Exhaustive generation of organic isomers. 1. Acyclic structures

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 singleor 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.