1
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Pirnia A, Maqdisi R, Mittal S, Sener M, Singharoy A. Perspective on Integrative Simulations of Bioenergetic Domains. J Phys Chem B 2024; 128:3302-3319. [PMID: 38562105 DOI: 10.1021/acs.jpcb.3c07335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Bioenergetic processes in cells, such as photosynthesis or respiration, integrate many time and length scales, which makes the simulation of energy conversion with a mere single level of theory impossible. Just like the myriad of experimental techniques required to examine each level of organization, an array of overlapping computational techniques is necessary to model energy conversion. Here, a perspective is presented on recent efforts for modeling bioenergetic phenomena with a focus on molecular dynamics simulations and its variants as a primary method. An overview of the various classical, quantum mechanical, enhanced sampling, coarse-grained, Brownian dynamics, and Monte Carlo methods is presented. Example applications discussed include multiscale simulations of membrane-wide electron transport, rate kinetics of ATP turnover from electrochemical gradients, and finally, integrative modeling of the chromatophore, a photosynthetic pseudo-organelle.
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Affiliation(s)
- Adam Pirnia
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287-1004, United States
| | - Ranel Maqdisi
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287-1004, United States
| | - Sumit Mittal
- VIT Bhopal University, Sehore 466114, Madhya Pradesh, India
| | - Melih Sener
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287-1004, United States
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Abhishek Singharoy
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287-1004, United States
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2
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Jha A, Zhang PP, Tiwari V, Chen L, Thorwart M, Miller RJD, Duan HG. Unraveling quantum coherences mediating primary charge transfer processes in photosystem II reaction center. SCIENCE ADVANCES 2024; 10:eadk1312. [PMID: 38446882 PMCID: PMC10917350 DOI: 10.1126/sciadv.adk1312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 01/31/2024] [Indexed: 03/08/2024]
Abstract
Photosystem II (PSII) reaction center (RC) is a unique complex that is capable of efficiently separating electronic charges across the membrane. The primary energy- and charge-transfer (CT) processes occur on comparable ultrafast timescales, which makes it extremely challenging to understand the fundamental mechanism responsible for the near-unity quantum efficiency of the transfer. Here, we elucidate the role of quantum coherences in the ultrafast energy and CT in the PSII RC by performing two-dimensional (2D) electronic spectroscopy at the cryogenic temperature of 20 kelvin, which captures the distinct underlying quantum coherences. Specifically, we uncover the electronic and vibrational coherences along with their lifetimes during the primary ultrafast processes of energy and CT. We construct an excitonic model that provides evidence for coherent energy and CT at low temperature in the 2D electronic spectra. The principles could provide valuable guidelines for creating artificial photosystems with exploitation of system-bath coupling and control of coherences to optimize the photon conversion efficiency to specific functions.
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Affiliation(s)
- Ajay Jha
- Department of Physics, School of Physical Science and Technology, Ningbo University, Ningbo, 315211, P.R. China
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761, Hamburg, Germany
- Rosalind Franklin Institute, Harwell, Oxfordshire OX11 0QX, UK
- Department of Pharmacology, University of Oxford, Oxford OX1 3QT, UK
| | - Pan-Pan Zhang
- Department of Physics, School of Physical Science and Technology, Ningbo University, Ningbo, 315211, P.R. China
| | - Vandana Tiwari
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761, Hamburg, Germany
- Department of Chemistry, University of Hamburg, Martin-Luther-King Platz 6, 20146 Hamburg, Germany
| | - Lipeng Chen
- Zhejiang Laboratory, Hangzhou 311100, P.R. China
| | - Michael Thorwart
- I. Institut für Theoretische Physik, Universität Hamburg, Notkestr. 9, 22607 Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - R. J. Dwayne Miller
- The Departments of Chemistry and Physics, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
| | - Hong-Guang Duan
- Department of Physics, School of Physical Science and Technology, Ningbo University, Ningbo, 315211, P.R. China
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761, Hamburg, Germany
- I. Institut für Theoretische Physik, Universität Hamburg, Notkestr. 9, 22607 Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
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3
