Automated conformational analysis and structure generation: algorithms for molecular perception

Abstract

Many methodologies for performing automated conformational analysis require some means of "perceiving" a molecule to determine features of interest. Algorithms for finding rings, bond orders, and stereocenters and detecting the presence of substructural fragments have been developed. These algorithms are described, emphasizing their importance in conformational analysis.

Reactive modeling of the initial stages of alkoxysilane polycondensation: effects of precursor molecule structure and solution composition

“…Through a list of siloxane bridges, the average number of bridges per silicon atom and cluster sizes are determined at each step. Additionally, Perlmol 47 is used to implement a siloxane ring-finding algorithm 48,49 which assembles the SSSR (smallest set of smallest rings) at each timestep.…”

Constitutional, configurational and conformational analysis of transition metal coordination complexes

“…Other equivalent configurations are found by comparing the configuration with those already discovered (as the symmetry check only considers intra-ligand symmetry it is possible that symmetrically equivalent configurations may also be generated if some of the ligands are identical). This comparison is performed using the substructure searching algorithms previously developed [6]. If the configuration is unique then the search of its conformational space is initiated.…”

“…computational conformational analysis, to search conformational space and locate conformations at or near energy minima [1][2][3][4][5][6]. Our objectives were to develop a means of rapidly and automatically exploring conformational space for a wide variety of molecules.…”

“…In the former case any 3D coordinate information serves only to define the stereochemistry of each atom. The molecule is then analysed to recognize features such as rings, bond orders, stereocentres and aromaticity [6]. The conformational units present in the molecule are then determined.…”

“…The carbon atoms in the cyclohexane unit would then be able to match any saturated sp 3 atom in the molecule and this unit would match a piperidine ring in the molecule. Two subsequent levels of generalization are possible, if necessary [6].…”