1
|
Yamaguchi K, Miyagawa K, Shoji M, Kawakami T, Isobe H, Yamanaka S, Nakajima T. Theoretical elucidation of the structure, bonding, and reactivity of the CaMn 4O x clusters in the whole Kok cycle for water oxidation embedded in the oxygen evolving center of photosystem II. New molecular and quantum insights into the mechanism of the O-O bond formation. PHOTOSYNTHESIS RESEARCH 2023:10.1007/s11120-023-01053-7. [PMID: 37945776 DOI: 10.1007/s11120-023-01053-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 09/25/2023] [Indexed: 11/12/2023]
Abstract
This paper reviews our historical developments of broken-symmetry (BS) and beyond BS methods that are applicable for theoretical investigations of metalloenzymes such as OEC in PSII. The BS hybrid DFT (HDFT) calculations starting from high-resolution (HR) XRD structure in the most stable S1 state have been performed to elucidate structure and bonding of whole possible intermediates of the CaMn4Ox cluster (1) in the Si (i = 0 ~ 4) states of the Kok cycle. The large-scale HDFT/MM computations starting from HR XRD have been performed to elucidate biomolecular system structures which are crucial for examination of possible water inlet and proton release pathways for water oxidation in OEC of PSII. DLPNO CCSD(T0) computations have been performed for elucidation of scope and reliability of relative energies among the intermediates by HDFT. These computations combined with EXAFS, XRD, XFEL, and EPR experimental results have elucidated the structure, bonding, and reactivity of the key intermediates, which are indispensable for understanding and explanation of the mechanism of water oxidation in OEC of PSII. Interplay between theory and experiments have elucidated important roles of four degrees of freedom, spin, charge, orbital, and nuclear motion for understanding and explanation of the chemical reactivity of 1 embedded in protein matrix, indicating the participations of the Ca(H2O)n ion and tyrosine(Yz)-O radical as a one-electron acceptor for the O-O bond formation. The Ca-assisted Yz-coupled O-O bond formation mechanisms for water oxidation are consistent with recent XES and very recent time-resolved SFX XFEL and FTIR results.
Collapse
Affiliation(s)
- Kizashi Yamaguchi
- Center for Quantum Information and Quantum Biology, Osaka University, Toyonaka, Osaka, 560-0043, Japan.
- RIKEN Center for Computational Science, Kobe, Hyogo, 650-0047, Japan.
- SANKEN, Osaka University, Ibaraki, Osaka, 567-0047, Japan.
| | - Koichi Miyagawa
- Center of Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8577, Japan
| | - Mitsuo Shoji
- Center of Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8577, Japan
| | - Takashi Kawakami
- RIKEN Center for Computational Science, Kobe, Hyogo, 650-0047, Japan
- Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan
| | - Hiroshi Isobe
- Research Institute for Interdisciplinary Science, and Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan
| | - Shusuke Yamanaka
- Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan
| | - Takahito Nakajima
- RIKEN Center for Computational Science, Kobe, Hyogo, 650-0047, Japan
| |
Collapse
|
2
|
Yamaguchi K, Shoji M, Isobe H, Kawakami T, Miyagawa K, Suga M, Akita F, Shen JR. Geometric, electronic and spin structures of the CaMn4O5 catalyst for water oxidation in oxygen-evolving photosystem II. Interplay between experiments and theoretical computations. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2022.214742] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
3
|
Relative energies among S3 intermediates in the photosystem II revealed by DLPNO coupled cluster and hybrid DFT calculations. Possible pathways of water insertion in the S2 to S3 transition. Chem Phys Lett 2022. [DOI: 10.1016/j.cplett.2022.139439] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
|
4
|
Miyagawa K, Yamanaka S, Isobe H, Shoji M, Kawakami T, Taniguchi M, Okumura M, Yamaguchi K. Electronic and spin structures of CaMn 4O x clusters in the S 0 state of the oxygen evolving complex of photosystem II. Domain-based local pair natural orbital (DLPNO) coupled-cluster (CC) calculations using optimized geometries and natural orbitals (UNO) by hybrid density functional theory (HDFT) calculations. Phys Chem Chem Phys 2021; 22:27191-27205. [PMID: 33226053 DOI: 10.1039/d0cp04762g] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Domain-based local pair natural orbital (DLPNO) coupled cluster single and double (CCSD) with triple perturbation (T) correction methods were performed to elucidate the relative stabilities of ten different intermediate structures of the CaMn4Ox cluster in the S0 state of the oxygen evolving complex (OEC) of photosystem II (PSII). Full geometry optimizations of all the S0 intermediates were performed by the UB3LYP-D3/Def2-TZVP methods, providing the assumed geometrical structures and starting natural orbitals (UNO) for DLPNO-CCSD(T)/Def2TZVP calculations. The effective exchange integrals (J) for the spin Hamiltonian models for the ten intermediates were obtained by the UB3LYP/Def2-TZVP calculations followed by the general spin projections. DLPNO-CCSD(T) calculations followed by the CBS extrapolation procedure elucidated that the (II, III, IV, IV) and (III, III, III, IV) valence states in the CaMn4O5 cluster of the OEC of the PS II were nearly degenerated in energy in the S0 state, indicating an important role of dynamical electron correlation effects for the valence and spin fluctuations in strongly correlated electron systems (SCESs) consisting of 3d transition metals.
Collapse
Affiliation(s)
- K Miyagawa
- Institute for Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan.
