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Cui X, Yan Y, Wei J. Theoretical Study on the Effect of Environment on Excitation Energy Transfer in Photosynthetic Light-Harvesting Systems. J Phys Chem B 2020; 124:2354-2362. [PMID: 32130013 DOI: 10.1021/acs.jpcb.0c00266] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In recent years, two-dimensional (2D) electronic spectroscopy experiments prove that the excitation energy transfer (EET) in photosynthetic light-harvesting systems presents long-lived electronic quantum beating signals. After being discovered in the light-harvesting system, the quantum coherence effect has aroused widespread discussion. To illustrate the EET process in the Fenna-Matthews-Olson (FMO) and phycocyanin 645 (PC645) complex, the local protein environment is often thought to be the same; however, this is ambivalent to the practical structural analysis of the light-harvesting complex. By adopting the dissipaton equation of motion theory, we present the effect of a heterogeneous protein environment on the energy transfer process with accurate numerical results. We demonstrate that the energy transfer process relies on the local heterogeneous environment for the FMO complex. A similar good agreement is found for the PC645 complex. Furthermore, we discuss the optimal value of different chromophores in the excitation energy transfer process by controlling the environmental characteristics.
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Affiliation(s)
- XueYan Cui
- Department of Physics & Beijing Key Laboratory of Optoelectronic Functional Materials and Micro-nano Devices, Renmin University of China, Beijing 100872, China
| | - YiJing Yan
- Department of Chemical Physics & Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - JianHua Wei
- Department of Physics & Beijing Key Laboratory of Optoelectronic Functional Materials and Micro-nano Devices, Renmin University of China, Beijing 100872, China
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2
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Saito S, Higashi M, Fleming GR. Site-Dependent Fluctuations Optimize Electronic Energy Transfer in the Fenna–Matthews–Olson Protein. J Phys Chem B 2019; 123:9762-9772. [DOI: 10.1021/acs.jpcb.9b07456] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Shinji Saito
- Institute for Molecular Science, Myodaiji, Okazaki, Aichi 444-8585, Japan
- The Graduate University for Advanced Studies, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Masahiro Higashi
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto daigaku-katsura, Nishikyo-ku, Kyoto 615-8510, Kyoto, Japan
- JST, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Graham R. Fleming
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Lab, Berkeley, California 94720, United States
- Kavli Energy Nanosciences Institute at Berkeley, Berkeley, California 94720, United States
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Abstract
A comprehensive approach to modeling open quantum systems consistent with thermodynamics is presented. The theory of open quantum systems is employed to define system bath partitions. The Markovian master equation defines an isothermal partition between the system and bath. Two methods to derive the quantum master equation are described: the weak coupling limit and the repeated collision model. The role of the eigenoperators of the free system dynamics is highlighted, in particular, for driven systems. The thermodynamical relations are pointed out. Models that lead to loss of coherence, i.e., dephasing are described. The implication of the laws of thermodynamics to simulating transport and spectroscopy is described. The indications for self-averaging in large quantum systems and thus its importance in modeling are described. Basic modeling by the surrogate Hamiltonian is described, as well as thermal boundary conditions using the repeated collision model and their use in the stochastic surrogate Hamiltonian. The problem of modeling with explicitly time dependent driving is analyzed. Finally, the use of the stochastic surrogate Hamiltonian for modeling ultrafast spectroscopy and quantum control is reviewed.
