1
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Sokolov M, Hoffmann DS, Dohmen PM, Krämer M, Höfener S, Kleinekathöfer U, Elstner M. Non-adiabatic molecular dynamics simulations provide new insights into the exciton transfer in the Fenna-Matthews-Olson complex. Phys Chem Chem Phys 2024. [PMID: 38979564 DOI: 10.1039/d4cp02116a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
A trajectory surface hopping approach, which uses machine learning to speed up the most time-consuming steps, has been adopted to investigate the exciton transfer in light-harvesting systems. The present neural networks achieve high accuracy in predicting both Coulomb couplings and excitation energies. The latter are predicted taking into account the environment of the pigments. Direct simulation of exciton dynamics through light-harvesting complexes on significant time scales is usually challenging due to the coupled motion of nuclear and electronic degrees of freedom in these rather large systems containing several relatively large pigments. In the present approach, however, we are able to evaluate a statistically significant number of non-adiabatic molecular dynamics trajectories with respect to exciton delocalization and exciton paths. The formalism is applied to the Fenna-Matthews-Olson complex of green sulfur bacteria, which transfers energy from the light-harvesting chlorosome to the reaction center with astonishing efficiency. The system has been studied experimentally and theoretically for decades. In total, we were able to simulate non-adiabatically more than 30 ns, sampling also the relevant space of parameters within their uncertainty. Our simulations show that the driving force supplied by the energy landscape resulting from electrostatic tuning is sufficient to funnel the energy towards site 3, from where it can be transferred to the reaction center. However, the high efficiency of transfer within a picosecond timescale can be attributed to the rather unusual properties of the BChl a molecules, resulting in very low inner and outer-sphere reorganization energies, not matched by any other organic molecule, e.g., used in organic electronics. A comparison with electron and exciton transfer in organic materials is particularly illuminating, suggesting a mechanism to explain the comparably high transfer efficiency.
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Affiliation(s)
- Monja Sokolov
- Institute of Physical Chemistry (IPC), Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany.
| | - David S Hoffmann
- Institute of Physical Chemistry (IPC), Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany.
| | - Philipp M Dohmen
- Institute of Physical Chemistry (IPC), Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany.
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany
| | - Mila Krämer
- Institute of Physical Chemistry (IPC), Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany.
| | - Sebastian Höfener
- Institute of Physical Chemistry (IPC), Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany.
| | | | - Marcus Elstner
- Institute of Physical Chemistry (IPC), Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany.
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2
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Runeson JE, Fay TP, Manolopoulos DE. Exciton dynamics from the mapping approach to surface hopping: comparison with Förster and Redfield theories. Phys Chem Chem Phys 2024; 26:4929-4938. [PMID: 38265093 PMCID: PMC10849040 DOI: 10.1039/d3cp05926j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 01/03/2024] [Indexed: 01/25/2024]
Abstract
We compare the recently introduced multi-state mapping approach to surface hopping (MASH) with the Förster and Redfield theories of excitation energy transfer. Whereas Förster theory relies on weak coupling between chromophores, and Redfield theory assumes the electronic excitations to be weakly coupled to fast chromophore vibrations, MASH is free from any perturbative or Markovian approximations. We illustrate this with an example application to the rate of energy transfer in a Frenkel-exciton dimer, showing that MASH interpolates correctly between the opposing regimes in which the Förster and Redfield results are reliable. We then compare the three methods for a realistic model of the Fenna-Matthews-Olson complex with a structured vibrational spectral density and static disorder in the excitation energies. In this case there are no exact results for comparison so we use MASH to assess the validity of Förster and Redfield theories. We find that Förster theory is the more accurate of the two on the picosecond timescale, as has been shown previously for a simpler model of this particular light-harvesting complex. We also explore various ways to sample the initial electronic state in MASH and find that they all give very similar results for exciton dynamics.
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Affiliation(s)
- Johan E Runeson
- Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford, OX1 3QZ, UK.
| | - Thomas P Fay
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - David E Manolopoulos
- Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford, OX1 3QZ, UK.
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3
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Götze JP, Maity S, Kleinekathöfer U. Incoherent Energy Transfer between the Baseplate and FMO Protein Explored at Ideal Geometries. J Phys Chem B 2023; 127:7829-7838. [PMID: 37691433 DOI: 10.1021/acs.jpcb.3c02568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
The Förster resonance energy transfer (FRET) between the Fenna-Matthews-Olson (FMO) protein complex and the chlorosomal baseplate (CBP) is investigated by using an idealized model. This simplified model is based on crystal structure and molecular dynamics conformations. Some of the further input, such as the transition dipole moments, was extracted from earlier molecular-level simulations. The resulting model mimics the effects of the relative position between the CBP and the FMO complex on the corresponding FRET efficiency under ideal conditions, involving about 1.3 billion FRET calculations per investigated model. In this idealized model and employing some approximations, it is found that FRET efficiency is almost completely independent of the FMO trimer orientation (displacement, distance, and rotation), despite FMO and CBP being highly structured complexes. Even removing individual FMO BChl triples will only reduce the FRET efficiency by up to 8.6%. An FMO containing only the least efficient BChl triple will retain about 25% of the FRET efficiency of a full FMO complex. In addition to its proposed function as an energetic funnel, FMO is thus identified to act as a highly robust spatial funnel for CBP excitation harvesting, independent of the mutual CBP-FMO orientation.
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Affiliation(s)
- Jan P Götze
- Institut für Chemie und Biochemie, Physikalische und Theoretische Chemie, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
| | - Sayan Maity
- School of Science, Constructor University, Campusring 1, 28759 Bremen, Germany
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4
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Fujihashi Y, Miwa K, Higashi M, Ishizaki A. Probing exciton dynamics with spectral selectivity through the use of quantum entangled photons. J Chem Phys 2023; 159:114201. [PMID: 37712788 DOI: 10.1063/5.0169768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 08/28/2023] [Indexed: 09/16/2023] Open
Abstract
Quantum light is increasingly recognized as a promising resource for developing optical measurement techniques. Particular attention has been paid to enhancing the precision of the measurements beyond classical techniques by using nonclassical correlations between quantum entangled photons. Recent advances in the quantum optics technology have made it possible to manipulate spectral and temporal properties of entangled photons, and photon correlations can facilitate the extraction of matter information with relatively simple optical systems compared to conventional schemes. In these respects, the applications of entangled photons to time-resolved spectroscopy can open new avenues for unambiguously extracting information on dynamical processes in complex molecular and materials systems. Here, we propose time-resolved spectroscopy in which specific signal contributions are selectively enhanced by harnessing nonclassical correlations of entangled photons. The entanglement time characterizes the mutual delay between an entangled twin and determines the spectral distribution of photon correlations. The entanglement time plays a dual role as the knob for controlling the accessible time region of dynamical processes and the degrees of spectral selectivity. In this sense, the role of the entanglement time is substantially equivalent to the temporal width of the classical laser pulse. The results demonstrate that the application of quantum entangled photons to time-resolved spectroscopy leads to monitoring dynamical processes in complex molecular and materials systems by selectively extracting desired signal contributions from congested spectra. We anticipate that more elaborately engineered photon states would broaden the availability of quantum light spectroscopy.
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Affiliation(s)
- Yuta Fujihashi
- Department of Molecular Engineering, Kyoto University, Kyoto 615-8510, Japan
- PRESTO, Japan Science and Technology Agency, Kawaguchi 332-0012, Japan
| | - Kuniyuki Miwa
- Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki 444-8585, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Okazaki 444-8585, Japan
| | - Masahiro Higashi
- Department of Molecular Engineering, Kyoto University, Kyoto 615-8510, Japan
- PRESTO, Japan Science and Technology Agency, Kawaguchi 332-0012, Japan
| | - Akihito Ishizaki
- Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki 444-8585, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Okazaki 444-8585, Japan
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5
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Kim Y, Mitchell Z, Lawrence J, Morozov D, Savikhin S, Slipchenko LV. Predicting Mutation-Induced Changes in the Electronic Properties of Photosynthetic Proteins from First Principles: The Fenna-Matthews-Olson Complex Example. J Phys Chem Lett 2023; 14:7038-7044. [PMID: 37524046 DOI: 10.1021/acs.jpclett.3c01461] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Multiscale molecular modeling is utilized to predict optical absorption and circular dichroism spectra of two single-point mutants of the Fenna-Matthews-Olson photosynthetic pigment-protein complex. The modeling approach combines classical molecular dynamics simulations with structural refinement of photosynthetic pigments and calculations of their excited states in a polarizable protein environment. The only experimental input to the modeling protocol is the X-ray structure of the wild-type protein. The first-principles modeling reproduces changes in the experimental optical spectra of the considered mutants, Y16F and Q198V. Interestingly, the Q198V mutation has a negligible effect on the electronic properties of the targeted bacteriochlorophyll a pigment. Instead, the electronic properties of several other pigments respond to this mutation. The molecular modeling demonstrates that a single-point mutation can induce long-range effects on the protein structure, while extensive structural changes near a pigment do not necessarily lead to significant changes in the electronic properties of that pigment.
