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ORCIDJournal of Computational Chemistry, Volume 21
Volume 21, Number 1, 15 January 2000
- Finn Drabløs:
Ab initio simulation of chemical shift effects from metal ion binding in Bacitracin A. 1-7 - Petr Bou:
Comparison of Hartree-Fock and Kohn-Sham determinants as wave functions. 8-16 - Gerrit Schüürmann:
Prediction of Henry's law constant of benzene derivatives using quantum chemical continuum-solvation models. 17-34 - E. Del Río, Ramón López, María Isabel Menéndez Rodríguez, Tomás Luis Sordo:
A theoretical study of the reaction of HCO+ with C2H2. 35-42 - Jose M. Mercero, Paul Barrett, Cheuk W. Lam, Joseph E. Fowler, Jesus M. Ugalde, Lee G. Pedersen:
Quantum mechanical calculations on phosphate hydrolysis reactions. 43-51 - Roberto Izzo, Martin Klessinger:
Optimization of conical intersections using the semiempirical MNDOC-CI method with analytic gradients. 52-62 - Marie C. Vicens, Gustavo E. López:
Density functional studies of cation-water complexes. 63-68 - Jon Baker, Peter Pulay:
Efficient geometry optimization of molecular clusters. 69-76 - Kenny B. Lipkowitz:
Book review. 77-78
Volume 21, Number 2, 30 January 2000
- Konrad Hinsen:
The molecular modeling toolkit: A new approach to molecular simulations. 79-85 - Nicolas Foloppe, Alexander D. MacKerell Jr.:
All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data. 86-104 - Alexander D. MacKerell Jr., Nilesh K. Banavali:
All-atom empirical force field for nucleic acids: II. Application to molecular dynamics simulations of DNA and RNA in solution. 105-120 - See-Wing Chiu, Michael M. Clark, Shankar Subramaniam, Eric Jakobsson:
Collective motion artifacts arising in long-duration molecular dynamics simulations. 121-131 - Araz Jakalian, Bruce L. Bush, David B. Jack, Christopher I. Bayly:
Fast, efficient generation of high-quality atomic charges. AM1-BCC model: I. Method. 132-146 - Luis B. Morales, Ramón Garduño-Juárez, J. M. Aguilar-Alvarado, F. J. Riveros-Castro:
A parallel tabu search for conformational energy optimization of oligopeptides. 147-156 - Timothy R. Forester, William Smith:
SHAKE, rattle, and roll: Efficient constraint algorithms for linked rigid bodies. 157
Volume 21, Number 3, February 2000
- Hon M. Chun, Carlos E. Padilla, Donovan N. Chin, Masakatsu Watanabe, Valeri I. Karlov, Howard E. Alper, Keto Soosaar, Kim B. Blair, Oren M. Becker, Leo S. D. Caves, Robert Nagle, David N. Haney, Barry L. Farmer:
MBO(N)D: A multibody method for long-time molecular dynamics simulations. 159-184 - C. R. Sarma, A. V. V. Nampoothiri:
A labeling scheme for young tableaux spanning representations of permutation group S(N). 185-190 - Vladimir A. Bushenkov
, J. P. Prates Ramalho, Georgi V. Smirnov:
Adsorption integral equation via complex approximation with constraints: The Langmuir kernel. 191-200 - Masaaki Kawata, Masuhiro Mikami:
Computationally efficient canonical molecular dynamics simulations by using a multiple time-step integrator algorithm combined with the particle mesh Ewald method and with the fast multipole method. 201-217 - H. Donald B. Jenkins, Luminita C. Jitariu, Ingo Krossing, Jack Passmore, Reijo Suontamo:
Basis set and correlation effects in the calculation of accurate gas phase dimerization energies of two M+2 to give M2+4 (M = S, Se). 218-226 - Fakhr Abu-Awwad, Peter Politzer:
Variation of parameters in Becke-3 hybrid exchange-correlation functional. 227-238 - Robert J. Bubel, Warthen Douglass, David P. White:
Molecular mechanics-based measures of steric effects: Customized code to compute Ligand repulsive energies. 239-246
Volume 21, Number 4, March 2000
- Denton S. Ebel, Mark S. Ghiorso, Richard O. Sack, Lawrence Grossman:
