<abstract xmlns="http://www.w3.org/1999/xhtml"><p>Combining a computationally efficient and affordable molecular dynamics approach, based on atom-centered density matrix propagation scheme, with the density functional tight binding semiempirical quantum mechanics, we study the vibrational dynamics of a single molecule at series of finite temperatures, spanning quite wide range. Data generated by molecular dynamics simulations are further analyzed and processed using time series analytic methods, based on correlation functions formalism, leading to both vibrational density of states spectra and infrared absorption spectra at finite temperatures. The temperature-induced dynamics in structural intramolecular parameters is correlated to the observed changes in the spectral regions relevant to molecular detection. In particular, we consider a case when an intramolecular X-H stretching vibrational states are notably dependent on the intramolecular torsional degree of freedom, the dynamics of which is, on the other hand, strongly temperature-dependent.</p></abstract>

Combining a computationally efficient and affordable molecular dynamics approach, based on atom-centered density matrix propagation scheme, with the density functional tight binding semiempirical quantum mechanics, we study the vibrational dynamics of a single molecule at series of finite temperatures, spanning quite wide range. Data generated by molecular dynamics simulations are further analyzed and processed using time series analytic methods, based on correlation functions formalism, leading to both vibrational density of states spectra and infrared absorption spectra at finite temperatures. The temperature-induced dynamics in structural intramolecular parameters is correlated to the observed changes in the spectral regions relevant to molecular detection. In particular, we consider a case when an intramolecular X-H stretching vibrational states are notably dependent on the intramolecular torsional degree of freedom, the dynamics of which is, on the other hand, strongly temperature-dependent.

Finite-Temperature Single Molecule Vibrational Dynamics from Combined Density Functional Tight Binding Extended Lagrangian Dynamics Simulations and Time Series Analysis

Faculty of Computer Science and Engineering

Faculty of Natural Sciences and Mathematics, Ss. Cyril and Methodius University

Department of Chemistry, Bioscience and Environmental Engineering, Faculty of Science and Technology

Cybernetics and Information Technologies

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

Combining a computationally efficient and affordable molecular dynamics approach, based on atom-centered density matrix propagation scheme, with the density...

Finite-Temperature Single Molecule Vibrational Dynamics from Combined Density Functional Tight Binding Extended Lagrangian Dynamics Simulations and Time Series Analysis

Published Online: Dec 31, 2020

Page range: 201 - 212

Received: Aug 25, 2020

Accepted: Nov 05, 2020

DOI: https://doi.org/10.2478/cait-2020-0074

Keywords
Atom-centered density matrix propagation, density functional tight binding, molecular dynamics, finite-temperature vibrational dynamics, formic acid, torsional motion

© 2020 Bojana Koteska et al., published by Sciendo

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

Finite-Temperature Single Molecule Vibrational Dynamics from Combined Density Functional Tight Binding Extended Lagrangian Dynamics Simulations and Time Series Analysis

Published Online: Dec 31, 2020

Page range: 201 - 212

Received: Aug 25, 2020

Accepted: Nov 05, 2020

DOI: https://doi.org/10.2478/cait-2020-0074

KeywordsAtom-centered density matrix propagation, density functional tight binding, molecular dynamics, finite-temperature vibrational dynamics, formic acid, torsional motion

© 2020 Bojana Koteska et al., published by Sciendo

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

Keywords
Atom-centered density matrix propagation, density functional tight binding, molecular dynamics, finite-temperature vibrational dynamics, formic acid, torsional motion