Reviews in Computational Chemistry

xxii Contributors to Previous Volumes

Jeffry D. Madura,* Malcolm E. Davis, Michael K. Gilson, Rebecca C. Wade, Brock A. Luty, and J. Andrew McCammon, Biological Applications of Electrostatic Calculations and Brownian Dynamics Simulations.

K. V. Damodaran and Kenneth M. Merz Jr., Computer Simulation of Lipid Systems.

Jeffrey M. Blaneyy and J. Scott Dixon, Distance Geometry in Molecular Modeling.

Lisa M. Balbes, S. Wayne Mascarella, and Donald B. Boyd, A Perspective of Modern Methods in Computer-Aided Drug Design.

Volume 6

Christopher J. Cramer and Donald G. Truhlar, Continuum Solvation Models: Classical and Quantum Mechanical Implementations.

Clark R. Landis, Daniel M. Root, and Thomas Cleveland, Molecular Mechanics Force Fields for Modeling Inorganic and Organometallic Compounds.

Vassilios Galiatsatos, Computational Methods for Modeling Polymers: An Introduction.

Rick A. Kendall,z Robert J. Harrison, Rik J. Littlefield, and Martyn F. Guest, High Performance Computing in Computational Chemistry: Methods and Machines.

Donald B. Boyd, Molecular Modeling Software in Use: Publication Trends.

Eiji Osawa and Kenny B. Lipkowitz, Appendix: Published Force Field Parameters.

*Current address: Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania 15282-1530 (Electronic mail: [e-mail]).

yCurrent address: DuPont Pharmaceuticals Research Laboratories, 150 California Street, Suite 1100, San Francisco, California 94111-4500 (Electronic mail: jblaney@combichem. com).

zCurrent address: Scalable Computing Laboratory, Ames Laboratory, Wilhelm Hall, Ames, lowa 50011 (Electronic mail: [e-mail]).

Contributors to Previous Volumes

xxiii

Volume 7

Geoffrey M. Downs and Peter Willett, Similarity Searching in Databases of Chemical Structures.

Andrew C. Good* and Jonathan S. Mason, Three-Dimensional Structure Database Searches.

Jiali Gao,y Methods and Applications of Combined Quantum Mechanical and Molecular Mechanical Potentials.

Libero J. Bartolotti and Ken Flurchick, An Introduction to Density Functional Theory.

Alain St-Amant, Density Functional Methods in Biomolecular Modeling.

Danya Yang and Arvi Rauk, The A Priori Calculation of Vibrational Circular Dichroism Intensities.

Donald B. Boyd, Appendix: Compendium of Software for Molecular Modeling.

Volume 8

Zdeneˇk Slanina,z Shyi-Long Lee, and Chin-hui Yu, Computations in Treating Fullerenes and Carbon Aggregates.

Gernot Frenking, Iris Antes, Marlis Bo¨hme, Stefan Dapprich, Andreas W. Ehlers, Volker Jonas, Arndt Neuhaus, Michael Otto, Ralf Stegmann, Achim Veldkamp, and Sergei F. Vyboishchikov, Pseudopotential Calculations of Transition Metal Compounds: Scope and Limitations.

Thomas R. Cundari, Michael T. Benson, M. Leigh Lutz, and Shaun O. Sommerer, Effective Core Potential Approaches to the Chemistry of the Heavier Elements.

*Current address: Bristol–Myers Squibb, 5 Research Parkway, P.O. Box 5100, Wallingford, Connecticut 06492-7660 (Electronic mail: [e-mail]).

yCurrent address: Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455-0431 (Electronic mail: [e-mail]).

zCurrent address: Institute of Chemistry, Academia Sinica, Nankang, Taipei 11529, Taiwan, Republic of China (Electronic mail: [e-mail]).

xxiv Contributors to Previous Volumes

Jan Almlo¨ f and Odd Gropen,* Relativistic Effects in Chemistry.

Donald B. Chesnut, The Ab Initio Computation of Nuclear Magnetic Resonance Chemical Shielding.

Volume 9

James R. Damewood, Jr., Peptide Mimetic Design with the Aid of Computational Chemistry.

