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ORCIDJournal of Computational Chemistry, Volume 24
Volume 24, Number 1, 15 January 2003
- Stephen C. Harvey, Chunlin Wang, Stephane Teletchea
, Richard Lavery:
Motifs in nucleic acids: Molecular mechanics restraints for base pairing and base stacking. 1-9 - Andrew Smellie, Robert V. Stanton, Randy Henne, Steven L. Teig:
Conformational analysis by intersection: CONAN. 10-20 - Asim Okur, Bentley Strockbine, Viktor Hornak, Carlos Simmerling:
Using PC clusters to evaluate the transferability of molecular mechanics force fields for proteins. 21-31 - Carles Curutchet, Albert Salichs, Xavier Barril, Modesto Orozco, Francisco Javier Luque:
Transferability of fragmental contributions to the octanol/water partition coefficient: An NDDO-based MST study. 32-45 - Giuliano Alagona, Caterina Ghio, Peter A. Kollman:
The intramolecular mechanism for the second proton transfer in triosephosphate isomerase (TIM): A QM/FE approach. 46-56 - Edward C. Sherer, Darrin M. York, Christopher J. Cramer:
Fast approximate methods for calculating nucleic acid base pair interaction energies. 57-67 - Scott Brown, Teresa Head-Gordon:
Cool walking: A new Markov chain Monte Carlo sampling method. 68-76 - Danny Barash, Linjing Yang, Xiaoliang Qian, Tamar Schlick:
Inherent speedup limitations in multiple time step/particle mesh Ewald algorithms. 77-88 - Chaok Seok, J. Ben Rosen, John D. Chodera, Ken A. Dill:
MOPED: Method for optimizing physical energy parameters using decoys. 89-97 - Gregori Ujaque, Dean J. Tantillo, Yunfeng Hu, Kendall N. Houk, Kinya Hotta, Donald Hilvert:
Catalysis on the coastline: Theozyme, molecular dynamics, and free energy perturbation analysis of antibody 21D8 catalysis of the decarboxylation of 5-nitro-3-carboxybenzisoxazole. 98-110 - Karl Nicholas Kirschner, Anita H. Lewin, J. Phillip Bowen:
Molecular mechanics force-field development for amino acid zwitterions. 111-128
Volume 24, Number 2, 30 January 2003
- Matteo Ceccarelli, Piero Procacci, Massimo Marchi:
An ab initio force field for the cofactors of bacterial photosynthesis. 129-142 - Francesca Massi, John E. Straub:
Structural and dynamical analysis of the hydration of the Alzheimer's beta-amyloid peptide. 143-153 - Alexander V. Mitin, Jon Baker, Krzysztof Wolinski, Peter Pulay:
Parallel stored-integral and semidirect Hartree-Fock and DFT methods with data compression. 154-160 - Jose Manuel Hermida-Ramón, Steve Brdarski, Gunnar Karlström, Ulf Berg:
Inter- and intramolecular potential for the N-formylglycinamide-water system. A comparison between theoretical modeling and empirical force fields. 161-176 - Mireia Garcia-Viloca, Cristóbal Alhambra, Donald G. Truhlar, Jiali Gao:
Hydride transfer catalyzed by xylose isomerase: Mechanism and quantum effects. 177-190 - John L. Klepeis, Christodoulos A. Floudas:
Prediction of beta-sheet topology and disulfide bridges in polypeptides. 191-208 - Takumi Hori, Hideaki Takahashi, Tomoshige Nitta:
Hybrid QM/MM molecular dynamics simulations for an ionic SN2 reaction in the supercritical water: OH- + CH3Cl -> CH3OH + Cl-. 209-221 - Robert J. Petrella, Ioan Andricioaei, Bernard R. Brooks, Martin Karplus:
An improved method for nonbonded list generation: Rapid determination of near-neighbor pairs. 222-231 - D. Benjamin Gordon, Geoffrey K. Hom, Stephen L. Mayo, Niles A. Pierce:
Exact rotamer optimization for protein design. 232-243 - Satoshi Okumoto, Shinichi Yamabe:
Computational study of epoxy-amine reactions. 244-253
- Vsevolod Katritch, Maxim Totrov, Ruben Abagyan:
ICFF: A new method to incorporate implicit flexibility into an internal coordinate force field. 254-265
Volume 24, Number 3, February 2003
- George A. Kaminski, Richard A. Friesner, Ruhong Zhou:
A computationally inexpensive modification of the point dipole electrostatic polarization model for molecular simulations. 267-276 - Genyuan Li, Herschel A. Rabitz, Sheng-Wei Wang, Panos G. Georgopoulos:
Correlation method for variance reduction of Monte Carlo integration in RS-HDMR. 277-283 - Carles Curutchet, Christopher J. Cramer, Donald G. Truhlar, Manuel F. Ruiz-López, Daniel Rinaldi, Modesto Orozco, F. Javier Luque:
Electrostatic component of solvation: Comparison of SCRF continuum models. 284-297 - Christopher S. Page, Massimo Olivucci:
Ground and excited state CASPT2 geometry optimizations of small organic molecules. 298-309 - Kazuyoshi Ikeda, Oxana V. Galzitskaya, Haruki Nakamura, Junichi Higo:
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. 310-318 - Takashi Yoshida, Kazuhisa Sakakibara, Masatoshi Asami, Kuo-Hsiang Chen, Jenn-Huei Lii, Norman L. Allinger:
Molecular mechanics (MM3) calculations on lithium amide compounds. 319-327 - Alicia C. Lorenzo, Pedro Geraldo Pascutti, Paulo Mascarello Bisch:
Nonspecific interaction forces at water-membrane interface by forced molecular dynamics simulations. 328-339 - Zheng-Wang Qu, Hui Zhu, Xing-Kang Zhang, Qi-Yuan Zhang:
Density functional investigation on electron-transfer catalysis of cycloreversion of cyclobutane: Radical anion mechanism. 340-344 - Jinshan Li, Feng Zhao, Fuqian Jing:
An ab initio study of intermolecular interactions of nitromethane dimer and nitromethane trimer. 345-352 - Andrew J. Bordner, G. A. Huber:
Boundary element solution of the linear Poisson-Boltzmann equation and a multipole method for the rapid calculation of forces on macromolecules in solution. 353-367 - Jaroslav Koca, Chang-Guo Zhan, Robert C. Rittenhouse, Rick L. Ornstein:
Coordination number of zinc ions in the phosphotriesterase active site by molecular dynamics and quantum mechanics. 368-378 - Yi-Gui Wang, Nick Henry Werstiuk:
A practical and efficient method to calculate AIM localization and delocalization indices at post-HF levels of theory. 379-385 - Christofer S. Tautermann, Andreas F. Voegele, Thomas Loerting, Peter Kaps, Klaus R. Liedl:
Extended method for adiabatic mode reordering. 386-395 - Asit K. Chandra, Tadafumi Uchimaru, Masaaki Sugie, Akira Sekiya:
Ab initio study on the structures of fluorinated formates and hydrogen abstraction reaction with OH radical. 396-407
Volume 24, Number 4, March 2003
- Shridhar R. Gadre:
Foreword. 408 - Christophe Chipot:
Rational determination of charge distributions for free energy calculations. 409-415 - Ibon Alkorta, José Elguero, Enrique Espinosa, Ignasi Mata, Elies Molins:
Comparison of electron density properties in frozen and relaxed electronic distributions. 416-421 - Carlo Gatti, Fausto Cargnoni, Luca Bertini:
Chemical information from the source function. 422-436 - Nathaniel O. J. Malcolm, Paul L. A. Popelier:
An improved algorithm to locate critical points in a 3D scalar field as implemented in the program MORPHY. 437-442 - George Maroulis:
Ab initio determination of the electric multipole moments and static (hyper)polarizability of HCCX, X = F, Cl, Br, and I. 443-452 - Chérif F. Matta:
Application of the quantum theory of atoms in molecules to selected physico-chemical and biophysical problems: Focus on correlation with experiment. 453-463 - Frank De Proft, Ricardo Vivas-Reyes, Anik Peeters, Christian Van Alsenoy, Paul Geerlings:
Hirshfeld partitioning of the electron density: Atomic dipoles and their relation with functional group properties. 463-470 - Daniel J. Grimwood, Ian Bytheway, Dylan Jayatilaka:
Wave functions derived from experiment. V. Investigation of electron densities, electrostatic potentials, and electron localization functions for noncentrosymmetric crystals. 470-483 - K. Babu, Shridhar R. Gadre:
Ab initio quality one-electron properties of large molecules: Development and testing of molecular tailoring approach. 484-495 - Eduardo Chamorro, Patricio Fuentealba, Andreas Savin:
Electron probability distribution in AIM and ELF basins. 496-504 - Peter Politzer, Jane S. Murray, Pat Lane:
Electrostatic potentials and covalent radii. 505-511 - Christopher E. Whitehead, Curt M. Breneman, Nagamani Sukumar, M. Dominic Ryan:
Transferable atom equivalent multicentered multipole expansion method. 512-529
Volume 24, Number 5, 15 April 2003
- Marcin Król:
Comparison of various implicit solvent models in molecular dynamics simulations of immunoglobulin G light chain dimer. 531-546 - Paola Facchini, Felice Grandinetti:
Concerning the reaction between singlet nitrenium ions and water: A computational investigation on competitive reaction paths. 547-564 - Marcus Elstner, Qiang Cui, Petra Munih, Efthimios Kaxiras, Thomas Frauenheim, Martin Karplus:
Modeling zinc in biomolecules with the self consistent charge-density functional tight binding (SCC-DFTB) method: Applications to structural and energetic analysis. 565-581 - Takashi Amisaki, Shinjiro Toyoda, Hiroh Miyagawa, Kunihiro Kitamura:
Development of hardware accelerator for molecular dynamics simulations: A computation board that calculates nonbonded interactions in cooperation with fast multipole method. 582-592 - Jia-Yan Wu, Jing-Yao Liu, Ze-Sheng Li, Xu-Ri Huang, Chia-Chung Sun:
Dual-level direct dynamics studies for the reactions of dimethyl ether with hydrogen atom and methyl radical. 593-600 - Gabriela L. Borosky:
Theoretical study concerning the reactivity of imine derivatives of polycyclic aromatic hydrocarbons. 601-608 - José-Vicente Pitarch Ruiz, José Sánchez-Marín, Daniel Maynau:
Vertical spectrum of the C2H2+ system. An open shell (SC)2-CAS-SDCI study. 609-617 - Chandra Saravanan, Yihan Shao, Roi Baer, Philip N. Ross, Martin Head-Gordon:
Sparse matrix multiplications for linear scaling electronic structure calculations in an atom-centered basis set using multiatom blocks. 618-622 - Meng-Sheng Liao, Yun Lu, Steve Scheiner:
Performance assessment of density-functional methods for study of charge-transfer complexes. 623-631 - Andrea C. Vaiana, Andreas Schulz, Jürgen Wolfrum, Markus Sauer, Jeremy C. Smith:
Molecular mechanics force field parameterization of the fluorescent probe rhodamine 6G using automated frequency matching. 632-639 - C. F. Cloud III, Martin Schwartz:
Systematic errors in DFT calculations of haloalkane heats of formation. 640-646 - Genyuan Li, Maxim Artamonov, Herschel A. Rabitz, Sheng-Wei Wang, Panos G. Georgopoulos, Metin Demiralp:
High-dimensional model representations generated from low order terms - lp-RS-HDMR. 647-656
- Tomasz Róg, Krzysztof Murzyn, Konrad Hinsen, Gerald R. Kneller:
nMoldyn: A program package for a neutron scattering oriented analysis of molecular dynamics simulations. 657-667
Volume 24, Number 6, 30 April 2003
- Maurizio Cossi, Nadia Rega, Giovanni Scalmani, Vincenzo Barone:
Energies, structures, and electronic properties of molecules in solution with the C-PCM solvation model. 669-681 - David Bosch, Mercedes Campillo, Leonardo Pardo:
Binding of proteins to the minor groove of DNA: What are the structural and energetic determinants for kinking a basepair step?. 682-691 - A. S. Zyubin, A. M. Mebel:
Performance of time-dependent density functional and Green functions methods for calculations of excitation energies in radicals and for Rydberg electronic states. 692-700 - Laura Masgrau, Àngels González-Lafont, José M. Lluch:
Dependence of the rate constants on the treatment of internal rotation modes: The reaction OH + CH3SH CH3S + H2O as an example. 701-706 - Luis Lorenzo, Ricardo A. Mosquera:
A box-counting-based algorithm for computing Shannon entropy in molecular dynamics simulations. 707-713 - Axel Koslowski, Michael E. Beck, Walter Thiel:
Implementation of a general multireference configuration interaction procedure with analytic gradients in a semiempirical context using the graphical unitary group approach. 714-726 - Yu-Dong Cai, Xiao-Jun Liu, Kuo-Chen Chou:
Prediction of protein secondary structure content by artificial neural network. 727-731 - Peter M. W. Gill, Siu-Hung Chien:
Radial quadrature for multiexponential integrands. 732-740 - Tanja Schulz-Gasch, Martin Stahl:
Mechanistic insights into oxidosqualene cyclizations through homology modeling. 741-753 - Markus Pernpointner, Lucas Visscher:
Parallelization of four-component calculations. II. Symmetry-driven parallelization of the 4-Spinor CCSD algorithm. 754-759 - Thom Vreven, Keiji Morokuma, Ödön Farkas, H. Bernhard Schlegel, Michael J. Frisch:
Geometry optimization with QM/MM, ONIOM, and other combined methods. I. Microiterations and constraints. 760-769 - David Zanuy, Carlos Alemán, Manuel Laso, Sebastián Muñoz-Guerra:
Thermally induced phase transition in helical comblike poly(-peptide)s: An atomistic simulation. 770-778 - Matteo Pappalardo, Danilo Milardi, Domenico M. Grasso, Carmelo La Rosa:
Free energy perturbation and molecular dynamics calculations of copper binding to azurin. 779-785 - Mark Pinsky, Dina Yogev-Einot, David Avnir:
