Computer generation of molecular structures by the SMOG program

Journal of Chemical Information and Computer Sciences

Volumn 36, Issue 4, 1996, Pages 888-899

  Molchanova, M S ^a   Shcherbukhin, V V ^a   Zefirov, N S ^a  

^a N D ZELINSKY INSTITUTE OF ORGANIC CHEMISTRY   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0000154023     PISSN: 00952338     EISSN: None     Source Type: Journal    
DOI: 10.1021/ci950393z     Document Type: Article

References (70)

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4. (d) Lindsay, R. K.; Buchanan, B. G.: Feigenbaum, E. A.; Lederberg, J. Applications of Artificial Intelligence for Organic Chemistry: The Dendral Project; McGraw-Hill: New York, 1980.
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26. Lomova, O. A.; Sukhachev, D. V.; Kumskov, M. I.; Palyulin, V. A.; Tratch, S. S.; Zefirov, N. S. The Generation of Molecular Graphs for QSAR Studies by the Acyclic Fragment Combining. Commun. Math. Chem. (MATCH) 1992, 27, 153-174.
27. Nilakantan, R.; Bauman, N.; Venkataraghavan, R. A Method for Automatic Generation of Novel Chemical Structures and Its Potential Applicability to Drug Discovery. J. Chem. Inf. Comput. Sci. 1991, 31, 527-530.
28. Another restriction that is common for all generation algorithms is the consideration of connectivity: structures comprising two or more disconnected parts should be disregarded.
29. The previous version of the program, named GEM (GEneration of Molecules), was mentioned in our earlier publications: Pivina, T. S.; Molchanova, M. S.; Shcherbukhin, V. V.; Zefirov, N. S. Computer Generation of Caged Frameworks Which Can Be Used as Synthons for Creating High-Energetic Materials. Propellants, Explosives, Pyrotechnics 1994, 19, 286-289; 1995, 20, 144-146, etc.
30. The previous version of the program, named GEM (GEneration of Molecules), was mentioned in our earlier publications: Pivina, T. S.; Molchanova, M. S.; Shcherbukhin, V. V.; Zefirov, N. S. Computer Generation of Caged Frameworks Which Can Be Used as Synthons for Creating High-Energetic Materials. Propellants, Explosives, Pyrotechnics 1994, 19, 286-289; 1995, 20, 144-146, etc.
31. (a) Faradjev, I. A. Constructive Enumeration of Combinatorial Objects. In Algorithmic Investigations in Combinatorics; Faradjev, I. A., Ed.; Nauka: Moscow, 1978; pp 3-11 (in Russian),
32. (b) Zaichenko, V. A.; Ivanov, A. B.; Rozenfeld, M. Z.; Faradjev, I. A. Algorithm for Verifying the Canonicity of a Partially Filled Adjacency Matrix of a Graph. In Algorithmic Investigations in Combinatorics; Faradjev, I. A., Ed.; Nauka: Moscow, 1978; pp 19-25 (in Russian).
33. The sets of valence states are selected in such a way that the total formal charge remains constant. For all examples in this paper, this charge is zero (electrical neutrality).
34. As is apparent from Figure 2a. atoms in SMOG-generated structures are numbered in accordance with their valences: atoms with higher valences have smaller ordinal numbers.
35. Among programs that use modifications of such an approach, we can mention the AEGIS software (ref 7).
36. Lowler, E. L.; Wood, D. E. Branch-and-Bound Methods: A Survey. J. Oper. Res. Soc. Am. 1966, 14, 217-282.
37. (a) Hendrickson, J. B.; Toczko, A. G. Unique Numbering and Cataloguing of Molecular Structures. J. Chem. Inf. Comput. Sci. 1983, 23, 171-177.
38. (b) Hendrickson, J. B.; Parks, C. A. Generation and Enumeration of Carbon Skeletons. J. Chem. Inf. Comput. Sci. 1991, 31, 101-107.
39. (a) Randić, M. Recognition of Identical Graphs Representing Molecular Topology. J. Chem. Phys. 1974, 60, 3920-3928.