| | | | | | | | | | | | | | | |
Collapse
|
5
|
Yamaguchi K, Miyagawa K, Isobe H, Shoji M, Kawakami T, Yamanaka S. Isolobal and isospin analogy between organic and inorganic open-shell molecules—Application to oxygenation reactions by active oxygen and oxy-radicals and water oxidation in the native and artificial photosynthesis. ADVANCES IN QUANTUM CHEMISTRY 2021. [DOI: 10.1016/bs.aiq.2021.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
6
|
Yamaguchi K, Yamanaka S, Isobe H, Shoji M, Miyagawa K, Kawakami T. Theory of chemical bonds in metalloenzymes XXIII fundamental principles for the photo-induced water oxidation in oxygen evolving complex of photosystem II. Mol Phys 2020. [DOI: 10.1080/00268976.2020.1725168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- K. Yamaguchi
- The Institute for Scientific and Industrial Research, Osaka University, Osaka, Japan
- Graduate School of Science, Osaka University, Toyonaka, Japan
- RIKEN Center for Computational Science, Kobe, Japan
- Institute for Nanoscience Design, Osaka University, Toyonaka, Japan
- Division of Quantum Information and Quantum Biology (QIQB), Osaka University, Toyonaka, Japan
| | - S. Yamanaka
- Graduate School of Science, Osaka University, Toyonaka, Japan
- Division of Quantum Information and Quantum Biology (QIQB), Osaka University, Toyonaka, Japan
| | - H. Isobe
- Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - M. Shoji
- Center of Computational Sciences, Tsukuba University, Tsukuba, Japan
| | - K. Miyagawa
- The Institute for Scientific and Industrial Research, Osaka University, Osaka, Japan
| | - T. Kawakami
- Graduate School of Science, Osaka University, Toyonaka, Japan
- RIKEN Center for Computational Science, Kobe, Japan
| |
Collapse
|
7
|
Yamaguchi K, Isobe H, Shoji M, Miyagawa K, Yamanaka S, Kawakami T, Nakajima T. Development of broken-symmetry (BS) methods in chemical reactions. A theoretical view of water oxidation in photosystem II and related systems. J Photochem Photobiol A Chem 2020. [DOI: 10.1016/j.jphotochem.2020.112791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
8
|
Miyagawa K, Kawakami T, Isobe H, Shoji M, Yamanaka S, Nakatani K, Okumura M, Nakajima T, Yamaguchi K. Domain-based local pair natural orbital CCSD(T) calculations of six different S1 structures of oxygen evolving complex of photosystem II. Proposal of multi-intermediate models for the S1 state. Chem Phys Lett 2019. [DOI: 10.1016/j.cplett.2019.136660] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
|
9
|
Miyagawa K, Kawakami T, Suzuki Y, Isobe H, Shoji M, Yamanaka S, Okumura M, Nakajima T, Yamaguchi K. Domain-based local pair natural orbital CCSD(T) calculations of strongly correlated electron systems: Examination of dynamic equilibrium models based on multiple intermediates in S1 state of photosystem II. Mol Phys 2019. [DOI: 10.1080/00268976.2019.1666171] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- K. Miyagawa
- Institute for Scientific and Industrial Research, Osaka University, Osaka 567-0047, Japan
| | - T. Kawakami
- Graduate School of Science, Osaka University, Toyonaka 560-0043, Japan
- RIKEN Center for Computational Science, Kobe, Hyogo 650-0047, Japan
| | - Y. Suzuki
- Graduate School of Science, Osaka University, Toyonaka 560-0043, Japan
| | - H. Isobe
- Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8530, Japan
| | - M. Shoji
- Center of Computational Sciences, Tsukuba University, Tsukuba, Ibaraki 305-8577, Japan
| | - S. Yamanaka
- Graduate School of Science, Osaka University, Toyonaka 560-0043, Japan
| | - M. Okumura
- Graduate School of Science, Osaka University, Toyonaka 560-0043, Japan
| | - T. Nakajima
- RIKEN Center for Computational Science, Kobe, Hyogo 650-0047, Japan
| | - K. Yamaguchi
- Institute for Scientific and Industrial Research, Osaka University, Osaka 567-0047, Japan
- RIKEN Center for Computational Science, Kobe, Hyogo 650-0047, Japan
- Insitute for Nanoscience Design, Osaka University, Toyonaka 560-0043, Japan
| |
Collapse
|
10
|
Yamaguchi K, Yamanaka S, Isobe H, Shoji M, Miyagawa K, Nakajima T, Kawakami T, Okumura M. Theoretical and computational investigations of geometrical, electronic and spin structures of the CaMn 4 O X (X = 5, 6) cluster in the Kok cycle S i (i = 0-3) of oxygen evolving complex of photosystem II. PHYSIOLOGIA PLANTARUM 2019; 166:44-59. [PMID: 30847925 DOI: 10.1111/ppl.12960] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 03/01/2019] [Accepted: 03/05/2019] [Indexed: 06/09/2023]
Abstract
The optimized geometries of the CaMn4 OX (X = 5, 6) cluster in the oxygen evolving complex (OEC) of photosystem II (PSII) by large-scale quantum mechanics (QM) and molecular mechanics (MM) calculations are compared with recent serial femtosecond crystallography (SFX) results for the Si (i = 0-3) states. The valence states of four Mn ions by the QM/MM calculations are also examined in relation to the experimental results by the X-ray emission spectroscopy (XES) for the Si intermediates. Geometrical and valence structures of right-opened Mn-hydroxide, Mn-oxo and Mn-peroxide intermediates in the S3 state are investigated in detail in relation to recent SFX and XES experiments for the S3 state. Interplay between theory and experiment indicates that the Mn-oxo intermediate is a new possible candidate for the S3 state. Implications of the computational results are discussed in relation to possible mechanisms of the oxygenoxygen bond formation for water oxidation in OEC of PSII.
