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Depenbrock F, Limpke T, Bill E, SantaLucia DJ, van Gastel M, Walleck S, Oldengott J, Stammler A, Bögge H, Glaser T. Reactivities and Electronic Structures of μ-1,2-Peroxo and μ-1,2-Superoxo Co IIICo III Complexes: Electrophilic Reactivity and O 2 Release Induced by Oxidation. Inorg Chem 2023; 62:17913-17930. [PMID: 37838986 DOI: 10.1021/acs.inorgchem.3c02782] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
Peroxo complexes are key intermediates in water oxidation catalysis (WOC). Cobalt plays an important role in WOC, either as oxides CoOx or as {CoIII(μ-1,2-peroxo)CoIII} complexes, which are the oldest peroxo complexes known. The oxidation of {CoIII(μ-1,2-peroxo)CoIII} complexes had usually been described to form {CoIII(μ-1,2-superoxo)CoIII} complexes; however, recently the formation of {CoIV(μ-1,2-peroxo)CoIII} species were suggested. Using a bis(tetradentate) dinucleating ligand, we present here the synthesis and characterization of {CoIII(μ-1,2-peroxo)(μ-OH)CoIII} and {CoIII(μ-OH)2CoIII} complexes. Oxidation of {CoIII(μ-1,2-peroxo)(μ-OH)CoIII} at -40 °C in CH3CN provides the stable {CoIII(μ-1,2-superoxo)(μ-OH)CoIII} species and activates electrophilic reactivity. Moreover, {CoIII(μ-1,2-peroxo)(μ-OH)CoIII} catalyzes water oxidation, not molecularly but rather via CoOx films. While {CoIII(μ-1,2-peroxo)(μ-OH)CoIII} can be reversibly deprotonated with DBU at -40 °C in CH3CN, {CoIII(μ-1,2-superoxo)(μ-OH)CoIII} undergoes irreversible conversions upon reaction with bases to a new intermediate that is also the decay product of {CoIII(μ-1,2-superoxo)(μ-OH)CoIII} in aqueous solution at pH > 2. Based on a combination of experimental methods, the new intermediate is proposed to have a {CoII(μ-OH)CoIII} core formed by the release of O2 from {CoIII(μ-1,2-superoxo)(μ-OH)CoIII} confirmed by a 100% yield of O2 upon photocatalytic oxidation of {CoIII(μ-1,2-peroxo)(μ-OH)CoIII}. This release of O2 by oxidation of a peroxo intermediate corresponds to the last step in molecular WOC.
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Affiliation(s)
- Felix Depenbrock
- Lehrstuhl für Anorganische Chemie I, Fakultät für Chemie, Universität Bielefeld, Universitätsstr. 25, Bielefeld D-33615, Germany
| | - Thomas Limpke
- Lehrstuhl für Anorganische Chemie I, Fakultät für Chemie, Universität Bielefeld, Universitätsstr. 25, Bielefeld D-33615, Germany
| | - Eckhard Bill
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstr. 34-36, Mülheim an der Ruhr D-45470, Germany
| | - Daniel J SantaLucia
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, Mülheim an der Ruhr D-45470, Germany
| | - Maurice van Gastel
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, Mülheim an der Ruhr D-45470, Germany
| | - Stephan Walleck
- Lehrstuhl für Anorganische Chemie I, Fakultät für Chemie, Universität Bielefeld, Universitätsstr. 25, Bielefeld D-33615, Germany
| | - Jan Oldengott
- Lehrstuhl für Anorganische Chemie I, Fakultät für Chemie, Universität Bielefeld, Universitätsstr. 25, Bielefeld D-33615, Germany
| | - Anja Stammler
- Lehrstuhl für Anorganische Chemie I, Fakultät für Chemie, Universität Bielefeld, Universitätsstr. 25, Bielefeld D-33615, Germany
| | - Hartmut Bögge
- Lehrstuhl für Anorganische Chemie I, Fakultät für Chemie, Universität Bielefeld, Universitätsstr. 25, Bielefeld D-33615, Germany
| | - Thorsten Glaser
- Lehrstuhl für Anorganische Chemie I, Fakultät für Chemie, Universität Bielefeld, Universitätsstr. 25, Bielefeld D-33615, Germany
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Monteiro DCF, Amoah E, Rogers C, Pearson AR. Using photocaging for fast time-resolved structural biology studies. Acta Crystallogr D Struct Biol 2021; 77:1218-1232. [PMID: 34605426 PMCID: PMC8489231 DOI: 10.1107/s2059798321008809] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 08/23/2021] [Indexed: 12/02/2022] Open
Abstract
Careful selection of photocaging approaches is critical to achieve fast and well synchronized reaction initiation and perform successful time-resolved structural biology experiments. This review summarizes the best characterized and most relevant photocaging groups previously described in the literature. It also provides a walkthrough of the essential factors to consider in designing a suitable photocaged molecule to address specific biological questions, focusing on photocaging groups with well characterized spectroscopic properties. The relationships between decay rates (k in s-1), quantum yields (ϕ) and molar extinction coefficients (ϵmax in M-1 cm-1) are highlighted for different groups. The effects of the nature of the photocaged group on these properties is also discussed. Four main photocaging scaffolds are presented in detail, o-nitrobenzyls, p-hydroxyphenyls, coumarinyls and nitrodibenzofuranyls, along with three examples of the use of this technology. Furthermore, a subset of specialty photocages are highlighted: photoacids, molecular photoswitches and metal-containing photocages. These extend the range of photocaging approaches by, for example, controlling pH or generating conformationally locked molecules.