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Affiliation(s)
- Yongbin Kim
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Zach Mitchell
- Department of Physics and Astronomy, Purdue University, 525 Northwestern Avenue, West Lafayette, Indiana 47907, United States
| | - Jack Lawrence
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Dmitry Morozov
- Nanoscience Center and Department of Chemistry, University of Jyväskylä, P.O. Box 35, 40014 Jyväskylä, Finland
| | - Sergei Savikhin
- Department of Physics and Astronomy, Purdue University, 525 Northwestern Avenue, West Lafayette, Indiana 47907, United States
| | - Lyudmila V Slipchenko
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
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6
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Delgado F, Enríquez M. Quantum Entanglement and State-Transference in Fenna-Matthews-Olson Complexes: A Post-Experimental Simulation Analysis in the Computational Biology Domain. Int J Mol Sci 2023; 24:10862. [PMID: 37446061 DOI: 10.3390/ijms241310862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/13/2023] [Accepted: 06/27/2023] [Indexed: 07/15/2023] Open
Abstract
Fenna-Mathews-Olson complexes participate in the photosynthetic process of Sulfur Green Bacteria. These biological subsystems exhibit quantum features which possibly are responsible for their high efficiency; the latter may comprise multipartite entanglement and the apparent tunnelling of the initial quantum state. At first, to study these aspects, a multidisciplinary approach including experimental biology, spectroscopy, physics, and math modelling is required. Then, a global computer modelling analysis is achieved in the computational biology domain. The current work implements the Hierarchical Equations of Motion to numerically solve the open quantum system problem regarding this complex. The time-evolved states obtained with this method are then analysed under several measures of entanglement, some of them already proposed in the literature. However, for the first time, the maximum overlap with respect to the closest separable state is employed. This authentic multipartite entanglement measure provides information on the correlations, not only based on the system bipartitions as in the usual analysis. Our study has led us to note a different view of FMO multipartite entanglement as tiny contributions to the global entanglement suggested by other more basic measurements. Additionally, in another related trend, the initial state, considered as a Förster Resonance Energy Transfer, is tracked using a novel approach, considering how it could be followed under the fidelity measure on all possible permutations of the FMO subsystems through its dynamical evolution by observing the tunnelling in the most probable locations. Both analyses demanded significant computational work, making for a clear example of the complexity required in computational biology.
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Affiliation(s)
- Francisco Delgado
- School of Engineering and Sciences, Tecnologico de Monterrey, Atizapan 52926, Mexico
| | - Marco Enríquez
- School of Engineering and Sciences, Tecnologico de Monterrey, Santa Fe 01389, Mexico
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7
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Hu Z, Liu Z, Sun X. Effects of Heterogeneous Protein Environment on Excitation Energy Transfer Dynamics in the Fenna-Matthews-Olson Complex. J Phys Chem B 2022; 126:9271-9287. [PMID: 36327977 DOI: 10.1021/acs.jpcb.2c06605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The Fenna-Matthews-Olson (FMO) complex of green sulfur bacteria has been serving as a prototypical light-harvesting protein for studying excitation energy transfer (EET) dynamics in photosynthesis. The most widely used Frenkel exciton model for FMO complex assumes that each excited bacteriochlorophyll site couples to an identical and isolated harmonic bath, which does not account for the heterogeneous local protein environment. To better describe the realistic environment, we propose to use the recently developed multistate harmonic (MSH) model, which contains a globally shared bath that couples to the different pigment sites according to the atomistic quantum mechanics/molecular mechanics simulations with explicit protein scaffold and solvent. In this work, the effects of heterogeneous protein environment on EET in FMO complexes from Prosthecochloris aestuarii and Chlorobium tepidum, specifically including realistic spectral density, site-dependent reorganization energies, and system-bath couplings are investigated. Semiclassical and mixed quantum-classical mapping dynamics were applied to obtain the nonadiabatic EET dynamics in several models ranging from the Frenkel exciton model to the MSH model and their variants. The MSH model with realistic spectral density and site-dependent system-bath couplings displays slower EET dynamics than the Frenkel exciton model. Our comparative study shows that larger average reorganization energy, heterogeneity in spectral densities, and low-frequency modes could facilitate energy dissipation, which is insensitive to the static disorder in reorganization energies. The effects of the spectral densities and system-bath couplings along with the MSH model can be used to optimize EET dynamics for artificial light-harvesting systems.
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Affiliation(s)
- Zhubin Hu
- Division of Arts and Sciences, NYU Shanghai, 1555 Century Avenue, Shanghai 200122, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, 3663 Zhongshan Road North, Shanghai 200062, China.,State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China
| | - Zengkui Liu
- Division of Arts and Sciences, NYU Shanghai, 1555 Century Avenue, Shanghai 200122, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, 3663 Zhongshan Road North, Shanghai 200062, China.,Department of Chemistry, New York University, New York, New York 10003, United States
| | - Xiang Sun
- Division of Arts and Sciences, NYU Shanghai, 1555 Century Avenue, Shanghai 200122, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, 3663 Zhongshan Road North, Shanghai 200062, China.,State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China.,Department of Chemistry, New York University, New York, New York 10003, United States
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8
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Abstract
Nonadiabatic quantum dynamics is important for understanding light-harvesting processes, but its propagation with traditional methods can be rather expensive. Here we present a one-shot trajectory learning approach that allows us to directly make an ultrafast prediction of the entire trajectory of the reduced density matrix for a new set of such simulation parameters as temperature and reorganization energy. The whole 10-ps-long propagation takes 70 ms as we demonstrate on the comparatively large quantum system, the Fenna-Matthews-Olsen (FMO) complex. Our approach also significantly reduces time and memory requirements for training.
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Affiliation(s)
- Arif Ullah
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Department of Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Pavlo O Dral
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Department of Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
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9
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Runeson JE, Lawrence JE, Mannouch JR, Richardson JO. Explaining the Efficiency of Photosynthesis: Quantum Uncertainty or Classical Vibrations? J Phys Chem Lett 2022; 13:3392-3399. [PMID: 35404611 PMCID: PMC9036581 DOI: 10.1021/acs.jpclett.2c00538] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 04/01/2022] [Indexed: 06/14/2023]
Abstract
Photosynthetic organisms are known to use a mechanism of vibrationally assisted exciton energy transfer to efficiently harvest energy from light. The importance of quantum effects in this mechanism is a long-standing topic of debate, which has traditionally focused on the role of excitonic coherences. Here, we address another recent claim: that the efficient energy transfer in the Fenna-Matthews-Olson complex relies on nuclear quantum uncertainty and would not function if the vibrations were classical. We present a counter-example to this claim, showing by trajectory-based simulations that a description in terms of quantum electrons and classical nuclei is indeed sufficient to describe the funneling of energy to the reaction center. We analyze and compare these findings to previous classical-nuclear approximations that predicted the absence of an energy funnel and conclude that the key difference and the reason for the discrepancy is the ability of the trajectories to properly account for Newton's third law.
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10
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Predicting the future of excitation energy transfer in light-harvesting complex with artificial intelligence-based quantum dynamics. Nat Commun 2022; 13:1930. [PMID: 35411054 PMCID: PMC9001686 DOI: 10.1038/s41467-022-29621-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 03/16/2022] [Indexed: 01/20/2023] Open
Abstract
Exploring excitation energy transfer (EET) in light-harvesting complexes (LHCs) is essential for understanding the natural processes and design of highly-efficient photovoltaic devices. LHCs are open systems, where quantum effects may play a crucial role for almost perfect utilization of solar energy. Simulation of energy transfer with inclusion of quantum effects can be done within the framework of dissipative quantum dynamics (QD), which are computationally expensive. Thus, artificial intelligence (AI) offers itself as a tool for reducing the computational cost. Here we suggest AI-QD approach using AI to directly predict QD as a function of time and other parameters such as temperature, reorganization energy, etc., completely circumventing the need of recursive step-wise dynamics propagation in contrast to the traditional QD and alternative, recursive AI-based QD approaches. Our trajectory-learning AI-QD approach is able to predict the correct asymptotic behavior of QD at infinite time. We demonstrate AI-QD on seven-sites Fenna–Matthews–Olson (FMO) complex. Simulations of energy transfer in light-harvesting complexes are computationally very demanding. Here the authors apply an artificial intelligence quantum dissipative algorithm to study the excited state energy transfer dynamics in a light-harvesting complex.
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11
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ZHU ZHE, Higashi M, Saito S. Excited states of chlorophyll a and b in solution by time-dependent density functional theory. J Chem Phys 2022; 156:124111. [DOI: 10.1063/5.0083395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The ground state and excited state electronic properties of chlorophyll (Chl) a and Chl b in diethyl ether, acetone, and ethanol solutions are investigated using quantum mechanical and molecular mechanical calculations with density functional theory (DFT) and time-dependent DFT (TDDFT). Although the DFT/TDDFT methods are widely used, the electronic structures of molecules, especially large molecules, calculated with these methods are known to be strongly dependent on the functionals and the parameters used in functionals. Here, we optimize the range-separated parameter, µ, of the CAM-B3LYP functional of Chl a and Chl b to reproduce the experimental excitation energy differences of these Chl molecules in solution. The optimal values of µ for Chl a and Chl b are smaller than the default value of µ and that for bacteriochlorophyll a, indicating the change in electronic distribution, i.e., an increase in electron delocalization, within the molecule. We find that the electronic distribution of Chl b with an extra formyl group is different from that of Chl a. We also find that the polarity of solution and hydrogen bond cause the decrease in the excitation energies and the increase in the widths of excitation energy distributions of Chl a and Chl b. The present results are expected to be useful for understanding the electronic properties of each pigment molecule in a local heterogeneous environment, which will play an important role in the excitation energy transfer in light-harvesting complex II.
