Journal of Chemical Information and Computer Sciences
Volume 39, Number 1, JANUARY/FEBRUARY 1999


TABLE OF CONTENTS


1 Molecular Diversity and Representativity in Chemical Databases
Denis M. Bayada, * Hans Hamersma, and Vincent J. van Geerestein

11 Evaluation and Use of BCUT Descriptors in QSAR and QSPR Studies
David T. Stanton

21 Application of Nearest-Neighbor and Cluster Analyses in Pharmaceutical Lead Discovery
David T. Stanton, Timothy W. Morris, Siddhartha Roychoudhury, and Christian N. Parker*

28 Metric Validation and the Receptor-Relevant Subspace Concept
R. S. Pearlman* and K. M, Smith

36 Design and Diversity Analysis of Large Combinatorial Libraries Using Cell-Based Methods
Dora Schnur

46 Design of Libraries To Explore Receptor Sites
Catherine M. Murray and Stephen J. Cato*

51 An Efficient Implementation of Distance-Based Diversity Measures Based on k~d Trees
Dimitris K. Agrafiotis* and Victor S, Lobanov

Papers from the MATH/CHEM/COMP97 International Course and Conference, Dubrovik,
Croatia.

59 Prediction of Gas-Chromatographic Retention Indices Using Topological Descriptors
Matevi Pompe and Marjana No vie

68 Time-Resolved Profiles in Modulated Polarization Spectroscopy
A. Vrancic, * K. Rupnik, L. Klasinc, and S, P. McGlynn

77 Szeged Index of Symmetric Graphs
Janez. Zerovnik

CHEMICAL INFORMATION

81 End-User Customized Chemistry Journal Articles
Steven M. Bachrach, * Anatoli Krassavine, and Darin C. Burleigh

86 Concept Design of Computer-Aided Study on Traditional Chinese Drugs
Xinjian Yan, * Jiaju Zhou, and Zhihong Xu

CHEMICAL COMPUTATION

90 Generalized Spectral Moments of the Iterated Line Graphs Sequence. A Novel Approach to QSPR
Studies
Ernesto Estrada

96 Mathematica-A.ssisted Learning in Physical Chemistry
R. W. Kaziro

104 Modeling Properties with Higher-Level Molecular Connectivity Descriptors
Lionello Pogliani

112 GA Strategy for Variable Selection in QSAR Studies: Application of GA-Based Region Selection to
a 3D-QSAR Study of Acetylcholinesterase Inhibitors
Kiyoshi Hasegawa, Toshiro Kimura, and Kimito Funatsu *

121 Multivariate Regression Outperforms Several Robust Architectures of Neural Networks in QSAR
Modeling
Bono Lucic* and Nenad Trinajstic

133 Wavelet Neural Network and Its Application to the Inclusion of^-Cyclodextrin with Benzene
Derivatives
Lei Liu and Qing-Xiang Guo*

139 A New Topological Index for QSPR of Alkanes
Biye Ren

144 The Most Stable Class of Benzenoid Hydrocarbons and Their Topological Characteristics — Total
Resonant Sextet Benzenoids Revisited
Jerry Ray Dias

151 Benzene Derivatives with Achiral and Chiral Substituents and Relevant Derivatives Derived from
D(6h) Skeletons. Symmetry-Itemized Enumeration and Symmetry Characterization by the
Unit-Subduced Cycle Index Approach
Shinsaku Fujita

164 Binary Quantitative Structure—Activity Relationship (QSAR) Analysis of Estrogen Receptor Ligands
Hua Gao, * Chris Williams, Paul Labute, and Jürgen Bajorath

MOLECULAR-MODELTNG

169 Selecting Combinatorial Libraries to Optimize Diversity and Physical Properties
Valerie J. Gillet, * Peter Willett, John Bradshaw, and Darren V. S. Green

BOOK REVIEWS

178 Molecular Modeling on the PC
Gordon G. Cash

178 Chemical Librarianship: Challenges and Opportunities
Matthew Clark

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Journal of Chemical Information and Computer Sciences
Volume 39, Number 3, MAY/JUNE 1999

