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Rankelytė G, Gelzinis A, Robert B, Valkunas L, Chmeliov J. Environment-dependent chlorophyll-chlorophyll charge transfer states in Lhca4 pigment-protein complex. FRONTIERS IN PLANT SCIENCE 2024; 15:1412750. [PMID: 39170787 PMCID: PMC11335733 DOI: 10.3389/fpls.2024.1412750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 07/02/2024] [Indexed: 08/23/2024]
Abstract
Photosystem I (PSI) light-harvesting antenna complexes LHCI contain spectral forms that absorb and emit photons of lower energy than that of its primary electron donor, P700. The most red-shifted fluorescence is associated with the Lhca4 complex. It has been suggested that this red emission is related to the inter-chlorophyll charge transfer (CT) states. In this work we present a systematic quantum-chemical study of the CT states in Lhca4, accounting for the influence of the protein environment by estimating the electrostatic interactions. We show that significant energy shifts result from these interactions and propose that the emission of the Lhca4 complex is related not only to the previously proposed a603+-a608- state, but also to the a602+-a603- state. We also investigate how different protonation patterns of protein amino acids affect the energetics of the CT states.
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Affiliation(s)
- Gabrielė Rankelytė
- Institute of Chemical Physics, Faculty of Physics, Vilnius University, Vilnius, Lithuania
- Department of Molecular Compound Physics, Center for Physical Sciences and Technology, Vilnius, Lithuania
| | - Andrius Gelzinis
- Institute of Chemical Physics, Faculty of Physics, Vilnius University, Vilnius, Lithuania
- Department of Molecular Compound Physics, Center for Physical Sciences and Technology, Vilnius, Lithuania
| | - Bruno Robert
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell, Gif-sur-Yvette, France
| | - Leonas Valkunas
- Department of Molecular Compound Physics, Center for Physical Sciences and Technology, Vilnius, Lithuania
| | - Jevgenij Chmeliov
- Institute of Chemical Physics, Faculty of Physics, Vilnius University, Vilnius, Lithuania
- Department of Molecular Compound Physics, Center for Physical Sciences and Technology, Vilnius, Lithuania
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2
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Zhang YZ, Li K, Qin BY, Guo JP, Zhang QB, Zhao DL, Chen XL, Gao J, Liu LN, Zhao LS. Structure of cryptophyte photosystem II-light-harvesting antennae supercomplex. Nat Commun 2024; 15:4999. [PMID: 38866834 PMCID: PMC11169493 DOI: 10.1038/s41467-024-49453-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 06/06/2024] [Indexed: 06/14/2024] Open
Abstract
Cryptophytes are ancestral photosynthetic organisms evolved from red algae through secondary endosymbiosis. They have developed alloxanthin-chlorophyll a/c2-binding proteins (ACPs) as light-harvesting complexes (LHCs). The distinctive properties of cryptophytes contribute to efficient oxygenic photosynthesis and underscore the evolutionary relationships of red-lineage plastids. Here we present the cryo-electron microscopy structure of the Photosystem II (PSII)-ACPII supercomplex from the cryptophyte Chroomonas placoidea. The structure includes a PSII dimer and twelve ACPII monomers forming four linear trimers. These trimers structurally resemble red algae LHCs and cryptophyte ACPI trimers that associate with Photosystem I (PSI), suggesting their close evolutionary links. We also determine a Chl a-binding subunit, Psb-γ, essential for stabilizing PSII-ACPII association. Furthermore, computational calculation provides insights into the excitation energy transfer pathways. Our study lays a solid structural foundation for understanding the light-energy capture and transfer in cryptophyte PSII-ACPII, evolutionary variations in PSII-LHCII, and the origin of red-lineage LHCIIs.
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Affiliation(s)
- Yu-Zhong Zhang
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China.
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China.
| | - Kang Li
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Bing-Yue Qin
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Jian-Ping Guo
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Quan-Bao Zhang
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Dian-Li Zhao
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Xiu-Lan Chen
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Jun Gao
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China.
| | - Lu-Ning Liu
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China.
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK.
| | - Long-Sheng Zhao
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China.
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3
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Zazubovich V, Jankowiak R. High-Resolution Frequency-Domain Spectroscopic and Modeling Studies of Photosystem I (PSI), PSI Mutants and PSI Supercomplexes. Int J Mol Sci 2024; 25:3850. [PMID: 38612659 PMCID: PMC11011720 DOI: 10.3390/ijms25073850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 03/23/2024] [Accepted: 03/26/2024] [Indexed: 04/14/2024] Open
Abstract
Photosystem I (PSI) is one of the two main pigment-protein complexes where the primary steps of oxygenic photosynthesis take place. This review describes low-temperature frequency-domain experiments (absorption, emission, circular dichroism, resonant and non-resonant hole-burned spectra) and modeling efforts reported for PSI in recent years. In particular, we focus on the spectral hole-burning studies, which are not as common in photosynthesis research as the time-domain spectroscopies. Experimental and modeling data obtained for trimeric cyanobacterial Photosystem I (PSI3), PSI3 mutants, and PSI3-IsiA18 supercomplexes are analyzed to provide a more comprehensive understanding of their excitonic structure and excitation energy transfer (EET) processes. Detailed information on the excitonic structure of photosynthetic complexes is essential to determine the structure-function relationship. We will focus on the so-called "red antenna states" of cyanobacterial PSI, as these states play an important role in photochemical processes and EET pathways. The high-resolution data and modeling studies presented here provide additional information on the energetics of the lowest energy states and their chlorophyll (Chl) compositions, as well as the EET pathways and how they are altered by mutations. We present evidence that the low-energy traps observed in PSI are excitonically coupled states with significant charge-transfer (CT) character. The analysis presented for various optical spectra of PSI3 and PSI3-IsiA18 supercomplexes allowed us to make inferences about EET from the IsiA18 ring to the PSI3 core and demonstrate that the number of entry points varies between sample preparations studied by different groups. In our most recent samples, there most likely are three entry points for EET from the IsiA18 ring per the PSI core monomer, with two of these entry points likely being located next to each other. Therefore, there are nine entry points from the IsiA18 ring to the PSI3 trimer. We anticipate that the data discussed below will stimulate further research in this area, providing even more insight into the structure-based models of these important cyanobacterial photosystems.
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Affiliation(s)
- Valter Zazubovich
- Department of Physics, Concordia University, Montreal, QC H4B 1R6, Canada
| | - Ryszard Jankowiak
- Department of Chemistry, Kansas State University, Manhattan, KS 66506, USA
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4
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Gera T, Chen L, Eisfeld A, Reimers JR, Taffet EJ, Raccah DIGB. Simulating optical linear absorption for mesoscale molecular aggregates: An adaptive hierarchy of pure states approach. J Chem Phys 2023; 158:2887556. [PMID: 37125709 DOI: 10.1063/5.0141882] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 03/07/2023] [Indexed: 05/02/2023] Open
Abstract
In this paper, we present dyadic adaptive HOPS (DadHOPS), a new method for calculating linear absorption spectra for large molecular aggregates. This method combines the adaptive HOPS (adHOPS) framework, which uses locality to improve computational scaling, with the dyadic HOPS method previously developed to calculate linear and nonlinear spectroscopic signals. To construct a local representation of dyadic HOPS, we introduce an initial state decomposition that reconstructs the linear absorption spectra from a sum over locally excited initial conditions. We demonstrate the sum over initial conditions can be efficiently Monte Carlo sampled and that the corresponding calculations achieve size-invariant [i.e., O(1)] scaling for sufficiently large aggregates while trivially incorporating static disorder in the Hamiltonian. We present calculations on the photosystem I core complex to explore the behavior of the initial state decomposition in complex molecular aggregates as well as proof-of-concept DadHOPS calculations on an artificial molecular aggregate inspired by perylene bis-imide to demonstrate the size-invariance of the method.
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Affiliation(s)
- Tarun Gera
- Department of Chemistry, Southern Methodist University, P.O. Box, Dallas, Texas 750314, USA
| | - Lipeng Chen
- Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Str. 38, Dresden, Germany
| | - Alexander Eisfeld
- Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Str. 38, Dresden, Germany
| | - Jeffrey R Reimers
- International Centre for Quantum and Molecular Structures and the School of Physics, Shanghai University, 200444 Shanghai, China
- School of Mathematical and Physical Sciences, University of Technology Sydney, Sydney NSW 2007, Australia
| | - Elliot J Taffet
- Department of Chemistry, Southern Methodist University, P.O. Box, Dallas, Texas 750314, USA
| | - Doran I G B Raccah
- Department of Chemistry, Southern Methodist University, P.O. Box, Dallas, Texas 750314, USA
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5
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Novoderezhkin VI, Croce R. The location of the low-energy states in Lhca1 favors excitation energy transfer to the core in the plant PSI-LHCI supercomplex. PHOTOSYNTHESIS RESEARCH 2023; 156:59-74. [PMID: 36374368 DOI: 10.1007/s11120-022-00979-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 10/19/2022] [Indexed: 06/16/2023]
Abstract
Lhca1 is one of the four pigment-protein complexes composing the outer antenna of plant Photosystem I-light-havesting I supercomplex (PSI-LHCI). It forms a functional dimer with Lhca4 but, differently from this complex, it does not contain 'red-forms,' i.e., pigments absorbing above 700 nm. Interestingly, the recent PSI-LHCI structures suggest that Lhca1 is the main point of delivering the energy harvested by the antenna to the core. To identify the excitation energy pathways in Lhca1, we developed a structure-based exciton model based on the simultaneous fit of the low-temperature absorption, linear dichroism, and fluorescence spectra of wild-type Lhca1 and two mutants, lacking chlorophylls contributing to the long-wavelength region of the absorption. The model enables us to define the locations of the lowest energy pigments in Lhca1 and estimate pathways and timescales of energy transfer within the complex and to the PSI core. We found that Lhca1 has a particular energy landscape with an unusual (compared to Lhca4, LHCII, and CP29) configuration of the low-energy states. Remarkably, these states are located near the core, facilitating direct energy transfer to it. Moreover, the low-energy states of Lhca1 are also coupled to the red-most state (red forms) of the neighboring Lhca4 antenna, providing a pathway for effective excitation energy transfer from Lhca4 to the core.