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Liu M, Zhang G, Ming R, Fu X, Jiang R, Tian L, Chen X. Reconstruction of Highly-Defective MgO and Exceptional Photochemical Activity on CO 2 Upgrade in Aqueous Solution. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2303405. [PMID: 37431200 DOI: 10.1002/smll.202303405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 06/21/2023] [Indexed: 07/12/2023]
Abstract
Defects on metal oxide have attracted extensive attention in photo-/electrocatalytic CO2 reduction. Herein, porous MgO nanosheets with abundant oxygen vacancies (Vo s) and three-coordinated oxygen atoms (O3c ) at corners are reported, which reconstruct into defective MgCO3 ·3H2 O exposing rich surface unsaturated -OH groups and vacancies to initiate photocatalytic CO2 reduction to CO and CH4 . In consecutive 7-cycle tests (each run for 6 h) in pure water, CO2 conversion keeps stable. The total production of CH4 and CO attains ≈367 µmol gcata -1 h-1 . The selectivity of CH4 gradually increases from ≈3.1% (1st run) to ≈24.5% (4th run) and then remains unchanged under UV-light irradiation. With triethanolamine (3.3 vol.%) as the sacrificial agent, the total production of CO and CH4 production rapidly increases to ≈28 000 µmol gcata -1 in 2 h reaction. Photoluminescence spectra reveal that Vo s induces the formation of donor bands to promote charge carrier seperation. A series of trace spectra and theoretical analysis indicate Mg-Vo sites in the derived MgCO3 ·3H2 O are active centers, which play a crucial role in modulating CO2 adsorption and triggering photoreduction reactions. These intriguing results on defective alkaline earth oxides as potential photocatalysts in CO2 conversion may spur some exciting and novel findings in this field.
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Affiliation(s)
- Mengping Liu
- Hubei Collaborative Innovation Center for Advanced Organochemical Materials, Ministry-of-Education Key Laboratory for the Synthesis and Applications of Organic Functional Molecules, Hubei University, Wuhan, 430062, P. R. China
| | - Ganbing Zhang
- Hubei Collaborative Innovation Center for Advanced Organochemical Materials, Ministry-of-Education Key Laboratory for the Synthesis and Applications of Organic Functional Molecules, Hubei University, Wuhan, 430062, P. R. China
| | - Ruiqi Ming
- Hubei Collaborative Innovation Center for Advanced Organochemical Materials, Ministry-of-Education Key Laboratory for the Synthesis and Applications of Organic Functional Molecules, Hubei University, Wuhan, 430062, P. R. China
| | - Xin Fu
- Hubei Collaborative Innovation Center for Advanced Organochemical Materials, Ministry-of-Education Key Laboratory for the Synthesis and Applications of Organic Functional Molecules, Hubei University, Wuhan, 430062, P. R. China
| | - Ruiyi Jiang
- Hubei Collaborative Innovation Center for Advanced Organochemical Materials, Ministry-of-Education Key Laboratory for the Synthesis and Applications of Organic Functional Molecules, Hubei University, Wuhan, 430062, P. R. China
| | - Lihong Tian
- Hubei Collaborative Innovation Center for Advanced Organochemical Materials, Ministry-of-Education Key Laboratory for the Synthesis and Applications of Organic Functional Molecules, Hubei University, Wuhan, 430062, P. R. China
| | - Xiaobo Chen
- Division of Energy, Matter, and Systems, School of Science and Engineering, University of Missouri - Kansas City, Kansas City, MO 64110, USA
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4
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Exact simulation of pigment-protein complexes unveils vibronic renormalization of electronic parameters in ultrafast spectroscopy. Nat Commun 2022; 13:2912. [PMID: 35614049 PMCID: PMC9133012 DOI: 10.1038/s41467-022-30565-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 05/04/2022] [Indexed: 12/04/2022] Open
Abstract
The primary steps of photosynthesis rely on the generation, transport, and trapping of excitons in pigment-protein complexes (PPCs). Generically, PPCs possess highly structured vibrational spectra, combining many discrete intra-pigment modes and a quasi-continuous of protein modes, with vibrational and electronic couplings of comparable strength. The intricacy of the resulting vibronic dynamics poses significant challenges in establishing a quantitative connection between spectroscopic data and underlying microscopic models. Here we show how to address this challenge using numerically exact simulation methods by considering two model systems, namely the water-soluble chlorophyll-binding protein of cauliflower and the special pair of bacterial reaction centers. We demonstrate that the inclusion of the full multi-mode vibronic dynamics in numerical calculations of linear spectra leads to systematic and quantitatively significant corrections to electronic parameter estimation. These multi-mode vibronic effects are shown to be relevant in the longstanding discussion regarding the origin of long-lived oscillations in multidimensional nonlinear spectra. Multimode vibronic mixing in model photosynthetic systems revealed by numerically exact simulations is shown to strongly modify linear and non-linear optical responses and facilitate the persistence of coherent dynamics.
