Last update:
Mon Sep 4 17:19:44 MDT 2023
Timothy R. Forester and
William Smith SHAKE, rattle, and roll: Efficient
constraint algorithms for linked rigid
bodies . . . . . . . . . . . . . . . . . 102--111
Finn Drablòs Ab initio simulation of chemical shift
effects from metal ion binding in
Bacitracin A . . . . . . . . . . . . . . 1--7
Petr Bou\vr Comparison of Hartree--Fock and
Kohn--Sham determinants as wave
functions . . . . . . . . . . . . . . . 8--16
Gerrit Schüürmann Prediction of Henry's law constant of
benzene derivatives using quantum
chemical continuum-solvation models . . 17--34
E. del Río and
R. López and
M. I. Menéndez and
T. L. Sordo A theoretical study of the reaction of
HCO$^+$ with C$_2$H$_2$ . . . . . . . . 35--42
Jose M. Mercero and
Paul Barrett and
Cheuk W. Lam and
Joseph E. Fowler and
Jesus M. Ugalde and
Lee G. Pedersen Quantum mechanical calculations on
phosphate hydrolysis reactions . . . . . 43--51
Roberto Izzo and
Martin Klessinger Optimization of conical intersections
using the semiempirical MNDOC--CI method
with analytic gradients . . . . . . . . 52--62
Marie C. Vicens and
Gustavo E. López Density functional studies of
cation--water complexes . . . . . . . . 63--68
Jon Baker and
Peter Pulay Efficient geometry optimization of
molecular clusters . . . . . . . . . . . 69--76
Kenny B. Lipkowitz Book review: \booktitleEncyclopedia of
Computational Chemistry, P. v. R.
Schleyer, editor-in-chief, John Wiley &
Sons, Chichester, UK, 1998, 3,500 pp.
\$3,150. ISBN 0-471-96588-X} . . . . . . 77--78
Konrad Hinsen The molecular modeling toolkit: a new
approach to molecular simulations . . . 79--85
Nicolas Foloppe and
Alexander D. MacKerell, Jr. All-atom empirical force field for
nucleic acids: I. Parameter optimization
based on small molecule and condensed
phase macromolecular target data . . . . 86--104
Alexander D. MacKerell Jr. and
Nilesh K. Banavali All-atom empirical force field for
nucleic acids: II. Application to
molecular dynamics simulations of DNA
and RNA in solution . . . . . . . . . . 105--120
See-Wing Chiu and
Michael Clark and
Shankar Subramaniam and
Eric Jakobsson Collective motion artifacts arising in
long-duration molecular dynamics
simulations . . . . . . . . . . . . . . 121--131
Araz Jakalian and
Bruce L. Bush and
David B. Jack and
Christopher I. Bayly Fast, efficient generation of
high-quality atomic charges. AM1-BCC
model: I. Method . . . . . . . . . . . . 132--146
L. B. Morales and
R. Garduño-Juárez and
J. M. Aguilar-Alvarado and
F. J. Riveros-Castro A parallel tabu search for
conformational energy optimization of
oligopeptides . . . . . . . . . . . . . 147--156
Timothy R. Forester and
William Smith Erratum: SHAKE, rattle, and roll:
Efficient constraint algorithms for
linked rigid bodies . . . . . . . . . . 157--157
Hon M. Chun and
Carlos E. Padilla and
Donovan N. Chin and
Masakatsu Watanabe and
Valeri I. Karlov and
Howard E. Alper and
Keto Soosaar and
Kim B. Blair and
Oren M. Becker and
Leo S. D. Caves and
Robert Nagle and
David N. Haney and
Barry L. Farmer MBO(N)D: a multibody method for
long-time molecular dynamics simulations 159--184
C. R. Sarma and
A. V. V. Nampoothiri A labeling scheme for young tableaux
spanning representations of permutation
group S (N) . . . . . . . . . . . . . . 185--190
Vladimir A. Bushenkov and
J. P. Prates Ramalho and
Georgi V. Smirnov Adsorption integral equation via complex
approximation with constraints: the
Langmuir kernel . . . . . . . . . . . . 191--200
Masaaki Kawata and
Masuhiro Mikami Computationally efficient canonical
molecular dynamics simulations by using
a multiple time-step integrator
algorithm combined with the particle
mesh Ewald method and with the fast
multipole method . . . . . . . . . . . . 201--217
H. Donald B. Jenkins and
Luminita C. Jitariu and
Ingo Krossing and
Jack Passmore and
Reijo Suontamo Basis set and correlation effects in the
calculation of accurate gas phase
dimerization energies of two M to give M
(M = S, Se) . . . . . . . . . . . . . . 218--226
Fakhr Abu-Awwad and
Peter Politzer Variation of parameters in Becke-3
hybrid exchange-correlation functional 227--238
Robert J. Bubel and
Warthen Douglass and
David P. White Molecular mechanics-based measures of
steric effects: Customized code to
compute Ligand repulsive energies . . . 239--246
Denton S. Ebel and
Mark S. Ghiorso and
Richard O. Sack and
Lawrence Grossman Gibbs energy minimization in gas +
liquid + solid systems . . . . . . . . . 247--256
Marta Forés and
Miquel Duran and
Miquel Sol\`a and
Ludwik Adamowicz Theoretical characterization of
intramolecular proton transfer in the
ground and the lowest-lying triplet
excited states of 1-amino-3-propenal: a
methodological comparison . . . . . . . 257--269
Bernd Mayer and
Giancarlo Marconi Circular dichroic constrained structure
optimization of homoalanine peptides . . 270--281
Jean-Didier Maréchal and
Guada Barea and
Feliu Maseras and
Agustí Lledós and
Liliane Mouawad and
David Pérahia Theoretical modeling of the heme group
with a hybrid QM/MM method . . . . . . . 282--294
Laurent David and
Ray Luo and
Michael K. Gilson Comparison of generalized Born and
Poisson models: Energetics and dynamics
of HIV protease . . . . . . . . . . . . 295--309
Eugene T. Knight A radial probability density function
for analysis of canonical molecular
orbitals . . . . . . . . . . . . . . . . 310--321
Redouan El-Bergmi and
J. A. Dobado and
Dolores Portal and
José Molina Molina Stabilization in neutral bicyclic
sulfoxide compounds . . . . . . . . . . 322--327
Guyan Liang and
Jennifer B. Sorensen and
David Whitmire and
J. Phillip Bowen Molecular mechanics (MM3)
parameterization for oxocarbenium ions 329--339
Derek M. Dolney and
Gregory D. Hawkins and
Paul Winget and
Daniel A. Liotard and
Christopher J. Cramer and
Donald G. Truhlar Universal solvation model based on
conductor-like screening model . . . . . 340--366
Emmanuelle Rousseau and
Didier Mathieu Atom equivalents for converting DFT
energies calculated on molecular
mechanics structures to formation
enthalpies . . . . . . . . . . . . . . . 367--379
Young Joo Lee and
Jae Yeol Maeng and
Eok-Kyun Lee and
Bongsoo Kim and
Sehun Kim and
Kyu-Kwang Han Melting behaviors of icosahedral metal
clusters studied by Monte Carlo
simulations . . . . . . . . . . . . . . 380--387
K. Tappura and
M. Lahtela-Kakkonen and
O. Teleman A new soft-core potential function for
molecular dynamics applied to the
prediction of protein loop conformations 388--397
Giovanni Talarico and
Peter H. M. Budzelaar and
Anton W. Gal Ethylene coordination, insertion, and
chain transfer at a cationic aluminum
center: a comparative study with Ab
Initio correlated level and density
functional methods . . . . . . . . . . . 398--410
Steven Feldgus and
Clark R. Landis and
Eric D. Glendening and
Frank Weinhold Natural resonance theory. I. General
formalism . . . . . . . . . . . . . . . 411--413
L. V. Moskaleva and
M. C. Lin Unimolecular isomerization/decomposition
of cyclopentadienyl and related
bimolecular reverse process: ab initio
MO/statistical theory study . . . . . . 415--425
Allan D. Headley and
Stephen D. Starnes Theoretical analysis of fluoroglycine
conformers . . . . . . . . . . . . . . . 426--431
Pawe\l K\kedzierski and
W. Andrzej Sokalski and
Morris Krauss Nonempirical analysis of nature of
catalytic effects in ribonuclease A
active site . . . . . . . . . . . . . . 432--445
M. F. O'Donohue and
E. Minasian and
S. J. Leach and
A. W. Burgess and
H. R. Treutlein PEPCAT --- a new tool for conformational
analysis of peptides . . . . . . . . . . 446--461
Luis Carballeira and
Ignacio Pérez-Juste An ab initio interpretation in gas phase
and aqueous solution of the generalized
anomeric effect in
R\bondO\bondCR$_2$\bondNR$_2$ (R = H,
CH$_3$) . . . . . . . . . . . . . . . . 462--477
Stuart R. Gooding and
Peter J. Winn and
Richard I. Maurer and
György G. Ferenczy and
John R. Miller and
Jayne E. Harris and
D. Vaughan Griffiths and
Christopher A. Reynolds Fully polarizable QM/MM calculations: an
application to the nonbonded
iodine--oxygen interaction in
dimethyl-2-iodobenzoylphosphonate . . . 478--482
Dominique Dehareng and
Georges Dive Hartree--Fock instabilities and
electronic properties . . . . . . . . . 483--504
John F. Stanton Book review: \booktitleReviews in
Computational Chemistry, Volume 13.
Edited by Kenny B. Lipkowitz and Donald
B. Boyd, Wiley-VCH, 1999, 426 pp.
\$139.00. ISBN 0-471-33135-X} . . . . . 505--507
Franck Fuster and
Alain Sevin and
Bernard Silvi Determination of substitutional sites in
heterocycles from the topological
analysis of the electron localization
function (ELF) . . . . . . . . . . . . . 509--514
S. Alcaro and
F. Gasparrini and
O. Incani and
S. Mecucci and
D. Misiti and
M. Pierini and
C. Villani A ``quasi-flexible'' automatic docking
processing for studying stereoselective
recognition mechanisms. Part I. Protocol
validation . . . . . . . . . . . . . . . 515--530
Reece K. Hart and
Rohit V. Pappu and
Jay W. Ponder Exploring the similarities between
potential smoothing and simulated
annealing . . . . . . . . . . . . . . . 531--552
Robert E. Tuzun and
Donald W. Noid and
Bobby G. Sumpter Computation of internal coordinates,
derivatives, and gradient expressions:
torsion and improper torsion . . . . . . 553--561
Ramón Bosque and
Feliu Maseras Performance of the semiempirical PM3
(tm) method in the geometry optimization
of transition metal complexes . . . . . 562--571
M. I. Bernal-Uruchurtu and
M. T. C. Martins-Costa and
C. Millot and
M. F. Ruiz-López Improving description of hydrogen bonds
at the semiempirical level: water--water
interactions as test case . . . . . . . 572--581
Philippe Derreumaux Predicting helical hairpins from
sequences by Monte Carlo simulations . . 582--589
Anonymous In memoriam: Michael C. Zerner . . . . . 591--591
Terry J. Frankcombe and
Sean C. Smith Solving the unimolecular master equation
with a weighted subspace projection
method . . . . . . . . . . . . . . . . . 592--606
Jordi Vill\`a and
Jörg Bentzien and
\`Angels González-Lafont and
José M. Lluch and
Juan Bertran and
Arieh Warshel Effective way of modeling chemical
catalysis: Empirical valence bond
picture of role of solvent and catalyst
in alkylation reactions . . . . . . . . 607--625
Imre Jákli and
András Perczel and
Ödön Farkas and
Attila G. Császár and
Carlos Sosa and
Imre G. Csizmadia Peptide models XXIII. Conformational
model for polar side-chain containing
amino acid residues: a comprehensive
analysis of RHF, DFT, and MP2 properties
of HCO-L-SER-NH$_2$ . . . . . . . . . . 626--655
M. Skowronek and
I. Roterman and
L. Konieczny and
B. Stopa and
J. Rybarska and
B. Piekarska Why do Congo Red, Evans Blue, and Trypan
Blue differ in their complexation
properties? . . . . . . . . . . . . . . 656--667
Willian R. Rocha and
Wagner B. De Almeida Carbonyl insertion reaction into the Pt
C bond in heterobimetallic
Pt(SnCl$_3$)(PH$_3$)$_2$(CO)(CH$_3$)
compound: Theoretical study . . . . . . 668--674
Roger Arnaud and
Valentina Vetere and
Vincenzo Barone Quantum mechanical study of
regioselectivity of radical additions to
substituted olefins . . . . . . . . . . 675--691
Delanie Lamprecht and
Gert J. Lamprecht A molecular mechanics force field for
rhodium(I) carbonyl phosphine complexes
and its application on the oxidative
addition reactions of these complexes 692--703
M. L. Sánchez and
M. E. Martín and
M. A. Aguilar and
F. J. Olivares del Valle Solvent effects by means of averaged
solvent electrostatic potentials:
Coupled method . . . . . . . . . . . . . 705--715
Isidoro García-Cruz and
Miguel Castro and
Annik Vivier-Bunge DFT and MP2 molecular orbital
determination of OH--toluene--O$_2$
isomeric structures in the atmospheric
oxidation of toluene . . . . . . . . . . 716--730
Steven M. LaValle and
Paul W. Finn and
Lydia E. Kavraki and
Jean-Claude Latombe A randomized kinematics-based approach
to pharmacophore-constrained
conformational search and database
screening . . . . . . . . . . . . . . . 731--747
Satoshi Ono and
Nobuyuki Nakajima and
Junichi Higo and
Haruki Nakamura Peptide free-energy profile is strongly
dependent on the force field: Comparison
of C96 and AMBER95 . . . . . . . . . . . 748--762
Laurie A. Christianson and
Melissa J. Lucero and
Daniel H. Appella and
Daniel A. Klein and
Samuel H. Gellman Improved treatment of cyclic
$\beta$-amino acids and successful
prediction of $\beta$-peptide secondary
structure using a modified force field:
AMBER*C . . . . . . . . . . . . . . . . 763--773
Wolfgang Damm and
Wilfred F. van Gunsteren Reversible peptide folding: Dependence
on molecular force field used . . . . . 774--787
Stephen P. Greatbanks and
Jill E. Gready and
Ajay C. Limaye and
Alistair P. Rendell Comparison of enzyme polarization of
ligands and charge-transfer effects for
dihydrofolate reductase using
point-charge embedded ab initio quantum
mechanical and linear-scaling
semiempirical quantum mechanical methods 788--811
Buyong Ma and
Jenn-Huei Lii and
Norman L. Allinger Molecular polarizabilities and induced
dipole moments in molecular mechanics 813--825
M. K. Shukla and
S. K. Mishra and
Anil Kumar and
P. C. Mishra An ab initio study of excited states of
guanine in the gas phase and aqueous
media: Electronic transitions and
mechanism of spectral oscillations . . . 826--846
Johan Wouters Use of theoretical descriptors to
characterize cation--$\pi$ binding sites
in (macro)molecules . . . . . . . . . . 847--855
Jian Wu and
Yuansheng Jiang The valence bond calculations for
conjugated hydrocarbons having 24--28
$\pi$-electrons . . . . . . . . . . . . 856--869
M. D. Di Benedetto and
P. Lucibello and
A. L. Sangiovanni-Vincentelli and
K. Yamaguchi A new procedure for exact ring closure 870--881
András Perczel and
Attila G. Császár Toward direct determination of
conformations of protein building units
from multidimensional NMR experiments I.
A theoretical case study of
For-Gly-NH$_2$ and For-L-Ala-NH$_2$ . . 882--900
Xavier Grabuleda and
Carlos Jaime and
Peter A. Kollman Molecular dynamics simulation studies of
liquid acetonitrile: New six-site model 901--908
F. Tielens and
W. Langenaeker and
A. R. Ocakoglu and
P. Geerlings Quantum chemical calculation of Henry
constants of diatomic molecules in
faujasite-type zeolites . . . . . . . . 909--922
Zlatko Vasilkoski and
David L. Weaver A generator of protein folding kinetics
states for the diffusion--collision
model . . . . . . . . . . . . . . . . . 923--932
Anthony S. Mitchell and
Mark A. Spackman Molecular surfaces from the promolecule:
a comparison with Hartree--Fock ab
initio electron density surfaces . . . . 933--942
Thomas A. Baker and
Gregory I. Gellene A hybrid ab initio /free electron
computational model for conjugated dye
molecules: Simple cyanines and oxonols 943--953
Kenji Sayano and
Hidetoshi Kono and
M. Michael Gromiha and
Akinori Sarai Multicanonical Monte Carlo calculation
of the free-energy map of the
base--amino acid interaction . . . . . . 954--962
Françoise Rogalewicz and
Gilles Ohanessian and
Nohad Gresh Interaction of neutral and zwitterionic
glycine with Zn$^{2+}$ in gas phase: ab
initio and SIBFA molecular mechanics
calculations . . . . . . . . . . . . . . 963--973
Karl Jug and
Gerald Geudtner and
Thorsten Homann MSINDO parameterization for third-row
main group elements . . . . . . . . . . 974--987
Jinn-Moon Yang and
Cheng-Yan Kao Flexible ligand docking using a robust
evolutionary algorithm . . . . . . . . . 988--998
N. A. Pierce and
J. A. Spriet and
J. Desmet and
S. L. Mayo Conformational splitting: a more
powerful criterion for dead-end
elimination . . . . . . . . . . . . . . 999--1009
Gilles Tiraboschi and
Nohad Gresh and
Claude Giessner-Prettre and
Lee G. Pedersen and
David W. Deerfield Parallel ab initio and molecular
mechanics investigation of
polycoordinated Zn(II) complexes with
model hard and soft ligands: Variations
of binding energy and of its components
with number and charges of ligands . . . 1011--1039
Friedrich Biegler-König Calculation of atomic integration data 1040--1048
Junmei Wang and
Piotr Cieplak and
Peter A. Kollman How well does a restrained electrostatic
potential (RESP) model perform in
calculating conformational energies of
organic and biological molecules? . . . 1049--1074
Takashi Amisaki Precise and efficient Ewald summation
for periodic fast multipole method . . . 1075--1087
Martin J. Field and
Marc Albe and
Céline Bret and
Flavien Proust-De Martin and
Aline Thomas The dynamo library for molecular
simulations using hybrid quantum
mechanical and molecular mechanical
potentials . . . . . . . . . . . . . . . 1088--1100
Y. Z. Xu and
Q. Ouyang and
J. G. Wu and
J. A. Yorke and
G. X. Xu and
D. F. Xu and
R. D. Soloway and
J. Q. Ren Using fractal to solve the multiple
minima problem in molecular mechanics
calculation . . . . . . . . . . . . . . 1101--1108
Yuan-Jie Ye and
Ling-Ling Shen DFT approach to calculate electronic
transfer through a segment of DNA double
helix . . . . . . . . . . . . . . . . . 1109--1117
Hermes F. de Souza and
Paulo H. Guadagnini and
Rogério Custodio and
John D. Goddard The correlation of proton affinities
with atomic charges and
electronegativities for the group 14 to
17 hydrides . . . . . . . . . . . . . . 1119--1131
Aaron R. Dinner Local deformations of polymers with
nonplanar rigid main-chain internal
coordinates . . . . . . . . . . . . . . 1132--1144
Ryan T. Koehler and
Hugo O. Villar Design of screening libraries biased for
pharmaceutical discovery . . . . . . . . 1145--1152
Carlo Adamo and
Vincenzo Barone Structures and properties of lanthanide
and actinide complexes by a new density
functional approach: Lanthanum,
gadolinium, lutetium, and thorium
halides as case studies . . . . . . . . 1153--1166
F. J. Meléndez and
B. Gallego-Luxan and
Jean Demaison and
Yves G. Smeyers Ab initio determination of the infrared
phosphine torsion spectrum in
vinylphosphine with ZPE correction . . . 1167--1175
M. Pernpointner and
L. Visscher and
W. A. de Jong and
R. Broer Parallelization of four-component
calculations. I. Integral generation,
SCF, and four-index transformation in
the Dirac--Fock package MOLFDIR . . . . 1176--1186
Kholmirzo Kholmurodov and
William Smith and
Kenji Yasuoka and
Tom Darden and
Toshikazu Ebisuzaki A smooth-particle mesh Ewald method for
DL\_POLY molecular dynamics simulation
package on the Fujitsu VPP700 . . . . . 1187--1191
Cristobal Alhambra and
Jiali Gao Hydrogen-bonding interactions in the
active site of a low molecular weight
protein-tyrosine phosphatase . . . . . . 1192--1203
F. A. Momany and
J. L. Willett Computational studies on carbohydrates:
I. Density functional ab initio geometry
optimization on maltose conformations 1204--1219
Petter Persson and
Johnny Bustad and
Michael C. Zerner INDO calculations of small copper
clusters and CO adsorbed on copper(100)
surfaces . . . . . . . . . . . . . . . . 1221--1228
Norman L. Allinger and
Kathleen A. Durkin Van der Waals effects between hydrogen
and first-row atoms in molecular
mechanics (MM3/MM4) . . . . . . . . . . 1229--1242
Nino Russo and
Marirosa Toscano and
André Grand Theoretical determination of electron
affinity and ionization potential of DNA
and RNA bases . . . . . . . . . . . . . 1243--1250
Fatih Ya\csar and
Tarik Çelik and
Bernd A. Berg and
Hagai Meirovitch Multicanonical procedure for continuum
peptide models . . . . . . . . . . . . . 1251--1261
M. C. Wells and
R. R. Lucchese Computing the superexchange electronic
factor of electron transfer theory using
a grid-based numerical method . . . . . 1262--1273
J. Elezgaray and
Y. H. Sanejouand Modal dynamics of proteins in water . . 1274--1282
Sreedhara V. Rao Mechanism of some 1:2 hydrogen transfer
reactions through bond variation indices 1283--1291
Yoshinao Nakagawa and
Nobuo Tajima and
Kimihiko Hirao A theoretical study of catalytic
hydration reactions of ethylene . . . . 1292--1304
Asit K. Chandra and
Tadafumi Uchimaru and
Masaaki Sugie Kinetics of the hydrogen abstraction
reactions of 1,1- and 1,2-difluoroethane
with hydroxyl radical: an ab initio
study . . . . . . . . . . . . . . . . . 1305--1318
M. Holst and
N. Baker and
F. Wang Adaptive multilevel finite element
solution of the Poisson--Boltzmann
equation I. Algorithms and examples . . 1319--1342
N. Baker and
M. Holst and
F. Wang Adaptive multilevel finite element
solution of the Poisson--Boltzmann
equation II. Refinement at
solvent-accessible surfaces in
biomolecular systems . . . . . . . . . . 1343--1352
Nenad Raos Iterative method for finding the
low-energy conformations based on the
concept of molecular volumes . . . . . . 1353--1360
Xavier Fradera and
Miquel Duran and
Jordi Mestres Atomic transferability within the
exchange-correlation density . . . . . . 1361--1374
Josep Maria Bofill and
Ibério de Pinho Ribeiro Moreira and
Josep Maria Anglada and
Francesc Illas Accurate and efficient determination of
higher roots in diagonalization of large
matrices based in function restricted
optimization algorithms . . . . . . . . 1375--1386
Yuxiang Bu and
Chengbu Liu The orientation and distance-dependence
analysis of the electron transfer
reactivity: an electron correlation
level investigation of
Mn$^{2+}$(H$_2$O)$_2$/Mn$^{3+}$(H$_2$O)$_2$ system 1387--1404
Rois Benassi and
Fernando Taddei Complete basis set model chemistry
applied to molecules of increasing
molecular complexity: Thermochemical
properties of organic sulfur derivatives 1405--1418
Thom Vreven and
Keiji Morokuma On the application of the IMOMO
(integrated molecular orbital +
molecular orbital) method . . . . . . . 1419--1432
Richard J. Hall and
Sally A. Hindle and
Neil A. Burton and
Ian H. Hillier Aspects of hybrid QM/MM calculations:
the treatment of the QM/MM interface
region and geometry optimization with an
application to chorismate mutase . . . . 1433--1441
R. B. Murphy and
D. M. Philipp and
R. A. Friesner A mixed quantum mechanics/molecular
mechanics (QM/MM) method for large-scale
modeling of chemistry in protein
environments . . . . . . . . . . . . . . 1442--1457
Yirong Mo and
Jiali Gao Ab initio QM/MM simulations with a
molecular orbital-valence bond (MOVB)
method: application to an S$_N$2
reaction in water . . . . . . . . . . . 1458--1469
Joachim Sauer and
Marek Sierka Combining quantum mechanics and
interatomic potential functions in ab
initio studies of extended systems . . . 1470--1493
Arjan van der Vaart and
Valentin Gogonea and
Steven L. Dixon and
Kenneth M. Merz, Jr. Linear scaling molecular orbital
calculations of biological systems using
the semiempirical divide and conquer
method . . . . . . . . . . . . . . . . . 1494--1504
Peter M. W. Gill and
Andrew T. B. Gilbert and
Terry R. Adams Rapid evaluation of two-center
two-electron integrals . . . . . . . . . 1505--1510
S. J. A. van Gisbergen and
C. Fonseca Guerra and
E. J. Baerends Towards excitation energies and
(hyper)polarizability calculations of
large molecules. Application of
parallelization and linear scaling
techniques to time-dependent density
functional response theory . . . . . . . 1511--1523
Philippe Y. Ayala and
Gustavo E. Scuseria Electron correlation in large molecular
systems using the atomic orbital
formalism. The case of intermolecular
interactions in crystalline urea as an
example . . . . . . . . . . . . . . . . 1524--1531
Jing Kong and
Christopher A. White and
Anna I. Krylov and
David Sherrill and
Ross D. Adamson and
Thomas R. Furlani and
Michael S. Lee and
Aaron M. Lee and
Steven R. Gwaltney and
Terry R. Adams and
Christian Ochsenfeld and
Andrew T. B. Gilbert and
Gary S. Kedziora and
Vitaly A. Rassolov and
David R. Maurice and
Nikhil Nair and
Yihan Shao and
Nicholas A. Besley and
Paul E. Maslen and
Jeremy P. Dombroski and
Holger Daschel and
Weimin Zhang and
Prakashan P. Korambath and
Jon Baker and
Edward F. C. Byrd and
Troy Van Voorhis and
Manabu Oumi and
So Hirata and
Chao-Ping Hsu and
Naoto Ishikawa and
Jan Florian and
Arieh Warshel and
Benny G. Johnson and
Peter M. W. Gill and
Martin Head-Gordon and
John A. Pople Q-Chem 2.0: a high-performance ab initio
electronic structure program package . . 1532--1548
Karl Jug and
Daniel Wichmann MSINDO study of large silsesquioxanes 1549--1553
Gongyi Hong and
Marek Strajbl and
Tomasz A. Wesolowski and
Arieh Warshel Constraining the electron densities in
DFT method as an effective way for ab
initio studies of metal-catalyzed
reactions . . . . . . . . . . . . . . . 1554--1561
Jana Khandogin and
Anguang Hu and
Darrin M. York Electronic structure properties of
solvated biomolecules: a quantum
approach for macromolecular
characterization . . . . . . . . . . . . 1562--1571
Bernard Kirtman and
Benoit Champagne and
Josep M. Luis Efficient treatment of the effect of
vibrations on electrical, magnetic, and
spectroscopic properties . . . . . . . . 1572--1588
Gernot Frenking Foreword . . . . . . . . . . . . . . . . v--v
Xiang-Yuan Li Electron transfer between tryptophan and
tyrosine: Theoretical calculation of
electron transfer matrix element for
intramolecular hole transfer . . . . . . 565--579
Anonymous New Section of the Journal of
Computational Chemistry . . . . . . . . 1--1
Donald E. Williams Improved intermolecular force field for
crystalline oxohydrocarbons including
O\bondH\dottedbondO hydrogen bonding . . 1--20
István Kolossváry and
György M. Keserü Hessian-free low-mode conformational
search for large-scale protein loop
optimization: application to $c$-jun
$N$-terminal kinase JNK3 . . . . . . . . 21--30
Masao Masamura Ab initio molecular orbital study of
OH$^-$(H$_2$O)$_n$ in the gas phase . . 31--37
Michael G. Razumov and
Vladimir L. Melnikov and
Igor V. Pletnev Molecular mechanics calculations of
$\beta$-diketonate, aqua, and
aqua-$\beta$-diketonate complexes of
lanthanide ions using Gillespie--Kepert
model . . . . . . . . . . . . . . . . . 38--50
Mikko Linnolahti and
Pipsa Hirva and
Tapani A. Pakkanen Geometry prediction of bridged
zirconocene dichlorides by quantum
chemical methods . . . . . . . . . . . . 51--64
Alfred D. French and
Anne-Marie Kelterer and
Glenn P. Johnson and
Michael K. Dowd and
Christopher J. Cramer HF/6-31G* energy surfaces for
disaccharide analogs . . . . . . . . . . 65--78
Marcel Swart and
Piet Th. van Duijnen and
Jaap G. Snijders A charge analysis derived from an atomic
multipole expansion . . . . . . . . . . 79--88
Thomas Bredow and
Gerald Geudtner and
Karl Jug Development of the cyclic cluster
approach for ionic systems . . . . . . . 89--101
K. Endo and
S. Koizumi and
T. Otsuka and
M. Suhara and
T. Morohasi and
E. Z. Kurmaev and
D. P. Chong Analysis of XPS and XES of diamond and
graphite by DFT calculations using model
molecules . . . . . . . . . . . . . . . 102--108
Michael Meyer and
Thomas Steinke and
Maria Brandl and
Jürgen Sühnel Density functional study of guanine and
uracil quartets and of guanine
quartet/metal ion complexes . . . . . . 109--124
Masao Masamura Ab initio molecular orbital study on the
structures and energetics of
CH$_3$OH(H$_2$O)$_n$ and
CH$_3$SH(H$_2$O)$_n$ in the gas phase 125--131
Matthias Prall VMD: a graphical tool for the modern
chemists . . . . . . . . . . . . . . . . 132--134
Luis Carballeira and
Ignacio Pérez-Juste Role of the anomeric effect in
methanediamines in the gas phase and
aqueous solutions . . . . . . . . . . . 135--150
Thomas Krüger and
Alexander F. Sax Distorted silicon hydrides--- a
comparative study with various density
functionals . . . . . . . . . . . . . . 151--161
Salvador León and
Carlos Alemán and
Francesc Escalé and
Manuel Laso MCDP: an advanced tool to simulate
comb-like polymers . . . . . . . . . . . 162--171
Daniel Beuve-Mery and
Mehdi Rahman and
Philippe Ducarme and
Robert Brasseur Practical aspects of computational
chemistry calculations through PC
networks: the RAMSES--Beowulf
implementation . . . . . . . . . . . . . 172--177
Sergey Vyazovkin Modification of the integral
isoconversional method to account for
variation in the activation energy . . . 178--183
Zhong-Hui Duan and
Robert Krasny An adaptive treecode for computing
nonbonded potential energy in classical
molecular systems . . . . . . . . . . . 184--195
Béla Paizs and
Pedro Salvador and
Attila G. Császár and
Miquel Duran and
Sándor Suhai Intermolecular bond lengths:
extrapolation to the basis set limit on
uncorrected and BSSE-corrected potential
energy hypersurfaces . . . . . . . . . . 196--207
Don Steiger and
Rainer Glaser Lattice sum calculations for $1/r^p$
interactions via multipole expansions
and Euler summation . . . . . . . . . . 208--215
Elfi Kraka and
Dieter Cremer The para-didehydropyridine,
para-didehydropyridinium, and related
biradicals --- a contribution to the
chemistry of enediyne antitumor drugs 216--229
Didier Bégué and
Claude Pouchan Density functional finite cluster method
for polarizability of large Be$_N$
three-dimensional systems . . . . . . . 230--240
Sándor Kristyán and
Gábor I. Csonka Fitting atomic correlation parameters
for RECEP (rapid estimation of
correlation energy from partial charges)
method to estimate molecular correlation
energies within chemical accuracy . . . 241--254
Xavier Gironés and
David Robert and
Ramon Carbó-Dorca TGSA: a molecular superposition program
based on topo-geometrical considerations 255--263
Hiroyuki Ito and
Hiroshi Nakatsuji Roles of proteins in the electron
transfer in the photosynthetic reaction
center of \em Rhodopseudomonas viridis:
bacteriopheophytin to ubiquinone . . . . 265--272
R. de Gelder and
R. Wehrens and
J. A. Hageman A generalized expression for the
similarity of spectra: application to
powder diffraction pattern
classification . . . . . . . . . . . . . 273--289
Siegfried Höfinger and
Thomas Simonson Dielectric relaxation in proteins: a
continuum electrostatics model
incorporating dielectric heterogeneity
of the protein and time-dependent
charges . . . . . . . . . . . . . . . . 290--305
Padeleimon Karafiloglou A method to calculate the weights of nbo
electronic structures from Moffitt's
theorem . . . . . . . . . . . . . . . . 306--315
Satoshi Okumoto and
Shinichi Yamabe A computational study of base-catalyzed
reactions between isocyanates and
epoxides affording 2-oxazolidones and
isocyanurates . . . . . . . . . . . . . 316--326
Yong Zhang and
Xiao-Zeng You Charge redistribution effect on the
properties of charge transfer complexes
H$_n$R$\cdot$XY and H$_n$R$\cdot$X$_2$
(X, Y = F, Cl, Br, I; R = O, S, N, P) 327--338
Marcos R. Betancourt and
Jeffrey Skolnick Finding the needle in a haystack:
educing native folds from ambiguous ab
initio protein structure predictions . . 339--353
Andrzej J. Gor\kaczko Multiisotopic modeling of fragmentation
ion patterns in mass spectra of
organometallic and coordination
compounds . . . . . . . . . . . . . . . 354--365
Nathaniel R. Luman and
Michael P. King and
Joseph D. Augspurger Predicting $^{15}$N amide chemical
shifts in proteins. I. An additive model
for the backbone contribution . . . . . 366--372
Dmitrii N. Rassokhin and
Victor S. Lobanov and
Dimitris K. Agrafiotis Nonlinear mapping of massive data sets
by fuzzy clustering and neural networks 373--386
Josep Maria Anglada and
Emili Besalú and
Josep Maria Bofill and
Ramon Crehuet On the quadratic reaction path evaluated
in a reduced potential energy surface
model and the problem to locate
transition states . . . . . . . . . . . 387--406
Ingolf Sommer and
Richard Brimacombe Methods for refining interactively
established models of ribosomal RNA
towards a physico-chemically plausible
structure . . . . . . . . . . . . . . . 407--417
Ingo Muegge Effect of ligand volume correction on
PMF scoring . . . . . . . . . . . . . . 418--425
Petr Bou\vr Computations of the Raman optical
activity via the sum-over-states
expansions . . . . . . . . . . . . . . . 426--435
Pei Tang and
Igor Zubryzcki and
Yan Xu Ab initio calculation of structures and
properties of halogenated general
anesthetics: halothane and sevoflurane 436--444
Kevin J. Naidoo and
Michelle Kuttel Water structure about the dimer and
hexamer repeat units of amylose from
molecular dynamics computer simulations 445--456
Alexey K. Mazur Molecular dynamics of minimal B-DNA . . 457--467
Leonel F. Murga and
Mary Jo Ondrechen Numerical Aspects of the Calculation of
Second Hyperpolarizabilities Using the
Finite Field Method Coupled with a
Simple Lanczos Algorithm . . . . . . . . 468--474
M. Holst and
N. Baker and
F. Wang Erratum: Adaptive multilevel finite
element solution of the
Poisson--Boltzmann equation I.
Algorithms and examples . . . . . . . . 475--475
Francisco Torrens and
José Sánchez-Marín and
Ignacio Nebot-Gil New dimension indices for the
characterization of the
solvent-accessible surface . . . . . . . 477--487
Dimitris K. Agrafiotis and
Dmitrii N. Rassokhin and
Victor S. Lobanov Multidimensional scaling and
visualization of large molecular
similarity tables . . . . . . . . . . . 488--500
Vincent Kräutler and
Wilfred F. van Gunsteren and
Philippe H. Hünenberger A fast SHAKE algorithm to solve distance
constraint equations for small molecules
in molecular dynamics simulations . . . 501--508
Kerstin Möhle and
Hans-Jörg Hofmann and
Walter Thiel Description of peptide and protein
secondary structures employing
semiempirical methods . . . . . . . . . 509--520
Yuhki Ohtsuka and
Kazufumi Ohkawa and
Hiroshi Nakatsuji Electron transfer in the $c$-type
cytochrome subunit of the photosynthetic
reaction center of \em Rhodopseudomonas
viridis: ab initio theoretical study . . 521--527
Shuhei Fukawa and
Masahiko Hada and
Ryoichi Fukuda and
Shinji Tanaka and
Hiroshi Nakatsuji Relativistic effects and the halogen
dependencies in the $^{13}$C chemical
shifts of CH$_{4 - n}$I$_n$, CH$_{4 -
n}$Br$_n$, CCl$_{4 - n}$I$_n$, and
CBr$_{4 - n}$I$_n$ ($n = 0$--$4$) . . . 528--536
Wolfgang Quapp Comment ``On the quadratic reaction path
evaluated in a reduced potential energy
surface model and the problem to locate
transition states'' [by J. M. Anglada,
E. Besalú, J. M. Bofill, and R. Crehuet,
J Comput Chem 2001, \bf 22, 4, 387--406] 537--540
Josep Maria Bofill Reply on the comment ``On the quadratic
reaction path evaluated in a reduced
potential energy surface model and the
problem to locate transition states''
[by J. M. Anglada, E. Besalú, J. M.
Bofill, and R. Crehuet, J Comput Chem
2001, \bf 22, 4, 387--406] . . . . . . . 541--544
Anonymous AIM2000 . . . . . . . . . . . . . . . . 545--559
Anonymous CI benchmark calculations on PC . . . . 560--563
Jean-Loup Faulon Stochastic generator of chemical
structure. 4. Building polymeric systems
with specified properties . . . . . . . 580--590
Linda Yu Zhang and
Emilio Gallicchio and
Richard A. Friesner and
Ronald M. Levy Solvent models for protein--ligand
binding: Comparison of implicit solvent
Poisson and surface generalized Born
models with explicit solvent simulations 591--607
J. Andrew Grant and
Barry T. Pickup and
Anthony Nicholls A smooth permittivity function for
Poisson--Boltzmann solvation methods . . 608--640
Oleg Borodin and
Grant D. Smith and
Richard L. Jaffe Ab initio quantum chemistry and
molecular dynamics simulations studies
of LiPF$_6$ /poly(ethylene oxide)
interactions . . . . . . . . . . . . . . 641--654
Fredrik Blomgren and
Sven Larsson and
Stephen F. Nelsen Electron transfer in bis(hydrazines), a
critical test for application of the
Marcus model . . . . . . . . . . . . . . 655--664
Fokke Dijkstra and
Joop H. van Lenthe Software news and updates . . . . . . . 665--672
Irene Nobeli and
John B. O. Mitchell and
Alexander Alex and
Janet M. Thornton Evaluation of a knowledge-based
potential of mean force for scoring
docked protein--ligand complexes . . . . 673--688
L. E. Dardenne and
A. S. Werneck and
M. Oliveira Neto and
P. M. Bisch Reassociation of fragments using
multicentered multipolar expansions:
peptide junction treatments to
investigate electrostatic properties of
proteins . . . . . . . . . . . . . . . . 689--701
L. F. Pacios and
P. C. Gómez Intramolecular interactions and
intramolecular hydrogen bonding in
conformers of gaseous glycine . . . . . 702--716
Bilha Sandak Multiscale fast summation of long-range
charge and dipolar interactions . . . . 717--731
Péter Hudáky and
Imre Jákli and
Attila G. Császár and
András Perczel Peptide models XXXI. Conformational
properties of hydrophobic residues
shaping the core of proteins. An ab
initio study of $N$-formyl- L-valinamide
and $N$-formyl- L-phenylalaninamide . . 732--751
A. M. Tokmachev and
A. L. Tchougréeff Semiempirical implementation of strictly
localized geminals for analysis of
molecular electronic structure . . . . . 752--764
Pedro Salvador and
Béla Paizs and
Miquel Duran and
Sándor Suhai On the effect of the BSSE on
intermolecular potential energy
surfaces. Comparison of a priori and a
posteriori BSSE correction schemes . . . 765--786
Zorka Smedarchina and
Antonio Fernández-Ramos and
Willem Siebrand DOIT: a program to calculate thermal
rate constants and mode-specific
tunneling splittings directly from
quantum-chemical calculations . . . . . 787--801
Pei Tang and
Igor Zubrzycki and
Yan Xu Erratum: Ab initio calculation of
structures and properties of halogenated
general anesthetics: halothane and
sevoflurane . . . . . . . . . . . . . . 802--802
Josep Maria Anglada and
Emili Besalú and
Josep Maria Bofill and
Ramon Crehuet Erratum: On the quadratic reaction path
evaluated in a reduced potential energy
surface model and the problem to locate
transition states . . . . . . . . . . . 803--803
Bouke P. van Eijck and
Wijnand T. M. Mooij and
Jan Kroon Ab initio crystal structure predictions
for flexible hydrogen-bonded molecules.
Part II. Accurate energy minimization 805--815
Bouke P. van Eijck Ab initio crystal structure predictions
for flexible hydrogen-bonded molecules.
Part III. Effect of lattice vibrations 816--826
Chang Kon Kim and
Jongok Won and
Hoon Sik Kim and
Yong Soo Kang and
Hong Guang Li and
Chan Kyung Kim Density functional theory studies on the
dissociation energies of metallic salts:
relationship between lattice and
dissociation energies . . . . . . . . . 827--834
Mayumi Kamishima and
Masaaki Kojima and
Yuzo Yoshikawa Calculation of stacking geometries by a
modified MM2 method . . . . . . . . . . 835--845
Hannes H. Loeffler and
Christoph A. Sotriffer and
Rudolf H. Winger and
Klaus R. Liedl and
Bernd M. Rode Calculation of sequence-dependent free
energies of hydration of dipeptides
formed by alanine and glycine . . . . . 846--860
Thomas Bredow and
Gerald Geudtner and
Karl Jug MSINDO parameterization for third-row
transition metals . . . . . . . . . . . 861--887
Chong Hak Chae and
Dong Gweon Oh and
Whanchul Shin Flexible molecular superposition:
development of a combined similarity
index and application of the constrained
optimization technique . . . . . . . . . 888--900
Rafa\l Wysoki\'nski and
Danuta Michalska The performance of different density
functional methods in the calculation of
molecular structures and vibrational
spectra of platinum(II) antitumor drugs:
cisplatin and carboplatin . . . . . . . 901--912
Luke Fisher and
Thomas Holme MM3 parameterization for the B N dative
bond . . . . . . . . . . . . . . . . . . 913--922
Sundaram Arulmozhiraja and
Tadatake Sato and
Akira Yabe Benzdiynes revisited: ab initio and
density functional theory . . . . . . . 923--930
G. te Velde and
F. M. Bickelhaupt and
E. J. Baerends and
C. Fonseca Guerra and
S. J. A. van Gisbergen and
J. G. Snijders and
T. Ziegler Chemistry with ADF . . . . . . . . . . . 931--967
A. Toniolo and
M. Persico Efficient calculation of Franck--Condon
factors and vibronic couplings in
polyatomics . . . . . . . . . . . . . . 968--975
Vitaly A. Rassolov and
Mark A. Ratner and
John A. Pople and
Paul C. Redfern and
Larry A. Curtiss 6-31G* basis set for third-row atoms . . 976--984
J. J. Borrás-Almenar and
J. M. Clemente-Juan and
E. Coronado and
B. S. Tsukerblat Software News and Updates: \tt MAGPACK:
a package to calculate the energy
levels, bulk magnetic properties, and
inelastic neutron scattering spectra of
high nuclearity spin clusters . . . . . 985--991
Paul D. Kirchhoff and
Rob Brown and
Scott Kahn and
Marvin Waldman and
C. M. Venkatachalam Application of structure-based focusing
to the estrogen receptor . . . . . . . . 993--1003
Kyu-Kwang Han and
Ki Hae Kim and
Byung Jin Mhin and
Hyeon S. Son Application of the multiensemble
sampling to the hydration free energy 1004--1009
Tran Trung Tran and
Herbert Treutlein and
Antony W. Burgess Conformational analysis of thiopeptides:
derivation of $sp^2$ sulfur parameters
for the CFF91 force field . . . . . . . 1010--1025
Tran Trung Tran and
Herbert Treutlein and
Antony W. Burgess Conformational analysis of thiopeptides:
$(\varphi, \psi)$ maps of
thio-substituted dipeptides . . . . . . 1026--1037
Gilles Tiraboschi and
Marie-Claude Fournié-Zaluski and
Bernard-Pierre Roques and
Nohad Gresh Intramolecular chelation of Zn$^{2+}$ by
$\alpha$- and
$\beta$-mercaptocarboxamides. A parallel
ab initio and polarizable molecular
mechanics investigation. Assessment of
the role of multipole transferability 1038--1047
Piotr Cieplak and
James Caldwell and
Peter Kollman Molecular mechanical models for organic
and biological systems going beyond the
atom centered two body additive
approximation: aqueous solution free
energies of methanol and $N$-methyl
acetamide, nucleic acid base, and amide
hydrogen bonding and chloroform/water
partition coefficients of the nucleic
acid bases . . . . . . . . . . . . . . . 1048--1057
Vladimir A. Bushenkov and
J. P. Prates Ramalho and
Georgi V. Smirnov Adsorption integral equation via complex
approximation with constraints: kernel
of general form . . . . . . . . . . . . 1058--1066
Xiang-Yuan Li and
Ji-Feng Liu A theoretical study of solvent effect
and reaction mechanism of electron
transfer reaction between indole side
chain and phenol side chain of peptide
involving tryptophan and tyrosine . . . 1067--1081
Pawel K\kedzierski and
W. Andrzej Sokalski Analysis of the transferability of
atomic multipoles for amino acids in
modeling macromolecular charge
distribution from fragments . . . . . . 1082--1097
Narutoshi Kamiya and
Junichi Higo Repeated-annealing sampling combined
with multicanonical algorithm for
conformational sampling of bio-molecules 1098--1106
Shoji Morita and
Shogo Sakai IMiCMO: a new integrated ab initio
multicenter molecular orbitals method
for molecular dynamics calculations in
solvent cluster systems . . . . . . . . 1107--1112
Christopher J. Van Zele and
Mark A. Cunningham and
Marvin W. Makinen Validation of nitroxyl spin-label
force-field parameters through molecular
dynamics simulations . . . . . . . . . . 1113--1123
M. Basma and
S. Sundara and
D. Çalgan and
T. Vernali and
R. J. Woods Solvated ensemble averaging in the
calculation of partial atomic charges 1125--1137
Annia Galano and
J. Raúl Alvarez-Idaboy and
Luis A. Montero and
Annik Vivier-Bunge OH hydrogen abstraction reactions from
alanine and glycine: a quantum
mechanical approach . . . . . . . . . . 1138--1153
Donald E. Williams Improved intermolecular force field for
molecules containing H, C, N, and O
atoms, with application to nucleoside
and peptide crystals . . . . . . . . . . 1154--1166
Edward C. Sherer and
Christopher J. Cramer Quantum chemical characterization of the
cytosine: 2-Aminopurine base pair . . . 1167--1179
Carles Curutchet and
Modesto Orozco and
F. Javier Luque Solvation in octanol: parametrization of
the continuum MST model . . . . . . . . 1180--1193
Christopher J. Cramer and
Anne-Marie Kelterer and
Alfred D. French When anomeric effects collide . . . . . 1194--1204
Lukas D. Schuler and
Xavier Daura and
Wilfred F. van Gunsteren An improved GROMOS96 force field for
aliphatic hydrocarbons in the condensed
phase . . . . . . . . . . . . . . . . . 1205--1218
Junmei Wang and
Peter A. Kollman Automatic parameterization of force
field by systematic search and genetic
algorithms . . . . . . . . . . . . . . . 1219--1228
Tommi Hassinen and
Mikael Peräkylä New energy terms for reduced protein
models implemented in an off-lattice
force field . . . . . . . . . . . . . . 1229--1242
Hiroaki Umeda and
Shiro Koseki and
Umpei Nagashima and
Michael W. Schmidt Parallelization of multireference
perturbation calculations with GAMESS 1243--1251
H. Takahashi and
T. Hori and
H. Hashimoto and
T. Nitta A hybrid QM/MM method employing real
space grids for QM water in the TIP4P
water solvents . . . . . . . . . . . . . 1252--1261
Christian Silvio Pomelli and
Jacopo Tomasi and
Roberto Cammi A Symmetry adapted tessellation of the
GEPOL surface: applications to molecular
properties in solution . . . . . . . . . 1262--1272
Gerhard Bringmann and
Jörg Mühlbacher and
Charlotte Repges and
Jörg Fleischhauer MD-based CD calculations for the
assignment of the absolute axial
configuration of the
naphthylisoquinoline alkaloid
dioncophylline A . . . . . . . . . . . . 1273--1278
Jerzy Cioslowski and
Agnieszka Szarecka First-principles conformational analysis
of the C$_{36}$H$_{36}$ spheriphane, a
prototype hydrocarbon host cage . . . . 1279--1286
Shura Hayryan and
Chin-Kun Hu and
Shun-Yun Hu and
Rung-Ji Shang Multicanonical parallel simulations of
proteins with continuous potentials . . 1287--1296
Glênisson de Oliveira and
Jan M. L. Martin and
Indira K. C. Silwal and
Joel F. Liebman Definitive heat of formation of
methylenimine, CH$_2$NH, and of
methylenimmonium ion, CH$_2$NH$_2^+$, by
means of W2 theory . . . . . . . . . . . 1297--1305
Wim Klopper and
Claire C. M. Samson and
György Tarczay and
Attila G. Császár Equilibrium inversion barrier of NH$_3$
from extrapolated coupled-cluster pair
energies . . . . . . . . . . . . . . . . 1306--1314
Noboru Watanabe and
Yohei Kamata and
Kota Yamauchi and
Yasuo Udagawa Calculation of X-ray scattering
intensities by means of the coupled
cluster singles and doubles model . . . 1315--1320
F. Wang and
H. Mackenzie-Ross and
D. A. Winkler and
I. E. McCarthy and
L. Campbell and
M. J. Brunger A high-resolution electron momentum
spectroscopy and density functional
theory study into the complete valence
electronic structure of allene . . . . . 1321--1333
Li Jie Wang and
Se Li and
Qian Shu Li Theoretical studies on a possible
synthesis reaction pathway on N$_8$
(C$_S$) clusters . . . . . . . . . . . . 1334--1339
Melissa L. P. Price and
Dennis Ostrovsky and
William L. Jorgensen Gas-phase and liquid-state properties of
esters, nitriles, and nitro compounds
with the OPLS-AA force field . . . . . . 1340--1352
Kaoru Kobayashi and
Yuko Sano and
Shigeru Nagase Theoretical study of endohedral
metallofullerenes: Sc$_{3 -
n}$La$_n$N@C$_{80}$ ($n = 0$--$3$) . . . 1353--1358
N. Balucani and
O. Asvany and
Y. T. Lee and
R. I. Kaiser and
N. Galland and
M. T. Rayez and
Y. Hannachi Gas-phase detection of the HBCC
(X$^1\Sigma$) molecule: a combined
crossed beam and computational study of
the B($^2$P) +
C$_2$H$_2$($^1\Sigma_g^+$) reaction . . 1359--1365
Stanislav Ya. Umanskii and
Konstantin P. Novoselov and
Airat Kh. Minushev and
Magdalena Siodmiak and
Gernot Frenking and
Anatoli A. Korkin Thermodynamics and kinetics of initial
gas phase reactions in chemical vapor
deposition of titanium nitride.
