Journal of Computational Chemistry

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Journal of Computational Chemistry

2004

CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations
by: Sandeep Patel, Charles L. Brooks III v. 25 i. 1 p. 1 - 16
Peptide backbone reconstruction using dead-end elimination and a knowledge-based forcefield
by: Stewart A. Adcock v. 25 i. 1 p. 16 - 27
Improving the efficiency and reliability of free energy perturbation calculations using overlap sampling methods
by: Nandou Lu, David A. Kofke, Thomas B. Woolf v. 25 i. 1 p. 28 - 40
Theoretical study of the internal conversion of sulfoxide precursors of poly-isothianaphthene and related polymers
by: Luc Claes, Jean-Pierre François, Michael S. Deleuze v. 25 i. 1 p. 40 - 50
DFT-GIAO calculations of 19F NMR chemical shifts for perfluoro compounds
by: Haruhiko Fukaya, Taizo Ono v. 25 i. 1 p. 51 - 60
Development and validation of COMPASS force field parameters for molecules with aliphatic azide chains
by: Michael J. McQuaid, Huai Sun, David Rigby v. 25 i. 1 p. 61 - 71
Ab initio direct dynamics studies on the reaction of H atom with CH3CH2Cl
by: Li Sheng, Ze-Sheng Li, Jing-Yao Liu, Jing-Fa Xiao, Chia-Chung Sun v. 25 i. 1 p. 72 - 82
Systematic quantum chemical study of DNA-base tautomers
by: Manuel Piacenza, Stefan Grimme v. 25 i. 1 p. 83 - 99
Testing electronic structure methods for describing intermolecular H · · · H interactions in supramolecular chemistry
by: Ricard Casadesús, Miquel Moreno, Àngels González-Lafont, José M. Lluch, Matthew P. Repasky v. 25 i. 1 p. 99 - 105
New reaction simulator LUMMOX and its application for prediction of catalytic activities
by: Takao Motoki, Akinobu Shiga v. 25 i. 1 p. 106 - 111
Ground- and excited-state properties of DNA base molecules from plane-wave calculations using ultrasoft pseudopotentials
by: Martin Preuss, Wolf G. Schmidt, Kaori Seino, Jürgen Furthmüller, Friedhelm Bechstedt v. 25 i. 1 p. 112 - 122
Semiempirical PM5 molecular orbital study on chlorophylls and bacteriochlorophylls: Comparison of semiempirical, ab initio, and density functional results
by: Juha Linnanto, Jouko Korppi-Tommola v. 25 i. 1 p. 123 - 138
Extension of the PDDG/PM3 and PDDG/MNDO semiempirical molecular orbital methods to the halogens
by: Ivan Tubert-Brohman, Cristiano Ruch Werneck Guimarães, Matthew P. Repasky, William L. Jorgensen v. 25 i. 1 p. 138 - 150
Solvent effects on glycine. I. A supermolecule modeling of tautomerization via intramolecular proton transfer - Erratum
by: Bülent Balta, Viktorya Aviyente v. 25 i. 1 p. 151 - 151
TGSA-Flex: Extending the capabilities of the Topo-Geometrical superposition algorithm to handle flexible molecules
by: Xavier Gironés, Ramon Carbó-Dorca v. 25 i. 2 p. 153 - 159
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
by: Nohad Gresh, Gen-Bin Shi v. 25 i. 2 p. 160 - 168
Computational study of conformational preferences of thioamide-containing azaglycine peptides
by: Ho-Jin Lee, Jong Hyun Kim, Hee Jung Jung, Kun-Young Kim, Eun-Jung Kim, Young-Sang Choi, Chang-Ju Yoon v. 25 i. 2 p. 169 - 178
Theoretical study on the excited states of psoralen compounds bonded to a thymine residue
by: A. Nakata, T. Baba, H. Takahashi, H. Nakai v. 25 i. 2 p. 179 - 188
Voronoi deformation density (VDD) charges: Assessment of the Mulliken, Bader, Hirshfeld, Weinhold, and VDD methods for charge analysis
by: Célia Fonseca Guerra, Jan-Willem Handgraaf, Evert Jan Baerends, F. Matthias Bickelhaupt v. 25 i. 2 p. 189 - 210
Characterization of dynamics and reactivities of solvated ions by ab initio simulations
by: Thomas S. Hofer, Hung T. Tran, Christian F. Schwenk, Bernd M. Rode v. 25 i. 2 p. 211 - 217
A dual-level ab initio and hybrid density functional theory dynamics study on the unimolecular decomposition reaction C2H5O CH2O + CH3
by: Yue Zhang, Shaowen Zhang, Qian Shu Li v. 25 i. 2 p. 218 - 226
Theoretical study of ribonucleotide reductase mechanism-based inhibition by 2-azido-2-deoxyribonucleoside 5-diphosphates
by: Susana Pereira, Pedro Alexandrino Fernandes, Maria João Ramos v. 25 i. 2 p. 227 - 237
Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf
by: Holger Gohlke, David A. Case v. 25 i. 2 p. 238 - 250
Direct dynamic study on the hydrogen abstraction reaction CH3CN + OH CH2CN + H2O
by: Qian-Shu Li, Chao Yang Wang v. 25 i. 2 p. 251 - 257
Density functional investigation of reaction of borohydride cation BH2+ with propylene
by: Zheng-Wang Qu, Hui Zhu, Ze-Sheng Li, Xing-Kang Zhang, Qi-Yuan Zhang v. 25 i. 2 p. 258 - 264
Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures
by: Michael Feig, Alexey Onufriev, Michael S. Lee, Wonpil Im, David A. Case, Charles L. Brooks III v. 25 i. 2 p. 265 - 284
On the flexibility of -peptides
by: Tamás Beke, Imre G. Csizmadia, András Perczel v. 25 i. 2 p. 285 - 307
Inclusion of the ligand field contribution in a polarizable molecular mechanics: SIBFA-LF
by: Jean-Philip Piquemal, Ben Williams-Hubbard, Natalie Fey, Robert J. Deeth, Nohad Gresh, Claude Giessner-Prettre v. 25 i. 2 p. 308 - 308