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5
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Do TN, Nguyen HL, Akhtar P, Zhong K, Jansen TLC, Knoester J, Caffarri S, Lambrev PH, Tan HS. Ultrafast Excitation Energy Transfer Dynamics in the LHCII-CP29-CP24 Subdomain of Plant Photosystem II. J Phys Chem Lett 2022; 13:4263-4271. [PMID: 35522529 DOI: 10.1021/acs.jpclett.2c00194] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
We measure the two-dimensional electronic spectra of the LHCII(M)-CP29-CP24 complex in photosystem II (PSII) and provide the first study of the ultrafast excitation energy transfer (EET) processes of an asymmetric and native light-harvesting assembly of the antenna of PSII. With comparisons to LHCII, we observe faster energy equilibrations in the intermediate levels of the LHCII(M)-CP29-CP24 complex at 662 and 670 nm. Notably, the putative "bottleneck" states in LHCII exhibit faster effective dynamics in the LHCII(M)-CP24-CP29 complex, with the average lifetime shortening from 2.5 ps in LHCII to 1.2 ps in the bigger assembly. The observations are supported by high-level structure-based calculations, and the accelerated dynamics can be attributed to the structural change of LHCII(M) in the bigger complex. This study shows that the biological functioning structures of the complexes are important to understand the overall EET dynamics of the PSII supercomplex.
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Affiliation(s)
- Thanh Nhut Do
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore
| | - Hoang Long Nguyen
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, Netherlands
| | - Parveen Akhtar
- Biological Research Center, Szeged, Temesvári körút 62, Szeged 6726, Hungary
- ELI-ALPS, ELI-HU Nonprofit Limited, Wolfgang Sandner utca 3, Szeged 6728, Hungary
| | - Kai Zhong
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, Netherlands
| | - Thomas L C Jansen
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, Netherlands
| | - Jasper Knoester
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, Netherlands
| | - Stefano Caffarri
- Aix Marseille Université, CEA, CNRS, BIAM, LGBP, 13009 Marseille, France
| | - Petar H Lambrev
- Biological Research Center, Szeged, Temesvári körút 62, Szeged 6726, Hungary
| | - Howe-Siang Tan
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore
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6
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Leng X, Yan YM, Zhu RD, Song K, Weng YX, Shi Q. Simulation of the Two-Dimensional Electronic Spectroscopy and Energy Transfer Dynamics of Light-Harvesting Complex II at Ambient Temperature. J Phys Chem B 2018; 122:4642-4652. [DOI: 10.1021/acs.jpcb.8b00674] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Xuan Leng
- Beijing National Laboratory for Condensed Matter Physics, CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ya-Ming Yan
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rui-Dan Zhu
- Beijing National Laboratory for Condensed Matter Physics, CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kai Song
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yu-Xiang Weng
- Beijing National Laboratory for Condensed Matter Physics, CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiang Shi
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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7
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Pan J, Gelzinis A, Chorošajev V, Vengris M, Senlik SS, Shen JR, Valkunas L, Abramavicius D, Ogilvie JP. Ultrafast energy transfer within the photosystem II core complex. Phys Chem Chem Phys 2018; 19:15356-15367. [PMID: 28574545 DOI: 10.1039/c7cp01673e] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
We report 2D electronic spectroscopy on the photosystem II core complex (PSII CC) at 77 K under different polarization conditions. A global analysis of the high time-resolution 2D data shows rapid, sub-100 fs energy transfer within the PSII CC. It also reveals the 2D spectral signatures of slower energy equilibration processes occurring on several to hundreds of picosecond time scales that are consistent with previous work. Using a recent structure-based model of the PSII CC [Y. Shibata, S. Nishi, K. Kawakami, J. R. Shen and T. Renger, J. Am. Chem. Soc., 2013, 135, 6903], we simulate the energy transfer in the PSII CC by calculating auxiliary time-resolved fluorescence spectra. We obtain the observed sub-100 fs evolution, even though the calculated electronic energy shows almost no dynamics at early times. On the other hand, the electronic-vibrational interaction energy increases considerably over the same time period. We conclude that interactions with vibrational degrees of freedom not only induce population transfer between the excitonic states in the PSII CC, but also reshape the energy landscape of the system. We suggest that the experimentally observed ultrafast energy transfer is a signature of excitonic-polaron formation.
