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Volume 11, Number 1, January, 1990R. J. Vos and R. Hendriks and F. B. Van Duijneveldt SCF, MP2, and CEPA-1 calculations on the OH\dottedbondO hydrogen bonded complexes (H$_2$O)$_2$ and (H$_2$O-H$_2$CO) . . . 1--18 P. Auffinger and G. Wipff High temperature annealed molecular dynamics simulations as a tool for conformational sampling. Application to the bicyclic ``222'' cryptand . . . . . 19--31 Julio C. Facelli and David M. Grant and Thomas D. Bouman and Aage E. Hansen A comparison of the IGLO and LORG methods for the calculations of nuclear magnetic shieldings . . . . . . . . . . 32--44 Ron Shepard A data compression method applicable to first-order convergent iterative procedures . . . . . . . . . . . . . . . 45--57 John F. Stanton and David E. Bernholdt An empirically adjusted Newton--Raphson algorithm for finding local minima on molecular potential energy surfaces . . 58--63 Olle Teleman A stringent formulation of the overall rotational diffusion in molecules and other flexible assemblies . . . . . . . 64--66 John D. Head Partial optimization of large molecules and clusters . . . . . . . . . . . . . . 67--75 Minoru Saito and Haruki Nakamura Hydration free energy calculations by the acceptance ratio method . . . . . . 76--81 Henry A. Kurtz and James J. P. Stewart and Kenneth M. Dieter Calculation of the nonlinear optical properties of molecules . . . . . . . . 82--87 Leon F. Phillips Calculation of Langevin-type capture rate constants for rotating molecules with arbitrary interaction potentials 88--93 Steven R. Kass Hydrocarbon acidities calculated with MINDO/3, MNDO, and AM1 . . . . . . . . . 94--104 Joseph D. Augspurger and Clifford E. Dykstra General quantum mechanical operators. An open-ended approach for one-electron integrals with Gaussian bases . . . . . 105--111 Jane S. Murray and M. Edward Grice and Peter Politzer and James R. Rabinowitz Evaluation of a finite multipole expansion technique for the computation of electrostatic potentials of dibenzo-$p$-dioxins and related systems 112--120 Michael J. Dudek and Harold A. Scheraga Protein structure prediction using a combination of sequence homology and global energy minimization I. Global energy minimization of surface loops . . 121--151 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
Gyorgy G. Ferenczy and Christopher A. Reynolds and W. Graham Richards Semiempirical AM1 electrostatic potentials and AM1 electrostatic potential derived charges: a comparison with ab initio values . . . . . . . . . 159--169 Miquel Sol\`a and Agustí Lledós and Miquel Duran and Juan Bertrán and Oscar N. Ventura Ab initio study of substituent effect on the addition of hydrogen fluoride to fluoroethylenes . . . . . . . . . . . . 170--180 Richard Däppen and Heinrich R. Karfunkel and Frank J. J. Leusen Computational chemistry applied to the design of chiral stationary phases for enantiomeric separation . . . . . . . . 181--193 U. Salzner and P. Otto and J. Ladik Numerical solution of a partial differential equation system describing chemical kinetics and diffusion in a cell with the aid of compartmentalization . . . . . . . . . . 194--204 Anne Imberty and Vinh Tran and Serge Pérez Relaxed potential energy surfaces of $N$-linked oligosaccharides: the mannose-$\alpha (1 \rightarrow 3)$-mannose case . . . . . . . . . . . . 205--216 Tomislav P. \vZivkovi\'c On the evaluation of the characteristic polynomial of a chemical graph . . . . . 217--222 W. R. Müller and K. Szymanski and J. V. Knop and S. Nikoli\'c and N. Trinajsti\'c On the enumeration and generation of polyhex hydrocarbons . . . . . . . . . . 223--235 D. W. Noid and B. G. Sumpter and B. Wunderlich and G. A. Pfeffer Molecular dynamics simulations of polymers: Methods for optimal Fortran programming . . . . . . . . . . . . . . 236--241 Miron G. Still and L. B. Rogers Effects of computational variations for determining binding energies of diastereomeric complexes when using MM2 242--248 Rainer Glaser and Andrew Streitwieser $\eta^5$-P- or $\eta^4$-P-coordination in apically oxygenated phosphoranes? An ab initio study of PH$_4$O$^-$, PH$_4$O$^-$ $\cdot$ E (E = Li$^+$, NH$_4^+$, and HF) and related fluorinated oxyphosphoranes . . . . . . 249--264 Jack D. Dunitz Book Review: \booktitleDistance geometry and molecular conformation, by G. M. Crippen and T. F. Havel, Research Studies Press, Taunton, England, John Wiley and Sons, New York, 1988. pp. 541 + x pp. Price: \$142.00} . . . . . . . . 265--266 John F. Garst Book Review: \booktitleAlternate realities --- mathematical models of nature and man, by John L. Casti, Institute for Econometrics, Operations Research, and System Theory, Technical University of Vienna, John Wiley & Sons, New York, 1989, xvii + 493 pp. \$34.95} 266--267 Anonymous Announcement . . . . . . . . . . . . . . 268--268 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
R. Voets and J.-P. François and J. M. L. Martin and J. Mullens and J. Yperman and L. C. Van Poucke Theoretical study of the proton affinities of 2-, 3-, and 4-monosubstituted phenolate ions in the gas phase by means of MINDO/3, MNDO, and AM1 . . . . . . . . . . . . . . . . . . 269--290 T. L. Sordo and J. A. Sordo and R. Flórez Theoretical study of adsorption of hydrocarbons on graphite . . . . . . . . 291--296 Robert J. Woods and Maged Khalil and Wendy Pell and Steven H. Moffat and Vedene H. Smith Jr. Derivation of net atomic charges from molecular electrostatic potentials . . . 297--310 Michael J. S. Dewar and Andrew J. Holder On the validity of polarization and correlation additivity in ab initio molecular orbital calculations . . . . . 311--313 Julia M. Goodfellow and Douglas M. Jones and Roman A. Laskowski and David S. Moss and Mansoor Saqi and Narmada Thanki and Richard Westlake Use of parallel processing in the study of protein. Ligand binding . . . . . . . 314--325 Yuzo Yoshikawa Molecular mechanics criterion for metal complex formation . . . . . . . . . . . 326--335 Kenneth J. Miller First and second derivative matrix elements for linear and out-of-plane bending motion . . . . . . . . . . . . . 336--345 Jian Shen and Chung F. Wong and Shankar Subramaniam and Thomas A. Albright and J. Andrew McCammon Partial electrostatic charges for the active center of Cu, Zn superoxide dismutase . . . . . . . . . . . . . . . 346--350 Terry G. Lenz and John D. Vaughan Force field calculation of equilibrium thermodynamic properties: Diels--Alder reaction of 1,3-butadiene and ethylene and Diels--Alder dimerization of 1,3-butadiene . . . . . . . . . . . . . 351--360 Curt M. Breneman and Kenneth B. Wiberg Determining atom-centered monopoles from molecular electrostatic potentials. The need for high sampling density in formamide conformational analysis . . . 361--373 Francis T. Marchese Coordination numbers for biomolecular hydration: a quantitative method based on pattern recognition analysis of Monte Carlo simulations of aqueous solutions 374--381 Douglas Poland On the use of series to integrate rate equations . . . . . . . . . . . . . . . 382--395 V. Galiatsatos and Wayne L. Mattice Efficient formulation of the large generator matrices required for computation of the higher moments, and mixed moments, of conformation-dependent properties of chain molecules with independent bonds . . . . . . . . . . . 396--400 M. E. Davis and J. A. McCammon Calculating electrostatic forces from grid-calculated potentials . . . . . . . 401--409 Phillip Christiansen Book Review: \booktitleMethods in computational chemistry, volume II, edited by Stephen Wilson, Plenum Press, New York, 1988 . . . . . . . . . . . . . 410--410 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
Carlos Jaime MM2' calculations on methylenecyclohexane, methylenecyclopentane, and cyclopentane. Pitfalls in the two-bond drive technique: How large should the ring be? 411--415 F. J. Luque and F. Illas and M. Orozco Comparative study of the molecular electrostatic potential obtained from different wavefunctions. Reliability of the semiempirical MNDO wavefunction . . 416--430 Brent H. Besler and Kenneth M. Merz Jr. and Peter A. Kollman Atomic charges derived from semiempirical methods . . . . . . . . . 431--439 Fariborz Mohamadi and Nigel G. J. Richards and Wayne C. Guida and Rob Liskamp and Mark Lipton and Craig Caufield and George Chang and Thomas Hendrickson and W. Clark Still Macromodel --- an integrated software system for modeling organic and bioorganic molecules using molecular mechanics . . . . . . . . . . . . . . . 440--467 Kenneth D. Gibson and Harold A. Scheraga Variable step molecular dynamics: an exploratory technique for peptides with fixed geometry . . . . . . . . . . . . . 468--486 Kenneth D. Gibson and Harold A. Scheraga Dynamics of peptides with fixed geometry: Kinetic energy terms and potential energy derivatives as functions of dihedral angles . . . . . . 487--492 Stelian Grigoras A structural approach to calculate physical properties of pure organic substances: the critical temperature, critical volume and related properties 493--510 Robert Kulver Free energy calculation of a soft sphere solid using an adaptive, importance sampling Monte Carlo algorithm . . . . . 511--517 Lillian M. Hansen and Dennis S. Marynick Extended basis sets for the transition metals yttrium through cadmium . . . . . 518--523 Toshiyuki Katagi Theoretical studies on the alkaline hydrolysis of $N$-methylcarbamates . . . 524--530 William J. Welsh and Vivian Cody Molecular modeling studies of novel heteroarotinoids . . . . . . . . . . . . 531--540 Michael J. S. Dewar and Eamonn F. Healy and Andrew J. Holder and Yate-Ching Yuan Comments on a comparison of AM1 with the recently developed PM3 method . . . . . 541--542 James J. P. Stewart Reply to ``Comments on a comparison of AM1 with the recently developed PM3 method'' . . . . . . . . . . . . . . . . 543--544 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
S. Ramasesha A new algorithm for solving large inhomogeneous linear system of algebraic equations . . . . . . . . . . . . . . . 545--547 W. Gründler and T. Steinke and P. Walther H/He molecules in strong electric fields 548--559 Philippe Derreumaux and Gérard Vergoten and Philippe Lagant A vibrational molecular force field of model compounds with biological interest. I. Harmonic dynamics of crystalline urea at 123 K . . . . . . . 560--568 Mozart N. Ramos and Benício de B. Neto Electronic structure and hypolipidemic activity of phthalimide and related compounds. A QSAR study . . . . . . . . 569--572 Anne-Marie Sapse and Duli C. Jain and Denyse De Gale and T. C. Wu Solvent effect and librational entropy calculations on $N$-acetylalanylglycine amide . . . . . . . . . . . . . . . . . 573--575 S. Tolosa and J. J. Esperilla and F. J. Olivares del Valle Overestimation of the coupling component in the CP technique. Application of the indirect counterpoise correction to the H$_2$O\dottedbondHF hydrogen-bonded system . . . . . . . . . . . . . . . . . 576--588 Xiaoyu Liu and K. Balasubramanian Computer generation of character tables of generalized wreath product groups . . 589--602 R. J. Zauhar and R. S. Morgan Computing the electric potential of biomolecules: Application of a new method of molecular surface triangulation . . . . . . . . . . . . . 603--622 C. W. Bock and Y. N. Panchenko and V. I. Pupyshev Effect of basic set quality and electron correlation on the scale factors of a harmonic force field . . . . . . . . . . 623--628 M. V. Rama Krishna On proper dissociation configurations of a molecule . . . . . . . . . . . . . . . 629--635 Edward Earl Adaptation of D$_{2h}$ ab initio computer code to higher-symmetry point groups . . . . . . . . . . . . . . . . . 636--643 William J. Welsh AM1 molecular orbital studies of the structures, conformations, protonation energies, and electronic properties of triazine dihydrofolate reductase inhibitors . . . . . . . . . . . . . . . 644--653 Frank A. Momany and Valentine J. Klimkowski and Lothar Schäfer On the use of conformationally dependent geometry trends from ab initio dipeptide studies to refine potentials for the empirical force field CHARMM . . . . . . 654--662 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
Rainer Glaser Diazonium ions. Topological electron density analysis of cyclopropeniumyldiazonium dications and of their stability toward dediazoniation 663--679 Andrew R. Leach and Keith Prout and Daniel P. Dolata The application of Artificial Intelligence to the conformational analysis of strained molecules . . . . . 680--693 Luca Baumer and Giordano Sala and Guido Sello A new method for the calculation of atomic and local hardness . . . . . . . 694--699 Martin J. Field and Paul A. Bash and Martin Karplus A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations . . . . . 700--733 L. Carballeira and A. J. Pereiras and M. A. Rios Design and application of a molecular mechanics force field for alkyl iodides including an electrostatic polarization model . . . . . . . . . . . . . . . . . 734--742 Alice Chung-Phillips and Thomas A. Stevenson Simulations of internal rotation potential energies for substituted ethanes . . . . . . . . . . . . . . . . 743--753 Harrell Sellers On the interaction of palladium with olefinic systems . . . . . . . . . . . . 754--763 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
Maarten C. Krol and Cornelis J. M. Huige and Cornelis Altona The anomeric effect: Ab-initio studies on molecules of the type X CH$_2$O CH$_3$ . . . . . . . . . . . . . . . . . 765--790 Peter L. Cummins and Jill E. Gready Mechanistic aspects of biological redox reactions involving NADH 2: a combined semiempirical and ab initio study of hydride-ion transfer between the NADH analogue, 1-methyl-dihydronicotinamide, and folate and dihydrofolate analogue substrates of dihydrofolate reductase 791--804 Paolo Catasti and Enrico Carrara and Claudio Nicolini Pepto: an expert system for automatic peak assignment of two-dimensional nuclear magnetic resonance spectra of proteins . . . . . . . . . . . . . . . . 805--818 Martin Badertscher and Stefano Musso and Martin Welti and Ernö Pretsch and Takuya Maruizumi and Tae-kyu Ha Combined application of pair potentials and the MM2 force field for the modeling of ionophores . . . . . . . . . . . . . 819--828 K. Balasubramanian Computer generation of distance polynomials of graphs . . . . . . . . . 829--836 Ivan Stibor and Petr Holý and Pavel Hobza and Petr \vCársky MM2 study of 20-hydroxy-4,7,13,16-tetraoxa-1,10-diazabicyclo [8,8,3] heneicosane and its formation controlled by hydrogen bonding 837--847 Norman L. Allinger and Fanbing Li and Liqun Yan Molecular mechanics. The MM3 force field for alkenes . . . . . . . . . . . . . . 848--867 Norman L. Allinger and Fanbing Li and Liqun Yan and Julia C. Tai Molecular mechanics (MM3) calculations on conjugated hydrocarbons . . . . . . . 868--895 Nathan L. Bauld The theoretical reaction path for the cation radical vinylcyclobutane rearrangement: a concerted SR path . . . 896--898 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
S. S. Tratch and M. I. Stankevitch and N. S. Zefirov Combinatorial models and algorithms in chemistry. The expanded Wiener number --- a novel topological index . . . . . 899--908 M. Orozco and F. J. Luque On the use of AM1 and MNDO wave functions to compute accurate electrostatic charges . . . . . . . . . 909--923 V. Musolino and M. Toscano and N. Russo Electronic structure and photoelectron spectra of Sb$_2$ and Sb$_4$ from local-spin-density calculations. Model potential for Sb . . . . . . . . . . . . 924--929 Giuliano Alagona and Caterina Ghio The effect of diffuse functions on minimal basis set superposition errors for H-bonded dimers . . . . . . . . . . 930--942 T. P. Straatsma and J. A. McCammon ARGOS, a vectorized general molecular dynamics program . . . . . . . . . . . . 943--951 Joseph M. Leonard and William P. Ashman Molecular mechanics parameterization: Bond lengths and angles for nitrogen and phosphorus containing compounds . . . . 952--957 James M. Briggs and Tooru Matsui and William L. Jorgensen Monte Carlo simulations of liquid alkyl ethers with the OPLS potential functions 958--971 Joseph D. Augspurger and David E. Bernholdt and Clifford E. Dykstra Concise, open-ended implementation of Rys polynomial evaluation of two-Electron integrals . . . . . . . . . 972--977 James M. Gruschus and Atsuo Kuki Partial charges by multipole constraint. Application to the amino acids . . . . . 978--993 Lillian M. Hansen and Peter A. Kollman Free energy perturbation calculations on models of active sites: Applications to adenosine deaminase inhibitors . . . . . 994--1002 Jian Shen and Chung F. Wong and J. Andrew McCammon Hydration of superoxide studied by molecular dynamics simulation . . . . . 1003--1008 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
Rafik Karaman and Jun-Tsu Luke Huang and James L. Fry Correlation of the acidity of substituted phenols, anilines, and benzoic acids calculated by MNDO, AM1, and PM3 with Hammett-type substituent constants . . . . . . . . . . . . . . . 1009--1016 Javier Fernändez Sanz and Alain Dargelos Theoretical analysis of the electronic spectrum of GeH$_4$ from ab initio CI calculations . . . . . . . . . . . . . . 1017--1020 Hans-Joachim Böhm and Gerhard Klebe and Thomas Lorenz and Thomas Mietzner and Lorenz Siggel Different approaches to conformational analysis: a comparison of completeness, efficiency, and reliability based on the study of a nine-membered lactam . . . . 1021--1028 M. Kaupp and H. Stoll and H. Preuss Pseudopotential calculations for methyl compounds of zinc and magnesium . . . . 1029--1037 Giuliano Alagona and Caterina Ghio and Péter Nagy and Kálmán Simon and Gábor Náray-Szabo Comparative study of imidazole hydration: ab initio and electrostatic calculations vs. Cambridge Structural Database analysis . . . . . . . . . . . 1038--1046 Juan Luis Pascual-Ahuir and Estanislao Silla GEPOL: an improved description of molecular surfaces. I. Building the spherical surface set . . . . . . . . . 1047--1060 David M. Ferguson and Douglas J. Raber Molecular mechanics calculations of several lanthanide complexes: an application of the random incremental pulse search . . . . . . . . . . . . . . 1061--1071 S. Roszak and P. C. Hariharan and Joyce J. Kaufman An ab initio method for approximation of the frozen molecular fragment . . . . . 1072--1075 S. Roszak and P. C. Hariharan and Joyce J. Kaufman and W. S. Koski MRD--CI calculations of proton affinity within the ab initio method for approximation of the frozen molecular fragment . . . . . . . . . . . . . . . . 1076--1079 Byung Jun Yoon and A. M. Lenhoff A boundary element method for molecular electrostatics with electrolyte effects 1080--1086 Richard D. Gilliom and Gerald L. Stoner Molecular mechanics study of myelin basic protein peptide 87-118: Some local energy minima . . . . . . . . . . . . . 1087--1093 Toshiyuki Katagi AM1 study of acid-catalyzed hydrolysis of maleamic (4-amino-4-oxo-2-butenoic) acids . . . . . . . . . . . . . . . . . 1094--1100 Dimitris K. Agrafiotis and Brian Tansy and Andrew Streitwieser PRODEN: a new program for calculating integrated projected populations . . . . 1101--1110 Hugo O. Villar and Gilda H. Loew A conformational study of cocaine and its diastereomers . . . . . . . . . . . 1111--1118 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
Ikchoon Lee and Chang Kon Kim Theoretical studies on the intramolecular cyclization of alkyl halide anions . . . . . . . . . . . . . 1119--1124 Jan L. M. Dillen An improved empirical force field for saturated hydrocarbons . . . . . . . . . 1125--1138 Catherine Burt and W. Graham Richards and Philip Huxley The application of molecular similarity calculations . . . . . . . . . . . . . . 1139--1146 Heinz Hofmann and Elke Hünsele and Timothy Clark A cautionary note on the use of the frozen-core approximation for correlation energy calculations involving alkali metals . . . . . . . . 1147--1150 Lawrence A. Covick and Kenneth M. Sando Four-Index transformation on distributed-memory parallel computers 1151--1159 John P. Paolini The bond order--bond length relationship 1160--1163 Johan H. van Lenthe and Peter Pulay A space-saving modification of Davidson's eigenvector algorithm . . . . 1164--1168 Douglas B. Kitchen and Fumio Hirata and John D. Westbrook and Ronald Levy and David Kofke and Martin Yarmush Conserving energy during molecular dynamics simulations of water, proteins, and proteins in water . . . . . . . . . 1169--1180 Paul S. Charifson and Richard G. Hiskey and Lee G. Pedersen Construction and molecular modeling of phospholipid surfaces . . . . . . . . . 1181--1186 Simon K. Kearsley An algorithm for the simultaneous superposition of a structural series . . 1187--1192 Andrew R. Leach and Keith Prout Automated conformational analysis: Directed conformational search using the A* algorithm . . . . . . . . . . . . . . 1193--1205 R. C. Binning Jr. and L. A. Curtiss Compact contracted basis sets for third-row atoms: Ga--Kr . . . . . . . . 1206--1216 John B. O. Mitchell and Sarah L. Price The nature of the N\bondH\dottedbondO\bondC hydrogen bond: an intermolecular perturbation theory study of the formamide/formaldehyde complex . . . . . . . . . . . . . . . . 1217--1233 U. Dinur and A. T. Hagler A novel decomposition of torsional potentials into pairwise interactions: a study of energy second derivatives . . . 1234--1246 Anonymous Announcement . . . . . . . . . . . . . . 1247--1247 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
H. Bruning and D. Feil Electrostatic interactions in host-guest complexes 2 . . . . . . . . . . . . . . 1--8 Pavel Hobza and Dana Nachtigallová and Zden\uek Havlas and Petr Malo\un and Jaroslav \vSponar Interaction of Lysine-Alanine-Alanine tripeptide with a fragment of DNA: an empirical potential study . . . . . . . 9--16 Walter M. F. Fabian Tautomeric equilibria of heterocyclic molecules. A test of the semiempirical AM1 and MNDO-PM3 methods . . . . . . . . 17--35 Alessandro Fortunelli and Oriano Salvetti A simplified representation of the potential produced by Gaussian charge distributions . . . . . . . . . . . . . 36--41 Stéphane Boudon and Georges Wipff Free energy calculations involving NH$_4^+$ in water . . . . . . . . . . . 42--51 J. M. L. Martin and J. P. François and R. Gijbels A critical comparison of MINDO/3, MNDO, AM1, and PM3 for a model problem: Carbon clusters C$_2$--C$_{10}$. An ad hoc reparametrization of MNDO well suited for the accurate prediction of their spectroscopic constants . . . . . . . . 52--70 Christer Elvingson A general Brownian dynamics simulation program for biopolymer dynamics and its implementation on a vector computer . . 71--77 Berta Fernández and Miguel A. Ríos and Luís Carballeira Molecular mechanics (MM2) and conformational analysis of compounds with N\bondC\bondO units. Parametrization of the force field and anomeric effect . . . . . . . . . . . . 78--90 Uri Dinur Force related atomic multipoles in planar molecules. Derivation of atomic quadrupole and octupole moments . . . . 91--105 K. Balasubramanian Computer enumeration of walks on directed graphs . . . . . . . . . . . . 106--112 Mohammad A. Al-Laham and G. A. Petersson and Paul Haake Ab initio study of ascorbic acid conformations . . . . . . . . . . . . . 113--118 Randall C. Boehm and Lawrence L. Lohr Ab initio characterization of several states of nitroxylium (NO). Comparison of fragmentation energies of nitroxylium, nitroxyl (NO$_3$), and nitrate . . . . . . . . . . . . . . . . 119--125 James E. Gano and E. Jean Jacob and Rebecca Roesner Evaluation of PM3, AM1, and MNDO for calculation of higher energy ionization potentials . . . . . . . . . . . . . . . 126--134 Tomoko Sotomatsu and Yoshiyuki Murata and Toshio Fujita Theoretical calculation of the steric effects of ortho substituents by the AM1 method . . . . . . . . . . . . . . . . . 135--138 Paul G. Mezey Book Review: \booktitleTopological methods in chemistry, by R. E. Merrifield and H. E. Simmons, Wiley Interscience, New York, 1989. pp. 233 + ix pp. Price: \$35.00} . . . . . . . . . 139--139 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
C. N. Cavasotto and C. G. Giribet and M. C. Ruiz de Azúa and R. H. Contreras Exo-exo and endo-endo vicinal proton spin-spin coupling constants in norbornane and norbornene. An IPPP-CLOPPA analysis . . . . . . . . . . 141--146 V. Fritsch and E. Westhof Minimization and molecular dynamics studies of guanosine and Z-DNA modified by $N$-2-acetylaminofluorene . . . . . . 147--166 T. Pötter and M. Klessinger Geometry optimization in semiempirical SCF--MO--CI calculations . . . . . . . . 167--171 P. Scano and C. Thomson Comparison of semiempirical MO methods applied to large molecules . . . . . . . 172--174 Robert D. Skeel Macromolecular dynamics on a shared-memory multiprocessor . . . . . . 175--179 D. H. Gregory and J. T. Gerig Structural effects of fluorine substitution in proteins . . . . . . . . 180--185 Jenn-Huei Lii and Norman L. Allinger The MM3 force field for amides, polypeptides and proteins . . . . . . . 186--199 Klaus Gundertofte and Jonas Palm and Ingrid Pettersson and Anders Stamvik A comparison of conformational energies calculated by molecular mechanics (MM2(85), Sybyl 5.1, Sybyl 5.21, and ChemX) and semiempirical (AM1 and PM3) methods . . . . . . . . . . . . . . . . 200--208 T. J. O'Donnell and Shashidhar N. Rao and Konrad Koehler and Yvonne C. Martin and Beverly Eccles A general approach for atom-type assignment and the interconversion of molecular structure files . . . . . . . 209--214 M. W. Wong and G. Corongiu and E. Clementi Two-electron integral evaluation for uncontracted geometrical-type Gaussian functions . . . . . . . . . . . . . . . 215--219 P. Duane Walker and Gustavo A. Arteca and Paul G. Mezey A complete shape characterization for molecular charge densities represented by Gaussian-type functions . . . . . . . 220--230 Richard E. Overill Towards the truly nonempirical computation of hyperfine interactions: a contribution to the debate on the $t$-butyl radical . . . . . . . . . . . 231--236 Mario Blanco Molecular silverware. I. General solutions to excluded volume constrained problems . . . . . . . . . . . . . . . . 237--247 K. Balasubramanian Comments on the characteristic polynomial of a graph . . . . . . . . . 248--253 P. S. Rao and R. J. McEachern and J. A. Weil On a proposed radiation-induced polaronic hole in silicon dioxide . . . 254--265 Donald G. Truhlar A simple approximation for the vibrational partition function of a hindered internal rotation . . . . . . . 266--270 Michael J. Mitchell and J. Andrew McCammon Free energy difference calculations by thermodynamic integration: Difficulties in obtaining a precise value . . . . . . 271--275 Abbas Farazdel and Michel Dupuis On the determination of the minimum on the crossing seam of two potential energy surfaces . . . . . . . . . . . . 276--282 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
F. Perez Pla and J. J. Baeza Baeza and G. Ramis Ramos and J. Palou OPKINE, a multipurpose program for kinetics . . . . . . . . . . . . . . . . 283--291 Mark J. Forster Comparison of compuational methods for simulating nuclear Overhauser effects in NMR spectroscopy . . . . . . . . . . . . 292--300 Rosanna Bonaccorsi and Roberto Cammi and Jacopo Tomasi On the ab initio geometry optimization of molecular solutes . . . . . . . . . . 301--309 Karel Zimmermann ORAL: All purpose molecular mechanics simulator and energy minimizer . . . . . 310--319 James J. P. Stewart Optimization of parameters for semiempirical methods. III Extension of PM3 to Be, Mg, Zn, Ga, Ge, As, Se, Cd, In, Sn, Sb, Te, Hg, Tl, Pb, and Bi . . . 320--341 Stephen R. Wilson and Weili Cui and Jules W. Moskowitz and Kevin E. Schmidt Applications of simulated annealing to the conformational analysis of flexible molecules . . . . . . . . . . . . . . . 342--349 Larry P. Davis and Larry W. Burggraf and Donn M. Storch Hydration of small anions: Calculations by the AM1 semiempirical method . . . . 350--358 Akio Kitao and Nobuhiro G\=o Conformational dynamics of polypeptides and proteins in the dihedral angle space and in the Cartesian coordinate space: Normal mode analysis of deca-alanine . . 359--368 John Mullay A simple method for calculating atomic charges in charged molecular systems of biochemical interest . . . . . . . . . . 369--375 Da-Hong Lu and Meishan Zhao and Donald G. Truhlar Projection operator method for geometry optimization with constraints . . . . . 376--384 K. Palmö and L.-O. Pietilä and S. Krimm Construction of molecular mechanics energy functions by mathematical transformation of ab initio force fields and structures . . . . . . . . . . . . . 385--390 Randall S. Dumont A Metropolis Monte Carlo method for computing microcanonical statistical rate constants . . . . . . . . . . . . . 391--401 Craig E. Kundrot and Jay W. Ponder and Frederic M. Richards Algorithms for calculating excluded volume and its derivatives as a function of molecular conformation and their use in energy minimization . . . . . . . . . 402--409 Louis Carlacci and Kuo-Chen Chou New development on energetic approach to the packing in proteins . . . . . . . . 410--415 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
W. S. Verwoerd and K. Weimer Comparison of semiempirical calculations for silicon compounds . . . . . . . . . 417--420 Jan H. Jensen and Mark S. Gordon Splicing I: Using mixed basis sets in ab initio calculations . . . . . . . . . . 421--426 Petko M. Ivanov and Tatyana G. Momchilova and Ivan G. Pojarlieff Molecular mechanics (MM) and MM-EHMO conformational analysis of the diastereoisomers of 3-amino-1,2,3-triphenyl-1-propyl chloride . . . . . . . . . . . . . . . . 427--434 Anthony Nicholls and Barry Honig A rapid finite difference algorithm, utilizing successive over-relaxation to solve the Poisson--Boltzmann equation 435--445 R. J. McEachern and P. S. Rao and J. A. Weil Ab initio calculations on CO$_4$ centers in silicon dioxide . . . . . . . . . . . 446--453 Kim Sharp Incorporating solvent and ion screening into molecular dynamics using the finite-difference Poisson--Boltzmann method . . . . . . . . . . . . . . . . . 454--468 Uri Dinur Atomic multipoles and perpendicular electrostatic forces in diatomic and planar molecules . . . . . . . . . . . . 469--486 S. P. Karna and M. Dupuis Frequency dependent nonlinear optical properties of molecules: Formulation and implementation in the HONDO program . . 487--504 Kathleen A. Palmer and Harold A. Scheraga Standard-geometry chains fitted to X-ray derived structures: Validation of the rigid-geometry approximation. I. Chain closure through a limited search of ``loop'' conformations . . . . . . . . . 505--526 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
