Generalized Normal Coordinates for the Vibrational Analysis of Molecular Dynamics Simulations

Area of Science:

• Computational Chemistry
• Spectroscopy
• Molecular Dynamics

Background:

• Vibrational spectra computation using molecular dynamics (MD) has advanced significantly.
• Ab initio MD enables infrared spectra calculation by computing the dipole moment on the fly.
• Analyzing spectra in terms of normal modes of intramolecular motion remains a theoretical challenge.

Purpose of the Study:

• To present a novel algorithm for extracting normal modes from MD trajectories.
• To compute normal modes and vibrational bands without the equipartition assumption.
• To analyze the infrared spectrum of isoprene using ab initio MD.

Main Methods:

• Developed an algorithm combining literature ideas for normal mode extraction from MD.
• Utilized a tensorial definition of vibrational density of states.
• Introduced generalized normal coordinates via iterative minimization and Jacobi diagonalization.
• Computed mode local temperatures for convergence assessment and intensity correction.

Main Results:

• Successfully extracted normal modes and vibrational bands from MD trajectories.
• Overcame limitations of previous methods by avoiding the equipartition assumption.
• Demonstrated the method's utility by analyzing the infrared spectrum of isoprene.
• Provided mode local temperatures for improved spectral analysis.

Conclusions:

• The presented algorithm offers a robust method for analyzing vibrational spectra from MD simulations.
• The approach enhances the accuracy of normal mode and vibrational band computation.
• The isoprene analysis showcases the algorithm's applicability to complex molecules.