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Affiliation(s)
| | - Masahiro Higashi
- Department of Molecular Engineering, Kyoto University - Katsura Campus, Japan
| | - Shinji Saito
- Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Japan
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12
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Cui X, Yan Y, Wei J. Role of Pigment-Protein Coupling in the Energy Transport Dynamics in the Fenna-Matthews-Olson Complex. J Phys Chem B 2021; 125:11884-11892. [PMID: 34669415 DOI: 10.1021/acs.jpcb.1c06844] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The role of pigment-protein coupling in the dynamics of photosynthetic energy transport in chromophoric complexes has not been fully understood. The excitation energy transfer in the photosynthetic system is tremendously efficient. In particular, we investigate the excitation energy transport in the Fenna-Matthews-Olson (FMO) complex. The exciton dynamics and excitation energy transfer (EET) depend on the interaction between the excited chromophores and their environment. Most theoretical models believe that all bacteriochlorophyll-a (BChla) sites are surrounded by the same local protein environment, which is contradicted by the structural analysis of the FMO complex. Based on different values of pigment-protein coupling for different sites, measured in the adiabatic limit, we have theoretically investigated the effect of the heterogeneous local protein environment on the EET process. By the realistic and site-dependent model of the system-bath couplings, the results show that this interaction may have a critical value for the coherent energy-transfer process. Furthermore, we verify that the two transport pathways are coherent and stable to the important parameter reorganization energy of environmental interactions. The quantum dynamical simulations show that the correlation fluctuation keeps the oscillation of the coherent excitation on a long timescale. In addition, due to the inhomogeneous pigment-protein coupling, different BChl sites have asymmetric excitation oscillation timescales.
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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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13
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Huai Z, Tong Z, Mei Y, Mo Y. Theoretical Study of the Spectral Differences of the Fenna-Matthews-Olson Protein from Different Species and Their Mutants. J Phys Chem B 2021; 125:8313-8324. [PMID: 34314175 DOI: 10.1021/acs.jpcb.1c01686] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The structural basis for the spectral differences between the Fenna-Matthews-Olson (FMO) proteins from Chlorobaculum tepidum (C. tepidum) and Prosthecochloris aestuarii 2K (P. aestuarii) is yet to be fully understood. Mutation-induced perturbation to the exciton structure and the optical spectra of the complex provide a suitable means to investigate the critical role played by the protein scaffold. In this work, we have performed quantum-mechanics/molecular-mechanics calculations over the molecular dynamics simulation trajectories with the polarized protein-specific charge scheme for both wild-type FMOs and two mutants. Our result reveals that a single-point mutation in the vicinity of BChl 6, namely, W183F of C. tepidum, significantly affects the absorption spectrum, resulting in a switch of the absorption spectrum from type 2, for which the 806 nm band is more pronounced than the 815 nm band, to type 1, for which the 815 nm band is pronounced. Our observations agree with the single-point mutation experiments reported by Saer et al. (Biochim. Biophys. Acta, Bioenerg. 2017, 1858, 288-296) and Khmelnitskiy et al. (J. Phys. Chem. Lett. 2018, 9, 3378-3386). In contrast, the absorption spectrum of the P. aestuarii experiences the opposite transition (from type 1 to type 2) upon the same mutation. Furthermore, by comparing the contributions of individual pigments to the spectra in the wild type and its mutant, we find that a single-point mutation near BChl 6 not only induces changes in excitation energy of BChl 6 per se but also affects the excitonic structures of the neighboring BChls 5 and 7 through strong interpigment electronic couplings, resulting in a significant change in the absorption spectra.
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Affiliation(s)
- Zhe Huai
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200062, China
| | - Zhengqing Tong
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200062, China
| | - Ye Mei
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200062, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China.,Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
| | - Yan Mo
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200062, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China.,Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
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14
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Renger T. Semiclassical Modified Redfield and Generalized Förster Theories of Exciton Relaxation/Transfer in Light-Harvesting Complexes: The Quest for the Principle of Detailed Balance. J Phys Chem B 2021; 125:6406-6416. [PMID: 34126008 PMCID: PMC8237266 DOI: 10.1021/acs.jpcb.1c01479] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
A conceptual problem
of transfer theories that use a semiclassical
description of the electron-vibrational coupling is the neglect of
the correlation between momenta and coordinates of nuclei. In the
Redfield theory of exciton relaxation, this neglect leads to a violation
of the principle of detailed balance; equal “uphill”
and “downhill” transfer rate constants are obtained.
Here, we investigate how this result depends on nuclear reorganization
effects, neglected in Redfield but taken into account in the modified
Redfield theory. These reorganization effects, resulting from a partial
localization of excited states, are found to promote a preferential
“downhill” relaxation of excitation energy. However,
for realistic spectral densities of light-harvesting antennae in photosynthesis,
the reorganization effects are too small to compensate for the missing
coordinate–momentum uncertainty. For weaker excitonic couplings
as they occur between domains of strongly coupled pigments, we find
the principle of detailed balance to be fulfilled in a semiclassical
variant of the generalized Förster theory. A qualitatively
correct description of the transfer is obtained with this theory at
a significantly lower computational cost as with the quantum generalized
Förster theory. Larger deviations between the two theories
are expected for large energy gaps as they occur in complexes with
chemically different pigments.
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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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15
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Lokstein H, Renger G, Götze JP. Photosynthetic Light-Harvesting (Antenna) Complexes-Structures and Functions. Molecules 2021; 26:molecules26113378. [PMID: 34204994 PMCID: PMC8199901 DOI: 10.3390/molecules26113378] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 02/07/2023] Open
Abstract
Chlorophylls and bacteriochlorophylls, together with carotenoids, serve, noncovalently bound to specific apoproteins, as principal light-harvesting and energy-transforming pigments in photosynthetic organisms. In recent years, enormous progress has been achieved in the elucidation of structures and functions of light-harvesting (antenna) complexes, photosynthetic reaction centers and even entire photosystems. It is becoming increasingly clear that light-harvesting complexes not only serve to enlarge the absorption cross sections of the respective reaction centers but are vitally important in short- and long-term adaptation of the photosynthetic apparatus and regulation of the energy-transforming processes in response to external and internal conditions. Thus, the wide variety of structural diversity in photosynthetic antenna “designs” becomes conceivable. It is, however, common for LHCs to form trimeric (or multiples thereof) structures. We propose a simple, tentative explanation of the trimer issue, based on the 2D world created by photosynthetic membrane systems.
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Affiliation(s)
- Heiko Lokstein
- Department of Chemical Physics and Optics, Charles University, Ke Karlovu 3, 12116 Prague, Czech Republic
- Correspondence:
| | - Gernot Renger
- Max-Volmer-Laboratorium, Technische Universität Berlin, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Jan P. Götze
- Institut für Chemie und Biochemie, Freie Universität Berlin, Arnimallee 22, D-14195 Berlin, Germany;
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16
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Rolczynski BS, Yeh SH, Navotnaya P, Lloyd LT, Ginzburg AR, Zheng H, Allodi MA, Otto JP, Ashraf K, Gardiner AT, Cogdell RJ, Kais S, Engel GS. Time-Domain Line-Shape Analysis from 2D Spectroscopy to Precisely Determine Hamiltonian Parameters for a Photosynthetic Complex. J Phys Chem B 2021; 125:2812-2820. [PMID: 33728918 DOI: 10.1021/acs.jpcb.0c08012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Optical signals come from coherences between quantum states, with spectral line widths determined by the coherences' dephasing dynamics. Using a 2D electronic spectrometer, we observe weak coherence- and rephasing-time-domain signals persisting to 1 ps in the Fenna-Matthews-Olson complex at 77 K. These are coherences between the ground and excited states prepared after the complex interacts once or three times with light, rather than zero-quantum coherences that are more frequently investigated following two interactions. Here, we use these small but persistent signal components to isolate spectral contributions with narrowed peaks and reveal the system's eigenenergies.