Gibbs energy minimization in gas + liquid + solid systems. 247-256 - Marta Forés, Miquel Duran, Miquel Solà, Ludwik Adamowicz:
Theoretical characterization of intramolecular proton transfer in the ground and the lowest-lying triplet excited states of 1-amino-3-propenal: a methodological comparison. 257-269 - Bernd Mayer, Giancarlo Marconi:
Circular dichroic constrained structure optimization of homoalanine peptides. 270-281 - Jean-Didier Maréchal, Guada Barea, Feliu Maseras, Agustí Lledós, Liliane Mouawad, David Pérahia:
Theoretical modeling of the heme group with a hybrid QM/MM method. 282-294 - Laurent David, Ray Luo, Michael K. Gilson:
Comparison of generalized born and poisson models: Energetics and dynamics of HIV protease. 295-309 - Eugene T. Knight:
A radial probability density function for analysis of canonical molecular orbitals. 310-321 - Redouan El-Bergmi, José Antonio Dobado Jimez, Dolores Portal, José Molina Molina:
Stabilization in neutral bicyclic sulfoxide compounds. 322-327
Volume 21, Number 5, 15 April 2000
- Guyan Liang, Jennifer B. Sorensen, David Whitmire, J. Phillip Bowen:
Molecular mechanics (MM3) parameterization for oxocarbenium ions. 329-339 - Derek M. Dolney, Gregory D. Hawkins, Paul Winget, Daniel A. Liotard, Christopher J. Cramer, Donald G. Truhlar:
Universal solvation model based on conductor-like screening model. 340-366 - Emmanuelle Rousseau, Didier Mathieu:
Atom equivalents for converting DFT energies calculated on molecular mechanics structures to formation enthalpies. 367-379 - Young Joo Lee, Jae Yeol Maeng, Eok-Kyun Lee, Bongsoo Kim, Sehun Kim, Kyu-Kwang Han:
Melting behaviors of icosahedral metal clusters studied by Monte Carlo simulations. 380-387 - Kirsi Tappura, Maija Lahtela-Kakkonen, Teleman:
A new soft-core potential function for molecular dynamics applied to the prediction of protein loop conformations. 388-397 - Giovanni Talarico, Peter H. M. Budzelaar, Anton W. Gal:
Ethylene coordination, insertion, and chain transfer at a cationic aluminum center: A comparative study with Ab Initio correlated level and density functional methods. 398-410 - Steven Feldgus, Clark R. Landis, Eric D. Glendening, Frank Weinhold:
Natural resonance theory. I. General formalism. 411-413
Volume 21, Number 6, 30 April 2000
- Ludmila V. Moskaleva, Ming-Chang Lin:
Unimolecular isomerization/decomposition of cyclopentadienyl and related bimolecular reverse process: ab initio MO/statistical theory study. 415-425 - Allan D. Headley, Stephen D. Starnes:
Theoretical analysis of fluoroglycine conformers. 426-431 - Pawel Kdzierski, W. Andrzej Sokalski, Morris Krauss:
Nonempirical analysis of nature of catalytic effects in ribonuclease A active site. 432-445 - M. F. O'Donohue, E. Minasian, Simon Joshua Leach, Antony W. Burgess, Herbert R. Treutlein:
PEPCAT - A new tool for conformational analysis of peptides. 446-461 - Luis Carballeira, Ignacio Pérez-Juste:
An ab initio interpretation in gas phase and aqueous solution of the generalized anomeric effect in ROCR2NR2 (R = H, CH3). 462-477 - Stuart R. Gooding, Peter J. Winn, Richard I. Maurer, György G. Ferenczy, John R. Miller, Jayne E. Harris, D. Vaughan Griffiths, Christopher A. Reynolds:
Fully polarizable QM/MM calculations: An application to the nonbonded iodine-oxygen interaction in dimethyl-2-iodobenzoylphosphonate. 478-482 - Dominique Dehareng, Georges Dive:
Hartree-Fock instabilities and electronic properties. 483-504 - John F. Stanton:
Book review. 505-507
Volume 21, Number 7, May 2000
- Franck Fuster, Alain Sevin, Bernard Silvi:
Determination of substitutional sites in heterocycles from the topological analysis of the electron localization function (ELF). 509-514 - Stefano Alcaro, Francesco Gasparrini, O. Incani, S. Mecucci, D. Misiti, Marco Pierini, Claudio Villani:
A quasi-flexible automatic docking processing for studying stereoselective recognition mechanisms. Part I. Protocol validation. 515-530 - Reece K. Hart, Rohit V. Pappu, Jay W. Ponder:
Exploring the similarities between potential smoothing and simulated annealing. 531-552 - Robert E. Tuzun, Donald W. Noid, Bobby G. Sumpter:
Computation of internal coordinates, derivatives, and gradient expressions: torsion and improper torsion. 553-561 - Ramón Bosque, Feliu Maseras:
Performance of the semiempirical PM3 (tm) method in the geometry optimization of transition metal complexes. 562-571 - Margarita Isabel Bernal-Uruchurtu, Marilia T. C. Martins-Costa, Claude Millot, Manuel F. Ruiz-López:
Improving description of hydrogen bonds at the semiempirical level: water-water interactions as test case. 572-581 - Philippe Derreumaux:
Predicting helical hairpins from sequences by Monte Carlo simulations. 582-589
Volume 21, Number 8, June 2000
- Terry J. Frankcombe, Sean C. Smith:
Solving the unimolecular master equation with a weighted subspace projection method. 592-606 - Jordi Villá, Jörg Bentzien, Àngels González-Lafont, José M. Lluch, Juan Bertrán, Arieh Warshel:
Effective way of modeling chemical catalysis: Empirical valence bond picture of role of solvent and catalyst in alkylation reactions. 607-625 - Imre Jákli, András Perczel, Ödön Farkas, Attila G. Császár, Carlos P. Sosa, Imre G. Csizmadia:
Peptide models XXIII. Conformational model for polar side-chain containing amino acid residues: A comprehensive analysis of RHF, DFT, and MP2 properties of HCO-L-SER-NH2 . 626-655 - Marek Skowronek, Irena Roterman, Leszek Konieczny, Barbara Stopa, Janina Rybarska, Barbara Piekarska:
Why do Congo Red, Evans Blue, and Trypan Blue differ in their complexation properties? 656-667 - Willian R. Rocha, Wagner B. De Almeida:
Carbonyl insertion reaction into the PtC bond in heterobimetallic Pt(SnCl3)(PH3)2(CO)(CH3) compound: Theoretical study. 668-674 - Roger Arnaud, Valentina Vetere, Vincenzo Barone:
Quantum mechanical study of regioselectivity of radical additions to substituted olefins. 675-691 - Delanie Lamprecht, Gert J. Lamprecht:
A molecular mechanics force field for rhodium(I) carbonyl phosphine complexes and its application on the oxidative addition reactions of these complexes. 692-703
Volume 21, Number 9, 15 July 2000
- M. Luz Sánchez, M. Elena Martín, Manuel Angel Aguilar Espinosa, Francisco Javier Olivares del Valle:
Solvent effects by means of averaged solvent electrostatic potentials: Coupled method. 705-715 - Isidoro García-Cruz, Miguel Castro, Annik Vivier Bunge:
DFT and MP2 molecular orbital determination of OH-toluene-O2 isomeric structures in the atmospheric oxidation of toluene. 716-730 - Steven M. LaValle, Paul W. Finn, Lydia E. Kavraki, Jean-Claude Latombe:
A randomized kinematics-based approach to pharmacophore-constrained conformational search and database screening. 731-747 - Satoshi Ono, Nobuyuki Nakajima, Junichi Higo, Haruki Nakamura:
Peptide free-energy profile is strongly dependent on the force field: Comparison of C96 and AMBER95. 748-762 - Laurie A. Christianson, Melissa J. Lucero, Daniel H. Appella, Daniel A. Klein, Samuel H. Gellman:
Improved treatment of cyclic -amino acids and successful prediction of -peptide secondary structure using a modified force field: AMBER*C. 763-773 - Wolfgang Damm, Wilfred F. van Gunsteren:
Reversible peptide folding: Dependence on molecular force field used. 774-787 - Stephen P. Greatbanks, Jill E. Gready, Ajay C. Limaye, Alistair P. Rendell:
