Table Of ContentFundamentals of Molecular
Similarity
MATHEMATICAL AND COMPUTATIONAL CHEMISTRY
Series Editor: PAUL G. MEZEY
University 01 Saskatchewan
Saskatoon, Saskatchewan
FUNDAMENfALS OF MOLECULAR SIMILARITY
Edited by Ramon Carb6-Dorca, Xavier Girones, and Paul G. Mezey
MANY-ELECTRON DENSmES AND REDUCED DENSIlY MATRICES
Edited by Jerzy Cioslowski
A Continuation Order Plan is available for tbis series. A continuation order will bring delivery of each new volume
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Fundamentals of Molecular
Similarity
Edited by
Ramon Carb6-Dorca
Xavier Girones
University of Girona
Girona, Catalonia, Spain
and
Paul G. Mezey
University of Saskatchewan
Saskatoon, Saskatchewan, Canada
Springer Science+Business Media, LLC
ISBN 978-1-4419-3344-7 ISBN 978-1-4757-3273-3 (eBook)
DOI 10.1007/978-1-4757-3273-3
©2001 Springer Science+Business Media New York
Originally published by Kluwer AcademiclPlenum Publishers, New York in 200l.
Softcover reprint ofthe hardcover 1st edition 2001
http://www.wkap.nl
10987654321
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No part of this book may be reproduced, stored in a retrieval system, or transmitted in any form or by any
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Contributors
ALLAN, N.L. SCHOOL OF CHEMISTRY, UNIVERSITY OF BRISTOL,
CANTOCKS CLOSE, BRISTOL BS8 1T S, UNITED KINGDOM
AMAT, L. INSTITUT OE QUiMICA COMPUTACIONAL,
UNIVERSITAT OE GIRONA, GIRONA 17071, CATALONIA, SPAIN
ANGLADA, J.M. INSTITUT D'INVESTIGACIONS QUiMIQUES I
AMBIENTALS. C.LD. -C.S.LC., JORDI GIRONA SALGADO 18 -26, E-
08034 BARCELONA, CATALUNY A, SPAIN
ARENAS, A. DEPARTAMENT D'ENGINYERIA QUIMICA, ESCOLA
TECNICA SUPERIOR D'ENGINYERIA QUIMICA, DEPARTAMENT
D'ENGINYERIA INFORMA TICA I MATEMATICA (ETSE),
UNIVERSITAT ROVIRA I VIRGILI, TARRAGONA, CATALUNYA, SPAIN
BARRIL, X. DEPARTAMENT OE BIOQUIMICA I BIOLOGIA
MOLECULAR, FACULTAT OE QUIMICA, UNIVERSITAT OE
BARCELONA, MARTI I FRANQUES 1, BARCELONA 08028, SPAIN
BESALU, E. INSTITUT OE QUIMICA COMPUTACIONAL,
UNIVERSITAT OE GIRONA, GIRONA 17071, CATALONIA, SPAIN
BOFILL, J.M. DEPARTAMENT OE QUiMICA ORGANICA I CENTRE
ESPECIAL OE RECERCA EN QUiMICA TEORICA, UNIVERSIT A T OE
BARCELONA, MARTI I FRANQUES 1, E-08028 BARCELONA,
CATALUNYA, SPAIN
v
vi Contributors
CARBO-DORCA, R. INSTITUT DE QUIMICA COMPUTACIONAL,
UNIVERSITAT DE GIRONA, GIRONA 17071, CATALONIA, SPAIN
CIOSLOWSKI, J. DEPARTMENT OF CHEMISTRY AND CSIT,
FLORIDA STA TE UNIVERSITY, T ALLAHASSEE, FL 32306-3006, USA
COOPER, D.L. DEPARTMENT OF CHEMISTRY, UNIVERSITY OF
LIVERPOOL, P.O. BOX 147, LIVERPOOL L69 7ZD, UNITED KINGDOM
CREHUET, R. INSTITUT D'INVESTIGACIONS QUIMIQUES I
AMBIENTALS. C.I.D. -C.S.I.C., JORDI GIRONA SALGADO 18 -26, E-
08034 BARCELONA, CATALUNYA, SPAIN