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Affiliation(s)
- Brian S Rolczynski
- Department of Chemistry, The Institute for Biophysical Dynamics, and The James Franck Institute, The University of Chicago, Chicago, Illinois 60637, United States
| | - Shu-Hao Yeh
- Department of Chemistry, The Institute for Biophysical Dynamics, and The James Franck Institute, The University of Chicago, Chicago, Illinois 60637, United States.,Qatar Environment and Energy Research Institute, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
| | - Polina Navotnaya
- Department of Chemistry, The Institute for Biophysical Dynamics, and The James Franck Institute, The University of Chicago, Chicago, Illinois 60637, United States
| | - Lawson T Lloyd
- Department of Chemistry, The Institute for Biophysical Dynamics, and The James Franck Institute, The University of Chicago, Chicago, Illinois 60637, United States
| | - Alan R Ginzburg
- Department of Chemistry, The Institute for Biophysical Dynamics, and The James Franck Institute, The University of Chicago, Chicago, Illinois 60637, United States
| | - Haibin Zheng
- Department of Chemistry, The Institute for Biophysical Dynamics, and The James Franck Institute, The University of Chicago, Chicago, Illinois 60637, United States
| | - Marco A Allodi
- Department of Chemistry, The Institute for Biophysical Dynamics, and The James Franck Institute, The University of Chicago, Chicago, Illinois 60637, United States
| | - John P Otto
- Department of Chemistry, The Institute for Biophysical Dynamics, and The James Franck Institute, The University of Chicago, Chicago, Illinois 60637, United States
| | - Khuram Ashraf
- Institute of Biomedical and Life Sciences, Glasgow Biomedical Research Centre, University of Glasgow, Glasgow G12 8QQ, Scotland, United Kingdom
| | - Alastair T Gardiner
- Institute of Biomedical and Life Sciences, Glasgow Biomedical Research Centre, University of Glasgow, Glasgow G12 8QQ, Scotland, United Kingdom
| | - Richard J Cogdell
- Institute of Biomedical and Life Sciences, Glasgow Biomedical Research Centre, University of Glasgow, Glasgow G12 8QQ, Scotland, United Kingdom
| | - Sabre Kais
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Gregory S Engel
- Department of Chemistry, The Institute for Biophysical Dynamics, and The James Franck Institute, The University of Chicago, Chicago, Illinois 60637, United States
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17
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Reinot T, Khmelnitskiy A, Kell A, Jassas M, Jankowiak R. Exciton Lifetime Distributions and Population Dynamics in the FMO Protein Complex from Prosthecochloris aestuarii. ACS OMEGA 2021; 6:5990-6008. [PMID: 33681637 PMCID: PMC7931385 DOI: 10.1021/acsomega.1c00286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 02/09/2021] [Indexed: 06/12/2023]
Abstract
Significant protein rearrangement upon excitation and energy transfer in Fenna-Matthews-Olson protein of Prosthecochloris aestuarii results in a modified energy landscape, which induces more changes in pigment site energies than predicted by the "standard" hole-burning theory. The energy changes are elucidated by simulations while investigating the effects of site-dependent disorder, both static (site-energy distribution widths) and dynamic (spectral density shapes). The resulting optimized site energies and their fluctuations are consistent with relative differences observed in inhomogeneous widths calculated by recent molecular dynamic simulations. Two sets of different spectral densities reveal how their shapes affect the population dynamics and distribution of exciton lifetimes. Calculations revealed the wavelength-dependent distributions of exciton lifetimes (T 1) in the femtosecond to picosecond time frame. We suggest that the calculated multimodal and asymmetric wavelength-dependent T 1 distributions offer more insight into the interpretation of resonant hole-burned (HB) spectra, kinetic traces in two-dimensional (2D) electronic spectroscopy experiments, and widely used global analyses in fitting data from transient absorption experiments.
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Affiliation(s)
- Tonu Reinot
- Department
of Chemistry, Department of Physics, Kansas State University, Manhattan, Kansas 66506, United States
| | - Anton Khmelnitskiy
- Department
of Chemistry, Department of Physics, Kansas State University, Manhattan, Kansas 66506, United States
| | - Adam Kell
- Department
of Chemistry, Department of Physics, Kansas State University, Manhattan, Kansas 66506, United States
| | - Mahboobe Jassas
- Department
of Chemistry, Department of Physics, Kansas State University, Manhattan, Kansas 66506, United States
| | - Ryszard Jankowiak
- Department
of Chemistry, Department of Physics, Kansas State University, Manhattan, Kansas 66506, United States
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18
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Chaillet M, Lengauer F, Adolphs J, Müh F, Fokas AS, Cole DJ, Chin AW, Renger T. Static Disorder in Excitation Energies of the Fenna-Matthews-Olson Protein: Structure-Based Theory Meets Experiment. J Phys Chem Lett 2020; 11:10306-10314. [PMID: 33227205 PMCID: PMC7751012 DOI: 10.1021/acs.jpclett.0c03123] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 11/17/2020] [Indexed: 06/11/2023]
Abstract
Inhomogeneous broadening of optical lines of the Fenna-Matthews-Olson (FMO) light-harvesting protein is investigated by combining a Monte Carlo sampling of low-energy conformational substates of the protein with a quantum chemical/electrostatic calculation of local transition energies (site energies) of the pigments. The good agreement between the optical spectra calculated for the inhomogeneous ensemble and the experimental data demonstrates that electrostatics is the dominant contributor to static disorder in site energies. Rotamers of polar amino acid side chains are found to cause bimodal distribution functions of site energy shifts, which can be probed by hole burning and single-molecule spectroscopy. When summing over the large number of contributions, the resulting distribution functions of the site energies become Gaussians, and the correlations in site energy fluctuations at different sites practically average to zero. These results demonstrate that static disorder in the FMO protein is in the realm of the central limit theorem of statistics.
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Affiliation(s)
- Marten
L. Chaillet
- Bijvoet
Centre for Biomolecular Research, University
of Utrecht, Heidelberglaan 8, 3584 CS Utrecht, The Netherlands
| | - Florian Lengauer
- Institute
of Theoretical Physics, Johannes Kepler
University Linz, Altenberger Str. 69, 4040 Linz, Austria
| | - Julian Adolphs
- Leibniz
Institute for Agricultural Engineering and Bioeconomy, Max-Eyth-Allee 100, 14469 Potsdam, Germany
| | - Frank Müh
- Institute
of Theoretical Physics, Johannes Kepler
University Linz, Altenberger Str. 69, 4040 Linz, Austria
| | - Alexander S. Fokas
- TCM
Group, Cavendish Laboratory, 19 J. J. Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Daniel J. Cole
- School
of Natural and Environmental Sciences, Newcastle
University, Newcastle
upon Tyne NE1 7RU, United
Kingdom
| | - Alex W. Chin
- Centre
National de la Recherce Scientifique, Institute des Nanosciences de
Paris, Sorbonne Université, Paris, France
| | - Thomas Renger
- Institute
of Theoretical Physics, Johannes Kepler
University Linz, Altenberger Str. 69, 4040 Linz, Austria
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19
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Klinger A, Lindorfer D, Müh F, Renger T. Normal mode analysis of spectral density of FMO trimers: Intra- and intermonomer energy transfer. J Chem Phys 2020; 153:215103. [PMID: 33291900 DOI: 10.1063/5.0027994] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The intermolecular contribution to the spectral density of the exciton-vibrational coupling of the homotrimeric Fenna-Matthews-Olson (FMO) light-harvesting protein of green sulfur bacteria P. aestuarii is analyzed by combining a normal mode analysis of the protein with the charge density coupling method for the calculation of local transition energies of the pigments. Correlations in site energy fluctuations across the whole FMO trimer are found at low vibrational frequencies. Including, additionally, the high-frequency intrapigment part of the spectral density, extracted from line-narrowing spectra, we study intra- and intermonomer exciton transfer. Whereas the intrapigment part of the spectral density is important for fast intramonomer exciton relaxation, the intermolecular contributions (due to pigment-environment coupling) determine the intermonomer exciton transfer. Neither the variations of the local Huang-Rhys factors nor the correlations in site energy fluctuations have a critical influence on energy transfer. At room temperature, the intermonomer transfer in the FMO protein occurs on a 10 ps time scale, whereas intramonomer exciton equilibration is roughly two orders of magnitude faster. At cryogenic temperatures, intermonomer transfer limits the lifetimes of the lowest exciton band. The lifetimes are found to increase between 20 ps in the center of this band up to 100 ps toward lower energies, which is in very good agreement with the estimates from hole burning data. Interestingly, exciton delocalization in the FMO monomers is found to slow down intermonomer energy transfer, at both physiological and cryogenic temperatures.
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Affiliation(s)
- Alexander Klinger
- Institut für Theoretische Physik, Johannes Kepler Universität Linz, Altenberger Str. 69, 4040 Linz, Austria
| | - Dominik Lindorfer
- Institut für Theoretische Physik, Johannes Kepler Universität Linz, Altenberger Str. 69, 4040 Linz, Austria
| | - Frank Müh
- Institut für Theoretische Physik, Johannes Kepler Universität Linz, Altenberger Str. 69, 4040 Linz, Austria
| | - Thomas Renger
- Institut für Theoretische Physik, Johannes Kepler Universität Linz, Altenberger Str. 69, 4040 Linz, Austria
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20
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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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21
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Suzuki Y, Watanabe H, Okiyama Y, Ebina K, Tanaka S. Comparative study on model parameter evaluations for the energy transfer dynamics in Fenna–Matthews–Olson complex. Chem Phys 2020. [DOI: 10.1016/j.chemphys.2020.110903] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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22
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Maity S, Bold BM, Prajapati JD, Sokolov M, Kubař T, Elstner M, Kleinekathöfer U. DFTB/MM Molecular Dynamics Simulations of the FMO Light-Harvesting Complex. J Phys Chem Lett 2020; 11:8660-8667. [PMID: 32991176 DOI: 10.1021/acs.jpclett.0c02526] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Because of the size of light-harvesting complexes and the involvement of electronic degrees of freedom, computationally these systems need to be treated with a combined quantum-classical description. To this end, Born-Oppenheimer molecular dynamics simulations have been employed in a quantum mechanics/molecular mechanics (QM/MM) fashion for the ground state followed by excitation energy calculations again in a QM/MM scheme for the Fenna-Matthews-Olson (FMO) complex. The self-consistent-charge density functional tight-binding (DFTB) method electrostatically coupled to a classical description of the environment was applied to perform the ground-state dynamics. Subsequently, long-range-corrected time-dependent DFTB calculations were performed to determine the excitation energy fluctuations of the individual bacteriochlorophyll a molecules. The spectral densities obtained using this approach show an excellent agreement with experimental findings. In addition, the fluctuating site energies and couplings were used to estimate the exciton transfer dynamics.