TABLE OF CONTENTS

423 Developments in Patents Documentation in Europe during the Last Decade
Stephen R. Adams

432 Creating Customized Shared Databases of Patent Information Using Lotus Notes
Carol Herzberg

439 Crossfile Searching with QPAT-US Using WordBasic Macro Tools
Elvin L. Hoel

448 Patents on the Internet versus Patents Online: A Snapshot in Time
Nancy Lambert*

453 Relevance Ranking in Patent Databases. Is It Relevant?
Edlyn S. Simmons

CHEMICAL INFORMATION

463 Molecular Structure Disassembly Program (MOSDAP): A Chemical Information Model To
Automate Structure-Based Physical Property Estimation
John W, Raymond* and Tony N. Rogers

475 Exhaustive Generation of Organic Isomers. 5. Unsaturated Optical and Geometrical Stereoisomers
and a New CIP Subrule
M. L. Contreras,* G. M. Trevisiol, J. Alvaret, G. Arias, and R. Rozas

483 Authentication of Internet-Based Distributed Computing Resources in Chemistry
Alan P. Tonge, Henry S, Rzepa, * and Hiroshi Yoshida

CHEMICAL COMPUTATION

491 Quantitative Structure-Property Relationships for the Estimation of Boiling Point and Flash Point
Using a Radial Basis Function Neural Network
John Tetteh, Takahiro Su^uki, Ed Metcalfe, * and Sian Howells

508 Prediction of Methyl Radical Addition Rate Constants from Molecular Structure
Gregory A. Bakken and Peter C. Jurs*

515 Estimation of the Liquid Viscosity of Organic Compounds with a Quantitative Structure—Property
Model
Ovidiu lvanciuc, Teodora lvanciuc, Petru A. Filip, and Daniel Cabrol-Bass*


525 MS-WHIM Scores for Amino Acids: A New 3D-Description for Peptide QSAR and QSPR Studies
A. Zaliani* and E. Gancia

534 Wiener-Number-Related Sequences
Douglas J. Klein and Ivan Gutman*

537 Ab Initio Study of Chlorosilanes: Dipole Moments and Charge Distributions
Dea-Sik Hong* and Soo Gyeong Cho*

543 Simulation Techniques in Parametric Hamiltonians
Mirba Romero, Morella Sänchez, Anibal Sierraalta, Luis Rincon, and Fernanda Ruette*

550 Path-Integral Calculation of the Mean Number of Overcrossings in an Entangled Polymer Network
Gustave) A. Artec a

558 Infrared Spectra Information and Their Correlation with QSAR Descriptors
Rornualdo Benigni, * Laura Passerini, David J. Livingstone, Mark A. Johnson, and
Alessandro Giuliani

563 Isomer Generation: Syntactic Rules for Detection of Isomorphism
Istvdn Lukovits

569 Pharmacophore Fingerprinting. l. Application to QSAR and Focused Library Design
Malcolm J. McGregor and Steven M. Muskal

575 On the Equivalence Between Different Descriptions of Molecules: Value for Computational
Approaches
Rornualdo Benigni, * Graua Gallo, Fabri^io Giorgi, and Alessandro Giuliani

579 Numerical Study of Tetrahedral Bond Angles
I gor Novak

MOLECULAR MODELING

582 Mining a Large Database for Peptidomimetic Ring Structures Using a Topological Index
Alan H. Lipkus

587 An Implementation of Configuration Interaction in a General Purpose Semiempirical Context
Daniel A. Liotard* and Andrew Holder

594 Alignment of 3D-Structures by the Method of 2D-Projections
Daniel D.Robinson, Paul D. Lyne, and W. Graham Richards*

601 Development of Three-Dimensional Descriptors Represented by Tensors: Free Energy of Hydration
Density Tensor
Su H\van Son, Cheol Kyu H an, Soon Kil Ahn, Jeong Hyeok Yoon, and Kyoung Tai No*