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Affiliation(s)
- Jie Pan
- Department of Physics, University of Michigan, Ann Arbor, 48109, USA.
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8
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Novoderezhkin VI, Romero E, Prior J, van Grondelle R. Exciton-vibrational resonance and dynamics of charge separation in the photosystem II reaction center. Phys Chem Chem Phys 2018; 19:5195-5208. [PMID: 28149991 DOI: 10.1039/c6cp07308e] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The dynamics of charge separation in the photosystem II reaction center (PSII-RC) in the presence of intramolecular vibrations with their frequency matching the energy gap between the exciton state acting as the primary electron donor and the first charge-transfer (CT) state are investigated. A reduced PSII-RC 4-state model explicitly including a CT state is analyzed within Redfield relaxation theory in the multidimensional exciton-vibrational (vibronic) basis. This model is used to study coherent energy/electron transfers and their spectral signatures obtained by two-dimensional electronic spectroscopy (2DES). Modeling of the time-resolved 2D frequency maps obtained by wavelet analysis reveals the origins of the coherences which produce the observed oscillating features in 2DES and allows comparing the lifetimes of the coherences. The results suggest faster excitonic decoherence as compared with longer-lived vibronic oscillations. The emerging picture of the dynamics unravels the role of resonant vibrations in sustaining the effective energy conversion in the PSII-RC. We demonstrate that the mixing of the exciton and CT states promoted by a resonant vibrational quantum allows faster penetration of excitation energy into the CT with subsequent dynamic localization at the bottom of the CT potential induced by the remaining non-resonant nuclear modes. The degree of vibration-assisted mixing and, correspondingly, the rate of primary charge separation, increases significantly in the case of electron-vibrational resonance. The observed features illustrate the principles of quantum design of the photosynthetic unit. These principles are connected with the phenomenon of coherent mixing within vibronic eigenstates, increasing the effectiveness of charge separation not only upon coherent and impulsive laser excitation utilized in the 2DES experiment, but also under natural conditions under non-coherent non-impulsive solar light illumination.
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Affiliation(s)
- Vladimir I Novoderezhkin
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Leninskie Gory, 119992, Moscow, Russia.
| | - Elisabet Romero
- Department of Biophysics, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Javier Prior
- Departamento de Física Aplicada, Universidad Politécnica de Cartagena, Cartagena 30202, Spain
| | - Rienk van Grondelle
- Department of Biophysics, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
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9
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Primary Charge Separation in the Photosystem II Reaction Center Revealed by a Global Analysis of the Two-dimensional Electronic Spectra. Sci Rep 2017; 7:12347. [PMID: 28955056 PMCID: PMC5617839 DOI: 10.1038/s41598-017-12564-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 09/12/2017] [Indexed: 11/08/2022] Open
Abstract
The transfer of electronic charge in the reaction center of Photosystem II is one of the key building blocks of the conversion of sunlight energy into chemical energy within the cascade of the photosynthetic reactions. Since the charge transfer dynamics is mixed with the energy transfer dynamics, an effective tool for the direct resolution of charge separation in the reaction center is still missing. Here, we use experimental two-dimensional optical photon echo spectroscopy in combination with the theoretical calculation to resolve its signature. A global fitting analysis allows us to clearly and directly identify a decay pathway associated to the primary charge separation. In particular, it can be distinguished from regular energy transfer and occurs on a time scale of 1.5 ps under ambient conditions. This technique provides a general tool to identify charge separation signatures from the energy transport in two-dimensional optical spectroscopy.
