetic coupling constants: The parent compounds of superconducting cuprates as a case study. 1234-1241
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• Martin Almlöf, Bjørn O. Brandsdal, Johan Åqvist:
  Binding affinity prediction with different force fields: Examination of the linear interaction energy method. 1242-1254
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• Nisanth N. Nair, Thomas Bredow, Karl Jug:
  Molecular dynamics implementation in MSINDO: Study of silicon clusters. 1255-1263
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• K. Fiaty, C. Charcosset, B. Perrin, R. Couturier, B. Maïsterrena:
  ATP-dependent active transport simulations based on a phosphatase-channel-kinase membrane structure. 1264-1276
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• Wolfgang Quapp:
  Reaction pathways and projection operators: Application to string methods. 1277-1285
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• Susana Pereira, Pedro Alexandrino Fernandes, Maria João Ramos:
  Mechanism for ribonucleotide reductase inactivation by the anticancer drug gemcitabine. 1286-1294
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• Robert M. Dirks, Niles A. Pierce:
  An algorithm for computing nucleic acid base-pairing probabilities including pseudoknots. 1295-1304
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• Gordon M. Crippen:
  Cluster distance geometry of polypeptide chains. 1305-1312
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Volume 25, Number 11, August 2004

• Yuri A. Kosinsky, Pavel E. Volynsky, Philippe Lagant, Gérard Vergoten, Ei-Ichiro Suzuki, Alexander S. Arseniev, Roman G. Efremov:
  Development of the force field parameters for phosphoimidazole and phosphohistidine. 1313-1321
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• Marina Udier-Blagovi, Patricia Morales De Tirado, Shoshannah A. Pearlman, William L. Jorgensen:
  Accuracy of free energies of hydration using CM1 and CM3 atomic charges. 1322-1332
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• Roberto Improta, Vincenzo Barone:
  Assessing the reliability of density functional methods in the conformational study of polypeptides: The treatment of intraresidue nonbonding interactions. 1333-1341
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• Kenneth B. Wiberg:
  Basis set effects on calculated geometries: 6-311++G** vs. aug-cc-pVDZ. 1342-1346
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• Jaime Fernández Rico, R. López, I. Ema, G. Ramírez:
  Electrostatic potentials and fields from density expansions of deformed atoms in molecules. 1347-1354
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• Jaime Fernández Rico, R. López, G. Ramírez, I. Ema, E. V. Ludeña:
  Analytical method for the representation of atoms-in-molecules densities. 1355-1363
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• Bo Liao, Tian-Ming Wang:
  New 2D graphical representation of DNA sequences. 1364-1368
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• Gennady N. Chuev, Maxim V. Fedorov:
  Wavelet algorithm for solving integral equations of molecular liquids. A test for the reference interaction site model. 1369-1377
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• Aisha El-Sherbiny, Raymond A. Poirier:
  An evaluation of the radial part of numerical integration commonly used in DFT. 1378-1384
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• Dawoon Jung, Jie Floyd, Tamara M. Gund:
  A comparative molecular field analysis (CoMFA) study using semiempirical, density functional, ab initio methods and pharmacophore derivation using DISCOtech on sigma 1 ligands. 1385-1399
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• Alexander D. MacKerell Jr., Michael Feig, Charles L. Brooks III:
  Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. 1400-1415
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• Peter A. Sims, Chung F. Wong, James Andrew McCammon:
  Charge optimization of the interface between protein kinases and their ligands. 1416-1429
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Volume 25, Number 12, September 2004

• Yun Xiang, Da W. Zhang, John Z. H. Zhang:
  Fully quantum mechanical energy optimization for protein-ligand structure. 1431-1437
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• Jörg-Rüdiger Hill, Johann Plank:
  Retardation of setting of plaster of Paris by organic acids: Understanding the mechanism through molecular modeling. 1438-1448
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• Hui Li, Jan H. Jensen:
  Improving the efficiency and convergence of geometry optimization with the polarizable continuum model: New energy gradients and molecular surface tessellation. 1449-1462
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• Stefan Grimme:
  Accurate description of van der Waals complexes by density functional theory including empirical corrections. 1463-1473
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• Tim N. Heinz, Philippe H. Hünenberger:
  A fast pairlist-construction algorithm for molecular simulations under periodic boundary conditions. 1474-1486
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• Daiqian Xie, Jun Zeng:
  Hydrogen bonding and solvatochromatic shift of the lowest 1(n, *) excitation of s-tetrazine in its hydrated clusters and dilute solutions. 1487-1495
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• Bahram Hemmateenejad, Mohammad A. Safarpour, Ramin Miri, Fariba Taghavi:
  Application of ab initio theory to QSAR study of 1, 4-dihydropyridine-based calcium channel blockers using GA-MLR and PC-GA-ANN procedures. 1495-1503
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• Sandeep Patel, Alexander D. MacKerell Jr., Charles L. Brooks III:
  CHARMM fluctuating charge force field for proteins: II Protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model. 1504-1514
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• Leslaw K. Bieniasz:
  A fourth-order accurate, Numerov-type, three-point finite-difference discretization of electrochemical reaction-diffusion equations on nonuniform (exponentially expanding) spatial grids in one-dimensional space geometry. 1515-1521
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• Ilona Hudáky, Péter Hudáky, András Perczel:
  Solvation model induced structural changes in peptides. A quantum chemical study on Ramachandran surfaces and conformers of alanine diamide using the polarizable continuum model. 1522-1531
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• Christian Silvio Pomelli:
  A tessellationless integration grid for the polarizable continuum model reaction field. 1532-1541
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• Xavier López, Jorge A. Fernández, Susanna Romo, Jean François Paul, Leonid Kazansky, Josep M. Poblet:
  Are the solvent effects critical in the modeling of polyoxoanions? 1542-1549
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Volume 25, Number 13, October 2004

• Karl Jug, Thomas Bredow:
  Models for the treatment of crystalline solids and surfaces. 1551-1567
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• Holger Merlitz, Thomas Herges, Wolfgang Wenzel:
  Fluctuation analysis and accuracy of a large-scale in silico screen. 1568-1575
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• Chinapong Kritayakornupong, Kristof Plankensteiner, Bernd M. Rode:
  Structure and dynamics of the Cr(III) ion in aqueous solution: Ab initio QM/MM molecular dynamics simulation. 1576-1583
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• Alexander D. MacKerell Jr.:
  Empirical force fields for biological macromolecules: Overview and issues. 1584-1604
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• Eric F. Pettersen, Thomas D. Goddard, Conrad C. Huang, Gregory S. Couch, Daniel M. Greenblatt, Elaine C. Meng, Thomas E. Ferrin:
  UCSF Chimera - A visualization system for exploratory research and analysis. 1605-1612
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• Felix Autenrieth, Emad Tajkhorshid, Jerome Baudry, Zaida Luthey-Schulten:
  Classical force field parameters for the heme prosthetic group of cytochrome c. 1613-1622
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• Jason Wagoner, Nathan A. Baker:
  Solvation forces on biomolecular structures: A comparison of explicit solvent and Poisson-Boltzmann models. 1623-1629
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• Richard E. Gillilan, Ryan H. Lilien:
  Optimization and dynamics of protein-protein complexes using B-splines. 1630-1646
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• Maria Del Carmen Michelini, Nino Russo, Mohammad Esmaïl Alikhani, Bernard Silvi:
  Energetic and topological analysis of the reaction of Mo and Mo2 with NH3, C2H2, and C2H4 molecules. 1647-1655
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• Chris Oostenbrink, Alessandra Villa, Alan E. Mark, Wilfred F. van Gunsteren:
  A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6. 1656-1676
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