Theoretical study of TiCl$_4$
ammonolysis . . . . . . . . . . . . . . 1366--1376
Amnon Stanger and
Elena Tkachenko Strain induced bond localization in
strained aromatic compounds with
extended $\pi$ systems . . . . . . . . . 1377--1386
Petar M. Mitrasinovic Quantitative characterization of the P C
bonds in ylides of phosphorus . . . . . 1387--1395
Charles H. Langley and
Jenn-Huei Lii and
Norman L. Allinger Molecular mechanics (MM4) calculations
on carbonyl compounds part I: aldehydes 1396--1425
Charles H. Langley and
Jenn-Huei Lii and
Norman L. Allinger Molecular mechanics calculations on
carbonyl compounds. II. Open-chain
ketones . . . . . . . . . . . . . . . . 1426--1450
Charles H. Langley and
Jenn-Huei Lii and
Norman L. Allinger Molecular mechanics calculations on
carbonyl compounds. III. Cycloketones 1451--1475
Charles H. Langley and
Jenn-Huei Lii and
Norman L. Allinger Molecular mechanics calculations on
carbonyl compounds. IV. Heats of
formation . . . . . . . . . . . . . . . 1476--1483
Cheol Ho Choi and
Klaus Ruedenberg and
Mark S. Gordon New parallel optimal-parameter fast
multipole method (OPFMM) . . . . . . . . 1484--1501
Masahiko Hada and
Jian Wan and
Ryoichi Fukuda and
Hiroshi Nakatsuji Quasirelativistic study of $^{125}$Te
nuclear magnetic shielding constants and
chemical shifts . . . . . . . . . . . . 1502--1508
Asit K. Chandra and
Tadafumi Uchimaru Reaction of OH radical with mono-, di-,
and trichloroacetaldehyde: an ab initio
study . . . . . . . . . . . . . . . . . 1509--1521
Trung Ngoc Le and
Alexander M. Mebel and
Ralf I. Kaiser Ab initio study of C$_4$H$_3$ potential
energy surface and reaction of
ground-state carbon atom with propargyl
radical . . . . . . . . . . . . . . . . 1522--1535
Masae Takahashi and
Mitsuo Kira and
Kenkichi Sakamoto and
Thomas Müller and
Yitzhak Apeloig Theoretical prediction of vertical
transition energies of diaminosilylenes
and aminosubstituted disilenes . . . . . 1536--1541
Eluvathingal D. Jemmis and
M. Ramalingam and
Elambalassery G. Jayasree Cationic closo carboranes --- promising
weakly coordinating ions . . . . . . . . 1542--1551
Brian J. Duke Choice of Spin--Orbit Correction Terms
in Gaussian Model Chemistries . . . . . 1552--1556
Corinne Lacaze-Dufaure and
Tzonka Mineva and
Nino Russo On the interaction of Mo and Mo$_2$ with
NH$_3$, C$_2$H$_4$, and C$_3$H$_6$ . . . 1557--1564
David A. Hrovat and
Richard Vaughan Williams and
Alan C. Goren and
Weston Thatcher Borden B3LYP calculations on bishomoaromaticity
in substituted semibullvalenes* . . . . 1565--1573
Matthew L. Leininger and
C. David Sherrill and
Wesley D. Allen and
Henry F. Schaefer III Systematic Study of Selected
Diagonalization Methods for
Configuration Interaction Matrices . . . 1574--1589
Kathryn N. Rankin and
Russell J. Boyd A density functional theory study of the
dimers of HX (X = F, Cl, and Br) . . . . 1590--1597
R. B. Sunoj and
P. Lakshminarasimhan and
V. Ramamurthy and
J. Chandrasekhar Configuration interaction and density
functional study of the influence of
lithium cation complexation on vertical
and adiabatic excitation energies of
enones . . . . . . . . . . . . . . . . . 1598--1604
Matthias Prall and
Alexander Wittkopp and
Andrey A. Fokin and
Peter R. Schreiner Substituent effects on the Bergman
cyclization of (Z)-1,5-hexadiyne-3-enes:
a systematic computational study . . . . 1605--1614
Gernot Frenking and
Norman L. Allinger Editors' preface . . . . . . . . . . . . vii--viii
Paul von R. Schleyer An appreciation . . . . . . . . . . . . ix--xi
Verónica Barone and
Juan E. Peralta and
Rubén H. Contreras NMR $^3$J(C$_1$,H$_3$) couplings in
1-X-bicyclo[1.1.1]pentanes. FPT--DFT and
NBO studies of hyperconjugative
interactions and heavy atom substituent
effects . . . . . . . . . . . . . . . . 1615--1621
Lewis Whitehead and
Colin M. Edge and
Jonathan W. Essex Molecular dynamics simulation of the
hydrocarbon region of a biomembrane
using a reduced representation model . . 1622--1633
P. E. M. Siegbahn Modeling aspects of mechanisms for
reactions catalyzed by metalloenzymes 1634--1645
Jayaraman Chandrasekhar and
Martin Saunders and
William L. Jorgensen Efficient exploration of conformational
space using the stochastic search
method: application to $\beta$-peptide
oligomers . . . . . . . . . . . . . . . 1646--1654
J. Fernández Rico and
R. López and
G. Ramírez and
I. Ema Correspondence between GTO and STO
molecular basis sets . . . . . . . . . . 1655--1665
Jordi Poater and
Miquel Duran and
Miquel Sol\`a Parametrization of the Becke3-LYP hybrid
functional for a series of small
molecules using quantum molecular
similarity techniques . . . . . . . . . 1666--1678
György G. Ferenczy and
János G. Ángyán Intra- and intermolecular interactions
in crystals of polar molecules. A study
by the mixed quantum
mechanical/molecular mechanical
SCMP-NDDO method . . . . . . . . . . . . 1679--1690
V. D. de Viterbo and
J. C. Belchior Artificial neural networks applied for
studying metallic complexes . . . . . . 1691--1701
D. B. Chesnut Localization function study of
excitation processes in a set of small
isoelectronic molecules . . . . . . . . 1702--1711
Dimitris K. Agrafiotis and
Victor S. Lobanov Multidimensional scaling of
combinatorial libraries without explicit
enumeration . . . . . . . . . . . . . . 1712--1722
Miroslav Pinak Molecular dynamics simulation of thymine
glycol-lesioned DNA reveals specific
hydration at the lesion . . . . . . . . 1723--1731
A. Jongejan and
J. A. Jongejan and
W. R. Hagen Direct hydride transfer in the reaction
mechanism of quinoprotein alcohol
dehydrogenases: a quantum mechanical
investigation . . . . . . . . . . . . . 1732--1749
Yuan-Ping Pang and
Emanuele Perola and
Kun Xu and
Franklyn G. Prendergast EUDOC: a computer program for
identification of drug interaction sites
in macromolecules and drug leads from
chemical databases . . . . . . . . . . . 1750--1771
Tatyana Kuznetsova and
Bjòrn Kvamme Viabilty of atomistic potentials for
thermodynamic properties of carbon
dioxide at low temperatures . . . . . . 1772--1781
Carl S. Ewig and
Rajiv Berry and
Uri Dinur and
Jörg-Rüdiger Hill and
Ming-Jing Hwang and
Haiying Li and
Chris Liang and
Jon Maple and
Zhengwei Peng and
Thomas P. Stockfisch and
Thomas S. Thacher and
Lisa Yan and
Xiangshan Ni and
Arnold T. Hagler Derivation of class II force fields.
VIII. Derivation of a general quantum
mechanical force field for organic
compounds . . . . . . . . . . . . . . . 1782--1800
Wolfgang Kliesch EQUIPATH --- an equilibrial path tracing
routine for the use with the program
package GAUSSIAN94 . . . . . . . . . . . 1801--1816
Odonírio Abrahão-Júnior and
Paulo G. B. D. Nascimento and
Sérgio E. Galembeck Conformational analysis of the HIV-1
virus reverse transcriptase
nonnucleoside inhibitors: TIBO and
nevirapine . . . . . . . . . . . . . . . 1817--1829
F. Fogolari and
G. Esposito and
P. Viglino and
H. Molinari Molecular mechanics and dynamics of
biomolecules using a solvent continuum
model . . . . . . . . . . . . . . . . . 1830--1842
Xiaoliang Qian and
Daniel Strahs and
Tamar Schlick A new program for optimizing periodic
boundary models of solvated biomolecules
(PBCAID) . . . . . . . . . . . . . . . . 1843--1850
Eduardo J. Delgado and
Joel B. Alderete Prediction of infinite dilution activity
coefficients of chlorinated organic
compounds in aqueous solution from
quantum-chemical descriptors . . . . . . 1851--1856
Michael Schaefer and
Christian Bartels and
Fabrice Leclerc and
Martin Karplus Effective atom volumes for implicit
solvent models: comparison between
Voronoi volumes and minimum fluctuation
volumes . . . . . . . . . . . . . . . . 1857--1879
Sor-Koon Goh and
Dennis S. Marynick Ability of fullerenes to act as $\eta^6$
ligands in transition metal complexes. A
comparative PM3(tm)--density functional
theory study . . . . . . . . . . . . . . 1881--1886
Bing Wang and
Ulrich Fleischer and
James F. Hinton and
Peter Pulay Accurate prediction of proton chemical
shifts. I. Substituted aromatic
hydrocarbons . . . . . . . . . . . . . . 1887--1895
Daniel K. W. Mok and
Edmond P. F. Lee and
Foo-Tim Chau and
John M. Dyke Ab initio calculations on the and states
of AlNC and simulation of the AlNC--
emission spectra . . . . . . . . . . . . 1896--1906
Yu-guo Tao and
Yi-hong Ding and
Jian-jun Liu and
Ze-sheng Li and
Xu-ri Huang and
Chia-Chung Sun Theoretical study on reaction mechanism
of the CF radical with nitrogen dioxide 1907--1919
Olivier Quinet and
Beno\^\it Champagne and
Bernard Kirtman Analytical TDHF second derivatives of
dynamic electronic polarizability with
respect to nuclear coordinates.
Application to the dynamic ZPVA
correction . . . . . . . . . . . . . . . 1920--1932
B. Mannfors and
N. G. Mirkin and
K. Palmo and
S. Krimm A polarizable electrostatic model of the
$N$-methylacetamide dimer . . . . . . . 1933--1943
J. Hauck and
K. Mika Ground-state structures of polymers . . 1944--1955
Nicolas Budin and
Nicolas Majeux and
Catherine Tenette-Souaille and
Amedeo Caflisch Structure-based ligand design by a
build-up approach and genetic algorithm
search in conformational space . . . . . 1956--1970
Michael Thormann and
Miquel Pons Massive docking of flexible ligands
using environmental niches in
parallelized genetic algorithms . . . . 1971--1982
Junichi Higo and
Yasunobu Sugimoto and
Katsuzo Wakabayashi and
Haruki Nakamura Collective motions of myosin head
derived from backbone molecular dynamics
and combination with X-ray solution
scattering data . . . . . . . . . . . . 1983--1994
Susumu Yanagisawa and
Takao Tsuneda and
Kimihiko Hirao Investigation of the use of density
functionals in second- and third-row
transition metal dimer calculations . . 1995--2009
Young-Kyu Han Density functional studies of AnF$_6$
(An = U, Np, and Pu) and UF$_{6 -
n}$Cl$_n$ ($n = 1$--$6$) using hybrid
functionals: geometries and vibrational
frequencies . . . . . . . . . . . . . . 2010--2017
Marta Filizola and
Silvina M. Tasso and
Gilda H. Loew and
Hugo O. Villar Global physicochemical properties as
activity discriminants for the mGluR1
subtype of metabotropic glutamate
receptors . . . . . . . . . . . . . . . 2018--2027
Chao-Ping Liu and
J. J. Soares Neto Revisiting the generator coordinate
approximation for calculating the
ro-vibrational energies of H . . . . . . 2028--2039
Robert J. Woods Book review: \booktitleComputational
Chemistry. A Practical Guide for
Applying Techniques to Real World
Problems, By David Young . . . . . . . . 2040--2040
B. Jayaram and
K. McConnell and
S. B. Dixit and
A. Das and
D. L. Beveridge Free-energy component analysis of 40
protein--DNA complexes: a consensus view
on the thermodynamics of binding at the
molecular level . . . . . . . . . . . . 1--14
Shuanghong Huo and
Irina Massova and
Peter A. Kollman Computational alanine scanning of the
1:1 human growth hormone--receptor
complex . . . . . . . . . . . . . . . . 15--27
Harold A. Scheraga and
Jaroslaw Pillardy and
Adam Liwo and
Jooyoung Lee and
Cezary Czaplewski and
Daniel R. Ripoll and
William J. Wedemeyer and
Yelena A. Arnautova Evolution of physics-based methodology
for exploring the conformational energy
landscape of proteins . . . . . . . . . 28--34
Lalith Perera and
Thomas A. Darden and
Lee G. Pedersen Predicted solution structure of zymogen
human coagulation FVII . . . . . . . . . 35--47
Martin J. Field Simulating enzyme reactions: Challenges
and perspectives . . . . . . . . . . . . 48--58
Maricel Torrent and
Djamaladdin G. Musaev and
Harold Basch and
Keiji Morokuma Computational studies of reaction
mechanisms of methane monooxygenase and
ribonucleotide reductase . . . . . . . . 59--76
Keith D. Ball and
Burak Erman and
Ken A. Dill The elastic net algorithm and protein
structure prediction . . . . . . . . . . 77--83
Dean J. Tantillo and
K. N. Houk Transition state docking: a probe for
noncovalent catalysis in biological
systems. Application to
antibody-catalyzed ester hydrolysis . . 84--95
Ramkumar Rajamani and
Jiali Gao Combined QM/MM study of the opsin shift
in bacteriorhodopsin . . . . . . . . . . 96--105
Marek Orzechowski and
Piotr Cieplak and
Lucjan Piela Theoretical calculation of the
coiled-coil stability in water in the
context of its possible use as a
molecular rack . . . . . . . . . . . . . 106--110
Jaroslaw Meller and
Michael Wagner and
Ron Elber Maximum feasibility guideline in the
design and analysis of protein folding
potentials . . . . . . . . . . . . . . . 111--118
Pemra Doruker and
Robert L. Jernigan and
Ivet Bahar Dynamics of large proteins through
hierarchical levels of coarse-grained
structures . . . . . . . . . . . . . . . 119--127
Walter Rocchia and
Sundaram Sridharan and
Anthony Nicholls and
Emil Alexov and
Alessandro Chiabrera and
Barry Honig Rapid grid-based construction of the
molecular surface and the use of induced
surface charge to calculate reaction
field energies: Applications to the
molecular systems and geometric objects 128--137
Corey Hardin and
Michael P. Eastwood and
Michael Prentiss and
Z. Luthey-Schulten and
Peter G. Wolynes Folding funnels: the key to robust
protein structure prediction . . . . . . 138--146
Brian N. Dominy and
Charles L. Brooks III Identifying native-like protein
structures using physics-based
potentials . . . . . . . . . . . . . . . 147--160
D. K. Klimov and
D. Thirumalai Is there a unique melting temperature
for two-state proteins? . . . . . . . . 161--165
Hagai Meirovitch Polymer collapse, protein folding, and
the percolation threshold . . . . . . . 166--171
Ailan Cheng and
David J. Diller and
Steven L. Dixon and
William J. Egan and
George Lauri and
Kenneth M. Merz Jr. Computation of the physio-chemical
properties and data mining of large
molecular collections . . . . . . . . . 172--183
Sam Kalat and
Geoff Mann and
Jan Hermans Qmd-plot: a graphical utility for rapid
preliminary analysis of time series of
fluctuating data, developed in the
context of molecular dynamics
simulations . . . . . . . . . . . . . . 184--188
Marek Wojciechowski and
Jeffrey Skolnick Docking of small ligands to
low-resolution and theoretically
predicted receptor structures . . . . . 189--197
I. Jen Chen and
Daxu Yin and
Alexander D. MacKerell Jr. Combined ab initio /empirical approach
for optimization of Lennard-Jones
parameters for polar-neutral compounds 199--213
Olgun Guvench and
Jörg Weiser and
Peter Shenkin and
István Kolossváry and
W. Clark Still Application of the frozen atom
approximation to the GB/SA continuum
model for solvation free energy . . . . 214--221
Aline Thaís Bruni and
Vitor B. P. Leite and
Márcia M. C. Ferreira Conformational analysis: a new approach
by means of chemometrics . . . . . . . . 222--236
Shuhua Li and
Jing Ma and
Yuansheng Jiang Linear scaling local correlation
approach for solving the coupled cluster
equations of large systems . . . . . . . 237--244
J. L. Klepeis and
C. A. Floudas Ab initio prediction of helical segments
in polypeptides . . . . . . . . . . . . 245--266
Yu-Dong Cai and
Xiao-Jun Liu and
Xue-Biao Xu and
Kuo-Chen Chou Support vector machines for predicting
HIV protease cleavage sites in protein 267--274
Andreas Klamt and
Frank Eckert and
Martin Hornig and
Michael E. Beck and
Thorsten Bürger Prediction of aqueous solubility of
drugs and pesticides with COSMO-RS . . . 275--281
Thomas Strassner and
Markus Busold and
Wolfgang A. Herrmann MM3 parametrization of four- and
five-coordinated rhenium complexes by a
genetic algorithm --- which factors
influence the optimization performance? 282--290
Patrizia Calaminici and
Karl Jug and
Andreas M. Köster and
Cécile Arbez-Gindre and
Constantinos G. Screttas Mechanism for large first
hyperpolarizabilities of phosphonic acid
stilbene derivatives . . . . . . . . . . 291--297
Raiker Witter and
Wolfram Prie and
Ulrich Sternberg Chemical shift driven geometry
optimization . . . . . . . . . . . . . . 298--305
Reinhart Ahlrichs and
Kakha Tsereteli Efficient linear algebra routines for
symmetric matrices stored in packed form 306--309
Tsutomu Ikegami and
Suehiro Iwata Spectral density calculation by using
the Chebyshev expansion . . . . . . . . 310--318
S. Dennis and
S. Vajda Semiglobal simplex optimization and its
application to determining the preferred
solvation sites of proteins . . . . . . 319--334
Primo\vz Pristov\vsek and
Heinz Rüterjans and
Roman Jerala Semiautomatic sequence-specific
assignment of proteins based on the
tertiary structure --- the program \tt
st2nmr . . . . . . . . . . . . . . . . . 335--340
Caterina Benzi and
Roberto Improta and
Giovanni Scalmani and
Vincenzo Barone Quantum mechanical study of the
conformational behavior of proline and
4R-hydroxyproline dipeptide analogues in
vacuum and in aqueous solution . . . . . 341--350
Emma Sigfridsson and
Ulf Ryde and
Bruce L. Bush Restrained point-charge models for
disaccharides . . . . . . . . . . . . . 351--364
Jacco Van de Streek and
Paul Verwer and
Piet Bennema and
Elias Vlieg On the irrelevance of electrostatics for
the crystal structures and polymorphism
of long even $n$-alkanes . . . . . . . . 365--370
Thomas Krüger and
Alexander F. Sax Oligovalent link atoms in embedding
calculations . . . . . . . . . . . . . . 371--377
Kazuhiro Ishida Accompanying coordinate expansion
formulas derived with the solid harmonic
gradient . . . . . . . . . . . . . . . . 378--393
Takao Otsuka and
Seiji Koizumi and
Kazunaka Endo and
Hiroyuki Kawabe and
Delano P. Chong Theoretical Auger electron spectra of
polymers by density functional theory
calculations using model dimers . . . . 394--401
Shuzo Yoshioki Dynamics of a protein and water
molecules surrounding the protein:
Hydrogen-bonding between vibrating water
molecules and a fluctuating protein . . 402--413
Zheng-wang Qu and
Hui Zhu and
Ze-sheng Li and
Qi-yuan Zhang Theoretical study on the mechanism of
the gas-phase reaction of diborane(3)
anion with carbon disulfide . . . . . . 414--419
Alexander A. Auer and
Trygve Helgaker and
Wim Klopper Basis-set completeness profiles in two
dimensions . . . . . . . . . . . . . . . 420--425
Wensheng Cai and
Xueguang Shao A fast annealing evolutionary algorithm
for global optimization . . . . . . . . 427--435
Kangcheng Zheng and
Juping Wang and
Yong Shen and
Wenlie Peng and
Fengcun Yun Studies on $4,7$-di-substitution effects
of one ligand in [Ru(Phen)$_3$]$^2$ with
DFT method . . . . . . . . . . . . . . . 436--443
H. Valdés and
J. A. Sordo Ab initio and DFT studies on van der
Waals trimers: The OCS $\cdot$
(CO$_2$)$_2$ complexes . . . . . . . . . 444--455
Bouke P. Van Eijck Crystal structure predictions using five
space groups with two independent
molecules. The case of small organic
acids . . . . . . . . . . . . . . . . . 456--462
Shugo Nakamura and
Daisuke Kyono and
Mitsunori Ikeguchi and
Kentaro Shimizu New method for parallel computation of
Hessian matrix of conformational energy
function in internal coordinates . . . . 463--469
Satoshi Ono and
Masataka Kuroda and
Junichi Higo and
Nobuyuki Nakajima and
Haruki Nakamura Calibration of force-field dependency in
free energy landscapes of peptide
conformations by quantum chemical
calculations . . . . . . . . . . . . . . 470--476
Gwon Hee Ko and
William H. Fink Rapidly converging lattice sums for
nonelectrostatic interactions . . . . . 477--483
Khuloud Jaqaman and
Peter J. Ortoleva New space warping method for the
simulation of large-scale macromolecular
conformational changes . . . . . . . . . 484--491
Bing Wang and
James F. Hinton and
Peter Pulay Accurate prediction of proton chemical
shifts. II. Peptide analogues . . . . . 492--497
Matthew P. Repasky and
Jayaraman Chandrasekhar and
William L. Jorgensen Improved semiempirical heats of
formation through the use of bond and
group equivalents . . . . . . . . . . . 498--510
Hideaki Nakamura Monte Carlo sampling algorithm for
searching a scale-transformed energy
space of polypeptides . . . . . . . . . 511--516
Emilio Gallicchio and
Linda Yu Zhang and
Ronald M. Levy The SGB/NP hydration free energy model
based on the surface generalized Born
solvent reaction field and novel
nonpolar hydration free energy
estimators . . . . . . . . . . . . . . . 517--529
S. K. Mishra and
P. C. Mishra An ab initio theoretical study of
electronic structure and properties of
2'-deoxyguanosine in gas phase and
aqueous media . . . . . . . . . . . . . 530--540
Philippe Marsal and
Michel Roche Variational treatment of the vibrational
Hamiltonian for NH$_3$ and H$_2$NO . . . 541--547
Alessandra Villa and
Alan E. Mark Calculation of the free energy of
solvation for neutral analogs of amino
acid side chains . . . . . . . . . . . . 548--553
J. Muñoz and
X. Barril and
B. Hernández and
Modesto Orozco and
F. Javier Luque Hydrophobic similarity between
molecules: a MST-based hydrophobic
similarity index . . . . . . . . . . . . 554--563
Wenjian Liu and
Robert Franke Comprehensive relativistic ab initio and
density functional theory studies on
PtH, PtF, PtCl, and Pt(NH$_3$)$_2$Cl$_2$ 564--575
Michal Dallos and
Hans Lischka and
Elizete Ventura Do Monte and
Michael Hirsch and
Wolfgang Quapp Determination of energy minima and
saddle points using multireference
configuration interaction methods in
combination with reduced gradient
following: the S$_0$ surface of H$_2$CO
and the T$_1$ and T$_2$ surfaces of
acetylene . . . . . . . . . . . . . . . 576--583
Chang Kon Kim and
Hongok Won and
Hoon Sik Kim and
Yong Soo Kang and
Hong Guang Li and
Chan Kyung Kim Erratum: Density functional theory
studies on the dissociation energies of
metallic salts: Relationship between
lattice and dissociation energies . . . 584--584
Roger A. Klein Ab initio conformational studies on
diols and binary diol-water systems
using DFT methods. Intramolecular
hydrogen bonding and 1:1 complex
formation with water . . . . . . . . . . 585--599
Oleg V. Tsodikov and
M. Thomas Record Jr. and
Yuri V. Sergeev Novel computer program for fast exact
calculation of accessible and molecular
surface areas and average surface
curvature . . . . . . . . . . . . . . . 600--609
Nicolas Ferré and
Xavier Assfeld and
Jean-Louis Rivail Specific force field parameters
determination for the hybrid ab initio
QM/MM LSCF method . . . . . . . . . . . 610--624
Jian-Jun Liu and
Yi-Hong Ding and
Yu-Guo Tao and
Ji-Kang Feng and
Chia-Chung Sun Theoretical study on the mechanism of
the $^1$CHCl + NO reaction . . . . . . . 625--649
Emma Langella and
Nadia Rega and
Roberto Improta and
Orlando Crescenzi and
Vincenzo Barone Conformational analysis of the tyrosine
dipeptide analogue in the gas phase and
in aqueous solution by a density
functional/continuum solvent model . . . 650--661
Jean-Luc Fattebert and
François Gygi Density functional theory for efficient
ab initio molecular dynamics simulations
in solution . . . . . . . . . . . . . . 662--666
John E. Carpenter Computation of pressure components due
to Class II force fields . . . . . . . . 667--672
Robert D. Skeel and
Ismail Tezcan and
David J. Hardy Multiple grid methods for classical
molecular dynamics . . . . . . . . . . . 673--684
Salvador León and
David Zanuy and
Carlos Alemán Influence of the presence of small gas
molecules in the structure of comblike
polyacrylates: a Monte Carlo study . . . 685--696
Peter Comba and
Rainer Remenyi A new molecular mechanics force field
for the oxidized form of blue copper
proteins . . . . . . . . . . . . . . . . 697--705
Paulo F. B. Gonçalves and
Hubert Stassen New approach to free energy of solvation
applying continuum models to molecular
dynamics simulation . . . . . . . . . . 706--714
Rajmund Ka\'zmierkiewicz and
Adam Liwo and
Harold A. Scheraga Energy-based reconstruction of a protein
backbone from its $\alpha$-carbon trace
by a Monte-Carlo method . . . . . . . . 715--723
Jérôme Golebiowski and
Véronique Lamare and
Manuel F. Ruiz-López Rb$^+$ /Cs$^+$ selectivity of benzo and
tribenzo derivatives of the 21C7 crown
ether. A density functional study . . . 724--731
Obis Castaño and
Raúl Palmeiro and
Luis Manuel Frutos and
José Luisandrés Role of bifurcation in the bond shifting
of cyclooctatetraene . . . . . . . . . . 732--736
Vladislav Vasilyev and
Enrico O. Purisima A fast pairwise evaluation of molecular
surface area . . . . . . . . . . . . . . 737--745
Patrick Bultinck and
Stijn Augustynen and
Hans W. Hilbers and
Ed E. Moret and
Jan P. Tollenaere Generate: a program for $3$-D structure
generation and conformational analysis
of peptides and peptidomimetics . . . . 746--754
John E. Carpenter and
Alan Christoffels and
Yael Weinbach and
Winston A. Hide Assessment of the parallelization
approach of \tt d2\_cluster for
high-performance sequence clustering . . 755--757
Lucas Visscher The Dirac equation in quantum chemistry:
Strategies to overcome the current
computational problems . . . . . . . . . 759--766
Hermann Stoll and
Bernhard Metz and
Michael Dolg Relativistic energy-consistent
pseudopotentials --- recent developments 767--778
Christoph Van Wüllen Spin densities in two-component
relativistic density functional
calculations: Noncollinear versus
collinear approach . . . . . . . . . . . 779--785
Kenneth G. Dyall A systematic sequence of relativistic
approximations . . . . . . . . . . . . . 786--793
Martin Kaupp and
Roman Reviakine and
Olga L. Malkina and
Alexei Arbuznikov and
Bernd Schimmelpfennig and
Vladimir G. Malkin Calculation of electronic $g$-tensors
for transition metal complexes using
hybrid density functionals and atomic
meanfield spin-orbit operators . . . . . 794--803
J. Autschbach and
S. Siekierski and
M. Seth and
P. Schwerdtfeger and
W. H. E. Schwarz Dependence of relativistic effects on
electronic configuration in the neutral
atoms of $d$- and $f$-block elements . . 804--813
Trond Saue and
Trygve Helgaker Four-component relativistic Kohn--Sham
theory . . . . . . . . . . . . . . . . . 814--823
Martin Kleinschmidt and
Jörg Tatchen and
Christel M. Marian Spin-orbit coupling of DFT/MRCI
wavefunctions: Method, test
calculations, and application to
thiophene . . . . . . . . . . . . . . . 824--833
Maite García-Hernández and
Christa Lauterbach and
Sven Krüger and
Alexei Matveev and
Notker Rösch Comparative study of relativistic
density functional methods applied to
actinide species AcO$_2^{2+}$ and
AcF$_6$ for Ac = U, Np . . . . . . . . . 834--846
Takahito Nakajima and
Takeshi Yanai and
Kimihiko Hirao Relativistic electronic structure theory 847--860
Richard H. Henchman and
J. Andrew McCammon Extracting hydration sites around
proteins from explicit water simulations 861--869
Andre Elvas Pereira Da Silva and
Geraldo Magela E. Silva Quantum bits with polyacetylene . . . . 870--873
Xiang-Yuan Li and
Chun-Xiu Hu Theoretical investigation of electron
transfer transition in
tetracyanoethylene-contained organic
complexes . . . . . . . . . . . . . . . 874--886
Michael Hirsch and
Wolfgang Quapp Improved RGF method to find saddle
points . . . . . . . . . . . . . . . . . 887--894
Johannes Neugebauer and
Markus Reiher and
Carsten Kind and
Bernd A. Hess Quantum chemical calculation of
vibrational spectra of large molecules
--- Raman and IR spectra for
Buckminsterfullerene . . . . . . . . . . 895--910
Effendi Widjaja and
Marc Garland Pure component spectral reconstruction
from mixture data using SVD, global
entropy minimization, and simulated
annealing. Numerical investigations of
admissible objective functions using a
synthetic 7-species data set . . . . . . 911--919
Fan Wang and
Lemin Li Analytical energy gradient evaluation in
relativistic and nonrelativistic density
functional calculations . . . . . . . . 920--927
Yoshiaki Amatatsu Ab initio study on the electronic
structures of styrene in the
Franck--Condon region . . . . . . . . . 928--937
Katherine R. Greene and
Kyle A. Beran Isomers of C$_{20}$: an energy profile 938--942
R. J. Buenker and
J. L. Whitten and
E. I. Izgorodina and
H.-P. Liebermann and
D. B. Kokh Use of exchange maximization to generate
starting vectors for self-consistent
field calculations on metal
cluster/adsorbate systems . . . . . . . 943--949
Yoshiaki Amatatsu Ab initio study on the photochemical
behavior of styrene . . . . . . . . . . 950--956
Henryk A. Witek and
Yoong-Kee Choe and
James P. Finley and
Kimihiko Hirao Intruder state avoidance multireference
Mòller--Plesset perturbation theory . . . 957--965
Mustafa R. Helal and
Yaser A. Yousef and
Akef T. Afaneh Ab initio calculations of the
stabilization energies of the
conformational and the structural
isomers of C$_3$H$_7$X where X = F, Cl,
and Br . . . . . . . . . . . . . . . . . 966--976
Kalju Kahn and
Thomas C. Bruice Parameterization of OPLS--AA force field
for the conformational analysis of
macrocyclic polyketides . . . . . . . . 977--996
Hajime Torii Intensity-carrying modes important for
vibrational polarizabilities and
hyperpolarizabilities of molecules:
Derivation from the algebraic properties
of formulas and applications . . . . . . 997--1006
André Severo Pereira Gomes and
Rogério Custodio Exact Gaussian expansions of Slater-type
atomic orbitals . . . . . . . . . . . . 1007--1012
A.-L. Derepas and
J.-M. Soudan and
V. Brenner and
J.-P. Dognon and
Ph. Millié Can we understand the different
coordinations and structures of
closed-shell metal cation-water
clusters? . . . . . . . . . . . . . . . 1013--1030
Jian-Jun Liu and
Yi-Hong Ding and
Yu-Guo Tao and
Ji-Kang Feng and
Chia-Chung Sun Theoretical study on the mechanism of
the $^3$CH$_2$ + NO$_2$ reaction . . . . 1031--1044
Daniel J. Price and
Charles L. Brooks III Modern protein force fields behave
comparably in molecular dynamics
simulations . . . . . . . . . . . . . . 1045--1057
Ulf Ryde and
Lars Olsen and
Kristina Nilsson Quantum chemical geometry optimizations
in proteins using crystallographic raw
data . . . . . . . . . . . . . . . . . . 1058--1070
T. Ida and
M. Mizuno and
K. Endo Electronic state of small and large
cavities for methane hydrate . . . . . . 1071--1075
Maciej Bobrowski and
Adam Liwo and
Stanis\law O\ldziej and
Danuta Jeziorek and
Tadeusz Ossowski Ab initio study of the mechanism of
singlet-dioxygen addition to
hydroxyaromatic compounds: Negative
evidence for the involvement of peroxa
and endoperoxide intermediates . . . . . 1076--1089
Buddhadeb Mallik and
Artem Masunov and
Themis Lazaridis Distance and exposure dependent
effective dielectric function . . . . . 1090--1099
T. W. Whitfield and
John E. Straub Gravitational smoothing as a global
optimization strategy . . . . . . . . . 1100--1103
A. S. Shalabi F$_A$(I):Au$^+$ and F$_A$(II):Cu$^+$
laser activity and photographic
sensitization at the low coordinated
surfaces of AgBr ab initio calculations 1104--1120
Ron Shepard and
Isaiah Shavitt and
Hans Lischka Reducing I/O costs for the eigenvalue
procedure in large-scale configuration
interaction calculations . . . . . . . . 1121--1125
Fatih Ya\csar and
Handan Arkin and
Tarik Çelik and
Bernd A. Berg and
Hagai Meirovitch Efficiency of the multicanonical
simulation method as applied to peptides
of increasing size: the heptapeptide
deltorphin . . . . . . . . . . . . . . . 1127--1134
L. Y. A. Dávila and
M. J. Caldas Applicability of MNDO techniques AM1 and
PM3 to ring-structured polymers . . . . 1135--1142
Sonja M. Schwarzl and
Thomas B. Tschopp and
Jeremy C. Smith and
Stefan Fischer Can the calculation of ligand binding
free energies be improved with continuum
solvent electrostatics and an ideal-gas
entropy correction? . . . . . . . . . . 1143--1149
Jon Baker and
Peter Pulay An efficient parallel algorithm for the
calculation of canonical MP2 energies 1150--1156
José Pitarch-Ruiz and
José Sánchez-Marín and
Daniel Maynau Reducing CAS-SDCI space. Using selected
spaces in configuration interaction
calculations in an efficient way . . . . 1157--1165
Haruyuki Nakano and
Ryuma Uchiyama and
Kimihiko Hirao Quasi-degenerate perturbation theory
with general multiconfiguration
self-consistent field reference
functions . . . . . . . . . . . . . . . 1166--1175
Thomas E. Exner and
Matthias Keil and
Jürgen Brickmann Pattern recognition strategies for
molecular surfaces. I. Pattern
generation using fuzzy set theory . . . 1176--1187
Thomas E. Exner and
Matthias Keil and
Jürgen Brickmann Pattern recognition strategies for
molecular surfaces. II. Surface
complementarity . . . . . . . . . . . . 1188--1197
F. De Proft and
C. Van Alsenoy and
A. Peeters and
W. Langenaeker and
P. Geerlings Atomic charges, dipole moments, and
Fukui functions using the Hirshfeld
partitioning of the electron density . . 1198--1209
Pekka Mark and
Lennart Nilsson Structure and dynamics of liquid water
with different long-range interaction
truncation and temperature control
methods in molecular dynamics
simulations . . . . . . . . . . . . . . 1211--1219
He Jiang and
Dominic Appadoo and
Evan Robertson and
Don McNaughton A comparison of predicted and
experimental vibrational spectra in some
small fluorocarbons . . . . . . . . . . 1220--1225
Kenzi Hori and
Nobumitsu Dou and
Katsuhiko Okano and
Ai Ohgami and
Hiroshi Tsukube Stable conformations of 12-crown-O$_3$N
and its Li$^+$ complex in aqueous
solution . . . . . . . . . . . . . . . . 1226--1235
Michelle Kuttel and
J. W. Brady and
Kevin J. Naidoo Carbohydrate solution simulations:
Producing a force field with
experimentally consistent primary
alcohol rotational frequencies and
populations . . . . . . . . . . . . . . 1236--1243
Ray Luo and
Laurent David and
Michael K. Gilson Accelerated Poisson--Boltzmann
calculations for static and dynamic
systems . . . . . . . . . . . . . . . . 1244--1253
Vladislav Vasilyev Determination of the effective
dielectric constant from the accurate
solution of the Poisson equation . . . . 1254--1265
Athanassios C. Tsipis and
Constantinos A. Tsipis Mechanistic aspects of the dehydration
and dehydrohalogenation of
halo-hydroxyformaldoxime conformers. A
quantum chemical model study . . . . . . 1266--1280
Jens Antony and
Nohad Gresh and
Lars Olsen and
Lars Hemmingsen and
Christopher J. Schofield and
Rogert Bauer Binding of D- and L-captopril inhibitors
to metallo-$\beta$-lactamase studied by
polarizable molecular mechanics and
quantum mechanics . . . . . . . . . . . 1281--1296
Alexey Onufriev and
David A. Case and
Donald Bashford Effective Born radii in the generalized
Born approximation: the importance of
being perfect . . . . . . . . . . . . . 1297--1304
Pere Constans Linear scaling approaches to quantum
macromolecular similarity: Evaluating
the similarity function . . . . . . . . 1305--1313
Stephen J. Titmuss and
Peter L. Cummins and
Alistair P. Rendell and
Andrey A. Bliznyuk and
Jill E. Gready Comparison of linear-scaling
semiempirical methods and combined
quantum mechanical/molecular mechanical
methods for enzymic reactions. II. An
energy decomposition analysis . . . . . 1314--1322
Junichi Higo and
Masayoshi Nakasako Hydration structure of human lysozyme
investigated by molecular dynamics
simulation and cryogenic X-ray crystal
structure analyses: On the correlation
between crystal water sites, solvent
density, and solvent dipole . . . . . . 1323--1336
Hajime Takashima and
So Yamada and
Shigeru Obara and
Kunihiro Kitamura and
Shinjiro Inabata and
Nobuaki Miyakawa and
Kazutoshi Tanabe and
Umpei Nagashima A novel parallel algorithm for
large-scale Fock matrix construction
with small locally distributed memory
architectures: RT parallel algorithm . . 1337--1346
Xavier Fradera and
Miquel Sol\`a Electron localization and delocalization
in open-shell molecules . . . . . . . . 1347--1356
Qingzhang Lu and
Guoli Shen and
Ruqin Yu Genetic training of network using chaos
concept: Application to QSAR studies of
vibration modes of tetrahedral halides 1357--1365
Yang Wu and
Yi-Hong Ding and
Jing-Fa Xiao and
Ze-Sheng Li and
Xu-Ri Huang and
Chia-Chung Sun Direct ab initio dynamics study on the
rate constants and kinetic isotope
effect for the reactions of H atoms with
GeD$_n$ (CH$_3$)$_{4 - n}$ ($n =
1$--$4$) . . . . . . . . . . . . . . . . 1366--1374
Konstantin P. Novoselov and
Denis B. Shirabaikin and
Stanislav Ya. Umanskii and
Alexander S. Vladimirov and
Airat Kh. Minushev and
Anatoli A. Korkin CHIMERA: a software tool for reaction
rate calculations and kinetics and
thermodynamics analysis . . . . . . . . 1375--1389
Meng-Sheng Liao and
Steve Scheiner Comparative study of metal-porphyrins,
-porphyrazines, and -phthalocyanines . . 1391--1403
Li Xie and
Haiyan Liu The treatment of solvation by a
generalized Born model and a
self-consistent charge-density
functional theory-based tight-binding
method . . . . . . . . . . . . . . . . . 1404--1415
D. Kony and
W. Damm and
S. Stoll and
W. F. Van Gunsteren An improved OPLS--AA force field for
carbohydrates . . . . . . . . . . . . . 1416--1429
Denis Jacquemin and
Beno\^\it Champagne and
Jean-Marie André and
Erik Deumens and
Yngve öhrn Integral algorithm and density matrix
integration scheme for ab initio band
structure calculations on polymeric
systems . . . . . . . . . . . . . . . . 1430--1444
Masahiro Kinoshita and
Yoshiki Sugai Methodology of predicting approximate
shapes and size distribution of
micelles: Illustration for simple models 1445--1455
Jing-Fa Xiao and
Ze-Sheng Li and
Jing-Yao Liu and
Li Sheng and
Chia-Chung Sun DFT and ab initio direct dynamics
studies on the hydrogen abstraction
reactions of chlorine atoms with CH$_{4
- n}$F$_n$ ($n = 1$--$3$) . . . . . . . 1456--1465
Akihiro Morita Water polarizability in condensed phase:
ab initio evaluation by cluster approach 1466--1471
Shingo Urata and
Seiji Tsuzuki and
Masuhiro Mikami and
Akira Takada and
Tadafumi Uchimaru and
Akira Sekiya Analysis of the intermolecular
interaction between CH$_3$OCH$_3$,
CF$_3$OCH$_3$, CF$_3$OCF$_3$, and
CH$_4$: High level ab initio
calculations . . . . . . . . . . . . . . 1472--1479
Grant D. Smith and
Oleg Borodin and
Dmitry Bedrov A revised quantum chemistry-based
potential for poly(ethylene oxide) and
its oligomers in aqueous solution . . . 1480--1488
Friedrich Biegler-König and
Jens Schönbohm Update of the AIM2000-Program for atoms
in molecules . . . . . . . . . . . . . . 1489--1494
Olivier Quinet and
Beno\^\it Champagne and
Bernard Kirtman Analytical TDHF second derivatives of
dynamic electronic polarizability with
respect to nuclear coordinates.
Application to the dynamic ZPVA
correction . . . . . . . . . . . . . . . 1495--1496
Pengyu Ren and
Jay W. Ponder Consistent treatment of inter- and
intramolecular polarization in molecular
mechanics calculations . . . . . . . . . 1497--1506
Jan Sefcik and
Ersan Demiralp and
Tahir Cagin and
William A. Goddard III Dynamic Charge Equilibration-Morse
stretch force field: Application to
energetics of pure silica zeolites . . . 1507--1514
George A. Kaminski and
Harry A. Stern and
B. J. Berne and
Richard A. Friesner and
Yixiang X. Cao and
Robert B. Murphy and
Ruhong Zhou and
Thomas A. Halgren Development of a polarizable force field
for proteins via ab initio quantum
chemistry: First generation model and
gas phase tests . . . . . . . . . . . . 1515--1531
Alain Chaumont and
Georges Wipff Macrotricyclic quaternary tetraammonium
receptors: Halide anion recognition and
interfacial activity at an aqueous
interface. A molecular dynamics
investigation . . . . . . . . . . . . . 1532--1543
E. Keith Davies and
Meir Glick and
Karl N. Harrison and
W. Graham Richards Pattern recognition and massively
distributed computing . . . . . . . . . 1544--1550
Jin-Qiu Lin and
Shi-Wei Luo and
Yun-Dong Wu Theoretical study of sheets formed by
$\beta$-peptides . . . . . . . . . . . . 1551--1558
Irina Massova and
Peter A. Kollman p K$_a$, MM, and QM studies of
mechanisms of $\beta$-lactamases and
penicillin-binding proteins: Acylation
step . . . . . . . . . . . . . . . . . . 1559--1576
Philippe Barthe and
Christian Roumestand and
Hél\`ene Déméné and
Laurent Chiche Helix motion in protein C12A-p8$^{MTCP}
1$: Comparison of molecular dynamics
simulations and multifield NMR
relaxation data . . . . . . . . . . . . 1577--1586
Dimas Suárez and
Natalia Díaz and
Kenneth M. Merz Jr. Molecular dynamics simulations of the
dinuclear zinc-$\beta$-lactamase from
Bacteroides fragilis complexed with
imipenem . . . . . . . . . . . . . . . . 1587--1600
Matthew P. Repasky and
Jayaraman Chandrasekhar and
William L. Jorgensen PDDG/PM3 and PDDG/MNDO: Improved
semiempirical methods . . . . . . . . . 1601--1622
Araz Jakalian and
David B. Jack and
Christopher I. Bayly Fast, efficient generation of
high-quality atomic charges. AM1-BCC
model: II. Parameterization and
validation . . . . . . . . . . . . . . . 1623--1641
Qian-Shu Li and
Rui-Hua Lü and
Yaoming Xie and
Henry F. Schaefer III Molecules for materials: Germanium
hydride neutrals and anions. Molecular
structures, electron affinities, and
thermochemistry of GeH$_n$ /GeH ($n =
0$--$4$) and Ge$_2$H$_n$ /Ge$_2$H ($n =
0$--$6$) . . . . . . . . . . . . . . . . 1642--1655
Visvaldas Kairys and
Michael K. Gilson Enhanced docking with the mining minima
optimizer: Acceleration and side-chain
flexibility . . . . . . . . . . . . . . 1656--1670
Gernot Frenking and
William L. Jorgensen Foreword . . . . . . . . . . . . . . . . vi--vii
Stephen C. Harvey and
Chunlin Wang and
Stephane Teletchea and
Richard Lavery Motifs in nucleic acids: Molecular
mechanics restraints for base pairing
and base stacking . . . . . . . . . . . 1--9
Andrew Smellie and
Robert Stanton and
Randy Henne and
Steve Teig Conformational analysis by intersection:
CONAN . . . . . . . . . . . . . . . . . 10--20
Asim Okur and
Bentley Strockbine and
Viktor Hornak and
Carlos Simmerling Using PC clusters to evaluate the
transferability of molecular mechanics
force fields for proteins . . . . . . . 21--31
C. Curutchet and
A. Salichs and
X. Barril and
Modesto Orozco and
F. Javier Luque Transferability of fragmental
contributions to the octanol/water
partition coefficient: an NDDO-based MST
study . . . . . . . . . . . . . . . . . 32--45
Giuliano Alagona and
Caterina Ghio and
Peter A. Kollman The intramolecular mechanism for the
second proton transfer in
triosephosphate isomerase (TIM): a QM/FE
approach . . . . . . . . . . . . . . . . 46--56
Edward C. Sherer and
Darrin M. York and
Christopher J. Cramer Fast approximate methods for calculating
nucleic acid base pair interaction
energies . . . . . . . . . . . . . . . . 57--67
Scott Brown and
Teresa Head-Gordon Cool walking: a new Markov chain Monte
Carlo sampling method . . . . . . . . . 68--76
Danny Barash and
Linjing Yang and
Xiaoliang Qian and
Tamar Schlick Inherent speedup limitations in multiple
time step/particle mesh Ewald algorithms 77--88
Chaok Seok and
J. B. Rosen and
John D. Chodera and
Ken A. Dill MOPED: Method for optimizing physical
energy parameters using decoys . . . . . 89--97
Gregori Ujaque and
Dean J. Tantillo and
Yunfeng Hu and
K. N. Houk and
Kinya Hotta and
Donald Hilvert Catalysis on the coastline: Theozyme,
molecular dynamics, and free energy
perturbation analysis of antibody 21D8
catalysis of the decarboxylation of
5-nitro-3-carboxybenzisoxazole . . . . . 98--110
K. N. Kirschner and
A. H. Lewin and
J. P. Bowen Molecular mechanics force-field
development for amino acid zwitterions 111--128
Matteo Ceccarelli and
Piero Procacci and
Massimo Marchi An ab initio force field for the
cofactors of bacterial photosynthesis 129--142
Francesca Massi and
John E. Straub Structural and dynamical analysis of the
hydration of the Alzheimer's
$\beta$-amyloid peptide . . . . . . . . 143--153
Alexander V. Mitin and
Jon Baker and
Krzysztof Wolinski and
Peter Pulay Parallel stored-integral and semidirect
Hartree--Fock and DFT methods with data
compression . . . . . . . . . . . . . . 154--160
Jose Manuel Hermida-Ramón and
Steve Brdarski and
Gunnar Karlström and
Ulf Berg Inter- and intramolecular potential for
the $N$-formylglycinamide-water system.
A comparison between theoretical
modeling and empirical force fields . . 161--176
Mireia Garcia-Viloca and
Cristóbal Alhambra and
Donald G. Truhlar and
Jiali Gao Hydride transfer catalyzed by xylose
isomerase: Mechanism and quantum effects 177--190
J. L. Klepeis and
C. A. Floudas Prediction of $\beta$-sheet topology and
disulfide bridges in polypeptides . . . 191--208
Takumi Hori and
Hideaki Takahashi and
Tomoshige Nitta Hybrid QM/MM molecular dynamics
simulations for an ionic S$_N$2 reaction
in the supercritical water: OH$^-$ +
CH$_3$Cl $\rightarrow$ CH$_3$OH + Cl$^-$ 209--221
Robert J. Petrella and
Ioan Andricioaei and
Bernard R. Brooks and
Martin Karplus An improved method for nonbonded list
generation: Rapid determination of
near-neighbor pairs . . . . . . . . . . 222--231
D. Benjamin Gordon and
Geoffrey K. Hom and
Stephen L. Mayo and
Niles A. Pierce Exact rotamer optimization for protein
design . . . . . . . . . . . . . . . . . 232--243
Satoshi Okumoto and
Shinichi Yamabe Computational study of epoxy-amine
reactions . . . . . . . . . . . . . . . 244--253
Vsevolod Katritch and
Maxim Totrov and
Ruben Abagyan ICFF: a new method to incorporate
implicit flexibility into an internal
coordinate force field . . . . . . . . . 254--265
George A. Kaminski and
Richard A. Friesner and
Ruhong Zhou A computationally inexpensive
modification of the point dipole
electrostatic polarization model for
molecular simulations . . . . . . . . . 267--276
Genyuan Li and
Herschel Rabitz and
Sheng-Wei Wang and
Panos G. Georgopoulos Correlation method for variance
reduction of Monte Carlo integration in
RS-HDMR . . . . . . . . . . . . . . . . 277--283
Carles Curutchet and
Christopher J. Cramer and
Donald G. Truhlar and
Manuel F. Ruiz-López and
Daniel Rinaldi and
Modesto Orozco and
F. Javier Luque Electrostatic component of solvation:
Comparison of SCRF continuum models . . 284--297
Christopher S. Page and
Massimo Olivucci Ground and excited state CASPT 2
geometry optimizations of small organic
molecules . . . . . . . . . . . . . . . 298--309
Kazuyoshi Ikeda and
Oxana V. Galzitskaya and
Haruki Nakamura and
Junichi Higo $\beta$-Hairpins, $\alpha$-helices, and
the intermediates among the secondary
structures in the energy landscape of a
peptide from a distal $\beta$-hairpin of
SH3 domain . . . . . . . . . . . . . . . 310--318
Takashi Yoshida and
Kazuhisa Sakakibara and
Masatoshi Asami and
Kuo-Hsiang Chen and
Jenn-Huei Lii and
Norman L. Allinger Molecular mechanics (MM3) calculations
on lithium amide compounds . . . . . . . 319--327
Alicia C. Lorenzo and
Pedro G. Pascutti and
Paulo M. Bisch Nonspecific interaction forces at
water--membrane interface by forced
molecular dynamics simulations . . . . . 328--339
Zheng-Wang Qu and
Hui Zhu and
Xing-Kang Zhang and
Qi-Yuan Zhang Density functional investigation on
electron-transfer catalysis of
cycloreversion of cyclobutane: Radical
anion mechanism . . . . . . . . . . . . 340--344
Jinshan Li and
Feng Zhao and
Fuqian Jing An ab initio study of intermolecular
interactions of nitromethane dimer and
nitromethane trimer . . . . . . . . . . 345--352
A. J. Bordner and
G. A. Huber Boundary element solution of the linear
Poisson--Boltzmann equation and a
multipole method for the rapid
calculation of forces on macromolecules
in solution . . . . . . . . . . . . . . 353--367
Jaroslav Koca and
Chang-Guo Zhan and
Robert C. Rittenhouse and
Rick L. Ornstein Coordination number of zinc ions in the
phosphotriesterase active site by
molecular dynamics and quantum mechanics 368--378
Yi-Gui Wang and
Nick Henry Werstiuk A practical and efficient method to
calculate AIM localization and
delocalization indices at post-HF levels
of theory . . . . . . . . . . . . . . . 379--385
Christofer S. Tautermann and
Andreas F. Voegele and
Thomas Loerting and
Peter Kaps and
Klaus R. Liedl Extended method for adiabatic mode
reordering . . . . . . . . . . . . . . . 386--395
Asit K. Chandra and
Tadafumi Uchimaru and
Masaaki Sugie and
Akira Sekiya Ab initio study on the structures of
fluorinated formates and hydrogen
abstraction reaction with OH radical . . 396--407
Christophe Chipot Rational determination of charge
distributions for free energy
calculations . . . . . . . . . . . . . . 409--415
Ibon Alkorta and
Jose Elguero and
Enrique Espinosa and
Ignasi Mata and
Elies Molins Comparison of electron density
properties in frozen and relaxed
electronic distributions . . . . . . . . 416--421
Carlo Gatti and
Fausto Cargnoni and
Luca Bertini Chemical information from the source
function . . . . . . . . . . . . . . . . 422--436
Nathaniel O. J. Malcolm and
Paul L. A. Popelier An improved algorithm to locate critical
points in a $3$D scalar field as
implemented in the program MORPHY . . . 437--442
George Maroulis Ab initio determination of the electric
multipole moments and static
(hyper)polarizability of HCCX, X = F,
Cl, Br, and I . . . . . . . . . . . . . 443--452
Chérif F. Matta Application of the quantum theory of
atoms in molecules to selected
physico-chemical and biophysical
problems: Focus on correlation with
experiment . . . . . . . . . . . . . . . 453--463
F. De Proft and
R. Vivas-Reyes and
A. Peeters and
C. Van Alsenoy and
P. Geerlings Hirshfeld partitioning of the electron
density: Atomic dipoles and their
relation with functional group
properties . . . . . . . . . . . . . . . 463--470
Daniel J. Grimwood and
Ian Bytheway and
Dylan Jayatilaka Wave functions derived from experiment.
V. Investigation of electron densities,
electrostatic potentials, and electron
localization functions for
noncentrosymmetric crystals . . . . . . 470--483
K. Babu and
Shridhar R. Gadre Ab initio quality one-electron
properties of large molecules:
Development and testing of molecular
tailoring approach . . . . . . . . . . . 484--495
E. Chamorro and
P. Fuentealba and
A. Savin Electron probability distribution in AIM
and ELF basins . . . . . . . . . . . . . 496--504
Peter Politzer and
Jane S. Murray and
Pat Lane Electrostatic potentials and covalent
radii . . . . . . . . . . . . . . . . . 505--511
C. E. Whitehead and
C. M. Breneman and
N. Sukumar and
M. D. Ryan Transferable atom equivalent
multicentered multipole expansion method 512--529
Shridhar R. Gadre Foreword . . . . . . . . . . . . . . . . vii--vii
Marcin Król Comparison of various implicit solvent
models in molecular dynamics simulations
of immunoglobulin G light chain dimer 531--546
Paola Facchini and
Felice Grandinetti Concerning the reaction between singlet
nitrenium ions and water: a
computational investigation on
competitive reaction paths . . . . . . . 547--564
Marcus Elstner and
Qiang Cui and
Petra Munih and
Efthimios Kaxiras and
Thomas Frauenheim and
Martin Karplus Modeling zinc in biomolecules with the
self consistent charge-density
functional tight binding (SCC-DFTB)
method: Applications to structural and
energetic analysis . . . . . . . . . . . 565--581
Takashi Amisaki and
Shinjiro Toyoda and
Hiroh Miyagawa and
Kunihiro Kitamura Development of hardware accelerator for
molecular dynamics simulations: a
computation board that calculates
nonbonded interactions in cooperation
with fast multipole method . . . . . . . 582--592
Jia-Yan Wu and
Jing-Yao Liu and
Ze-Sheng Li and
Xu-Ri Huang and
Chia-Chung Sun Dual-level direct dynamics studies for
the reactions of dimethyl ether with
hydrogen atom and methyl radical . . . . 593--600
Gabriela L. Borosky Theoretical study concerning the
reactivity of imine derivatives of
polycyclic aromatic hydrocarbons . . . . 601--608
José Pitarch-Ruiz and
José Sánchez-Marín and
Daniel Maynau Vertical spectrum of the C$_2$H system.
