51
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Tay BA. Attenuation of excitation decay rate due to collective effect. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 90:022142. [PMID: 25215723 DOI: 10.1103/physreve.90.022142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Indexed: 06/03/2023]
Abstract
We study a series of N oscillators, each coupled to its nearest neighbors, and linearly to a phonon field through the oscillator's number operator. We show that the Hamiltonian of a pair of adjacent oscillators, or a dimer, within the series of oscillators can be transformed into a form in which they are collectively coupled to the phonon field as a composite unit. In the weak coupling and rotating-wave approximation, the system behaves effectively as the trilinear boson model in the one excitation subspace of the dimer subsystem. The reduced dynamics of the one excitation subspace of the dimer subsystem coupled weakly to a phonon bath is similar to that of a two-level system, with a metastable state against the vacuum. The decay constant of the subsystem is proportional to the dephasing rate of the individual oscillator in a phonon bath, attenuated by a factor that depends on site asymmetry, intersite coupling, and the resonance frequency between the transformed oscillator modes, or excitons. As a result of the collective effect, the excitation relaxation lifetime is prolonged over the dephasing lifetime of an individual oscillator coupled to the same bath.
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Affiliation(s)
- B A Tay
- Foundation Studies, Faculty of Engineering, University of Nottingham Malaysia Campus, Jalan Broga, 43500 Semenyih, Selangor, Malaysia
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52
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Dong H, Fleming GR. Inhomogeneous Broadening Induced Long-Lived Integrated Two-Color Coherence Photon Echo Signal. J Phys Chem B 2014; 118:8956-61. [DOI: 10.1021/jp503045z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hui Dong
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Graham R. Fleming
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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53
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Goez A, Jacob CR, Neugebauer J. Modeling environment effects on pigment site energies: Frozen density embedding with fully quantum-chemical protein densities. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2014.02.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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54
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Fujita T, Huh J, Aspuru-Guzik A. A stochastic reorganizational bath model for electronic energy transfer. J Chem Phys 2014; 140:244103. [DOI: 10.1063/1.4883862] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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55
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Zhang L, Silva DA, Zhang H, Yue A, Yan Y, Huang X. Dynamic protein conformations preferentially drive energy transfer along the active chain of the photosystem II reaction centre. Nat Commun 2014; 5:4170. [PMID: 24954746 PMCID: PMC4083425 DOI: 10.1038/ncomms5170] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 05/20/2014] [Indexed: 11/11/2022] Open
Abstract
One longstanding puzzle concerning photosystem II, a core component of photosynthesis, is that only one of the two symmetric branches in its reaction centre is active in electron transfer. To investigate the effect of the photosystem II environment on the preferential selection of the energy transfer pathway (a prerequisite for electron transfer), we have constructed an exciton model via extensive molecular dynamics simulations and quantum mechanics/molecular mechanics calculations based on a recent X-ray structure. Our results suggest that it is essential to take into account an ensemble of protein conformations to accurately compute the site energies. We identify the cofactor CLA606 of active chain as the most probable site for the energy excitation. We further pinpoint a number of charged protein residues that collectively lower the CLA606 site energy. Our work provides insights into the understanding of molecular mechanisms of the core machinery of the green-plant photosynthesis. Cofactor-mediated energy and electron transfer in photosystem II occurs preferentially through one branch of the reaction centre, despite there being a symmetric path available. Here, the authors use computational methods to determine the influence of protein conformation on this selectivity.
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Affiliation(s)
- Lu Zhang
- Department of Chemistry, Institute for Advance Study and School of Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Daniel-Adriano Silva
- 1] Department of Chemistry, Institute for Advance Study and School of Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong [2]
| | - Houdao Zhang
- Department of Chemistry, Institute for Advance Study and School of Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Alexander Yue
- Division of Biomedical Engineering, Institute for Advance Study and School of Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - YiJing Yan
- 1] Department of Chemistry, Institute for Advance Study and School of Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong [2] Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, China
| | - Xuhui Huang
- 1] Department of Chemistry, Institute for Advance Study and School of Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong [2] Division of Biomedical Engineering, Institute for Advance Study and School of Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong [3] Centre of Systems Biology and Human Health, Institute for Advance Study and School of Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong
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56
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Kell A, Acharya K, Blankenship RE, Jankowiak R. On destabilization of the Fenna-Matthews-Olson complex of Chlorobaculum tepidum. PHOTOSYNTHESIS RESEARCH 2014; 120:323-329. [PMID: 24584903 DOI: 10.1007/s11120-014-9990-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Accepted: 02/17/2014] [Indexed: 06/03/2023]
Abstract
The Fenna-Matthews-Olson (FMO) complex from the green sulfur bacterium Chlorobaculum tepidum was studied with respect to its stability. We provide a critical assessment of published and recently measured optical spectra. FMO complexes were found to destabilize over time producing spectral shifts, with destabilized samples having significantly higher hole-burning efficiencies; indicating a remodeled protein energy landscape. Observed correlated peak shifts near 825 and 815 nm suggest possible correlated (protein) fluctuations. It is proposed that the value of 35 cm(-1) widely used for reorganization energy (E λ ), which has important implications for the contributions to the coherence rate (Kreisbeck and Kramer 3:2828-2833, 2012), in various modeling studies of two-dimensional electronic spectra is overestimated. We demonstrate that the value of E λ is most likely about 15-22 cm(-1) and suggest that spectra reported in the literature (often measured on different FMO samples) exhibit varied peak positions due to different purification/isolation procedures or destabilization effects.
