Reviews in Computational Chemistry Volume 18

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xii Epilogue and Dedication sustained usefulness in learning, teaching, and research. With this volume, the eighteenth, more than 7300 pages have been published since the series began in 1990. More than 200 authors have contributed the chapters. Appreciating the value of these chapters, scientists and libraries around the world have purchased more than 13,000 copies of the books since the series began. My vision of computational chemistry, as embodied in this book series as well as in the Gordon Conference on Computational Chemistry that I initiated, was that there were synergies to be gained by juxtaposing all the various methodologies available to computational chemists. Thus, computational chemistry is more than quantum chemistry, more than molecular modeling, more than simulations, more than molecular design. Versatility is possible when scientists can draw from their toolbox the most appropriate methodologies for modeling molecules and data. Important goals of this book series have been to nurture the development of the field of computational chemistry, advance its recognition, strengthen its foundations, expand its dimensions, aid practitioners working in the field, and assist newcomers wanting to enter the field. However, it is now time for me to rest my keyboard-weary hands. I wish Ken and his new co-editors every success as the book series continues. Ken could not have paid me a higher compliment than by enlisting not one, but two, excellent people to carry on the work I did. I have every confidence that as computational chemistry continues to evolve, its spectrum of methods and applications will further expand and increase in brilliance. Dedication With completion of this, my final, volume, I am reminded of my blessings to live in a country conceived by the Founding Fathers of the United States of America. Nothing would have been possible for me without the selflessness and devotion of Howard Milton Boyd, Ph.G., B.S., M.S. Nothing would have been worthwhile without the following: Andy Cynthia Douglas Drew Elisabeth Emma Joanne Mary Richard Susanne Donald B. Boyd Indianapolis January 2002
Contents 1. Clustering Methods and Their Uses in Computational Chemistry 1 Geoff M. Downs and John M. Barnard Introduction 1 Clustering Algorithms 6 Hierarchical Methods 6 Nonhierarchical Methods 9 Progress in Clustering Methodology 14 Algorithm Developments 14 Comparative Studies on Chemical Data Sets 23 How Many Clusters? 24 Chemical Applications 28 Conclusions 33 References 34 2. The Use of Scoring Functions in Drug Discovery Applications 41 Hans-Joachim Böhm and Martin Stahl Introduction 41 The Process of Virtual Screening 43 Major Contributions to Protein–Ligand Interactions 45 Description of Scoring Functions for Receptor–Ligand Interactions 49 Force Field-Based Methods 51 Empirical Scoring Functions 53 Knowledge-Based Methods 56 Critical Assessment of Current Scoring Functions 58 Influence of the Training Data 58 Molecular Size 59 Other Penalty Terms 59 Specific Attractive Interactions 60 Water Structure and Protonation State 61 Performance in Structure Prediction 61 Rank Ordering Sets of Related Ligands 63 xiii
Page 1 and 2: Reviews in Computational Chemistry
Page 3 and 4: Kenny B. Lipkowitz Department of Ch
Page 5 and 6: vi Preface three-dimensional struct
Page 7 and 8: viii Preface some descriptors and i
Page 9: Epilogue and Dedication My associat
Page 13 and 14: Contents xv Electron Transfer in Po
Page 15 and 16: Contributors John M. Barnard, Barna
Page 17 and 18: Contributors to Previous Volumes *
Page 19 and 20: Volume 3 (1992) Tamar Schlick, Opti
Page 21 and 22: Volume 7 (1996) Geoffrey M. Downs a
Page 23 and 24: Volume 11 (1997) Mark A. Murcko, Re
Page 25 and 26: T. Daniel Crawford* and Henry F. Sc
Page 27 and 28: Topics Covered in Volumes 1-18 * Ab
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32 Clustering Methods and Their Use
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42 The Use of Scoring Functions in
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Table 1 Reference List for the Most
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CHAPTER 3 Potentials and Algorithms
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Vn (1 + cos(nω + γ)) 2 K θ (θ
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are modified by their environment w
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Table 1 Polarizability Parameters f
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The polarizable point dipole models
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two to three orders of magnitude sl
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M i z i + q i d i k i and shell cha
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Shell Models 103 on estimates of sh
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minimization can be replaced by mor
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The energy required to create a cha
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for all i ði:e:; 8 iÞ: @U @qi l
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where we have used q Cl ¼ qNa. The
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Electronegativity Equalization Mode
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Electronegativity Equalization Mode
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of N molecules is taken as a Hartre
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is treated using variable charges.
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water have been developed, includin
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Applications 123 classical and rigi
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developing polarizable models. A va
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Comparison of the Polarization Mode
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negligible errors in such propertie
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ecome significant at field strength
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noteworthy in this regard because t
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References 135 9. P. Cieplak and P.
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References 137 48. E. L. Pollock an
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References 139 Computational Chemis
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References 141 139. J. Hinze and H.
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References 143 178. J. J. P. Stewar
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References 145 216. M. W. Mahoney a
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CHAPTER 4 New Developments in the T
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Introduction 149 applications). For
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FCWD(∆E ) FCWD(0) ∆E = 0 ∆E
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Introduction 153 Equations [6]-[12]
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Paradigm of Free Energy Surfaces 15
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Paradigm of Free Energy Surfaces 15
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In Eqs. [18] and [19], F0i is the e
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where ‘‘þ’’ and ‘‘ ’
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is, however, small for the usual co
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solute-solvent coupling through the
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where Z is the electrode overpotent
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energy surfaces of ET. 33,50-56 It
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This result indicates a fundamental
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βF i (X ) 40 20 0 −20 1 2 βλ 1
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Table 1 Main Features of the Two-Pa
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and Hss ¼ U rep ss 1 2 X j;k ðmj
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λ i /eV 4 3 2 1 0 0 10 20 30 40 Bo
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the width/Stokes shift relation (Eq
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Table 3 Mapping of the Q Model on S
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This situation is of course not sat
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F ± (Y ad )/λ I 0.8 0.4 0 −0.4
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it by choosing the GMH basis set 7
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Anharmonic higher order terms gain
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of the radiation is the perturbatio
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individual vibrational excitations
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m 12 /D 6 5.5 5 4.5 4 3.5 17 18 19
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In Eq. [144], the coordinates Y km
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ε/M −1 cm −1 4000 2000 0 analy
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βσ 2 /10 3 cm −1 14 12 10 8 Opt
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0.2 0.1 0 12 16 20 24 28 32 The app
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References 207 7. M. D. Newton, Adv
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References 209 59. R. Kubo and Y. T
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Reviews in Computational Chemistry Volume 18

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