Statistical analysis of the estimation of distance measures. 786-796
Volume 24, Number 7, May 2003
- Philippe Arnaud, Krystyna Zakrzewska, Bernard Meunier:
Theoretical study of the interaction between a high-valent manganese porphyrin oxyl-(hydroxo)-Mn(IV)-TMPyP and double-stranded DNA. 797-805 - Majda Sekkal-Rahal, Nezha Sekkal, Dirk C. Kleb, Paul Bleckmann:
Structures and energies of D-galactose and galabiose conformers as calculated by ab initio and semiempirical methods. 806-818 - José Mario Martínez, Leandro Martínez:
Packing optimization for automated generation of complex system's initial configurations for molecular dynamics and docking. 819-825 - Kenshu Kamiya, Yoko Sugawara, Hideaki Umeyama:
Algorithm for normal mode analysis with general internal coordinates. 826-841 - Yu-Ren Jiang, Jing-Ya Liu, Yue-Hua Hu, Toyohisa Fujita:
Novel topological index for research on structure-property relationships of complex organic compounds. 842-849 - Valentina Vetere, Pascale Maldivi, Carlo Adamo:
Comparative studies of quasi-relativistic density functional methods for the description of lanthanide and actinide complexes. 850-858 - Ignacio Ema, J. M. García de la Vega, Guillermo Ramírez, Rafael López, Jaime Fernández Rico, H. Meissner, J. Paldus:
Polarized basis sets of Slater-type orbitals: H to Ne atoms. 859-868 - Carlos Renato Zacharias, Maurício Ruv Lemes, Arnaldo Dal Pino Júnior, David Santo Orcero:
Predicting structural models for silicon clusters. 869-875 - Mark Bathe, Gregory C. Rutledge:
Inverse Monte Carlo procedure for conformation determination of macromolecules. 876-890 - Joseph V. Turner, David J. Cutler, Ian Spence, Desmond J. Maddalena:
Selective descriptor pruning for QSAR/QSPR studies using artificial neural networks. 891-897 - Miroslav Pinak:
8-oxoguanine lesioned B-DNA molecule complexed with repair enzyme hOGG1: A molecular dynamics study. 898-907
Volume 24, Number 8, June 2003
- Fillmore Freeman, Elika Derek:
A computational study of conformational interconversions in 1, 4-dithiacyclohexane (1, 4-dithiane). 909-919 - Wataru Shinoda, Masuhiro Mikami:
Rigid-body dynamics in the isothermal-isobaric ensemble: A test on the accuracy and computational efficiency. 920-930 - Yong Wu, Daiqian Xie, Ying Xue:
Ab initio studies for the photodissociation mechanism of hydroxyacetone. 931-938 - Shinichi Yamabe, Noriko Tsuchida:
A computational study of interactions between acetic acid and water molecules. 939-947 - Zhongfang Chen, Haijun Jiao, Gotthard Seifert, Anselm H. C. Horn, Dengke Yu, Timothy Clark, Walter Thiel, Paul von Ragué Schleyer:
The structure and stability of Si60 and Ge60 cages: A computational study. 948-953 - Kathryn N. Rankin, Traian Sulea, Enrico O. Purisima:
On the transferability of hydration-parametrized continuum electrostatics models to solvated binding calculations. 954-962 - Ying Xue, Chun Ho Kang, Chan Kyung Kim, Ikchoon Lee:
Theoretical studies on the gas-phase pyrolysis of 2-phenoxycarboxylic acids: An ONIOM approach. 963-972 - Marcelo Zaldini Hernandes, João Bosco P. Da Silva, Ricardo L. Longo:
Chemometric study of liquid water simulations. I. The parameters of the TIP4P model potential. 973-981 - Eliseo Ruiz, Antonio Rodríguez-Fortea, Joan Cano, Santiago Alvarez, Pere Alemany:
About the calculation of exchange coupling constants in polynuclear transition metal complexes. 982-989 - Dominic R. Alfonso, Kenneth D. Jordan:
A flexible nudged elastic band program for optimization of minimum energy pathways using ab initio electronic structure methods. 990-996
- János G. Ángyán, Christophe Chipot, François Dehez, Christof Hättig, Georg Jansen, Claude Millot:
OPEP: A tool for the optimal partitioning of electric properties. 997-1008
Volume 24, Number 9, 15 July 2003
- Christopher C. Lovallo, Mariusz Klobukowski:
Development of new pseudopotential methods: Improved model core potentials for the first-row transition metals. 1009-1015 - Kristin L. Meagher, Luke T. Redman, Heather A. Carlson:
Development of polyphosphate parameters for use with the AMBER force field. 1016-1025 - András Perczel, Ödön Farkas, Imre Jákli, Igor A. Topol, Imre G. Csizmadia:
Peptide models. XXXIII. Extrapolation of low-level Hartree-Fock data of peptide conformation to large basis set SCF, MP2, DFT, and CCSD(T) results. The Ramachandran surface of alanine dipeptide computed at various levels of theory. 1026-1042 - Jos A. Hageman, Ron Wehrens, René de Gelder, Lutgarde M. C. Buydens:
Powder pattern indexing using the weighted crosscorrelation and genetic algorithms. 1043-1051 - David C. Chatfield, Alberto Augsten, Cassian D'Cunha, Sergio Ernesto Wong:
Methyl dynamics in crystalline amino acids: MD and NMR. 1052-1058 - Shenghua Shi, Lisa Yan, Yang Yang, Jodi Fisher-Shaulsky, Tom Thacher:
An extensible and systematic force field, ESFF, for molecular modeling of organic, inorganic, and organometallic systems. 1059-1076 - Toshimasa Ishida, George C. Schatz:
A local interpolation scheme using no derivatives in potential sampling: Application to O(1D) + H2 system. 1077-1086 - Alice Glättli, Xavier Daura, Wilfred F. van Gunsteren:
A novel approach for designing simple point charge models for liquid water with three interaction sites. 1087-1096 - Lionello Pogliani:
Complete graph conjecture for inner-core electrons: Homogeneous index case. 1097-1109 - Suzanne W. Sirois, Emil I. Proynov, Jean-François Truchon, Christos M. Tsoukas, Dennis R. Salahub:
A density functional study of the hydrogen-bond network within the HIV-1 protease catalytic site cleft. 1110-1119 - Roger A. Klein:
Hydrogen bonding in diols and binary diol-water systems investigated using DFT methods. II. Calculated infrared OH-stretch frequencies, force constants, and NMR chemical shifts correlate with hydrogen bond geometry and electron density topology. A reevaluation of geometrical criteria for hydrogen bonding. 1120-1131 - Nikolay A. Anikin, Vladislav L. Bugaenko, M. V. Frash, Leonid Gorb, Jerzy Leszczynski:
Localized basis orbitals: Minimization of 2-electron integrals array and orthonormality of basis set. 1132-1141 - Erik Van Lenthe, Evert Jan Baerends:
Optimized Slater-type basis sets for the elements 1-118. 1142-1156
Volume 24, Number 10, 30 July 2003
- András Perczel, Anna K. Füzéry, Attila G. Császár:
Toward direct determination of conformations of protein building units from multidimensional NMR experiments. V. NMR chemical shielding analysis of N-formyl-serinamide, a model for polar side-chain containing peptides. 1157-1171 - Vladimir Hnizdo, Adam Fedorowicz, Harshinder Singh, Eugene Demchuk:
Statistical thermodynamics of internal rotation in a hindering potential of mean force obtained from computer simulations. 1172-1183 - Jon Baker, Peter Pulay:
Assessment of the OLYP and O3LYP density functionals for first-row transition metals. 1184-1191 - Michio Iwaoka, Shuji Tomoda:
The SAAP force field. A simple approach to a new all-atom protein force field by using single amino acid potential (SAAP) functions in various solvents. 1192-1200 - Sean A. C. McDowell:
A computational study of the LiH dimer. 1201-1207 - David Curcó, David Zanuy, Carlos Alemán:
EVEBAT: A fast strategy for the examination of the empty space in polymer matrices. 1208-1214 - Dimitris K. Agrafiotis:
Stochastic proximity embedding. 1215-1221 - Bedamati Das, Hagai Meirovitch, Ionel Michael Navon:
Performance of hybrid methods for large-scale unconstrained optimization as applied to models of proteins. 1222-1231 - Hannes H. Loeffler:
Many-body effects on structure and dynamics of aqueous ionic solutions. 1232-1239 - Markus J. Loferer, Hannes H. Loeffler, Klaus R. Liedl:
A QM-MM interface between CHARMM and TURBOMOLE: Implementation and application to systems in bulk phase and biologically active systems. 1240-1249 - Joseph Ivanic, Klaus Ruedenberg:
A MCSCF method for ground and excited states based on full optimizations of successive Jacobi rotations. 1250-1262 - Carles Curutchet, Josep Maria Bofill, Begoña Hernández, Modesto Orozco, F. Javier Luque:
Energy decomposition in molecular complexes: Implications for the treatment of polarization in molecular simulations. 1263-1275
- Nathaniel O. J. Malcolm, Paul L. A. Popelier:
An algorithm to delineate and integrate topological basins in a three-dimensional quantum mechanical density function. 1276-1282
- Charles H. Langley, Jenn-Huei Lii, Norman L. Allinger:
Molecular mechanics (MM4) calculations on carbonyl compounds. I-IV - Erratum. 1283-1286