Collapse
Affiliation(s)
- Kizashi Yamaguchi
- Institute of Scientific and Industrial Research, Osaka University, Suita, Osaka, 567-0047, Japan
- Riken Center for Computational Science, Kobe, Hyogo 650-0047, Japan
| | - Shusuke Yamanaka
- Department of Chemistry, Graduate School of Science, Osaka University, Suita, Osaka 560-0043, Japan
| | - Hiroshi Isobe
- Research Institute for Interdisciplinary Science, Okayama University, Okayama, Okayama 700-8530, Japan
| | - Mitsuo Shoji
- Center of Computational Sciences, Tsukuba University, Tsukuba, Ibaraki 305-8577, Japan
| | - Kouichi Miyagawa
- Institute of Scientific and Industrial Research, Osaka University, Suita, Osaka, 567-0047, Japan
| | | | - Takashi Kawakami
- Department of Chemistry, Graduate School of Science, Osaka University, Suita, Osaka 560-0043, Japan
| | - Mitsutaka Okumura
- Department of Chemistry, Graduate School of Science, Osaka University, Suita, Osaka 560-0043, Japan
| |
Collapse
|
11
|
Shoji M, Isobe H, Miyagawa K, Yamaguchi K. Possibility of the right-opened Mn-oxo intermediate (R-oxo(4444)) among all nine intermediates in the S3 state of the oxygen-evolving complex of photosystem II revealed by large-scale QM/MM calculations. Chem Phys 2019. [DOI: 10.1016/j.chemphys.2018.11.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
|
12
|
Shoji M, Isobe H, Yamanaka S, Umena Y, Kawakami K, Kamiya N, Yamaguchi K. Theoretical Elucidation of Geometrical Structures of the CaMn4O5 Cluster in Oxygen Evolving Complex of Photosystem II Scope and Applicability of Estimation Formulae of Structural Deformations via the Mixed-Valence and Jahn–Teller Effects. ADVANCES IN QUANTUM CHEMISTRY 2019. [DOI: 10.1016/bs.aiq.2018.05.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
|
13
|
Yamaguchi K, Shoji M, Isobe H, Miyagawa K, Nakatani K. Theory of chemical bonds in metalloenzymes XXII: a concerted bond-switching mechanism for the oxygen–oxygen bond formation coupled with one electron transfer for water oxidation in the oxygen-evolving complex of photosystem II. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1552799] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- K. Yamaguchi
- Institute for Nanoscience Design, Osaka University, Toyonaka, Osaka, Japan
- The Institute for Scientific and Industrial Research, Osaka University, Osaka, Japan
- Handairigaku Techno-Research, Toyonaka, Osaka, Japan
| | - M. Shoji
- Center of Computational Sciences, Tsukuba University, Tsukuba, Ibaraki, Japan
| | - H. Isobe
- Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - K. Miyagawa
- The Institute for Scientific and Industrial Research, Osaka University, Osaka, Japan
| | - K. Nakatani
- The Institute for Scientific and Industrial Research, Osaka University, Osaka, Japan
| |
Collapse
|
14
|
Shoji M, Isobe H, Tanaka A, Fukushima Y, Kawakami K, Umena Y, Kamiya N, Nakajima T, Yamaguchi K. Understanding Two Different Structures in the Dark Stable State of the Oxygen-Evolving Complex of Photosystem II: Applicability of the Jahn-Teller Deformation Formula. CHEMPHOTOCHEM 2018; 2:257-270. [PMID: 29577075 PMCID: PMC5861676 DOI: 10.1002/cptc.201700162] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 11/02/2017] [Indexed: 11/11/2022]
Abstract
Tanaka et al. (J. Am. Chem. Soc., 2017, 139, 1718) recently reported the three-dimensional (3D) structure of the oxygen evolving complex (OEC) of photosystem II (PSII) by X-ray diffraction (XRD) using extremely low X-ray doses of 0.03 and 0.12 MGy. They observed two different 3D structures of the CaMn4O5 cluster with different hydrogen-bonding interactions in the S1 state of OEC keeping the surrounding polypeptide frameworks of PSII the same. Our Jahn-Teller (JT) deformation formula based on large-scale quantum mechanics/molecular mechanics (QM/MM) was applied for these low-dose XRD structures, elucidating important roles of JT effects of the MnIII ion for subtle geometric distortions of the CaMn4O5 cluster in OEC of PSII. The JT deformation formula revealed the similarity between the low-dose XRD and damage-free serial femtosecond X-ray diffraction (SFX) structures of the CaMn4O5 cluster in the dark stable state. The extremely low-dose XRD structures were not damaged by X-ray irradiation. Implications of the present results are discussed in relation to recent SFX results and a blue print for the design of artificial photocatalysts for water oxidation.
Collapse
Affiliation(s)
- Mitsuo Shoji
- Center of Computational SciencesTsukuba University, TsukubaIbaraki305–8577Japan
| | - Hiroshi Isobe
- Graduate School of Natural Science and TechnologyOkayama UniversityOkayama700–8530Japan
| | - Ayako Tanaka
- The OUC Advanced Research Institute for Natural Science and Technology (OCARNA)Osaka City UniversityOsaka558–8585Japan
| | - Yoshimasa Fukushima
- The OUC Advanced Research Institute for Natural Science and Technology (OCARNA)Osaka City UniversityOsaka558–8585Japan
| | - Keisuke Kawakami
- The OUC Advanced Research Institute for Natural Science and Technology (OCARNA)Osaka City UniversityOsaka558–8585Japan
| | - Yasufumi Umena
- The OUC Advanced Research Institute for Natural Science and Technology (OCARNA)Osaka City UniversityOsaka558–8585Japan
| | - Nobuo Kamiya
- The OUC Advanced Research Institute for Natural Science and Technology (OCARNA)Osaka City UniversityOsaka558–8585Japan
| | - Takahito Nakajima
- Riken Advanced Institute for Computational Science, Chuo-KuKobe, Hyogo650-0047Japan
| | - Kizashi Yamaguchi
- Riken Advanced Institute for Computational Science, Chuo-KuKobe, Hyogo650-0047Japan
- Institute for Nanoscience DesignOsaka University, ToyonakaOsaka560–8531Japan
- Handairigaku Techno-Research, ToyonakaOsaka560-0043Japan
| |
Collapse
|
15
|
Yamaguchi K, Shoji M, Isobe H, Yamanaka S, Kawakami T, Yamada S, Katouda M, Nakajima T. Theory of chemical bonds in metalloenzymes XXI. Possible mechanisms of water oxidation in oxygen evolving complex of photosystem II. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1428375] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Kizashi Yamaguchi
- Institute for Nanoscience Design, Osaka University, Osaka, Japan
- Handairigaku Techno-Research, Osaka Univeristy, Osaka, Japan
- Riken Advanced Institute for Computational Science (AICS), Hyogo, Japan
| | - Mitsuo Shoji
- Center for Computational Sciences, University of Tsukuba, Ibaraki, Japan
| | - Hiroshi Isobe
- Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | | | - Takashi Kawakami
- Graduate School of Science, Osaka University, Osaka, Japan
- Riken Advanced Institute for Computational Science (AICS), Hyogo, Japan
| | - Satoru Yamada
- Riken Advanced Institute for Computational Science (AICS), Hyogo, Japan
| | - Michio Katouda
- Riken Advanced Institute for Computational Science (AICS), Hyogo, Japan
| | - Takahito Nakajima
- Riken Advanced Institute for Computational Science (AICS), Hyogo, Japan
| |
Collapse
|
16
|
Baituti B. Computational studies of the Mn 4/Ca cluster in photosystem II. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2018. [DOI: 10.1142/s0219633618500074] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Computational chemistry with the data from more detailed X-ray diffraction (XRD) oxygen evolving complex (OEC) structure has been used extensively of late in exploring the mechanisms of water oxidation in the OEC. The study reported in this paper involves density functional theory (DFT) calculations to investigate whether the data are in agreement with the four manganese ions in the OEC, being organized as a ‘3[Formula: see text]1’ (trimer plus one) model [Gatt et al. Angewandte Chemie International Edition, 51, 12025–12028, 2012; Petrie et al. Chemistry - A European Journal, 21, 6780–6792, 2015; Terrett et al. Chemical Communications, 50, 3187–3190, 2014] or ‘dimer of dimers’ model. [Terrett et al. Journal of Inorganic Biochemistry, 162, 178–189, 2016]. The data analysis method used involves quantum chemical DFT calculations on relevant models of the OEC cluster. DFT calculations were performed using both the so-called ‘open’ and ‘closed’ forms [Terrett et al. Journal of Inorganic Biochemistry, 162, 178–189, 2016] of the S2 OEC structure models with total spin ([Formula: see text]) 1/2, 7/2, 9/2 and 15/2 within the MnIII MnIV MnIII MnIII ‘low’ oxidation paradigm to examine exchange coupling within the OEC cluster. The results show that the [Formula: see text]-coupling in the ‘closed’ form: [Formula: see text][Formula: see text]cm[Formula: see text], [Formula: see text][Formula: see text]cm[Formula: see text], [Formula: see text][Formula: see text]cm[Formula: see text] and [Formula: see text]–[Formula: see text][Formula: see text]cm[Formula: see text]. In the ‘closed’ form, [Formula: see text] and [Formula: see text] represent the two largest exchange interactions within the manganese cluster, whereas [Formula: see text] and [Formula: see text] are small and almost net cancel. The magnetic coupling between the four Mn ions is close to ‘dimer of dimers’, with both dimers anti-ferromagnetically coupled internally and with weak inter-dimer net coupling.
