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
Electronic Edition (link) BibTeX
- Andrew Smellie, Robert Stanton, Randy Henne, Steven L. Teig:
Conformational analysis by intersection: CONAN.
10-20
Electronic Edition (link) BibTeX
- Asim Okur, Bentley Strockbine, Viktor Hornak, Carlos Simmerling:
Using PC clusters to evaluate the transferability of molecular mechanics force fields for proteins.
21-31
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Edward C. Sherer, Darrin M. York, Christopher J. Cramer:
Fast approximate methods for calculating nucleic acid base pair interaction energies.
57-67
Electronic Edition (link) BibTeX
- Scott Brown, Teresa Head-Gordon:
Cool walking: A new Markov chain Monte Carlo sampling method.
68-76
Electronic Edition (link) BibTeX
- Danny Barash, Linjing Yang, Xiaoliang Qian, Tamar Schlick:
Inherent speedup limitations in multiple time step/particle mesh Ewald algorithms.
77-88
Electronic Edition (link) BibTeX
- Chaok Seok, J. Ben Rosen, John D. Chodera, Ken A. Dill:
MOPED: Method for optimizing physical energy parameters using decoys.
89-97
Electronic Edition (link) BibTeX
- Gregori Ujaque, Dean J. Tantillo, Yunfeng Hu, K. 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
Electronic Edition (link) BibTeX
- Karl Nicholas Kirschner, Anita H. Lewin, J. Phillip Bowen:
Molecular mechanics force-field development for amino acid zwitterions.
111-128
Electronic Edition (link) BibTeX
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
Electronic Edition (link) BibTeX
- Francesca Massi, John E. Straub:
Structural and dynamical analysis of the hydration of the Alzheimer's beta-amyloid peptide.
143-153
Electronic Edition (link) BibTeX
- Alexander V. Mitin, Jon Baker, Krzysztof Wolinski, Peter Pulay:
Parallel stored-integral and semidirect Hartree-Fock and DFT methods with data compression.
154-160
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Mireia Garcia-Viloca, Cristóbal Alhambra, Donald G. Truhlar, Jiali Gao:
Hydride transfer catalyzed by xylose isomerase: Mechanism and quantum effects.
177-190
Electronic Edition (link) BibTeX
- John L. Klepeis, Christodoulos A. Floudas:
Prediction of beta-sheet topology and disulfide bridges in polypeptides.
191-208
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- D. Benjamin Gordon, Geoffrey K. Hom, Stephen L. Mayo, Niles A. Pierce:
Exact rotamer optimization for protein design.
232-243
Electronic Edition (link) BibTeX
- Satoshi Okumoto, Shinichi Yamabe:
Computational study of epoxy-amine reactions.
244-253
Electronic Edition (link) BibTeX
Software News and Updates
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
Electronic Edition (link) BibTeX
- Genyuan Li, Herschel Rabitz, Sheng-Wei Wang, Panos G. Georgopoulos:
Correlation method for variance reduction of Monte Carlo integration in RS-HDMR.
277-283
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Christopher S. Page, Massimo Olivucci:
Ground and excited state CASPT2 geometry optimizations of small organic molecules.
298-309
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Alicia C. Lorenzo, Pedro G. Pascutti, Paulo Mascarello Bisch:
Nonspecific interaction forces at water-membrane interface by forced molecular dynamics simulations.
328-339
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Jinshan Li, Feng Zhao, Fuqian Jing:
An ab initio study of intermolecular interactions of nitromethane dimer and nitromethane trimer.
345-352
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Christofer S. Tautermann, Andreas F. Voegele, Thomas Loerting, Peter Kaps, Klaus R. Liedl:
Extended method for adiabatic mode reordering.
386-395
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
Volume 24,
Number 4,
March 2003
- Shridhar R. Gadre:
Foreword.
408
Electronic Edition (link) BibTeX
- Christophe Chipot:
Rational determination of charge distributions for free energy calculations.
409-415
Electronic Edition (link) BibTeX
- Ibon Alkorta, Jose Elguero, Enrique Espinosa, Ignasi Mata, Elies Molins:
Comparison of electron density properties in frozen and relaxed electronic distributions.
416-421
Electronic Edition (link) BibTeX
- Carlo Gatti, Fausto Cargnoni, Luca Bertini:
Chemical information from the source function.
422-436
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- George Maroulis:
Ab initio determination of the electric multipole moments and static (hyper)polarizability of HCCX, X = F, Cl, Br, and I.
