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Hamiltonian flow over saddles for exploring molecular phase space structures.

Stavros C Farantos^1,2

¹Department of Chemistry, University of Crete, 70013 Heraklion-Crete, Greece farantos@iesl.forth.gr.

Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences

|February 13, 2018

Summary

Molecules behave in phase space, not just potential energy surfaces. Geometrical structures in phase space, revealed by Hamiltonian flow, dictate molecular dynamics and reveal unique trajectories.

Keywords:

adiabatic potential energy surface alanine dipeptide phase space geometry stable and unstable manifold

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Area of Science:

Chemical Dynamics
Theoretical Chemistry
Molecular Physics

Background:

Traditional molecular dynamics studies utilize potential energy surfaces.
Molecular behavior is fundamentally governed by phase space, encompassing coordinates and momenta.
A phase space perspective offers a more complete understanding of chemical dynamics.

Purpose of the Study:

To demonstrate that geometrical structures in phase space dictate molecular dynamics.
To investigate the role of Hamiltonian flow above saddles in tracing molecular dynamics.
To explore the existence of internally free rotor trajectories in molecular systems.

Main Methods:

Theoretical analysis of molecular dynamics.
Numerical simulations using alanine dipeptide as a model system.
Examination of Hamiltonian flow in phase space.

Main Results:

Geometrical structures within phase space were identified as key determinants of molecular dynamics.
Hamiltonian flow above saddles was used to trace dynamic fingerprints.
Internally free rotor trajectories were observed and justified through a phase space lens.

Conclusions:

Molecular dynamics are dictated by phase space geometry, not solely potential energy surfaces.
Phase space analysis provides crucial insights into molecular behavior and trajectory formation.
The study highlights the importance of considering both coordinates and momenta for a full understanding of chemical dynamics.