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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.
| | - Roberta Croce
- Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
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6
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Reiter S, Kiss FL, Hauer J, de Vivie-Riedle R. Thermal site energy fluctuations in photosystem I: new insights from MD/QM/MM calculations. Chem Sci 2023; 14:3117-3131. [PMID: 36970098 PMCID: PMC10034153 DOI: 10.1039/d2sc06160k] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 02/03/2023] [Indexed: 02/09/2023] Open
Abstract
Cyanobacterial photosystem I (PSI) is one of the most efficient photosynthetic machineries found in nature. Due to the large scale and complexity of the system, the energy transfer mechanism from the antenna complex to the reaction center is still not fully understood. A central element is the accurate evaluation of the individual chlorophyll excitation energies (site energies). Such an evaluation must include a detailed treatment of site specific environmental influences on structural and electrostatic properties, but also their evolution in the temporal domain, because of the dynamic nature of the energy transfer process. In this work, we calculate the site energies of all 96 chlorophylls in a membrane-embedded model of PSI. The employed hybrid QM/MM approach using the multireference DFT/MRCI method in the QM region allows to obtain accurate site energies under explicit consideration of the natural environment. We identify energy traps and barriers in the antenna complex and discuss their implications for energy transfer to the reaction center. Going beyond previous studies, our model also accounts for the molecular dynamics of the full trimeric PSI complex. Via statistical analysis we show that the thermal fluctuations of single chlorophylls prevent the formation of a single prominent energy funnel within the antenna complex. These findings are also supported by a dipole exciton model. We conclude that energy transfer pathways may form only transiently at physiological temperatures, as thermal fluctuations overcome energy barriers. The set of site energies provided in this work sets the stage for theoretical and experimental studies on the highly efficient energy transfer mechanisms in PSI.
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Affiliation(s)
- Sebastian Reiter
- Department of Chemistry, Ludwig-Maximilians-Universität München Butenandtstr. 11 81377 Munich Germany
| | - Ferdinand L Kiss
- Department of Chemistry, Ludwig-Maximilians-Universität München Butenandtstr. 11 81377 Munich Germany
| | - Jürgen Hauer
- Department of Chemistry, Technical University of Munich Lichtenbergstr. 4, Garching 85747 Germany
| | - Regina de Vivie-Riedle
- Department of Chemistry, Ludwig-Maximilians-Universität München Butenandtstr. 11 81377 Munich Germany
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7
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Förster A, Visscher L. Quasiparticle Self-Consistent GW-Bethe-Salpeter Equation Calculations for Large Chromophoric Systems. J Chem Theory Comput 2022; 18:6779-6793. [PMID: 36201788 PMCID: PMC9648197 DOI: 10.1021/acs.jctc.2c00531] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
The GW-Bethe–Salpeter equation
(BSE) method
is promising for calculating the low-lying excitonic states of molecular
systems. However, so far it has only been applied to rather small
molecules and in the commonly implemented diagonal approximations
to the electronic self-energy, it depends on a mean-field starting
point. We describe here an implementation of the self-consistent and
starting-point-independent quasiparticle self-consistent (qsGW)-BSE approach, which is suitable for calculations on
large molecules. We herein show that eigenvalue-only self-consistency
can lead to an unfaithful description of some excitonic states for
chlorophyll dimers while the qsGW-BSE vertical excitation
energies (VEEs) are in excellent agreement with spectroscopic experiments
for chlorophyll monomers and dimers measured in the gas phase. Furthermore,
VEEs from time-dependent density functional theory calculations tend
to disagree with experimental values and using different range-separated
hybrid (RSH) kernels does change the VEEs by up to 0.5 eV. We use
the new qsGW-BSE implementation to calculate the
lowest excitation energies of the six chromophores of the photosystem
II (PSII) reaction center (RC) with nearly 2000 correlated electrons.
Using more than 11,000 (6000) basis functions, the calculation could
be completed in less than 5 (2) days on a single modern compute node.
In agreement with previous TD-DFT calculations using RSH kernels on
models that also do not include environmental effects, our qsGW-BSE calculations only yield states with local characters
in the low-energy spectrum of the hexameric complex. Earlier works
with RSH kernels have demonstrated that the protein environment facilitates
the experimentally observed interchromophoric charge transfer. Therefore,
future research will need to combine correlation effects beyond TD-DFT
with an explicit treatment of environmental electrostatics.
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Affiliation(s)
- Arno Förster
- Theoretical Chemistry, Vrije Universiteit, De Boelelaan 1083, NL-1081 HVAmsterdam, The Netherlands
| | - Lucas Visscher
- Theoretical Chemistry, Vrije Universiteit, De Boelelaan 1083, NL-1081 HVAmsterdam, The Netherlands
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8
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Cherepanov DA, Semenov AY, Mamedov MD, Aybush AV, Gostev FE, Shelaev IV, Shuvalov VA, Nadtochenko VA. Current state of the primary charge separation mechanism in photosystem I of cyanobacteria. Biophys Rev 2022; 14:805-820. [PMID: 36124265 PMCID: PMC9481807 DOI: 10.1007/s12551-022-00983-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 07/10/2022] [Indexed: 11/24/2022] Open
Abstract
This review analyzes new data on the mechanism of ultrafast reactions of primary charge separation in photosystem I (PS I) of cyanobacteria obtained in the last decade by methods of femtosecond absorption spectroscopy. Cyanobacterial PS I from many species harbours 96 chlorophyll a (Chl a) molecules, including six specialized Chls denoted Chl1A/Chl1B (dimer P700, or PAPB), Chl2A/Chl2B, and Chl3A/Chl3B arranged in two branches, which participate in electron transfer reactions. The current data indicate that the primary charge separation occurs in a symmetric exciplex, where the special pair P700 is electronically coupled to the symmetrically located monomers Chl2A and Chl2B, which can be considered together as a symmetric exciplex Chl2APAPBChl2B with the mixed excited (Chl2APAPBChl2B)* and two charge-transfer states P700 +Chl2A - and P700 +Chl2B -. The redistribution of electrons between the branches in favor of the A-branch occurs after reduction of the Chl2A and Chl2B monomers. The formation of charge-transfer states and the symmetry breaking mechanisms were clarified by measuring the electrochromic Stark shift of β-carotene and the absorption dynamics of PS I complexes with the genetically altered Chl 2B or Chl 2A monomers. The review gives a brief description of the main methods for analyzing data obtained using femtosecond absorption spectroscopy. The energy levels of excited and charge-transfer intermediates arising in the cyanobacterial PS I are critically analyzed.
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Affiliation(s)
- Dmitry A. Cherepanov
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119991, Kosygina Street 1, Moscow, Russia
| | - Alexey Yu Semenov
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119991, Kosygina Street 1, Moscow, Russia
- A.N. Belozersky Institute of Physical-Chemical Biology, M.V. Lomonosov Moscow State University, 119992 Leninskye gory 1 building, 40 Moscow, Russia
| | - Mahir D. Mamedov
- A.N. Belozersky Institute of Physical-Chemical Biology, M.V. Lomonosov Moscow State University, 119992 Leninskye gory 1 building, 40 Moscow, Russia
| | - Arseniy V. Aybush
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119991, Kosygina Street 1, Moscow, Russia
| | - Fedor E. Gostev
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119991, Kosygina Street 1, Moscow, Russia
| | - Ivan V. Shelaev
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119991, Kosygina Street 1, Moscow, Russia
| | - Vladimir A. Shuvalov
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119991, Kosygina Street 1, Moscow, Russia
| | - Victor A. Nadtochenko
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119991, Kosygina Street 1, Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, 119991, Leninskiye Gory 1-3, Moscow, Russia
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9
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Mikalčiūtė A, Gelzinis A, Mačernis M, Büchel C, Robert B, Valkunas L, Chmeliov J. Structure-based model of fucoxanthin-chlorophyll protein complex: Calculations of chlorophyll electronic couplings. J Chem Phys 2022; 156:234101. [PMID: 35732526 DOI: 10.1063/5.0092154] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Diatoms are a group of marine algae that are responsible for a significant part of global oxygen production. Adapted to life in an aqueous environment dominated by the blue-green light, their major light-harvesting antennae-fucoxanthin-chlorophyll protein complexes (FCPs)-exhibit different pigment compositions than of plants. Despite extensive experimental studies, until recently the theoretical description of excitation energy dynamics in these complexes was limited by the lack of high-resolution structural data. In this work, we use the recently resolved crystallographic information of the FCP complex from Phaeodactylum tricornutum diatom [Wang et al., Science 363, 6427 (2019)] and quantum chemistry-based calculations to evaluate the chlorophyll transition dipole moments, atomic transition charges from electrostatic potential, and the inter-chlorophyll couplings in this complex. The obtained structure-based excitonic couplings form the foundation for any modeling of stationary or time-resolved spectroscopic data. We also calculate the inter-pigment Förster energy transfer rates and identify two quickly equilibrating chlorophyll clusters.
