Software Development in Chemistry 4: Proceedings of the 4th Workshop “Computers in Chemistry” Hochfilzen, Tyrol, November 22–24, 1989 PDF
Preview Software Development in Chemistry 4: Proceedings of the 4th Workshop “Computers in Chemistry” Hochfilzen, Tyrol, November 22–24, 1989
1. Gasteiger (Ed.) Software Development in Chemistry 4 Proceedings of the 4th Workshop "Computers in Chemistry" Hochfilzen, Tyrol, November 22-24,1989 Organized by the working group der G DCh-Fachgruppe Chemic-Information Springer-Verlag Berlin Heidelberg New York London Paris Tokyo Hong Kong Prof. Dr. Johann Gasteiger Institute of Organic Chemistry Technical University of Munich LichtenbergstraBe 4, 0-8046 Garching FRG ISBN-13: 978-3-540-52173-0 e-ISBN-13: 978-3-642-75430-2 DOl: 10.1007/978-3-642-75430-2 This work is subject to copyright. All rights are reserved, whether the whole or part of the material is concerned. specifically the rights of translation, reprinting, re-use of illustrations, recitation. broadcasting, reproduction on microfilms or in other ways, and storage in data banks. Duplication of this publication or parts thereof is only permitted under the provisions of the German Copyright Law of September 9,1965, in its current version, and a copyright fee must always be paid. Violations fall under the prosecution act of the German Copyright Law. © Springer-Verlag, Berlin Heidelberg 1990 The use of registered names, trademarks, etc. in this publication does not imply, even in the absence of a specific stakment. that such names are exempt from the relevant protective laws and regulations and therefore free for general use. 216113020 5 4 3 2 I 0 - Printed on acid-free paper Geleitwort Neben Arbeit und Kapital wird die Produktion, Verteilung und Nut zung von Information in unserer modernen Industriegesellschaft im mer mehr zum Produktionsfaktor. Dies gilt insbesondere fur innova tionsorientierte Forschungs- und Entwicklungsbereiche, wie etwa die Mikroelektronik, die Biotechnologie und die Chemie. 1m weltweiten Informationsangebot behaupten wir mit den Daten banken BEILSTEIN ONLINE und GMELIN ONLINE, deren Aufbau Schwer punkt im Fachinformationsprogramm der Bundesregierung ist, unsere traditionelle Kompetenz fur den Bereich der stoffbezogenen Fakten information. Erganzend dazu spielen spektroskopische Methoden eine erhebliche Rolle fur viele Arbeitsbereiche der Chemie. Mit den kurzlich begonnenen Aktivitaten zum Aufbau eines Informationssy stems Spektroskopie auf der Basis von SPECINFO werden entscheiden de Verbesserungen zur Automatisierung in der Strukturaufklarung und Analytik erwartet. Angesichts der Informationsfulle in der Chemie ist, neben der Auf arbeitung und Speicherung, die Entwicklung moderner Werkzeuge zur Erschlie~ung des gespeicherten Wissens von gro~er Bedeutung. Ande rerseits ist fur eine Vielzahl der bekannten Stoffe das Eigen schaftsprofil nicht annahernd vollstandig verfugbar. Durch die sy stematische Auswertung strukturorientierter Datenbanken k6nnen Zu sammenhange zwischen den Stoffdaten ermittelt werden, die sich in Regeln fur eine Datenprognose niederschlagen. Hier besteht eine wichtige Zukunftsaufgabe fur die Fachinformation, und hier setzt auch das Thema Ihrer Veranstaltung "Software-Entwicklung in der Chemie" an. Fur die Vortrage, die Diskussionen und Prasentationen wtinsche ich den Veranstaltern und Teilnehmern viel Erfolg und vielfaltige An regungen fur ihre Tatigkeit in ihren Einrichtungen. Dr. Heinz Riesenhuber Bundesminister fur Forschung und Technologie der Bundesrepublik Deutschland Foreword Besides work and finance. the production. distribution. and the use of information are increasingly becoming production factors in our modern industrial society. This is particularly valid for in novatory fields of research and development such as microelectron ics. biotechnology. and chemistry. In the worldwide supply of information. we are maintaining our traditional competence in the field of