1
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Li M, Maisuradze M, Mullaliu A, Carlomagno I, Aquilanti G, Plaisier JR, Giorgetti M. Structural Evolution of Manganese Prussian Blue Analogue in Aqueous ZnSO 4 Electrolyte. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2404584. [PMID: 39105446 DOI: 10.1002/smll.202404584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 07/22/2024] [Indexed: 08/07/2024]
Abstract
Among different Prussian Blue Analogues (PBAs), manganese hexacyanoferrate (MnHCF), with open framework and two abundant electroactive metal sites, exhibits high potential for the grid-scale aqueous rechargeable zinc-ion batteries (ARZIBs) application. Until now, the intercalation mechanism of Zn2+ into MnHCF has not been clearly illustrated. In this work, combining different synchrotron X-ray techniques, the structural and microscopic evolution of MnHCF in 3 m ZnSO4 electrolyte is comprehensively studied, and a thorough understanding of the intercalation/release dynamic, in terms of local and long-range domain, is provided. The elemental distribution and structural information of Fe, Mn, Zn inside MnHCF electrodes is obtained from the X-ray fluorescence (XRF) elemental maps and X-ray absorption spectroscopy (XAS). The in-depth analysis of extended X-ray absorption fine structure (EXAFS) signals confirm that the rearrangement of Mn site, evidencing the cleavage of the Mn─N bond with the formation of a Mn─O bond, in an octahedral environment. The phase transformation of MnHCF takes place exclusively during the 1st cycle, and a mixture of rhombohedral and cubic zinc hexacynoferrate (ZnHCF) phases are formed during the first charge process. Thereafter, the newly formed cubic ZnHCF phase becomes the only stable one, existing in the subsequent cycles and exhibiting excellent electrochemical stability.
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Affiliation(s)
- Min Li
- Department of Industrial Chemistry, University of Bologna, Campus Navile, Via Piero Gobetti 85, Bologna, 40139, Italy
| | - Mariam Maisuradze
- Department of Industrial Chemistry, University of Bologna, Campus Navile, Via Piero Gobetti 85, Bologna, 40139, Italy
| | | | - Ilaria Carlomagno
- Elettra - Sincrotrone Trieste, s.s. 14, km 163.5, Trieste, 34149, Italy
| | | | | | - Marco Giorgetti
- Department of Industrial Chemistry, University of Bologna, Campus Navile, Via Piero Gobetti 85, Bologna, 40139, Italy
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2
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Mandal A, Berquist EJ, Herbert JM. A new parameterization of the DFT/CIS method with applications to core-level spectroscopy. J Chem Phys 2024; 161:044114. [PMID: 39051834 DOI: 10.1063/5.0220535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2024] [Accepted: 07/08/2024] [Indexed: 07/27/2024] Open
Abstract
Time-dependent density functional theory (TD-DFT) within a restricted excitation space is an efficient means to compute core-level excitation energies using only a small subset of the occupied orbitals. However, core-to-valence excitation energies are significantly underestimated when standard exchange-correlation functionals are used, which is partly traceable to systemic issues with TD-DFT's description of Rydberg and charge-transfer excited states. To mitigate this, we have implemented an empirically modified combination of configuration interaction with single substitutions (CIS) based on Kohn-Sham orbitals, which is known as "DFT/CIS." This semi-empirical approach is well-suited for simulating x-ray near-edge spectra, as it contains sufficient exact exchange to model charge-transfer excitations yet retains DFT's low-cost description of dynamical electron correlation. Empirical corrections to the matrix elements enable semi-quantitative simulation of near-edge x-ray spectra without the need for significant a posteriori shifts; this should be useful in complex molecules and materials with multiple overlapping x-ray edges. Parameter optimization for use with a specific range-separated hybrid functional makes this a black-box method intended for both core and valence spectroscopy. Results herein demonstrate that realistic K-edge absorption and emission spectra can be obtained for second- and third-row elements and 3d transition metals, with promising results for L-edge spectra as well. DFT/CIS calculations require absolute shifts that are considerably smaller than what is typical in TD-DFT.