Mircea V. Diudea and Ovidiu Minailiuc and Alexandru T. Balaban Molecular topology. IV. Regressive vertex degrees (new graph invariants) and derived topological indices . . . . 527--535 Rafik Karaman and Jun-Tsu Luke Huang and James L. Fry Correlation of singlet-triplet gaps for aryl carbenes calculated by MINDO/3, MNDO, AM1, and PM3 with Hammett-type substituent constants . . . . . . . . . 536--545 D. B. Chesnut and D. W. Wright Chemical shift bond derivatives for molecules containing first-row atoms . . 546--559 D. Frye and A. Preiskorn and E. Clementi The Hylleraas--CI method in molecular calculations. III. Implementation and numerical verification of a three-electron many-center theory . . . 560--564 Brian J. Smith and Colin J. Marsden Conformational preferences of XONO$_2$ systems (X = H, F, Cl, CH$_3$) from ab initio techniques . . . . . . . . . . . 565--574 R. J. Zauhar The incorporation of hydration forces determined by continuum electrostatics into molecular mechanics simulations . . 575--583 Maged Khalil and Robert J. Woods and Donald F. Weaver and Vedene H. Smith Jr. An examination of inter molecular and intra molecular hydrogen bonding in biomolecules by AM1 and MNDO/M semiempirical molecular orbital studies 584--593 Akbar Nayeem and Jorge Vila and Harold A. Scheraga A comparative study of the simulated-annealing and Monte Carlo-with-minimization approaches to the minimum-energy structures of polypeptides: [Met]-enkephalin . . . . . 594--605 Jon Baker and Warren J. Hehre Geometry optimization in Cartesian coordinates: the end of the $Z$-matrix? 606--610 S. Tolosa and J. Espinosa and F. J. Olivares del Valle Computation of spectroscopic properties of van der Waals systems from post-SCF ab initio potentials including the EICP alternative counterpoise technique . . . 611--619 David M. Ferguson and Peter A. Kollman Can the Lennard-Jones $6$--$12$ function replace the $10$--$12$ form in molecular mechanics calculations? . . . . . . . . 620--626 Tahir Ça\ugin and Michael Holder and B. Montgomery Pettitt A method for modeling icosahedral virions: Rotational symmetry boundary conditions . . . . . . . . . . . . . . . 627--634 Donald B. Boyd and John D. Snoddy and Ho-Shen Lin Molecular simulations of DD-peptidase, a model ß-lactam-binding protein: Synergy between X-ray crystallography and computational chemistry . . . . . . . . 635--644 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
Martin Saunders Searching for conformers of nine- to twelve-ring hydrocarbons on the MM2 and MM3 energy surfaces: Stochastic search for interconversion pathways . . . . . . 645--663 Carlos Alemán and Enric I. Canela and Rafael Franco and Modesto Orozco A new strategy for the evaluation of force parameters from quantum mechanical computations . . . . . . . . . . . . . . 664--674 Miroslaw Szafran and Jacek Koput PM3 study of the proton affinities of 2-, 3-, and 4-monosubstituted pyridines in the gas phase . . . . . . . . . . . . 675--680 Angelina Kantola and Hugo O. Villar and Gilda H. Loew Atom based parametrization for a conformationally dependent hydrophobic index . . . . . . . . . . . . . . . . . 681--689 V. J. Barclay and James S. Wright MRD--CI potential surfaces using balanced basis sets. VI. Correlation of bond order with bond function composition for first-row diatomic molecules . . . . . . . . . . . . . . . 690--696 James S. Wright and V. J. Barclay Bond functions, covalent potential curves, and the basis set superposition error . . . . . . . . . . . . . . . . . 697--704 Gustavo A. Arteca and Alfonso Hernández-Laguna and Juan J. Rández and Yves G. Smeyers and Paul G. Mezey A topological analysis of molecular electrostatic potential on van der Waals surfaces for histamine and 4-substituted derivatives as H$_2$-receptor agonists 705--716 Yasuhiko Shiratori and Setsuko Nakagawa Parametrization of calcium binding site in proteins and molecular dynamics simulation on phospholipase A$_2$ . . . 717--730 Philippe Lagant and Philippe Derreumaux and Gerard Vergoten and Warner Peticolas The use of ultraviolet resonance Raman intensities to test proposed molecular force fields for nucleic acid bases . . 731--741 David R. Fagerburg Comparison of AM1 and ab initio calculation of the carbon-carbon bond rotation in ethylene glycol diacetate 742--745 Huajun Wang Grid-search molecular accessible surface algorithm for solving the protein docking problem . . . . . . . . . . . . 746--750 Edgar W. Ignacio and H. Bernhard Schlegel On the additivity of basis set effects in some simple fluorine containing systems . . . . . . . . . . . . . . . . 751--760 Robert W. Williams and Alfred H. Lowrey Effects of hydration on scale factors for ab initio force constants . . . . . 761--777 Anonymous Announcements . . . . . . . . . . . . . 778--778 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
P. Venuvanalingam and P. Thangavel Parallel algorithm for the computation of characteristic polynomials of chemical graphs . . . . . . . . . . . . 779--783 F. M. Floris and J. Tomasi and J. L. Pascual Ahuir Dispersion and repulsion contributions to the solvation energy: Refinements to a simple computational model in the continuum approximation . . . . . . . . 784--791 Santiago Olivella and José Salvador The half-projected Hartree--Fock model for computing thermally ``forbidden'' pericyclic reactions . . . . . . . . . . 792--802 Yufei Guo and M. A. Whitehead An alternative self-interaction correction in the generalized exchange local-density functional theory . . . . 803--810 M. P. Fülscher and E. L. Mehler Self-consistent, nonorthogonal group function approximation. III. Approaches for modeling intermolecular interactions 811--828 Jan Hlavá\vcek and Václav Mat\uejka and Petr \vCársky MM2 study on the conformation of $N$-acetyl- L-amino acid $N$'-methylamides with aliphatic side chain and their N$^\alpha$-methyl derivatives . . . . . . . . . . . . . . 829--838 Ingrid Pettersson and Klaus Gundertofte Conformational energies and rotational barriers in 3-methyl-1-butene and 1-butene: an ab initio and molecular mechanics study . . . . . . . . . . . . 839--843 Dora M. Schnur and Mark V. Grieshaber and J. Phillip Bowen Development of an internal searching algorithm for parameterization of the MM2/MM3 force fields . . . . . . . . . . 844--849 Carol A. Venanzi and Christopher Plant and Thomas J. Venanzi A molecular orbital study of amiloride 850--861 C. S. Wu and W. C. Neely and S. D. Worley A semiempirical theoretical study of the molecular interaction of cocaine with the biological substrate glycine . . . . 862--867 Huajun Wang and Cyrus Levinthal A vectorized algorithm for calculating the accessible surface area of macromolecules . . . . . . . . . . . . . 868--871 Saulo A. Vázquez and Miguel A. Ríos and Luis Carballeira A molecular mechanics study of conformational trends in simple alcohols and ethers. Part I: Geometric trends . . 872--879 G. A. Crowder and G. O. Carlisle Conformational studies of 2-methylbutyronitrile and 3-methyl-1-pentyne by vibrational spectroscopy and molecular mechanics . . 880--884 Elisabete Suto and M. M. C. Ferreira and Roy E. Bruns Principal component analysis of dipole moment derivative signs of chloroform 885--890 Elaine C. Meng and Richard A. Lewis Determination of molecular topology and atomic hybridization states from heavy atom coordinates . . . . . . . . . . . . 891--898 Paul S. Charifson and Richard G. Hiskey and Lee G. Pedersen and Lee F. Kuyper Free energy calculations on calcium and magnesium complexes: Protein and phospholipid model systems . . . . . . . 899--908 Malcolm E. Davis and J. Andrew McCammon Dielectric boundary smoothing in finite difference solutions of the Poisson equation: an approach to improve accuracy and convergence . . . . . . . . 909--912 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
György G. Ferenczy Charges derived from distributed multipole series . . . . . . . . . . . . 913--917 Philippe Alard and Shoshana J. Wodak Detection of cavities in a set of interpenetrating spheres . . . . . . . . 918--922 Andrew L. Sargent and Michael B. Hall Basis sets for geometry optimizations of second-row transition metal inorganic and organometallic complexes . . . . . . 923--933 Giuliano Alagona and Caterina Ghio and Claudio Pratesi Force field parameters for molecular mechanical simulation of dehydroamino acid residues . . . . . . . . . . . . . 934--942 Rob W. W. Hooft and Jan A. Kanters and Jan Kroon Implementation and use of the method of prudent ascent in conformational analysis using molecular mechanics . . . 943--947 Michael B. Coolidge and John E. Marlin and James J. P. Stewart Calculations of molecular vibrational frequencies using semiempirical methods 948--952 C. Kozmutza and E. Kapuy Counterpoise corrected calculations at the correlated level: a simplified method using LMOs . . . . . . . . . . . 953--958 Ann M. Richard Quantitative comparison of molecular electrostatic potentials for structure-activity studies . . . . . . . 959--969 Milan Randi\'c On computation of optimal parameters for multivariate analysis of structure-property relationship . . . . 970--980 Alexander A. Rashin and Joseph Malinsky New method for the computation of ionic distribution around rod-like polyelectrolytes with the helical distribution of charges. I. General approach and a nonlinearized Poisson--Boltzmann equation . . . . . . 981--993 P. V. Maye and C. A. Venanzi Host-guest preorganization and complementarity: a molecular mechanics and molecular dynamics study of cation complexes of a cyclic urea-anisole spherand . . . . . . . . . . . . . . . . 994--1007 Shahul H. Nilar Applications of the simulated annealing method to intermolecular interactions 1008--1013 Xiche Hu and William L. Hase and Tony Pirraglia Vectorization of the general Monte Carlo classical trajectory program VENUS . . . 1014--1024 Gilles Klopman and Shaomeng Wang A computer automated structure evaluation (CASE) approach to calculation of partition coefficient . . 1025--1032 Terry R. Stouch and Keith B. Ward and Amanda Altieri and Arnold T. Hagler Simulations of lipid crystals: Characterization of potential energy functions and parameters for lecithin molecules . . . . . . . . . . . . . . . 1033--1046 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
J. J. C. Teixeira-Dias and R. Fausto and L. A. E. Batista de Carvalho The C$_\alpha$\bondC internal rotation in $\alpha$-alkyl substituted carbonyls and thiocarbonyls: CH(CH$_3$)$_2$C (\doublebondX) Y H (X, Y\doublebondO or S) . . . . . . . . . . . . . . . . . . . 1047--1057 Hans Horn and Horst Weiß and Marco Háser and Michael Ehrig and Reinhart Ahlrichs Prescreening of two-electron integral derivatives in SCF gradient and Hessian calculations . . . . . . . . . . . . . . 1058--1064 Berthold von Freyberg and Werner Braun Efficient search for all low energy conformations of polypeptides by Monte Carlo methods . . . . . . . . . . . . . 1065--1076 Estanislao Silla and Iñaki Tuñón and Juan Luis Pascual-Ahuir GEPOL: an improved description of molecular surfaces II. Computing the molecular area and volume . . . . . . . 1077--1088 Michael Lehd and Frank Jensen A general procedure for obtaining wave functions obeying the virial theorem . . 1089--1096 Hiroshi Kato and Eishi Tanaka Stabilities of small Be$_n$ and B$_n$ clusters ($4 \leq n \leq 8$) by vibrational analysis . . . . . . . . . . 1097--1109 Jonathan M. Goodman and W. Clark Still An unbounded systematic search of conformational space . . . . . . . . . . 1110--1117 T. J. N. Brown and R. B. Mallion and P. Pollak and Branca R. M. de Castro and J. A. N. F. Gomes The number of spanning trees in Buckminsterfullerene . . . . . . . . . . 1118--1124 Libero J. Bartolotti and Lee G. Pedersen and Paul S. Charifson Long range nonbonded attractive constants for some charged atoms . . . . 1125--1128 Mark Froimowitz Molecular geometries and heats of formation of C$_{60}$ and C$_{70}$ as computed by MM2-87 . . . . . . . . . . . 1129--1133 Jeffrey P. Jones and Jeffrey L. Urbauer Theoretical kinetic isotope effects for the hydride transfer from formate to carbon dioxide: a comparison of theory with experiment . . . . . . . . . . . . 1134--1141 Shahrzad Kabir and Anne-Marie Sapse An ab initio study of the proton affinities of some heteroatomic rings: Imidazole, oxazole, and thiazole . . . . 1142--1146 Rudolf Zahradník and V. Balaji and Josef Michl An SCF study of 10-vertex and 12-vertex boranes and heteroboranes . . . . . . . 1147--1156 James J. P. Stewart and Michael B. Coolidge Semiempirical vibrational and electronic structures of C$_{60}$ and C$_{70}$ . . 1157--1162 Anonymous Announcements . . . . . . . . . . . . . 1163--1163 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
Angels González-Lafont and José M. Lluch and Antonio Oliva and Juan Bertrán A Monte Carlo simulation of free energy relationships for the electron transfer reaction between Fe$^+$ and Fe$^{2+}$ in water . . . . . . . . . . . . . . . . . 1165--1171 J. M. García de la Vega and B. Miguel Approximate STO functions for the first-row transition metal atoms . . . . 1172--1181 Nicholas Bodor and Ming-Ju Huang Predicting partition coefficients for isomeric diastereoisomers of some tripeptide analogs . . . . . . . . . . . 1182--1186 S. L. Price and C. H. Faerman and C. W. Murray Toward accurate transferable electrostatic models for polypeptides: a distributed multipole study of blocked amino acid residue charge distributions 1187--1197 Gustavo A. Arteca and Naomi D. Grant and Paul G. Mezey Variable atomic radii based on some approximate configurational invariance and transferability properties of the electron density . . . . . . . . . . . . 1198--1210 Rita Kakkar and Vibha Walia Unimolecular rearrangements of ethylnitrene: an exploratory theoretical study . . . . . . . . . . . . . . . . . 1211--1216 Herbert W. Jones Analytic Löwdin alpha-function method for two-center electron-repulsion integrals over Slater-type orbitals . . . . . . . 1217--1222 Mark H. Holmes and Jonathan Bell The application of symbolic computing to chemical kinetic reaction schemes . . . 1223--1231 Piotr Cieplak and Peter Kollman On the use of electrostatic potential derived charges in molecular mechanics force fields. The relative solvation free energy of cis- and trans-$N$-methyl-acetamide . . . . . . . 1232--1236 J. J. Soares Neto and Jan Linderberg A fully three-dimensional finite element method calculation for the vibrational levels of H$_2$O and D$_2$O . . . . . . 1237--1242 X. Liu and D. J. Klein The graph isomorphism problem . . . . . 1243--1251 X. Liu and D. J. Klein and T. G. Schmalz and W. A. Seitz Generation of carbon-cage polyhedra . . 1252--1259 D. J. Klein and X. Liu Many-body conjugated-circuit computations . . . . . . . . . . . . . . 1260--1264 X. Liu and D. J. Klein and W. A. Seitz and T. G. Schmalz Sixty-atom carbon cages . . . . . . . . 1265--1269 John E. Mertz and Douglas J. Tobias and Charles L. Brooks III and U. C. Singh Vector and parallel algorithms for the molecular dynamics simulation of macromolecules on shared-memory computers . . . . . . . . . . . . . . . 1270--1277 Marcus E. Brewster and Ming-Ju Huang and James J. Kaminski and Emil Pop and Nicholas Bodor Reactivity of biologically important reduced pyridines. VIII. A semiempirical (AM1) study of the oxidation of 3-substituted-1-methyl-1,4-dihydropyridines 1278--1282 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
G. Perrot and B. Cheng and K. D. Gibson and J. Vila and K. A. Palmer and A. Nayeem and B. Maigret and H. A. Scheraga MSEED: a program for the rapid analytical determination of accessible surface areas and their derivatives . . 1--11 Shuichi Yahiro and Yasuhiko Gondo A vector processing algorithm of auxiliary integral evaluation for two-electron Gaussian integrals . . . . 12--16 M. V. Szombathely and P. Bräuer and M. Jaroniec The solution of adsorption integral equations by means of the regularization method . . . . . . . . . . . . . . . . . 17--32 Yaxiong Sun and Peter A. Kollman Conformational sampling and ensemble generation by molecular dynamics simulations: 18-Crown-6 as a test case 33--40 David A. Wertz and Chen-Xi Shi and Carol A. Venanzi A comparison of distance geometry and molecular dynamics simulation techniques for conformational analysis of $\beta$-cyclodextrin . . . . . . . . . . 41--56 Maria Kontoyianni and Andrew J. Hoffman and J. Phillip Bowen Ab initio and molecular mechanics calculations on imine derivatives: a study of the rotational barriers and the development of MM2 parameters . . . . . 57--65 Jacqueline J. Sines and J. Andrew McCammon and Stuart A. Allison Kinetic effects of multiple charge modifications in enzyme-substrate reactions: Brownian dynamics simulations of Cu, Zn superoxide dismutase . . . . . 66--69 T. Ziegler and G. L. Gutsev On the evaluation of molecular electron affinities by approximate density functional theory . . . . . . . . . . . 70--75 Carl-Dieter Zachmann and Wolfgang Heiden and Micheal Schlenkrich and Jürgen Brickmann Topological analysis of complex molecular surfaces . . . . . . . . . . . 76--84 Jian Li and Paulo Correa De Mello and Karl Jug Extension of SINDO1 to transition metal compounds . . . . . . . . . . . . . . . 85--92 Jian Li and Karl Jug Application of SINDO1 to organo-transition metal compounds . . . 93--101 Michael K. Dowd and Peter J. Reilly and Alfred D. French Conformational analysis of trehalose disaccharides and analogues using MM3 102--114 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
F. J. Olivares del Valle and M. A. Aguilar Correlation and solvation effects. IV. A systematic analysis of the influence of cavity size and shape on solvation properties in the polarizable continuum model with electron correlation . . . . 115--134 J. R. Alvarez-Collado and Robert J. Buenker On the numerical solution of the multidimensional vibrational time-independent Schroedinger equation 135--141 Martin Speis and Volker Buss Basis set and correlation energy dependence of geometry and harmonic frequencies of difluoroethane, CHF$_2$CH$_3$ . . . . . . . . . . . . . 142--147 C. Sousa and J. Rubio and F. Illas Reliability of atomic natural orbital basis sets in calculations involving pseudopotentials . . . . . . . . . . . . 148--154 Ramon Carbo and Lluís Molino and Blanca Calabuig A concurrent algorithm for parallel calculation of eigenvalues and eigenvectors of real symmetric matrices 155--159 Hans P. Lüthi and John E. Mertz and Martin W. Feyereisen and Jan E. Almlöf A coarse-grain parallel implementation of the direct SCF method . . . . . . . . 160--164 Jürgen Breidung and Walter Thiel A systematic ab initio study of the group V trihalides MX$_3$ and pentahalides MX$_5$ (M = P Bi, X = F I) 165--176 Jorge M. Seminario and Monica C. Concha and Peter Politzer Calculated structures and relative stabilities of furoxan, some 1,2-dinitrosoethylenes and other isomers 177--182 Ruifeng Liu and Peter Pulay Ab initio evidence for the stepwise mechanism of the McLafferty rearrangement of the butanal radical cation . . . . . . . . . . . . . . . . . 183--186 Yubin Wang and Zhenyi Wen and Zhiyong Zhang and Quishi Du New realization of loop driven direct CI 187--198 V. Luzhkov and A. Warshel Microscopic models for quantum mechanical calculations of chemical processes in solutions: LD/AMPAC and SCAAS/AMPAC calculations of solvation energies . . . . . . . . . . . . . . . . 199--213 Wayne C. Guida and Regine S. Bohacek and Mark D. Erion Probing the conformational space available to inhibitors in the thermolysin active site using Monte Carlo/energy minimization techniques . . 214--228 George P. Ford and Bingze Wang The optimized ellisoidal cavity and its application to the self-consistent reaction field calculation of hydration energies of cations and neutral molecules . . . . . . . . . . . . . . . 229--239 Jon Baker Geometry optimization in Cartesian coordinates: Constrained optimization 240--253 Elisheva Goldstein Book Review: \booktitleAlgorithms for chemists, by Jure Zupan, Wiley, New York, 1989, pp. 290. Price: \$120.00} 254--254 Tereza Varnali Book Review: \booktitleComputational chemistry using the P.C., by Donald W. Rogers, VCH Publishers, Inc., New York, 1990. pp. 224. Price: \$55.00} . . . . . 254--255 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
Jan L. M. Dillen PEFF: a program for the development of empirical force fields . . . . . . . . . 257--267 T. C. Chang Pauli repulsion in the open shell species BeH and Co$^+$ . . . . . . . . . 268--274 Wolfgang Förner Davydov soliton dynamics: Initial state, boundary conditions, and numerical procedure . . . . . . . . . . . . . . . 275--313 Reiner Sustmann and Willi Sicking and Helmut Quast Analysis of an intermediate in a 1,3-dipolar cycloaddition of methylsulfonyl azide . . . . . . . . . . 314--317 M. Schaumberger and J. Köhler Charge distributions of phosphorylcholine and its derivatives 318--328 Kathleen A. Palmer and Harold A. Scheraga Standard-geometry chains fitted to X-ray derived structures: Validation of the rigid-geometry approximation. II. Systematic searches for short loops in proteins: Applications to bovine pancreatic ribonuclease A and human lysozyme . . . . . . . . . . . . . . . . 329--350 Gordon M. Crippen Exploring the conformation space of cycloalkanes by linearized embedding . . 351--361 David M. Ferguson and David A. Pearlman and William C. Swope and Peter A. Kollman Free energy perturbation calculations involving potential function changes . . 362--370 Gyula Tasi and Imre Kiricsi and Horst Förster Representation of molecules by atomic charges: a new population analysis . . . 371--379 Brian K. Shoichet and Irwin D. Kuntz and Dale L. Bodian Molecular docking using shape descriptors . . . . . . . . . . . . . . 380--397 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
Jeanne G. C. M. van Duijneveldt-van de Rijdt and Frans B. van Duijneveldt Methods for the calculation of V$_{oh}$ in OH O hydrogen bonds . . . . . . . . . 399--407 John Kendrick and Elizabeth Robson and Sara McIntyre Ab initio and molecular mechanics study of $n$-phenyl phthalimide and its crystal structure . . . . . . . . . . . 408--413 S. Kindermann and E. Michel and P. Otto Parallelization of quantum mechanical integral calculations . . . . . . . . . 414--422 Mustafa R. Ibrahim and Michael Bühl and Reinhard Knab and Paul von Ragué Schleyer Vinyloxyborane and its isomers. An ab initio study of the C$_2$H$_5$BO potential energy surface, the barrier to 1,3-shifts in $\beta$-ketoboranes, and the mechanism of the carbonylation reaction of boranes . . . . . . . . . . 423--428 Jan Hermans and R. H. Yun and Amil G. Anderson Precision of free energies calculated by molecular dynamics simulations of peptides in solution . . . . . . . . . . 429--442 Antonio Rey and Jeffrey Skolnick Efficient algorithm for the reconstruction of a protein backbone from the $\alpha$-carbon coordinates . . 443--456 K. Hirao and K. Mogi Floating functions satisfying the Hellmann--Feynman Theorem: single floating scheme . . . . . . . . . . . . 457--467 William J. Dunn III and Peter I. Nagy Relative $\log P$ and solution structure for small organic solutes in the chloroform/water system using Monte Carlo methods . . . . . . . . . . . . . 468--477 Michael Sabio and Sid Topiol A conformational analysis of 3'-azido-3'-deoxythymidine . . . . . . . 478--491 Steven L. Dixon and Peter C. Jurs Atomic charge calculations for quantitative structure--property relationships . . . . . . . . . . . . . 492--504 Elaine C. Meng and Brian K. Shoichet and Irwin D. Kuntz Automated docking with grid-based energy evaluation . . . . . . . . . . . . . . . 505--524 David M. Ferguson and Ian R. Gould and William A. Glauser and Stefan Schroeder and Peter A. Kollman Comparison of ab initio, semiempirical, and molecular mechanics calculations for the conformational analysis of ring systems . . . . . . . . . . . . . . . . 525--532 J. F. Janak and P. C. Pattnaik Protein calculations on parallel processors. I. Parallel algorithm for the potential energy . . . . . . . . . . 533--538 Gilles Klopmand Book Review: \booktitleConcepts and applications of molecular similarity, by Mark A. Johnson and Gerald M. Maggiora, eds., John Wiley & Sons, New York, 1990, 393 pp. Price: \$65.00} . . . . . . . . 539--540 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
Anusch Peyman and Hans-Dieter Beckhaus Modeling a reaction path by molecular mechanics: Dimerization of carbon free radicals . . . . . . . . . . . . . . . . 541--550 Ulrich Meier and Christoph Van Wüllen and Michael Schindler Ab initio calculation of magnetic properties by the ``direct'' IGLO method 551--559 Yasuyuki Kurita and Chiyozo Takayama and Mitsuru Sasaki Conformational analysis of 4 h-1,3,2-benzodioxaphosphorin 2-sulfides with ab initio molecular orbital calculations . . . . . . . . . . . . . . 560--564 Catherine E. Peishoff and J. Scott Dixon Improvements to the distance geometry algorithm for conformational sampling of cyclic structures . . . . . . . . . . . 565--569 Desiderio A. Vasquez Locally implicit solution of a reaction-diffusion system with stiff kinetics . . . . . . . . . . . . . . . . 570--578 Mark E. Snow Powerful simulated-annealing algorithm locates global minimum of protein-folding potentials from multiple starting conformations . . . . . . . . . 579--584 William C. Swope and David M. Ferguson Alternative expressions for energies and forces due to angle bending and torsional energy . . . . . . . . . . . . 585--594 Sang Yeon Lee and Yoon Sup Lee Kramers' restricted Hartree--Fock method for polyatomic molecules using ab initio relativistic effective core potentials with spin--orbit operators . . . . . . . 595--601 Pawel M. Kozlowski and Ludwik Adamowicz Multicenter and multiparticle integrals for explicitly correlated Cartesian Gaussian-type functions . . . . . . . . 602--613 Weida Tong and Hongping Ye and Ding Rong and Valerian T. D'Souza Artificial redox enzymes. II. A computational chemistry study . . . . . 614--621 T. R. Stouch and Donald E. Williams Conformational dependence of electrostatic potential derived charges of a lipid headgroup: Glycerylphosphorylcholine . . . . . . . 622--632 Andrzej Sygula and Peter W. Rabideau Pathways for ring inversion in 9, 10-dihydroanthracene, 9, 10-dihydrophenanthrene, and 7, 12-dihydropleiadene: Combined molecular orbital and molecular mechanics study 633--639 Douglas A. Smith and Charles W. Ulmer II and Matthew J. Gilbert Structural studies of aromatic amines and the DNA intercalating compounds m-AMSA and o-AMSA: Comparison of MNDO, AM1, and PM3 to experimental and ab initio results . . . . . . . . . . . . . 640--650 Mihaly Mezei Polynomial path for the calculation of liquid state free energies from computer simulations tested on liquid water . . . 651--656 Maria Kontoyianni and J. Phillip Bowen An ab initio and molecular mechanical investigation of ureas and amide derivatives . . . . . . . . . . . . . . 657--666 Timothy P. Wunz Nucleoside free energy perturbation calculations: Mutation of purine-to-pyrimidine and pyrimidine-to-purine nucleosides . . . . 667--673 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
Daniel Rinaldi and Jean-Louis Rivail and Noureddine Rguini Fast geometry optimizationin self-cosistent reaction field computations on solvated molecules . . . 675--680 J. Frau and J. Donoso and F. Muñoz and F. García Blanco Theoretical calculations of $\beta$-lactam antibiotics. III. AM1, MNDO, and MINDO/3 calculations of hydrolysis of $\beta$-lactam compound (azetidin-2-one ring) . . . . . . . . . 681--692 S. D. Morley and D. E. Jackson and M. R. Saunders and J. G. Vinter DMC: a multifunctional hybrid dynamics/Monte Carlo simulation algorithm for the evaluation of conformational space . . . . . . . . . . 693--703 Alexander Alex and Timothy Clark MO-Studies of enzyme reaction mechanisms. I. Model molecular orbital study of the cleavage of peptides by carboxypeptidase A . . . . . . . . . . . 704--717 Charles W. Bock and Alexander V. Abramenkov and George R. De Maré and Yurii N. Panchenko Effective internal rotation potential energy function of acryloyl fluoride, CH$_2$CHCFO . . . . . . . . . . . . . . 718--721 Berta Fernández and Saulo A. Vázquez and Miguel A. Ríos Theoretical study of some nitriles: Intramolecular hydrogen bonds and anomeric effect . . . . . . . . . . . . 722--729 Andrew R. Leach and Irwin D. Kuntz Conformational analysis of flexible ligands in macromolecular receptor sites 730--748 Kenneth M. Merz Jr. Analysis of a large data base of electrostatic potential derived atomic charges . . . . . . . . . . . . . . . . 749--767 Brock A. Luty and Malcolm E. Davis and J. Andrew McCammon Electrostatic energy calculations by a Finite-difference method: Rapid calculation of charge--solvent interaction energies . . . . . . . . . . 768--771 Ya-Jun Zheng and Scott M. Le Grand and Kenneth M. Merz Jr. Conformational preferences for hydroxyl groups in substituted tetrahydropyrans 772--791 Milan Randi\'c Book Review: \booktitleComputational chemical graph theory, Dennis H. Rouvray, ed., Nova Science Publisher, Inc., New York, 1990, 331 pp. ISBN 0-947143-84-5. Price: \$72.00} . . . . . 792--792 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
E. W. Knapp Long time dynamics of a polymer with rigid body monomer units relating to a protein model: Comparison with the rouse model . . . . . . . . . . . . . . . . . 793--798 R. Fausto and L. A. E. Batista De Carvalho and J. J. C. Teixeira-Dias Conformational analysis of carbonyl and thiocarbonyl ethyl esters: the PHC(X) (X, Y = O or S) internal rotation . . . 799--809 J. J. Baeza Baeza and G. Ramis Ramos and F. Pérez Plá Stiffness-Adaptive Taylor method for the integration of non-stiff and stiff kinetic models . . . . . . . . . . . . . 810--820 Josep Martí and Agustí Lledós and Juan Bertrán and Miquel Duran Vibrational Stark effect: Theoretical determination through the semiempirical AM1 method . . . . . . . . . . . . . . . 821--829 György G. Ferenczy and Jean-Louis Rivail and Péter R. Surján and Gábor Náray-Szabó NDDO fragment self-consistent field approximation for large electronic systems . . . . . . . . . . . . . . . . 830--837 Norman L. Allinger and Lawrence R. Schmitz and Ioan Motoc and Charles Bender and Jan K. Labanowski Heats of formation of organic molecules by Ab Initio calculations: Carboxylic acids and esters . . . . . . . . . . . . 838--841 L. Bonati and U. Cosentino and E. Fraschini and G. Moro and D. Pitea Molecular electrostatic potential of substituted aromatic compounds: Factors affecting the differences between Ab Initio and semiempirical results . . . . 842--850 Saulo A. Vázquez and Miguel A. Ríos and LuíS Carballeira Molecular mechanics study of conformational trends in simple alcohols and ethers. II. Intramolecular hydrogen bonding . . . . . . . . . . . . . . . . 851--859 Miguel A. Ríos and JesúS Rodríguez Semiempirical study of compounds with O-H O intramolecular hydrogen bond . . . 860--866 German Urbina-Villalba and Leonardo J. Rodriguez and German R. Castro and Fernando Ruette Semiempirical study of electronic and bonding properties of cobalt silicide clusters . . . . . . . . . . . . . . . . 867--873 Alice Chung-Phillips Torsional energy levels and wave functions . . . . . . . . . . . . . . . 874--882 W. A. Sokalski and M. Shibata and R. Rein and R. L. Ornstein Cumulative atomic multipole moments complement any atomic charge model to obtain more accurate electrostatic properties . . . . . . . . . . . . . . . 883--887 Frank A. Momany and Rebecca Rone Validation of the general purpose QUANTA\reg 3.2/CHARMm\reg force field 888--900 J. M. Cullen Localized electron pair theory for the calculation of ground state energies of large molecules . . . . . . . . . . . . 901--911 Sanchita Hati and Dipankar Datta Electronegativity and Bader's bond critical point . . . . . . . . . . . . . 912--918 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
