1
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Singh A, Roy L. Evolution in the Design of Water Oxidation Catalysts with Transition-Metals: A Perspective on Biological, Molecular, Supramolecular, and Hybrid Approaches. ACS OMEGA 2024; 9:9886-9920. [PMID: 38463281 PMCID: PMC10918817 DOI: 10.1021/acsomega.3c07847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 02/05/2024] [Accepted: 02/07/2024] [Indexed: 03/12/2024]
Abstract
Increased demand for a carbon-neutral sustainable energy scheme augmented by climatic threats motivates the design and exploration of novel approaches that reserve intermittent solar energy in the form of chemical bonds in molecules and materials. In this context, inspired by biological processes, artificial photosynthesis has garnered significant attention as a promising solution to convert solar power into chemical fuels from abundantly found H2O. Among the two redox half-reactions in artificial photosynthesis, the four-electron oxidation of water according to 2H2O → O2 + 4H+ + 4e- comprises the major bottleneck and is a severe impediment toward sustainable energy production. As such, devising new catalytic platforms, with traditional concepts of molecular, materials and biological catalysis and capable of integrating the functional architectures of the natural oxygen-evolving complex in photosystem II would certainly be a value-addition toward this objective. In this review, we discuss the progress in construction of ideal water oxidation catalysts (WOCs), starting with the ingenuity of the biological design with earth-abundant transition metal ions, which then diverges into molecular, supramolecular and hybrid approaches, blurring any existing chemical or conceptual boundaries. We focus on the geometric, electronic, and mechanistic understanding of state-of-the-art homogeneous transition-metal containing molecular WOCs and summarize the limiting factors such as choice of ligands and predominance of environmentally unrewarding and expensive noble-metals, necessity of high-valency on metal, thermodynamic instability of intermediates, and reversibility of reactions that create challenges in construction of robust and efficient water oxidation catalyst. We highlight how judicious heterogenization of atom-efficient molecular WOCs in supramolecular and hybrid approaches put forth promising avenues to alleviate the existing problems in molecular catalysis, albeit retaining their fascinating intrinsic reactivities. Taken together, our overview is expected to provide guiding principles on opportunities, challenges, and crucial factors for designing novel water oxidation catalysts based on a synergy between conventional and contemporary methodologies that will incite the expansion of the domain of artificial photosynthesis.
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Affiliation(s)
- Ajeet
Kumar Singh
- Institute of Chemical Technology
Mumbai−IOC Odisha Campus Bhubaneswar, IIT Kharagpur Extension
Centre, Bhubaneswar − 751013 India
| | - Lisa Roy
- Institute of Chemical Technology
Mumbai−IOC Odisha Campus Bhubaneswar, IIT Kharagpur Extension
Centre, Bhubaneswar − 751013 India
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2
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Maximova O, Allen W, Yee G, Israel C, Leshchev D, Stavitski E, Ding Y, Davis K, Wessells C, Friebel D, Pushkar Y. Spectroscopic Characterization of Mn 1+ Low Oxidation State in Prussian Blue-Based Battery Anodes. J Phys Chem Lett 2024; 15:1521-1528. [PMID: 38299494 DOI: 10.1021/acs.jpclett.3c03516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2024]
Abstract
Stabilization of ions in exotic oxidation states is beneficial for the development of new materials for green energy technologies. Exotic Mn1+ was proposed to play a role in the function of sodium-based Prussian blue analogues (PBA) batteries, a highly sought-out technology for industrial energy storage. Here, we report the detailed electronic structure characterization of uncharged and charged sodium-based manganese hexacyanomanganate anodes via Mn K-edge X-ray absorption spectroscopy (XAS), Kβ nonresonant X-ray emission (XES), and resonant inelastic X-ray scattering (RIXS). The latter allowed us to obtain site-selective XANES information about two distinct Mn centers. The obtained spectroscopic data represent the first electronic structure characterization of low-spin Mn1+ using hard X-ray RIXS and XES and allowed us to confirm its role in anode reduction. Our experimental approach can be expanded to analysis of analogues with other 3d transition metals broadening the application of exotic ionic states in materials engineering.