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Affiliation(s)
- Ronnie Kosloff
- The Institute of Chemistry and The Fritz Haber Centre for Theoretical Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
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4
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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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5
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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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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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8
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Lee MH, Troisi A. Quantum dynamics of a vibronically coupled linear chain using a surrogate Hamiltonian approach. J Chem Phys 2016; 144:214106. [DOI: 10.1063/1.4953043] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Myeong H. Lee
- Department of Chemistry and Centre for Scientific Computing, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Alessandro Troisi
- Department of Chemistry and Centre for Scientific Computing, University of Warwick, Coventry CV4 7AL, United Kingdom
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10
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Kim HW, Rhee YM. Improving long time behavior of Poisson bracket mapping equation: A non-Hamiltonian approach. J Chem Phys 2014; 140:184106. [DOI: 10.1063/1.4874268] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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11
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Kais S. Introduction to Quantum Information and Computation for Chemistry. ADVANCES IN CHEMICAL PHYSICS 2014. [DOI: 10.1002/9781118742631.ch01] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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12
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Impact of a single base pair substitution on the charge transfer rate along short DNA hairpins. Proc Natl Acad Sci U S A 2013; 110:14867-71. [PMID: 23980166 DOI: 10.1073/pnas.1309139110] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Numerical studies of hole migration along short DNA hairpins were performed with a particular emphasis on the variations of the rate and quantum yield of the charge separation process with the location of a single guanine:cytosine (G:C) base pair. Our calculations show that the hole arrival rate increases as the position of the guanine:cytosine base pair shifts from the beginning to the end of the sequence. Although these results are in agreement with recent experimental findings, the mechanism governing the charge migration along these sequences is revisited here. Instead of the phenomenological two-step hopping mechanism via the guanine base, the charge propagation occurs through a delocalization of the hole density along the base pair stack. Furthermore, the variations of the charge transfer with the position of the guanine base are explained by the impact of the base pair substitutions on the delocalized conduction channels.
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Banchi L, Costagliola G, Ishizaki A, Giorda P. An analytical continuation approach for evaluating emission lineshapes of molecular aggregates and the adequacy of multichromophoric Förster theory. J Chem Phys 2013; 138:184107. [DOI: 10.1063/1.4803694] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
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König C, Neugebauer J. Protein Effects on the Optical Spectrum of the Fenna–Matthews–Olson Complex from Fully Quantum Chemical Calculations. J Chem Theory Comput 2013; 9:1808-20. [DOI: 10.1021/ct301111q] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Carolin König
- Theoretische Organische
Chemie, Organisch-Chemisches
Institut, Westfälische Wilhelms-Universität Münster, Corrensstraße 40, 48149 Münster,
Germany
| | - Johannes Neugebauer
- Theoretische Organische
Chemie, Organisch-Chemisches
Institut, Westfälische Wilhelms-Universität Münster, Corrensstraße 40, 48149 Münster,
Germany
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Renaud N, Berlin YA, Lewis FD, Ratner MA. Between superexchange and hopping: an intermediate charge-transfer mechanism in poly(A)-poly(T) DNA hairpins. J Am Chem Soc 2013; 135:3953-63. [PMID: 23402652 DOI: 10.1021/ja3113998] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
We developed a model for hole migration along relatively short DNA hairpins with fewer that seven adenine (A):thymine (T) base pairs. The model was used to simulate hole migration along poly(A)-poly(T) sequences with a particular emphasis on the impact of partial hole localization on the different rate processes. The simulations, performed within the framework of the stochastic surrogate Hamiltonian approach, give values for the arrival rate in good agreement with experimental data. Theoretical results obtained for hairpins with fewer than three A:T base pairs suggest that hole transfer along short hairpins occurs via superexchange. This mechanism is characterized by the exponential distance dependence of the arrival rate on the donor/acceptor distance, k(a) ≃ e(-βR), with β = 0.9 Å(-1). For longer systems, up to six A:T pairs, the distance dependence follows a power law k(a) ≃ R(-η) with η = 2. Despite this seemingly clear signature of unbiased hopping, our simulations show the complete delocalization of the hole density along the entire hairpin. According to our analysis, the hole transfer along relatively long sequences may proceed through a mechanism which is distinct from both coherent single-step superexchange and incoherent multistep hopping. The criterion for the validity of this mechanism intermediate between superexchange and hopping is proposed. The impact of partial localization on the rate of hole transfer between neighboring A bases was also investigated.
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Affiliation(s)
- Nicolas Renaud
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, USA.