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10
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Gelzinis A, Abramavicius D, Ogilvie JP, Valkunas L. Spectroscopic properties of photosystem II reaction center revisited. J Chem Phys 2017; 147:115102. [DOI: 10.1063/1.4997527] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Andrius Gelzinis
- Department of Theoretical Physics, Faculty of Physics, Vilnius University, Sauletekio 9-III, 10222 Vilnius, Lithuania
- Department of Molecular Compound Physics, Center for Physical Sciences and Technology, Sauletekio 3, 10257 Vilnius, Lithuania
| | - Darius Abramavicius
- Department of Theoretical Physics, Faculty of Physics, Vilnius University, Sauletekio 9-III, 10222 Vilnius, Lithuania
| | - Jennifer P. Ogilvie
- Department of Physics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Leonas Valkunas
- Department of Theoretical Physics, Faculty of Physics, Vilnius University, Sauletekio 9-III, 10222 Vilnius, Lithuania
- Department of Molecular Compound Physics, Center for Physical Sciences and Technology, Sauletekio 3, 10257 Vilnius, Lithuania
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11
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Kramer T, Rodríguez M, Zelinskyy Y. Modeling of Transient Absorption Spectra in Exciton–Charge-Transfer Systems. J Phys Chem B 2017; 121:463-470. [DOI: 10.1021/acs.jpcb.6b09858] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tobias Kramer
- Konrad-Zuse-Zentrum für Informationstechnik Berlin, 14195 Berlin, Germany
- Department
of Physics, Harvard University, 17 Oxford Street, 02138 Cambridge, Massachusetts, United States
| | - Mirta Rodríguez
- Konrad-Zuse-Zentrum für Informationstechnik Berlin, 14195 Berlin, Germany
| | - Yaroslav Zelinskyy
- Konrad-Zuse-Zentrum für Informationstechnik Berlin, 14195 Berlin, Germany
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12
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13
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Novoderezhkin VI, Romero E, van Grondelle R. How exciton-vibrational coherences control charge separation in the photosystem II reaction center. Phys Chem Chem Phys 2016; 17:30828-41. [PMID: 25854607 DOI: 10.1039/c5cp00582e] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
In photosynthesis absorbed sun light produces collective excitations (excitons) that form a coherent superposition of electronic and vibrational states of the individual pigments. Two-dimensional (2D) electronic spectroscopy allows a visualization of how these coherences are involved in the primary processes of energy and charge transfer. Based on quantitative modeling we identify the exciton-vibrational coherences observed in 2D photon echo of the photosystem II reaction center (PSII-RC). We find that the vibrations resonant with the exciton splittings can modify the delocalization of the exciton states and produce additional states, thus promoting directed energy transfer and allowing a switch between the two charge separation pathways. We conclude that the coincidence of the frequencies of the most intense vibrations with the splittings within the manifold of exciton and charge-transfer states in the PSII-RC is not occurring by chance, but reflects a fundamental principle of how energy conversion in photosynthesis was optimized.
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Affiliation(s)
- Vladimir I Novoderezhkin
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Leninskie Gory, 119992, Moscow, Russia.
| | - Elisabet Romero
- Department of Biophysics, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Rienk van Grondelle
- Department of Biophysics, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
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14
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Abramavicius D, Valkunas L. Role of coherent vibrations in energy transfer and conversion in photosynthetic pigment-protein complexes. PHOTOSYNTHESIS RESEARCH 2016; 127:33-47. [PMID: 25618783 DOI: 10.1007/s11120-015-0080-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 01/05/2015] [Indexed: 06/04/2023]
Abstract
Oscillatory features of two-dimensional spectra of photosynthetic pigment-protein complexes during few picoseconds after electronic excitations of chlorophylls in various pigment-proteins were recently related to the coherent nuclear vibrations. It has been also speculated that the vibrations may assist the excitonic energy transfer and charge separation, hence contributing to energy transport and energy conversion efficiency. Here, we consider three theoretical approaches usually used for characterization of the excitation dynamics and charge separation, namely Redfield, Förster, and Marcus model descriptions, regarding this question. We show that two out of the three mechanisms require explicit resonances of excitonic splittings and the nuclear vibration frequencies. However, the third one related to the electron transfer is in principle off resonant.