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Affiliation(s)
- Sayan Maity
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Beatrix M Bold
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany
| | | | - Monja Sokolov
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany
| | - Tomáš Kubař
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany
| | - Marcus Elstner
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany
- Institute of Biological Interfaces, Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany
| | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
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23
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Singh D, Dasgupta S. Importance of Intermonomer Couplings of the FMO Complex in Coherently Initiated Dynamics. J Phys Chem B 2020; 124:4056-4061. [PMID: 32338901 DOI: 10.1021/acs.jpcb.0c01215] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
In this work, the hierarchical equation of motion approach was employed to study the excitation transfer efficiency (ETE) from the Fenna-Matthews-Olson (FMO) complex to the reaction center core complex (RCC). Further, the realistic initial pure state (created by the interaction of femtosecond laser pulse with the isolated FMO complex) was used in the presence of an inhomogeneous protein environment. We observed the same amount of excitation transfer from the FMO to the RCC, in agreement with the experiment using femtosecond absorption spectroscopy. Simulation analysis shows weak intermonomer couplings are strongly affecting the dynamics of ETE, which implies that all the monomers of the FMO complex need to be considered as connected with the RCC pigment for a better estimate of the ETE.
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Affiliation(s)
- Davinder Singh
- Department of Physics, Indian Institute of Technology Ropar, Rupnagar 140001, Punjab, India
| | - Shubhrangshu Dasgupta
- Department of Physics, Indian Institute of Technology Ropar, Rupnagar 140001, Punjab, India
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24
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Cao J, Cogdell RJ, Coker DF, Duan HG, Hauer J, Kleinekathöfer U, Jansen TLC, Mančal T, Miller RJD, Ogilvie JP, Prokhorenko VI, Renger T, Tan HS, Tempelaar R, Thorwart M, Thyrhaug E, Westenhoff S, Zigmantas D. Quantum biology revisited. SCIENCE ADVANCES 2020; 6:eaaz4888. [PMID: 32284982 PMCID: PMC7124948 DOI: 10.1126/sciadv.aaz4888] [Citation(s) in RCA: 175] [Impact Index Per Article: 43.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 01/06/2020] [Indexed: 05/21/2023]
Abstract
Photosynthesis is a highly optimized process from which valuable lessons can be learned about the operating principles in nature. Its primary steps involve energy transport operating near theoretical quantum limits in efficiency. Recently, extensive research was motivated by the hypothesis that nature used quantum coherences to direct energy transfer. This body of work, a cornerstone for the field of quantum biology, rests on the interpretation of small-amplitude oscillations in two-dimensional electronic spectra of photosynthetic complexes. This Review discusses recent work reexamining these claims and demonstrates that interexciton coherences are too short lived to have any functional significance in photosynthetic energy transfer. Instead, the observed long-lived coherences originate from impulsively excited vibrations, generally observed in femtosecond spectroscopy. These efforts, collectively, lead to a more detailed understanding of the quantum aspects of dissipation. Nature, rather than trying to avoid dissipation, exploits it via engineering of exciton-bath interaction to create efficient energy flow.
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Affiliation(s)
- Jianshu Cao
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Richard J. Cogdell
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Science, University of Glasgow, Glasgow G12 8QQ, UK
| | - David F. Coker
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, MA 02215, USA
| | - Hong-Guang Duan
- Atomically Resolved Dynamics Department, Max Planck Institute for the Structure and Dynamics of Matter, 22761 Hamburg, Germany
- I. Institut für Theoretische Physik, Universität Hamburg, Jungiusstrasse 9, 20355 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, 22761 Hamburg, Germany
| | - Jürgen Hauer
- Technische Universität München, Dynamische Spektroskopien, Fakultät für Chemie, Lichtenbergstr. 4, 85748 Garching, Germany, and Photonics Institute, TU Wien, 1040 Vienna, Austria
| | - Ulrich Kleinekathöfer
- Department of Physics and Earth Science, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Thomas L. C. Jansen
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, Netherlands
| | - Tomáš Mančal
- Faculty of Mathematics and Physics, Charles University, Ke Karlovu 5, CZ-12116 Prague 2, Czech Republic
| | - R. J. Dwayne Miller
- Atomically Resolved Dynamics Department, Max Planck Institute for the Structure and Dynamics of Matter, 22761 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, 22761 Hamburg, Germany
- Departments of Chemistry and Physics, University of Toronto, Toronto, ON M5S 3H6, Canada
| | | | - Valentyn I. Prokhorenko
- Atomically Resolved Dynamics Department, Max Planck Institute for the Structure and Dynamics of Matter, 22761 Hamburg, Germany
| | - Thomas Renger
- Institute of Theoretical Physics, Department of Theoretical Biophysics, Johannes Kepler University Linz, Altenberger Str. 69, 4040 Linz, Austria
| | - Howe-Siang Tan
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore
| | - Roel Tempelaar
- Department of Chemistry, Columbia University, 3000 Broadway, New York, NY 10027, USA
| | - Michael Thorwart
- I. Institut für Theoretische Physik, Universität Hamburg, Jungiusstrasse 9, 20355 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, 22761 Hamburg, Germany
| | - Erling Thyrhaug
- Technische Universität München, Dynamische Spektroskopien, Fakultät für Chemie, Lichtenbergstr. 4, 85748 Garching, Germany, and Photonics Institute, TU Wien, 1040 Vienna, Austria
| | - Sebastian Westenhoff
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg 40530, Sweden
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25
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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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26
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Kim Y, Morozov D, Stadnytskyi V, Savikhin S, Slipchenko LV. Predictive First-Principles Modeling of a Photosynthetic Antenna Protein: The Fenna-Matthews-Olson Complex. J Phys Chem Lett 2020; 11:1636-1643. [PMID: 32013435 DOI: 10.1021/acs.jpclett.9b03486] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
High efficiency of light harvesting in photosynthetic pigment-protein complexes is governed by evolutionary-perfected protein-assisted tuning of individual pigment properties and interpigment interactions. Due to the large number of spectrally overlapping pigments in a typical photosynthetic complex, experimental methods often fail to unambiguously identify individual chromophore properties. Here, we report a first-principles-based modeling protocol capable of predicting properties of pigments in protein environment to a high precision. The technique was applied to successfully uncover electronic properties of the Fenna-Matthews-Olson (FMO) pigment-protein complex. Each of the three subunits of the FMO complex contains eight strongly coupled bacteriochlorophyll a (BChl a) pigments. The excitonic structure of FMO can be described by an electronic Hamiltonian containing excitation (site) energies of BChl a pigments and electronic couplings between them. Several such Hamiltonians have been developed in the past based on the information from various spectroscopic measurements of FMO; however, fine details of the excitonic structure and energy transfer in FMO, especially assignments of short-lived high-energy sites, remain elusive. Utilizing polarizable embedding quantum mechanics/molecular mechanics with the effective fragment potentials, we computed the electronic Hamiltonian of FMO that is in general agreement with previously reported empirical Hamiltonians and quantitatively reproduces experimental absorption and circular dichroism spectra of the FMO protein. The developed computational protocol is sufficiently simple and can be utilized for predictive modeling of other wild-type and mutated photosynthetic pigment-protein complexes.
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Affiliation(s)
- Yongbin Kim
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Dmitry Morozov
- Nanoscience Center and Department of Chemistry, University of Jyväskylä, P.O. Box 35, Jyväskylä 40014, Finland
| | - Valentyn Stadnytskyi
- Department of Physics and Astronomy, Purdue University, 525 Northwestern Avenue, West Lafayette, Indiana 47907, United States
- Laboratory of Chemical Physics, National Institute of Diabetes, Digestion and Kidney Diseases, National Institutes of Health, 5 Memorial Drive, Bethesda, Maryland 20892, United States
| | - Sergei Savikhin
- Department of Physics and Astronomy, Purdue University, 525 Northwestern Avenue, West Lafayette, Indiana 47907, United States
| | - Lyudmila V Slipchenko
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
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27
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Kaliakin DS, Nakata H, Kim Y, Chen Q, Fedorov DG, Slipchenko LV. FMOxFMO: Elucidating Excitonic Interactions in the Fenna-Matthews-Olson Complex with the Fragment Molecular Orbital Method. J Chem Theory Comput 2020; 16:1175-1187. [PMID: 31841349 DOI: 10.1021/acs.jctc.9b00621] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In order to study Förster resonance energy transfer (FRET), the fragment molecular orbital (FMO) method is extended to compute electronic couplings between local excitations via the excited state transition density model, enabling efficient calculations of nonlocal excitations in a large molecular system and overcoming the previous limitation of being able to compute only local excitations. The results of these simple but accurate models are validated against full quantum calculations without fragmentation. The developed method is applied to a very important photosynthetic pigment-protein complex, the Fenna-Matthews-Olson complex (FMOc), that is responsible for the energy transfer from a chlorosome to the reaction center in the green sulfur bacteria. Absorption and circular dichroism spectra of FMOc are simulated, and the role of the molecular environment on the excitations is revealed.