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16
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Yeh SH, Zhu J, Kais S. Population and coherence dynamics in light harvesting complex II (LH2). J Chem Phys 2013; 137:084110. [PMID: 22938221 DOI: 10.1063/1.4747622] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The electronic excitation population and coherence dynamics in the chromophores of the photosynthetic light harvesting complex 2 (LH2) B850 ring from purple bacteria (Rhodopseudomonas acidophila) have been studied theoretically at both physiological and cryogenic temperatures. Similar to the well-studied Fenna-Matthews-Olson (FMO) protein, oscillations of the excitation population and coherence in the site basis are observed in LH2 by using a scaled hierarchical equation of motion approach. However, this oscillation time (300 fs) is much shorter compared to the FMO protein (650 fs) at cryogenic temperature. Both environment and high temperature are found to enhance the propagation speed of the exciton wave packet yet they shorten the coherence time and suppress the oscillation amplitude of coherence and the population. Our calculations show that a long-lived coherence between chromophore electronic excited states can exist in such a noisy biological environment.
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Affiliation(s)
- Shu-Hao Yeh
- Department of Chemistry and Birck Nanotechnology Center, Purdue University, West Lafayette, Indiana 47907, USA
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17
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Renaud N, Powell D, Zarea M, Movaghar B, Wasielewski MR, Ratner MA. Quantum Interferences and Electron Transfer in Photosystem I. J Phys Chem A 2012; 117:5899-908. [DOI: 10.1021/jp308216y] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Nicolas Renaud
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston,
Illinois 60208-3113, United States
| | - Daniel Powell
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston,
Illinois 60208-3113, United States
| | - Mahdi Zarea
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston,
Illinois 60208-3113, United States
| | - Bijan Movaghar
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston,
Illinois 60208-3113, United States
| | - Michael R. Wasielewski
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston,
Illinois 60208-3113, United States
| | - Mark A. Ratner
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston,
Illinois 60208-3113, United States
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18
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Zhu J, Kais S, Aspuru-Guzik A, Rodriques S, Brock B, Love PJ. Multipartite quantum entanglement evolution in photosynthetic complexes. J Chem Phys 2012; 137:074112. [DOI: 10.1063/1.4742333] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
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19
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Kim HW, Kelly A, Park JW, Rhee YM. All-Atom Semiclassical Dynamics Study of Quantum Coherence in Photosynthetic Fenna–Matthews–Olson Complex. J Am Chem Soc 2012; 134:11640-51. [DOI: 10.1021/ja303025q] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hyun Woo Kim
- Institute of Theoretical
and Computational Chemistry, Department of Chemistry, Pohang University of Science and Technology, Pohang
790-784, Korea
| | - Aaron Kelly
- Institute of Theoretical
and Computational Chemistry, Department of Chemistry, Pohang University of Science and Technology, Pohang
790-784, Korea
| | - Jae Woo Park
- Institute of Theoretical
and Computational Chemistry, Department of Chemistry, Pohang University of Science and Technology, Pohang
790-784, Korea
| | - Young Min Rhee
- Institute of Theoretical
and Computational Chemistry, Department of Chemistry, Pohang University of Science and Technology, Pohang
790-784, Korea
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20
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Thilagam A. Multipartite entanglement in the Fenna-Matthews-Olson (FMO) pigment-protein complex. J Chem Phys 2012; 136:175104. [PMID: 22583269 DOI: 10.1063/1.4705396] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- A Thilagam
- Minerals and Materials Science and Technology, Mawson Institute, Division of ITEE, University of South Australia, Adelaide, South Australia 5095, Australia.
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Franco I, Brumer P. Electronic coherence dynamics in trans-polyacetylene oligomers. J Chem Phys 2012; 136:144501. [PMID: 22502527 DOI: 10.1063/1.3700445] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Ignacio Franco
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, USA.
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22
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Berkelbach TC, Markland TE, Reichman DR. Reduced density matrix hybrid approach: Application to electronic energy transfer. J Chem Phys 2012; 136:084104. [DOI: 10.1063/1.3687342] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
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23
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Thilagam A. Non-Hermitian exciton dynamics in a photosynthetic unit system. J Chem Phys 2012; 136:065104. [DOI: 10.1063/1.3684654] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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