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Affiliation(s)
- Darius Abramavicius
- Department of Theoretical Physics, Vilnius University, Sauletekio al. 9-III, 10222, Vilnius, Lithuania.
| | - Leonas Valkunas
- Department of Theoretical Physics, Vilnius University, Sauletekio al. 9-III, 10222, Vilnius, Lithuania.
- Center for Physical Sciences and Technology, A. Gostauto 11, 01108, Vilnius, Lithuania.
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15
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Novoderezhkin VI, Croce R, Wahadoszamen M, Polukhina I, Romero E, van Grondelle R. Mixing of exciton and charge-transfer states in light-harvesting complex Lhca4. Phys Chem Chem Phys 2016; 18:19368-77. [DOI: 10.1039/c6cp02225a] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Structure-based modeling of spectra of the wild-type Lhca4 and NH mutant enables us to build the exciton model of the complex that includes a charge-transfer state mixed with the excited-state manifold.
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Affiliation(s)
| | - Roberta Croce
- Department of Biophysics
- Faculty of Sciences
- VU University Amsterdam
- 1081 HV Amsterdam
- The Netherlands
| | - Md. Wahadoszamen
- Department of Biophysics
- Faculty of Sciences
- VU University Amsterdam
- 1081 HV Amsterdam
- The Netherlands
| | - Iryna Polukhina
- Department of Biophysics
- Faculty of Sciences
- VU University Amsterdam
- 1081 HV Amsterdam
- The Netherlands
| | - Elisabet Romero
- Department of Biophysics
- Faculty of Sciences
- VU University Amsterdam
- 1081 HV Amsterdam
- The Netherlands
| | - Rienk van Grondelle
- Department of Biophysics
- Faculty of Sciences
- VU University Amsterdam
- 1081 HV Amsterdam
- The Netherlands
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16
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Duan HG, Dijkstra AG, Nalbach P, Thorwart M. Efficient tool to calculate two-dimensional optical spectra for photoactive molecular complexes. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 92:042708. [PMID: 26565273 DOI: 10.1103/physreve.92.042708] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Indexed: 06/05/2023]
Abstract
We combine the coherent modified Redfield theory (CMRT) with the equation of motion-phase matching approach (PMA) to calculate two-dimensional photon-echo spectra for photoactive molecular complexes with an intermediate strength of the coupling to their environment. Both techniques are highly efficient, yet they involve approximations at different levels. By explicitly comparing with the numerically exact quasiadiabatic path integral approach, we show for the Fenna-Matthews-Olson complex that the CMRT describes the decay rates in the population dynamics well, but final stationary populations and the oscillation frequencies differ slightly. In addition, we use the combined CMRT+PMA to calculate two-dimensional photon-echo spectra for a simple dimer model. We find excellent agreement with the exact path integral calculations at short waiting times where the dynamics is still coherent. For long waiting times, differences occur due to different final stationary states, specifically for strong system-bath coupling. For weak to intermediate system-bath couplings, which is most important for natural photosynthetic complexes, the combined CMRT+PMA gives reasonable results with acceptable computational efforts.
