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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.
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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
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Drosou M, Comas-Vilà G, Neese F, Salvador P, Pantazis DA. Does Serial Femtosecond Crystallography Depict State-Specific Catalytic Intermediates of the Oxygen-Evolving Complex? J Am Chem Soc 2023; 145:10604-10621. [PMID: 37137865 DOI: 10.1021/jacs.3c00489] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Recent advances in serial femtosecond crystallography (SFX) of photosystem II (PSII), enabled by X-ray free electron lasers (XFEL), provided the first geometric models of distinct intermediates in the catalytic S-state cycle of the oxygen-evolving complex (OEC). These models are obtained by flash-advancing the OEC from the dark-stable state (S1) to more oxidized intermediates (S2 and S3), eventually cycling back to the most reduced S0. However, the interpretation of these models is controversial because geometric parameters within the Mn4CaO5 cluster of the OEC do not exactly match those expected from coordination chemistry for the spectroscopically verified manganese oxidation states of the distinct S-state intermediates. Here we focus on the first catalytic transition, S1 → S2, which represents a one-electron oxidation of the OEC. Combining geometric and electronic structure criteria, including a novel effective oxidation state approach, we analyze existing 1-flash (1F) SFX-XFEL crystallographic models that should depict the S2 state of the OEC. We show that the 1F/S2 equivalence is not obvious, because the Mn oxidation states and total unpaired electron counts encoded in these models are not fully consistent with those of a pure S2 state and with the nature of the S1 → S2 transition. Furthermore, the oxidation state definition in two-flashed (2F) structural models is practically impossible to elucidate. Our results advise caution in the extraction of electronic structure information solely from the literal interpretation of crystallographic models and call for re-evaluation of structural and mechanistic interpretations that presume exact correspondence of such models to specific catalytic intermediates of the OEC.
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Affiliation(s)
- Maria Drosou
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
| | - Gerard Comas-Vilà
- Institute of Computational Chemistry and Catalysis, Chemistry Department, University of Girona, Montilivi Campus, Girona, Catalonia 17003, Spain
| | - Frank Neese
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
| | - Pedro Salvador
- Institute of Computational Chemistry and Catalysis, Chemistry Department, University of Girona, Montilivi Campus, Girona, Catalonia 17003, Spain
| | - Dimitrios A Pantazis
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
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Guo Y, Messinger J, Kloo L, Sun L. Alternative Mechanism for O 2 Formation in Natural Photosynthesis via Nucleophilic Oxo-Oxo Coupling. J Am Chem Soc 2023; 145:4129-4141. [PMID: 36763485 DOI: 10.1021/jacs.2c12174] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
O2 formation in photosystem II (PSII) is a vital event on Earth, but the exact mechanism remains unclear. The presently prevailing theoretical model is "radical coupling" (RC) involving a Mn(IV)-oxyl unit in an "open-cubane" Mn4CaO6 cluster, which is supported experimentally by the S3 state of cyanobacterial PSII featuring an additional Mn-bound oxygenic ligand. However, it was recently proposed that the major structural form of the S3 state of higher plants lacks this extra ligand, and that the resulting S4 state would feature instead a penta-coordinate dangler Mn(V)=oxo, covalently linked to a "closed-cubane" Mn3CaO4 cluster. For this proposal, we explore here a large number of possible pathways of O-O bond formation and demonstrate that the "nucleophilic oxo-oxo coupling" (NOOC) between Mn(V)=oxo and μ3-oxo is the only eligible mechanism in such a system. The reaction is facilitated by a specific conformation of the cluster and concomitant water binding, which is delayed compared to the RC mechanism. An energetically feasible process is described starting from the valid S4 state through the sequential formation of peroxide and superoxide, followed by O2 release and a second water insertion. The newly found mechanism is consistent with available experimental thermodynamic and kinetic data and thus a viable alternative pathway for O2 formation in natural photosynthesis, in particular for higher plants.
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Affiliation(s)
- Yu Guo
- Center of Artificial Photosynthesis for Solar Fuels and Department of Chemistry, School of Science, Westlake University, Hangzhou 310024, China
- Institute of Natural Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, China
| | - Johannes Messinger
- Department of Chemistry, Umeå University, Linnaeus väg 6 (KBC huset), Umeå SE-90187, Sweden
- Molecular Biomimetics, Department of Chemistry─Ångström Laboratory, Uppsala University, Uppsala SE-75120, Sweden
| | - Lars Kloo
- Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm SE-10044, Sweden
| | - Licheng Sun
- Center of Artificial Photosynthesis for Solar Fuels and Department of Chemistry, School of Science, Westlake University, Hangzhou 310024, China
- Institute of Natural Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, China
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Chen Y, Xu B, Yao R, Chen C, Zhang C. Mimicking the Oxygen-Evolving Center in Photosynthesis. FRONTIERS IN PLANT SCIENCE 2022; 13:929532. [PMID: 35874004 PMCID: PMC9302449 DOI: 10.3389/fpls.2022.929532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 06/20/2022] [Indexed: 06/15/2023]
Abstract
The oxygen-evolving center (OEC) in photosystem II (PSII) of oxygenic photosynthetic organisms is a unique heterometallic-oxide Mn4CaO5-cluster that catalyzes water splitting into electrons, protons, and molecular oxygen through a five-state cycle (Sn, n = 0 ~ 4). It serves as the blueprint for the developing of the man-made water-splitting catalysts to generate solar fuel in artificial photosynthesis. Understanding the structure-function relationship of this natural catalyst is a great challenge and a long-standing issue, which is severely restricted by the lack of a precise chemical model for this heterometallic-oxide cluster. However, it is a great challenge for chemists to precisely mimic the OEC in a laboratory. Recently, significant advances have been achieved and a series of artificial Mn4XO4-clusters (X = Ca/Y/Gd) have been reported, which closely mimic both the geometric structure and the electronic structure, as well as the redox property of the OEC. These new advances provide a structurally well-defined molecular platform to study the structure-function relationship of the OEC and shed new light on the design of efficient catalysts for the water-splitting reaction in artificial photosynthesis.
