Computer Generation of Molecular Structures by the SMOG Program

The SMOG program for exhaustive and irredundant generation of chemical structures by the given molecular formula is described. The program makes use of the graph-theoretical Faradjev algorithm, which was essentially modified to be efficiently applied for chemical purposes. The major improvements of the algorithm include adequate consideration of the sets of required and forbidden structural fragments (“Goodlist” and “Badlist”, respectively), effective use of invariant substructures (“core” fragments), possible consideration of various atomic valence states (atoms with formal charges, etc.), and rigorous treatment of aromatic structures. The output structures are visualized as 2D graphs according to an original algorithm. The advantages and possible applications of this software are discussed.

[1]  Dennis H. Smith,et al.  Applications of artificial intelligence for chemical inference. XVII. Approach to computer-assisted elucidation of molecular structure , 1975 .

[2]  Louis Hodes,et al.  Selection of Descriptors According to Discrimination and Redundancy. Application to Chemical Structure Searching , 1976, J. Chem. Inf. Comput. Sci..

[3]  Yoshihiro Kudo,et al.  The Connectivity Stack, a New Format for Representation of Organic Chemical Structures , 1974 .

[4]  Simona Bohanec.  Structure Generation by the Combination of Structure Reduction and Structure Assembly , 1995, J. Chem. Inf. Comput. Sci..

[5]  Vladimír Kvasnička,et al.  An improved version of the constructive enumeration of molecular graphs with prescribed sequence of valence states , 1993 .

[6]  Craig A. Shelley,et al.  Heuristic approach for displaying chemical structures , 1983, J. Chem. Inf. Comput. Sci..

[7]  E. Fontain.  The B6H14 problem: Generation of a catalogue of conceivable isomers† , 1994 .

[8]  James B. Hendrickson,et al.  Generation and enumeration of carbon skeletons , 1991, J. Chem. Inf. Comput. Sci..

[9]  Shinsaku Fujita.  Subductive and inductive derivation for designing molecules of high symmetry , 1991, J. Chem. Inf. Comput. Sci..

[10]  Ramaswamy Nilakantan,et al.  A method for automatic generation of novel chemical structures and its potential applications to drug discovery , 1991, J. Chem. Inf. Comput. Sci..

[11]  N. S. Sridharan,et al.  Applications of artificial intelligence for chemical inference. XIII. Labeling of objects having symmetry , 1974 .

[12]  Nobuhide Tanaka,et al.  A reasonable triamantane rearrangement path searched by the selective disource propagation algorithm , 1983, J. Chem. Inf. Comput. Sci..

[13]  Adalbert Kerber,et al.  Ein strukturgenerator für molekulare graphen , 1990 .

[14]  Simona Bohanec,et al.  Structure generation of constitutional isomers from structural fragments , 1991, J. Chem. Inf. Comput. Sci..

[15]  I. P. Bangov.  Computer-assisted structure generation from a gross formula. 3. Alleviation of the combinatorial problem , 1990, J. Chem. Inf. Comput. Sci..

[16]  Dennis H. Smith,et al.  Applications of artificial intelligence for chemical inference. 37. GENOA: a computer program for structure elucidation utilizing overlapping and alternative substructures , 1981 .

[17]  Milan Randic,et al.  On Canonical Numbering of Atoms in a Molecule and Graph Isomorphism , 1977, J. Chem. Inf. Comput. Sci..

[18]  Heribert Popp,et al.  ELDAR, a knowledge base system on microcomputer for electrolyte solutions. The factual knowledge of ELDAR , 1991, J. Chem. Inf. Comput. Sci..

[19]  Kimito Funatsu,et al.  Further development of structure generation in the automated structure elucidation system CHEMICS , 1988, J. Chem. Inf. Comput. Sci..

[20]  Cheng Qian,et al.  Enhanced algorithm for finding the smallest set of smallest rings , 1990, J. Chem. Inf. Comput. Sci..

[21]  James B. Hendrickson,et al.  Unique numbering and cataloging of molecular structures , 1983, J. Chem. Inf. Comput. Sci..

[22]  Jiri Pospichal,et al.  Canonical indexing and constructive enumeration of molecular graphs , 1990, J. Chem. Inf. Comput. Sci..

[23]  Bradley D. Christie,et al.  Structure generation by reduction: a new strategy for computer-assisted structure elucidation , 1988, J. Chem. Inf. Comput. Sci..

[24]  Arndt Simon,et al.  Über die ersten monosubstituierten Derivate von Triboran(7). – Kristall‐ und Molekülstruktur von Benzoyloxytriboran(7) , 1989 .

[25]  Shu Shu Yang,et al.  DAST (diethylaminosulfur trifluoride) induced epimerization of a 2-(acetoxymethyl)myoinositol , 1981 .

[26]  Alan H. Lipkus,et al.  Automated classification of candidate structures for computer-assisted structure elucidation , 1988, J. Chem. Inf. Comput. Sci..

[27]  Milan Randić,et al.  On the recognition of identical graphs representing molecular topology , 1974 .