Journal of ^ Computational Chemistry ORGANIC INORGANIC PHYSICAL BIOLOGICAL Volume Contents ' Volume 23, 2002 Issue 1, January 15, 2002 Free Energy Component Analysis of 40 Protein-DSA Complexes: 4 Consensus View on the Thermodynamics of Binding at the Molecular I^evel B. JAYARAM. K. MCCONNKLL. S. B. DIXIT. A. DA.S. AND D L. BKVERlIXiK 1 Computational Alanine Scanning of the 1:1 Human Growth Hormone-Receptor Complex SHLANCiHDNG HL(X IRINA MA.SSOVA. AND PETER A. KILLMAN 15 Evolution of Physics-Based Methodology for Exploring the Conformational Energy iMudscape of Proteins HAROLD A. .SCHERAGA. JAROSLAVV PII.LARDY. ADAM I.IWO, JOOYOl NG LEE. CEXARY C/.APLEW.SKI. DANIEL R RIPOI.L. WILLIAM J. WEDEMEYER. AND YELENA A. ARNAl TOVA 28 Predicted Solution of Zymogen Human Coagulation EVH LALITH PERERA. THOMAS A. DARDEN. AND LEE G. PEDERSON 35 Simulating Enzyme Reactions: Challenges and Perspectives MARTIN J. FIELD 48 Computational Studies of Reaction Mechanisms of Methane Monooxygenase and Ribonucleotide Reductase MARICEL TORRENT. DIAMALADDIN G. ML SAEV. HAROLD BASCH. AND KEl I MOROKl'MA 59 The Elastic Set Algorithm and Protein Structure Prediction KEITH D. BALL. BLRAK ERM.AN. AND KEN A. DILL 77 Transition State Docking: A Probe for Soncovalent Catalysis in Biological Systems. Application to Antibody-Catalyzed Ester Hydrolysis DEAN J. TANTILLO AND K N. HOLK 84 Combined QM/MM Study of the Opsin Shift in Bacteriorhodopsin RAMKL MAR RAJAMANI AND JIALI GAO 96 Theoretical Calculation of the Coiled-Coil Stability in Water in the Context of its Possible Use as a Molecular Rack MAREK ORZECHOWSKI. PIOTR CIEPLAK. AND LI’CIAN PIELA 106 Maximum Feasibility Guideline in the Design and Analysis of Protein Folding Potentials JAROSLAW MELLER. MICHAEL WAGNER. AND RON ELBER 111 Dynamics of Ixirge Proteins through Hierarchical Levels of Coarse-Grained Structures PEMRA DORL KER. ROBERT L. JERNIGAN. AND IVET BAHAR 119 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 WALTER ROCCHIA. SUNDARAM SRIDHARAN. ANTHONY NICHOLES. EMIL ALEXOV. ALESSANDRO CHIABRERA. AND BARRY HONIG 128 Folding Funnels: The Key to Robust Protein Structure Prediction COREY HARDIN. MICHAEL P. E:ASTW(X)D, MICHAEL PRENTISS. Z. LLTHEY-.SCHL'LTEN. AND PETER G. WOLYNES 138 Identifying Native-Like Protein Structures Using Physics-Based Potentials BRIAN N. DOMINY AND CHARLES L BRCXJKS. Ill 147 Volume Contents • Vol. 23, So. 16 • Journal of Computational Chemistry Is there a Unique .Melting Temperature for Two-State Proteinis? D. K. KLIMOV AND D. THIRLMALAl Polymer Collapse, Protein Folding, and the Percolation Threshold HAGAI MEIROVITCH Computation of the Physio-Chemical Properties and Data .Mining of iMrge Molecular Collections AILAN CHENG. DAVID J DILLER. STEVEN L. DIXON. WILLIAM J EGAN. GEORGE LAL RI. AND KENNETH M. MERZ. JR. Qmd-Plot: A Graphical Utility for Rapid Preliminary .Analysis of Time Series of Fluctuating Data, Developed in the Context of .Molecular Dynamics Simulations SA.M KAL.AT. GEOFF MANN. AND JAN HERMANS Docking of Small Ligands to Low-Resolution and Theoretically Predicted Receptor Structures MAREK WOJCIECHOWSKI AND JEFFREY SKOLNICK Issue 2, January 30, 2002 Combined .Ab mWAolEmpirical .Approach for Optimization of Lennard-Jones Parameters for PolarSeutral Compounds I-JEN CHEN. DAXU YIN. AND .ALEXANDER D. MACKEREL!.. JR. .Application of the Frozen .Atom .Approximation