An open shell (SC)$^2$--CAS--SDCI study 609--617
Chandra Saravanan and
Yihan Shao and
Roi Baer and
Philip N. Ross and
Martin Head-Gordon Sparse matrix multiplications for linear
scaling electronic structure
calculations in an atom-centered basis
set using multiatom blocks . . . . . . . 618--622
Meng-Sheng Liao and
Yun Lu and
Steve Scheiner Performance assessment of
density-functional methods for study of
charge-transfer complexes . . . . . . . 623--631
Andrea C. Vaiana and
Andreas Schulz and
Jürgen Wolfrum and
Markus Sauer and
Jeremy C. Smith Molecular mechanics force field
parameterization of the fluorescent
probe rhodamine 6G using automated
frequency matching . . . . . . . . . . . 632--639
C. F. Cloud III and
M. Schwartz Systematic errors in DFT calculations of
haloalkane heats of formation . . . . . 640--646
Genyuan Li and
Maxim Artamonov and
Herschel Rabitz and
Sheng-wei Wang and
Panos G. Georgopoulos and
Metin Demiralp High-dimensional model representations
generated from low order terms ---
lp-RS-HDMR . . . . . . . . . . . . . . . 647--656
T. Róg and
K. Murzyn and
K. Hinsen and
G. R. Kneller n Moldyn: a program package for a
neutron scattering oriented analysis of
molecular dynamics simulations . . . . . 657--667
Maurizio Cossi and
Nadia Rega and
Giovanni Scalmani and
Vincenzo Barone Energies, structures, and electronic
properties of molecules in solution with
the C-PCM solvation model . . . . . . . 669--681
David Bosch and
Mercedes Campillo and
Leonardo Pardo Binding of proteins to the minor groove
of DNA: What are the structural and
energetic determinants for kinking a
basepair step? . . . . . . . . . . . . . 682--691
A. S. Zyubin and
A. M. Mebel Performance of time-dependent density
functional and Green functions methods
for calculations of excitation energies
in radicals and for Rydberg electronic
states . . . . . . . . . . . . . . . . . 692--700
Laura Masgrau and
\`Angels González-Lafont and
José M. Lluch Dependence of the rate constants on the
treatment of internal rotation modes:
the reaction OH + CH$_3$SH $\rightarrow$
CH$_3$S + H$_2$O as an example . . . . . 701--706
Luis Lorenzo and
Ricardo A. Mosquera A box-counting-based algorithm for
computing Shannon entropy in molecular
dynamics simulations . . . . . . . . . . 707--713
Axel Koslowski and
Michael E. Beck and
Walter Thiel Implementation of a general
multireference configuration interaction
procedure with analytic gradients in a
semiempirical context using the
graphical unitary group approach . . . . 714--726
Yu-Dong Cai and
Xiao-Jun Liu and
Kuo-Chen Chou Prediction of protein secondary
structure content by artificial neural
network . . . . . . . . . . . . . . . . 727--731
Peter M. W. Gill and
Siu-Hung Chien Radial quadrature for multiexponential
integrands . . . . . . . . . . . . . . . 732--740
Tanja Schulz-Gasch and
Martin Stahl Mechanistic insights into oxidosqualene
cyclizations through homology modeling 741--753
Markus Pernpointner and
Lucas Visscher Parallelization of four-component
calculations. II. Symmetry-driven
parallelization of the 4-Spinor CCSD
algorithm . . . . . . . . . . . . . . . 754--759
Thom Vreven and
Keiji Morokuma and
Ödön Farkas and
H. Bernhard Schlegel and
Michael J. Frisch Geometry optimization with QM/MM, ONIOM,
and other combined methods. I.
Microiterations and constraints . . . . 760--769
David Zanuy and
Carlos Alemán and
Manuel Laso and
Sebastián Muñoz-Guerra Thermally induced phase transition in
helical comblike poly($\beta$-peptide)s:
an atomistic simulation . . . . . . . . 770--778
Matteo Pappalardo and
Danilo Milardi and
Domenico M. Grasso and
Carmelo La Rosa Free energy perturbation and molecular
dynamics calculations of copper binding
to azurin . . . . . . . . . . . . . . . 779--785
Mark Pinsky and
Dina Yogev-Einot and
David Avnir Statistical analysis of the estimation
of distance measures . . . . . . . . . . 786--796
Philippe Arnaud and
Krystyna Zakrzewska and
Bernard Meunier Theoretical study of the interaction
between a high-valent manganese
porphyrin oxyl-(hydroxo)-Mn(IV)-TMPyP
and double-stranded DNA . . . . . . . . 797--805
Majda Rahal-Sekkal and
Nezha Sekkal and
Dirk C. Kleb and
Paul Bleckmann Structures and energies of D-galactose
and galabiose conformers as calculated
by ab initio and semiempirical methods 806--818
José Mario Martínez and
Leandro Martínez Packing optimization for automated
generation of complex system's initial
configurations for molecular dynamics
and docking . . . . . . . . . . . . . . 819--825
Kenshu Kamiya and
Yoko Sugawara and
Hideaki Umeyama Algorithm for normal mode analysis with
general internal coordinates . . . . . . 826--841
Yu-Ren Jiang and
Jing-Ya Liu and
Yue-Hua Hu and
Toyohisa Fujita Novel topological index for research on
structure-property relationships of
complex organic compounds . . . . . . . 842--849
Valentina Vetere and
Pascale Maldivi and
Carlo Adamo Comparative studies of
quasi-relativistic density functional
methods for the description of
lanthanide and actinide complexes . . . 850--858
I. Ema and
J. M. García de la Vega and
G. Ramírez and
R. López and
J. Fernández Rico and
H. Meissner and
J. Paldus Polarized basis sets of Slater-type
orbitals: H to Ne atoms . . . . . . . . 859--868
Carlos Renato Zacharias and
Maurício Ruv Lemes and
Arnaldo Dal Pino Júnior and
David Santo Orcero Predicting structural models for silicon
clusters . . . . . . . . . . . . . . . . 869--875
Mark Bathe and
Gregory C. Rutledge Inverse Monte Carlo procedure for
conformation determination of
macromolecules . . . . . . . . . . . . . 876--890
Joseph V. Turner and
David J. Cutler and
Ian Spence and
Desmond J. Maddalena Selective descriptor pruning for
QSAR/QSPR studies using artificial
neural networks . . . . . . . . . . . . 891--897
Miroslav Pinak 8-oxoguanine lesioned B-DNA molecule
complexed with repair enzyme hOGG1: a
molecular dynamics study . . . . . . . . 898--907
Fillmore Freeman and
Elika Derek A computational study of conformational
interconversions in
1,4-dithiacyclohexane (1,4-dithiane) . . 909--919
Wataru Shinoda and
Masuhiro Mikami Rigid-body dynamics in the
isothermal-isobaric ensemble: a test on
the accuracy and computational
efficiency . . . . . . . . . . . . . . . 920--930
Yong Wu and
Daiqian Xie and
Ying Xue Ab initio studies for the
photodissociation mechanism of
hydroxyacetone . . . . . . . . . . . . . 931--938
Shinichi Yamabe and
Noriko Tsuchida A computational study of interactions
between acetic acid and water molecules 939--947
Zhongfang Chen and
Haijun Jiao and
Gotthard Seifert and
Anselm H. C. Horn and
Dengke Yu and
Tim Clark and
Walter Thiel and
Paul von Ragué Schleyer The structure and stability of Si$_{60}$
and Ge$_{60}$ cages: a computational
study . . . . . . . . . . . . . . . . . 948--953
Kathryn N. Rankin and
Traian Sulea and
Enrico O. Purisima On the transferability of
hydration-parametrized continuum
electrostatics models to solvated
binding calculations . . . . . . . . . . 954--962
Ying Xue and
Chun Ho Kang and
Chan Kyung Kim and
Ikchoon Lee Theoretical studies on the gas-phase
pyrolysis of 2-phenoxycarboxylic acids:
an ONIOM approach . . . . . . . . . . . 963--972
Marcelo Zaldini Hernandes and
João Bosco P. Da Silva and
Ricardo L. Longo Chemometric study of liquid water
simulations. I. The parameters of the
TIP4P model potential . . . . . . . . . 973--981
Eliseo Ruiz and
Antonio Rodríguez-Fortea and
Joan Cano and
Santiago Alvarez and
Pere Alemany About the calculation of exchange
coupling constants in polynuclear
transition metal complexes . . . . . . . 982--989
Dominic R. Alfonso and
Kenneth D. Jordan A flexible nudged elastic band program
for optimization of minimum energy
pathways using ab initio electronic
structure methods . . . . . . . . . . . 990--996
János G. Ángyán and
Christophe Chipot and
François Dehez and
Christof Hättig and
Georg Jansen and
Claude Millot OPEP: a tool for the optimal
partitioning of electric properties . . 997--1008
Christopher C. Lovallo and
Mariusz Klobukowski Development of new pseudopotential
methods: Improved model core potentials
for the first-row transition metals . . 1009--1015
Kristin L. Meagher and
Luke T. Redman and
Heather A. Carlson Development of polyphosphate parameters
for use with the AMBER force field . . . 1016--1025
András Perczel and
Ödön Farkas and
Imre Jákli and
Igor A. Topol and
Imre G. Csizmadia Peptide models. XXXIII. Extrapolation of
low-level Hartree--Fock data of peptide
conformation to large basis set SCF,
MP2, DFT, and CCSD(T) results. The
Ramachandran surface of alanine
dipeptide computed at various levels of
theory . . . . . . . . . . . . . . . . . 1026--1042
J. A. Hageman and
R. Wehrens and
R. De Gelder and
L. M. C. Buydens Powder pattern indexing using the
weighted crosscorrelation and genetic
algorithms . . . . . . . . . . . . . . . 1043--1051
David C. Chatfield and
Alberto Augsten and
Cassian D'Cunha and
Sergio E. Wong Methyl dynamics in crystalline amino
acids: MD and NMR . . . . . . . . . . . 1052--1058
Shenghua Shi and
Lisa Yan and
Yang Yang and
Jodi Fisher-Shaulsky and
Tom Thacher An extensible and systematic force
field, ESFF, for molecular modeling of
organic, inorganic, and organometallic
systems . . . . . . . . . . . . . . . . 1059--1076
Toshimasa Ishida and
George C. Schatz A local interpolation scheme using no
derivatives in potential sampling:
Application to O($^1$D) + H$_2$ system 1077--1086
Alice Glättli and
Xavier Daura and
Wilfred F. Van Gunsteren A novel approach for designing simple
point charge models for liquid water
with three interaction sites . . . . . . 1087--1096
Lionello Pogliani Complete graph conjecture for inner-core
electrons: Homogeneous index case . . . 1097--1109
S. Sirois and
E. I. Proynov and
J.-F. Truchon and
C. M. Tsoukas and
D. R. Salahub A density functional study of the
hydrogen-bond network within the HIV-1
protease catalytic site cleft . . . . . 1110--1119
Roger A. Klein Hydrogen bonding in diols and binary
diol--water systems investigated using
DFT methods. II. Calculated infrared
OH-stretch frequencies, force constants,
and NMR chemical shifts correlate with
hydrogen bond geometry and electron
density topology. A reevaluation of
geometrical criteria for hydrogen
bonding . . . . . . . . . . . . . . . . 1120--1131
N. A. Anikin and
V. L. Bugaenko and
M. V. Frash and
L. Gorb and
J. Leszczynski Localized basis orbitals: Minimization
of 2-electron integrals array and
orthonormality of basis set . . . . . . 1132--1141
E. Van Lenthe and
E. J. Baerends Optimized Slater-type basis sets for the
elements 1--118 . . . . . . . . . . . . 1142--1156
András Perczel and
Anna K. Füzéry and
Attila G. Császár Toward direct determination of
conformations of protein building units
from multidimensional NMR experiments.
V. NMR chemical shielding analysis of
N-formyl-serinamide, a model for polar
side-chain containing peptides . . . . . 1157--1171
Vladimir Hnizdo and
Adam Fedorowicz and
Harshinder Singh and
Eugene Demchuk Statistical thermodynamics of internal
rotation in a hindering potential of
mean force obtained from computer
simulations . . . . . . . . . . . . . . 1172--1183
Jon Baker and
Peter Pulay Assessment of the OLYP and O3LYP density
functionals for first-row transition
metals . . . . . . . . . . . . . . . . . 1184--1191
Michio Iwaoka and
Shuji Tomoda The SAAP force field. A simple approach
to a new all-atom protein force field by
using single amino acid potential (SAAP)
functions in various solvents . . . . . 1192--1200
Sean A. C. McDowell A computational study of the LiH dimer 1201--1207
David Curcó and
David Zanuy and
Carlos Alemán EVEBAT: a fast strategy for the
examination of the empty space in
polymer matrices . . . . . . . . . . . . 1208--1214
Dimitris K. Agrafiotis Stochastic proximity embedding . . . . . 1215--1221
B. Das and
H. Meirovitch and
I. M. Navon Performance of hybrid methods for
large-scale unconstrained optimization
as applied to models of proteins . . . . 1222--1231
Hannes H. Loeffler Many-body effects on structure and
dynamics of aqueous ionic solutions . . 1232--1239
Markus J. Loferer and
Hannes H. Loeffler and
Klaus R. Liedl A QM--MM interface between CHARMM and
TURBOMOLE: Implementation and
application to systems in bulk phase and
biologically active systems . . . . . . 1240--1249
Joseph Ivanic and
Klaus Ruedenberg A MCSCF method for ground and excited
states based on full optimizations of
successive Jacobi rotations . . . . . . 1250--1262
Carles Curutchet and
Josep María Bofill and
Begoña Hernández and
Modesto Orozco and
F. Javier Luque Energy decomposition in molecular
complexes: Implications for the
treatment of polarization in molecular
simulations . . . . . . . . . . . . . . 1263--1275
Nathaniel O. J. Malcolm and
Paul L. A. Popelier An algorithm to delineate and integrate
topological basins in a
three-dimensional quantum mechanical
density function . . . . . . . . . . . . 1276--1282
Charles H. Langley and
Jenn-Huei Lii and
Norman Allinger Molecular mechanics (MM4) calculations
on carbonyl compounds. I--IV. . . . . . 1283--1286
Kyle A. Beran Isomers of C$_{20}$: an energy profile
II . . . . . . . . . . . . . . . . . . . 1287--1290
Jason D. Thompson and
Christopher J. Cramer and
Donald G. Truhlar Parameterization of charge model 3 for
AM1, PM3, BLYP, and B3LYP . . . . . . . 1291--1304
Clovis Darrigan and
Michel Rérat and
Giuseppe Mallia and
Roberto Dovesi Implementation of the finite field
perturbation method in the CRYSTAL
program for calculating the dielectric
constant of periodic systems . . . . . . 1305--1312
Shandar Ahmad and
M. Michael Gromiha Design and training of a neural network
for predicting the solvent accessibility
of proteins . . . . . . . . . . . . . . 1313--1320
Julio Peiró-García and
Víctor M. Ramírez-Ramírez and
Ignacio Nebot-Gil A theoretical ab initio study on the
H$_2$NO + O$_3$ reaction . . . . . . . . 1321--1328
Osamu Takahashi and
Masanori Joyabu and
Masaki Mitani and
Ko Saito and
Suehiro Iwata Theoretical studies on the molecular
dependence of bond dissociation after
core excitations II:
CH$_3$CO(CH$_2$)$_n$CN, $n = 0$--$3$ . . 1329--1335
D. M. Upadhyay and
P. C. Mishra An ab initio study of microsolvation of
LiF in water: Structures and properties
of LiF--W$_n$, $n = 1$--$9$ complexes 1336--1347
Michael S. Lee and
Michael Feig and
Freddie R. Salsbury Jr. and
Charles L. Brooks III New analytic approximation to the
standard molecular volume definition and
its application to generalized Born
calculations . . . . . . . . . . . . . . 1348--1356
Marco Garavelli and
Fabrizio Ruggeri and
François Ogliaro and
Michael J. Bearpark and
Fernando Bernardi and
Massimo Olivucci and
Michael A. Robb A simple approach for improving the
hybrid MMVB force field: Application to
the photoisomerization of $s$-cis
butadiene . . . . . . . . . . . . . . . 1357--1363
Sean Cahill and
Michael Cahill and
Kevin Cahill On the kinematics of protein folding . . 1364--1370
Lillian T. Chong and
Pradipta Bandyopadhyay and
Thomas S. Scanlan and
Irwin D. Kuntz and
Peter A. Kollman Direct hydroxide attack is a plausible
mechanism for amidase antibody 43C9 . . 1371--1377
Mutsumi Hirama and
Toshimasa Ishida and
Jun-Ichi Aihara Possible molecular hydrogen formation
mediated by the radical cations of
anthracene and pyrene . . . . . . . . . 1378--1382
Peter Carlsson and
Lennart Nilsson Improved precision and efficiency of
free energy calculations for small
systems using $\lambda$-scaled atomic
masses and separating conformational and
transformational sampling . . . . . . . 1383--1389
Henryk A. Witek and
Haruyuki Nakano and
Kimihiko Hirao Multireference perturbation theory with
optimized partitioning. II. Applications
to molecular systems . . . . . . . . . . 1390--1400
Masahiro Yamanaka and
Akiko Inagaki and
Eiichi Nakamura Theoretical studies on structures and
reactivities of organocuprate(I) and
organocopper(III) species . . . . . . . 1401--1409
A. V. Nemukhin and
B. L. Grigorenko and
I. A. Topol and
S. K. Burt Flexible effective fragment QM/MM
method: Validation through the
challenging tests . . . . . . . . . . . 1410--1420
Abhijit K. Das and
Jun-Ya Hasegawa and
Tomoo Miyahara and
Masahiro Ehara and
Hiroshi Nakatsuji Electronic excitations of the green
fluorescent protein chromophore in its
protonation states: SAC/SAC--CI study 1421--1431
Bojan Zagrovic and
Vijay Pande Solvent viscosity dependence of the
folding rate of a small protein:
Distributed computing study . . . . . . 1432--1436
Mark N. Kobrak Systematic and statistical error in
histogram-based free energy calculations 1437--1446
Norman L. Allinger and
Kuo-Hsiang Chen and
Jenn-Huei Lii and
Kathleen A. Durkin Alcohols, ethers, carbohydrates, and
related compounds. I. The MM4 force
field for simple compounds . . . . . . . 1447--1472
Jenn-Huei Lii and
Kuo-Hsiang Chen and
Kathleen A. Durkin and
Norman L. Allinger Alcohols, ethers, carbohydrates, and
related compounds. II. The anomeric
effect . . . . . . . . . . . . . . . . . 1473--1489
Jenn-Huei Lii and
Kuo-Hsiang Chen and
T. Bruce Grindley and
Norman L. Allinger Alcohols, ethers, carbohydrates, and
related compounds. III. The
1,2-dimethoxyethane system . . . . . . . 1490--1503
Jenn-Huei Lii and
Kuo-Hsiang Chen and
Norman L. Allinger Alcohols, ethers, carbohydrates, and
related compounds. IV. carbohydrates . . 1504--1513
H. Bernhard Schlegel Exploring potential energy surfaces for
chemical reactions: an overview of some
practical methods . . . . . . . . . . . 1514--1527
Stefan Grimme Improved third-order Mòller--Plesset
perturbation theory . . . . . . . . . . 1529--1537
Tadafumi Uchimaru and
Asit K. Chandra and
Seiji Tsuzuki and
Masaaki Sugie and
Akira Sekiya Ab initio investigation on the reaction
path and rate for the gas-phase reaction
of HO + H$_2$O $\leftrightarrow$ H$_2$O
+ OH . . . . . . . . . . . . . . . . . . 1538--1548
Guosheng Wu and
Daniel H. Robertson and
Charles L. Brooks III and
Michal Vieth Detailed analysis of grid-based
molecular docking: a case study of
CDOCKER --- a CHARMm-based MD docking
algorithm . . . . . . . . . . . . . . . 1549--1562
Brian W. Hopkins and
Gregory S. Tschumper A multicentered approach to integrated
QM/QM calculations. Applications to
multiply hydrogen bonded systems . . . . 1563--1568
Niall J. English and
J. M. D. Macelroy Structural and dynamical properties of
methane clathrate hydrates . . . . . . . 1569--1581
Delano P. Chong and
Myrta Grüning and
Evert Jan Baerends STO and GTO field-induced polarization
functions for H to Kr . . . . . . . . . 1582--1591
Takao Tsuneda and
Muneaki Kamiya and
Kimihiko Hirao Regional self-interaction correction of
density functional theory . . . . . . . 1592--1598
Rajeev Prabhakar and
Per E. M. Siegbahn A comparison of the mechanism for the
reductive half-reaction between pea
seedling and other copper amine oxidases
(CAOs) . . . . . . . . . . . . . . . . . 1599--1609
Antonio Morreale and
Josep Lluis Gelpí and
F. Javier Luque and
Modesto Orozco Continuum and discrete calculation of
fractional contributions to solvation
free energy . . . . . . . . . . . . . . 1610--1623
Dirk Reith and
Mathias Pütz and
Florian Müller-Plathe Deriving effective mesoscale potentials
from atomistic simulations . . . . . . . 1624--1636
Richard D. Taylor and
Philip J. Jewsbury and
Jonathan W. Essex FDS: Flexible ligand and receptor
docking with a continuum solvent model
and soft-core energy function . . . . . 1637--1656
Julio Peiró-García and
Ignacio Nebot-Gil Ab initio study of the mechanism of the
atmospheric reaction: NO$_2$ + O$_3$
$\rightarrow$ NO$_3$ + O$_2$ . . . . . . 1657--1663
Robert M. Dirks and
Niles A. Pierce A partition function algorithm for
nucleic acid secondary structure
including pseudoknots . . . . . . . . . 1664--1677
Mikhail Kozhin and
Ilya Yanov and
Jerzy Leszczynski Network visualization system for
computational chemistry . . . . . . . . 1678--1687
Hannes H. Loeffler and
Bernd M. Rode Erratum: Many-body effects on structure
and dynamics of aqueous ionic solutions 1688--1688
Wonpil Im and
Michael S. Lee and
Charles L. Brooks III Generalized Born model with a simple
smoothing function . . . . . . . . . . . 1691--1702
M. B. Darkhovskii and
I. V. Pletnev and
A. L. Tchougréeff Low- and high-spin iron (II) complexes
studied by effective crystal field
method combined with molecular mechanics 1703--1719
Yi-Gui Wang and
Cherif Matta and
Nick Henry Werstiuk Comparison of localization and
delocalization indices obtained with
Hartree--Fock and conventional
correlated methods: Effect of Coulomb
correlation . . . . . . . . . . . . . . 1720--1729
Chris Oostenbrink and
Wilfred F. Van Gunsteren Single-step perturbations to calculate
free energy differences from unphysical
reference states: Limits on size,
flexibility, and character . . . . . . . 1730--1739
Frank Neese An improvement of the resolution of the
identity approximation for the formation
of the Coulomb matrix . . . . . . . . . 1740--1747
Alain Laederach and
Peter J. Reilly Specific empirical free energy function
for automated docking of carbohydrates
to proteins . . . . . . . . . . . . . . 1748--1757
Paulo F. B. Gonçalves and
Hubert Stassen Free energy of solvation from molecular
dynamics simulations for low dielectric
solvents . . . . . . . . . . . . . . . . 1758--1765
Scott Habershon and
Kenneth D. M. Harris and
Roy L. Johnston Development of a multipopulation
parallel genetic algorithm for structure
solution from powder diffraction data 1766--1774
Ramkumar Rajamani and
Kevin J. Naidoo and
Jiali Gao Implementation of an adaptive umbrella
sampling method for the calculation of
multidimensional potential of mean force
of chemical reactions in solution . . . 1775--1781
Aimée Tomlinson and
David Yaron Direct INDO/SCI method for excited state
calculations . . . . . . . . . . . . . . 1782--1788
Bülent Balata and
Viktorya Aviyente Solvent effects on glycine. I. A
supermolecule modeling of
tautomerization via intramolecular
proton transfer . . . . . . . . . . . . 1789--1802
Brian D. Wladkowski and
Paul Ostazeski and
Sarah Chenoweth and
Steven J. Broadwater and
Morris Krauss Hydrolysis of cyclic phosphates by
ribonuclease A: a computational study
using a simplified ab initio quantum
model . . . . . . . . . . . . . . . . . 1803--1811
Feng Yang and
Zhen-Dong Wang and
Yun-Ping Huang and
Hai-Liang Zhu Novel topological index F based on
incidence matrix . . . . . . . . . . . . 1812--1820
Michael S. Lee and
Michael Feig and
Freddie R. Salsbury Jr. and
Charles L. Brooks III Erratum: New analytic approximation to
the standard molecular volume definition
and its application to generalized Born
calculations . . . . . . . . . . . . . . 1821--1821
Hiroshi Tatewaki and
Yoshihiro Watanabe Gaussian-type function set without
prolapse for the Dirac--Fock--Roothaan
equation . . . . . . . . . . . . . . . . 1823--1828
Robert Ponec and
Gleb Yuzhakov and
Ramon Carbó-Dorca Chemical structures from the analysis of
domain-averaged Fermi holes: Multiple
metal metal bonding in transition metal
compounds . . . . . . . . . . . . . . . 1829--1838
Hua Zhu and
Daiqian Xie and
Guosen Yan Theoretical studies for structures and
energetics of Rg$_n$N$_2$O (Rg = He, Ne,
Ar) clusters . . . . . . . . . . . . . . 1839--1845
D. W. Zhang and
X. H. Chen and
J. Z. H. Zhang Molecular caps for full quantum
mechanical computation of peptide--water
interaction energy . . . . . . . . . . . 1846--1852
Adélia J. A. Aquino and
Daniel Tunega and
Georg Haberhauer and
Martin H. Gerzabek and
Hans Lischka Adsorption of organic substances on
broken clay surfaces: a quantum chemical
study . . . . . . . . . . . . . . . . . 1853--1863
Natalia Díaz and
Dimas Suárez and
Tomás L. Sordo Conformational properties of
penicillins: Quantum chemical
calculations and molecular dynamics
simulations of benzylpenicillin . . . . 1864--1873
Kazuhiro Ishida Molecular integrals over the
gauge-including atomic orbitals. II. The
Breit--Pauli interaction . . . . . . . . 1874--1890
Filip Ryjá\vcek and
Tomá\vs Kuba\vr and
Pavel Hobza New parameterization of the Cornell et
al. empirical force field covering amino
group nonplanarity in nucleic acid bases 1891--1902
R. Bochicchio and
L. Lain and
A. Torre Determination of atomic valence indices
from population analyses at correlated
level . . . . . . . . . . . . . . . . . 1902--1909
Karine Bastard and
Aurélien Thureau and
Richard Lavery and
Chantal Prévost Docking macromolecules with flexible
segments . . . . . . . . . . . . . . . . 1910--1920
Illia Horenko and
Martin Weiser Adaptive integration of molecular
dynamics . . . . . . . . . . . . . . . . 1921--1929
Justin L. MacCallum and
D. Peter Tieleman Calculation of the water--cyclohexane
transfer free energies of neutral amino
acid side-chain analogs using the OPLS
all-atom force field . . . . . . . . . . 1930--1935
Urs Haberthür and
Nicolas Majeux and
Philipp Werner and
Amedeo Caflisch Efficient evaluation of the effective
dielectric function of a macromolecule
in aqueous solution . . . . . . . . . . 1936--1949
R. Gautier and
P. Tufféry Critical assessment of side-chain
conformational space sampling procedures
designed for quantifying the effect of
side-chain environment . . . . . . . . . 1950--1961
Jean-Philip Piquemal and
Ben Williams-Hubbard and
Natalie Fey and
Robert J. Deeth and
Nohad Gresh and
Claude Giessner-Prettre Inclusion of the ligand field
contribution in a polarizable molecular
mechanics: SIBFA-LF . . . . . . . . . . 1963--1970
Pablo A. Molina and
Hui Li and
Jan H. Jensen Intraprotein electrostatics derived from
first principles: Divide-and-conquer
approaches for QM/MM calculations . . . 1971--1979
Thomas E. Exner and
Paul G. Mezey Ab initio quality properties for
macromolecules using the ADMA approach 1980--1986
Chia-En Chang and
Michael K. Gilson Tork: Conformational analysis method for
molecules and complexes . . . . . . . . 1987--1998
Yong Duan and
Chun Wu and
Shibasish Chowdhury and
Mathew C. Lee and
Guoming Xiong and
Wei Zhang and
Rong Yang and
Piotr Cieplak and
Ray Luo and
Taisung Lee and
James Caldwell and
Junmei Wang and
Peter Kollman A point-charge force field for molecular
mechanics simulations of proteins based
on condensed-phase quantum mechanical
calculations . . . . . . . . . . . . . . 1999--2012
Karl Jug and
Gerald Geudtner Bond energies for molecules, clusters,
and deposit systems . . . . . . . . . . 2013--2022
L. Claes and
J.-P. François and
M. S. Deleuze Theoretical study of the internal
elimination reactions of xanthate
precursors . . . . . . . . . . . . . . . 2023--2031
Jorng-Tzong Horng and
Hsien-Da Huang and
Shih-Hsien Wang and
Ming-You Chen and
Shir-Ly Huang and
Jenn-Kang Hwang Computing motif correlations in proteins 2032--2043
Pedro Braña and
José A. Sordo Theoretical approach to the mechanism of
reactions between halogen atoms and
unsaturated hydrocarbons: the Cl +
propene reaction . . . . . . . . . . . . 2044--2062
Qing Zhang and
Daniel A. Beard and
Tamar Schlick Constructing irregular surfaces to
enclose macromolecular complexes for
mesoscale modeling using the discrete
surface charge optimization (DISCO)
algorithm . . . . . . . . . . . . . . . 2063--2074
E. Valderrama and
R. J. Wheatley An environmental pseudopotential
approach to molecular interactions:
Implementation in MOLPRO . . . . . . . . 2075--2082
Satoshi Yokojima and
Guanhua Chen and
Ruixue Xu and
Yijing Yan A dynamic mean field theory for
dissipative interacting many-electron
systems: Markovian formalism and its
implementation . . . . . . . . . . . . . 2083--2092
Alberto Del Rio and
Abdou Boucekkine and
Jean Meinnel Reassessment of methyl rotation barriers
and conformations by correlated quantum
chemistry methods . . . . . . . . . . . 2093--2100
Sandeep Patel and
Charles L. Brooks III CHARMM fluctuating charge force field
for proteins: I parameterization and
application to bulk organic liquid
simulations . . . . . . . . . . . . . . 1--16
Stewart A. Adcock Peptide backbone reconstruction using
dead-end elimination and a
knowledge-based forcefield . . . . . . . 16--27
Nandou Lu and
David A. Kofke and
Thomas B. Woolf Improving the efficiency and reliability
of free energy perturbation calculations
using overlap sampling methods . . . . . 28--40
Luc Claes and
Jean-Pierre François and
Michael S. Deleuze Theoretical study of the internal
conversion of sulfoxide precursors of
poly-isothianaphthene and related
polymers . . . . . . . . . . . . . . . . 40--50
Haruhiko Fukaya and
Taizo Ono DFT--GIAO calculations of $^{19}$F NMR
chemical shifts for perfluoro compounds 51--60
Michael J. McQuaid and
Huai Sun and
David Rigby Development and validation of COMPASS
force field parameters for molecules
with aliphatic azide chains . . . . . . 61--71
Li Sheng and
Ze-Sheng Li and
Jing-Yao Liu and
Jing-Fa Xiao and
Chia-Chung Sun Ab initio direct dynamics studies on the
reaction of H atom with CH$_3$CH$_2$Cl 72--82
M. Piacenza and
S. Grimme Systematic quantum chemical study of
DNA-base tautomers . . . . . . . . . . . 83--99
Ricard Casadesús and
Miquel Moreno and
\`angels González-Lafont and
José M. Lluch and
Matthew P. Repasky Testing electronic structure methods for
describing intermolecular H\dottedbondH
interactions in supramolecular chemistry 99--105
Takao Motoki and
Akinobu Shiga New reaction simulator ``LUMMOX'' and
its application for prediction of
catalytic activities . . . . . . . . . . 106--111
M. Preuss and
W. G. Schmidt and
K. Seino and
J. Furthmüller and
F. Bechstedt Ground- and excited-state properties of
DNA base molecules from plane-wave
calculations using ultrasoft
pseudopotentials . . . . . . . . . . . . 112--122
Juha Linnanto and
Jouko Korppi-Tommola Semiempirical PM5 molecular orbital
study on chlorophylls and
bacteriochlorophylls: Comparison of
semiempirical, ab initio, and density
functional results . . . . . . . . . . . 123--138
Ivan Tubert-Brohman and
Cristiano Ruch Werneck Guimarães and
Matthew P. Repasky and
William L. Jorgensen Extension of the PDDG/PM3 and PDDG/MNDO
semiempirical molecular orbital methods
to the halogens . . . . . . . . . . . . 138--150
Bülent Balata and
Viktorya Aviyente Erratum: Solvent effects on glycine. I.
A supermolecule modeling of
tautomerization via intramolecular
proton transfer . . . . . . . . . . . . 151--151
North American Editorship Announcement . . . . . . . . . . . . . . i--i
Xavier Gironés and
Ramon Carbó-Dorca TGSA-Flex: Extending the capabilities of
the Topo-Geometrical superposition
algorithm to handle flexible molecules 153--159
Nohad Gresh and
Gen-Bin Shi Conformation-dependent intermolecular
interaction energies of the triphosphate
anion with divalent metal cations.
Application to the ATP-binding site of a
binuclear bacterial enzyme. A parallel
quantum chemical and polarizable
molecular mechanics investigation . . . 160--168
Ho-Jin Lee and
Jong Hyun Kim and
Hee Jung Jung and
Kun-Young Kim and
Eun-Jung Kim and
Young-Sang Choi and
Chang-Ju Yoon Computational study of conformational
preferences of thioamide-containing
azaglycine peptides . . . . . . . . . . 169--178
A. Nakata and
T. Baba and
H. Takahashi and
H. Nakai Theoretical study on the excited states
of psoralen compounds bonded to a
thymine residue . . . . . . . . . . . . 179--188
Célia Fonseca Guerra and
Jan-Willem Handgraaf and
Evert Jan Baerends and
F. Matthias Bickelhaupt Voronoi deformation density (VDD)
charges: Assessment of the Mulliken,
Bader, Hirshfeld, Weinhold, and VDD
methods for charge analysis . . . . . . 189--210
Thomas S. Hofer and
Hung T. Tran and
Christian F. Schwenk and
Bernd M. Rode Characterization of dynamics and
reactivities of solvated ions by ab
initio simulations . . . . . . . . . . . 211--217
Yue Zhang and
Shaowen Zhang and
Qian Shu Li A dual-level ab initio and hybrid
density functional theory dynamics study
on the unimolecular decomposition
reaction C$_2$H$_5$O $\rightarrow$
CH$_2$O + CH$_3$ . . . . . . . . . . . . 218--226
Susana Pereira and
Pedro Alexandrino Fernandes and
Maria João Ramos Theoretical study of ribonucleotide
reductase mechanism-based inhibition by
2'-azido-2'-deoxyribonucleoside
5'-diphosphates . . . . . . . . . . . . 227--237
Holger Gohlke and
David A. Case Converging free energy estimates:
MM-PB(GB)SA studies on the
protein--protein complex Ras--Raf . . . 238--250
Qian-Shu Li and
Chao Yang Wang Direct dynamic study on the hydrogen
abstraction reaction CH$_3$CN + OH
$\rightarrow$ CH$_2$CN + H$_2$O . . . . 251--257
Zheng-Wang Qu and
Hui Zhu and
Ze-Sheng Li and
Xing-Kang Zhang and
Qi-Yuan Zhang Density functional investigation of
reaction of borohydride cation BH with
propylene . . . . . . . . . . . . . . . 258--264
Michael Feig and
Alexey Onufriev and
Michael S. Lee and
Wonpil Im and
David A. Case and
Charles L. Brooks III Performance comparison of generalized
Born and Poisson methods in the
calculation of electrostatic solvation
energies for protein structures . . . . 265--284
Tamás Beke and
Imre G. Csizmadia and
András Perczel On the flexibility of $\beta$-peptides 285--307
Jean-Philip Piquemal and
Ben Williams-Hubbard and
Natalie Fey and
Robert J. Deeth and
Nohad Gresh and
Claude Giessner-Prettre Erratum: Inclusion of the ligand field
contribution in a polarizable molecular
mechanics: SIBFA-LF . . . . . . . . . . 308--308
Yi-Gui Wang and
Cherif F. Matta and
Nick Henry Werstiuk Erratum: Comparison of localization and
delocalization indices obtained with
Hartree--Fock and conventional
correlated methods: Effect of Coulomb
correlation . . . . . . . . . . . . . . 309--309
A. Nakata and
T. Baba and
H. Takahashi and
H. Nakai Erratum: Theoretical study on the
excited states of psoralen compounds
bonded to a thymine residue . . . . . . 309--309
Vladimir Pelmenschikov and
Kyung-Bin Cho and
Per E. M. Siegbahn Class I ribonucleotide reductase
revisited: the effect of removing a
proton on Glu441 . . . . . . . . . . . . 311--321
Jennifer I. Chavez and
Maira M. Carrillo and
Kyle A. Beran Isomers of C$_{20}$: an energy profile
III . . . . . . . . . . . . . . . . . . 322--327
Robert J. Harrison Krylov subspace accelerated inexact
Newton method for linear and nonlinear
equations . . . . . . . . . . . . . . . 328--334
Ji\vrí Kolafa Time-reversible always stable
predictor--corrector method for
molecular dynamics of polarizable
molecules . . . . . . . . . . . . . . . 335--342
Vinzenz Bachler A simple computational scheme for
obtaining localized bonding schemes and
their weights from a CASSCF wave
function . . . . . . . . . . . . . . . . 343--367
A. N. Artemyev and
E. V. Ludeña and
V. V. Karasiev and
A. J. Hernández A finite B-spline basis set for accurate
diatomic molecule calculations . . . . . 368--374
Luca Frediani and
Roberto Cammi and
Christian S. Pomelli and
Jacopo Tomasi and
Kenneth Ruud New developments in the symmetry-adapted
algorithm of the Polarizable Continuum
Model . . . . . . . . . . . . . . . . . 375--385
Ivan Infante and
Lucas Visscher QM/MM study of aqueous solvation of the
uranyl fluoride [UO$_2$F] complex . . . 386--392
Serena Donnini and
André H. Juffer Calculation of affinities of peptides
for proteins . . . . . . . . . . . . . . 393--411
Marco Cecchini and
Peter Kolb and
Nicolas Majeux and
Amedeo Caflisch Automated docking of highly flexible
ligands by genetic algorithms: a
critical assessment . . . . . . . . . . 412--422
Li Sheng and
Ze-Sheng Li and
Jing-Yao Liu and
Jing-Fa Xiao and
Chia-Chung Sun Theoretical study on the rate constants
for the C$_2$H$_5$ + HBr $\rightarrow$
C$_2$H$_6$ + Br reaction . . . . . . . . 423--428
Rachel Crespo-Otero and
Luis A. Montero and
Giselle Rosquete and
J. Alexander Padrón-García and
Raúl H. González-Jonte Theoretical model of internal rotation
in monosubstituted derivatives of
furfural . . . . . . . . . . . . . . . . 429--438
Xavier Fradera and
Miquel Sol\`a Second-order atomic Fukui indices from
the electron-pair density in the
framework of the atoms in molecules
theory . . . . . . . . . . . . . . . . . 439--446
Shingo Urata and
Seiji Tsuzuki and
Akira Takada and
Masuhiro Mikami and
Tadafumi Uchimaru and
Akira Sekiya Analysis of the intermolecular
interactions between CH$_3$OCH$_3$,
CF$_3$OCH$_3$, CF$_3$OCF$_3$, and
CH$_2$F$_2$, CHF$_3$ . . . . . . . . . . 447--459
Yi Ren and
San-Yan Chu Modified Gaussian-2 level investigation
of the identity ion-pair S$_N$2
reactions of lithium halide and methyl
halide with inversion and retention
mechanisms . . . . . . . . . . . . . . . 461--471
Lingchun Song and
Wei Wu and
Qianer Zhang and
Sason Shaik A practical valence bond method: a
configuration interaction method
approach with perturbation theoretic
facility . . . . . . . . . . . . . . . . 472--478
Emilio Gallicchio and
Ronald M. Levy AGBNP: an analytic implicit solvent
model suitable for molecular dynamics
simulations and high-resolution modeling 479--499
Xiang-Yuan Li and
Ke-Xiang Fu Continuous medium theory for
nonequilibrium solvation: I. How to
correctly evaluate solvation free energy
of nonequilibrium . . . . . . . . . . . 500--509
Evangelos A. Coutsias and
Chaok Seok and
Matthew P. Jacobson and
Ken A. Dill A kinematic view of loop closure . . . . 510--528
Mitsunori Ikeguchi Partial rigid-body dynamics in NPT, NPAT
and NP$\gamma$T ensembles for proteins
and membranes . . . . . . . . . . . . . 529--541
Michael J. Liddell and
Davor Margetic and
Anthony S. Mitchell and
Ronald N. Warrener An AM1 semiempirical study of
host--guest complexation in
hemicarcerand complexes . . . . . . . . 542--557
Li Wang and
Jing-Yao Liu and
Ze-Sheng Li and
Chia-Chung Sun Direct ab initio dynamics studies on the
hydrogen-abstraction reactions of OH
radicals with HOX (X = F, Cl, and Br) 558--564
S. Banu Ozkan and
Hagai Meirovitch Conformational search of peptides and
proteins: Monte Carlo minimization with
an adaptive bias method applied to the
heptapeptide deltorphin . . . . . . . . 565--572
Francisco Corzana and
Mohammed S. Motawia and
Catherine Hervé Du Penhoat and
Serge Perez and
Sarah M. Tschampel and
Robert J. Woods and
Sòren B. Engelsen A hydration study of (1$\rightarrow$4)
and (1$\rightarrow$6) linked
$\alpha$-glucans by comparative 10 ns
molecular dynamics simulations and
500-MHz NMR . . . . . . . . . . . . . . 573--586
Johannes Neugebauer and
Markus Reiher Vibrational center--ligand couplings in
transition metal complexes . . . . . . . 587--597
Shinichi Yamabe and
Noriko Tsuchida A computational study of the role of
hydrogen bonds in S$_N$1 and E1
reactions . . . . . . . . . . . . . . . 598--608
Maxim Totrov Accurate and efficient generalized Born
model based on solvent accessibility:
Derivation and application for Log P
octanol/water prediction and flexible
peptide docking . . . . . . . . . . . . 609--619
Martin Saunders Stochastic search for isomers on a
quantum mechanical surface . . . . . . . 621--626
Richard I. Maurer and
Christopher A. Reynolds A multilayered approach to approximating
solute polarization . . . . . . . . . . 627--631
Zheng Yuan and
John S. Mattick and
Rohan D. Teasdale SVM\TM: Support vector machines to
predict transmembrane segments . . . . . 632--636
John Cullen Performance of the Harris functional for
extended basis sets at the Hartree--Fock
and density functional levels . . . . . 637--648
Siân T. Howard and
Colin D. Abernethy Intramolecular C H\ldotsC$_{carbene}$
hydrogen bonds and competing
interactions in monoprotonated tripodal
carbenes . . . . . . . . . . . . . . . . 649--659
Ali Khalaf Al-Matar and
David A. Rockstraw A generating equation for mixing rules
and two new mixing rules for interatomic
potential energy parameters . . . . . . 660--668
Fan Wang and
Lemin Li Numerical examination of performance of
some exchange-correlation functionals
for molecules containing heavy elements 669--677
Michael Patra and
Mikko Karttunen Systematic comparison of force fields
for microscopic simulations of NaCl in
aqueous solutions: Diffusion, free
energy of hydration, and structural
properties . . . . . . . . . . . . . . . 678--689
Bülent Balta and
Viktorya Aviyente Solvent effects on glycine II.
Water-assisted tautomerization . . . . . 690--703
P. Zarzycki and
R. Charmas and
P. Szabelski Study of proton adsorption at
heterogeneous oxide/electrolyte
interface. Prediction of the surface
potential using Monte Carlo simulations
and 1-pK approach . . . . . . . . . . . 704--711
Eran Eyal and
Rafael Najmanovich and
Brendan J. Mcconkey and
Marvin Edelman and
Vladimir Sobolev Importance of solvent accessibility and
contact surfaces in modeling side-chain
conformations in proteins . . . . . . . 712--724
Paul Winget and
Timothy Clark Enthalpies of formation from B3LYP
calculations . . . . . . . . . . . . . . 725--733
D. B. Chesnut and
L. D. Quin Nature of bonding in the sulfuryl group 734--738
Kazuhiro Ishida Accurate and fast algorithm of the
molecular incomplete gamma function with
a complex argument . . . . . . . . . . . 739--748
Harry A. Stern Simple algorithm for
isothermal--isobaric molecular dynamics 749--761
M. Michael Gromiha and
Shandar Ahmad and
Makiko Suwa Neural network-based prediction of
transmembrane $\beta$-strand segments in
outer membrane proteins . . . . . . . . 762--767
M. K. Shukla and
Jerzy Leszczynski TDDFT investigation on nucleic acid
bases: Comparison with experiments and
standard approach . . . . . . . . . . . 768--778
Matthias Keil and
Thomas E. Exner and
Jürgen Brickmann Pattern recognition strategies for
molecular surfaces: III. Binding site
prediction with a neural network . . . . 779--789
David Curcó and
Carlos Alemán Performance of SuSi: a method for
generating atomistic models of amorphous
polymers based on a random search of
energy minima . . . . . . . . . . . . . 790--798
Rochus Schmid Car--Parrinello simulations with a real
space method . . . . . . . . . . . . . . 799--812
Jun Zeng and
Daiqian Xie Hydrogen bonding and solvent effects on
the lowest $^1$(n, $\pi^*$) excitations
of triazines in water . . . . . . . . . 813--822
Nohad Gresh and
Sherif A. Kafafi and
Jean-François Truchon and
Dennis R. Salahub Intramolecular interaction energies in
model alanine and glycine tetrapeptides.
Evaluation of anisotropy, polarization,
and correlation effects. A parallel ab
initio HF/MP2, DFT, and polarizable
molecular mechanics study . . . . . . . 823--834
Xiang-Yuan Li and
Ke-Xiang Fu and
Quan Zhu and
Min-Hua Shan Continuous medium theory for
nonequilibrium solvation: II.
