Dynamic embedding of effective harmonic normal mode vibrations in all-atomistic energy gap fluctuations: Case study of light harvesting 2 complex

Author:

Cho Kwang Hyun1ORCID,Jang Seogjoo J.234ORCID,Rhee Young Min1ORCID

Affiliation:

1. Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST) 1 , Daejeon 34141, South Korea

2. Department of Chemistry and Biochemistry, Queens College, City University of New York 2 , Queens, New York 11367, USA and , New York, New York 10016, USA

3. Ph.D. Programs in Chemistry and Physics, Graduate Center of the City University of New York 2 , Queens, New York 11367, USA and , New York, New York 10016, USA

4. Korea Institute for Advanced Study 3 , Seoul 02455, South Korea

Abstract

Environmental effects in excitation energy transfer have mostly been modeled by baths of harmonic oscillators, but to what extent such modeling provides a reliable description of actual interactions between molecular systems and environments remains an open issue. We address this issue by investigating fluctuations in the excitation energies of the light harvesting 2 complex using a realistic all-atomistic simulation of the potential energy surface. Our analyses reveal that molecular motions exhibit significant anharmonic features, even for underdamped intramolecular vibrations. In particular, we find that the anharmonicity contributes to the broadening of spectral densities and substantial overlaps between neighboring peaks, which complicates the meaning of mode frequencies constituting a bath model. Thus, we develop a strategy to construct a minimally underdamped harmonic bath that has a clear connection to all-atomistic dynamics by utilizing actual normal modes of molecules but optimizing their frequencies such that the resulting bath model can best reproduce the all-atomistic simulation results. By subtracting the underdamped contribution from the entire fluctuations, we also show that identifying a residual spectral density representing all other contributions with overdamped behavior is possible. We find that this can be fitted well with a well-established analytic form of a spectral density function or, alternatively, modeled as explicit time dependent fluctuations with muti-exponential or power law type correlation functions. We provide an assessment and the implications of these possibilities. The approach presented here can also serve as a general strategy to construct a simplified bath model that can effectively represent the underlying all-atomistic bath dynamics.

Funder

National Research Foundation of Korea

National Science Foundation

U.S. Department of Energy

Publisher

AIP Publishing

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