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Affiliation(s)
- Hong-Guang Duan
- I. Institut für Theoretische Physik, Universität Hamburg, Jungiusstraße 9, 20355 Hamburg, Germany
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Arend G Dijkstra
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Peter Nalbach
- I. Institut für Theoretische Physik, Universität Hamburg, Jungiusstraße 9, 20355 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Michael Thorwart
- I. Institut für Theoretische Physik, Universität Hamburg, Jungiusstraße 9, 20355 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
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Chen L, Shenai P, Zheng F, Somoza A, Zhao Y. Optimal Energy Transfer in Light-Harvesting Systems. Molecules 2015; 20:15224-72. [PMID: 26307957 PMCID: PMC6332264 DOI: 10.3390/molecules200815224] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 08/03/2015] [Accepted: 08/14/2015] [Indexed: 01/25/2023] Open
Abstract
Photosynthesis is one of the most essential biological processes in which specialized pigment-protein complexes absorb solar photons, and with a remarkably high efficiency, guide the photo-induced excitation energy toward the reaction center to subsequently trigger its conversion to chemical energy. In this work, we review the principles of optimal energy transfer in various natural and artificial light harvesting systems. We begin by presenting the guiding principles for optimizing the energy transfer efficiency in systems connected to dissipative environments, with particular attention paid to the potential role of quantum coherence in light harvesting systems. We will comment briefly on photo-protective mechanisms in natural systems that ensure optimal functionality under varying ambient conditions. For completeness, we will also present an overview of the charge separation and electron transfer pathways in reaction centers. Finally, recent theoretical and experimental progress on excitation energy transfer, charge separation, and charge transport in artificial light harvesting systems is delineated, with organic solar cells taken as prime examples.
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Affiliation(s)
- Lipeng Chen
- Division of Materials Science, Nanyang Technological University, 50 Nanyang Avenue,Singapore 639798, Singapore.
| | - Prathamesh Shenai
- Division of Materials Science, Nanyang Technological University, 50 Nanyang Avenue,Singapore 639798, Singapore.
| | - Fulu Zheng
- Division of Materials Science, Nanyang Technological University, 50 Nanyang Avenue,Singapore 639798, Singapore.
| | - Alejandro Somoza
- Division of Materials Science, Nanyang Technological University, 50 Nanyang Avenue,Singapore 639798, Singapore.
| | - Yang Zhao
- Division of Materials Science, Nanyang Technological University, 50 Nanyang Avenue,Singapore 639798, Singapore.
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18
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Gelzinis A, Abramavicius D, Valkunas L. Absorption lineshapes of molecular aggregates revisited. J Chem Phys 2015; 142:154107. [DOI: 10.1063/1.4918343] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Affiliation(s)
- Andrius Gelzinis
- Department of Theoretical Physics, Faculty of Physics, Vilnius University, Sauletekio 9-III, 10222 Vilnius, Lithuania
- Center for Physical Sciences and Technology, Gostauto 9, 01108 Vilnius, Lithuania
| | - Darius Abramavicius
- Department of Theoretical Physics, Faculty of Physics, Vilnius University, Sauletekio 9-III, 10222 Vilnius, Lithuania
| | - Leonas Valkunas
- Department of Theoretical Physics, Faculty of Physics, Vilnius University, Sauletekio 9-III, 10222 Vilnius, Lithuania
- Center for Physical Sciences and Technology, Gostauto 9, 01108 Vilnius, Lithuania
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19
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Romero E, Augulis R, Novoderezhkin VI, Ferretti M, Thieme J, Zigmantas D, van Grondelle R. Quantum Coherence in Photosynthesis for Efficient Solar Energy Conversion. NATURE PHYSICS 2014; 10:676-682. [PMID: 26870153 PMCID: PMC4746732 DOI: 10.1038/nphys3017] [Citation(s) in RCA: 335] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 06/06/2014] [Indexed: 05/19/2023]
Abstract
The crucial step in the conversion of solar to chemical energy in Photosynthesis takes place in the reaction center where the absorbed excitation energy is converted into a stable charge separated state by ultrafast electron transfer events. However, the fundamental mechanism responsible for the near unity quantum efficiency of this process is unknown. Here we elucidate the role of coherence in determining the efficiency of charge separation in the plant photosystem II reaction centre (PSII RC) by comprehensively combining experiment (two-dimensional electronic spectroscopy) and theory (Redfield theory). We reveal the presence of electronic coherence between excitons as well as between exciton and charge transfer states which we argue to be maintained by vibrational modes. Furthermore, we present evidence for the strong correlation between the degree of electronic coherence and efficient and ultrafast charge separation. We propose that this coherent mechanism will inspire the development of new energy technologies.