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Affiliation(s)
- Yang Chen
- Laboratory of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Boran Xu
- Laboratory of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ruoqing Yao
- Laboratory of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Changhui Chen
- Laboratory of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
| | - Chunxi Zhang
- Laboratory of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
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Bigness A, Vaddypally S, Zdilla MJ, Mendoza-Cortes JL. Ubiquity of cubanes in bioinorganic relevant compounds. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2021.214168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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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.
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Affiliation(s)
- K Miyagawa
- Institute for Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan.
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7
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Evaluation of new low-valent computational models for the oxygen-evolving complex of photosystem II. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2020.137629] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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8
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Water-oxidizing complex in Photosystem II: Its structure and relation to manganese-oxide based catalysts. Coord Chem Rev 2020. [DOI: 10.1016/j.ccr.2020.213183] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Petrie S, Terrett R, Stranger R, Pace RJ. Rationalizing the Geometries of the Water Oxidising Complex in the Atomic Resolution, Nominal S 3 State Crystal Structures of Photosystem II. Chemphyschem 2020; 21:785-801. [PMID: 32133758 DOI: 10.1002/cphc.201901106] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 01/14/2020] [Indexed: 11/06/2022]
Abstract
Three atomic resolution crystal structures of Photosystem II, in the double flashed, nominal S3 intermediate state of its Mn4 Ca Water Oxidising Complex (WOC), have now been presented, at 2.25, 2.35 and 2.08 Å resolution. Although very similar overall, the S3 structures differ within the WOC catalytic site. The 2.25 Å structure contains only one oxy species (O5) in the WOC cavity, weakly associated with Mn centres, similar to that in the earlier 1.95 Å S1 structure. The 2.35 Å structure shows two such species (O5, O6), with the Mn centres and O5 positioned as in the 2.25 Å structure and O5-O6 separation of ∼1.5 Å. In the latest S3 variant, two oxy species are also seen (O5, Ox), with the Ox group appearing only in S3 , closely ligating one Mn, with O5-Ox separation <2.1 Å. The O5 and O6/Ox groups were proposed to be substrate water derived species. Recently, Petrie et al. (Chem. Phys. Chem., 2017) presented large scale Quantum Chemical modelling of the 2.25 Å structure, quantitatively explaining all significant features within the WOC region. This, as in our earlier studies, assumed a 'low' Mn oxidation paradigm (mean S1 Mn oxidation level of +3.0, Petrie et al., Angew. Chem. Int. Ed., 2015), rather than a 'high' oxidation model (mean S1 oxidation level of +3.5). In 2018 we showed (Chem. Phys. Chem., 2018) this oxidation state assumption predicted two energetically close S3 structural forms, one with the metal centres and O5 (as OH- ) positioned as in the 2.25 Å structure, and the other with the metals similarly placed, but with O5 (as H2 O) located in the O6 position of the 2.35 Å structure. The 2.35 Å two flashed structure was likely a crystal superposition of two such forms. Here we show, by similar computational analysis, that the latest 2.08 Å S3 structure is also a likely superposition of forms, but with O5 (as OH- ) occupying either the O5 or Ox positions in the WOC cavity. This highlights a remarkable structural 'lability' of the WOC centre in the S3 state, which is likely catalytically relevant to its water splitting function.
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Affiliation(s)
- Simon Petrie
- Research School of Chemistry, College of Physical and Mathematical Sciences, The Australian National University, Acton, ACT 2601, Australia
| | - Richard Terrett
- Research School of Chemistry, College of Physical and Mathematical Sciences, The Australian National University, Acton, ACT 2601, Australia
| | - Robert Stranger
- Research School of Chemistry, College of Physical and Mathematical Sciences, The Australian National University, Acton, ACT 2601, Australia
| | - Ron J Pace
- Research School of Chemistry, College of Physical and Mathematical Sciences, The Australian National University, Acton, ACT 2601, Australia
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Abstract
The oxygen-evolving center (OEC) in photosystem II (PSII) of plants, algae and cyanobacteria is a unique natural catalyst that splits water into electrons, protons and dioxygen. The crystallographic studies of PSII have revealed that the OEC is an asymmetric Mn4CaO5-cluster. The understanding of the structure-function relationship of this natural Mn4CaO5-cluster is impeded mainly due to the complexity of the protein environment and lack of a rational chemical model as a reference. Although it has been a great challenge for chemists to synthesize the OEC in the laboratory, significant advances have been achieved recently. Different artificial complexes have been reported, especially a series of artificial Mn4CaO4-clusters that closely mimic both the geometric and electronic structures of the OEC in PSII, which provides a structurally well-defined chemical model to investigate the structure-function relationship of the natural Mn4CaO5-cluster. The deep investigations on this artificial Mn4CaO4-cluster could provide new insights into the mechanism of the water-splitting reaction in natural photosynthesis and may help the development of efficient catalysts for the water-splitting reaction in artificial photosynthesis.