Volker Jonas and Gernot Frenking and Manfred T. Reetz Theoretical studies of organometallic compounds. I. All electron and pseudopotential calculations of Ti(CH$_3$)$_n$Cl$_{4 - n}$ ($n = 0$--$4$) . . . . . . . . . . . . . . . . 919--934 Volker Jonas and Gernot Frenking and Manfred T. Reetz Theoretical studies of organometallic compounds. II. All electron and pseudopotential calculations of M (CH$_3$)$_n$Cl$_{4 - n}$ (M = C, Si, Ge, Sn, Pb; $n = 0$--$4$) . . . . . . . . . 935--943 Szczepan Roszak and W. Andrzej Sokalski and Joyce J. Kaufman Correlated molecular and multicenter multipole moments in ground and excited states from multiple reference double-excitation configuration interaction calculations . . . . . . . . 944--951 Shuichi Miyamoto and Peter A. Kollman Settle: an analytical version of the SHAKE and RATTLE algorithm for rigid water models . . . . . . . . . . . . . . 952--962 Craig A. Gough and Stephen E. Debolt and Peter A. Kollman Derivation of fluorine and hydrogen atom parameters using liquid simulations . . 963--970 David L. Veenstra and David M. Ferguson and Peter A. Kollman How transferable are hydrogen parameters in molecular mechanics calculations? . . 971--978 John D. Westbrook and Ronald M. Levy and Karsten Krogh-Jespersen Molecular electrostatic potentials and partial atomic charges from correlated wave functions: Applications to the electronic ground and excited states of 3-methylindole . . . . . . . . . . . . . 979--989 John J. Houser and Gilles Klopman Rapid estimation of charge distribution. II. Heteroatoms . . . . . . . . . . . . 990--996 Paul von Ragué Schleyer and José Walkimar De M. Carneiro Does CH prefer a C$_{2v}$ rather than a C$_s$ structure? . . . . . . . . . . . . 997--1003 Robert C. Morrison and Guanghua Liu Extended Koopmans' theorem: Approximate ionization energies from MCSCF wave functions . . . . . . . . . . . . . . . 1004--1010 Shankar Kumar and John M. Rosenberg and Djamal Bouzida and Robert H. Swendsen and Peter A. Kollman THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method . . . . . . 1011--1021 S. L. Lin and J. Mellor-Crummey and B. M. Pettitt and G. N. Phillips Jr. Molecular dynamics on a distributed-memory multiprocessor . . . 1022--1035 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
Oscar N. Ventura and Elena L. CoitiñO and Agustí Lledós and Juan Bertran Analysis of the gas-phase addition of water to formaldehyde: a semiempirical and ab initio study of bifunctional catalysis by H$_2$O . . . . . . . . . . 1037--1046 F. Bockisch and J. C. Rayez and D. Liotard and B. Duguay Theoretical studies of $[n]$paracyclophanes and their valence isomers. I. Geometries, strain energies, and enthalpies of the inter-conversions of $[n]$paracyclophanes and their Dewar benzene isomers . . . . . . . . . . . . 1047--1056 Victor Pérez and José M. Lluch and Juan Bertrán Monte Carlo simulation of the diabatic free energy curves for a dissociative electron transfer reaction in a polar solvent . . . . . . . . . . . . . . . . 1057--1065 Alexander I. Boldyrev and Paul v. R. Schleyer and D. Higgins and Colin Thomson and Sofia S. Kramarenko Ab initio investigation of the structures and stabilities of CH$_2$N$_2$, CHFN$_2$, and CF$_2$N$_2$ isomers: Important consequences of MP2 optimizations . . . . . . . . . . . . . 1066--1078 Raúl E. Valdés-Pérez Algorithm to generate reaction pathways for computer-assisted elucidation . . . 1079--1088 Christopher J. Cramer and Donald G. Truhlar PM3-SM3: a general parameterization for including aqueous solvation effects in the PM3 molecular orbital model . . . . 1089--1097 J. F. Janak and P. C. Pattnaik Protein calculations on parallel processors. II. Parallel algorithm for the forces and molecular dynamics . . . 1098--1102 Mahmoud Korek and Hafez Kobeissi Highly accurate diatomic centrifugal distortion constants for high orders and high levels . . . . . . . . . . . . . . 1103--1108 Y. W. Xu and C. X. Wang and Y. Y. Shi Improvements on the protein--dipole Langevin--dipole model . . . . . . . . . 1109--1113 Brock A. Luty and Malcolm E. Davis and J. Andrew McCammon Solving the finite-difference non-linear Poisson--Boltzmann equation . . . . . . 1114--1118 Juan J. Morales and María J. Nuevo General expression for the density dependence of the mori coefficients . . 1119--1124 Eugene L. Stewart and J. Phillip Bowen Molecular mechanics studies of ketene derivatives and related structures . . . 1125--1137 Jenn-Huei Lii and Norman L. Allinger Intensities of infrared bands in molecular mechanics (MM3) . . . . . . . 1138--1141 K. Palmö and L.-O. Pietilä and S. Krimm Treatment of redundancies among internal coordinates in optimizing molecular mechanics force constants . . . . . . . 1142--1150 Ya-Jun Zheng and Kenneth M. Merz Jr. Study of hydrogen bonding interactions relevant to biomolecular structure and function . . . . . . . . . . . . . . . . 1151--1169 Anonymous Announcement . . . . . . . . . . . . . . 1170--1170 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
H. R. Karfunkel and R. J. Gdanitz Ab initio prediction of possible crystal structures for general organic molecules 1171--1183 Achim Veldkamp and Gernot Frenking Theoretical studies of organometallic compounds. III. Structures and bond energies of FeCH$_n$ and FeCH ($n = 1, 2, 3$) . . . . . . . . . . . . . . . . . 1184--1198 Jesús R. Flores From linear combinations to integrals: a new approach to the basis function problem . . . . . . . . . . . . . . . . 1199--1209 M. Depner and B. L. Schürmann Molecular dynamics simulation of a poly(oxyethylene) chain dissolved in benzene . . . . . . . . . . . . . . . . 1210--1215 B. Velikson and T. Garel and J.-C. Niel and H. Orland and J. C. Smith Conformational distribution of heptaalanine: Analysis using a new Monte Carlo chain growth method . . . . . . . 1216--1233 François Colonna and Earl Evleth and János G. Ángyán Critical analysis of electric field modeling: Formamide . . . . . . . . . . 1234--1245 Shuichi Yahiro and Yasuhiko Gondo Vector processing algorithm for electron repulsion integrals in Ab Initio HF calculation based upon the PK supermatrix . . . . . . . . . . . . . . 1246--1254 P. L. Polavarapu and C. S. Ewig Ab initio computed molecular structures and energies of the conformers of glucose . . . . . . . . . . . . . . . . 1255--1261 Gordon M. Crippen and Andrew S. Smellie and Wendy W. Richardson Conformational sampling by a general linearized embedding algorithm . . . . . 1262--1274 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
Norman L. Allinger and Paul von R. Schleyer Editorial . . . . . . . . . . . . . . . 1--1 Wolfgang W. Schoeller and Jörg Strutwolf and Wilfried Haug and Thilo Busch Rotational barrier in phosphatriafulvene: an MCSCF study . . . 3--7 Markus P. Fülscher and Per-Olof Widmark An electron repulsion integral compression algorithm . . . . . . . . . 8--12 Vyacheslav G. Zakrzewski and Wolfgang von Niessen Vectorizable algorithm for green function and many-body perturbation methods . . . . . . . . . . . . . . . . 13--18 E. W. Knapp and A. Irgens-Defregger Off-lattice Monte Carlo method with constraints: Long-time dynamics of a protein model without nonbonded interactions . . . . . . . . . . . . . . 19--29 Ungsik Ryu and Myeongcheol Kim and Yoon Sup Lee Optimal use of the recurrence relations for the evaluation of molecular integrals over Cartesian Gaussian basis functions . . . . . . . . . . . . . . . 30--36 Matthias Kolb and Walter Thiel MNDO parameters for helium: Optimization, tests, and application to endohedral fullerene--helium complexes 37--44 Ji\vrí Kozelka and Roger Savinelli and Gaston Berthier and Jean-Pierre Flament and Richard Lavery Force field for platinum binding to adenine . . . . . . . . . . . . . . . . 45--53 Eric Magnusson Supplementary $d$ and $f$ functions in molecular wave functions: Optimum and nonoptimum exponents . . . . . . . . . . 54--66 Eric Magnusson Supplementary $d$ and $f$ functions in molecular wave functions at large and small internuclear separations . . . . . 67--74 Alan A. Shaffer and Scott G. Wierschke Comparison of computational methods applied to oxazole, thiazole, and other heterocyclic compounds . . . . . . . . . 75--88 Marcus W. Jurema and George C. Shields Ability of the PM3 quantum-mechanical method to model inter molecular hydrogen bonding between neutral molecules . . . 89--104 Michael Holst and Faisal Saied Multigrid solution of the Poisson--Boltzmann equation . . . . . . 105--113 W. Glunt and T. L. Hayden and M. Raydan Molecular conformations from distance matrices . . . . . . . . . . . . . . . . 114--120 Kenny B. Lipkowitz and Michael A. Peterson Benzene is not very rigid . . . . . . . 121--125 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
Douglas M. Jones and Julia M. Goodfellow Parallelization strategies for molecular simulation using the Monte Carlo algorithm . . . . . . . . . . . . . . . 127--137 W. Hanebeck and J. Gasteiger Rapid empirical calculation of the first ($n$ or $\pi$) ionization potential of organic molecules . . . . . . . . . . . 138--154 Alexandru T. Balaban and Cornel Catana Search for nondegenerate real vertex invariants and derived topological indexes . . . . . . . . . . . . . . . . 155--160 Frederick S. Lee and Zhen Tao Chu and Arieh Warshel Microscopic and semimicroscopic calculations of electrostatic energies in proteins by the POLARIS and ENZYMIX programs . . . . . . . . . . . . . . . . 161--185 Elisheva Goldstein and Suqian Jin and M. Robyn Carrillo and Robert J. Cave Ab initio study of the ground and excited states of HCP and its isomer HPC 186--194 William L. Jorgensen and Toan B. Nguyen Monte Carlo simulations of the hydration of substituted benzenes with OPLS potential functions . . . . . . . . . . 195--205 William L. Jorgensen and Ellen R. Laird and Toan B. Nguyen and Julian Tirado-Rives Monte Carlo simulations of pure liquid substituted benzenes with OPLS potential functions . . . . . . . . . . . . . . . 206--215 Clarke W. Earley Use of effective core potentials for ab initio calculations on molecular siloxanes and silicates . . . . . . . . 216--225 JoëL Pothier and Jacques Gabarro-Arpa and Marc Le Bret MORMIN: a quasi-Newtonian energy minimizer fitting the nuclear Overhauser data . . . . . . . . . . . . . . . . . . 226--236 Atul Agarwal and Ethan Will Taylor $3$-D QSAR for intrinsic activity of 5-HT$_{1A}$ receptor ligands by the method of comparative molecular field analysis . . . . . . . . . . . . . . . . 237--245 W. Heiden and T. Goetze and J. Brickmann Fast generation of molecular surfaces from 3D data fields with an enhanced ``marching cube'' algorithm . . . . . . 246--250 Andrew Holder Further comments on the lack of homoaromaticity in triquinacene . . . . 251--251 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
Thomas Fox and Notker Rösch and Randy J. Zauhar Electrostatic solvent effects on the electronic structure of ground and excited states of molecules: Applications of a cavity model based upon a finite element method . . . . . . 253--262 Manuel Dauchez and Philippe Derreumaux and Gérard Vergoten Vibrational molecular force field of model compounds with biologic interest. II. Harmonic dynamics of both anomers of glucose in the crystalline state . . . . 263--277 K. Tasaki and S. McDonald and J. W. Brady Observations concerning the treatment of long-range interactions in molecular dynamics simulations . . . . . . . . . . 278--284 Mikhail N. Glukhovtsev and Paul von Ragué Schleyer and Nicolaas J. R. van Eikema Hommes and Jose Walkimar De M. Carneiro and Wolfram Koch Is tetrahedral H$_4^{2+}$ a minimum? Anomalous behavior of popular basis sets with the standard $p$ exponents on hydrogen . . . . . . . . . . . . . . . . 285--294 Jeanmarie Guenot and Peter A. Kollman Conformational and energetic effects of truncating nonbonded interactions in an aqueous protein dynamics simulation . . 295--311 Stephen E. Debolt and Peter A. Kollman AMBERCUBE MD, parallelization of AMBER's molecular dynamics module for distributed-memory hypercube computers 312--329 Martin Saunders and Hugo Alejandro Jiménez-Vázquez Stochastic searches for lactone and cycloalkene conformers . . . . . . . . . 330--348 Scott M. Le Grand and Kenneth M. Merz Jr. Rapid approximation to molecular surface area via the use of Boolean logic and look-up tables . . . . . . . . . . . . . 349--352 Joseph J. Urban and George R. Famini Conformational dependence of the electrostatic potential-derived charges of dopamine: Ramifications in molecular mechanics force field calculations in the gas phase and in aqueous solution 353--362 Milan Randi\'c Fitting of nonlinear regressions by orthogonalized power series . . . . . . 363--370 Miroslaw Szafran and Mati M. Karelson and Alan R. Katritzky and Jacek Koput and Michael C. Zerner Reconsideration of solvent effects calculated by semiempirical quantum chemical methods . . . . . . . . . . . . 371--377 Anonymous Announcements . . . . . . . . . . . . . 378--378 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
Rois Benassi and Ugo Folli and Silvia Sbardellati and Ferdinando Taddei Conformational properties and homolytic bond cleavage of organic peroxides. I. An empirical approach based upon molecular mechanics and ab initio calculations . . . . . . . . . . . . . . 379--391 Andreas Ritter von Onciul and Timothy Clark Molecular orbital studies of enzyme mechanisms. II. Catalytic oxidation of alcohols by liver alcohol dehydrogenase 392--400 Pierre Valiron and Ágnes Vibók and István Mayer Comparison of a posteriori and a priori BSSE correction schemes for SCF intermolecular energies . . . . . . . . 401--409 L. Fernandez Pacios Analytical density-dependent representation of Hartree--Fock atomic potentials . . . . . . . . . . . . . . . 410--421 James R. Holden and Zuyue Du and Herman L. Ammon Prediction of possible crystal structures for C-, H-, N-, O-, and F-containing organic compounds . . . . . 422--437 Joseph M. Salvino and Peter R. Seoane and Roland E. Dolle Conformational analysis of bradykinin by annealed molecular dynamics and comparison to NMR-derived conformations 438--444 Rajendra N. Shirsat and Ajay C. Limaye and Shridhar R. Gadre Development of a restricted Hartree--Fock program INDMOL on PARAM: a highly parallel computer . . . . . . . . 445--451 Gerardo Cisneros Improved solutions to the one-center McMurchie--Davidson tree search problem 452--454 Robert K.-Z. Tan and Stephen C. Harvey Yammp: Development of a molecular mechanics program using the modular programming method . . . . . . . . . . . 455--470 Maciej Bagi\'nki and Lucjan Piela and Jeffrey Skolnick The ethylene group as a peptide bond mimicking unit: a theoretical conformational analysis . . . . . . . . 471--477 Maciej Bagi\'nki and Lucjan Piela Theoretical comparison of conformational properties of molecules: Conformational probability maps and similarity index 478--483 Tony J. You and Stephen C. Harvey Finite element approach to the electrostatics of macromolecules with arbitrary geometries . . . . . . . . . . 484--501 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
Guntram Rauhut and Timothy Clark Multicenter point charge model for high-quality molecular electrostatic potentials from AM1 calculations . . . . 503--509 Berthold Von Freyberg and Werner Braun Minimization of empirical energy functions in proteins including hydrophobic surface area effects . . . . 510--521 Peng Wang and Yala Zhang and Rainer Glaser and Andrew Streitwieser and Paul von R. Schleyer Ab initio calculations on phosphorus compounds. II. Effects of disubstitution on ligand apicophilicity in phosphoranes 522--529 Ibon Alkorta and Hugo O. Villar and Gustavo A. Arteca Comparative study between ab initio and semiempirical electrostatic potentials on molecular surfaces . . . . . . . . . 530--540 Michael B. Bass and Rick L. Ornstein Substrate specificity of cytochrome P450cam for L- and D-norcamphor as studied by molecular dynamics simulations . . . . . . . . . . . . . . 541--548 Taijin Zhou Study of localized molecular orbitals using group theory methods and its approach to the many-electron correlation problem. III. Orthogonal bonded functions . . . . . . . . . . . . 549--555 Qiang Zheng and Rakefet Rosenfeld and Sandor Vajda and Charles Delisi Loop closure via bond scaling and relaxation . . . . . . . . . . . . . . . 556--565 Eric Schwegler and Pawel M. Kozlowski and Ludwik Adamowicz Application of explicitly correlated Gaussian functions for calculations of the ground state of the beryllium atom 566--570 Ibon Alkorta and Hugo O. Villar and Raul E. Cachau Conformational analysis of 2,3,6,7-tetrahydroazepines with implications for D$_1$-selective benzazepines . . . . . . . . . . . . . . 571--578 Franco Battaglia and Emilio Gallicchio FORTRAN routine to compute Born--Oppenheimer potential energy curves directly from spectroscopic data 579--586 Modesto Orozco and F. J. Luque Molecular interaction potential: a new tool for the theoretical study of molecular reactivity . . . . . . . . . . 587--602 K. Balasubramanian Computer generation of Hadamard matrices 603--619 Ibon Alkorta and Hugo O. Villar and Juan J. Perez Comparison of methods to estimate the free energy of solvation:Importance in the modulation of the affinity of 3-benzazepines for the D$_1$ receptor 620--626 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
M. Natália D. S. Cordeiro and José A. N. F. Gomes Ab initio copper--water interaction potential for the simulation of aqueous solutions . . . . . . . . . . . . . . . 629--638 Karl Jug and Gerald Geudtner Treatment of hydrogen bonding in SINDO1 639--646 Mercedes Rubio and Francisco Torrens and José Sánchez-Marín Are most of the stationary points in a molecular association minima? Application of Fraga's potential to benzene--benzene . . . . . . . . . . . . 647--654 Norman L. Allinger and Yi Fan Molecular mechanics calculations (MM3) on sulfones . . . . . . . . . . . . . . 655--666 Katalin Tóth and Tapani A. Pakkanen Model calculations for small closed-ring CdS clusters and chemisorption processes by a quantum chemical cluster approach 667--672 Omar G. Stradella and Giorgina Corongiu and Enrico Clementi Techniques for the compression of sequences of integer numbers and real numbers with fixed absolute precision 673--679 C. Sousa and J. Casanovas and J. Rubio and F. Illas Madelung fields from optimized point charges for ab initio cluster model calculations on ionic systems . . . . . 680--684 Julianto Pranata Relative basicities of carboxylate lone pairs in aqueous solution . . . . . . . 685--690 István Kolossváry and Wayne C. Guida Torsional flexing: Conformational searching of cyclic molecules in biased internal coordinate space . . . . . . . 691--698 Kathryn E. Norris and George B. Bacskay and Jill E. Gready Theoretical study of ``protonated pyruvate'': a methylhydroxycarbene--carbon dioxide complex --- implications for the decarboxylation of pyruvic acid . . . . 699--714 Carl W. David Sprouting side chain conformations in X-PLOR simulations of peptides . . . . . 715--717 Gustavo A. Arteca Global measure of molecular flexibility and shape fluctuations about conformational minima . . . . . . . . . 718--727 Juan J. Morales Path integral theory: an improved simulation for the forces in semiclassic systems . . . . . . . . . . . . . . . . 728--735 James W. Boughton and Peter Pulay Comparison of the Boys and Pipek--Mezey localizations in the local correlation approach and automatic virtual basis selection . . . . . . . . . . . . . . . 736--740 Robert B. Hermann Calculation of hydrophobic interactions from molecular dynamics, surface areas, and experimental hydrocarbon solubilities . . . . . . . . . . . . . . 741--750 P. L. Polavarapu Chiral force constants: Recommendations for the presentation of internal coordinate force constants . . . . . . . 751--752 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
Kuohsiang Chen and Norman L. Allinger A molecular mechanics study of alkyl peroxides . . . . . . . . . . . . . . . 755--768 T. Koslowski and W. Von Niessen Linear combination of Lanczos vectors: a storage-efficient algorithm for sparse matrix eigenvector computations . . . . 769--774 Matthias Kolb and Walter Thiel Beyond the MNDO model: Methodical considerations and numerical results . . 775--789 P. Tufféry and C. Etchebest and S. Hazout and R. Lavery A critical comparison of search algorithms applied to the optimization of protein side-chain conformations . . 790--798 Carlos Alemán and F. J. Luque and M. Orozco Suitability of the PM3-derived molecular electrostatic potentials . . . . . . . . 799--808 Lawrence M. Pratt and C. C. Chu Hydrolytic degradation of $\alpha$-substituted polyglycolic acids: a semiempirical computational study . . 809--817 Martin W. Feyereisen and Rick A. Kendall and Jeff Nichols and David Dame and Joseph T. Golab Implementation of the direct SCF and RPA methods on loosely coupled networks of workstations . . . . . . . . . . . . . . 818--830 B. J. Hardy and A. Sarko Conformational analysis and molecular dynamics simulation of cellobiose and larger cellooligomers . . . . . . . . . 831--847 B. J. Hardy and A. Sarko Molecular dynamics simulation of cellobiose in water . . . . . . . . . . 848--857 Terry R. Stouch and Donald E. Williams Conformational dependence of electrostatic potential-derived charges: Studies of the fitting procedure . . . . 858--866 Jiro Shimada and Hiroki Kaneko and Toshikazu Takada Efficient calculations of Coulombic interactions in biomolecular simulations with periodic boundary conditions . . . 867--878 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
Modesto Orozco and F. J. Luque Ab initio study of bond stretching: Implications in force-field parametrization for molecular mechanics and dynamics . . . . . . . . . . . . . . 881--894 G. I. Csonka Analysis of the core-repulsion functions used in AM1 and PM3 semiempirical calculations: Conformational analysis of ring systems . . . . . . . . . . . . . . 895--898 E. T. H. Leuwerink and S. Harkema and W. J. Briels and D. Feil Molecular dynamics of 18-crown-6 complexes with alkali--metal cations and urea: Prediction of their conformations and comparison with data from the Cambridge Structural Database . . . . . 899--906 Frank Haase and Reinhart Ahlrichs Semidirect MP2 gradient evaluation on workstation computers: the MPGRAD program . . . . . . . . . . . . . . . . 907--912 Peter Schwerdtfeger and Josef Ischtwan Theoretical investigations on thallium halides: Relativistic and electron correlation effects in T1 X and T1 X$_3$ compounds (X F, C1, Br, and I) . . . . . 913--921 Jesús Rodríguez and Francesc Manaut and Ferran Sanz Quantitative comparison of molecular electrostatic potential distributions from several semiempirical and ab initio wave functions . . . . . . . . . . . . . 922--927 J. D. Petke Cumulative and discrete similarity analysis of electrostatic potentials and fields . . . . . . . . . . . . . . . . . 928--933 Mark Froimowitz Conformational analysis of cocaine, the potent analog 2$\beta$-carbomethoxy-3$\beta$-(4-fluorophenyl)tropane (CFT), and other dopamine reuptake blockers 934--943 Hanoch Senderowitz and Pinchas Aped and Benzion Fuchs Modified MM2 scheme for computation of O\bondC\bondN-containing systems . . . . 944--960 Eric Magnusson and Nigel W. Moriarty Computational convergence of electronic structure calculations of transition metal ligand complexes . . . . . . . . . 961--969 W. A. Sokalski and D. A. Keller and R. L. Ornstein and R. Rein Multipole correction of atomic monopole models of molecular charge distribution. I. Peptides . . . . . . . . . . . . . . 970--976 Robert C. Schweitzer and Gary W. Small Application of parallel processing techniques to improving the efficiency of MM2 molecular mechanics calculations 977--985 James O. Jensen and Arthur H. Carrieri and Constantine P. Vlahacos and Daniel Zeroka and Hendrik F. Hameka and Clifton N. Merrow Evaluation of one-electron integrals for arbitrary operators $V(r)$ over Cartesian Gaussians: Application to inverse-square distance and Yukawa operators . . . . . . . . . . . . . . . 986--994 John F. Cannon AMBER force-field parameters for guanosine triphosphate and its imido and methylene analogs . . . . . . . . . . . 995--1005 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
William R. Pitt and Judith Murray-Rust and Julia M. Goodfellow AQUARIUS2: Knowledge-based modeling of solvent sites around proteins . . . . . 1007--1018 Vellarkad N. Viswanadhan and M. Rami Reddy and Russell J. Bacquet and Mark D. Erion Assessment of methods used for predicting lipophilicity: Application to nucleosides and nucleoside bases . . . . 1019--1026 David Feller and Martin W. Feyereisen Ab initio study of hydrogen bonding in the phenol--water system . . . . . . . . 1027--1035 Zhengwei Su New method for the derivation of net atomic charges from the electrostatic potential . . . . . . . . . . . . . . . 1036--1041 David White and B. Craig Taverner and P. G. L. Leach and Neil J. Coville Quantification of substituent and ligand size by the use of solid angles . . . . 1042--1049 A. K. Ghose and E. P. Jaeger and P. J. Kowalczyk and M. L. Peterson and A. M. Treasurywala Conformational searching methods for small molecules. I. Study of the sybyl search method . . . . . . . . . . . . . 1050--1065 Donald E. Williams and Terry R. Stouch Characterization of force fields for lipid molecules: Applications to crystal structures . . . . . . . . . . . . . . . 1066--1076 Marvin Waldman and A. T. Hagler New combining rules for rare gas van der Waals parameters . . . . . . . . . . . . 1077--1084 Jon Baker Techniques for geometry optimization: a comparison of Cartesian and natural internal coordinates . . . . . . . . . . 1085--1100 George P. Ford and Bingze Wang New approach to the rapid semiempirical calculation of molecular electrostatic potentials based on the AM1 wave function: Comparison with ab initio HF/6-31g* results . . . . . . . . . . . 1101--1111 Robert W. Harrison Stiffness and energy conservation in molecular dynamics: an improved integrator . . . . . . . . . . . . . . . 1112--1122 Anonymous Announcement . . . . . . . . . . . . . . 1123--1123 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
H. R. Karfunkel and B. Rohde and F. J. J. Leusen and R. J. Gdanitz and G. Rihs Continuous similarity measure between nonoverlapping X-ray powder diagrams of different crystal modifications . . . . 1125--1135 C. Kozmutza and E. Kapuy and E. M. Evleth Calculation of the interaction energy in a localized representation for a trimer (Ne$_3$) system . . . . . . . . . . . . 1136--1141 Stefan Brode and Hans Horn and Michael Ehrig and Diane Moldrup and Julia E. Rice and Reinhart Ahlrichs Parallel direct SCF and gradient program for workstation clusters . . . . . . . . 1142--1148 Dietmar Heidrich and Nicolaas J. R. Van Eikema Hommes and Paul von Ragué Schleyer Ab initio models for multiple-hydrogen exchange: Comparison of cyclic four- and six-center systems . . . . . . . . . . . 1149--1163 Von-Wun Soo and Jan-Fu Hwang and Tung-Bo Chen and Chin Yu Divide-and-conquer, pattern matching, and relaxation methods in interpretation of 2-D NMR spectra of polypeptides . . . 1164--1171 P. Duane Walker and Gustavo A. Arteca and Paul G. Mezey Shape groups of the electronic isodensity surfaces for small molecules: Shapes of 10-electron hydrides . . . . . 1172--1183 David A. Pearlman and Mark A. Murcko CONCEPTS: New dynamic algorithm for de novo drug suggestion . . . . . . . . . . 1184--1193 Adam Godzik and Andrzej Kolinski and Jeffrey Skolnick Lattice representations of globular proteins: How good are they? . . . . . . 1194--1202 J. Fernández Rico Long-range multicenter integrals with Slater functions: Gauss transform-based methods . . . . . . . . . . . . . . . . 1203--1211 Guihua Zhang and Tamar Schlick LIN: a new algorithm to simulate the dynamics of biomolecules by combining implicit-integration and normal mode techniques . . . . . . . . . . . . . . . 1212--1233 Mariusz Klobukowski Ab initio SCF and Mòller--Plesset studies on hexafluorides of selenium and tellurium . . . . . . . . . . . . . . . 1234--1239 Heather A. Carlson and Toan B. Nguyen and Modesto Orozco and William L. Jorgensen Accuracy of free energies of hydration for organic molecules from 6-31g*-derived partial charges . . . . . 1240--1249 Toshiyuki Katagi MNDO-PM3 study on model cytochrome P450-mediated desulfuration of thiophosphoryl trifluoride, trimethylphosphine sulfide, and trimethyl phosphorothionate . . . . . . 1250--1257 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
Pnina Dauber-Osguthorpe and David J. Osguthorpe Partitioning the motion in molecular dynamics simulations into characteristic modes of motion . . . . . . . . . . . . 1259--1271 Frank Eisenhaber and Patrick Argos Improved strategy in analytic surface calculation for molecular systems: Handling of singularities and computational efficiency . . . . . . . . 1272--1280 M. L. C. E. Kouwijzer and B. P. Van Eijck and S. J. Kroes and J. Kroon Comparison of two force fields by molecular dynamics simulations of glucose crystals: Effect of using Ewald sums . . . . . . . . . . . . . . . . . . 1281--1289 Carl-Dieter Zachmann and Stefan Michael Kast and Alla Sariban and Jürgen Brickmann Self-Similarity of solvent-accessible surfaces of biological and synthetical macromolecules . . . . . . . . . . . . . 1290--1300 Ernst Anders and Rainer Koch and Peter Freunscht Optimization and application of lithium parameters for PM3 . . . . . . . . . . . 1301--1312 Douglas A. Smith and Douglas A. Smith and S. Vijayakumar Critical reevaluation of proximity effects in the barton oxidation and related intramolecular reactions . . . . 1313--1319 M. Dagher and H. Kobeissi and M. Kobressi and J. D'Incan and C. Effantin Generalized Morse analytic function for the ``true'' diatomic potential of the RKR type . . . . . . . . . . . . . . . . 1320--1325 Marcus W. Jurema and Karl N. Kirschner and George C. Shields Modeling of magic water clusters (H$_2$O)$_{20}$ and (H$_2$O)$_{21}$H$^+$ with the PM3 quantum-mechanical method 1326--1332 Ulrich H. E. Hansmann and Yuko Okamoto Prediction of peptide conformation by multicanonical algorithm: New approach to the multiple-minima problem . . . . . 1333--1338 Jon Baker and Doreen Bergeron Constrained optimization in Cartesian coordinates . . . . . . . . . . . . . . 1339--1346 Michael W. Schmidt and Kim K. Baldridge and Jerry A. Boatz and Steven T. Elbert and Mark S. Gordon and Jan H. Jensen and Shiro Koseki and Nikita Matsunaga and Kiet A. Nguyen and Shujun Su and Theresa L. Windus and Michel Dupuis and John A. Montgomery Jr. General atomic and molecular electronic structure system . . . . . . . . . . . . 1347--1363 D. B. Chesnut and B. E. Rusiloski and K. D. Moore and D. A. Egolf Use of locally dense basis sets for nuclear magnetic resonance shielding calculations . . . . . . . . . . . . . . 1364--1375 Henry N. Po and Fillmore Freeman and Choonsun Lee and Warren J. Hehre Ab initio molecular orbital calculations for 3,6-dihydro-1,2-dithiin and 3,6-dihydro-1,2-dioxin . . . . . . . . . 1376--1384 D. B. McGarrah and R. S. Judson Analysis of the genetic algorithm method of molecular conformation determination 1385--1395 Angel E. García and Lewis Stiller Computation of the mean residence time of water in the hydration shells of biomolecules . . . . . . . . . . . . . . 1396--1406 R. S. Judson and E. P. Jaeger and A. M. Treasurywala and M. L. Peterson Conformational searching methods for small molecules. II. Genetic algorithm approach . . . . . . . . . . . . . . . . 1407--1414 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
