1
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Cho KH, Rhee YM. Computational elucidations on the role of vibrations in energy transfer processes of photosynthetic complexes. Phys Chem Chem Phys 2021; 23:26623-26639. [PMID: 34842245 DOI: 10.1039/d1cp04615b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Coupling between pigment excitations and nuclear movements in photosynthetic complexes is known to modulate the excitation energy transfer (EET) efficiencies. Toward providing microscopic information, researchers often apply simulation techniques and investigate how vibrations are involved in EET processes. Here, reports on such roles of nuclear movements are discussed from a theory perspective. While vibrations naturally present random thermal fluctuations that can affect energy transferring characteristics, they can also be intertwined with exciton structures and create more specific non-adiabatic energy transfer pathways. For reliable simulations, a bath model that accurately mimics a given molecular system is required. Methods for obtaining such a model in combination with quantum chemical electronic structure calculations and molecular dynamics trajectory simulations are discussed. Various quantum dynamics simulation tools that can handle pigment-to-pigment energy transfers together with their vibrational characters are also touched on. Behaviors of molecular vibrations often deviate from ideality, especially when all-atom details are included, which practically forces us to treat them classically. We conclude this perspective by considering some recent reports that suggest that classical descriptions of bath effects with all-atom details may still produce valuable information for analyzing sophisticated contributions by vibrations to EET processes.
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Affiliation(s)
- Kwang Hyun Cho
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea.
| | - Young Min Rhee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea.
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2
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Wang YC, Zhao Y. The hierarchical stochastic schrödinger equations: Theory and applications. CHINESE J CHEM PHYS 2020. [DOI: 10.1063/1674-0068/cjcp2009165] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Yu-Chen Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, iChEM, Fujian Provincial Key Lab of Theoretical and Computational Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Yi Zhao
- State Key Laboratory of Physical Chemistry of Solid Surfaces, iChEM, Fujian Provincial Key Lab of Theoretical and Computational Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
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3
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Sato Y, Navarro Hernández A, Gillespie LD, Valete D. Effects of intramolecular vibrations on excitation energy transfer dynamics of the Fenna-Matthews-Olson complex. Chem Phys 2020. [DOI: 10.1016/j.chemphys.2020.110940] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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4
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Sato Y. A scalable algorithm of numerical real-time path integral for quantum dissipative systems. J Chem Phys 2019; 150:224108. [PMID: 31202255 DOI: 10.1063/1.5100881] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Numerical real-time path integration has been a practical method to study a quantum system under the influence of its environment. Performing the path integral computations, however, is a resource-demanding task in general, and implementing it is less straightforward with modern hardware architectures of massively parallel platforms. In this article, a numerical algorithm based on the quasiadiabatic propagator path integral scheme is proposed and shown to scale for systems with large size. As a case study of performance, the quantum dynamics of excitation energy transfer in the Fenna-Matthews-Olson complex is discussed, employing a vibronic model in which the system size can be varied simply by adding vibrational excitations.
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Affiliation(s)
- Yoshihiro Sato
- Department of Physics, Gettysburg College, Gettysburg Pennsylvania 17325, USA
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5
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Wang YC, Zhao Y. Effect of an underdamped vibration with both diagonal and off-diagonal exciton-phonon interactions on excitation energy transfer. J Comput Chem 2019; 40:1097-1104. [PMID: 30549065 DOI: 10.1002/jcc.25611] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 08/29/2018] [Accepted: 09/06/2018] [Indexed: 11/08/2022]
Abstract
A numerically exact approach, named as the hierarchical stochastic Schrödinger equation, is employed to investigate the resonant vibration-assisted excitation energy transfer in a dimer system, where an underdamped vibration with both diagonal and off-diagonal exciton-phonon interactions is incorporated. From a large parameter space over the site-energy difference, excitonic coupling, and reorganization energy, it is found that the promotion effect of the underdamped vibration is significant only when the excitonic coupling is smaller than the site-energy difference. Under the circumstance, there is an optimal strength ratio between diagonal and off-diagonal exciton-phonon interactions for the resonant vibration-assisted excitation energy transfer as the site-energy difference is greater than the reorganization energy, whereas in the opposite situation the most efficient energy transfer occurs as the exciton-phonon interaction is totally off-diagonal. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Yu-Chen Wang
- State Key Laboratory for Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Fujian Provincial Key Lab of Theoretical and Computational Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Yi Zhao
- State Key Laboratory for Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Fujian Provincial Key Lab of Theoretical and Computational Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
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6
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Oh SA, Coker DF, Hutchinson DAW. Optimization of energy transport in the Fenna-Matthews-Olson complex via site-varying pigment-protein interactions. J Chem Phys 2019; 150:085102. [DOI: 10.1063/1.5048058] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Affiliation(s)
