CONFORMER CLUSTERING-ALGORITHM AND ITS APPLICATION FOR CROWN-TYPE MACROCYCLES

An efficient conformer clustering algorithm designed for treating mole cular modeling problems of flexible molecules associated with a large variety of conformers is described. It incorporates a fast algorithm f or the generation of chemical graph automorphisms allowing to easily d iscard equivalent conformers for symmetrical structures. The cluster i s defined as a set of conformers deviating from the ''central conforme r'' less than the allowed threshold. The deviation is calculated as a maximum distance between the matched atoms. Matched atoms can include all heavy atoms that can be superimposed according to graph automorphi sm mappings or a special subset of atoms indicated by the user. Using the ''central conformer'' as a meaningful representative of a cluster significantly reduces molecular modeling efforts without losing the fe atures of the system. Application of the algorithm to the ion recognit ion study of the newly synthesized macrocyclic host is presented.