to the GB/S.A Continuum .Model for Solvation Free Energy OLGLN GLVENCH. JORG VVELSER. PETER SHENKIN. ISTV.AN KOLOSSV.ARY. AND W. CLARK STILL Conformational Analysis: A Sew .Approach by Means of Chemonietrics ALINE THAIS BRLNI. VITOR B P. LEITE. AND MARCIA M. C. FERREIRA Linear Scaling Local Correlation .Approach for Solving the Coupled Cluster Equations of iMrge Systems SHL'HL'A LI. JING MA. AND YL ANSHENG JIANG .Ab Initio Prediction of Helical Segments in Polypeptides J. L. KLEPEIS AND C. A. FLOL DAS Support Vector Machines for Predicting HIV Protease Cleavage Sites in Protein ^ L-DONG CAL XIAO-JLN LIU. XLE-BIAO XU. AND KUO-CHEN CHOU Prediction of Aqueous Solubility of Drugs and Pesticides with COSMO-RS ANDREAS KLAMT. FRANK ECKERT. MARTIN HORNING. .MICHAEL E. BECK. AND THOR.STEN BURGER MM3 Parametrization of Eour- and Eive-Coordinated Rhenium Complexes by a Genetic Algorithm—Which Eactors Influence the Optimization Performance? THOMAS STRASSNER. MARKUS BUSOLD. AND WOLFGANG A. HERRMANN .Mechanism for Large Eirst Hyperpolarizabilities of Phosphonic .Acid Stilbene Derivatives PATRIZIA CALAMINICI. KARL JUG. ANDREAS M. KO.STER. CECILE ARBEZ-GINDRE. AND CON.STANTINOS G. SCRETTAS Chemical Shift Driven Geometry Optimization RAIKER WITTER. WOLFRAM PRIEB. AND ULRICH STERNBERG Efficient Linear Algebra Routines for Symmetric Matrices Stores in Packed Eorm REINHART AHLRICHS AND KAKHA TSERETELI Spectral Density Calculation by Using the Chebyshev Expansion TSUTOMU IKEGAMI AND SUEHIRO IWATA Issue 3, February 2002 Semiglobal Simplex Optimization and Its .Application to Determining the Preferred Solvation Sites of Proteins S DENNIS AND S. VAJDA Semiautomatic Sequence-Specific .Assignment of Proteins Based on the Tertiary Structure—The Program st2nmr PRIMOZ PRISTOV-SEK. HEINZ RUTEJANS. AND ROMAN JERALA Volume Contents • Vol. 23, .\o. 16 • Journal of Computational Chemistry Quantum Mechanical Study of the Conformational Behavior of Proline and 4R-Hydroxyproline Dipeptide Analogues in Vacuum and in Aqueous Solution CATERINA BENZl. ROBERTO IMPROTA. GIOVANNI SCALMANT. AND VINCENZO BARONE Restrained Point-Charge Models for Disaccharides EMMA SIGFRIDSSON. LEE RYDE. AND BRUCE L. BUSH On the Irrelevance of Electrostatics for the Crystal Structures and Polymorphism of Long Even n-Alkanes JACCO VAN DE STREEK. PAUL VERWER, PIET BENNEMA. AND ELIAS VLIEG Oligovalent Link Atoms in Embedding Calculations THOMAS KRUGER AND ALEXANDER F. SAX Accompanying Coordinate Expansion Formulas Derived with the Solid Harmonic Gradient KAZUHIRO ISHIDA Theoretical Auger Electron Spectra of Polymers by Density Functional Theory Calculations using Mode Dimers TAKAO OTSUKA, SEIJI KOIZUMI. K.AZUNAKA ENDO. HIROYUKI K.AWABE. AND DELANO P. CHONG Dynamics of a Protein and Water Molecules Surrounding the Protein: Hydrogen-Bonding between Vibrating Water Molecules and a Fluctuating Protein SHUZO YOSHIOKI Theoretical Study on the Mechanism of the Gas-Phase Reaction of DihoranetJ) Anion with Carbon Disulfide ZHENG-WANG QU, HUI ZHU. ZE-SHENG LI. .AND QI-YUAN ZHANG Software News and Updates Basis-Set Completeness Profiles in Two Dimensions ALEXANDER A. AUER. TRYGVE HELGAKER. AND WIM KLOPPER Issue 4, March 2002 A Fast Annealing Evolutionary Algorithm for Global Optimization WENSHENG CAI AND XUEGUANG SHAO Studies on 4,7-di-Substitution Effects of One Ligand in [RulPhenjjfi'*' with DFT Method KANGCHENG ZHENG. JUPING WANG. YONG SHEN. WENLIE PENG. AND FENGCUN YUN .