- S. A. Oh
- Dodd-Walls Centre for Photonic and Quantum Technologies, Department of Physics, University of Otago, Dunedin 9016, New Zealand
| | - D. F. Coker
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
| | - D. A. W. Hutchinson
- Dodd-Walls Centre for Photonic and Quantum Technologies, Department of Physics, University of Otago, Dunedin 9016, New Zealand
- Centre for Quantum Technologies, National University of Singapore, 3 Science Drive 2, Singapore 117543, Singapore
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7
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Liang XT. Long-Lived Coherence Originating from Electronic-Vibrational Couplings in Light-Harvesting Complexes. CHINESE J CHEM PHYS 2017. [DOI: 10.1063/1674-0068/30/cjcp1609188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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8
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Lee MH, Troisi A. Vibronic enhancement of excitation energy transport: Interplay between local and non-local exciton-phonon interactions. J Chem Phys 2017; 146:075101. [DOI: 10.1063/1.4976558] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Affiliation(s)
- Myeong H. Lee
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Alessandro Troisi
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
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9
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Stross C, Van der Kamp MW, Oliver TAA, Harvey JN, Linden N, Manby FR. How Static Disorder Mimics Decoherence in Anisotropy Pump-Probe Experiments on Purple-Bacteria Light Harvesting Complexes. J Phys Chem B 2016; 120:11449-11463. [PMID: 27723973 DOI: 10.1021/acs.jpcb.6b09916] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Anisotropy pump-probe experiments have provided insights into the character of excitons formed in photosynthetic complexes. Rapid decay in the observed anisotropy is cited as evidence of the strength of coupling of the excitonic degrees of freedom to their environment. Here we show that ensemble averaging over realistic model Hamiltonians leads to a rapid decay of anisotropy to a value close to the observed asymptote, and at a rate comparable to observed decay rates, even in the absence of coupling to the environment. While coupling to the environment will clearly play a role in the dynamics of such systems, our calculations suggest that caution is needed in deducing the strength of this coupling from anisotropy experiments. We also set out to clarify the nature of the quantum states and processes involved in the dynamics of such systems and the associated terminology.
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Affiliation(s)
- Clement Stross
- Centre for Computational Chemistry, School of Chemistry, University of Bristol , Bristol BS8 1TS, U.K.,School of Mathematics, University of Bristol , Bristol BS8 1TW, U.K
| | - Marc W Van der Kamp
- Centre for Computational Chemistry, School of Chemistry, University of Bristol , Bristol BS8 1TS, U.K
| | | | - Jeremy N Harvey
- Centre for Computational Chemistry, School of Chemistry, University of Bristol , Bristol BS8 1TS, U.K.,Department of Chemistry, KU Leuven , Celestijnenlaan 200F, B-3001 Leuven, Belgium
| | - Noah Linden
- School of Mathematics, University of Bristol , Bristol BS8 1TW, U.K
| | - Frederick R Manby
- Centre for Computational Chemistry, School of Chemistry, University of Bristol , Bristol BS8 1TS, U.K
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Flanagan ML, Long PD, Dahlberg PD, Rolczynski BS, Massey SC, Engel GS. Mutations to R. sphaeroides Reaction Center Perturb Energy Levels and Vibronic Coupling but Not Observed Energy Transfer Rates. J Phys Chem A 2015; 120:1479-87. [PMID: 26630123 DOI: 10.1021/acs.jpca.5b08366] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The bacterial reaction center is capable of both efficiently collecting and quickly transferring energy within the complex; therefore, the reaction center serves as a convenient model for both energy transfer and charge separation. To spectroscopically probe the interactions between the electronic excited states on the chromophores and their intricate relationship with vibrational motions in their environment, we examine coherences between the excited states. Here, we investigate this question by introducing a series of point mutations within 12 Å of the special pair of bacteriochlorophylls in the Rhodobacter sphaeroides reaction center. Using two-dimensional spectroscopy, we find that the time scales of energy transfer dynamics remain unperturbed by these mutations. However, within these spectra, we detect changes in the mixed vibrational-electronic coherences in these reaction centers. Our results indicate that resonance between bacteriochlorophyll vibrational modes and excitonic energy gaps promote electronic coherences and support current vibronic models of photosynthetic energy transfer.
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Affiliation(s)
| | | | | | - Brian S Rolczynski
- Department of Chemistry, The James Franck Institute and The Institute for Biophysical Dynamics, The University of Chicago , Chicago, Illinois 60637, United States
| | - Sara C Massey
- Department of Chemistry, The James Franck Institute and The Institute for Biophysical Dynamics, The University of Chicago , Chicago, Illinois 60637, United States
| | - Gregory S Engel
- Department of Chemistry, The James Franck Institute and The Institute for Biophysical Dynamics, The University of Chicago , Chicago, Illinois 60637, United States
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11
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Wilkins DM, Dattani NS. Why Quantum Coherence Is Not Important in the Fenna–Matthews–Olsen Complex. J Chem Theory Comput 2015; 11:3411-9. [DOI: 10.1021/ct501066k] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- David M. Wilkins
- Physical and Theoretical
Chemistry Laboratory, Oxford University, South Parks Road, Oxford, OX1 3QZ, United Kingdom
| | - Nikesh S. Dattani
- Quantum
Chemistry Laboratory,
Department of Chemistry, Kyoto University, 606-8502, Kyoto, Japan
- School of Materials Science
and Engineering, Nanyang Technological University, Block N4.1, Nanyang Avenue, Singapore 639798
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