Comparison of localization and delocalization indices obtained with Hartree-Fock and conventional correlated methods: Effect of Coulomb correlation
by: Yi-Gui Wang, Cherif F. Matta, Nick Henry Werstiuk v. 25 i. 2 p. 309 - 459
Theoretical study on the excited states of psoralen compounds bonded to a thymine residue
by: A. Nakata, T. Baba, H. Takahashi, H. Nakai v. 25 i. 3 p. 309 - 309
Class I ribonucleotide reductase revisited: The effect of removing a proton on Glu441
by: Vladimir Pelmenschikov, Kyung-Bin Cho, Per E. M. Siegbahn v. 25 i. 3 p. 311 - 321
Isomers of C20: An energy profile III
by: Jennifer I. Chavez, Maira M. Carrillo, Kyle A. Beran v. 25 i. 3 p. 322 - 327
Krylov subspace accelerated inexact Newton method for linear and nonlinear equations
by: Robert J. Harrison v. 25 i. 3 p. 328 - 334
Time-reversible always stable predictor-corrector method for molecular dynamics of polarizable molecules
by: Jií Kolafa v. 25 i. 3 p. 335 - 342
A simple computational scheme for obtaining localized bonding schemes and their weights from a CASSCF wave function
by: Vinzenz Bachler v. 25 i. 3 p. 343 - 367
A finite B-spline basis set for accurate diatomic molecule calculations
by: A. N. Artemyev, Eduardo V. Ludeña, Valentin V. Karasiev, Antonio J. Hernández v. 25 i. 3 p. 368 - 374
New developments in the symmetry-adapted algorithm of the Polarizable Continuum Model
by: Luca Frediani, Roberto Cammi, Christian Silvio Pomelli, Jacopo Tomasi, Kenneth Ruud v. 25 i. 3 p. 375 - 385
QM/MM study of aqueous solvation of the uranyl fluoride [UO2F42-] complex
by: Ivan Infante, Lucas Visscher v. 25 i. 3 p. 386 - 392
Calculation of affinities of peptides for proteins
by: Serena Donnini, André H. Juffer v. 25 i. 3 p. 393 - 411
Automated docking of highly flexible ligands by genetic algorithms: A critical assessment
by: Marco Cecchini, Peter Kolb, Nicolas Majeux, Amedeo Caflisch v. 25 i. 3 p. 412 - 422
Theoretical study on the rate constants for the C2H5 + HBr C2H6 + Br reaction
by: Li Sheng, Ze-Sheng Li, Jing-Yao Liu, Jing-Fa Xiao, Chia-Chung Sun v. 25 i. 3 p. 423 - 428
Theoretical model of internal rotation in monosubstituted derivatives of furfural
by: Rachel Crespo-Otero, Luis A. Montero, Giselle Rosquete, J. Alexander Padrón-García, Raúl H. González-Jonte v. 25 i. 3 p. 429 - 438
Second-order atomic Fukui indices from the electron-pair density in the framework of the atoms in molecules theory
by: Xavier Fradera, Miquel Solà v. 25 i. 3 p. 439 - 446
Analysis of the intermolecular interactions between CH3OCH3, CF3OCH3, CF3OCF3, and CH2F2, CHF3
by: Shingo Urata, Seiji Tsuzuki, Akira Takada, Masuhiro Mikami, Tadafumi Uchimaru, Akira Sekiya v. 25 i. 3 p. 447 - 459
Modified Gaussian-2 level investigation of the identity ion-pair SN2 reactions of lithium halide and methyl halide with inversion and retention mechanisms
by: Yi Ren, San-Yan Chu v. 25 i. 4 p. 461 - 471
A practical valence bond method: A configuration interaction method approach with perturbation theoretic facility
by: Lingchun Song, Wei Wu, Qianer Zhang, Sason Shaik v. 25 i. 4 p. 472 - 478
AGBNP: An analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling
by: Emilio Gallicchio, Ronald M. Levy v. 25 i. 4 p. 479 - 499
Continuous medium theory for nonequilibrium solvation: I. How to correctly evaluate solvation free energy of nonequilibrium
by: Xiang-Yuan Li, Ke-Xiang Fu v. 25 i. 4 p. 500 - 509
A kinematic view of loop closure
by: Evangelos A. Coutsias, Chaok Seok, Matthew P. Jacobson, Ken A. Dill v. 25 i. 4 p. 510 - 528
Partial rigid-body dynamics in NPT, NPAT and NPT ensembles for proteins and membranes
by: Mitsunori Ikeguchi v. 25 i. 4 p. 529 - 541
An AM1 semiempirical study of host-guest complexation in hemicarcerand complexes
by: Michael J. Liddell, Davor Margetic, Anthony S. Mitchell, Ronald N. Warrener v. 25 i. 4 p. 542 - 557
Direct ab initio dynamics studies on the hydrogen-abstraction reactions of OH radicals with HOX (X = F, Cl, and Br)
by: Li Wang, Jing-Yao Liu, Ze-Sheng Li, Chia-Chung Sun v. 25 i. 4 p. 558 - 564
Conformational search of peptides and proteins: Monte Carlo minimization with an adaptive bias method applied to the heptapeptide deltorphin
by: S. Banu Ozkan, Hagai Meirovitch v. 25 i. 4 p. 565 - 572
A hydration study of (1-&gt4) and (1-&gt6) linked alpha-glucans by comparative 10 ns molecular dynamics simulations and 500-MHz NMR
by: Francisco Corzana, Mohammed S. Motawia, Catherine Hervé du Penhoat, Serge Pérez, Sarah M. Tschampel, Robert J. Woods, Søren Balling Engelsen v. 25 i. 4 p. 573 - 586
Vibrational center-ligand couplings in transition metal complexes
by: Johannes Neugebauer, Markus Reiher v. 25 i. 4 p. 587 - 597
A computational study of the role of hydrogen bonds in SN1 and E1 reactions
by: Shinichi Yamabe, Noriko Tsuchida v. 25 i. 4 p. 598 - 608
Accurate and efficient generalized born model based on solvent accessibility: Derivation and application for LogP octanol/water prediction and flexible peptide docking
by: Maxim Totrov v. 25 i. 4 p. 609 - 619
Stochastic search for isomers on a quantum mechanical surface
by: Martin Saunders v. 25 i. 5 p. 621 - 626