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Affiliation(s)
- Austėja Mikalčiūtė
- Institute of Chemical Physics, Faculty of Physics, Vilnius University, Saulėtekio Avenue 9, LT-10222 Vilnius, Lithuania
| | - Andrius Gelzinis
- Institute of Chemical Physics, Faculty of Physics, Vilnius University, Saulėtekio Avenue 9, LT-10222 Vilnius, Lithuania
| | - Mindaugas Mačernis
- Institute of Chemical Physics, Faculty of Physics, Vilnius University, Saulėtekio Avenue 9, LT-10222 Vilnius, Lithuania
| | - Claudia Büchel
- Institute of Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue Straße 9, 60438 Frankfurt, Germany
| | - Bruno Robert
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Leonas Valkunas
- Institute of Chemical Physics, Faculty of Physics, Vilnius University, Saulėtekio Avenue 9, LT-10222 Vilnius, Lithuania
| | - Jevgenij Chmeliov
- Institute of Chemical Physics, Faculty of Physics, Vilnius University, Saulėtekio Avenue 9, LT-10222 Vilnius, Lithuania
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10
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Li M, Kobayashi R, Amos RD, Ford MJ, Reimers JR. Density functionals with asymptotic-potential corrections are required for the simulation of spectroscopic properties of materials. Chem Sci 2022; 13:1492-1503. [PMID: 35222934 PMCID: PMC8809424 DOI: 10.1039/d1sc03738b] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 12/31/2021] [Indexed: 11/21/2022] Open
Abstract
Five effects of correction of the asymptotic potential error in density functionals are identified that significantly improve calculated properties of molecular excited states involving charge-transfer character. Newly developed materials-science computational methods are used to demonstrate how these effects manifest in materials spectroscopy. Connection is made considering chlorophyll-a as a paradigm for molecular spectroscopy, 22 iconic materials as paradigms for 3D materials spectroscopy, and the VN - defect in hexagonal boron nitride as an example of the spectroscopy of defects in 2D materials pertaining to nanophotonics. Defects can equally be thought of as being "molecular" and "materials" in nature and hence bridge the relms of molecular and materials spectroscopies. It is concluded that the density functional HSE06, currently considered as the standard for accurate calculations of materials spectroscopy, should be replaced, in most instances, by the computationally similar but asymptotically corrected CAM-B3LYP functional, with some specific functionals for materials-use only providing further improvements.
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Affiliation(s)
- Musen Li
- International Centre for Quantum and Molecular Structures and Department of Physics, Shanghai University Shanghai 200444 China
| | - Rika Kobayashi
- ANU Supercomputer Facility Leonard Huxley Bldg. 56, Mills Rd Canberra ACT 2601 Australia
| | - Roger D Amos
- ANU Supercomputer Facility Leonard Huxley Bldg. 56, Mills Rd Canberra ACT 2601 Australia
| | - Michael J Ford
- University of Technology Sydney, School of Mathematical and Physical Sciences Ultimo New South Wales 2007 Australia
| | - Jeffrey R Reimers
- International Centre for Quantum and Molecular Structures and Department of Physics, Shanghai University Shanghai 200444 China
- University of Technology Sydney, School of Mathematical and Physical Sciences Ultimo New South Wales 2007 Australia
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11
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Mao R, Wang X, Gao J. Bridging Carotenoid-to-Bacteriochlorophyll Energy Transfer of Purple Bacteria LH2 With Temperature Variations: Insights From Conformational Changes. Front Chem 2021; 9:764107. [PMID: 34671594 PMCID: PMC8521103 DOI: 10.3389/fchem.2021.764107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 09/20/2021] [Indexed: 11/13/2022] Open
Abstract
Photosynthesis is a key process for converting light energy into chemical energy and providing food for lives on Earth. Understanding the mechanism for the energy transfers could provide insights into regulating energy transfers in photosynthesis and designing artificial photosynthesis systems. Many efforts have been devoted to exploring the mechanism of temperature variations affecting the excitonic properties of LH2. In this study, we performed all-atom molecular dynamics (MD) simulations and quantum mechanics calculations for LH2 complex from purple bacteria along with its membrane environment under three typical temperatures: 270, 300, and 330 K. The structural analysis from validated MD simulations showed that the higher temperature impaired interactions at N-terminus of both α and β polypeptide helices and led to the dissociation of this hetero polypeptide dimer. Rhodopin-β-D-glucosides (RG1) moved centripetally with α polypeptide helices when temperature increased and enlarged their distances with bacteriochlorophylls molecules that have the absorption peak at 850 nm (B850), which resulted in reducing the coupling strengths between RG1 and B850 molecules. The present study reported a cascading mechanism for temperature regulating the energy transfers in LH2 of purple bacteria.
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Affiliation(s)
- Ruichao Mao
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Xiaocong Wang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Jun Gao
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
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12
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Akhtar P, Caspy I, Nowakowski PJ, Malavath T, Nelson N, Tan HS, Lambrev PH. Two-Dimensional Electronic Spectroscopy of a Minimal Photosystem I Complex Reveals the Rate of Primary Charge Separation. J Am Chem Soc 2021; 143:14601-14612. [PMID: 34472838 DOI: 10.1021/jacs.1c05010] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Photosystem I (PSI), found in all oxygenic photosynthetic organisms, uses solar energy to drive electron transport with nearly 100% quantum efficiency, thanks to fast energy transfer among antenna chlorophylls and charge separation in the reaction center. There is no complete consensus regarding the kinetics of the elementary steps involved in the overall trapping, especially the rate of primary charge separation. In this work, we employed two-dimensional coherent electronic spectroscopy to follow the dynamics of energy and electron transfer in a monomeric PSI complex from Synechocystis PCC 6803, containing only subunits A-E, K, and M, at 77 K. We also determined the structure of the complex to 4.3 Å resolution by cryoelectron microscopy with refinements to 2.5 Å. We applied structure-based modeling using a combined Redfield-Förster theory to compute the excitation dynamics. The absorptive 2D electronic spectra revealed fast excitonic/vibronic relaxation on time scales of 50-100 fs from the high-energy side of the absorption spectrum. Antenna excitations were funneled within 1 ps to a small pool of chlorophylls absorbing around 687 nm, thereafter decaying with 4-20 ps lifetimes, independently of excitation wavelength. Redfield-Förster energy transfer computations showed that the kinetics is limited by transfer from these red-shifted pigments. The rate of primary charge separation, upon direct excitation of the reaction center, was determined to be 1.2-1.5 ps-1. This result implies activationless electron transfer in PSI.
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Affiliation(s)
- Parveen Akhtar
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Nanyang Link 21, 637371 Singapore.,Biological Research Centre, Szeged, Temesvári krt. 62, Szeged 6726, Hungary.,ELI-ALPS, ELI-HU Non-profit Ltd., Wolfgang Sandner u. 3, Szeged 6728, Hungary
| | - Ido Caspy
- Department of Biochemistry and Molecular Biology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Paweł J Nowakowski
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Nanyang Link 21, 637371 Singapore
| | - Tirupathi Malavath
- Department of Biochemistry and Molecular Biology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Nathan Nelson
- Department of Biochemistry and Molecular Biology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Howe-Siang Tan
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Nanyang Link 21, 637371 Singapore
| | - Petar H Lambrev
- Biological Research Centre, Szeged, Temesvári krt. 62, Szeged 6726, Hungary
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13
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Cherepanov DA, Shelaev IV, Gostev FE, Nadtochenko VA, Xu W, Golbeck JH, Semenov AY. Symmetry breaking in photosystem I: ultrafast optical studies of variants near the accessory chlorophylls in the A- and B-branches of electron transfer cofactors. Photochem Photobiol Sci 2021; 20:1209-1227. [PMID: 34478050 DOI: 10.1007/s43630-021-00094-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 08/18/2021] [Indexed: 11/25/2022]
Abstract
Femtosecond absorption spectroscopy of Photosystem I (PS I) complexes from the cyanobacterium Synechocystis sp. PCC 6803 was carried out on three pairs of complementary amino acid substitutions located near the second pair of chlorophyll molecules Chl2A and Chl2B (also termed A-1A and A-1B). The absorption dynamics at delays of 0.1-500 ps were analyzed by decomposition into discrete decay-associated spectra and continuously distributed exponential components. The multi-exponential deconvolution of the absorption changes revealed that the electron transfer reactions in the PsaA-N600M, PsaA-N600H, and PsaA-N600L variants near the B-branch of cofactors are similar to those of the wild type, while the PsaB-N582M, PsaB-N582H, and PsaB-N582L variants near the A-branch of cofactors cause significant alterations of the photochemical processes, making them heterogeneous and poorly described by a discrete exponential kinetic model. A redistribution of the unpaired electron between the second and the third monomers Chl2A/Chl2B and Chl3A/Chl3B was identified in the time range of 9-20 ps, and the subsequent reduction of A1 was identified in the time range of 24-70 ps. In the PsaA-N600L and PsaB-N582H/L variants, the reduction of A1 occurred with a decreased quantum yield of charge separation. The decreased quantum yield correlates with a slowing of the phylloquinone A0 → A1 reduction, but not with the initial transient spectra measured at the shortest time delay. The results support a branch competition model, where the electron is sheared between Chl2A-Chl3A and Chl2B-Chl3B cofactors before its transfer to phylloquinone in either A1A or A1B sites.