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Affiliation(s)
- Adam Kell
- Department of Chemistry, Kansas State University, Manhattan, KS, 66506, USA
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57
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Fassioli F, Dinshaw R, Arpin PC, Scholes GD. Photosynthetic light harvesting: excitons and coherence. J R Soc Interface 2014; 11:20130901. [PMID: 24352671 PMCID: PMC3899860 DOI: 10.1098/rsif.2013.0901] [Citation(s) in RCA: 165] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Accepted: 11/29/2013] [Indexed: 12/15/2022] Open
Abstract
Photosynthesis begins with light harvesting, where specialized pigment-protein complexes transform sunlight into electronic excitations delivered to reaction centres to initiate charge separation. There is evidence that quantum coherence between electronic excited states plays a role in energy transfer. In this review, we discuss how quantum coherence manifests in photosynthetic light harvesting and its implications. We begin by examining the concept of an exciton, an excited electronic state delocalized over several spatially separated molecules, which is the most widely available signature of quantum coherence in light harvesting. We then discuss recent results concerning the possibility that quantum coherence between electronically excited states of donors and acceptors may give rise to a quantum coherent evolution of excitations, modifying the traditional incoherent picture of energy transfer. Key to this (partially) coherent energy transfer appears to be the structure of the environment, in particular the participation of non-equilibrium vibrational modes. We discuss the open questions and controversies regarding quantum coherent energy transfer and how these can be addressed using new experimental techniques.
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Affiliation(s)
| | | | | | - Gregory D. Scholes
- Department of Chemistry, University of Toronto, 80 St George St., Toronto, Ontario, CanadaM5S 3H6
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58
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Herascu N, Kell A, Acharya K, Jankowiak R, Blankenship RE, Zazubovich V. Modeling of Various Optical Spectra in the Presence of Slow Excitation Energy Transfer in Dimers and Trimers with Weak Interpigment Coupling: FMO as an Example. J Phys Chem B 2014; 118:2032-40. [DOI: 10.1021/jp410586f] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Nicoleta Herascu
- Department
of Physics, Concordia University, Montreal, H4B 1R6 Quebec, Canada
| | | | | | | | | | - Valter Zazubovich
- Department
of Physics, Concordia University, Montreal, H4B 1R6 Quebec, Canada
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59
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Sato Y, Reynolds MF. Resonant Coherence in Photosynthetic Electronic Energy Transfer by Site-Dependent Pigment–Protein Interactions. J Phys Chem B 2014; 118:1229-33. [DOI: 10.1021/jp410190n] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yoshihiro Sato
- Department of Physics & Astronomy, Colby College, Waterville, Maine 04901, United States
| | - Meredith F. Reynolds
- Department of Physics & Astronomy, Colby College, Waterville, Maine 04901, United States
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60
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Mohseni M, Shabani A, Lloyd S, Rabitz H. Energy-scales convergence for optimal and robust quantum transport in photosynthetic complexes. J Chem Phys 2014; 140:035102. [DOI: 10.1063/1.4856795] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
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61
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Butkus V, Valkunas L, Abramavicius D. Vibronic phenomena and exciton–vibrational interference in two-dimensional spectra of molecular aggregates. J Chem Phys 2014; 140:034306. [DOI: 10.1063/1.4861466] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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62
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Halpin A, Johnson PJM, Tempelaar R, Murphy RS, Knoester J, Jansen TLC, Miller RJD. Two-dimensional spectroscopy of a molecular dimer unveils the effects of vibronic coupling on exciton coherences. Nat Chem 2014; 6:196-201. [DOI: 10.1038/nchem.1834] [Citation(s) in RCA: 193] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 11/22/2013] [Indexed: 12/31/2022]
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63
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Viani L, Corbella M, Curutchet C, O'Reilly EJ, Olaya-Castro A, Mennucci B. Molecular basis of the exciton–phonon interactions in the PE545 light-harvesting complex. Phys Chem Chem Phys 2014; 16:16302-11. [DOI: 10.1039/c4cp01477d] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
A fully polarizable QM/MM approach is used in combination with classical MD simulations to predict the pigment-dependent spectral densities of the PE545 antenna complex and account for their effects on the exciton dynamics.