40. (b) Randić, M. On Canonical Numbering of Atoms in a Molecule and Graph Isomorphism. J. Chem. Inf. Comput. Sci. 1977, 17, 171-180.
41. 23 or its parts. As is easy to show, the criteria of a maximum (minimum) matrix or maximum (minimum) upper triangle are equivalent.
42. A similar modification of the canonicity criterion was mentioned in ref 10c. but it was not quite correctly implemented in that study, as is shown by example 4 of this paper.
43. A ring is not regarded as aromatic by SMOG if additional short "cross-linking" bridges connect its atoms and thus form an extremely strained structure (for example, an extra chain of one or two atoms between the 1- and 4-positions of benzene). The consequence of this rule is that two aromatic rings cannot have more than two atoms in common, and these have to be adjacent. The SMOG user may specify the minimum lengths of cross-linking bridges at which the structure is already regarded as aromatic.
44. 2, CH, OH, etc. Generation proceeds on the basis of a set of these new vertices. This procedure makes generation significantly faster but is inapplicable in many important cases, such as the presence of core fragments.
45. SMOG explicitly assumes an additional limitation concerning the numbers of free valences at vertices of quasistructures: the number of hydrogens bound to any non-hydrogen atom may not exceed 3.
46. 8b However, there are at least two points of difference: in Kvasnicka's approach, classification of vertices by initial sets of stability (i.e., by different vertex types) is disregarded, but at the same time each atom must obey some explicit rules limiting the number and type of its multiple bonds.
47. The method for combinatorial enumeration of permutations in the 5(I,J) group and some of the ways to optimize this search are thoroughly described in ref 17b. We modified this procedure so that the S(I,J,C) group might be considered.
48. The importance of considering alternative substructures was shown in refs 1e, 5a and numerous other works dealing with problems of structural generation.
49. Hereafter, free valences and bonds with an unspecified terminus in the structural formulas of fragments may be saturated by any atom(s), including hydrogen, unless explicitly stated otherwise.
50. Nechepurenko, M. I.; Popkov, V. K.; Mainagashev, S. M.; Kaul', S. B.; Proskuryakov, V. A.; Kokhov, V. A.; Gryzunov, A. B. Algorithms and Programs for the Solution of Problems on Graphs and Networks; Nauka: Novosibirsk, 1990 (in Russian).
51. Arlazarov, V. L.; Zuev, I. I.; Uskov, A. V.; Faradjev, I. A. The Algorithm for Bringing Finite Nonoriented Graphs to the Canonical Form. Zh. Vychisl. Mat. Mat. Fiz. 1974, 14, 3, 737-743 (in Russian).
52. Carhart, R. E. A. Model-based Approach to the Teletype Printing of Chemical Structures. J. Chem. Inf. Comput. Sci. 1976, 16, 82-88.
53. Shelley, C. A. Heuristic Approach for Displaying Chemical Structures. J. Chem. Inf. Comput. Sci. 1983, 23, 61-65.
54. Contreras, M.; Valdivia, R.; Rozas, R. Exhaustive Generation of Organic Isomers. (a) 1. Acyclic Structures. J. Chem. Inf. Comput. Sci. 1992, 32, 323-330. (b) 2. Cyclic Structures: New Compact Molecular Code. J. Chem. Inf. Comput. Sci. 1992, 32, 481-491. (c) 3. Acyclic, Cyclic, and Mixed Compounds. J. Chem. Inf. Comput. Sci. 1994, 34, 610-616.
55. Contreras, M.; Valdivia, R.; Rozas, R. Exhaustive Generation of Organic Isomers. (a) 1. Acyclic Structures. J. Chem. Inf. Comput. Sci. 1992, 32, 323-330. (b) 2. Cyclic Structures: New Compact Molecular Code. J. Chem. Inf. Comput. Sci. 1992, 32, 481-491. (c) 3. Acyclic, Cyclic, and Mixed Compounds. J. Chem. Inf. Comput. Sci. 1994, 34, 610-616.