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Affiliation(s)
- Olga Maximova
- Department of Physics and Astronomy, Purdue University, West Lafayette, Indiana 47907, United States
| | - Winter Allen
- Department of Physics and Astronomy, Purdue University, West Lafayette, Indiana 47907, United States
| | - Grace Yee
- Natron Energy, 3542 Bassett St., Santa Clara, California 95054, United States
| | - Charlotte Israel
- Natron Energy, 3542 Bassett St., Santa Clara, California 95054, United States
| | - Denis Leshchev
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, New York 11793, United States
| | - Eli Stavitski
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, New York 11793, United States
| | - Yujia Ding
- Department of Physics and CSRRI, Illinois Institute of Technology, Chicago, Illinois 60616, United States
| | - Katherine Davis
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Colin Wessells
- Natron Energy, 3542 Bassett St., Santa Clara, California 95054, United States
| | - Daniel Friebel
- Natron Energy, 3542 Bassett St., Santa Clara, California 95054, United States
| | - Yulia Pushkar
- Department of Physics and Astronomy, Purdue University, West Lafayette, Indiana 47907, United States
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3
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Cutsail GE, Banerjee R, Rice DB, McCubbin Stepanic O, Lipscomb JD, DeBeer S. Determination of the iron(IV) local spin states of the Q intermediate of soluble methane monooxygenase by Kβ X-ray emission spectroscopy. J Biol Inorg Chem 2022; 27:573-582. [PMID: 35988092 PMCID: PMC9470658 DOI: 10.1007/s00775-022-01953-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 08/07/2022] [Indexed: 11/29/2022]
Abstract
Soluble methane monooxygenase (sMMO) facilitates the conversion of methane to methanol at a non-heme FeIV2 intermediate MMOHQ, which is formed in the active site of the sMMO hydroxylase component (MMOH) during the catalytic cycle. Other biological systems also employ high-valent FeIV sites in catalysis; however, MMOHQ is unique as Nature’s only identified FeIV2 intermediate. Previous 57Fe Mössbauer spectroscopic studies have shown that MMOHQ employs antiferromagnetic coupling of the two FeIV sites to yield a diamagnetic cluster. Unfortunately, this lack of net spin prevents the determination of the local spin state (Sloc) of each of the irons by most spectroscopic techniques. Here, we use Fe Kβ X-ray emission spectroscopy (XES) to characterize the local spin states of the key intermediates of the sMMO catalytic cycle, including MMOHQ trapped by rapid-freeze-quench techniques. A pure XES spectrum of MMOHQ is obtained by subtraction of the contributions from other reaction cycle intermediates with the aid of Mössbauer quantification. Comparisons of the MMOHQ spectrum with those of known Sloc = 1 and Sloc = 2 FeIV sites in chemical and biological models reveal that MMOHQ possesses Sloc = 2 iron sites. This experimental determination of the local spin state will help guide future computational and mechanistic studies of sMMO catalysis.
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Affiliation(s)
- George E Cutsail
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470, Mülheim an der Ruhr, Germany.
- Institute of Inorganic Chemistry, University of Duisburg-Essen, Universitätsstrasse 5-7, 45117, Essen, Germany.
| | - Rahul Banerjee
- Department of Biochemistry Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Derek B Rice
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470, Mülheim an der Ruhr, Germany
| | - Olivia McCubbin Stepanic
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470, Mülheim an der Ruhr, Germany
| | - John D Lipscomb
- Department of Biochemistry Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Serena DeBeer
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470, Mülheim an der Ruhr, Germany.
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4
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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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5
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Holfelder I, Wansleben M, Kayser Y, Gnewkow R, Müller M, Weser J, Zech C, Beckhoff B. A double crystal von Hamos spectrometer for traceable x-ray emission spectroscopy. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2021; 92:123105. [PMID: 34972394 DOI: 10.1063/5.0061183] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 11/21/2021] [Indexed: 06/14/2023]
Abstract
A novel double full-cylinder crystal x-ray spectrometer for x-ray emission spectroscopy (XES) has been realized based on a modified von Hamos geometry. The spectrometer is characterized by its compact dimensions, its versatility with respect to the number of crystals used in series in the detection path, and the option to perform calibrated XES measurements. The full-cylinder crystals used are based on highly annealed pyrolytic graphite with a thickness of 40 μm, which was bent to a radius of curvature of 50 mm. The flexible design of the spectrometer allows for an easy change-within the same setup-between measurements with one crystal for maximized efficiency or two crystals for increased spectral resolving power. The spectrometer realized can be used at different end-stations of synchrotron radiation beamlines or can be laboratory-based. The main application focus of the spectrometer is the determination of x-ray fundamental atomic parameters in the photon energy range from 2.4 to 18 keV. The evaluation of chemical speciation is also an area of application, as demonstrated in the example of battery electrodes using resonant inelastic x-ray scattering.