Interaction energy between solute charge
and reaction field and single-sphere
model for spectral shift . . . . . . . . 835--842
Jinn-Moon Yang Development and evaluation of a generic
evolutionary method for protein--ligand
docking . . . . . . . . . . . . . . . . 843--857
Ricardo L. Mancera and
Per Källblad and
Nikolay P. Todorov Ligand--protein docking using a quantum
stochastic tunneling optimization method 858--864
Yang Zhang and
Jeffrey Skolnick SPICKER: a clustering approach to
identify near-native protein folds . . . 865--871
Dmitri G. Fedorov and
Ryan M. Olson and
Kazuo Kitaura and
Mark S. Gordon and
Shiro Koseki A new hierarchical parallelization
scheme: Generalized distributed data
interface (GDDI), and an application to
the fragment molecular orbital method
(FMO) . . . . . . . . . . . . . . . . . 872--880
Feng Yang and
Zhen-Dong Wang and
Yun-Ping Huang Modification of the Wiener index 4 . . . 881--887
F. Pascale and
C. M. Zicovich-Wilson and
F. López Gejo and
B. Civalleri and
R. Orlando and
R. Dovesi The calculation of the vibrational
frequencies of crystalline compounds and
its implementation in the CRYSTAL code 888--897
Harold Basch and
Mark A. Ratner Reduced basis set for the gold atom in
cluster complexes . . . . . . . . . . . 899--906
Yi Zhao and
Wenguo Xu and
Qianshu Li and
Yaoming Xie and
Henry F. Schaefer III The arsenic clusters As$_n$ ($n =
1$--$5$) and their anions: Structures,
thermochemistry, and electron affinities 907--920
Anatoliy Volkov and
Philip Coppens Calculation of electrostatic interaction
energies in molecular dimers from atomic
multipole moments obtained by different
methods of electron density partitioning 921--934
Alexander H. Boschitsch and
Marcia O. Fenley Hybrid boundary element and finite
difference method for solving the
nonlinear Poisson--Boltzmann equation 935--955
J. Cortés and
T. Siméon and
M. Remaud-Siméon and
V. Tran Geometric algorithms for the
conformational analysis of long protein
loops . . . . . . . . . . . . . . . . . 956--967
Xiaoping Han and
Yue Zhang and
Huibin Xu First-principles pair potentials across
the metal--ceramic interface . . . . . . 968--973
Massimiliano Aschi and
Costantino Zazza and
Riccardo Spezia and
Cecilia Bossa and
Alfredo Di Nola and
Maurizio Paci and
Andrea Amadei Conformational fluctuations and
electronic properties in myoglobin . . . 974--984
Arnaud Blondel Ensemble variance in free energy
calculations by thermodynamic
integration: Theory, optimal
``Alchemical'' path, and practical
solutions . . . . . . . . . . . . . . . 985--993
Mihai V. Putz and
Nino Russo and
Emilia Sicilia On the applicability of the HSAB
principle through the use of improved
computational schemes for chemical
hardness evaluation . . . . . . . . . . 994--1003
Olgun Guvench and
Charles L. Brooks III Efficient approximate all-atom solvent
accessible surface area method
parameterized for folded and denatured
protein conformations . . . . . . . . . 1005--1014
Nathalie Basdevant and
Daniel Borgis and
Tap Ha-Duong A semi-implicit solvent model for the
simulation of peptides and proteins . . 1015--1029
Delano P. Chong and
Erik Van Lenthe and
Stan Van Gisbergen and
Evert Jan Baerends Even-tempered Slater-type orbitals
revisited: From hydrogen to krypton . . 1030--1036
Henk Bekker and
Jur P. Van Den Berg and
Tsjerk A. Wassenaar A method to obtain a near-minimal-volume
molecular simulation of a macromolecule,
using periodic boundary conditions and
rotational constraints . . . . . . . . . 1037--1046
Anil Kumar and
Michaela Knapp-Mohammady and
P. C. Mishra and
Sándor Suhai A theoretical study of structures and
electron affinities of radical anions of
guanine-cytosine, adenine-thymine, and
hypoxanthine-cytosine base pairs . . . . 1047--1059
Arturo Robertazzi and
James A. Platts Hydrogen bonding, solvation, and
hydrolysis of cisplatin: a theoretical
study . . . . . . . . . . . . . . . . . 1060--1067
Abdallah Sayyed-Ahmad and
Kagan Tuncay and
Peter J. Ortoleva Efficient solution technique for solving
the Poisson--Boltzmann equation . . . . 1068--1074
Les\law K. Bieniasz Improving the accuracy of the spatial
discretization in finite-difference
electrochemical kinetic simulations, by
means of the extended Numerov method . . 1075--1083
András Perczel and
Péter Hudáky and
Anna K. Füzéry and
Imre G. Csizmadia Stability issues of covalently and
noncovalently bonded peptide subunits 1084--1100
Zlatko Vasilkoski and
David L. Weaver Diffusion--collision model algorithms
for protein folding kinetics . . . . . . 1101--1107
J. Ulises Reveles and
Andreas M. Köster Geometry optimization in density
functional methods . . . . . . . . . . . 1109--1116
A. Becue and
N. Meurice and
L. Leherte and
D. P. Vercauteren Evaluation of the protein
solvent-accessible surface using reduced
representations in terms of critical
points of the electron density . . . . . 1117--1126
Kenneth B. Wiberg and
Yi-Gui Wang Conformational energies for
2-substituted butanes . . . . . . . . . 1127--1132
Ming Lei and
Maria I. Zavodszky and
Leslie A. Kuhn and
M. F. Thorpe Sampling protein conformations and
pathways . . . . . . . . . . . . . . . . 1133--1148
Genyuan Li and
Jacqueline Schoendorf and
Tak-San Ho and
Herschel Rabitz Multicut-HDMR with an application to an
ionospheric model . . . . . . . . . . . 1149--1156
Junmei Wang and
Romain M. Wolf and
James W. Caldwell and
Peter A. Kollman and
David A. Case Development and testing of a general
AMBER force field . . . . . . . . . . . 1157--1174
Hiroaki Umeda and
Shiro Koseki and
Umpei Nagashima Improvement of parallelization
performance of GAMESS: Global sum and
(semi-)direct integral calculation in
multireference perturbation calculation 1175--1183
Jia-Xu Zhang and
Jing-Yao Liu and
Ze-Sheng Li and
Chia-Chung Sun Theoretical study on the mechanism of
the $^1$CHCl + NO$_2$ reactions . . . . 1184--1190
Sergio Aragon A precise boundary element method for
macromolecular transport properties . . 1191--1205
Christopher C. Lovallo and
Mariusz Klobukowski Improved model core potentials for the
second- and third-row transition metals 1206--1213
Anonymous Publisher's note: Sir John A. Pople,
1925--2004 . . . . . . . . . . . . . . . fmv--viii
Delia Soto-Castro and
Patricia Guadarrama Macrocyclic vs. dendrimeric effect. A
DFT study . . . . . . . . . . . . . . . 1215--1226
I. Fdez. Galván and
M. E. Martín and
M. A. Aguilar A new method to locate saddle points for
reactions in solution by using the
free-energy gradient method and the mean
field approximation . . . . . . . . . . 1227--1233
D. Muñoz and
C. De Graaf and
F. Illas Putting error bars on the Ab Initio
theoretical estimates of the magnetic
coupling constants: the parent compounds
of superconducting cuprates as a case
study . . . . . . . . . . . . . . . . . 1234--1241
Martin Almlöf and
BjÒrn O. Brandsdal and
Johan Åqvist Binding affinity prediction with
different force fields: Examination of
the linear interaction energy method . . 1242--1254
Nisanth N. Nair and
Thomas Bredow and
Karl Jug Molecular dynamics implementation in
MSINDO: Study of silicon clusters . . . 1255--1263
K. Fiaty and
C. Charcosset and
B. Perrin and
R. Couturier and
B. Ma\"\isterrena ATP-dependent active transport
simulations based on a
phosphatase--channel--kinase membrane
structure . . . . . . . . . . . . . . . 1264--1276
Wolfgang Quapp Reaction pathways and projection
operators: Application to string methods 1277--1285
Susana Pereira and
Pedro Alexandrino Fernandes and
Maria João Ramos Mechanism for ribonucleotide reductase
inactivation by the anticancer drug
gemcitabine . . . . . . . . . . . . . . 1286--1294
Robert M. Dirks and
Niles A. Pierce An algorithm for computing nucleic acid
base-pairing probabilities including
pseudoknots . . . . . . . . . . . . . . 1295--1304
Gordon M. Crippen Cluster distance geometry of polypeptide
chains . . . . . . . . . . . . . . . . . 1305--1312
Yuri A. Kosinsky and
Pavel E. Volynsky and
Philippe Lagant and
Gerard Vergoten and
Ei-Ichiro Suzuki and
Alexander S. Arseniev and
Roman G. Efremov Development of the force field
parameters for phosphoimidazole and
phosphohistidine . . . . . . . . . . . . 1313--1321
Marina Udier-Blagovi\'c and
Patricia Morales De Tirado and
Shoshannah A. Pearlman and
William L. Jorgensen Accuracy of free energies of hydration
using CM1 and CM3 atomic charges . . . . 1322--1332
Roberto Improta and
Vincenzo Barone Assessing the reliability of density
functional methods in the conformational
study of polypeptides: the treatment of
intraresidue nonbonding interactions . . 1333--1341
Kenneth B. Wiberg Basis set effects on calculated
geometries: 6-311++G** vs. aug-cc-pVDZ 1342--1346
J. Fernández Rico and
R. López and
I. Ema and
G. Ramírez Electrostatic potentials and fields from
density expansions of deformed atoms in
molecules . . . . . . . . . . . . . . . 1347--1354
J. Fernández Rico and
R. López and
G. Ramírez and
I. Ema and
E. V. Ludeña Analytical method for the representation
of atoms-in-molecules densities . . . . 1355--1363
Bo Liao and
Tian-Ming Wang New $2$D graphical representation of DNA
sequences . . . . . . . . . . . . . . . 1364--1368
Gennady N. Chuev and
Maxim V. Fedorov Wavelet algorithm for solving integral
equations of molecular liquids. A test
for the reference interaction site model 1369--1377
Aisha El-Sherbiny and
Raymond A. Poirier An evaluation of the radial part of
numerical integration commonly used in
DFT . . . . . . . . . . . . . . . . . . 1378--1384
Dawoon Jung and
Jie Floyd and
Tamara M. Gund A comparative molecular field analysis
(CoMFA) study using semiempirical,
density functional, ab initio methods
and pharmacophore derivation using
DISCOtech on sigma 1 ligands . . . . . . 1385--1399
Alexander D. Mackerell Jr. and
Michael Feig and
Charles L. Brooks III Extending the treatment of backbone
energetics in protein force fields:
Limitations of gas-phase quantum
mechanics in reproducing protein
conformational distributions in
molecular dynamics simulations . . . . . 1400--1415
Peter A. Sims and
Chung F. Wong and
J. Andrew McCammon Charge optimization of the interface
between protein kinases and their
ligands . . . . . . . . . . . . . . . . 1416--1429
Yun Xiang and
Da W. Zhang and
John Z. H. Zhang Fully quantum mechanical energy
optimization for protein--ligand
structure . . . . . . . . . . . . . . . 1431--1437
Jörg-Rüdiger Hill and
Johann Plank Retardation of setting of plaster of
Paris by organic acids: Understanding
the mechanism through molecular modeling 1438--1448
Hui Li and
Jan H. Jensen Improving the efficiency and convergence
of geometry optimization with the
polarizable continuum model: New energy
gradients and molecular surface
tessellation . . . . . . . . . . . . . . 1449--1462
Stefan Grimme Accurate description of van der Waals
complexes by density functional theory
including empirical corrections . . . . 1463--1473
Tim N. Heinz and
Philippe H. Hünenberger A fast pairlist-construction algorithm
for molecular simulations under periodic
boundary conditions . . . . . . . . . . 1474--1486
Daiqian Xie and
Jun Zeng Hydrogen bonding and solvatochromatic
shift of the lowest$^1$ (n, $\pi^*$)
excitation of s-tetrazine in its
hydrated clusters and dilute solutions 1487--1495
Bahram Hemmateenejad and
Mohammad A. Safarpour and
Ramin Miri and
Fariba Taghavi Application of ab initio theory to QSAR
study of 1,4-dihydropyridine-based
calcium channel blockers using GA-MLR
and PC-GA-ANN procedures . . . . . . . . 1495--1503
Sandeep Patel and
Alexander D. Mackerell Jr. and
Charles L. Brooks III CHARMM fluctuating charge force field
for proteins: II. Protein/solvent
properties from molecular dynamics
simulations using a nonadditive
electrostatic model . . . . . . . . . . 1504--1514
Les\law K. Bieniasz A fourth-order accurate, Numerov-type,
three-point finite-difference
discretization of electrochemical
reaction-diffusion equations on
nonuniform (exponentially expanding)
spatial grids in one-dimensional space
geometry . . . . . . . . . . . . . . . . 1515--1521
Ilona Hudáky and
Péter Hudáky and
András Perczel Solvation model induced structural
changes in peptides. A quantum chemical
study on Ramachandran surfaces and
conformers of alanine diamide using the
polarizable continuum model . . . . . . 1522--1531
Christian Silvio Pomelli A tessellationless integration grid for
the polarizable continuum model reaction
field . . . . . . . . . . . . . . . . . 1532--1541
Xavier López and
Jorge A. Fernández and
Susanna Romo and
Jean François Paul and
Leonid Kazansky and
Josep M. Poblet Are the solvent effects critical in the
modeling of polyoxoanions? . . . . . . . 1542--1549
Karl Jug and
Thomas Bredow Models for the treatment of crystalline
solids and surfaces . . . . . . . . . . 1551--1567
H. Merlitz and
T. Herges and
W. Wenzel Fluctuation analysis and accuracy of a
large-scale in silico screen . . . . . . 1568--1575
Chinapong Kritayakornupong and
Kristof Plankensteiner and
Bernd M. Rode Structure and dynamics of the Cr(III)
ion in aqueous solution: ab initio QM/MM
molecular dynamics simulation . . . . . 1576--1583
Alexander D. Mackerell Jr. Empirical force fields for biological
macromolecules: Overview and issues . . 1584--1604
Eric F. Pettersen and
Thomas D. Goddard and
Conrad C. Huang and
Gregory S. Couch and
Daniel M. Greenblatt and
Elaine C. Meng and
Thomas E. Ferrin UCSF Chimera --- a visualization system
for exploratory research and analysis 1605--1612
Felix Autenrieth and
Emad Tajkhorshid and
Jerome Baudry and
Zaida Luthey-Schulten Classical force field parameters for the
heme prosthetic group of cytochrome c 1613--1622
Jason Wagoner and
Nathan A. Baker Solvation forces on biomolecular
structures: a comparison of explicit
solvent and Poisson--Boltzmann models 1623--1629
Richard E. Gillilan and
Ryan H. Lilien Optimization and dynamics of
protein--protein complexes using
B-splines . . . . . . . . . . . . . . . 1630--1646
Maria Del Carmen Michelini and
Nino Russo and
Mohammad Esma\"\il Alikhani and
Bernard Silvi Energetic and topological analysis of
the reaction of Mo and Mo$_2$ with
NH$_3$, C$_2$H$_2$, and C$_2$H$_4$
molecules . . . . . . . . . . . . . . . 1647--1655
Chris Oostenbrink and
Alessandra Villa and
Alan E. Mark and
Wilfred F. Van Gunsteren A biomolecular force field based on the
free enthalpy of hydration and
solvation: the GROMOS force-field
parameter sets 53A5 and 53A6 . . . . . . 1656--1676
Edward N. Brothers and
Dimas Suarez and
David W. Deerfield II and
Kenneth M. Merz Jr. PM3-compatible zinc parameters optimized
for metalloenzyme active sites . . . . . 1677--1692
Xueguang Shao and
Longjiu Cheng and
Wensheng Cai A dynamic lattice searching method for
fast optimization of Lennard-Jones
clusters . . . . . . . . . . . . . . . . 1693--1698
Zhi-Xiang Wang and
Yong Duan Solvation effects on alanine dipeptide:
a MP2/cc-pVTZ//MP2/6-31G** study of
$(\Phi, \Psi)$ energy maps and
conformers in the gas phase, ether, and
water . . . . . . . . . . . . . . . . . 1699--1716
Joseph P. Kenny and
Steven J. Benson and
Yuri Alexeev and
Jason Sarich and
Curtis L. Janssen and
Lois Curfman Mcinnes and
Manojkumar Krishnan and
Jarek Nieplocha and
Elizabeth Jurrus and
Carl Fahlstrom and
Theresa L. Windus Component-based integration of chemistry
and optimization software . . . . . . . 1717--1725
Qi Shen and
Jian-Hui Jiang and
Chen-Xu Jiao and
Wei-Qi Lin and
Guo-Li Shen and
Ru-Qin Yu Hybridized particle swarm algorithm for
adaptive structure training of
multilayer feed-forward neural network:
QSAR studies of bioactivity of organic
compounds . . . . . . . . . . . . . . . 1726--1735
Cristina P. Gonçalves and
José R. Mohallem A new algorithm to handle finite nuclear
mass effects in electronic calculations:
the ISOTOPE program . . . . . . . . . . 1736--1739
Oh-Seuk Lee and
Kiyull Yang and
Keum Duck Kang and
In Sun Koo and
Chan-Kyung Kim and
Ikchoon Lee Ab initio and DFT studies on hydrolyses
of phosphorus halides . . . . . . . . . 1740--1748
F. Marty Ytreberg and
Daniel M. Zuckerman Efficient use of nonequilibrium
measurement to estimate free energy
differences for molecular systems . . . 1749--1759
Julien Michel and
Richard D. Taylor and
Jonathan W. Essex The parameterization and validation of
generalized Born models using the
pairwise descreening approximation . . . 1760--1770
Masao Masamura The effect of basis set superposition
error on the convergence of
intermolecular interaction energies for
deprotonated complexes . . . . . . . . . 1771--1778
Pawe\l Szabelski and
Julian Talbot Kinetics and equilibrium of
multicomponent adsorption on chiraly
templated surfaces . . . . . . . . . . . 1779--1786
Ernesto Estrada and
Eduardo J. Delgado and
Joel B. Alderete and
Gonzalo A. Jaña Quantum-connectivity descriptors in
modeling solubility of environmentally
important organic compounds . . . . . . 1787--1796
Premal S. Shah and
Geoffrey K. Hom and
Stephen L. Mayo Preprocessing of rotamers for protein
design calculations . . . . . . . . . . 1797--1800
Jason Wagoner and
Nathan A. Baker Erratum: Jason Wagoner and Nathan A.
Baker, ``Solvation forces on
biomolecular structures: A comparison of
explicit solvent and Poisson--Boltzmann
models,'' Journal of Computational
Chemistry (2004) \bf 25(13) 1623--1629 1801--1801
Anonymous Publisher's Note: ``Software News and
Updates'' section of the Journal of
Computational Chemistry . . . . . . . . i--i
Shunzhou Wan and
Peter Coveney and
Darren R. Flower Large-scale molecular dynamics
simulations of HLA-A*0201 complexed with
a tumor-specific antigenic peptide: Can
the $\alpha$3 and $\beta_2 m$ domains be
neglected? . . . . . . . . . . . . . . . 1803--1813
M. Belmares and
M. Blanco and
W. A. Goddard III and
R. B. Ross and
G. Caldwell and
S.-H. Chou and
J. Pham and
P. M. Olofson and
Cristina Thomas Hildebrand and Hansen solubility
parameters from Molecular Dynamics with
applications to electronic nose polymer
sensors . . . . . . . . . . . . . . . . 1814--1826
Jian Wan and
Li Zhang and
Guangfu Yang Quantitative structure--activity
relationships for phenyl triazolinones
of protoporphyrinogen oxidase
inhibitors: a density functional theory
study . . . . . . . . . . . . . . . . . 1827--1832
Weizhong Yan and
Ying Xue and
Hua Zhu and
Jun Zeng and
Daiqian Xie A theoretical study of solvent effects
on tautomerism and electronic absorption
spectra of 3-hydroxy-2-mercaptopyridine
and 2,3-dihydroxypyridine . . . . . . . 1833--1839
Robert J. Deeth and
Natalie Fey The performance of nonhybrid density
functionals for calculating the
structures and spin states of Fe(II) and
Fe(III) complexes . . . . . . . . . . . 1840--1848
Evangelos A. Coutsias and
Chaok Seok and
Ken A. Dill Using quaternions to calculate RMSD . . 1849--1857
Henryk A. Witek and
Keiji Morokuma Systematic study of vibrational
frequencies calculated with the
self-consistent charge density
functional tight-binding method . . . . 1858--1864
Bernd Kuhn and
Peter A. Kollman and
Martin Stahl Prediction of pK$_a$ shifts in proteins
using a combination of molecular
mechanical and continuum solvent
calculations . . . . . . . . . . . . . . 1865--1872
C. M. Zicovich-Wilson and
F. Pascale and
C. Roetti and
V. R. Saunders and
R. Orlando and
R. Dovesi Calculation of the vibration frequencies
of $\alpha$-quartz: the effect of
Hamiltonian and basis set . . . . . . . 1873--1881
Yoshiumi Kawamura and
Hiromi Nakai A hybrid approach combining energy
density analysis with the interaction
energy decomposition method . . . . . . 1882--1887
Jia-Xu Zhang and
Jing-Yao Liu and
Ze-Sheng Li and
Chia-Chung Sun Theoretical study on reaction mechanism
of the fluoromethylene radical with
nitrogen dioxide . . . . . . . . . . . . 1888--1894
Eric Martineau and
Pierre-Jean L'Heureux and
John R. Gunn Biased fragment distribution in MC
simulation of protein folding . . . . . 1895--1903
Roberto L. A. Haiduke and
Luiz G. M. De Macedo and
Rugles C. Barbosa and
Albérico B. F. Da Silva A polynomial version of the generator
coordinate Dirac--Fock method . . . . . 1904--1909
Yasuhito Ohta and
Koji Ohta Interconversion behavior of the C H bond
in the CH radical cation: ab initio
molecular dynamics study . . . . . . . . 1910--1919
Philippe Soler and
Franck Fuster and
Hilaire Chevreau Fast topological analysis of $2$D and
$3$D grids of data: Application to the
atoms in molecule (AIM) and the electron
localization function (ELF) . . . . . . 1920--1925
Heather M. Netzloff and
Mark S. Gordon Fast fragments: the development of a
parallel effective fragment potential
method . . . . . . . . . . . . . . . . . 1926--1936
Francesc J. Corcho and
Josep Canto and
Juan J. Perez Comparative analysis of the
conformational profile of substance P
using simulated annealing and molecular
dynamics . . . . . . . . . . . . . . . . 1937--1952
Joseph M. Hayes and
James C. Greer and
David A. Morton-Blake A force-field description of short-range
repulsions for high density alkane
molecular dynamics simulations . . . . . 1953--1966
Michael S. Lee and
Freddie R. Salsbury Jr. and
Mark A. Olson An efficient hybrid explicit/implicit
solvent method for biomolecular
simulations . . . . . . . . . . . . . . 1967--1978
Otto Exner and
Stanislav Böhm Enthalpies of formation of
monoderivatives of hydrocarbons:
Interaction of polar groups with an
alkyl group . . . . . . . . . . . . . . 1979--1986
J. Fernández Rico and
R. López and
I. Ema and
G. Ramírez Efficiency of the algorithms for the
calculation of Slater molecular
integrals in polyatomic molecules . . . 1987--1994
Rie Tatsumi and
Yoshifumi Fukunishi and
Haruki Nakamura A hybrid method of molecular dynamics
and harmonic dynamics for docking of
flexible ligand to flexible receptor . . 1995--2005
Ramkumar V. Vadali and
Yan Shi and
Sameer Kumar and
Laxmikant V. Kale and
Mark E. Tuckerman and
Glenn J. Martyna Scalable fine-grained parallelization of
plane-wave--based ab initio molecular
dynamics for large supercomputers . . . 2006--2022
Xingfa Gao and
Hui Yuan and
Zhenling Chen and
Yuliang Zhao Theoretical studies of structures and
stabilities of a new odd-numbered
fullerene dimer: C$_{141}$ . . . . . . . 2023--2030
Nuno M. F. S. A. Cerqueira and
Pedro Alexandrino Fernandes and
Leif A. Eriksson and
Maria João Ramos Ribonucleotide activation by enzyme
ribonucleotide reductase: Understanding
the role of the enzyme . . . . . . . . . 2031--2037
John Mongan and
David A. Case and
J. Andrew McCammon Constant pH molecular dynamics in
generalized Born implicit solvent . . . 2038--2048
Ninad V. Prabhu and
Peijuan Zhu and
Kim A. Sharp Implementation and testing of stable,
fast implicit solvation in molecular
dynamics using the smooth-permittivity
finite difference Poisson--Boltzmann
method . . . . . . . . . . . . . . . . . 2049--2064
Joris van Droogenbroeck and
Ben Swerts and
Lothar Schäfer and
Christian van Alsenoy Solids modeled by ab initio crystal
field methods, part 22: the Fock matrix
transformed supermolecule model and the
structure determination of D-erythronic
acid-3,4-carbonate . . . . . . . . . . . 2065--2072
Chan Kyung Kim and
Kyung A. Lee and
Kwan Hoon Hyun and
Heung Jin Park and
In Young Kwack and
Chang Kon Kim and
Hai Whang Lee and
Bon-Su Lee Prediction of physicochemical properties
of organic molecules using van der Waals
surface electrostatic potentials . . . . 2073--2079
Kaori Fukuzawa and
Kazuo Kitaura and
Masami Uebayasi and
Kotoko Nakata and
Tsuguchika Kaminuma and
Tatsuya Nakano Ab initio quantum mechanical study of
the binding energies of human estrogen
receptor $\alpha$ with its ligands: an
application of fragment molecular
orbital method . . . . . . . . . . . . . 1--10
Maria Kontoyianni and
Glenn S. Sokol and
Laura M. Mcclellan Evaluation of library ranking efficacy
in virtual screening . . . . . . . . . . 11--22
Steve Dixon and
Kenneth M. Merz Jr. and
Giorgio Lauri and
James C. Ianni QMQSAR: Utilization of a semiempirical
probe potential in a field-based QSAR
method . . . . . . . . . . . . . . . . . 23--34
Zhong-Zhi Yang and
Li-Dong Gong and
Dong-Xia Zhao and
Ming-Bo Zhang Method and algorithm of obtaining the
molecular intrinsic characteristic
contours (MICCs) of organic molecules 35--47
Art E. Cho and
John A. Wendel and
Nagarajan Vaidehi and
Peter M. Kekenes-Huskey and
Wely B. Floriano and
Prabal K. Maiti and
William A. Goddard III The MPSim--Dock hierarchical docking
algorithm: Application to the eight
trypsin inhibitor cocrystals . . . . . . 48--71
Malek O. Khan and
Gareth Kennedy and
Derek Y. C. Chan A scalable parallel Monte Carlo method
for free energy simulations of molecular
systems . . . . . . . . . . . . . . . . 72--77
Kyoungrim Lee and
Cezary Czaplewski and
Seung-Yeon Kim and
Jooyoung Lee An efficient molecular docking using
conformational space annealing . . . . . 78--87
Bing Suo and
Gaohong Zhai and
Yubin Wang and
Zhenyi Wen and
Xiangqian Hu and
Lemin Li Parallelization of MRCI based on
hole-particle symmetry . . . . . . . . . 88--96
F. Martin and
H. Zipse Charge distribution in the water
molecule --- a comparison of methods . . 97--105
Wenli Zou and
Wenjian Liu Extensive theoretical studies on the
low-lying electronic states of indium
monochloride cation, InCl$^+$ . . . . . 106--113
Junmei Wang and
Romain M. Wolf and
James W. Caldwell and
Peter A. Kollman and
David A. Case Erratum: Junmei Wang, Romain M. Wolf,
James W. Caldwell, Peter A. Kollman, and
David A. Case, ``Development and testing
of a general AMBER force field'' Journal
of Computational Chemistry (2004) \bf
25(9) 1157--1174 . . . . . . . . . . . . 114--114
Serena Donnini and
Alan E. Mark and
André H. Juffer and
Alessandra Villa Incorporating the effect of ionic
strength in free energy calculations
using explicit ions . . . . . . . . . . 115--122
Robert J. Deeth and
Natalie Fey and
Benjamin Williams-Hubbard DommiMOE: an implementation of ligand
field molecular mechanics in the
molecular operating environment . . . . 123--130
David De Sancho and
Lidia Prieto and
Ana M. Rubio and
Antonio Rey Evolutionary method for the assembly of
rigid protein fragments . . . . . . . . 131--141
Daniela Bertolini Depizzol and
Marcia Helena Moreira Paiva and
Thiago Oliveira Dos Santos and
Anderson Coser Gaudio MoCalc: a new graphical user interface
for molecular calculations . . . . . . . 142--144
Zuzana Benkova and
Andrzej J. Sadlej and
Roma E. Oakes and
Steven E. J. Bell Reduced-size polarized basis sets for
calculations of molecular electric
properties. I. The basis set generation 145--153
Roma E. Oakes and
Steven E. J. Bell and
Zuzana Benkova and
Andrzej J. Sadlej Reduced-size polarized basis sets for
calculations of molecular electric
properties. II. Simulation of the Raman
spectra . . . . . . . . . . . . . . . . 154--159
Mitsuhito Wada and
Minoru Sakurai A quantum chemical method for rapid
optimization of protein structures . . . 160--168
H. Sun and
P. W.-C. Kung Urea: an ab initio and force field study
of the gas and solid phases . . . . . . 169--174
S. Chiodo and
N. Russo and
E. Sicilia Newly developed basis sets for density
functional calculations . . . . . . . . 175--184
Li Wang and
Jing-Yao Liu and
Ze-Sheng Li and
Chia-Chung Sun Theoretical study and rate constant
calculation for the reactions of SH (SD)
with Cl$_2$, Br$_2$, and BrCl . . . . . 184--193
W. Dean Harman and
Carl Trindle Charge donation to and dearomatization
of benzene attending complexation: DFT
estimates of binding energies of
TpMXO(L) with benzene, for Tp =
hydridotris(pyrazolyl) borate, MXO =
MoNO, ReCO, and WNO, and L = ammonia,
$N$-methylimidazole, pyridine,
phosphine, methyl isocyanide, and carbon
monoxide . . . . . . . . . . . . . . . . 194--200
K. Fiaty and
C. Charcosset and
B. Perrin and
R. Couturier and
B. Ma\"\isterrena Simulations of the active transport of a
neutral solute based on a
kinase-channel-phosphatase topology . . 201--213
Robert J. Gdanitz and
Gary D. Black and
Carina S. Lansing and
Bruce J. Palmer and
Karen L. Schuchardt Registering the Amica electronic
structure code in the Extensible
Computational Chemistry Environment . . 214--225
Yuhui Qu and
Xiufang Bian Electronic structure and stability of
Al$_n$P$_n$ ($n = 2$--$4$) clusters . . 226--234
Joanna Makowska and
Mariusz Makowski and
Adam Liwo and
Lech Chmurzy\'nski Theoretical calculations of
homoconjugation equilibrium constants in
systems modeling acid--base interactions
in side chains of biomolecules using the
potential of mean force . . . . . . . . 235--242
Charles F. F. Karney and
Jason E. Ferrara and
Stephan Brunner Method for computing protein binding
affinity . . . . . . . . . . . . . . . . 243--251
Matthew A. Meineke and
Charles F. Vardeman II and
Teng Lin and
Christopher J. Fennell and
J. Daniel Gezelter OOPSE: an object-oriented parallel
simulation engine for molecular dynamics 252--271
Minoru Saito and
Isao Okazaki and
Masayuki Oda and
Ikuo Fujii A free energy calculation study of the
effect of H$\rightarrow$F substitution
on binding affinity in ligand--antibody
interactions . . . . . . . . . . . . . . 272--282
F. Wennmohs and
M. Schindler Development of a multipoint model for
sulfur in proteins: a new
parametrization scheme to reproduce
high-level ab initio interaction
energies . . . . . . . . . . . . . . . . 283--293
Josef \vSeda and
Jaroslav V. Burda and
Jerzy Leszczynski Study of electronic spectra of free-base
porphin and Mg-porphin: Comprehensive
comparison of variety of ab initio, DFT,
and semiempirical methods . . . . . . . 294--303
Panagiotis G. Karamertzanis and
Constantinos C. Pantelides Ab initio crystal structure prediction
--- I. Rigid molecules . . . . . . . . . 304--324
Yasuyo Hatano and
Shigeyoshi Yamamoto and
Hiroshi Tatewaki Characterization of molecular orbitals
by counting nodal regions . . . . . . . 325--333
Shura Hayryan and
Chin-Kun Hu and
Jaroslav Sk\vrivánek and
Edik Hayryane and
Imrich Pokorný A new analytical method for computing
solvent-accessible surface area of
macromolecules and its gradients . . . . 334--343
A. Martín Pendás and
E. Francisco and
M. A. Blanco Two-electron integrations in the Quantum
Theory of Atoms in Molecules with
correlated wave functions . . . . . . . 344--351
Michael Meyer and
Alexandre Hocquet and
Jürgen Sühnel Interaction of sodium and potassium ions
with sandwiched cytosine-, guanine-,
thymine-, and uracil-base tetrads . . . 352--364
Pablo Campomanes and
M. Isabel Menéndez and
Ramón López and
Tomás L. Sordo Stereodynamics of bond rotation in
tertiary 1-naphthoic acid amides: a
computational study . . . . . . . . . . 365--373
Eckart Bindewald and
Jeffrey Skolnick A scoring function for docking ligands
to low-resolution protein structures . . 374--383
Philippe Carbonniere and
Tecla Lucca and
Claude Pouchan and
Nadia Rega and
Vincenzo Barone Vibrational computations beyond the
harmonic approximation: Performances of
the B3LYP density functional for
semirigid molecules . . . . . . . . . . 384--388
Mehdi Mobli and
Raymond J. Abraham Quantum vs. classical models of the
nitro group for proton chemical shift
calculations and conformational analysis 389--398
Quan Zhu and
Ke-Xiang Fu and
Xiang-Yuan Li and
Zhen Gong and
Jian-Yi Ma Continuous medium theory for
nonequilibrium solvation: III. Solvation
shift by monopole approximation and
multipole expansion in spherical cavity 399--409
Veronika Kasalová and
Henry F. Schaefer III Structures and electron affinities of
the di-arsenic fluorides As$_2$F$_n$
/As$_2$F ($n = 1$--$8$) . . . . . . . . 411--435
Mari Tamaoki and
Yusuke Yamauchi and
Hiromi Nakai Short-time Fourier transform analysis of
ab initio molecular dynamics simulation:
Collision reaction between CN and
C$_4$H$_6$ . . . . . . . . . . . . . . . 436--442
Rajeev Prabhakar and
Keiji Morokuma and
Djamaladdin G. Musaev A comparative study of various
computational approaches in calculating
the structure of pyridoxal 5'-phosphate
(PLP)-dependent $\beta$-lyase protein.
The importance of protein environment 443--446
Robert Ponec and
Gleb Yuzhakov and
Markku R. Sundberg Chemical structures from the analysis of
domain-averaged Fermi holes. Nature of
the Mn Mn bond in
bis(pentacarbonylmanganese) . . . . . . 447--454
A. Gallegos and
R. Carbó-Dorca and
F. Lodier and
E. Canc\`es and
A. Savin Maximal probability domains in linear
molecules . . . . . . . . . . . . . . . 455--460
Qishi Du and
P. G. Mezey and
Kuo-Chen Chou Heuristic molecular lipophilicity
potential (HMLP): a $2$D-QSAR study to
LADH of molecular family pyrazole and
derivatives . . . . . . . . . . . . . . 461--470
Carlos A. Stortz Comparative performance of MM3(92) and
two TINKER\TM MM3 versions for the
modeling of carbohydrates . . . . . . . 471--483
Bing Liu and
Jiaju Zhou SARS-CoV protease inhibitors design
using virtual screening method from
natural products libraries . . . . . . . 484--490
A. M. Tokmachev and
A. L. Tchougréeff Transferability of parameters of
strictly local geminals' wave function
and possibility of sequential derivation
of molecular mechanics . . . . . . . . . 491--505
Pierre Tuffery and
Frédéric Guyon and
Philippe Derreumaux Improved greedy algorithm for protein
structure reconstruction . . . . . . . . 506--513
Lingchun Song and
Yirong Mo and
Qianer Zhang and
Wei Wu XMVB: a program for ab initio
nonorthogonal valence bond computations 514--521
Anonymous Announcements . . . . . . . . . . . . . v--v
Raúl A. Bustos Marún and
Eduardo A. Coronado and
Juan C. Ferrero Fitting complex potential energy
surfaces to simple model potentials:
Application of the simplex-annealing
method . . . . . . . . . . . . . . . . . 523--531
Vinzenz Bachler The behavior of transition metal nitrido
bonds towards protonation rationalized
by means of localized bonding schemes
and their weights . . . . . . . . . . . 532--551
Ping Li and
Yuxiang Bu Double proton transfer and one-electron
oxidation behavior in double H-bonded
glycinamide--glycine complex in the gas
phase . . . . . . . . . . . . . . . . . 552--560
Peter L. Cummins and
Jill E. Gready Computational methods for the study of
enzymic reaction mechanisms III: a
perturbation plus QM/MM approach for
calculating relative free energies of
protonation . . . . . . . . . . . . . . 561--568
Núria González-García and
\`Angels González-Lafont and
José M. Lluch Electronic structure study of the
initiation routes of the dimethyl
sulfide oxidation by OH . . . . . . . . 569--583
Qingyu Kong and
Li Zhao and
Wenning Wang and
Chen Wang and
Can Xu and
Wingham Zhang and
Lei Liu and
Kangnian Fan and
Yufen Li and
Jun Zhuang Magic number silicon dioxide-based
clusters: Laser ablation-mass
spectrometric and density functional
theory studies . . . . . . . . . . . . . 584--598
Peter Pulay and
Svein Saebo and
Massimo Malagoli and
Jon Baker Accuracy and efficiency of atomic basis
set methods versus plane wave
calculations with ultrasoft
pseudopotentials for DNA base molecules 599--605
T. K. Manojkumar and
Chunzhi Cui and
Kwang S. Kim Theoretical insights into the mechanism
of acetylcholinesterase-catalyzed
acylation of acetylcholine . . . . . . . 606--611
Pedro L. Muiño The OH$^\bullet$ + CH$_3$SH reaction:
Support for an addition-elimination
mechanism from ab initio calculations 612--618
Manfred Rudolph Attaining exponential convergence for
the flux error with second- and
fourth-order accurate finite-difference
equations. I. Presentation of the basic
concept and application to a pure
diffusion system . . . . . . . . . . . . 619--632
Manfred Rudolph Attaining exponential convergence for
the flux error with second- and
fourth-order accurate finite-difference
equations. II. Application to systems
comprising first-order chemical
reactions . . . . . . . . . . . . . . . 633--641
Hong-Qing He and
Jing-Yao Liu and
Ze-Sheng Li and
Chia-Chung Sun Theoretical study for the reaction of
CH$_3$OCl with Cl atom . . . . . . . . . 642--650
Eva Darian and
Vladimir Hnizdo and
Adam Fedorowicz and
Harshinder Singh and
Eugene Demchuk Estimation of the absolute
internal-rotation entropy of molecules
with two torsional degrees of freedom
from stochastic simulations . . . . . . 651--660
Marcus Lundberg and
Per E. M. Siegbahn Agreement between experiment and hybrid
DFT calculations for O H bond
dissociation enthalpies in manganese
complexes . . . . . . . . . . . . . . . 661--667
Peter A. Sims and
Chung F. Wong and
Danka Vuga and
J. Andrew McCammon and
Bartholomew M. Sefton Relative contributions of desolvation,
inter- and intramolecular interactions
to binding affinity in protein kinase
systems . . . . . . . . . . . . . . . . 668--681
Eric J. Sorin and
Vijay S. Pande Empirical force-field assessment: the
interplay between backbone torsions and
noncovalent term scaling . . . . . . . . 682--690
Min-Yi Shen and
Karl F. Freed A simple method for faster nonbonded
force evaluations . . . . . . . . . . . 691--698
L. Renee Olano and
Steven W. Rick Fluctuating charge normal modes: an
algorithm for implementing molecular
dynamics simulations with polarizable
potentials . . . . . . . . . . . . . . . 699--707
Alán Aspuru-Guzik and
Romelia Salomón-Ferrer and
Brian Austin and
William A. Lester Jr. A sparse algorithm for the evaluation of
the local energy in quantum Monte Carlo 708--715
Anti Liivat and
Alvo Aabloo and
John O. Thomas Development of a force field for
Li$_2$SiF$_6$ . . . . . . . . . . . . . 716--724
Thereza A. Soares and
Philippe H. Hünenberger and
Mika A. Kastenholz and
Vincent Kräutler and
Thomas Lenz and
Roberto D. Lins and
Chris Oostenbrink and
Wilfred F. van Gunsteren An improved nucleic acid parameter set
for the GROMOS force field . . . . . . . 725--737
Fredrik Blomgren and
Sven Larsson Exploring the potential energy surface
of retinal, a comparison of the
performance of different methods . . . . 738--742
Neil Gohaud and
Didier Begue and
Clovis Darrigan and
Claude Pouchan New parallel software (\tt P\_Anhar) for
anharmonic vibrational calculations:
Application to (CH$_3$Li)$_2$ . . . . . 743--754
Robert J. Petrella and
Martin Karplus Electrostatic energies and forces
computed without explicit interparticle
interactions: a linear time complexity
formulation . . . . . . . . . . . . . . 755--787
Hirofumi Fujimoto and
Miroslav Pinak and
Toshiyuki Nemoto and
Peter O'Neill and
Etsuo Kume and
Kimiaki Saito and
Hideaki Maekawa Molecular dynamics simulation of
clustered DNA damage sites containing
8-oxoguanine and abasic site . . . . . . 788--798
Si-Dian Li and
Chang-Qing Miao and
Jin-Chang Guo and
Guang-Ming Ren Carbon boronyls: Species with higher
viable possibility than boron carbonyls
at the density functional theory . . . . 799--802
Frank J. Owens Stability of (C$_{60}$)$_2$ and epoxide
dimers, (C$_{60}$)$_2$O$_N$, and their
anions . . . . . . . . . . . . . . . . . 803--806
Jia-Xu Zhang and
Jing-Yao Liu and
Ze-Sheng Li and
Chia-Chung Sun Theoretical study on the reaction
mechanism of the methyl radical with
nitrogen oxides . . . . . . . . . . . . 807--817
Akifumi Oda and
Noriyuki Yamaotsu and
Shuichi Hirono New AMBER force field parameters of heme
iron for cytochrome P450s determined by
quantum chemical calculations of
simplified models . . . . . . . . . . . 818--826
Alessandro Genoni and
Arianna Fornili and
Maurizio Sironi Optimal virtual orbitals to relax wave
functions built up with transferred
extremely localized molecular orbitals 827--835
Theodore S. Dibble Computations on the $\tilde{A}$--X$^-$;
transition of isoprene-OH-O$_2$ peroxy
radicals . . . . . . . . . . . . . . . . 836--845
J. Fernández Rico and
R. López and
I. Ema and
G. Ramírez Translation of STO charge distributions 846--855
Alán Aspuru-Guzik and
Romelia Salomón-Ferrer and
Brian Austin and
Raul Perusquía-Flores and
Mary A. Griffin and
Ricardo A. Oliva and
David Skinner and
Dominik Domin and
William A. Lester Jr. Zori 1.0: a parallel quantum Monte Carlo
electronic structure package . . . . . . 856--862
Jason Wagoner and
Nathan A. Baker Erratum to ``Solvation forces on
biomolecular structures: A comparison of
explicit solvent and Poisson--Boltzmann
models,'' by Jason Wagoner and Nathan A.
Baker . . . . . . . . . . . . . . . . . 863--863
Ia. I. Dobrogorskaia-Méreau and
A. V. Nemukhin Quantum chemical modeling of the
reduction of cis-diammineplatinum(IV)
tetrachloride [Pt(NH$_3$)$_2$Cl$_4$] by
methyl thiolate anion . . . . . . . . . 865--870
Gui-Chang Wang and
Jun Li and
Xiu-Fang Xu and
Rui-Fang Li and
Junji Nakamura The relationship between adsorption
energies of methyl on metals and the
metallic electronic properties: a
first-principles DFT study . . . . . . . 871--878
Andreas Schreiber and
Michael Humbert and
Alexander Benz and
Ursula Dietrich $3$D-Epitope-Explorer (3DEX):
Localization of conformational epitopes
within three-dimensional structures of
proteins . . . . . . . . . . . . . . . . 879--887
Per E. M. Siegbahn and
Alexander F. Shestakov Quantum chemical modeling of CO
oxidation by the active site of
molybdenum CO dehydrogenase . . . . . . 888--898
Wayne Pullan An unbiased population-based search for
the geometry optimization of
Lennard-Jones clusters: $2 \leq {N} \leq
372$ . . . . . . . . . . . . . . . . . . 899--906
Jaroslav V. Burda and
Michal Zeizinger and
Jerzy Leszczynski Hydration process as an activation of
trans- and cisplatin complexes in
anticancer treatment. DFT and ab initio
computational study of thermodynamic and
kinetic parameters . . . . . . . . . . . 907--914
Art E. Cho and
Victor Guallar and
Bruce J. Berne and
Richard Friesner Importance of accurate charges in
molecular docking: Quantum
mechanical/molecular mechanical (QM/MM)
approach . . . . . . . . . . . . . . . . 915--931
Roberto L. A. Haiduke and
Luiz G. M. de Macedo and
Albérico B. F. da Silva An accurate relativistic universal
Gaussian basis set for hydrogen through
Nobelium without variational prolapse
and to be used with both uniform sphere
and Gaussian nucleus models . . . . . . 932--940
Illia Horenko and
Sönke Lorenz and
Christof Schütte and
Wilhelm Huisinga Adaptive approach for nonlinear
sensitivity analysis of reaction
kinetics . . . . . . . . . . . . . . . . 941--948
Thomas S. Hofer and
Bernhard R. Randolf and
Bernd M. Rode Structure-breaking effects of solvated
Rb(I) in dilute aqueous solution --- an
ab initio QM/MM MD approach . . . . . . 949--956
Sanjay Banerjee and
John A. Board Jr. Efficient charge assignment and back
interpolation in multigrid methods for
molecular dynamics . . . . . . . . . . . 957--967
Li Yang and
Ji-Kang Feng and
Ai-Min Ren Theoretical studies on the electronic
and optical properties of two new
alternating fluorene/carbazole
copolymers . . . . . . . . . . . . . . . 969--979
Chang-Guo Zhan and
Shi-Xian Deng and
Jaime G. Skiba and
Beth A. Hayes and
Sarah M. Tschampel and
George C. Shields and
Donald W. Landry First-principle studies of
intermolecular and intramolecular
catalysis of protonated cocaine . . . . 980--986
Toru Inaba and
Saisei Tahara and
Nobutaka Nisikawa and
Hiroshi Kashiwagi and
Fumitoshi Sato All-electron density functional
calculation on insulin with
quasi-canonical localized orbitals . . . 987--993
Ying Xue and
Chan Kyung Kim and
Yong Guo and
Dai Qian Xie and
Guo Sen Yan DFT study and Monte Carlo simulation on
proton transfers of 2-amino-2-oxazoline,
2-amino-2-thiazoline, and
2-amino-2-imidazoline in the gas phase
and in water . . . . . . . . . . . . . . 994--1005
G. Theodoor De Jong and
Daan P. Geerke and
Axel Diefenbach and
Miquel Sol\`a and
F. Matthias Bickelhaupt Oxidative addition of the ethane C C
bond to Pd. An ab initio benchmark and
DFT validation study . . . . . . . . . . 1006--1020
Michael S. Crocker and
Scott S. Hampton and
Thierry Matthey and
Jesús A. Izaguirre \sc MDSimAid: Automatic parameter
optimization in fast electrostatic
algorithms . . . . . . . . . . . . . . . 1021--1031
Hsien-Da Huang and
Tzong-Yi Lee and
Shih-Wei Tzeng and
Li-Cheng Wu and
Jorng-Tzong Horng and
Ann-Ping Tsou and
Kuan-Tsae Huang Incorporating hidden Markov models for
identifying protein kinase-specific
phosphorylation sites . . . . . . . . . 1032--1041
Stefano Borini and
Daniel Maynau and
Stefano Evangelisti A combined freeze-and-cut strategy for
the description of large molecular
systems using a localized orbitals
approach . . . . . . . . . . . . . . . . 1042--1051
Jean-Philip Piquemal and
Antonio Marquez and
Olivier Parisel and
Claude Giessner-Prettre A CSOV study of the difference between
HF and DFT intermolecular interaction
energy values: the importance of the
charge transfer contribution . . . . . . 1052--1062
Jerod Parsons and
J. Bradley Holmes and
J. Maurice Rojas and
Jerry Tsai and
Charlie E. M. Strauss Practical conversion from torsion space
to Cartesian space for in silico protein
synthesis . . . . . . . . . . . . . . . 1063--1068
Lesley D. Lloyd and
Roy L. Johnston and
Said Salhi Strategies for increasing the efficiency
of a genetic algorithm for the
structural optimization of nanoalloy
clusters . . . . . . . . . . . . . . . . 1069--1078
Piotr Zarzycki and
Pawe\l Szabelski and
Robert Charmas Role of the surface heterogeneity in
adsorption of hydrogen ions on metal
oxides: Theory and simulations . . . . . 1079--1088
A. M. Ruvinsky and
A. V. Kozintsev New and fast statistical-thermodynamic
method for computation of protein-ligand
binding entropy substantially improves
docking accuracy . . . . . . . . . . . . 1089--1095
Caterina Benzi and
Maurizio Cossi and
Roberto Improta and
Vincenzo Barone Building cavities in a fluid of
spherical or rod-like particles: a
contribution to the solvation free
energy in isotropic and anisotropic
polarizable continuum model . . . . . . 1096--1105
Michael S. Schuurman and
Wesley D. Allen and
Henry F. Schaefer III The ab initio limit quartic force field
of BH$_3$ . . . . . . . . . . . . . . . 1106--1112
Nohad Gresh and
Jean-Philip Piquemal and
Morris Krauss Representation of Zn(II) complexes in
polarizable molecular mechanics. Further
refinements of the electrostatic and
short-range contributions. Comparisons
with parallel ab initio computations . . 1113--1130
Jens Antony and
Jean-Philip Piquemal and
Nohad Gresh Complexes of thiomandelate and captopril
mercaptocarboxylate inhibitors to
metallo-$\beta$-lactamase by polarizable
molecular mechanics. Validation on model
binding sites by quantum chemistry . . . 1131--1147
Siegfried Höfinger Solving the Poisson--Boltzmann equation
with the specialized computer chip
MD-GRAPE-2 . . . . . . . . . . . . . . . 1148--1154
András Perczel and
Zoltán Gáspári and
Imre G. Csizmadia Structure and stability of
$\beta$-pleated sheets . . . . . . . . . 1155--1168
Florian Koskowski and
Bernd Hartke Towards protein folding with
evolutionary techniques . . . . . . . . 1169--1179
Maxence Launay and
Richard Dronskowski A theoretical study on the structures
and energetics of hypothetical
TiM(NCN)$_3$ compounds of the $3 d$
transition metals . . . . . . . . . . . 1180--1188
Hongzhi Li and
Yaoqi Zhou SCUD: Fast structure clustering of
decoys using reference state to remove
overall rotation . . . . . . . . . . . . 1189--1192
Manfred Rudolph Attaining exponential convergence for
the flux error with second- and
fourth-order accurate finite-difference
equations. Part 3. Application to
electrochemical systems comprising
second-order chemical reactions . . . . 1193--1204
Robert Ponec and
Joaquin Chaves Electron pairing and chemical bonds.
Electron fluctuation and pair
localization in ELF domains . . . . . . 1205--1213
Zexing Cao and
Qianer Zhang Computational analyses of
singlet--singlet and singlet--triplet
transitions in mononuclear gold-capped
carbon-rich conjugated complexes . . . . 1214--1221
Po-Ssu Huang and
John J. Love and
Stephen L. Mayo Adaptation of a fast Fourier
transform-based docking algorithm for
protein design . . . . . . . . . . . . . 1222--1232
Thanh Ha Nguyen and
David E. Hibbs and
Siân T. Howard Conformations, energies, and
intramolecular hydrogen bonds in
dicarboxylic acids: Implications for the
design of synthetic dicarboxylic acid
receptors . . . . . . . . . . . . . . . 1233--1241
Andreas W. Götz and
Christian Kollmar and
Bernd A. Hess Optimization of auxiliary basis sets for
the LEDO expansion and a projection
technique for LEDO--DFT . . . . . . . . 1242--1253
J. M. Junquera-Hernández and
J. Pitarch-Ruiz and
J. Sánchez-Marín and
S. Evangelisti and
D. Maynau Multistate active spaces from local
CAS-SCF molecular orbitals: the
photodissociation of HFCO as an example 1254--1262
Xue-Hai Ju and
Xin Wang and
Feng-Li Bei Substituent effects on heats of
formation, group interactions, and
detonation properties of
polyazidocubanes . . . . . . . . . . . . 1263--1269
Marek Freindorf and
Yihan Shao and
Thomas R. Furlani and
Jing Kong Lennard-Jones parameters for the
combined QM/MM method using the
B3LYP/6-31G*/AMBER potential . . . . . . 1270--1278
Zhigang Wang and
Keyan Lian and
Shoufu Pan and
Xianhong Fan A path from I$_h$ to C$_1$ symmetry for
C$_{20}$ cage molecule . . . . . . . . . 1279--1283
Maria Del Carmen Michelini and
Nino Russo and
Mohammad Esma\"\il Alikhani and
Bernard Silvi Energetic and topological analyses of
the oxidation reaction between Mo$_n$
($n = 1, 2$) and N$_2$O . . . . . . . . 1284--1293
Christian Bartels and
Armin Widmer and
Claus Ehrhardt Absolute free energies of binding of
peptide analogs to the HIV-1 protease
from molecular dynamics simulations . . 1294--1305
Péter Hudáky and
András Perczel Toward direct determination of
conformations of protein building units
from multidimensional NMR experiments
VI. Chemical shift analysis of his to
gain $3$D structure and protonation
state information . . . . . . . . . . . 1307--1317
David E. Shaw A fast, scalable method for the parallel
evaluation of distance-limited pairwise
particle interactions . . . . . . . . . 1318--1328
Pathumwadee Intharathep and
Anan Tongraar and
Kritsana Sagarik Structure and dynamics of hydrated NH:
an ab initio QM/MM molecular dynamics
simulation . . . . . . . . . . . . . . . 1329--1338
Yu-Hua Yao and
Xu-Ying Nan and
Tian-Ming Wang A class of $2$D graphical
representations of RNA secondary
structures and the analysis of
similarity based on them . . . . . . . . 1339--1346
R. Villar and
M. J. Gil and
J. I. García and
V. Martínez-Merino Are AM1 ligand-protein binding
enthalpies good enough for use in the
rational design of new drugs? . . . . . 1347--1358
Sonja M. Schwarzl and
Danzhi Huang and
Jeremy C. Smith and
Stefan Fischer Nonuniform charge scaling (NUCS): a
practical approximation of solvent
electrostatic screening in proteins . . 1359--1371
Hitoshi Kusama and
Hideki Sugihara Theoretical study of quinolines--I$_2$
intermolecular interaction and
implications on dye-sensitized solar
cell performance . . . . . . . . . . . . 1372--1382
Zoe Cournia and
Jeremy C. Smith and
G. Matthias Ullmann A molecular mechanics force field for
biologically important sterols . . . . . 1383--1399
Roberto D. Lins and
Philippe H. Hünenberger A new GROMOS force field for
hexopyranose-based carbohydrates . . . . 1400--1412
Youdong Lin and
Mark A. Stadtherr Deterministic global optimization of
molecular structures using interval
analysis . . . . . . . . . . . . . . . . 1413--1420
Hui Zhang and
Jia-Yan Wu and
Ze-Sheng Li and
Jing-Yao Liu and
Li Sheng and
Chia-Chung Sun Dual-level direct dynamics studies on
the reaction Cl + CHBr$_2$Cl . . . . . . 1421--1426
Victor Polo and
Juan Andrés A joint study based on the electron
localization function and catastrophe
theory of the chameleonic and centauric
models for the Cope rearrangement of
1,5-hexadiene and its cyano derivatives 1427--1437
Gernot Katzer and
Alexander F. Sax Identification and thermodynamic
treatment of several types of
large-amplitude motions . . . . . . . . 1438--1451
Alba T. Macias and
Alexander D. MacKerell Jr. CH/$\pi$ interactions involving aromatic
amino acids: Refinement of the CHARMM
tryptophan force field . . . . . . . . . 1452--1463
Nicholas P. Labello and
Antonio M. Ferreira and
Henry A. Kurtz An augmented effective core potential
basis set for the calculation of
molecular polarizabilities . . . . . . . 1464--1471
Marian Nanias and
Maurizio Chinchio and
Stanis\law O\ldziej and
Cezary Czaplewski and
Harold A. Scheraga Protein structure prediction with the
UNRES force-field using Replica-Exchange
Monte Carlo-with-Minimization;
Comparison with MCM, CSA, and CFMC . . . 1472--1486
Daiqian Xie and
Jun Zeng Electronic excitations of green
fluorescent proteins: Protonation states
of chromophore model compound in
solutions . . . . . . . . . . . . . . . 1487--1496
A. Patrícia Bento and
Miquel Sol\`a and
F. Matthias Bickelhaupt Ab initio and DFT benchmark study for
nucleophilic substitution at carbon
(S$_N$2@C) and silicon (S$_N$2@Si) . . . 1497--1504
Max C. Holthausen Benchmarking approximate density
functional theory. I. $s/d$ excitation
energies in $3 d$ transition metal
cations . . . . . . . . . . . . . . . . 1505--1518
Bo Liao and
Kequan Ding Graphical approach to analyzing DNA
sequences . . . . . . . . . . . . . . . 1519--1523
Ricardo O. Freire and
Gerd B. Rocha and
Alfredo M. Simas Modeling lanthanide complexes:
Sparkle/AM1 parameters for ytterbium
(III) . . . . . . . . . . . . . . . . . 1524--1528
Daniel J. Price and
Charles L. Brooks III Detailed considerations for a balanced
and broadly applicable force field: a
study of substituted benzenes modeled
with OPLS-AA . . . . . . . . . . . . . . 1529--1541
Hui-Yin Wu and
Ajay Chaudhari and
Shyi-Long Lee Theoretical studies on nonlinear optical
properties of formaldehyde oligomers by
ab initio and density functional theory
methods . . . . . . . . . . . . . . . . 1543--1564
Jianhan Chen and
Wonpil Im and
Charles L. Brooks III Application of torsion angle molecular
dynamics for efficient sampling of
protein conformations . . . . . . . . . 1565--1578
M. Tafipolsky and
R. Schmid Calculation of rotational partition
functions by an efficient Monte Carlo
importance sampling technique . . . . . 1579--1591
Chompoonut Rungnim and
Vithaya Ruangpornvisuti A density functional study of propylene
glycol conversion to propanal and
propanone of various acid-catalyzed
reaction models: a water-addition effect 1592--1599
Yoong-Kee Choe and
Shigeru Nagase Effect of the axial cysteine ligand on
the electronic structure and reactivity
of high-valent iron(IV) oxo-porphyrins
(Compound I): a theoretical study . . . 1600--1611
Sanghyun Park and
Randall J. Radmer and
Teri E. Klein and
Vijay S. Pande A new set of molecular mechanics
parameters for hydroxyproline and its
use in molecular dynamics simulations of
collagen-like peptides . . . . . . . . . 1612--1616
Shantenu Jha and
Peter V. Coveney and
Charles A. Laughton Force field validation for nucleic acid
simulations: Comparing energies and
dynamics of a DNA dodecamer . . . . . . 1617--1627
Emanuel H. Rubensson and
Pawe\l Sa\lek Systematic sparse matrix error control
for linear scaling electronic structure
calculations . . . . . . . . . . . . . . 1628--1637
Mark T. Oakley and
Jonathan M. Garibaldi and
Jonathan D. Hirst Lattice models of peptide aggregation:
Evaluation of conformational search
algorithms . . . . . . . . . . . . . . . 1638--1646
Michael A. Johnston and
Ignacio Fdez. Galván and
Jordi Vill\`a-Freixa Framework-based design of a new
all-purpose molecular simulation
application: the Adun simulator . . . . 1647--1659
G. R. Kneller Comment on ``Using quaternions to
calculate RMSD'' [J. Comp. Chem. \bf 25,
1849 (2004)] . . . . . . . . . . . . . . 1660--1662
Evangelos A. Coutsias and
Chaok Seok and
Ken A. Dill Rotational superposition and least
squares: the SVD and quaternions
approaches yield identical results.