Robert E. Bruccoleri Grid positioning independence and the reduction of self-energy in the solution of the Poisson--Boltzmann equation . . . 1417--1422 B. W. Clare and P. J. Jennings and J. C. L. Cornish and G. Talukder and C. P. Lund and G. T. Hefter Simulation of the electronic and vibrational structure of hydrogenated amorphous silicon using cluster models 1423--1428 Alistair P. Rendell and Martyn F. Guest and Rick A. Kendall Distributed data parallel coupled-cluster algorithm: Application to the 2-hydroxypyridine/2-pyridone tautomerism . . . . . . . . . . . . . . 1429--1439 S. Huzinaga and E. Miyoshi and M. Sekiya Electric dipole polarity of diatomic molecules . . . . . . . . . . . . . . . 1440--1445 Mark A. Murcko and B. Govinda Rao Conformational analysis of HIV protease inhibitors. I. Rotation of the amide group adjacent to the P'$_1$ decahydroisoquinoline ring system in Ro 31-8959 and related systems . . . . . . 1446--1453 Raúal E. Valdés-Pérez Algorithm to test the structural plausibility of a proposed elementary reaction . . . . . . . . . . . . . . . . 1454--1459 Steven L. Dixon and Peter C. Jurs Estimation of $pK_a$ for organic oxyacids using calculated atomic charges 1460--1467 Jerzy Cioslowski and Ernst Joachim Weniger Bulk properties from finite cluster calculations. VIII. Benchmark calculations of the efficiency of extrapolation methods for the HF and MP2 energies of polyacenes . . . . . . . . . 1468--1481 Je Myung Park and Kyoung Tai No and Mu Shik Jhon and Harold A. Scheraga Determination of net atomic charges using a modified partial equalization of orbital electronegativity method. III. Application to halogenated and aromatic molecules . . . . . . . . . . . . . . . 1482--1490 Gy. Dömötör and M. I. Bán and L. L. Stachó Experiences and practical hints on using the DDRP method, illustrated by the example of the H$_2$ + H reaction . . . 1491--1497 Modesto Orozco and William L. Jorgensen and F. J. Luque Comparison of 6-31G*-based MST/SCRF and FEP evaluations of the free energies of hydration for small neutral molecules 1498--1503 Kenneth B. Wiberg and Paul R. Rablen Comparison of atomic charges derived via different procedures . . . . . . . . . . 1504--1518 Hafez Kobeissi and Chafia H. Trad and Majida Kobeissi ``Full numerical'' diatomic matrix elements: Simplified shooting method . . 1519--1522 Peter J. Gardner and Steve R. Preston and Rachel Siertsema and Derek Steele Ab initio molecular orbital studies for compounds of magnesium . . . . . . . . . 1523--1533 F. Illas and L. Roset and J. M. Ricart and J. Rubio Basis-Modified hydrogen atoms as embedding atoms in ab initio chemisorption cluster model calculations on Si surfaces . . . . . . . . . . . . . 1534--1544 J. Frau and J. Donoso and F. Muñoz and F. García Blanco Theoretical calculations of $\beta$-lactam antibiotics. V. AM1 calculations of hydrolysis of cephalothin in gaseous phase and influence of the solvent . . . . . . . . 1545--1552 Rolf Eggenberger and Stefan Gerber and Hanspeter Huber and Debra Searles and Marc Welker Use of molecular dynamics simulations with ab initio SCF calculations for the determination of the deuterium quadrupole coupling constant in liquid water and bond lengths in ice . . . . . 1553--1560 Lawrence L. Griffin and David J. McAdoo and Santiago Olivella Evaluation of AM1-calculated radical cation ion-neutral complexes . . . . . . 1561--1574 Chris L. Waller and James D. McKinney Theoretical investigation into the potential of halogenated methanes to undergo reductive metabolism . . . . . . 1575--1579 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
Josep Maria Bofill Updated Hessian matrix and the restricted step method for locating transition structures . . . . . . . . . 1--11 C. Alhambra and F. J. Luque and Modesto Orozco Comparison of NDDO and quasi- ab initio approaches to compute semiempirical molecular electrostatic potentials . . . 12--22 Carl W. David Hydrating peptides using a sprouting technique . . . . . . . . . . . . . . . 23--27 Jiro Shimada and Hiroki Kaneko and Toshikazu Takada Performance of fast multipole methods for calculating electrostatic interactions in biomacromolecular simulations . . . . . . . . . . . . . . 28--43 William S. Young and Charles L. Brooks III Implementation of a data parallel, logical domain decomposition method for interparticle interactions in molecular dynamics of structured molecular fluids 44--53 Zhenghong Zhang and Pawel M. Kozlowski and Ludwik Adamowicz Newton--Raphson optimization of the explicitly correlated Gaussian functions for calculations of the ground state of the helium atom . . . . . . . . . . . . 54--60 D. M. York and L. J. Bartolotti and T. A. Darden and L. G. Pedersen and M. W. Anderson Simulations of the solution structure of HIV-1 protease in the presence and absence of bound zinc . . . . . . . . . 61--71 Daniel I. Okunbor and Robert D. Skeel Canonical numerical methods for molecular dynamics simulations . . . . . 72--79 Charles D. Schwieters and Herschel Rabitz Display of the flow of energy in molecules . . . . . . . . . . . . . . . 80--89 Takao Furuki and Akihiro Umeda and Minoru Sakurai and Yoshio Inoue and Riichirô Chûjô and Kazuaki Harata General parameterization of a reaction field theory combined with the boundary element method . . . . . . . . . . . . . 90--104 David A. Pearlman Free energy derivatives: a new method for probing the convergence problem in free energy calculations . . . . . . . . 105--123 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
Ricard Gelabert and Miquel Moreno and José M. Lluch Applicability of the WKB method in asymmetric double wells with degenerate and nondegenerate minima . . . . . . . . 125--131 Rudolf Janoschek and Walter M. F. Fabian and Gert Kollenz and C. Oliver Kappe Conformation and reactivity of $\alpha$-oxo-ketenes: ab initio and semiempirical (AM1, PM3) calculations 132--143 J. J. Soares Neto Parallel algorithm for calculating ro-vibrational states of diatomic molecules . . . . . . . . . . . . . . . 144--148 Ching-Lung Lin and Robert H. Wood Free energy of solvation of a small Lennard-Jones particle . . . . . . . . . 149--154 Mark J. Forster and Barbara Mulloy Rationalizing nuclear Overhauser effect data for compounds adopting multiple-solution conformations . . . . 155--161 J. R. Maple and M.-J. Hwang and T. P. Stockfisch and U. Dinur and M. Waldman and C. S. Ewig and A. T. Hagler Derivation of class II force fields. I. Methodology and quantum force field for the alkyl functional group and alkane molecules . . . . . . . . . . . . . . . 162--182 Jesús Rodríguez Semiempirical study of compounds with intramolecular O H\ldotsO hydrogen bonds. II. Further verification of a modified MNDO method . . . . . . . . . . 183--189 Arun Malhotra and Robert K.-Z. Tan and Stephen C. Harvey Utilization of shape data in molecular mechanics using a potential based on spherical harmonic surfaces . . . . . . 190--199 Bingze Wang and George P. Ford Atomic charges derived from a fast and accurate method for electrostatic potentials based on modified AM1 calculations . . . . . . . . . . . . . . 200--207 Barry J. Hardy and Richard W. Pastor Conformational sampling of hydrocarbon and lipid chains in an orienting potential . . . . . . . . . . . . . . . 208--226 W. Glunt and T. L. Hayden and M. Raydan Preconditioners for distance matrix algorithms . . . . . . . . . . . . . . . 227--232 Andrew R. Leach and Richard A. Lewis A ring-bracing approach to computer-assisted ligand design . . . . 233--240 Lawrence M. Pratt and C. C. Chu Computational study of the hydrolysis of degradable polysaccharide biomaterials: Substituent effects on the hydrolytic mechanism . . . . . . . . . . . . . . . 241--248 Anonymous Announcement . . . . . . . . . . . . . . 249--249 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
Norman L. Allinger and Yi Fan Force field calculations (MM3) on glyoxal, quinones, and related compounds 251--268 Vincent Théry and Daniel Rinaldi and Jean-Louis Rivail and Bernard Maigret and György G. Ferenczy Quantum mechanical computations on very large molecular systems: the local self-consistent field method . . . . . . 269--282 Ruifeng Liu and Norman L. Allinger Molecular mechanics (MM3) calculations on alkyl radicals . . . . . . . . . . . 283--299 Ljubomir J. Buturovi\'c and Temple F. Smith and Sandor Vajda Finite-state and reduced-parameter representations of protein backbone conformations . . . . . . . . . . . . . 300--312 Anibal Sierraalta and Fernando Ruette A comparative study of effective core potential and full-electron calculations in Mo compounds. I. An analysis of topological properties of bond charge distribution . . . . . . . . . . . . . . 313--321 Andrea Dorigo and Paul von Ragué Schleyer and Pavel Hobza The structures of LiNC, NaNC, and KNC: Potential energy surface for the orbiting motion of the metal cation around the CN group . . . . . . . . . . 322--332 Xiannong Chen and Libero Bartolotti and Khalid Ishaq and Alexander Tropsha Molecular simulation of alkyl boronic acids: Molecular mechanics and solvation free energy calculations . . . . . . . . 333--345 Z.-L. Cai Ab initio study of low-lying electronic states of the PF$_2$ radical . . . . . . 346--350 Stephen E. Debolt and David A. Pearlman and Peter A. Kollman Free energy perturbation calculations on parallel computers: Demonstrations of scalable linear speedup . . . . . . . . 351--373 Anonymous Announcement . . . . . . . . . . . . . . 374--374 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
J. R. Alvarez-Collado Normal coordinates--finite elements calculation of 3D vibrational energy levels: Henon--Heiles and Eckart potentials, H molecule . . . . . . . . . 377--384 G. I. Csonka and P. Hencsei Ab initio molecular orbital study of 1-fluorosilatrane . . . . . . . . . . . 385--394 Vincenzo Barone and Carlo Adamo Modulation of intramolecular proton transfer by electronic excitation and environment: 2-Pyridone as a case study 395--404 F. J. Ramírez and V. Hernández and J. T. López Navarrete Transferable semiempirical quadratic force fields: the case of polythiophene and shorter oligomers . . . . . . . . . 405--423 S. Grimme MRD--CI studies of vertical excitation energies of unsaturated hydrocarbon molecules . . . . . . . . . . . . . . . 424--432 Mahmoud Ghomi and Jean-Marc Victor and Charles Henriet Monte Carlo simulations on short single-stranded oligonucleotides. I. Application to RNA trimers . . . . . . . 433--445 M. Bachs and F. J. Luque and Modesto Orozco Optimization of solute cavities and van der Waals parameters in ab initio MST-SCRF calculations of neutral molecules . . . . . . . . . . . . . . . 446--454 Berta Fernández and Miguel A. Ríos Parametrization of a force field for studying some beta-lactams . . . . . . . 455--465 L. Pisani and E. Clementi Relativistic Dirac--Fock calculations for closed-shell molecules . . . . . . . 466--474 Anonymous Announcements . . . . . . . . . . . . . 475--475 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
X. Assfeld and M. F. Ruiz-Lopez and J. Gonzalez and R. Lopez and J. A. Sordo and T. L. Sordo Theoretical analysis of the role of the solvent on the reaction mechanisms: One-step versus two-step ketene--imine cycloaddition . . . . . . . . . . . . . 479--487 Ruben Abagyan and Maxim Totrov and Dmitry Kuznetsov ICM --- a new method for protein modeling and design: applications to docking and structure prediction from the distorted native conformation . . . 488--506 Michel Petitjean On the analytical calculation of van der Waals surfaces and volumes: Some numerical aspects . . . . . . . . . . . 507--523 Ulrich Sternberg and Frank-Thomas Koch and Margit Möllhoff New approach to the semiempirical calculation of atomic charges for polypeptides and large molecular systems 524--531 Philippe Derreumaux and Guihua Zhang and Tamar Schlick and Bernard Brooks A truncated Newton minimizer adapted for CHARMM and biomolecular applications . . 532--552 Jan FloriáN and Steve Scheiner Variation of atomic charges during proton transfer in hydrogen bonds . . . 553--560 Alfred D. French and Michael K. Dowd Analysis of the ring-form tautomers of psicose with MM3 (92) . . . . . . . . . 561--570 Anonymous Announcement . . . . . . . . . . . . . . 571--571 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
Olav Vahtras and Hans Årgren and Hans Jòrgen Aa. Jensen Direct one-index transformations in multiconfiguration response calculations 573--579 P. Battersby and J. R. Dean and S. M. Hitchen and W. R. Tomlinson and P. M. Myers Interaction between carbon dioxide and naphthalene: a molecular modeling approach . . . . . . . . . . . . . . . . 580--587 Tilman Brodmeier and Ernö Pretsch Application of genetic algorithms in molecular modeling . . . . . . . . . . . 588--595 Ahmed M. El-Nahas and Paul von Ragué Schleyer Structures and stabilization energies of methyl anions with main group substituents from the first five periods 596--626 J. C. Meza and M. L. Martinez Direct search methods for the molecular conformation problem . . . . . . . . . . 627--632 Gustavo A. Arteca Shape analysis of hydrogen-bonded networks in solvation clusters . . . . . 633--643 B. W. Clare and G. Talukder and P. J. Jennings and J. C. L. Cornish and G. T. Hefter Effect of charge on bond strength in hydrogenated amorphous silicon . . . . . 644--652 Herbert F. M. Da Costa and David A. Micha Atomic orbital basis sets for molecular interactions . . . . . . . . . . . . . . 653--661 Carl W. David X-PLORing extraribosomal peptide folding during synthesis . . . . . . . . . . . . 662--665 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
Peter J. Steinbach and Bernard R. Brooks New spherical-cutoff methods for long-range forces in macromolecular simulation . . . . . . . . . . . . . . . 667--683 Shuzo Yoshioki Internal dynamics of a globular protein under external force field . . . . . . . 684--703 Peter L. Cummins and Jill E. Gready Thermodynamic integration calculations on the relative free energies of complex ions in aqueous solution: Application to ligands of dihydrofolate reductase . . . 704--718 Donald E. Williams Failure of net atomic charge models to represent the van der Waals envelope electric potential of $n$-alkanes . . . 719--732 Steven L. Dixon and Peter C. Jurs Fast geometry optimization using a modified extended Hückel method: Results for molecules containing H, C, N, O, and F . . . . . . . . . . . . . . . . . . . 733--746 Alexander V. Mitin Iterative methods for the calculation of a few of the lowest eigenvalues and corresponding eigenvectors of the $A X = \lambda B X$ equation with real symmetric matrices of large dimension 747--751 H. Sun Force field for computation of conformational energies, structures, and vibrational frequencies of aromatic polyesters . . . . . . . . . . . . . . . 752--768 Fanbing Li and Weili Cui and Norman L. Allinger Expanding molecular dynamics simulations to the NMR time scale. I. Studies of conformational interconversions of 1, 1-difluoro-4, 4-dimethylcycloheptane using MM3-MD . . . . . . . . . . . . . . 769--781 Jesús R. Flores and P. Redondo High-precision atomic computations from finite element techniques: Second-order correlation energies for Be, Ca, Sr, Cd, Ba, Yb, and Hg . . . . . . . . . . . . . 782--790 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
Wolf Dietrich Ihlenfeldt and Johann Gasteiger Hash codes for the identification and classification of molecular structure elements . . . . . . . . . . . . . . . . 793--813 Ian J. Palmer and Janos Ladik New implementation of a program to calculate correlated band structures of polymers: an application to the band structure of polyparaphenylene (PPP) . . 814--819 Jean-françois Gibrat and Jean Garnier and Nobuhiro G\=o Normal mode analysis of oligomeric proteins: Reduction of the memory requirement by consideration of rigid geometry and molecular symmetry . . . . 820--837 M. E. Clamp and P. G. Baker and C. J. Stirling and A. Brass Hybrid Monte Carlo: an efficient algorithm for condensed matter simulation . . . . . . . . . . . . . . . 838--846 F. J. Luque and M. Bachs and Modesto Orozco An optimized AM1/MST method for the MST-SCRF representation of solvated systems . . . . . . . . . . . . . . . . 847--857 Taijin Zhou and Aimin Liu Study of localized molecular orbitals using group theory methods and its approach to the many-electron correlation problem. IV. The symmetry-adaptation of many-center integrals and Hamiltonian matrix elements in MCSCF calculations . . . . . 858--865 Guyan Liang and J. Phillip Bowen and James A. Bentley Molecular mechanics (MM3) parameterization of hydroxylamine and methyl derivatives . . . . . . . . . . . 866--874 Ann M. Schmiedekamp and Igor A. Topol and Stanley K. Burt and Holy Razafinjanahary and Henry Chermette and Timothy Pfaltzgraff and Christopher J. Michejda Triazene proton affinities: a comparison between density functional, Hartree--Fock, and post-Hartree--Fock methods . . . . . . . . . . . . . . . . 875--892 Zhenghong Zhang and Ludwik Adamowicz Explicitly correlated Gaussian functions with $r$ factors for calculations of the ground state of the helium atom . . . . 893--898 Peter S. Shenkin and D. Quentin McDonald Cluster analysis of molecular conformations . . . . . . . . . . . . . 899--916 Anonymous Announcement . . . . . . . . . . . . . . 917--917 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
U. Dinur and A. T. Hagler On the functional representation of bond energy functions . . . . . . . . . . . . 919--924 Gábor I. Csonka and Miklós Erdösy and József Réffy Structure of disiloxane: a semiempirical and Post-Hartree--Fock study . . . . . . 925--936 Lud\uek Matyska and Jaroslav Ko\vca D-CICADA: a software for conformational PES elucidation on network of workstations . . . . . . . . . . . . . . 937--946 Roberta Susnow and Clarence Schutt and Herschel Rabitz and Shankar Subramaniam Conformational study of dipeptides: a sensitivity analysis approach . . . . . 947--962 Roberta Susnow and Clarence Schutt and Herschel Rabitz Principal component analysis of dipeptides . . . . . . . . . . . . . . . 963--980 R. Santamaria and A. Vázquez Structural and electronic property changes of the nucleic acid bases upon base pair formation . . . . . . . . . . 981--996 Niels Grònbech-Jensen and Sebastian Doniach Long-time overdamped Langevin dynamics of molecular chains . . . . . . . . . . 997--1012 Yasuyuki Kurita and Chiyozo Takayama and Shizuya Tanaka Decomposition analyses of the intermolecular interaction energies in two $\pi$ $\pi$ stacking complexes: Quinhydrone and N, N, N', N'-tetramethyl-P-diaminobenzene-chloranil complex 1013--1018 Timothy M. Glennon and Ya-Jun Zheng and Scott M. Le Grand and Brad A. Shutzberg and Kenneth M. Merz Jr. A force field for monosaccharides and ($1 \rightarrow 4$) linked polysaccharides . . . . . . . . . . . . 1019--1040 Gilles Klopman and Dan Fercu Application of the multiple computer automated structure evaluation methodology to a quantitative structure--activity relationship study of acidity . . . . . . . . . . . . . . . 1041--1050 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
W. Biemolt and A. P. J. Jansen Potential energy surfaces for Rh CO from DFT calculations . . . . . . . . . . . . 1053--1063 Bernd Beck and Guntram Rauhut and Timothy Clark The natural atomic orbital point charge model for PM3: Multipole moments and molecular electrostatic potentials . . . 1064--1073 Roberta Susnow and Nancie Senko and Timothy Ocain Conformational sensitivity analysis of FKBP-FK506/rapamycin complexes . . . . . 1074--1090 Jean M. J. Tronchet and Istvan Komaromi Conformation energy around the N(sp$^3$)O single bond . . . . . . . . . 1091--1104 Maxim Totrov and Ruben Abagyan Efficient parallelization of the energy, surface, and derivative calculations for internal coordinate mechanics . . . . . 1105--1112 Jordi Mestres and Miquel Sol\`a and Miquel Duran and Ramon Carbó On the calculation of ab initio quantum molecular similarities for large systems: Fitting the electron density 1113--1120 Alexander J. Pertsin and Jutta Hahn and Hans P. Grossmann Incorporation of bond-length constraints in Monte Carlo simulations of cyclic and linear molecules: Conformational sampling for cyclic alkanes as test systems . . . . . . . . . . . . . . . . 1121--1126 J. L. Pascual-ahuir and E. Silla and I. Tuñon GEPOL: an improved description of molecular surfaces. III. A new algorithm for the computation of a solvent-excluding surface . . . . . . . 1127--1138 Alain-Dominique Gorse and Michel Pesquer The use of Fraga's potential with AM1 atomic point charges in the evaluation of spectral shifts: Application to TICT molecules . . . . . . . . . . . . . . . 1139--1150 Uwe Versteeg and Wolfram Koch The valence isomers of (CH)$_8$ and (SiH)$_8$: an ab initio MO study . . . . 1151--1162 Brian K. Schmitz and William B. Euler A computational study of azine, azoethene, and diimine linkages in the poly/oligoazine system . . . . . . . . . 1163--1175 Brian T. Luke Stable conformations of CH$_3$CH$_2$OCH$_2$CH$_2$OH: a comparison of theoretical methods . . . 1176--1185 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
Richard J. Wheatley and John B. O. Mitchell Gaussian multipoles in practice: Electrostatic energies for intermolecular potentials . . . . . . . 1187--1198 Frank Jensen Transition structure modeling by intersecting potential energy surfaces 1199--1216 K. Baldridge and R. Fine and A. Hagler The effects of solvent screening in quantum mechanical calculations in protein systems . . . . . . . . . . . . 1217--1227 Peter I. Nagy and Joseph E. Bitar and Douglas A. Smith Comparison of the molecular mechanics + generalized Born/surface area and the ab initio + Monte Carlo simulation methods in estimating conformational equilibria in aqueous solution . . . . . . . . . . 1228--1240 B. G. Rao and M. A. Murcko Reversed stereochemical preference in binding of Ro 31-8959 to HIV-1 proteinase: a free energy perturbation analysis . . . . . . . . . . . . . . . . 1241--1253 Mangalya Kar and Terry G. Lenz and John D. Vaughan Thermodynamic molecular mechanics force field: Modified QCFF program . . . . . . 1254--1265 Raúl E. Valdés-Pérez Algorithm to infer the structures of molecular formulas within a reaction pathway . . . . . . . . . . . . . . . . 1266--1277 Junichi Higo and Mariko Yamaki and Michiru Hogyoku and Takuya Takahashi and Shigeru Endo and Kuniaki Nagayama Stability of two-dimensional crystalline aggregates of a protein studied by molecular dynamics . . . . . . . . . . . 1278--1290 Fransiska S. Ganda-Kesuma and Kenneth J. Miller Linear dependency in the refinement of force constants with the Jacobian method 1291--1301 Frank Guarnieri and W. Clark Still A rapidly convergent simulation method: Mixed Monte Carlo/stochastic dynamics 1302--1310 Haiyan Liu and Yunyu Shi Combined molecular mechanical and quantum mechanical potential study of a nucleophilic addition reaction in solution . . . . . . . . . . . . . . . . 1311--1318 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
N. L. Allinger and Liqun Yan and Kuohsiang Chen Molecular mechanics calculations (MM2 and MM3) on enamines and aniline derivatives . . . . . . . . . . . . . . 1321--1330 Andrew E. Torda and Wilfred F. van Gunsteren Algorithms for clustering molecular dynamics configurations . . . . . . . . 1331--1340 R. Arnaud Ab initio study of some CH$_3$OCXYCH$_2$ radicals: the influence of anomeric effects on their structure and their stability . . . . . . . . . . . . . . . 1341--1356 Nathaniel O. J. Malcolm and Joseph J. W. McDouall A variational biorthogonal valence bond method . . . . . . . . . . . . . . . . . 1357--1364 Nathaniel O. J. Malcolm and Joseph J. W. McDouall Variational biorthogonal valence bond descriptions of 1,3-dipoles . . . . . . 1365--1371 Junichi Higo and Shigeru Endo and Kuniaki Nagayama and Tomoyoshi Ito and Toshiyuki Fukushige and Toshikazu Ebisuzaki and Daiichiro Sugimoto and Hiroo Miyagawa and Kunihiro Kitamura and Junichiro Makino Application of a high-performance, special-purpose computer, GRAPE-2A, to molecular dynamics . . . . . . . . . . . 1372--1376 A. J. Stone and C.-S. Tong Anisotropy of atom--atom repulsions . . 1377--1392 Alexander A. Cohen and Shimon E. Shatzmiller Implementation of artificial intelligence for automatic drug design. I. Stepwise computation of the interactive drug-design sequence . . . . 1393--1402 Kenneth D. Gibson and Harold A. Scheraga A rapid and efficient algorithm for packing polypeptide chains by energy minimization . . . . . . . . . . . . . . 1403--1413 Kenneth D. Gibson and Harold A. Scheraga An algorithm for packing regular multistrand polypeptide structures by energy minimization . . . . . . . . . . 1414--1428 M. L. Verdonk and R. W. Tjerkstra and I. S. Ridder and J. A. Kanters and J. Kroon and W. J. M. van der Kemp ToBaD: a method for the estimation of torsion barriers from crystal structure data; conformational analysis of N, $N$-dimethylaniline and derivatives . . 1429--1436 Lawrence R. Schmitz and Yi Ren Chen Heats of formation of organic molecules calculated from ab initio theory and a group equivalent scheme: Alkenes . . . . 1437--1445 Yi Fan and Norman L. Allinger Molecular mechanics (MM3) calculations on azoxy compounds . . . . . . . . . . . 1446--1460 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
A. A. Varnek and G. Wipff and A. S. Glebov and D. Feil An application of the Miertus--Scrocco--Tomasi solvation model in molecular mechanics and dynamics simulations . . . . . . . . . . . . . . 1--19 Elena L. Coitiño and Jacopo Tomasi and Roberto Cammi On the evaluation of the solvent polarization apparent charges in the polarizable continuum model: a new formulation . . . . . . . . . . . . . . 20--30 Rolf Gleiter and Karl-Heinz Pfeifer and Wolfram Koch Propella[3$_4$] prismane and its congeners: a MO-theoretical study . . . 31--36 A. H. De Vries and P. Th. Van Duijnen and A. H. Juffer and J. A. C. Rullmann and J. P. Dijkman and H. Merenga and B. T. Thole Implementation of reaction field methods in quantum chemistry computer codes . . 37--55 Cornelis J. M. Huige and Cornelis Altona Force field parameters for sulfates and sulfamates based on ab initio calculations: Extensions of AMBER and CHARMm fields . . . . . . . . . . . . . 56--79 Michel Petitjean Geometric molecular similarity from volume-based distance minimization: Application to saxitoxin and tetrodotoxin . . . . . . . . . . . . . . 80--90 Thomas R. Furlani and Harry F. King Implementation of a parallel direct SCF algorithm on distributed memory computers . . . . . . . . . . . . . . . 91--104 Juan J. Morales and María J. Nuevo Path integral molecular dynamics methods: Application to neon . . . . . . 105--112 Robert V. Stanton and David S. Hartsough and Kenneth M. Merz Jr. An examination of a density functional/molecular mechanical coupled potential . . . . . . . . . . . . . . . 113--128 Anonymous Announcement . . . . . . . . . . . . . . 129--129 Roberta Susnow and Clarence Schutt and Herschel Rabitz Errata: Principal component analysis of dipeptides . . . . . . . . . . . . . . . 130--130 Yasuyuki Kurita and Chiyozo Takayama and Shizuya Tanaka Errata: Decomposition analyses of the intermolecular interaction energies in two $\pi$--$\pi$ stacking complexes: Quinhydrone and N, N, N', N tetramethyl-P-diaminobenzene-chloranil complex . . . . . . . . . . . . . . . . 131--131 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
L. Fernández Pacios Atomic radii scales and electron properties deduced from the charge density . . . . . . . . . . . . . . . . 133--145 Hans-Joachim Böhm and Stefan Brode Ab initio SCF calculations on low-energy conformers of cyclohexaglycine . . . . . 146--153 U. Dinur and A. T. Hagler Geometry-dependent atomic charges: Methodology and application to alkanes, aldehydes, ketones, and amides . . . . . 154--170 Andrew Smellie and Steven L. Teig and Peter Towbin Poling: Promoting conformational variation . . . . . . . . . . . . . . . 171--187 Manuel Dauchez and Philippe Derreumaux and Philippe Lagant and Gérard Vergoten A vibrational molecular force field of model compounds with biological interest. IV. Parameters for the different glycosidic linkages of oligosaccharides . . . . . . . . . . . . 188--199 Xiang Zhexin and Shi Yunyu and Xu Yinwu Solving the finite-difference, nonlinear, Poisson--Boltzmann equation under a linear approach . . . . . . . . 200--206 Melanie J. M. Pepper and Isaiah Shavitt and Paul von Ragué Schleyer and Mikhail N. Glukhovtsev and Rudolf Janoschek and Martin Quack Is the stereomutation of methane possible? . . . . . . . . . . . . . . . 207--225 Y. S. Li and M. C. Wrinn and J. M. Newsam and M. P. Sears Parallel implementation of a mesh-based density functional electronic structure code . . . . . . . . . . . . . . . . . . 226--234 Tooru Taga and Kazuhumi Masuda Monte Carlo study of lipid membranes: Simulation of diparmitoylphosphatidylcholine bilayers in gel and liquid-crystalline phases . . 235--242 Allison E. Howard and Piotr Cieplak and Peter A. Kollman A molecular mechanical model that reproduces the relative energies for chair and twist-boat conformations of 1,3-dioxanes . . . . . . . . . . . . . . 243--261 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
Antonio L. Llamas-Saiz and Concepción Foces-Foces and Otilia Mó and Manuel Yáñez and Eric Elguero and José Elguero The geometry of pyrazole: a test for ab initio calculations . . . . . . . . . . 263--272 Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and Michael Scharf The double cubic lattice method: Efficient approaches to numerical integration of surface area and volume and to dot surface contouring of molecular assemblies . . . . . . . . . . 273--284 Kenny B. Lipkowitz and Michael A. Peterson Evaluation of moment statistics for molecular modeling . . . . . . . . . . . 285--295 Jaroslav Ko\vca and Serge Pérez and Anne Imberty Conformational analysis and flexibility of carbohydrates using the CICADA approach with MM3 . . . . . . . . . . . 296--310 Daniel L. Severance and Jonathan W. Essex and William L. Jorgensen Generalized alteration of structure and parameters: a new method for free-energy perturbations in systems containing flexible degrees of freedom . . . . . . 311--327 Shinji Sunada and Nobuhiro Go Small-amplitude protein conformational dynamics: Second-order analytic relation between Cartesian coordinates and dihedral angles . . . . . . . . . . . . 328--336 Michael J. Holst and Faisal Saied Numerical solution of the nonlinear Poisson--Boltzmann equation: Developing more robust and efficient methods . . . 337--364 Mei-Qing Zhang and Robert D. Skeel Symplectic integrators and the conservation of angular momentum . . . . 365--369 Bo Svensson and Bo Jönsson An efficient simulation technique for electrostatic free energies with applications to azurin . . . . . . . . . 370--377 Takao Furuki and Minoru Sakurai and Yoshio Inoue An application of the reaction field theory to hydrated metal cations in the framework of the MNDO, AM1, and PM3 methods . . . . . . . . . . . . . . . . 378--384 Ming Wah Wong and Kenneth B. Wiberg and Michael J. Frisch Ab initio calculation of molar volumes: Comparison with experiment and use in solvation models . . . . . . . . . . . . 385--394 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