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Affiliation(s)
- I Holfelder
- Physikalisch-Technische Bundesanstalt (PTB), Abbestr. 2-12, 10587 Berlin, Germany
| | - M Wansleben
- Physikalisch-Technische Bundesanstalt (PTB), Abbestr. 2-12, 10587 Berlin, Germany
| | - Y Kayser
- Physikalisch-Technische Bundesanstalt (PTB), Abbestr. 2-12, 10587 Berlin, Germany
| | - R Gnewkow
- Analytical X-ray Physics, TU Berlin, Hardenbergstr. 36, 10623 Berlin, Germany
| | - M Müller
- Physikalisch-Technische Bundesanstalt (PTB), Abbestr. 2-12, 10587 Berlin, Germany
| | - J Weser
- Physikalisch-Technische Bundesanstalt (PTB), Abbestr. 2-12, 10587 Berlin, Germany
| | - C Zech
- Physikalisch-Technische Bundesanstalt (PTB), Abbestr. 2-12, 10587 Berlin, Germany
| | - B Beckhoff
- Physikalisch-Technische Bundesanstalt (PTB), Abbestr. 2-12, 10587 Berlin, Germany
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6
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Fransson T, Alonso-Mori R, Chatterjee R, Cheah MH, Ibrahim M, Hussein R, Zhang M, Fuller F, Gul S, Kim IS, Simon PS, Bogacz I, Makita H, de Lichtenberg C, Song S, Batyuk A, Sokaras D, Massad R, Doyle M, Britz A, Weninger C, Zouni A, Messinger J, Yachandra VK, Yano J, Kern J, Bergmann U. Effects of x-ray free-electron laser pulse intensity on the Mn K β 1,3 x-ray emission spectrum in photosystem II-A case study for metalloprotein crystals and solutions. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2021; 8:064302. [PMID: 34849380 PMCID: PMC8610604 DOI: 10.1063/4.0000130] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 10/24/2021] [Indexed: 05/21/2023]
Abstract
In the last ten years, x-ray free-electron lasers (XFELs) have been successfully employed to characterize metalloproteins at room temperature using various techniques including x-ray diffraction, scattering, and spectroscopy. The approach has been to outrun the radiation damage by using femtosecond (fs) x-ray pulses. An example of an important and damage sensitive active metal center is the Mn4CaO5 cluster in photosystem II (PS II), the catalytic site of photosynthetic water oxidation. The combination of serial femtosecond x-ray crystallography and Kβ x-ray emission spectroscopy (XES) has proven to be a powerful multimodal approach for simultaneously probing the overall protein structure and the electronic state of the Mn4CaO5 cluster throughout the catalytic (Kok) cycle. As the observed spectral changes in the Mn4CaO5 cluster are very subtle, it is critical to consider the potential effects of the intense XFEL pulses on the Kβ XES signal. We report here a systematic study of the effects of XFEL peak power, beam focus, and dose on the Mn Kβ1,3 XES spectra in PS II over a wide range of pulse parameters collected over seven different experimental runs using both microcrystal and solution PS II samples. Our findings show that for beam intensities ranging from ∼5 × 1015 to 5 × 1017 W/cm2 at a pulse length of ∼35 fs, the spectral effects are small compared to those observed between S-states in the Kok cycle. Our results provide a benchmark for other XFEL-based XES studies on metalloproteins, confirming the viability of this approach.
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Affiliation(s)
- Thomas Fransson
- Department of Theoretical Chemistry and Biology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Roberto Alonso-Mori
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Ruchira Chatterjee
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Mun Hon Cheah
- Department of Chemistry – Ångström Laboratory, Molecular Biomimetics, Uppsala University, SE 75120 Uppsala, Sweden
| | - Mohamed Ibrahim
- Humboldt-Universität zu Berlin, Department of Biology, 10099 Berlin, Germany
| | - Rana Hussein
- Humboldt-Universität zu Berlin, Department of Biology, 10099 Berlin, Germany
| | - Miao Zhang
- Humboldt-Universität zu Berlin, Department of Biology, 10099 Berlin, Germany
| | - Franklin Fuller
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Sheraz Gul
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - In-Sik Kim
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Philipp S. Simon
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Isabel Bogacz
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Hiroki Makita
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | | | - Sanghoon Song
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Alexander Batyuk
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Dimosthenis Sokaras
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Ramzi Massad
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Margaret Doyle
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | | | | | - Athina Zouni
- Humboldt-Universität zu Berlin, Department of Biology, 10099 Berlin, Germany
| | | | - Vittal K. Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Uwe Bergmann
- Department of Physics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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7
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Solovyev MA, Lockard JV, Huang X, Heald SM, Sun CJ. High resolution x-ray emission spectrometer for multiple hard x-ray emission lines: Demonstration for Cu Kα and Kβ emissions. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2021; 92:073105. [PMID: 34340408 DOI: 10.1063/5.0048726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 06/20/2021] [Indexed: 06/13/2023]
Abstract
We present a compact 3D printed x-ray emission spectrometer based on the von Hamos geometry that represents a significant upgrade to the existing von Hamos geometry-based miniature x-ray emission spectrometer (miniXES) [Mattern et al., Rev. Sci. Instrum. 83(2), 023901 (2012)]. The upgrades include the incorporation of a higher pixel density 500K detector for improved energy resolution and an enlarged sample area to accommodate a wider range of sample formats. The versatile spectrometer houses removable crystal holders that can be easily exchanged, as well as movable alignment eyelets that give flexibility in Bragg angle selection. Designed for ease of manufacture, all the components, except for the apertures, can be 3D printed and readily assembled. We describe its implementation in measurements of resonant and non-resonant Cu Kα and Kβ x-ray emission and report the theoretical and measured energy resolution and collected solid angle of the emission.