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Affiliation(s)
- Dmitry A Cherepanov
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Kosygina St. 4, Moscow, 117977, Russian Federation.
| | - Ivan V Shelaev
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Kosygina St. 4, Moscow, 117977, Russian Federation
| | - Fedor E Gostev
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Kosygina St. 4, Moscow, 117977, Russian Federation
| | - Victor A Nadtochenko
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Kosygina St. 4, Moscow, 117977, Russian Federation.,Department of Chemistry, Lomonosov Moscow State University, Leninskiye Gory 1-3, Moscow, 119991, Russian Federation
| | - Wu Xu
- Department of Chemistry, University of Louisiana at Lafayette, Lafayette, LA, 70504, USA
| | - John H Golbeck
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16801, USA.,Department of Chemistry, The Pennsylvania State University, University Park, PA, 16801, USA
| | - Alexey Yu Semenov
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Kosygina St. 4, Moscow, 117977, Russian Federation.,A.N. Belozersky Institute of Physical-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, 1, Moscow, 119992, Russian Federation
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14
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Gorka M, Charles P, Kalendra V, Baldansuren A, Lakshmi KV, Golbeck JH. A dimeric chlorophyll electron acceptor differentiates type I from type II photosynthetic reaction centers. iScience 2021; 24:102719. [PMID: 34278250 PMCID: PMC8267441 DOI: 10.1016/j.isci.2021.102719] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 05/17/2021] [Accepted: 06/09/2021] [Indexed: 01/09/2023] Open
Abstract
This research addresses one of the most compelling issues in the field of photosynthesis, namely, the role of the accessory chlorophyll molecules in primary charge separation. Using a combination of empirical and computational methods, we demonstrate that the primary acceptor of photosystem (PS) I is a dimer of accessory and secondary chlorophyll molecules, Chl2A and Chl3A, with an asymmetric electron charge density distribution. The incorporation of highly coupled donors and acceptors in PS I allows for extensive delocalization that prolongs the lifetime of the charge-separated state, providing for high quantum efficiency. The discovery of this motif has widespread implications ranging from the evolution of naturally occurring reaction centers to the development of a new generation of highly efficient artificial photosynthetic systems. Video abstract
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Affiliation(s)
- Michael Gorka
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Philip Charles
- Department of Chemistry and Chemical Biology and The Baruch '60 Center for Biochemical Solar Energy Research, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Vidmantas Kalendra
- Department of Chemistry and Chemical Biology and The Baruch '60 Center for Biochemical Solar Energy Research, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Amgalanbaatar Baldansuren
- Department of Chemistry and Chemical Biology and The Baruch '60 Center for Biochemical Solar Energy Research, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - K V Lakshmi
- Department of Chemistry and Chemical Biology and The Baruch '60 Center for Biochemical Solar Energy Research, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - John H Golbeck
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.,Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
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15
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Li M, Reimers JR, Ford MJ, Kobayashi R, Amos RD. Accurate prediction of the properties of materials using the CAM-B3LYP density functional. J Comput Chem 2021; 42:1486-1497. [PMID: 34013573 DOI: 10.1002/jcc.26558] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/21/2021] [Accepted: 04/26/2021] [Indexed: 12/25/2022]
Abstract
Density functionals with asymptotic corrections to the long-range potential provide entry-level methods for calculations on molecules that can sustain charge transfer, but similar applications in materials science are rare. We describe an implementation of the CAM-B3LYP range-separated functional within the Vienna Ab-initio Simulation Package (VASP) framework, together with its analytical functional derivatives. Results obtained for eight representative materials: aluminum, diamond, graphene, silicon, NaCl, MgO, 2D h-BN, and 3D h-BN, indicate that CAM-B3LYP predictions embody mean-absolute deviations (MAD) compared to HSE06 that are reduced by a factor of six for lattice parameters, four for quasiparticle band gaps, three for the lowest optical excitation energies, and six for exciton binding energies. Further, CAM-B3LYP appears competitive compared to ab initio G0 W0 and Bethe-Salpeter equation approaches. The CAM-B3LYP implementation in VASP was verified by comparison of optimized geometries and reaction energies for isolated molecules taken from the ACCDB database, evaluated in large periodic unit cells, to analogous results obtained using Gaussian basis sets. Using standard GW pseudopotentials and energy cutoffs for the plane-wave calculations and the aug-cc-pV5Z basis set for the atomic-basis ones, the MAD in energy for 1738 chemical reactions was 0.34 kcal mol-1 , while for 480 unique bond lengths this was 0.0036 Å; these values reduced to 0.28 kcal mol-1 (largest error 0.94 kcal mol-1 ) and 0.0009 Å by increasing the plane-wave cutoff energy to 850 eV.
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Affiliation(s)
- Musen Li
- International Centre for Quantum and Molecular Structures and Department of Physics, Shanghai University, Shanghai, China
| | - Jeffrey R Reimers
- International Centre for Quantum and Molecular Structures and Department of Physics, Shanghai University, Shanghai, China.,School of Mathematical and Physical Sciences, University of Technology Sydney, Ultimo, Australia
| | - Michael J Ford
- School of Mathematical and Physical Sciences, University of Technology Sydney, Ultimo, Australia
| | - Rika Kobayashi
- ANU Supercomputer Facility, Leonard Huxley Building 56, Mills Rd, Acton, ACT, 2601, Australia
| | - Roger D Amos
- ANU Supercomputer Facility, Leonard Huxley Building 56, Mills Rd, Acton, ACT, 2601, Australia
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16
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Wang Z, Suo B, Yin S, Zou W. Quantum Chemical Simulation of the Qy Absorption Spectrum of Zn Chlorin Aggregates for Artificial Photosynthesis. Molecules 2021; 26:1086. [PMID: 33669551 PMCID: PMC7922025 DOI: 10.3390/molecules26041086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 02/13/2021] [Accepted: 02/15/2021] [Indexed: 11/16/2022] Open
Abstract
Zn chlorin (Znchl) is easy to synthesize and has similar optical properties to those of bacteriochlorophyll c in the nature, which is expected to be used as a light-harvesting antenna system in artificial photosynthesis. In order to further explore the optical characteristics of Znchl, various sizes of a parallel layered Znchl-aggregate model and the THF-Znchl explicit solvent monomer model were constructed in this study, and their Qy excited state properties were simulated by using time-dependent density functional theory (TDDFT) and exciton theory. For the Znchl monomer, with a combination of the explicit solvent model and the implicit solvation model based on density (SMD), the calculated Qy excitation energy agreed very well with the experimental one. The Znchl aggregates may be simplified to a Zn36 model to reproduce the experimental Qy absorption spectrum by the Förster coupling theory. The proposed Znchl aggregate model provides a good foundation for the future exploration of other properties of Znchl and simulations of artificial light-harvesting antennas. The results also indicate that J-aggregrates along z-direction, due to intermolecular coordination bonds, are the dominant factor in extending the Qy band of Znchl into the near infrared region.
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Affiliation(s)
- Zhimo Wang
- Institute of Modern Physics, Northwest University, and Shaanxi Key Laboratory for Theoretical Physics Frontiers, Xi’an 710127, China;
| | - Bingbing Suo
- Institute of Modern Physics, Northwest University, and Shaanxi Key Laboratory for Theoretical Physics Frontiers, Xi’an 710127, China;
| | - Shiwei Yin
- Key Laboratory for Macromolecular Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi’an 710062, China;
| | - Wenli Zou
- Institute of Modern Physics, Northwest University, and Shaanxi Key Laboratory for Theoretical Physics Frontiers, Xi’an 710127, China;
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17
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Cherepanov DA, Shelaev IV, Gostev FE, Petrova A, Aybush AV, Nadtochenko VA, Xu W, Golbeck JH, Semenov AY. Primary charge separation within the structurally symmetric tetrameric Chl 2AP AP BChl 2B chlorophyll exciplex in photosystem I. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2021; 217:112154. [PMID: 33636482 DOI: 10.1016/j.jphotobiol.2021.112154] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 01/05/2021] [Accepted: 02/12/2021] [Indexed: 12/01/2022]
Abstract
In Photosystem I (PS I), the role of the accessory chlorophyll (Chl) molecules, Chl2A and Chl2B (also termed A-1A and A-1B), which are directly adjacent to the special pair P700 and fork into the A- and B-branches of electron carriers, is incompletely understood. In this work, the Chl2A and Chl2B transient absorption ΔA0(λ) at a time delay of 100 fs was identified by ultrafast pump-probe spectroscopy in three pairs of PS I complexes from Synechocystis sp. PCC 6803 with residues PsaA-N600 or PsaB-N582 (which ligate Chl2B or Chl2A through a H2O molecule) substituted by Met, His, and Leu. The ΔA0(λ) spectra were quantified using principal component analysis, the main component of which was interpreted as a mutation-induced shift of the equilibrium between the excited state of primary donor P700⁎ and the primary charge-separated state P700+Chl2-. This equilibrium is shifted to the charge-separated state in wild-type PS I and to the excited P700 in the PS I complexes with the substituted ligands to the Chl2A and Chl2B monomers. The results can be rationalized within the framework of an adiabatic model in which the P700 is electronically coupled with the symmetrically arranged monomers Chl2A and Chl2B; such a structure can be considered a symmetric tetrameric exciplex Chl2APAPBChl2B, in which the excited state (Chl2APAPBChl2B)* is mixed with two charge-transfer states P700+Chl2A- and P700+Chl2B-. The electron redistribution between the two branches in favor of the A-branch apparently takes place in the picosecond time scale after reduction of the Chl2A and Chl2B monomers.