443-452
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- K. Babu, Shridhar R. Gadre:
Ab initio quality one-electron properties of large molecules: Development and testing of molecular tailoring approach.
484-495
Electronic Edition (link) BibTeX
- Eduardo Chamorro, Patricio Fuentealba, Andreas Savin:
Electron probability distribution in AIM and ELF basins.
496-504
Electronic Edition (link) BibTeX
- Peter Politzer, Jane S. Murray, Pat Lane:
Electrostatic potentials and covalent radii.
505-511
Electronic Edition (link) BibTeX
- Christopher E. Whitehead, Curt M. Breneman, Nagamani Sukumar, M. D. Ryan:
Transferable atom equivalent multicentered multipole expansion method.
512-529
Electronic Edition (link) BibTeX
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
Electronic Edition (link) BibTeX
- Paola Facchini, Felice Grandinetti:
Concerning the reaction between singlet nitrenium ions and water: A computational investigation on competitive reaction paths.
547-564
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Gabriela L. Borosky:
Theoretical study concerning the reactivity of imine derivatives of polycyclic aromatic hydrocarbons.
601-608
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Meng-Sheng Liao, Yun Lu, Steve Scheiner:
Performance assessment of density-functional methods for study of charge-transfer complexes.
623-631
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- C. F. Cloud III, M. Schwartz:
Systematic errors in DFT calculations of haloalkane heats of formation.
640-646
Electronic Edition (link) BibTeX
- Genyuan Li, Maxim Artamonov, Herschel Rabitz, Sheng-Wei Wang, Panos G. Georgopoulos, Metin Demiralp:
High-dimensional model representations generated from low order terms - lp-RS-HDMR.
647-656
Electronic Edition (link) BibTeX
Software News and Updates
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
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Luis Lorenzo, Ricardo A. Mosquera:
A box-counting-based algorithm for computing Shannon entropy in molecular dynamics simulations.
707-713
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Yu-Dong Cai, Xiao-Jun Liu, Kuo-Chen Chou:
Prediction of protein secondary structure content by artificial neural network.
727-731
Electronic Edition (link) BibTeX
- Peter M. W. Gill, Siu-Hung Chien:
Radial quadrature for multiexponential integrands.
732-740
Electronic Edition (link) BibTeX
- Tanja Schulz-Gasch, Martin Stahl:
Mechanistic insights into oxidosqualene cyclizations through homology modeling.
741-753
Electronic Edition (link) BibTeX
- Markus Pernpointner, Lucas Visscher:
Parallelization of four-component calculations. II. Symmetry-driven parallelization of the 4-Spinor CCSD algorithm.
754-759
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- David Zanuy, Carlos Alemán, Manuel Laso, Sebastián Muñoz-Guerra:
Thermally induced phase transition in helical comblike poly(-peptide)s: An atomistic simulation.
770-778
Electronic Edition (link) BibTeX
- Matteo Pappalardo, Danilo Milardi, Domenico M. Grasso, Carmelo La Rosa:
Free energy perturbation and molecular dynamics calculations of copper binding to azurin.
779-785
Electronic Edition (link) BibTeX
- Mark Pinsky, Dina Yogev-Einot, David Avnir:
Statistical analysis of the estimation of distance measures.
786-796
Electronic Edition (link) BibTeX
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
Electronic Edition (link) BibTeX
- Majda Rahal-Sekkal, 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
Electronic Edition (link) BibTeX
- José Mario Martínez, Leandro Martínez:
Packing optimization for automated generation of complex system's initial configurations for molecular dynamics and docking.
819-825
Electronic Edition (link) BibTeX
- Kenshu Kamiya, Yoko Sugawara, Hideaki Umeyama:
Algorithm for normal mode analysis with general internal coordinates.
826-841
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Valentina Vetere, Pascale Maldivi, Carlo Adamo:
Comparative studies of quasi-relativistic density functional methods for the description of lanthanide and actinide complexes.
850-858
Electronic Edition (link) BibTeX
- I. Ema, J. M. García de la Vega, G. Ramírez, R. López, Jaime Fernández Rico, H. Meissner, J. Paldus:
Polarized basis sets of Slater-type orbitals: H to Ne atoms.
859-868
Electronic Edition (link) BibTeX
- Carlos Renato Zacharias, Maurício Ruv Lemes, Arnaldo Dal Pino Júnior, David Santo Orcero:
Predicting structural models for silicon clusters.