DE CACERES, M. GRUP DE RECERCA EN INFORMA TICA MEDICA,
INSTITUT MUNICIPAL D'INVESTIGACIO MEDICA, UNIVERSITAT
POMPEU FABRA,C/ DR. AIGUADER 80, E-08003 BARCELONA, SPAIN
ESPINOSA, G. DEPARTAMENT D'ENGINYERIA QUIMICA, ESCOLA
TECNICA SUPERIOR D'ENGINYERIA QUIMICA, DEPARTAMENT
D'ENGINYERIA INFORMATICA I MATEMATICA (ETSE),
UNIVERSITAT ROVlRA I VIRGILI, TARRAGONA, CATALUNYA, SPAIN
GALVEZ, J. UNIDAD DE INVESTIGACION DE DISENO DE
FARMACOS Y CONECTIVIDAD MOLECULAR SEC. DEPT. QUIMICA
FISICA. FACULT AD DE FARMACIA, UNIVERSITAT DE VALENCIA
GARCIA-DOMENECH, R. UNIDAD DE INVESTIGACION DE DISENO
DE FARMACOS Y CONECTIVIDAD MOLECULAR SEC. DEPT. QUIMICA
FISICA. FACULTAD DE FARMACIA, UNIVERSITAT DE VALENCIA
GELPI, J.L. DEPARTAMENT DE BIOQUIMICA I BIOLOGIA
MOLECULAR, FACULTAT DE QUIMICA, UNIVERSITAT DE
BARCELONA, MARTI I FRANQUES 1, BARCELONA 08028, SPAIN
GERBER, P.R. PHARMACEUTICAL RESEARCH AND
DEVELOPMENT, F. HOFFMANN-LA ROCHE, BASEL, SWITZERLAND
GIRALT, F. DEPARTAMENT D'ENGINYERIA QUIMICA, ESCOLA
TECNICA SUPERIOR D'ENGINYERIA QUIMICA, DEPARTAMENT
D'ENGINYERIA INFORMATICA I MA TEMATICA (ETSE),
UNIVERSITAT ROVlRA I VIRGILI, TARRAGONA, CATALUNYA, SPAIN
Contributors vii
GIRONES, X. INSTITUT DE QUIMICA COMPUTACIONAL,
UNIVERSITAT DE GIRONA, GIRONA 17071, CATALONIA (SPAIN)
HALL, L.H. DEPARTMENT OF CHEMISTRY, EASTERN NAZARENE
COLLEGE, QUINCY, MASSACHUSETTS
JULIAN-ORTIZ, J.V. UNIDAD DE INVESTIGACION DE DISENO DE
FARMACOS Y CONECTIVIDAD MOLECULAR SEC. DEPT. QUIMICA
FISICA. FACULTAD DE FARMACIA, UNIVERSITAT DE VALENCIA
KARADAKOV, P.B. DEPARTMENT OF CHEMISTRY, UNIVERSITY
OF SURREY, GUILDFORD, SURREY GU2 5XH, UNI TED KINGDOM
KARWOWSKI, J. INSTYTUT FIZYKI, UNIVERSYTET MIKOLAJA
KOPERNIKA, GRUDZIl\DZKA 5, 87-100 TORUN, POLAND
KIER, L.B. DEPARTMENT OF MEDICINAL CHEMISTRY, VIRGINIA
COMMONWEALTH UNIVERSITY, RICHMOND, VIRGINIA, 23298
LUQUE, F.J. DEPARTAMENT DE BIOQUIMICA I BIOLOGIA
MOLECULAR, FACULTAT DE QUIMICA, UNIVERSITAT DE
BARCELONA, MARTI I FRANQUES I, BARCELONA 08028, SPAIN
MEZEY, P.G. INSTITUTE FOR ADV ANCED STUDY, COLLEGIUM
BUDAPEST,1014 BUDAPEST,I. SZENTHAROMSAG U. 2, HUNGARY AND
MATHEMATICAL CHEMISTRY RESEARCH UNIT, DEPARTMENT OF
CHEMISTRY AND DEPARTMENT OF MATHEMA TICS AND
STA TISTICS. UNIVERSITY OF SASKA TCHEWAN, 110 SCIENCE PLACE,
SASKA TOON, SK, CANADA, S7N 5C9
MUNOZ, J. DEPARTAMENT DE BIOQUIMICA I BIOLOGIA
MOLECULAR, FACULTAT DE QUIMICA, UNIVERSITAT DE
BARCELONA, MARTI I FRANQUES I, BARCELONA 08028, SPAIN
OROZCO, M. DEPARTAMENT DE BIOQUIMICA I BIOLOGIA
MOLECULAR, FACULTAT DE QUIMICA, UNIVERSITAT DE
BARCELONA, MARTI I FRANQUES I, BARCELONA 08028, SPAIN
RICHARDS, W.G. PHYSICAL AND THEORETICAL CHEMISTRY
LABORATORY, THE UNIVERSITY OF OXFORD, OXFORD, UNITED
KINGDOM
viii Contributors
ROBERT, D. INSTITUT DE QUiMICA COMPUTACIONAL,
UNIVERSITAT DE GIRONA, GIRONA 17071, CATALONIA, SPAIN
