Last update:
Sat Jun 1 08:22:34 MDT 2019
R. 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