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11
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Assessment of the manganese cluster's oxidation state via photoactivation of photosystem II microcrystals. Proc Natl Acad Sci U S A 2019; 117:141-145. [PMID: 31848244 DOI: 10.1073/pnas.1915879117] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Knowledge of the manganese oxidation states of the oxygen-evolving Mn4CaO5 cluster in photosystem II (PSII) is crucial toward understanding the mechanism of biological water oxidation. There is a 4 decade long debate on this topic that historically originates from the observation of a multiline electron paramagnetic resonance (EPR) signal with effective total spin of S = 1/2 in the singly oxidized S2 state of this cluster. This signal implies an overall oxidation state of either Mn(III)3Mn(IV) or Mn(III)Mn(IV)3 for the S2 state. These 2 competing assignments are commonly known as "low oxidation (LO)" and "high oxidation (HO)" models of the Mn4CaO5 cluster. Recent advanced EPR and Mn K-edge X-ray spectroscopy studies converge upon the HO model. However, doubts about these assignments have been voiced, fueled especially by studies counting the number of flash-driven electron removals required for the assembly of an active Mn4CaO5 cluster starting from Mn(II) and Mn-free PSII. This process, known as photoactivation, appeared to support the LO model since the first oxygen is reported to evolve already after 7 flashes. In this study, we improved the quantum yield and sensitivity of the photoactivation experiment by employing PSII microcrystals that retained all protein subunits after complete manganese removal and by oxygen detection via a custom built thin-layer cell connected to a membrane inlet mass spectrometer. We demonstrate that 9 flashes by a nanosecond laser are required for the production of the first oxygen, which proves that the HO model provides the correct description of the Mn4CaO5 cluster's oxidation states.
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The S3 State of the Oxygen-Evolving Complex: Overview of Spectroscopy and XFEL Crystallography with a Critical Evaluation of Early-Onset Models for O–O Bond Formation. INORGANICS 2019. [DOI: 10.3390/inorganics7040055] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The catalytic cycle of the oxygen-evolving complex (OEC) of photosystem II (PSII) comprises five intermediate states Si (i = 0–4), from the most reduced S0 state to the most oxidized S4, which spontaneously evolves dioxygen. The precise geometric and electronic structure of the Si states, and hence the mechanism of O–O bond formation in the OEC, remain under investigation, particularly for the final steps of the catalytic cycle. Recent advances in protein crystallography based on X-ray free-electron lasers (XFELs) have produced new structural models for the S3 state, which indicate that two of the oxygen atoms of the inorganic Mn4CaO6 core of the OEC are in very close proximity. This has been interpreted as possible evidence for “early-onset” O–O bond formation in the S3 state, as opposed to the more widely accepted view that the O–O bond is formed in the final state of the cycle, S4. Peroxo or superoxo formation in S3 has received partial support from computational studies. Here, a brief overview is provided of spectroscopic information, recent crystallographic results, and computational models for the S3 state. Emphasis is placed on computational S3 models that involve O–O formation, which are discussed with respect to their agreement with structural information, experimental evidence from various spectroscopic studies, and substrate exchange kinetics. Despite seemingly better agreement with some of the available crystallographic interpretations for the S3 state, models that implicate early-onset O–O bond formation are hard to reconcile with the complete line of experimental evidence, especially with X-ray absorption, X-ray emission, and magnetic resonance spectroscopic observations. Specifically with respect to quantum chemical studies, the inconclusive energetics for the possible isoforms of S3 is an acute problem that is probably beyond the capabilities of standard density functional theory.
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Bikas R, Shahmoradi E, Reinoso S, Emami M, Lezama L, Sanchiz J, Noshiranzadeh N. The effect of the orientation of the Jahn–Teller distortion on the magnetic interactions of trinuclear mixed-valence Mn(ii)/Mn(iii) complexes. Dalton Trans 2019; 48:13799-13812. [DOI: 10.1039/c9dt01652j] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The effect of the orientation of the Jahn–Teller distortion on the magnetic interactions in two new mixed-valence trinuclear Mn(iii)–Mn(ii)–Mn(iii) complexes has been investigated.
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Affiliation(s)
- Rahman Bikas
- Department of Chemistry
- Faculty of Science
- Imam Khomeini International University
- 34148-96818 Qazvin
- Iran
| | - Elaheh Shahmoradi
- Department of Chemistry
- Faculty of Science
- University of Zanjan
- 45371-38791 Zanjan
- Iran
| | - Santiago Reinoso
- Institute for Advanced Materials (InaMat)
- Universidad Pública de Navarra
- 31006 Pamplona
- Spain
| | - Marzieh Emami
- Department of Chemistry
- Faculty of Science
- University of Zanjan
- 45371-38791 Zanjan
- Iran
| | - Luis Lezama
- Departamento de Química Inorgánica
- Facultad de Ciencia y Tecnología
- Universidad del País Vasco UPV/EHU
- 48080 Bilbao
- Spain
| | - Joaquín Sanchiz
- Department of Chemistry
- Faculty of Science
- Instituto de Materiales y Nanotecnología
- University of La Laguna
- 38206 Tenerife
| | - Nader Noshiranzadeh
- Department of Chemistry
- Faculty of Science
- University of Zanjan
- 45371-38791 Zanjan
- Iran
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14
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Chen H, Case DA, Dismukes GC. Reconciling Structural and Spectroscopic Fingerprints of the Oxygen-Evolving Complex of Photosystem II: A Computational Study of the S 2 State. J Phys Chem B 2018; 122:11868-11882. [PMID: 30444623 DOI: 10.1021/acs.jpcb.8b08147] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The catalytic cycle of photosynthetic water oxidation occurs at the Mn4CaO5 oxygen-evolving complex (OEC) of photosystem II. Extensive spectroscopic data have been collected on the intermediates, especially the S2 (Kok) state, although the proton and electron inventories (Mn oxidation states) are still uncertain. The "high oxidation" paradigm assigns S2 Mn oxidation level (III, IV, IV, IV) or (IV, IV, IV, III), whereas a "low oxidation" paradigm posits two additional electrons. Here, we investigate the geometric (X-ray diffraction, extended X-ray absorption fine structure) and spectroscopic (electron paramagnetic resonance (EPR), electron nuclear double resonance (ENDOR)) properties of the S2 state using quantum chemical density functional theory calculations, focusing on the neglected low paradigm. Two interconvertible electronic spin configurations are predicted as ground states, producing multiline ( S = 1/2) and broad ( S = 5/2) EPR signals in the low paradigm oxidation state (III, IV, III, III) and with W2 as OH- and O5 as OH-. They have "open" ( S = 5/2) and "closed" ( S = 1/2) Mn3CaO4-cubane geometries. Other energetically accessible isomers with ground spin states 1/2, 7/2, 9/2, or 11/2 can be obtained through perturbations of hydrogen-bonding networks (e.g., H+ from His337 to O3 or W2), consistent with experimental observations. Conformers with the low oxidation state configuration (III, IV, IV, II) also become energetically accessible when the protonation states are O5 (OH-), W2 (H2O), and neutral His337. The configuration with (III, IV, III, III) agrees well with earlier low-temperature EPR and ENDOR interpretations, whereas the MnII-containing configuration agrees partially with recent ENDOR data. However, the low oxidation paradigm does not yield isotropic ligand hyperfine interactions in good agreement with observed values. We conclude that the low Mn oxidation state proposal for the OEC can closely fit most of the available structural and electronic data for S2 at accessible energies.
