Algorithm for Exhaustive and Nonredundant Organic Stereoisomer Generation

Abstract

Generation of organic stereoisomers with R/S, Z/E, and/or M/P configurations that may contain heteroatoms, multiple bonds, and any kind of cycle (isolated, spiro, condensed, and nested) is described. Inputs for processing are molecular structures in a N_tuple format resident on an automatic (canonical) or manual (non canonical) generated file which are processed by doing internal molecular graph construction, a weighted bipartite tree construction for all atoms and bonds to detect stereocenters, and symmetrical atom groups (SAG) with some specific SAG parameters that constitute a novel way for redundancy elimination of meso structures. Finally, determination of ligand CIP priorities allows for writing the output N_tuples with stereoisomer description. Several examples showing application of this methology to a wide number of structures are also presented.

Understanding topological symmetry: A heuristic approach to its determination

“…This is one of the merits of this method. It does not P1: {(1,1); (2,14); (3,13);(4,4);(5,5); (6,10); (7,9); (8,8); (11,11); (12,12); (15,15);(16,16)} P2: {(1,8);(2,7); (3,6);(4,5); (9,14); (10,13); (11,15); (12,16) No No 0.06 13 P1: {(1,1);(2,6);(3,5);(4,4);(7,13); (8,14); (9,15); (10,16); (11,17); (12,18); (19,19); (20,21); (22,22);(23,24)} P2: {(1,3);(2,2);(4,6);(5,5);(7,7); (8,9);(10,10); (11,12); (13,19); (14,20); (15,21); (16,22); (17,23);(18,24)} P3: {(1,5);(2,4);(3,3);(6,6); (7,...…”

“…(6,6);(7,10); (8,11); (9,12); (13,16); (14,17); (15,18); (19,22); (20,23 ,7); (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) require a special procedure to determine stereochemical centers neither the number or size or kind of cycle (isolated, nested, spiro, fused) or even to know if there is any cycle present. Processing time in general depends on the number of atoms and also on the structure complexity more than on the number of symmetry elements.…”

“…Its value has been already proved for detecting meso structures (symmetrical molecules having more than one chiral center) appearing as redundant structures in an exhaustive isomer generation work. 20 Here, a detailed algorithm has been developed showing the heuristic approach applied for determining topological SPs and SAGs for cases of recognized established difficulties 9,13 valid for neutral species and also for transient intermediates such as radical, ions, radical ions and the like.…”

Implementation of Stereochemistry in Automatic Kinetic Model Generation

“…The algorithm is also used when the user defines reactants that have stereocenters without specifying the stereoconfiguration. A number of stereoisomer generation algorithms exist in the literature , but free and publicly available codes based on them were not found. The methodology used in this work is based on the algorithm by Razinger et al .…”

Efficient enumeration of stereoisomers of tree structured molecules using dynamic programming

“…Then stereoisomers caused only by asymmetry around carbon atoms are fundamental and practically important. As to enumeration of such stereoisomers, several methods have been proposed [1,3,12], which mostly follow the work by Nourse [7]. Given a chemical compound with m stereocenters, these methods first create a list of all 2 m combinations of the two choices of asymmetries around each carbon atom, and remove each set S of combinations that represent the same stereoisomer leaving one of them as their representative.…”