Reply to the preceding comment by G.
Kneller . . . . . . . . . . . . . . . . 1663--1665
Charles L. Brooks III Editorial . . . . . . . . . . . . . . . 1667--1667
David A. Case and
Thomas E. Cheatham III and
Tom Darden and
Holger Gohlke and
Ray Luo and
Kenneth M. Merz Jr. and
Alexey Onufriev and
Carlos Simmerling and
Bing Wang and
Robert J. Woods The AMBER biomolecular simulation
programs . . . . . . . . . . . . . . . . 1668--1688
William L. Jorgensen and
Julian Tirado-Rives Molecular modeling of organic and
biomolecular systems using BOSS and
MCPRO . . . . . . . . . . . . . . . . . 1689--1700
David Van Der Spoel and
Erik Lindahl and
Berk Hess and
Gerrit Groenhof and
Alan E. Mark and
Herman J. C. Berendsen GROMACS: Fast, flexible, and free . . . 1701--1718
Markus Christen and
Philippe H. Hünenberger and
Dirk Bakowies and
Riccardo Baron and
Roland Bürgi and
Daan P. Geerke and
Tim N. Heinz and
Mika A. Kastenholz and
Vincent Kräutler and
Chris Oostenbrink and
Christine Peter and
Daniel Trzesniak and
Wilfred F. van Gunsteren The GROMOS software for biomolecular
simulation: GROMOS05 . . . . . . . . . . 1719--1751
Jay L. Banks and
Hege S. Beard and
Yixiang Cao and
Art E. Cho and
Wolfgang Damm and
Ramy Farid and
Anthony K. Felts and
Thomas A. Halgren and
Daniel T. Mainz and
Jon R. Maple and
Robert Murphy and
Dean M. Philipp and
Matthew P. Repasky and
Linda Y. Zhang and
Bruce J. Berne and
Richard A. Friesner and
Emilio Gallicchio and
Ronald M. Levy Integrated Modeling Program, Applied
Chemical Theory (IMPACT) . . . . . . . . 1752--1780
James C. Phillips and
Rosemary Braun and
Wei Wang and
James Gumbart and
Emad Tajkhorshid and
Elizabeth Villa and
Christophe Chipot and
Robert D. Skeel and
Laxmikant Kalé and
Klaus Schulten Scalable molecular dynamics with NAMD 1781--1802
Anonymous Erratum: David E. Shaw. ``A fast,
scalable method for the parallel
evaluation of distance-limited pairwise
particle interactions'', Journal of
Computational Chemistry (2005) \bf 26
(13) 1318--1328 . . . . . . . . . . . . 1803--1803
Zhong-Zhi Yang and
Qiang Zhang Study of peptide conformation in terms
of the ABEEM/MM method . . . . . . . . . 1--10
Frank Eckert and
Andreas Klamt Accurate prediction of basicity in
aqueous solution with COSMO-RS . . . . . 11--19
Tamás Beke and
Csaba Somlai and
András Perczel Toward a rational design of
$\beta$-peptide structures . . . . . . . 20--38
Jing Ma and
Shuhua Li and
Wei Li A multireference configuration
interaction method based on the
separated electron pair wave functions 39--47
Yoshihiro Watanabe and
Hiroshi Tatewaki and
Toshikatsu Koga and
Osamu Matsuoka Relativistic Gaussian basis sets for
molecular calculations: Fully optimized
single-family exponent basis sets for H
Hg . . . . . . . . . . . . . . . . . . . 48--52
Kaori Ueno-Noto and
Miki Hara-Yokoyama and
Keiko Takano Recognition of tandem sialic acid
residues by CD38: a theoretical study 53--60
Roberto L. A. Haiduke and
Albérico B. F. da Silva Accurate relativistic adapted Gaussian
basis sets for hydrogen through xenon
without variational prolapse and to be
used with both uniform sphere and
Gaussian nucleus models . . . . . . . . 61--71
Zhiyun Yu and
Matthew P. Jacobson and
Richard A. Friesner What role do surfaces play in GB models?
A new-generation of surface-generalized
Born model based on a novel Gaussian
surface for biomolecules . . . . . . . . 72--89
Yasemin Kurtulus and
Michael Gilleßen and
Richard Dronskowski Electronic structure, chemical bonding,
and finite-temperature magnetic
properties of full Heusler alloys . . . 90--102
Brent A. Gregersen and
Darrin M. York A charge-scaling implementation of the
variational electrostatic projection
method . . . . . . . . . . . . . . . . . 103--115
Carlos Silva López and
Olalla Nieto Faza and
Susana López Estévez and
Angel R. de Lera Computation of vertical excitation
energies of retinal and analogs: Scope
and limitations . . . . . . . . . . . . 116--123
Hairong Ma and
Martin Gruebele Low barrier kinetics: Dependence on
observables and free energy surface . . 125--134
Christoph van Wüllen Numerical instabilities in the
computation of pseudopotential matrix
elements . . . . . . . . . . . . . . . . 135--141
Christophe Gourlaouen and
Jean-Philip Piquemal and
Trond Saue and
Olivier Parisel Revisiting the geometry of $nd^{10} (n +
1)s^0$ [M(H$_2$O)]$^{p+}$ complexes
using four-component relativistic DFT
calculations and scalar relativistic
correlated CSOV energy decompositions
(M$^{p+}$ = Cu$^+$, Zn$^{2+}$, Ag$^+$,
Cd$^{2+}$, Au$^+$, Hg$^{2+}$) . . . . . 142--156
Anne Milet and
Yves Gimbert and
Andrew E. Greene Reaction of nitrones with silyl ketene
acetals: a DFT study . . . . . . . . . . 157--162
Chantal T. Falzon and
Delano P. Chong and
Feng Wang Prediction of spectroscopic constants
for diatomic molecules in the ground and
excited states using time-dependent
density functional theory . . . . . . . 163--173
Ivan Rivalta and
Nino Russo and
Emilia Sicilia Methane activation by chromium oxide
cations in the gas phase: a theoretical
study . . . . . . . . . . . . . . . . . 174--187
Fernando D. Suvire and
Luis N. Santagata and
José A. Bombasaro and
Ricardo D. Enriz Dynamics of flexible cycloalkanes. Ab
initio and DFT study of the
conformational energy hypersurface of
cyclononane . . . . . . . . . . . . . . 188--202
Jie Hu and
Ao Ma and
Aaron R. Dinner Monte Carlo simulations of biomolecules:
the MC module in CHARMM . . . . . . . . 203--216
Marcelo Alves-Santos and
Liliana Y. A. Dávila and
Helena M. Petrilli and
Rodrigo B. Capaz and
Marília J. Caldas Application of standard DFT theory for
nonbonded interactions in soft matter:
Prototype study of poly-para-phenylene 217--227
Chultack Lim and
Hee Soon Lee and
Young-Woo Kwak and
Cheol Ho Choi A theoretical study of thermal
[1,3]-sigmatropic rearrangements of
3-trimethylsilyl-1-pyrazoline: Concerted
vs. stepwise mechanisms . . . . . . . . 228--237
José Luis Alonso and
Pablo Echenique A physically meaningful method for the
comparison of potential energy functions 238--252
J. A. L. Rabone and
N. H. De Leeuw Interatomic potential models for natural
apatite crystals: Incorporating
strontium and the lanthanides . . . . . 253--266
Zhijian Wu Electronic structures of $3 d$-metal
mononitrides . . . . . . . . . . . . . . 267--276
Kaushalya S. Ekanayake and
Pierre R. Lebreton Activation barriers for DNA alkylation
by carcinogenic methane diazonium ions 277--286
Andrzej Bil and
Zdzis\law Latajka The hydroperoxy radical as a hydrogen
bond acceptor. HOO HCl complexes --- ab
initio study . . . . . . . . . . . . . . 287--295
A. M. Tokmachev and
R. Dronskowski Electron group functions for the
analysis of the electronic structures of
molecules . . . . . . . . . . . . . . . 296--308
Heinz Sklenar and
Daniel Wüstner and
Remo Rohs Using internal and collective variables
in Monte Carlo simulations of nucleic
acid structures: Chain breakage/closure
algorithm and associated Jacobians . . . 309--315
Tsjerk A. Wassenaar and
Alan E. Mark The effect of box shape on the dynamic
properties of proteins simulated under
periodic boundary conditions . . . . . . 316--325
Eirik Fossgård and
Kenneth Ruud Superlinear scaling in master-slave
quantum chemical calculations using
in-core storage of two-electron
integrals . . . . . . . . . . . . . . . 326--333
Prasad V. Bharatam and
Pansy Iqbal Theoretical studies on electron
delocalization in diaminoguanidine . . . 334--343
Inmaculada García Cuesta and
Alfredo M. J. Sánchez De Merás and
Paolo Lazzeretti Structure, magnetizability, and nuclear
magnetic shielding tensors of
bis-heteropentalenes. IV.
Dihydrophospholophosphole isomers . . . 344--351
Timothy J. Dudley and
Ryan M. Olson and
Michael W. Schmidt and
Mark S. Gordon Parallel coupled perturbed CASSCF
equations and analytic CASSCF second
derivatives . . . . . . . . . . . . . . 352--362
Jian Wang and
Yi-Hong Ding and
Gong-Bing Wu and
Chia-Chung Sun Gaseous reaction mechanism of C$_2$F
radical with water . . . . . . . . . . . 363--367
Ke-Xiang Fu and
Quan Zhu and
Xiang-Yuan Li and
Zhen Gong and
Jian-Yi Ma and
Rong-Xing He Continuous medium theory for
nonequilibrium solvation: IV. Solvent
reorganization energy of electron
transfer based on conductor-like
screening model . . . . . . . . . . . . 368--374
Geoffrey K. Hom and
Stephen L. Mayo A search algorithm for fixed-composition
protein design . . . . . . . . . . . . . 375--378
Hisashi Okumura and
Yuko Okamoto Multibaric--multithermal ensemble
molecular dynamics simulations . . . . . 379--395
R. Svobodová Va\vreková and
J. Ko\vca Optimized and parallelized
implementation of the electronegativity
equalization method and the atom-bond
electronegativity equalization method 396--405
Kazuya Ishimura and
Peter Pulay and
Shigeru Nagase A new parallel algorithm of MP2 energy
calculations . . . . . . . . . . . . . . 407--413
Arnaldo Rapallo An algorithm for the uniform sampling of
iso-energy surfaces and for the
calculation of microcanonical averages 414--425
Hiroyuki Nakashima and
Jun-Ya Hasegawa and
Hiroshi Nakatsuji On the reversible O$_2$ binding of the
Fe--porphyrin complex . . . . . . . . . 426--433
Pekka Manninen and
Juha Vaara Systematic Gaussian basis-set limit
using completeness-optimized primitive
sets. A case for magnetic properties . . 434--445
Franci Merzel and
Milan Hodo\vs\vcek and
Du\vsanka Jane\vzi\vc and
Alain Sanson New force field for calcium binding
sites in annexin--membrane complexes . . 446--452
Norio Yoshida and
Fumio Hirata A new method to determine electrostatic
potential around a macromolecule in
solution from molecular wave functions 453--462
Masahiro Sekiya and
Takeshi Noro and
Eisaku Miyoshi and
You Osanai and
Toshikatsu Koga Relativistic correlating basis sets for
lanthanide atoms from Ce to Lu . . . . . 463--470
Hideaki Nakamura and
Masaru Aniya Thermodynamic properties of
Ag$_2$OB$_2$O$_3$ glasses by a modified
scale-transformed energy space sampling
Monte Carlo method . . . . . . . . . . . 471--477
Xuan Xiao and
Shi-Huang Shao and
Zheng-De Huang and
Kuo-Chen Chou Using pseudo amino acid composition to
predict protein structural classes:
Approached with complexity measure
factor . . . . . . . . . . . . . . . . . 478--482
Gerald Geudtner and
Florian Janetzko and
Andreas M. Köster and
Alberto Vela and
Patrizia Calaminici Parallelization of the deMon2k code . . 483--490
Mark P. Waller and
Arturo Robertazzi and
James A. Platts and
David E. Hibbs and
Peter A. Williams Hybrid density functional theory for
$\pi$-stacking interactions: Application
to benzenes, pyridines, and DNA bases 491--504
Qiang Wang and
Yi-Hong Ding and
Hong-Bin Xie and
Chia-Chung Sun Theoretical study on structures and
stabilities of [H,Ge,C,N] . . . . . . . 505--514
Arianna Fornili and
Yohann Moreau and
Maurizio Sironi and
Xavier Assfeld On the suitability of strictly localized
orbitals for hybrid QM/MM calculations 515--523
Josep M. Oliva and
Luis Serrano-Andrés A computational study of the lowest
singlet and triplet states of neutral
and dianionic 1,2-substituted
icosahedral and octahedral
$o$-carboranes . . . . . . . . . . . . . 524--535
Min Hsien Liu and
Cheng Chen Modified calculations of hydrocarbon
thermodynamic properties . . . . . . . . 537--544
Hong-Bin Xie and
Yi-Hong Ding and
Chia-Chung Sun Ylidic radical--molecule reactions . . . 545--551
Mikhail V. Basilevsky and
Igor V. Leontyev and
Sofia V. Luschekina and
Olga A. Kondakova and
Vladimir B. Sulimov Computation of hydration free energies
of organic solutes with an implicit
water model . . . . . . . . . . . . . . 552--570
Stanislav Böhm and
Otto Exner Are calculated enthalpies of formation
sometimes more reliable than
experimental? A test on alkyl
substituted benzoic acids . . . . . . . 571--577
Li-Ming Yang and
Yi-Hong Ding and
Qiang Wang and
Chia-Chung Sun Monosilicon-substituted cyanoacetylene:
a computational study . . . . . . . . . 578--595
Diego R. Alcoba and
Luis Lain and
Alicia Torre and
Roberto C. Bochicchio An orbital localization criterion based
on the theory of ``fuzzy'' atoms . . . . 596--608
Anna Fiorentino and
Deepangi Pandit and
Kathleen M. Gilbert and
Milind Misra and
Rose Dios and
Carol A. Venanzi Singular value decomposition of
torsional angles of analogs of the
dopamine reuptake inhibitor GBR 12909 609--620
Giulio Gianese and
Stefano Pascarella A consensus procedure improving solvent
accessibility prediction . . . . . . . . 621--626
P. Cassam-Chena\"\i and
J. Liévin The VMFCI method: a flexible tool for
solving the molecular vibration problem 627--640
Hong-Bin Xie and
Yi-Hong Ding and
Chia-Chung Sun Radical reaction C$_3$H + NO: a
mechanistic study . . . . . . . . . . . 641--660
Jia-Xu Zhang and
Ze-Sheng Li and
Jing-Yao Liu and
Chia-Chung Sun Theoretical mechanistic study on the
radical-molecule reaction of CHCl$_2$
/CCl$_3$ with NO$_2$ . . . . . . . . . . 661--671
Håkan W. Hugosson and
Alessandro Laio and
Patrick Maurer and
Ursula Rothlisberger A comparative theoretical study of
dipeptide solvation in water . . . . . . 672--684
Qi-Shi Du and
Da-Peng Li and
Wen-Zhang He and
Kuo-Chen Chou Heuristic molecular lipophilicity
potential (HMLP): Lipophilicity and
hydrophilicity of amino acid side chains 685--692
Satyavani Vemparala and
Ivaylo Ivanov and
Vojislava Pophristic and
Katrin Spiegel and
Michael L. Klein Ab initio calculations of intramolecular
parameters for a class of arylamide
polymers . . . . . . . . . . . . . . . . 693--700
Yasunobu Seno Allostery of the two-state model of
hemoglobin studied by ECEPP energy
minimization . . . . . . . . . . . . . . 701--710
Chunsheng Shi and
Masahiko Morinaga Doping effects on proton incorporation
and conduction in SrZrO$_3$ . . . . . . 711--718
Jana Chocholou\vsová and
Michael Feig Balancing an accurate representation of
the molecular surface in generalized
Born formalisms with integrator
stability in molecular dynamics
simulations . . . . . . . . . . . . . . 719--729
Siu-Hung Chien and
Peter M. W. Gill SG-0: a small standard grid for DFT
quadrature on large systems . . . . . . 730--739
Tomasz Borowski and
Ewa Broclawik and
Christopher J. Schofield and
Per E. M. Siegbahn Epimerization and desaturation by
carbapenem synthase (CarC). A hybrid DFT
study . . . . . . . . . . . . . . . . . 740--748
Guang-Tao Yu and
Xu-Ri Huang and
Yi-Hong Ding and
Chia-Chung Sun and
Au-Chin Tang Theoretical study on the [Si, C, N, O]
potential energy surface . . . . . . . . 749--761
Fabio E. Penotti Orbital-orthogonality constraints and
basis-set optimization . . . . . . . . . 762--772
Ram Kinkar Roy and
V. Usha and
Bhisma K. Patel and
Kimihiko Hirao Acetalization and thioacetalization of
cabonyl compounds: a case study based on
global and local electrophilicity
descriptors . . . . . . . . . . . . . . 773--780
Zhi-Xiang Wang and
Wei Zhang and
Chun Wu and
Hongxing Lei and
Piotr Cieplak and
Yong Duan Strike a balance: Optimization of
backbone torsion parameters of AMBER
polarizable force field for simulations
of proteins and peptides . . . . . . . . 781--790
Primo\vz Pristov\vsek and
Lorella Franzoni Stereospecific assignments of protein
NMR resonances based on the tertiary
structure and $2$D/$3$D NOE data . . . . 791--797
Li-Cheng Wu and
Jorng-Tzong Horng and
Shir-Ly Huang and
Hsien-Da Huang and
Baw-Jhiune Liu Detection of discriminative sequence
motifs in proteins obtained from
prokaryotes grown at various
temperatures . . . . . . . . . . . . . . 798--808
Peng Bao and
Zhong-Heng Yu Theoretical studies on the role of
$\pi$-electron delocalization in
determining the conformation of
$N$-benzylideneaniline with three types
of LMO basis sets . . . . . . . . . . . 809--824
Seongho Moon and
David A. Case A comparison of quantum chemical models
for calculating NMR shielding parameters
in peptides: Mixed basis set and ONIOM
methods combined with a complete basis
set extrapolation . . . . . . . . . . . 825--836
Jean-François Fuchs and
Hristo Nedev and
David Poger and
Michel Ferrand and
Valérie Brenner and
Jean-Pierre Dognon and
Serge Crouzy New model potentials for
sulfur--copper(I) and
sulfur--mercury(II) interactions in
proteins: From ab initio to molecular
dynamics . . . . . . . . . . . . . . . . 837--856
Yu Zhou and
Chris Oostenbrink and
Aldo Jongejan and
Wilfred F. Van Gunsteren and
Wilfred R. Hagen and
Simon W. De Leeuw and
Jaap A. Jongejan Computational study of ground-state
chiral induction in small peptides:
Comparison of the relative stability of
selected amino acid dimers and oligomers
in homochiral and heterochiral
combinations . . . . . . . . . . . . . . 857--867
Lionello Pogliani The hydrogen perturbation in molecular
connectivity computations . . . . . . . 868--882
Lin Jin and
Yi-Hong Ding and
Jian Wang and
Chia-Chung Sun Reaction mechanism of the CCN radical
with nitric oxide . . . . . . . . . . . 883--893
Jia-Xu Zhang and
Ze-Sheng Li and
Jing-Yao Liu and
Chia-Chung Sun Theoretical study on the mechanism of
the CH$_2$F + NO$_2$ reaction . . . . . 894--905
Kazuki Ohno and
Minoru Sakurai Linear-scaling molecular orbital
calculations for the pKa values of
ionizable residues in proteins . . . . . 906--916
Hiromi Nakai and
Yasuaki Kikuchi Energy density analysis of cluster size
dependence of surface--molecule
interactions (II): Formate adsorption
onto a Cu(111) surface . . . . . . . . . 917--925
J. H. Van Lenthe and
R. Zwaans and
H. J. J. Van Dam and
M. F. Guest Starting SCF calculations by
superposition of atomic densities . . . 926--932
Ju Xie and
Dacheng Feng and
Shengyu Feng Theoretical study on the isomeric
structures and the stability of
silylenoid (Tsi)Cl$_2$SiLi (Tsi =
C(SiMe$_3$)$_3$) . . . . . . . . . . . . 933--940
Shiqi Zhou Rapidly convergent procedure to solve
the density profile equation in the
classical density functional theory . . 941--947
Kaori Fukuzawa and
Yuto Komeiji and
Yuji Mochizuki and
Akifumi Kato and
Tatsuya Nakano and
Shigenori Tanaka Intra- and intermolecular interactions
between cyclic-AMP receptor protein and
DNA: ab initio fragment molecular
orbital study . . . . . . . . . . . . . 948--960
K. Darowicki and
W. Felisiak On the joint time-frequency
characteristics of chemical oscillations 961--965
Alexandra T. P. Carvalho and
P. A. Fernandes and
Maria J. Ramos Determination of the $\Delta$pKa between
the active site cysteines of thioredoxin
and DsbA . . . . . . . . . . . . . . . . 966--975
Dmitri G. Fedorov and
Kazuo Kitaura and
Hui Li and
Jan H. Jensen and
Mark S. Gordon The polarizable continuum model (PCM)
interfaced with the fragment molecular
orbital method (FMO) . . . . . . . . . . 976--985
Zhi-Ru Li and
Fang-Fang Wang and
Di Wu and
Ying Li and
Wei Chen and
Xiao-Ying Sun and
Feng Long Gu and
Yuriko Aoki Royal crown-shaped electride
Li$_3$--N$_3$--Be containing two
superatoms: New knowledge on aromaticity 986--993
Anonymous Erratum: Zhi-Xiang Wang, Wei Zhang, Chun
Wu, Hongxing Lei, Piotr Cieplak, Yong
Duan, ``Strike a balance: Optimization
of backbone torsion parameters of AMBER
polarizable force field for simulations
of proteins and peptides'', Journal of
Computational Chemistry (2006) \bf 27(6)
781--790 . . . . . . . . . . . . . . . . 994--994
Antonio Cervellino and
Cinzia Giannini and
Antonietta Guagliardi On the efficient evaluation of Fourier
patterns for nanoparticles and clusters 995--1008
Roberto Flores-Moreno and
Rodrigo J. Alvarez-Mendez and
Alberto Vela and
Andreas M. Köster Half-numerical evaluation of
pseudopotential integrals . . . . . . . 1009--1019
Tzong-Yi Lee and
Jorng-Tzong Horng and
Hsueh-Fen Juan and
Hsien-Da Huang and
Li-Cheng Wu and
Meng-Fong Tsai and
Hsuan-Cheng Huang An agent-based system to discover
protein--protein interactions, identify
protein complexes and proteins with
multiple peptide mass fingerprints . . . 1020--1032
Aggeliki Kosmopoulou and
Metaxia Vlassi and
Athanassios Stavrakoudis and
Constantinos Sakarellos and
Maria Sakarellos-Daitsiotis T-cell epitopes of the La/SSB
autoantigen: Prediction based on the
homology modeling of HLA-DQ2/DQ7 with
the insulin-B peptide/HLA-DQ8 complex 1033--1044
Hua Zhu and
Yong Guo and
Ying Xue and
Daiqian Xie Ab initio potential energy surface and
predicted microwave spectra for
Ar\bondOCS dimer and structures of
Ar$_n$\bondOCS ($n = 2$--$14$) clusters 1045--1053
Patrick Musch and
Bernd Engels DIESEL--MP2: a new program to perform
large-scale multireference-MP2
computations . . . . . . . . . . . . . . 1055--1062
Andrew E. Whitten and
Joshua J. McKinnon and
Mark A. Spackman Electric field-derived point charges to
mimic the electrostatics in molecular
crystals . . . . . . . . . . . . . . . . 1063--1070
Benjamin D. Allen and
Stephen L. Mayo Dramatic performance enhancements for
the FASTER optimization algorithm . . . 1071--1075
Pablo Echenique and
J. L. Alonso Definition of Systematic, Approximately
Separable, and Modular Internal
Coordinates (SASMIC) for macromolecular
simulation . . . . . . . . . . . . . . . 1076--1087
Karl Jug and
Viatcheslav A. Tikhomirov Anion substitution in zinc chalcogenides 1088--1092
T. S. Venkatesan and
K. Deepika and
S. Mahapatra The Jahn--Teller and pseudo-Jahn--Teller
effects in the anion photoelectron
spectroscopy of B$_3$ cluster . . . . . 1093--1100
Gerd B. Rocha and
Ricardo O. Freire and
Alfredo M. Simas and
James J. P. Stewart RM1: a reparameterization of AM1 for H,
C, N, O, P, S, F, Cl, Br, and I . . . . 1101--1111
Genyuan Li and
Herschel Rabitz Ratio control variate method for
efficiently determining high-dimensional
model representations . . . . . . . . . 1112--1118
Liwei Liu and
Tianming Wang $2$D representation of protein secondary
structure sequences and its applications 1119--1124
Bahram Hemmateenejad and
Ramin Miri and
Mohammad A. Safarpour and
Ahmad R. Mehdipour Accurate prediction of the blood--brain
partitioning of a large set of solutes
using ab initio calculations and genetic
neural network modeling . . . . . . . . 1125--1135
Hyunbum Jang and
Thomas B. Woolf Multiple pathways in conformational
transitions of the alanine dipeptide: an
application of dynamic importance
sampling . . . . . . . . . . . . . . . . 1136--1141
Flavia P. Agostini and
Diogo De O. Soares-Pinto and
Marcelo A. Moret and
Carla Osthoff and
Pedro G. Pascutti Generalized simulated annealing applied
to protein folding studies . . . . . . . 1142--1155
Ivan Infante and
Bas van Stralen and
Lucas Visscher A QM/MM study on the aqueous solvation
of the tetrahydroxouranylate [UO$_2$
(OH)$_4$]$^{2-}$ complex ion . . . . . . 1156--1162
Vincent Kräutler and
Philippe H. Hünenberger A multiple time step algorithm
compatible with a large number of
distance classes and an arbitrary
distance dependence of the time step
size for the fast evaluation of
nonbonded interactions in molecular
simulations . . . . . . . . . . . . . . 1163--1176
Dusan P. Djurdjevic and
Mark J. Biggs Ab initio protein fold prediction using
evolutionary algorithms: Influence of
design and control parameters on
performance . . . . . . . . . . . . . . 1177--1195
Bo Liao and
Xuyu Xiang and
Wen Zhu Coronavirus phylogeny based on $2$D
graphical representation of DNA sequence 1196--1202
Annia Galano and
J. Raúl Alvarez-Idaboy A new approach to counterpoise
correction to BSSE . . . . . . . . . . . 1203--1210
E. S. Ferrari and
R. C. Burton and
R. J. Davey and
A. Gavezzotti Simulation of phase separation in
alcohol/water mixtures using two-body
force field and standard molecular
dynamics . . . . . . . . . . . . . . . . 1211--1219
Gernot Frenking and
Max C. Holthausen Foreword . . . . . . . . . . . . . . . . 1221--1222
Carmen Herrmann and
Lian Yu and
Markus Reiher Spin states in polynuclear clusters: The
[Fe$_2$O$_2$] core of the methane
monooxygenase active site . . . . . . . 1223--1239
Guillermina Estiu and
Dimas Suárez and
Kenneth M. Merz Quantum mechanical and molecular
dynamics simulations of ureases and Zn
$\beta$-lactamases . . . . . . . . . . . 1240--1262
Mihail Atanasov and
Peter Comba and
Bodo Martin and
Vera Müller and
Gopalan Rajaraman and
Heidi Rohwer and
Steffen Wunderlich DFT models for copper(II) bispidine
complexes: Structures, stabilities,
isomerism, spin distribution, and
spectroscopy . . . . . . . . . . . . . . 1263--1277
Felix Studt and
Felix Tuczek Theoretical, spectroscopic, and
mechanistic studies on transition-metal
dinitrogen complexes: Implications to
reactivity and relevance to the
nitrogenase problem . . . . . . . . . . 1278--1291
Wen-Ge Han and
Tiqing Liu and
Timothy Lovell and
Louis Noodleman DFT calculations of $^{57}$Fe Mössbauer
isomer shifts and quadrupole splittings
for iron complexes in polar dielectric
media: Applications to methane
monooxygenase and ribonucleotide
reductase . . . . . . . . . . . . . . . 1292--1306
Jonathan P. McNamara and
Mahesh Sundararajan and
Ian H. Hillier and
Jun Ge and
Andrew Campbell and
Claudio Morgado Can the semiempirical PM3 scheme
describe iron-containing bioinorganic
molecules? . . . . . . . . . . . . . . . 1307--1323
Ahmet Altun and
Sason Shaik and
Walter Thiel Systematic QM/MM investigation of
factors that affect the cytochrome
P450-catalyzed hydrogen abstraction of
camphor . . . . . . . . . . . . . . . . 1324--1337
Nicolai Lehnert and
V. K. K. Praneeth and
Florian Paulat Electronic structure of
iron(II)--porphyrin nitroxyl complexes:
Molecular mechanism of fungal nitric
oxide reductase (P450nor) . . . . . . . 1338--1351
Jeremy N. Harvey and
Christine M. Bathelt and
Adrian J. Mulholland QM/MM modeling of compound I active
species in cytochrome P450, cytochrome C
peroxidase, and ascorbate peroxidase . . 1352--1362
Hiroyuki Nakashima and
Jun-ya Hasegawa and
Hiroshi Nakatsuji On the O$_2$ binding of Fe--porphyrin,
Fe--porphycene, and Fe--corrphycene
complexes . . . . . . . . . . . . . . . 1363--1372
Margareta R. A. Blomberg and
Per E. M. Siegbahn Quantum chemistry applied to the
mechanisms of transition metal
containing enzymes --- Cytochrome $c$
oxidase, a particularly challenging case 1373--1384
Robert K. Szilagyi and
Mark A. Winslow On the accuracy of density functional
theory for iron--sulfur clusters . . . . 1385--1397
Lubomír Rulí\vsek and
Kasper P. Jensen and
Kristoffer Lundgren and
Ulf Ryde The reaction mechanism of iron and
manganese superoxide dismutases studied
by theoretical calculations . . . . . . 1398--1414
Edward I. Solomon and
Serge I. Gorelsky and
Abhishek Dey Metal--thiolate bonds in bioinorganic
chemistry . . . . . . . . . . . . . . . 1415--1428
Jadwiga Kuta and
Seguei Patchkovskii and
Marek Z. Zgierski and
Pawel M. Kozlowski Performance of DFT in modeling
electronic and structural properties of
cobalamins . . . . . . . . . . . . . . . 1429--1437
Rajeev Prabhakar and
Keiji Morokuma and
Djamaladdin G. Musaev A DFT study of the mechanism of Ni
superoxide dismutase (NiSOD): Role of
the active site cysteine-6 residue in
the oxidative half-reaction . . . . . . 1438--1445
Jean-Didier Maréchal and
Feliu Maseras and
Agustí Lledós and
Liliane Mouawad and
David Perahia A DFT study on the relative affinity for
oxygen of the $\alpha$ and $\beta$
subunits of hemoglobin . . . . . . . . . 1446--1453
Jesse W. Tye and
Marcetta Y. Darensbourg and
Michael B. Hall Correlation between computed gas-phase
and experimentally determined
solution-phase infrared spectra: Models
of the iron--iron hydrogenase enzyme
active site . . . . . . . . . . . . . . 1454--1462
Sebastian Sinnecker and
Frank Neese QM/MM calculations with DFT for taking
into account protein effects on the EPR
and optical spectra of metalloproteins.
Plastocyanin as a case study . . . . . . 1463--1475
Myungshim Kang and
Paul E. Smith A Kirkwood-Buff derived force field for
amides . . . . . . . . . . . . . . . . . 1477--1485
Marcel Swart and
Ernst Rösler and
F. Matthias Bickelhaupt Proton affinities of maingroup-element
hydrides and noble gases: Trends across
the periodic table, structural effects,
and DFT validation . . . . . . . . . . . 1486--1493
Haibo Yu and
Daan P. Geerke and
Haiyan Liu and
Wilfred F. van Gunsteren Molecular dynamics simulations of liquid
methanol and methanol--water mixtures
with polarizable models . . . . . . . . 1494--1504
P. Salvador and
D. Asturiol and
I. Mayer A general efficient implementation of
the BSSE-free SCF and MP2 methods based
on the chemical Hamiltonian approach . . 1505--1516
Alexey Aleksandrov and
Thomas Simonson The tetracycline: Mg$^{2+}$ complex: a
molecular mechanics force field . . . . 1517--1533
Elena Herzog and
Tomaso Frigato and
Volkhard Helms and
C. Roy D. Lancaster Energy barriers of proton transfer
reactions between amino acid side chain
analogs and water from ab initio
calculations . . . . . . . . . . . . . . 1534--1547
Anders Irbäck and
Sandipan Mohanty PROFASI: a Monte Carlo simulation
package for protein folding and
aggregation . . . . . . . . . . . . . . 1548--1555
Yi-Yu Ke and
Yun-Chu Chen and
Thy-Hou Lin Structure of the virus capsid protein
VP1 of enterovirus 71 predicted by some
homology modeling and molecular docking
studies . . . . . . . . . . . . . . . . 1556--1570
Zhen Xi and
Zhihong Yu and
Congwei Niu and
Shurong Ban and
Guangfu Yang Development of a general
quantum-chemical descriptor for steric
effects: Density functional theory based
QSAR study of herbicidal sulfonylurea
analogues . . . . . . . . . . . . . . . 1571--1576
Meng-Sheng Liao and
John D. Watts and
Ming-Ju Huang Assessment of the performance of
density-functional methods for
calculations on iron porphyrins and
related compounds . . . . . . . . . . . 1577--1592
Yuedong Yang and
Haiyan Liu Genetic algorithms for protein
conformation sampling and optimization
in a discrete backbone dihedral angle
space . . . . . . . . . . . . . . . . . 1593--1602
Marcin Makowski and
Jacek Korchowiec and
Feng Long Gu and
Yuriko Aoki Efficiency and accuracy of the
elongation method as applied to the
electronic structures of large systems 1603--1619
Anonymous Erratum: Matteo Ceccarelli, Piero
Procacci, Massimo Marchi ``An ab initio
force field for the cofactors of
bacterial photosynthesis,'' Journal of
Computational Chemistry (2003) \bf 24(2)
129--142 . . . . . . . . . . . . . . . . 1620--1620
Anonymous Erratum: Felix Studt, Felix Tuczek,
``Theoretical, spectroscopic, and
mechanistic studies on transition-metal
dinitrogen complexes: Implications to
reactivity and relevance to the
nitrogenase problem,'' Journal of
Computational Chemistry (2006) \bf
27(12) 1278--1291 . . . . . . . . . . . 1621--1621
Azuma Matsuura and
Hiroyuki Sato and
Hirohiko Houjou and
Shino Saito and
Tomohiko Hayashi and
Minoru Sakurai Accurate evaluation of the absorption
maxima of retinal proteins based on a
hybrid QM/MM method . . . . . . . . . . 1623--1630
Peter C. Anderson and
Sandro Mecozzi Minimum sequence requirements for
selective RNA-ligand binding: a
molecular mechanics algorithm using
molecular dynamics and free-energy
techniques . . . . . . . . . . . . . . . 1631--1640
Luis F. Pacios Computational study of the process of
hydrogen bond breaking: the case of the
formamide--formic acid complex . . . . . 1641--1649
Luis F. Pacios and
Pedro C. Gómez and
Oscar Gálvez Variation of atomic charges on proton
transfer in strong hydrogen bonds: the
case of anionic and neutral
imidazole--acetate complexes . . . . . . 1650--1661
Russell A. Brown and
David A. Case Second derivatives in generalized Born
theory . . . . . . . . . . . . . . . . . 1662--1675
N. N. Medvedev and
V. P. Voloshin and
V. A. Luchnikov and
M. L. Gavrilova An algorithm for three-dimensional
Voronoi S-network . . . . . . . . . . . 1676--1692
Oliver F. Lange and
Lars V. Schäfer and
Helmut Grubmüller Flooding in GROMACS: Accelerated barrier
crossings in molecular dynamics . . . . 1693--1702
S. Knippenberg and
J.-P. François and
M. S. Deleuze Green's function study of the
one-electron and shake-up ionization
spectra of unsaturated hydrocarbon cage
compounds . . . . . . . . . . . . . . . 1703--1722
Pathumwadee Intharathep and
Anan Tongraar and
Kritsana Sagarik Ab initio QM/MM dynamics of H$_3$O$^+$
in water . . . . . . . . . . . . . . . . 1723--1732
Pablo Echenique and
Iván Calvo and
J. L. Alonso Quantum mechanical calculation of the
effects of stiff and rigid constraints
in the conformational equilibrium of the
alanine dipeptide . . . . . . . . . . . 1733--1747
Pablo Echenique and
Iván Calvo Explicit factorization of external
coordinates in constrained statistical
mechanics models . . . . . . . . . . . . 1748--1755
Jian Wang and
Yi-Hong Ding and
Chia-Chung Sun Theoretical mechanistic study on the
radical--molecule reactions of
cyanomethylidyne with PH$_3$, H$_2$S,
and HCl . . . . . . . . . . . . . . . . 1756--1764
Nicholas M. Glykos Software news and updates carma: a
molecular dynamics analysis program . . 1765--1768
Carles Curutchet and
Modesto Orozco and
F. Javier Luque and
Benedetta Mennucci and
Jacopo Tomasi Dispersion and repulsion contributions
to the solvation free energy: Comparison
of quantum mechanical and classical
approaches in the polarizable continuum
model . . . . . . . . . . . . . . . . . 1769--1780
Leticia González and
Chantal Daniel Photochemistry of CH$_3$Mn(CO)$_5$: a
multiconfigurational ab initio study . . 1781--1786
Stefan Grimme Semiempirical GGA-type density
functional constructed with a long-range
dispersion correction . . . . . . . . . 1787--1799
Laurence Leherte Similarity measures based on
Gaussian-type promolecular electron
density models: Alignment of small rigid
molecules . . . . . . . . . . . . . . . 1800--1816
Jian Zhang and
Mingyu Zhang and
Yuanyuan Zhao and
Baoguo Chen and
Chia-Chung Sun Ab initio studies on isomers of
macropolyhedral borane ions
[B$_{20}$H$_{18}$]$^n$ ($n = 0$, $-2$,
$-4$) . . . . . . . . . . . . . . . . . 1817--1821
Rogério Custodio and
André Severo Pereira Gomes and
Fabrício Ronil Sensato and
Júlio Murilo dos Santos Trevas Analysis of the segmented contraction of
basis functions using density matrix
theory . . . . . . . . . . . . . . . . . 1822--1829
Qi Dai and
Xiao-Qing Liu and
Tian-Ming Wang Numerical characterization of DNA
sequences based on the $k$-step Markov
chain transition probability . . . . . . 1830--1842
Vincent Zoete and
Markus Meuwly Importance of individual side chains for
the stability of a protein fold:
Computational alanine scanning of the
insulin monomer . . . . . . . . . . . . 1843--1857
Si-Dian Li and
Chang-Qing Miao and
Jin-Chang Guo and
Guang-Ming Ren Transition metal--boron complexes
B$_n$M: From bowls ($n = 8$--$14$) to
tires ($n = 14$) . . . . . . . . . . . . 1858--1865
Sheng-You Huang and
Xiaoqin Zou An iterative knowledge-based scoring
function to predict protein--ligand
interactions: I. Derivation of
interaction potentials . . . . . . . . . 1866--1875
Sheng-You Huang and
Xiaoqin Zou An iterative knowledge-based scoring
function to predict protein--ligand
interactions: II. Validation of the
scoring function . . . . . . . . . . . . 1876--1882
Padeleimon Karafiloglou Control of delocalization and structural
changes by means of an electric field 1883--1891
Hugo R. R. Santos and
Gregori Ujaque and
Maria J. Ramos and
José A. N. F. Gomes QM/QM study of the coverage effects on
the adsorption of amino-cyclopentene at
the Si(100) surface . . . . . . . . . . 1892--1897
Sathesh Bhat and
Traian Sulea and
Enrico O. Purisima Coupled atomic charge selectivity for
optimal ligand-charge distributions at
protein binding sites . . . . . . . . . 1899--1907
Yu Sun and
Robert A. Latour Comparison of implicit solvent models
for the simulation of protein--surface
interactions . . . . . . . . . . . . . . 1908--1922
Mark S. Formaneck and
Qiang Cui The use of a generalized Born model for
the analysis of protein conformational
transitions: a comparative study with
explicit solvent simulations for
chemotaxis Y protein (CheY) . . . . . . 1923--1943
Hannes H. Loffler and
Ahmed M. Mohammed and
Yasuhiro Inada and
Shigenobu Funahashi Water exchange dynamics of
manganese(II), cobalt(II), and
nickel(II) ions in aqueous solution . . 1944--1949
Benjamin F. Gherman and
William B. Tolman and
Christopher J. Cramer Characterization of the structure and
reactivity of monocopper--oxygen
complexes supported by
$\beta$-diketiminate and anilido-imine
ligands . . . . . . . . . . . . . . . . 1950--1961
Sergei Izrailev and
Fangqiang Zhu and
Dimitris K. Agrafiotis A distance geometry heuristic for
expanding the range of geometries
sampled during conformational search . . 1962--1969
Roberto L. A. Haiduke and
Albérico B. F. Da Silva Accurate relativistic adapted Gaussian
basis sets for cesium through radon
without variational prolapse and to be
used with both uniform sphere and
Gaussian nucleus models . . . . . . . . 1970--1979
I. García Cuesta and
A. Sánchez de Merás and
P. Lazzeretti Diatropicity of tetraazanaphthalenes . . 1980--1989
Christopher S. Page and
Paul A. Bates Can MM-PBSA calculations predict the
specificities of protein kinase
inhibitors? . . . . . . . . . . . . . . 1990--2007
Gernot Frenking and
Sason Shaik Foreword . . . . . . . . . . . . . . . . 1--3
R. F. W. Bader and
J. Hernández-Trujillo and
F. Cortés-Guzmán Essay: Chemical bonding: from Lewis to
atoms in molecules . . . . . . . . . . . 4--14
Gernot Frenking and
Andreas Krapp Essay: Unicorns in the world of chemical
bonding models . . . . . . . . . . . . . 15--24
Werner Kutzelnigg Essay: What I like about Hückel theory 25--34
Jean-Paul Malrieu and
Nathalie Guihéry and
Carmen Jiménez Calzado and
Celestino Angeli Essay: Bond electron pair: Its relevance
and analysis from the quantum chemistry
point of view . . . . . . . . . . . . . 35--50
Sason Shaik Essay: The Lewis legacy: the chemical
bond --- a territory and heartland of
chemistry . . . . . . . . . . . . . . . 51--61
Ana Simões Essay: In between worlds: G. N. Lewis,
the shared pair bond and its
multifarious contexts . . . . . . . . . 62--72
Donald G. Truhlar Essay: Valence bond theory for chemical
dynamics . . . . . . . . . . . . . . . . 73--86
R. J. Gillespie and
E. A. Robinson Essay: Gilbert N. Lewis and the chemical
bond: the electron pair and the octet
rule from 1916 to the present day . . . 87--97
Mary Jo Nye Essay: Working tools for theoretical
chemistry: Polanyi, Eyring, and debates
over the ``semiempirical method'' . . . 98--108
Robert Ponec and
Joaquin Chaves Electron pairing and chemical bonds:
Pair localization in ELF domains from
the analysis of domain averaged Fermi
holes . . . . . . . . . . . . . . . . . 109--116
Gernot Frenking and
Christoph Loschen and
Andreas Krapp and
Stefan Fau and
Steven H. Strauss Electronic structure of CO --- an
exercise in modern chemical bonding
theory . . . . . . . . . . . . . . . . . 117--126
Marcos Mandado and
María J. González-Moa and
Ricardo A. Mosquera QTAIM $n$-center delocalization indices
as descriptors of aromaticity in mono
and poly heterocycles . . . . . . . . . 127--136
Philippe C. Hiberty and
Sason Shaik A survey of recent developments in ab
initio valence bond theory . . . . . . . 137--151
Patrick Bultinck and
Robert Ponec and
Ramon Carbó-Dorca Aromaticity in linear polyacenes:
Generalized population analysis and
molecular quantum similarity approach 152--160
A. Martín Pendás and
M. A. Blanco and
E. Francisco Chemical fragments in real space:
Definitions, properties, and energetic
decompositions . . . . . . . . . . . . . 161--184
Peifeng Su and
Lingchun Song and
Wei Wu and
Philippe C. Hiberty and
Sason Shaik A valence bond study of the dioxygen
molecule . . . . . . . . . . . . . . . . 185--197
C. R. Landis and
F. Weinhold Valence and extra-valence orbitals in
main group and transition metal bonding 198--203
I. Mayer Bond order and valence indices: a
personal account . . . . . . . . . . . . 204--221
Dmitri G. Fedorov and
Kazuo Kitaura Pair interaction energy decomposition
analysis . . . . . . . . . . . . . . . . 222--237
F. M. Bickelhaupt and
M. Sol\`a and
C. Fonseca Guerra Covalent versus ionic bonding in
alkalimetal fluoride oligomers . . . . . 238--250
Dmitry Yu. Zubarev and
Alexander I. Boldyrev Comprehensive analysis of chemical
bonding in boron clusters . . . . . . . 251--268
Lionel Goodman and
Ronald R. Sauers Diffuse functions in natural bond
orbital analysis . . . . . . . . . . . . 269--275
Lyudmila V. Slipchenko and
Mark S. Gordon Electrostatic energy in the effective
fragment potential method: Theory and
application to benzene dimer . . . . . . 276--291
M. Rafat and
P. L. A. Popelier Atom--atom partitioning of total
(super)molecular energy: the hidden
terms of classical force fields . . . . 292--301
Thomas Heine and
Rafael Islas and
Gabriel Merino $\sigma$ and $\pi$ contributions to the
induced magnetic field: Indicators for
the mobility of electrons in molecules 302--309
Dandamudi Usha Rani and
Dasari L. V. K. Prasad and
John F. Nixon and
Eluvathingal D. Jemmis Electronic structure and bonding studies
on triple-decker sandwich complexes with
a P$_6$ middle ring . . . . . . . . . . 310--319
Martin Kaupp The role of radial nodes of atomic
orbitals for chemical bonding and the
periodic table . . . . . . . . . . . . . 320--325
Iñigo García-Yoldi and
Fernando Mota and
Juan J. Novoa The origin of the
two-electron/four-centers C\bondC bond
in $\pi$-TCNE$_2^{2-}$ dimers:
Electrostatic or dispersion? . . . . . . 326--334
B. Sateesh and
A. Srinivas Reddy and
G. Narahari Sastry Towards design of the smallest planar
tetracoordinate carbon and boron systems 335--343
Chaitanya S. Wannere and
Ankan Paul and
Rainer Herges and
K. N. Houk and
Henry F. Schaefer III and
Paul von Ragué Schleyer The existence of secondary orbital
interactions . . . . . . . . . . . . . . 344--361
Gabriel Merino and
Miguel A. Méndez-Rojas and
Alberto Vela and
Thomas Heine Recent advances in planar
tetracoordinate carbon chemistry . . . . 362--372
Igor V. Alabugin and
Mariappan Manoharan Rehybridization as a general mechanism
for maximizing chemical and
supramolecular bonding and a driving
force for chemical reactions . . . . . . 373--390
Klaus Ruedenberg and
Michael W. Schmidt Why does electron sharing lead to
covalent bonding? A variational analysis 391--410
T. Bitter and
K. Ruedenberg and
W. H. E. Schwarz Toward a physical understanding of
electron-sharing two-center bonds. I.
General aspects . . . . . . . . . . . . 411--422
Dmitry V. Khoroshun and
Djamaladdin G. Musaev and
Keiji Morokuma Electronic reorganization: Origin of
sigma trans promotion effect . . . . . . 423--441
Anthony Scemama and
Michel Caffarel and
Andreas Savin Maximum probability domains from Quantum
Monte Carlo calculations . . . . . . . . 442--454
John Frederick Beck and
Yirong Mo How resonance assists hydrogen bonding
interactions: an energy decomposition
analysis . . . . . . . . . . . . . . . . 455--466
Zi-Zhang Wei and
Bu-Tong Li and
Hong-Xing Zhang and
Chia-Chung Sun and
Ke-Li Han A theoretical investigation of the
excited states of OCLO radical, cation,
and anion using the CASSCF/CASPT2 method 467--477
Ross C. Walker and
Ian P. Mercer and
Ian R. Gould and
David R. Klug Comparison of basis set effects and the
performance of ab initio and DFT methods
for probing equilibrium fluctuations . . 478--490
M. Rami Reddy and
U. C. Singh and
Mark D. Erion Ab initio quantum mechanics-based free
energy perturbation method for
calculating relative solvation free
energies . . . . . . . . . . . . . . . . 491--494
Evelyn Mayaan and
Adam Moser and
Alexander D. MacKerell Jr. and
Darrin M. York CHARMM force field parameters for
simulation of reactive intermediates in
native and thio-substituted ribozymes 495--507
Chun Li and
Ai-hua Wang and
Lili Xing Similarity of RNA secondary structures 508--512
Sheng-Yong Yang and
Ming-Li Xiang and
Li-Juan Chen and
Guo-Bin Xie and
Bing Shi and
Yu-Quan Wei and
Tom Ziegler Free energy profiles for monomer capture
in Grubbs- and SHOP-type olefin
polymerization catalysts: a constraint
ab initio molecular dynamics study . . . 513--518
Wei-Qi Lin and
Jian-Hui Jiang and
Yan-Ping Zhou and
Hai-Long Wu and
Guo-Li Shen and
Ru-Qin Yu Support vector machine based training of
multilayer feedforward neural networks
as optimized by particle swarm
algorithm: Application in QSAR studies
of bioactivity of organic compounds . . 519--527
S. A. De Marothy and
M. R. A. Blomberg and
P. E. M. Siegbahn Elucidating the mechanism for the
reduction of nitrite by copper nitrite
reductase --- a contribution from
quantum chemical studies . . . . . . . . 528--539
Jose M. Hermida-Ramón and
Ana M. Graña Blue-shifting hydrogen bond in the
benzene--benzene and
benzene--naphthalene complexes . . . . . 540--546
Kalju Kahn and
Alex A. Granovsky and
Jozef Noga Convergence of third order correlation
energy in atoms and molecules . . . . . 547--554
Petr Jure\vcka and
Ji\vrí \vCerný and
Pavel Hobza and
Dennis R. Salahub Density functional theory augmented with
an empirical dispersion term.
