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ORCIDJournal of Computational Chemistry, Volume 20
Volume 20, Number 1, 15 January 1999
- Walter Kohn:
Thoughts about density functional theory in 1998. 1 - Shubin Liu, Robert G. Parr:
Consequences for exchange energy density functional of exponentially decaying nature of atomic electron densities. 2-11 - Manfred Lein, John F. Dobson, Eberhard K. U. Gross:
Toward the description of van der Waals interactions within density functional theory. 12-22 - Helmut Eschrig, Vito Domenico Pietro Servedio:
Relativistic density functional approach to open shells. 23-30 - Eberhard Engel, Reiner M. Dreizler:
From explicit to implicit density functionals. 31-50 - Christoph Van Wüllen:
Relativistic all-electron density functional calculations. 51-62 - Axel D. Becke:
Exploring the limits of gradient corrections in density functional theory. 63-69 - Georg Schreckenbach, P. Jeffrey Hay, Richard L. Martin:
Density functional calculations on actinide compounds: Survey of recent progress and application to [UO2X4]2- (X=F, Cl, OH) and AnF6 (An=U, Np, Pu). 70-90 - Michael Bühl, Martin Kaupp, Olga L. Malkina, Vladimir G. Malkin:
The DFT route to NMR chemical shifts. 91-105 - Nicholas C. Handy, David J. Tozer:
Excitation energies of benzene from Kohn-Sham theory. 106-113 - F. Matthias Bickelhaupt:
Understanding reactivity with Kohn-Sham molecular orbital theory: E2-SN2 mechanistic spectrum and other concepts. 114-128 - H. Chermette:
Chemical reactivity indexes in density functional theory. 129-154 - Eduardo V. Ludeña, Valentin V. Karasiev, R. López-Boada, E. Valderrama, J. Maldonado:
Local-scaling transformation version of density functional theory: Application to atoms and diatomic molecules. 155-183
Volume 20, Number 2, 30 January 1999
- Shinjiro Toyoda, Hiroh Miyagawa, Kunihiro Kitamura, Takashi Amisaki, Eiri Hashimoto, Hitoshi Ikeda, Akihiro Kusumi, Nobuaki Miyakawa:
Development of MD Engine: High-speed accelerator with parallel processor design for molecular dynamics simulations. 185-199 - María Eugenia Costas, Rodolfo Acevedo-Chávez:
Density functional study of neutral allopurinol tautomeric forms. 200-206 - Kevin S. Raymond, Ralph A. Wheeler:
Compatibility of correlation-consistent basis sets with a hybrid Hartree-Fock/density functional method. 207-216 - Jörg Weiser, Peter S. Shenkin, W. Clark Still:
Approximate atomic surfaces from linear combinations of pairwise overlaps (LCPO). 217-230 - George P. Ford, P. S. Herman, Jon W. Thompson:
Syn and anti aryl nitrenium ions. 231-243 - Jean-Yves Trosset, Harold A. Scheraga:
Flexible docking simulations: Scaled collective variable Monte Carlo minimization approach using Bezier splines, and comparison with a standard Monte Carlo algorithm. 244-252 - Jozef Noga, Pavol Baacký, Stanislav Biskupic, Roman Boa, Peter Pelikán, Michal Svrek, Anton Zajac:
Approaching bulk limit for three-dimensional solids via the cyclic cluster approximation: Semiempirical INDO study. 253-261 - R. S. Payne, Raymond C. Rowe, R. J. Roberts, M. H. Charlton, R. Docherty:
Potential polymorphs of aspirin. 262-273 - G. J. Halász, Ágnes Vibók, István Mayer:
Comparison of basis set superposition error corrected perturbation theories for calculating intermolecular interaction energies. 274-283 - Ethan Will Taylor:
Book review. 284-286
Volume 20, Number 3, February 1999
- Martin Zacharias, Heinz Sklenar:
Harmonic modes as variables to approximately account for receptor flexibility in ligand-receptor docking simulations: Application to DNA minor groove ligand complex. 287-300 - Karl Jug, Christian Kölle, Frank Neumann:
Treatment of reactions in solutions with isodensity surfaces. 301-304 - Taijin Zhou, Yirong Mo:
General method for symmetry orbitals and tensors in electronic structure calculations. 305-321 - François Wagner, Thomas Simonson:
Implicit solvent models: Combining an analytical formulation of continuum electrostatics with simple models of the hydrophobic effect. 322-335 - Martin Stahl, Daniel Bur, Gisbert Schneider:
Mapping of proteinase active sites by projection of surface-derived correlation vectors. 336-347 - Zhong-Hui Duan, Louis N. Howard:
Loop entanglement of semicrystalline polyethylene in amorphous region: Diamond lattice approach. 348-353 - Canan Baysal, Hagai Meirovitch, Ionel Michael Navon:
Performance of efficient minimization algorithms as applied to models of peptides and proteins. 354-364 - P. N. V. Pavankumar, Peddaiahgari Seetharamulu, S. Yao, Jeffrey D. Saxe, Dasharatha G. Reddy, Frederick H. Hausheer:
Comprehensive ab initio quantum mechanical and molecular orbital (MO) analysis of cisplatin: Structure, bonding, charge density, and vibrational frequencies. 365-382
Volume 20, Number 4, March 1999
- David W. Ritchie, Graham J. L. Kemp:
Fast computation, rotation, and comparison of low resolution spherical harmonic molecular surfaces. 383-395 - Harold Baumann, Rainer E. Martin, François Diederich:
PM3 geometry optimization and CNDO/S-CI computation of UV/Vis spectra of large organic structures: Program description and application to poly(triacetylene) hexamer and taxotere. 396-411 - Jean-Yves Trosset, Harold A. Scheraga:
Prodock: Software package for protein modeling and docking. 412-427 - Brian J. Smith
:
Solvation parameters for amino acids. 428-442 - Hajime Takashima, Kunihiro Kitamura, Kazutoshi Tanabe, Umpei Nagashima:
Is large-scale ab initio Hartree-Fock calculation chemically accurate? Toward improved calculation of biological molecule properties. 443-454 - J. Hunger, G. Huttner:
Optimization and analysis of force field parameters by combination of genetic algorithms and neural networks. 455-471
Volume 20, Number 5, 15 April 1999
- Jacqueline Ridard, Bernard Lévy:
Effective atomic charges in alanine dipeptide. 473-482 - Richard H. Henchman, Jonathan W. Essex:
Generation of OPLS-like charges from molecular electrostatic potential using restraints. 483-498 - Richard H. Henchman, Jonathan W. Essex:
Free energies of hydration using restrained electrostatic potential derived charges via free energy perturbations and linear response. 499-510 - Ruben Santamaria, E. Charro, A. Zacarías, M. Castro:
Vibrational spectra of nucleic acid bases and their Watson-Crick pair complexes. 511-530 - Alexander M. Smondyrev, Max L. Berkowitz:
United atom force field for phospholipid membranes: Constant pressure molecular dynamics simulation of dipalmitoylphosphatidicholine/water system. 531-545 - Ying-Chieh Sun, Shu-Fen Yang, I-Lung Hwang, Tzu-Hsien Wu:
A 500-ps molecular dynamics simulation trajectory of cardiotoxin II from Taiwan cobra venom in solution: Correlation with NMR and X-ray crystallography data. 546-562
Volume 20, Number 6, 30 April 1999
- Bernd Ahlswede, Karl Jug:
Consistent modifications of SINDO1: I. Approximations and parameters. 563-571 - Bernd Ahlswede, Karl Jug:
Consistent modifications of SINDO1: II. Applications to first- and second-row elements. 572-578 - Donald E. Williams, Aron Abraha:
Site charge models for molecular electrostatic potentials of cycloalkanes and tetrahedrane. 579-585 - Jörg Weiser, Peter S. Shenkin, W. Clark Still:
Fast, approximate algorithm for detection of solvent-inaccessible atoms. 586-596 - Xiang-Yuan Li, Fu-Cheng He:
Electron transfer between biphenyl and biphenyl anion radicals: Reorganization energies and electron transfer matrix elements. 597-603 - Juan C. Cesco, Claudia C. Denner, Graciela O. Giubergia, Ana E. Rosso, Jorge E. Pérez, F. S. Ortiz, Oscar E. Taurian, Rubén H. Contreras:
Implementation of atomic basis set composed of 1s Gaussian and 1s Slater-type orbitals to carry out quantum mechanics molecular calculations. 604-609 - Robert Brotherus:
Infia - program for rotational analysis of linear molecule spectra. 610-622 - Xi-Jing Ning, Qi-Zong Qin:
Molecular dynamics simulation of O3 photolysis by ultraviolet light in solid argon. 623-628 - Andrey A. Bliznyuk, Alistair P. Rendell:
Faster gradients for semiempirical methods. 629-635 - John L. Klepeis, Christodoulos A. Floudas:
Comparative study of global minimum energy conformations of hydrated peptides. 636-654
Volume 20, Number 7, May 1999
- A. Hu, Peter Otto, Janos Ladik:
Relativistic Gaussian functions for atoms by fitting numerical results with adaptive nonlinear least-square algorithm. 655-664 - Carles Colominas, F. Javier Luque, Modesto Orozco:
Monte Carlo-MST: New strategy for representation of solvent configurational space in solution. 665-678 - Heribert Reis, Manthos G. Papadopoulos:
Nonlinear optical properties of the rhombic B4-cluster. 679-687 - Jörg Weiser, Peter S. Shenkin, W. Clark Still:
Optimization of Gaussian surface calculations and extension to solvent-accessible surface areas. 688-703 - Peter J. Winn, György G. Ferenczy, Christopher A. Reynolds:
Towards improved force fields: III. Polarization through modified atomic charges. 704-712 - Takeshi Kikuchi:
Study of protein fluctuation with an effective inter-C atomic potential derived from average distances between amino acids in proteins. 713-719 - Thomas A. Halgren:
MMFF VI. MMFF94s option for energy minimization studies. 720-729 - Thomas A. Halgren:
MMFF VII. Characterization of MMFF94, MMFF94s, and other widely available force fields for conformational energies and for intermolecular-interaction energies and geometries. 730-748
Volume 20, Number 8, June 1999
- Xin Chen, Alexander Tropsha:
Generalized linear response method: Application to hydration free energy calculations. 749-759 - Robert Ponec, Anthony J. Duben:
Electron pairing and chemical bonds: Bonding in hypervalent molecules from analysis of Fermi holes. 760-771 - Yair Salomon, David Avnir:
Continuous symmetry measures: Finding the closest C2-symmetric object or closest reflection-symmetric object using unit quaternions. 772-780 - Peter Comba, Norbert Okon, Rainer Remenyi:
Computation of cavity shapes, sizes, and plasticities. 781-785 - K. Anton Feenstra, Berk Hess, Herman J. C. Berendsen:
Improving efficiency of large time-scale molecular dynamics simulations of hydrogen-rich systems. 786-798 - Bouke P. van Eijck, Jan Kroon:
Upack program package for crystal structure prediction: Force fields and crystal structure generation for small carbohydrate molecules. 799-812 - Brett A. Harris, Stephen C. Harvey:
Program for analyzing knots represented by polygonal paths. 813-818 - William J. Wedemeyer, Harold A. Scheraga:
Exact analytical loop closure in proteins using polynomial equations. 819-844 - Isidoro García-Cruz, M. E. Ruiz-Santoyo, J. Raúl Alvarez-Idaboy, Annik Vivier Bunge:
Ab-initio study of initial atmospheric oxidation reactions of C3 and C4 alkanes. 845-856 - Vladimír Lukes, Viliam Laurinc, Stanislav Biskupic:
Perturbative formulation of dispersion contributions to interaction energy of van der Waals systems of closed-shell-open-shell type. 857-866 - Theo H. Reijmers, Ron Wehrens, Lutgarde M. C. Buydens:
Quality criteria of genetic algorithms for construction of phylogenetic trees. 867-876 - Srikanta Sen, Lennart Nilsson:
Some practical aspects of free energy calculations from molecular dynamics simulation. 877-885 - Marc F. Lensink, Janez Mavri, Herman J. C. Berendsen:
Simulation of slow reaction with quantum character: Neutral hydrolysis of carboxylic ester. 886-895
Volume 20, Number 9, 15 July 1999
- Isabelle Fourré, Bernard Silvi, Patrick Chaquin, Alain Sevin:
Electron localization function comparative study of ground state, triplet state, radical anion, and cation in model carbonyl and imine compounds. 897-910 - Lluís Amat, Ramon Carbó-Dorca:
Fitted electronic density functions from H to Rn for use in quantum similarity measures: cis-diamminedichloroplatinum(II) complex as an application example. 911-920 - Ross D. Adamson, Jeremy P. Dombroski, Peter M. W. Gill:
Efficient calculation of short-range Coulomb energies. 921-927 - Andriy Kovalenko, Seiichiro Ten-no, Fumio Hirata:
Solution of three-dimensional reference interaction site model and hypernetted chain equations for simple point charge water by modified method of direct inversion in iterative subspace. 928-936 - Begoña Hernández, F. Javier Luque, Modesto Orozco:
Parametrization of the GMIPp for the study of stacking interactions. 937-946 - J. M. R. Parker:
The relationship between peptide plane rotation (PPR) and similar conformations. 947-955 - Michael J. Potter, Paul D. Kirchhoff, Heather A. Carlson, James Andrew McCammon:
Molecular dynamics of cryptophane and its complexes with tetramethylammonium and neopentane using a continuum solvent model. 956-970 - Pedro G. Pascutti, Kleber C. Mundim, Amando S. Ito, Paulo Mascarello Bisch:
Polarization effects on peptide conformations at water-membrane interface by molecular dynamics simulation. 971-982 - Andrey A. Bliznyuk, Jill E. Gready:
Simple method for locating possible ligand binding sites on protein surfaces. 983-988
Volume 20, Number 10, 30 July 1999
- Yuxiang Bu, Haitao Sun, Hongbo Niu:
Electron transfer reactivity of O2+O2- system in low-spin coupling: Ab Initio study at electron correlation level. 989-998 - John Cullen:
Is GVB-CI superior to CASSCF? 999-1008 - Roland Faller, Heiko Schmitz, Oliver Biermann, Florian Müller-Plathe:
Automatic parameterization of force fields for liquids by simplex optimization. 1009-1017 - M. Rami Reddy, Mark D. Erion:
Calculation of relative solvation free energy differences by thermodynamic perturbation method: Dependence of free energy results on simulation length. 1018-1027 - Peter L. Cummins, Jill E. Gready:
Coupled semiempirical quantum mechanics and molecular mechanics (QM/MM) calculations on the aqueous solvation free energies of ionized molecules. 1028-1038 - P. Aplincourt, Manuel F. Ruiz-López, Xavier Assfeld, F. Bohr:
Structure of isolated and solvated peroxyl radicals. 1039-1048 - Izydor Apostol, Wojciech Szpankowski:
Indexing and mapping of proteins using a modified nonlinear Sammon projection. 1049-1059 - Paulo Hora Acioli, Geraldo Magela e Silva:
Investigating charge transport in molecular switches with neural networks. 1060-1066 - Sang-Ho Lee, Kim Palmö, Samuel Krimm:
New out-of-plane angle and bond angle internal coordinates and related potential energy functions for molecular mechanics and dynamics simulations. 1067-1084 - Alícia Torre, Luis Lain, Roberto C. Bochicchio, Robert Ponec:
Nature of nonclassical bonds in Closo-Boranes: Nonlinear population analysis approach. 1085-1090
Volume 20, Number 11, August 1999
- Velin Z. Spassov, Donald Bashford:
Multiple-site ligand binding to flexible macromolecules: Separation of global and local conformational change and an iterative mobile clustering approach. 1091-1111 - Josep Maria Anglada, Emili Besalú, Josep Maria Bofill, Ramon Crehuet:
Prediction of approximate transition states by Bell-Evans-Polanyi principle: I. 1112-1129 - Josep Maria Anglada, Emili Besalú, Josep Maria Bofill, Ramon Crehuet:
Prediction of approximate transition states by Bell-Evans-Polanyi principle: II. Gas phase unimolecular decomposition of methyldioxirane. 1130-1137 - Masao Masamura, Shigeru Ikuta:
Ab initio molecular orbital study on structures and energetics of CH3O-(H2O)n and CH3S-(H2O)n in gas phase. 1138-1144 - Norge Cruz Hernández, Javier Fdez. Sanz:
Ab initio compact group model potentials for describing environment effects in cluster calculations. 1145-1152 - See-Wing Chiu, Michael M. Clark, Eric Jakobsson, Shankar Subramaniam, H. Larry Scott:
Application of combined Monte Carlo and molecular dynamics method to simulation of dipalmitoyl phosphatidylcholine lipid bilayer. 1153-1164 - John B. O. Mitchell, Roman A. Laskowski, Alexander Alex, Janet M. Thornton:
BLEEP - potential of mean force describing protein-ligand interactions: I. Generating potential. 1165-1176 - John B. O. Mitchell, Roman A. Laskowski, Alexander Alex, Mark J. Forster, Janet M. Thornton:
BLEEP - potential of mean force describing protein-ligand interactions: II. Calculation of binding energies and comparison with experimental data. 1177-1185 - Nadia Rega, Maurizio Cossi, Vincenzo Barone:
Improving performance of polarizable continuum model for study of large molecules in solution. 1186-1198
Volume 20, Number 12, September 1999
- Werner Kutzelnigg:
Relativistic corrections to magnetic properties. 1199-1219 - Serguei Patchkovskii, Walter Thiel:
NMR chemical shifts in MNDO approximation: Parameters and results for H, C, N, and O. 1220-1245 - Hubert Ebert, M. Battocletti, M. Deng, Harald Freyer, J. Voitländer:
Fully relativistic description of static magnetic hyperfine interaction in magnetic and nonmagnetic solids. 1246-1253 - Michael Bühl:
Theoretical study of a vanadate peptide complex. 1254-1261 - Lucas Visscher, Thomas Enevoldsen, Trond Saue, Hans Jorgen Aagard Jensen, Jens Oddershede:
Full four-component relativistic calculations of NMR shielding and indirect spin-spin coupling tensors in hydrogen halides. 1262-1273 - Shashi P. Karna:
Ab initio coupled Hartree-Fock study of the Bloembergen effect on paramagnetic systems: SiH3 radical. 1274-1280 - Kurt V. Mikkelsen, Kenneth Ruud, Trygve Helgaker:
Solvent effects on the NMR parameters of H2S and HCN. 1281-1291 - Patrick J. O'malley:
Hybrid density functional studies of a bacteriopheophytin a model and its anion radical form: Geometry, spin densities, and hyperfine couplings. 1292-1298 - Kenneth B. Wiberg:
Comparison of density functional theory models' ability to reproduce experimental 13C-NMR shielding values. 1299-1303 - Martin Kaupp, Olga L. Malkina, Vladimir G. Malkin:
The role of -type nonbonding orbitals for spin-orbit induced NMR chemical shifts: DFT study of 13C and 19F shifts in the series CF3IFn (n=0, 2, 4, 6). 1304-1313 - Juha Vaara, Kenneth Ruud, Olav Vahtras:
Correlated response calculations of the spin-orbit interaction contribution to nuclear spin-spin couplings. 1314-1327
Volume 20, Number 13, October 1999
- A. Y. Jin, F. Y. Leung, D. F. Weaver:
Three variations of genetic algorithm for searching biomolecular conformation space: Comparison of GAP 1.0, 2.0, and 3.0. 1329-1342 - François Gilardoni, Jacques Weber, Andreas Hauser, Claude Daul:
A comparison of ground- and excited-state properties of [Ru(bz)2]2+ and bis(6-benzene)ruthenium(II) p-toluenesulfonate using the density functional theory. 1343-1353 - John L. Klepeis, Christodoulos A. Floudas, Dimitrios Morikis, John D. Lambris:
Predicting peptide structures using NMR data and deterministic global optimization. 1354-1370 - Anita H. Lewin, Jennifer B. Sorensen, John A. Dustman, J. Phillip Bowen:
Computational methods for conformational analysis of unsymmetrical 1, 3-diamines: 3-aminotropanes. 1371-1378 - Gilles Tiraboschi, Bernard-Pierre Roques, Nohad Gresh:
Joint quantum chemical and polarizable molecular mechanics investigation of formate complexes with penta- and hexahydrated Zn2+: Comparison between energetics of model bidentate, monodentate, and through-water Zn2+ binding modes and evaluation of nonadditivity effects. 1379-1390