Exhaustive generation of organic isomers. 1. Acyclic structures

Abstract

The system reported here describes selective, exhaustive, and nonredundant generation and counting algorithms for acyclic connectivity isomers associated with any molecular formula. Isomer structures can have multiple bonds and heteroatoms with mixed valences, as in the case of thiosulfonic acids. Structural isomer characteristics (IC) for each molecular formula are determined according to an expression derived from basic graph principles. The generation process uses a tuple notation and the concept of lexicographic order (see ref 13) and is done in three steps: (i) generation of the skeleton of the acyclic structure; (ii) incorporation of heteroatoms to the structure; (iii) incorporation of multiple bonds. Isomer redundant filtering processes and algorithms for doing a single-or a multiple-pattern restriction over the structures to be generated were developed. The code describing the generated isomers is compact and allows for both efficient molecular database storage and interaction with a graphic interface and with different calculation modules of CAMD such as those of topological indexes, molecular volume, and other molecular properties derived from semiempirical and ab initio methods. The system is therefore of great utility in structure elucidation, in organic synthesis, and especially in molecular design.

Can topological indices transmit information on properties but not on structures?

“…A fourth group is constituted by research undertaken by Drs Vladimir Kvasnicˇka and Jirˇı´Pospı´chal [72][73][74][75]. Finally, other authors have published one paper each in this area [76][77][78][79].…”

Chemical Structure Indices in In Silico Molecular Design

“…The main challenge of in silico molecular design approaches is generation of structural fragments from de facto modeling descriptors. Inverse-QSAR is an attempt in this direction [83][84][85][86][87][88][89]. Developments in new metrics are required to address different features of drug-receptor interactions so far not tamed.…”

“…This process of molecule rebuilding from QSAR equations is also addressed by other names such as graph reconstruction, inverse structure generation, inverse imaging etc [84]. Different algorithms have comeup in inverse QSAR to tackle the reconstruction of molecules from their identified characteristics [85][86][87][88]. The utility of these inverse QSAR approaches have been validated by reconstruction of structures of interest in various studies involving biological [84,88], physicochemical [89] and spectral activities and properties [87].…”

Algorithm for Exhaustive and Nonredundant Organic Stereoisomer Generation

“…SAG "identification parameters" are specified as follows: active major value (AMV), total active value (TAV), inactive (8,8); (9,9);(10,10); (11,11); (12,12); (13,13); (14,14); (15,15); (16,16); (17,17); (18,18); (19,19); (20,20); (21,21); (22,23); (24,24); (25,25); (26,26); (27,27); (28,28) (10,17); (11,20); (12,19); (13,18); (14,15); …”

“…[15][16][17] For solving some stereoisomer generation problem we have used molecular graphs processing of increasing complexity, first for acyclic structures 44,45 and then for cyclic ones with isolated and spiro cycles. 46 The approach now is to solve stereoisomer generation for molecular structures containing cycles of whatever type (isolated, spiro, condensed, and nested).…”