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Affiliation(s)
- Elisabet Romero
- Department of Physics and Astronomy, VU University, Amsterdam, The Netherlands
- Contact information: Dr. Elisabet Romero, , Phone +31 20 5987426, Fax +31 20 5987999
| | - Ramunas Augulis
- Department of Chemical Physics, Lund University, Lund, Sweden
| | | | - Marco Ferretti
- Department of Physics and Astronomy, VU University, Amsterdam, The Netherlands
| | - Jos Thieme
- Department of Physics and Astronomy, VU University, Amsterdam, The Netherlands
| | | | - Rienk van Grondelle
- Department of Physics and Astronomy, VU University, Amsterdam, The Netherlands
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20
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Vibronic coherence in oxygenic photosynthesis. Nat Chem 2014; 6:706-11. [DOI: 10.1038/nchem.2005] [Citation(s) in RCA: 303] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 06/16/2014] [Indexed: 01/05/2023]
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21
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Zhang L, Silva DA, Zhang H, Yue A, Yan Y, Huang X. Dynamic protein conformations preferentially drive energy transfer along the active chain of the photosystem II reaction centre. Nat Commun 2014; 5:4170. [PMID: 24954746 PMCID: PMC4083425 DOI: 10.1038/ncomms5170] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 05/20/2014] [Indexed: 11/11/2022] Open
Abstract
One longstanding puzzle concerning photosystem II, a core component of photosynthesis, is that only one of the two symmetric branches in its reaction centre is active in electron transfer. To investigate the effect of the photosystem II environment on the preferential selection of the energy transfer pathway (a prerequisite for electron transfer), we have constructed an exciton model via extensive molecular dynamics simulations and quantum mechanics/molecular mechanics calculations based on a recent X-ray structure. Our results suggest that it is essential to take into account an ensemble of protein conformations to accurately compute the site energies. We identify the cofactor CLA606 of active chain as the most probable site for the energy excitation. We further pinpoint a number of charged protein residues that collectively lower the CLA606 site energy. Our work provides insights into the understanding of molecular mechanisms of the core machinery of the green-plant photosynthesis. Cofactor-mediated energy and electron transfer in photosystem II occurs preferentially through one branch of the reaction centre, despite there being a symmetric path available. Here, the authors use computational methods to determine the influence of protein conformation on this selectivity.
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Affiliation(s)
- Lu Zhang
- Department of Chemistry, Institute for Advance Study and School of Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Daniel-Adriano Silva
- 1] Department of Chemistry, Institute for Advance Study and School of Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong [2]
| | - Houdao Zhang
- Department of Chemistry, Institute for Advance Study and School of Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Alexander Yue
- Division of Biomedical Engineering, Institute for Advance Study and School of Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - YiJing Yan
- 1] Department of Chemistry, Institute for Advance Study and School of Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong [2] Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, China
| | - Xuhui Huang
- 1] Department of Chemistry, Institute for Advance Study and School of Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong [2] Division of Biomedical Engineering, Institute for Advance Study and School of Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong [3] Centre of Systems Biology and Human Health, Institute for Advance Study and School of Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong
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22
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Pishchalnikov RY, Razjivin AP. From localized excited States to excitons: changing of conceptions of primary photosynthetic processes in the twentieth century. BIOCHEMISTRY (MOSCOW) 2014; 79:242-50. [PMID: 24821451 DOI: 10.1134/s0006297914030109] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
A short description of two theories of the primary photosynthetic processes is given. Generally accepted in 1950s-1990s, the localized excited states theory has been changed to the modern exciton theory. Appearance of the new experimental data and the light-harvesting complex crystal structure are reasons why the exciton theory has become important. The bulk of data for the old theory and outstanding experiments that have been the driving force for a new theory are discussed in detail.
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Affiliation(s)
- R Y Pishchalnikov
- Lomonosov Moscow State University, Belozersky Institute of Physico-Chemical Biology, Moscow, 119992, Russia.
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