T. P. Straatsma, Free Energy by Molecular Simulation.

Robert J. Woods, The Application of Molecular Modeling Techniques to the Determination of Oligosaccharide Solution Conformations.

Ingrid Pettersson and Tommy Liljefors, Molecular Mechanics Calculated Conformational Energies of Organic Molecules: A Comparison of Force Fields.

Gustavo A. Arteca, Molecular Shape Descriptors.

Volume 10

Richard Judson,y Genetic Algorithms and Their Use in Chemistry.

Eric C. Martin, David C. Spellmeyer, Roger E. Critchlow Jr., and Jeffrey M. Blaney, Does Combinatorial Chemistry Obviate Computer-Aided Drug Design?

Robert Q. Topper, Visualizing Molecular Phase Space: Nonstatistical Effects in Reaction Dynamics.

Raima Larter and Kenneth Showalter, Computational Studies in Nonlinear

Dynamics.

*Address: Institute of Mathematical and Physical Sciences, University of Tromsø, N-9037 Tromsø, Norway (Electronic mail: [e-mail]).

yCurrent address: Genaissance Pharmaceuticals, Five Science Park, New Haven, Connecticut 06511 (Electronic mail: [e-mail]).

Contributors to Previous Volumes

xxv

Stephen J. Smith and Brian T. Sutcliffe, The Development of Computational Chemistry in the United Kingdom.

Volume 11

Mark A. Murcko, Recent Advances in Ligand Design Methods.

David E. Clark,* Christopher W. Murray, and Jin Li, Current Issues in De Novo Molecular Design.

Tudor I. Oprea and Chris L. Waller, Theoretical and Practical Aspects of Three-Dimensional Quantitative Structure–Activity Relationships.

Giovanni Greco, Ettore Novellino, and Yvonne Connolly Martin, Approaches to Three-Dimensional Quantitative Structure–Activity Relationships.

Pierre-Alain Carrupt, Bernard Testa, and Patrick Gaillard, Computational Approaches to Lipophilicity: Methods and Applications.

Ganesan Ravishanker, Pascal Auffinger, David R. Langley, Bhyravabhotla Jayaram, Matthew A. Young, and David L. Beveridge, Treatment of Counterions in Computer Simulations of DNA.

Donald B. Boyd, Appendix: Compendium of Software and Internet Tools for Computational Chemistry.

Volume 12

Hagai Meirovitch, Calculation of the Free Energy and the Entropy of Macromolecular Systems by Computer Simulation.

Ramzi Kutteh and T. P. Straatsma, Molecular Dynamics with General Holonomic Constraints and Application to Internal Coordinate Constraints.

John C. Shelley and Daniel R. Be´rard, Computer Simulation of Water Physisorption at Metal–Water Interfaces.

*Current address: Computer-Aided Drug Design, Argenta Discovery Ltd., c/o Aventis Pharma Ltd., Rainham Road South, Dagenham, Essex, RM10 7XS, United Kingdom (Electronic mail: [e-mail]).

xxvi Contributors to Previous Volumes

Donald W. Brenner, Olga A. Shenderova, and Denis A. Areshkin, QuantumBased Analytic Interatomic Forces and Materials Simulation.

Henry A. Kurtz and Douglas S. Dudis, Quantum Mechanical Methods for Predicting Nonlinear Optical Properties.

Chung F. Wong,* Tom Thacher, and Herschel Rabitz, Sensitivity Analysis in Biomolecular Simulation.

Paul Verwer and Frank J. J. Leusen, Computer Simulation to Predict Possible Crystal Polymorphs.

Jean-Louis Rivail and Bernard Maigret, Computational Chemistry in France: A Historical Survey.

Volume 13

Thomas Bally and Weston Thatcher Borden, Calculations on Open-Shell Molecules: A Beginner’s Guide.

Neil R. Kestner and Jaime E. Combariza, Basis Set Superposition Errors: Theory and Practice.

James B. Anderson, Quantum Monte Carlo: Atoms, Molecules, Clusters, Liquids, and Solids.

Anders Wallqvist and Raymond D. Mountain, Molecular Models of Water: Derivation and Description.