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Affiliation(s)
- Diana C. F. Monteiro
- Hauptman–Woodward Medical Research Institute, 700 Ellicot Street, Buffalo, NY 14203, USA
| | - Emmanuel Amoah
- Hauptman–Woodward Medical Research Institute, 700 Ellicot Street, Buffalo, NY 14203, USA
| | - Cromarte Rogers
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Department of Chemistry, Universität Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Arwen R. Pearson
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
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Szundi I, Funatogawa C, Soulimane T, Einarsdóttir Ó. The Reactions of O 2 and NO with Mixed-Valence ba 3 Cytochrome c Oxidase from Thermus thermophilus. Biophys J 2019; 118:386-395. [PMID: 31870538 DOI: 10.1016/j.bpj.2019.11.3390] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 11/22/2019] [Accepted: 11/25/2019] [Indexed: 12/12/2022] Open
Abstract
Earlier CO flow-flash experiments on the fully reduced Thermus thermophilus ba3 (Tt ba3) cytochrome oxidase revealed that O2 binding was slowed down by a factor of 10 in the presence of CO (Szundi et al., 2010, PNAS 107, 21010-21015). The goal of the current study is to explore whether the long apparent lifetime (∼50 ms) of the CuB+-CO complex generated upon photolysis of the CO-bound mixed-valence Tt ba3 (Koutsoupakis et al., 2019, Acc. Chem. Res. 52, 1380-1390) affects O2 and NO binding and the ability of CuB to act as an electron donor during O-O bond splitting. The CO recombination, NO binding, and the reaction of mixed-valence Tt ba3 with O2 were investigated by time-resolved optical absorption spectroscopy using the CO flow-flash approach and photolabile O2 and NO carriers. No electron backflow was detected after photolysis of the mixed-valence CO-bound Tt ba3. The rate of O2 and NO binding was two times slower than in the fully reduced enzyme in the presence of CO and 20 times slower than in the absence of CO. The purported long-lived CuB+-CO complex did not prevent O-O bond splitting and the resulting PM formation, which was significantly faster (5-10 times) than in the bovine heart enzyme. We propose that O2 binding to heme a3 in Tt ba3 causes CO to dissociate from CuB+ in a concerted manner through steric and/or electronic effects, thus allowing CuB+ to act as an electron donor in the mixed-valence enzyme. The significantly faster O2 binding and O-O bond cleavage in Tt ba3 compared to analogous steps in the aa3 oxidases could reflect evolutionary adaptation of the enzyme to the microaerobic conditions of the T. thermophilus HB8 species.
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Affiliation(s)
- Istvan Szundi
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California
| | - Chie Funatogawa
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California
| | - Tewfik Soulimane
- Deparment of Chemical Sciences, Bernal Institute, University of Limerick, Limerick, Ireland
| | - Ólőf Einarsdóttir
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California.
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Dedushko MA, Schweitzer D, Blakely MN, Swartz RD, Kaminsky W, Kovacs JA. Geometric and electronic structure of a crystallographically characterized thiolate-ligated binuclear peroxo-bridged cobalt(III) complex. J Biol Inorg Chem 2019; 24:919-926. [PMID: 31342141 PMCID: PMC6948190 DOI: 10.1007/s00775-019-01686-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 07/11/2019] [Indexed: 10/26/2022]
Abstract
In order to shed light on metal-dependent mechanisms for O-O bond cleavage, and its microscopic reverse, we compare herein the electronic and geometric structures of O2-derived binuclear Co(III)- and Mn(III)-peroxo compounds. Binuclear metal peroxo complexes are proposed to form as intermediates during Mn-promoted photosynthetic H2O oxidation, and a Co-containing artificial leaf inspired by nature's photosynthetic H2O oxidation catalyst. Crystallographic characterization of an extremely activated peroxo is made possible by working with substitution-inert, low-spin Co(III). Density functional theory (DFT) calculations show that the frontier orbitals of the Co(III)-peroxo compound differ noticeably from the analogous Mn(III)-peroxo compound. The highest occupied molecular orbital (HOMO) associated with the Co(III)-peroxo is more localized on the peroxo in an antibonding π*(O-O) orbital, whereas the HOMO of the structurally analogous Mn(III)-peroxo is delocalized over both the metal d-orbitals and peroxo π*(O-O) orbital. With low-spin d6 Co(III), filled t2g orbitals prevent π-back-donation from the doubly occupied antibonding π*(O-O) orbital onto the metal ion. This is not the case with high-spin d4 Mn(III), since these orbitals are half-filled. This weakens the peroxo O-O bond of the former relative to the latter.