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Affiliation(s)
- Mikhail A Solovyev
- Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439, USA
| | | | - XianRong Huang
- Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439, USA
| | - Steve M Heald
- Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439, USA
| | - Cheng-Jun Sun
- Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439, USA
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8
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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
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9
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Hayashi H, Takaishi M. Highly Resolved Mn Kβ Emission: A Potential Probe in Laboratory for Analysis of Ligand Coordination around Mn Atoms in Gels and Solutions. ANAL SCI 2020; 36:1197-1201. [PMID: 32389903 DOI: 10.2116/analsci.20p088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 05/01/2020] [Indexed: 08/09/2023]
Abstract
Mn Kβ spectra of Mn, MnO, MnSO4·H2O, KMnO4, 0.50 M MnSO4 aqueous solution, and the precipitation bands of Mn-Fe-based Prussian blue analogs formed in 2.4 wt.% agarose gel ("Gel") were measured using a laboratory-use X-ray setup with ∼2.6 eV instrumental resolution, which comprises a cylindrically bent Si (400) crystal monochromator and a spherically bent Ge (440) crystal analyzer. The oxidation-state dependent shift of the Mn Kβ1,3 peak (∼1 eV) was clearly observed for Mn, MnO, and KMnO4, confirming that the employed setup can acquire the key features of Mn Kβ spectra. The Mn Kβ spectra of MnSO4·H2O, the 0.50 M solution, and Gel exhibited small but distinguishable differences, whereas the spectra acquired at two positions in Gel were almost the same. These results suggest that highly resolved Mn Kβ spectra can be helpful for assessing ligand coordination around Mn atoms in gels and solutions.
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Affiliation(s)
- Hisashi Hayashi
- Department of Chemical and Biological Sciences, Faculty of Science, Japan Women's University, 2-8-1 Mejirodai, Bunkyo, Tokyo, 112-8681, Japan.
| | - Mao Takaishi
- Department of Chemical and Biological Sciences, Faculty of Science, Japan Women's University, 2-8-1 Mejirodai, Bunkyo, Tokyo, 112-8681, Japan
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10
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Corry TA, O'Malley PJ. Electronic-Level View of O-O Bond Formation in Nature's Water Oxidizing Complex. J Phys Chem Lett 2020; 11:4221-4225. [PMID: 32374174 DOI: 10.1021/acs.jpclett.0c00794] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The crucial O-O bond forming step in the water oxidizing complex (WOC) of photosystem II is modeled using density functional theory calculations and compared with structural X-ray free electron laser (XFEL) determinations for the penultimate S3 state. Concerted electron flow between the Mn4O5 and Mn1O6 bonds of the complex and the nascent O-O bond is monitored using intrinsic bond orbital analysis along the reaction path. Concerted transfer to Mn1 and Mn4 of two electrons from the reactant oxos, O5 and O6, resulting in an unoccupied antibonding σ2p* orbital is the key to low barrier O-O bond formation. The potential energy surface for O-O bond formation shows a rather broad energy minimum for the oxo-oxo form ranging from 2.4-2.0 Å which may explain the relatively short O5-O6 bond distance reported in experimental structure studies. Alternatively the short O5-O6 bond distance may reflect a dynamic equilibrium model across the whole O-O potential energy surface.
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Affiliation(s)
- Thomas A Corry
- Department of Chemistry, School of Natural Sciences, The University of Manchester, Manchester M13 9PL, U.K
| | - Patrick J O'Malley
- Department of Chemistry, School of Natural Sciences, The University of Manchester, Manchester M13 9PL, U.K
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11
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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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12
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13
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Pushkar Y, K Ravari A, Jensen SC, Palenik M. Early Binding of Substrate Oxygen Is Responsible for a Spectroscopically Distinct S 2 State in Photosystem II. J Phys Chem Lett 2019; 10:5284-5291. [PMID: 31419136 DOI: 10.1021/acs.jpclett.9b01255] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The biological generation of oxygen by the oxygen-evolving complex (OEC) in photosystem II (PS II) is one of nature's most important reactions. The OEC is a Mn4Ca cluster that has multiple Mn-O-Mn and Mn-O-Ca bridges and binds four water molecules. Previously, binding of an additional oxygen was detected in the S2 to S3 transition. Here we demonstrate that early binding of the substrate oxygen to the five-coordinate Mn1 center in the S2 state is likely responsible for the S2 high-spin EPR signal. Substrate binding in the Mn1-OH form explains the prevalence of the high-spin S2 state at higher pH and its low-temperature conversion into the S3 state. The given interpretation was confirmed by X-ray absorption spectroscopic measurements, DFT, and broken symmetry DFT calculations of structures and magnetic properties. Structural, electronic, and spectroscopic properties of the high-spin S2 state model are provided and compared with the available S3 state models. New interpretation of the high-spin S2 state opens opportunity for analysis of factors controlling the oxygen substrate binding in PS II.