Collapse
Affiliation(s)
- Bernard Baituti
- Botswana International University of Science and Technology, Private Bag 16, Palapye, Botswana
| |
Collapse
|
17
|
Roemelt M, Krewald V, Pantazis DA. Exchange Coupling Interactions from the Density Matrix Renormalization Group and N-Electron Valence Perturbation Theory: Application to a Biomimetic Mixed-Valence Manganese Complex. J Chem Theory Comput 2017; 14:166-179. [PMID: 29211960 DOI: 10.1021/acs.jctc.7b01035] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The accurate description of magnetic level energetics in oligonuclear exchange-coupled transition-metal complexes remains a formidable challenge for quantum chemistry. The density matrix renormalization group (DMRG) brings such systems for the first time easily within reach of multireference wave function methods by enabling the use of unprecedentedly large active spaces. But does this guarantee systematic improvement in predictive ability and, if so, under which conditions? We identify operational parameters in the use of DMRG using as a test system an experimentally characterized mixed-valence bis-μ-oxo/μ-acetato Mn(III,IV) dimer, a model for the oxygen-evolving complex of photosystem II. A complete active space of all metal 3d and bridge 2p orbitals proved to be the smallest meaningful starting point; this is readily accessible with DMRG and greatly improves on the unrealistic metal-only configuration interaction or complete active space self-consistent field (CASSCF) values. Orbital optimization is critical for stabilizing the antiferromagnetic state, while a state-averaged approach over all spin states involved is required to avoid artificial deviations from isotropic behavior that are associated with state-specific calculations. Selective inclusion of localized orbital subspaces enables probing the relative contributions of different ligands and distinct superexchange pathways. Overall, however, full-valence DMRG-CASSCF calculations fall short of providing a quantitative description of the exchange coupling owing to insufficient recovery of dynamic correlation. Quantitatively accurate results can be achieved through a DMRG implementation of second order N-electron valence perturbation theory (NEVPT2) in conjunction with a full-valence metal and ligand active space. Perspectives for future applications of DMRG-CASSCF/NEVPT2 to exchange coupling in oligonuclear clusters are discussed.
Collapse
Affiliation(s)
- Michael Roemelt
- Lehrstuhl für Theoretische Chemie, Ruhr-University Bochum , 44780 Bochum, Germany.,Max Planck Institute for Coal Research, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Vera Krewald
- Department of Chemistry, University of Bath , Bath BA2 7AY, United Kingdom
| | - Dimitrios A Pantazis
- Max Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, 45470 Mülheim an der Ruhr, Germany
| |
Collapse
|
18
|
Yamaguchi K, Shoji M, Isobe H, Yamanaka S, Umena Y, Kawakami K, Kamiya N. On the guiding principles for understanding of geometrical structures of the CaMn4O5 cluster in oxygen-evolving complex of photosystem II. Proposal of estimation formula of structural deformations via the Jahn–Teller effects. Mol Phys 2017. [DOI: 10.1080/00268976.2016.1278476] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- K. Yamaguchi
- Institute for Nanoscience Design, Osaka University, Toyonaka, Japan
- Handairigaku Techno-Research , Toyonaka, Japan
| | - M. Shoji
- Center of Computational Sciences, Tsukuba University , Tsukuba, Japan
| | - H. Isobe
- Graduate School of Natural Science and Technology, Okayama University , Okayama, Japan
| | - S. Yamanaka
- Graduate School of Science, Osaka University , Osaka, Japan
| | - Y. Umena
- The OUC Advanced Research Institute for Natural Science and Technology (OCARNA), Osaka City University , Osaka, Japan
| | - K. Kawakami
- The OUC Advanced Research Institute for Natural Science and Technology (OCARNA), Osaka City University , Osaka, Japan
| | - N. Kamiya
- The OUC Advanced Research Institute for Natural Science and Technology (OCARNA), Osaka City University , Osaka, Japan
| |
Collapse
|
19
|
Isobe H. Functional significance of the “distorted chair” topology of the Mn cluster for oxygen evolution in photosynthesis. ACTA ACUST UNITED AC 2017. [DOI: 10.4019/bjscc.70.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- Hiroshi Isobe
- Research Institute for Interdisciplinary Science, Okayama University
| |
Collapse
|
20
|
Shoji M, Isobe H, Nakajima T, Shigeta Y, Suga M, Akita F, Shen JR, Yamaguchi K. Large-scale QM/MM calculations of the CaMn4O5 cluster in the S3 state of the oxygen evolving complex of photosystem II. Comparison between water-inserted and no water-inserted structures. Faraday Discuss 2017; 198:83-106. [DOI: 10.1039/c6fd00230g] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Large-scale QM/MM calculations were performed to elucidate an optimized geometrical structure of a CaMn4O5 cluster with and without water insertion in the S3 state of the oxygen evolving complex (OEC) of photosystem II (PSII). The left (L)-opened structure was found to be stable under the assumption of no hydroxide anion insertion in the S3 state, whereas the right (R)-opened structure became more stable if one water molecule is inserted to the Mn4Ca cluster. The optimized Mna(4)–Mnd(1) distance determined by QM/MM was about 5.0 Å for the S3 structure without an inserted hydroxide anion, but this is elongated by 0.2–0.3 Å after insertion. These computational results are discussed in relation to the possible mechanisms of O–O bond formation in water oxidation by the OEC of PSII.