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Affiliation(s)
- Danil S Kaliakin
- Department of Chemistry , Purdue University , 560 Oval Drive , West Lafayette , Indiana 47907 , United States
| | - Hiroya Nakata
- Research Institute for Advanced Materials and Devices , Kyocera , 5-3 Hikaridai-3 , Seika-cho Soraku-gun, Kyoto 619-0237 , Japan
| | - Yongbin Kim
- Department of Chemistry , Purdue University , 560 Oval Drive , West Lafayette , Indiana 47907 , United States
| | - Qifeng Chen
- Department of Chemistry , Purdue University , 560 Oval Drive , West Lafayette , Indiana 47907 , United States
| | - Dmitri G Fedorov
- Research Center for Computational Design of Advanced Functional Materials (CD-FMat) , National Institute of Advanced Industrial Science and Technology (AIST) , Central 2, Umezono 1-1-1 , Tsukuba 305-8568 , Japan
| | - Lyudmila V Slipchenko
- Department of Chemistry , Purdue University , 560 Oval Drive , West Lafayette , Indiana 47907 , United States
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28
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Gong Z, Wu J. Absorption matrix of multi-site systems calculated by a hybrid quantum-classical Liouville equation. J Chem Phys 2019; 151:224109. [DOI: 10.1063/1.5138217] [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] Open
Affiliation(s)
- Zhihao Gong
- Physics Department, Zhejiang University, 38 ZheDa Road, Hangzhou, Zhejiang 310027, China
| | - Jianlan Wu
- Physics Department, Zhejiang University, 38 ZheDa Road, Hangzhou, Zhejiang 310027, China
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29
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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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30
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Eckert PA, Kubarych KJ. Vibrational coherence transfer illuminates dark modes in models of the FeFe hydrogenase active site. J Chem Phys 2019. [DOI: 10.1063/1.5111016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Peter A. Eckert
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Kevin J. Kubarych
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
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31
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Cupellini L, Bondanza M, Nottoli M, Mennucci B. Successes & challenges in the atomistic modeling of light-harvesting and its photoregulation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1861:148049. [PMID: 31386831 DOI: 10.1016/j.bbabio.2019.07.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 07/10/2019] [Accepted: 07/15/2019] [Indexed: 12/21/2022]
Abstract
Light-harvesting is a crucial step of photosynthesis. Its mechanisms and related energetics have been revealed by a combination of experimental investigations and theoretical modeling. The success of theoretical modeling is largely due to the application of atomistic descriptions combining quantum chemistry, classical models and molecular dynamics techniques. Besides the important achievements obtained so far, a complete and quantitative understanding of how the many different light-harvesting complexes exploit their structural specificity is still missing. Moreover, many questions remain unanswered regarding the mechanisms through which light-harvesting is regulated in response to variable light conditions. Here we show that, in both fields, a major role will be played once more by atomistic descriptions, possibly generalized to tackle the numerous time and space scales on which the regulation takes place: going from the ultrafast electronic excitation of the multichromophoric aggregate, through the subsequent conformational changes in the embedding protein, up to the interaction between proteins.
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Affiliation(s)
- Lorenzo Cupellini
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, Pisa 56124, Italy
| | - Mattia Bondanza
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, Pisa 56124, Italy
| | - Michele Nottoli
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, Pisa 56124, Italy
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, Pisa 56124, Italy.
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32
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Saer RG, Schultz RL, Blankenship RE. The influence of quaternary structure on the stability of Fenna-Matthews-Olson (FMO) antenna complexes. PHOTOSYNTHESIS RESEARCH 2019; 140:39-49. [PMID: 30315435 DOI: 10.1007/s11120-018-0591-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 10/03/2018] [Indexed: 06/08/2023]
Abstract
The trimeric nature of the Fenna-Matthews-Olson (FMO) protein antenna complex from green sulfur phototrophic bacteria was investigated. Mutations were introduced into the protein at positions 142 and 198, which were chosen to destabilize the intra-trimer salt bridges between adjacent monomers. Strains bearing the mutations R142L, R198L, or their combination, exhibited altered optical absorption spectra of purified membranes and fluoresced more intensely than the wild type. In particular, the introduction of the R142L mutation resulted in slower culture growth rates, as well as an FMO complex that was not able to be isolated in appreciable quantities, while the R198L mutation yielded an FMO complex with increased sensitivity to sodium thiocyanate and Triton X-100 treatments. Native and denaturing PAGE experiments suggest that much of the FMO complexes in the mutant strains pool with the insoluble material upon membrane solubilization with n-dodecyl β-D-maltoside, a mild nonionic detergent. Taken together, our results suggest that the quaternary structure of the FMO complex, the homotrimer, is an important factor in the maintenance of the complex's tertiary structure.
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Affiliation(s)
- Rafael G Saer
- Department of Biology, Washington University in St. Louis, 1 Brookings Drive, St. Louis, MO, 63130, USA
- Photosynthetic Antenna Research Center (PARC), Washington University in St. Louis, 1 Brookings Drive, St. Louis, MO, 63130, USA
| | - Rebecca L Schultz
- Department of Chemistry, Washington University in St. Louis, 1 Brookings Drive, St. Louis, MO, 63130, USA
- Department of Chemistry, University of Wisconsin Madison, Madison, WI, 53706, USA
| | - Robert E Blankenship
- Department of Biology, Washington University in St. Louis, 1 Brookings Drive, St. Louis, MO, 63130, USA.
- Department of Chemistry, Washington University in St. Louis, 1 Brookings Drive, St. Louis, MO, 63130, USA.
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33
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Singh D, Dasgupta S. Role of Coherence in Excitation Transfer Efficiency to the Reaction Center in Photosynthetic Bacteria
Chlorobium tepidum. ChemistrySelect 2019. [DOI: 10.1002/slct.201803554] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Davinder Singh
- Department of PhysicsIndian Institute of Technology Ropar, Rupnagar Punjab - 140001 India
| | - Shubhrangshu Dasgupta
- Department of PhysicsIndian Institute of Technology Ropar, Rupnagar Punjab - 140001 India
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34
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Lu X, Selvaraj B, Ghimire-Rijal S, Orf GS, Meilleur F, Blankenship RE, Cuneo MJ, Myles DAA. Neutron and X-ray analysis of the Fenna-Matthews-Olson photosynthetic antenna complex from Prosthecochloris aestuarii. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2019; 75:171-175. [PMID: 30839291 DOI: 10.1107/s2053230x19000724] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 01/16/2019] [Indexed: 11/10/2022]
Abstract
The Fenna-Matthews-Olson protein from Prosthecochloris aestuarii (PaFMO) has been crystallized in a new form that is amenable to high-resolution X-ray and neutron analysis. The crystals belonged to space group H3, with unit-cell parameters a = b = 83.64, c = 294.78 Å, and diffracted X-rays to ∼1.7 Å resolution at room temperature. Large PaFMO crystals grown to volumes of 0.3-0.5 mm3 diffracted neutrons to 2.2 Å resolution on the MaNDi neutron diffractometer at the Spallation Neutron Source. The resolution of the neutron data will allow direct determination of the positions of H atoms in the structure, which are believed to be fundamentally important in tuning the individual excitation energies of bacteriochlorophylls in this archetypal photosynthetic antenna complex. This is one of the largest unit-cell systems yet studied using neutron diffraction, and will allow the first high-resolution neutron analysis of a photosynthetic antenna complex.
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Affiliation(s)
- Xun Lu
- Neutron Science Directorate, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Brinda Selvaraj
- Neutron Science Directorate, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Sudipa Ghimire-Rijal
- Neutron Science Directorate, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Gregory S Orf
- Departments of Biology and Chemistry, Washington University in St Louis, St Louis, MO 63130, USA
| | - Flora Meilleur
- Neutron Science Directorate, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Robert E Blankenship
- Departments of Biology and Chemistry, Washington University in St Louis, St Louis, MO 63130, USA
| | - Matthew J Cuneo
- Neutron Science Directorate, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Dean A A Myles
- Neutron Science Directorate, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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35
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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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36
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Lee SH, Matula AJ, Hu G, Troiano JL, Karpovich CJ, Crabtree RH, Batista VS, Brudvig GW. Strongly Coupled Phenazine-Porphyrin Dyads: Light-Harvesting Molecular Assemblies with Broad Absorption Coverage. ACS APPLIED MATERIALS & INTERFACES 2019; 11:8000-8008. [PMID: 30698407 DOI: 10.1021/acsami.8b20996] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The development of light-harvesting architectures with broad absorption coverage in the visible region continues to be an important research area in the field of artificial photosynthesis. Here, we introduce a new class of ethynyl-linked panchromatic dyads composed of dibenzophenazines coupled ortho and meta to tetrapyrroles with an anchoring group that can be grafted onto metal oxide surfaces. Quantum chemical calculations and photophysical measurements of the synthesized materials reveal that both of the dibenzophenazine dyads absorb broadly from 300 to 636 nm and exhibit absorption bands different from those of the constituent chromophore units. Moreover, the different points of attachment of dibenzophenazines to tetrapyrroles give different absorption profiles which computations suggest result from differences in the planarity of the two dyads. Applicability of the dyads in artificial photosynthesis systems was assessed by their incorporation and characterization of their performance in dye-sensitized solar cells.