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15
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Shamsipur M, Pashabadi A. Latest advances in PSII features and mechanism of water oxidation. Coord Chem Rev 2018. [DOI: 10.1016/j.ccr.2018.07.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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16
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Petrie S, Stranger R, Pace RJ. Explaining the Different Geometries of the Water Oxidising Complex in the Nominal S 3 State Crystal Structures of Photosystem II at 2.25 Å and 2.35 Å. Chemphyschem 2018; 19:3296-3309. [PMID: 30290080 DOI: 10.1002/cphc.201800686] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Indexed: 11/10/2022]
Abstract
Recently two atomic resolution crystal structures of Photosystem II, in the double flashed, nominal S3 intermediate state of its Mn4 Ca water oxidising complex (WOC), have been presented (Young et al., Nature 2016, 540, 453; Suga et al., Nature 2017, 543, 131). These structures are at 2.25 Å and 2.35 Å resolution, respectively. Although highly similar in most respects, the structures differ in a key region within the WOC catalytic site. In the 2.25 Å structure, one oxy species (O5) is observed within the WOC cavity, weakly associated with the Mn centres, similar to that seen earlier in the 1.95 Å XRD structure of the S1 intermediate (Suga et al., Nature, 2015, 517, 99). In the 2.35 Å structure, two such species are seen (O5, O6), with the Mn centres and O5 positioned as in the 2.25 Å structure and an O5-O6 separation of ∼1.5 Å, consistent with peroxo formation. This suggests O5 and O6 are substrate water derived species in this double flashed form. Recently we have presented (Petrie, et al., Chem. Phys. Chem., 2017) a large scale (220 atom) quantum chemical model of the Young et al. 2.25 Å structure, which quantitatively explains all significant features within the WOC region of that structure, particularly the positions of the metal centres and O5 group. Critical to this was our assumption of a 'low' Mn oxidation paradigm (mean S1 Mn oxidation level of +3.0, Petrie et al., Angew. Chem. Int. Ed., 2015), rather than a 'high' oxidation model (mean S1 oxidation level of +3.5), widely assumed in the literature. Here we show that our same oxidation state model predicts two classes of energetically close S3 structural forms, analogous to the S1 state, one with the metal centres and O5 positioned as in the 2.25 Å structure, and the other with the metals similarly placed, but with O5 located in the O6 position of the 2.35 Å structure. We show that the Suga et al. 2.35 Å structure is likely a superposition of two such forms, one from each class, which is consistent with reported atomic occupancies for that structure and the relative total energies we calculate for the two structural forms.
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Affiliation(s)
- Simon Petrie
- Research School of Chemistry, College of Physical and Mathematical Sciences, The Australian National University, Acton ACT, Australia, 2601
| | - Robert Stranger
- Research School of Chemistry, College of Physical and Mathematical Sciences, The Australian National University, Acton ACT, Australia, 2601
| | - Ron J Pace
- Research School of Chemistry, College of Physical and Mathematical Sciences, The Australian National University, Acton ACT, Australia, 2601
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Affiliation(s)
- Dimitrios A. Pantazis
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
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Petrie S, Stranger R, Pace RJ. What Mn K β spectroscopy reveals concerning the oxidation states of the Mn cluster in photosystem II. Phys Chem Chem Phys 2018; 19:27682-27693. [PMID: 28983541 DOI: 10.1039/c7cp04797e] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The oxygen evolving complex, (OEC) in Photosystem II contains a Mn4Ca cluster and catalyses oxidation of water to molecular oxygen and protons, the most energetically demanding reaction in nature. The catalytic mechanism remains unresolved and the precise Mn oxidation levels through which the cluster cycles during functional turnover are controversial. Two proposals for these redox levels exist; the 'high' and 'low' oxidation state paradigms, which differ systematically by two oxidation equivalents throughout the redox accumulating catalytic S state cycle (states S0…S3). Presently the 'high' paradigm is more favored. For S1 the assumed mean redox levels of Mn are 3.5 (high) and 3.0 (low) respectively. Mn K region X-ray spectroscopy has been extensively used to examine the OEC Mn oxidation levels, with Kβ emission spectroscopy increasingly the method of choice. Here we review the results from application of this and closely related techniques to PS II, building on our earlier examination of these and other data on the OEC oxidation states (Pace et al., Dalton Trans., 2012, 41, 11145). We compare the most recent results with a range of earlier Mn Kβ experiments on the photosystem and related model Mn systems. New analyses of these data are given, highlighting certain key spectral considerations which appear not to have been sufficiently appreciated earlier. These show that the recent and earlier PS II Kβ results have a natural internal consistency, leading to the strong conclusion that the low paradigm oxidation state assignment for the functional OEC is favoured.
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Affiliation(s)
- Simon Petrie
- Research School of Chemistry, College of Physical & Mathematical Sciences, College of Science, Australian National University, Canberra, ACT 0200, Australia.