Collapse
Affiliation(s)
- Mitsuo Shoji
- Center for Computational Sciences
- University of Tsukuba
- Tsukuba
- Japan
- Graduate School of Pure and Applied Sciences
| | - Hiroshi Isobe
- Research Institute for Interdisciplinary Science
- Graduate School of Natural Science and Technology
- Okayama University
- Okayama
- Japan
| | | | - Yasuteru Shigeta
- Center for Computational Sciences
- University of Tsukuba
- Tsukuba
- Japan
- Graduate School of Pure and Applied Sciences
| | - Michihiro Suga
- Research Institute for Interdisciplinary Science
- Graduate School of Natural Science and Technology
- Okayama University
- Okayama
- Japan
| | - Fusamichi Akita
- Research Institute for Interdisciplinary Science
- Graduate School of Natural Science and Technology
- Okayama University
- Okayama
- Japan
| | - Jian-Ren Shen
- Research Institute for Interdisciplinary Science
- Graduate School of Natural Science and Technology
- Okayama University
- Okayama
- Japan
| | - Kizashi Yamaguchi
- Riken Advanced Institute for Computational Science
- Kobe
- Japan
- Institute for NanoScience Design
- Osaka University
| |
Collapse
|
21
|
Chernev P, Zaharieva I, Rossini E, Galstyan A, Dau H, Knapp EW. Merging Structural Information from X-ray Crystallography, Quantum Chemistry, and EXAFS Spectra: The Oxygen-Evolving Complex in PSII. J Phys Chem B 2016; 120:10899-10922. [DOI: 10.1021/acs.jpcb.6b05800] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Petko Chernev
- Institute of Chemistry and Biochemistry and ‡Department of Physics, Freie Universität Berlin, D-14195 Berlin, Germany
| | - Ivelina Zaharieva
- Institute of Chemistry and Biochemistry and ‡Department of Physics, Freie Universität Berlin, D-14195 Berlin, Germany
| | - Emanuele Rossini
- Institute of Chemistry and Biochemistry and ‡Department of Physics, Freie Universität Berlin, D-14195 Berlin, Germany
| | - Artur Galstyan
- Institute of Chemistry and Biochemistry and ‡Department of Physics, Freie Universität Berlin, D-14195 Berlin, Germany
| | - Holger Dau
- Institute of Chemistry and Biochemistry and ‡Department of Physics, Freie Universität Berlin, D-14195 Berlin, Germany
| | - Ernst-Walter Knapp
- Institute of Chemistry and Biochemistry and ‡Department of Physics, Freie Universität Berlin, D-14195 Berlin, Germany
| |
Collapse
|
22
|
Shoji M, Isobe H, Nakajima T, Yamaguchi K. Large-scale QM/MM calculations of the CaMn4O5 cluster in the oxygen-evolving complex of photosystem II: Comparisons with EXAFS structures. Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2016.06.067] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
23
|
Krewald V, Retegan M, Neese F, Lubitz W, Pantazis DA, Cox N. Spin State as a Marker for the Structural Evolution of Nature’s Water-Splitting Catalyst. Inorg Chem 2015; 55:488-501. [DOI: 10.1021/acs.inorgchem.5b02578] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Vera Krewald
- Max Planck Institute for Chemical Energy Conversion, Stiftstr.
34–36, Mülheim an der Ruhr 45470, Germany
| | - Marius Retegan
- Max Planck Institute for Chemical Energy Conversion, Stiftstr.
34–36, Mülheim an der Ruhr 45470, Germany
| | - Frank Neese
- Max Planck Institute for Chemical Energy Conversion, Stiftstr.
34–36, Mülheim an der Ruhr 45470, Germany
| | - Wolfgang Lubitz
- Max Planck Institute for Chemical Energy Conversion, Stiftstr.
34–36, Mülheim an der Ruhr 45470, Germany
| | - Dimitrios A. Pantazis
- Max Planck Institute for Chemical Energy Conversion, Stiftstr.
34–36, Mülheim an der Ruhr 45470, Germany
| | - Nicholas Cox
- Max Planck Institute for Chemical Energy Conversion, Stiftstr.
34–36, Mülheim an der Ruhr 45470, Germany
| |
Collapse
|
24
|
Yamaguchi K, Isobe H, Shoji M, Yamanaka S, Okumura M. Theory of chemical bonds in metalloenzymes XX: magneto-structural correlations in the CaMn4O5cluster in oxygen-evolving complex of photosystem II. Mol Phys 2015. [DOI: 10.1080/00268976.2015.1114162] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
25
|
Shoji M, Isobe H, Nakajima T, Yamaguchi K. Full geometry optimizations of the CaMn4O4 model cluster for the oxygen evolving complex of photosystem II. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.10.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
26
|
Shoji M, Isobe H, Yamanaka S, Suga M, Akita F, Shen JR, Yamaguchi K. On the guiding principles for lucid understanding of the damage-free S1 structure of the CaMn4O5 cluster in the oxygen evolving complex of photosystem II. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.03.033] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
27
|
Fernando A, Weerawardene KLDM, Karimova NV, Aikens CM. Quantum Mechanical Studies of Large Metal, Metal Oxide, and Metal Chalcogenide Nanoparticles and Clusters. Chem Rev 2015; 115:6112-216. [PMID: 25898274 DOI: 10.1021/cr500506r] [Citation(s) in RCA: 217] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Amendra Fernando
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, United States
| | | | - Natalia V Karimova
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, United States
| | - Christine M Aikens
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, United States
| |
Collapse
|
28
|
Isobe H, Shoji M, Yamanaka S, Mino H, Umena Y, Kawakami K, Kamiya N, Shen JR, Yamaguchi K. Generalized approximate spin projection calculations of effective exchange integrals of the CaMn4O5 cluster in the S1 and S3 states of the oxygen evolving complex of photosystem II. Phys Chem Chem Phys 2015; 16:11911-23. [PMID: 24632787 DOI: 10.1039/c4cp00282b] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Full geometry optimizations followed by the vibrational analysis were performed for eight spin configurations of the CaMn4O4X(H2O)3Y (X = O, OH; Y = H2O, OH) cluster in the S1 and S3 states of the oxygen evolution complex (OEC) of photosystem II (PSII). The energy gaps among these configurations obtained by vertical, adiabatic and adiabatic plus zero-point-energy (ZPE) correction procedures have been used for computation of the effective exchange integrals (J) in the spin Hamiltonian model. The J values are calculated by the (1) analytical method and the (2) generalized approximate spin projection (AP) method that eliminates the spin contamination errors of UB3LYP solutions. Using J values derived from these methods, exact diagonalization of the spin Hamiltonian matrix was carried out, yielding excitation energies and spin densities of the ground and lower-excited states of the cluster. The obtained results for the right (R)- and left (L)-opened structures in the S1 and S3 states are found to be consistent with available optical and magnetic experimental results. Implications of the computational results are discussed in relation to (a) the necessity of the exact diagonalization for computations of reliable energy levels, (b) magneto-structural correlations in the CaMn4O5 cluster of the OEC of PSII, (c) structural symmetry breaking in the S1 and S3 states, and (d) the right- and left-handed scenarios for the O-O bond formation for water oxidation.