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Affiliation(s)
- Shin Hee Lee
- Department of Chemistry, and Yale Energy Sciences Institute , Yale University , New Haven , Connecticut 06520-8107 , United States
| | - Adam J Matula
- Department of Chemistry, and Yale Energy Sciences Institute , Yale University , New Haven , Connecticut 06520-8107 , United States
| | - Gongfang Hu
- Department of Chemistry, and Yale Energy Sciences Institute , Yale University , New Haven , Connecticut 06520-8107 , United States
| | - Jennifer L Troiano
- Department of Chemistry, and Yale Energy Sciences Institute , Yale University , New Haven , Connecticut 06520-8107 , United States
| | - Christopher J Karpovich
- Department of Chemistry, and Yale Energy Sciences Institute , Yale University , New Haven , Connecticut 06520-8107 , United States
| | - Robert H Crabtree
- Department of Chemistry, and Yale Energy Sciences Institute , Yale University , New Haven , Connecticut 06520-8107 , United States
| | - Victor S Batista
- Department of Chemistry, and Yale Energy Sciences Institute , Yale University , New Haven , Connecticut 06520-8107 , United States
| | - Gary W Brudvig
- Department of Chemistry, and Yale Energy Sciences Institute , Yale University , New Haven , Connecticut 06520-8107 , United States
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37
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Gong ZH, Tang ZF, Cao JS, Wu J. Optimal initialization of a quantum system for an efficient coherent energy transfer. CHINESE J CHEM PHYS 2018. [DOI: 10.1063/1674-0068/31/cjcp1804068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Zhi-hao Gong
- Department of Physics, Zhejiang University, Hangzhou 310027, China
| | - Zhou-fei Tang
- Department of Physics, Zhejiang University, Hangzhou 310027, China
| | - Jian-shu Cao
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Jianlan Wu
- Department of Physics, Zhejiang University, Hangzhou 310027, China
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38
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Richter M, Fingerhut BP. Coarse-grained representation of the quasi adiabatic propagator path integral for the treatment of non-Markovian long-time bath memory. J Chem Phys 2018; 146:214101. [PMID: 28576089 DOI: 10.1063/1.4984075] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The description of non-Markovian effects imposed by low frequency bath modes poses a persistent challenge for path integral based approaches like the iterative quasi-adiabatic propagator path integral (iQUAPI) method. We present a novel approximate method, termed mask assisted coarse graining of influence coefficients (MACGIC)-iQUAPI, that offers appealing computational savings due to substantial reduction of considered path segments for propagation. The method relies on an efficient path segment merging procedure via an intermediate coarse grained representation of Feynman-Vernon influence coefficients that exploits physical properties of system decoherence. The MACGIC-iQUAPI method allows us to access the regime of biological significant long-time bath memory on the order of hundred propagation time steps while retaining convergence to iQUAPI results. Numerical performance is demonstrated for a set of benchmark problems that cover bath assisted long range electron transfer, the transition from coherent to incoherent dynamics in a prototypical molecular dimer and excitation energy transfer in a 24-state model of the Fenna-Matthews-Olson trimer complex where in all cases excellent agreement with numerically exact reference data is obtained.
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Affiliation(s)
- Martin Richter
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, D-12489 Berlin, Germany
| | - Benjamin P Fingerhut
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, D-12489 Berlin, Germany
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39
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Reprint of “The effect of site-specific spectral densities on the high-dimensional exciton-vibrational dynamics in the FMO complex”. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2018.05.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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40
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Collette F, Renger T, Müh F, Schmidt am Busch M. Red/Green Color Tuning of Visual Rhodopsins: Electrostatic Theory Provides a Quantitative Explanation. J Phys Chem B 2018; 122:4828-4837. [DOI: 10.1021/acs.jpcb.8b02702] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Florimond Collette
- Institut für Theoretische Physik, Johannes Kepler University Linz, Altenberger Strasse 69, 4040 Linz, Austria
| | - Thomas Renger
- Institut für Theoretische Physik, Johannes Kepler University Linz, Altenberger Strasse 69, 4040 Linz, Austria
| | - Frank Müh
- Institut für Theoretische Physik, Johannes Kepler University Linz, Altenberger Strasse 69, 4040 Linz, Austria
| | - Marcel Schmidt am Busch
- Institut für Theoretische Physik, Johannes Kepler University Linz, Altenberger Strasse 69, 4040 Linz, Austria
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41
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Khmelnitskiy A, Saer RG, Blankenship RE, Jankowiak R. Excitonic Energy Landscape of the Y16F Mutant of the Chlorobium tepidum Fenna-Matthews-Olson (FMO) Complex: High Resolution Spectroscopic and Modeling Studies. J Phys Chem B 2018; 122:3734-3743. [PMID: 29554425 DOI: 10.1021/acs.jpcb.7b11763] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
We report high-resolution (low-temperature) absorption, emission, and nonresonant/resonant hole-burned (HB) spectra and results of excitonic calculations using a non-Markovian reduced density matrix theory (with an improved algorithm for parameter optimization in heterogeneous samples) obtained for the Y16F mutant of the Fenna-Matthews-Olson (FMO) trimer from the green sulfur bacterium Chlorobium tepidum. We show that the Y16F mutant is a mixture of FMO complexes with three independent low-energy traps (located near 817, 821, and 826 nm), in agreement with measured composite emission and HB spectra. Two of these traps belong to mutated FMO subpopulations characterized by significantly modified low-energy excitonic states. Hamiltonians for the two major subpopulations (Sub821 and Sub817) provide new insight into extensive changes induced by the single-point mutation in the vicinity of BChl 3 (where tyrosine Y16 was replaced with phenylalanine F16). The average decay time(s) from the higher exciton state(s) in the Y16F mutant depends on frequency and occurs on a picosecond time scale.
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Affiliation(s)
| | - Rafael G Saer
- Departments of Biology and Chemistry , Washington University in St. Louis , Saint Louis , Missouri 63130 , United States
| | - Robert E Blankenship
- Departments of Biology and Chemistry , Washington University in St. Louis , Saint Louis , Missouri 63130 , United States
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42
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Jurinovich S, Cupellini L, Guido CA, Mennucci B. EXAT: EXcitonic analysis tool. J Comput Chem 2017; 39:279-286. [PMID: 29151259 DOI: 10.1002/jcc.25118] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 11/02/2017] [Accepted: 11/03/2017] [Indexed: 01/09/2023]
Abstract
We introduce EXcitonic Analysis Tool (EXAT), a program able to compute optical spectra of large excitonic systems directly from the output of quantum mechanical calculations performed with the popular Gaussian 16 package. The software is able to combine in an excitonic scheme the single-chromophore properties and exciton couplings to simulate energies, coefficients, and excitonic spectra (UV-vis, CD, and LD). The effect of the environment can also be included using a Polarizable Continuum Model. EXAT also presents a simple graphical user interface, which shows on-screen both site and exciton properties. To show the potential of the method, we report two applications on a a chiral perturbed BODIPY system and DNA G-quadruplexes, respectively. The program is available online at http://molecolab.dcci.unipi.it/tools/. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Sandro Jurinovich
- Dipartimento di Chimica, Università di Pisa, Via G. Moruzzi 13, Pisa, 56124, Italy
| | - Lorenzo Cupellini
- Dipartimento di Chimica, Università di Pisa, Via G. Moruzzi 13, Pisa, 56124, Italy
| | - Ciro A Guido
- Laboratoire CEISAM - UMR CNRS 6230, Université de Nantes, 2 Rue de la Houssinière, BP 92208, 44322 Nantes Cedex 3, France
| | - Benedetta Mennucci
- Dipartimento di Chimica, Università di Pisa, Via G. Moruzzi 13, Pisa, 56124, Italy
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43
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Ke Y, Zhao Y. Perturbation expansions of stochastic wavefunctions for open quantum systems. J Chem Phys 2017; 147:184103. [DOI: 10.1063/1.4996737] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Yaling Ke
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, and Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
| | - Yi Zhao
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, and Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
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44
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Schulze J, Shibl MF, Al-Marri MJ, Kühn O. The effect of site-specific spectral densities on the high-dimensional exciton-vibrational dynamics in the FMO complex. Chem Phys 2017. [DOI: 10.1016/j.chemphys.2017.09.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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45
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Padula D, Lee MH, Claridge K, Troisi A. Chromophore-Dependent Intramolecular Exciton–Vibrational Coupling in the FMO Complex: Quantification and Importance for Exciton Dynamics. J Phys Chem B 2017; 121:10026-10035. [DOI: 10.1021/acs.jpcb.7b08020] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Daniele Padula
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
| | - Myeong H. Lee
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
| | - Kirsten Claridge
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
| | - Alessandro Troisi
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
- Department
of Chemistry and Materials Innovation Factory, University of Liverpool, Liverpool L69 7ZD, U.K
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46
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Baker LA, Habershon S. Photosynthesis, pigment-protein complexes and electronic energy transport: simple models for complicated processes. Sci Prog 2017; 100:313-330. [PMID: 28779762 PMCID: PMC10365183 DOI: 10.3184/003685017x14967574639964] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In this review, we discuss our recent work on modelling biological pigment-protein complexes, such as the Fenna-Matthews-Olson complex and light-harvesting complex-II, to explain their electronic energy transport properties. In particular, we highlight how a network-based analysis approach, where the light-absorbing pigments are treated as a network of interconnected nodes, can provide a qualitative picture of quantum dynamic energy transport. With this in mind, we demonstrate how other properties such as robustness to environmental changes can be assessed in a simple and computationally tractable manner. Such analyses could prove useful for the design of artificial energy transport networks such as those which might find application in solar cells.