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Beal NJ, Corry TA, O’Malley PJ. Comparison between Experimental and Broken Symmetry Density Functional Theory (BS-DFT) Calculated Electron Paramagnetic Resonance (EPR) Parameters of the S2 State of the Oxygen-Evolving Complex of Photosystem II in Its Native (Calcium) and Strontium-Substituted Form. J Phys Chem B 2017; 121:11273-11283. [DOI: 10.1021/acs.jpcb.7b09498] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Nathan J. Beal
- School of Chemistry, The University of Manchester, Manchester M13 9PL, United Kingdom
| | - Thomas A. Corry
- School of Chemistry, The University of Manchester, Manchester M13 9PL, United Kingdom
| | - Patrick J. O’Malley
- School of Chemistry, The University of Manchester, Manchester M13 9PL, United Kingdom
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Petrie S, Stranger R, Pace RJ. Rationalizing the 2.25 Å Resolution Crystal Structure of the Water Oxidising Complex of Photosystem II in the S3State. Chemphyschem 2017; 18:2924-2931. [DOI: 10.1002/cphc.201700640] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Indexed: 12/14/2022]
Affiliation(s)
- Simon Petrie
- Research School of Chemistry, College of Physical and Mathematical Sciences; The Australian National University; Acton ACT 2601 Australia
| | - Rob Stranger
- Research School of Chemistry, College of Physical and Mathematical Sciences; The Australian National University; Acton ACT 2601 Australia
| | - Ron J. Pace
- Research School of Chemistry, College of Physical and Mathematical Sciences; The Australian National University; Acton ACT 2601 Australia
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21
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Najafpour MM, Heidari S, Balaghi SE, Hołyńska M, Sadr MH, Soltani B, Khatamian M, Larkum AW, Allakhverdiev SI. Proposed mechanisms for water oxidation by Photosystem II and nanosized manganese oxides. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2017; 1858:156-174. [DOI: 10.1016/j.bbabio.2016.11.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 11/05/2016] [Accepted: 11/08/2016] [Indexed: 12/18/2022]
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22
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Terrett R, Petrie S, Stranger R, Pace RJ. What computational chemistry and magnetic resonance reveal concerning the oxygen evolving centre in Photosystem II. J Inorg Biochem 2016; 162:178-189. [PMID: 27157978 DOI: 10.1016/j.jinorgbio.2016.04.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Revised: 03/01/2016] [Accepted: 04/04/2016] [Indexed: 11/18/2022]
Abstract
Density Functional Theory (DFT) computational studies of the Mn4/Ca Oxygen Evolving Complex (OEC) region of Photosystem II in the paramagnetic S2 and S3 states of the water oxdizing catalytic cycle are described. These build upon recent advances in computationally understanding the detailed S1 state OEC geometries, revealed by the recent high resolution Photosystem II crystal structures of Shen et al., at 1.90Å and 1.95Å (Petrie et al., 2015, Angew. Chem. Int. Ed., 54, 7120). The models feature a 'Low Oxidation Paradigm' assumption for the mean Mn oxidation states in the functional enzyme, with the mean oxidation levels being 3.0, 3.25 and 3.5 in S1, S2 and S3, respectively. These calculations are used to infer magnetic exchange interactions within the coupled OEC cluster, particularly in the Electron Paramagnetic Resonance (EPR)-visible S2 and S3 states. Detailed computational estimates of the intrinsic magnitudes and molecular orientations of the 55Mn hyperfine tensors in the S2 state are presented. These parameters, together with the resultant spin projected hyperfine values are compared with recent appropriate experimental EPR data (Continuous Wave (CW), Electron-Nuclear Double Resonance (ENDOR) and ELDOR (Electron-Electron Double Resonance)-Detected Nuclear Magnetic Resonance (EDNMR)) from the OEC. It is found that an effective Coupled Dimer magnetic organization of the four Mn in the OEC cluster in the S2 and S3 states is able to quantitatively rationalize the observed 55Mn hyperfine data. This is consistent with structures we propose to represent the likely state of the OEC in the catalytically active form of the enzyme.
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Affiliation(s)
- Richard Terrett
- Research School of Chemistry, College of Physical and Mathematical Sciences, Australian National University, Canberra, ACT 0200, Australia
| | - Simon Petrie
- Research School of Chemistry, College of Physical and Mathematical Sciences, Australian National University, Canberra, ACT 0200, Australia
| | - Rob Stranger
- Research School of Chemistry, College of Physical and Mathematical Sciences, Australian National University, Canberra, ACT 0200, Australia
| | - Ron J Pace
- Research School of Chemistry, College of Physical and Mathematical Sciences, Australian National University, Canberra, ACT 0200, Australia.
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Chuah WY, Stranger R, Pace RJ, Krausz E, Frankcombe TJ. Deprotonation of Water/Hydroxo Ligands in Clusters Mimicking the Water Oxidizing Complex of PSII and Its Effect on the Vibrational Frequencies of Ligated Carboxylate Groups. J Phys Chem B 2016; 120:377-85. [PMID: 26727127 DOI: 10.1021/acs.jpcb.5b09987] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The IR absorptions of several first-shell carboxylate ligands of the water oxidizing complex (WOC) have been experimentally shown to be unaffected by oxidation state changes in the WOC during its catalytic cycle. Several model clusters that mimic the Mn4O5Ca core of the WOC in the S1 state, with electronic configurations that correspond to both the so-called "high" and "low" oxidation paradigms, were investigated. Deprotonation at W2, W1, or O3 sites was found to strongly reduce carboxylate ligand frequency shifts on oxidation of the metal cluster. The frequency shifts were smallest in neutrally charged clusters where the initial mean Mn oxidation state was +3, with W2 as an hydroxide and O5 a water. Deprotonation also reduced and balanced the oxidation energy of all clusters in successive oxidations.