Collapse
Affiliation(s)
- H Isobe
- Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8530, Japan
| | | | | | | | | | | | | | | | | |
Collapse
|
29
|
Theoretical studies of the damage-free S1 structure of the CaMn4O5 cluster in oxygen-evolving complex of photosystem II. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.01.030] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
|
30
|
Krewald V, Retegan M, Cox N, Messinger J, Lubitz W, DeBeer S, Neese F, Pantazis DA. Metal oxidation states in biological water splitting. Chem Sci 2015; 6:1676-1695. [PMID: 29308133 PMCID: PMC5639794 DOI: 10.1039/c4sc03720k] [Citation(s) in RCA: 230] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 12/31/2014] [Indexed: 12/20/2022] Open
Abstract
A central question in biological water splitting concerns the oxidation states of the manganese ions that comprise the oxygen-evolving complex of photosystem II.
A central question in biological water splitting concerns the oxidation states of the manganese ions that comprise the oxygen-evolving complex of photosystem II. Understanding the nature and order of oxidation events that occur during the catalytic cycle of five Si states (i = 0–4) is of fundamental importance both for the natural system and for artificial water oxidation catalysts. Despite the widespread adoption of the so-called “high-valent scheme”—where, for example, the Mn oxidation states in the S2 state are assigned as III, IV, IV, IV—the competing “low-valent scheme” that differs by a total of two metal unpaired electrons (i.e. III, III, III, IV in the S2 state) is favored by several recent studies for the biological catalyst. The question of the correct oxidation state assignment is addressed here by a detailed computational comparison of the two schemes using a common structural platform and theoretical approach. Models based on crystallographic constraints were constructed for all conceivable oxidation state assignments in the four (semi)stable S states of the oxygen evolving complex, sampling various protonation levels and patterns to ensure comprehensive coverage. The models are evaluated with respect to their geometric, energetic, electronic, and spectroscopic properties against available experimental EXAFS, XFEL-XRD, EPR, ENDOR and Mn K pre-edge XANES data. New 2.5 K 55Mn ENDOR data of the S2 state are also reported. Our results conclusively show that the entire S state phenomenology can only be accommodated within the high-valent scheme by adopting a single motif and protonation pattern that progresses smoothly from S0 (III, III, III, IV) to S3 (IV, IV, IV, IV), satisfying all experimental constraints and reproducing all observables. By contrast, it was impossible to construct a consistent cycle based on the low-valent scheme for all S states. Instead, the low-valent models developed here may provide new insight into the over-reduced S states and the states involved in the assembly of the catalytically active water oxidizing cluster.
Collapse
Affiliation(s)
- Vera Krewald
- Max Planck Institute for Chemical Energy Conversion , Stiftstr. 34-38 , 45470 Mülheim an der Ruhr , Germany .
| | - Marius Retegan
- Max Planck Institute for Chemical Energy Conversion , Stiftstr. 34-38 , 45470 Mülheim an der Ruhr , Germany .
| | - Nicholas Cox
- Max Planck Institute for Chemical Energy Conversion , Stiftstr. 34-38 , 45470 Mülheim an der Ruhr , Germany .
| | - Johannes Messinger
- Department of Chemistry , Chemical Biological Center (KBC) , Umeå University , 90187 Umeå , Sweden
| | - Wolfgang Lubitz
- Max Planck Institute for Chemical Energy Conversion , Stiftstr. 34-38 , 45470 Mülheim an der Ruhr , Germany .
| | - Serena DeBeer
- Max Planck Institute for Chemical Energy Conversion , Stiftstr. 34-38 , 45470 Mülheim an der Ruhr , Germany .
| | - Frank Neese
- Max Planck Institute for Chemical Energy Conversion , Stiftstr. 34-38 , 45470 Mülheim an der Ruhr , Germany .
| | - Dimitrios A Pantazis
- Max Planck Institute for Chemical Energy Conversion , Stiftstr. 34-38 , 45470 Mülheim an der Ruhr , Germany .
| |
Collapse
|
31
|
Shoji M, Isobe H, Yamanaka S, Umena Y, Kawakami K, Kamiya N, Shen JR, Nakajima T, Yamaguchi K. Large-Scale QM/MM Calculations of Hydrogen Bonding Networks for Proton Transfer and Water Inlet Channels for Water Oxidation—Theoretical System Models of the Oxygen-Evolving Complex of Photosystem II. ADVANCES IN QUANTUM CHEMISTRY 2015. [DOI: 10.1016/bs.aiq.2014.10.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|
32
|
Shen JR. The Structure of Photosystem II and the Mechanism of Water Oxidation in Photosynthesis. ANNUAL REVIEW OF PLANT BIOLOGY 2015; 66:23-48. [PMID: 25746448 DOI: 10.1146/annurev-arplant-050312-120129] [Citation(s) in RCA: 453] [Impact Index Per Article: 50.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Oxygenic photosynthesis forms the basis of aerobic life on earth by converting light energy into biologically useful chemical energy and by splitting water to generate molecular oxygen. The water-splitting and oxygen-evolving reaction is catalyzed by photosystem II (PSII), a huge, multisubunit membrane-protein complex located in the thylakoid membranes of organisms ranging from cyanobacteria to higher plants. The structure of PSII has been analyzed at 1.9-Å resolution by X-ray crystallography, revealing a clear picture of the Mn4CaO5 cluster, the catalytic center for water oxidation. This article provides an overview of the overall structure of PSII followed by detailed descriptions of the specific structure of the Mn4CaO5 cluster and its surrounding protein environment. Based on the geometric organization of the Mn4CaO5 cluster revealed by the crystallographic analysis, in combination with the results of a vast number of experimental studies involving spectroscopic and other techniques as well as various theoretical studies, the article also discusses possible mechanisms for water splitting that are currently under consideration.