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Affiliation(s)
- Lucas Viani
- Dipartimento di Chimica e Chimica Industriale
- Università di Pisa
- 56126 Pisa, Italy
| | - Marina Corbella
- Departament de Fisicoquímica
- Facultat de Farmàcia
- Universitat de Barcelona
- 08028 Barcelona, Spain
| | - Carles Curutchet
- Departament de Fisicoquímica
- Facultat de Farmàcia
- Universitat de Barcelona
- 08028 Barcelona, Spain
| | - Edward J. O'Reilly
- Department of Physics and Astronomy
- University College London
- London WC1E 6BT, UK
| | | | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale
- Università di Pisa
- 56126 Pisa, Italy
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64
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Plenio MB, Almeida J, Huelga SF. Origin of long-lived oscillations in 2D-spectra of a quantum vibronic model: Electronic versus vibrational coherence. J Chem Phys 2013; 139:235102. [DOI: 10.1063/1.4846275] [Citation(s) in RCA: 111] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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65
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Renger T, Madjet MEA, Schmidt am Busch M, Adolphs J, Müh F. Structure-based modeling of energy transfer in photosynthesis. PHOTOSYNTHESIS RESEARCH 2013; 116:367-388. [PMID: 23921525 DOI: 10.1007/s11120-013-9893-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2013] [Accepted: 07/08/2013] [Indexed: 06/02/2023]
Abstract
We provide a minimal model for a structure-based simulation of excitation energy transfer in pigment-protein complexes (PPCs). In our treatment, the PPC is assembled from its building blocks. The latter are defined such that electron exchange occurs only within, but not between these units. The variational principle is applied to investigate how the Coulomb interaction between building blocks changes the character of the electronic states of the PPC. In this way, the standard exciton Hamiltonian is obtained from first principles and a hierarchy of calculation schemes for the parameters of this Hamiltonian arises. Possible extensions of this approach are discussed concerning (i) the inclusion of dispersive site energy shifts and (ii) the inclusion of electron exchange between pigments. First results on electron exchange within the special pair of photosystem II of cyanobacteria and higher plants are presented and compared with earlier results on purple bacteria. In the last part of this mini-review, the coupling of electronic and nuclear degrees of freedom is considered. First, the standard exciton-vibrational Hamiltonian is parameterized with the help of a normal mode analysis of the PPC. Second, dynamical theories are discussed that exploit this Hamiltonian in the study of dissipative exciton motion.
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Affiliation(s)
- Thomas Renger
- Institut für Theoretische Physik, Johannes Kepler Universität Linz, Altenberger Str. 69, 4040, Linz, Austria,
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66
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Aghtar M, Strümpfer J, Olbrich C, Schulten K, Kleinekathöfer U. The FMO complex in a glycerol-water mixture. J Phys Chem B 2013; 117:7157-63. [PMID: 23697741 PMCID: PMC3714603 DOI: 10.1021/jp311380k] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Experimental findings of long-lived quantum coherence in the Fenna-Matthews-Olson (FMO) complex and other photosynthetic complexes have led to theoretical studies searching for an explanation of this unexpected phenomenon. Extending in this regard our own earlier calculations, we performed simulations of the FMO complex in a glycerol-water mixture at 310 K as well as 77 K, matching the conditions of earlier 2D spectroscopic experiments by Engel et al. The calculations, based on an improved quantum procedure employed by us already, yielded spectral densities of each individual pigment of FMO, in water and glycerol-water solvents at ambient temperature that compare well to prior experimental estimates. Due to the slow solvent dynamics at 77 K, the present results strongly indicate the presence of static disorder, i.e., disorder on a time scale beyond that relevant for the construction of spectral densities.
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67
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Bhattacharyya P, Sebastian KL. Adiabatic eigenfunction-based approach for coherent excitation transfer: an almost analytical treatment of the Fenna-Matthews-Olson complex. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 87:062712. [PMID: 23848720 DOI: 10.1103/physreve.87.062712] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Revised: 05/24/2013] [Indexed: 06/02/2023]
Abstract
We suggest a method of studying coherence in finite-level systems coupled to the environment and use it for the Hamiltonian that has been used to describe the light-harvesting pigment-protein complex. The method works with the adiabatic states and transforms the Hamiltonian to a form in which the terms responsible for decoherence and population relaxation are separated out. Decoherence is then accounted for nonperturbatively and population relaxation using a Markovian master equation. Almost analytical results can be obtained for the seven-level system, and the calculations are very simple for systems with more levels. We apply the treatment to the seven-level system, and the results are in excellent agreement with the exact numerical results of Nalbach et al. [Nalbach, Braun, and Thorwart, Phys. Rev. E 84, 041926 (2011)]. Our approach is able to account for decoherence and population relaxation separately. It is found that decoherence causes only damping of oscillations and does not lead to transfer to the reaction center. Population relaxation is necessary for efficient transfer to the reaction center, in agreement with earlier findings. Our results show that the transformation to the adiabatic basis followed by a Redfield type of approach leads to results in good agreement with exact simulation.
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Affiliation(s)
- Pallavi Bhattacharyya
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India.