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47
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Duan HG, Prokhorenko VI, Cogdell RJ, Ashraf K, Stevens AL, Thorwart M, Miller RJD. Nature does not rely on long-lived electronic quantum coherence for photosynthetic energy transfer. Proc Natl Acad Sci U S A 2017; 114:8493-8498. [PMID: 28743751 PMCID: PMC5559008 DOI: 10.1073/pnas.1702261114] [Citation(s) in RCA: 171] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
During the first steps of photosynthesis, the energy of impinging solar photons is transformed into electronic excitation energy of the light-harvesting biomolecular complexes. The subsequent energy transfer to the reaction center is commonly rationalized in terms of excitons moving on a grid of biomolecular chromophores on typical timescales [Formula: see text]100 fs. Today's understanding of the energy transfer includes the fact that the excitons are delocalized over a few neighboring sites, but the role of quantum coherence is considered as irrelevant for the transfer dynamics because it typically decays within a few tens of femtoseconds. This orthodox picture of incoherent energy transfer between clusters of a few pigments sharing delocalized excitons has been challenged by ultrafast optical spectroscopy experiments with the Fenna-Matthews-Olson protein, in which interference oscillatory signals up to 1.5 ps were reported and interpreted as direct evidence of exceptionally long-lived electronic quantum coherence. Here, we show that the optical 2D photon echo spectra of this complex at ambient temperature in aqueous solution do not provide evidence of any long-lived electronic quantum coherence, but confirm the orthodox view of rapidly decaying electronic quantum coherence on a timescale of 60 fs. Our results can be considered as generic and give no hint that electronic quantum coherence plays any biofunctional role in real photoactive biomolecular complexes. Because in this structurally well-defined protein the distances between bacteriochlorophylls are comparable to those of other light-harvesting complexes, we anticipate that this finding is general and directly applies to even larger photoactive biomolecular complexes.
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Affiliation(s)
- Hong-Guang Duan
- Atomically Resolved Dynamics Department, Max Planck Institute for the Structure and Dynamics of Matter, 22761 Hamburg, Germany
- I. Institut für Theoretische Physik, Universität Hamburg, 20355 Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, 22761 Hamburg, Germany
| | - Valentyn I Prokhorenko
- Atomically Resolved Dynamics Department, Max Planck Institute for the Structure and Dynamics of Matter, 22761 Hamburg, Germany
| | - Richard J Cogdell
- Institute of Molecular, Cell, and Systems Biology, College of Medical, Veterinary, and Life Science, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Khuram Ashraf
- Institute of Molecular, Cell, and Systems Biology, College of Medical, Veterinary, and Life Science, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Amy L Stevens
- Atomically Resolved Dynamics Department, Max Planck Institute for the Structure and Dynamics of Matter, 22761 Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, 22761 Hamburg, Germany
- Department of Chemistry, University of Toronto, Toronto, ON, Canada M5S 3H6
- Department of Physics, University of Toronto, Toronto, ON, Canada M5S 3H6
| | - Michael Thorwart
- I. Institut für Theoretische Physik, Universität Hamburg, 20355 Hamburg, Germany;
- The Hamburg Center for Ultrafast Imaging, 22761 Hamburg, Germany
| | - R J Dwayne Miller
- Atomically Resolved Dynamics Department, Max Planck Institute for the Structure and Dynamics of Matter, 22761 Hamburg, Germany;
- The Hamburg Center for Ultrafast Imaging, 22761 Hamburg, Germany
- Department of Chemistry, University of Toronto, Toronto, ON, Canada M5S 3H6
- Department of Physics, University of Toronto, Toronto, ON, Canada M5S 3H6
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Baker LA, Habershon S. Photosynthetic pigment-protein complexes as highly connected networks: implications for robust energy transport. Proc Math Phys Eng Sci 2017; 473:20170112. [PMID: 28588417 PMCID: PMC5454362 DOI: 10.1098/rspa.2017.0112] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 05/04/2017] [Indexed: 02/01/2023] Open
Abstract
Photosynthetic pigment-protein complexes (PPCs) are a vital component of the light-harvesting machinery of all plants and photosynthesizing bacteria, enabling efficient transport of the energy of absorbed light towards the reaction centre, where chemical energy storage is initiated. PPCs comprise a set of chromophore molecules, typically bacteriochlorophyll species, held in a well-defined arrangement by a protein scaffold; this relatively rigid distribution leads to a viewpoint in which the chromophore subsystem is treated as a network, where chromophores represent vertices and inter-chromophore electronic couplings represent edges. This graph-based view can then be used as a framework within which to interrogate the role of structural and electronic organization in PPCs. Here, we use this network-based viewpoint to compare excitation energy transfer (EET) dynamics in the light-harvesting complex II (LHC-II) system commonly found in higher plants and the Fenna-Matthews-Olson (FMO) complex found in green sulfur bacteria. The results of our simple network-based investigations clearly demonstrate the role of network connectivity and multiple EET pathways on the efficient and robust EET dynamics in these PPCs, and highlight a role for such considerations in the development of new artificial light-harvesting systems.
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Affiliation(s)
| | - Scott Habershon
- Department of Chemistry and Centre for Scientific Computing, University of Warwick, Coventry CV4 7AL, UK
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Saer RG, Stadnytskyi V, Magdaong NC, Goodson C, Savikhin S, Blankenship RE. Probing the excitonic landscape of the Chlorobaculum tepidum Fenna-Matthews-Olson (FMO) complex: a mutagenesis approach. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2017; 1858:288-296. [PMID: 28159567 DOI: 10.1016/j.bbabio.2017.01.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 01/27/2017] [Accepted: 01/30/2017] [Indexed: 12/17/2022]
Abstract
In this paper we report the steady-state optical properties of a series of site-directed mutants in the Fenna-Matthews-Olson (FMO) complex of Chlorobaculum tepidum, a photosynthetic green sulfur bacterium. The FMO antenna complex has historically been used as a model system for energy transfer due to the water-soluble nature of the protein, its stability at room temperature, as well as the availability of high-resolution structural data. Eight FMO mutants were constructed with changes in the environment of each of the bacteriochlorophyll a pigments found within each monomer of the homotrimeric FMO complex. Our results reveal multiple changes in low temperature absorption, as well as room temperature CD in each mutant compared to the wild-type FMO complex. These datasets were subsequently used to model the site energies of each pigment in the FMO complex by employing three different Hamiltonians from the literature. This enabled a basic approximation of the site energy shifts imparted on each pigment by the changed amino acid residue. These simulations suggest that, while the three Hamiltonians used in this work provide good fits to the wild-type FMO absorption spectrum, further efforts are required to obtain good fits to the mutant minus wild-type absorption difference spectra. This demonstrates that the use of FMO mutants can be a valuable tool to refine and iterate the current models of energy transfer in this system.
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Affiliation(s)
- Rafael G Saer
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, United States; Photosynthetic Antenna Research Center, Washington University in St. Louis, St. Louis, MO 63130, United States
| | - Valentyn Stadnytskyi
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907, United States
| | - Nikki C Magdaong
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, United States; Photosynthetic Antenna Research Center, Washington University in St. Louis, St. Louis, MO 63130, United States; Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, United States
| | - Carrie Goodson
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, United States
| | - Sergei Savikhin
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907, United States
| | - Robert E Blankenship
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, United States; Photosynthetic Antenna Research Center, Washington University in St. Louis, St. Louis, MO 63130, United States; Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, United States.
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Schulze J, Shibl MF, Al-Marri MJ, Kühn O. Multi-layer multi-configuration time-dependent Hartree (ML-MCTDH) approach to the correlated exciton-vibrational dynamics in the FMO complex. J Chem Phys 2017; 144:185101. [PMID: 27179506 DOI: 10.1063/1.4948563] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The coupled quantum dynamics of excitonic and vibrational degrees of freedom is investigated for high-dimensional models of the Fenna-Matthews-Olson complex. This includes a seven- and an eight-site model with 518 and 592 harmonic vibrational modes, respectively. The coupling between local electronic transitions and vibrations is described within the Huang-Rhys model using parameters that are obtained by discretization of an experimental spectral density. Different pathways of excitation energy flow are analyzed in terms of the reduced one-exciton density matrix, focussing on the role of vibrational and vibronic excitations. Distinct features due to both competing time scales of vibrational and exciton motion and vibronically assisted transfer are observed. The question of the effect of initial state preparation is addressed by comparing the case of an instantaneous Franck-Condon excitation at a single site with that of a laser field excitation.
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Affiliation(s)
- Jan Schulze
- Institut für Physik, Universität Rostock, Albert-Einstein-Str. 23-24, 18059 Rostock, Germany
| | - Mohamed F Shibl
- Gas Processing Center, College of Engineering, Qatar University, P.O. Box 2713, Doha, Qatar
| | - Mohammed J Al-Marri
- Gas Processing Center, College of Engineering, Qatar University, P.O. Box 2713, Doha, Qatar
| | - Oliver Kühn
- Institut für Physik, Universität Rostock, Albert-Einstein-Str. 23-24, 18059 Rostock, Germany
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