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Affiliation(s)
- Yulia Pushkar
- Department of Physics and Astronomy, Purdue University, West Lafayette, Indiana 47907, United States
| | - Alireza K Ravari
- Department of Physics and Astronomy, Purdue University, West Lafayette, Indiana 47907, United States
| | - Scott C Jensen
- Department of Physics and Astronomy, Purdue University, West Lafayette, Indiana 47907, United States
| | - Mark Palenik
- Code 6189, Chemistry Division, Naval Research Laboratory, Washington, DC 20375, United States
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14
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Jensen SC, Sullivan B, Hartzler DA, Pushkar Y. DIY XES - development of an inexpensive, versatile, and easy to fabricate XES analyzer and sample delivery system. X-RAY SPECTROMETRY : XRS 2019; 48:336-344. [PMID: 32606482 PMCID: PMC7326317 DOI: 10.1002/xrs.3005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 12/18/2018] [Indexed: 06/11/2023]
Abstract
The application of X-ray emission spectroscopy (XES) has grown substantially with the development of X-ray free electron lasers, third and fourth generation synchrotron sources and high-power benchtop sources. By providing the high X-ray flux required for XES, these sources broaden the availability and application of this method of probing electronic structure. As the number of sources increase, so does the demand for X-ray emission detection and sample delivery systems that are cost effective and customizable. Here, we present a detailed fabrication protocol for von Hamos X-ray optics and give details for a 3D-printed spectrometer design. Additionally, we outline an automated, externally triggered liquid sample delivery system that can be used to repeatedly deliver nanoliter droplets onto a plastic substrate for measurement. These systems are both low cost, efficient and easy to recreate or modify depending on the application. A low cost multiple X-ray analyzer system enables measurement of dilute samples, whereas the sample delivery limits sample loss and replaces spent sample with fresh sample in the same position. While both systems can be used in a wide range of applications, the design addresses several challenges associated specifically with time-resolved XES (TRXES). As an example application, we show results from TRXES measurements of photosystem II, a dilute, photoactive protein.
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Affiliation(s)
- Scott C Jensen
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907, USA
| | - Brendan Sullivan
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907, USA
| | - Daniel A Hartzler
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907, USA
| | - Yulia Pushkar
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907, USA
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15
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Shoji M, Isobe H, Shen JR, Suga M, Akita F, Miyagawa K, Shigeta Y, Yamaguchi K. Elucidation of the entire Kok cycle for photosynthetic water oxidation by the large-scale quantum mechanics/molecular mechanics calculations: Comparison with the experimental results by the recent serial femtosecond crystallography. Chem Phys Lett 2019. [DOI: 10.1016/j.cplett.2019.06.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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16
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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.
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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
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17
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Isobe H, Shoji M, Suzuki T, Shen JR, Yamaguchi K. Spin, Valence, and Structural Isomerism in the S 3 State of the Oxygen-Evolving Complex of Photosystem II as a Manifestation of Multimetallic Cooperativity. J Chem Theory Comput 2019; 15:2375-2391. [PMID: 30855953 DOI: 10.1021/acs.jctc.8b01055] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Photosynthetic water oxidation is catalyzed by a Mn4CaO5-cluster in photosystem II through an S-state cycle. Understanding the roles of heterogeneity in each S-state, as identified recently by the EPR spectroscopy, is very important to gain a complete description of the catalytic mechanism. We performed herein hybrid DFT calculations within the broken-symmetry formalism and associated analyses of Heisenberg spin models to study the electronic and spin structures of various isomeric structural motifs (hydroxo-oxo, oxyl-oxo, peroxo, and superoxo species) in the S3 state. Our extensive study reveals several factors that affect the spin ground state: (1) (formal) Mn oxidation state; (2) metal-ligand covalency; (3) coordination geometry; and (4) structural change of the Mn cluster induced by alternations in Mn···Mn distances. Some combination of these effects could selectively stabilize/destabilize some spin states. We found that the high spin state ( Stotal = 6) of the oxyl-oxo species can be causative for catalytic function, which manifests through mixing of the metal-ligand character in magnetic orbitals at relatively short O5···O6 distances (<2.0 Å) and long MnA···O5 distances (>2.0 Å). These results will serve as a basis to conceptually identify and rationalize the physicochemical synergisms that can be evoked by the unique "distorted chair" topology of the cluster through cooperative Jahn-Teller effects on multimetallic centers.
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Affiliation(s)
- Hiroshi Isobe
- Research Institute for Interdisciplinary Science , Okayama University , Okayama 700-8530 , Japan
| | - Mitsuo Shoji
- Center for Computational Science , University of Tsukuba , Tsukuba , Ibaraki 305-8577 , Japan
| | - Takayoshi Suzuki
- Research Institute for Interdisciplinary Science , Okayama University , Okayama 700-8530 , Japan
| | - Jian-Ren Shen
- Research Institute for Interdisciplinary Science , Okayama University , Okayama 700-8530 , Japan
| | - Kizashi Yamaguchi
- Institute for NanoScience Design , Osaka University , Toyonaka , Osaka 560-0043 , Japan
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18
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Jensen SC, Sullivan B, Hartzler D, Aguilar JM, Awel S, Bajt S, Basu S, Bean R, Chapman H, Conrad C, Frank M, Fromme R, Martin-Garcia JM, Grant TD, Heymann M, Hunter MS, Ketawala G, Kirian RA, Knoska J, Kupitz C, Li X, Liang M, Lisova S, Mariani V, Mazalova V, Messerschmidt M, Moran M, Nelson G, Oberthür D, Schaffer A, Sierra RG, Vaughn N, Weierstall U, Wiedorn MO, Xavier L, Yang JH, Yefanov O, Zatsepin NA, Aquila A, Fromme P, Boutet S, Seidler GT, Pushkar Y. X-ray Emission Spectroscopy at X-ray Free Electron Lasers: Limits to Observation of the Classical Spectroscopic Response for Electronic Structure Analysis. J Phys Chem Lett 2019; 10:441-446. [PMID: 30566358 PMCID: PMC7047744 DOI: 10.1021/acs.jpclett.8b03595] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
X-ray free electron lasers (XFELs) provide ultrashort intense X-ray pulses suitable to probe electron dynamics but can also induce a multitude of nonlinear excitation processes. These affect spectroscopic measurements and interpretation, particularly for upcoming brighter XFELs. Here we identify and discuss the limits to observing classical spectroscopy, where only one photon is absorbed per atom for a Mn2+ in a light element (O, C, H) environment. X-ray emission spectroscopy (XES) with different incident photon energies, pulse intensities, and pulse durations is presented. A rate equation model based on sequential ionization and relaxation events is used to calculate populations of multiply ionized states during a single pulse and to explain the observed X-ray induced spectral lines shifts. This model provides easy estimation of spectral shifts, which is essential for experimental designs at XFELs and illustrates that shorter X-ray pulses will not overcome sequential ionization but can reduce electron cascade effects.