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Affiliation(s)
- Wooi Yee Chuah
- Research School of Chemistry, Australian National University , Canberra, Australian Capital Territory 2601, Australia
| | - Rob Stranger
- Research School of Chemistry, Australian National University , Canberra, Australian Capital Territory 2601, Australia
| | - Ron J Pace
- Research School of Chemistry, Australian National University , Canberra, Australian Capital Territory 2601, Australia
| | - Elmars Krausz
- Research School of Chemistry, Australian National University , Canberra, Australian Capital Territory 2601, Australia
| | - Terry J Frankcombe
- Research School of Chemistry, Australian National University , Canberra, Australian Capital Territory 2601, Australia.,School of Physical, Environmental and Mathematical Sciences, University of New South Wales , Canberra, Australian Capital Territory 2600, Australia
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Krewald V, Neese F, Pantazis DA. Resolving the Manganese Oxidation States in the Oxygen-evolving Catalyst of Natural Photosynthesis. Isr J Chem 2015. [DOI: 10.1002/ijch.201500051] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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25
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Jin L, Smith P, Noble CJ, Stranger R, Hanson GR, Pace RJ. Electronic structure of the oxygen evolving complex in photosystem II, as revealed by 55Mn Davies ENDOR studies at 2.5 K. Phys Chem Chem Phys 2015; 16:7799-812. [PMID: 24643307 DOI: 10.1039/c3cp55189j] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We report the first (55)Mn pulsed ENDOR studies on the S2 state multiline spin ½ centre of the oxygen evolving complex (OEC) in Photosystem II (PS II), at temperatures below 4.2 K. These were performed on highly active samples of spinach PS II core complexes, developed previously in our laboratories for photosystem spectroscopic use, at temperatures down to 2.5 K. Under these conditions, relaxation effects which have previously hindered observation of most of the manganese ENDOR resonances from the OEC coupled Mn cluster are suppressed. (55)Mn ENDOR hyperfine couplings ranging from ∼50 to ∼680 MHz are now seen on the S2 state multiline EPR signal. These, together with complementary high resolution X-band CW EPR measurements and detailed simulations, reveal that at least two and probably three Mn hyperfine couplings with large anisotropy are seen, indicating that three Mn(III) ions are likely present in the functional S2 state of the enzyme. This suggests a low oxidation state paradigm for the OEC (mean Mn oxidation level 3.0 in the S1 state) and unexpected Mn exchange coupling in the S2 state, with two Mn ions nearly magnetically silent. Our results rationalize a number of previous ligand ESEEM/ENDOR studies and labelled water exchange experiments on the S2 state of the photosystem, in a common picture which is closely consistent with recent photo-assembly (Kolling et al., Biophys. J. 2012, 103, 313-322) and large scale computational studies on the OEC (Gatt et al., Angew. Chem., Int. Ed. 2012, 51, 12025-12028, Kurashige et al. Nat. Chem. 2013, 5, 660-666).
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Affiliation(s)
- Lu Jin
- Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia.
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26
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Petrie S, Pace RJ, Stranger R. Resolving the Differences Between the 1.9 Å and 1.95 Å Crystal Structures of Photosystem II: A Single Proton Relocation Defines Two Tautomeric Forms of the Water-Oxidizing Complex. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201502463] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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27
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Petrie S, Pace RJ, Stranger R. Resolving the Differences Between the 1.9 Å and 1.95 Å Crystal Structures of Photosystem II: A Single Proton Relocation Defines Two Tautomeric Forms of the Water-Oxidizing Complex. Angew Chem Int Ed Engl 2015; 54:7120-4. [PMID: 25917648 DOI: 10.1002/anie.201502463] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Indexed: 11/11/2022]
Abstract
Great progress has been made in characterizing the water-oxidizing complex (WOC) in photosystem II (PSII) with the publication of a 1.9 Å resolution X-ray diffraction (XRD) and recently a 1.95 Å X-ray free-electron laser (XFEL) structure. However, these achievements are under threat because of perceived conflicts with other experimental data. For the earlier 1.9 Å structure, lack of agreement with extended X-ray absorption fine structure (EXAFS) data led to the notion that the WOC suffered from X-ray photoreduction. In the recent 1.95 Å structure, Mn photoreduction is not an issue, but poor agreement with computational models which adopt the 'high' oxidation state paradigm, has again resulted in criticism of the structure on the basis of contamination with lower S states of the WOC. Here we use DFT modeling to show that the distinct WOC geometries in the 1.9 and 1.95 Å structures can be straightforwardly accounted for when the Mn oxidation states are consistent with the 'low' oxidation state paradigm. Remarkably, our calculations show that the two structures are tautomers, related by a single proton relocation.
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Affiliation(s)
- Simon Petrie
- Research School of Chemistry, Australian National University, Canberra ACT 0200 (Australia)
| | - Ron J Pace
- Research School of Chemistry, Australian National University, Canberra ACT 0200 (Australia).
| | - Rob Stranger
- Research School of Chemistry, Australian National University, Canberra ACT 0200 (Australia).