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Affiliation(s)
- Dmitry A Cherepanov
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 117977 Moscow, Kosygina st., 4, Russia.
| | - Ivan V Shelaev
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 117977 Moscow, Kosygina st., 4, Russia
| | - Fedor E Gostev
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 117977 Moscow, Kosygina st., 4, Russia
| | - Anastasia Petrova
- A.N. Belozersky Institute of Physical-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Leninskie gory, 1, Building 40, Russia
| | - Arseniy V Aybush
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 117977 Moscow, Kosygina st., 4, Russia
| | - Victor A Nadtochenko
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 117977 Moscow, Kosygina st., 4, Russia; Department of Chemistry, Lomonosov Moscow State University, Leninskiye Gory 1-3, Moscow 119991, Russian Federation
| | - Wu Xu
- Department of Chemistry, University of Louisiana at Lafayette, Lafayette, LA 70504, USA
| | - John H Golbeck
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16801, USA; Department of Chemistry, The Pennsylvania State University, University Park, PA 16801, USA
| | - Alexey Yu Semenov
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 117977 Moscow, Kosygina st., 4, Russia; A.N. Belozersky Institute of Physical-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Leninskie gory, 1, Building 40, Russia
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18
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Cherepanov DA, Shelaev IV, Gostev FE, Aybush AV, Mamedov MD, Shuvalov VA, Semenov AY, Nadtochenko VA. Generation of ion-radical chlorophyll states in the light-harvesting antenna and the reaction center of cyanobacterial photosystem I. PHOTOSYNTHESIS RESEARCH 2020; 146:55-73. [PMID: 32144697 DOI: 10.1007/s11120-020-00731-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 02/24/2020] [Indexed: 05/09/2023]
Abstract
The energy and charge-transfer processes in photosystem I (PS I) complexes isolated from cyanobacteria Thermosynechococcus elongatus and Synechocystis sp. PCC 6803 were investigated by pump-to-probe femtosecond spectroscopy. The formation of charge-transfer (CT) states in excitonically coupled chlorophyll a complexes (exciplexes) was monitored by measuring the electrochromic shift of β-carotene in the spectral range 500-510 nm. The excitation of high-energy chlorophyll in light-harvesting antenna of both species was not accompanied by immediate appearance of an electrochromic shift. In PS I from T. elongatus, the excitation of long-wavelength chlorophyll (LWC) caused a pronounced electrochromic effect at 502 nm assigned to the appearance of CT states of chlorophyll exciplexes. The formation of ion-radical pair P700+A1- at 40 ps was limited by energy transfer from LWC to the primary donor P700 and accompanied by carotenoid bleach at 498 nm. In PS I from Synechocystis 6803, the excitation at 720 nm produced an immediate bidentate bleach at 690/704 nm and synchronous carotenoid response at 508 nm. The bidentate bleach was assigned to the formation of primary ion-radical state PB+Chl2B-, where negative charge is localized predominantly at the accessory chlorophyll molecule in the branch B, Chl2B. The following decrease of carotenoid signal at ~ 5 ps was ascribed to electron transfer to the more distant molecule Chl3B. The reduction of phylloquinone in the sites A1A and A1B was accompanied by a synchronous blue-shift of the carotenoid response to 498 nm, pointing to fast redistribution of unpaired electron between two branches in favor of the state PB+A1A-.
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Affiliation(s)
- Dmitry A Cherepanov
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, Russia.
| | - Ivan V Shelaev
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Fedor E Gostev
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Arseniy V Aybush
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Mahir D Mamedov
- A.N. Belozersky Institute of Physical-Chemical Biology, Moscow State University, Kosygina st., 4, Moscow, Russia, 117991
| | - Vladimir A Shuvalov
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, Russia
- A.N. Belozersky Institute of Physical-Chemical Biology, Moscow State University, Kosygina st., 4, Moscow, Russia, 117991
- Institute of Basic Biological Problems, Pushchino Scientific Center for Biological Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Alexey Yu Semenov
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, Russia
- A.N. Belozersky Institute of Physical-Chemical Biology, Moscow State University, Kosygina st., 4, Moscow, Russia, 117991
| | - Victor A Nadtochenko
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, Russia
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The structure of a red-shifted photosystem I reveals a red site in the core antenna. Nat Commun 2020; 11:5279. [PMID: 33077842 PMCID: PMC7573975 DOI: 10.1038/s41467-020-18884-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 09/11/2020] [Indexed: 12/12/2022] Open
Abstract
Photosystem I coordinates more than 90 chlorophylls in its core antenna while achieving near perfect quantum efficiency. Low energy chlorophylls (also known as red chlorophylls) residing in the antenna are important for energy transfer dynamics and yield, however, their precise location remained elusive. Here, we construct a chimeric Photosystem I complex in Synechocystis PCC 6803 that shows enhanced absorption in the red spectral region. We combine Cryo-EM and spectroscopy to determine the structure−function relationship in this red-shifted Photosystem I complex. Determining the structure of this complex reveals the precise architecture of the low energy site as well as large scale structural heterogeneity which is probably universal to all trimeric Photosystem I complexes. Identifying the structural elements that constitute red sites can expand the absorption spectrum of oxygenic photosynthetic and potentially modulate light harvesting efficiency. Cyanobacterial photosystem I has a highly conserved core antenna consisting of eleven subunits and more than 90 chlorophylls. Here via CryoEM and spectroscopy, the authors determine the location of a red-shifted low-energy chlorophyll that allows harvesting of longer wavelengths of light.
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20
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Khmelnitskiy A, Toporik H, Mazor Y, Jankowiak R. On the Red Antenna States of Photosystem I Mutants from Cyanobacteria Synechocystis PCC 6803. J Phys Chem B 2020; 124:8504-8515. [DOI: 10.1021/acs.jpcb.0c05201] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Anton Khmelnitskiy
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, United States
| | - Hila Toporik
- School of Molecular Sciences and The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Yuval Mazor
- School of Molecular Sciences and The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Ryszard Jankowiak
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, United States
- Department of Physics, Kansas State University, Manhattan, Kansas 66506, United States
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21
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Evidence that chlorophyll f functions solely as an antenna pigment in far-red-light photosystem I from Fischerella thermalis PCC 7521. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1861:148184. [PMID: 32179058 DOI: 10.1016/j.bbabio.2020.148184] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 02/21/2020] [Accepted: 03/09/2020] [Indexed: 11/20/2022]
Abstract
The Photosystem I (PSI) reaction center in cyanobacteria is comprised of ~96 chlorophyll (Chl) molecules, including six specialized Chl molecules denoted Chl1A/Chl1B (P700), Chl2A/Chl2B, and Chl3A/Chl3B that are arranged in two branches and function in primary charge separation. It has recently been proposed that PSI from Chroococcidiopsis thermalis (Nürnberg et al. (2018) Science 360, 1210-1213) and Fischerella thermalis PCC 7521 (Hastings et al. (2019) Biochim. Biophys. Acta 1860, 452-460) contain Chl f in the positions Chl2A/Chl2B. We tested this proposal by exciting RCs from white-light grown (WL-PSI) and far-red light grown (FRL-PSI) F. thermalis PCC 7521 with femtosecond pulses and analyzing the optical dynamics. If Chl f were in the position Chl2A/Chl2B in FRL-PSI, excitation at 740 nm should have produced the charge-separated state P700+A0- followed by electron transfer to A1 with a τ of ≤25 ps. Instead, it takes ~230 ps for the charge-separated state to develop because the excitation migrates uphill from Chl f in the antenna to the trapping center. Further, we observe a strong electrochromic shift at 685 nm in the final P700+A1- spectrum that can only be explained if Chl a is in the positions Chl2A/Chl2B. Similar arguments rule out the presence of Chl f in the positions Chl3A/Chl3B; hence, Chl f is likely to function solely as an antenna pigment in FRL-PSI. We additionally report the presence of an excitonically coupled homo- or heterodimer of Chl f absorbing around 790 nm that is kinetically independent of the Chl f population that absorbs around 740 nm.
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22
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Cherepanov DA, Brady NG, Shelaev IV, Nguyen J, Gostev FE, Mamedov MD, Nadtochenko VA, Bruce BD. PSI-SMALP, a Detergent-free Cyanobacterial Photosystem I, Reveals Faster Femtosecond Photochemistry. Biophys J 2020; 118:337-351. [PMID: 31882247 PMCID: PMC6976803 DOI: 10.1016/j.bpj.2019.11.3391] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 11/17/2019] [Accepted: 11/26/2019] [Indexed: 12/12/2022] Open
Abstract
Cyanobacterial photosystem I (PSI) functions as a light-driven cyt c6-ferredoxin/oxidoreductase located in the thylakoid membrane. In this work, the energy and charge transfer processes in PSI complexes isolated from Thermosynechococcus elongatus via conventional n-dodecyl-β-D-maltoside solubilization (DM-PSI) and a, to our knowledge, new detergent-free method using styrene-maleic acid copolymers (SMA-PSI) have been investigated by pump-to-probe femtosecond laser spectroscopy. In DM-PSI preparations excited at 740 nm, the excitation remained localized on the long-wavelength chlorophyll forms within 0.1-20 ps and revealed little or no charge separation and oxidation of the special pair, P700. The formation of ion-radical pair P700+A1- occurred with a characteristic time of 36 ps, being kinetically controlled by energy transfer from the long-wavelength chlorophyll to P700. Quite surprisingly, the detergent-free SMA-PSI complexes upon excitation by these long-wave pulses undergo an ultrafast (<100 fs) charge separation in ∼45% of particles. In the remaining complexes (∼55%), the energy transfer to P700 occurred at ∼36 ps, similar to the DM-PSI. Both isolation methods result in a trimeric form of PSI, yet the SMA-PSI complexes display a heterogenous kinetic behavior. The much faster rate of charge separation suggests the existence of an ultrafast pathway for charge separation in the SMA-PSI that may be disrupted during detergent isolation.
