Reviews in Computational Chemistry Volume 18

More documents

Recommendations

Info

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
Page 29 and 30: Reviews in Computational Chemistry
Page 31 and 32: 2 Clustering Methods and Their Uses
Page 39 and 40: 10 Clustering Methods and Their Use
Page 61 and 62:
32 Clustering Methods and Their Use
Page 63 and 64:
Page 65 and 66:
Page 67 and 68:
Page 69 and 70:
Page 71 and 72:
42 The Use of Scoring Functions in
Page 73 and 74:
Page 75 and 76:
Page 77 and 78:
Page 79 and 80:
Table 1 Reference List for the Most
Page 81 and 82:
Page 83 and 84:
Page 85 and 86:
Page 87 and 88:
Page 89 and 90:
Page 91 and 92:
Page 93 and 94:
Page 95 and 96:
Page 97 and 98:
Page 99 and 100:
Page 101 and 102:
Page 103 and 104:
Page 105 and 106:
Page 107 and 108:
Page 109 and 110:
Page 111 and 112:
Page 113 and 114:
Page 115 and 116:
Page 117 and 118:
CHAPTER 3 Potentials and Algorithms
Page 119 and 120:
Vn (1 + cos(nω + γ)) 2 K θ (θ
Page 121 and 122:
are modified by their environment w
Page 123 and 124:
Table 1 Polarizability Parameters f
Page 125 and 126:
The polarizable point dipole models
Page 127 and 128:
two to three orders of magnitude sl
Page 129 and 130:
M i z i + q i d i k i and shell cha
Page 131 and 132:
Shell Models 103 on estimates of sh
Page 133 and 134:
minimization can be replaced by mor
Page 135 and 136:
The energy required to create a cha
Page 137 and 138:
for all i ði:e:; 8 iÞ: @U @qi l
Page 139 and 140:
where we have used q Cl ¼ qNa. The
Page 141 and 142:
Electronegativity Equalization Mode
Page 143 and 144:
Electronegativity Equalization Mode
Page 145 and 146:
of N molecules is taken as a Hartre
Page 147 and 148:
is treated using variable charges.
Page 149 and 150:
water have been developed, includin
Page 151 and 152:
Applications 123 classical and rigi
Page 153 and 154:
developing polarizable models. A va
Page 155 and 156:
Comparison of the Polarization Mode
Page 157 and 158:
negligible errors in such propertie
Page 159 and 160:
ecome significant at field strength
Page 161 and 162:
noteworthy in this regard because t
Page 163 and 164:
References 135 9. P. Cieplak and P.
Page 165 and 166:
References 137 48. E. L. Pollock an
Page 167 and 168:
References 139 Computational Chemis
Page 169 and 170:
References 141 139. J. Hinze and H.
Page 171 and 172:
References 143 178. J. J. P. Stewar
Page 173 and 174:
References 145 216. M. W. Mahoney a
Page 175 and 176:
CHAPTER 4 New Developments in the T
Page 177 and 178:
Introduction 149 applications). For
Page 179 and 180:
FCWD(∆E ) FCWD(0) ∆E = 0 ∆E
Page 181 and 182:
Introduction 153 Equations [6]-[12]
Page 183 and 184:
Paradigm of Free Energy Surfaces 15
Page 185 and 186:
Paradigm of Free Energy Surfaces 15
Page 187 and 188:
In Eqs. [18] and [19], F0i is the e
Page 189 and 190:
where ‘‘þ’’ and ‘‘ ’
Page 191 and 192:
is, however, small for the usual co
Page 193 and 194:
solute-solvent coupling through the
Page 195 and 196:
where Z is the electrode overpotent
Page 197 and 198:
energy surfaces of ET. 33,50-56 It
Page 199 and 200:
This result indicates a fundamental
Page 201 and 202:
βF i (X ) 40 20 0 −20 1 2 βλ 1
Page 203 and 204:
Table 1 Main Features of the Two-Pa
Page 205 and 206:
and Hss ¼ U rep ss 1 2 X j;k ðmj
Page 207 and 208:
λ i /eV 4 3 2 1 0 0 10 20 30 40 Bo
Page 209 and 210:
the width/Stokes shift relation (Eq
Page 211 and 212:
Table 3 Mapping of the Q Model on S
Page 213 and 214:
This situation is of course not sat
Page 215 and 216:
F ± (Y ad )/λ I 0.8 0.4 0 −0.4
Page 217 and 218:
it by choosing the GMH basis set 7
Page 219 and 220:
Anharmonic higher order terms gain
Page 221 and 222:
of the radiation is the perturbatio
Page 223 and 224:
individual vibrational excitations
Page 225 and 226:
m 12 /D 6 5.5 5 4.5 4 3.5 17 18 19
Page 227 and 228:
In Eq. [144], the coordinates Y km
Page 229 and 230:
ε/M −1 cm −1 4000 2000 0 analy
Page 231 and 232:
βσ 2 /10 3 cm −1 14 12 10 8 Opt
Page 233 and 234:
0.2 0.1 0 12 16 20 24 28 32 The app
Page 235 and 236:
References 207 7. M. D. Newton, Adv
Page 237 and 238:
References 209 59. R. Kubo and Y. T
show all

Reviews in Computational Chemistry Volume 18

You also want an ePaper? Increase the reach of your titles

Delete template?

Save as template?