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Vibrational energy transport in the presence of intrasite vibrational energy redistribution


Schade, M; Hamm, P (2009). Vibrational energy transport in the presence of intrasite vibrational energy redistribution. Journal of Chemical Physics, 131(4):044511.

Abstract

The mechanism of vibrational energy flow is studied in a regime where a diffusion equation is likely to break down, i.e., on length scales of a few chemical bonds and time scales of a few picoseconds. This situation occurs, for example, during photochemical reactions in protein environment. To that end, a toy model is introduced that on the one hand mimics the vibrational normal mode distribution of proteins, and on the other hand is small enough to numerically time propagate the system fully quantum mechanically. Comparing classical and quantum-mechanical results, the question is addressed to what extent the classical nature of the molecular dynamics simulations (which would be the only choice for the modeling of a real molecular system) affects the vibrational energy flow mechanism. Small differences are found which are due to the different ways classical and quantum mechanics distribute thermal energy over vibrational modes. In either case, a ballistic and a diffusive phase can be identified. For these small length and time scales, the latter is governed by intrasite vibrational energy redistribution, since vibrational energy does not necessarily thermalize completely within individual peptide units. Overall, the model suggests a picture that unifies many of the observations made recently in experiments.

The mechanism of vibrational energy flow is studied in a regime where a diffusion equation is likely to break down, i.e., on length scales of a few chemical bonds and time scales of a few picoseconds. This situation occurs, for example, during photochemical reactions in protein environment. To that end, a toy model is introduced that on the one hand mimics the vibrational normal mode distribution of proteins, and on the other hand is small enough to numerically time propagate the system fully quantum mechanically. Comparing classical and quantum-mechanical results, the question is addressed to what extent the classical nature of the molecular dynamics simulations (which would be the only choice for the modeling of a real molecular system) affects the vibrational energy flow mechanism. Small differences are found which are due to the different ways classical and quantum mechanics distribute thermal energy over vibrational modes. In either case, a ballistic and a diffusive phase can be identified. For these small length and time scales, the latter is governed by intrasite vibrational energy redistribution, since vibrational energy does not necessarily thermalize completely within individual peptide units. Overall, the model suggests a picture that unifies many of the observations made recently in experiments.

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Additional indexing

Item Type:Journal Article, refereed, original work
Communities & Collections:07 Faculty of Science > Department of Chemistry
Dewey Decimal Classification:540 Chemistry
Language:English
Date:July 2009
Deposited On:31 Dec 2009 08:40
Last Modified:06 Jun 2016 07:45
Publisher:American Institute of Physics
ISSN:0021-9606
Funders:Swiss National Science Foundation (SNF)
Additional Information:Copyright 2009 American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the American Institute of Physics. The following article appeared in J. Chem. Phys. 131, 044511 (2009) and may be found at http://link.aip.org/link/?JCPSA6/131/044511/1
Free access at:Publisher DOI. An embargo period may apply.
Publisher DOI:https://doi.org/10.1063/1.3185152
Permanent URL: https://doi.org/10.5167/uzh-24980

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