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Affiliation(s)
- Dmitry A Cherepanov
- N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Nathan G Brady
- Biochemistry and Cellular and Molecular Biology Department, University of Tennessee, Knoxville, Tennessee
| | - Ivan V Shelaev
- N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Jon Nguyen
- Biochemistry and Cellular and Molecular Biology Department, University of Tennessee, Knoxville, Tennessee
| | - Fedor E Gostev
- N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Mahir D Mamedov
- A. N. Belozersky Institute of Physical-Chemical Biology, Moscow State University, Moscow, Russia
| | - Victor A Nadtochenko
- N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, Russia.
| | - Barry D Bruce
- Biochemistry and Cellular and Molecular Biology Department, University of Tennessee, Knoxville, Tennessee; Energy Science & Engineering Program, The Bredesen Center, University of Tennessee, Knoxville, Tennessee.
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23
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Kato K, Shinoda T, Nagao R, Akimoto S, Suzuki T, Dohmae N, Chen M, Allakhverdiev SI, Shen JR, Akita F, Miyazaki N, Tomo T. Structural basis for the adaptation and function of chlorophyll f in photosystem I. Nat Commun 2020; 11:238. [PMID: 31932639 PMCID: PMC6957486 DOI: 10.1038/s41467-019-13898-5] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 12/05/2019] [Indexed: 12/03/2022] Open
Abstract
Chlorophylls (Chl) play pivotal roles in energy capture, transfer and charge separation in photosynthesis. Among Chls functioning in oxygenic photosynthesis, Chl f is the most red-shifted type first found in a cyanobacterium Halomicronema hongdechloris. The location and function of Chl f in photosystems are not clear. Here we analyzed the high-resolution structures of photosystem I (PSI) core from H. hongdechloris grown under white or far-red light by cryo-electron microscopy. The structure showed that, far-red PSI binds 83 Chl a and 7 Chl f, and Chl f are associated at the periphery of PSI but not in the electron transfer chain. The appearance of Chl f is well correlated with the expression of PSI genes induced under far-red light. These results indicate that Chl f functions to harvest the far-red light and enhance uphill energy transfer, and changes in the gene sequences are essential for the binding of Chl f. Chlorophyll f (Chl f) is the most red-shifted Chl in oxygenic photosynthesis but its localization in photosystem I (PSI) has been unknown so far. Here the authors determine the cryo-EM structures of PSI complexes from a Chl f-containing cyanobacterium grown either under white light or far-red light conditions and identify seven Chls f in the far-red light PSI structure, whereas PSI from cells grown under white light contains only Chl a.
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Affiliation(s)
- Koji Kato
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan
| | - Toshiyuki Shinoda
- Faculty of Science, Tokyo University of Science, Tokyo, 162-8601, Japan
| | - Ryo Nagao
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan
| | - Seiji Akimoto
- Graduate School of Science, Kobe University, Kobe, 657-8501, Japan
| | - Takehiro Suzuki
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, Wako, Japan
| | - Naoshi Dohmae
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, Wako, Japan
| | - Min Chen
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | - Suleyman I Allakhverdiev
- K.A. Timiryazev Institute of Plant Physiology RAS, Moscow, Russia.,Institute of Basic Biological Problems RAS, Pushchino, Moscow Region, Russia.,M.V. Lomonosov Moscow State University, Moscow, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny, Moscow region, Russia.,Institute of Molecular Biology and Biotechnology ANAS, -Baku, Azerbaijan
| | - Jian-Ren Shen
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan.
| | - Fusamichi Akita
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan. .,Japan Science and Technology Agency, PRESTO, Saitama, 332-0012, Japan.
| | - Naoyuki Miyazaki
- Institute for Protein Research, Laboratory of Protein Synthesis and Expression, Osaka University, Osaka, 565-0871, Japan. .,Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance, University of Tsukuba, Ibaraki, 305-8577, Japan.
| | - Tatsuya Tomo
- Faculty of Science, Tokyo University of Science, Tokyo, 162-8601, Japan.
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24
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Kitoh-Nishioka H, Shigeta Y, Itoh S, Kimura A. Excitonic Coupling on a Heliobacterial Symmetrical Type-I Reaction Center: Comparison with Photosystem I. J Phys Chem B 2019; 124:389-403. [DOI: 10.1021/acs.jpcb.9b11290] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Hirotaka Kitoh-Nishioka
- JST, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8571, Japan
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8571, Japan
| | - Shigeru Itoh
- Department of Physics, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Akihiro Kimura
- Department of Physics, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
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25
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26
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Pishchalnikov R, Shubin V, Razjivin A. Single Molecule Fluorescence Spectroscopy of PSI Trimers from Arthrospira platensis: A Computational Approach. Molecules 2019; 24:molecules24040822. [PMID: 30823581 PMCID: PMC6412541 DOI: 10.3390/molecules24040822] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 02/20/2019] [Accepted: 02/21/2019] [Indexed: 11/16/2022] Open
Abstract
Based on single molecule spectroscopy analysis and our preliminary theoretical studies, the linear and fluorescence spectra of the PSI trimer from Arthrospira platensis with different realizations of the static disorder were modeled at cryogenic temperature. Considering the previously calculated spectral density of chlorophyll, an exciton model for the PSI monomer and trimer including the red antenna states was developed taking into account the supposed similarity of PSI antenna structures from Thermosynechococcus e., Synechocystis sp. PCC6803, and Arthrospira platensis. The red Chls in the PSI monomer were assumed to be in the nearest proximity of the reaction center. The PSI trimer model allowed the simulation of experimentally measured zero phonon line distribution of the red states considering a weak electron-phonon coupling for the antenna exciton states. However, the broad absorption and fluorescence spectra of an individual emitter at 760 nm were calculated by adjusting the Huang-Rhys factors of the chlorophyll lower phonon modes assuming strong electron-phonon coupling.
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Affiliation(s)
- Roman Pishchalnikov
- Prokhorov General Physics Institute of the Russian Academy of Sciences, 119991 Moscow, Russia.
| | - Vladimir Shubin
- Bach Institute of Biochemistry of the Russian Academy of Sciences, 119071 Moscow, Russia.
| | - Andrei Razjivin
- Belozersky Research Institute of Physico-Chemical Biology, Moscow State University, 119992 Moscow, Russia.
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27
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Mandal A, Swain P, Nath B, Sau S, Mal P. Unipolar to ambipolar semiconductivity switching in charge transfer cocrystals of 2,7-di-tert-butylpyrene. CrystEngComm 2019. [DOI: 10.1039/c8ce01806e] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Charge transfer cocrystals of 2,7-di-tert-butylpyrene donor and tetracyanoquinodimethane, tetracyanobenzene and 1,3-dinitrobenzene acceptor exhibited switchable semi-conductivity.