869-875
Electronic Edition (link) BibTeX
- Mark Bathe, Gregory C. Rutledge:
Inverse Monte Carlo procedure for conformation determination of macromolecules.
876-890
Electronic Edition (link) BibTeX
- Joseph V. Turner, David J. Cutler, Ian Spence, Desmond J. Maddalena:
Selective descriptor pruning for QSAR/QSPR studies using artificial neural networks.
891-897
Electronic Edition (link) BibTeX
- Miroslav Pinak:
8-oxoguanine lesioned B-DNA molecule complexed with repair enzyme hOGG1: A molecular dynamics study.
898-907
Electronic Edition (link) BibTeX
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
Electronic Edition (link) BibTeX
- Wataru Shinoda, Masuhiro Mikami:
Rigid-body dynamics in the isothermal-isobaric ensemble: A test on the accuracy and computational efficiency.
920-930
Electronic Edition (link) BibTeX
- Yong Wu, Daiqian Xie, Ying Xue:
Ab initio studies for the photodissociation mechanism of hydroxyacetone.
931-938
Electronic Edition (link) BibTeX
- Shinichi Yamabe, Noriko Tsuchida:
A computational study of interactions between acetic acid and water molecules.
939-947
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Kathryn N. Rankin, Traian Sulea, Enrico O. Purisima:
On the transferability of hydration-parametrized continuum electrostatics models to solvated binding calculations.
954-962
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
Software News and Updates
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
Electronic Edition (link) BibTeX
- Kristin L. Meagher, Luke T. Redman, Heather A. Carlson:
Development of polyphosphate parameters for use with the AMBER force field.
1016-1025
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Jos A. Hageman, Ron Wehrens, René de Gelder, Lutgarde M. C. Buydens:
Powder pattern indexing using the weighted crosscorrelation and genetic algorithms.
1043-1051
Electronic Edition (link) BibTeX
- David C. Chatfield, Alberto Augsten, Cassian D'Cunha, Sergio E. Wong:
Methyl dynamics in crystalline amino acids: MD and NMR.
1052-1058
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Toshimasa Ishida, George C. Schatz:
A local interpolation scheme using no derivatives in potential sampling: Application to O(1D) + H2 system.
1077-1086
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Lionello Pogliani:
Complete graph conjecture for inner-core electrons: Homogeneous index case.
1097-1109
Electronic Edition (link) BibTeX
- Suzanne W. Sirois, Emil I. Proynov, Jean-François Truchon, C. M. Tsoukas, Dennis R. Salahub:
A density functional study of the hydrogen-bond network within the HIV-1 protease catalytic site cleft.
1110-1119
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Erik Van Lenthe, Evert Jan Baerends:
Optimized Slater-type basis sets for the elements 1-118.
1142-1156
Electronic Edition (link) BibTeX
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
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Jon Baker, Peter Pulay:
Assessment of the OLYP and O3LYP density functionals for first-row transition metals.
1184-1191
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Sean A. C. McDowell:
A computational study of the LiH dimer.
1201-1207
Electronic Edition (link) BibTeX
- David Curcó, David Zanuy, Carlos Alemán:
EVEBAT: A fast strategy for the examination of the empty space in polymer matrices.
1208-1214
Electronic Edition (link) BibTeX
- Dimitris K. Agrafiotis:
Stochastic proximity embedding.
1215-1221
Electronic Edition (link) BibTeX
- B. Das, Hagai Meirovitch, I. Michael Navon:
Performance of hybrid methods for large-scale unconstrained optimization as applied to models of proteins.
1222-1231
Electronic Edition (link) BibTeX
- Hannes H. Loeffler:
Many-body effects on structure and dynamics of aqueous ionic solutions.
1232-1239
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Joseph Ivanic, Klaus Ruedenberg:
A MCSCF method for ground and excited states based on full optimizations of successive Jacobi rotations.
1250-1262
Electronic Edition (link) BibTeX
- Carles Curutchet, Josep María Bofill, Begoña Hernández, Modesto Orozco, F. Javier Luque:
Energy decomposition in molecular complexes: Implications for the treatment of polarization in molecular simulations.
1263-1275
Electronic Edition (link) BibTeX
Software News and Updates
Erratum
Volume 24,
Number 11,
August 2003
- Kyle A. Beran:
Isomers of C20: An energy profile II.
1287-1290
Electronic Edition (link) BibTeX
- Jason D. Thompson, Christopher J. Cramer, Donald G. Truhlar:
Parameterization of charge model 3 for AM1, PM3, BLYP, and B3LYP.