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68
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Haverkort F, Stradomska A, de Vries AH, Knoester J. Investigating the Structure of Aggregates of an Amphiphilic Cyanine Dye with Molecular Dynamics Simulations. J Phys Chem B 2013; 117:5857-67. [DOI: 10.1021/jp4005696] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Frank Haverkort
- Zernike Institute for Advanced
Materials, University of Groningen, Nijenborgh
4, 9747 AG Groningen, The Netherlands
| | - Anna Stradomska
- Zernike Institute for Advanced
Materials, University of Groningen, Nijenborgh
4, 9747 AG Groningen, The Netherlands
| | - Alex H. de Vries
- Zernike Institute for Advanced
Materials, University of Groningen, Nijenborgh
4, 9747 AG Groningen, The Netherlands
- Groningen Biomolecular Sciences
and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Jasper Knoester
- Zernike Institute for Advanced
Materials, University of Groningen, Nijenborgh
4, 9747 AG Groningen, The Netherlands
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69
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Rivera E, Montemayor D, Masia M, Coker DF. Influence of Site-Dependent Pigment–Protein Interactions on Excitation Energy Transfer in Photosynthetic Light Harvesting. J Phys Chem B 2013; 117:5510-21. [DOI: 10.1021/jp4011586] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Eva Rivera
- Department
of Physics, and Complex
Adaptive Systems Laboratory, University College Dublin, Belfield, Dublin 4, Ireland
| | - Daniel Montemayor
- Department
of Physics, and Complex
Adaptive Systems Laboratory, University College Dublin, Belfield, Dublin 4, Ireland
| | - Marco Masia
- Institut für Physikalische
und Theoretische Chemie, Goethe Universität Frankfurt, Max von Laue Str. 7, D-60438 Frankfurt am Main, Germany, and Dipartimento
di Chimica e Farmacia, Universita’ degli Studi di Sassari, Via Vienna 2, 07100 Sassari, Italy
| | - David F. Coker
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston,
Massachusetts 02215, United States
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70
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Gao J, Shi WJ, Ye J, Wang X, Hirao H, Zhao Y. QM/MM Modeling of Environmental Effects on Electronic Transitions of the FMO Complex. J Phys Chem B 2013; 117:3488-95. [DOI: 10.1021/jp3109418] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Junkuo Gao
- Division of Materials Science, Nanyang Technological University, 50 Nanyang Avenue,
Singapore 639798
| | - Wu-Jun Shi
- Division of Materials Science, Nanyang Technological University, 50 Nanyang Avenue,
Singapore 639798
| | - Jun Ye
- Institute of High Performance Computing, Agency for Science, Technology
and Research, 1 Fusionopolis Way, 16-16 Connexis, Singapore 138632
| | - Xiaoqing Wang
- Division of Chemistry & Biological Chemistry, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
| | - Hajime Hirao
- Division of Chemistry & Biological Chemistry, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
| | - Yang Zhao
- Division of Materials Science, Nanyang Technological University, 50 Nanyang Avenue,
Singapore 639798
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71
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Berkelbach TC, Hybertsen MS, Reichman DR. Microscopic theory of singlet exciton fission. I. General formulation. J Chem Phys 2013; 138:114102. [DOI: 10.1063/1.4794425] [Citation(s) in RCA: 184] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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72
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Kolli A, O'Reilly EJ, Scholes GD, Olaya-Castro A. The fundamental role of quantized vibrations in coherent light harvesting by cryptophyte algae. J Chem Phys 2013; 137:174109. [PMID: 23145719 DOI: 10.1063/1.4764100] [Citation(s) in RCA: 174] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The influence of fast vibrations on energy transfer and conversion in natural molecular aggregates is an issue of central interest. This article shows the important role of high-energy quantized vibrations and their non-equilibrium dynamics for energy transfer in photosynthetic systems with highly localized excitonic states. We consider the cryptophyte antennae protein phycoerythrin 545 and show that coupling to quantized vibrations, which are quasi-resonant with excitonic transitions is fundamental for biological function as it generates non-cascaded transport with rapid and wider spatial distribution of excitation energy. Our work also indicates that the non-equilibrium dynamics of such vibrations can manifest itself in ultrafast beating of both excitonic populations and coherences at room temperature, with time scales in agreement with those reported in experiments. Moreover, we show that mechanisms supporting coherent excitonic dynamics assist coupling to selected modes that channel energy to preferential sites in the complex. We therefore argue that, in the presence of strong coupling between electronic excitations and quantized vibrations, a concrete and important advantage of quantum coherent dynamics is precisely to tune resonances that promote fast and effective energy distribution.
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Affiliation(s)
- Avinash Kolli
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, United Kingdom
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73
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Viani L, Curutchet C, Mennucci B. Spatial and Electronic Correlations in the PE545 Light-Harvesting Complex. J Phys Chem Lett 2013; 4:372-377. [PMID: 26281726 DOI: 10.1021/jz301987u] [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: 06/04/2023]
Abstract
The recent discovery of long-lasting quantum coherence effects in photosynthetic pigment-protein complexes has challenged our view of the role that protein motions play in light-harvesting processes. Several groups have suggested that correlated fluctuations involving the pigments site energies and couplings could be at the origin of such unexpected behavior. Here we combine molecular dynamics simulations with quantum mechanics/molecular mechanics calculations to analyze the degree of correlated fluctuations in the PE545 complex of Rhodomonas sp. strain CS24. We find that correlations between the motions of the chromophores, which are significantly assisted by the water solvent, do not translate into appreciable site energy correlations but do lead to significant cross-correlations of energies and couplings. Such behavior, not observed in a recent study on the Fenna-Mathews-Olson complex, seems to provide phycobiliproteins with an additional fundamental mechanism to control quantum coherence and light-harvesting efficiency compared with chlorophyll-containing complexes.