Interaction energies and geometries of
80 noncovalent complexes compared with
ab initio quantum mechanics calculations 555--569
Pedro Gonnet A simple algorithm to accelerate the
computation of non-bonded interactions
in cell-based molecular dynamics
simulations . . . . . . . . . . . . . . 570--573
Miquel Torrent-Sucarrat and
Pedro Salvador and
Paul Geerlings and
Miquel Sol\`a On the quality of the hardness kernel
and the Fukui function to evaluate the
global hardness . . . . . . . . . . . . 574--583
R. Conte and
G. P. Arrighini and
C. Guidotti Direct evaluation via forced oscillation
method of the electronic state density
of sizable clusters . . . . . . . . . . 584--593
Hong Seok Kang A theoretical study of
fullerene--ferrocene hybrids . . . . . . 594--600
Svetlana Stepanenko and
Bernd Engels Gradient tabu search . . . . . . . . . . 601--611
Hung-Ming Chen and
Bo-Fu Liu and
Hui-Ling Huang and
Shiow-Fen Hwang and
Shinn-Ying Ho SODOCK: Swarm optimization for highly
flexible protein--ligand docking . . . . 612--623
Chang K. Kim and
Dong J. Kim and
Y. Hsieh and
Hai W. Lee and
Bon-Su Lee and
Chan K. Kim Effects of entropy on the gas-phase
pyrolysis of ethyl N,
$N$-dimethylcarbamate . . . . . . . . . 625--631
Beno\^\it Bories and
Daniel Maynau and
Marie-Laure Bonnet Selected excitation for CAS-SDCI
calculations . . . . . . . . . . . . . . 632--643
Irina S. Moreira and
Pedro A. Fernandes and
Maria J. Ramos Computational alanine scanning
mutagenesis --- an improved
methodological approach . . . . . . . . 644--654
Vladimir Hnizdo and
Eva Darian and
Adam Fedorowicz and
Eugene Demchuk and
Shengqiao Li and
Harshinder Singh Nearest-neighbor nonparametric method
for estimating the configurational
entropy of complex molecules . . . . . . 655--668
Jinhyuk Lee and
Wonpil Im Implementation and application of
helix--helix distance and crossing angle
restraint potentials . . . . . . . . . . 669--680
Tomasz Panczyk Collisions of ideal gas molecules with a
rough/fractal surface. A computational
study . . . . . . . . . . . . . . . . . 681--688
Zhitao Xu and
Harry H. Luo and
D. Peter Tieleman Modifying the OPLS-AA force field to
improve hydration free energies for
several amino acid side chains using new
atomic charges and an off-plane charge
model for aromatic residues . . . . . . 689--697
Dimitri N. Laikov Neglect of four- and approximation of
one-, two-, and three-center
two-electron integrals in a
symmetrically orthogonalized basis . . . 698--702
Z. J. Wu and
M. Y. Wang and
Z. M. Su Electronic structures and chemical
bonding in diatomic ScX to ZnX (X = S,
Se, Te) . . . . . . . . . . . . . . . . 703--714
Ruben G. Ghulghazaryan and
Shura Hayryan and
Chin-Kun Hu Efficient combination of Wang--Landau
and transition matrix Monte Carlo
methods for protein simulations . . . . 715--726
Yoong-Kee Choe and
Shigeru Nagase and
Kichisuke Nishimoto Theoretical study of the electronic
spectra of oxidized and reduced states
of lumiflavin and its derivative . . . . 727--739
Terutaka Yoshizawa and
Masahiko Hada Calculations of frequency-dependent
molecular magnetizabilities with
quasi-relativistic time-dependent
generalized unrestricted Hartree--Fock
method . . . . . . . . . . . . . . . . . 740--747
J. Fernández Rico and
R. López and
I. Ema and
G. Ramírez Generation of basis sets with high
degree of fulfillment of the
Hellmann--Feynman theorem . . . . . . . 748--758
Bryan M. Wong and
Sumathy Raman Thermodynamic calculations for molecules
with asymmetric internal rotors ---
application to 1,3-butadiene . . . . . . 759--766
Ernesto Estrada Point scattering: a new geometric
invariant with applications from
(Nano)clusters to biomolecules . . . . . 767--777
Vladimir I. Bolshakov and
Vladimir V. Rossikhin and
Eugene O. Voronkov and
Sergiy I. Okovytyy and
Jerzy Leszczynski The performance of the new
6-31G$^{\#\#}$ basis set: Molecular
structures and vibrational frequencies
of transition metal carbonyls . . . . . 778--782
Hsiu-Feng Lu and
Feng-Yin Li and
S. H. Lin Site specificity of $\alpha$-H
abstraction reaction among secondary
structure motif --- an ab initio study 783--794
Xingfa Gao and
Yuliang Zhao The way of stabilizing non-IPR
fullerenes and structural elucidation of
C$_{54}$Cl$_8$ . . . . . . . . . . . . . 795--801
Ying Wang and
Jing-Yao Liu and
Ze-Sheng Li and
Li Wang and
Chia-Chung Sun Theoretical study and rate constant
calculation for reaction of
CF$_3$CH$_2$OH with OH . . . . . . . . . 802--810
M. L. Ellzey Jr. Finite group theory for large systems.
3. Symmetry-generation of reduced matrix
elements for icosahedral C$_{20}$ and
C$_{60}$ molecules . . . . . . . . . . . 811--817
Jeb Kegerreis and
Nancy Makri Optimized Monte Carlo sampling in
forward--backward semiclassical dynamics 818--824
Dorota Rutkowska-Zbik and
Ma\lgorzata Witko and
Grazyna Stochel Theoretical density functional theory
studies on interactions of small
biologically active molecules with
isolated heme group . . . . . . . . . . 825--831
Michel Rafat and
Paul L. A. Popelier Long range behavior of high-rank
topological multipole moments . . . . . 832--838
Robert A. Distasio, Jr. and
Ryan P. Steele and
Young Min Rhee and
Yihan Shao and
Martin Head-Gordon An improved algorithm for analytical
gradient evaluation in
resolution-of-the-identity second-order
Mòller--Plesset perturbation theory:
Application to alanine tetrapeptide
conformational analysis . . . . . . . . 839--856
Victor Polo and
Juan Andres and
Bernard Silvi New insights on the bridge
carbon--carbon bond in propellanes: a
theoretical study based on the analysis
of the electron localization function 857--864
Jian Wang and
Yi-Hong Ding and
Shao-Wen Zhang and
Chia-Chung Sun Theoretical study on the methyl radical
with chlorinated methyl radicals CH$_{3
- n}$Cl$_n$ ($n = 1$, $2$, $3$) and
CCl$_2$ . . . . . . . . . . . . . . . . 865--876
Martin R. Siegert and
Matthias Heuchel and
Dieter Hofmann A generalized direct-particle-deletion
scheme for the calculation of chemical
potential and solubilities of small- and
medium-sized molecules in amorphous
polymers . . . . . . . . . . . . . . . . 877--889
Frits Daeyaert and
Marc De Jonge and
Luc Koymans and
Maarten Vinkers An ant algorithm for the conformational
analysis of flexible molecules . . . . . 890--898
Edward Sanville and
Steven D. Kenny and
Roger Smith and
Graeme Henkelman Improved grid-based algorithm for Bader
charge allocation . . . . . . . . . . . 899--908
Alexander H. Boschitsch and
Marcia O. Fenley A new outer boundary formulation and
energy corrections for the nonlinear
Poisson--Boltzmann equation . . . . . . 909--921
Hassan Sabzyan and
Davood Farmanzadeh Electric field effects on the
performance of a candidate multipole
molecular switch: a quantum
computational study . . . . . . . . . . 922--931
Ravichandra Mutyala and
R. N. Reddy and
M. Sumakanth and
P. Reddanna and
M. Rami Reddy Calculation of relative binding
affinities of fructose
1,6-bisphosphatase mutants with
adenosine monophosphate using free
energy perturbation method . . . . . . . 932--937
Celine Roux and
Nohad Gresh and
Lalith E. Perera and
Jean-Philip Piquemal and
Laurent Salmon Binding of 5-phospho-
D-arabinonohydroxamate and 5-phospho-
D-arabinonate inhibitors to zinc
phosphomannose isomerase from Candida
albicans studied by polarizable
molecular mechanics and quantum
mechanics . . . . . . . . . . . . . . . 938--957
V. R. Ferro and
R. López and
S. Omar and
J. M. García De La Vega On the molecular electron structure of
three phosphinine-containing macrocycles 958--966
W. J. Fan and
R. Q. Zhang and
Shubin Liu Computation of large systems with an
economic basis set: Structures and
reactivity indices of nucleic acid base
pairs from density functional theory . . 967--974
Yue-meng Ji and
Xiao-lei Zhao and
Ze-sheng Li and
Jing-yao Liu Kinetic mechanism of the hydrogen
abstraction reactions of the chlorine
atoms with CH$_3$CF$_2$Cl and
CH$_3$CFCl$_2$: a dual level direct
dynamics study . . . . . . . . . . . . . 975--983
Toru Inaba and
Fumitoshi Sato Development of parallel density
functional program using distributed
matrix to calculate all-electron
canonical wavefunction of large
molecules . . . . . . . . . . . . . . . 984--995
Ismael Tejero and
\`Angels González-Lafont and
José M. Lluch A PM3/d specific reaction
parameterization for iron atom in the
hydrogen abstraction catalyzed by
soybean lipoxygenase-1 . . . . . . . . . 997--1005
Viwat Vchirawongkwin and
Thomas S. Hofer and
Bernhard R. Randolf and
Bernd M. Rode Tl(I)-the strongest structure-breaking
metal ion in water? A quantum
mechanical/molecular mechanical
simulation study . . . . . . . . . . . . 1006--1016
Arnau Cordomí and
Olle Edholm and
Juan J. Perez Effect of different treatments of
long-range interactions and sampling
conditions in molecular dynamic
simulations of rhodopsin embedded in a
dipalmitoyl phosphatidylcholine bilayer 1017--1030
Anna Marabotti and
Giovanni Colonna and
Angelo Facchiano New computational strategy to analyze
the interactions of ER$\alpha$ and
ER$\beta$ with different ERE sequences 1031--1041
Humberto González-díaz and
Liane Saíz-urra and
Reinaldo Molina and
Yenny González-díaz and
Angeles Sánchez-gonzález Computational chemistry approach to
protein kinase recognition using $3$D
stochastic van der Waals spectral
moments . . . . . . . . . . . . . . . . 1042--1048
Humberto González-díaz and
Guillermín Agüero-chapin and
Javier Varona and
Reinaldo Molina and
Giovanna Delogu and
Lourdes Santana and
Eugenio Uriarte and
Gianni Podda $2$D-RNA-coupling numbers: a new
computational chemistry approach to link
secondary structure topology with
biological function . . . . . . . . . . 1049--1056
Viwat Vchirawongkwin and
Thomas S. Hofer and
Bernhard R. Randolf and
Bernd M. Rode Quantum mechanical/molecular mechanical
simulations of the Tl(III) ion in water 1057--1067
Anna Jagielska and
Harold A. Scheraga Influence of temperature, friction, and
random forces on folding of the B-domain
of staphylococcal protein A: All-atom
molecular dynamics in implicit solvent 1068--1082
P. Söderhjelm and
J. W. Krogh and
G. Karlström and
U. Ryde and
R. Lindh Accuracy of distributed multipoles and
polarizabilities: Comparison between the
LoProp and MpProp models . . . . . . . . 1083--1090
Hitomi Yuki and
Yoshikazu Tanaka and
Masayuki Hata and
Hidenori Ishikawa and
Saburo Neya and
Tyuji Hoshino Implementation of $\pi$-$\pi$
interactions in molecular dynamics
simulation . . . . . . . . . . . . . . . 1091--1099
Kyoung Hoon Kim and
Jaehoon Jung and
Bo Keun Park and
Young-Kyu Han and
Joon T. Park Cyclic voltammetry modeling, geometries,
and electronic properties for
metallofullerene complexes with
$\mu_3$--$\eta^2$: $\eta^2$:
$\eta^2$-C$_{60}$ bonding mode . . . . . 1100--1106
Sang-Ho Lee and
Kim Palmo and
Samuel Krimm A comparative study of molecular
dynamics in Cartesian and in internal
coordinates: Dynamical instability in
the latter caused by nonlinearity of the
equations of motion . . . . . . . . . . 1107--1118
S. Alcaro and
F. Gasparrini and
O. Incani and
L. Caglioti and
M. Pierini and
C. Villani ``Quasi flexible'' automatic docking
processing for studying stereoselective
recognition mechanisms, part 2:
Prediction of $\Delta\Delta$G of
complexation and $^1$H-NMR NOE
correlation . . . . . . . . . . . . . . 1119--1128
Minoru Saito and
Isao Okazaki A 45-ns molecular dynamics simulation of
hemoglobin in water by vectorizing and
parallelizing COSMOS90 on the earth
simulator: Dynamics of tertiary and
quaternary structures . . . . . . . . . 1129--1136
Takao Otsuka and
Hiromi Nakai Wavelet transform analysis of ab initio
molecular dynamics simulation:
Application to core-excitation dynamics
of BF$_3$ . . . . . . . . . . . . . . . 1137--1144
Ruth Huey and
Garrett M. Morris and
Arthur J. Olson and
David S. Goodsell A semiempirical free energy force field
with charge-based desolvation . . . . . 1145--1152
Hui Zhang and
Gui-Ling Zhang and
Li Wang and
Bo Liu and
Xiao-Yang Yu and
Ze-Sheng Li Theoretical study on the Br +
CH$_3$SCH$_3$ reaction . . . . . . . . . 1153--1159
Sérgio Filipe Sousa and
Pedro Alexandrino Fernandes and
Maria João Ramos Theoretical studies on farnesyl
transferase: Evidence for thioether
product coordination to the active-site
zinc sphere . . . . . . . . . . . . . . 1160--1168
Maxim Tafipolsky and
Saeed Amirjalayer and
Rochus Schmid Ab initio parametrized MM3 force field
for the metal-organic framework MOF-5 1169--1176
Seth T. Call and
Dmitry Yu. Zubarev and
Alexander I. Boldyrev Global minimum structure searches via
particle swarm optimization . . . . . . 1177--1186
David De Sancho and
Antonio Rey Evaluation of coarse grained models for
hydrogen bonds in proteins . . . . . . . 1187--1199
Adelio R. Matamala and
Daniel E. Almonacid and
Maximiliano F. Figueroa and
José Martínez-oyanedel and
Marta C. Bunster A semiempirical approach to the
intra-phycocyanin and inter-phycocyanin
fluorescence resonance energy-transfer
pathways in phycobilisomes . . . . . . . 1200--1207
Nicholas Y. Palermo and
József Csontos and
Michael C. Owen and
Richard F. Murphy and
Sándor Lovas Aromatic-backbone interactions in model
$\alpha$-helical peptides . . . . . . . 1208--1214
Alan R. Ford and
Tomasz Janowski and
Peter Pulay Array files for computational chemistry:
MP2 energies . . . . . . . . . . . . . . 1215--1220
Yan-Li Zhao and
Wei Kan and
Hua Zhong and
Hai-Tao Yu and
Hong-Gang Fu Combined DFT, QCISD(T), and G2 mechanism
investigation for the reactions of
carbon monophosphide CP with unsaturated
hydrocarbons allene CH$_2$CCH$_2$ and
methylacetylene CH$_3$CCH . . . . . . . 1221--1233
Fangqiang Zhu and
Dimitris K. Agrafiotis Self-organizing superimposition
algorithm for conformational sampling 1234--1239
Evgueni B. Kadossov and
Karen J. Gaskell and
Marjorie A. Langell Effect of surrounding point charges on
the density functional calculations of
Ni$_x$O$_x$ clusters ($x = 4$--$12$) . . 1240--1251
Manuel Urbano Cuadrado and
Irene Luque Ruiz and
Miguel Ángel Gómez-Nieto QSAR models based on isomorphic and
nonisomorphic data fusion for predicting
the blood brain barrier permeability . . 1252--1260
Dennis Elking and
Tom Darden and
Robert J. Woods Gaussian induced dipole polarization
model . . . . . . . . . . . . . . . . . 1261--1274
Chanin Nantasenamat and
Chartchalerm Isarankura-Na-Ayudhya and
Natta Tansila and
Thanakorn Naenna and
Virapong Prachayasittikul Prediction of GFP spectral properties
using artificial neural network . . . . 1275--1289
Anthony K. Grafton Vibalizer: a free, Web-based tool for
rapid, quantitative comparison and
analysis of calculated vibrational modes 1290--1305
David P. Tew and
Wim Klopper and
Trygve Helgaker Electron correlation: the many-body
problem at the heart of chemistry . . . 1307--1320
N. R. Jena and
P. C. Mishra Formation of 8-nitroguanine and
8-oxoguanine due to reactions of
peroxynitrite with guanine . . . . . . . 1321--1335
Andrew Leaver-Fay and
Glenn L. Butterfoss and
Jack Snoeyink and
Brian Kuhlman Maintaining solvent accessible surface
area under rotamer substitution for
protein design . . . . . . . . . . . . . 1336--1341
Michael L. Mckee Modeling the nitrogenase FeMo cofactor
with high-spin Fe$_8$S$_9$X$^+$ (X = N,
C) clusters. Is the first step for N$_2$
reduction to NH$_3$ a concerted
dihydrogen transfer? . . . . . . . . . . 1342--1356
Chin-Hung Lai and
Pi-Tai Chou Can an OH radical form a strong hydrogen
bond? A theoretical comparison with
H$_2$O . . . . . . . . . . . . . . . . . 1357--1363
Anatoly M. Ruvinsky Role of binding entropy in the
refinement of protein--ligand docking
predictions: Analysis based on the use
of 11 scoring functions . . . . . . . . 1364--1372
Veronika Kasalová and
Wesley D. Allen and
Henry F. Schaefer III and
Eszter Czinki and
Attila G. Császár Molecular structures of the two most
stable conformers of free glycine . . . 1373--1383
Sönke Lorenz and
Elmar Diederichs and
Regina Telgmann and
Christof Schütte Discrimination of dynamical system
models for biological and chemical
processes . . . . . . . . . . . . . . . 1384--1399
Kilho Eom and
Seung-Chul Baek and
Jung-Hee Ahn and
Sungsoo Na Coarse-graining of protein structures
for the normal mode studies . . . . . . 1400--1410
Carlos Silva López and
Olalla Nieto Faza and
José A. Souto and
Rosana Álvarez and
Ángel R. De Lera Pseudopericyclic design drives
antara-antara [1,5] methylene
sigmatropic shifts from a stepwise to a
concerted mechanism . . . . . . . . . . 1411--1416
Jin Qiang Hou and
Hong Seok Kang A DFT study on the dimerization of
C$_{62}$, H$_2$C$_{62}$, and
F$_2$C$_{62}$ . . . . . . . . . . . . . 1417--1426
Xiaoli Yang and
Wensheng Cai and
Xueguang Shao A dynamic lattice searching method with
constructed core for optimization of
large Lennard-Jones clusters . . . . . . 1427--1433
Qi Dai and
Xiao-Qing Liu and
Tian-Ming Wang and
Damir Vukicevic Linear regression model of DNA sequences
and its application . . . . . . . . . . 1434--1445
Qian Shu Li and
Yu Xu A quantum chemistry study: a new kind of
boron nitrides . . . . . . . . . . . . . 1446--1455
Didier Begue and
Claude Pouchan Vibrational anharmonic calculations in
solution: Performance of various DFT
approaches . . . . . . . . . . . . . . . 1456--1462
Hao Lin and
Qian-Zhong Li Using pseudo amino acid composition to
predict protein structural class:
Approached by incorporating 400
dipeptide components . . . . . . . . . . 1463--1466
Wei-Qi Li and
Wei-Quan Tian and
Ji-Kang Feng and
Zi-Zhong Liu and
Ai-Min Ren and
Chia-Chung Sun and
Yuriko Aoki Electronic properties of tricoordinated
phosphorus in hexagonal phosphininium
compounds and molecular aromaticity . . 1467--1475
Dmitri G. Fedorov and
Kazuya Ishimura and
Toyokazu Ishida and
Kazuo Kitaura and
Peter Pulay and
Shigeru Nagase Accuracy of the three-body fragment
molecular orbital method applied to
Mòller--Plesset perturbation theory . . . 1476--1484
H. Lee Woodcock III and
Milan Hodo\vs\vcek and
Andrew T. B. Gilbert and
Peter M. W. Gill and
Henry F. Schaefer III and
Bernard R. Brooks Interfacing Q-Chem and CHARMM to perform
QM/MM reaction path calculations . . . . 1485--1502
Stephan Raub and
Christel M. Marian Quantum chemical investigation of
hydrogen-bond strengths and partition
into donor and acceptor contributions 1503--1515
Antonio Vila and
Ricardo A. Mosquera Atoms in molecules interpretation of the
anomeric effect in the O\bondC\bondO
unit . . . . . . . . . . . . . . . . . . 1516--1530
Mark P. Waller and
Michael Bühl Vibrational corrections to geometries of
transition metal complexes from density
functional theory . . . . . . . . . . . 1531--1537
Setsuko Nakagawa Polarizable model potential function for
nucleic acid bases . . . . . . . . . . . 1538--1550
Marcel Swart and
Miquel Sol\`a and
F. Matthias Bickelhaupt Energy landscapes of nucleophilic
substitution reactions: a comparison of
density functional theory and coupled
cluster methods . . . . . . . . . . . . 1551--1560
Shinichi Yamabe and
Noriko Tsuchida and
Shoko Yamazaki Theoretical study of the role of solvent
H$_2$O in neopentyl and pinacol
rearrangements . . . . . . . . . . . . . 1561--1571
Matthew C. Zwier and
Justin M. Shorb and
Brent P. Krueger Hybrid molecular dynamics-quantum
mechanics simulations of solute spectral
properties in the condensed phase:
Evaluation of simulation parameters . . 1572--1581
Edmond P. F. Lee and
John M. Dyke and
Wan-Ki Chow and
Foo-Tim Chau and
Daniel K. W. Mok DFT and ab initio calculations on two
reactions between hydrogen atoms and the
fire suppressants 2-H heptafluoropropane
and CF$_3$Br . . . . . . . . . . . . . . 1582--1592
Dominik Gront and
Sebastian Kmiecik and
Andrzej Kolinski Backbone building from quadrilaterals: a
fast and accurate algorithm for protein
backbone reconstruction from alpha
carbon coordinates . . . . . . . . . . . 1593--1597
Olexandr Isayev and
Leonid Gorb and
Jerzy Leszczynski Theoretical calculations: Can Gibbs free
energy for intermolecular complexes be
predicted efficiently and accurately? 1598--1609
T. Daniel Crawford and
C. David Sherrill and
Edward F. Valeev and
Justin T. Fermann and
Rollin A. King and
Matthew L. Leininger and
Shawn T. Brown and
Curtis L. Janssen and
Edward T. Seidl and
Joseph P. Kenny and
Wesley D. Allen PSI3: an open-source Ab Initio
electronic structure package . . . . . . 1610--1616
Petr Dan\ue\vcek and
Petr Bou\vr Comparison of the numerical stability of
methods for anharmonic calculations of
vibrational molecular energies . . . . . 1617--1624
Marcos Mandado and
María J. González-Moa and
Ricardo A. Mosquera Chemical graph theory and $n$-center
electron delocalization indices: a study
on polycyclic aromatic hydrocarbons . . 1625--1633
José D. Faraldo-Gómez and
Beno\^\it Roux Characterization of conformational
equilibria through Hamiltonian and
temperature replica-exchange
simulations: Assessing entropic and
environmental effects . . . . . . . . . 1634--1647
Anna Jagielska and
Jeffrey Skolnick Origin of intrinsic $3_{10}$-helix
versus strand stability in
homopolypeptides and its implications
for the accuracy of the AMBER force
field . . . . . . . . . . . . . . . . . 1648--1657
Yongjian Li and
Jian Wan and
Xin Xu Theoretical study of the vertical
excited states of benzene, pyrimidine,
and pyrazine by the symmetry adapted
cluster--configuration interaction
method . . . . . . . . . . . . . . . . . 1658--1667
Dorota Latek and
Dariusz Ekonomiuk and
Andrzej Kolinski Protein structure prediction: Combining
de novo modeling with sparse
experimental data . . . . . . . . . . . 1668--1676
Ying Li and
Di Wu and
Zhi-Ru Li and
Chia-Chung Sun Structural and electronic properties of
boron-doped lithium clusters: ab initio
and DFT studies . . . . . . . . . . . . 1677--1684
Yuri Alexeev and
Michael W. Schmidt and
Theresa L. Windus and
Mark S. Gordon A parallel distributed data CPHF
algorithm for analytic Hessians . . . . 1685--1694
A. V. Larin and
W. J. Mortier and
D. P. Vercauteren Quick scheme for evaluation of atomic
charges in arbitrary aluminophosphate
sieves on the basis of electron
densities calculated with DFT methods 1695--1703
M. Qaiser Fatmi and
Thomas S. Hofer and
Bernhard R. Randolf and
Bernd M. Rode Quantum mechanical charge field
molecular dynamics simulation of the
TiO$^{2+}$ ion in aqueous solution . . . 1704--1710
Pedro J. Ballester and
W. Graham Richards Ultrafast shape recognition to search
compound databases for similar molecular
shapes . . . . . . . . . . . . . . . . . 1711--1723
S. F. Braga and
D. S. Galvão Molecular dynamics simulation of single
wall carbon nanotubes polymerization
under compression . . . . . . . . . . . 1724--1734
Rungtiwa Chidthong and
Supa Hannongbua and
Adelia J. A. Aquino and
Peter Wolschann and
Hans Lischka Excited state properties, fluorescence
energies, and lifetime of a
poly(fluorene-pyridine) copolymer, based
on TD-DFT investigation . . . . . . . . 1735--1742
David Curcó and
Carlos Alemán Computational tool to model the packing
of polycyclic chains: Structural
analysis of amorphous polythiophene . . 1743--1749
Yuto Komeiji and
Toyokazu Ishida and
Dmitri G. Fedorov and
Kazuo Kitaura Change in a protein's electronic
structure induced by an explicit
solvent: an ab initio fragment molecular
orbital study of ubiquitin . . . . . . . 1750--1762
Hossein Eslami and
Florian Müller-Plathe Molecular dynamics simulation in the
grand canonical ensemble . . . . . . . . 1763--1773
Charles L. Brooks III and
Gernot Frenking and
Shigeyoshi Sakaki Letter from the Editors . . . . . . . . 1775--1775
Remmick So and
Saman Alavi Vertical excitation energies for ribose
and deoxyribose nucleosides . . . . . . 1776--1782
Stanislav Böhm and
Otto Exner Inductive effects in radicals calculated
from DFT energies; substituted
bicyclo[2.2.2]octan-1-yloxy radicals . . 1783--1789
Jiande Gu and
Jing Wang and
Jerzy Leszczynski Iso-guanine quintet complexes
coordinated by mono valent cations
(Na$^+$, K$^+$, Rb$^+$, and Cs$^+$) . . 1790--1795
Michael L. Mckee Modeling hydrogen evolution from the
Fe$_4$S$_4$ and Fe$_8$S$_9$X (X = N, C)
clusters. Can a FeS high-spin cluster
serve as a surrogate for the FeMo
cofactor? . . . . . . . . . . . . . . . 1796--1808
Yao-Yuan Chuang Calculating rate constants with updated
Hessians using variational transition
state theory with multidimensional
tunneling . . . . . . . . . . . . . . . 1809--1816
R. Maul and
F. Ortmann and
M. Preuss and
K. Hannewald and
F. Bechstedt DFT studies using supercells and
projector-augmented waves for structure,
energetics, and dynamics of glycine,
alanine, and cysteine . . . . . . . . . 1817--1833
Wolfgang Quapp Finding the transition state without
initial guess: the growing string method
for Newton trajectory to isomerization
and enantiomerization reaction of
alanine dipeptide and poly(15)alanine 1834--1847
Tian Zhang and
Haoping Zheng and
Shu Yan Equivalent potential of water molecules
for electronic structure of glutamic
acid . . . . . . . . . . . . . . . . . . 1848--1857
Thenmalarchelvi Rathinavelan and
Wonpil Im Explicit treatment of force contribution
from alignment tensor using
overdetermined linear equations and its
application in NMR structure
determination . . . . . . . . . . . . . 1858--1864
V. A. Levashov and
S. J. L. Billinge and
M. F. Thorpe Quantum correction to the pair
distribution function . . . . . . . . . 1865--1882
Yu Sun and
Brian N. Dominy and
Robert A. Latour Comparison of solvation-effect methods
for the simulation of peptide
interactions with a hydrophobic surface 1883--1892
Constantinos A. Tsipis and
Ioannis G. Depastas and
Christos E. Kefalidis Growth format, electronic architecture,
magnetic, and optical properties of
aromatic cyclo-Cu$_3$Au$_3$ homotops . . 1893--1908
Maykel Cruz-Monteagudo and
Humberto González-Díaz and
Guillermín Agüero-Chapín and
Lourdes Santana and
Fernanda Borges and
Elena Rosa Domínguez and
Gianni Podda and
Eugenio Uriarte Computational chemistry development of a
unified free energy Markov model for the
distribution of 1300 chemicals to 38
different environmental or biological
systems . . . . . . . . . . . . . . . . 1909--1923
Sofie Van Damme and
Patrick Bultinck A new computer program for
QSAR-analysis: ARTE-QSAR . . . . . . . . 1924--1928
David Curcó and
Carlos Alemán Coarse-graining: a procedure to generate
equilibrated and relaxed models of
amorphous polymers . . . . . . . . . . . 1929--1935
Imre Berente and
Eszter Czinki and
Gábor Náray-szabó A combined electronegativity
equalization and electrostatic potential
fit method for the determination of
atomic point charges . . . . . . . . . . 1936--1942
Gaurav Porwal and
Swapnil Jain and
S. Dhilly Babu and
Deepak Singh and
Hemant Nanavati and
Santosh Noronha Protein structure prediction aided by
geometrical and probabilistic
constraints . . . . . . . . . . . . . . 1943--1952
Yousung Jung and
Yihan Shao and
Martin Head-Gordon Fast evaluation of scaled opposite spin
second-order Mòller--Plesset correlation
energies using auxiliary basis
expansions and exploiting sparsity . . . 1953--1964
Ian R. Gould and
Hoda Abdel-Aal Bettley and
Richard A. Bryce Correlated ab initio quantum chemical
calculations of di- and trisaccharide
conformations . . . . . . . . . . . . . 1965--1973
Georgy Rychkov and
Michael Petukhov Joint neighbors approximation of
macromolecular solvent accessible
surface area . . . . . . . . . . . . . . 1974--1989
Humberto González-Díaz and
Yunierkis Pérez-Castillo and
Gianni Podda and
Eugenio Uriarte Computational chemistry comparison of
stable/nonstable protein mutants
classification models based on $3$D and
topological indices . . . . . . . . . . 1990--1995
Andrew J. Moad and
Charles W. Moad and
John M. Perry and
Ronald D. Wampler and
G. Scott Goeken and
Nathan J. Begue and
Tian Shen and
Randy Heiland and
Garth J. Simpson NLOPredict: Visualization and data
analysis software for nonlinear optics 1996--2002
Tomoko Akama and
Masato Kobayashi and
Hiromi Nakai Implementation of divide-and-conquer
method including Hartree--Fock exchange
interaction . . . . . . . . . . . . . . 2003--2012
Vinzenz Bachler Orthogonal natural atomic orbitals form
an appropriate one-electron basis for
expanding CASSCF wave functions into
localized bonding schemes and their
weights . . . . . . . . . . . . . . . . 2013--2019
Alexei M. Nikitin and
Alexander P. Lyubartsev New six-site acetonitrile model for
simulations of liquid acetonitrile and
its aqueous mixtures . . . . . . . . . . 2020--2026
T. Zeng and
Z. Jamshidi and
H. Mori and
E. Miyoshi and
M. Klobukowski Electron affinities of heavier
phosphoryl and thiophosphoryl halides
APX$_3$ (A = O, S and X = Br, I) . . . . 2027--2033
Kazuya Ishimura and
Peter Pulay and
Shigeru Nagase New parallel algorithm for MP2 energy
gradient calculations . . . . . . . . . 2034--2042
Qi-Shi Du and
Ri-Bo Huang and
Yu-Tuo Wei and
Cheng-Hua Wang and
Kuo-Chen Chou Peptide reagent design based on physical
and chemical properties of amino acid
residues . . . . . . . . . . . . . . . . 2043--2050
Balázs Jójárt and
Tamás A. Martinek Performance of the general AMBER force
field in modeling aqueous POPC membrane
bilayers . . . . . . . . . . . . . . . . 2051--2058
Liliana Wroblewska and
Jeffrey Skolnick Can a physics-based, all-atom potential
find a protein's native structure among
misfolded structures? I. Large scale
AMBER benchmarking . . . . . . . . . . . 2059--2066
Yutaka Imamura and
Takao Otsuka and
Hiromi Nakai Description of core excitations by
time-dependent density functional theory
with local density approximation,
generalized gradient approximation,
meta-generalized gradient approximation,
and hybrid functionals . . . . . . . . . 2067--2074
Carsten Kutzner and
David Van Der Spoel and
Martin Fechner and
Erik Lindahl and
Udo W. Schmitt and
Bert L. De Groot and
Helmut Grubmüller Speeding up parallel GROMACS on
high-latency networks . . . . . . . . . 2075--2084
Francesco Ferrante and
Gianfranco La Manna Theoretical study of the interaction
between sodium ion and a cyclopeptidic
tubular structure . . . . . . . . . . . 2085--2090
Run-Feng Chen and
Chao Zheng and
Qu-Li Fan and
Wei Huang Structural, electronic, and optical
properties of 9-heterofluorenes: a
quantum chemical study . . . . . . . . . 2091--2101
Javier González and
Xavier Giménez and
Josep Maria Bofill Algorithm to evaluate rate constants for
polyatomic chemical reactions. I. Theory
and computational details . . . . . . . 2102--2110
Javier González and
Xavier Giménez and
Josep Maria Bofill Algorithm to evaluate rate constants for
polyatomic chemical reactions. II.
Applications . . . . . . . . . . . . . . 2111--2121
Chen Yanover and
Menachem Fromer and
Julia M. Shifman Dead-end elimination for multistate
protein design . . . . . . . . . . . . . 2122--2129
Bård Buttingsrud and
Bjòrn K. Alsberg and
Per-Olof Åstrand Validation of critical points in the
electron density as descriptors by
building quantitative
structure--property relationships for
the atomic polar tensor . . . . . . . . 2130--2139
Mine Ilk Capar and
Emine Cebe Odd--even effects in the homologous
series of alkyl-cyanobiphenyl liquid
crystals: a molecular dynamic study . . 2140--2146
Jingjing Zheng and
Ahmet Altun and
Walter Thiel Common system setup for the entire
catalytic cycle of cytochrome
P450$_{cam}$ in quantum
mechanical/molecular mechanical studies 2147--2158
R. Zanasi and
S. Pelloni and
P. Lazzeretti Chiral discrimination via nuclear
magnetic shielding polarisabilities from
NMR spectroscopy: Theoretical study of
(R$_a$)-1,3-dimethylallene, (2
R)-2-methyloxirane, and (2 R)-
$N$-methyloxaziridine . . . . . . . . . 2159--2163
Yuanqiang Zhu and
Yong Guo and
Lidong Zhang and
Daiqian Xie A computational investigation on the
sequential rearrangement mechanism of
2-allyl-2,4,5-hexatrienaldehyde
involving [1,5]-hydrogen migration and
8$\pi$-electrocyclization . . . . . . . 2164--2169
Josep M. Porta and
Lluís Ros and
Federico Thomas and
Francesc Corcho and
Josep Cantó and
Juan Jesús Pérez Complete maps of molecular-loop
conformational spaces . . . . . . . . . 2170--2189
L. Cheng and
M. Y. Wang and
Z. J. Wu and
Z. M. Su Electronic structures and chemical
bonding in 4d transition metal
monohalides . . . . . . . . . . . . . . 2190--2202
G. Milani and
F. Milani Genetic algorithm for the determination
of binodal curves in ternary systems
polymer--liquid(1)--liquid(2) and
polymer(1)--polymer(2)--solvent . . . . 2203--2215
Santiago Vilar and
M. Carmen Villaverde and
Fredy Sussman Inhibitor docking screened by the
modified SAFE\_p scoring function:
Application to cyclic urea HIV-1 PR
inhibitors . . . . . . . . . . . . . . . 2216--2225
Peter H. M. Budzelaar Geometry optimization using generalized,
chemically meaningful constraints . . . 2226--2236
Kaori Fukuzawa and
Yuto Komeiji and
Yuji Mochizuki and
Akifumi Kato and
Tatsuya Nakano and
Shigenori Tanaka Intra- and intermolecular interactions
between cyclic-AMP receptor protein and
DNA: ab initio fragment molecular
orbital study . . . . . . . . . . . . . 2237--2239
Huynh-Hoa Bui and
Alexandra J. Schiewe and
Ian S. Haworth WATGEN: an algorithm for modeling water
networks at protein--protein interfaces 2241--2251
Mikhail Pykavy and
Christoph Van Wüllen A systematic quantum chemical
investigation of the C H bond activation
in methane by gas phase vanadium oxide
cation VO$^+$ . . . . . . . . . . . . . 2252--2259
Guiling Zhang and
Hui Zhang and
Miao Sun and
Yanhong Liu and
Xiaohong Pang and
Xiaoyang Yu and
Bo Liu and
Zesheng Li Substitution effect on the geometry and
electronic structure of the ferrocene 2260--2274
M. Piacenza and
I. Hyla-Kryspin and
S. Grimme A comparative quantum chemical study of
the ruthenium catalyzed olefin
metathesis . . . . . . . . . . . . . . . 2275--2285
Wenli Zou and
Wenjian Liu Theoretical study on the low-lying
electronic states of NiH and NiAt . . . 2286--2298
Marko Schreiber and
Leticia González Structure and bonding of Ag(I)--DNA base
complexes and Ag(I)--adenine--cytosine
mispairs: an ab initio study . . . . . . 2299--2308
David R. Kent IV and
Richard P. Muller and
Amos G. Anderson and
William A. Goddard III and
Michael T. Feldmann Efficient algorithm for ``on-the-fly''
error analysis of local or distributed
serially correlated data . . . . . . . . 2309--2316
Julian Henn and
Dirk Leusser and
Dietmar Stalke Chemical interpretation of molecular
electron density distributions . . . . . 2317--2324
Edda Kloppmann and
G. Matthias Ullmann and
Torsten Becker An extended dead-end elimination
algorithm to determine gap-free lists of
low energy states . . . . . . . . . . . 2325--2335
Xinliang Yu and
Bing Yi and
Xueye Wang Prediction of refractive index of vinyl
polymers by using density functional
theory . . . . . . . . . . . . . . . . . 2336--2341
Xizhen Zhang and
Jiawei Luo and
Li Yang New invariant of DNA sequence based on
$3$DD-curves and its application on
phylogeny . . . . . . . . . . . . . . . 2342--2346
Zengjian Hu and
William Southerland Windock: Structure-based drug discovery
on Windows-based PCs . . . . . . . . . . 2347--2351
Kaushalya S. Ekanayake and
Pierre R. Lebreton Model transition states for methane
diazonium ion methylation of guanine
runs in oligomeric DNA . . . . . . . . . 2352--2365
Riccardo Nifosí and
Pietro Amat and
Valentina Tozzini Variation of spectral, structural, and
vibrational properties within the
intrinsically fluorescent proteins
family: a density functional study . . . 2366--2377
Arnab B. Chowdry and
Kimberly A. Reynolds and
Melinda S. Hanes and
Mark Voorhies and
Navin Pokala and
Tracy M. Handel An object-oriented library for
computational protein design . . . . . . 2378--2388
Klaus Ruedenberg and
Michael W. Schmidt Erratum: Why does electron sharing lead
to covalent bonding? A variational
analysis . . . . . . . . . . . . . . . . 2389--2389
Kuo-Hsiang Chen and
Jenn-Huei Lii and
Yi Fan and
Norman L. Allinger Molecular mechanics (MM4) study of
amines . . . . . . . . . . . . . . . . . 2391--2412
Congyi Zhou and
Changming Nie and
Shan Li and
Zhonghai Li A novel semi-empirical topological
descriptor Nt and the application to
study on QSPR/QSAR . . . . . . . . . . . 2413--2423
Hidenori Anjima and
Shinya Tsukamoto and
Hirotoshi Mori and
Masaki Mine and
Mariusz Klobukowski and
Eisaku Miyoshi Revised model core potentials of
$s$-block elements . . . . . . . . . . . 2424--2430
Anan Wu and
Ying Zhang and
Xin Xu and
Yijing Yan Systematic studies on the computation of
nuclear magnetic resonance shielding
constants and chemical shifts: the
density functional models . . . . . . . 2431--2442
Jun-Ya Hasegawa and
Kazuhiro Fujimoto and
Ben Swerts and
Tomoo Miyahara and
Hiroshi Nakatsuji Excited states of GFP chromophore and
active site studied by the SAC--CI
method: Effect of protein-environment
and mutations . . . . . . . . . . . . . 2443--2452
Alexander Fischer and
Sonja Waldhausen and
Illia Horenko and
Eike Meerbach and
Christof Schütte Identification of biomolecular
conformations from incomplete torsion
angle observations by hidden Markov
models . . . . . . . . . . . . . . . . . 2453--2464
A. Slepoy and
M. D. Peters and
A. P. Thompson Searching for globally optimal
functional forms for interatomic
potentials using genetic programming
with parallel tempering . . . . . . . . 2465--2471
Wei Kan and
Hai-Tao Yu and
Hong-Gang Fu and
Yi-Qun Wu Theoretical investigation on the
protonation reactions and products of
the stable [N,C,C,S] isomers . . . . . . 2472--2482
D. Duca and
G. Barone and
S. Giuffrida and
Zs. Varga IDEA: Interface dynamics and energetics
algorithm . . . . . . . . . . . . . . . 2483--2499
Yan-Ling Liu and
Ji-Kang Feng and
Ai-Min Ren Structural, electronic, and optical
properties of phosphole-containing
$\pi$-conjugated oligomers for
light-emitting diodes . . . . . . . . . 2500--2509
Nicholas Y. Palermo and
József Csontos and
Michael C. Owen and
R. F. Murphy and
Sándor Lovas Erratum: Aromatic-backbone interactions
in model $\alpha$-helical peptides . . . 2510--2510
Takeshi Noro and
Masahiro Sekiya and
You Osanai and
Toshikatsu Koga and
Hisashi Matsuyama Relativistic correlating basis sets for
actinide atoms from $_{90}$Th to
$_{103}$Lr . . . . . . . . . . . . . . . 2511--2516
Ying Wang and
Jing-Yao Liu and
Ze-Sheng Li Ab initio direct dynamics studies on the
reactions of chlorine atom with CH$_{3 -
n}$F$_n$CH$_2$OH ($n = 1$--$3$) . . . . 2517--2530
Emanuel H. Rubensson and
Elias Rudberg and
Pawe\l Sa\lek A hierarchic sparse matrix data
structure for large-scale
Hartree--Fock/Kohn--Sham calculations 2531--2537
Parimal Kar and
Yanjie Wei and
Ulrich H. E. Hansmann and
Siegfried Höfinger Systematic study of the boundary
composition in Poisson Boltzmann
calculations . . . . . . . . . . . . . . 2538--2544
Xiaoqing Liu and
Zhilong Xiu and
Xiaohui Li Numerical characterization of the
conformation of cyclic peptides and its
application . . . . . . . . . . . . . . 2545--2551
Abhinav Verma and
Srinivasa M. Gopal and
Jung S. Oh and
Kyu H. Lee and
Wolfgang Wenzel All-atom de novo protein folding with a
scalable evolutionary algorithm . . . . 2552--2558
Ángel J. Pérez-Jiménez and
José M. Pérez-Jordá and
Ibério de P. R. Moreira and
Francesc Illas Merging multiconfigurational
wavefunctions and correlation
functionals to predict magnetic coupling
constants . . . . . . . . . . . . . . . 2559--2568
Pawe\l Sa\lek and
Andreas Hesselmann A self-contained and portable density
functional theory library for use in Ab
Initio quantum chemistry programs . . . 2569--2575
K. Hamacher Information theoretical measures to
analyze trajectories in rational
molecular design . . . . . . . . . . . . 2576--2580
Jon Baker and
Krzysztof Wolinski and
Peter Pulay Parallel DFT gradients using the Fourier
Transform Coulomb method . . . . . . . . 2581--2588
D. Heringer and
T. A. Niehaus and
M. Wanko and
Th. Frauenheim Analytical excited state forces for the
time-dependent density-functional
tight-binding method . . . . . . . . . . 2589--2601
M. Rafat and
P. L. A. Popelier Visualization and integration of quantum
topological atoms by spatial
discretization into finite elements . . 2602--2617
John E. Stone and
James C. Phillips and
Peter L. Freddolino and
David J. Hardy and
Leonardo G. Trabuco and
Klaus Schulten Accelerating molecular modeling
applications with graphics processors 2618--2640
Tanja Van Mourik Comment on ``Aromatic-Backbone
Interactions in Model $\alpha$-Helical
Peptides'' [Palermo et al., J. Comput
Chem 2007, 28, 1208] . . . . . . . . . . 1--3
József Csontos and
Nicholas Y. Palermo and
Richard F. Murphy and
Sándor Lovas Reply to ``Comment on Aromatic-Backbone
Interactions in Model $\alpha$-Helical
Peptides'' . . . . . . . . . . . . . . . 4--7
Michael T. Feldmann and
Julian C. Cummings and
David R. Kent IV and
Richard P. Muller and
William A. Goddard III Manager--worker-based model for the
parallelization of quantum Monte Carlo
on heterogeneous and homogeneous
networks . . . . . . . . . . . . . . . . 8--16
Kun Song and
Viktor Hornak and
Carlos De Los Santos and
Arthur P. Grollman and
Carlos Simmerling Molecular mechanics parameters for the
FapydG DNA lesion . . . . . . . . . . . 17--23
Lula Rosso and
Ian R. Gould Structure and dynamics of phospholipid
bilayers using recently developed
general all-atom force fields . . . . . 24--37
Katrin Spiegel and
Alessandra Magistrato and
Patrick Maurer and
Paolo Ruggerone and
Ursula Rothlisberger and
Paolo Carloni and
Jan Reedijk and
Michael L. Klein Parameterization of azole-bridged
dinuclear platinum anticancer drugs via
a QM/MM force matching procedure . . . . 38--49
R. J. Milgram and
Guanfeng Liu and
J. C. Latombe On the structure of the inverse
kinematics map of a fragment of protein
backbone . . . . . . . . . . . . . . . . 50--68
Francisco Rodríguez-Ropero and
Jordi Casanovas and
Carlos Alemán Ab initio calculations on $\pi$-stacked
thiophene dimer, trimer, and tetramer:
Structure, interaction energy,
cooperative effects, and intermolecular
electronic parameters . . . . . . . . . 69--78
Evgenii V. Kovalyov and
Vladimir I. Elokhin and
Aleksandr V. Myshlyavtsev Stochastic simulation of physicochemical
processes performance over supported
metal nanoparticles . . . . . . . . . . 79--86
Y. C. Zhou and
Michael Feig and
G. W. Wei Highly accurate biomolecular
electrostatics in continuum dielectric
environments . . . . . . . . . . . . . . 87--97
N. R. Jena and
P. S. Kushwaha and
P. C. Mishra Reaction of hypochlorous acid with
imidazole: Formation of 2-chloro- and
2-oxoimidazoles . . . . . . . . . . . . 98--107
Ewgenij Proschak and
Matthias Rupp and
Swetlana Derksen and
Gisbert Schneider Shapelets: Possibilities and limitations
of shape-based virtual screening . . . . 108--114
Chinapong Kritayakornupong The Jahn--Teller effect of the Cr$^{2+}$
ion in aqueous solution: ab initio QM/MM
molecular dynamics simulations . . . . . 115--121
Matej Praprotnik and
Stanko Ho\vcevar and
Milan Hodo\vs\vcek and
Matej Penca and
Du\vsanka Jane\vzi\vc New all-atom force field for molecular
dynamics simulation of an AlPO$_4$-34
molecular sieve . . . . . . . . . . . . 122--129
A. V. Larin and
D. N. Trubnikov and
D. P. Vercauteren Electric field convergence versus atomic
basis sets in all-siliceous zeolites . . 130--138
Ignacio Fdez. Galván and
Martin J. Field Improving the efficiency of the NEB
reaction path finding algorithm . . . . 139--143
Josep M. Porta and
Lluís Ros and
Federico Thomas and
Francesc Corcho and
Josep Cantó and
Juan Jesús Pérez Complete maps of molecular-loop
conformational spaces . . . . . . . . . 144--155
Markus Christen and
Wilfred F. van Gunsteren On searching in, sampling of, and
dynamically moving through
conformational space of biomolecular
systems: a review . . . . . . . . . . . 157--166
Florian Weigend Hartree--Fock exchange fitting basis
sets for H to Rn . . . . . . . . . . . . 167--175
Weihua Zhu and
Heming Xiao Ab initio study of electronic structure
and optical properties of heavy-metal
azides: TlN$_3$, AgN$_3$, and CuN$_3$ 176--184
Nathan E. Schultz and
Yan Zhao and
Donald G. Truhlar Benchmarking approximate density
functional theory for $s/d$ excitation
energies in $3d$ transition metal
cations . . . . . . . . . . . . . . . . 185--189
Mark Pinsky and
David Casanova and
Pere Alemany and
Santiago Alvarez and
David Avnir and
Chaim Dryzun and
Ziv Kizner and
Alexander Sterkin Symmetry operation measures . . . . . . 190--197
Jian-Yi Ma and
Jing-Bo Wang and
Xiang-Yuan Li and
Yao Huang and
Quan Zhu and
Ke-Xiang Fu A study on orientation and absorption
spectrum of interfacial molecules by
using continuum model . . . . . . . . . 198--210
Qi-Shi Du and
Ri-Bo Huang and
Yu-Tuo Wei and
Li-Qin Du and
Kuo-Chen Chou Multiple field three dimensional
quantitative structure--activity
relationship (MF-3D-QSAR) . . . . . . . 211--219
D. N. Tarasov and
R. P. Tiger Numerical computations of molecular
reactions in associated systems caused
by the formation of fractal structures 220--224
Yasuji Inada and
Hideo Orita Efficiency of numerical basis sets for
predicting the binding energies of
hydrogen bonded complexes: Evidence of
small basis set superposition error
compared to Gaussian basis sets . . . . 225--232
Milan On\vcák and
Martin Srnec Electronic structure and physical
properties of M$_i$ X$_i$ clusters (M =
B, Al; X = N, P; i = 1, 2, 3): ab initio
study . . . . . . . . . . . . . . . . . 233--246
Jing Yang and
Qian Shu Li and
Shaowen Zhang Direct dynamics study on the reaction of
acetaldehyde with ozone . . . . . . . . 247--255
Kun Liu and
Wensheng Bian Extensive theoretical study on the
low-lying electronic states of silicon
monofluoride cation including spin-orbit
coupling . . . . . . . . . . . . . . . . 256--265
Bahram Hemmateenejad and
Afshan Mohajeri Application of quantum topological
molecular similarity descriptors in QSPR
study of the O-methylation of
substituted phenols . . . . . . . . . . 266--274
Yun Ding and
Ye Mei and
John Z. H. Zhang and
Fu-Ming Tao Efficient bond function basis set for
$\pi$-$\pi$ interaction energies . . . . 275--279
Miguel A. Zamora and
Fernando D. Suvire and
Ricardo D. Enriz Ring inversion in 1,4,7 cyclononatriene
and analogues: ab initio and DFT
calculations and topological analysis 280--290
Y. Wei and
T. Singer and
H. Mayr and
G. N. Sastry and
H. Zipse Assessment of theoretical methods for
the calculation of methyl cation
affinities . . . . . . . . . . . . . . . 291--297
Sean A. C. McDowell A comparative study of some red- and
blue-shifted linear H-bonded complexes
of N$_2$ . . . . . . . . . . . . . . . . 298--305
Mohamed Zerara pyVib, a computer program for the
analysis of infrared and Raman optical
activity . . . . . . . . . . . . . . . . 306--311
Willem-Jan Van Zeist and
Célia Fonseca Guerra and
F. Matthias Bickelhaupt PyFrag --- streamlining your reaction
path analysis . . . . . . . . . . . . . 312--315
Yoanna María Alvarez-Ginarte and
Yovani Marrero-Ponce and
José Alberto Ruiz-García and
Luis Alberto Montero-Cabrera and
Jose Manuel García De La Vega and
Pedro Noheda Marin and
Rachel Crespo-Otero and
Francisco Torrens Zaragoza and
Ramón García-Domenech Applying pattern recognition methods
plus quantum and physico-chemical
molecular descriptors to analyze the
anabolic activity of structurally
diverse steroids . . . . . . . . . . . . 317--333
Koji Yasuda Two-electron integral evaluation on the
graphics processor unit . . . . . . . . 334--342
Arvids Stashans and
Gaston Chamba and
Henry Pinto Electronic structure, chemical bonding,
and geometry of pure and Sr-doped
CaCO$_3$ . . . . . . . . . . . . . . . . 343--349
Ruibo Wu and
Zexing Cao QM/MM study of catalytic methyl transfer
by the N$^5$-glutamine SAM-dependent
methyltransferase and its inhibition by
the nitrogen analogue of coenzyme . . . 350--357
Stijn Fias and
Sofie Van Damme and
Patrick Bultinck Multidimensionality of delocalization
indices and nucleus independent chemical
shifts in polycyclic aromatic
hydrocarbons . . . . . . . . . . . . . . 358--366
Norberto Castillo and
Katherine N. Robertson and
S. C. Choi and
Russell J. Boyd and
Osvald Knop Bond length and the electron density at
the bond critical point: X\bondX,
Z\bondZ, and C\bondZ bonds (X = Li--F, Z
= Na--Cl) . . . . . . . . . . . . . . . 367--379
P. W. Bates and
G. W. Wei and
Shan Zhao Minimal molecular surfaces and their
applications . . . . . . . . . . . . . . 380--391
Daniel Norberg and
Nessima Salhi-Benachenhou McLafferty rearrangement of the radical
cations of butanal and 3-fluorobutanal:
a theoretical investigation of the
concerted and stepwise mechanisms . . . 392--406
Sebastian Schlund and
Robert Müller and
Carsten Graßmann and
Bernd Engels Conformational analysis of arginine in
gas phase --- a strategy for scanning
the potential energy surface effectively 407--415
Gilles Frison and
Gilles Ohanessian A comparative study of semiempirical, ab
initio, and DFT methods in evaluating
metal--ligand bond strength, proton
affinity, and interactions between first
and second shell ligands in
Zn-biomimetic complexes . . . . . . . . 416--433
Bin Gao and
Jun Jiang and
Kai Liu and
Ziyu Wu and
Wei Lu and
Yi Luo An efficient first-principle approach
for electronic structures calculations
of nanomaterials . . . . . . . . . . . . 434--444
Richard J. Wheatley Time-dependent coupled-cluster
calculations of polarizabilities and
dispersion energy coefficients . . . . . 445--450
M. Piacenza and
F. Della Sala and
E. Fabiano and
T. Maiolo and
G. Gigli Torsional effects on excitation energies
of thiophene derivatives induced by
$\beta$-substituents: Comparison between
time-dependent density functional theory
and approximated coupled cluster
approaches . . . . . . . . . . . . . . . 451--457
Toshiaki Matsubara and
Michel Dupuis and
Misako Aida An insight into the environmental
effects of the pocket of the active site
of the enzyme. Ab initio ONIOM-molecular
dynamics (MD) study on cytosine
deaminase . . . . . . . . . . . . . . . 458--465
Chao Deng and
Qiang-Gen Li and
Yi Ren and
Ning-Bew Wong and
San-Yan Chu and
Hua-Jie Zhu A comprehensive theoretical study on the
hydrolysis of carbonyl sulfide in the
neutral water . . . . . . . . . . . . . 466--480
Bryan M. Wong and
Maria M. Fadri and
Sumathy Raman Thermodynamic calculations for molecules
with asymmetric internal rotors. II.
