Periodic orbits in biological molecules: Phase space structures and selectivity in alanine dipeptide

Abstract

Small and large molecules may localize their energy in specific bonds or generally in vibrational modes for extended periods of time, an effect which may have dramatic consequences in reaction dynamics. Periodic orbits offer the means to identify phase space regions with localized motions. The author demonstrate that techniques to locate periodic orbits developed for small molecules can be applied to large molecules such as alanine dipeptide. The widely used empirical force fields are employed and principal families of periodic orbits associated with local-type motions and emanated from the lowest energy minima and saddle points are investigated. Continuation of these families at high energies unravels the stable and unstable regions of phase space as well as elementary bifurcations such as saddle nodes.