A multilayered approach to approximating solute polarization
by: Richard I. Maurer, Christopher A. Reynolds v. 25 i. 5 p. 627 - 631
SVMtm: Support vector machines to predict transmembrane segments
by: Zheng Yuan, John S. Mattick, Rohan D. Teasdale v. 25 i. 5 p. 632 - 636
Performance of the Harris functional for extended basis sets at the Hartree-Fock and density functional levels
by: John Cullen v. 25 i. 5 p. 637 - 648
Intramolecular CHCcarbene hydrogen bonds and competing interactions in monoprotonated tripodal carbenes
by: Siân T. Howard, Colin D. Abernethy v. 25 i. 5 p. 649 - 659
A generating equation for mixing rules and two new mixing rules for interatomic potential energy parameters
by: Ali Khalaf Al-Matar, David A. Rockstraw v. 25 i. 5 p. 660 - 668
Numerical examination of performance of some exchange-correlation functionals for molecules containing heavy elements
by: Fan Wang, Lemin Li v. 25 i. 5 p. 669 - 677
Systematic comparison of force fields for microscopic simulations of NaCl in aqueous solutions: Diffusion, free energy of hydration, and structural properties
by: Michael Patra, Mikko Karttunen v. 25 i. 5 p. 678 - 689
Solvent effects on glycine II. Water-assisted tautomerization
by: Bülent Balta, Viktorya Aviyente v. 25 i. 5 p. 690 - 703
Study of proton adsorption at heterogeneous oxide/electrolyte interface. Prediction of the surface potential using Monte Carlo simulations and 1-pK approach
by: P. Zarzycki, R. Charmas, P. Szabelski v. 25 i. 5 p. 704 - 711
Importance of solvent accessibility and contact surfaces in modeling side-chain conformations in proteins
by: Eran Eyal, Rafael Najmanovich, Brendan J. Mcconkey, Marvin Edelman, Vladimir Sobolev v. 25 i. 5 p. 712 - 724
Enthalpies of formation from B3LYP calculations
by: Paul Winget, Timothy Clark v. 25 i. 5 p. 725 - 733
Nature of bonding in the sulfuryl group
by: D. B. Chesnut, L. D. Quin v. 25 i. 5 p. 734 - 738
Accurate and fast algorithm of the molecular incomplete gamma function with a complex argument
by: Kazuhiro Ishida v. 25 i. 5 p. 739 - 748
Simple algorithm for isothermal-isobaric molecular dynamics
by: Harry A. Stern v. 25 i. 5 p. 749 - 761
Neural network-based prediction of transmembrane -strand segments in outer membrane proteins
by: M. Michael Gromiha, Shandar Ahmad, Makiko Suwa v. 25 i. 5 p. 762 - 767
TDDFT investigation on nucleic acid bases: Comparison with experiments and standard approach
by: M. K. Shukla, Jerzy Leszczynski v. 25 i. 5 p. 768 - 778
Pattern recognition strategies for molecular surfaces: III. Binding site prediction with a neural network
by: Matthias Keil, Thomas E. Exner, Jürgen Brickmann v. 25 i. 6 p. 779 - 789
Performance of SuSi: A method for generating atomistic models of amorphous polymers based on a random search of energy minima
by: David Curcó, Carlos Alemán v. 25 i. 6 p. 790 - 798
Car-Parrinello simulations with a real space method
by: Rochus Schmid v. 25 i. 6 p. 799 - 812
Hydrogen bonding and solvent effects on the lowest 1(n, *) excitations of triazines in water
by: Jun Zeng, Daiqian Xie v. 25 i. 6 p. 813 - 822
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
by: Nohad Gresh, Sherif A. Kafafi, Jean-François Truchon, Dennis R. Salahub v. 25 i. 6 p. 823 - 834
Continuous medium theory for nonequilibrium solvation: II. Interaction energy between solute charge and reaction field and single-sphere model for spectral shift
by: Xiang-Yuan Li, Ke-Xiang Fu, Quan Zhu, Min-Hua Shan v. 25 i. 6 p. 835 - 842
Development and evaluation of a generic evolutionary method for protein-ligand docking
by: Jinn-Moon Yang v. 25 i. 6 p. 843 - 857
Ligand-protein docking using a quantum stochastic tunneling optimization method
by: Ricardo L. Mancera, Per Källblad, Nikolay P. Todorov v. 25 i. 6 p. 858 - 864
SPICKER: A clustering approach to identify near-native protein folds
by: Yang Zhang, Jeffrey Skolnick v. 25 i. 6 p. 865 - 871
A new hierarchical parallelization scheme: Generalized distributed data interface (GDDI), and an application to the fragment molecular orbital method (FMO)
by: Dmitri G. Fedorov, Ryan M. Olson, Kazuo Kitaura, Mark S. Gordon, Shiro Koseki v. 25 i. 6 p. 872 - 880
Modification of the Wiener index 4
by: Feng Yang, Zhen-Dong Wang, Yun-Ping Huang v. 25 i. 6 p. 881 - 887
The calculation of the vibrational frequencies of crystalline compounds and its implementation in the CRYSTAL code
by: Fabien Pascale, C. M. Zicovich-Wilson, F. López Gejo, Bartolomeo Civalleri, Roberto Orlando, Roberto Dovesi v. 25 i. 6 p. 888 - 897
Reduced basis set for the gold atom in cluster complexes
by: Harold Basch, Mark A. Ratner v. 25 i. 7 p. 899 - 906
The arsenic clusters Asn (n = 1-5) and their anions: Structures, thermochemistry, and electron affinities
by: Yi Zhao, Wenguo Xu, Qianshu Li, Yaoming Xie, Henry F. Schaefer III v. 25 i. 7 p. 907 - 920
Calculation of electrostatic interaction energies in molecular dimers from atomic multipole moments obtained by different methods of electron density partitioning
by: Anatoliy Volkov, Philip Coppens v. 25 i. 7 p. 921 - 934
Hybrid boundary element and finite difference method for solving the nonlinear Poisson-Boltzmann equation
