Reviews in Computational Chemistry Volume 18

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Preface ix also is very fast and appears to provide a quite complete and up-to-date picture of what information is available on the World Wide Web. We are also glad to note that our publisher has plans to make our most recent volumes available in an online form through Wiley InterScience. Please check the Web (http://www.interscience.wiley.com/onlinebooks) or contact reference@wiley.com for the latest information. For readers who appreciate the permanence and convenience of bound books, these will, of course, continue. We thank the authors of this volume for their excellent chapters. Mrs. Joanne Hequembourg Boyd is acknowledged for editorial assistance. Donald B. Boyd and Kenny B. Lipkowitz Indianapolis January 2002
Epilogue and Dedication My association with Ken Lipkowitz began a couple of years after he arrived in Indianapolis in 1977. Ken, trained as an synthetic organic chemist, was a new young assistant professor at Indiana University–Purdue University Indianapolis, and I was a research scientist at Eli Lilly & Company, where I, a quantum chemist by training, had been working in the field of computer-aided drug design for nine years. Ken approached me to learn about computational chemistry. I was glad to help him, and he was an enthusiastic ‘‘student’’. Our first paper together was published in 1980. Unsure whether his career as a fledging computational chemist would lead anywhere, he made a distinction in this and other papers he wrote between his organic persona (Kenneth B. Lipkowitz) and his computational persona (Kenny B. Lipkowitz). Over the subsequent years, he focused his career more and more on computational chemistry and established himself as a highly productive and creative scientist. He has always been a hard-working, amiable, and obliging collaborator and friend. In the late 1980s, Ken had the idea of initiating a book series on computational chemistry. The field was starting to come into full blossom, but few books for it were being published. Whereas review series on other subjects tended to be of mainly archival value and to remain on library shelves, his inspiration for Reviews in Computational Chemistry was to include as many tutorial chapters as possible, so that the books would be more used for teaching and individual study. The chapters would be ones that a professor could give new graduate students to bring them up to speed in a particular topic. The chapters would also be substantive, so that the books would not be just a journal with hard covers. As much as possible, the contents of the books would be material that could not be found in any other source. Ken persuaded me to join him in this endeavor. I have viewed an editor’s prime duties to set high standards and to heed the needs of both readers and authors. Hence, every effort has been made to produce volumes of the highest quality. It has been a keen pleasure working with authors who take exceptional pride in their workmanship. The expertise and hard work of many authors have been essential for producing books of xi
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: viii Preface some descriptors and i
Page 11 and 12: Contents 1. Clustering Methods and
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
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30 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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