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Affiliation(s)
- Maksym A Dedushko
- The Department of Chemistry, University of Washington, Box 351700, Seattle, WA, 98195-1700, USA
| | - Dirk Schweitzer
- The Department of Chemistry, University of Washington, Box 351700, Seattle, WA, 98195-1700, USA
| | - Maike N Blakely
- The Department of Chemistry, University of Washington, Box 351700, Seattle, WA, 98195-1700, USA
| | - Rodney D Swartz
- The Department of Chemistry, University of Washington, Box 351700, Seattle, WA, 98195-1700, USA
| | - Werner Kaminsky
- The Department of Chemistry, University of Washington, Box 351700, Seattle, WA, 98195-1700, USA
| | - Julie A Kovacs
- The Department of Chemistry, University of Washington, Box 351700, Seattle, WA, 98195-1700, USA.
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Gao J, Fischer A, Svensson PH, Kloo L. Crystallography as Forensic Tool for Understanding Electrolyte Degradation in Dye-sensitized Solar Cells. ChemistrySelect 2017. [DOI: 10.1002/slct.201601756] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Jiajia Gao
- Applied Physical Chemistry; KTH Royal Institue of Technology; SE-100 44 Stockhjolm Sweden
| | - Andreas Fischer
- Applied Physical Chemistry; KTH Royal Institue of Technology; SE-100 44 Stockhjolm Sweden
| | - Per H. Svensson
- Applied Physical Chemistry; KTH Royal Institue of Technology; SE-100 44 Stockhjolm Sweden
- SP Process Development, Fordskargatan; SE-151 21 Södertälje Sweden
| | - Lars Kloo
- Applied Physical Chemistry; KTH Royal Institue of Technology; SE-100 44 Stockhjolm Sweden
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Funatogawa C, Li Y, Chen Y, McDonald W, Szundi I, Fee JA, Stout CD, Einarsdóttir Ó. Role of the Conserved Valine 236 in Access of Ligands to the Active Site of Thermus thermophilus ba3 Cytochrome Oxidase. Biochemistry 2016; 56:107-119. [DOI: 10.1021/acs.biochem.6b00590] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Chie Funatogawa
- Department
of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - Yang Li
- Department
of Molecular Biology, The Scripps Institute, MB-8, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Ying Chen
- Department
of Molecular Biology, The Scripps Institute, MB-8, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - William McDonald
- Department
of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - Istvan Szundi
- Department
of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - James A. Fee
- Department
of Molecular Biology, The Scripps Institute, MB-8, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - C. David Stout
- Department
of Molecular Biology, The Scripps Institute, MB-8, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Ólöf Einarsdóttir
- Department
of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
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Stich TA, McAlpin JG, Wall RM, Rigsby ML, Britt RD. Electron Paramagnetic Resonance Characterization of Dioxygen-Bridged Cobalt Dimers with Relevance to Water Oxidation. Inorg Chem 2016; 55:12728-12736. [PMID: 27989208 DOI: 10.1021/acs.inorgchem.6b01954] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A variety of metal oxides can catalyze the oxidation of water to molecular oxygen when polarized by a sufficiently high electrochemical potential. Minimizing the overpotential and increasing the rate of the oxygen-evolving reaction (OER) are key goals in making such materials a component of viable energy storage devices. However, the structural factors that imbue the metal oxides with their catalytic power are difficult to assess as these solids contain many distinct metal-ion sites, have a varying amount of defect sites within the lattice, and can be composed of multiple phases. In the present study, we determined the magnetic properties for a series of dimeric cobalt complexes in which the two metal centers are bridged by a dioxygen moiety. Our spectroscopically validated electronic structure description indicates that each species is best described as two Co(III) ions that are bound to a μ-η1η1 superoxide ligand. Intriguingly, we found evidence that the two compounds that possess oxygen-evolving activity coordinate the superoxide ion in an unusual, nonplanar fashion. It appears as if the intermediately long Co···Co distance of 3.9 Å is responsible for the unusual superoxide binding geometry. This structural factor may be an important element in the design of solid-state OER catalysts.
