Cheminformatics and Organic Chemistry. Computer-Assisted Synthetic Analysis

The interest in the use of computers in synthetic organic chemistry has shown a considerable increase over the last decades, possibly reflected in the special ‘Computer Session’ at the 8th International IUPAC Conference on Organic Synthesis in Helsinki [1]. However, the impact of computerization has been less than in other disciplines of science, and certainly less than in other chemical disciplines. For example, molecular modeling is a technique that was developed around the same time and its use is widespread now, as is reflected, for instance, in Chapters 5 and 7 of this book. One might speculate on the reasons for this observation, but among them certainly the following are important.

[1]  Jan-Willem Boiten,et al.  Cationic polyene cyclizations. A computer assisted synthesis approach , 1993, J. Chem. Inf. Comput. Sci..

[2]  W. T. Wipke,et al.  Computer-Assisted Organic Synthesis , 1977 .

[3]  Ivar Ugi,et al.  Transparent formal methods for reducing the combinatorial abundance of conceivable solutions to a chemical problem : Computer-assisted elucidation of complex reaction mechanisms☆ , 1990 .

[4]  William L. Jorgensen,et al.  Computer-assisted mechanistic evaluation of organic reactions. 12. pKa predictions for organic compounds in Me2SO , 1986 .

[5]  Johann Gasteiger,et al.  EROS A computer program for generating sequences of reactions , 1978 .

[6]  E. Corey,et al.  The Logic of Chemical Synthesis , 1989 .

[7]  E. Corey General methods for the construction of complex molecules , 1967 .

[8]  James B. Hendrickson,et al.  Organische Synthese im Computerzeitalter , 1990 .

[9]  Computer-assisted synthetic analysis. Performance of long-range strategies for stereoselective olefin synthesis , 1978 .

[10]  William L. Jorgensen,et al.  Computer-assisted synthetic analysis. Synthetic strategies based on appendages and the use of reconnective transforms , 1976 .

[11]  Eric Fontain,et al.  The generation of reaction networks with RAIN. 1. The reaction generator , 1991, J. Chem. Inf. Comput. Sci..

[12]  Stephen Hanessian,et al.  The psychobiological basis of heuristic synthesis planning - man, machine and the chiron approach , 1990 .

[13]  Johann Gasteiger,et al.  Berechnung der Ladungsverteilung in konjugierten Systemen durch eine Quantifizierung des Mesomeriekonzeptes , 1985 .

[14]  W. L. Jorgensen,et al.  Computer-assisted mechanistic evaluation of organic reactions. 1. Overview , 1980 .

[15]  Gushurst Computer-assisted mechanistic evaluation of organic reactions , 1988 .

[16]  J. B. Hendrickson,et al.  Systematic synthesis design: the SYNGEN program , 1989 .

[17]  Johann Gasteiger,et al.  COMPUTER-ASSISTED DESIGN OF SYNTHESES FOR HETEROCYCLIC COMPOUNDS , 1995 .

[18]  James B. Hendrickson,et al.  SYNGEN program for synthesis design: basic computing techniques , 1989, J. Chem. Inf. Comput. Sci..

[19]  Joshua Lederberg,et al.  Applications of Artificial Intelligence for Organic Chemistry: The DENDRAL Project , 1980 .

[20]  Alan K. Long,et al.  Computer-assisted synthetic analysis. Techniques for efficient long-range retrosynthetic searches applied to the Robinson annulation process , 1980 .

[21]  David A. Pensak,et al.  COMPUTER-ASSISTED SYNTHETIC ANALYSIS. THE IDENTIFICATION AND PROTECTION OF INTERFERING FUNCTIONALITY IN MACHINE-GENERATED SYNTHETIC INTERMEDIATES , 1976 .

[22]  Johann Gasteiger,et al.  Automatic estimation of heats of atomization and heats of reaction , 1979 .

[23]  Alan K. Long,et al.  Computer-assisted synthetic analysis. Performance of tactical combinations of transforms , 1994, J. Chem. Inf. Comput. Sci..

[24]  J. Gasteiger,et al.  Computer-assisted synthesis and reaction planning in combinatorial chemistry , 2000 .

[25]  Johann Gasteiger,et al.  Computer‐Assisted Planning of Organic Syntheses: The Second Generation of Programs , 1996 .

