Quantifying near-symmetric molecular distortion using symmetry-coordinate structural decomposition

Abstract

We imagine molecules to be perfect, but rigidified units can be designed to bend from their ideal shape, discarding their symmetric elements as they progress through vibrations and larger, more permanent distortions. The shape of molecules is either simulated or measured by crystallography and strongly affects chemical properties but, beyond an image or tabulation of atom-to-atom distances, little is often discussed of the accessed conformation. We have simplified the process of shape quantification across multiple molecular types with a new web-accessible program – SCSD – through which a molecular subunit possessing near-symmetry can be dissected into symmetry coordinates with ease. This parameterization allows a common set of numbers for comparing and understanding molecular shape, and is a simple method for database analysis.