Antonio M. Márquez and Michel Dupuis Parallel computation of the MP2 energy on distributed memory computers . . . . 395--404 Heiko Gerwens and Karl Jug SINDO1 study of the photoreaction of tetramethylene sulfone . . . . . . . . . 405--413 Bjòrn K. Alsberg Fast, fuzzy $c$-means clustering of data sets with many features . . . . . . . . 414--421 Daniel A. Liotard and Gregory D. Hawkins and Gillian C. Lynch and Christopher J. Cramer and Donald G. Truhlar Improved methods for semiempirical solvation models . . . . . . . . . . . . 422--440 H. Behnejad and A. Maghari and M. Najafi The extended law of corresponding states and the intermolecular potentials for He He and Ne Ne . . . . . . . . . . . . . . 441--444 Jian Shen and Florante A. Quiocho Calculation of binding energy differences for receptor--ligand systems using the Poisson--Boltzmann method . . 445--448 Sung-Eun Yoo and Ok Ja Cha Prediction of LUMO energy and rate constant by comparative molecular field analysis (CoMFA) . . . . . . . . . . . . 449--453 Brock A. Luty and Zelda R. Wasserman and Pieter F. W. Stouten and C. Nicholas Hodge and Martin Zacharias and J. Andrew McCammon A molecular mechanics/grid method for evaluation of ligand--receptor interactions . . . . . . . . . . . . . . 454--464 F. Matthias Bickelhaupt and Miquel Sol\`a and Paul von Ragué Schleyer Theoretical investigation of the relative stabilities of XSSX and X$_2$SS isomers (X = F, Cl, H, and CH$_3$) . . . 465--477 Jeong Hyeok Yoon and Jae Kwang Shin and Mu Shik Jhon Determination of C-terminal structure of human C Ha ras oncogenic protein . . . . 478--485 Gordon M. Crippen Intervals and the deduction of drug binding site models . . . . . . . . . . 486--500 David M. Ferguson Parameterization and evaluation of a flexible water model . . . . . . . . . . 501--511 Xiang Zhexin and Shi Yunyu and Xu Yingwu Calculating the electric potential of macromolecules: a simple method for molecular surface triangulation . . . . 512--516 T. \vZivkovi\'c and M. Randi\'c and D. J. Klein and H.-Y. Zhu and N. Trinajsti\'c Analytical approach to very large benzenoid polymers . . . . . . . . . . . 517--526 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
H. Bekker and H. J. C. Berendsen and W. F. van Gunsteren Force and virial of torsional-angle-dependent potentials . . 527--533 Frederico F. Campos and John S. Rollett The exponents method for calculating equilibrium concentrations of complex species in solution . . . . . . . . . . 534--544 R. Bursi and M. Lankhorst and D. Feil Uncoupled Hartree--Fock calculations of the polarizability and hyperpolarizabilities of nitrophenols 545--562 Modesto Orozco and M. Bachs and F. J. Luque Development of optimized MST/SCRF methods for semiempirical calculations: the MNDO and PM3 Hamiltonians . . . . . 563--575 Roland H. Hertwig and Wolfram Koch On the accuracy of density functionals and their basis set dependence: an extensive study on the main group homonuclear diatomic molecules Li$_2$ to Br$_2$ . . . . . . . . . . . . . . . . . 576--585 O. V. Sizova and V. I. Baranovski INDO parameters for the elements of the I and II transition rows . . . . . . . . 586--594 Jan L. M. Dillen An empirical force field. I. Alkanes . . 595--609 Jan L. M. Dillen An empirical force field. II. Crystalline alkanes . . . . . . . . . . 610--619 Per-Ola Norrby and Kenneth Wärnmark and Björn Åkermark and Christina Moberg Unusual conformational-determining interactions in oxymethylpyridines: an ab initio study and an improved method for refining molecular mechanics parameters . . . . . . . . . . . . . . . 620--627 D. J. Willock and S. L. Price and M. Leslie and C. R. A. Catlow The relaxation of molecular crystal structures using a distributed multipole electrostatic model . . . . . . . . . . 628--647 Frank Guarnieri and Stephen R. Wilson Conformational memories and a simulated annealing program that learns: Application to LTB$_4$ . . . . . . . . . 648--653 Dariush Habibollahzadeh and M. Edward Grice and Monica C. Concha and Jane S. Murray and Peter Politzer Nonlocal density functional calculation of gas phase heats of formation . . . . 654--658 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
M. I. Menéndez and D. Suárez and J. A. Sordo and T. L. Sordo Theoretical study of the gas-phase addition of HF and HCl to ethylene: Analysis of the catalytic action of dimeric halides . . . . . . . . . . . . 659--666 H. A. Gabb and R. Lavery and C. Prévost Efficient conformational space sampling for nucleosides using internal coordinate Monte Carlo simulations and a modified furanose description . . . . . 667--680 Enrico O. Purisima and Shahul H. Nilar A simple yet accurate boundary element method for continuum dielectric calculations . . . . . . . . . . . . . . 681--689 Beno\^\it Roux and Martin Karplus Potential energy function for cation--peptide interactions: an ab initio study . . . . . . . . . . . . . . 690--704 Weida Tong and Valerian T. D'Souza The role of the carboxylate ion in models of acyl-chymotrypsin . . . . . . 705--714 William S. Young and Charles L. Brooks III Dynamic load balancing algorithms for replicated data molecular dynamics . . . 715--722 Mounzer Dagher and Mounif Kobersi and Hafez Kobeissi The true diatomic potential as a perturbed Morse function . . . . . . . . 723--728 Jordi Mestres and Gustavo E. Scuseria Genetic algorithms: a robust scheme for geometry optimizations and global minimum structure problems . . . . . . . 729--742 Tony You and Donald Bashford An analytical algorithm for the rapid determination of the solvent accessibility of points in a three-dimensional lattice around a solute molecule . . . . . . . . . . . . 743--757 Gustavo E. López The electronic structure of weakly bound systems. I. Rare-gas bimolecular cations 758--767 Gustavo E. López The electronic structure of weakly bound systems. II. Ne X$^+$ and Ar X$^+$ (X = H$_2$O, HCl, and HF) bimolecular cations 768--776 James P. Ritchie and Ann S. Copenhaver Comparison of potential-derived charge and atomic multipole models in calculating electrostatic potentials and energies of some nucleic acid bases and pairs . . . . . . . . . . . . . . . . . 777--789 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
Michael J. Dudek and Jay W. Ponder Accurate modeling of the intramolecular electrostatic energy of proteins . . . . 791--816 Valentin Gogonea and Eiji \=Osawa An improved algorithm for the analytical computation of solvent-excluded volume. The treatment of singularities in solvent-accessible surface area and volume functions . . . . . . . . . . . . 817--842 Nohad Gresh and Walter J. Stevens and Morris Krauss Mono- and poly-ligated complexes of Zn$^{2+}$: an ab initio analysis of the metal--ligand interaction energy . . . . 843--855 Nohad Gresh Energetics of Zn$^{2+}$ binding to a series of biologically relevant ligands: a molecular mechanics investigation grounded on ab initio self-consistent field supermolecular computations . . . 856--882 Congxin Liang and Liqun Yan and Jörg-R. Hill and Carl S. Ewig and Terry R. Stouch and Arnold T. Hagler Force field studies of cholesterol and cholesteryl acetate crystals and cholesterol--cholesterol intermolecular interactions . . . . . . . . . . . . . . 883--897 Ranganathan Bharadwaj and Andreas Windemuth and S. Sridharan and Barry Honig and Anthony Nicholls The fast multipole boundary element method for molecular electrostatics: an optimal approach for large systems . . . 898--913 J. Aerts An improved molecular modeling method for the prediction of enantioselectivity 914--922 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
Thomas H. Fischer and Wesley P. Petersen and Hans Peter Lüthi A new optimization technique for artificial neural networks applied to prediction of force constants of large molecules . . . . . . . . . . . . . . . 923--936 Uwe Koch and Ernst Egert An improved description of the molecular charge density in force fields with atomic multipole moments . . . . . . . . 937--944 P. C. Chen The molecular structures and the absorption maxima of the H-chromophores of the indigoid dyes . . . . . . . . . . 945--950 Jonathan W. Essex and William L. Jorgensen An empirical boundary potential for water droplet simulations . . . . . . . 951--972 Mark Sulkes Conformational analysis of jet-cooled tryptophan analogs and Histamine using the MM3(94) force field: Comparison with experiment . . . . . . . . . . . . . . . 973--983 David S. Maxwell and Julian Tirado-Rives and William L. Jorgensen A comprehensive study of the rotational energy profiles of organic systems by ab initio MO theory, forming a basis for peptide torsional parameters . . . . . . 984--1010 Je Myung Park and Oh Young Kwon and Kyoung Tai No and Mu Shik Jhon and Harold A. Scheraga Determination of net atomic charges using a modified partial equalization of orbital electronegativity method. IV. Application to hypervalent sulfur- and phosphorus-containing molecules . . . . 1011--1026 Eric Magnusson Electrostatic bonding models: a test on group 1 and 2 metal complexes with H$_2$O, NH$_3$, H$_2$S, PH$_3$, and related ligands . . . . . . . . . . . . 1027--1037 S. Sridharan and Anthony Nicholls and Kim A. Sharp A rapid method for calculating derivatives of solvent accessible surface areas of molecules . . . . . . . 1038--1044 Ikchoon Lee and Chang Kon Kim and Bon-Su Lee Ab initio molecular orbital studies of nonidentity allyl transfer reactions . . 1045--1054 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
Bruce A. Smart and Carl H. Schiesser On the existence of SH$_3$, SeH$_3$, and TeH$_3$: Discrepancies between all-electron and pseudopotential calculations . . . . . . . . . . . . . . 1055--1066 Lawrence M. Pratt and Ishrat M. Khan A density functional treatment of organolithium compounds: Comparison to ab initio, semiempirical, and experimental results . . . . . . . . . . 1067--1080 Michael K. Gilson and J. Andrew McCammon and Jeffry D. Madura Molecular dynamics simulation with a continuum electrostatic model of the solvent . . . . . . . . . . . . . . . . 1081--1095 Sòren Balling Engelsen and Serge Pérez and Isabelle Braccini and Catherine Hervé Du Penhoat Internal motions of carbohydrates as probed by comparative molecular modeling and nuclear magnetic resonance of ethyl $\beta$-lactoside . . . . . . . . . . . 1096--1119 Takashi Amisaki and Takaji Fujiwara and Akihiro Kusumi and Hiroo Miyagawa and Kunihiro Kitamura Error evaluation in the design of a special-purpose processor that calculates nonbonded forces in molecular dynamics simulations . . . . . . . . . . 1120--1130 Eric Swanson and Terry P. Lybrand PVM-AMBER: a parallel implementation of the AMBER molecular mechanics package for workstation clusters . . . . . . . . 1131--1140 Dan N. Bernardo and Yanbo Ding and Karsten Krogh-Jespersen and Ronald M. Levy Evaluating polarizable potentials on distributed memory parallel computers: Program development and applications . . 1141--1152 D. R. Ripoll and M. S. Pottle and K. D. Gibson and H. A. Scheraga and A. Liwo Implementation of the ECEPP algorithm, the Monte Carlo minimization method, and the electrostatically driven Monte Carlo method on the Kendall square research KSR1 computer . . . . . . . . . . . . . 1153--1163 Yaxiong Sun and Peter A. Kollman Hydrophobic solvation of methane and nonbond parameters of the TIP3P water model . . . . . . . . . . . . . . . . . 1164--1169 Feliu Maseras and Keiji Morokuma IMOMM: a new integrated ab initio + molecular mechanics geometry optimization scheme of equilibrium structures and transition states . . . . 1170--1179 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
Marc R. Roussel and Carmay Lim Discrete, dynamic polymer modeling: a pseudo-diatomic model of lignin . . . . 1181--1191 Eric Barth and Krzysztof Kuczera and Benedict Leimkuhler and Robert D. Skeel Algorithms for constrained molecular dynamics . . . . . . . . . . . . . . . . 1192--1209 Kevin P. Clark and Ajay Flexible ligand docking without parameter adjustment across four ligand--receptor complexes . . . . . . . 1210--1226 D. B. Chesnut A comparative quantum mechanical study of bond separation energies as a measure of cyclic conjugation . . . . . . . . . 1227--1237 P. Duane Walker and Paul G. Mezey Toward similarity measures for macromolecular bodies: Medla test calculations for substituted benzene systems . . . . . . . . . . . . . . . . 1238--1249 Georgia B. McGaughey and Eugene L. Stewart and J. Phillip Bowen Ab initio and molecular mechanics (MM2 and MM3) calculations of nonconjugated positively charged nitrogen-containing compounds . . . . . . . . . . . . . . . 1250--1260 Warner L. Peticolas and Thomas Rush III Ab initio calculations of the ultraviolet resonance Raman spectra of uracil . . . . . . . . . . . . . . . . . 1261--1270 James Turner and Paul Weiner and Barry Robson and Ravi Venugopal and Harry Schubele III and Ramen Singh Reduced variable molecular dynamics . . 1271--1290 Adrian T. Wong and Robert J. Harrison Approaches to large-scale parallel self-consistent field calculations . . . 1291--1300 Ida M. B. Nielsen and Edward T. Seidl Parallel direct implementations of second-order perturbation theories . . . 1301--1313 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
Pavel Hobza and Ji\vrí \vsponer and Tomá\vs Reschel Density functional theory and molecular clusters . . . . . . . . . . . . . . . . 1315--1325 Josep Maria Bofill and Móanica Comajuan Analysis of the updated Hessian matrices for locating transition structures . . . 1326--1338 Shankar Kumar and John M. Rosenberg and Djamal Bouzida and Robert H. Swendsen and Peter A. Kollman Multidimensional free-energy calculations using the weighted histogram analysis method . . . . . . . 1339--1350 Yong Duan and Shankar Kumar and John M. Rosenberg and Peter A. Kollman Gradient SHAKE: an improved method for constrained energy minimization in macromolecular simulations . . . . . . . 1351--1356 Piotr Cieplak and Wendy D. Cornell and Christopher Bayly and Peter A. Kollman Application of the multimolecule and multiconformational RESP methodology to biopolymers: Charge derivation for DNA, RNA, and proteins . . . . . . . . . . . 1357--1377 Andrew R. Leach and Teri E. Klein A molecular dynamics study of the inhibition of chicken dihydrofolate reductase by a phenyl triazine . . . . . 1378--1393 Boris B. Stefanov and Jerzy Cioslowski An efficient approach to calculation of zero-flux atomic surfaces and generation of atomic integration data . . . . . . . 1394--1404 R. S. Judson and Y. T. Tan and E. Mori and C. Melius and E. P. Jaeger and A. M. Treasurywala and A. Mathiowetz Docking flexible molecules: a case study of three proteins . . . . . . . . . . . 1405--1419 James J. Vincent and Kenneth M. Merz Jr. A highly portable parallel implementation of AMBER4 using the message passing interface standard . . . 1420--1427 Razif R. Gabdoulline and Chong Zheng Effects of the cutoff center on the mean potential and pair distribution functions in liquid water . . . . . . . 1428--1433 Frank Herrmann and Sándor Suhai Energy minimization of peptide analogues using genetic algorithms . . . . . . . . 1434--1444 A. H. De Vries and P. Th. Van Duijnen and A. H. Juffer and J. A. C. Rullmann and J. P. Dijkman and H. Merenga and B. T. Thole Implementation of reaction field methods in quantum chemistry computer codes . . 1445--1446 Anonymous Announcement . . . . . . . . . . . . . . 1447--1447 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
R. Cammi and J. Tomasi Remarks on the use of the apparent surface charges (ASC) methods in solvation problems: Iterative versus matrix-inversion procedures and the renormalization of the apparent charges 1449--1458 Alexander A. Cohen and Shimon E. Shatzmiller Localization and quantitative evaluation of potent local binding sites on the accessible Lennard-Jones surface . . . . 1459--1467 Xiang Zhexin and Huang Fuhua and Shi Yunyu and Xu Yinwu Incorporating the protein--dipole Langevin--dipole model into Tanford--Kirkwood theory . . . . . . . . 1468--1473 P. Duane Walker and Paul G. Mezey and Gerald M. Maggiora and Mark A. Johnson and James D. Petke Application of the shape group method to conformational processes: Shape and conjugation changes in the conformers of 2-phenyl pyrimidine . . . . . . . . . . 1474--1482 Alain St.-Amant and Wendy D. Cornell and Peter A. Kollman and Thomas A. Halgren Calculation of molecular geometries, relative conformational energies, dipole moments, and molecular electrostatic potential fitted charges of small organic molecules of biochemical interest by density functional theory 1483--1506 J. C. Cesco and C. C. Denner and A. E. Rosso and J. E. Perez and F. S. Ortiz and R. H. Contreras and C. G. Giribet and M. C. Ruiz De Azúa Numerical evaluation of three- and four-center bielectronic integrals using exponential-type atomic orbitals . . . . 1507--1512 Mark D. Erion and M. Rami Reddy Calculation of relative free energy differences for the covalent hydration of organic compounds: a combined quantum mechanical and free energy perturbation study . . . . . . . . . . . . . . . . . 1513--1521 Bernard R. Brooks and Du\vsanka Jane\vzi\vc and Martin Karplus Harmonic analysis of large systems. I. Methodology . . . . . . . . . . . . . . 1522--1542 D\vsanka Jane\vzi\vc and Bernard R. Brooks Harmonic analysis of large systems. II. Comparison of different protein models 1543--1553 Du\vsanka Jane\vzi\vc and Richard M. Venable and Bernard R. Brooks Harmonic analysis of large systems. III. Comparison with molecular dynamics . . . 1554--1566 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
Mark A. Spackman Potential derived charges using a geodesic point selection scheme . . . . 1--18 I. Tuñón and M. T. C. Martins-Costa and C. Millot and M. F. Ruiz-López and J. L. Rivail A coupled density functional-molecular mechanics Monte Carlo simulation method: the water molecule in liquid water . . . 19--29 Peeter Burk and Ilmar A. Koppel and Ivar Koppel and Lev M. Yagupolskii and Robert W. Taft Superacidity of neutral Brönsted acids in gas phase . . . . . . . . . . . . . . . 30--41 O. Castell and V. M. García and C. Bo and R. Caballol Relative stability of the $^3$A$_2$, $^1$A$_2$, and $^1$A$_1$ states of phenylnitrene: a difference-dedicated configuration interaction calculation 42--48 Chunyang Peng and Philippe Y. Ayala and H. Bernhard Schlegel and Michael J. Frisch Using redundant internal coordinates to optimize equilibrium geometries and transition states . . . . . . . . . . . 49--56 Maurizio Cossi and Benedetta Mennucci and Roberto Cammi Analytical first derivatives of molecular surfaces with respect to nuclear coordinates . . . . . . . . . . 57--73 D. Delfini and C. Nicolini and E. A. Carrara Performance analysis of the double-iterated Kalman filter for molecular structure estimation . . . . . 74--86 Dirk Bakowies and Walter Thiel Semiempirical treatment of electrostatic potentials and partial charges in combined quantum mechanical and molecular mechanical approaches . . . . 87--108 Ian T. Foster and Jeffrey L. Tilson and Albert F. Wagner and Ron L. Shepard and Robert J. Harrison and Rick A. Kendall and Rik J. Littlefield Toward high-performance computational chemistry: I. Scalable Fock matrix construction algorithms . . . . . . . . 109--123 Robert J. Harrison and Martyn F. Guest and Rick A. Kendall and David E. Bernholdt and Adrian T. Wong and Mark Stave and James L. Anchell and Anthony C. Hess and Rik J. Littlefield and George L. Fann and Jaroslaw Nieplocha and Greg S. Thomas and David Elwood and Jeffrey L. Tilson and Ron L. Shepard and Albert F. Wagner and Ian T. Foster and Ewing Lusk and Rick Stevens Toward high-performance computational chemistry: II. A scalable self-consistent field program . . . . . 124--132 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
Stephan Reiling and Jürgen Brickmann and Michael Schlenkrich and Philippe A. Bopp Theoretical investigations on 1,2-ethanediol: the problem of intramolecular hydrogen bonds . . . . . 133--147 Iñaki Tuñón and Manuel F. Ruiz-López and Daniel Rinaldi and Juan Bertrán Computation of hydration free energies using a parameterized continuum model: Study of equilibrium geometries and reactive processes in water solution . . 148--155 Marcelo Giordan and Rogério Custodio and José Roberto Trigo Pyrrolizidine alkaloids necine bases: ab initio, semiempirical, and molecular mechanics approaches to molecular properties . . . . . . . . . . . . . . . 156--166 Ana Luiza M. S. de Azevedo and Benício B. Neto and Ieda S. Scarminio and Anselmo E. de Oliveira and Roy E. Bruns A chemometric analysis of ab initio vibrational frequencies and infrared intensities of methyl fluoride . . . . . 167--177 A. I. Panin and O. V. Sizova Direct CI method in restricted configuration spaces . . . . . . . . . . 178--184 Kenneth B. Wiberg and Henry Castejon and Todd A. Keith Solvent effects: 6. A comparison between gas phase and solution acidities . . . . 185--190 Shigetaka Yoneda and Masako Kitazawa and Hideaki Umeyama Molecular dynamics simulation of a rhinovirus capsid under rotational symmetry boundary conditions . . . . . . 191--203 Alesia Sawyer and Erica Sullivan and Yitbarek H. Mariam A semiempirical computational study of electron transfer reactivity of one- vs. two-ring model systems for anthracycline pharmacophores. I. A rationale for mode of action . . . . . . . . . . . . . . . 204--225 Takeshi Kikuchi Inter-C$^\alpha$ atomic potentials derived from the statistics of average interresidue distances in proteins: Application to bovine pancreatic trypsin inhibitor . . . . . . . . . . . . . . . 226--237 Seunho Jung and Dugki Min and Rawle I. Hollingsworth A Metropolis Monte Carlo method for analyzing the energetics and dynamics of lipopolysaccharide supramolecular structure and organization . . . . . . . 238--249 Grant S. Heffelfinger and Martin E. Lewitt A comparison between two massively parallel algorithms for Monte Carlo computer simulation: an investigation in the grand canonical ensemble . . . . . . 250--265 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
H. J. J. Van Dam and J. H. Van Lenthe and G. L. G. Sleijpen and H. A. Van Der Vorst An improvement of Davidson's iteration method: Applications to MRCI and MRCEPA calculations . . . . . . . . . . . . . . 267--272 Dan Harris and Gilda Loew Comparative study of free energies of solvation of phenylimidazole inhibitors of cytochrome P450 \em cam by free energy simulation, AMSOL, and Poisson Boltzmann methods . . . . . . . . . . . 273--288 Gy. Dömötör and M. I. Bán and L. L. Stachó Theoretical and practical aspects of the convergence properties of the dynamically defined reaction path method 289--297 Branko S. Jursic and Zoran Zdravkovski An ab initio study of heterodienophiles addition to 2,3-diaza-1,3-butadiene: an example of endo-lone-pair effect on the reaction energy barrier . . . . . . . . 298--305 B. W. Clare and P. J. Jennings and J. C. L. Cornish and G. T. Hefter and D. J. Santjojo Simulation of the infrared spectra of amorphous silicon alloys . . . . . . . . 306--312 Youliang Wang and Raymond A. Poirier Computational developments in generalized valence bond calculations 313--325 Steve Plimpton and Bruce Hendrickson A new parallel method for molecular dynamics simulation of macromolecular systems . . . . . . . . . . . . . . . . 326--337 Yanbo Ding and Karsten Krogh-Jespersen The 1:1 glycine zwitterion-water complex: an ab initio electronic structure study . . . . . . . . . . . . 338--349 Jian Shen and John Wendoloski Electrostatic binding energy calculation using the finite difference solution to the linearized Poisson--Boltzmann equation: Assessment of its accuracy . . 350--357 Daniel E. Platt and B. David Silverman Registration, orientation, and similarity of molecular electrostatic potentials through multipole matching 358--366 Michelle Miller Francl and Christina Carey and Lisa Emily Chirlian and David M. Gange Charges fit to electrostatic potentials. II. Can atomic charges be unambiguously fit to electrostatic potentials? . . . . 367--383 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
Norman L. Allinger and Paul von R. Schleyer Editorial . . . . . . . . . . . . . . . 385--385 Marek Freindorf and Jiali Gao Optimization of the Lennard-Jones parameters for a combined ab initio quantum mechanical and molecular mechanical potential using the 3-21G basis set . . . . . . . . . . . . . . . 386--395 Ulf Berg and Nina Bladh Molecular mechanics calculations of conjugated amides and an ab initio investigation of acrylamide and its $\beta$-amino derivative: Conformational analysis and rotational barriers . . . . 396--408 Michael Falk and Peter F. Spierenburg and John A. Walter Determination of the stereochemistry of natural products from nuclear magnetic resonance data by constrained molecular dynamics . . . . . . . . . . . . . . . . 409--417 Kamalakar Gulukota and Sandor Vajda and Charles Delisi Peptide docking using dynamic programming . . . . . . . . . . . . . . 418--428 Klaus Gundertofte and Tommy Liljefors and Per-ola Norrby and Ingrid Pettersson A comparison of conformational energies calculated by several molecular mechanics methods . . . . . . . . . . . 429--449 Stephan Reiling and Michael Schlenkrich and Jürgen Brickmann Force field parameters for carbohydrates 450--468 P. Ballestrero and P. Baglietto and C. Ruggiero Molecular dynamics for proteins: Performance evaluation on massively parallel computers based on mesh networks using a space decomposition approach . . . . . . . . . . . . . . . . 469--475 Shigeru Endo and Junichi Higo and Kuniaki Nagayama and Hiroshi Wako New implementation of and the modeling by the extended simulated annealing process to structures of T4 lysozyme mutants at the 86th residue . . . . . . 476--488 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
Norman L. Allinger and Paul von R. Schleyer Editorial . . . . . . . . . . . . . . . 489--489 Thomas A. Halgren Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94 . . . . . . . . . 490--519 Thomas A. Halgren Merck molecular force field. II. MMFF94 van der Waals and electrostatic parameters for intermolecular interactions . . . . . . . . . . . . . . 520--552 Thomas A. Halgren Merck molecular force field. III. Molecular geometries and vibrational frequencies for MMFF94 . . . . . . . . . 553--586 Thomas A. Halgren and Robert B. Nachbar Merck molecular force field. IV. conformational energies and geometries for MMFF94 . . . . . . . . . . . . . . . 587--615 Thomas A. Halgren Merck molecular force field. V. Extension of MMFF94 using experimental data, additional computational data, and empirical rules . . . . . . . . . . . . 616--641 Norman L. Allinger and Kuohsiang Chen and Jenn-Huei Lii An improved force field (MM4) for saturated hydrocarbons . . . . . . . . . 642--668 Neysa Nevins and Kuohsiang Chen and Norman L. Allinger Molecular mechanics (MM4) calculations on alkenes . . . . . . . . . . . . . . . 669--694 Neysa Nevins and Jenn-Huei Lii and Norman L. Allinger Molecular mechanics (MM4) calculations on conjugated hydrocarbons . . . . . . . 695--729 Neysa Nevins and Norman L. Allinger Molecular mechanics (MM4) vibrational frequency calculations for alkenes and conjugated hydrocarbons . . . . . . . . 730--746 Norman L. Allinger and Kuohsiang Chen and J. A. Katzenellenbogen and Scott R. Wilson and Gregory M. Anstead Hyperconjugative effects on carbon--carbon bond lengths in molecular mechanics (MM4) . . . . . . . . . . . . 747--755 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
John R. Kneisler and Norman L. Allinger Ab initio and density functional theory study of structures and energies for dimethoxymethane as a model for the anomeric effect . . . . . . . . . . . . 757--766 Gábor I. Csonka and Pál Hencsei The structure of 1-chlorosilatrane: an ab initio molecular orbital and a density functional theory study . . . . 767--780 Ralf Stegmann and Gernot Frenking Silaacetylene: a possible target for experimental studies . . . . . . . . . . 781--789 Hideo Nakajima and Ohgi Takahashi and Osamu Kikuchi Rapid evaluation of molecular electrostatic potential maps for amino acids, peptides, and proteins by empirical functions . . . . . . . . . . 790--805 F. J. Luque and M. Bachs and C. Alemán and Modesto Orozco Extension of MST/SCRF method to organic solvents: ab initio and semiempirical parametrization for neutral solutes in CCl$_4$ . . . . . . . . . . . . . . . . 806--820 András Perczel and Ödön Farkas and Imre G. Csizmadia Peptide models XVI. The identification of selected HCO--L--SER--NH$_2$ conformers via a systematic grid search using ab initio potential energy surfaces . . . . . . . . . . . . . . . . 821--834 Branko S. Jursic Density functional Gaussian-type orbital approach in theoretical study of S$_2$F$_2$ isomerization . . . . . . . . 835--840 Jireí Seponer and Jerzy Leszczynski and Pavel Hobza Base stacking in cytosine dimer. A comparison of correlated ab initio calculations with three empirical potential models and density functional theory calculations . . . . . . . . . . 841--850 Xiaoping Cao and Muzhen Liao and Xuejun Chen and Bo Li Molecular symmetry and ab initio calculations. II. Symmetry-matrix and symmetry-supermatrix in the Dirac-Fock method . . . . . . . . . . . . . . . . . 851--863 Randy J. Zauhar and Alexander Varnek A fast and Space-efficient boundary element method for computing electrostatic and hydration effects in large molecules . . . . . . . . . . . . 864--877 Shuzo Yoshioki Internal dynamics of a globular protein in water . . . . . . . . . . . . . . . . 878--887 Jon Baker and Fora Chan The location of transition states: a comparison of Cartesian, $Z$-matrix, and natural internal coordinates . . . . . . 888--904 Ramón López and José A. Sordo and Tomás L. Sordo and Paul von Ragué Schleyer Ab initio study of the formation of C$_3$H$_3^+$ from the reaction of CH$_3^+$ with acetylene . . . . . . . . 905--909 Masaki Tomimoto and Nobuhiro Go and Hiroshi Wako Conformational analysis of nucleic acid molecules with flexible furanose rings in dihedral angle space . . . . . . . . 910--917 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
A. A. Buchachenko and A. Yu. Baisogolov and N. F. Stepanov Decoupling approximations for quantum vibrational predissociation dynamics: the tests on the low-level golden rule approaches for some rare gas --- Cl$_2$, ICl complexes . . . . . . . . . . . . . 919--930 Delbert R. Black and Craig G. Parker and S. Scott Zimmerman and Milton L. Lee Enantioselective binding of $\alpha$-pinene and of some cyclohexanetriol derivatives by cyclodextrin hosts: a molecular modeling study . . . . . . . . . . . . . . . . . 931--939 Guyan Liang and Peter C. Fox and J. Phillip Bowen Parameter analysis and refinement toolkit system and its application in MM3 parameterization for phosphine and its derivatives . . . . . . . . . . . . 940--953 Wendell Forst Sum and density of states of polyatomic systems with hindered rotors . . . . . . 954--961 Andrey A. Bliznyuk and Jill E. Gready Numerical calculation of molecular surface area. I. Assessment of errors 962--969 Andrey A. Bliznyuk and Jill E. Gready Numerical calculation of molecular surface area. II. Speed of calculation 970--975 Marcia O. Fenley and Wilma K. Olson and Kiat Chua and Alexander H. Boschitsch Fast adaptive multipole method for computation of electrostatic energy in simulations of polyelectrolyte DNA . . . 976--991 Lawrence A. Covick and Kenneth M. Sando Portable, parallel transformation: Distributed-Memory approach . . . . . . 992--1001 Louis Carlacci and S. Walter Englander Loop problem in proteins: Developments on Monte Carlo simulated annealing approach . . . . . . . . . . . . . . . . 1002--1012 Shusen Li and Ching-Hsien Huang Molecular mechanics simulation studies of dienoic hydrocarbons: From alkenes to 1-Palmitoyl-2-linoleoyl-phosphatidylcholines 1013--1024 Boris A. Reva and Michel F. Sanner and Arthur J. Olson and Alexei V. Finkelstein Lattice modeling: Accuracy of energy calculations . . . . . . . . . . . . . . 1025--1032 Rohit V. Pappu and William J. Schneller and David L. Weaver Electrostatic multipole representation of a polypeptide chain: an algorithm for simulation of polypeptide properties . . 1033--1055 Hiroshi Tatewaki and Shinichi Katsuki and Yoshiko Sakai and Eisaku Miyoshi Applications of spectral-Representation model as a potential method for Cu clusters . . . . . . . . . . . . . . . . 1056--1067 Karl-Heinz Ott and Bernd Meyer Parametrization of GROMOS force field for oligosaccharides and assessment of efficiency of molecular dynamics simulations . . . . . . . . . . . . . . 1068--1084 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