[26]  Johannes M. Bauer IGOR2: a PC-program for generating new reactions and molecular structures , 1989 .

[27]  Johann Gasteiger,et al.  A new treatment of chemical reactivity: Development of EROS, an expert system for reaction prediction and synthesis design , 1987 .

[28]  G. A. Petersson,et al.  General methods of synthetic analysis. Strategic bond disconnections for bridged polycyclic structures , 1975 .

[29]  E. Corey,et al.  COMPUTER‐ASSISTED SYNTHETIC ANALYSIS. A RAPID COMPUTER METHOD FOR THE SEMIQUANTITATIVE ASSIGNMENT OF CONFORMATION OF SIX‐MEMBERED RING SYSTEMS. 1. DERIVATION OF A PRELIMINARY CONFORMATIONAL DESCRIPTION OF THE SIX‐MEMBERED RING , 1980 .

[30]  Chris Marshall,et al.  Starting material oriented retrosynthetic analysis in the LHASA program. 3. Heuristic estimation of synthetic proximity , 1992, J. Chem. Inf. Comput. Sci..

[31]  E. Corey,et al.  Computer-assisted analysis in organic synthesis. , 1985, Science.

[32]  E J Corey,et al.  Computer-assisted design of complex organic syntheses. , 1969, Science.

[33]  J. Gasteiger,et al.  ITERATIVE PARTIAL EQUALIZATION OF ORBITAL ELECTRONEGATIVITY – A RAPID ACCESS TO ATOMIC CHARGES , 1980 .

[34]  Ivar Ugi,et al.  Computer assistance in the design of syntheses and a new generation of computer programs for the solution of chemical problems by molecular logic , 1988 .

[35]  Johann Gasteiger,et al.  Similarity concepts for the planning of organic reactions and syntheses , 1992, J. Chem. Inf. Comput. Sci..

[36]  Ivar Ugi,et al.  Computer assisted bilateral generation of reaction networks from educts and products , 1987 .

[37]  W. T. Wipke,et al.  Computer-assisted synthetic analysis. Facile man-machine communication of chemical structure by interactive computer graphics , 1972 .

[38]  E. Fontain The generation of reaction networks with RAIN. 2. Resonance structures and tautomerism , 1990 .

[39]  Chris Marshall,et al.  Starting material oriented retrosynthetic analysis in the LHASA program. 2. Mapping the SM and target structures , 1992, J. Chem. Inf. Comput. Sci..

[40]  Martin A. Ott,et al.  Long-Range Strategies in the LHASA Program: The Quinone Diels-Alder Transform , 1997, J. Chem. Inf. Comput. Sci..

[41]  James B. Hendrickson,et al.  Systematic synthesis design. 6. Yield analysis and convergency , 1977 .

[42]  W. L. Jorgensen,et al.  Computer-assisted mechanistic evaluation of organic reactions. 3. Ylide chemistry and the organometallic chemistry of lithium, magnesium, and lithium cuprates , 1981 .

[43]  Z. Hippe Self-adapting computer program system for designing organic syntheses , 1981 .

[44]  Wolf-Dietrich Ihlenfeldt,et al.  An efficient approach toward a flexible and general knowledge definition and program control language system for a synthesis-planning program , 1994, J. Chem. Inf. Comput. Sci..

[45]  Willi Sieber Reaction Retrieval and Synthesis Planning , 1988 .

[46]  James Dugundji,et al.  An algebraic model of constitutional chemistry as a basis for chemical computer programs , 1973 .

[47]  G. Smith,et al.  SECS—Simulation and Evaluation of Chemical Synthesis: Strategy and Planning , 1977 .

[48]  J. Gasteiger,et al.  Computer-assisted reaction prediction and synthesis design , 1990 .

[49]  P. Hodge,et al.  Protective groups in organic synthesis , 1981 .

[50]  James B. Hendrickson,et al.  A logic-based program for synthesis design , 1985 .

[51]  William L. Jorgensen,et al.  Computer-assisted mechanistic evaluation of organic reactions. 22. The generation and use of three-dimensional structures , 1993 .

[52]  W. L. Jorgensen,et al.  Computer-assisted mechanistic evaluation of organic reactions. VII: Six-electron cycloadditions , 1983 .

