Development of spherical topology of conformational space

Abstract

Conformational search program CONFLEX can quickly find the chemically significant conformers of large and flexible molecules. However, as the number of conformers increase, network topology in conformational space that consists of the interconversion relationships between conformers is more complex. To analyze and understand the dynamic behaviors of such molecules with conformational exchanges, development of visualization technique for conformational topology is quit important. In this paper, we propose a visualization technique by multiple spherical representations of conformational space and topology: whole conformational space is represented by one central large sphere and a conformation is drawn as a point or a small sphere on the central sphere. If there are a large number of conformations, all conformations are classified by several conformational clusters and each cluster can be represented by a middle size of sphere (like a moon) having a partial conformational topology. In this study, accuracy and qualitative evaluation for our visualization technique of conformational topology have been examined in comparison with general 2D and 3D representations for well-known conformational topologies of cyclohexane, cycloheptane and cyclooctane. New supporting tool for exploring the transition state structure coupled to both this visualization system and CONFLEX will be also discussed.