Collapse
Affiliation(s)
- Jian-Ren Shen
- Photosynthesis Research Center, Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8530, Japan;
| |
Collapse
|
33
|
Shoji M, Isobe H, Yamanaka S, Umena Y, Kawakami K, Kamiya N, Shen JR, Nakajima T, Yamaguchi K. Theoretical modelling of biomolecular systems I. Large-scale QM/MM calculations of hydrogen-bonding networks of the oxygen evolving complex of photosystem II. Mol Phys 2014. [DOI: 10.1080/00268976.2014.960021] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
|
34
|
Theoretical study on mechanism of dioxygen evolution in photosystem II. II. Molecular and electronic structures at the S3 and S4 states of oxygen-evolving complex. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2014.02.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
35
|
Yamaguchi K, Kitagawa Y, Isobe H, Shoji M, Yamanaka S, Okumura M. Reprint of “Theory of chemical bonds in metalloenzymes XVIII. Importance of mixed-valence configurations for Mn5O5, CaMn4O5 and Ca2Mn3O5 clusters revealed by UB3LYP computations. A bio-inspired strategy for artificial photosynthesis”. Polyhedron 2013. [DOI: 10.1016/j.poly.2013.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
36
|
Yamaguchi K, Yamanaka S, Shoji M, Isobe H, Kitagawa Y, Kawakami T, Yamada S, Okumura M. Theory of chemical bonds in metalloenzymes XIX: labile manganese oxygen bonds of the CaMn4O5cluster in oxygen evolving complex of photosystem II. Mol Phys 2013. [DOI: 10.1080/00268976.2013.842009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
37
|
Retegan M, Neese F, Pantazis DA. Convergence of QM/MM and Cluster Models for the Spectroscopic Properties of the Oxygen-Evolving Complex in Photosystem II. J Chem Theory Comput 2013; 9:3832-42. [PMID: 26584129 DOI: 10.1021/ct400477j] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The latest crystal structure of photosystem II at 1.9 Å resolution, which resolves the topology of the Mn4CaO5 oxygen evolving complex (OEC) at atomistic detail, enables a better correlation between structural features and spectroscopic properties than ever before. Building on the refined crystallographic model of the OEC and the protein, we present combined quantum mechanical/molecular mechanical (QM/MM) studies of the spectroscopic properties of the natural catalyst embedded in the protein matrix. Focusing on the S2 state of the catalytic cycle, we examine the convergence of not only structural parameters but also of the intracluster magnetic interactions in terms of exchange coupling constants and of experimentally relevant (55)Mn, (17)O, and (14)N hyperfine coupling constants with respect to QM/MM partitioning using five QM regions of increasing size. This enables us to assess the performance of the method and to probe second sphere effects by identifying amino acid residues that principally affect the spectroscopic properties of the OEC. Comparison between QM-only and QM/MM treatments reveals that whereas QM/MM models converge quickly to stable values, the QM cluster models need to incorporate significantly larger parts of the second coordination sphere and surrounding water molecules to achieve convergence for certain properties. This is mainly due to the sensitivity of the QM-only models to fluctuations in the hydrogen bonding network and ligand acidity. Additionally, a hydrogen bond that is typically omitted in QM-only treatments is shown to determine the hyperfine coupling tensor of the unique Mn(III) ion by regulating the rotation plane of the ligated D1-His332 imidazole ring, the only N-donor ligand of the OEC.
Collapse
Affiliation(s)
- Marius Retegan
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-38, 45470 Mülheim an der Ruhr, Germany
| | - Frank Neese
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-38, 45470 Mülheim an der Ruhr, Germany
| | - Dimitrios A Pantazis
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-38, 45470 Mülheim an der Ruhr, Germany
| |
Collapse
|
38
|
Yamaguchi K, Kitagawa Y, Isobe H, Shoji M, Yamanaka S, Okumura M. Theory of chemical bonds in metalloenzymes XVIII. Importance of mixed-valence configurations for Mn5O5, CaMn4O5 and Ca2Mn3O5 clusters revealed by UB3LYP computations. A bio-inspired strategy for artificial photosynthesis. Polyhedron 2013. [DOI: 10.1016/j.poly.2013.04.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
39
|
Ichino T, Yoshioka Y. Theoretical Study on the Mechanism of Dioxygen Evolution in Photosystem II. I. Molecular and Electronic Structures at the S0, S1, and S2States of Oxygen-Evolving Complex. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2013. [DOI: 10.1246/bcsj.20120223] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Tomoya Ichino
- Chemistry Department for Materials, Graduate School of Engineering, Mie University
| | - Yasunori Yoshioka
- Chemistry Department for Materials, Graduate School of Engineering, Mie University
| |
Collapse
|
40
|
Shoji M, Isobe H, Yamanaka S, Umena Y, Kawakami K, Kamiya N, Shen JR, Yamaguchi K. Theoretical insight in to hydrogen-bonding networks and proton wire for the CaMn4O5 cluster of photosystem II. Elongation of Mn–Mn distances with hydrogen bonds. Catal Sci Technol 2013. [DOI: 10.1039/c3cy00051f] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
41
|
Which oxidation state is preferable at S0 state in oxygen-evolving complex, Mn4(II, III, IV, IV) or Mn4(III, III, III, IV)? A B3LYP study. Chem Phys Lett 2012. [DOI: 10.1016/j.cplett.2012.07.029] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
42
|
Similarities of artificial photosystems by ruthenium oxo complexes and native water splitting systems. Proc Natl Acad Sci U S A 2012; 109:15600-5. [PMID: 22761310 DOI: 10.1073/pnas.1120705109] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The nature of chemical bonds of ruthenium(Ru)-quinine(Q) complexes, mononuclear [Ru(trpy)(3,5-t-Bu(2)Q)(OH(2))](ClO(4))(2) (trpy = 2,2':6',2''-terpyridine, 3,5-di-tert-butyl-1,2-benzoquinone) (1), and binuclear [Ru(2)(btpyan)(3,6-di-Bu(2)Q)(2)(OH(2))](2+) (btpyan = 1,8-bis(2,2':6',2''-terpyrid-4'-yl)anthracene, 3,6-t-Bu(2)Q = 3,6-di-tert-butyl-1,2-benzoquinone) (2), has been investigated by broken-symmetry (BS) hybrid density functional (DFT) methods. BS DFT computations for the Ru complexes have elucidated that the closed-shell structure (2b) Ru(II)-Q complex is less stable than the open-shell structure (2bb) consisting of Ru(III) and semiquinone (SQ) radical fragments. These computations have also elucidated eight different electronic and spin structures of tetraradical intermediates that may be generated in the course of water splitting reaction. The Heisenberg spin Hamiltonian model for these species has been derived to elucidate six different effective exchange interactions (J) for four spin systems. Six J values have been determined using total energies of the eight (or seven) BS solutions for different spin configurations. The natural orbital analyses of these BS DFT solutions have also been performed in order to obtain natural orbitals and their occupation numbers, which are useful for the lucid understanding of the nature of chemical bonds of the Ru complexes. Implications of the computational results are discussed in relation to the proposed reaction mechanisms of water splitting reaction in artificial photosynthesis systems and the similarity between artificial and native water splitting systems.