factual information on com pounds with the databases BEILSTEIN ONLINE and GMELIN ONLINE. The development of these databases is a high priority of the Special ized Information Program of the Federal Republic. In addition. spectroscopic methods playa major role in many areas of chemis try. Recently. action was taken to initiate an Information System of Spectroscopy based on SPECINFO. It is expected that this system will lead to decisive improvements in the automation of structure elucidation and analytical chemistry. In view of the large amount of information in chemistry. not only the processing and storage of knowledge is of great importance but also the development of modern tools for retrieving it. On the other hand. the set of characteristics for a large number of com pounds is far from being completely accessible. The relationships between the data on compounds can be derived by systematically evaluating structure oriented databases. These re lationships can be put down in rules for data prediction. This is an important task for technical information in the future and this is also a focal point of your workshop "Software-Development in Chemistry" . For the lectures. discussions. and presentations. I wish the or ganizers and participants every success and a great deal of inspi ration for their work in their organizations. Dr. Heinz Riesenhuber The Federal Minister for Research and Technology of the Federal Republic of Germany (translated by Prof. Dr. J. Gasteiger) Preface This monograph contains papers presented at the 4th Workshop "Software-Entwicklung in der Chemie" (Software Development in Chemistry) held in November 1989 in Hochfilzenl Austria. It was the 4th workshop organized by the Working Party ''CIC - Computer in der Chemie". The proceedings of the first three workshops have all been published in German: Software-Entwicklung in der Chemie 1, 2, and 3; Springer Verlag, Berlin, 1987, 1988, 1989. As this is the first one to have the proceedings in English some retrospective views on the history of this Working Party and its Workshop are appropriate. The Division of "Chemie Information" of the German Chemical Society (GDCh) set up a Working Party "CIC - Computer in der Chemie" in December 1985. As a first scientific event this Working Party organized a Workshop "Software-Development in Chemistry" in November 1986 in the tiny alpine village of HochfiIzen/Tirol in Austria. The main objective of this workshop was to bring together scientists from the various disciplines of chemistry that are actively engaged in developing software or using the computer for the solution of chemical problems. The various activities in organic, inorganic, analytical, and theoretical chemistry are usually presented at highly speCialized meetings to experts from their own field. It was thought that a synergistic effect should develop by bringing these speCialists together at a meeting that has as a common denominator the use of the computer in chemistry and that this should provide new scientific impulses. Another intention was to further the development of software for chemistry in the German speaking countries. Even the humblest beginnings of venturing into programm ing the computer to perform tasks for the chemist should be attracted to assess the state of the art in Germany and then lay a foundation to aim for international standards of excellence. Therefore, the language of the workshop was German. Only a few dozens of "computer freaks" were expected. Thus we were in for a big surprise when already 135 participants showed up at this first workshop in 1986. The scientific atmosphere was so good, the discussions so intense that it was unanimously agreed to make this workshop an annual event. The second CIC-Workshop was in 1987 again in HochfiIzen, the third one, organized by Prof. G. Gauglitz, in 1988 at the University of Tiibingen drawing 265 partiCipants. For the fourth workshop the number of participants had