ROBINSON, D.D. PHYSICAL AND THEORETICAL CHEMISTRY
LA BORA TORY, THE UNIVERSITY OF OXFORD, OXFORD, UNITED
KINGDOM
SANZ, F. GRUP DE RECERCA EN INFORMA TICA MEDICA,
INSTITUT MUNICIPAL D'INVESTIGACIO MEDICA, UNIVERSITAT
POMPEU FABRA,CI DR. AIGUADER 80, E-08003 BARCELONA, SPAIN
SELLO, G. DIPARTIMENTO DI CHIMICA ORGANICA E
INDUSTRIALE, UNIVERSITA' DEGLI STUDI DI MILANO
VILLA, J. GRUP DE RECERCA EN INFORMA TICA MEDICA,
INSTITUT MUNICIPAL D'INVESTIGACIO MEDICA, UNIVERSITAT
POMPEU FABRA,CI DR. AIGUADER 80, E-08003 BARCELONA, SPAIN;
DEPARTMENT OF CHEMISTRY, UNIVERSITY OF SOUTHERN
CALIFORNIA, LOS ANGELES, CA, 90089, USA.
WILLETT, P. KREBS INSTITUTE FOR BIOMOLECULAR RESEARCH
AND DEPARTMENT OF INFORMATION STUDIES, UNIVERSITY OF
SHEFFIELD, WESTERN BANK, SHEFFIELD S10 2TN, UK.
WINN, P.J. PHYSICAL AND THEORETICAL CHEMISTRY
LABORA TORY, THE UNIVERSITY OF OXFORD, OXFORD, UK
Foreword
This volume edited by Ramon Carb6-Dorca, Xavier Girones and Paul G.
Mezey deals with Molecular Similarity, a very specialised topic, which
provides, however, an answer, even if limited, on a very modern, broad and
relevant trend in the evolution of the scientific method. Let me start a bit far
from this specific topic in order to put it into perspective.
Today society expects science to be useful toward the solution of its (real
or imaginary) survival needs, blurring in this process the traditional
separation between "pure" and "applied" sciences. Thus, "theory" and
"applications ", "models" and "experimental reality", "verification" and
"prediction" are interwoven components in the flow of our scientific
technical-industrial-commercial -sociallife.
In the last half of the twentieth century "computers and computations"
appeared as new tools of ever increasing strength, originally envisaged
mainly to solve complex numericalor statistical problems and to simulate a
limited range of natural events, thus connecting pure and formal scientific
theories to laboratory data, with the dual ability to verify theoretical
hypotheses and predict phenomena.
In general, theory attempts to rationalise events in our ordinary x,y,z, t,
space-time frame. The motion of objects did capture man's interest and
fascination since the beginning of civilisation, and its rationalisation required
notions of geometry, and related algebra but mainly a variety of hypotheses
concerning the origin and nature of the causes responsible for the transit
from A to B for the object. Soon it appeared that different kinds of objects
are in motion due to different but not unrelated causes, and science was born.
Thus, "grosso modo", recalling Pythagoras, Democritus, Galilei and
Kepler, and later Newton, we arrive at the theory of gases, at the
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