by: Alexander H. Boschitsch, Marcia O. Fenley v. 25 i. 7 p. 935 - 955
Geometric algorithms for the conformational analysis of long protein loops
by: Juan Cortés, Thierry Siméon, Magali Remaud-Siméon, Vinh Tran v. 25 i. 7 p. 956 - 967
First-principles pair potentials across the metal-ceramic interface
by: Xiaoping Han, Yue Zhang, Huibin Xu v. 25 i. 7 p. 968 - 973
Conformational fluctuations and electronic properties in myoglobin
by: Massimiliano Aschi, Costantino Zazza, Riccardo Spezia, Cecilia Bossa, Alfredo Di Nola, Maurizio Paci, Andrea Amadei v. 25 i. 7 p. 974 - 984
Ensemble variance in free energy calculations by thermodynamic integration: Theory, optimal Alchemical path, and practical solutions
by: Arnaud Blondel v. 25 i. 7 p. 985 - 993
On the applicability of the HSAB principle through the use of improved computational schemes for chemical hardness evaluation
by: Mihai V. Putz, Nino Russo, Emilia Sicilia v. 25 i. 7 p. 994 - 1003
Efficient approximate all-atom solvent accessible surface area method parameterized for folded and denatured protein conformations
by: Olgun Guvench, Charles L. Brooks III v. 25 i. 8 p. 1005 - 1014
A semi-implicit solvent model for the simulation of peptides and proteins
by: Nathalie Basdevant, Daniel Borgis, Tap Ha-Duong v. 25 i. 8 p. 1015 - 1029
Even-tempered slater-type orbitals revisited: From hydrogen to krypton
by: Delano P. Chong, Erik Van Lenthe, Stan Van Gisbergen, Evert Jan Baerends v. 25 i. 8 p. 1030 - 1036
A method to obtain a near-minimal-volume molecular simulation of a macromolecule, using periodic boundary conditions and rotational constraints
by: Henk Bekker, Jur P. van den Berg, Tsjerk A. Wassenaar v. 25 i. 8 p. 1037 - 1046
A theoretical study of structures and electron affinities of radical anions of guanine-cytosine, adenine-thymine, and hypoxanthine-cytosine base pairs
by: Anil Kumar, Michaela Knapp-Mohammady, P. C. Mishra, Sándor Suhai v. 25 i. 8 p. 1047 - 1059
Hydrogen bonding, solvation, and hydrolysis of cisplatin: A theoretical study
by: Arturo Robertazzi, James A. Platts v. 25 i. 8 p. 1060 - 1067
Efficient solution technique for solving the Poisson-Boltzmann equation
by: Abdallah Sayyed-Ahmad, Kagan Tuncay, Peter J. Ortoleva v. 25 i. 8 p. 1068 - 1074
Improving the accuracy of the spatial discretization in finite-difference electrochemical kinetic simulations, by means of the extended Numerov method
by: Leslaw K. Bieniasz v. 25 i. 8 p. 1075 - 1083
Stability issues of covalently and noncovalently bonded peptide subunits
by: András Perczel, Péter Hudáky, Anna K. Füzéry, Imre G. Csizmadia v. 25 i. 8 p. 1084 - 1100
Diffusion-collision model algorithms for protein folding kinetics
by: Zlatko Vasilkoski, David L. Weaver v. 25 i. 8 p. 1101 - 1107
Publisher's note: Sir John A. Pople, 1925-2004
v. 25 i. 9 p. 1108 - 1108
Geometry optimization in density functional methods
by: J. Ulises Reveles, Andreas M. Köster v. 25 i. 9 p. 1109 - 1116
Evaluation of the protein solvent-accessible surface using reduced representations in terms of critical points of the electron density
by: A. Becue, N. Meurice v. 25 i. 9 p. 1117 - 1126
Conformational energies for 2-substituted butanes
by: Kenneth B. Wiberg, Yi-Gui Wang v. 25 i. 9 p. 1127 - 1132
Sampling protein conformations and pathways
by: Ming Lei, Maria I. Zavodszky, Leslie A. Kuhn, M. F. Thorpe v. 25 i. 9 p. 1133 - 1148
Multicut-HDMR with an application to an ionospheric model
by: Genyuan Li, Jacqueline Schoendorf, Tak-San Ho, Herschel Rabitz v. 25 i. 9 p. 1149 - 1156
Development and testing of a general amber force field
by: Junmei Wang, Romain M. Wolf, James W. Caldwell, Peter A. Kollman, David A. Case v. 25 i. 9 p. 1157 - 1174
Improvement of parallelization performance of GAMESS: Global sum and (semi-)direct integral calculation in multireference perturbation calculation
by: Hiroaki Umeda, Shiro Koseki, Umpei Nagashima v. 25 i. 9 p. 1175 - 1183
Theoretical study on the mechanism of the 1CHCl + NO2 reactions
by: Jia-Xu Zhang, Jing-Yao Liu, Ze-Sheng Li, Chia-Chung Sun v. 25 i. 9 p. 1184 - 1190
A precise boundary element method for macromolecular transport properties
by: Sergio Aragon v. 25 i. 9 p. 1191 - 1205
Improved model core potentials for the second- and third-row transition metals
by: Christopher C. Lovallo, Mariusz Klobukowski v. 25 i. 9 p. 1206 - 1213
Macrocyclic vs. dendrimeric effect. A DFT study
by: Delia Soto-Castro, Patricia Guadarrama v. 25 i. 10 p. 1215 - 1226
A new method to locate saddle points for reactions in solution by using the free-energy gradient method and the mean field approximation
by: I. Fdez. Galván, M. E. Martín, M. A. Aguilar v. 25 i. 10 p. 1227 - 1233
Putting error bars on the Ab Initio theoretical estimates of the magnetic coupling constants: The parent compounds of superconducting cuprates as a case study
by: David Muñoz, Coen De Graaf, Francesc Illas v. 25 i. 10 p. 1234 - 1241
Binding affinity prediction with different force fields: Examination of the linear interaction energy method
by: Martin Almlöf, Bjørn O. Brandsdal, Johan Âqvist v. 25 i. 10 p. 1242 - 1254
