Issue 39, 2022

The principal component analysis of the ring deformation in the nonadiabatic surface hopping dynamics

Abstract

The analysis of the leading active molecular motions in the on-the-fly trajectory surface hopping simulation provides the essential information to understand the geometric evolution in nonadiabatic dynamics. When the ring deformation is involved, the identification of the key active coordinates becomes challenging. A “hierarchical” protocol based on the dimensionality reduction and clustering approaches is proposed for the automatic analysis of the ring deformation in the nonadiabatic molecular dynamics. The representative system keto isocytosine is taken as the prototype to illustrate this protocol. The results indicate that the current hierarchical analysis protocol is a powerful way to clearly clarify both the major and minor active molecular motions of the ring distortion in nonadiabatic dynamics.

Graphical abstract: The principal component analysis of the ring deformation in the nonadiabatic surface hopping dynamics

Supplementary files

Article information

Article type
Paper
Submitted
20 iyl 2022
Accepted
13 sen 2022
First published
14 sen 2022

Phys. Chem. Chem. Phys., 2022,24, 24362-24382

The principal component analysis of the ring deformation in the nonadiabatic surface hopping dynamics

Y. Zhu, J. Peng, X. Kang, C. Xu and Z. Lan, Phys. Chem. Chem. Phys., 2022, 24, 24362 DOI: 10.1039/D2CP03323B

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