Volume 24, Number 11, August 2003
- Kyle A. Beran:
Isomers of C20: An energy profile II. 1287-1290 - Jason D. Thompson, Christopher J. Cramer, Donald G. Truhlar:
Parameterization of charge model 3 for AM1, PM3, BLYP, and B3LYP. 1291-1304 - Clovis Darrigan, Michel Rérat, Giuseppe Mallia, Roberto Dovesi:
Implementation of the finite field perturbation method in the CRYSTAL program for calculating the dielectric constant of periodic systems. 1305-1312 - Shandar Ahmad, M. Michael Gromiha:
Design and training of a neural network for predicting the solvent accessibility of proteins. 1313-1320 - Julio Peiró-García, Víctor M. Ramírez-Ramírez, Ignacio Nebot-Gil:
A theoretical ab initio study on the H2NO + O3 reaction. 1321-1328 - Osamu Takahashi, Masanori Joyabu, Masaki Mitani, Ko Saito, Suehiro Iwata:
Theoretical studies on the molecular dependence of bond dissociation after core excitations II: CH3CO(CH2)nCN, n = 0-3. 1329-1335 - D. M. Upadhyay, P. C. Mishra:
An ab initio study of microsolvation of LiF in water: Structures and properties of LiF-Wn, n = 1-9 complexes. 1336-1347 - Michael S. Lee, Michael Feig, Freddie R. Salsbury Jr., Charles L. Brooks III:
New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations. 1348-1356 - Marco Garavelli, Fabrizio Ruggeri, Francois Ogliaro, Michael J. Bearpark, Fernando Bernardi, Massimo Olivucci, Michael A. Robb:
A simple approach for improving the hybrid MMVB force field: Application to the photoisomerization of s-cis butadiene. 1357-1363 - Sean Cahill, Michael J. Cahill, Kevin Cahill:
On the kinematics of protein folding. 1364-1370
Volume 24, Number 12, September 2003
- Lillian T. Chong, Pradipta Bandyopadhyay, Thomas S. Scanlan, Irwin D. Kuntz, Peter A. Kollman:
Direct hydroxide attack is a plausible mechanism for amidase antibody 43C9. 1371-1377 - Mutsumi Hirama, Toshimasa Ishida, Jun-Ichi Aihara:
Possible molecular hydrogen formation mediated by the radical cations of anthracene and pyrene. 1378-1382 - Peter Carlsson, Lennart Nilsson:
Improved precision and efficiency of free energy calculations for small systems using lambda-scaled atomic masses and separating conformational and transformational sampling. 1383-1389 - Henryk A. Witek, Haruyuki Nakano, Kimihiko Hirao:
Multireference perturbation theory with optimized partitioning. II. Applications to molecular systems. 1390-1400 - Masahiro Yamanaka, Akiko Inagaki, Eiichi Nakamura:
Theoretical studies on structures and reactivities of organocuprate(I) and organocopper(III) species. 1401-1409 - Alexander V. Nemukhin, Bella L. Grigorenko, Igor A. Topol, Stanley K. Burt:
Flexible effective fragment QM/MM method: Validation through the challenging tests. 1410-1420 - Abhijit K. Das, Jun-Ya Hasegawa, Tomoo Miyahara, Masahiro Ehara, Hiroshi Nakatsuji:
Electronic excitations of the green fluorescent protein chromophore in its protonation states: SAC/SAC-CI study. 1421-1431 - Bojan Zagrovic, Vijay Pande:
Solvent viscosity dependence of the folding rate of a small protein: Distributed computing study. 1432-1436 - Mark N. Kobrak:
Systematic and statistical error in histogram-based free energy calculations. 1437-1446 - Norman L. Allinger, Kuo-Hsiang Chen, Jenn-Huei Lii, Kathleen A. Durkin:
Alcohols, ethers, carbohydrates, and related compounds. I. The MM4 force field for simple compounds. 1447-1472 - Jenn-Huei Lii, Kuo-Hsiang Chen, Kathleen A. Durkin, Norman L. Allinger:
Alcohols, ethers, carbohydrates, and related compounds. II. The anomeric effect. 1473-1489 - Jenn-Huei Lii, Kuo-Hsiang Chen, T. Bruce Grindley, Norman L. Allinger:
Alcohols, ethers, carbohydrates, and related compounds. III. The 1, 2-dimethoxyethane system. 1490-1503 - Jenn-Huei Lii, Kuo-Hsiang Chen, Norman L. Allinger:
Alcohols, ethers, carbohydrates, and related compounds. IV. carbohydrates. 1504-1513 - H. Bernhard Schlegel:
Exploring potential energy surfaces for chemical reactions: An overview of some practical methods. 1514-1527
Volume 24, Number 13, October 2003
- Stefan Grimme:
Improved third-order Møller-Plesset perturbation theory. 1529-1537 - Tadafumi Uchimaru, Asit K. Chandra, Seiji Tsuzuki, Masaaki Sugie, Akira Sekiya:
Ab initio investigation on the reaction path and rate for the gas-phase reaction of HO + H2O H2O + OH. 1538-1548 - Guosheng Wu, Daniel H. Robertson, Charles L. Brooks III, Michal Vieth:
Detailed analysis of grid-based molecular docking: A case study of CDOCKER - A CHARMm-based MD docking algorithm. 1549-1562 - Brian W. Hopkins, Gregory S. Tschumper:
A multicentered approach to integrated QM/QM calculations. Applications to multiply hydrogen bonded systems. 1563-1568 - Niall J. English, J. M. D. MacElroy:
Structural and dynamical properties of methane clathrate hydrates. 1569-1581 - Delano P. Chong, Myrta Grüning, Evert Jan Baerends:
STO and GTO field-induced polarization functions for H to Kr. 1582-1591 - Takao Tsuneda, Muneaki Kamiya, Kimihiko Hirao:
Regional self-interaction correction of density functional theory. 1592-1598 - Rajeev Prabhakar, Per E. M. Siegbahn:
A comparison of the mechanism for the reductive half-reaction between pea seedling and other copper amine oxidases (CAOs). 1599-1609 - Antonio Morreale, Josep Lluis Gelpí, F. Javier Luque, Modesto Orozco:
Continuum and discrete calculation of fractional contributions to solvation free energy. 1610-1623 - Dirk Reith, Mathias Pütz, Florian Müller-Plathe:
Deriving effective mesoscale potentials from atomistic simulations. 1624-1636 - Richard D. Taylor, Philip J. Jewsbury, Jonathan W. Essex:
FDS: Flexible ligand and receptor docking with a continuum solvent model and soft-core energy function. 1637-1656 - Julio Peiró-García, Ignacio Nebot-Gil:
Ab initio study of the mechanism of the atmospheric reaction: NO2 + O3 NO3 + O2. 1657-1663 - Robert M. Dirks, Niles A. Pierce:
A partition function algorithm for nucleic acid secondary structure including pseudoknots. 1664-1677
- Mikhail Kozhin, Ilya Yanov, Jerzy Leszczynski:
Network visualization system for computational chemistry. 1678-1687
- Hannes H. Loeffler, Bernd M. Rode:
Many-body effects on structure and dynamics of aqueous ionic solutions- Erratum. 1688
Volume 24, Number 14, 15 November 2003
- Wonpil Im, Michael S. Lee, Charles L. Brooks III:
Generalized born model with a simple smoothing function. 1691-1702 - Mikhail B. Darkhovskii, Igor V. Pletnev, Andreì L. Tchougréeff:
Low- and high-spin iron (II) complexes studied by effective crystal field method combined with molecular mechanics. 1703-1719 - 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. 1720-1729 - Chris Oostenbrink, Wilfred F. van Gunsteren:
Single-step perturbations to calculate free energy differences from unphysical reference states: Limits on size, flexibility, and character. 1730-1739 - Frank Neese:
An improvement of the resolution of the identity approximation for the formation of the Coulomb matrix. 1740-1747 - Alain Laederach, Peter J. Reilly:
Specific empirical free energy function for automated docking of carbohydrates to proteins. 1748-1757 - Paulo Fernando Bruno Gonçalves, Hubert Stassen:
Free energy of solvation from molecular dynamics simulations for low dielectric solvents. 1758-1765 - Scott Habershon, Kenneth D. M. Harris, Roy L. Johnston:
Development of a multipopulation parallel genetic algorithm for structure solution from powder diffraction data. 1766-1774 - Ramkumar Rajamani, Kevin J. Naidoo, Jiali Gao:
Implementation of an adaptive umbrella sampling method for the calculation of multidimensional potential of mean force of chemical reactions in solution. 1775-1781 - Aimée Tomlinson, David Yaron:
Direct INDO/SCI method for excited state calculations. 1782-1788 - Bülent Balta, Viktorya Aviyente:
Solvent effects on glycine. I. A supermolecule modeling of tautomerization via intramolecular proton transfer. 1789-1802 - Brian D. Wladkowski, Paul Ostazeski, Sarah Chenoweth, Steven J. Broadwater, Morris Krauss:
Hydrolysis of cyclic phosphates by ribonuclease A: A computational study using a simplified ab initio quantum model. 1803-1811 - Feng Yang, Zhen-Dong Wang, Yun-Ping Huang, Hai-Liang Zhu:
Novel topological index F based on incidence matrix. 1812-1820
- Michael S. Lee, Michael Feig, Freddie R. Salsbury Jr., Charles L. Brooks III:
New analytic approximation to the standard molecular volume definition and its application to generalized born calculations - Erratum. 1821
Volume 24, Number 15, 30 November 2003