\b Initio and DFT Studies on van der Waals Trimers: The OCS • (CO^lj Complexes H VALDES AND J. A. SORDO Crystal Structure Predictions Using Five Space Groups with Two Independent Molecules. The Case of Small Organic Acids BOL KE P. VAN EIJCK .Wh’ Method for Parallel Computation of Hessian Matrix of Conformational Energy Function in Internal Coordinates SHUGO NAKAMURA. DAISUKE KYONO. MITSUNORI IKEGUCHI. AND KENTARO SHI.MIZl Calibration of Force-Field Dependency in Free Energy Landscapes of Peptide Conformations by Quantum Chemical Calculations SATOSHI ONO. M.AS.ATAKA KURODA. JUNICHI HIGO. NOBUYUKI NAK.AJIMA. AND HARUKI NAKAMURA Rapidly Converging iMttice Sums for Sonelectrostatic Interactions GWON HEE KO AND WILLIAM H FINK Sew Space Warping Method for the Simulation of Large-Scale Macromolecular Conformational Changes KHULOUD J.AQAMAN AND PETER J. ORTOLEVA Accurate Prediction of Proton Chemical Shifts. H. Peptide .Analogues BING WANG. JAMES F. HINTON. AND PETER PULAY Improved Semiempirical Heats of Formation through the Use of Bond and Group Equivalents MATTHEW P. REP.ASKY. JAYARAMAN CHANDRASEKHAR. AND WILLIAM L. JORGEN.SEN 498 Volume Contents • Vol. 23, So. 16 • Journal of Computational Chemistry Monte Carlo Sampling Algorithm for Searching a Scale-Transformed Energy Space of Polypeptides HIDEAKl NAKAMURA 511 Issue 5, April 15, 2002 The SGB/SP Hydration Free Energy Model Based on the Surface Generalized Born Solvent Reaction Field and \ovel Sonpolar Hydration Free Energy Estimators EMILIO GALLICCHIO. LINDA YU ZHANG. AND RONALD M. LEVY 517 An Ah Initio Theoretical Study of Electronic Structure and Properties of 2'-Deoxyguanosine in Gas Phase and Aqueous Media S, K. MISHRA AND P, C. MISHRA 530 Variational Treatment of the Vibrational Hamiltonian for A// , and H^NO PHILIPPE MARSAL AND MICHEL RIXTHE 541 Calculation of the Free Energy of Solvation for Neutral Analogs of Amino Acid Side Chains ALESSANDRA VILLA AND ALAN E. MARK 548 Hydrophobic Similarity between Molecules: A MST-Based Hydrophobic Similarity Index J. MUNOZ. X. BARRIE. B. HERN.ANDEZ. MODESTO OROZCO. AND F. JAVIER LUQUE 554 Comprehensive Relativistic .4b Initio and Density Functional Theory Studies on PtH, PtF, PtCl, and Pt(NHd^Cf WENJIAN LIU AND ROBERT FR.ANKE 564 Determination of Energy Minima and Saddle Points Using Multireference Configuration Interaction Methods in Combination with Reduced Gradient Following: The S,; Surface of H^CO and the T/ and T, Surfaces of Acetylene MICHAL DALLOS. HANS LLSCHK.A. ELIZETE VENTURA DO MONTE. MICHAEL HIRSCH. AND WOLFGANG QUAPP 576 Erratum Density Functional Theory Studies on the Dissociation Energies of Metallic Salts: Relationship between iMttice and Dissociation Energies CHANG KON KIM. HONGOK WON. HOON SIK KIM. YONG SOO KANG. HONG GUANG LI. AND CHAN KYUNG KIM 584 Issue 6, April 30, 2002 4Ab Initio Conformational Studies on Diols and Binary Diol-Water Systems Using DFT Methods. Intramolecular Hydrogen Bonding and l:l Complex Formation with Water ROGER A. KLEIN 585 Novel Computer Program for Fast Exact Calculation of Accessible and Molecular Surface Areas and Average Surface Curvature OLEG V. TSODIKOV. M. THOMAS RECORD. JR.. AND YURI V. SERGEEV 6(H) Specific Force Field Parameters Determination for the Hybrid Ab Initio QM/MM LSCF