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Affiliation(s)
- Lucas Viani
- †Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Risorgimento 35, 56126 Pisa, Italy
| | - Carles Curutchet
- ‡Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII s/n, 08028 Barcelona, Spain
| | - Benedetta Mennucci
- †Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Risorgimento 35, 56126 Pisa, Italy
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74
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Renger T, Müh F. Understanding photosynthetic light-harvesting: a bottom up theoretical approach. Phys Chem Chem Phys 2013; 15:3348-71. [PMID: 23361062 DOI: 10.1039/c3cp43439g] [Citation(s) in RCA: 125] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We discuss a bottom up approach for modeling photosynthetic light-harvesting. Methods are reviewed for a full structure-based parameterization of the Hamiltonian of pigment-protein complexes (PPCs). These parameters comprise (i) the local transition energies of the pigments in their binding sites in the protein, the site energies; (ii) the couplings between optical transitions of the pigments, the excitonic couplings; and (iii) the spectral density characterizing the dynamic modulation of pigment transition energies and excitonic couplings by protein vibrations. Starting with quantum mechanics perturbation theory, we provide a microscopic foundation for the standard PPC Hamiltonian and relate the expressions obtained for its matrix elements to quantities that can be calculated with classical molecular mechanics/electrostatics approaches including the whole PPC in atomic detail and using charge and transition densities obtained with quantum chemical calculations on the isolated building blocks of the PPC. In the second part of this perspective, the Hamiltonian is utilized to describe the quantum dynamics of excitons. Situations are discussed that differ in the relative strength of excitonic and exciton-vibrational coupling. The predictive power of the approaches is demonstrated in application to different PPCs, and challenges for future work are outlined.
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Affiliation(s)
- Thomas Renger
- Institut für Theoretische Physik, Johannes Kepler Universität Linz, Linz, Austria.
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75
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Renger T, Klinger A, Steinecker F, Schmidt am Busch M, Numata J, Müh F. Normal mode analysis of the spectral density of the Fenna-Matthews-Olson light-harvesting protein: how the protein dissipates the excess energy of excitons. J Phys Chem B 2012; 116:14565-80. [PMID: 23163520 PMCID: PMC3557933 DOI: 10.1021/jp3094935] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Revised: 11/19/2012] [Indexed: 11/29/2022]
Abstract
We report a method for the structure-based calculation of the spectral density of the pigment-protein coupling in light-harvesting complexes that combines normal-mode analysis with the charge density coupling (CDC) and transition charge from electrostatic potential (TrEsp) methods for the computation of site energies and excitonic couplings, respectively. The method is applied to the Fenna-Matthews-Olson (FMO) protein in order to investigate the influence of the different parts of the spectral density as well as correlations among these contributions on the energy transfer dynamics and on the temperature-dependent decay of coherences. The fluctuations and correlations in excitonic couplings as well as the correlations between coupling and site energy fluctuations are found to be 1 order of magnitude smaller in amplitude than the site energy fluctuations. Despite considerable amplitudes of that part of the spectral density which contains correlations in site energy fluctuations, the effect of these correlations on the exciton population dynamics and dephasing of coherences is negligible. The inhomogeneous charge distribution of the protein, which causes variations in local pigment-protein coupling constants of the normal modes, is responsible for this effect. It is seen thereby that the same building principle that is used by nature to create an excitation energy funnel in the FMO protein also allows for efficient dissipation of the excitons' excess energy.
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Affiliation(s)
- Thomas Renger
- Institut für Theoretische Physik, Johannes Kepler Universität Linz, Altenberger Str. 69, 4040 Linz, Austria.
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76
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Shim S, Aspuru-Guzik A. Path integral Monte Carlo with importance sampling for excitons interacting with an arbitrary phonon bath. J Chem Phys 2012; 137:22A538. [DOI: 10.1063/1.4751487] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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77
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Chang HT, Cheng YC. Coherent versus incoherent excitation energy transfer in molecular systems. J Chem Phys 2012; 137:165103. [DOI: 10.1063/1.4761929] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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78
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Roy A, Post CB. Detection of long-range concerted motions in protein by a distance covariance. J Chem Theory Comput 2012; 8:3009-3014. [PMID: 23610564 PMCID: PMC3630994 DOI: 10.1021/ct300565f] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We asses the ability of a distance correlation coefficient (DiCC), calculated from distance covariance, for detecting long-range concerted motion in proteins. We establish a set of criteria for ideal correlation coefficient values based on the coefficient of determination in multi-dimension, R2. We compare in detail DiCC and conventional coefficients against these criteria. We demonstrate that in contrast to conventional correlation coefficients, which capture long-distance correlation adequately only with certain restrictions in multi-dimension, DiCC reflects appropriate correlation in both one- and multi-dimension. Finally we demonstrate the usefulness of DiCC for assessing long-distance correlated fluctuation in protein dynamics.
