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

Area of Science:

• Chemical Physics
• Molecular Dynamics
• Computational Chemistry

Background:

• Molecules can localize energy in specific bonds or vibrational modes, impacting reaction dynamics.
• Identifying these localized motions is crucial for understanding molecular behavior.

Purpose of the Study:

• To demonstrate the applicability of periodic orbit theory to large molecules.
• To investigate energy localization and phase space structures in alanine dipeptide.

Main Methods:

• Utilized established techniques for locating periodic orbits.
• Employed widely used empirical force fields for molecular modeling.
• Investigated families of periodic orbits originating from minima and saddle points.

Main Results:

• Periodic orbit techniques are transferable from small to large molecules (e.g., alanine dipeptide).
• Identified principal families of periodic orbits linked to local motions.
• High-energy continuation revealed stable/unstable phase space regions and bifurcations.

Conclusions:

• Periodic orbit theory provides a robust framework for analyzing energy localization in large molecules.
• This approach enhances the understanding of complex molecular reaction dynamics.