Method NICOLAS FERRE. XAVIER ASSFELD. AND JEAN-LOUIS RIVAIL 610 Theoretical Study on the Mechanism of the 'CHCl + NO Reaction JIA.N-JUN LIU, YI-HONG DING. YU-GUO TAO. JI-KANG FENG. AND CHI.A-CHUNG SUN 625 Conformational Analysis of the Tyrosine Dipeptide Analogue in the Gas Phase and in Aqueous Solution by a Density Functional/Continuum Solvent Model EMMA LANGELLA. NADIA REGA. ROBERTO IMPROTA. ORLANDO CRESCENZI. AND VINCENZO BARONE 650 Density Functional Theory for Efficient Ab Initio Molecular Dynamics Simulations in Solution JEAN-LUC FATTEBERT AND FRANCOIS GYGI 662 Volume Contents • Vo/. 23, \o. 16 • Journal of Computational Chemistry Compiitatwn of Pressure Components due to Class // Force Fields JOHN E. CARPENTER Multiple Grid Methods for Classical Molecular Dynamics ROBERT D. SKEEL. ISMAIL TEZCAN. AND DAVID J HARDY 673 Issue 7, May 2002 Influence of the Presence of Small Gas Molecules in the Structure of Comhlike Polyacrylates: A Monte Carlo Study SALVADtJR LEON. DAVID ZANL Y. AND CARLOS ALEMAN 685 A .\ew Molecular Mechanics Force Field for the Oxidized Form of Blue Copper Proteins PETER COMBA AND RAINER REMENYI 697 ,\Vh' Approach to Free Energy of Solvation Applying Continuum Models to Molecular Dynamics Simulation PALLO F. B. GON’CALVES AND HUBERT STASSEN 7()6 Energy-Based Reconstruction of a Protein Backbone from its a-Carhon Trace by a Monte-Carlo Method RAJML ND K.AZMIERKIEW ICZ. ADAM LIWC). AND HAROLD A. SCHER.AC1A 715 Rh'^/Cs'^ Selectivity of Benzo and Tribenzo Derivatives of the 21C7 Crown Ether. A Density Functional Study JEROME GOLEBIOWSKI. VERONIQUE LAMARE. AND MANUEL F. RUIZ-LOPEZ 724 Role of Bifurcation in the Bond Shifting of Cyclooctatetraene OBIS CASTANO. RAUL PALMEIRO. LUIS MANUEL FRUTOS. AND JOSE LUISANDRES 732 .-4 Fast Pairwise Evaluation of Molecular Surface Area VLADISLAV VASILYEV AND ENRICO O. PURISIMA 737 Software News and Updates Generate: A Program for 3-D Structure Generation and Conformational Analysis of Peptides and Peptidomimetics PATRICK BULTINCK. STUN AUGUSTYNEN. HANS \V. HILBERS. ED E. MORET. AND JAN P TOLLENAERE 746 Assessment of the Parallelization Approach of d2_cluster for High-Performance Sequence Clustering JOHN E. CARPENTER. ALAN CHRISTOFFELS. YAEL WEINB.ACH. AND WINSTON A. HIDE 755 Issue 8, June 2002 The Dirac Equation in Quantum Chemistry: Strategies to Overcome the Current Computational Problems LUCAS VISSCHER 759 Relativistic Energy-Consistent Pseudopotentials—Recent Developments HERMANN STOLL. BERNHARD METZ. AND MICHAEL DOLG 767 Spin Densities in Two-Component Relativistic Density Functional Calculations: Soncollinear versus Collinear Approach CHRISTOPH VAN WLLLEN 779 .4 Systematic Sequence of Relativistic Approximations KENNETH G. DYALL 786 Calculation of Electronic g-Tensors for Transition Metal Complexes Using Hybrid Density Functionals and Atomic Meanfield Spin-Orbit Operators MARTIN KAUPP. ROM.YN REVIAKINE. OLGA L. MALKIN.A. ALE.XEI ARBUZNIKOV. BERND SCHI.M.MELPFENNIG. AND VLADI.MIR G M.ALKIN 794 Dependence of Relativistic Effects on Electronic Configuration in the Seutral Atoms of d- and f-Block Elements J AUTSCHB.ACH. S. SIEKIERSKI. M. SETH. P. .SCHW ERDTFEGER. AND W H. E. SCHWARZ 804 Four-Component Relativistic Kohn-Sham Theory TROND SALE AND TRYGVE HELGAKER 814 Volume Contents • Vol. 23, So. 16 • Journal of Computational Chemistry Spin-Orbit Coupling of