1291-1304
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Shandar Ahmad, M. Michael Gromiha:
Design and training of a neural network for predicting the solvent accessibility of proteins.
1313-1320
Electronic Edition (link) BibTeX
- Julio Peiró-García, Víctor M. Ramírez-Ramírez, Ignacio Nebot-Gil:
A theoretical ab initio study on the H2NO + O3 reaction.
1321-1328
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Sean Cahill, Michael Cahill, Kevin Cahill:
On the kinematics of protein folding.
1364-1370
Electronic Edition (link) BibTeX
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
Electronic Edition (link) BibTeX
- Mutsumi Hirama, Toshimasa Ishida, Jun-Ichi Aihara:
Possible molecular hydrogen formation mediated by the radical cations of anthracene and pyrene.
1378-1382
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Henryk A. Witek, Haruyuki Nakano, Kimihiko Hirao:
Multireference perturbation theory with optimized partitioning. II. Applications to molecular systems.
1390-1400
Electronic Edition (link) BibTeX
- Masahiro Yamanaka, Akiko Inagaki, Eiichi Nakamura:
Theoretical studies on structures and reactivities of organocuprate(I) and organocopper(III) species.
1401-1409
Electronic Edition (link) BibTeX
- A. V. Nemukhin, B. L. Grigorenko, Igor A. Topol, Stanley K. Burt:
Flexible effective fragment QM/MM method: Validation through the challenging tests.
1410-1420
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Bojan Zagrovic, Vijay Pande:
Solvent viscosity dependence of the folding rate of a small protein: Distributed computing study.
1432-1436
Electronic Edition (link) BibTeX
- Mark N. Kobrak:
Systematic and statistical error in histogram-based free energy calculations.
1437-1446
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Jenn-Huei Lii, Kuo-Hsiang Chen, Kathleen A. Durkin, Norman L. Allinger:
Alcohols, ethers, carbohydrates, and related compounds. II. The anomeric effect.
1473-1489
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Jenn-Huei Lii, Kuo-Hsiang Chen, Norman L. Allinger:
Alcohols, ethers, carbohydrates, and related compounds. IV. carbohydrates.
1504-1513
Electronic Edition (link) BibTeX
- H. Bernhard Schlegel:
Exploring potential energy surfaces for chemical reactions: An overview of some practical methods.
1514-1527
Electronic Edition (link) BibTeX
Volume 24,
Number 13,
October 2003
- Stefan Grimme:
Improved third-order Møller-Plesset perturbation theory.
1529-1537
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Brian W. Hopkins, Gregory S. Tschumper:
A multicentered approach to integrated QM/QM calculations. Applications to multiply hydrogen bonded systems.
1563-1568
Electronic Edition (link) BibTeX
- Niall J. English, J. M. D. Macelroy:
Structural and dynamical properties of methane clathrate hydrates.
1569-1581
Electronic Edition (link) BibTeX
- Delano P. Chong, Myrta Grüning, Evert Jan Baerends:
STO and GTO field-induced polarization functions for H to Kr.
1582-1591
Electronic Edition (link) BibTeX
- Takao Tsuneda, Muneaki Kamiya, Kimihiko Hirao:
Regional self-interaction correction of density functional theory.
1592-1598
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Antonio Morreale, Josep Lluis Gelpí, F. Javier Luque, Modesto Orozco:
Continuum and discrete calculation of fractional contributions to solvation free energy.
1610-1623
Electronic Edition (link) BibTeX
- Dirk Reith, Mathias Pütz, Florian Müller-Plathe:
Deriving effective mesoscale potentials from atomistic simulations.
1624-1636
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Julio Peiró-García, Ignacio Nebot-Gil:
Ab initio study of the mechanism of the atmospheric reaction: NO2 + O3 NO3 + O2.
1657-1663
Electronic Edition (link) BibTeX
- Robert M. Dirks, Niles A. Pierce:
A partition function algorithm for nucleic acid secondary structure including pseudoknots.
1664-1677
Electronic Edition (link) BibTeX
Software News and Updates
Erratum
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
Electronic Edition (link) BibTeX
- Mikhail B. Darkhovskii, Igor V. Pletnev, Anderì L. Tchougréeff:
Low- and high-spin iron (II) complexes studied by effective crystal field method combined with molecular mechanics.
1703-1719
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Frank Neese:
An improvement of the resolution of the identity approximation for the formation of the Coulomb matrix.