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Affiliation(s)
- Scott C Jensen
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907, USA
| | - Brendan Sullivan
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907, USA
| | - Daniel Hartzler
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907, USA
| | - Jose Meza Aguilar
- Biodesign Institute, Arizona State University, Tempe, AZ 85287-7401, USA
| | - Salah Awel
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, D-22607 Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, 22761 Hamburg, Germany
| | - Saša Bajt
- Photon Science, Deutsches Elektronen-Synchrotron, D-22607 Hamburg, Germany
| | - Shibom Basu
- Paul Sherrer Institut, 5232 Villigen PSI, Switzerland
| | | | - Henry Chapman
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, D-22607 Hamburg, Germany
| | - Chelsie Conrad
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287-7401, USA
| | - Matthias Frank
- Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Raimund Fromme
- Biodesign Institute, Arizona State University, Tempe, AZ 85287-7401, USA
| | | | - Thomas D Grant
- Hauptman-Woodward Institute, Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, SUNY University at Buffalo, Buffalo, NY 14203
- BioXFEL Science and Technology Center, Buffalo, NY 14203, USA
| | - Michael Heymann
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, D-22607 Hamburg, Germany
- Max Planck Institute of Biochemistry, 82152 Planegg, Germany
| | - Mark S. Hunter
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Gihan Ketawala
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287-7401, USA
| | - Richard A Kirian
- Department of Physics, Arizona State University, Tempe, AZ 85287-7401, USA
| | - Juraj Knoska
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, D-22607 Hamburg, Germany
| | - Christopher Kupitz
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI 53201, USA
| | - Xuanxuan Li
- Beijing Computational Science Research Center, Beijing 100193, China
| | - Mengning Liang
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Stella Lisova
- Department of Physics, Arizona State University, Tempe, AZ 85287-7401, USA
| | - Valerio Mariani
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, D-22607 Hamburg, Germany
| | - Victoria Mazalova
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, D-22607 Hamburg, Germany
| | | | - Michael Moran
- Biodesign Institute, Arizona State University, Tempe, AZ 85287-7401, USA
| | - Garrett Nelson
- Department of Physics, Arizona State University, Tempe, AZ 85287-7401, USA
| | - Dominik Oberthür
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, D-22607 Hamburg, Germany
| | - Alex Schaffer
- Department of Biochemistry, University of California Davis, Davis, CA 95616, USA
| | - Raymond G Sierra
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Natalie Vaughn
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287-7401, USA
| | - Uwe Weierstall
- Biodesign Institute, Arizona State University, Tempe, AZ 85287-7401, USA
- Department of Physics, Arizona State University, Tempe, AZ 85287-7401, USA
| | - Max O. Wiedorn
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, D-22607 Hamburg, Germany
| | - Lourdu Xavier
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, D-22607 Hamburg, Germany
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Jay-How Yang
- Biodesign Institute, Arizona State University, Tempe, AZ 85287-7401, USA
| | - Oleksandr Yefanov
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, D-22607 Hamburg, Germany
| | - Nadia A Zatsepin
- Department of Physics, Arizona State University, Tempe, AZ 85287-7401, USA
| | - Andrew Aquila
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Petra Fromme
- Biodesign Institute, Arizona State University, Tempe, AZ 85287-7401, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ85287-1604
| | - Sébastien Boutet
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Gerald T Seidler
- Department of Physics, University of Washington, Seattle, Washington 98195-1560, USA
| | - Yulia Pushkar
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907, USA
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19
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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]
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20
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Ananyev G, Roy-Chowdhury S, Gates C, Fromme P, Dismukes GC. The Catalytic Cycle of Water Oxidation in Crystallized Photosystem II Complexes: Performance and Requirements for Formation of Intermediates. ACS Catal 2019. [DOI: 10.1021/acscatal.8b04513] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
| | - Shatabdi Roy-Chowdhury
- Biodesign Center for Applied Structural Discovery, The Biodesign Institute and School of Molecular Sciences Arizona State University, Tempe, Arizona 85287, United States
| | | | - Petra Fromme
- Biodesign Center for Applied Structural Discovery, The Biodesign Institute and School of Molecular Sciences Arizona State University, Tempe, Arizona 85287, United States
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21
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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
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22
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Soldatov MA, Martini A, Bugaev AL, Pankin I, Medvedev PV, Guda AA, Aboraia AM, Podkovyrina YS, Budnyk AP, Soldatov AA, Lamberti C. The insights from X-ray absorption spectroscopy into the local atomic structure and chemical bonding of Metal–organic frameworks. Polyhedron 2018. [DOI: 10.1016/j.poly.2018.08.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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23