DFT/MRCI Wavefunctions: Method, Test Calculations, and Application to Thiophene MARTIN KLEINSCHMIDT. JORG TATCHEN. AND CHRISTEL M MARIAN 824 Comparative Study of Relativistic Density Functional Methods Applied to Actinide Species AcOj''*’ and AcFf^for .4c = U, \p MAITE GARCiA-HERNANDEZ. CHRISTA LALTERBACH. SV EN KRUGER. ALEXEI MATVEEV. AND NOTKER ROSCH 834 Relativistic Electronic Structure Theory T.AKAHITO NAK.VJI.MA. TAKESHI YANAI. AND KI.MIHIKO HIR.AO 847 Issue 9, July 15, 2002 Extracting Hydration Sites around Proteins front E.vplicit Water Simulations RICHARD H. HENCHM AN AND J. ANDREW McCAMMON 861 Quantum Bits with Polyacetylene ANDRE ELVAS PEREIRA DA SILV A AND GERALDO MAGELA E SILVA 870 Theoretical Investigation of Electron Transfer Transition in Tetracyanoethylene-Contained Organic Complexes XIANG-YLAN LI AND CHUN-XIL HU 874 Improved RGF .Method to Eind Saddle Points MICHAEL HIRSCH AND WOLFGANG QUAPP 887 Quantum Chemical Calculation of Vibrational Spectra of luirge Molecules—Raman and IR Spectra for Biickminsterfullerene JOHANNES NEUGEBAUER. MARKUS REIHER. CARSTEN KIND. AND BERND A. HESS 895 Pure Component Spectral Reconstruction from .Mixture Data Using SVD, Global Entropy .Minimization, and Simulated Annealing. Sumerical Investigations of .Admissible Objective Eunctions Using a Synthetic 7-Species Data Set EFFENDI WIDJ.AJA AND MARC GARLAND 911 .Analytical Energy Gradient Evaluation in Relativistic and Sonrelativistic Density Eunctional Calculations FAN WANG AND LEMIN LI 920 .\b Initio Study on the Electronic Structures of Styrene in the Franck-Condon Region YOSHIAKI AMAT.ATSL 928 Isomers of C,„; An Energy Profile K.ATHERINE R GREENE AND KYLE A BERAN 938 Issue 10, July 30, 2002 Use of Exchange Maximization to Generate Starting Vectors for Self-Consistent Field Calculations on .Metal Cluster/Adsorbate Systems R. J. BUENKER. J. L. WHITTEN. E. 1. IZGORODINA. H.-P. LIEBER.VIANN. AND D. B. KOKH 943 .\b Initio Study on the Photochemical Behavior of .Styrene YOSHIAKI AM.ATATSU 950 Intruder State .Avoidance .Multireference Moller-Plesset Perturbation Theory HENRYK A. VVITEK. YOONG-KEE CHOE. JAMES P. FINLEY. AND KIMIHIKO HIR.AO 957 .4b Initio Calculations of the Stabilization Energies of the Conformational and the Structural Isomers of C^H^X where X = F, Cl, and Br MUSTAFA R. HELAL. YASER A. YOUSEF. AND AKEF T. AFANEH 966 Parameterization of OPLS-A.A Force Field for the Conformational Analysis of Macrocyclic Polyketides KALJU KAHN AND THOMAS C. BRUTCE 977 Intensity-Carrying .Modes Important for Vibrational Polarizabilities and Hyperpolarizabilities of .Molecules: Derivation from the .Algebraic Properties of Formulas and .Applications H.AJIME TORII 997 Volume Contents • Vol. 23. So. 16 • Journal of Computational Chemistry Exact Gaussian Expansions of Slater-Type .Atomic Orbitals ANDRE SEVERO PEREIRA GOMES AND ROGERIO CLSTODIO 1(M)7 Can We L'nderstand the Different Coordinations and Structures of Closed-Shell .Metal Cation-Water Clusters? A.-L. DEREPAS. J.-.M. SOLDAN. V. BRENNER. J.-P CKX3NON. AND PH. .MILLIE 1013 Issue 11, August 2002 Theoretical Study on the Mechanism of the ^CH^ + .VO, Reaction JI.AN-JLN LIL. YI-HONG DING. YL'-GUO T.AO. JI-KANG FENG. AND CHI.A-CHLNG SLN 1031 Modern Protein Eorce Eields Behave Comparably in Molecular Dynamics Simulations D.ANIEL J. PRICE AND CHARLES L. BROOKS III 1045 Quantum Chemical Geometry Optimizations in Proteins Using Crystallographic Raw Data LLF RYDE. LARS OLSEN. AND KRISTINA NILSSON 1058 Electronic State of Small and Ixirge Cavities for Methane Hydrate T. ID.A. M. MIZLNO. AND K. ENDO 1071 .