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Affiliation(s)
- Troy A Stich
- Department of Chemistry, University of California , 1 Shields Avenue, Davis, California 95616-0935, United States
| | - J Gregory McAlpin
- Department of Chemistry, University of California , 1 Shields Avenue, Davis, California 95616-0935, United States
| | - Ryan M Wall
- Department of Chemistry, University of California , 1 Shields Avenue, Davis, California 95616-0935, United States
| | - Matthew L Rigsby
- Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706-1322, United States
| | - R David Britt
- Department of Chemistry, University of California , 1 Shields Avenue, Davis, California 95616-0935, United States
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von Stetten D, Giraud T, Carpentier P, Sever F, Terrien M, Dobias F, Juers DH, Flot D, Mueller-Dieckmann C, Leonard GA, de Sanctis D, Royant A. In crystallo optical spectroscopy (icOS) as a complementary tool on the macromolecular crystallography beamlines of the ESRF. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:15-26. [PMID: 25615856 PMCID: PMC4304682 DOI: 10.1107/s139900471401517x] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 06/27/2014] [Indexed: 01/04/2023]
Abstract
The analysis of structural data obtained by X-ray crystallography benefits from information obtained from complementary techniques, especially as applied to the crystals themselves. As a consequence, optical spectroscopies in structural biology have become instrumental in assessing the relevance and context of many crystallographic results. Since the year 2000, it has been possible to record such data adjacent to, or directly on, the Structural Biology Group beamlines of the ESRF. A core laboratory featuring various spectrometers, named the Cryobench, is now in its third version and houses portable devices that can be directly mounted on beamlines. This paper reports the current status of the Cryobench, which is now located on the MAD beamline ID29 and is thus called the ID29S-Cryobench (where S stands for `spectroscopy'). It also reviews the diverse experiments that can be performed at the Cryobench, highlighting the various scientific questions that can be addressed.
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Affiliation(s)
| | - Thierry Giraud
- European Synchrotron Radiation Facility, F-38043 Grenoble, France
| | | | - Franc Sever
- European Synchrotron Radiation Facility, F-38043 Grenoble, France
| | - Maxime Terrien
- Université Grenoble Alpes, IBS, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
- CEA, IBS, F-38044 Grenoble, France
| | - Fabien Dobias
- European Synchrotron Radiation Facility, F-38043 Grenoble, France
| | - Douglas H. Juers
- Department of Physics, Whitman College, Walla Walla, WA 99362, USA
| | - David Flot
- European Synchrotron Radiation Facility, F-38043 Grenoble, France
| | | | | | | | - Antoine Royant
- European Synchrotron Radiation Facility, F-38043 Grenoble, France
- Université Grenoble Alpes, IBS, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
- CEA, IBS, F-38044 Grenoble, France
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McDonald W, Funatogawa C, Li Y, Chen Y, Szundi I, Fee JA, Stout CD, Einarsdóttir O. Conserved glycine 232 in the ligand channel of ba3 cytochrome oxidase from Thermus thermophilus. Biochemistry 2014; 53:4467-75. [PMID: 24937405 PMCID: PMC4216187 DOI: 10.1021/bi500289h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Knowing how the protein environment modulates ligand pathways and redox centers in the respiratory heme-copper oxidases is fundamental for understanding the relationship between the structure and function of these enzymes. In this study, we investigated the reactions of O2 and NO with the fully reduced G232V mutant of ba3 cytochrome c oxidase from Thermus thermophilus (Tt ba3) in which a conserved glycine residue in the O2 channel of the enzyme was replaced with a bulkier valine residue. Previous studies of the homologous mutant of Rhodobacter sphaeroides aa3 cytochrome c oxidase suggested that the valine completely blocked the access of O2 to the active site [Salomonsson, L., et al. (2004) Proc. Natl. Acad. Sci. U.S.A. 101, 11617-11621]. Using photolabile O2 and NO carriers, we find by using time-resolved optical absorption spectroscopy that the rates of O2 and NO binding are not significantly affected in the Tt ba3 G232V mutant. Classical molecular dynamics simulations of diffusion of O2 to the active site in the wild-type enzyme and G232V mutant show that the insertion of the larger valine residue in place of the glycine appears to open up other O2 and NO exit/entrance pathways that allow these ligands unhindered access to the active site, thus compensating for the larger valine residue.
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Affiliation(s)
- William McDonald
- Department of Chemistry and Biochemistry, University of California , Santa Cruz, California 95064, United States
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