[53]  H. L. Morgan The Generation of a Unique Machine Description for Chemical Structures-A Technique Developed at Chemical Abstracts Service. , 1965 .

[54]  W. L. Jorgensen,et al.  CAMEO: a program for the logical prediction of the products of organic reactions , 1990 .

[55]  Richard D. Cramer,et al.  Computer-assisted synthetic analysis for complex molecules. Methods and procedures for machine generation of synthetic intermediates , 1972 .

[56]  David A. Pensak,et al.  Computer-assisted synthetic analysis. Methods for machine generation of synthetic intermediates involving multistep look-ahead , 1974 .

[57]  M. G. Hutchings,et al.  Quantification of effective polarisability. Applications to studies of X-ray photoelectron spectroscopy and alkylamine protonation , 1984 .

[58]  Rainer Herges Reaction planning: prediction of new organic reactions , 1990, J. Chem. Inf. Comput. Sci..

[59]  M. G. Hutchings,et al.  Residual electronegativity - an empirical quantification of polar influences and its application to the proton affinity of amines , 1983 .

[60]  William L. Jorgensen,et al.  Computer-assisted mechanistic evaluation of organic reactions. 14. Reactions of sulfur and phosphorus ylides, iminophosphoranes, and P=X-activated anions , 1988 .

[61]  Krishna K. Agarwal,et al.  Application of chemical transforms in EYNCHEMZ: a computer program for organic synthesis route discovery , 1978, Comput. Chem..

[62]  William L. Jorgensen,et al.  Computer-assisted evaluation of oxidation reactions , 1989 .

[63]  A F Sanders,et al.  Empirical Explorations of SYNCHEM , 1977, Science.

[64]  Chris Marshall,et al.  Implementation of the Cahn-Ingold-Prelog System for Stereochemical Perception in the LHASA Program , 1994, J. Chem. Inf. Comput. Sci..

[65]  J. Gasteiger,et al.  Automated derivation of reaction rules for the EROS 6.0 system for reaction prediction , 1990 .

[66]  W. T. Wipke,et al.  SIMULATION AND EVALUATION OF CHEMICAL SYNTHESIS, COMPUTER REPRESENTATION AND MANIPULATION OF STEREOCHEMISTRY , 1974 .

[67]  William L. Jorgensen,et al.  Computer assisted analysis of reactions involving organic free radicals and diradicals , 1990, J. Chem. Inf. Comput. Sci..

[68]  R. Herges,et al.  Reaction Planning: Computer-Aided Discovery of a Novel Elimination Reaction , 1992, Science.

[69]  W. L. Jorgensen,et al.  Computer-assisted mechanistic evaluation of organic reactions. 4. Organosilicon chemistry , 1983 .

[70]  Philip N. Judson,et al.  Starting material oriented retrosynthetic analysis in the LHASA program. 1. General description , 1992, J. Chem. Inf. Comput. Sci..

[71]  Andreas Dietz,et al.  Models, concepts, theories, and formal languages in chemistry and their use as a basis for computer assistance in chemistry , 1994, Journal of chemical information and computer sciences.

[72]  W. T. Wipke,et al.  Techniques for perception by a computer of synthetically significant structural features in complex molecules , 1972 .

[73]  E. J. Corey,et al.  Algorithm for machine perception of synthetically significant rings in complex cyclic organic structures , 1972 .

[74]  Alan K. Long,et al.  Computer-assisted synthetic analysis. A generalized procedure for subgoal transform selection based on a two-dimensional pattern language , 1994, J. Chem. Inf. Comput. Sci..

[75]  Johann Mulzer,et al.  Computer-Assisted Synthetic Analysis. Long-Range Search Procedures for Antithetic Simplification of Complex Targets by Application of the Halolactonization Transform , 1980, J. Chem. Inf. Comput. Sci..

[76]  W. L. Jorgensen,et al.  Computer-assisted synthetic analysis. Generation of synthetic sequences involving sequential functional group interchanges , 1976 .

[77]  J. B. Hendrickson The SYNGEN approach to synthesis design , 2010 .

[78]  G. É. Vléduts,et al.  Concerning one system of classification and codification of organic reactions , 1963, Inf. Storage Retr..

[79]  David Weininger,et al.  SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules , 1988, J. Chem. Inf. Comput. Sci..