Evgenii B. Krissinel' and Noam Agmon Spherical symmetric diffusion problem 1085--1098 Per E. M. Siegbahn Models for the description of the H$_3$O$^+$ and OH$^-$ ions in water . . 1099--1107 Xiang-Yuan Li and An-Min Tian and Fu-Cheng He and Guo-Sen Yan Electron transfer integral between two zero-overlap states . . . . . . . . . . 1108--1111 Christophe Chipot and Peter A. Kollman and David A. Pearlman Alternative approaches to potential of mean force calculations: Free energy perturbation versus thermodynamic integration. Case study of some representative nonpolar interactions . . 1112--1131 Arnaud Blondel and Martin Karplus New formulation for derivatives of torsion angles and improper torsion angles in molecular mechanics: Elimination of singularities . . . . . . 1132--1141 J. C. Meza and R. S. Judson and T. R. Faulkner and A. M. Treasurywala A comparison of a direct search method and a genetic algorithm for conformational searching . . . . . . . . 1142--1151 Bernard Delley High order integration schemes on the unit sphere . . . . . . . . . . . . . . 1152--1155 Bo R. Svensson and Clifford E. Woodward Constant-NT$\mu$ simulations: Free energy difference method for excess adsorption . . . . . . . . . . . . . . . 1156--1162 Takako Kudo and Fujiko Hashimoto and Mark S. Gordon Ab initio study of cyclic siloxanes (H$_2$SiO)$_n$: $n = 3$, $4$, $5$ . . . 1163--1170 A. M. Treasurywala and E. P. Jaeger and M. L. Peterson Conformational searching methods for small molecules. III. Study of stochastic methods available in SYBYL and MACROMODEL . . . . . . . . . . . . . 1171--1182 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
Paulo J. A. Ribeiro-Claro and Ana Margarida Amado and J. J. C. Teixeira-Dias Structures and vibrational frequencies of vanadium (V) oligomers: an ab initio study using effective core potentials 1183--1196 Bjòrn K. Alsberg and Vidar R. Jensen and Knut J. Bòrve Use of multivariate methods in the analysis of calculated reaction pathways 1197--1216 John R. Gunn and Richard A. Friesner Parallel implementation of a protein structure refinement algorithm . . . . . 1217--1228 P. Beroza and D. R. Fredkin Calculation of amino acid $pK_a$s in a protein from a continuum electrostatic model: Method and sensitivity analysis 1229--1244 Guang Wu and S. Jacobs and M. G. Verbruggen and A. T. H. Lenstra and C. van Alsenoy and H. J. Geise and L. van Meervelt Phenylene vinylene oligomers studied by theoretical methods: Joint analysis of computational and X-ray results of the configurational isomers of 1,4-bis[2-(3,4,5-trimethoxyphenyl)ethenyl]benzene 1245--1257 Qishi Du and Gustavo A. Arteca Derivation of fused-sphere molecular surfaces from properties of the electrostatic potential distribution . . 1258--1268 Shankar Kumar and Philip W. Payne and Maximiliano Vásquez Method for free-energy calculations using iterative techniques . . . . . . . 1269--1275 T. Komatsu and T. Noro and F. Sasaki and H. Tatewaki Quality of correlating functions generated from commonly used basis sets 1276--1286 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
Marc F. Lensink and Janez Mavri and Herman J. C. Berendsen Simultaneous integration of mixed quantum-classical systems by density matrix evolution equations using interaction representation and adaptive time step integrator . . . . . . . . . . 1287--1295 Romano T. Kroemer and Peter Hecht and Klaus R. Liedl Different electrostatic descriptors in comparative molecular field analysis: a comparison of molecular electrostatic and Coulomb potentials . . . . . . . . . 1296--1308 Oscar N. Ventura and Martina Kieninger and Elena L. Coitiño Density functional study of isomerization of fluoro- and chloroformaldehyde radical cations . . . 1309--1317 Serguei Patchkovskii and Walter Thiel Analytical second derivatives of the energy in MNDO methods . . . . . . . . . 1318--1327 N. Swamy Kandadai and M. Rami Reddy Solution structure of papain as studied by molecular mechanics and molecular dynamics techniques . . . . . . . . . . 1328--1338 S. A. C. McDowell Dipole moment derivatives and integrated intensities for the vibrational transitions of N$_2$ \ldots HF . . . . . 1339--1343 Zhongxiang Zhou and Philip Payne and Max Vasquez and Nat Kuhn and Michael Levitt Finite-difference solution of the Poisson--Boltzmann equation: Complete elimination of self-energy . . . . . . . 1344--1351 Jerzy Cioslowski and Boris B. Stefanov and Pere Constans Efficient algorithm for quantitative assessment of similarities among atoms in molecules . . . . . . . . . . . . . . 1352--1358 Marc Couty and Michael B. Hall Basis sets for transition metals: Optimized outer $p$ functions . . . . . 1359--1370 Jorge Llano and Luis A. Montero $\pi$-Bonding contribution to restricted internal rotations in saccharides . . . 1371--1384 Julian Tirado-Rives and William L. Jorgensen Viability of molecular modeling with Pentium-based PCs . . . . . . . . . . . 1385--1386 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
Jun-Ichi Aihara and Sumio Oe and Mitsuho Yoshida and Eiji \=Osawa Further test of the isolated pentagon rule: Thermodynamic and kinetic stabilities of C$_{84}$ fullerene isomers . . . . . . . . . . . . . . . . 1387--1394 Georgia B. McGaughey and Eugene L. Stewart and J. Phillip Bowen Ab initio and molecular mechanics (MM2 and MM3) calculations of positively charged conjugated nitrogen-containing compounds . . . . . . . . . . . . . . . 1395--1405 Bernd Reindl and Timothy Clark and Paul v. R. Schleyer A new method for empirical force field calculations on localized and delocalized carbocations . . . . . . . . 1406--1430 D. B. Chesnut and E. F. C. Byrd Accurate estimation of correlation energies using locally dense basis sets 1431--1443 George L. Heard and Brian F. Yates Hybrid supermolecule-polarizable continuum approach to solvation: Application to the mechanism of the Stevens rearrangement . . . . . . . . . 1444--1452 Betty Cheng and Akbar Nayeem and Harold A. Scheraga From secondary structure to three-dimensional structure: Improved dihedral angle probability distribution function for use with energy searches for native structures of polypeptides and proteins . . . . . . . . . . . . . . 1453--1480 Nohad Gresh and David R. Garmer Comparative binding energetics of Mg$^{2+}$, Ca$^{2+}$, Zn$^{2+}$, and Cd$^{2+}$ to biologically relevant ligands: Combined ab initio SCF supermolecule and molecular mechanics investigation . . . . . . . . . . . . . 1481--1495 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
M. Danielewski and R. Filipek Generalized solution of interdiffusion problem: Optimal approach for multicomponent bounded systems . . . . . 1497--1507 Martina Kieninger and Sándor Suhai Conformational and energetic properties of the ammonia dimer --- comparison of post-Hartree--Fock and density functional methods . . . . . . . . . . . 1508--1519 A. Varnek and G. Wipff Theoretical calculations of extraction selectivity: Alkali cation complexes of calix[4]-bis-crown6 in pure water, chloroform, and at a water/chloroform interface . . . . . . . . . . . . . . . 1520--1531 Charles E. Hudson and David J. McAdoo and C. S. Giam The isomers of ionized ethane . . . . . 1532--1540 Wendy D. Cornell and Maria P. Ha and Yax Sun and Peter A. Kollman Application of a simple diagonal force field to the simulation of cyclopentane conformational dynamics . . . . . . . . 1541--1548 Joseph D. Augspurger and Harold A. Scheraga An efficient, differentiable hydration potential for peptides and proteins . . 1549--1558 J. P. Braga and J. C. Belchior Normalization of the Fox--Goodwin algorithm to calculate scattering matrices in an adiabatic basis at low and high collision energies . . . . . . 1559--1563 Teerakiat Kerdcharoen and Klaus R. Liedl and Bernd M. Rode Bidirectional molecular dynamics: Interpretation in terms of a modern formulation of classical mechanics . . . 1564--1570 David Feller The role of databases in support of computational chemistry calculations . . 1571--1586 Anonymous Announcement . . . . . . . . . . . . . . ii--ii Anonymous Masthead . . . . . . . . . . . . . . . . fmi
Johan Åqvist Calculation of absolute binding free energies for charged ligands and effects of long-range electrostatic interactions 1587--1597 Peter L. Cummins and Jill E. Gready Solvent effects in active-site molecular dynamics simulations on the binding of 8-methyl-N5-deazapterin and 8-methylpterin to dihydrofolate reductase . . . . . . . . . . . . . . . 1598--1611 B. Craig Taverner Improved algorithm for accurate computation of molecular solid angles 1612--1623 Chuan-Bao Zhu and Ji-Min Yan Investigation of interaction in C$_{60}$ embedded complexes (X@C$_{60}$) (X = alkali or halogen) at a series of radial positions by Buckingham potential function . . . . . . . . . . . . . . . . 1624--1632 Jan Antosiewicz and James M. Briggs and Adrian H. Elcock and Michael K. Gilson and J. Andrew McCammon Computing ionization states of proteins with a detailed charge model . . . . . . 1633--1644 Daniel A. Jelski and Randall H. Haley and Joel M. Bowman New vibrational self-consistent field program for large molecules . . . . . . 1645--1652 J. A. Grant and M. A. Gallardo and B. T. Pickup A fast method of molecular shape comparison: a simple application of a Gaussian description of molecular shape 1653--1666 Hidetoshi Kono and Junta Doi A new method for side-chain conformation prediction using a Hopfield network and reproduced rotamers . . . . . . . . . . 1667--1683 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
A. S. Lemak and N. K. Balabaev Molecular dynamics simulation of a polymer chain in solution by collisional dynamics method . . . . . . . . . . . . 1685--1695 Stephen D. Williams and Warren Harper and Gleb Mamantov and Louis J. Tortorelli and George Shankle Ab initio MO study of selected aluminum and boron chlorides and fluorides: Comparison with $^{11}$B NMR spectra of a tetrachloroborate melt . . . . . . . . 1696--1711 Graham Campbell and Yuefan Deng and James Glimm and Yuan Wang and Qiqing Yu and Moisés Eisenberg and Arthur Grollman Analysis and prediction of hydrogen bonding in protein-DNA complexes using parallel processors . . . . . . . . . . 1712--1725 Krzysztof Kuczera One- and multidimensional conformational free energy simulations . . . . . . . . 1726--1749 R. E. Bradley and S. Windwer Loop-erased self-avoiding random walks in four and five dimensions . . . . . . 1750--1756 Tahmid I. Mizan and Phillip E. Savage and Robert M. Ziff Comparison of rigid and flexible simple point charge water models at supercritical conditions . . . . . . . . 1757--1770 Keith E. Laidig and Andrew Streitwieser Origins of relative acidity: First and second period hydrides . . . . . . . . . 1771--1781 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
A. H. Juffer and P. Argos and J. de Vlieg Adsorption of proteins onto charged surfaces: a Monte Carlo approach with explicit ions . . . . . . . . . . . . . 1783--1803 Attila Kovács and István Kolossváry and Gábor I. Csonka and István Hargittai Theoretical study of intramolecular hydrogen bonding and molecular geometry of 2-trifluoromethylphenol . . . . . . . 1804--1819 G. Wu and S. Jacobs and A. T. H. Lenstra and C. van Alsenoy and H. J. Geise 2,5-Dimethoxy-1,4-bis[2-(2,4-dimethoxyphenyl) ethenyl]benzene studied by quantum chemical calculations and single crystal X-ray diffraction 1820--1835 Irina V. Ionova and Emily A. Carter Error vector choice in direct inversion in the iterative subspace method . . . . 1836--1847 Guntram Rauhut Combined ab initio and density functional study of ring chain tautomerism in benzofurazan-1-oxide . . 1848--1856 Nathan G. Hunt and Fred E. Cohen Fast lookup tables for interatomic interactions . . . . . . . . . . . . . . 1857--1862 Anonymous Masthead . . . . . . . . . . . . . . . . fmi
Christian Kölle and Karl Jug Solvation effects in SINDO1: Application to organic molecules . . . . . . . . . . 1--8 Elso M. Cruz and Xabier Lopez and Martín Sarobe and Fernando P. Cossío and Jesus M. Ugalde G2 study of triplet [H$_4$, Si, P]$^+$ potential energy surface: Mechanism for reaction of P$^+$ ($^3$P) with silane 9--19 Wim Klopper Simple recipe for implementing computation of first-order relativistic corrections to electron correlation energies in framework of direct perturbation theory . . . . . . . . . . 20--27 Bernd Reindl and Timothy Clark and Paul von R. Schleyer Empirical force-field and ab initio calculations on delocalized open chain cations . . . . . . . . . . . . . . . . 28--44 Attila Bérces Geometry optimization of metal complexes using natural internal coordinates: Representation of skeletal degrees of freedom . . . . . . . . . . . . . . . . 45--55 Doyoung Lee and Chang Kon Kim and Bon-Su Lee and Ikchoon Lee and Byung Choon Lee A theoretical study on keto-enol tautomerization involving simple carbonyl derivatives . . . . . . . . . . 56--69 Thomas G. Metzger and David M. Ferguson and William A. Glauser A computational analysis of interaction energies in methane and neopentane dimer systems . . . . . . . . . . . . . . . . 70--79 Mariusz Milik and Andrzej Kolinski and Jeffrey Skolnick Algorithm for rapid reconstruction of protein backbone from alpha carbon coordinates . . . . . . . . . . . . . . 80--85 Richard G. A. Bone and Hugo O. Villar Exhaustive enumeration of molecular substructures . . . . . . . . . . . . . 86--107 Kenneth B. Wiberg and Joseph W. Ochterski Comparison of different ab initio theoretical models for calculating isodesmic reaction energies for small ring and related compounds . . . . . . . 108--114 Robert B. Hermann Modeling hydrophobic solvation of nonspherical systems: Comparison of use of molecular surface area with accessible surface area . . . . . . . . 115--125 Horst M. Sulzbach and George Vacek and Peter R. Schreiner and John Morrison Galbraith and Paul von R. Schleyer and Henry F. Schaefer III NMR chemical shielding surface of $N$-acetyl-N'-methylalaninamide: a density functional study . . . . . . . . 126--138 Christian Bartels and Peter Güntert and Martin Billeter and Kurt Wüthrich GARANT-a general algorithm for resonance assignment of multidimensional nuclear magnetic resonance spectra . . . . . . . 139--149
Alan J. McMahon and Paul M. King Optimization of Carbó molecular similarity index using gradient methods 151--158 Antonio M. Márquez and Jaime Oviedo and Javier Fernández Sanz and Michel Dupuis Parallel computation of second derivatives of RHF energy on distributed memory computers . . . . . . . . . . . . 159--168 D. M. F. Van Aalten and B. L. De Groot and J. B. C. Findlay and H. J. C. Berendsen and A. Amadei A comparison of techniques for calculating protein essential dynamics 169--181 Curt M. Breneman and Marlon Rhem QSPR analysis of HPLC column capacity factors for a set of high-energy materials using electronic van der Waals surface property descriptors computed by transferable atom equivalent method . . 182--197 Ulrike Salzner and Steven M. Bachrach and Debbie C. Mulhearn Ab initio investigation of the Diels--Alder reaction between 2 H-phosphole and phosphaethene: a model for phosphole dimerization . . . . . . . 198--210 Jörg-R. Hill Use of test particle calculations for the derivation of van der Waals parameters used in force fields . . . . 211--220 Joseph J. Pavelites and Jiali Gao and Paul A. Bash and Alexander D. Mackerell Jr. A molecular mechanics force field for NAD$^+$, NADH, and the pyrophosphate groups of nucleotides . . . . . . . . . 221--239 Hagai Meirovitch and Eva Meirovitch Efficiency of Monte Carlo minimization procedures and their use in analysis of NMR data obtained from flexible peptides 240--253 Willian R. Rocha and Wagner B. De Almeida Quantum-mechanical and molecular mechanics conformational analysis of 1,5-cyclooctadiene . . . . . . . . . . . 254--259 Isaac B. Bersuker Limitations of density functional theory in application to degenerate states . . 260--267 Robert E. Bruccoleri and Jiri Novotny and Malcolm E. Davis and Kim A. Sharp Finite difference Poisson--Boltzmann electrostatic calculations: Increased accuracy achieved by harmonic dielectric smoothing and charge antialiasing . . . 268--276 Cheuk-San Wang Efficient algorithm for conformational search of macrocyclic molecules . . . . 277--289 K. F. C. Yiu and K. Y. Tam and S. C. Tsang Crystal indexing method using a simulated annealing algorithm with particular applications in nanocrystal research . . . . . . . . . . . . . . . . 290--299
Matthias Krack and Andreas M. Köster and Karl Jug Approximate molecular electrostatic potentials from semiempirical wavefunctions . . . . . . . . . . . . . 301--312 M. L. Sanchez and M. A. Aguilar and F. J. Olivares del Valle Study of solvent effects by means of averaged solvent electrostatic potentials obtained from molecular dynamics data . . . . . . . . . . . . . 313--322 Zhiqiang Wang and Ruth Pachter Prediction of peptide conformation: the adaptive simulated annealing approach 323--329 Gabor I. Csonka and Krisztina Éliás and Imre G. Csizmadia Ab initio and density functional study of the conformational space of $^1$C$_4\alpha$-L-fucose . . . . . . . . 330--342 Laurent David and Martin J. Field Basis set approach to solution of Poisson equation for small molecules immersed in solvent . . . . . . . . . . 343--350 Dino R. Ferro and Paolo Pumilia and Massimo Ragazzi An improved force field for conformational analysis of sulfated polysaccharides . . . . . . . . . . . . 351--367 Konrad Hinsen and Beno\^\it Roux A potential function for computer simulation studies of proton transfer in acetylacetone . . . . . . . . . . . . . 368--380 Mario E. Fajardo and Jerry A. Boatz Monte Carlo simulations of Na atoms in dynamically disordered Ar systems: Solid, liquid, and critical-point fluid Ar . . . . . . . . . . . . . . . . . . . 381--392 Sergey Vyazovkin Evaluation of activation energy of thermally stimulated solid-state reactions under arbitrary variation of temperature . . . . . . . . . . . . . . 393--402 K. D. Gibson and H. A. Scheraga Energy minimization of rigid-geometry polypeptides with exactly closed disulfide loops . . . . . . . . . . . . 403--415 Sergei F. Vyboishchikov and Anibal Sierraalta and Gernot Frenking Topological analysis of electron density distribution taken from a pseudopotential calculation . . . . . . 416--429 Holger Dachsel and Hans Lischka and Ron Shepard and Jaroslaw Nieplocha and Robert J. Harrison A massively parallel multireference configuration interaction program: the parallel COLUMBUS program . . . . . . . 430--448
Volkhard Helms and Rebecca C. Wade Free energies of hydration from thermodynamic integration: Comparison of molecular mechanics force fields and evaluation of calculation accuracy . . . 449--462 Uwe Eichler and Christoph M. Kölmel and Joachim Sauer Combining ab initio techniques with analytical potential functions for structure predictions of large systems: Method and application to crystalline silica polymorphs . . . . . . . . . . . 463--477 Mark R. Wilson and Michael P. Allen and Mark A. Warren and Alain Sauron and William Smith Replicated data and domain decomposition molecular dynamics techniques for simulation of anisotropic potentials . . 478--488 Guntram Rauhut and Andrzej A. Jarzecki and Peter Pulay Density functional based vibrational study of conformational isomers: Molecular rearrangement of benzofuroxan 489--500 Kian-Tat Lim and Sharon Brunett and Mihail Iotov and Richard B. McClurg and Nagarajan Vaidehi and Siddharth Dasgupta and Stephen Taylor and William A. Goddard III Molecular dynamics for very large systems on massively parallel computers: the MPSim program . . . . . . . . . . . 501--521 L. Young and I. A. Topol and A. A. Rashin and S. K. Burt Building molecular charge distributions from fragments: Application to HIV-1 protease inhibitors . . . . . . . . . . 522--532 Bernd Reindl and Timothy Clark and Paul v. R. Schleyereeee Empirical force field and ab initio calculations on allyl cations . . . . . 533--551 Ajay C. Limaye Parallel MP2-energy evaluation: Simulated shared memory approach on distributed memory parallel machines . . 552--561 Stephen P. Greatbanks and Ian H. Hillier and Paul Sherwood Comparison of embedded cluster models to study zeolite catalysis: Proton transfer reactions in acidic chabazite . . . . . 562--568 Yury N. Vorobjev and Harold A. Scheraga A fast adaptive multigrid boundary element method for macromolecular electrostatic computations in a solvent 569--583 D. B. Chesnut and K. M. Davis Resonance revisited: a consideration of the calculation of cyclic conjugation energies . . . . . . . . . . . . . . . . 584--593 Aaron F. Stanton and Richard E. Bleil and Sabre Kais A new approach to global minimization 594--599
Jacek Styszy\'nski and Xiaoping Cao and Gulzari L. Malli and Lucas Visscher Relativistic all-electron Dirac--Fock--Breit calculations on xenon fluorides (XeF$_n$, $n = 1$, $2$, $4$, $6$) . . . . . . . . . . . . . . . . . . 601--608 László Nyulászi and Péter Várnai and Wolfgang Eisfeld and Manfred Regitz Regioselectivity in cycloaddition reaction between phosphaacetylene and diazomethane: an ab initio study . . . . 609--616 Gianfranco Pacchioni and Anna Maria Ferrari and Antonio M. Márquez and Francesc Illas Importance of Madelung potential in quantum chemical modeling of ionic surfaces . . . . . . . . . . . . . . . . 617--628 K. Pointet and A. Milliet and S. Hoyau and M. F. Renou-Gonnord Proton affinities of polybenzenoid aromatic hydrocarbons and those with five-membered rings . . . . . . . . . . 629--637 J. W. M. Nissink and M. L. Verdonk and J. Kroon and T. Mietzner and G. Klebe Superposition of molecules: Electron density fitting by application of Fourier transforms . . . . . . . . . . . 638--645 Petr Bou\vr and Jana Sopková and Lucie Bednárová and Petr Malo\un and Timothy A. Keiderling Transfer of molecular property tensors in Cartesian coordinates: a new algorithm for simulation of vibrational spectra . . . . . . . . . . . . . . . . 646--659 H. Dufner and S. M. Kast and J. Brickmann and M. Schlenkrich Ewald summation versus direct summation of shifted-force potentials for the calculation of electrostatic interactions in solids: a quantitative study . . . . . . . . . . . . . . . . . 660--676 Marco Nonella Effect of charge distribution on electrostatic chromophore--protein interactions in Bacteriorhodopsin . . . 677--693 Béla Paizs and Sándor Suhai Extension of SCF and DFT versions of chemical Hamiltonian approach to $N$ interacting subsystems and an algorithm for their efficient implementation . . . 694--701 Clifford E. Dykstra and Troy A. Van Voorhis Quantum Monte Carlo vibrational dynamics in a property-based interaction potential scheme for weakly bound clusters . . . . . . . . . . . . . . . . 702--711 Maria Cristina Andreazza Costa and Yuji Takahata Conformational analysis of synthetic neolignans active against leishmaniasis, using the molecular mechanics method (MM2) . . . . . . . . . . . . . . . . . 712--721
Amedeo Caflisch and Stefan Fischer and Martin Karplus Docking by Monte Carlo minimization with a solvation correction: Application to an FKBP-substrate complex . . . . . . . 723--743 Bernd Beck and Timothy Clark and Robert C. Glen VESPA: a new, fast approach to electrostatic potential-derived atomic charges from semiempirical methods . . . 744--756 Jos P. M. Lommerse and Sarah L. Price and Robin Taylor Hydrogen bonding of carbonyl, ether, and ester oxygen atoms with alkanol hydroxyl groups . . . . . . . . . . . . . . . . . 757--774 Andrew C. Scheiner and Jon Baker and Jan W. Andzelm Molecular energies and properties from density functional theory: Exploring basis set dependence of Kohn--Sham equation using several density functionals . . . . . . . . . . . . . . 775--795 Tap Ha Duong and Krystyna Zakrzewska Calculation and analysis of low frequency normal modes for DNA . . . . . 796--811 Mihaly Mezei Optimal position of solute for simulations . . . . . . . . . . . . . . 812--815 Krzysztof Wolinski and Robert Haacke and James F. Hinton and Peter Pulay Methods for parallel computation of SCF NMR chemical shifts by GIAO method: Efficient integral calculation, multi-Fock algorithm, and pseudodiagonalization . . . . . . . . . 816--825 Pere Constans and Lluís Amat and Ramon Carbó-Dorca Toward a global maximization of the molecular similarity function: Superposition of two molecules . . . . . 826--846
A. Liwo and S. O\ldziej and M. R. Pincus and R. J. Wawak and S. Rackovsky and H. A. Scheraga A united-residue force field for off-lattice protein-structure simulations. I. Functional forms and parameters of long-range side-chain interaction potentials from protein crystal data . . . . . . . . . . . . . . 849--873 A. Liwo and M. R. Pincus and R. J. Wawak and S. Rackovsky and S. O\ldziej and H. A. Scheraga A united-residue force field for off-lattice protein-structure simulations. II. Parameterization of short-range interactions and determination of weights of energy terms by Z-score optimization . . . . . . . . 874--887 Arnaud J. A. Soirat and Chung F. Wong and Roman Osman and Harel Weinstein Brownian dynamics simulations of the reactions of hydrated electrons with components of DNAs and a DNA double-helix . . . . . . . . . . . . . . 888--901 Randall J. Radmer and Peter A. Kollman Free energy calculation methods: a theoretical and empirical comparison of numerical errors and a new method qualitative estimates of free energy changes . . . . . . . . . . . . . . . . 902--919 Ulrich H. E. Hansmann and Yuko Okamoto Numerical comparisons of three recently proposed algorithms in the protein folding problem . . . . . . . . . . . . 920--933 Jordi Mestres and Douglas C. Rohrer and Gerald M. Maggiora MIMIC: a molecular-field matching program. Exploiting applicability of molecular similarity approaches . . . . 934--954 Dennis S. Marynick Accurate molecular electrostatic potentials based on modified PRDDO/M wave functions. I. Electrostatic potential derived atomic charges . . . . 955--969
Xiaoping Cao and Yan Wang Molecular symmetry and ab initio calculations: IV. Symmetry-matrix and symmetry-supermatrix in calculations of two-electron repulsion integrals . . . . 971--979 Robert Soliva and Modesto Orozco and F. Javier Luque Suitability of density functional methods for calculation of electrostatic properties . . . . . . . . . . . . . . . 980--991 Josep Maria Anglada and Josep Maria Bofill A reduced-restricted-quasi-Newton--Raphson method for locating and optimizing energy crossing points between two potential energy surfaces . . . . . . . 992--1003 Struan H. Robertson and Michael J. Pilling and Kevin E. Gates and Sean C. Smith Application of inverse iteration to 2-dimensional master equations . . . . . 1004--1010 J. Papadakis and G. S. Fanourgakis and S. C. Farantos and M. Founargiotakis Comparison of line search minimization algorithms for exploring topography of multidimensional potential energy surfaces: Mg$^+$Ar$_n$ case . . . . . . 1011--1022 Rainer Glaser and Grace Shiahuy Chen and Hansjörg Grützmacher Effects of electron correlation and spin projection on rotational barriers of trithiocarbenium ion [C(SH)$_3$]$^+$ and Radical Dication [C(SH)$_3$]$^{cdot,2+}$ 1023--1035 Bouke P. Van Eijck and Jan Kroon Fast clustering of equivalent structures in crystal structure prediction . . . . 1036--1042 Delphine Flatters and Krystyna Zakrzewska and Richard Lavery Internal coordinate modeling of DNA: Force field comparisons . . . . . . . . 1043--1055 Marc C. Nicklaus Conformational energies calculated by the molecular mechanics program CHARMm 1056--1060 Jiali Gao Energy components of aqueous solution: Insight from hybrid QM/MM simulations using a polarizable solvent model . . . 1061--1071 Joseph D. Augspurger and Harold A. Scheraga An assessment of the accuracy of the RRIGS hydration potential: Comparison to solutions of the Poisson--Boltzmann equation . . . . . . . . . . . . . . . . 1072--1078 Jon Baker Constrained optimization in delocalized internal coordinates . . . . . . . . . . 1079--1095 W. J. Pullan Energy minimization of mixed argon--xenon microclusters using a genetic algorithm . . . . . . . . . . . 1096--1111
A. Goede and R. Preissner and C. Frömmel Voronoi cell: New method for allocation of space among atoms: Elimination of avoidable errors in calculation of atomic volume and density . . . . . . . 1113--1123 Leticia González and Otilia Mó and Manuel Yáñez High-level ab initio versus DFT calculations on (H$_2$O$_2$)$_2$ and H$_2$O$_2$--H$_2$O complexes as prototypes of multiple hydrogen bond systems . . . . . . . . . . . . . . . . 1124--1135 Pavel Hobza and Martin Kabelá\vc and Ji\vrí \vSponer and Petr Mejzlík and Ji\vrí Vondrá\vsek Performance of empirical potentials (AMBER, CFF95, CVFF, CHARMM, OPLS, POLTEV), semiempirical quantum chemical methods (AM1, MNDO/M, PM3), and ab initio Hartree--Fock method for interaction of DNA bases: Comparison with nonempirical beyond Hartree--Fock results . . . . . . . . . . . . . . . . 1136--1150 Mark A. Murcko and B. Govinda Rao and Roberto Gomperts Conformational analysis of HIV-1 protease inhibitors: 2. Thioproline P$_1$' residue in the potent inhibitor KNI-272 . . . . . . . . . . . . . . . . 1151--1166 Shijun Zheng and Lingpeng Meng and Xinhua Cai and Zhenfeng Xu and Xiaoyuan Fu Topological studies on IRC paths of X + H$_2$ $\rightarrow$ XH + H reactions . . 1167--1174 Todd J. A. Ewing and Irwin D. Kuntz Critical evaluation of search algorithms for automated molecular docking and database screening . . . . . . . . . . . 1175--1189 Sanja Seku\vsak and Aleksandar Sablji\'c Reactivity of haloethanes with hydroxyl radicals: Effects of basis set and correlation energy on reaction energetics . . . . . . . . . . . . . . . 1190--1199 Alexander V. Mitin and Gerhard Hirsch and Robert J. Buenker Accurate atomic Gaussian basis functions for second-row atoms: Small split-valence 3-21SP and 4-22SP basis sets . . . . . . . . . . . . . . . . . . 1200--1210 R. Griffith and J. B. Bremner and S. J. Titmuss Molecular mechanics study of transannular amine--ketone (N $\rightarrow$ C\doublebondO) interaction in medium-sized heterocycles . . . . . . 1211--1221 Jooyoung Lee and Harold A. Scheraga and S. Rackovsky New optimization method for conformational energy calculations on polypeptides: Conformational space annealing . . . . . . . . . . . . . . . 1222--1232 J. A. Niesse and Howard R. Mayne Global optimization of atomic and molecular clusters using the space-fixed modified genetic algorithm method . . . 1233--1244 Nidhi Arora and B. Jayaram Strength of hydrogen bonds in $\alpha$ helices . . . . . . . . . . . . . . . . 1245--1252
David Ayma and Jean Pierre Campillo and Michel Rérat and Mauro Caus\`a Ab initio calculation of dynamic polarizability and dielectric constant of carbon and silicon cubic crystals . . 1253--1263 Jörg Weiser and Max C. Holthausen and Lutz Fitjer HUNTER: a conformational search program for acyclic to polycyclic molecules with special emphasis on stereochemistry . . 1264--1281 Zoran Konkoli and Dieter Cremer and Elfi Kraka Diabatic ordering of vibrational normal modes in reaction valley studies . . . . 1282--1294 Gianpaolo Bravi and Emanuela Gancia and Andrea Zaliani and Monica Pegna SONHICA (Simple optimized non-HIerarchical Cluster Analysis): a new tool for analysis of molecular conformations . . . . . . . . . . . . . 1295--1311 R. Berger and M. Klessinger Algorithms for exact counting of energy levels of spectroscopic transitions at different temperatures . . . . . . . . . 1312--1319 Masahiro Kinoshita and Yuko Okamoto and Fumio Hirata Calculation of hydration free energy for a solute with many atomic sites using the RISM theory: a robust and efficient algorithm . . . . . . . . . . . . . . . 1320--1326 Xuefeng Zhou Book Review: \booktitleReviews in Computational Chemistry, Volume 7 . . . 1327--1327 Ernest R. Davidson Book Review: \booktitleModern Electronic Structure Theory, Edited by David R. Yarkony, World Scientific Publishing Co. Pte. Ltd., 1995, Part I, 768 pp., \$152 cloth\slash \$89 paperback, Part II, 784 pp., \$152 cloth\slash \$89 paperback 1328--1328