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Affiliation(s)
- Arkalekha Mandal
- School of Chemical Sciences
- National Institute of Science Education and Research (NISER)
- India
| | - Pravasini Swain
- School of Physical Sciences
- National Institute of Science Education and Research (NISER)
- HBNI
- Bhubaneswar
- India
| | - Bhaskar Nath
- Department of Educational Science
- Assam Central University
- Silchar
- India
| | - Sudip Sau
- School of Chemical Sciences
- National Institute of Science Education and Research (NISER)
- India
| | - Prasenjit Mal
- School of Chemical Sciences
- National Institute of Science Education and Research (NISER)
- India
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28
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29
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Hou J, Zou Q, Wang Y, Gao Q, Yao W, Yao Q, Zhang J. Screening for the selective inhibitors of MMP-9 from natural products based on pharmacophore modeling and molecular docking in combination with bioassay experiment, hybrid QM/MM calculation, and MD simulation. J Biomol Struct Dyn 2018; 37:3135-3149. [PMID: 30079817 DOI: 10.1080/07391102.2018.1509019] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Matrix metalloproteinase-9 (MMP-9) has been considered as an attractive target involving cancer therapy. In this study, the 3D QSAR pharmacophore model of MMP-9 inhibitors is built, and its reliability is subsequently validated based on different methods. The built pharmacophore model consists of the four chemical features, including two hydrogen bond acceptors (HBA), one hydrophobic (HY), and one ring aromatic (RA). Among them, both HY and RA are found to be especially important features because they involve the interactions of inhibitors with the S1' pocket of MMP-9, which determines the selectivity of MMP-9 inhibitors. By combining pharmacophore model with molecular docking, the virtual screening is carried out to identify the selective MMP-9 inhibitors from natural products. The four potential selective MMP-9 inhibitors of natural products are found. One of them was used to carry out the bioassay experiment inhibiting MMP-9, and the estimated IC50 value of only 26.94 µM clearly shows its strongly inhibitory activity; besides, both the hybrid quantum mechanics/molecular mechanics (QM/MM) calculation and the molecular dynamics simulation are performed to examine the reliability regarding the binding mode of this inhibitor with MMP-9 active sites predicted by molecular docking. All the screened four natural products are found to well bind with the MMP-9 active sites by different kinds of interactions. Finally, the ADMET properties of screened four natural products are assessed. These screened MMP-9 inhibitors of natural products could be used as the lead compounds to perform structural modifications and optimizations in the future work. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jiaying Hou
- a Department of Physical Chemistry , China Pharmaceutical University , Nanjing , People's Republic of China
| | - Qing Zou
- a Department of Physical Chemistry , China Pharmaceutical University , Nanjing , People's Republic of China
| | - Yijun Wang
- a Department of Physical Chemistry , China Pharmaceutical University , Nanjing , People's Republic of China
| | - Qi Gao
- a Department of Physical Chemistry , China Pharmaceutical University , Nanjing , People's Republic of China
| | - Wenhui Yao
- a Department of Physical Chemistry , China Pharmaceutical University , Nanjing , People's Republic of China
| | - Qizheng Yao
- c School of Pharmacy , China Pharmaceutical University , Nanjing , People's Republic of China
| | - Ji Zhang
- a Department of Physical Chemistry , China Pharmaceutical University , Nanjing , People's Republic of China.,b State Key Laboratory of Natural Medicines , China Pharmaceutical University , Nanjing , People's Republic of China
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30
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Lee Y, Gorka M, Golbeck JH, Anna JM. Ultrafast Energy Transfer Involving the Red Chlorophylls of Cyanobacterial Photosystem I Probed through Two-Dimensional Electronic Spectroscopy. J Am Chem Soc 2018; 140:11631-11638. [DOI: 10.1021/jacs.8b04593] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Yumin Lee
- Deparment of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, Pennsylvania 19104, United States
| | - Michael Gorka
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - John H. Golbeck
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Jessica M. Anna
- Deparment of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, Pennsylvania 19104, United States
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31
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Polyakov IV, Khrenova MG, Moskovsky AA, Shabanov BM, Nemukhin AV. Towards first-principles calculation of electronic excitations in the ring of the protein-bound bacteriochlorophylls. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2018.03.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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32
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Herascu N, Hunter MS, Shafiei G, Najafi M, Johnson TW, Fromme P, Zazubovich V. Spectral Hole Burning in Cyanobacterial Photosystem I with P700 in Oxidized and Neutral States. J Phys Chem B 2016; 120:10483-10495. [PMID: 27661089 DOI: 10.1021/acs.jpcb.6b07803] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nicoleta Herascu
- Department
of Physics, Concordia University, 7141 Sherbrooke Street West, Montreal, H4B 1R4, Quebec, Canada
| | - Mark S. Hunter
- Department
of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona, United States
| | - Golia Shafiei
- Department
of Physics, Concordia University, 7141 Sherbrooke Street West, Montreal, H4B 1R4, Quebec, Canada
| | - Mehdi Najafi
- Department
of Physics, Concordia University, 7141 Sherbrooke Street West, Montreal, H4B 1R4, Quebec, Canada
| | - T. Wade Johnson
- Department
of Chemistry, Susquehanna University, Selinsgrove, Pennsylvania, United States
| | - Petra Fromme
- Department
of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona, United States
| | - Valter Zazubovich
- Department
of Physics, Concordia University, 7141 Sherbrooke Street West, Montreal, H4B 1R4, Quebec, Canada
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33
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Challenges facing an understanding of the nature of low-energy excited states in photosynthesis. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1627-1640. [PMID: 27372198 DOI: 10.1016/j.bbabio.2016.06.010] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 06/27/2016] [Accepted: 06/28/2016] [Indexed: 01/09/2023]
Abstract
While the majority of the photochemical states and pathways related to the biological capture of solar energy are now well understood and provide paradigms for artificial device design, additional low-energy states have been discovered in many systems with obscure origins and significance. However, as low-energy states are naively expected to be critical to function, these observations pose important challenges. A review of known properties of low energy states covering eight photochemical systems, and options for their interpretation, are presented. A concerted experimental and theoretical research strategy is suggested and outlined, this being aimed at providing a fully comprehensive understanding.
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34
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Abstract
The design of optimal light-harvesting (supra)molecular systems and materials is one of the most challenging frontiers of science. Theoretical methods and computational models play a fundamental role in this difficult task, as they allow the establishment of structural blueprints inspired by natural photosynthetic organisms that can be applied to the design of novel artificial light-harvesting devices. Among theoretical strategies, the application of quantum chemical tools represents an important reality that has already reached an evident degree of maturity, although it still has to show its real potentials. This Review presents an overview of the state of the art of this strategy, showing the actual fields of applicability but also indicating its current limitations, which need to be solved in future developments.
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Affiliation(s)
- Carles Curutchet
- Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona , Av. Joan XXIII s/n, 08028 Barcelona, Spain
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, University of Pisa , via G. Moruzzi 13, 56124 Pisa, Italy
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35
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Jurinovich S, Viani L, Prandi IG, Renger T, Mennucci B. Towards an ab initio description of the optical spectra of light-harvesting antennae: application to the CP29 complex of photosystem II. Phys Chem Chem Phys 2016; 17:14405-16. [PMID: 25872495 DOI: 10.1039/c4cp05647g] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Light-harvesting pigment-protein complexes (PPC) represent the fundamental units through which the photosynthetic organisms absorb sunlight and funnel the energy to the reaction centre for carrying out the primary energy conversion reactions of photosynthesis. Here we apply a multiscale computational strategy to a specific PPC present in the photosystem II of plants and algae (CP29) to investigate in what detail should the environment effects due to protein and membrane/solvent be included for an accurate description of optical spectra. We find that a refinement of the crystal structure is needed before any meaningful quantum chemical calculations of pigment transition energies can be performed. For this purpose we apply classical molecular dynamics simulations of the PPC within its natural environment and we perform ab initio computations of the exciton Hamiltonian of the complex, including the environment either implicitly by the polarizable continuum model (PCM) or explicitly using the polarizable QM/MM methodology (MMPol). However, PCM essentially leads to an unspecific redshift of all transition energies, and MMPol is able to reveal site-specific changes in the optical properties of the pigments. Based on the latter and the excitonic couplings obtained within a polarizable QM/MM methodology, optical spectra are calculated, which are in good qualitative agreement with experimental data. A weakness of the approach is however found in the overestimation of the fluctuations of the excitonic parameters of the pigments along the MD trajectory. An explanation for such a finding in terms of the limits of the force fields commonly used for protein cofactors is presented and discussed.
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Affiliation(s)
- Sandro Jurinovich
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, Via G. Moruzzi 3, I-56124 Pisa, Italy.
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36
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Abstract
David Craig (1919–2015) left us with a lasting legacy concerning basic understanding of chemical spectroscopy and bonding. This is expressed in terms of some of the recent achievements of my own research career, with a focus on integration of Craig’s theories with those of Noel Hush to solve fundamental problems in photosynthesis, molecular electronics (particularly in regard to the molecules synthesized by Maxwell Crossley), and self-assembled monolayer structure and function. Reviewed in particular is the relation of Craig’s legacy to: the 50-year struggle to assign the visible absorption spectrum of arguably the world’s most significant chromophore, chlorophyll; general theories for chemical bonding and structure extending Hush’s adiabatic theory of electron-transfer processes; inelastic electron-tunnelling spectroscopy (IETS); chemical quantum entanglement and the Penrose–Hameroff model for quantum consciousness; synthetic design strategies for NMR quantum computing; Gibbs free-energy measurements and calculations for formation and polymorphism of organic self-assembled monolayers on graphite surfaces from organic solution; and understanding the basic chemical processes involved in the formation of gold surfaces and nanoparticles protected by sulfur-bound ligands, ligands whose form is that of Au0-thiyl rather than its commonly believed AuI-thiolate tautomer.
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37
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Kobayashi R, Reimers JR. Free energies for the coordination of ligands to the magnesium of chlorophyll-a in solvents. Mol Phys 2015. [DOI: 10.1080/00268976.2014.1003620] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Rika Kobayashi
- Australian National University Supercomputer Facility, Mills Rd, Canberra, Australia
| | - Jeffrey R. Reimers
- International Centre for Quantum and Molecular Structure, Shanghai University, Shanghai, China
- School of Physics and Advanced Materials, University of Technology, Sydney, Australia
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38
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Frankcombe TJ. Explicit calculation of the excited electronic states of the photosystem II reaction centre. Phys Chem Chem Phys 2015; 17:3295-302. [DOI: 10.1039/c4cp04468a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The excited states of the photosystem II reaction centre cofactors have been calculated as a single “supermolecule”. Charge transfer states are shown to be dependent on electrostatic environment.
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39
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Goerigk L, Collyer CA, Reimers JR. Recommending Hartree–Fock Theory with London-Dispersion and Basis-Set-Superposition Corrections for the Optimization or Quantum Refinement of Protein Structures. J Phys Chem B 2014; 118:14612-26. [DOI: 10.1021/jp510148h] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Lars Goerigk
- School
of Chemistry, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Charles A. Collyer
- School
of Molecular Bioscience, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Jeffrey R. Reimers
- Centre
for Quantum and Molecular Structure, College of Sciences, Shanghai University, Shanghai 200444, China
- School
of Physics and Advanced Materials, The University of Technology, Sydney, New South Wales 2007, Australia
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40
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Zhou ZG, Yao QZ, Lei D, Zhang QQ, Zhang J. Investigations on the mechanisms of interactions between matrix metalloproteinase 9 and its flavonoid inhibitors using a combination of molecular docking, hybrid quantum mechanical/molecular mechanical calculations, and molecular dynamics simulations. CAN J CHEM 2014. [DOI: 10.1139/cjc-2014-0180] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Many experimental studies have found that flavonoids can inhibit the activities of matrix metalloproteinases (MMPs), but the relevant mechanisms are still unclear. In this paper, the interaction mechanisms of MMP-9 with its five flavonoid inhibitors are investigated using a combination of molecular docking, hybrid quantum mechanical and molecular mechanical (QM/MM) calculations, and molecular dynamics simulations. The molecular dynamics simulation results show a good linear correlation between the calculated binding free energies of QM/MM−Poisson–Boltzmann surface area (PBSA) and the experimental −log(EC50) regarding the studied five flavonoids on MMP-9 inhibition in explicit solvent. It is found that compared with the MM−PBSA method, the QM/MM−PBSA method can obviously improve the accuracy for the calculated binding free energies. The predicted binding modes of the five flavonoid−MMP-9 complexes reveal that the different hydrogen bond networks can form besides producing the Zn−O coordination bonds, which can reasonably explain previous experimental results. The agreement between our calculated results and the previous experimental facts indicates that the force field parameters used here are effective and reliable for investigating the systems of flavonoid−MMP-9 interactions, and thus, these simulations and analyses could be reproduced for the other related systems involving protein−ligand interactions. This paper may be helpful for designing the new MMP-9 inhibitors having higher biological activities by carrying out the structural modifications of flavonoid molecules.