Application to the 1,2-dihaloethanes . . 481--487
V. Ganesh and
Ritwik Kavathekar and
Anuja Rahalkar and
Shridhar R. Gadre WebProp: Web interface for ab initio
calculation of molecular one-electron
properties . . . . . . . . . . . . . . . 488--495
John Cullen An approximate diatomics in molecules
formulation of generalized valence bond
theory . . . . . . . . . . . . . . . . . 497--504
Xiao-Wei Fan and
Xue-Hai Ju Theoretical studies on four-membered
ring compounds with NF$_2$, ONO$_2$,
N$_3$, and NO$_2$ groups . . . . . . . . 505--513
Jiali Gao and
Kin-Yiu Wong and
Dan T. Major Combined QM/MM and path integral
simulations of kinetic isotope effects
in the proton transfer reaction between
nitroethane and acetate ion in water . . 514--522
J. Pitarch-Ruiz and
J. Sánchez-Marín and
A. M. Velasco Full configuration interaction
calculation of the low lying valence and
Rydberg states of BeH . . . . . . . . . 523--532
Maykel Cruz-Monteagudo and
M. Natália D. S. Cordeiro and
Fernanda Borges Computational chemistry approach for the
early detection of drug-induced
idiosyncratic liver toxicity . . . . . . 533--549
Lei Yang and
Jing-Yao Liu and
Li Wang and
Hong-Qing He and
Ying Wang and
Ze-Sheng Li Theoretical study of the reactions
CF$_3$CH$_2$OCHF$_2$ + OH/Cl and its
product radicals and parent ether
(CH$_3$CH$_2$OCH$_3$) with OH . . . . . 550--561
Joseph P. Kenny and
Curtis L. Janssen and
Edward F. Valeev and
Theresa L. Windus Components for integral evaluation in
quantum chemistry . . . . . . . . . . . 562--577
Flavio Forti and
Xavier Barril and
F. Javier Luque and
Modesto Orozco Extension of the MST continuum solvation
model to the RM1 semiempirical
Hamiltonian . . . . . . . . . . . . . . 578--587
M. L. Contreras and
J. Alvarez and
D. Guajardo and
R. Rozas Understanding topological symmetry: a
heuristic approach to its determination 588--600
Aibing Liu and
Steven J. Stuart Empirical bond-order potential for
hydrocarbons: Adaptive treatment of van
der Waals interactions . . . . . . . . . 601--611
Yasushi Honda and
Atsushi Kurihara and
Masahiko Hada and
Hiroshi Nakatsuji Excitation and circular dichroism
spectra of (-)-(3a S, 7a
S)-2-chalcogena-trans-hydrindans (Ch =
S, Se, Te): SAC and SAC--CI calculations 612--621
Karl N. Kirschner and
Austin B. Yongye and
Sarah M. Tschampel and
Jorge González-Outeiriño and
Charlisa R. Daniels and
B. Lachele Foley and
Robert J. Woods GLYCAM06: a generalizable biomolecular
force field. Carbohydrates . . . . . . . 622--655
Humberto González-Díaz and
Francisco J. Prado-Prado Unified QSAR and network-based
computational chemistry approach to
antimicrobials, part 1: Multispecies
activity models for antifungals . . . . 656--667
Wei Yang and
Hugh Nymeyer and
Huan-Xiang Zhou and
Bernd Berg and
Rafael Brüschweiler Quantitative computer simulations of
biomolecules: a snapshot . . . . . . . . 668--672
Kitiyaporn Wittayanarakul and
Supot Hannongbua and
Michael Feig Accurate prediction of protonation state
as a prerequisite for reliable
MM-PB(GB)SA binding free energy
calculations of HIV-1 protease
inhibitors . . . . . . . . . . . . . . . 673--685
Cai-Yun Geng and
Ji-Lai Li and
Xu-Ri Huang and
Hui-Ling Liu and
Zhuo Li and
Chia-Chung Sun Theoretical elucidation of the
rhodium-catalyzed [4 + 2] annulation
reactions . . . . . . . . . . . . . . . 686--693
Alex Robertson and
Edgar Luttmann and
Vijay S. Pande Effects of long-range electrostatic
forces on simulated protein folding
kinetics . . . . . . . . . . . . . . . . 694--700
Urs Haberthür and
Amedeo Caflisch FACTS: Fast analytical continuum
treatment of solvation . . . . . . . . . 701--715
R. C. Binning Jr. and
Daniel E. Bacelo High-spin versus broken symmetry ---
effect of DFT spin density
representation on the geometries of
three diiron (III) model compounds . . . 716--723
Marcel Swart and
F. Matthias Bickelhaupt QUILD: QUantum-regions interconnected by
local descriptions . . . . . . . . . . . 724--734
Yutaka Imamura and
Hiroyoshi Kiryu and
Hiromi Nakai Colle--Salvetti-type correction for
electron--nucleus correlation in the
nuclear orbital plus molecular orbital
theory . . . . . . . . . . . . . . . . . 735--740
Robert M. Whitnell and
Dow P. Hurst and
Patricia H. Reggio and
Frank Guarnieri Conformational memories with variable
bond angles . . . . . . . . . . . . . . 741--752
Mikael P. Johansson and
Ville R. I. Kaila and
Liisa Laakkonen Charge parameterization of the metal
centers in cytochrome $c$ oxidase . . . 753--767
Svetlana Stepanenko and
Bernd Engels New tabu search based global
optimization methods outline of
algorithms and study of efficiency . . . 768--780
Zhen Zhou and
Jijun Zhao and
Paul von Ragué Schleyer and
Zhongfang Chen Insertion of C$_{50}$ into single-walled
carbon nanotubes: Selectivity in
interwall spacing and C$_{50}$ isomers 781--787
Emilio Gallicchio and
Ronald M. Levy and
Manish Parashar Asynchronous replica exchange for
molecular simulations . . . . . . . . . 788--794
Matteo Masetti and
Andrea Cavalli and
Maurizio Recanatini Modeling the hERG potassium channel in a
phospholipid bilayer: Molecular dynamics
and drug docking studies . . . . . . . . 795--808
Yue-meng Ji and
Xiao-lei Zhao and
Jing-yao Liu and
Ying Wang and
Ze-sheng Li Theoretical dynamic studies on the
reactions of CH$_3$C(O)CH$_{3 -
n}$Cl$_n$ ($n = 0$--$3$) with the
chlorine atom . . . . . . . . . . . . . 809--819
Mark A. Olson and
Michael Feig and
Charles L. Brooks III Prediction of protein loop conformations
using multiscale modeling methods with
physical energy scoring functions . . . 820--831
Mahmoud Mirzaei and
Nasser L. Hadipour A computational NQR study on the
hydrogen-bonded lattice of
cytosine-5-acetic acid . . . . . . . . . 832--838
Noel M. O'Boyle and
Adam L. Tenderholt and
Karol M. Langner \tt cclib: a library for
package-independent computational
chemistry algorithms . . . . . . . . . . 839--845
Rainer Grohmann and
Torsten Schindler Toward robust QSPR models: Synergistic
utilization of robust regression and
variable elimination . . . . . . . . . . 847--860
Haydée Valdés and
Vojt\uech Klusák and
Michal Pito\unák and
Otto Exner and
Ivo Starý and
Pavel Hobza and
Lubomír Rulí\vsek Evaluation of the intramolecular basis
set superposition error in the
calculations of larger molecules:
$[n]$helicenes and Phe-Gly-Phe
tripeptide . . . . . . . . . . . . . . . 861--870
Tatsuhiko Miyata and
Fumio Hirata Combination of molecular dynamics method
and 3D-RISM theory for conformational
sampling of large flexible molecules in
solution . . . . . . . . . . . . . . . . 871--882
Huancong Shi and
David C. Roettger and
Allan L. L. East Photochemistry studied with ab initio
orbital-correlation and
state-correlation plots: Classic
cyclobutene ring opening, and the
reaction of N$_2$ with photoexcited
O$_2$ . . . . . . . . . . . . . . . . . 883--891
Fabienne Bessac and
Feliu Maseras DFT modeling of reactivity in an ionic
liquid: How many ion pairs? . . . . . . 892--899
Kalju Kahn and
Iiris Kahn Improved efficiency of focal point
conformational analysis with truncated
correlation consistent basis sets . . . 900--911
Sandro Chiodo and
Nino Russo Determination of spin-orbit coupling
contributions in the framework of
density functional theory . . . . . . . 912--920
Denis Jacquemin and
Eric A. Perpéte and
Ilaria Ciofini and
Carlo Adamo Revisiting the relationship between the
bond length alternation and the first
hyperpolarizability with range-separated
hybrid functionals . . . . . . . . . . . 921--925
C. H. Mak RNA conformational sampling. I.
Single-nucleotide loop closure . . . . . 926--933
Stefan Duret and
Ahmed Bouferguene and
Hassan Safouhi Strategies for an efficient
implementation of the Gauss--Bessel
quadrature for the evaluation of
multicenter integral over STFs . . . . . 934--944
Lívia B. Pártay and
György Hantal and
Pál Jedlovszky and
Árpád Vincze and
George Horvai A new method for determining the
interfacial molecules and characterizing
the surface roughness in computer
simulations. Application to the
liquid--vapor interface of water . . . . 945--956
Fabrizio Santoro and
Vincenzo Barone and
Roberto Improta Can TD-DFT calculations accurately
describe the excited states behavior of
stacked nucleobases? The cytosine dimer
as a test case . . . . . . . . . . . . . 957--964
Deepak Bandyopadhyay and
Dimitris K. Agrafiotis A self-organizing algorithm for
molecular alignment and pharmacophore
development . . . . . . . . . . . . . . 965--982
Alicia M. Davis and
Gary Joanis and
Lorena Tribe Molecular modeling of polymer--clay
nanocomposite precursors: Lysine in
montmorillonite interlayers . . . . . . 983--987
Grzegorz Mazur An improved SCPF scheme for polarization
energy calculations . . . . . . . . . . 988--993
Núria Queralt and
David Taratiel and
Coen de Graaf and
Rosa Caballol and
Renzo Cimiraglia and
Celestino Angeli On the applicability of multireference
second-order perturbation theory to
study weak magnetic coupling in
molecular complexes . . . . . . . . . . 994--1003
Sabine Schweizer and
Jörg Kussmann and
Bernd Doser and
Christian Ochsenfeld Linear-scaling Cholesky decomposition 1004--1010
Christoph R. Jacob and
Johannes Neugebauer and
Lucas Visscher A flexible implementation of
frozen-density embedding for use in
multilevel simulations . . . . . . . . . 1011--1018
Ross C. Walker and
Michael F. Crowley and
David A. Case The implementation of a fast and
accurate QM/MM potential method in AMBER 1019--1031
Sunil Patil and
R. C. Aiyer and
K. C. Sharma Globally convergent computation of
chemical equilibrium composition . . . . 1032--1036
Mette Alstrup Lie and
Birgit Schiòtt A DFT study of solvation effects on the
tautomeric equilibrium and catalytic
ylide generation of thiamin models . . . 1037--1047
Sven Lammers and
Stephan Lutz and
Markus Meuwly Reactive force fields for proton
transfer dynamics . . . . . . . . . . . 1048--1063
Miquel Torrent-Sucarrat and
Pedro Salvador and
Miquel Sol\`a and
Paul Geerlings The hardness kernel as the basis for
global and local reactivity indices . . 1064--1072
Woo Youn Kim and
Kwang S. Kim Carbon nanotube, graphene, nanowire, and
molecule-based electron and spin
transport phenomena using the
nonequilibrium Green's function method
at the level of first principles theory 1073--1083
Asbjòrn Holt and
Gunnar Karlström An intramolecular induction correction
model of the molecular dipole moment . . 1084--1091
Marcel Schmidt Am Busch and
Anne Lopes and
David Mignon and
Thomas Simonson Computational protein design: Software
implementation, parameter optimization,
and performance of a simple model . . . 1092--1102
Udo Schnupf and
Julious L. Willett and
Wayne B. Bosma and
Frank A. Momany DFT conformational studies of
$\alpha$-maltotriose . . . . . . . . . . 1103--1112
Ninad V. Prabhu and
Manoranjan Panda and
Qingyi Yang and
Kim A. Sharp Explicit ion, implicit water solvation
for molecular dynamics of nucleic acids
and highly charged molecules . . . . . . 1113--1130
Anthony D. Hill and
Peter J. Reilly A Gibbs free energy correlation for
automated docking of carbohydrates . . . 1131--1141
Yang Zhong and
G. Lee Warren and
Sandeep Patel Thermodynamic and structural properties
of methanol--water solutions using
nonadditive interaction models . . . . . 1142--1152
Christina L. Vizcarra and
Naigong Zhang and
Shannon A. Marshall and
Ned S. Wingreen and
Chen Zeng and
Stephen L. Mayo An improved pairwise decomposable
finite-difference Poisson--Boltzmann
method for computational protein design 1153--1162
Elad Project and
Esther Nachliel and
Menachem Gutman Parameterization of Ca$^{+2}$--protein
interactions for molecular dynamics
simulations . . . . . . . . . . . . . . 1163--1169
Hui Zhang and
Gui-Ling Zhang and
Jing-Yao Liu and
Bo Liu and
Xiao-Yang Yu and
Ze-Sheng Li Theoretical study on the OH +
CH$_3$NHC(O)OCH$_3$ reaction . . . . . . 1170--1176
Oliver J. Clarke and
Martin J. Parker Time-averaged predictions of folded and
misfolded peptides using a reduced
physicochemical model . . . . . . . . . 1177--1185
Seiken Tokura and
Takeshi Sato and
Takao Tsuneda and
Takahito Nakajima and
Kimihiko Hirao A dual-level state-specific
time-dependent density-functional theory 1187--1197
Viktor Bezugly and
Pawel Wielgus and
Frank R. Wagner and
Miroslav Kohout and
Yuri Grin Electron localizability indicators ELI
and ELIA: the case of highly correlated
wavefunctions for the argon atom . . . . 1198--1207
Seung Kyu Min and
Eun Cheol Lee and
Han Myoung Lee and
Dong Young Kim and
Dongwook Kim and
Kwang S. Kim Complete basis set limit of ab initio
binding energies and geometrical
parameters for various typical types of
complexes . . . . . . . . . . . . . . . 1208--1221
Yong Wu and
Lu Jin and
Ying Xue and
Dai Qian Xie and
Chan Kyung Kim and
Yong Guo and
Guo Sen Yan Theoretical study on the hydrolysis
mechanism of N, N-dimethyl--N'-(2-oxo-1,
2-dihydro-pyrimidinyl)formamidine:
Water-assisted mechanism and
cluster-continuum model . . . . . . . . 1222--1232
Francisco Rodríguez-Ropero and
David Zanuy and
Carlos Alemán Molecular dynamics of a
calix[4]arene-containing polymer in
dichloromethane solution: Ability of the
solvent molecules to fill the cavity of
the macrocycle . . . . . . . . . . . . . 1233--1241
Alexander G. Donchev and
Nikolay G. Galkin and
Alexey A. Illarionov and
Oleg V. Khoruzhii and
Michael A. Olevanov and
Vladimir D. Ozrin and
Leonid B. Pereyaslavets and
Vladimir I. Tarasov Assessment of performance of the general
purpose polarizable force field QMPFF3
in condensed phase . . . . . . . . . . . 1242--1249
Yong Wu and
Ying Xue and
Chan Kyung Kim Computational studies on the dimers and
the thermal dimerization of
norbornadiene . . . . . . . . . . . . . 1250--1258
Ying Xiong and
Hai-Ting Lu and
Chang-Guo Zhan Dynamic structures of
phosphodiesterase-5 active site by
combined molecular dynamics simulations
and hybrid quantum mechanical/molecular
mechanical calculations . . . . . . . . 1259--1267
Chen Levi and
Jan M. L. Martin and
Ilana Bar Fundamental vibrational frequencies and
dominant resonances in methylamine
isotopologues by ab initio and density
functional theory methods . . . . . . . 1268--1276
Maciej Haranczyk and
John Holliday and
Peter Willett and
Maciej Gutowski Structure and singly occupied molecular
orbital analysis of anionic tautomers of
guanine . . . . . . . . . . . . . . . . 1277--1291
Qi Dai and
Tian-Ming Wang Use of statistical measures for
analyzing RNA secondary structures . . . 1292--1305
Wai-Leung Yim and
Thorsten Klüner Atoms-in-molecules analysis for
planewave DFT calculations --- a
numerical approach on a successively
interpolated charge density grid . . . . 1306--1315
Ryangguk Kim and
Jeffrey Skolnick Assessment of programs for ligand
binding affinity prediction . . . . . . 1316--1331
Olexander Yakovenko and
Alexander A. Oliferenko and
Volodymyr G. Bdzhola and
Vladimir A. Palyulin and
Nikolai S. Zefirov Kirchhoff atomic charges fitted to
multipole moments: Implementation for a
virtual screening system . . . . . . . . 1332--1343
József Csontos and
Nicholas Y. Palermo and
Richard F. Murphy and
Sándor Lovas Calculation of weakly polar interaction
energies in polypeptides using density
functional and local Mòller--Plesset
perturbation theory . . . . . . . . . . 1344--1352
Sophie Barbe and
Marc Le Bret Ab initio determination of the
flexibility of 2'-aminoribonucleosides
and 2'-aminoarabinonucleosides inserted
in duplexes . . . . . . . . . . . . . . 1353--1363
Yi-yuan Chiu and
Jenn-kang Hwang and
Jinn-moon Yang Soft energy function and generic
evolutionary method for discriminating
native from nonnative protein
conformations . . . . . . . . . . . . . 1364--1373
Vill\Ho K. Pálfi and
András Perczel How stable is a collagen triple helix?
An ab initio study on various collagen
and $\beta$-sheet forming sequences . . 1374--1386
Robert Ponec and
György Lendvay and
Joaquin Chaves Structure and bonding in binuclear metal
carbonyls from the analysis of domain
averaged Fermi holes. I. Fe$_2$ (CO)$_9$
and Co$_2$ (CO)$_8$ . . . . . . . . . . 1387--1398
Hajime Hirao A reactive bond orbital investigation of
the Diels--Alder reaction between
1,3-butadiene and ethylene: Energy
decomposition, state correlation
diagram, and electron density analyses 1399--1407
Pablo Echenique and
José Luis Alonso Efficient model chemistries for
peptides. I. General framework and a
study of the heterolevel approximation
in RHF and MP2 with Pople split-valence
basis sets . . . . . . . . . . . . . . . 1408--1422
Xueye Wang and
Hengliang Wang and
Yuanqiang Tan DFT study of the cryptand and
benzocryptand and their complexes with
alkali metal cations: Li$^+$, Na$^+$,
K$^+$ . . . . . . . . . . . . . . . . . 1423--1428
Karine Voltz and
Joanna Trylska and
Valentina Tozzini and
Vandana Kurkal-Siebert and
Jörg Langowski and
Jeremy Smith Coarse-grained force field for the
nucleosome from self-consistent
multiscaling . . . . . . . . . . . . . . 1429--1439
Julien Pilmé and
Jean-Philip Piquemal Advancing beyond charge analysis using
the electronic localization function:
Chemically intuitive distribution of
electrostatic moments . . . . . . . . . 1440--1449
Mauro Ferrero and
Michel Rérat and
Roberto Orlando and
Roberto Dovesi The calculation of static
polarizabilities of $1$--$3$D periodic
compounds. The implementation in the
CRYSTAL code . . . . . . . . . . . . . . 1450--1459
Piotr Rotkiewicz and
Jeffrey Skolnick Fast procedure for reconstruction of
full-atom protein models from reduced
representations . . . . . . . . . . . . 1460--1465
József Csontos and
Péter Kálmán and
Gyula Tasi and
Miklós Kálmán and
Richard F. Murphy and
Sándor Lovas The effect of electron correlation on
the conformational space of melatonin 1466--1471
Laurence Leherte and
Daniel P. Vercauteren Collective motions of rigid fragments in
protein structures from smoothed
electron density distributions . . . . . 1472--1489
Asit K. Chandra and
Salma Parveen and
Subojit Das and
Thér\`ese Zeegers-Huyskens Blue shifts of the C H stretching
vibrations in hydrogen-bonded and
protonated trimethylamine. Effect of
hyperconjugation on bond properties . . 1490--1496
Matthew A. Addicoat and
Mark A. Buntine and
Brian Yates and
Gregory F. Metha Associative versus dissociative binding
of CO to $4 d$ transition metal trimers:
a density functional study . . . . . . . 1497--1506
Riccardo Chelli and
Victor V. Volkov and
Roberto Righini Retrieval of spectral and dynamic
properties from two-dimensional infrared
pump-probe experiments . . . . . . . . . 1507--1516
Qi Liu and
V. Olman and
Huiqing Liu and
Xiuzi Ye and
Shilun Qiu and
Ying Xu RNACluster: an integrated tool for RNA
secondary structure comparison and
clustering . . . . . . . . . . . . . . . 1517--1526
Ivelin Georgiev and
Ryan H. Lilien and
Bruce R. Donald The minimized dead-end elimination
criterion and its application to protein
redesign in a hybrid scoring and search
algorithm for computing partition
functions over molecular ensembles . . . 1527--1542
Ferran Feixas and
Eduard Matito and
Jordi Poater and
Miquel Sol\`a On the performance of some aromaticity
indices: a critical assessment using a
test set . . . . . . . . . . . . . . . . 1543--1554
Yutaka Imamura and
Hiromi Nakai Energy density analysis for second-order
Mòller--Plesset perturbation theory and
coupled-cluster theory with singles and
doubles: Application to C$_2$H$_4$CH$_4$
complexes . . . . . . . . . . . . . . . 1555--1563
Juan Torras and
Gustavo de M. Seabra and
Erik Deumens and
S. B. Trickey and
Adrian E. Roitberg A versatile AMBER--Gaussian QM/MM
interface through PUPIL . . . . . . . . 1564--1573
Michal Brylinski and
Jeffrey Skolnick Q-Dock: Low-resolution flexible ligand
docking with pocket-specific threading
restraints . . . . . . . . . . . . . . . 1574--1588
L. A. Zotti and
G. Teobaldi and
K. Palotás and
W. Ji and
H.-J. Gao and
W. A. Hofer Adsorption of benzene, fluorobenzene and
meta-di-fluorobenzene on Cu(110): a
computational study . . . . . . . . . . 1589--1595
Ke Chen and
Lukasz A. Kurgan and
Jishou Ruan Prediction of protein structural class
using novel evolutionary
collocation-based sequence
representation . . . . . . . . . . . . . 1596--1604
Vladimir Hnizdo and
Jun Tan and
Benjamin J. Killian and
Michael K. Gilson Efficient calculation of configurational
entropy from molecular simulations by
combining the mutual-information
expansion and nearest-neighbor methods 1605--1614
Pawe\l Szabelski Spontaneous segregation on a hybrid
chiral surface . . . . . . . . . . . . . 1615--1625
Jong Chan Kim and
Kyoung Hoon Kim and
Jaehoon Jung and
Young-Kyu Han Reaction mechanisms of dissociative
chemisorption of HI, I$_2$, and CH$_3$I
on a magic cluster Al . . . . . . . . . 1626--1631
Yu-hua Yao and
Qi Dai and
Xu-Ying Nan and
Ping-An He and
Zuo-Ming Nie and
Song-Ping Zhou and
Yao-Zhou Zhang Analysis of similarity/dissimilarity of
DNA sequences based on a class of $2$D
graphical representation . . . . . . . . 1632--1639
Thenmalarchelvi Rathinavelan and
Wonpil Im A novel strategy to determine protein
structures using exclusively residual
dipolar coupling . . . . . . . . . . . . 1640--1649
Qingxu Li and
Yuanping Yi and
Zhigang Shuai Local approach to coupled cluster
evaluation of polarizabilities for long
conjugated molecules . . . . . . . . . . 1650--1655
F. Iori and
S. Corni Including image charge effects in the
molecular dynamics simulations of
molecules on metal surfaces . . . . . . 1656--1666
Xiao-Jing Liu and
Chuan-Lu Yang and
Xiang Zhang and
Ke-Li Han and
Zi-Chao Tang Theoretical study on the structure and
formation mechanism of
[C$_6$H$_5$M$_m$]$^-$ (M = Ag, Au; $m =
1$--$3$) . . . . . . . . . . . . . . . . 1667--1674
Liang-Tsung Huang and
M. Michael Gromiha Analysis and prediction of protein
folding rates using quadratic response
surface models . . . . . . . . . . . . . 1675--1683
David de Sancho and
Antonio Rey Energy minimizations with a combination
of two knowledge-based potentials for
protein folding . . . . . . . . . . . . 1684--1692
Paul Labute The generalized Born/volume integral
implicit solvent model: Estimation of
the free energy of hydration using
London dispersion instead of atomic
surface area . . . . . . . . . . . . . . 1693--1698
Nitin S. Sapre and
Nilanjana Pancholi and
Swagata Gupta and
Neelima Sapre Computational modeling of
tetrahydroimidazo-[4,5,1-jk][1,4]-benzodiazepinone derivatives: an atomistic drug design approach using Kier-Hall electrotopological state (E-state) indices 1699--1706
Michel Masella and
Daniel Borgis and
Philippe Cuniasse Combining a polarizable force-field and
a coarse-grained polarizable solvent
model: Application to long dynamics
simulations of bovine pancreatic trypsin
inhibitor . . . . . . . . . . . . . . . 1707--1724
Laban Bondesson and
Elias Rudberg and
Yi Luo and
Pawe\l Sa\lek Basis set dependence of solute--solvent
interaction energy of benzene in water:
a HF/DFT study . . . . . . . . . . . . . 1725--1732
Alexander G. Donchev Nonadditive effects in ternary H$_2$
--cation--PAH systems . . . . . . . . . 1733--1739
Luca Monticelli and
Eric J. Sorin and
D. Peter Tieleman and
Vijay S. Pande and
Giorgio Colombo Molecular simulation of multistate
peptide dynamics: a comparison between
microsecond timescale sampling and
multiple shorter trajectories . . . . . 1740--1752
Max W. Chang and
Richard K. Belew and
Kate S. Carroll and
Arthur J. Olson and
David S. Goodsell Empirical entropic contributions in
computational docking: Evaluation in APS
reductase complexes . . . . . . . . . . 1753--1761
Naigong Zhang and
Chen Zeng Reference energy extremal optimization:
a stochastic search algorithm applied to
computational protein design . . . . . . 1762--1771
Xueguang Shao and
Xiaoli Yang and
Wensheng Cai A dynamic lattice searching method with
interior operation for unbiased
optimization of large Lennard-Jones
clusters . . . . . . . . . . . . . . . . 1772--1779
Tian Zhang and
Haoping Zheng and
Shu Yan The equivalent potential of water for
electronic structure of aspartic acid 1780--1787
Siamkhanthang Neihsial and
Richard H. Duncan Lyngdoh Novel H-bonded base dimers as repeat
units for information-bearing
self-associative duplexes: a
B3LYP/6-31G* search . . . . . . . . . . 1788--1797
Ying Zhang and
Xin Xu and
Yijing Yan Systematic investigation on the
geometric dependence of the calculated
nuclear magnetic shielding constants . . 1798--1807
K. Periya Vijayalakshmi and
Cherumuttathu H. Suresh Theoretical studies on the
carcinogenicity of polycyclic aromatic
hydrocarbons . . . . . . . . . . . . . . 1808--1817
Chan Kyung Kim and
Soo Gyeong Cho and
Chang Kon Kim and
Hyung-Yeon Park and
Hui Zhang and
Hai Whang Lee Prediction of densities for solid
energetic molecules with molecular
surface electrostatic potentials . . . . 1818--1824
M. Y. Wang and
L. Cheng and
Z. J. Wu Density functional study on the reaction
mechanism of palladium-catalyzed
addition of cyanoboranes to alkynes . . 1825--1839
Cherumuttathu H. Suresh and
Aswathy Mary Vargheese and
K. Periya Vijayalakshmi and
Neetha Mohan and
Nobuaki Koga Role of structural water molecule in HIV
protease-inhibitor complexes: a QM/MM
study . . . . . . . . . . . . . . . . . 1840--1849
Ning He and
Hong-Bin Xie and
Yi-Hong Ding Structures and stability of lithium
monosilicide clusters SiLi$_n$ ($n =
4$--$16$): What is the maximum number,
magic number, and core number for
lithium coordination to silicon? . . . . 1850--1858
Sunhwan Jo and
Taehoon Kim and
Vidyashankara G. Iyer and
Wonpil Im CHARMM-GUI: a Web-based graphical user
interface for CHARMM . . . . . . . . . . 1859--1865
Xiuzhen Hu and
Qianzhong Li Using support vector machine to predict
$\beta$- and $\gamma$-turns in proteins 1867--1875
Witold Dyrka and
Andy T. Augousti and
Ma\lgorzata Kotulska Ion flux through membrane channels ---
an enhanced algorithm for the
Poisson--Nernst--Planck model . . . . . 1876--1888
Fahrettin Gogtas Time-dependent quantum study of the
kinetics of the H($^2$S) + FO($^2\Pi$)
$\rightarrow$ OH($^2\Pi$) + F($^2$P)
reaction . . . . . . . . . . . . . . . . 1889--1894
Timothy J. Giese and
Darrin M. York Extension of adaptive tree code and fast
multipole methods to high angular
momentum particle charge densities . . . 1895--1904
Asbjòrn Holt and
Gunnar Karlstròm Induction correction model for rotation
of two or three dihedral angles . . . . 1905--1911
Keiko Shinoda and
Wataru Shinoda and
Masuhiro Mikami Efficient free energy calculation of
water across lipid membranes . . . . . . 1912--1918
Rong-Zhen Liao and
Wan-Jian Ding and
Jian-Guo Yu and
Wei-Hai Fang and
Ruo-Zhuang Liu Theoretical studies on pyridoxal
5'-phosphate-dependent transamination of
$\alpha$-amino acids . . . . . . . . . . 1919--1929
Daisuke Katagiri and
Hideyoshi Fuji and
Saburo Neya and
Tyuji Hoshino Ab initio protein structure prediction
with force field parameters derived from
water-phase quantum chemical calculation 1930--1944
Pankaj R. Daga and
Robert J. Doerksen Stereoelectronic properties of
spiroquinazolinones in differential PDE7
inhibitory activity . . . . . . . . . . 1945--1954
Anna Marabotti and
Francesca Spyrakis and
Angelo Facchiano and
Pietro Cozzini and
Saverio Alberti and
Glen E. Kellogg and
Andrea Mozzarelli Energy-based prediction of amino
acid-nucleotide base recognition . . . . 1955--1969
Magdalena Gruziel and
Pawel Grochowski and
Joanna Trylska The Poisson--Boltzmann model for tRNA:
Assessment of the calculation set-up and
ionic concentration cutoff . . . . . . . 1970--1981
Inés Corral and
Leticia González Theoretical investigation of
anthracene-9,10-endoperoxide vertical
singlet and triplet excitation spectra 1982--1991
Amit Mor and
Guy Ziv and
Yaakov Levy Simulations of proteins with
inhomogeneous degrees of freedom: the
effect of thermostats . . . . . . . . . 1992--1998
István Komáromi and
Michael C. Owen and
Richard F. Murphy and
Sándor Lovas Development of glycyl radical parameters
for the OPLS-AA/L force field . . . . . 1999--2009
Guang-Jiu Zhao and
Ke-Li Han Time-dependent density functional theory
study on hydrogen-bonded intramolecular
charge-transfer excited state of
4-dimethylamino-benzonitrile in methanol 2010--2017
Xuan Xiao and
Wei-Zhong Lin and
Kuo-Chen Chou Using grey dynamic modeling and pseudo
amino acid composition to predict
protein structural classes . . . . . . . 2018--2024
Hujun Xie and
Ruibo Wu and
Fei Xia and
Zexing Cao Effects of electron attachment on
C$_{5'}$O$_{5'}$ and C$_{1'}$N$_1$ bond
cleavages of pyrimidine nucleotides: a
theoretical study . . . . . . . . . . . 2025--2032
Asbjòrn Holt and
Gunnar Karlström Inclusion of the quadrupole moment when
describing polarization. The effect of
the dipole-quadrupole polarizability . . 2033--2038
Richard Dronskowski and
Gernot Frenking Foreword . . . . . . . . . . . . . . . . 2039--2043
Jürgen Hafner Ab-initio simulations of materials using
VASP: Density-functional theory and
beyond . . . . . . . . . . . . . . . . . 2044--2078
R. A. Evarestov and
A. V. Bandura and
M. V. Losev and
E. A. Kotomin and
Yu. F. Zhukovskii and
D. Bocharov A first-principles DFT study of UN bulk
and (001) surface: Comparative LCAO and
PW calculations . . . . . . . . . . . . 2079--2087
Torsten Kerber and
Marek Sierka and
Joachim Sauer Application of semiempirical long-range
dispersion corrections to periodic
systems in density functional theory . . 2088--2097
M. J. Gillan and
D. Alf\`e and
S. de Gironcoli and
F. R. Manby High-precision calculation of
Hartree--Fock energy of crystals . . . . 2098--2106
Elena Voloshina and
Beate Paulus Cohesive properties of CeN and LaN from
first principles . . . . . . . . . . . . 2107--2112
Cesare Pisani and
Lorenzo Maschio and
Silvia Casassa and
Migen Halo and
Martin Schütz and
Denis Usvyat Periodic local MP2 method for the study
of electronic correlation in crystals:
Theory and preliminary applications . . 2113--2124
Sheng-Qing Xia and
Svilen Bobev Are Ba$_{11}$Cd$_6$Sb$_{12}$ and
Sr$_{11}$Cd$_6$Sb$_{12}$ Zintl phases or
not? A density-functional theory study 2125--2133
Jianxiao Xu and
Holger Kleinke Unusual Sb--Sb bonding in high
temperature thermoelectric materials . . 2134--2143
Pere Alemany and
Miquel Llunell and
Enric Canadell Roles of cations, electronegativity
difference, and anionic interlayer
interactions in the metallic versus
nonmetallic character of Zintl phases
related to arsenic . . . . . . . . . . . 2144--2153
Changhoon Lee and
Myung-Hwan Whangbo and
Jürgen Köhler Analysis of electronic structures and
chemical bonding of metal-rich
compounds. I. Density functional study
of Pt metal, LiPt$_2$, LiPt, and
Li$_2$Pt . . . . . . . . . . . . . . . . 2154--2160
A. I. Baranov and
M. Kohout Electron localizability for hexagonal
element structures . . . . . . . . . . . 2161--2171
Dong-Kyun Seo and
Sang-Hwan Kim Nature of Stoner condition for metallic
ferromagnetism . . . . . . . . . . . . . 2172--2176
German D. Samolyuk and
Gordon J. Miller Relation between chemical bonding and
exchange coupling approaches to the
description of ordering in itinerant
magnets . . . . . . . . . . . . . . . . 2177--2186
Dadi Dai and
Hongjun Xiang and
Myung-Hwan Whangbo Effects of spin-orbit coupling on
magnetic properties of discrete and
extended magnetic systems . . . . . . . 2187--2209
Daniel Fritsch and
Klaus Koepernik and
Manuel Richter and
Helmut Eschrig Transition metal dimers as potential
molecular magnets: a challenge to
computational chemistry . . . . . . . . 2210--2219
Anderi L. Tchougréeff and
Richard Dronskowski A computational study of the crystal and
electronic structure of the room
temperature organometallic ferromagnet
V(TCNE)$_2$ . . . . . . . . . . . . . . 2220--2233
C. Richard A. Catlow and
Samuel A. French and
Alexey A. Sokol and
Abdullah A. Al-Sunaidi and
Scott M. Woodley Zinc oxide: a case study in contemporary
computational solid state chemistry . . 2234--2249
Karl Jug and
Viatcheslav A. Tikhomirov Influence of intrinsic defects on the
properties of zinc oxide . . . . . . . . 2250--2254
Atsushi Togo and
Peter Kroll First-principles lattice dynamics
calculations of the phase boundary
between $\beta$-Si$_3$N$_4$ and
$\gamma$-Si$_3$N$_4$ at elevated
temperatures and pressures . . . . . . . 2255--2259
Holger Wolff and
Richard Dronskowski First-principles and molecular-dynamics
study of structure and bonding in
perovskite-type oxynitrides ABO$_2$N (A
= Ca, Sr, Ba; B = Ta, Nb) . . . . . . . 2260--2267
C. M. Zicovich-Wilson and
F. J. Torres and
F. Pascale and
L. Valenzano and
R. Orlando and
R. Dovesi Ab initio simulation of the IR spectra
of pyrope, grossular, and andradite . . 2268--2278
Jerome Cuny and
Sabri Messaoudi and
Veronique Alonzo and
Eric Furet and
Jean-François Halet and
Eric Le Fur and
Sharon E. Ashbrook and
Chris J. Pickard and
Regis Gautier and
Laurent Le Polles DFT calculations of quadrupolar
solid-state NMR properties: Some
examples in solid-state inorganic
chemistry . . . . . . . . . . . . . . . 2279--2287
Lindsay E. Roy and
Tomasz Durakiewicz and
Richard L. Martin and
Juan E. Peralta and
Gustavo E. Scuseria and
Cliff G. Olson and
John J. Joyce and
Ela Guziewicz Dispersion in the Mott insulator UO$_2$:
a comparison of photoemission
spectroscopy and screened hybrid density
functional theory . . . . . . . . . . . 2288--2294
Florian Janetzko and
Thomas Bredow and
Gerald Geudtner and
Andreas M. Köster Boron-doped diamond: Investigation of
the stability of surface-doping versus
bulk-doping using cyclic cluster model
calculations . . . . . . . . . . . . . . 2295--2301
Ilka Hegemann and
Andreas Schwaebe and
Karin Fink Adsorption of single Cu atoms at
differently stabilized polar ZnO
surfaces: an ab initio study . . . . . . 2302--2310
Takashi Tsuchimochi and
Masato Kobayashi and
Ayako Nakata and
Yutaka Imamura and
Hiromi Nakai Application of the Sakurai-Sugiura
projection method to core-excited-state
calculation by time-dependent density
functional theory . . . . . . . . . . . 2311--2316
Masato Morita and
Satoshi Yabushita Photoionization cross sections with
optimized orbital exponents within the
complex basis function method . . . . . 2317--2329
Andreas B. Pribil and
Thomas S. Hofer and
Bernhard R. Randolf and
Bernd M. Rode Structure and dynamics of phosphate ion
in aqueous solution: an ab initio QMCF
MD study . . . . . . . . . . . . . . . . 2330--2334
Daniel R. Fisher and
David R. Kent IV and
Michael T. Feldmann and
William A. Goddard III An optimized initialization algorithm to
ensure accuracy in quantum Monte Carlo
calculations . . . . . . . . . . . . . . 2335--2343
A. V. Larin and
I. K. Sakodynskaya and
D. N. Trubnikov Convergence of electric field and
electric field gradient versus atomic
basis sets in all-siliceous and Mg
substituted phillipsites . . . . . . . . 2344--2358
Carl-Johan Högberg and
Alexei M. Nikitin and
Alexander P. Lyubartsev Modification of the CHARMM force field
for DMPC lipid bilayer . . . . . . . . . 2359--2369
Zdenek Chval and
Miroslav Sip and
Jaroslav V. Burda The trans effect in square-planar
platinum(II) complexes --- a density
functional study . . . . . . . . . . . . 2370--2381
Paraskevas A. Karipidis and
Constantinos A. Tsipis The dramatic effect of NH$_3$
co-ligation on the FE$^+$-assisted
activation of carbon dioxide in the gas
phase: From bare metal ions to complexes 2382--2396
Lula Rosso and
Antony D. Gee and
Ian R. Gould Ab initio computational study of
positron emission tomography ligands
interacting with lipid molecule for the
prediction of nonspecific binding . . . 2397--2405
Gennady N. Chuev and
Maxim V. Fedorov and
Sandro Chiodo and
Nino Russo and
Emilia Sicilia Hydration of ionic species studied by
the reference interaction site model
with a repulsive bridge correction . . . 2406--2415
Jens Krüger and
Wolfgang B. Fischer Exploring the conformational space of
Vpu from HIV-1: a versatile adaptable
protein . . . . . . . . . . . . . . . . 2416--2424
Karmen \vCondi\'c-Jurki\'c and
V. Tamara Perchyonok and
Hendrik Zipse and
David M. Smith On the modeling of arginine-bound
carboxylates: a case study with Pyruvate
Formate-Lyase . . . . . . . . . . . . . 2425--2433
G. G. Camiletti and
S. F. Machado and
F. E. Jorge Gaussian basis set of double zeta
quality for atoms K through Kr:
Application in DFT calculations of
molecular properties . . . . . . . . . . 2434--2444
Maykel Cruz-Monteagudo and
Fernanda Borges and
M. Natália D. S. Cordeiro Desirability-based multiobjective
optimization for global QSAR studies:
Application to the design of novel
NSAIDs with improved analgesic,
antiinflammatory, and ulcerogenic
profiles . . . . . . . . . . . . . . . . 2445--2459
Carmen Herrmann and
Johannes Neugebauer and
Markus Reiher QM/MM vibrational mode tracking . . . . 2460--2470
Masato Morita and
Satoshi Yabushita Photoionization cross sections of H and
H$_2$ with complex Gaussian-type basis
functions optimized for the
frequency-dependent polarizabilities . . 2471--2478
Jinwoo Lee and
Keehyoung Joo and
Seung-Yeon Kim and
Jooyoung Lee Re-examination of structure optimization
of off-lattice protein AB models by
conformational space annealing . . . . . 2479--2484
Asbjòrn Holt and
Gunnar Karlström Erratum: Inclusion of the quadrupole
moment when describing polarization. The
effect of the dipole-quadrupole
polarizability . . . . . . . . . . . . . 2485--2486
Chin-Hung Lai and
Ming-Der Su Theoretical characterizations of HAsXH
(X = N, P, As, Sb, and Bi) isomers in
the singlet and triplet states . . . . . 2487--2499
Juan A. Castillo-Garit and
Yovani Marrero-Ponce and
Francisco Torrens and
Ramón García-Domenech and
Vicente Romero-Zaldivar Bond-based 3D-chiral linear indices:
Theory and QSAR applications to central
chirality codification . . . . . . . . . 2500--2512
Yajun Liu and
Hongyan Xiao and
Mengtao Sun and
Weihai Fang Spin-orbit ab initio investigation of
the photodissociation of dibromomethane
in the gas and solution phases . . . . . 2513--2519
Wei Shi and
Edward J. Maginn Improvement in molecule exchange
efficiency in Gibbs ensemble Monte
Carlo: Development and implementation of
the continuous fractional component move 2520--2530
Hirotaka Ode and
Yuri Matsuo and
Saburo Neya and
Tyuji Hoshino Force field parameters for rotation
around $\chi$ torsion axis in nucleic
acids . . . . . . . . . . . . . . . . . 2531--2542
Olgun Guvench and
Shannon N. Greene and
Ganesh Kamath and
John W. Brady and
Richard M. Venable and
Richard W. Pastor and
Alexander D. Mackerell Jr. Additive empirical force field for
hexopyranose monosaccharides . . . . . . 2543--2564
Natércia F. Brás and
Sara A. Moura-Tamames and
Pedro A. Fernandes and
Maria J. Ramos Mechanistic studies on the formation of
glycosidase-substrate and
glycosidase-inhibitor covalent
intermediates . . . . . . . . . . . . . 2565--2574
Gernot Kieseritzky and
E. W. Knapp Improved $pK_a$ prediction: Combining
empirical and semimicroscopic methods 2575--2581
P. Poulain and
A. Saladin and
B. Hartmann and
C. Prévost Insights on protein-DNA recognition by
coarse grain modelling . . . . . . . . . 2582--2592
Giovanni Grazioso and
Andrea Cavalli and
Marco De Amici and
Maurizio Recanatini and
Carlo De Micheli Alpha7 nicotinic acetylcholine receptor
agonists: Prediction of their binding
affinity through a molecular mechanics
Poisson--Boltzmann surface area approach 2593--2602
Jakob Schluttig and
Michael Bachmann and
Wolfhard Janke Comparative molecular dynamics and Monte
Carlo study of statistical properties
for coarse-grained heteropolymers . . . 2603--2612
Santiago Vilar and
Humberto González-Díaz and
Lourdes Santana and
Eugenio Uriarte QSAR model for alignment-free prediction
of human breast cancer biomarkers based
on electrostatic potentials of protein
pseudofolding HP-lattice networks . . . 2613--2622
Yan-Hong Cui and
Wei Quan Tian and
Ji-Kang Feng and
De-Li Chen Structures, stabilities, electronic, and
optical properties of C$_{64}$ fullerene
isomers, anions (C and C$_{64}^{4-}$),
metallofullerene Sc$_2$@C$_{64}$, and
Sc$_2$C$_2$@C$_{64}$ . . . . . . . . . . 2623--2630
Lili Sun and
Shuwei Tang and
Yingfei Chang and
Zhanliang Wang and
Rongshun Wang Searching for stable hept-C$_{62}$X$_2$
(X = F, Cl, and Br): Structures and
stabilities of heptagon-containing
C$_{62}$ halogenated derivatives . . . . 2631--2635
Jiazhong Li and
Beilei Lei and
Huanxiang Liu and
Shuyan Li and
Xiaojun Yao and
Mancang Liu and
Paola Gramatica QSAR study of malonyl-CoA decarboxylase
inhibitors using GA-MLR and a new
strategy of consensus modeling . . . . . 2636--2647
Guoming Liang and
Xiaoguang Bao and
Jiande Gu The possibility of the decomposition of
2'-deoxyribose moiety of thymidine
induced by the low energy electron
attachment . . . . . . . . . . . . . . . 2648--2655
Tomonaga Ozawa and
Kosuke Okazaki CH/$\pi$ hydrogen bonds determine the
selectivity of the Src homology 2 domain
to tyrosine phosphotyrosyl peptides: an
ab initio fragment molecular orbital
study . . . . . . . . . . . . . . . . . 2656--2666
Mahito Chiba and
Dmitri G. Fedorov and
Kazuo Kitaura Polarizable continuum model with the
fragment molecular orbital-based
time-dependent density functional theory 2667--2676
Karolina Kisowska and
Slawomir Berski and
Zdzislaw Latajka The structure and chemical bonding in
the N$_2$CuX and N$_2$\dottedbondXCu (X
= F, Cl, Br) systems studied by means of
the molecular orbital and Quantum
Chemical Topology methods . . . . . . . 2677--2692
Valery Andrushchenko and
Petr Bou\vr Circular dichroism enhancement in large
DNA aggregates simulated by a
generalized oscillator model . . . . . . 2693--2703
María Suárez and
Pablo Tortosa and
Javier Carrera and
Alfonso Jaramillo Pareto optimization in computational
protein design with multiple objectives 2704--2711
Mark Pinsky and
Chaim Dryzun and
David Casanova and
Pere Alemany and
David Avnir Analytical methods for calculating
Continuous Symmetry Measures and the
Chirality Measure . . . . . . . . . . . 2712--2721
N. Flocke and
V. Lotrich Efficient electronic integrals and their
generalized derivatives for object
oriented implementations of electronic
structure calculations . . . . . . . . . 2722--2736
Gernot Frenking and
Charles L. Brooks III and
Shigeyoshi Sakiki Editors' note . . . . . . . . . . . . . 1--1
Vincenzo Barone and
Mirco Zerbetto and
Antonino Polimeno Hydrodynamic modeling of diffusion
tensor properties of flexible molecules 2--13
Olga Yuzlenko and
Katarzyna Kie\'c-Kononowicz Molecular modeling of A$_1$ and A$_{2A}$
adenosine receptors: Comparison of
rhodopsin- and
$\beta_2$-adrenergic-based homology
models through the docking studies . . . 14--32
Bing Niu and
Lin Lu and
Liang Liu and
Tian Hong Gu and
Kai-Yan Feng and
Wen-Cong Lu and
Yu-Dong Cai HIV-1 protease cleavage site prediction
based on amino acid property . . . . . . 33--39
Yuto Komeiji and
Takeshi Ishikawa and
Yuji Mochizuki and
Hiroshi Yamataka and
Tatsuya Nakano Fragment Molecular Orbital method-based
Molecular Dynamics (FMO--MD) as a
simulator for chemical reactions in
explicit solvation . . . . . . . . . . . 40--50
Bryan M. Wong Noncovalent interactions in
supramolecular complexes: a study on
corannulene and the double concave
buckycatcher . . . . . . . . . . . . . . 51--56
Matthew A. Addicoat and
Gregory F. Metha Kick: Constraining a stochastic search
procedure with molecular fragments . . . 57--64
Luká\vs Bu\vcinský and
Stanislav Biskupi\vc and
Michal Il\vcin and
Vladimír Luke\vs and
Viliam Laurinc On relativistic effects in ground state
potential curves of Zn$_2$, Cd$_2$, and
Hg$_2$ dimers. A CCSD(T) study . . . . . 65--74
Daniel Escudero and
Antonio Frontera and
David Quiñonero and
Pere M. Dey\`a Interplay between anion-$\pi$ and
hydrogen bonding interactions . . . . . 75--82
Wissam Helal and
Stefano Evangelisti and
Thierry Leininger and
Daniel Maynau Ab-initio multireference study of an
organic mixed-valence Spiro molecular
system . . . . . . . . . . . . . . . . . 83--92
Weiyang Chen and
Bo Liao and
Wen Zhu and
Hao Liu and
Qingguang Zeng An ant colony pairwise alignment based
on the dot plots . . . . . . . . . . . . 93--97
A. Martín Pendás and
M. A. Blanco and
E. Francisco Steric repulsions, rotation barriers,
and stereoelectronic effects: a real
space perspective . . . . . . . . . . . 98--109
Gota Kikugawa and
Rossen Apostolov and
Narutoshi Kamiya and
Makoto Taiji and
Ryutaro Himeno and
Haruki Nakamura and
Yasushige Yonezawa Application of MDGRAPE-3, a special
purpose board for molecular dynamics
simulations, to periodic biomolecular
systems . . . . . . . . . . . . . . . . 110--118
A. S. Zyubin and
A. M. Mebel and
M. Hayashi and
H. C. Chang and
S. H. Lin Quantum chemical modeling of
photoadsorption properties of the
nitrogen-vacancy point defect in diamond 119--131
Michael D. Altman and
Jaydeep P. Bardhan and
Jacob K. White and
Bruce Tidor Accurate solution of multi-region
continuum biomolecule electrostatic
problems using the linearized
Poisson--Boltzmann equation with curved
boundary elements . . . . . . . . . . . 132--153
Nikolaj Otte and
Marco Bocola and
Walter Thiel Force-field parameters for the
simulation of tetrahedral intermediates
of serine hydrolases . . . . . . . . . . 154--162
Ke Chen and
Yingfu Jiang and
Li Du and
Lukasz Kurgan Prediction of integral membrane protein
type by collocated hydrophobic amino
acid pairs . . . . . . . . . . . . . . . 163--172
Juan M. Ramírez-Anguita and
\`Angels González-Lafont and
José M. Lluch Formation pathways of DMSO from DMS-OH
in the presence of O$_2$ and NO$_x$: a
theoretical study . . . . . . . . . . . 173--182
Wen Lai Huang and
Qingshan Zhu DFT calculations on the electronic
structures of BiOX (X = F, Cl, Br, I)
photocatalysts with and without semicore
Bi $5 d$ states . . . . . . . . . . . . 183--190
Dmitri V. Sakharov and
Carmay Lim Force fields including charge transfer
and local polarization effects:
Application to proteins containing
multi/heavy metal ions . . . . . . . . . 191--202
Artur Galstyan and
Ernst-Walter Knapp Accurate redox potentials of mononuclear
iron, manganese, and nickel model
complexes* . . . . . . . . . . . . . . . 203--211
Chris Oostenbrink Efficient free energy calculations on
small molecule host-guest systems --- a
combined linear interaction
energy/one-step perturbation approach 212--221
Anmin Zheng and
Shang-Bin Liu and
Feng Deng $^{13}$C shielding tensors of
crystalline amino acids and peptides:
Theoretical predictions based on
periodic structure models . . . . . . . 222--235
Hui Zhang and
Gui-Ling Zhang and
Jing-Yan Liu and
Miao Sun and
Bo Liu and
Ze-Sheng Li Theoretical study on the reaction of
SiH(CH$_3$)$_3$ with SiH$_3$ radical . . 236--242
Alexey Aleksandrov and
Thomas Simonson Molecular mechanics models for
tetracycline analogs . . . . . . . . . . 243--255
Xiaolei Zhu and
Luhua Lai A novel method for enzyme design . . . . 256--267
Edgar Luttmann and
Daniel L. Ensign and
Vishal Vaidyanathan and
Mike Houston and
Noam Rimon and
Jeppe Òland and
Guha Jayachandran and
Mark Friedrichs and
Vijay S. Pande Accelerating molecular dynamic
simulation on the Cell processor and
Playstation 3 . . . . . . . . . . . . . 268--274
Albert Poater and
Ana Gallegos Saliner and
Ramon Carbó-Dorca and
Jordi Poater and
Miquel Sol\`a and
Luigi Cavallo and
Andrew P. Worth Modeling the structure-property
relationships of nanoneedles: a journey
toward nanomedicine . . . . . . . . . . 275--284
Chao Deng and
Xiao-Peng Wu and
Xiao-Ming Sun and
Yi Ren and
Ying-Hong Sheng Neutral hydrolyses of carbon disulfide:
an ab initio study of water catalysis 285--294
Qi-Shi Du and
Ri-Bo Huang and
Yu-Tuo Wei and
Zong-Wen Pang and
Li-Qin Du and
Kuo-Chen Chou Fragment-based quantitative
structure--activity relationship
(FB-QSAR) for fragment-based drug design 295--304
Li-Ping Ju and
Ke-Li Han and
John Z. H. Zhang Global dynamics and transition state
theories: Comparative study of reaction
rate constants for gas-phase chemical
reactions . . . . . . . . . . . . . . . 305--316