Collapse
|
43
|
Saito K, Shen JR, Ishikita H. Influence of the axial ligand on the cationic properties of the chlorophyll pair in photosystem II from Thermosynechococcus vulcanus. Biophys J 2012; 102:2634-40. [PMID: 22713579 DOI: 10.1016/j.bpj.2012.04.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Revised: 04/12/2012] [Accepted: 04/16/2012] [Indexed: 11/26/2022] Open
Abstract
Influence of the axial ligand of PD1 chlorophyll (D1-His-198) on the Em of monomer chlorophylls PD1 and PD2, and the PD1•+/PD2•+ charge ratio was investigated by theoretical calculations using the PSII crystal structure of Thermosynechococcus vulcanus analyzed at 1.9-Å resolution. It was found that the Em(PD1)/Em(PD2) values and PD1•+/PD2•+ ratio remained unchanged upon D1-H198Q mutation. However, Em(PD1) was increased in the D1-H198A mutant, resulting in a more even distribution of the positive charge over PD1/PD2. Introduction of a water molecule as an axial ligand resulted in equal Em values and PD1•+/PD2•+ ratios between the mutant and wild-type, thus confirming the presence of the water ligand in the mutant.
Collapse
Affiliation(s)
- Keisuke Saito
- Career-Path Promotion Unit for Young Life Scientists, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | | | | |
Collapse
|
44
|
Galstyan A, Robertazzi A, Knapp EW. Oxygen-Evolving Mn Cluster in Photosystem II: The Protonation Pattern and Oxidation State in the High-Resolution Crystal Structure. J Am Chem Soc 2012; 134:7442-9. [DOI: 10.1021/ja300254n] [Citation(s) in RCA: 141] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Artur Galstyan
- Department of Biology,
Chemistry and Pharmacy, Institute
of Chemistry and Biochemistry, Freie Universität Berlin, Fabeckstrasse 36a, D-14195 Berlin, Germany
| | - Arturo Robertazzi
- Department of Biology,
Chemistry and Pharmacy, Institute
of Chemistry and Biochemistry, Freie Universität Berlin, Fabeckstrasse 36a, D-14195 Berlin, Germany
| | - Ernst Walter Knapp
- Department of Biology,
Chemistry and Pharmacy, Institute
of Chemistry and Biochemistry, Freie Universität Berlin, Fabeckstrasse 36a, D-14195 Berlin, Germany
| |
Collapse
|
45
|
Ichino T, Yamaguchi K, Yoshioka Y. Effectiveness of Optimizing Geometry for CaMn4O5 Cluster at 1.9 Å Resolved OEC and Proposal for Oxidation Mechanism from S0 to S3 States. CHEM LETT 2012. [DOI: 10.1246/cl.2012.18] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Tomoya Ichino
- Chemistry Department for Materials, Graduate School of Engineering, Mie University
| | | | - Yasunori Yoshioka
- Chemistry Department for Materials, Graduate School of Engineering, Mie University
| |
Collapse
|
46
|
Yamanaka S, Kanda K, Saito T, Umena Y, Kawakami K, Shen JR, Kamiya N, Okumura M, Nakamura H, Yamaguchi K. Electronic and Spin Structures of the CaMn4O5(H2O)4 Cluster in OEC of PSII Refined to 1.9Å X-ray Resolution. ADVANCES IN QUANTUM CHEMISTRY 2012. [DOI: 10.1016/b978-0-12-396498-4.00016-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
|
47
|
Does B3LYP correctly describe magnetism of manganese complexes with various oxidation numbers and various structural motifs? Chem Phys Lett 2012. [DOI: 10.1016/j.cplett.2011.11.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
48
|
Petrie S, Gatt P, Stranger R, Pace RJ. Modelling the metal atom positions of the Photosystem II water oxidising complex: a density functional theory appraisal of the 1.9 Å resolution crystal structure. Phys Chem Chem Phys 2012; 14:11333-43. [DOI: 10.1039/c2cp41020f] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
|
49
|
Isobe H, Shoji M, Yamanaka S, Umena Y, Kawakami K, Kamiya N, Shen JR, Yamaguchi K. Theoretical illumination of water-inserted structures of the CaMn4O5 cluster in the S2 and S3 states of oxygen-evolving complex of photosystem II: full geometry optimizations by B3LYP hybrid density functional. Dalton Trans 2012; 41:13727-40. [DOI: 10.1039/c2dt31420g] [Citation(s) in RCA: 162] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
50
|
Saito K, Shen JR, Ishikita H. Cationic state distribution over the chlorophyll d-containing P(D1)/P(D2) pair in photosystem II. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1817:1191-5. [PMID: 22192718 DOI: 10.1016/j.bbabio.2011.12.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2011] [Revised: 12/02/2011] [Accepted: 12/06/2011] [Indexed: 11/25/2022]
Abstract
Most of the chlorophyll (Chl) cofactors in photosystem II (PSII) from Acaryochloris marina are Chld, although a few Chla molecules are also present. To evaluate the possibility that Chla may participate in the P(D1)/P(D2) Chl pair in PSII from A. marina, the P(D1)(•+)/P(D2)(•+) charge ratio was investigated using the PSII crystal structure analyzed at 1.9-Å resolution, while considering all possibilities for the Chld-containing P(D1)/P(D2) pair, i.e., Chld/Chld, Chla/Chld, and Chld/Chla pairs. Chld/Chld and Chla/Chld pairs resulted in a large P(D1)(•+) population relative to P(D2)(•+), as identified in Chla/Chla homodimer pairs in PSII from other species, e.g., Thermosynechococcus elongatus PSII. However, the Chld/Chla pair possessed a P(D1)(•+)/P(D2)(•+) ratio of approximately 50/50, which is in contrast to previous spectroscopic studies on A. marina PSII. The present results strongly exclude the possibility that the Chld/Chla pair serves as P(D1)/P(D2) in A. marina PSII. This article is part of a Special Issue entitled: Photosynthesis Research for Sustainability: from Natural to Artificial.
Collapse
Affiliation(s)
- Keisuke Saito
- Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | | | | |
Collapse
|