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28
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Tomson NC, Williams KD, Dai X, Sproules S, DeBeer S, Warren TH, Wieghardt K. Re-evaluating the Cu K pre-edge XAS transition in complexes with covalent metal-ligand interactions. Chem Sci 2015; 6:2474-2487. [PMID: 29308158 PMCID: PMC5647745 DOI: 10.1039/c4sc03294b] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 02/11/2015] [Indexed: 01/10/2023] Open
Abstract
Three [Me2NN]Cu(η2-L2) complexes (Me2NN = HC[C(Me)NAr]2; L2 = PhNO (2), (3), PhCH[double bond, length as m-dash]CH2 (4); Ar = 2,6-Me2-C6H3; ArF = 3,5-(CF3)2-C6H3) have been studied by Cu K-edge X-ray absorption spectroscopy, as well as single- and multi-reference computational methods (DFT, TD-DFT, CASSCF, MRCI, and OVB). The study was extended to a range of both known and theoretical compounds bearing 2p-element donors as a means of deriving a consistent view of how the pre-edge transition energy responds in systems with significant ground state covalency. The ground state electronic structures of many of the compounds under investigation were found to be strongly influenced by correlation effects, resulting in ground state descriptions with majority contributions from a configuration comprised of a Cu(ii) metal center anti-ferromagentically coupled to radical anion O2, PhNO, and ligands. In contrast, the styrene complex 4, which displays a Cu K pre-edge transition despite its formal d10 electron configuration, exhibits what can best be described as a Cu(i):(styrene)0 ground state with strong π-backbonding. The Cu K pre-edge features for these complexes increase in energy from 1 to 4, a trend that was tracked to the percent Cu(ii)-character in the ground state. The unexpected shift to higher pre-edge transition energies with decreasing charge on copper (Q Cu) contributed to an assignment of the pre-edge features for these species as arising from metal-to-ligand charge transfer instead of the traditional Cu1s → Cu3d designation.
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Affiliation(s)
- Neil C Tomson
- Max Planck Institute for Chemical Energy Conversion , Stiftstrasse 34-36 , 45470 Mülheim an der Ruhr , Germany . ;
| | - Kamille D Williams
- Department of Chemistry , Georgetown University , Box 571227-1227 , Washington, D. C. 20057 , USA .
| | - Xuliang Dai
- Department of Chemistry , Georgetown University , Box 571227-1227 , Washington, D. C. 20057 , USA .
| | - Stephen Sproules
- Max Planck Institute for Chemical Energy Conversion , Stiftstrasse 34-36 , 45470 Mülheim an der Ruhr , Germany . ;
| | - Serena DeBeer
- Max Planck Institute for Chemical Energy Conversion , Stiftstrasse 34-36 , 45470 Mülheim an der Ruhr , Germany . ;
- Department of Chemistry and Chemical Biology , Cornell University , Ithaca , NY 14853 , USA
| | - Timothy H Warren
- Department of Chemistry , Georgetown University , Box 571227-1227 , Washington, D. C. 20057 , USA .
| | - Karl Wieghardt
- Max Planck Institute for Chemical Energy Conversion , Stiftstrasse 34-36 , 45470 Mülheim an der Ruhr , Germany . ;
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Petrie S, Stranger R, Pace RJ. Rationalising the Geometric Variation between the A and B Monomers in the 1.9 Å Crystal Structure of Photosystem II. Chemistry 2015; 21:6780-92. [DOI: 10.1002/chem.201406419] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Indexed: 11/12/2022]
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30
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Xiao J, Khan M, Singh A, Suljoti E, Spiccia L, Aziz EF. Enhancing catalytic activity by narrowing local energy gaps--X-ray studies of a manganese water oxidation catalyst. CHEMSUSCHEM 2015; 8:872-877. [PMID: 25605663 DOI: 10.1002/cssc.201403219] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Indexed: 06/04/2023]
Abstract
Changes in the local electronic structure of the Mn 3d orbitals of a Mn catalyst derived from a dinuclear Mn(III) complex during the water oxidation cycle were investigated ex situ by X-ray absorption spectroscopy (XAS) and resonant inelastic X-ray scattering (RIXS) analyses. Detailed information about the Mn 3d orbitals, especially the local HOMO-LUMO gap on Mn sites revealed by RIXS analyses, indicated that the enhancement in catalytic activity (water oxidation) originated from the narrowing of the local HOMO-LUMO gap when electrical voltage and visible light illumination were applied simultaneously to the Mn catalytic system.
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Affiliation(s)
- Jie Xiao
- Institute of Methods for Material Development, Helmholtz-Zentrum Berlin fur Materialien und Energie, Albert-Einstein-Str. 15, 12489 Berlin (Germany).
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31
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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.
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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 .
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Abstract
Nature relies on a unique and intricate biochemical setup to achieve sunlight-driven water splitting. Combined experimental and computational efforts have produced significant insights into the structural and functional principles governing the operation of the water-oxidizing enzyme Photosystem II in general, and of the oxygen-evolving manganese-calcium cluster at its active site in particular. Here we review the most important aspects of biological water oxidation, emphasizing current knowledge on the organization of the enzyme, the geometric and electronic structure of the catalyst, and the role of calcium and chloride cofactors. The combination of recent experimental work on the identification of possible substrate sites with computational modeling have considerably limited the possible mechanistic pathways for the critical O-O bond formation step. Taken together, the key features and principles of natural photosynthesis may serve as inspiration for the design, development, and implementation of artificial systems.
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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: 441] [Impact Index Per Article: 49.0] [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.
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Affiliation(s)
- Jian-Ren Shen
- Photosynthesis Research Center, Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8530, Japan;
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Substrate-water exchange in photosystem II is arrested before dioxygen formation. Nat Commun 2014; 5:4305. [PMID: 24993602 PMCID: PMC4102119 DOI: 10.1038/ncomms5305] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Accepted: 06/04/2014] [Indexed: 11/17/2022] Open
Abstract
Light-driven oxidation of water into dioxygen, catalysed by the oxygen-evolving complex (OEC) in photosystem II, is essential for life on Earth and provides the blueprint for devices for producing fuel from sunlight. Although the structure of the OEC is known at atomic level for its dark-stable state, the mechanism by which water is oxidized remains unsettled. Important mechanistic information was gained in the past two decades by mass spectrometric studies of the H218O/H216O substrate–water exchange in the four (semi) stable redox states of the OEC. However, until now such data were not attainable in the transient states formed immediately before the O–O bond formation. Using modified photosystem II complexes displaying up to 40-fold slower O2 production rates, we show here that in the transient state the substrate–water exchange is dramatically slowed as compared with the earlier S states. This further constrains the possible sites for substrate–water binding in photosystem II. The oxygen-evolving complex of photosystem II converts water into oxygen during photosynthesis, but how this process occurs is not yet fully understood. Here, the authors use modified complexes with reduced reaction rates to study the process of oxygen evolution in more detail.