\b Initio Study of the .Mechanism of Singlet-Dioxygen .Addition to Hydroxyaromatic Compounds: Segative Evidence for the Involvement of Peroxa and Endoperoxide Intermediates MACIEJ BOBROWSKI. ADAM LIWO. STANISLAW OLDZIEJ. DANCTA JEZIOREK. AND TADEL SZ OSSOW SKI 1076 Distance and Exposure Dependent Effective Dielectric Function BLDDHADEB MALLIK. ARTE.M MASLNOV. AND THE.MIS LAZARIDIS 1090 Gravitational Smoothing as a Global Optimization Strategy T. \V. WHITFIELD AND JOHN E. STRALB 1 KHJ ¥ ^flpAu'*' and V ^(II):Cu'^ iMser .Activity and Photographic Sensitization at the Low Coordinated Surfaces of .AgBr .\b Initio Calculations A. S. SHALABI 1104 Software News and Updates Reducing I/O Costs for the Eigenvalue Procedure in Ixirge-Scale Config iration Interaction Calculations RON SHEPARD. ISAIAH SHAVITT. AND HANS LISCHKA 1121 Issue 12, September 2002 Efficiency of the Multicanonical Simulation Method as .Applied to Peptides of Increasing Size: The Ileptapeptide Deltorphin FATIH YA§AR. HANDAN ARKIN. TARIK (^ELIK. BERND A. BERG. AND H.AGAI MEIROVITCH 1127 .Applicability of MS DO Techniques AMI and P.M3 to Ring-Structured Polymers 1. Y A. D.AVILA AND M. J. CALDAS 1135 Can the Calculation of Ligand Binding Free Energies Be Improved with Continuum Solvent Electrostatics and an Ideal-Gas Entropy Correction? SONJA M. SCHWARZL. THOMAS B. TSCHOPP. JEREMY C. SMITH. AND STEFAN FISCHER 1143 .4/1 Efficient Parallel .Algorithm for the Calculation of Canonical .MP2 Energies JON BAKER .AND PETER PLL.AY 1150 Reducing CAS-SDCI Space. Using Selected Spaces in Configuration Interaction Calculations in an Efficient UViv JOSE PITARCH-RLTZ. JOSE S.ANCHEZ .MARIN, AND DANIEL MAYNAL 1157 Quasi-Degenerate Perturbation Theory with (General .Multiconfiguration Self-Consistent Field Reference Functions HARLYL’KI NAKANO. RYL'MA LCHIYAMA. AND KIMIHIKO HIR.AO 1166 Pattern Recognition Strategies for Molecular Surfaces. /. Pattern Generation Using Fuzzy Set Theory THOMAS E. EXNER. MATTHIAS KEIL. AND JLRGEN BRICKMANN 1176 Volume Contents • Vol. 23, So. 16 • Journal of Computational Chemistry Pattern Recognition Strategies for .Molecular Surfaces. II. Surface Complementarity THOMAS E. EXNER. MATTHIAS KEIL. AND JL RGEN BRICKMANN 1188 .Atomic Charges, Dipole Moments, and Fuktii Functions Using the Hirshfeld Partitioning of the Electron Density F. DE PROFT. C. VAN ALSENOV. A. PEETERS. W. LANGENAEKER. AND P. GEERLINGS 1198 Issue 13, October 2002 Structure and Dynamics of Liquid Water with Different Long-Range Interaction Truncation and Temperature Control Methods in .Molecular Dynamics Simulations PEKKA MARK. LENNART NILSSON 1211 A Comparison of Predicted and Experimental Vibrational Spectra in Some Small Fluorocarbons HE JIANG. DOMINIC APPADOO. E\ AN ROBERTSON. DON .MCNALGHTON 1220 Stable Conformations of l2-Crown-O^S and Its Li Complex in .Aqueous Solution KENZI HORI. NOBL'MITSU DOL. K.ATSL HIKO OKANO. AI OHGA.MI. HIROSHI TSL KL BE 1226 Carbohydrate Solution Simulations: Producing a Force Field with Experimentally Consistent Primary .Alcohol Rotational Frequencies and Populations MICHELLE KCTTEL. J. \V. BRADV. KEVIN J. NAIDOO 1236 .Accelerated