- Hiroshi Tatewaki, Yoshihiro Watanabe:
Gaussian-type function set without prolapse for the Dirac-Fock-Roothaan equation. 1823-1828 - Robert Ponec, Gleb Yuzhakov, Ramon Carbó-Dorca:
Chemical structures from the analysis of domain-averaged Fermi holes: Multiple metalmetal bonding in transition metal compounds. 1829-1838 - Hua Zhu, Daiqian Xie, Guosen Yan:
Theoretical studies for structures and energetics of RgnN2O (RgHe, Ne, Ar) clusters. 1839-1845 - Da W. Zhang, X. H. Chen, John Z. H. Zhang:
Molecular caps for full quantum mechanical computation of peptide-water interaction energy. 1846-1852 - Adélia J. A. Aquino, Daniel Tunega, Georg Haberhauer, Martin H. Gerzabek, Hans Lischka:
Adsorption of organic substances on broken clay surfaces: A quantum chemical study. 1853-1863 - Natalia Díaz, Dimas Suárez, Tomás Luis Sordo:
Conformational properties of penicillins: Quantum chemical calculations and molecular dynamics simulations of benzylpenicillin. 1864-1873 - Kazuhiro Ishida:
Molecular integrals over the gauge-including atomic orbitals. II. The Breit-Pauli interaction. 1874-1890 - Filip Ryjáek, Tomá Kuba, Pavel Hobza:
New parameterization of the Cornell et al. empirical force field covering amino group nonplanarity in nucleic acid bases. 1891-1902 - R. Bochicchio, L. Lain, Alícia Torre:
Determination of atomic valence indices from population analyses at correlated level. 1902-1909 - Karine Bastard, Aurélien Thureau, Richard Lavery, Chantal Prévost:
Docking macromolecules with flexible segments. 1910-1920 - Illia Horenko, Martin Weiser:
Adaptive integration of molecular dynamics. 1921-1929 - Justin L. MacCallum, D. Peter Tieleman:
Calculation of the water-cyclohexane transfer free energies of neutral amino acid side-chain analogs using the OPLS all-atom force field. 1930-1935 - Urs Haberthür, Nicolas Majeux, Philipp Werner, Amedeo Caflisch:
Efficient evaluation of the effective dielectric function of a macromolecule in aqueous solution. 1936-1949 - R. Gautier, Pierre Tufféry:
Critical assessment of side-chain conformational space sampling procedures designed for quantifying the effect of side-chain environment. 1950-1961
Volume 24, Number 16, December 2003
- 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. 1963-1970 - Pablo A. Molina, Hui Li, Jan H. Jensen:
Intraprotein electrostatics derived from first principles: Divide-and-conquer approaches for QM/MM calculations. 1971-1979 - Thomas E. Exner, Paul G. Mezey:
Ab initio quality properties for macromolecules using the ADMA approach. 1980-1986 - Chia-En Chang, Michael K. Gilson:
Tork: Conformational analysis method for molecules and complexes. 1987-1998 - Yong Duan, Chun Wu, Shibasish Chowdhury, Mathew C. Lee, Guoming Xiong, Wei Zhang, Rong Yang, Piotr Cieplak, Ray Luo, Tai-Sung Lee, James W. Caldwell, Junmei Wang, Peter A. Kollman:
A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. 1999-2012 - Karl Jug, Gerald Geudtner:
Bond energies for molecules, clusters, and deposit systems. 2013-2022 - Luc Claes, Jean-Pierre François, Michael S. Deleuze:
Theoretical study of the internal elimination reactions of xanthate precursors. 2023-2031 - Jorng-Tzong Horng, Hsien-Da Huang, Shih-Hsien Wang, Ming-You Chen, Shir-Ly Huang, Jenn-Kang Hwang:
Computing motif correlations in proteins. 2032-2043 - Pedro Braña, José A. Sordo:
Theoretical approach to the mechanism of reactions between halogen atoms and unsaturated hydrocarbons: The Cl + propene reaction. 2044-2062 - Qing Zhang, Daniel A. Beard, Tamar Schlick:
Constructing irregular surfaces to enclose macromolecular complexes for mesoscale modeling using the discrete surface charge optimization (DISCO) algorithm. 2063-2074 - E. Valderrama, Richard J. Wheatley:
An environmental pseudopotential approach to molecular interactions: Implementation in MOLPRO. 2075-2082 - Satoshi Yokojima, Guanhua Chen, Ruixue Xu, Yijing Yan:
A dynamic mean field theory for dissipative interacting many-electron systems: Markovian formalism and its implementation. 2083-2092 - Alberto Del Rio, Abdou Boucekkine, Jean Meinnel:
Reassessment of methyl rotation barriers and conformations by correlated quantum chemistry methods. 2093-2100
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