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Corry TA, O'Malley PJ. Evidence of O-O Bond Formation in the Final Metastable S 3 State of Nature's Water Oxidizing Complex Implying a Novel Mechanism of Water Oxidation. J Phys Chem Lett 2018; 9:6269-6274. [PMID: 30336040 DOI: 10.1021/acs.jpclett.8b02793] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
A novel mechanism for the final stages of Nature's photosynthetic water oxidation to molecular oxygen is proposed. This is based on a comparison of experimental and broken symmetry density functional theory (BS-DFT) calculated geometries and magnetic resonance properties of water oxidizing complex models in the final metastable oxidation state, S3. We show that peroxo models of the S3 state are in vastly superior agreement with the current experimental structural determinations compared with oxo-hydroxo models. Comparison of experimental and BS-DFT calculated 55Mn hyperfine couplings for the electron paramagnetic resonance (EPR) visible form shows better agreement for the oxo-hydroxo model. An equilibrium between oxo-hydroxo and peroxo models is proposed for the S3 state and the major implications for the final steps in the water oxidation mechanism are analyzed and discussed.
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Affiliation(s)
- Thomas A Corry
- School of Chemistry , The University of Manchester , Manchester , M13 9PL , U.K
| | - Patrick J O'Malley
- School of Chemistry , The University of Manchester , Manchester , M13 9PL , U.K
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24
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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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25
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Davis KM, Sullivan BT, Palenik MC, Yan L, Purohit V, Robison G, Kosheleva I, Henning RW, Seidler GT, Pushkar Y. Rapid evolution of the Photosystem II electronic structure during water splitting. PHYSICAL REVIEW. X 2018; 8:041014. [PMID: 31231592 PMCID: PMC6588194 DOI: 10.1103/physrevx.8.041014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Photosynthetic water oxidation is a fundamental process that sustains the biosphere. A Mn4Ca cluster embedded in the photosystem II protein environment is responsible for the production of atmospheric oxygen. Here, time-resolved x-ray emission spectroscopy (XES) was used to observe the process of oxygen formation in real time. These experiments reveal that the oxygen evolution step, initiated by three sequential laser flashes, is accompanied by rapid (within 50 μs) changes to the Mn Kβ XES spectrum. However, no oxidation of the Mn4Ca core above the all MnIV state was detected to precede O-O bond formation, and the observed changes were therefore assigned to O-O bond formation dynamics. We propose that O-O bond formation occurs prior to the transfer of the final (4th) electron from the Mn4Ca cluster to the oxidized tyrosine YZ residue. This model resolves the kinetic limitations associated with O-O bond formation, and suggests an evolutionary adaptation to avoid releasing of harmful peroxide species.
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Affiliation(s)
- Katherine M. Davis
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907, USA
| | - Brendan T. Sullivan
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907, USA
| | | | - Lifen Yan
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907, USA
| | - Vatsal Purohit
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907, USA
| | - Gregory Robison
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907, USA
| | - Irina Kosheleva
- Center for Advanced Radiation Sources, The University of Chicago, Chicago, IL 60637, USA
| | - Robert W. Henning
- Center for Advanced Radiation Sources, The University of Chicago, Chicago, IL 60637, USA
| | - Gerald T. Seidler
- Department of Physics, University of Washington, Seattle, WA 98195, USA
| | - Yulia Pushkar
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907, USA
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26
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Fransson T, Chatterjee R, Fuller FD, Gul S, Weninger C, Sokaras D, Kroll T, Alonso-Mori R, Bergmann U, Kern J, Yachandra VK, Yano J. X-ray Emission Spectroscopy as an in Situ Diagnostic Tool for X-ray Crystallography of Metalloproteins Using an X-ray Free-Electron Laser. Biochemistry 2018; 57:4629-4637. [PMID: 29906115 DOI: 10.1021/acs.biochem.8b00325] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Serial femtosecond crystallography (SFX) using the ultrashort X-ray pulses from a X-ray free-electron laser (XFEL) provides a new way of collecting structural data at room temperature that allows for following the reaction in real time after initiation. XFEL experiments are conducted in a shot-by-shot mode as the sample is destroyed and replenished after each X-ray pulse, and therefore, monitoring and controlling the data quality by using in situ diagnostic tools is critical. To study metalloenzymes, we developed the use of simultaneous collection of X-ray diffraction of crystals along with X-ray emission spectroscopy (XES) data that is used as a diagnostic tool for crystallography, by monitoring the chemical state of the metal catalytic center. We have optimized data analysis methods and sample delivery techniques for fast and active feedback to ensure the quality of each batch of samples and the turnover of the catalytic reaction caused by reaction triggering methods. Here, we describe this active in situ feedback system using Photosystem II as an example that catalyzes the oxidation of H2O to O2 at the Mn4CaO5 active site. We used the first moments of the Mn Kβ1,3 emission spectra, which are sensitive to the oxidation state of Mn, as the primary diagnostics. This approach is applicable to different metalloproteins to determine the integrity of samples and follow changes in the chemical states of the reaction that can be initiated by light or activated by substrates and offers a metric for determining the diffraction images that are used for the final data sets.