Comparison of enzyme polarization of ligands and charge-transfer effects for dihydrofolate reductase using point-charge embedded ab initio quantum mechanical and linear-scaling semiempirical quantum mechanical methods. 788-811
Volume 21, Number 10, 30 July 2000
- Buyong Ma, Jenn-Huei Lii, Norman L. Allinger:
Molecular polarizabilities and induced dipole moments in molecular mechanics. 813-825 - Manish Kumar Shukla, S. K. Mishra, Anil Kumar, P. C. Mishra:
An ab initio study of excited states of guanine in the gas phase and aqueous media: Electronic transitions and mechanism of spectral oscillations. 826-846 - Johan Wouters:
Use of theoretical descriptors to characterize cation- binding sites in (macro)molecules. 847-855 - Jian Wu, Yuansheng Jiang:
The valence bond calculations for conjugated hydrocarbons having 24-28 -electrons. 856-869 - Maria Domenica Di Benedetto, Pasquale Lucibello, Alberto L. Sangiovanni-Vincentelli, Ken Yamaguchi:
A new procedure for exact ring closure. 870-881 - András Perczel, Attila G. Császár:
Toward direct determination of conformations of protein building units from multidimensional NMR experiments I. A theoretical case study of For-Gly-NH2 and For-L-Ala-NH2. 882-900 - Xavier Grabuleda, Carlos Jaime, Peter A. Kollman:
Molecular dynamics simulation studies of liquid acetonitrile: New six-site model. 901-908
Volume 21, Number 11, August 2000
- Frederik J. Tielens, Wilfried Langenaeker, Ahmet R. Ocakoglu, Paul Geerlings:
Quantum chemical calculation of Henry constants of diatomic molecules in faujasite-type zeolites. 909-922 - Zlatko Vasilkoski, David L. Weaver:
A generator of protein folding kinetics states for the diffusion-collision model. 923-932 - Anthony S. Mitchell, Mark A. Spackman:
Molecular surfaces from the promolecule: A comparison with Hartree-Fock ab initio electron density surfaces. 933-942 - Thomas A. Baker, Gregory I. Gellene:
A hybrid ab initio/free electron computational model for conjugated dye molecules: Simple cyanines and oxonols. 943-953 - Kenji Sayano, Hidetoshi Kono, M. Michael Gromiha, Akinori Sarai:
Multicanonical Monte Carlo calculation of the free-energy map of the base-amino acid interaction. 954-962 - Francoise Rogalewicz, Gilles Ohanessian, Nohad Gresh:
Interaction of neutral and zwitterionic glycine with Zn2+ in gas phase: ab initio and SIBFA molecular mechanics calculations. 963-973 - Karl Jug, Gerald Geudtner, Thorsten Homann:
MSINDO parameterization for third-row main group elements. 974-987 - Jinn-Moon Yang, Cheng-Yan Kao:
Flexible ligand docking using a robust evolutionary algorithm. 988 - Niles A. Pierce, Jan A. Spriet, J. Desmet, Stephen L. Mayo:
Conformational splitting: A more powerful criterion for dead-end elimination. 999-1009
Volume 21, Number 12, September 2000
- Gilles Tiraboschi, Nohad Gresh, Claude Giessner-Prettre, Lee G. Pedersen, David W. Deerfield:
Parallel ab initio and molecular mechanics investigation of polycoordinated Zn(II) complexes with model hard and soft ligands: Variations of binding energy and of its components with number and charges of ligands. 1011-1039 - Friedrich Biegler-König:
Calculation of atomic integration data. 1040-1048 - Junmei Wang, Piotr Cieplak, Peter A. Kollman:
How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? 1049-1074 - Takashi Amisaki:
Precise and efficient Ewald summation for periodic fast multipole method. 1075-1087 - Martin J. Field, Marc Albe, Céline Bret, Flavien Proust-De Martin, Aline Thomas:
The dynamo library for molecular simulations using hybrid quantum mechanical and molecular mechanical potentials. 1088-1100 - Yizhuang Xu, Q. Ouyang, Jinguang Wu, J. A. Yorke, Guangxian Xu, Duanfu Xu, R. D. Soloway, J. Q. Ren:
Using fractal to solve the multiple minima problem in molecular mechanics calculation. 1101-1108 - Yuan-Jie Ye, Ling-Ling Shen:
DFT approach to calculate electronic transfer through a segment of DNA double helix. 1109-1117
Volume 21, Number 13, October 2000
- Hermes F. de Souza, Paulo H. Guadagnini, Rogério Custodio, John D. Goddard:
The correlation of proton affinities with atomic charges and electronegativities for the group 14 to 17 hydrides. 1119-1131 - Aaron R. Dinner:
Local deformations of polymers with nonplanar rigid main-chain internal coordinates. 1132-1144 - Ryan T. Koehler, Hugo O. Villar:
Design of screening libraries biased for pharmaceutical discovery. 1145-1152 - Carlo Adamo, Vincenzo Barone:
Structures and properties of lanthanide and actinide complexes by a new density functional approach: Lanthanum, gadolinium, lutetium, and thorium halides as case studies. 1153-1166 - Fco. Javier Meléndez, Blanca Gallego Luxan, Jean Demaison, Yves G. Smeyers:
Ab initio determination of the infrared phosphine torsion spectrum in vinylphosphine with ZPE correction. 1167-1175 - Markus Pernpointner, Lucas Visscher, Wibe A. de Jong, Ria Broer:
Parallelization of four-component calculations. I. Integral generation, SCF, and four-index transformation in the Dirac-Fock package MOLFDIR. 1176-1186 - Kholmirzo Kholmurodov, William Smith, Kenji Yasuoka, Thomas A. Darden, Toshikazu Ebisuzaki:
A smooth-particle mesh Ewald method for DL_POLY molecular dynamics simulation package on the Fujitsu VPP700. 1187-1191 - Cristóbal Alhambra, Jiali Gao:
Hydrogen-bonding interactions in the active site of a low molecular weight protein-tyrosine phosphatase. 1192-1203 - Frank A. Momany, Julious L. Willett:
Computational studies on carbohydrates: I. Density functional ab initio geometry optimization on maltose conformations. 1204-1219
Volume 21, Number 14, 15 November 2000
- Petter Persson, Johnny Bustad, Michael C. Zerner:
INDO calculations of small copper clusters and CO adsorbed on copper(100) surfaces. 1221-1228 - Norman L. Allinger, Kathleen A. Durkin:
Van der Waals effects between hydrogen and first-row atoms in molecular mechanics (MM3/MM4). 1229-1242 - Nino Russo, Marirosa Toscano, André Grand:
Theoretical determination of electron affinity and ionization potential of DNA and RNA bases. 1243-1250 - Fatih Yaar, Tarik Çelik, Bernd A. Berg, Hagai Meirovitch:
Multicanonical procedure for continuum peptide models. 1251-1261 - Mona C. Wells, Robert R. Lucchese:
Computing the superexchange electronic factor of electron transfer theory using a grid-based numerical method. 1262-1273 - Juan Elezgaray, Yves-Henri Sanejouand:
Modal dynamics of proteins in water. 1274-1282 - Sreedhara V. Rao:
Mechanism of some 1: 2 hydrogen transfer reactions through bond variation indices. 1283-1291 - Yoshinao Nakagawa, Nobuo Tajima, Kimihiko Hirao:
A theoretical study of catalytic hydration reactions of ethylene. 1292-1304 - Asit K. Chandra, Tadafumi Uchimaru, Masaaki Sugie:
Kinetics of the hydrogen abstraction reactions of 1, 1- and 1, 2-difluoroethane with hydroxyl radical: an ab initio study. 1305-1318
Volume 21, Number 15, 30 November 2000
- Michael J. Holst, Nathan A. Baker, Feng Wang:
Adaptive multilevel finite element solution of the Poisson-Boltzmann equation I. Algorithms and examples. 1319-1342 - Michael J. Holst, Nathan A. Baker, Feng Wang:
Adaptive multilevel finite element solution of the Poisson-Boltzmann equation II. Refinement at solvent-accessible surfaces in biomolecular systems. 1343-1352 - Nenad Raos:
Iterative method for finding the low-energy conformations based on the concept of molecular volumes. 1353-1360 - Xavier Fradera, Miquel Duran, Jordi Mestres:
Atomic transferability within the exchange-correlation density. 1361-1374 - Josep Maria Bofill, Ibério de Pinho Ribeiro Moreira, Josep Maria Anglada, Francesc Illas:
Accurate and efficient determination of higher roots in diagonalization of large matrices based in function restricted optimization algorithms. 1375-1386 - Yuxiang Bu, Chengbu Liu:
The orientation and distance-dependence analysis of the electron transfer reactivity: An electron correlation level investigation of Mn2+(H2O)2/Mn3+(H2O)2 system. 1387-1404 - Rois Benassi, Fernando Taddei:
Complete basis set model chemistry applied to molecules of increasing molecular complexity: Thermochemical properties of organic sulfur derivatives. 1405-1418
Volume 21, Number 16, December 2000
- Thom Vreven, Keiji Morokuma:
On the application of the IMOMO (integrated molecular orbital + molecular orbital) method. 1419-1432 - Richard J. Hall, Sally A. Hindle, Neil A. Burton, Ian H. Hillier:
Aspects of hybrid QM/MM calculations: The treatment of the QM/MM interface region and geometry optimization with an application to chorismate mutase. 1433-1441 - Robert B. Murphy, Dean M. Philipp, Richard A. Friesner:
A mixed quantum mechanics/molecular mechanics (QM/MM) method for large-scale modeling of chemistry in protein environments. 1442-1457 - Yirong Mo, Jiali Gao:
Ab initio QM/MM simulations with a molecular orbital-valence bond (MOVB) method: application to an SN2 reaction in water. 1458-1469 - Joachim Sauer, Marek Sierka:
Combining quantum mechanics and interatomic potential functions in ab initio studies of extended systems. 1470-1493 - Arjan van der Vaart, Valentin Gogonea, Steven L. Dixon, Kenneth M. Merz Jr.:
Linear scaling molecular orbital calculations of biological systems using the semiempirical divide and conquer method. 1494-1504 - Peter M. W. Gill, Andrew T. B. Gilbert, Terry R. Adams:
Rapid evaluation of two-center two-electron integrals. 1505-1510 - Stan J. A. van Gisbergen, Célia Fonseca Guerra, Evert Jan Baerends:
Towards excitation energies and (hyper)polarizability calculations of large molecules. Application of parallelization and linear scaling techniques to time-dependent density functional response theory. 1511-1523 - Philippe Y. Ayala, Gustavo E. Scuseria:
Electron correlation in large molecular systems using the atomic orbital formalism. The case of intermolecular interactions in crystalline urea as an example. 1524-1531 - Jing Kong, Christopher A. White, Anna I. Krylov, David Sherrill, Ross D. Adamson, Thomas R. Furlani, Michael S. Lee, Aaron M. Lee, Steven R. Gwaltney, Terry R. Adams, Christian Ochsenfeld, Andrew T. B. Gilbert, Gary S. Kedziora, Vitaly A. Rassolov, David R. Maurice, Nikhil Nair, Yihan Shao, Nicholas A. Besley, Paul E. Maslen, Jeremy P. Dombroski, Holger Daschel, Weimin Zhang, Prakashan P. Korambath, Jon Baker, Edward F. C. Byrd, Troy A. Van Voorhis, Manabu Oumi, So Hirata, Chao-Ping Hsu, Naoto Ishikawa, Jan Florián, Arieh Warshel, Benny G. Johnson, Peter M. W. Gill, Martin Head-Gordon, John A. Pople:
Q-Chem 2.0: a high-performance ab initio electronic structure program package. 1532-1548 - Karl Jug, Daniel Wichmann:
MSINDO study of large silsesquioxanes. 1549-1553 - Gongyi Hong, Marek Strajbl, Tomasz A. Wesolowski, Arieh Warshel:
Constraining the electron densities in DFT method as an effective way for ab initio studies of metal-catalyzed reactions. 1554-1561 - Jana Khandogin, Anguang Hu, Darrin M. York:
Electronic structure properties of solvated biomolecules: A quantum approach for macromolecular characterization. 1562-1571 - Bernard Kirtman, Benoît Champagne, Josep M. Luis:
Efficient treatment of the effect of vibrations on electrical, magnetic, and spectroscopic properties. 1572-1588
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