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35
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Chuah WY, Stranger R, Pace RJ, Krausz E, Frankcombe TJ. Ab Initio modeling of the effect of oxidation coupled with HnO deprotonation on carboxylate ligands in Mn/Ca clusters. J Phys Chem B 2014; 118:3553-8. [PMID: 24606611 DOI: 10.1021/jp500362q] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Oxidation of some manganese complexes containing both carboxylate and water/hydroxo ligands does not result in changes to the carboxylate stretching frequencies. The water oxidizing complex of photosystem II is one motivating example. On the basis of electronic structure theory calculations, we here suggest that the deprotonation of water or hydroxo ligands minimizes changes in the vibrational frequencies of coligating carboxylates, rendering the carboxylate modes "invisible" in FTIR difference spectroscopy. This deprotonation of water/hydroxo ligands was also found to balance the redox potentials of the Mn(II)/Mn(III) and Mn(III)/Mn(IV) couples, allowing the possibility for successive manganese oxidations at a relatively constant redox potential.
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Affiliation(s)
- Wooi Yee Chuah
- Research School of Chemistry, Australian National University , ACT 0200, Australia
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36
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Terrett R, Petrie S, Pace RJ, Stranger R. What does the Sr-substituted 2.1 Å resolution crystal structure of photosystem II reveal about the water oxidation mechanism? Chem Commun (Camb) 2014; 50:3187-90. [DOI: 10.1039/c3cc49324e] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The structure of the water oxidising complex in the Sr-substituted X-ray crystal structure of photosystem II and its differences relative to the Ca-containing system, have been rationalized by a density functional study.
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Affiliation(s)
- Richard Terrett
- Research School of Chemistry
- College of Physical Sciences and Mathematics
- The Australian National University
- , Australia
| | - Simon Petrie
- Research School of Chemistry
- College of Physical Sciences and Mathematics
- The Australian National University
- , Australia
| | - Ron J. Pace
- Research School of Chemistry
- College of Physical Sciences and Mathematics
- The Australian National University
- , Australia
| | - Robert Stranger
- Research School of Chemistry
- College of Physical Sciences and Mathematics
- The Australian National University
- , Australia
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37
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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.
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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
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38
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Vinyard DJ, Ananyev GM, Charles Dismukes G. Photosystem II: The Reaction Center of Oxygenic Photosynthesis. Annu Rev Biochem 2013; 82:577-606. [DOI: 10.1146/annurev-biochem-070511-100425] [Citation(s) in RCA: 279] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- David J. Vinyard
- Department of Chemistry and Chemical Biology and the Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854; ,
- Department of Chemistry, Princeton University, Princeton, New Jersey 08540;
| | - Gennady M. Ananyev
- Department of Chemistry and Chemical Biology and the Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854; ,
| | - G. Charles Dismukes
- Department of Chemistry and Chemical Biology and the Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854; ,
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39
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Krewald V, Neese F, Pantazis DA. On the magnetic and spectroscopic properties of high-valent Mn3CaO4 cubanes as structural units of natural and artificial water-oxidizing catalysts. J Am Chem Soc 2013; 135:5726-39. [PMID: 23527603 DOI: 10.1021/ja312552f] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Mn(IV)3CaO4 cubane is a structural motif present in the oxygen-evolving complex (OEC) of photosystem II and in water-oxidizing Mn/Ca layered oxides. This work investigates the magnetic and spectroscopic properties of two recently synthesized complexes and a series of idealized models that incorporate this structural unit. Magnetic interactions, accessible spin states, and (55)Mn isotropic hyperfine couplings are computed with quantum chemical methods and form the basis for structure-property correlations. Additionally, the effects of oxo-bridge protonation and one-electron reduction are examined. The calculated properties are found to be in excellent agreement with available experimental data. It is established that all synthetic and model Mn(IV)3CaO4 cubane complexes have the same high-spin S = (9)/2 ground state. The magnetic coupling conditions under which different ground spin states can be accessed are determined. Substitution of Mn(IV) magnetic centers by diamagnetic ions [e.g., Ge(IV)] allows one to "switch off" specific spin sites in order to examine the magnetic orbitals along individual Mn-Mn exchange pathways, which confirms the predominance of ferromagnetic interactions within the cubane framework. The span of the Heisenberg spin ladder is found to correlate inversely with the number of protonated oxo bridges. Energetic comparisons for protonated models show that the tris-μ-oxo bridge connecting only Mn ions in the cubane has the lowest proton affinity and that the average relaxation energy per additional proton is on the order of 18 kcal·mol(-1), thus making access to ground states other than the high-spin S = (9)/2 state in these cubanes unlikely. The relevance of these cubanes for the OEC and synthetic oxides is discussed.
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Affiliation(s)
- Vera Krewald
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-38, 45470 Mülheim an der Ruhr, Germany
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40
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Gatt P, Petrie S, Stranger R, Pace RJ. Rationalizing the 1.9 Å Crystal Structure of Photosystem II-A Remarkable Jahn-Teller Balancing Act Induced by a Single Proton Transfer. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201206316] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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41
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Gatt P, Petrie S, Stranger R, Pace RJ. Rationalizing the 1.9 Å crystal structure of photosystem II--A remarkable Jahn-Teller balancing act induced by a single proton transfer. Angew Chem Int Ed Engl 2012; 51:12025-8. [PMID: 23108989 DOI: 10.1002/anie.201206316] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Indexed: 01/01/2023]
Affiliation(s)
- Phillip Gatt
- Research School of Chemistry, Australian National University, Canberra ACT 0200, Australia
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