Molecular dynamics implementation in MSINDO: Study of silicon clusters
by: Nisanth N. Nair, Thomas Bredow, Karl Jug v. 25 i. 10 p. 1255 - 1263
ATP-dependent active transport simulations based on a phosphatase-channel-kinase membrane structure
by: K. Fiaty, C. Charcosset, B. Perrin, R. Couturier, B. Maïsterrena v. 25 i. 10 p. 1264 - 1276
Reaction pathways and projection operators: Application to string methods
by: Wolfgang Quapp v. 25 i. 10 p. 1277 - 1285
Mechanism for ribonucleotide reductase inactivation by the anticancer drug gemcitabine
by: Susana Pereira, Pedro Alexandrino Fernandes, Maria João Ramos v. 25 i. 10 p. 1286 - 1294
An algorithm for computing nucleic acid base-pairing probabilities including pseudoknots
by: Robert M. Dirks, Niles A. Pierce v. 25 i. 10 p. 1295 - 1304
Cluster distance geometry of polypeptide chains
by: Gordon M. Crippen v. 25 i. 10 p. 1305 - 1312
Development of the force field parameters for phosphoimidazole and phosphohistidine
by: Yuri A. Kosinsky, Pavel E. Volynsky, Philippe Lagant, Gerard Vergoten, Ei-Ichiro Suzuki, Alexander S. Arseniev, Roman G. Efremov v. 25 i. 11 p. 1313 - 1321
Accuracy of free energies of hydration using CM1 and CM3 atomic charges
by: Marina Udier-Blagovi, Patricia Morales De Tirado, Shoshannah A. Pearlman, William L. Jorgensen v. 25 i. 11 p. 1322 - 1332
Assessing the reliability of density functional methods in the conformational study of polypeptides: The treatment of intraresidue nonbonding interactions
by: Roberto Improta, Vincenzo Barone v. 25 i. 11 p. 1333 - 1341
Basis set effects on calculated geometries: 6-311++G** vs. aug-cc-pVDZ
by: Kenneth B. Wiberg v. 25 i. 11 p. 1342 - 1346
Electrostatic potentials and fields from density expansions of deformed atoms in molecules
by: Jaime Fernández Rico, R. López, I. Ema, G. Ramírez v. 25 i. 11 p. 1347 - 1354
Analytical method for the representation of atoms-in-molecules densities
by: Jaime Fernández Rico, R. López, G. Ramírez, I. Ema, E. V. Ludeña v. 25 i. 11 p. 1355 - 1363
New 2D graphical representation of DNA sequences
by: Bo Liao, Tian-Ming Wang v. 25 i. 11 p. 1364 - 1368
Wavelet algorithm for solving integral equations of molecular liquids. A test for the reference interaction site model
by: Gennady N. Chuev, Maxim V. Fedorov v. 25 i. 11 p. 1369 - 1377
An evaluation of the radial part of numerical integration commonly used in DFT
by: Aisha El-Sherbiny, Raymond A. Poirier v. 25 i. 11 p. 1378 - 1384
A comparative molecular field analysis (CoMFA) study using semiempirical, density functional, ab initio methods and pharmacophore derivation using DISCOtech on sigma 1 ligands
by: Dawoon Jung, Jie Floyd, Tamara M. Gund v. 25 i. 11 p. 1385 - 1399
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
by: Alexander D. MacKerell Jr., Michael Feig, Charles L. Brooks III v. 25 i. 11 p. 1400 - 1415
Charge optimization of the interface between protein kinases and their ligands
by: Peter A. Sims, Chung F. Wong, J. Andrew McCammon v. 25 i. 11 p. 1416 - 1429
Fully quantum mechanical energy optimization for protein-ligand structure
by: Yun Xiang, Da W. Zhang, John Z. H. Zhang v. 25 i. 12 p. 1431 - 1437
Retardation of setting of plaster of Paris by organic acids: Understanding the mechanism through molecular modeling
by: Jörg-Rüdiger Hill, Johann Plank v. 25 i. 12 p. 1438 - 1448
Improving the efficiency and convergence of geometry optimization with the polarizable continuum model: New energy gradients and molecular surface tessellation
by: Hui Li, Jan H. Jensen v. 25 i. 12 p. 1449 - 1462
Accurate description of van der Waals complexes by density functional theory including empirical corrections
by: Stefan Grimme v. 25 i. 12 p. 1463 - 1473
A fast pairlist-construction algorithm for molecular simulations under periodic boundary conditions
by: Tim N. Heinz, Philippe H. Hünenberger v. 25 i. 12 p. 1474 - 1486
Hydrogen bonding and solvatochromatic shift of the lowest 1(n, *) excitation of s-tetrazine in its hydrated clusters and dilute solutions
by: Daiqian Xie, Jun Zeng v. 25 i. 12 p. 1487 - 1495
Application of ab initio theory to QSAR study of 1, 4-dihydropyridine-based calcium channel blockers using GA-MLR and PC-GA-ANN procedures
by: Bahram Hemmateenejad, Mohammad A. Safarpour, Ramin Miri, Fariba Taghavi v. 25 i. 12 p. 1495 - 1503
CHARMM fluctuating charge force field for proteins: II Protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model
by: Sandeep Patel, Alexander D. MacKerell Jr., Charles L. Brooks III v. 25 i. 12 p. 1504 - 1514
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
by: Leslaw K. Bieniasz v. 25 i. 12 p. 1515 - 1521
Solvation model induced structural changes in peptides. A quantum chemical study on Ramachandran surfaces and conformers of alanine diamide using the polarizable continuum model
by: Ilona Hudáky, Péter Hudáky, András Perczel v. 25 i. 12 p. 1522 - 1531
A tessellationless integration grid for the polarizable continuum model reaction field
by: Christian Silvio Pomelli v. 25 i. 12 p. 1532 - 1541
Are the solvent effects critical in the modeling of polyoxoanions?
