Version 1
: Received: 15 July 2024 / Approved: 17 July 2024 / Online: 17 July 2024 (13:30:55 CEST)
How to cite:
Tikhonov, D. S. PyRAMD Scheme: A Protocol for Computing the Infrared Spectra of Polyatomic Molecules Using Ab Initio Molecular Dynamics. Preprints2024, 2024071381. https://doi.org/10.20944/preprints202407.1381.v1
Tikhonov, D. S. PyRAMD Scheme: A Protocol for Computing the Infrared Spectra of Polyatomic Molecules Using Ab Initio Molecular Dynamics. Preprints 2024, 2024071381. https://doi.org/10.20944/preprints202407.1381.v1
Tikhonov, D. S. PyRAMD Scheme: A Protocol for Computing the Infrared Spectra of Polyatomic Molecules Using Ab Initio Molecular Dynamics. Preprints2024, 2024071381. https://doi.org/10.20944/preprints202407.1381.v1
APA Style
Tikhonov, D. S. (2024). PyRAMD Scheme: A Protocol for Computing the Infrared Spectra of Polyatomic Molecules Using Ab Initio Molecular Dynamics. Preprints. https://doi.org/10.20944/preprints202407.1381.v1
Chicago/Turabian Style
Tikhonov, D. S. 2024 "PyRAMD Scheme: A Protocol for Computing the Infrared Spectra of Polyatomic Molecules Using Ab Initio Molecular Dynamics" Preprints. https://doi.org/10.20944/preprints202407.1381.v1
Abstract
Here, we present a general framework for computing the infrared anharmonic vibrational spectra of polyatomic molecules using the Born-Oppenheimer molecular dynamics (BOMD) with the software PyRAMD. To account for the nuclear quantum effects, we suggest using the simplified Wigner sampling (SWS) approach [\textit{Phys. Chem. Chem. Phys.}, 2023, \textbf{25}, 18406-18423] simultaneously coupled with the Andersen and Berendsen thermostats. We propose a new criterion for selecting the parameter of the SWS based on the molecules' harmonic vibrational frequencies and usage of the large-time-step blue shift correction, allowing for a decrease in computational expenses. For the Fourier transform of the dipole moment autocorrelation function, we propose to use the regularized least-squares analysis, which allows us to obtain higher frequency resolution than the direct application of fast Fourier transform. Finally, we suggest the usage of the pre-parameterized scaling factors for the IR spectra from BOMD, also providing the scaling factors for the spectra at the BLYP-D3(BJ)/6-31G, PBE-D3(BJ)/6-31G, and PBEh-3c levels of theory.
Chemistry and Materials Science, Theoretical Chemistry
Copyright:
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