Laura Gagliardi and Gian Luigi Bendazzoli and Stefano Evangelisti Direct-list algorithm for configuration interaction calculations . . . . . . . . 1329--1343 Martin F. Parretti and Romano T. Kroemer and Jeffrey H. Rothman and W. Graham Richards Alignment of molecules by the Monte Carlo optimization of molecular similarity indices . . . . . . . . . . . 1344--1353 Alexey K. Mazur Quasi-Hamiltonian equations of motion for internal coordinate molecular dynamics of polymers . . . . . . . . . . 1354--1364 Zhuo-Min Chen and Tahir Ça\ugin and William A. Goddard III Fast Ewald sums for general van der Waals potentials . . . . . . . . . . . . 1365--1370 Guyan Liang and Xiannong Chen and J. A. Dustman and Anita H. Lewin and J. Phillip Bowen Ab initio calculations and molecular mechanics (MM3) force field development for ammonium and protonated aliphatic amines . . . . . . . . . . . . . . . . . 1371--1391 Fillmore Freeman and Choonsun Lee and Warren J. Hehre and Henry N. Po Ab initio molecular orbital calculations of 3,4-dihydro-1,2-dioxin, 3,6-dihydro-1,2-dioxin, 4 H-1,3-dioxin (1,3-diox-4-ene), and 2,3-dihydro-1,4-dioxin (1,4-dioxene) . . 1392--1406 Geraldo Magela e Silva and Paulo Hora Acioli and Antonio Carlos Pedroza Estimating correlation energy of diatomic molecules and atoms with neural networks . . . . . . . . . . . . . . . . 1407--1414 Kerstin Möhle and Martin Gußmann and Hans-Jörg Hofmann Structural and energetic relations between $\beta$ turns . . . . . . . . . 1415--1430
Miroslav Kohout and Andreas Savin Influence of core--valence separation of electron localization function . . . . . 1431--1439 Shun Zhou Wan and Cun Xin Wang and Zhe Xin Xiang and Yun Yu Shi Stochastic dynamics simulation of alanine dipeptide: Including solvation interaction determined by boundary element method . . . . . . . . . . . . . 1440--1449 Christian Bartels and Martin Karplus Multidimensional adaptive umbrella sampling: Applications to main chain and side chain peptide conformations . . . . 1450--1462 Berk Hess and Henk Bekker and Herman J. C. Berendsen and Johannes G. E. M. Fraaije LINCS: a linear constraint solver for molecular simulations . . . . . . . . . 1463--1472 Frank Eckert and Peter Pulay and Hans-Joachim Werner Ab initio geometry optimization for large molecules . . . . . . . . . . . . 1473--1483 Christian D. Berweger and Wilfred F. van Gunsteren and Florian Müller-Plathe Finite element interpolation for combined classical/quantum mechanical molecular dynamics simulations . . . . . 1484--1495 Peter L. Cummins and Jill E. Gready Coupled semiempirical molecular orbital and molecular mechanics model (QM/MM) for organic molecules in aqueous solution . . . . . . . . . . . . . . . . 1496--1512 Robert E. Tuzun and Donald W. Noid and Bobby G. Sumpter Treatment of multibody interactions in molecular simulations of systems with general bond networks . . . . . . . . . 1513--1522 Soo Gyeong Cho and One Kwon Rim and Gyoosoon Park Rotational barriers of disilane, hexafluorodisilane, and hexamethyldisilane: ab initio, density functional, and molecular mechanics (MM3) studies . . . . . . . . . . . . . 1523--1533 Gábor I. Csonka and Nam Anh Nguyen and István Kolossváry Simple tests for density functional methods . . . . . . . . . . . . . . . . 1534--1545 Yuto Komeiji and Masami Uebayasi and Ryo Takata and Akihiro Shimizu and Keiji Itsukashi and Makoto Taiji Fast and accurate molecular dynamics simulation of a protein using a special-purpose computer . . . . . . . . 1546--1563
F. E. Jorge and E. V. R. De Castro and A. B. F. Da Silva A universal Gaussian basis set for atoms cerium through lawrencium generated with the generator coordinate Hartree--Fock method . . . . . . . . . . . . . . . . . 1565--1569 Christian M. Cortis and Richard A. Friesner An automatic three-dimensional finite element mesh generation system for the Poisson--Boltzmann equation . . . . . . 1570--1590 Christian M. Cortis and Richard A. Friesner Numerical solution of the Poisson--Boltzmann equation using tetrahedral finite-element meshes . . . 1591--1608 D. T. Nguyen and A. C. Scheiner and J. W. Andzelm and S. Sirois and D. R. Salahub and A. T. Hagler A density functional study of the glycine molecule: Comparison with post-Hartree--Fock calculations and experiment . . . . . . . . . . . . . . . 1609--1631 Richard W. Dixon and Peter A. Kollman Advancing beyond the atom-centered model in additive and nonadditive molecular mechanics . . . . . . . . . . . . . . . 1632--1646 Emilio Martínez-Núñez and Saulo A. Vázquez and Ricardo A. Mosquera Conformational analysis of model compounds of vitamin D by theoretical calculations . . . . . . . . . . . . . . 1647--1655 Yoshifumi Fukunishi and Makoto Suzuki Potential of mean force calculation of solute molecules in water by a modified solvent-accessible surface method . . . 1656--1663 Sean A. C. McDowell Relation of the force constant of a bond to the electric field at a nucleus . . . 1664--1667 Adam Liwo and Dariusz Dyl and Danuta Jeziorek and Ma\lgorzata Nowacka and Tadeusz Ossowski and Wies\law Wo\'znicki MCSCF study of singlet oxygen addition to ethenol --- a model of photooxidation reactions of unsaturated and aromatic compounds bearing hydroxy groups . . . . 1668--1681 Dennis S. Marynick Accurate molecular electrostatic potentials based on modified PRDDO/M wave functions: II. Electrostatic potentials inside the molecular van der Waals envelope . . . . . . . . . . . . . 1682--1693
Christoph Maerker and Paul von R. Schleyer and Klaus R. Liedl and T.-K. Ha and Martin Quack and Martin A. Suhm A critical analysis of electronic density functionals for structural, energetic, dynamic, and magnetic properties of hydrogen fluoride clusters 1695--1719 Vincenzo Barone and Gabriella Capecchi and Yvon Brunel and Marie-Louise Dheu Andriés and Robert Subra Development and validation of force-field parameters for molecular simulations of peptides and proteins containing open-shell residues . . . . . 1720--1728 M. Eichinger and H. Grubmüller and Helmut Heller and Paul Tavan FAMUSAMM: an algorithm for rapid evaluation of electrostatic interactions in molecular dynamics simulations . . . 1729--1749 Jason L. Smart and Tami J. Marrone and J. Andrew McCammon Conformational sampling with Poisson--Boltzmann forces and a stochastic dynamics/Monte Carlo method: Application to alanine dipeptide . . . . 1750--1759 Omar A. Sharafeddin and Konrad Hinsen and Tucker Carrington Jr. and Beno\^\it Roux Mixing quantum-classical molecular dynamics methods applied to intramolecular proton transfer in acetylacetone . . . . . . . . . . . . . 1760--1772 In-Suk Han and Chang Kon Kim and Chan Kyung Kim and Bon-Su Lee and Ikchoon Lee Ab initio studies of three-membered ring formation through intramolecular nucleophilic substitution . . . . . . . 1773--1784 Thomas C. Bishop and Robert D. Skeel and Klaus Schulten Difficulties with multiple time stepping and fast multipole algorithm in molecular dynamics . . . . . . . . . . . 1785--1791 Ruslan M. Minyaev and Wolfgang Quapp and Govindan Subramanian and Paul von R. Schleyer and Yirong Mo Internal conrotation and disrotation in H$_2$BCH$_2$BH$_2$ and diborylmethane 1,3 H exchange . . . . . . . . . . . . . 1792--1803 Robert E. Tuzun and Donald W. Noid and Bobby G. Sumpter Efficient treatment of out-of-plane bend and improper torsion interactions in MM2, MM3, and MM4 molecular mechanics calculations . . . . . . . . . . . . . . 1804--1811 Shingo Makino and Irwin D. Kuntz Automated flexible ligand docking method and its application for database search 1812--1825
Norman L. Allinger and Yi Fan Molecular mechanics studies (MM4) of sulfides and mercaptans . . . . . . . . 1827--1847 Piero Procacci and Tom A. Darden and Emanuele Paci and Massimo Marchi ORAC: a molecular dynamics program to simulate complex molecular systems with realistic electrostatic interactions . . 1848--1862 Daniel T. Mainz and Jasna J. Klicic and Richard A. Friesner and Jean-Marc Langlois and Jason K. Perry Extension of the PS-GVB electronic structure code to transition metal complexes . . . . . . . . . . . . . . . 1863--1874 Aliette Cossé-Barbi and Mourad Raji Discrete pattern recognition by fitting onto a continuous function . . . . . . . 1875--1892 Oren M. Becker Representing protein and peptide structures with parallel-coordinates . . 1893--1902 Patrick Jemmer Symbolic algebra in mathematical analysis of chemical-kinetic systems . . 1903--1917 Marcelo Giordan and Rogério Custodio Basis set modeling for molecular calculations using effective core potential . . . . . . . . . . . . . . . 1918--1929 H. Bekker Unification of box shapes in molecular simulations . . . . . . . . . . . . . . 1930--1942 U. Salzner and J. B. Lagowski and P. G. Pickup and R. A. Poirier Design of low band gap polymers employing density functional theory --- hybrid functionals ameliorate band gap problem . . . . . . . . . . . . . . . . 1943--1953
Wolfgang Damm and Antonio Frontera and Julian Tirado-Rives and William L. Jorgensen OPLS all-atom force field for carbohydrates . . . . . . . . . . . . . 1955--1970 A. Y. Jin and F. Y. Leung and D. F. Weaver Development of a novel genetic algorithm search method (GAP1.0) for exploring peptide conformational space . . . . . . 1971--1984 Christoph Van Wüllen Molecular structure and binding energies of monosubstituted hexacarbonyls of chromium, molybdenum, and tungsten: Relativistic density functional study 1985--1992 Carlo Adamo and Maurizio Cossi and Vincenzo Barone Catalytic and bulk solvent effects on proton transfer: Formamide as a case study . . . . . . . . . . . . . . . . . 1993--2000 H. A. Gabb and C. Prévost and G. Bertucat and C. H. Robert and R. Lavery Collective-variable Monte Carlo simulation of DNA . . . . . . . . . . . 2001--2011 A. Pullman and G. Berthier and R. Savinelli Theoretical study of binding of tetramethylammonium ion with aromatics 2012--2022 Lluís Amat and Ramon Carbó-Dorca Quantum similarity measures under atomic shell approximation: First order density fitting using elementary Jacobi rotations . . . . . . . . . . . . . . . 2023--2039 Jaros\law Pillardy and Lucjan Piela Smoothing techniques of global optimization: Distance scaling method in searches for most stable Lennard-Jones atomic clusters . . . . . . . . . . . . 2040--2049 J. Grunenberg and R. Herges Calculation of molecular vibrations: Selective scaling factors for semiempirical force constants . . . . . 2050--2059 I. Nobeli and S. L. Price and J. P. M. Lommerse and R. Taylor Hydrogen bonding properties of oxygen and nitrogen acceptors in aromatic heterocycles . . . . . . . . . . . . . . 2060--2074 Randall C. Boehm and Joel D. Kress and Richard L. Martin and P. Jeffrey Hay A theoretical study of bond energies in model Si--H--Cl molecules using density functional approaches for representing Si surface chemistry . . . . . . . . . . 2075--2085 Junichi Higo and Nobuyuki Nakajima and Hiroki Shirai and Akinori Kidera and Haruki Nakamura Two-component multicanonical Monte Carlo method for effective conformation sampling . . . . . . . . . . . . . . . . 2086--2092 Anonymous Additions and corrections: ``Force field calculations (MM3) on glyoxal, quinones, and related compounds,'' N. L. Allinger and Y. Fan, J. Comput. Chem., \bf 15:251 (1994) . . . . . . . . . . . . . . . . . 2093--2093
R. S. Payne and R. J. Roberts and R. C. Rowe and R. Docherty Generation of crystal structures of acetic acid and its halogenated analogs 1--20 Joannis Apostolakis and Andreas Plückthun and Amedeo Caflisch Docking small ligands in flexible binding sites . . . . . . . . . . . . . 21--37 György G. Ferenczy and Gábor I. Csonka and Gábor Náray-Szabó and János G. Ángyán Quantum mechanical/molecular mechanical self-consistent Madelung potential method for treatment of polar molecular crystals . . . . . . . . . . . . . . . . 38--50 Ulf Norinder and Peter Svensson Descriptors for amino acids using MolSurf parametrization . . . . . . . . 51--59 Zhenqin Li and Keith E. Laidig and Valerie Daggett Conformational search using a molecular dynamics--minimization procedure: Applications to clusters of Coulombic charges, Lennard-Jones particles, and waters . . . . . . . . . . . . . . . . . 60--70 Daniel Oberlin and Harold A. Scheraga B-spline method for energy minimization in grid-based molecular mechanics calculations . . . . . . . . . . . . . . 71--85 Jane J. Ou and Shaw H. Chen Molecular dynamics simulation of organic glass formers: I. ortho-terphenyl and 1,3,5-tri-$\alpha$-naphthyl benzene . . 86--93 Alexander V. Mitin Calculation of rovibrational energy levels of diatomic molecules by Dunham method with potential obtained from ab initio calculations . . . . . . . . . . 94--101 Timothy R. Forester and William Smith SHAKE, rattle, and roll: Efficient constraint algorithms for linked rigid bodies . . . . . . . . . . . . . . . . . 102--111
Michael Bühl and Fred A. Hamprecht Theoretical investigations of NMR chemical shifts and reactivities of oxovanadium(v) compounds . . . . . . . . 113--122 Heinz Oberhammer Molecular structures and conformations: Experiment and theory . . . . . . . . . 123--128 Martin \vCuma and Clifton Thompson and Steve Scheiner Effect of nonproximate atomic substitution on excited state intramolecular proton transfer . . . . . 129--138 R. C. Haddon Organometallic chemistry of fullerenes: $\eta^2$- and $\eta^5$-($\pi$) complexes 139--143 Brian J. Teppen and Ching-Hsing Yu and David M. Miller and Lothar Schäfer Molecular dynamics simulations of sorption of organic compounds at the clay mineral/aqueous solution interface 144--153 E. Goldstein and M. Haught and Y. Tang Evaluation of density functional theory in the bond rupture of octane . . . . . 154--167 James J. P. Stewart Symmetry groups for unit cells in solids 168--180 C. G. Giribet and M. C. Ruiz de Azúa and S. B. Gómez and E. L. Botek and R. H. Contreras and W. Adcock and E. W. Della and A. R. Krstic and I. J. Lochert C$_3$\bondM$_\alpha$ bond contribution to polarizability tensor and $^3$J(C$_1$M$_\alpha$) NMR coupling constant in 1-X-3-M-bicyclo[1.1.1]pentanes . . . . . 181--188 Jerome M. Schulman and Raymond L. Disch Bowl-shaped hydrocarbons related to C$_{60}$ . . . . . . . . . . . . . . . . 189--194 Asit K. Chandra and Minh Tho Nguyen Approach to regiochemistry using local softness in 1,3-dipolar cycloadditions 195--202 Feng Long Gu and Xiaomei Yang and Au-Chin Tang and Haijun Jiao and Paul von R. Schleyer Structure and stability of B$^+_{13}$ clusters . . . . . . . . . . . . . . . . 203--214 Keiji Iwao and Kazuhisa Sakakibara and Minoru Hirota Evaluation of reactivity for nitroxide radical trapping by correlation analysis using steric substituent parameter ($\Omega_S$) . . . . . . . . . . . . . . 215--221 John E. Baldwin Thermal isomerizations of vinylcyclopropanes to cyclopentenes . . 222--231 Shigeru Nagase and Kaoru Kobayashi and Takeshi Akasaka Recent advances in the structural determination of endohedral metallofullerenes . . . . . . . . . . . 232--239 Ruifeng Liu and Xuefeng Zhou and Lei Zhai Theoretical investigation of unimolecular decomposition channels of furan4 . . . . . . . . . . . . . . . . . 240--249 Nathan J. Harris and Tomohiko Ohwada and Koop Lammertsma Protonation enthalpies in fluorosulfonic acid using ab initio self-consistent reaction field theory . . . . . . . . . 250--257 J. Philip Bowen A portrait of the chemist: the Lou Allinger story . . . . . . . . . . . . . vii--ix Paul von R. Schleyer Editor's preface . . . . . . . . . . . . v--v
A. Liwo and R. Ka\'zmierkiewicz and C. Czaplewski and M. Groth and S. O\ldziej and R. J. Wawak and S. Rackovsky and M. R. Pincus and H. A. Scheraga United-residue force field for off-lattice protein-structure simulations: III. Origin of backbone hydrogen-bonding cooperativity in united-residue potentials . . . . . . . 259--276 Haruhiko Fukaya and Taizo Ono and Takashi Abe Theoretical study of reaction of trifluoromethyl radical with hydroxyl and hydrogen radicals . . . . . . . . . 277--289 Tzonka Mineva and Nino Russo and Emilia Sicilia Solvation effects on reaction profiles by the polarizable continuum model coupled with the Gaussian density functional method . . . . . . . . . . . 290--299 Patrick Jemmer and Peter J. Knowles Symbolic algebra in functional derivative potential calculations . . . 300--307 Attila Kovács and Gábor I. Csonka and György M. Keser\Hu Comparison of ab initio and density functional methods for vibrational analysis of TeCl$_4$ . . . . . . . . . . 308--318 Robert Fraczkiewicz and Werner Braun Exact and efficient analytical calculation of the accessible surface areas and their gradients for macromolecules . . . . . . . . . . . . . 319--333 Daxu Yin and Alexander D. MacKerell Jr. Combined ab initio /empirical approach for optimization of Lennard-Jones parameters . . . . . . . . . . . . . . . 334--348 Josep Maria Anglada and Josep Maria Bofill How good is a Broyden--Fletcher--Goldfarb--Shanno-like update Hessian formula to locate transition structures? Specific reformulation of Broyden--Fletcher--Goldfarb--Shanno for optimizing saddle points . . . . . . . . 349--362 Timothy Astley and Gordon G. Birch and Michael G. B. Drew and P. Mark Rodger and Gareth R. H. Wilden Effect of available volumes on radial distribution functions . . . . . . . . . 363--367 Josep Maria Bofill and Hugo Bono and Jaime Rubio Analysis of the convergence of the general coupling operator method for one-configuration-type wave functions 368--376
Emma Sigfridsson and Ulf Ryde Comparison of methods for deriving atomic charges from the electrostatic potential and moments . . . . . . . . . 377--395 Dario Duca and Péter Baranyai and Tamás Vidóczy Monte--Carlo model for the hydrogenation of alkenes on metal catalyst . . . . . . 396--403 Vincenzo Barone and Maurizio Cossi and Jacopo Tomasi Geometry optimization of molecular structures in solution by the polarizable continuum model . . . . . . 404--417 Carlo Adamo and Vincenzo Barone Implementation and validation of the Lacks--Gordon exchange functional in conventional density functional and adiabatic connection methods . . . . . . 418--429 J. R. Maple and M.-J. Hwang and K. J. Jalkanen and T. P. Stockfisch and A. T. Hagler Derivation of class II force fields: V. Quantum force field for amides, peptides, and related compounds . . . . 430--458 Wijnand T. M. Mooij and Bouke P. van Eijck and Sarah L. Price and Paul Verwer and Jan Kroon Crystal structure predictions for acetic acid . . . . . . . . . . . . . . . . . . 459--474
Julia C. Tai and Norman L. Allinger Effect of inclusion of electron correlation in MM3 studies of cyclic conjugated compounds . . . . . . . . . . 475--487 L. F. Pacios and P. C. Gómez Radial behavior of gradient expansion approximation to atomic Fukui function and shell structure of atoms . . . . . . 488--503 Cory C. Pye and Raymond A. Poirier Graphical approach for defining natural internal coordinates . . . . . . . . . . 504--511 Johan E. Bol and Christian Buning and Peter Comba and Jan Reedijk and Marc Ströhle Molecular mechanics modeling of organic backbone of metal-free and coordinated ligands . . . . . . . . . . . . . . . . 512--523 Willian R. Rocha and Josefredo R. Pliego Jr. and Stella M. Resende and Hélio F. Dos Santos and Marcos A. De Oliveira and Wagner B. De Almeida Ab initio conformational analysis of cyclooctane molecule . . . . . . . . . . 524--534 Xavier Daura and Alan E. Mark and Wilfred F. Van Gunsteren Parametrization of aliphatic CH$_n$ united atoms of GROMOS96 force field . . 535--547 Michael J. Dudek and K. Ramnarayan and Jay W. Ponder Protein structure prediction using a combination of sequence homology and global energy minimization: II. Energy functions . . . . . . . . . . . . . . . 548--573
Béla Paizs and Sándor Suhai Comparative study of BSSE correction methods at DFT and MP2 levels of theory 575--584 Ahmed M. El-Nahas and Essam Hammam and El-Zeiny M. Ebeid Quantum chemical studies on structures and spectra of 2,5-distyrylpyrazine (DSP) laser dye . . . . . . . . . . . . 585--592 E. D. Glendening and F. Weinhold Natural resonance theory: I. General formalism . . . . . . . . . . . . . . . 593--609 E. D. Glendening and F. Weinhold Natural resonance theory: II. Natural bond order and valency . . . . . . . . . 610--627 E. D. Glendening and J. K. Badenhoop and F. Weinhold Natural resonance theory: III. Chemical applications . . . . . . . . . . . . . . 628--646 M. A. Moret and P. G. Pascutti and P. M. Bisch and K. C. Mundim Stochastic molecular optimization using generalized simulated annealing . . . . 647--657 Elda Rossi and Gian Luigi Bendazzoli and Stefano Evangelisti Full configuration interaction algorithm on a massively parallel architecture: Direct-list implementation . . . . . . . 658--672 James R. Rabinowitz and Stephen B. Little and Eric M. Gifford Interactions between chlorinated dioxins and a positively charged molecular probe: New molecular interaction potential . . . . . . . . . . . . . . . 673--684
D. Roccatano and R. Bizzarri and G. Chillemi and N. Sanna and A. Di Nola Development of a parallel molecular dynamics code on SIMD computers: Algorithm for use of pair list criterion 685--694 M. L. M. Beckers and L. M. C. Buydens Multivariate analysis of a data matrix containing A-DNA and B-DNA dinucleoside monophosphate steps: Multidimensional Ramachandran plots for nucleic acids . . 695--715 Marcus Gastreich and Christel M. Marian Ab initio prediction of $^{15}$N-NMR chemical shift in $\alpha$-boron nitride based on an analysis of connectivities 716--725 Stephen C. Harvey and Robert K.-Z. Tan and Thomas E. Cheatham III The flying ice cube: Velocity rescaling in molecular dynamics leads to violation of energy equipartition . . . . . . . . 726--740 Andrew V. Zeigarnik and Raúl E. Valdés-Pérez Systematic prediction of the products and intermediates of isotopic labeling in reaction pathway studies . . . . . . 741--753 Kim Palmo and Samuel Krimm Electrostatic model for infrared intensities in a spectroscopically determined molecular mechanics force field . . . . . . . . . . . . . . . . . 754--768 M. Rami Reddy and Mark D. Erion and Atul Agarwal and Vellarkad N. Viswanadhan and D. Quentin McDonald and W. Clark Still Solvation free energies calculated using the GB/SA model: Sensitivity of results on charge sets, protocols, and force fields . . . . . . . . . . . . . . . . . 769--780 Greg M. Pearl and M. C. Zerner and Anders Broo and John McKelvey Method of calculating band shape for molecular electronic spectra . . . . . . 781--796 Jörg Weiser and Armin A. Weiser and Peter S. Shenkin and W. Clark Still Neighbor-list reduction: Optimization for computation of molecular van der Waals and solvent-accessible surface areas . . . . . . . . . . . . . . . . . 797--808
J. Raúl Alvarez-Idaboy and Irina Díaz-Acosta and Annik Vivier-Bunge Energetics of mechanism of OH-propene reaction at low pressures in inert atmosphere . . . . . . . . . . . . . . . 811--819 Alexandre Varnek and Severine Helissen and Georges Wipff and André Collet van der Waals host--guest complexes: Can one predict complexation selectivity of neutral guests by a cryptophane? MD-FEP studies in gas phase and chloroform solution . . . . . . . . . . . . . . . . 820--832 Maurizio Cossi and Benedetta Mennucci and Jesus Pitarch and Jacopo Tomasi Correction of cavity-induced errors in polarization charges of continuum solvation models . . . . . . . . . . . . 833--846 Elena Fraschini and Anthony J. Stone H\dottedbondH model potential for exchange--repulsion energy of methane dimer . . . . . . . . . . . . . . . . . 847--857 F. E. Jorge and P. R. Librelon and A. Canal Neto Adapted Gaussian basis sets for atoms Cs to Lr based on the generator coordinate Hartree--Fock method . . . . . . . . . . 858--865 F. Javier Luque and Modesto Orozco Polarization effects in generalized molecular interaction potential: New Hamiltonian for reactivity studies and mixed QM/MM calculations . . . . . . . . 866--881 Erh-Hao Chen and Tse-Chiang Chang Photoelectron spectra, Penning ionization electron spectra, and character of canonical molecular orbitals . . . . . . . . . . . . . . . . 882--892 Sebastian Tomac and Astrid Gräslund Multi-multigrid solution of modified Poisson--Boltzmann equation for arbitrarily shaped molecules . . . . . . 893--901 Thomas R. Cundari and Akihiko Yoshikawa Computational study of methane activation by mercury(II) complexes . . 902--911 Saturnino Calvo-Losada and José Joaquín Quirante and Dimas Suárez and Tomás Luis Sordo Rearrangement of azirine intermediates to nitriles: Theoretical study of cleavage of 3,4-dihydro-1a H-azirine[2,3-c]pyrrol-2-one to cyanoketene--formaldimine complex . . . 912--922 Kazuhiro Ishida Rapid algorithm for computing the electron repulsion integral over higher order Gaussian-type orbitals: Accompanying coordinate expansion method 923--934 Katrin Gaedt and Hans-Dieter Höltje Consistent valence force-field parameterization of bond lengths and angles with quantum chemical ab initio methods applied to some heterocyclic dopamine D$_3$-receptor agonists . . . . 935--946 Vidar R. Jensen and Knut J. Bòrve An investigation of the quantum chemical description of the ethylenic double bond in reactions: II. Insertion of ethylene into a titanium--carbon bond . . . . . . 947--960 Luis Carballeira and Ignacio Pérez-Juste Influence of calculation level and effect of methylation on axial/equatorial equilibria in piperidines . . . . . . . . . . . . . . 961--976 Peter L. Cummins and Jill E. Gready Molecular dynamics and free energy perturbation study of hydride-ion transfer step in dihydrofolate reductase using combined quantum and molecular mechanical model . . . . . . . . . . . . 977--988
Nino Russo and Marirosa Toscano and André Grand and Franck Jolibois Protonation of thymine, cytosine, adenine, and guanine DNA nucleic acid bases: Theoretical investigation into the framework of density functional theory . . . . . . . . . . . . . . . . . 989--1000 Jenn-Huei Lii and Norman L. Allinger Directional hydrogen bonding in the MM3 force field: II . . . . . . . . . . . . 1001--1016 David Chasman and Michael D. Beachy and Limin Wang and Richard A. Friesner Parallel pseudospectral electronic structure: I. Hartree--Fock calculations 1017--1029 Michael D. Beachy and David Chasman and Richard A. Friesner and Robert B. Murphy Parallel pseudospectral electronic structure: II. Localized Mòller--Plesset calculations . . . . . . . . . . . . . . 1030--1038 Wendell T. Duncan and Robert L. Bell and Thanh N. Truong TheRate: Program for ab initio direct dynamics calculations of thermal and vibrational-state-selected rate constants . . . . . . . . . . . . . . . 1039--1052 C. P. Sosa and J. Ochterski and J. Carpenter and M. J. Frisch Ab initio quantum chemistry on the Cray T3E massively parallel supercomputer: II 1053--1063 Fillmore Freeman and Choonsun Lee and Henry N. Po and Warren J. Hehre Ab initio molecular orbital study of energies and conformers of 3,4-dihydro-1,2-dithiin, 3,6-dihydro-1,2-dithiin, 4 H-1,3-dithiin, and 2,3-dihydro-1,4-dithiin . . . . . . . . 1064--1071 M. Alcamí and O. Mó and M. Yáñez G2 ab initio calculations on three-membered rings: Role of hydrogen atoms . . . . . . . . . . . . . . . . . 1072--1086 Wolfgang Quapp and Michael Hirsch and Olaf Imig and Dietmar Heidrich Searching for saddle points of potential energy surfaces by following a reduced gradient . . . . . . . . . . . . . . . . 1087--1100 Wei Pan and Tai-Sung Lee and Weitao Yang Parallel implementation of divide-and-conquer semiempirical quantum chemistry calculations . . . . . . . . . 1101--1109 Jörg Weiser and Armin A. Weiser and Peter S. Shenkin and W. Clark Still Erratum: Neighbor-list reduction: Optimization for computation of molecular van der Waals and solvent-accessible surface areas . . . . 1110--1110
Susan E. Barrows and Joey W. Storer and Christopher J. Cramer and Alfred D. French and Donald G. Truhlar Factors controlling relative stability of anomers and hydroxymethyl conformers of glucopyranose . . . . . . . . . . . . 1111--1129 Rainer Glaser and Grace Shiahuy Chen Asymmetrization effects on structures and populations of the ground state of dipolar donor--acceptor-substituted molecular organic NLO materials . . . . 1130--1140 Vladimir S. Mastryukov and Svein Samdal Asymmetry in methyl group of ethane during internal rotation: ab initio study . . . . . . . . . . . . . . . . . 1141--1145 Per-Ola Norrby and Tommy Liljefors Automated molecular mechanics parameterization with simultaneous utilization of experimental and quantum mechanical data . . . . . . . . . . . . 1146--1166 Joseph J. Gajewski and Kevin E. Gilbert and Thomas W. Kreek General molecular mechanics approach to transition metal complexes . . . . . . . 1167--1178 William L. Jorgensen and Corky Jenson Temperature dependence of TIP3P, SPC, and TIP4P water from NPT Monte Carlo simulations: Seeking temperatures of maximum density . . . . . . . . . . . . 1179--1186 Jon Baker and Peter Pulay Predicting the vibrational spectra of some simple fluorocarbons by direct scaling of primitive valence force constants . . . . . . . . . . . . . . . 1187--1204
M. E. Alikhani and B. Silvi DFT-predicted structural, vibrational, and bonding properties of XSiO and X$_2$SiO (X = F, Cl, or Br) molecules 1205--1214 Abigail J. Dobbyn and Peter J. Knowles and Robert J. Harrison Parallel internally contracted multireference configuration interaction 1215--1228 Alfredo Di Nola and Axel T. Brünger Free energy calculations in globular proteins: Methods to reduce errors . . . 1229--1240 Guntram Rauhut and Peter Pulay and Hans-Joachim Werner Integral transformation with low-order scaling for large local second-order Mòller--Plesset calculations . . . . . . 1241--1254 Oren M. Becker Principal coordinate maps of molecular potential energy surfaces . . . . . . . 1255--1267 Shek Ling Chan and Enrico O. Purisima Molecular surface generation using marching tetrahedra . . . . . . . . . . 1268--1277 Paul H. Axelsen and Daohui Li Improved convergence in dual-topology free energy calculations through use of harmonic restraints . . . . . . . . . . 1278--1283 J. Fernández Rico and R. López and A. Aguado and I. Ema and G. Ramírez Reference program for molecular calculations with Slater-type orbitals 1284--1293 Hanoch Senderowitz and W. Clark Still Sampling potential energy surface of glycyl glycine peptide: Comparison of Metropolis Monte Carlo and stochastic dynamics . . . . . . . . . . . . . . . . 1294--1299 Claudine C. Tazartes and Christopher R. Anderson and Emily A. Carter Automated selection of optimal Gaussian fits to arbitrary functions in electronic structure theory . . . . . . 1300--1314 Parviz Hassanzedeh and Karl K. Irikura Inexpensive vibrational anharmonicities from estimated derivatives: Diatomic molecules . . . . . . . . . . . . . . . 1315--1324