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Affiliation(s)
- Amitava Roy
- Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, USA
| | - Carol Beth Post
- Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, USA
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79
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Chin AW, Huelga SF, Plenio MB. Coherence and decoherence in biological systems: principles of noise-assisted transport and the origin of long-lived coherences. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2012; 370:3638-57. [PMID: 22753818 DOI: 10.1098/rsta.2011.0224] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The quantum dynamics of transport networks in the presence of noisy environments has recently received renewed attention with the discovery of long-lived coherences in different photosynthetic complexes. This experimental evidence has raised two fundamental questions: firstly, what are the mechanisms supporting long-lived coherences; and, secondly, how can we assess the possible functional role that the interplay of noise and quantum coherence might play in the seemingly optimal operation of biological systems under natural conditions? Here, we review recent results, illuminate them by means of two paradigmatic systems (the Fenna-Matthew-Olson complex and the light-harvesting complex LHII) and present new progress on both questions.
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Affiliation(s)
- A W Chin
- Institute of Theoretical Physics, Universität Ulm, Albert-Einstein-Allee 11, 89069 Ulm, Germany.
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80
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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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81
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Christensson N, Kauffmann HF, Pullerits T, Mančal T. Origin of long-lived coherences in light-harvesting complexes. J Phys Chem B 2012; 116:7449-54. [PMID: 22642682 PMCID: PMC3789255 DOI: 10.1021/jp304649c] [Citation(s) in RCA: 284] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A vibronic exciton model is applied to explain the long-lived oscillatory features in the two-dimensional (2D) electronic spectra of the Fenna-Matthews-Olson (FMO) complex. Using experimentally determined parameters and uncorrelated site energy fluctuations, the model predicts oscillations with dephasing times of 1.3 ps at 77 K, which is in a good agreement with the experimental results. These long-lived oscillations originate from the coherent superposition of vibronic exciton states with dominant contributions from vibrational excitations on the same pigment. The oscillations obtain a large amplitude due to excitonic intensity borrowing, which gives transitions with strong vibronic character a significant intensity despite the small Huang-Rhys factor. Purely electronic coherences are found to decay on a 200 fs time scale.
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Affiliation(s)
- Niklas Christensson
- Faculty of Physics, University of Vienna, Strudlhofgasse 4, 1090 Vienna, Austria
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82
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Zhang L, Silva DA, Yan Y, Huang X. Force field development for cofactors in the photosystem II. J Comput Chem 2012; 33:1969-80. [DOI: 10.1002/jcc.23016] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Revised: 04/05/2012] [Accepted: 04/22/2012] [Indexed: 01/03/2023]
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83
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84
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Wong CY, Alvey RM, Turner DB, Wilk KE, Bryant DA, Curmi PMG, Silbey RJ, Scholes GD. Electronic coherence lineshapes reveal hidden excitonic correlations in photosynthetic light harvesting. Nat Chem 2012; 4:396-404. [DOI: 10.1038/nchem.1302] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Accepted: 02/10/2012] [Indexed: 12/11/2022]
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85
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Huo P, Coker DF. Influence of environment induced correlated fluctuations in electronic coupling on coherent excitation energy transfer dynamics in model photosynthetic systems. J Chem Phys 2012; 136:115102. [DOI: 10.1063/1.3693019] [Citation(s) in RCA: 42] [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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86
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Mühlbacher L, Kleinekathöfer U. Preparational effects on the excitation energy transfer in the FMO complex. J Phys Chem B 2012; 116:3900-6. [PMID: 22360690 DOI: 10.1021/jp301444q] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Using numerically exact path integral Monte Carlo simulations, the excitation energy transfer in the Fenna-Matthews-Olson (FMO) complex is determined at room temperature. The employed system and environment parameters are based on previously reported atomistic simulations. When starting with excitations localized at specific chromophores, no coherence features can be observed. In contrast, when starting with delocalized excitations, traces of coherent motion become apparent. On the one hand, as experimental findings account for much stronger quantum coherent motion, these results suggest a reevaluation of the underlying spectral densities. On the other hand, the results emphasize that the initial preparation of the excitonic system needs to be taken into account carefully when attempting to reproduce the respective experiments.
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Affiliation(s)
- Lothar Mühlbacher
- Physikalisches Institut, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany.