James M. Briggs and Jan Antosiewicz, Simulation of pH-dependent Properties of Proteins Using Mesoscopic Models.

Harold E. Helson, Structure Diagram Generation.

Volume 14

Michelle Miller Francl and Lisa Emily Chirlian, The Pluses and Minuses of Mapping Atomic Charges to Electrostatic Potentials.

*Current address: Howard Hughes Medical Institutes, School of Medicine, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093-0365 (Electronic mail: [e-mail]).

Contributors to Previous Volumes

xxvii

T. Daniel Crawford* and Henry F. Schaefer III, An Introduction to Coupled Cluster Theory for Computational Chemists.

Bastiaan van de Graaf, Swie Lan Njo, and Konstantin S. Smirnov, Introduction to Zeolite Modeling.

Sarah L. Price, Toward More Accurate Model Intermolecular Potentials for Organic Molecules.

Christopher J. Mundy, Sundaram Balasubramanian, Ken Bagchi, Mark E. Tuckerman, Glenn J. Martyna, and Michael L. Klein, Nonequilibrium Molecular Dynamics.

Donald B. Boyd and Kenny B. Lipkowitz, History of the Gordon Research Conferences on Computational Chemistry.

Mehran Jalaie and Kenny B. Lipkowitz, Appendix: Published Force Field Parameters for Molecular Mechanics, Molecular Dynamics, and Monte Carlo Simulations.

Volume 15

F. Matthias Bickelhaupt and Evert Jan Baerends, Kohn–Sham Density Functional Theory: Predicting and Understanding Chemistry.

Michael A. Robb, Marco Garavelli, Massimo Olivucci, and Fernando Bernardi, A Computational Strategy for Organic Photochemistry.

Larry A. Curtiss, Paul C. Redfern, and David J. Frurip, Theoretical Methods for Computing Enthalpies of Formation of Gaseous Compounds.

Russell J. Boyd, The Development of Computational Chemistry in Canada.

Volume 16

Richard A. Lewis, Stephen D. Pickett, and David E. Clark, Computer-Aided Molecular Diversity Analysis and Combinatorial Library Design.

*Current address: Department of Chemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061-0212 (Electronic mail: [e-mail]).

xxviii Contributors to Previous Volumes

Keith L. Peterson, Artificial Neural Networks and Their Use in Chemistry.

Jo¨ rg-Ru¨ diger Hill, Clive M. Freeman, and Lalitha Subramanian, Use of Force Fields in Materials Modeling.

M. Rami Reddy, Mark D. Erion, and Atul Agarwal, Free Energy Calculations: Use and Limitations in Predicting Ligand Binding Affinities.

Reviews in

Computational

Chemistry

Volume 17

Author Index

Abagyan, R., 52, 94, 95, 96

Abe, M., 299, 303

Abe, R., 302

Abegg, P. W., 199

Abraham, D. J., 48

Abronin, I. A., 308

Adachi, G., 276

Adachi, H., 321, 330

Advani, S. G., 348

Aerts, P. J. C., 199, 201

Aflalo, C., 95

Agarwal, A., 93

˚

Agren, H., 201, 203 Ahern, K., 278 Ahlrichs, R., 319 Ahmed, F. R., 290 Air, G. M., 47, 59 Aishima, T., 288 Ajay, 51, 54, 58 Ajersch, F., 281 Alagona, G., 50 Albeck, S., 93 Albertsson, A.-C., 333 Albright, T. A., 300 Alcock, C. B., 292 Alder, B. J., 319 Alekseyev, A. B., 200 Alex, A., 55, 57 Allen, D. T., 276 Allen, F. H., 50

Allen, M. P., 250, 282, 339, 340 Allinger, N. L., 94, 337, 357 Almlo¨f, J., 196, 200

Alonso, M., 296 Aloy, P., 95 Althaus, E., 94 Alvarez, J. C., 58 Amadei, A., 96 Amann, A., 321, 333