Simon Shun-Wang Leung and Andrew Streitwieser Theoretical study of structure of alkali metal cyanates and isocyanates and their related ion pair S$_N$2 reactions . . . 1325--1336 Paul G. Mezey Averaged electron densities for averaged conformations . . . . . . . . . . . . . 1337--1344 Ganesh A. Kumar and Yongping Pan and C. Jay Smallwood and Michael A. McAllister Low-barrier hydrogen bonds: ab initio and DFT investigation . . . . . . . . . 1345--1352 Anwar G. Baboul and H. Bernhard Schlegel and Mikhail N. Glukhovtsev and Robert D. Bach Computational study on nature of transition structure for oxygen transfer from dioxirane and carbonyloxide . . . . 1353--1369 Joong-Youn Shim and J. Phillip Bowen Molecular mechanics studies of acyl halides: I. Molecular structures and conformational analysis . . . . . . . . 1370--1386 Joong-Youn Shim and J. Phillip Bowen Molecular mechanics studies of acyl halides: II. Vibrational spectra . . . . 1387--1401 Bernd Reindl and Paul von R. Schleyer Molecular mechanics and ab initio calculations on cyclopentadienyl cations 1402--1420 Jan Labanowski and Lawrence Schmitz and Kuo-Hsiang Chen and Norman L. Allinger Heats of formation of organic molecules calculated by density functional theory: II. Alkanes . . . . . . . . . . . . . . 1421--1430
Michael R. Salazar and Richard L. Bell General methodology in two dimensions for classical simulation of reactive and nonreactive events on ab initio potential energy surfaces . . . . . . . 1431--1444 Ioan Andricioaei and John E. Straub Global optimization using bad derivatives: Derivative-free method for molecular energy minimization . . . . . 1445--1455 Dennis S. Marynick Accurate molecular electrostatic potentials based on modified PRDDO/M wave functions: III. Extension of the PESP method for calculation of electrostatic potential-derived atomic charges to compounds containing Li$^+$, Na$^+$, Mg$^{2+}$, K$^+$, Ca$^{2+}$, Zn$^{2+}$, and I . . . . . . . . . . . . 1456--1469 Christian T. Klein and Bernd Mayer and Gottfried Köhler and Peter Wolschann Systematic stepsize variation: Efficient method for searching conformational space of polypeptides . . . . . . . . . 1470--1481 Brian J. Smith and Nathan E. Hall Atomic radii: Incorporation of solvation effects . . . . . . . . . . . . . . . . 1482--1493 Enrico O. Purisima Fast summation boundary element method for calculating solvation free energies of macromolecules . . . . . . . . . . . 1494--1504 D. Benjamin Gordon and Stephen L. Mayo Radical performance enhancements for combinatorial optimization algorithms based on the dead-end elimination theorem . . . . . . . . . . . . . . . . 1505--1514 Oreola Donini and Donald F. Weaver Development of modified force field for cation--amino acid interactions: ab initio-derived empirical correction terms with comments on cation--$\pi$ interactions . . . . . . . . . . . . . . 1515--1525 Young-Kyu Han and Cheolbeom Bae and Yoon Sup Lee and Sang Yeon Lee Spin-orbit effects on structures of closed-shell polyatomic molecules containing heavy atoms calculated by two-component Hartree--Fock method . . . 1526--1533 Helmut Grubmüller and Paul Tavan Multiple time step algorithms for molecular dynamics simulations of proteins: How good are they? . . . . . . 1534--1552 Kenneth G. Dyall Review of Relativistic Effects in Chemistry Part A: Theory and Techniques 1553--1554
Xiong-Wu Wu and Shen-Shu Sung Constraint dynamics algorithm for simulation of semiflexible macromolecules . . . . . . . . . . . . . 1555--1566 N. J. Smeyers and F. J. Melendez and Y. G. Smeyers Exploring potential energy hypersurfaces for triple symmetric inversion in 3-azabicyclo[3.3.1]nonan-9-one and its $N$-methyl derivative . . . . . . . . . 1567--1574 Lluís Amat and Ramon Carbó-Dorca and Robert Ponec Molecular quantum similarity measures as an alternative to $\log P$ values in QSAR studies . . . . . . . . . . . . . . 1575--1583 Andreas B. J. Parusel and Rudolf Schamschule and Gottfried Köhler Theoretical description of solvent effects on fluorescence spectra of bulky charge transfer compound DMA-DMPP . . . 1584--1595 Robert Franke and Christoph Van Wüllen First-order relativistic corrections to MP2 energy from standard gradient codes: Comparison with results from density functional theory . . . . . . . . . . . 1596--1603 Roland H. Hertwig and Wolfram Koch and Brian F. Yates Economical treatments of relativistic effects and electron correlation in WH$_6$ . . . . . . . . . . . . . . . . . 1604--1611 Michal Vieth and Jonathan D. Hirst and Andrzej Kolinski and Charles L. Brooks III Assessing energy functions for flexible docking . . . . . . . . . . . . . . . . 1612--1622 Michal Vieth and Jonathan D. Hirst and Brian N. Dominy and Heidi Daigler and Charles L. Brooks III Assessing search strategies for flexible docking . . . . . . . . . . . . . . . . 1623--1631 Tom J. Evans and Thanh N. Truong Optimizing efficiency of perturbative Monte Carlo method . . . . . . . . . . . 1632--1638 Garrett M. Morris and David S. Goodsell and Robert S. Halliday and Ruth Huey and William E. Hart and Richard K. Belew and Arthur J. Olson Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function . . . . . . 1639--1662 Anthony K. Grafton and Ralph A. Wheeler Vibrational projection analysis: New tool for quantitatively comparing vibrational normal modes of similar molecules . . . . . . . . . . . . . . . 1663--1674
G.-S. Li and B. Maigret and D. Rinaldi and M. F. Ruiz-López Influence of environment on proton-transfer mechanisms in model triads from theoretical calculations . . 1675--1688 Alexander Fischer and Frank Cordes and Christof Schütte Hybrid Monte Carlo with adaptive temperature in mixed-canonical ensemble: Efficient conformational analysis of RNA 1689--1697 S. G. Raptis and S. M. Nasiou and I. N. Demetropoulos and M. G. Papadopoulos Static and frequency dependent polarizabilities and hyperpolarizabilities of H$_2$S$_n$ . . 1698--1715 Shugo Nakamura and Mitsunori Ikeguchi and Kentaro Shimizu Parallel algorithm for efficient calculation of second derivatives of conformational energy function in internal coordinates . . . . . . . . . . 1716--1723 Masahiro Kinoshita and Yuko Okamoto and Fumio Hirata Calculation of solvation free energy using RISM theory for peptide in salt solution . . . . . . . . . . . . . . . . 1724--1735 Hanoch Senderowitz and W. Clark Still MC(JBW): Simple but smart Monte Carlo algorithm for free energy simulations of multiconformational molecules . . . . . 1736--1745 Malte Von Arnim and Reinhart Ahlrichs Performance of parallel TURBOMOLE for density functional calculations . . . . 1746--1757 Christian S. Pomelli and Jacopo Tomasi DefPol: New procedure to build molecular surfaces and its use in continuum solvation methods . . . . . . . . . . . 1758--1776 Emili Besalú and Josep Maria Bofill Calculation of clustered eigenvalues of large matrices using variance minimization method . . . . . . . . . . 1777--1785 Anatoly M. Belostotskii and Alfred Hassner Meshed tert-butyl gears on a quasirigid backbone . . . . . . . . . . . . . . . . 1786--1794
Eric C. Magnuson and Julianto Pranata Theoretical study of 1,3-dipolar cycloadditions of nitrone and fulminic acid with substituted ethylenes . . . . 1795--1804 Wensheng Cai and Maosen Zhang and Bernard Maigret New approach for representation of molecular surface . . . . . . . . . . . 1805--1815 Jose M. Hermida-Ramón and Ola Engkvist and Gunnar Karlström Theoretical study of intermolecular potential energy surface for HCl dimer: Example of nonspherical atom--atom exchange repulsion interaction . . . . . 1816--1825 E. Del Río and R. López and M. I. Menéndez and T. L. Sordo and M. F. Ruiz-López Theoretical study of ester enolate--imine condensation route to $\beta$-lactams . . . . . . . . . . . . 1826--1833 Shingo Makino and Irwin D. Kuntz ELECT++: Faster conformational search method for docking flexible molecules using molecular similarity . . . . . . . 1834--1852 Marcelo Giordan Pyrrolizidine alkaloids necine bases: II. Conformational analysis of free bases . . . . . . . . . . . . . . . . . 1853--1861 Kui Zhang and Alice Chung-Phillips Conformers of gaseous protonated glycine 1862--1876 Alexander V. Mitin Use of symmetric rank-one Hessian update in molecular geometry optimization . . . 1877--1886 F. Moscardó and Angel J. Pérez-Jiménez Self-consistent field calculations using two-body density functionals for correlation energy component: I. Atomic systems . . . . . . . . . . . . . . . . 1887--1898 F. Moscardó and Angel J. Pérez-Jiménez and J. Américo Cjuno Self-consistent field calculations using two-body density functionals for correlation energy component: II. Small molecules . . . . . . . . . . . . . . . 1899--1908
Walter Kohn Thoughts about density functional theory in 1998 . . . . . . . . . . . . . . . . 1--1 Shubin Liu and Robert G. Parr Consequences for exchange energy density functional of exponentially decaying nature of atomic electron densities . . 2--11 M. Lein and J. F. Dobson and E. K. U. Gross Toward the description of van der Waals interactions within density functional theory . . . . . . . . . . . . . . . . . 12--22 H. Eschrig and V. D. P. Servedio Relativistic density functional approach to open shells . . . . . . . . . . . . . 23--30 E. Engel and R. 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 and P. Jeffrey Hay and Richard L. Martin Density functional calculations on actinide compounds: Survey of recent progress and application to [UO$_2$X$_4$]$^{2-}$ (X = F, Cl, OH) and AnF$_6$ (An = U, Np, Pu) . . . . . . . . 70--90 Michael Bühl and Martin Kaupp and Olga L. Malkina and Vladimir G. Malkin The DFT route to NMR chemical shifts . . 91--105 Nicholas C. Handy and 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--S$_N$2 mechanistic spectrum and other concepts 114--128 H. Chermette Chemical reactivity indexes in density functional theory . . . . . . . . . . . 129--154 E. V. Ludeña and V. Karasiev and R. López-Boada and E. Valderrama and J. Maldonado Local-scaling transformation version of density functional theory: Application to atoms and diatomic molecules . . . . 155--183 Gernot Frenking Foreword . . . . . . . . . . . . . . . . v--vi
Shinjiro Toyoda and Hiroh Miyagawa and Kunihiro Kitamura and Takashi Amisaki and Eiri Hashimoto and Hitoshi Ikeda and Akihiro Kusumi and Nobuaki Miyakawa Development of MD Engine: High-speed accelerator with parallel processor design for molecular dynamics simulations . . . . . . . . . . . . . . 185--199 María Eugenia Costas and Rodolfo Acevedo-Chávez Density functional study of neutral allopurinol tautomeric forms . . . . . . 200--206 Kevin S. Raymond and Ralph A. Wheeler Compatibility of correlation-consistent basis sets with a hybrid Hartree--Fock/density functional method 207--216 Jörg Weiser and Peter S. Shenkin and W. Clark Still Approximate atomic surfaces from linear combinations of pairwise overlaps (LCPO) 217--230 George P. Ford and P. S. Herman and Jon W. Thompson Syn and anti aryl nitrenium ions . . . . 231--243 Jean-Yves Trosset and 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 and Pavol Ba\unacký and Stanislav Biskupi\vc and Roman Bo\vca and Peter Pelikán and Michal Svr\vcek and Anton Zajac Approaching bulk limit for three-dimensional solids via the cyclic cluster approximation: Semiempirical INDO study . . . . . . . . . . . . . . . 253--261 R. S. Payne and R. C. Rowe and R. J. Roberts and M. H. Charlton and R. Docherty Potential polymorphs of aspirin . . . . 262--273 G. J. Halász and Á. Vibók and I. Mayer Comparison of basis set superposition error corrected perturbation theories for calculating intermolecular interaction energies . . . . . . . . . . 274--283 Ethan Will Taylor Book Review: \booktitleRational Molecular Design in Drug Research, Alfred Benzon Symposium No. 42. Edited by T. Liljefors, F. S. Jòrgensen, and P. Krogsgaard-Larsen, Munksgaard, Copenhagen, 1998, 399 pp. ISBN 87-16-12049-3 . . . . . . . . . . . . . 284--286
Martin Zacharias and 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 and Christian Kölle and Frank Neumann Treatment of reactions in solutions with isodensity surfaces . . . . . . . . . . 301--304 Taijin Zhou and Yirong Mo General method for symmetry orbitals and tensors in electronic structure calculations . . . . . . . . . . . . . . 305--321 François Wagner and Thomas Simonson Implicit solvent models: Combining an analytical formulation of continuum electrostatics with simple models of the hydrophobic effect . . . . . . . . . . . 322--335 Martin Stahl and Daniel Bur and Gisbert Schneider Mapping of proteinase active sites by projection of surface-derived correlation vectors . . . . . . . . . . 336--347 Zhong-Hui Duan and Louis N. Howard Loop entanglement of semicrystalline polyethylene in amorphous region: Diamond lattice approach . . . . . . . . 348--353 C. Baysal and H. Meirovitch and I. M. Navon Performance of efficient minimization algorithms as applied to models of peptides and proteins . . . . . . . . . 354--364 P. N. V. Pavankumar and P. Seetharamulu and S. Yao and Jeffrey D. Saxe and Dasharatha G. Reddy and Frederick H. Hausheer Comprehensive ab initio quantum mechanical and molecular orbital (MO) analysis of cisplatin: Structure, bonding, charge density, and vibrational frequencies . . . . . . . . . . . . . . 365--382
David W. Ritchie and Graham J. L. Kemp Fast computation, rotation, and comparison of low resolution spherical harmonic molecular surfaces . . . . . . 383--395 Harold Baumann and Rainer E. Martin and 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 and Harold A. Scheraga \sc Prodock: Software package for protein modeling and docking . . . . . . 412--427 Brian J. Smith Solvation parameters for amino acids . . 428--442 Hajime Takashima and Kunihiro Kitamura and Kazutoshi Tanabe and Umpei Nagashima Is large-scale ab initio Hartree--Fock calculation chemically accurate? Toward improved calculation of biological molecule properties . . . . . . . . . . 443--454 J. Hunger and G. Huttner Optimization and analysis of force field parameters by combination of genetic algorithms and neural networks . . . . . 455--471
J. Ridard and B. Lévy Effective atomic charges in alanine dipeptide . . . . . . . . . . . . . . . 473--482 Richard H. Henchman and Jonathan W. Essex Generation of OPLS-like charges from molecular electrostatic potential using restraints . . . . . . . . . . . . . . . 483--498 Richard H. Henchman and Jonathan W. Essex Free energies of hydration using restrained electrostatic potential derived charges via free energy perturbations and linear response . . . 499--510 R. Santamaria and E. Charro and A. Zacarías and M. Castro Vibrational spectra of nucleic acid bases and their Watson--Crick pair complexes . . . . . . . . . . . . . . . 511--530 Alexander M. Smondyrev and Max L. Berkowitz United atom force field for phospholipid membranes: Constant pressure molecular dynamics simulation of dipalmitoylphosphatidicholine/water system . . . . . . . . . . . . . . . . . 531--545 Ying-Chieh Sun and Shu-Fen Yang and I-Lung Hwang and 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
Bernd Ahlswede and Karl Jug Consistent modifications of SINDO1: I. Approximations and parameters . . . . . 563--571 Bernd Ahlswede and Karl Jug Consistent modifications of SINDO1: II. Applications to first- and second-row elements . . . . . . . . . . . . . . . . 572--578 Donald E. Williams and Aron Abraha Site charge models for molecular electrostatic potentials of cycloalkanes and tetrahedrane . . . . . . . . . . . . 579--585 Jörg Weiser and Peter S. Shenkin and W. Clark Still Fast, approximate algorithm for detection of solvent-inaccessible atoms 586--596 Xiang-Yuan Li and Fu-Cheng He Electron transfer between biphenyl and biphenyl anion radicals: Reorganization energies and electron transfer matrix elements . . . . . . . . . . . . . . . . 597--603 J. C. Cesco and C. C. Denner and G. O. Giubergia and A. E. Rosso and J. E. Pérez and F. S. Ortiz and O. E. Taurian and R. 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 and Qi-Zong Qin Molecular dynamics simulation of O$_3$ photolysis by ultraviolet light in solid argon . . . . . . . . . . . . . . . . . 623--628 Andrey A. Bliznyuk and Alistair P. Rendell Faster gradients for semiempirical methods . . . . . . . . . . . . . . . . 629--635 J. L. Klepeis and C. A. Floudas Comparative study of global minimum energy conformations of hydrated peptides . . . . . . . . . . . . . . . . 636--654
A. Hu and P. Otto and J. Ladik Relativistic Gaussian functions for atoms by fitting numerical results with adaptive nonlinear least-square algorithm . . . . . . . . . . . . . . . 655--664 Carles Colominas and F. Javier Luque and Modesto Orozco Monte Carlo--MST: New strategy for representation of solvent configurational space in solution . . . 665--678 H. Reis and M. G. Papadopoulos Nonlinear optical properties of the rhombic B$_4$-cluster . . . . . . . . . 679--687 Jörg Weiser and Peter S. Shenkin and W. Clark Still Optimization of Gaussian surface calculations and extension to solvent-accessible surface areas . . . . 688--703 Peter J. Winn and György G. Ferenczy and 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$^\alpha$ 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
Xin Chen and Alexander Tropsha Generalized linear response method: Application to hydration free energy calculations . . . . . . . . . . . . . . 749--759 Robert Ponec and Anthony J. Duben Electron pairing and chemical bonds: Bonding in hypervalent molecules from analysis of Fermi holes . . . . . . . . 760--771 Yair Salomon and David Avnir Continuous symmetry measures: Finding the closest C$_2$-symmetric object or closest reflection-symmetric object using unit quaternions . . . . . . . . . 772--780 Peter Comba and Norbert Okon and Rainer Remenyi Computation of cavity shapes, sizes, and plasticities . . . . . . . . . . . . . . 781--785 K. Anton Feenstra and Berk Hess and Herman J. C. Berendsen Improving efficiency of large time-scale molecular dynamics simulations of hydrogen-rich systems . . . . . . . . . 786--798 Bouke P. van Eijck and Jan Kroon U pack program package for crystal structure prediction: Force fields and crystal structure generation for small carbohydrate molecules . . . . . . . . . 799--812 Brett A. Harris and Stephen C. Harvey Program for analyzing knots represented by polygonal paths . . . . . . . . . . . 813--818 William J. Wedemeyer and Harold A. Scheraga Exact analytical loop closure in proteins using polynomial equations . . 819--844 Isidoro García-Cruz and M. E. Ruiz-Santoyo and J. Raúl Alvarez-Idaboy and Annik Vivier-Bunge Ab-initio study of initial atmospheric oxidation reactions of C$_3$ and C$_4$ alkanes . . . . . . . . . . . . . . . . 845--856 Vladimír Luke\vs and Viliam Laurinc and Stanislav Biskupi\vc Perturbative formulation of dispersion contributions to interaction energy of van der Waals systems of ``closed-shell--open-shell'' type . . . 857--866 T. H. Reijmers and R. Wehrens and L. M. C. Buydens Quality criteria of genetic algorithms for construction of phylogenetic trees 867--876 Srikanta Sen and Lennart Nilsson Some practical aspects of free energy calculations from molecular dynamics simulation . . . . . . . . . . . . . . . 877--885 Marc F. Lensink and Janez Mavri and Herman J. C. Berendsen Simulation of slow reaction with quantum character: Neutral hydrolysis of carboxylic ester . . . . . . . . . . . . 886--895
Isabelle Fourré and Bernard Silvi and Patrick Chaquin and 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 and 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 and Jeremy P. Dombroski and Peter M. W. Gill Efficient calculation of short-range Coulomb energies . . . . . . . . . . . . 921--927 Andriy Kovalenko and Seiichiro Ten-no and 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 and F. Javier Luque and 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 and Paul D. Kirchhoff and Heather A. Carlson and J. Andrew McCammon Molecular dynamics of cryptophane and its complexes with tetramethylammonium and neopentane using a continuum solvent model . . . . . . . . . . . . . . . . . 956--970 Pedro G. Pascutti and Kleber C. Mundim and Amando S. Ito and Paulo M. Bisch Polarization effects on peptide conformations at water--membrane interface by molecular dynamics simulation . . . . . . . . . . . . . . . 971--982 Andrey A. Bliznyuk and Jill E. Gready Simple method for locating possible ligand binding sites on protein surfaces 983--988
Yuxiang Bu and Haitao Sun and Hongbo Niu Electron transfer reactivity of O$_2$ +O 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 and Heiko Schmitz and Oliver Biermann and Florian Müller-Plathe Automatic parameterization of force fields for liquids by simplex optimization . . . . . . . . . . . . . . 1009--1017 M. Rami Reddy and 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 and 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 and M. F. Ruiz-López and X. Assfeld and F. Bohr Structure of isolated and solvated peroxyl radicals . . . . . . . . . . . . 1039--1048 Izydor Apostol and Wojciech Szpankowski Indexing and mapping of proteins using a modified nonlinear Sammon projection . . 1049--1059 Paulo Hora Acioli and Geraldo Magela e Silva Investigating charge transport in molecular switches with neural networks 1060--1066 Sang-Ho Lee and Kim Palmo and 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 A. Torre and L. Lain and R. Bochicchio and R. Ponec Nature of nonclassical bonds in Closo-Boranes: Nonlinear population analysis approach . . . . . . . . . . . 1085--1090
Velin Z. Spassov and 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 and Emili Besalú and Josep Maria Bofill and Ramon Crehuet Prediction of approximate transition states by Bell--Evans--Polanyi principle: I . . . . . . . . . . . . . . 1112--1129 Josep Maria Anglada and Emili Besalú and Josep Maria Bofill and Ramon Crehuet Prediction of approximate transition states by Bell--Evans--Polanyi principle: II. Gas phase unimolecular decomposition of methyldioxirane . . . . 1130--1137 Masao Masamura and Shigeru Ikuta Ab initio molecular orbital study on structures and energetics of CH$_3$O$^-$(H$_2$O)$_n$ and CH$_3$S$^-$(H$_2$O)$_n$ in gas phase . . 1138--1144 Norge Cruz Hernández and Javier Fdez. Sanz Ab initio compact group model potentials for describing environment effects in cluster calculations . . . . . . . . . . 1145--1152 S. W. Chiu and M. M. Clark and Eric Jakobsson and Shankar Subramaniam and 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 and Roman A. Laskowski and Alexander Alex and Janet M. Thornton \sc Bleep --- potential of mean force describing protein--ligand interactions: I. Generating potential . . . . . . . . 1165--1176 John B. O. Mitchell and Roman A. Laskowski and Alexander Alex and Mark J. Forster and Janet M. Thornton \sc Bleep --- potential of mean force describing protein--ligand interactions: II. Calculation of binding energies and comparison with experimental data . . . 1177--1185 Nadia Rega and Maurizio Cossi and Vincenzo Barone Improving performance of polarizable continuum model for study of large molecules in solution . . . . . . . . . 1186--1198
Werner Kutzelnigg Relativistic corrections to magnetic properties . . . . . . . . . . . . . . . 1199--1219 S. Patchkovskii and W. Thiel NMR chemical shifts in MNDO approximation: Parameters and results for H, C, N, and O . . . . . . . . . . . 1220--1245 H. Ebert and M. Battocletti and M. Deng and H. Freyer and 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 and Thomas Enevoldsen and Trond Saue and Hans Jòrgen Aagard Jensen and 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: SiH$_3$ radical . . . . . . . . 1274--1280 Kurt V. Mikkelsen and Kenneth Ruud and Trygve Helgaker Solvent effects on the NMR parameters of H$_2$S 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 $^{13}$C-NMR shielding values . . . . . . . . . . . . . . . . . 1299--1303 Martin Kaupp and Olga L. Malkina and Vladimir G. Malkin The role of $\pi$-type nonbonding orbitals for spin--orbit induced NMR chemical shifts: DFT study of $^{13}$C and $^{19}$F shifts in the series CF$_3$IF$_n$ ($n = 0$, $2$, $4$, $6$) 1304--1313 Juha Vaara and Kenneth Ruud and Olav Vahtras Correlated response calculations of the spin--orbit interaction contribution to nuclear spin--spin couplings . . . . . . 1314--1327 Martin Kaupp and Vladimir G. Malkin Foreword . . . . . . . . . . . . . . . . v--vii
A. Y. Jin and F. Y. Leung and 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 F. Gilardoni and J. Weber and A. Hauser and C. Daul A comparison of ground- and excited-state properties of [Ru(bz)$_2$]$^{2+}$ and bis($\eta^6$-benzene)ruthenium(II) $p$-toluenesulfonate using the density functional theory . . . . . . . . . . . 1343--1353 J. L. Klepeis and C. A. Floudas and D. Morikis and J. D. Lambris Predicting peptide structures using NMR data and deterministic global optimization . . . . . . . . . . . . . . 1354--1370 Anita H. Lewin and Jennifer B. Sorensen and John A. Dustman and J. Phillip Bowen Computational methods for conformational analysis of unsymmetrical 1,3-diamines: 3-aminotropanes . . . . . . . . . . . . 1371--1378 Gilles Tiraboschi and Bernard-Pierre Roques and Nohad Gresh Joint quantum chemical and polarizable molecular mechanics investigation of formate complexes with penta- and hexahydrated Zn$^{2+}$: Comparison between energetics of model bidentate, monodentate, and through-water Zn$^{2+}$ binding modes and evaluation of nonadditivity effects . . . . . . . . . 1379--1390 Eliseo Ruiz and Joan Cano and Santiago Alvarez and Pere Alemany Broken symmetry approach to calculation of exchange coupling constants for homobinuclear and heterobinuclear transition metal complexes . . . . . . . 1391--1400 Jesús Pitarch and Juan-Luis Pascual-Ahuir and Estanislao Silla and Iñaki Tuñón and Manuel F. Ruiz-López Modeling $\beta$-lactam interactions in aqueous solution through combined quantum mechanics--molecular mechanics methods . . . . . . . . . . . . . . . . 1401--1411 Santiago Melchor Ferrer and Jose Molina Molina Theoretical calculations on C$_{30}$H$_{12}$ bowl-shaped hydrocarbons: NMR shielding constants, stability, and aromaticity . . . . . . . 1412--1421 Marta Forés and Ludwik Adamowicz A CASSCF-CASPT2 study of the excited-state intramolecular proton transfer reaction in 1-amino-3-propenal using different active spaces . . . . . 1422--1431 R. López and E. Del Río and M. I. Menéndez and T. L. Sordo Ab initio study of the reaction of CHO$^+$ with H$_2$O and NH$_3$ . . . . . 1432--1443 Ana M. Graña and Ricardo A. Mosquera Atomic and bond properties in functionalized esters and amides . . . . 1444--1454
Thomas Huber and Andrew E. Torda Protein sequence threading, the alignment problem, and a two-step strategy . . . . . . . . . . . . . . . . 1455--1467 Dean M. Philipp and Richard A. Friesner Mixed ab initio QM/MM modeling using frozen orbitals and tests with alanine dipeptide and tetrapeptide . . . . . . . 1468--1494 Bruce L. Bush and Christopher I. Bayly and Thomas A. Halgren Consensus bond-charge increments fitted to electrostatic potential or field of many compounds: Application to MMFF94 training set . . . . . . . . . . . . . . 1495--1516 Rosa Llusar and Armando Beltrán and Juan Andrés and Stéphane Noury and Bernard Silvi Topological analysis of electron density in depleted homopolar chemical bonds . . 1517--1526 K. W. Foreman and A. T. Phillips and J. B. Rosen and K. A. Dill Comparing search strategies for finding global optima on energy landscapes . . . 1527--1532 Marco Scarsi and Amedeo Caflisch Comment on the validation of continuum electrostatics models . . . . . . . . . 1533--1536 H. L. Kennedy and Y. Zhao Use of STOs in Hartree--Fock calculations: Error analysis and variance-minimized pseudospectral method 1537--1548 Jessica Bartol and Peter Comba and Michael Melter and Marc Zimmer Conformational searching of transition metal compounds . . . . . . . . . . . . 1549--1558 P. Stampfuss and W. Wenzel and H. Keiter The parallel implementation of configuration-selecting multireference configuration interaction method . . . . 1559--1570 D. Genest Correlated motions analysis from molecular dynamics trajectories: Statistical accuracy on the determination of canonical correlation coefficients . . . . . . . . . . . . . . 1571--1576 Gordon M. Crippen VRI: 3D QSAR at variable resolution . . 1577--1585 James E. Boggs Guidelines for presentation of methodological choices in the publication of computational results: Ab initio electronic structure calculations 1587--1590 Douglas J. Raber and Wayne C. Guida Guidelines for publication of research results from force-field calculations 1591--1592
Jenn-Huei Lii and Buyong Ma and Norman L. Allinger Importance of selecting proper basis set in quantum mechanical studies of potential energy surfaces of carbohydrates . . . . . . . . . . . . . 1593--1603 Heiko Schäfer and Wilfred F. Van Gunsteren and Alan E. Mark Estimating relative free energies from a single ensemble: Hydration free energies 1604--1617 Robert W. Harrison Integrating quantum and molecular mechanics . . . . . . . . . . . . . . . 1618--1633 Jeffrey W. Godden and Florence L. Stahura and Jürgen Bajorath Statistical analysis of computational docking of large compound data bases to distinct protein binding sites . . . . . 1634--1643 Serge Crouzy and Jerôme Baudry and Jeremy C. Smith and Beno\^\it Roux Efficient calculation of two-dimensional adiabatic and free energy maps: Application to the isomerization of the C13 C14 and C15 N16 bonds in the retinal of bacteriorhodopsin . . . . . . . . . . 1644--1658 Canan Baysal and Hagai Meirovitch Efficiency of simulated annealing for peptides with increasing geometrical restrictions . . . . . . . . . . . . . . 1659--1670 István Kolossváry and Wayne C. Guida Low-mode conformational search elucidated: Application to C$_{39}$H$_{80}$ and flexible docking of 9-deazaguanine inhibitors into PNP . . . 1671--1684
Laura Masgrau and \`Angels González-Lafont and José M. Lluch Effect of a complex formation on the calculated low-pressure rate constant of a bimolecular gas-phase reaction governed by tunneling . . . . . . . . . 1685--1692 Christian Silvio Pomelli and Jacopo Tomasi and Maurizio Cossi and Vincenzo Barone Effective generation of molecular cavities in polarizable continuum model by DefPol procedure . . . . . . . . . . 1693--1701 Ming-Jing Hwang and Pei-Ying Chu and Jye-Chan Chen and Ito Chao Conformational analysis of three pyrophosphate model species: Diphosphate, methyl diphosphate, and triphosphate . . . . . . . . . . . . . . 1702--1715 R. G. Della Valle and L. Halonen and E. Venuti Molecular anharmonicity: a computer-aided treatment . . . . . . . . 1716--1730 Thomas L. Beck Multigrid high-order mesh refinement techniques for composite grid electrostatics calculations . . . . . . 1731--1739 David J. Diller and Christophe L. M. J. Verlinde A critical evaluation of several global optimization algorithms for the purpose of molecular docking . . . . . . . . . . 1740--1751 Bernd Hartke Global cluster geometry optimization by a phenotype algorithm with Niches: Location of elusive minima, and low-order scaling with cluster size . . 1752--1759 Wilhelm Huisinga and Christoph Best and Rainer Roitzsch and Christof Schütte and Frank Cordes From simulation data to conformational ensembles: Structure and dynamics-based methods . . . . . . . . . . . . . . . . 1760--1774
Timothy R. Forester and William Smith Erratum: SHAKE, rattle, and roll: Efficient constraint algorithms for linked rigid bodies . . . . . . . . . . 157--157
Anonymous Erratum to Csonka, G. I., Nguyen, N. A., & Kolossváry, I. (1997). Simple tests for density functional methods. Journal of Computational Chemistry, 18 (12), 1534--1545. (DOI: \url10.1002/(SICI)1096-987X(199709)18:12<1534::AID-JCC10>3.0.CO;2-K) 2270--2270