by: Xavier López, Jorge A. Fernández, Susanna Romo, Jean François Paul, Leonid Kazansky, Josep M. Poblet v. 25 i. 12 p. 1542 - 1549
Models for the treatment of crystalline solids and surfaces
by: Karl Jug, Thomas Bredow v. 25 i. 13 p. 1551 - 1567
Fluctuation analysis and accuracy of a large-scale in silico screen
by: H. Merlitz, T. Herges, W. Wenzel v. 25 i. 13 p. 1568 - 1575
Structure and dynamics of the Cr(III) ion in aqueous solution: Ab initio QM/MM molecular dynamics simulation
by: Chinapong Kritayakornupong, Kristof Plankensteiner, Bernd M. Rode v. 25 i. 13 p. 1576 - 1583
Empirical force fields for biological macromolecules: Overview and issues
by: Alexander D. MacKerell Jr. v. 25 i. 13 p. 1584 - 1604
UCSF Chimera - A visualization system for exploratory research and analysis
by: Eric F. Pettersen, Thomas D. Goddard, Conrad C. Huang, Gregory S. Couch, Daniel M. Greenblatt, Elaine C. Meng, Thomas E. Ferrin v. 25 i. 13 p. 1605 - 1612
Classical force field parameters for the heme prosthetic group of cytochrome c
by: Felix Autenrieth, Emad Tajkhorshid, Jerome Baudry, Zaida Luthey-Schulten v. 25 i. 13 p. 1613 - 1622
Solvation forces on biomolecular structures: A comparison of explicit solvent and Poisson-Boltzmann models
by: Jason Wagoner, Nathan A. Baker v. 25 i. 13 p. 1623 - 1629
Optimization and dynamics of protein-protein complexes using B-splines
by: Richard E. Gillilan, Ryan H. Lilien v. 25 i. 13 p. 1630 - 1646
Energetic and topological analysis of the reaction of Mo and Mo2 with NH3, C2H2, and C2H4 molecules
by: Maria Del Carmen Michelini, Nino Russo, Mohammad Esmaïl Alikhani, Bernard Silvi v. 25 i. 13 p. 1647 - 1655
A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6
by: Chris Oostenbrink, Alessandra Villa, Alan E. Mark, Wilfred F. van Gunsteren v. 25 i. 13 p. 1656 - 1676

2003

Motifs in nucleic acids: Molecular mechanics restraints for base pairing and base stacking
by: Stephen C. Harvey, Chunlin Wang, Stephane Teletchea, Richard Lavery v. 24 i. 1 p. 1 - 9
Conformational analysis by intersection: CONAN
by: Andrew Smellie, Robert Stanton, Randy Henne, Steve Teig v. 24 i. 1 p. 10 - 20
Using PC clusters to evaluate the transferability of molecular mechanics force fields for proteins
by: Asim Okur, Bentley Strockbine, Viktor Hornak, Carlos Simmerling v. 24 i. 1 p. 21 - 31
Transferability of fragmental contributions to the octanol/water partition coefficient: An NDDO-based MST study
by: Carles Curutchet, Albert Salichs, Xavier Barril, Modesto Orozco, Francisco Javier Luque v. 24 i. 1 p. 32 - 45
The intramolecular mechanism for the second proton transfer in triosephosphate isomerase (TIM): A QM/FE approach
by: Giuliano Alagona, Caterina Ghio, Peter A. Kollman v. 24 i. 1 p. 46 - 56
Fast approximate methods for calculating nucleic acid base pair interaction energies
by: Edward C. Sherer, Darrin M. York, Christopher J. Cramer v. 24 i. 1 p. 57 - 67
Cool walking: A new Markov chain Monte Carlo sampling method
by: Scott Brown, Teresa Head-Gordon v. 24 i. 1 p. 68 - 76
Inherent speedup limitations in multiple time step/particle mesh Ewald algorithms
by: Danny Barash, Linjing Yang, Xiaoliang Qian, Tamar Schlick v. 24 i. 1 p. 77 - 88
MOPED: Method for optimizing physical energy parameters using decoys
by: Chaok Seok, J. Ben Rosen, John D. Chodera, Ken A. Dill v. 24 i. 1 p. 89 - 97
Catalysis on the coastline: Theozyme, molecular dynamics, and free energy perturbation analysis of antibody 21D8 catalysis of the decarboxylation of 5-nitro-3-carboxybenzisoxazole
by: Gregori Ujaque, Dean J. Tantillo, Yunfeng Hu, K. N. Houk, Kinya Hotta, Donald Hilvert v. 24 i. 1 p. 98 - 110
Molecular mechanics force-field development for amino acid zwitterions
by: Karl Nicholas Kirschner, Anita H. Lewin, J. Phillip Bowen v. 24 i. 1 p. 111 - 128
An ab initio force field for the cofactors of bacterial photosynthesis
by: Matteo Ceccarelli, Piero Procacci, Massimo Marchi v. 24 i. 2 p. 129 - 142
Structural and dynamical analysis of the hydration of the Alzheimer's beta-amyloid peptide
by: Francesca Massi, John E. Straub v. 24 i. 2 p. 143 - 153
Parallel stored-integral and semidirect Hartree-Fock and DFT methods with data compression
by: Alexander V. Mitin, Jon Baker, Krzysztof Wolinski, Peter Pulay v. 24 i. 2 p. 154 - 160
Inter- and intramolecular potential for the N-formylglycinamide-water system. A comparison between theoretical modeling and empirical force fields
by: Jose Manuel Hermida-Ramón, Steve Brdarski, Gunnar Karlström, Ulf Berg v. 24 i. 2 p. 161 - 176
Hydride transfer catalyzed by xylose isomerase: Mechanism and quantum effects
by: Mireia Garcia-Viloca, Cristóbal Alhambra, Donald G. Truhlar, Jiali Gao v. 24 i. 2 p. 177 - 190
Prediction of beta-sheet topology and disulfide bridges in polypeptides
by: John L. Klepeis, Christodoulos A. Floudas v. 24 i. 2 p. 191 - 208
Hybrid QM/MM molecular dynamics simulations for an ionic SN2 reaction in the supercritical water: OH- + CH3Cl -&gt CH3OH + Cl-
by: Takumi Hori, Hideaki Takahashi, Tomoshige Nitta v. 24 i. 2 p. 209 - 221
An improved method for nonbonded list generation: Rapid determination of near-neighbor pairs
by: Robert J. Petrella, Ioan Andricioaei, Bernard R. Brooks, Martin Karplus v. 24 i. 2 p. 222 - 231