Poisson-Boltzmann Calculations for Static and Dynamic Systems RAV LLO. LALRENT DAVID. MICHAEL K. GILSON 1244 Determination of the Effective Dielectric Constant from the .Accurate Solution of the Poisson Equation VLADISLAV V.ASILVEV 1254 .Mechanistic .Aspects of the Dehydration and Dehydrohalogenation of Halo-Hydroxyformaldoxime Conformers. .4 Quantum Chemical Model Study .ATHAN.ASSIOS C. TSIPIS. CONSTA.NTINOS A. TSIPIS 1266 Binding of /> and i-Captopril Inhibitors to .Metallo-li-Lactamase Studied by Polarizable Molecular .Mechanics and Quantum .Mechanics JENS ANTONY. NOHAD GRESH. LARS OLSEN. LARS HE.M.MINGSEN. CHRISTOPHER J. SCHOFIELD. ROGERT BALER 1281 Issue 14, November 15, 2002 Effective Born Radii in the Generalized Born .Approximation: The Importance of Being Perfect ALE.XEY ONLFRIEV. DAV ID A. CASE. AND DONALD BASHFORD 1297 Linear Scaling .Approaches to Quantum Macromolecular Similarity: Evaluating the Similarity Function PERE CONSTANS 1305 Comparison of Linear-Scaling Semiempirical .Methods and Combined Quantum Mechanical/Molecular .Mechanical Methods for Enzymic Reactions. 11. .An Energy Decomposition .Analysis STEPHEN J. TITMUSS. PETER L. CLMMINS. ALISTAIR P. RENDELL. ANDREY A. BLIZNYLK. AND JILL E. GREADY 1314 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 JLNTCHI HIGO AND MASAYOSHI NAKASAKO 1323 .4 Sovel Parallel .Algorithm for luirge-Scale Fock Matrix Construction with Small Locally Distributed Memory .Architectures: RT Parallel .Algorithm H.AJIME TAKASHIMA. SO YAMADA. SHIGERL OBARA. KLNTHIRO KITA.MURA. SHINJIRO INAB.ATA. NOBUAKI MIYAKAWA. K.AZLTOSHI TANABE. AND UMPEI NAGASHIMA 1337 Electron Localization and Delocalization in Open-Shell .Molecules XAVIER FRADERA AND MIQLEL SOL.A 1347 Genetic Training of Setwork Using Chaos Concept: .Application to QS.AR Studies of Vibration Modes of Tetrahedral Halides QINGZHANG LL. GLOLI SHEN. AND RLQIN YC 1357 Volume Contents • Vol. 23, .\o. 16 • Journal of Computational Chemistry Direct Ab Initio Dynamics Study on the Rate Constants and Kinetic Isotope Effect for the Reactions of H Atoms with GeDJCHfn = 1-4) YANG \VL'. YI-HONG DING. JING-FA XI AO. ZE-SHENG LI. XL-RI HL ANG. AND CHI.A-CHL NG SL N 1366 Software News and I pdates CHIMERA: A Software Tool for Reaction Rate Calculations and Kinetics and Thermodynamics Analysis KON.STANT1N P. NOVOSELOV. DENIS B SHIRABAIKIN. STANISLAV YA. LMANSKII. ALEXANDER S VL.ADI.MIROV. AIR.AT KH. MINLSHEV. .AND ANATOLI A. KORKIN 1375 Issue 15, November 30, 2002 Comparative Study of Metal-Porphyrins, -Porphyrazines, and -Phthalocyanines MENG-SHE.NG LIAO AND STEVE SCHEINER 1391 The Treatment of Solvation by a Generalized Born Model and a Self-Consistent Charge-Density Functional Theory-Based Tight-Binding Method LI XIE AND H.AIYA.N LIL 1404 .4/1 Improved OPLS-AA Force Field for Carbohydrates D KONY. W DAM.M. S. STOLL. AND W F V AN GL NSTEREN 1416 Integral Algorithm and Density Matrix Integration Scheme for Ab Initio Band Structure Calculations on Polymeric Systems DENIS J.ACQL EMIN. BENOiT CHAMPAGNE. JEAN-MARIE ANDRE. ERIK DEL MENS. AND YNGVE OHRN 1430 Methodology of Predicting Approximate Shapes and Size Distribution of Micelles: Illustration for Simple Models M.AS.AHIRO KINOSHITA AND YOSHIKI SLG.AI 1445 DFT and .Ab Initio Direct Dynamics Studies on the Hydrogen Abstraction Reactions of Chlorine Atoms with CH_,_J-\ (n = 1-3) JING-FA XI