56. Contreras, M.; Valdivia, R.; Rozas, R. Exhaustive Generation of Organic Isomers. (a) 1. Acyclic Structures. J. Chem. Inf. Comput. Sci. 1992, 32, 323-330. (b) 2. Cyclic Structures: New Compact Molecular Code. J. Chem. Inf. Comput. Sci. 1992, 32, 481-491. (c) 3. Acyclic, Cyclic, and Mixed Compounds. J. Chem. Inf. Comput. Sci. 1994, 34, 610-616.
57. Contreras, M.; Valdivia, R.; Rozas, R. Exhaustive Generation of Organic Isomers. (a) 1. Acyclic Structures. J. Chem. Inf. Comput. Sci. 1992, 32, 323-330. (b) 2. Cyclic Structures: New Compact Molecular Code. J. Chem. Inf. Comput. Sci. 1992, 32, 481-491. (c) 3. Acyclic, Cyclic, and Mixed Compounds. J. Chem. Inf. Comput. Sci. 1994, 34, 610-616.
58. Barone, R.; Barberis, F.; Chanou, M. Exhaustive Generation of Organic Isomers from Base 2 and Base 4 Numbers. Commun. Math. Chem. (MATCH) 1995, 32, 19-25.
59. (a) Faulon, J.-L. On Using Graph Equivalence Classes for the Structure Elucidation of Large Molecules. J. Chem. Inf. Comput. Sci. 1992, 32, 338-348.
60. (b) Faulon, J.-L. Stochastic Generator of Chemical Structure. 1. Application to the Structure Elucidation of Large Molecules. J. Chem. Inf. Comput. Sci. 1994, 34, 1204-1218.
61. 10b,c However, this comparative slowness is largely due to the fact that SMOG is initially oriented at the presence of constraints; therefore, SMOG represents and calculates some characteristics of the partially generated structure at each stage of generation in such a way that various constraints may be quickly and easily considered. Such "data processing" is an important source of retardation: if we exclude it from SMOG, the performance of such a program in the absence of constraints becomes comparable to that of MOLGEN and GENM.
62. Ugi, I.; Wischhöfer, E. Isonitrile, XI. Synthase einfacher Penicillansäure-Derivate. Chem. Ber. 1962, 95, 136-140.
63. The generation of chemical isomers is one of the possible applications of the well-known IGOR and RAIN software.
64. 14: Application of the combined ab initiol IGLO/NMR Method. Heteroat. Chem. 1991, 2, 4, 499-506.
65. (b) Binder, H.; Brellochs, B.; Frei, B.; Simon, A.; Hettich, B. Über die ersten monosubstituierten Derivate von Triboran (7) -Kristall- und Molekülstruktur von Benzoyloxytriboran (7). Chem. Ber. 1989, 122, 6, 1049-1056.
66. 14 Problem: Generation of a Catalogue of Conceivable Isomers. Heteroat. Chem. 1994, 5, 61-64.
67. (a) Cyvin, S. J.; Cyvin, B. N.; Brunvoll, J. The Number of Pyrene Isomers is Still Unknown. Commun. Math. Chem. (MATCH) 1994, 30, 73-77.
68. (b) Cyvin, S. J.; Brunvoll, J.; Cyvin, B. N. Number and Forms of Tetracyclic Polygonal Pyrene Isomers. Commun. Math. Chem. (MATCH) 1995, 32, 59-70.
69. Actually, there are six Kekulé structures for the pyrene system, but they represent three pairs of topologically equivalent mirror images. Since SMOG always avoids topologically equivalent structures, it considers only one formal distribution of double bonds out of each such pair.
70. This program is available from the Archives of Computational Chemistry list (top page is http://ccl.osc.edu/chemistry.html). To go directly to the program, use the following URLs: gopher://infomeister.osc.edu:73/11/software/MS-DOS/SMOG or ftp://ccl.osc.edu/pub/ chemistry/software/MS-DOS/SMOG. It is also available via e-mail if the message [select chemistry; limit 2Mbytes, cd software/MS-DOS/ SMOG, get*; quit] is sent to MAILSERV@ccl.osc.edu.