610 A New Efficient Approach for Variable Selection Based on Multiregression: Prediction of Gas
Chromatographie Retention Times and Response Factors
Bono Lucic,* Nenad Trinajstic, Side v Sild, Mati Karelson, and Alan R. Katritzky*

622 Clustering Peptide Structures through Identification of Commonly Exposed Groups
Thy-Hou Lin, * Jia-Jiunn Lin, Yung-Feng Huang, and Jin-Hwang Liu

CORRESPONDENCE

630 Comment on "Isomorphism, Automorphism Partitioning, and Canonical Labeling Can Be Solved in
Polynomial-Time for Molecular Graphs"
Bo Tao Fan, Annick P anaye, and Jean-Pierre Doucet*

COMPUTER SOFTWARE REVIEWS

632 Symantec Norton Antivirus 5.0 for Windows
Stephen R. Heller

633 Norton 2000 Version 1.0 for Windows
Stephen R. Heller

634 Chemical Manufacturers Electronic Directory of Trade Name Products 1997 Edition on CD-ROM
Robert E. Buntrock

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Journal of Chemical Information and Computer Sciences
Volume 39, Number 2, MARCH/APRIL 1999

TABLE OF CONTENTS

179 First Indo—U.S. Workshop on Mathematical Chemistry with Applications in Molecular Design and
Hazard Assessment of Chemicals
Subhash C. Basak, George W. A. Milne, Milan Randic, Dilip K. Sinha

180 Chemical Structure and Superconductivity
R. B. King

192 Topological Index and Thermodynamic Properties. 5. How Can We Explain the Topological
Dependency of Thermodynamic Properties of Alkanes with the Topology of Graphs?
Haruo Hosoya, * Machiko Gotoh, Miyuki Murakami, and Shigeko Ikeda

197 Directed toward the Development of a Unified Structure Theory of Polycyclic Conjugated
Hydrocarbons: The Aufbau Principle in Structure/Similarity Studies
Jerry Ray Dias

204 Three-Dimensional Quantitative Structure—Activity Relationship (QSAR) and Receptor Mapping of
Cytochrome P-450i4(iDM Inhibiting Azoic Antifungal Agents
Tanaji T. Talele and Vithal M. Kulkarni*

211 A Theoretical Concept To Rank Environmentally Significant Chemicals
Rainer Brüggemann* and Hans-Georg Bartel

218 Heats of Adsorption of Hydrocarbons on Zeolite Surfaces: A Mathematical Approach
Lalji Dixit* and T. S. R. P rasada Rao

224 Holographic Electron Density Shape Theorem and Its Role in Drug Design and Toxicological Risk
Assessment
Paul G, Mezey*

231 Hydrogen Bonding Parameters for QSAR: Comparison of Indicator Variables, Hydrogen Bond
Counts, Molecular Orbital and Other Parameters
J . C. Dearden* and T. Ghafourian

236 New QSAR Methods Applied to Structure-Activity Mapping and Combinatorial Chemistry
Frank R. Burden* and David A. Winkler

243 Indexing Scheme and Similarity Measures for Macromolecular Sequences
C.RaychaudhuryandA.Nandy*

248 Topological Shape and Size of Peptides: Identification of Potential Allele Specific Helper T Cell
Antigenic Sites
Chandan Raychaudhury, * Asok Banerjee, Partha Bag, and Syamal Roy
255 Prediction of Complement-Inhibitory Activity of Benzamidines Using Topological and Geometric
Parameters
Subhash C. Basak, * Brian D. Gute, and Shibnath Ghatak

261 Optimal Molecular Descriptors Based on Weighted Path Numbers
Milan Randic* and Subhash C Basak

267 Proton Induced Structural Reorganization of a Few Carbonyl Molecules in the Ground and Excited
States
T. Thakuria, M. L. Das, P. K. Bhattacharyya, and C. Medhi*

272 Superpendentic Index: A Novel Topological Descriptor for Predicting Biological Activity
S. Gupta, M, Singh, and A. K. Madan*