Ambos, M. M., 282

Amusia, M. Ya., 318

Andersen, K., 336

Andersen, L. H., 253

Anderson, A., 93

Anderson, J. M., 295

Andrae, D., 198

Andre, J.-M., 285, 320, 321

Andreani, R., 57

Andrews, F. C., 336

Andzelm, J. W., 311, 313

Angyan, J., 312

Animalu, A. O. E., 320

Anno, T., 302

Ansel’m, A. A., 300

Antes, I., 197

Antonov, V. N., 321

Antony, A., 273

Apeloig, Y., 315

Apostolakis, J., 52, 56

Appelt, K., 55

Aqvist, J., 54

Arai, K., 280

Ariens, E. J., 345

Arnaut, L. G., 282

Arnett, E. M., 271

Arrighini, P., 309

Asbrink, L., 311

Aseev, G. G., 264, 273

Ash, J. E., 272, 273

Ashida, T., 291

Aso, Y., 265

Ataka, S., 279

Atashroo, T., 197

Atkins, P. W., 253, 295, 299, 301,

302

Atkinson, D. E., 339

Auton, T. R., 53, 55, 57

Avery, J., 310, 320

359

360 Author Index

Aviles, F. X., 95

Avouris, P., 203

Babe, L. M., 58

Babic, D., 268

Babkin, V. A., 318

Babu, Y. S., 47

Bachrach, S. M., 278, 283, 285

Bader, R. F. W., 302

Bae, C., 201

Baerends, E. J., 201

Bagatur’yants, A. A., 308

Baggott, J., 301

Bahar, I., 55, 57, 96

Baker, B. M., 93

Baker, C. T., 48

Balaban, A. T., 345, 351, 352

Balashov, V. V., 300

Balasubramanian, K., 202, 303

Balbuena, P. B., 344

Balescu, R., 336

Balian, R., 340

Balint, S., 285

Balke, S. T., 287

Ballentine, L. E., 303

Banci, L., 334

Banner, D. W., 53

Bantia, S., 47

Barandiara´n, Z., 197, 202

Baranov, V. I., 291

Baras, F., 341

Bargon, J., 264

Barkema, G. T., 53, 344

Barker, J. R., 250

Barlin, G. B., 253

Barnard, J. M., 273

Barnes, A. J., 316

Barnikel, G., 58

Barone, V., 331

Barrett, R. W., 47

Barriol, J., 296

Barry, T. I., 291, 292

Bartlett, R. J., 311, 317

Bashford, D., 96

Bastin, T., 300

Batalin, G. I., 263

Bathias, C., 275

Bauer, D., 273

Bauman, R. P., 340

Bawden, D., 275

Bax, A., 46

Baxevanis, A. D., 279

Baxter, C. A., 52, 57, 59

Bayada, D. M., 58

Bayly, C. I., 95

Beard, D. B., 295

Beard, G. B., 295

Bearpark, M. J., 200

Beck, D. R., 308

Becker, E. R., 348

Beebe, K. R., 288

Beech, G., 262

Begley, E. F., 278

Beineke, L. W., 352

Belashchenko, D. K., 298

Belaya, A. A., 271

Belevantsev, V. I., 262

Belew, R. K., 51

Bellard, S., 50

Bellmann, K., 273

Bellomo, N., 335

Bellott, M., 96

Ben-Naim, A., 57, 340

Bendazzoli, G. L., 200

Bender, A., 264

Benedek, P., 291

Benjamin, I., 252

Bennett, L. H., 292

Benson, M. T., 197

Bentley, G. A., 92

Berendsen, H. J. C., 51, 96, 337

Berezin, F. A., 294

Bergmann, E. D., 323, 324

Berman, H. M., 46, 97

Bernardi, F., 270, 283, 286, 319

Bernd, C., 53

Berne, B. J., 252

Berning, A., 198, 202

Bernstein, F. C., 46, 97

Berryman, H. S., 254

Bersuker, I. B., 312, 317

Berthier, G., 307

Bertran, J., 282

Bethe, H. A., 295

Bethell, R. C., 59

Betts, M. J., 93

Beveridge, D. L., 251, 304, 338,

339

Beyermann, K., 331

Bhat, T. N., 46, 92, 97

Bicerano, J., 282

Bicout, D., 316

Bidaux, R., 251

Bigham, E. C., 60

Billeter, M., 52

Billing, G. D., 342, 343