AO. ZE-SHENG LI. JING-Y.AO LIL. LI SHENG. AND CHI.A-CHLNG SLN 1456 Water Polarizability in Condensed Phase: .Ab Initio Evaluation by Cluster Approach AKIHIRO MORIT.A 1466 Analysis of the Intermolecular Interaction between CH,OCH^ CF,OCHf, CF,()CFf, and CH_,: High Level Ab Initio Calculations SHINGO LR.AT.A. SEIJI TSLZLKI. M.ASLHIRO MIK.AMI. AKIRA T.AK.AD.A. T.ADAFLMI LCHIM.ARL. AND AKIRA SEKIYA 1472 .4 Revised Quantum Chemistry-Based Potential for Polyfethylene oxide) and Its Oligomers in Aqueous Solution GRANT D. SMITH. OLEG BORODIN. AND DMITRY BEDROV 14X6 Software News and Updates Update of the AIM2000-Program for Atoms in Molecules FRIEDRICH BIEGLER-KONIG AND JENS SCHONBOHM 1489 Erratum Analytical TDHF Second Derivatives of Dynamic Electronic Polarizability with Respect to Suclear Coordinates. Application to the Dynamic ZPVA Correction OLIVIER QLTNET. BE.NOIT CH.A.MP.AGNE. AND BERNARD KIRTM.A.N 1495 Issue 16, December 2002 Foreword GERNOT FRENKING AND WILLIAM L. JORGENSEN vii Consistent Treatment of Inter- and Intramolecular Polarization in Molecular Mechanics Calculations PENGYL REN AND JAY W PONDER 1497 Dynamic Charge Equilibration-Morse Stretch Force Field: Application to Energetics of Pure Silica Zeolites JAN SEFCIK. ERSAN DE.MIR.ALP. TAHIR C.AGIN. AND WILLLA.M A. GODDARD III 1507 Volume Contents • Vol. 23, .\o. 16 • Journal of Computational Chemistry Development of a Polarizable Force Field For Proteins via Ah Initio Quantum Chemistry: First Generation Model and Gas Phase Tests 1515 GEORGE A. KAMINSKI. HARRY A STERN. B. J. BERNE. RICHARD A. FRIESNER. YIXIANG X. CAO. ROBERT B MURPHY. RUHONG ZHOC. AND THOMAS A. HALGREN Macrotricyclic Quaternary Tetraammonium Receptors: Halide Anion Recognition and Interfacial Activity at an Aqueous Interface. A Molecular Dynamics Investigation ALAIN CHALMONT AND GEORGES WIPFF 1532 Pattern Recognition and Massively Distributed Computing E. KEITH DAVIES. MEIR GLICK. KARL N. HARRISON. AND W. GRAHAM RICHARDS 1544 Theoretical Study of Sheets Formed by (i-Peptides JIN-QIL LIN. SHI-WEI LL'O. AND YI N-DONG \VC 1551 /?K„, MM, and QM Studies of Mechanisms of fi-lMctamases and Penicillin-Binding Proteins: Acylation Step IRINA MASSOVA .AND PETER A. KOLLMAN 1559 Helix Motion in Protein CI2A-p8^"*-'‘*: Comparison of Molecular Dynamics Simulations and Multifield \MR Relaxation Data PHILIPPE BARTHE. CHRISTIAN ROL'ViESTAND. HELENE DEMENE. AND LAURENT CHICHE 1577 Molecular Dynamics Simulations of the Dinuclear Zinc-fi-lMctamase from Bacteroides t'ragilis Complexed with Imipenem DIMAS SU.AREZ. NATALIA DIAZ. AND KENNETH M MERZ. JR. 1587 PDDG/PM3 and PDDG/MSDO: Improved Semiempirical Methods MATTHEW P. REPASKY. JAYARAMAN CHANDRASEKHAR. AND WILLIAM L. JORGENSEN 1601 Fast, Efficient Generation of High-Quality Atomic Charges. AMl-BCC Model: //. Parameterization and Validation .AR.AZ JAKALIAN. DAVID B. J.ACK. AND CHRISTOPHER I BAYLY 1623 Molecules for Materials: Germanium Hydride Neutrals and Anions. Molecular Structures, Electron Affinities, and Thermochemistry of GeHJGeH~ (n = 0-4) and GejHJGejH~ fn = 0-6) QI.AN-SHU LI. RLT-HUA LU. Y.AOMING XIE. AND HENRY F. SCHAEFER III 1642 Enhanced Docking with the Mining Minima Optimizer: Acceleration and Side-Chain Flexibility VTSVALDAS K.AIRYS AND MICHAEL K. GILSON 1656 Author Index to Volume 23, 2002 1673 Subject Index to Volume 23, 2002 1681 Volume Contents