to be limited to 180 with 190 eventually coming again to HochfiIzen. Concurrent with the success of the workshop the standing of the Working Party "CIC - Computer in der Chemie" within the Division of "Chemie Information" was increasing. To recognize the achievements of the Working Party and the impact of computers on chemistry the DiviSion of the German Chemical Society (GDCh) changed its name in November 1989 to "Chemie - Information - Computer (CIC)". This should lay the foundation for an increase in the promotion of the computer in chemical information and chemistry in general. VIII The 4th workshop in 1989 encompassed 28 oral presentations, 27 posters, and 26 demonstrations of a variety of software products from academic, industrial, and commercial sources. The proceedings contain those contributions (oral and poster presentations and some software demonstrations) for which manuscripts were submitted. The papers are grouped according to their topics. As in the previous workshops, main features were the processing of structural information, the bUilding of databases, the processing of spectroscopic data, and molecular modelling. A new major topic was the processing of information on chemical reactions. We also succeeded to open our perspectives to new developments in computer science, and attracted presentations on the simulation of structures and processes. On the other hand, we have to realize that some areas are still not well represented at this workshop. Chemometrics is one such topic that should deserve more attention in the future. A highlight of the workshop was the evening address by Prof. J. Brickmann on "Art and Computer" with its slide and video show. We all went away impressed and moved by realizing that we have met a person that has managed to combine work and hobby and has brought that to perfection. Clearly, a printed medium is too poor to give only the slightest hint at what is going on at the forefront of computer graphics and computer art. Thus we refrain from presenting any contribution of this apogee. The success of any meeting depends on the collaboration of many persons. The scientific committee, Prof. J. Brickmann, Prof. G. Gauglitz, Dr. C. Jochum, Dr. R. Neudert, Dr. V. Schubert, Prof. K. Varmuza, Dr. j. H. Winter, and Prof. D. Ziessow were instrumental in attracting contributions and shaping the program. The Division of "Chemie-Information" of GDCh and the Working Party "EDV in der Chemie" of the Austrian Chemical Society (GOCh) helped in spreading the news of the meeting and in the organisation. Computer hardware was prOVided by SUN Microsystems, Mtinchen, Digital Equipment, Frankfurt, Silicon Graphics, Geneva, and W & S-Computersysteme, Innsbruck. The Workshop was held under the auspices of the Bundesminster fUr Forschung und Technologie (BMFT) of the Federal Republic of Germany. Sponsorship came from the Federation of European Chemical Societies (FECS) and its Working Party "Computational Chemistry". Last not least, most of the work On orgamZIng and running the meeting} rested on Ms. Tanja PietraS who obtained assistance by Ms. Claudia Hofmann. In the final and hectic days my entire research group - V. Dimpfl, W. Hanebeck, W. D. Ihlenfeldt, K. Rafeiner, P. Rose, C. Rudolph, K.-P. Schulz, M. Wagener, W. Witzenbichler - provided every necessary help. As in previous years again valuable on-site assistance came in the village of Hochfilzen from the mayor, J. Bergmann, and from Ms. H. Gfaller, Ms. Perterer, and j. Arnold. The music band of Hochfilzen welcomed us and made us feel at home from the very beginning. I can only thank these persons and institutions for making the 4th CIC-Workshop again a big success. Johann Gasteiger Table of Contents 1. Representation of Chemical Structures; Factual Databases H. Maier, D. Walkowiak Chemical Substructure Search on CD-ROM 1 H. Noth, E. Striedl Documentation of Special Bond Types and Evaluation of Factual Data from "B-Base" 11 J.L. Wisniewski, L. Goebels, A. Lawson AUTONOM: Automatic Generation of IUPAC-Names from Structural Input 19 L. Domokos Keys to the Beilstein Database (A Ring Searching Algorithm) 31 E. Lang, T. Forster, C.