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Affiliation(s)
- Zhi-Guang Zhou
- School of Pharmacy, China Pharmaceutical University, Nanjing 210009, People’s Republic of China
| | - Qi-Zheng Yao
- School of Pharmacy, China Pharmaceutical University, Nanjing 210009, People’s Republic of China
| | - Dong Lei
- School of Pharmacy, China Pharmaceutical University, Nanjing 210009, People’s Republic of China
| | - Qing-Qing Zhang
- School of Pharmacy, China Pharmaceutical University, Nanjing 210009, People’s Republic of China
| | - Ji Zhang
- Department of Physical Chemistry, China Pharmaceutical University, Nanjing 210009, People’s Republic of China
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, People’s Republic of China
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41
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Reimers JR, Cai ZL, Kobayashi R, Rätsep M, Freiberg A, Krausz E. Formation of water–chlorophyll clusters in dilute samples of chlorophyll-a in ether at low temperature. Phys Chem Chem Phys 2014; 16:2323-30. [PMID: 24352346 DOI: 10.1039/c3cp53729c] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Jeffrey R Reimers
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia.
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42
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Reimers JR, Cai ZL, Kobayashi R, Rätsep M, Freiberg A, Krausz E. Assignment of the Q-bands of the chlorophylls: coherence loss via Qx - Qy mixing. Sci Rep 2013; 3:2761. [PMID: 24067303 PMCID: PMC3783888 DOI: 10.1038/srep02761] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 09/03/2013] [Indexed: 01/12/2023] Open
Abstract
We provide a new and definitive spectral assignment for the absorption, emission, high-resolution fluorescence excitation, linear dichroism, and/or magnetic circular dichroism spectra of 32 chlorophyllides in various environments. This encompases all data used to justify previous assignments and provides a simple interpretation of unexplained complex decoherence phenomena associated with Qx → Qy relaxation. Whilst most chlorophylls conform to the Gouterman model and display two independent transitions Qx (S2) and Qy (S1), strong vibronic coupling inseparably mixes these states in chlorophyll-a. This spreads x-polarized absorption intensity over the entireQ-band system to influence all exciton-transport, relaxation and coherence properties of chlorophyll-based photosystems. The fraction of the total absorption intensity attributed to Qx ranges between 7% and 33%, depending on chlorophyllide and coordination, and is between 10% and 25% for chlorophyll-a. CAM-B3LYP density-functional-theory calculations of the band origins, relative intensities, vibrational Huang-Rhys factors, and vibronic coupling strengths fully support this new assignment.
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43
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Falklöf O, Durbeej B. Modeling of phytochrome absorption spectra. J Comput Chem 2013; 34:1363-74. [DOI: 10.1002/jcc.23265] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Revised: 01/31/2013] [Accepted: 02/07/2013] [Indexed: 11/07/2022]
Affiliation(s)
- Olle Falklöf
- Division of Computational Physics; IFM; Linköping University; SE-581 83; Linköping; Sweden
| | - Bo Durbeej
- Division of Computational Physics; IFM; Linköping University; SE-581 83; Linköping; Sweden
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44
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Renger T, Müh F. Understanding photosynthetic light-harvesting: a bottom up theoretical approach. Phys Chem Chem Phys 2013; 15:3348-71. [PMID: 23361062 DOI: 10.1039/c3cp43439g] [Citation(s) in RCA: 125] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We discuss a bottom up approach for modeling photosynthetic light-harvesting. Methods are reviewed for a full structure-based parameterization of the Hamiltonian of pigment-protein complexes (PPCs). These parameters comprise (i) the local transition energies of the pigments in their binding sites in the protein, the site energies; (ii) the couplings between optical transitions of the pigments, the excitonic couplings; and (iii) the spectral density characterizing the dynamic modulation of pigment transition energies and excitonic couplings by protein vibrations. Starting with quantum mechanics perturbation theory, we provide a microscopic foundation for the standard PPC Hamiltonian and relate the expressions obtained for its matrix elements to quantities that can be calculated with classical molecular mechanics/electrostatics approaches including the whole PPC in atomic detail and using charge and transition densities obtained with quantum chemical calculations on the isolated building blocks of the PPC. In the second part of this perspective, the Hamiltonian is utilized to describe the quantum dynamics of excitons. Situations are discussed that differ in the relative strength of excitonic and exciton-vibrational coupling. The predictive power of the approaches is demonstrated in application to different PPCs, and challenges for future work are outlined.
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Affiliation(s)
- Thomas Renger
- Institut für Theoretische Physik, Johannes Kepler Universität Linz, Linz, Austria.
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45
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Yang F, Zhang Z, He X. A DFT study of the regeneration process of zinc porphyrin analogues in dye-sensitized solar cells. Dalton Trans 2013; 42:13874-81. [DOI: 10.1039/c3dt51181b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Fan Yang
- Department of Polymer Science and Engineering, School of Chemical Engineering and Technology Tianjin University, 300072 Tianjin, China
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46
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Zhang J, Geng H, Virk TS, Zhao Y, Tan J, Di CA, Xu W, Singh K, Hu W, Shuai Z, Liu Y, Zhu D. Sulfur-bridged annulene-TCNQ co-crystal: a self-assembled ''molecular level heterojunction'' with air stable ambipolar charge transport behavior. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2012; 24:2603-7. [PMID: 22499500 DOI: 10.1002/adma.201200578] [Citation(s) in RCA: 125] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Indexed: 05/24/2023]
Affiliation(s)
- Jing Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
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47
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Jing Y, Zheng R, Li HX, Shi Q. Theoretical Study of the Electronic–Vibrational Coupling in the Qy States of the Photosynthetic Reaction Center in Purple Bacteria. J Phys Chem B 2012; 116:1164-71. [DOI: 10.1021/jp209575q] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Yuanyuan Jing
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing 100190, China
| | - Renhui Zheng
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing 100190, China
| | - Hui-Xue Li
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing 100190, China
| | - Qiang Shi
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing 100190, China
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48
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Kitagawa Y, Matsuda K, Hasegawa JY. Theoretical study of the excited states of the photosynthetic reaction center in photosystem II: Electronic structure, interactions, and their origin. Biophys Chem 2011; 159:227-36. [DOI: 10.1016/j.bpc.2011.06.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2011] [Revised: 06/17/2011] [Accepted: 06/17/2011] [Indexed: 11/29/2022]
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König C, Neugebauer J. Quantum chemical description of absorption properties and excited-state processes in photosynthetic systems. Chemphyschem 2011; 13:386-425. [PMID: 22287108 DOI: 10.1002/cphc.201100408] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Indexed: 11/07/2022]
Abstract
The theoretical description of the initial steps in photosynthesis has gained increasing importance over the past few years. This is caused by more and more structural data becoming available for light-harvesting complexes and reaction centers which form the basis for atomistic calculations and by the progress made in the development of first-principles methods for excited electronic states of large molecules. In this Review, we discuss the advantages and pitfalls of theoretical methods applicable to photosynthetic pigments. Besides methodological aspects of excited-state electronic-structure methods, studies on chlorophyll-type and carotenoid-like molecules are discussed. We also address the concepts of exciton coupling and excitation-energy transfer (EET) and compare the different theoretical methods for the calculation of EET coupling constants. Applications to photosynthetic light-harvesting complexes and reaction centers based on such models are also analyzed.
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Affiliation(s)
- Carolin König
- Institute for Physical and Theoretical Chemistry, Technical University Braunschweig, Braunschweig, Germany
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50
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Rostov IV, Amos RD, Kobayashi R, Scalmani G, Frisch MJ. Studies of the ground and excited-state surfaces of the retinal chromophore using CAM-B3LYP. J Phys Chem B 2010; 114:5547-55. [PMID: 20369810 DOI: 10.1021/jp911329g] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The isomerization of the 11-cis isomer (PSB11) of the retinal chromophore to its all-trans isomer (PSBT) is examined. Optimized structures on both the ground state and the excited state are calculated, and the dependence on torsional angles in the carbon chain is investigated. Time-dependent density functional theory is used to produce excitation energies and the excited-state surface. To avoid problems with the description of excited states that can arise with standard DFT methods, the CAM-B3LYP functional was used. Comparing CAM-B3LYP with B3LYP results indicates that the former is significantly more accurate, as a consequence of which detailed cross sections of the retinal excited-state surface are obtained.
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Affiliation(s)
- Ivan V Rostov
- Australian National University Supercomputer Facility, Mills Road, Canberra, ACT 0200, Australia
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