CHEMICAL INFORMATION

278 Estimation of the Information Content in Ultraviolet—Visible Molecular Absorption Spectrometry
Victor David

281 Comparison of Beilstein CrossFirePlus Reactions and the Selective Reaction Databases under ISIS
Faiz A, Parkar and Don Parking

CHEMICAL COMPUTATION

289 Spectral Moments of the Edge Adjacency Matrix in Molecular Graphs. Benzenoid Hydrocarbons
Svetlana Markovic' and Ivan Gutman

294 Validation and Subsequent Development of the Derek Skin Sensitization Rulebase by Analysis of
the BgVV List of Contact Allergens
M. D, Barratt and J. J. Langowski*

299 An Effective Topological Symmetry Perception and Unique Numbering Algorithm
Zheng Ou yang, Shengang Yuan, * Josef Brandt, and Chongzhi Zheng

304 Response-Surface Analyses for Toxicity to Tetrahymena pyriformis: Reactive Carbonyl-Containing
Aliphatic Chemicals
T. Wayne Schulte and Mark T. D. Cronin

310 Conservative Electrostatic Potential Patterns at Enzyme Active Sites: The Anion-Cation-Anion
Triad
Timea Gerczei, Bence Asboth, and Gabor Näray-Szabö*

316 A Novel Approach to Retrosynthetic Analysis Using Knowledge Bases Derived from Reaction
Databases
Koji Satoh and Kimito Funatsu*

326 A Cellular Automata Model of the Percolation Process
Lemont B. Kier, * Chao-Kun Cheng, and Bernard Testa

333 Three-Dimensional Quantitative Structure-Activity Relationships from Tuned Molecular Quantum
Similarity Measures: Prediction of the Corticosteroid-Binding Globulin Binding Affinity for a
Steroid Family
David Robert, Lluis Amat, and Ramon Carbo-Dorca

MOLECULAR MODELING

345 Development and Validation of a Novel Variable Selection Technique with Application to
Multidimensional Quantitative Structure-Activity Relationship Studies
Chris L. Waller* and Mary P. Bradley

356 Modeling Antileukemic Activity of Carboquinones with Electrotopological State and Chi Indices
Jonathan D. Gough and Lowell H. Hall*

362 Definition of a Pharmacophore for Partial Agonists of Serotonin 5-HT3 Receptors
Cyril Daveu, Ronan Bureau, lsabelle Baglin, Herve Prunier, Jean-Charles Lancelot, and
Sylvain Rault*

370 Modeling the Solvation Sites in Rare-Gas Matrices with the Simulated Annealing Monte Carlo
Technique
Alexander Moskovsky and Alexander Nernukhin

376 PM3(tm) Analysis of Transition-Metal Complexes
Thomas R. Cundari* and Jun Deng

382 A Computational Study of Intramolecular Proton Transfer in Gaseous Protonated Glycine
Kui Zhang and Alice Chung-Phillips*

396 Prediction of the Brain—Blood Distribution of a Large Set of Drugs from Structurally Derived
Descriptors Using Partial Least-Squares (PLS) Modeling
Juan M. Luco*

405 Prediction of Solvation Free Energies of Small Organic Molecules: Additive-Constitutive Models
Based on Molecular Fingerprints and Atomic Constants
Vellarkad N. Viswanadhan, Arup K. Ghose,* U. Chandra Singh, and John J. Wendoloski

413 Modeling of the Interaction between New Ethidium Derivatives and TAR RNA of HIV-1
R. Terreux, D. Cabrol-Bass* V. Peytou, R. Condom, andR. Guedj

COMPUTER SOFTWARE REVIEWS

420 Fillers, Extenders, and Diluents Electronic Handbook
Elizabeth Brown

421 OmniPage Pro 9.0 for Windows
Stephen R. Heller

BOOK REVIEWS

422 Patent Strategy for Researchers and Research Managers
Adele Hoskin

422 A Practical Guide to Combinatorial Chemistry
Bruce Slutsky

422 Combinatorial Chemistry and Molecular Diversity in Drug Discovery
Bruce Slutsky

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