The Principal Component Analysis of the Ring Deformation in the Nonadiabatic Surface Hopping Dynamics

29 June 2022, Version 1
This content is a preprint and has not undergone peer review at the time of posting.


The analysis of the leading active molecular motions in the on-the-fly trajectory surface hopping stimulation provides the essential information to understand the geometrical 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 method 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 of the major and minor active molecular motions of the ring distortion in nonadiabatic dynamics.


Unsupervised machine learning
Nonadiabatic dynamics
Active coordinates
Dimensionality reduction

Supplementary materials

Supporting information
Several relevant information: The time-dependent occupations of electronic states; more additional PCA results; the structural information of the S0 minimum, the averaged structure and the typical one of each channel.


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