-W. von der Lieth The Integration of the Cambridge Crystallographic Data Files into the Relational Information Network of the German Cancer Research Center 43 A. Nebel, G. Olbrich, R. Deplanque The Gmelin Information System - The Connection between Handbook and Database 51 J. Gasteiger, W.D. Ihlenfeldt The WODCA System (An Integrating Environment for the Chemist) 57 2. Structure and Properties; Bridging the Gap K. Bley, I. Ugi Computer-Assisted Analysis of Qualitative Structure/Activity Relations of Organic Molecules 67 W. Degen prediction of the Threshold Soot Index for Hydrocarbon Fuels with Randic's TOpological Indices 75 R. Bruggemann, B. MUnzer A Graph Theoretical Method to Estimate Substance Date 85 B. Heinrich, E. Schreiner, D. Spielbauer, M. Wolperdinger, H.-U. Wagner PIMO. a Program Visualizing HMO Results by Producing Transferable Graphics Output 97 J. Barthel, H. Popp, G. Schmeer The Calculation of Electrolyte Solution Properties with the Help of the ELDAR Data and Method Bank Exemplified by Electrolyte Conductance 101 x 3. Molecular Modelling W. Heiden, M. schlenkrich, C.-D. Zachmann, J. Brickmann Triangulation of Molecular Surfaces 115 U. Howeler MOBY: Molecular Modelling on the PC 123 B. Krieg, P. Keller ROCOCO: Reference Online Library for the Computer Aided Construction of Molecular Geometries. Computer Aided Construction of Realistic Molecular Models Using a Knowledge Base (I) 127 N. Reuter MMGEO - A Versatile Tool for MMX Users 141 4. Spectral Datai Acquisition and Interpretation A.N. Davies, H. Hilliq, M. Linscheid JCAMP - DX, A Standard 147 P. Haas, W. Robien Automatic Interpretation of 2D-NMR-Spectra [1] 157 H. Lohninger CDDS - A Personal Computer Based System for Automated Interpretation of GC/MS-Analyses 165 W. Werther, K. Varmuza EDAS-MS - Exploratory Data Analysis of Mass Spectra 175 W. Hanebeck, K. Rafeiner, K.-P. Schulz, P. Rose, J. Gasteiqer Towards the Automatic Generation of a Mass Spectrum from the Structure of a Compound 187 G. Gauqlitz, S. Wei~ Factor Analysis of Spectral Data from Chemical Reactions 197 S. Ebel, J.S. Kanq, W. Windmann Normalization of in Situ-Spectra in Thin Layer Chromatography 207 S. Ebel, C. Urban, S. Windmann Algorithms for Use in Purity Control of Drugs Using a UV-Spectroscopy 221 S. Goudetsidis, G. Haqele DSYM-PC A Novel Program to Simulate HR-NMR Spectra for Spins 1=1/2 on IBM-Compatible Computers of PC/XT/AT Type 233 XI 5. Chemical Reactions and Synthesis Planning J. Bauer IGOR2: A Program System for Generating Chemical Reactions and Structures 237 E. Zass Reaction Databases in a University Chemistry Department - Online or In-house? 243 E. Blurock, T. Strelow Towards Synthesis Planning Aids Through Databank Analysis 255 M. Wagener, J. Gasteiger Implementation of Synthesis Strategies in PROLOG 265 P. Rose, J. Gasteiger EROS 6.0, A Knowledge Based System for Reaction Prediction - Application to the Regioselectivity of the Diels-Alder Reaction 275 R. Moll CARSA (Computer-Assisted Research in Synthesis and Application) 289 6. Simulations of Structures, Reactions and Properties J. Kinkel, H.J. Ederer, K.H. Ebert Modelling of Polymer Gel Formation and Gel Reactions with Monte Carlo Methods for 3-Dimensional Networks 297 K. Nicklas, J. BOcker, M. Schlenkrich, P. Bopp, J. Brickmann Molecular Dynamic Simulation of the Interface Aqueous Ionic Solution / Lipid Membrane 311 B. Speiser Electroanalytical Simulations. 10. The Simulation of Fast Second Order Reactions in Electrochemical Systems 321 M. Klein, G. Baier, O.E. Rossler The Rashevsky-Turing System: Two Coupled Oscillators as a Generic Reaction-Diffusion Model 331 D. Frohlich, G. Gauglitz Photoreactions in Solids - Experiment and Simulation 345
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