Exact rotamer optimization for protein design
by: D. Benjamin Gordon, Geoffrey K. Hom, Stephen L. Mayo, Niles A. Pierce v. 24 i. 2 p. 232 - 243
Computational study of epoxy-amine reactions
by: Satoshi Okumoto, Shinichi Yamabe v. 24 i. 2 p. 244 - 253
ICFF: A new method to incorporate implicit flexibility into an internal coordinate force field
by: Vsevolod Katritch, Maxim Totrov, Ruben Abagyan v. 24 i. 2 p. 254 - 265
A computationally inexpensive modification of the point dipole electrostatic polarization model for molecular simulations
by: George A. Kaminski, Richard A. Friesner, Ruhong Zhou v. 24 i. 3 p. 267 - 276
Correlation method for variance reduction of Monte Carlo integration in RS-HDMR
by: Genyuan Li, Herschel Rabitz, Sheng-Wei Wang, Panos G. Georgopoulos v. 24 i. 3 p. 277 - 283
Electrostatic component of solvation: Comparison of SCRF continuum models
by: Carles Curutchet, Christopher J. Cramer, Donald G. Truhlar, Manuel F. Ruiz-López, Daniel Rinaldi, Modesto Orozco, F. Javier Luque v. 24 i. 3 p. 284 - 297
Ground and excited state CASPT2 geometry optimizations of small organic molecules
by: Christopher S. Page, Massimo Olivucci v. 24 i. 3 p. 298 - 309
beta-Hairpins, alpha-helices, and the intermediates among the secondary structures in the energy landscape of a peptide from a distal beta-hairpin of SH3 domain
by: Kazuyoshi Ikeda, Oxana V. Galzitskaya, Haruki Nakamura, Junichi Higo v. 24 i. 3 p. 310 - 318
Molecular mechanics (MM3) calculations on lithium amide compounds
by: Takashi Yoshida, Kazuhisa Sakakibara, Masatoshi Asami, Kuo-Hsiang Chen, Jenn-Huei Lii, Norman L. Allinger v. 24 i. 3 p. 319 - 327
Nonspecific interaction forces at water-membrane interface by forced molecular dynamics simulations
by: Alicia C. Lorenzo, Pedro G. Pascutti, Paulo Mascarello Bisch v. 24 i. 3 p. 328 - 339
Density functional investigation on electron-transfer catalysis of cycloreversion of cyclobutane: Radical anion mechanism
by: Zheng-Wang Qu, Hui Zhu, Xing-Kang Zhang, Qi-Yuan Zhang v. 24 i. 3 p. 340 - 344
An ab initio study of intermolecular interactions of nitromethane dimer and nitromethane trimer
by: Jinshan Li, Feng Zhao, Fuqian Jing v. 24 i. 3 p. 345 - 352
Boundary element solution of the linear Poisson-Boltzmann equation and a multipole method for the rapid calculation of forces on macromolecules in solution
by: Andrew J. Bordner, G. A. Huber v. 24 i. 3 p. 353 - 367
Coordination number of zinc ions in the phosphotriesterase active site by molecular dynamics and quantum mechanics
by: Jaroslav Koca, Chang-Guo Zhan, Robert C. Rittenhouse, Rick L. Ornstein v. 24 i. 3 p. 368 - 378
A practical and efficient method to calculate AIM localization and delocalization indices at post-HF levels of theory
by: Yi-Gui Wang, Nick Henry Werstiuk v. 24 i. 3 p. 379 - 385
Extended method for adiabatic mode reordering
by: Christofer S. Tautermann, Andreas F. Voegele, Thomas Loerting, Peter Kaps, Klaus R. Liedl v. 24 i. 3 p. 386 - 395
Ab initio study on the structures of fluorinated formates and hydrogen abstraction reaction with OH radical
by: Asit K. Chandra, Tadafumi Uchimaru, Masaaki Sugie, Akira Sekiya v. 24 i. 3 p. 396 - 407
Foreword
by: Shridhar R. Gadre v. 24 i. 4 p. 408 - 408
Rational determination of charge distributions for free energy calculations
by: Christophe Chipot v. 24 i. 4 p. 409 - 415
Comparison of electron density properties in frozen and relaxed electronic distributions
by: Ibon Alkorta, Jose Elguero, Enrique Espinosa, Ignasi Mata, Elies Molins v. 24 i. 4 p. 416 - 421
Chemical information from the source function
by: Carlo Gatti, Fausto Cargnoni, Luca Bertini v. 24 i. 4 p. 422 - 436
An improved algorithm to locate critical points in a 3D scalar field as implemented in the program MORPHY
by: Nathaniel O. J. Malcolm, Paul L. A. Popelier v. 24 i. 4 p. 437 - 442
Ab initio determination of the electric multipole moments and static (hyper)polarizability of HCCX, X = F, Cl, Br, and I
by: George Maroulis v. 24 i. 4 p. 443 - 452
Application of the quantum theory of atoms in molecules to selected physico-chemical and biophysical problems: Focus on correlation with experiment
by: Chérif F. Matta v. 24 i. 4 p. 453 - 463
Hirshfeld partitioning of the electron density: Atomic dipoles and their relation with functional group properties
by: Frank De Proft, Ricardo Vivas-Reyes, Anik Peeters, Christian Van Alsenoy, Paul Geerlings v. 24 i. 4 p. 463 - 470
Wave functions derived from experiment. V. Investigation of electron densities, electrostatic potentials, and electron localization functions for noncentrosymmetric crystals
by: Daniel J. Grimwood, Ian Bytheway, Dylan Jayatilaka v. 24 i. 4 p. 470 - 483
Ab initio quality one-electron properties of large molecules: Development and testing of molecular tailoring approach
by: K. Babu, Shridhar R. Gadre v. 24 i. 4 p. 484 - 495
Electron probability distribution in AIM and ELF basins
by: Eduardo Chamorro, Patricio Fuentealba, Andreas Savin v. 24 i. 4 p. 496 - 504
Electrostatic potentials and covalent radii
by: Peter Politzer, Jane S. Murray, Pat Lane v. 24 i. 4 p. 505 - 511
Transferable atom equivalent multicentered multipole expansion method
