Collective coordinates and the mechanism for conformational transitions of complex molecules

Yanao, T., W. S. Koon, J. E. Marsden, and I. G. Kevrekidis

Proc. Appl. Math. Mech., 7, (2007), 1080503-4

Abstract:

Reduction of dimensionality is crucial for the deeper understanding of the mechanism for large-amplitude conformational transitions of complex molecules. By taking up a six-atomcluster as an illustrative example, we present a general methodology to understand conformational transitions of molecules in terms of the low-dimensional dynamics of molecular gyration radii. The dynamics of gyration radii is generally governed by the interplay between the ordinary potential force and a dynamical force called the internal centrifugal force. We show that the internal centrifugal force can be more important than the original potential barrier and gives rise to a new dynamical barrier that truly dominates the conformational transitions of the system. This kind of dynamical effect should be crucially important in a wide class of molecular reaction dynamics.