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Affiliation(s)
- Thomas Fransson
- Stanford PULSE Institute, SLAC National Accelerator Laboratory , Menlo Park , California United States
| | - Ruchira Chatterjee
- Molecular Biophysics and Integrated Bioimaging Division , Lawrence Berkeley National Laboratory , Berkeley , California United States
| | - Franklin D Fuller
- LCLS, SLAC National Accelerator Laboratory , Menlo Park , California United States
| | - Sheraz Gul
- Molecular Biophysics and Integrated Bioimaging Division , Lawrence Berkeley National Laboratory , Berkeley , California United States
| | - Clemens Weninger
- LCLS, SLAC National Accelerator Laboratory , Menlo Park , California United States
| | - Dimosthenis Sokaras
- SSRL, SLAC National Accelerator Laboratory , Menlo Park , California United States
| | - Thomas Kroll
- SSRL, SLAC National Accelerator Laboratory , Menlo Park , California United States
| | - Roberto Alonso-Mori
- LCLS, SLAC National Accelerator Laboratory , Menlo Park , California United States
| | - Uwe Bergmann
- Stanford PULSE Institute, SLAC National Accelerator Laboratory , Menlo Park , California United States
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division , Lawrence Berkeley National Laboratory , Berkeley , California United States
| | - Vittal K Yachandra
- Molecular Biophysics and Integrated Bioimaging Division , Lawrence Berkeley National Laboratory , Berkeley , California United States
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division , Lawrence Berkeley National Laboratory , Berkeley , California United States
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27
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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
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28
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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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29
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Guo M, Lee YM, Gupta R, Seo MS, Ohta T, Wang HH, Liu HY, Dhuri SN, Sarangi R, Fukuzumi S, Nam W. Dioxygen Activation and O-O Bond Formation Reactions by Manganese Corroles. J Am Chem Soc 2017; 139:15858-15867. [PMID: 29056043 PMCID: PMC5711437 DOI: 10.1021/jacs.7b08678] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Activation of dioxygen (O2) in enzymatic and biomimetic reactions has been intensively investigated over the past several decades. More recently, O-O bond formation, which is the reverse of the O2-activation reaction, has been the focus of current research. Herein, we report the O2-activation and O-O bond formation reactions by manganese corrole complexes. In the O2-activation reaction, Mn(V)-oxo and Mn(IV)-peroxo intermediates were formed when Mn(III) corroles were exposed to O2 in the presence of base (e.g., OH-) and hydrogen atom (H atom) donor (e.g., THF or cyclic olefins); the O2-activation reaction did not occur in the absence of base and H atom donor. Moreover, formation of the Mn(V)-oxo and Mn(IV)-peroxo species was dependent on the amounts of base present in the reaction solution. The role of the base was proposed to lower the oxidation potential of the Mn(III) corroles, thereby facilitating the binding of O2 and forming a Mn(IV)-superoxo species. The putative Mn(IV)-superoxo species was then converted to the corresponding Mn(IV)-hydroperoxo species by abstracting a H atom from H atom donor, followed by the O-O bond cleavage of the putative Mn(IV)-hydroperoxo species to form a Mn(V)-oxo species. We have also shown that addition of hydroxide ion to the Mn(V)-oxo species afforded the Mn(IV)-peroxo species via O-O bond formation and the resulting Mn(IV)-peroxo species reverted to the Mn(V)-oxo species upon addition of proton, indicating that the O-O bond formation and cleavage reactions between the Mn(V)-oxo and Mn(IV)-peroxo complexes are reversible. The present study reports the first example of using the same manganese complex in both O2-activation and O-O bond formation reactions.
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Affiliation(s)
- Mian Guo
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
| | - Yong-Min Lee
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
| | - Ranjana Gupta
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
| | - Mi Sook Seo
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
| | - Takehiro Ohta
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, RSC-UH LP Center, Hyogo 679-5148, Japan
| | - Hua-Hua Wang
- Department of Chemistry, South China University of Technology, Guangzhou 510641, China
| | - Hai-Yang Liu
- Department of Chemistry, South China University of Technology, Guangzhou 510641, China
| | - Sunder N. Dhuri
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
- Department of Chemistry, Goa University, Goa 403 206, India
| | - Ritimukta Sarangi
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Shunichi Fukuzumi
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
| | - Wonwoo Nam
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
- State Key Laboratory for Oxo Synthesis and Selective Oxidation, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou 730000, China
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