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87
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Shim S, Rebentrost P, Valleau S, Aspuru-Guzik A. Atomistic study of the long-lived quantum coherences in the Fenna-Matthews-Olson complex. Biophys J 2012; 102:649-60. [PMID: 22325289 PMCID: PMC3274801 DOI: 10.1016/j.bpj.2011.12.021] [Citation(s) in RCA: 180] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Revised: 11/08/2011] [Accepted: 12/05/2011] [Indexed: 12/16/2022] Open
Abstract
A remarkable amount of theoretical research has been carried out to elucidate the physical origins of the recently observed long-lived quantum coherence in the electronic energy transfer process in biological photosynthetic systems. Although successful in many respects, several widely used descriptions only include an effective treatment of the protein-chromophore interactions. In this work, by combining an all-atom molecular dynamics simulation, time-dependent density functional theory, and open quantum system approaches, we successfully simulate the dynamics of the electronic energy transfer of the Fenna-Matthews-Olson pigment-protein complex. The resulting characteristic beating of populations and quantum coherences is in good agreement with the experimental results and the hierarchy equation of motion approach. The experimental absorption, linear, and circular dichroism spectra and dephasing rates are recovered at two different temperatures. In addition, we provide an extension of our method to include zero-point fluctuations of the vibrational environment. This work thus presents, to our knowledge, one of the first steps to explain the role of excitonic quantum coherence in photosynthetic light-harvesting complexes based on their atomistic and molecular description.
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Affiliation(s)
| | | | | | - Alán Aspuru-Guzik
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts
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88
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Gelin MF, Sharp LZ, Egorova D, Domcke W. Bath-induced correlations and relaxation of vibronic dimers. J Chem Phys 2012; 136:034507. [DOI: 10.1063/1.3676063] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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89
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Jing Y, Zheng R, Li HX, Shi Q. Theoretical Study of the Electronic–Vibrational Coupling in the Qy States of the Photosynthetic Reaction Center in Purple Bacteria. J Phys Chem B 2012; 116:1164-71. [DOI: 10.1021/jp209575q] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Yuanyuan Jing
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing 100190, China
| | - Renhui Zheng
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing 100190, China
| | - Hui-Xue Li
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing 100190, China
| | - Qiang Shi
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing 100190, China
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90
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Pachón LA, Brumer P. Computational methodologies and physical insights into electronic energy transfer in photosynthetic light-harvesting complexes. Phys Chem Chem Phys 2012; 14:10094-108. [DOI: 10.1039/c2cp40815e] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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91
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König C, Neugebauer J. Quantum chemical description of absorption properties and excited-state processes in photosynthetic systems. Chemphyschem 2011; 13:386-425. [PMID: 22287108 DOI: 10.1002/cphc.201100408] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Indexed: 11/07/2022]
Abstract
The theoretical description of the initial steps in photosynthesis has gained increasing importance over the past few years. This is caused by more and more structural data becoming available for light-harvesting complexes and reaction centers which form the basis for atomistic calculations and by the progress made in the development of first-principles methods for excited electronic states of large molecules. In this Review, we discuss the advantages and pitfalls of theoretical methods applicable to photosynthetic pigments. Besides methodological aspects of excited-state electronic-structure methods, studies on chlorophyll-type and carotenoid-like molecules are discussed. We also address the concepts of exciton coupling and excitation-energy transfer (EET) and compare the different theoretical methods for the calculation of EET coupling constants. Applications to photosynthetic light-harvesting complexes and reaction centers based on such models are also analyzed.
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Affiliation(s)
- Carolin König
- Institute for Physical and Theoretical Chemistry, Technical University Braunschweig, Braunschweig, Germany
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92
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Gelin MF, Egorova D, Domcke W. Exact quantum master equation for a molecular aggregate coupled to a harmonic bath. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2011; 84:041139. [PMID: 22181119 DOI: 10.1103/physreve.84.041139] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2011] [Revised: 09/04/2011] [Indexed: 05/31/2023]
Abstract
We consider a molecular aggregate consisting of N identical monomers. Each monomer comprises two electronic levels and a single harmonic mode. The monomers interact with each other via dipole-dipole forces. The monomer vibrational modes are bilinearly coupled to a bath of harmonic oscillators. This is a prototypical model for the description of coherent exciton transport, from quantum dots to photosynthetic antennae. We derive an exact quantum master equation for such systems. Computationally, the master equation may be useful for the testing of various approximations employed in theories of quantum transport. Physically, it offers a plausible explanation of the origins of long-lived coherent optical responses of molecular aggregates in dissipative environments.
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Affiliation(s)
- Maxim F Gelin
- Department of Chemistry, Technische Universität München, D-85747 Garching, Germany
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93
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Nalbach P, Braun D, Thorwart M. Exciton transfer dynamics and quantumness of energy transfer in the Fenna-Matthews-Olson complex. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2011; 84:041926. [PMID: 22181194 DOI: 10.1103/physreve.84.041926] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2011] [Indexed: 05/31/2023]
Abstract
We present numerically exact results for the quantum coherent energy transfer in the Fenna-Matthews-Olson molecular aggregate under realistic physiological conditions, including vibrational fluctuations of the protein and the pigments for an experimentally determined fluctuation spectrum. We find coherence times shorter than observed experimentally. Furthermore, we determine the energy transfer current and quantify its "quantumness" as the distance of the density matrix to the classical pointer states for the energy current operator. Most importantly, we find that the energy transfer happens through a "Schrödinger-cat-like" superposition of energy current pointer states.