1740-1747
Electronic Edition (link) BibTeX
- Alain Laederach, Peter J. Reilly:
Specific empirical free energy function for automated docking of carbohydrates to proteins.
1748-1757
Electronic Edition (link) BibTeX
- Paulo Fernando Bruno Gonçalves, Hubert Stassen:
Free energy of solvation from molecular dynamics simulations for low dielectric solvents.
1758-1765
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Aimée Tomlinson, David Yaron:
Direct INDO/SCI method for excited state calculations.
1782-1788
Electronic Edition (link) BibTeX
- Bülent Balta, Viktorya Aviyente:
Solvent effects on glycine. I. A supermolecule modeling of tautomerization via intramolecular proton transfer.
1789-1802
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Feng Yang, Zhen-Dong Wang, Yun-Ping Huang, Hai-Liang Zhu:
Novel topological index F based on incidence matrix.
1812-1820
Electronic Edition (link) BibTeX
Erratum
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
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Hua Zhu, Daiqian Xie, Guosen Yan:
Theoretical studies for structures and energetics of RgnN2O (RgHe, Ne, Ar) clusters.
1839-1845
Electronic Edition (link) BibTeX
- D. W. Zhang, X. H. Chen, J. Z. H. Zhang:
Molecular caps for full quantum mechanical computation of peptide-water interaction energy.
1846-1852
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Natalia Díaz, Dimas Suárez, Tomás Luis Sordo:
Conformational properties of penicillins: Quantum chemical calculations and molecular dynamics simulations of benzylpenicillin.
1864-1873
Electronic Edition (link) BibTeX
- Kazuhiro Ishida:
Molecular integrals over the gauge-including atomic orbitals. II. The Breit-Pauli interaction.
1874-1890
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- R. Bochicchio, L. Lain, A. Torre:
Determination of atomic valence indices from population analyses at correlated level.
1902-1909
Electronic Edition (link) BibTeX
- Karine Bastard, Aurélien Thureau, Richard Lavery, Chantal Prévost:
Docking macromolecules with flexible segments.
1910-1920
Electronic Edition (link) BibTeX
- Illia Horenko, Martin Weiser:
Adaptive integration of molecular dynamics.
1921-1929
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Urs Haberthür, Nicolas Majeux, Philipp Werner, Amedeo Caflisch:
Efficient evaluation of the effective dielectric function of a macromolecule in aqueous solution.
1936-1949
Electronic Edition (link) BibTeX
- R. Gautier, Pierre Tufféry:
Critical assessment of side-chain conformational space sampling procedures designed for quantifying the effect of side-chain environment.
1950-1961
Electronic Edition (link) BibTeX
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
Electronic Edition (link) BibTeX
- Pablo A. Molina, Hui Li, Jan H. Jensen:
Intraprotein electrostatics derived from first principles: Divide-and-conquer approaches for QM/MM calculations.
1971-1979
Electronic Edition (link) BibTeX
- Thomas E. Exner, Paul G. Mezey:
Ab initio quality properties for macromolecules using the ADMA approach.
1980-1986
Electronic Edition (link) BibTeX
- Chia-En Chang, Michael K. Gilson:
Tork: Conformational analysis method for molecules and complexes.
1987-1998
Electronic Edition (link) BibTeX
- Yong Duan, Chun Wu, Shibasish Chowdhury, Mathew C. Lee, Guoming Xiong, Wei Zhang, Rong Yang, Piotr Cieplak, Ray Luo, Taisung 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
Electronic Edition (link) BibTeX
- Karl Jug, Gerald Geudtner:
Bond energies for molecules, clusters, and deposit systems.
2013-2022
Electronic Edition (link) BibTeX
- L. Claes, J.-P. François, M. S. Deleuze:
Theoretical study of the internal elimination reactions of xanthate precursors.
2023-2031
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Pedro Braña, José A. Sordo:
Theoretical approach to the mechanism of reactions between halogen atoms and unsaturated hydrocarbons: The Cl + propene reaction.
2044-2062
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- E. Valderrama, R. J. Wheatley:
An environmental pseudopotential approach to molecular interactions: Implementation in MOLPRO.
2075-2082
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Alberto Del Rio, Abdou Boucekkine, Jean Meinnel:
Reassessment of methyl rotation barriers and conformations by correlated quantum chemistry methods.
2093-2100
Electronic Edition (link) BibTeX
Copyright © Sun May 17 00:07:16 2009
by Michael Ley (ley@uni-trier.de)