Jon Baker and
Krzysztof Wolinski and
Massimo Malagoli and
Don Kinghorn and
Pawel Wolinski and
Gábor Magyarfalvi and
Svein Saebo and
Tomasz Janowski and
Peter Pulay Quantum chemistry in parallel with PQS 317--335
Edmond P. F. Lee and
Daniel K. W. Mok and
Foo-Tim Chau and
John M. Dyke A combined ab initio and Franck--Condon
factor simulation study on the
photodetachment spectrum of ScO$_2^-$ 337--345
Ján Bu\vsa and
Shura Hayryan and
Chin-Kun Hu and
Jaroslav Sk\vrivánek and
Ming-Chya Wu Enveloping triangulation method for
detecting internal cavities in proteins
and algorithm for computing their
surface areas and volumes . . . . . . . 346--357
Yi Ren and
Hiroshi Yamataka Does $\alpha$-effect exist in E2
reactions? A G2(+) investigation . . . . 358--365
Ivo Cacelli and
Carlo Federico Lami and
Giacomo Prampolini Force-field modeling through quantum
mechanical calculations: Molecular
dynamics simulations of a nematogenic
molecule in its condensed phases . . . . 366--378
A. J. C. Varandas Mòller--Plesset perturbation energies and
distances for HeC$_{20}$ extrapolated to
the complete basis set limit . . . . . . 379--388
Al Mokhtar Lamsabhi and
Otilia Mó and
Soledad Gutiérrez-Oliva and
Patricia Pérez and
Alejandro Toro-Labbé and
Manuel Yáñez The mechanism of double proton transfer
in dimers of uracil and 2-thiouracil ---
the reaction force perspective . . . . . 389--398
Lingchun Song and
Jinshuai Song and
Yirong Mo and
Wei Wu An efficient algorithm for energy
gradients and orbital optimization in
valence bond theory . . . . . . . . . . 399--406
Wan-Chun Cheng and
Soonmin Jang and
Chen-Chang Wu and
Ren-Jie Lin and
Hsiu-Feng Lu and
Feng-Yin Li Site specificity of the
$^{\alpha}$C\bond H bond dissociation
energy for a naturally occurring
$\beta$-hairpin peptide --- an ab initio
study . . . . . . . . . . . . . . . . . 407--414
C. Mediavilla and
J. Tortajada and
V. G. Baonza Modeling high pressure reactivity in
unsaturated systems: Application to
dimethylacetylene . . . . . . . . . . . 415--422
Yinglong Miao and
Peter J. Ortoleva Molecular dynamics/order parameter
extrapolation for bionanosystem
simulations . . . . . . . . . . . . . . 423--437
Li-Qin Xue and
Xian-Yong Pang and
Gui-Chang Wang Selective oxidation of styrene on an
oxygen-adsorbed Au(111): a density
functional theory study . . . . . . . . 438--446
Maik Goette and
Helmut Grubmüller Accuracy and convergence of free energy
differences calculated from
nonequilibrium switching processes . . . 447--456
Loukas Petridis and
Jeremy C. Smith A molecular mechanics force field for
lignin . . . . . . . . . . . . . . . . . 457--467
Cristopher Camacho and
Henryk A. Witek and
Shigeyoshi Yamamoto Intruder states in multireference
perturbation theory: the ground state of
manganese dimer . . . . . . . . . . . . 468--478
Stephan Frickenhaus and
Srinivasaraghavan Kannan and
Martin Zacharias Efficient evaluation of sampling quality
of molecular dynamics simulations by
clustering of dihedral torsion angles
and Sammon mapping . . . . . . . . . . . 479--492
Hao Zhang and
Yun-Hong Zhang and
Feng Wang Theoretical understanding on the v$_1$
-SO band perturbed by the formation of
magnesium sulfate ion pairs . . . . . . 493--503
Rong Wang and
Jian-Sheng Wang and
Gui-Rong Liu and
Jongyoon Han and
Yu-Zong Chen Simulation of DNA electrophoresis in
systems of large number of solvent
particles by coarse-grained hybrid
molecular dynamics approach . . . . . . 505--513
Daan P. Geerke and
Sandra Luber and
Koni H. Marti and
Wilfred F. Van Gunsteren On the direct calculation of the free
energy of quantization for molecular
systems in the condensed phase . . . . . 514--523
Wenli Zou and
Wenjian Liu Comprehensive ab initio calculation and
simulation on the low-lying electronic
states of TlX (X = F, Cl, Br, I, and At) 524--539
Katalin E. Kövér and
Tamás Beke and
András Lipták and
András Perczel Combined NMR three-bond scalar coupling
measurements and QM calculations to
calculate OH-rotamer equilibrium of
polyalcohols . . . . . . . . . . . . . . 540--550
Inmaculada Garíca Cuesta and
Alfredo Sánchez De Merás and
Stefano Pelloni and
Paolo Lazzeretti Understanding the ring current effects
on magnetic shielding of hydrogen and
carbon nuclei in naphthalene and
anthracene . . . . . . . . . . . . . . . 551--564
Lei Yang and
Jing-Yao Liu and
Su-Qin Wan and
Ze-Sheng Li Theoretical studies of the reactions of
CF$_3$CHCLOCHF$_2$/CF$_3$CHFOCHF$_2$
with OH radical and Cl atom and their
product radicals with OH . . . . . . . . 565--580
Darren J. Simpson and
Thomas Bredow and
Andrea R. Gerson MSINDO study of acid promoted
dissolution of planar MgO and NiO
surfaces . . . . . . . . . . . . . . . . 581--588
Wenbo Yu and
Lei Liang and
Zijing Lin and
Sanliang Ling and
Maciej Haranczyk and
Maciej Gutowski Comparison of some representative
density functional theory and wave
function theory methods for the studies
of amino acids . . . . . . . . . . . . . 589--600
Keith T. Butler and
F. Javier Luque and
Xavier Barril Toward accurate relative energy
predictions of the bioactive
conformation of drugs . . . . . . . . . 601--610
Li Wang and
Jing-yao Liu and
Hong Gao and
Su-qin Wan and
Ze-sheng Li Dual-level direct dynamics studies for
the reactions of OH radical with
bromine-substituted ethanes . . . . . . 611--620
Oliver J. Clarke and
Martin J. Parker Identification of amyloidogenic peptide
sequences using a coarse-grained
physicochemical model . . . . . . . . . 621--630
Zunnan Huang and
Chung F. Wong Conformational selection of protein
kinase A revealed by flexible-ligand
flexible-protein docking . . . . . . . . 631--644
Zanxia Cao and
Zhixiong Lin and
Jun Wang and
Haiyan Liu Refining the description of peptide
backbone conformations improves protein
simulations using the GROMOS 53A6 force
field . . . . . . . . . . . . . . . . . 645--660
V. Ganesh MeTA studio: a cross platform,
programmable IDE for computational
chemist . . . . . . . . . . . . . . . . 661--672
Andreas Vitalis and
Rohit V. Pappu ABSINTH: a new continuum solvation model
for simulations of polypeptides in
aqueous solutions . . . . . . . . . . . 673--699
Pei-Kun Yang and
Carmay Lim Strategies to model the near-solute
solvent molecular density/polarization 700--709
Alexandra T. P. Carvalho and
Pedro A. Fernandes and
Marcel Swart and
Joost N. P. Van Stralen and
F. Matthias Bickelhaupt and
Maria J. Ramos Role of the variable active site
residues in the function of thioredoxin
family oxidoreductases . . . . . . . . . 710--724
Yun-Xiang Lu and
Jian-Wei Zou and
Ji-Cai Fan and
Wen-Na Zhao and
Yong-Jun Jiang and
Qing-Sen Yu Ab initio calculations on halogen-bonded
complexes and comparison with density
functional methods . . . . . . . . . . . 725--732
Jeffrey S. Tan and
Stephan X. M. Boerrigter and
Raymond P. Scaringe and
Kenneth R. Morris Application of error-ranked singular
value decomposition for the
determination of potential-derived
atomic-centered point charges . . . . . 733--742
Lonnie D. Crosby and
Shawn M. Kathmann and
Theresa L. Windus Implementation of dynamical nucleation
theory with quantum potentials . . . . . 743--749
Pär Söderhjelm and
Ulf Ryde Conformational dependence of charges in
protein simulations . . . . . . . . . . 750--760
Volker Hähnke and
Bettina Hofmann and
Tomislav Grgat and
Ewgenij Proschak and
Dieter Steinhilber and
Gisbert Schneider PhAST: Pharmacophore alignment search
tool . . . . . . . . . . . . . . . . . . 761--771
Yingfu Jiang and
Paul Iglinski and
Lukasz Kurgan Prediction of protein folding rates from
primary sequences using hybrid sequence
representation . . . . . . . . . . . . . 772--783
Victor M. Anisimov and
Vladislav L. Bugaenko QM/QM docking method based on the
variational finite localized molecular
orbital approximation . . . . . . . . . 784--798
Frank Eckert and
Ivo Leito and
Ivari Kaljurand and
Agnes Kütt and
Andreas Klamt and
Michael Diedenhofen Prediction of acidity in acetonitrile
solution with COSMO-RS . . . . . . . . . 799--810
Grzegorz Mazur and
Rados\law W\lodarczyk Application of the dressed
time-dependent density functional theory
for the excited states of linear
polyenes . . . . . . . . . . . . . . . . 811--817
Loriano Storchi and
Giuseppe Vitillaro and
Francesco Tarantelli Implementation and use of a direct,
partially integral-driven non-Dyson
propagator method for molecular
ionization . . . . . . . . . . . . . . . 818--825
Hiroaki Umeda and
Yuichi Inadomi and
Hiroaki Honda and
Umpei Nagashima Parallel Fock matrix construction
program for molecular orbital
calculation --- specific computer with a
hierarchical network . . . . . . . . . . 826--831
Sandro G. Chiodo and
Nino Russo One-electron spin-orbit contribution by
effective nuclear charges . . . . . . . 832--839
Hua Zhu and
Daiqian Xie N$_2$O in small para-hydrogen clusters:
Structures and energetics . . . . . . . 841--846
Hua-Qing Yang and
Song Qin and
Song Qin and
Chang-Wei Hu Theoretical study on the gas-phase
reaction mechanism between nickel
monoxide and methane for syngas
production . . . . . . . . . . . . . . . 847--863
Mark S. Friedrichs and
Peter Eastman and
Vishal Vaidyanathan and
Mike Houston and
Scott Legrand and
Adam L. Beberg and
Daniel L. Ensign and
Christopher M. Bruns and
Vijay S. Pande Accelerating molecular dynamic
simulation on graphics processing units 864--872
Gwonchan Yoon and
Hyeong-Jin Park and
Sungsoo Na and
Kilho Eom Mesoscopic model for mechanical
characterization of biological protein
materials . . . . . . . . . . . . . . . 873--880
Jason Martin and
Jon Baker and
Peter Pulay Comments on the molecular geometry of
ferrocene: the dangers of using quantum
chemistry programs as black boxes . . . 881--883
Jorge A. Vila and
Héctor A. Baldoni and
Harold A. Scheraga Performance of density functional models
to reproduce observed $^{13}$C$^\alpha$
chemical shifts of proteins in solution 884--892
T. R. Walsh and
T. Liang A multipole-based water potential with
implicit polarization for biomolecular
simulations . . . . . . . . . . . . . . 893--899
Shuyan Li and
Lili Xi and
Chengqi Wang and
Jiazhong Li and
Beilei Lei and
Huanxiang Liu and
Xiaojun Yao A novel method for protein-ligand
binding affinity prediction and the
related descriptors exploration . . . . 900--909
Amanda M. Salisburg and
Ashley L. Deline and
Katrina W. Lexa and
George C. Shields and
Karl N. Kirschner Ramachandran-type plots for glycosidic
linkages: Examples from molecular
dynamic simulations using the Glycam06
force field . . . . . . . . . . . . . . 910--921
Nitin S. Sapre and
Swagata Gupta and
Nilanjana Pancholi and
Neelima Sapre A group center overlap based approach
for ``3D QSAR'' studies on TIBO
derivatives . . . . . . . . . . . . . . 922--933
Vincenzo Barone and
Maurizio Casarin and
Daniel Forrer and
Michele Pavone and
Mauro Sambi and
Andrea Vittadini Role and effective treatment of
dispersive forces in materials:
Polyethylene and graphite crystals as
test cases . . . . . . . . . . . . . . . 934--939
Peng Zhou and
Feifei Tian and
Zhicai Shang $2$D depiction of nonbonding
interactions for protein complexes . . . 940--951
Yi Luo and
Satoshi Maeda and
Koichi Ohno Automated exploration of stable isomers
of H$^+$(H$_2$O)$_n$ ($n = 5$--$7$) via
ab initio calculations: an application
of the anharmonic downward distortion
following algorithm . . . . . . . . . . 952--961
Hajime Okamoto and
Tetsuo Yamada and
Shuichiro Kihara and
Kazumasa Takechi and
Hiroyuki Takagi and
Kyozaburo Takeda Conformational transitions of cyclic D,
L-peptides . . . . . . . . . . . . . . . 962--973
Emanuel H. Rubensson and
Elias Rudberg and
Pawe\l Sa\lek Truncation of small matrix elements
based on the Euclidean norm for blocked
data structures . . . . . . . . . . . . 974--977
Guohua Gao and
Xiang Xu and
Hong Seok Kang A theoretical study on
fullerene-dizincocene hybrids . . . . . 978--982
Jakub Kaminský and
Ji\vrí \vSebek and
Petr Bou\vr Molecular dynamics with restrictions
derived from optical spectra . . . . . . 983--991
Sarah Remmert and
Carol Parish Energetic analyses of chair and boat
conformations of maleimide substituted
cyclohexane derivatives . . . . . . . . 992--998
Ilya V. Loksha and
James R. Maiolo III and
Cheng W. Hong and
Albert Ng and
Christopher D. Snow SHARPEN --- Systematic Hierarchical
Algorithms for Rotamers and Proteins on
an Extended Network . . . . . . . . . . 999--1005
Cun-Xi Liu and
Ze-Rong Li and
Chong-Wen Zhou and
Xiang-Yuan Li Accurate prediction of thermodynamic
properties of alkyl peroxides by
combining density functional theory
calculation with least-square
calibration . . . . . . . . . . . . . . 1007--1015
James S. Wright and
Hooman Shadnia and
Leonid L. Chepelev Stability of carbon-centered radicals:
Effect of functional groups on the
energetics of addition of molecular
oxygen . . . . . . . . . . . . . . . . . 1016--1026
Erika Ivonne López-Martínez and
Luz María Rodríguez-Valdez and
Norma Flores-Holguín and
Alfredo Márquez-Lucero and
Daniel Glossman-Mitnik Theoretical study of electronic
properties of organic photovoltaic
materials . . . . . . . . . . . . . . . 1027--1037
Shunzhou Wan and
Peter V. Coveney A comparative study of the COX-1 and
COX-2 isozymes bound to lipid membranes 1038--1050
Lixin Zhan and
Jeff Z. Y. Chen and
Wing-Ki Liu Comparison of predicted native
structures of Met-enkephalin based on
various accessible-surface-area solvent
models . . . . . . . . . . . . . . . . . 1051--1058
Xavier Periole and
Lucy R. Allen and
Kamil Tamiola and
Alan E. Mark and
Emanuele Paci Probing the free energy landscape of the
FBP28WW domain using multiple techniques 1059--1068
Stanislav Böhm and
Otto Exner Interaction of two functional groups
through the benzene ring: Theory and
experiment . . . . . . . . . . . . . . . 1069--1074
Miguel A. F. de Souza and
Elizete Ventura and
Regiane C. M. U. Araújo and
Mozart N. Ramos and
Silmar A. do Monte CASSCF and multireference CI with
singles and doubles study of low-lying
valence and Rydberg states of
2H-tetrazole . . . . . . . . . . . . . . 1075--1081
Juan I. Rodríguez and
Andreas M. Köster and
Paul W. Ayers and
Ana Santos-Valle and
Alberto Vela and
Gabriel Merino An efficient grid-based scheme to
compute QTAIM atomic properties without
explicit calculation of zero-flux
surfaces . . . . . . . . . . . . . . . . 1082--1092
Heiko Jacobsen Chemical bonding in view of electron
charge density and kinetic energy
density descriptors . . . . . . . . . . 1093--1102
Jin Wang and
Jin Huai Liu Novel bi-transition metallic
encapsulated naphthalene-like Si$_{20}$
prismatic cage: a DFT investigation . . 1103--1110
Laura R. Hofto and
Caroline E. Lee and
Mauricio Cafiero The importance of aromatic-type
interactions in serotonin synthesis:
Protein--ligand interactions in
tryptophan hydroxylase and aromatic
amino acid decarboxylase . . . . . . . . 1111--1115
Young Kee Kang and
Nam Sook Kang Conformational preferences of
$N$-methoxycarbonyl proline dipeptide 1116--1127
Hong-Liang Xu and
Fang-Fang Wang and
Zhi-Ru Li and
Bing-Qiang Wang and
Di Wu and
Wei Chen and
Guang-Tao Yu and
Feng Long Gu and
Yuriko Aoki The nitrogen edge-doped effect on the
static first hyperpolarizability of the
supershort single-walled carbon nanotube 1128--1134
Ji-Lai Li and
Cai-Yun Geng and
Yuxiang Bu and
Xu-Ri Huang and
Chia-Chung Sun Conformational transition pathway in the
allosteric process of calcium-induced
recoverin: Molecular dynamics
simulations . . . . . . . . . . . . . . 1135--1145
Ramon Carbó-Dorca and
Ana Gallegos and
Ángel J. Sánchez Notes on quantitative
structure-properties relationships
(QSPR) (1): a discussion on a QSPR
dimensionality paradox (QSPR DP) and its
quantum resolution . . . . . . . . . . . 1146--1159
Daniel Seeliger and
Bert L. De Groot tCONCOORD-GUI: Visually supported
conformational sampling of bioactive
molecules . . . . . . . . . . . . . . . 1160--1166
Ritwik Kavathekar and
Subodh Khire and
V. Ganesh and
Anuja P. Rahalkar and
Shridhar R. Gadre WebMTA: a web-interface for ab initio
geometry optimization of large molecules
using molecular tailoring approach . . . 1167--1173
Zuzana Jirou\vsková and
Radka Svobodová Va\vreková and
Jakub Van\uek and
Jaroslav Ko\vca Software news and updates
electronegativity equalization method:
Parameterization and validation for
organic molecules using the
Merz-Kollman-Singh charge distribution
scheme . . . . . . . . . . . . . . . . . 1174--1178
Ahmed Dkhissi and
Jean Marie Ducéré and
Ralf Blossey and
Claude Pouchan Can the hybrid meta GGA and DFT-D
methods describe the stacking
interactions in conjugated polymers? . . 1179--1184
K. S. Kang and
J. W. Davenport and
J. Glimm and
D. E. Keyes and
M. McGuigan Linear augmented Slater-type orbital
method for free standing clusters . . . 1185--1193
Oana Cramariuc and
Terttu I. Hukka and
Tapio T. Rantala and
Helge Lemmetyinen Ab initio description of photoabsorption
and electron transfer in a doubly-linked
porphyrin-fullerene dyad . . . . . . . . 1194--1201
Xue-Gang Yang and
Duan Chen and
Min Wang and
Ying Xue and
Yu-Zong Chen Prediction of antibacterial compounds by
machine learning approaches . . . . . . 1202--1211
M. Fernanda Rey-Stolle and
Marta Enciso and
Antonio Rey Topology-based models and NMR structures
in protein folding simulations . . . . . 1212--1219
Pedro A. Derosa A combined semiempirical-DFT study of
oligomers within the finite-chain
approximation, evolution from oligomers
to polymers . . . . . . . . . . . . . . 1220--1228
Miguel Arenas and
M. Carmen Villaverde and
Fredy Sussman Prediction and analysis of binding
affinities for chemically diverse HIV-1
PR inhibitors by the modified SAFE\_p
approach . . . . . . . . . . . . . . . . 1229--1240
Aneta Jezierska and
Jaros\law J. Panek Investigations of an OH\dottedbondS
hydrogen bond via Car--Parrinello and
path integral molecular dynamics . . . . 1241--1250
Yan Zhang and
Chang-Sheng Wang Estimation on the intramolecular
10-membered ring N H\dottedbondO C
hydrogen-bonding energies in glycine and
alanine peptides . . . . . . . . . . . . 1251--1260
Vincent Liégeois and
Beno\^\it Champagne Vibrational Raman optical activity of
$\pi$-conjugated helical systems:
Hexahelicene and heterohelicenes . . . . 1261--1278
Lin Jin and
Yi-Hong Ding Stability of $N$-based sandwich-like
energetic complexes
[N$_4$TiN$_4$]$^{2-}$: Effect of spins
and counterions . . . . . . . . . . . . 1279--1289
Michael Gilleßen and
Richard Dronskowski A combinatorial study of full Heusler
alloys by first-principles computational
methods . . . . . . . . . . . . . . . . 1290--1299
Michael Devereux and
Paul L. A. Popelier and
Iain M. McLay Toward an ab initio fragment database
for bioisosterism: Dependence of QCT
properties on level of theory,
conformation, and chemical environment 1300--1318
Celestino Angeli On the nature of the $\pi$ $\rightarrow$
$\pi^*$ ionic excited states: the $V$
state of ethene as a prototype . . . . . 1319--1333
Jinhyuk Lee and
Sihyun Ham and
Wonpil Im Beta-hairpin restraint potentials for
calculations of potentials of mean force
as a function of beta-hairpin tilt,
rotation, and distance . . . . . . . . . 1334--1343
Jian-Ding Qiu and
San-Hua Luo and
Jian-Hua Huang and
Ru-Ping Liang Using support vector machines for
prediction of protein structural classes
based on discrete wavelet transform . . 1344--1350
Yasuomi Kiyota and
Jun-Ya Hasegawa and
Kazuhiro Fujimoto and
Ben Swerts and
Hiroshi Nakatsuji A multicore QM/MM approach for the
geometry optimization of chromophore
aggregate in protein . . . . . . . . . . 1351--1359
Liuming Yan and
Changle Shao and
Xiaobo Ji Evaluation of electroosmotic drag
coefficient of water in hydrated sodium
perfluorosulfonate electrolyte polymer 1361--1370
Jan Fuhrmann and
Alexander Rurainski and
Hans-Peter Lenhof and
Dirk Neumann A new method for the gradient-based
optimization of molecular complexes . . 1371--1378
Anatoliy Volkov and
Tibor Koritsanszky and
Michal Chodkiewicz and
Harry F. King On the basis-set dependence of local and
integrated electron density properties:
Application of a new computer program
for quantum-chemical density analysis 1379--1391
Cherumuttathu H. Suresh and
Neetha Mohan and
K. Periya Vijayalakshmi and
Renjumon George and
Janice M. Mathew Typical aromatic noncovalent
interactions in proteins: a theoretical
study using phenylalanine . . . . . . . 1392--1404
Arghya Barman and
Woody Taves and
Rajeev Prabhakar Insights into the mechanism of
methionine oxidation catalyzed by metal
(Cu$^{2+}$, Zn$^{2+}$, and Fe$^{3+}$)
--- Amyloid beta (A$\beta$) peptide
complexes: a computational study . . . . 1405--1413
Xuan Xiao and
Pu Wang and
Kuo-Chen Chou GPCR-CA: a cellular automaton image
approach for predicting
G-protein--coupled receptor functional
classes . . . . . . . . . . . . . . . . 1414--1423
Jianming Wu and
Xin Xu Accurate prediction of heats of
formation by a combined method of B3LYP
and neural network correction . . . . . 1424--1444
Sandor Kristyan Interesting properties of Thomas--Fermi
kinetic and Parr
electron--electron-repulsion DFT energy
functional generated compact
one-electron density approximation for
ground-state electronic energy of
molecular systems . . . . . . . . . . . 1445--1453
Johannes Schwöbel and
Ralf-Uwe Ebert and
Ralph Kühne and
Gerrit Schüürmann Modeling the H bond donor strength of
OH, NH, and CH sites by local molecular
parameters . . . . . . . . . . . . . . . 1454--1464
F. Iori and
R. Di Felice and
E. Molinari and
S. Corni GolP: an atomistic force-field to
describe the interaction of proteins
with Au(111) surfaces in water . . . . . 1465--1476
Juan M. Ramírez-Anguita and
\`Angels González-Lafont and
José M. Lluch Formation pathways of DMSO$_2$ in the
addition channel of the OH-initiated DMS
oxidation: a theoretical study . . . . . 1477--1489
Lennart Nilsson Efficient table lookup without inverse
square roots for calculation of pair
wise atomic interactions in classical
simulations . . . . . . . . . . . . . . 1490--1498
Alexander Rurainski and
Andreas Hildebrandt and
Hans-Peter Lenhof A consensus line search algorithm for
molecular potential energy functions . . 1499--1509
Riccardo Concu and
Gianni Podda and
Eugenio Uriarte and
Humberto González-Díaz Computational chemistry study of
3D-structure-function relationships for
enzymes based on Markov models for
protein electrostatic, HINT, and van der
Waals potentials . . . . . . . . . . . . 1510--1520
Meiyan Wang and
Lin Cheng and
Bo Hong and
Zhijian Wu Reaction mechanism of
palladium-catalyzed silastannation of
allenes by density functional theory . . 1521--1531
Dray-Ming Shien and
Tzong-Yi Lee and
Wen-Chi Chang and
Justin Bo-Kai Hsu and
Jorng-Tzong Horng and
Po-Chiang Hsu and
Ting-Yuan Wang and
Hsien-Da Huang Incorporating structural characteristics
for identification of protein
methylation sites . . . . . . . . . . . 1532--1543
B. R. Brooks and
C. L. Brooks III and
A. D. Mackerell Jr. and
L. Nilsson and
R. J. Petrella and
B. Roux and
Y. Won and
G. Archontis and
C. Bartels and
S. Boresch and
A. Caflisch and
L. Caves and
Q. Cui and
A. R. Dinner and
M. Feig and
S. Fischer and
J. Gao and
M. Hodoscek and
W. Im and
K. Kuczera and
T. Lazaridis and
J. Ma and
V. Ovchinnikov and
E. Paci and
R. W. Pastor and
C. B. Post and
J. Z. Pu and
M. Schaefer and
B. Tidor and
R. M. Venable and
H. L. Woodcock and
X. Wu and
W. Yang and
D. M. York and
M. Karplus CHARMM: the biomolecular simulation
program . . . . . . . . . . . . . . . . 1545--1614
M. Bonomi and
A. Barducci and
M. Parrinello Reconstructing the equilibrium Boltzmann
distribution from well-tempered
metadynamics . . . . . . . . . . . . . . 1615--1621
Wonpil Im and
Jinhyuk Lee and
Taehoon Kim and
Huan Rui Novel free energy calculations to
explore mechanisms and energetics of
membrane protein structure and function 1622--1633
Edina Rosta and
H. Lee Woodcock and
Bernard R. Brooks and
Gerhard Hummer Artificial reaction coordinate
``tunneling'' in free-energy
calculations: the catalytic reaction of
RNase H . . . . . . . . . . . . . . . . 1634--1641
Jan H. Meinke and
Ulrich H. E. Hansmann Free-energy-driven folding and
thermodynamics of the 67-residue protein
GS-$\alpha_3$W --- a large-scale Monte
Carlo study . . . . . . . . . . . . . . 1642--1648
Mengen Chen and
Wei Yang On-the-path random walk sampling for
efficient optimization of minimum
free-energy path . . . . . . . . . . . . 1649--1653
Payel Das and
Jingyuan Li and
Ajay K. Royyuru and
Ruhong Zhou Free energy simulations reveal a double
mutant avian H5N1 virus hemagglutinin
with altered receptor binding
specificity . . . . . . . . . . . . . . 1654--1663
Clara D. Christ and
Wilfred F. Van Gunsteren Comparison of three enveloping
distribution sampling Hamiltonians for
the estimation of multiple free energy
differences from a single simulation . . 1664--1679
Xin Zhang and
Artem B. Mamonov and
Daniel M. Zuckerman Absolute free energies estimated by
combining precalculated molecular
fragment libraries . . . . . . . . . . . 1680--1691
Jennifer L. Knight and
Charles L. Brooks III $\lambda$-Dynamics free energy
simulation methods . . . . . . . . . . . 1692--1700
Dian Jiao and
Jiajing Zhang and
Robert E. Duke and
Guohui Li and
Michael J. Schnieders and
Pengyu Ren Trypsin-ligand binding free energies
from explicit and implicit solvent
simulations with polarizable potential 1701--1711
Gerhard König and
Stefan Bruckner and
Stefan Boresch Unorthodox uses of Bennett's acceptance
ratio method . . . . . . . . . . . . . . 1712--1718
Mikolai Fajer and
Robert V. Swift and
J. Andrew McCammon Using multistate free energy techniques
to improve the efficiency of replica
exchange accelerated molecular dynamics 1719--1725
Harald Oberhofer and
Christoph Dellago Efficient extraction of free energy
profiles from nonequilibrium experiments 1726--1736
Eric Vanden-Eijnden Some recent techniques for free energy
calculations . . . . . . . . . . . . . . 1737--1747
Sofie Van Damme and
Patrick Bultinck Conceptual DFT properties-based 3D QSAR:
Analysis of inhibitors of the nicotine
metabolizing CYP2A6 enzyme . . . . . . . 1749--1757
Zden\uek Futera and
Julia Klenko and
Judit E. \vSponer and
Ji\vrí \vSponer and
Jaroslav V. Burda Interactions of the ``piano-stool''
[ruthenium(II)
($\eta^6$-arene)(en)CL]$^+$ complexes
with water and nucleobases; ab initio
and DFT study . . . . . . . . . . . . . 1758--1770
Adri\`a Gil and
Mariona Sodupe and
Juan Bertran Influence of ionization on the
conformational preferences of peptide
models. Ramachandran surfaces of
$N$-formyl-glycine amide and
$N$-formyl-alanine amide radical cations 1771--1784
Guo-Xu Zhang and
Ying Xie and
Hai-Tao Yu and
Hong-Gang Fu First-principles calculations of the
stability and electronic properties of
the PbTiO$_3$ (110) polar surface . . . 1785--1798
Séverine Queyroy and
Haruki Nakamura and
Ikuo Fukuda Numerical examination of the extended
phase-space volume-preserving integrator
by the Nosé--Hoover molecular dynamics
equations . . . . . . . . . . . . . . . 1799--1815
Xinli Song and
Jicun Li and
Hua Hou and
Baoshan Wang Extensive theoretical studies of a new
energetic material:
Tetrazino-tetrazine-tetraoxide (TTTO) 1816--1820
Pedro E. M. Lopes and
Guillaume Lamoureux and
Alexander D. Mackerell Jr. Polarizable empirical force field for
nitrogen-containing heteroaromatic
compounds based on the classical Drude
oscillator . . . . . . . . . . . . . . . 1821--1838
Shih-Wei Chao and
Arvin Huang-Te Li and
Sheng D. Chao Molecular dynamics simulations of fluid
methane properties using ab initio
intermolecular interaction potentials 1839--1849
Shun Sakuraba and
Akio Kitao Multiple Markov transition matrix
method: Obtaining the stationary
probability distribution from multiple
simulations . . . . . . . . . . . . . . 1850--1858
Kai Lüder and
Lennart Lindfors and
Jan Westergren and
Sture Nordholm and
Rasmus Persson and
Mikaela Pedersen In silico prediction of drug solubility:
4. Will simple potentials suffice? . . . 1859--1871
Ujjal Das and
Krishnan Raghavachari Predicting PH vibrations of gas phase
molecules and surface-adsorbed species
using bond length-frequency correlations 1872--1881
Wen Lai Huang Electronic structures and optical
properties of BiOX (X = F, Cl, Br, I)
via DFT calculations . . . . . . . . . . 1882--1891
Huaiyong Li and
Siyuan Zhang and
Shihong Zhou and
Xueqiang Cao Investigation of chemical bond
characteristics, thermal expansion
coefficients and bulk moduli of
$\alpha$-R$_2$MoO$_6$ and
R$_2$Mo$_2$O$_7$ (R = rare earths) by
using a dielectric chemical bond method 1892--1898
Max K. Leong and
Yen-Ming Chen and
Tzu-Hsien Chen Prediction of human cytochrome P450
2B6-substrate interactions using
hierarchical support vector regression
approach . . . . . . . . . . . . . . . . 1899--1909
Robert Grybos and
Lubomir Benco and
Tomas Bu\vcko and
Jürgen Hafner Interaction of NO molecules with Pd
clusters: Ab initio density--functional
study . . . . . . . . . . . . . . . . . 1910--1922
Eun-Jong Hong and
Shaun M. Lippow and
Bruce Tidor and
Tomás Lozano-Pérez Rotamer optimization for protein design
through MAP estimation and problem-size
reduction . . . . . . . . . . . . . . . 1923--1945
Frederik Tielens Exploring the reactivity of framework
vanadium, niobium, and tantalum sites in
zeolitic materials using DFT reactivity
descriptors . . . . . . . . . . . . . . 1946--1951
William J. Allen and
Justin A. Lemkul and
David R. Bevan GridMAT-MD: a grid-based membrane
analysis tool for use with molecular
dynamics . . . . . . . . . . . . . . . . 1952--1958
Shuang Chen and
Jing Ma Charge transport in stacking metal and
metal-free phthalocyanine iodides.
Effects of packing, dopants, external
electric field, central metals, core
modification, and substitutions . . . . 1959--1972
Seonah Kim and
Anita M. Orendt and
Marta B. Ferraro and
Julio C. Facelli Crystal structure prediction of flexible
molecules using parallel genetic
algorithms with a standard force field 1973--1985
Junmeng Cai and
Siyu Chen A new iterative linear integral
isoconversional method for the
determination of the activation energy
varying with the conversion degree . . . 1986--1991
Xia Wu and
Wensheng Cai and
Xueguang Shao Optimization of bimetallic Cu--Au and
Ag--Au clusters by using a modified
adaptive immune optimization algorithm 1992--2000
Bahram Hemmateenejad and
Ahmad R. Mehdipour and
Ramin Miri and
Mojtaba Shamsipur Application of MOLMAP approach for QSAR
modeling of various biological
activities using substituent electronic
descriptors . . . . . . . . . . . . . . 2001--2009
Konrad H. Marti and
Markus Reiher Haptic quantum chemistry . . . . . . . . 2010--2020
Aurélien Grosdidier and
Vincent Zoete and
Olivier Michielin Blind docking of 260 protein--ligand
complexes with EADock 2.0 . . . . . . . 2021--2030
Weiyang Chen and
Bo Liao and
Wen Zhu and
Xuyu Xiang Multiple sequence alignment algorithm
based on a dispersion graph and ant
colony algorithm . . . . . . . . . . . . 2031--2038
Michio Iwaoka and
Naoki Kimura and
Daisuke Yosida and
Toshiya Minezaki The SAAP force field: Development of the
single amino acid potentials for 20
proteinogenic amino acids and Monte
Carlo molecular simulation for short
peptides . . . . . . . . . . . . . . . . 2039--2055
Jian Lin and
Kechen Wu and
Mingxin Zhang A new hybrid DFT approach to electronic
excitation and first
hyperpolarizabilities of transition
metal complexes . . . . . . . . . . . . 2056--2063
Brecht M. R. Donckels and
Dirk J. W. De Pauw and
Peter A. Vanrolleghem and
Bernard De Baets A kernel-based method to determine
optimal sampling times for the
simultaneous estimation of the
parameters of rival mathematical models 2064--2077
M. Piris and
J. M. Ugalde Iterative diagonalization for orbital
optimization in natural orbital
functional theory . . . . . . . . . . . 2078--2086
Vinzenz Bachler Time-dependent density functional
calculations on the electronic spectra
of the neutral nickel complex
[Ni(L$^{ISQ}$)$_2$] (L$^{ISQ}$ =
3,5-di-tert-butyl-o-diiminobenzosemiquinonate(1$^-$)) and its monoanion and dication 2087--2098
Ramon Carbó-Dorca and
Ana Gallegos Saliner Notes on quantitative
structure-properties relationships
(QSPR) part 2: the role of the number of
atoms as a molecular descriptor . . . . 2099--2104
Wenbo Yu and
Xuee Xu and
Hongbao Li and
Rui Pang and
Kun Fang and
Zijing Lin Extensive conformational searches of 13
representative dipeptides and an
efficient method for dipeptide structure
determinations based on amino acid
conformers . . . . . . . . . . . . . . . 2105--2121
Yang Wang Perfect planar tetracoordinate carbon in
neutral unsaturated hydrocarbon cages: a
new strategy utilizing three-dimensional
electron delocalization . . . . . . . . 2122--2126
Yi He and
Yi Xiao and
Adam Liwo and
Harold A. Scheraga Exploring the parameter space of the
coarse-grained UNRES force field by
random search: Selecting a transferable
medium-resolution force field . . . . . 2127--2135
Yongqi Huang and
Huifang Li and
Yuxiang Bu Molecular dynamics simulation
exploration of cooperative migration
mechanism of calcium ions in
sarcoplasmic reticulum Ca$^{2+}$-ATPase 2136--2145
Nigel J. Brookes and
David C. Graham and
Gemma Christian and
Robert Stranger and
Brian F. Yates The influence of peripheral ligand bulk
on nitrogen activation by
three-coordinate molybdenum complexes
--- a theoretical study using the ONIOM
method . . . . . . . . . . . . . . . . . 2146--2156
L. Martínez and
R. Andrade and
E. G. Birgin and
J. M. Martínez \sc Packmol: a package for building
initial configurations for molecular
dynamics simulations . . . . . . . . . . 2157--2164
Zhigang Zhou and
Yanli Wang and
Stephen H. Bryant Computational analysis of the cathepsin
B inhibitors activities through
LR-MMPBSA binding affinity calculation
based on docked complex . . . . . . . . 2165--2175
Shih-I Lu Gibbs energy of activation for thermal
isomerization of (1Z)-acetaldehyde
hydrazone and (1Z)-acetaldehyde
N,N-dimethylhydrazone by Gaussian-4
theory and CCSD(T)/CBS computations . . 2176--2180
Gab-Yong Lee Substituent effect on electron affinity,
gas-phase basicity, and structure of
monosubstituted propynyl radicals and
their anions: a theoretical study . . . 2181--2186
C. David Sherrill and
Bobby G. Sumpter and
Mutasem O. Sinnokrot and
Michael S. Marshall and
Edward G. Hohenstein and
Ross C. Walker and
Ian R. Gould Assessment of standard force field
models against high-quality ab initio
potential curves for prototypes of
$\pi$\doublebond$\pi$, CH\slash$\pi$,
and SH/$\pi$ interactions . . . . . . . 2187--2193
Hong-Xia Liu and
Ying Wang and
Lei Yang and
Jing-Yao Liu and
Hong Gao and
Ze-Sheng Li and
Chia-Chung Sun CH$_3$NHNH$_2$ + OH reaction: Mechanism
and dynamics studies . . . . . . . . . . 2194--2204
Bo Liao and
Weiyang Chen and
Xingming Sun and
Wen Zhu A binary coding method of RNA secondary
structure and its application . . . . . 2205--2212
Masanori Miura and
Yuriko Aoki Ab initio theory for treating local
electron excitations in molecules and
its performance for computing optical
properties . . . . . . . . . . . . . . . 2213--2230
Yifan Song and
Junjun Mao and
M. R. Gunner MCCE2: Improving protein $pK_a$
calculations with extensive side chain
rotamer sampling . . . . . . . . . . . . 2231--2247
Lei Chen and
Lin Lu and
Kairui Feng and
Wenjin Li and
Jie Song and
Lulu Zheng and
Youlang Yuan and
Zhenbin Zeng and
Kaiyan Feng and
Wencong Lu and
Yudong Cai Multiple classifier integration for the
prediction of protein structural classes 2248--2254
Chenggang Zhou and
Jinping Wu and
Liang Chen and
Yang Wang and
Hansong Cheng and
Robert C. Forrey Force field for copper clusters and
nanoparticles . . . . . . . . . . . . . 2255--2266
Yumi N. Imai and
Yoshihisa Inoue and
Isao Nakanishi and
Kazuo Kitaura Amide-$\pi$ interactions between
formamide and benzene . . . . . . . . . 2267--2276
Dongsheng Zou and
Zhongshi He and
Jingyuan He $\beta$-Hairpin prediction with
quadratic discriminant analysis using
diversity measure . . . . . . . . . . . 2277--2284
Matthias Rupp and
Petra Schneider and
Gisbert Schneider Distance phenomena in high-dimensional
chemical descriptor spaces: Consequences
for similarity-based approaches . . . . 2285--2296
Conrad Shyu and
F. Marty Ytreberg Reducing the bias and uncertainty of
free energy estimates by using
regression to fit thermodynamic
integration data . . . . . . . . . . . . 2297--2304
Ute F. Röhrig and
Aurélien Grosdidier and
Vincent Zoete and
Olivier Michielin Docking to heme proteins . . . . . . . . 2305--2315
Pablo Rivero and
Christoph Loschen and
Ibério De P. R. Moreira and
Francesc Illas Performance of plane-wave-based LDA + U
and GGA + U approaches to describe
magnetic coupling in molecular systems 2316--2326
Mikaël Kepenekian and
Vincent Robert and
Boris Le Guennic and
Coen De Graaf Energetics of [Fe(NCH)$_6$]$^{2+}$ via
CASPT2 calculations: a spin-crossover
perspective . . . . . . . . . . . . . . 2327--2333
Wei Kan and
Hua Zhong and
Hai-Tao Yu Theoretical prediction regarding
structural and thermodynamical
characteristics of stable CH$_3$PO$_2$
isomers and unimolecular decomposition
mechanisms of species
CH$_3$P(\doublebondO)$_2$,
CH$_3$O\bondP\doublebondO, and
CH$_2$\doublebondP(\doublebondO)OH . . . 2334--2350
Tetsu Narumi and
Kenji Yasuoka and
Makoto Taiji and
Siegfried Höfinger Current performance gains from utilizing
the GPU or the ASIC MDGRAPE-3 within an
enhanced Poisson Boltzmann approach . . 2351--2357
Erjun Zhao and
Bo Hong and
Jian Meng and
Zhijian Wu First principles investigation on the
ultra-incompressible and hard TaN . . . 2358--2363
Adam Górecki and
Marcin Szypowski and
Maciej D\lugosz and
Joanna Trylska RedMD --- reduced molecular dynamics
package . . . . . . . . . . . . . . . . 2364--2373
Olivier Delalande and
Nicolas Férey and
Gilles Grasseau and
Marc Baaden Complex molecular assemblies at hand via
interactive simulations . . . . . . . . 2375--2387
Xin Zhang and
Ruibo Wu and
Lingchun Song and
Yuchun Lin and
Menghai Lin and
Zexing Cao and
Wei Wu and
Yirong Mo Molecular dynamics simulations of the
detoxification of paraoxon catalyzed by
phosphotriesterase . . . . . . . . . . . 2388--2401
James R. Apgar and
Seungsoo Hahn and
Gevorg Grigoryan and
Amy E. Keating Cluster expansion models for
flexible-backbone protein energetics . . 2402--2413
Gergely Gidofalvi and
Ron Shepard Computation of determinant expansion
coefficients within the graphically
contracted function method . . . . . . . 2414--2419
Luis F. Pacios and
Víctor M. Campos and
Irene Merino and
Luis Gómez Structures and thermodynamics of
biphenyl dihydrodiol stereoisomers and
their metabolites in the enzymatic
degradation of arene xenobiotics . . . . 2420--2432
Hsin-Tsung Chen and
Jee-Gong Chang and
Hui-Lung Chen and
Shin-Pon Ju Identifying the O$_2$ diffusion and
reduction mechanisms on CeO$_2$
electrolyte in solid oxide fuel cells: a
DFT + U study . . . . . . . . . . . . . 2433--2442
Jacopo Sgrignani and
Claudia Bonaccini and
Giovanni Grazioso and
Matteo Chioccioli and
Andrea Cavalli and
Paola Gratteri Insights into docking and scoring
neuronal $\alpha$4$\beta$2 nicotinic
receptor agonists using molecular
dynamics simulations and QM/MM
calculations . . . . . . . . . . . . . . 2443--2454
Hassan Golmohammadi Prediction of octanol--water partition
coefficients of organic compounds by
multiple linear regression, partial
least squares, and artificial neural
network . . . . . . . . . . . . . . . . 2455--2465
N. M. F. S. A. Cerqueira and
P. J. Gonzalez and
C. D. Brondino and
M. J. Romão and
C. C. Romão and
I. Moura and
J. J. G. Moura The effect of the sixth sulfur ligand in
the catalytic mechanism of periplasmic
nitrate reductase . . . . . . . . . . . 2466--2484
A. G. Bailey and
C. P. Lowe MILCH SHAKE: an efficient method for
constraint dynamics applied to alkanes 2485--2493
Jagdish C. Patra and
Onkar Singh Artificial neural networks-based
approach to design ARIs using QSAR for
diabetes mellitus . . . . . . . . . . . 2494--2508
Lu Wang and
Jijun Zhao and
Zhen Zhou and
S. B. Zhang and
Zhongfang Chen First-principles study of molecular
hydrogen dissociation on doped
Al$_{12}$X (X = B, Al, C, Si, P, Mg, and
Ca) clusters . . . . . . . . . . . . . . 2509--2514
Jacek Korchowiec and
Jakub Lewandowski and
Marcin Makowski and
Feng Long Gu and
Yuriko Aoki Elongation cutoff technique armed with
quantum fast multipole method for linear
scaling . . . . . . . . . . . . . . . . 2515--2525
Wen-Chi Chang and
Tzong-Yi Lee and
Dray-Ming Shien and
Justin Bo-Kai Hsu and
Jorng-Tzong Horng and
Po-Chiang Hsu and
Ting-Yuan Wang and
Hsien-Da Huang and
Rong-Long Pan Incorporating support vector machine for
identifying protein tyrosine sulfation
sites . . . . . . . . . . . . . . . . . 2526--2537
Oscar Gálvez and
Pedro C. Gómez and
Luis F. Pacios Characterization of two types of
intermolecular interactions on halogen
monoxide monohydrates . . . . . . . . . 2538--2549
Terutaka Yoshizawa and
Masahiko Hada Relativistic and electron-correlation
effects on magnetizabilities
investigated by the Douglas-Kroll-Hess
method and the second-order
Mòller--Plesset perturbation theory . . . 2550--2566
Chang-Liang Sun and
Xiao-Nan Jiang and
Chang-Sheng Wang An analytic potential energy function
for the amide--amide and amide--water
intermolecular hydrogen bonds in
peptides . . . . . . . . . . . . . . . . 2567--2575
Andrey A. Toropov and
Alla P. Toropova and
Emilio Benfenati and
Alberto Manganaro QSPR modeling of enthalpies of formation
for organometallic compounds by
SMART-based optimal descriptors . . . . 2576--2582
Ayako Nakata and
Takao Tsuneda and
Kimihiko Hirao Modified regional self-interaction
corrected time-dependent density
functional theory for core excited-state
calculations . . . . . . . . . . . . . . 2583--2593
Takeshi Ishikawa and
Takakazu Ishikura and
Kazuo Kuwata Theoretical study of the prion protein
based on the fragment molecular orbital
method . . . . . . . . . . . . . . . . . 2594--2601
Satoshi Omori and
Sotaro Fuchigami and
Mitsunori Ikeguchi and
Akinori Kidera Linear response theory in dihedral angle
space for protein structural change upon
ligand binding . . . . . . . . . . . . . 2602--2608
Art E. Cho and
David Rinaldo Extension of QM/MM docking and its
applications to metalloproteins . . . . 2609--2616
Yin Wei and
Bandaru Sateesh and
Boris Maryasin and
G. N. Sastry and
Hendrik Zipse The performance of computational
techniques in locating the charge
separated intermediates in
organocatalytic transformations . . . . 2617--2624
Takashi Nakamura and
Azusa Yamaguchi and
Hirotaka Kondo and
Hirofumi Watanabe and
Tatsuo Kurihara and
Nobuyoshi Esaki and
Shuichi Hirono and
Shigenori Tanaka Roles of K151 and D180 in L-2-haloacid
dehalogenase from Pseudomonas sp. YL:
Analysis by molecular dynamics and ab
initio fragment molecular orbital
calculations . . . . . . . . . . . . . . 2625--2634
Mehdi Bagheri Hamaneh and
Matthias Buck Refinement of the primary hydration
shell model for molecular dynamics
simulations of large proteins . . . . . 2635--2644
R. A. Evarestov and
M. V. Losev All-electron LCAO calculations of the
LiF crystal phonon spectrum: Influence
of the basis set, the
exchange-correlation functional, and the
supercell size . . . . . . . . . . . . . 2645--2655
Minoru Saito and
Isao Okazaki Force-field parameters of the $\Psi$ and
$\Phi$ around glycosidic bonds to oxygen
and sulfur atoms . . . . . . . . . . . . 2656--2665
Thomas Sandberg and
Matti Hotokka Conformational analysis of
hydroxymatairesinol in aqueous solution
with molecular dynamics . . . . . . . . 2666--2673
Xiaoyan Zheng and
Xueye Wang and
Shanfeng Yi and
Nuanqing Wang and
Yueming Peng DFT study of the carbon- and
nitrogen-pivot lariat crown ethers and
their complexes with alkali metal
cations: Na$^+$, K$^+$ . . . . . . . . . 2674--2683
Wen Lai Huang First-principles calculations on the
energetics, electronic structures and
magnetism of SrFeO$_2$ . . . . . . . . . 2684--2693
Xiaohua Chen and
Dianxiang Xing and
Liang Zhang and
Robert I. Cukier and
Yuxiang Bu Effect of metal ions on radical type and
proton-coupled electron transfer
channel: $\sigma$-Radical vs
$\pi$-radical and $\sigma$-channel vs
$\pi$-channel in the imide units . . . . 2694--2705
Han Zheng and
Shenglong Wang and
Yingkai Zhang Increasing the time step with mass
scaling in Born--Oppenheimer ab initio
QM/MM molecular dynamics simulations . . 2706--2711
Indrani Mitra and
Kunal Roy and
Achintya Saha QSAR of antilipid peroxidative activity
of substituted benzodioxoles using
chemometric tools . . . . . . . . . . . 2712--2722
Yufang Liu and
Junxia Ding and
Ruiqiong Liu and
Deheng Shi and
Jinfeng Sun Time-dependent density functional theory
study on the electronic excited-state
geometric structure, infrared spectra,
and hydrogen bonding of a doubly
hydrogen-bonded complex . . . . . . . . 2723--2727
Akifumi Oda and
Noriyuki Yamaotsu and
Shuichi Hirono Evaluation of the searching abilities of
HBOP and HBSITE for binding pocket
detection . . . . . . . . . . . . . . . 2728--2737
Peng Zhou and
Jianwei Zou and
Feifei Tian and
Zhicai Shang Geometric similarity between
protein--RNA interfaces . . . . . . . . 2738--2751
Sérgio F. Sousa and
Emanuela S. Carvalho and
Diana M. Ferreira and
Isabel S. Tavares and
Pedro A. Fernandes and
Maria João Ramos and
José A. N. F. Gomes Comparative analysis of the performance
of commonly available density
functionals in the determination of
geometrical parameters for zinc
complexes . . . . . . . . . . . . . . . 2752--2763
J. Oscar C. Jiménez-Halla and
Eduard Matito and
Lluís Blancafort and
Juvencio Robles and
Miquel Sol\`a Tuning aromaticity in trigonal alkaline
earth metal clusters and their alkali
metal salts . . . . . . . . . . . . . . 2764--2776
Chinapong Kritayakornupong Structural and dynamical properties of
the V$^{3+}$ ion in dilute aqueous
solution: an ab initio QM/MM molecular
dynamics simulation . . . . . . . . . . 2777--2783
F. Matthias Bickelhaupt Book Review: \booktitleA chemist's guide
to valence bond theory, by Sason S.
Shaik and Philippe C. Hiberty, John
Wiley & Sons, Inc., Hoboken, New Jersey,
2008, 311 pp. ISBN-10 0-470-03735-0 . . 2784--2784
Garrett M. Morris and
Ruth Huey and
William Lindstrom and
Michel F. Sanner and
Richard K. Belew and
David S. Goodsell and
Arthur J. Olson AutoDock4 and AutoDockTools4: Automated
docking with selective receptor
flexibility . . . . . . . . . . . . . . 2785--2791
J. Oscar C. Jiménez-Halla and
Eduard Matito and
Lluís Blancafort and
Juvencio Robles and
Miquel Sol\`a Erratum: Tuning aromaticity in trigonal
alkaline earth metal clusters and their
alkali metal salts . . . . . . . . . . . 372--373
Laban Bondesson and
Elias Rudberg and
Yi Luo and
Pawe\l Sa\lek Erratum: ``Basis set dependence of
solute--solvent interaction energy of
benzene in water: a HF/DFT study'' . . . 354--354
D. Heringer and
T. A. Niehaus and
M. Wanko and
Th. Frauenheim Erratum: ``Analytical excited state
forces for the time-dependent
density-functional tight-binding
method'' [J. Comp. Chem. \bf 28, 2589] 593--593
J. H. van Lenthe and
H. B. Broer-Braam and
Z. Rashid Letters to the Editor: On the efficiency
of VBSCF algorithms, a comment on ``An
efficient algorithm for energy gradients
and orbital optimization in valence bond
theory'' . . . . . . . . . . . . . . . . 911--913
Wei Wu and
Yirong Mo Letters to the Editor: Reply to comment
on the paper ``An Efficient Algorithm
for Energy Gradients and Orbital
Optimization in Valence Bond Theory'' 914--915
Kameron R. Jorgensen and
Angela K. Wilson Letters to the Editor: Comment on the
paper ``Extensive Theoretical Studies of
a New Energetic Material:
Tetrazino-Tetrazine-Tetraoxide (TTTO)''
by Xinli Song, Jicun Li, Hua Hou, and
Baoshan Wang . . . . . . . . . . . . . . 1967--1968
M. E. Chen and
W. Yang Erratum: On-the-path random walk
sampling for efficient optimization of
minimum free energy path . . . . . . . . 2400--2400