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Affiliation(s)
- P Nalbach
- I. Institut für Theoretische Physik, Universität Hamburg, Jungiusstraße 9, D-20355 Hamburg, Germany
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94
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Olbrich C, Jansen TLC, Liebers J, Aghtar M, Strümpfer J, Schulten K, Knoester J, Kleinekathöfer U. From atomistic modeling to excitation transfer and two-dimensional spectra of the FMO light-harvesting complex. J Phys Chem B 2011; 115:8609-21. [PMID: 21635010 PMCID: PMC3140161 DOI: 10.1021/jp202619a] [Citation(s) in RCA: 183] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The experimental observation of long-lived quantum coherences in the Fenna-Matthews-Olson (FMO) light-harvesting complex at low temperatures has challenged general intuition in the field of complex molecular systems and provoked considerable theoretical effort in search of explanations. Here we report on room-temperature calculations of the excited-state dynamics in FMO using a combination of molecular dynamics simulations and electronic structure calculations. Thus we obtain trajectories for the Hamiltonian of this system which contains time-dependent vertical excitation energies of the individual bacteriochlorophyll molecules and their mutual electronic couplings. The distribution of energies and couplings is analyzed together with possible spatial correlations. It is found that in contrast to frequent assumptions the site energy distribution is non-Gaussian. In a subsequent step, averaged wave packet dynamics is used to determine the exciton dynamics in the system. Finally, with the time-dependent Hamiltonian, linear and two-dimensional spectra are determined. The thus-obtained linear absorption line shape agrees well with experimental observation and is largely determined by the non-Gaussian site energy distribution. The two-dimensional spectra are in line with what one would expect by extrapolation of the experimental observations at lower temperatures and indicate almost total loss of long-lived coherences.
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95
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Olbrich C, Strümpfer J, Schulten K, Kleinekathöfer U. Theory and Simulation of the Environmental Effects on FMO Electronic Transitions. J Phys Chem Lett 2011; 2011:1771-1776. [PMID: 21804928 PMCID: PMC3144632 DOI: 10.1021/jz2007676] [Citation(s) in RCA: 127] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Long-lived quantum coherence has been experimentally observed in the Fenna-Matthews-Olson (FMO) light-harvesting complex. It is much debated which role thermal effects play and if the observed low-temperature behavior arises also at physiological temperature. To contribute to this debate we use molecular dynamics simulations to study the coupling between the protein environment and the vertical excitation energies of individual bacteriochlorophyll molecules in the FMO complex of the green sulphur bacterium Chlorobaculum tepidum. The so-called spectral densities, which account for the environmental influence on the excited state dynamics, are determined from temporal autocorrelation functions of the energy gaps between ground and first excited states of the individual pigments. Although the overall shape of the spectral density is found to be rather similar for all pigments, variations in their magnitude can be seen. Differences between the spectral densities for the pigments of the FMO monomer and FMO trimer are also presented.
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Affiliation(s)
- Carsten Olbrich
- School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Johan Strümpfer
- Center for Biophysics and Computational Biology and Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Klaus Schulten
- Center for Biophysics and Computational Biology and Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Ulrich Kleinekathöfer
- School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
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96
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Mennucci B, Curutchet C. The role of the environment in electronic energy transfer: a molecular modeling perspective. Phys Chem Chem Phys 2011; 13:11538-50. [PMID: 21597605 DOI: 10.1039/c1cp20601j] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The key role of the environment in electronic energy transfer has been underscored in recent experimental and theoretical studies. In this perspective, we provide an overview of novel quantum-mechanical methodologies aimed at describing environment effects in energy transfers. The techniques described include continuum dielectric and atomistic descriptions of the surroundings. We discuss the advantages and limitations of each technique, as well as the main insights that have emerged from their application to solvated dyads and photosynthetic pigment-protein complexes. We finally highlight the aspects that still need to be solved in order to provide a full theoretical route to the study of energy transfer phenomena in complex environments.
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Affiliation(s)
- Benedetta Mennucci
- Department of Chemistry, University of Pisa, via Risorgimento 35, 56126 Pisa, Italy.
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97
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Strümpfer J, Schulten K. The effect of correlated bath fluctuations on exciton transfer. J Chem Phys 2011; 134:095102. [PMID: 21385000 PMCID: PMC3064689 DOI: 10.1063/1.3557042] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2010] [Accepted: 02/01/2011] [Indexed: 01/27/2023] Open
Abstract
Excitation dynamics of various light harvesting systems have been investigated with many theoretical methods including various non-Markovian descriptions of dissipative quantum dynamics. It is typically assumed that each excited state is coupled to an independent thermal environment, i.e., that fluctuations in different environments are uncorrelated. Here the assumption is dropped and the effect of correlated bath fluctuations on excitation transfer is investigated. Using the hierarchy equations of motion for dissipative quantum dynamics it is shown for models of the B850 bacteriochlorophylls of LH2 that correlated bath fluctuations have a significant effect on the LH2→LH2 excitation transfer rate. It is also demonstrated that inclusion of static disorder is crucial for an accurate description of transfer dynamics.
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Affiliation(s)
- Johan Strümpfer
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, USA
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