by: Christopher E. Whitehead, Curt M. Breneman, Nagamani Sukumar, M. D. Ryan v. 24 i. 4 p. 512 - 529
Comparison of various implicit solvent models in molecular dynamics simulations of immunoglobulin G light chain dimer
by: Marcin Król v. 24 i. 5 p. 531 - 546
Concerning the reaction between singlet nitrenium ions and water: A computational investigation on competitive reaction paths
by: Paola Facchini, Felice Grandinetti v. 24 i. 5 p. 547 - 564
Modeling zinc in biomolecules with the self consistent charge-density functional tight binding (SCC-DFTB) method: Applications to structural and energetic analysis
by: Marcus Elstner, Qiang Cui, Petra Munih, Efthimios Kaxiras, Thomas Frauenheim, Martin Karplus v. 24 i. 5 p. 565 - 581
Development of hardware accelerator for molecular dynamics simulations: A computation board that calculates nonbonded interactions in cooperation with fast multipole method
by: Takashi Amisaki, Shinjiro Toyoda, Hiroh Miyagawa, Kunihiro Kitamura v. 24 i. 5 p. 582 - 592
Dual-level direct dynamics studies for the reactions of dimethyl ether with hydrogen atom and methyl radical
by: Jia-Yan Wu, Jing-Yao Liu, Ze-Sheng Li, Xu-Ri Huang, Chia-Chung Sun v. 24 i. 5 p. 593 - 600
Theoretical study concerning the reactivity of imine derivatives of polycyclic aromatic hydrocarbons
by: Gabriela L. Borosky v. 24 i. 5 p. 601 - 608
Vertical spectrum of the C2H2+ system. An open shell (SC)2-CAS-SDCI study
by: José Pitarch-Ruiz, José Sánchez-Marín, Daniel Maynau v. 24 i. 5 p. 609 - 617
Sparse matrix multiplications for linear scaling electronic structure calculations in an atom-centered basis set using multiatom blocks
by: Chandra Saravanan, Yihan Shao, Roi Baer, Philip N. Ross, Martin Head-Gordon v. 24 i. 5 p. 618 - 622
Performance assessment of density-functional methods for study of charge-transfer complexes
by: Meng-Sheng Liao, Yun Lu, Steve Scheiner v. 24 i. 5 p. 623 - 631
Molecular mechanics force field parameterization of the fluorescent probe rhodamine 6G using automated frequency matching
by: Andrea C. Vaiana, Andreas Schulz, Jürgen Wolfrum, Markus Sauer, Jeremy C. Smith v. 24 i. 5 p. 632 - 639
Systematic errors in DFT calculations of haloalkane heats of formation
by: C. F. Cloud III, M. Schwartz v. 24 i. 5 p. 640 - 646
High-dimensional model representations generated from low order terms - lp-RS-HDMR
by: Genyuan Li, Maxim Artamonov, Herschel Rabitz, Sheng-Wei Wang, Panos G. Georgopoulos, Metin Demiralp v. 24 i. 5 p. 647 - 656
nMoldyn: A program package for a neutron scattering oriented analysis of molecular dynamics simulations
by: Tomasz Róg, Krzysztof Murzyn, Konrad Hinsen, G. R. Kneller v. 24 i. 5 p. 657 - 667
Energies, structures, and electronic properties of molecules in solution with the C-PCM solvation model
by: Maurizio Cossi, Nadia Rega, Giovanni Scalmani, Vincenzo Barone v. 24 i. 6 p. 669 - 681
Binding of proteins to the minor groove of DNA: What are the structural and energetic determinants for kinking a basepair step?
by: David Bosch, Mercedes Campillo, Leonardo Pardo v. 24 i. 6 p. 682 - 691
Performance of time-dependent density functional and Green functions methods for calculations of excitation energies in radicals and for Rydberg electronic states
by: A. S. Zyubin, A. M. Mebel v. 24 i. 6 p. 692 - 700
Dependence of the rate constants on the treatment of internal rotation modes: The reaction OH + CH3SH CH3S + H2O as an example
by: Laura Masgrau, Àngels González-Lafont, José M. Lluch v. 24 i. 6 p. 701 - 706
A box-counting-based algorithm for computing Shannon entropy in molecular dynamics simulations
by: Luis Lorenzo, Ricardo A. Mosquera v. 24 i. 6 p. 707 - 713
Implementation of a general multireference configuration interaction procedure with analytic gradients in a semiempirical context using the graphical unitary group approach
by: Axel Koslowski, Michael E. Beck, Walter Thiel v. 24 i. 6 p. 714 - 726
Prediction of protein secondary structure content by artificial neural network
by: Yu-Dong Cai, Xiao-Jun Liu, Kuo-Chen Chou v. 24 i. 6 p. 727 - 731
Radial quadrature for multiexponential integrands
by: Peter M. W. Gill, Siu-Hung Chien v. 24 i. 6 p. 732 - 740
Mechanistic insights into oxidosqualene cyclizations through homology modeling
by: Tanja Schulz-Gasch, Martin Stahl v. 24 i. 6 p. 741 - 753
Parallelization of four-component calculations. II. Symmetry-driven parallelization of the 4-Spinor CCSD algorithm
by: Markus Pernpointner, Lucas Visscher v. 24 i. 6 p. 754 - 759
Geometry optimization with QM/MM, ONIOM, and other combined methods. I. Microiterations and constraints
by: Thom Vreven, Keiji Morokuma, Ödön Farkas, H. Bernhard Schlegel, Michael J. Frisch v. 24 i. 6 p. 760 - 769
Thermally induced phase transition in helical comblike poly(-peptide)s: An atomistic simulation
by: David Zanuy, Carlos Alemán, Manuel Laso, Sebastián Muñoz-Guerra v. 24 i. 6 p. 770 - 778
Free energy perturbation and molecular dynamics calculations of copper binding to azurin
by: Matteo Pappalardo, Danilo Milardi, Domenico M. Grasso, Carmelo La Rosa v. 24 i. 6 p. 779 - 785
Statistical analysis of the estimation of distance measures
by: Mark Pinsky, Dina Yogev-Einot, David Avnir v. 24 i. 6 p. 786 - 796