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Affiliation(s)
- Aniket Mandal
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | | | - John M Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
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3
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Azadmanesh J, Slobodnik K, Struble LR, Lutz WE, Coates L, Weiss KL, Myles DAA, Kroll T, Borgstahl GEO. Revealing the atomic and electronic mechanism of human manganese superoxide dismutase product inhibition. Nat Commun 2024; 15:5973. [PMID: 39013847 PMCID: PMC11252399 DOI: 10.1038/s41467-024-50260-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 07/05/2024] [Indexed: 07/18/2024] Open
Abstract
Human manganese superoxide dismutase (MnSOD) is a crucial oxidoreductase that maintains the vitality of mitochondria by converting superoxide (O2●-) to molecular oxygen (O2) and hydrogen peroxide (H2O2) with proton-coupled electron transfers (PCETs). Human MnSOD has evolved to be highly product inhibited to limit the formation of H2O2, a freely diffusible oxidant and signaling molecule. The product-inhibited complex is thought to be composed of a peroxide (O22-) or hydroperoxide (HO2-) species bound to Mn ion and formed from an unknown PCET mechanism. PCET mechanisms of proteins are typically not known due to difficulties in detecting the protonation states of specific residues that coincide with the electronic state of the redox center. To shed light on the mechanism, we combine neutron diffraction and X-ray absorption spectroscopy of the product-bound, trivalent, and divalent states of the enzyme to reveal the positions of all the atoms, including hydrogen, and the electronic configuration of the metal ion. The data identifies the product-inhibited complex, and a PCET mechanism of inhibition is constructed.
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Affiliation(s)
- Jahaun Azadmanesh
- Eppley Institute for Research in Cancer and Allied Diseases, 986805 Nebraska Medical Center, Omaha, NE, 68198-6805, USA
| | - Katelyn Slobodnik
- Eppley Institute for Research in Cancer and Allied Diseases, 986805 Nebraska Medical Center, Omaha, NE, 68198-6805, USA
| | - Lucas R Struble
- Eppley Institute for Research in Cancer and Allied Diseases, 986805 Nebraska Medical Center, Omaha, NE, 68198-6805, USA
| | - William E Lutz
- Eppley Institute for Research in Cancer and Allied Diseases, 986805 Nebraska Medical Center, Omaha, NE, 68198-6805, USA
| | - Leighton Coates
- Second Target Station, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN, 37831, USA
| | - Kevin L Weiss
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN, 37831, USA
| | - Dean A A Myles
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN, 37831, USA
| | - Thomas Kroll
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Gloria E O Borgstahl
- Eppley Institute for Research in Cancer and Allied Diseases, 986805 Nebraska Medical Center, Omaha, NE, 68198-6805, USA.
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4
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Borgstahl G, Azadmanesh J, Slobodnik K, Struble L, Cone E, Dasgupta M, Lutz W, Kumar S, Natarajan A, Coates L, Weiss K, Myles D, Kroll T. The role of Tyr34 in proton-coupled electron transfer of human manganese superoxide dismutase. RESEARCH SQUARE 2024:rs.3.rs-4494128. [PMID: 38946943 PMCID: PMC11213228 DOI: 10.21203/rs.3.rs-4494128/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Human manganese superoxide dismutase (MnSOD) plays a crucial role in controlling levels of reactive oxygen species (ROS) by converting superoxide (O2 ●-) to molecular oxygen (O2) and hydrogen peroxide (H2O2) with proton-coupled electron transfers (PCETs). The reactivity of human MnSOD is determined by the state of a key catalytic residue, Tyr34, that becomes post-translationally inactivated by nitration in various diseases associated with mitochondrial dysfunction. We previously reported that Tyr34 has an unusual pKa due to its proximity to the Mn metal and undergoes cyclic deprotonation and protonation events to promote the electron transfers of MnSOD. To shed light on the role of Tyr34 MnSOD catalysis, we performed neutron diffraction, X-ray spectroscopy, and quantum chemistry calculations of Tyr34Phe MnSOD in various enzymatic states. The data identifies the contributions of Tyr34 in MnSOD activity that support mitochondrial function and presents a thorough characterization of how a single tyrosine modulates PCET catalysis.
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5
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Azadmanesh J, Slobodnik K, Struble LR, Cone EA, Dasgupta M, Lutz WE, Kumar S, Natarajan A, Coates L, Weiss KL, Myles DAA, Kroll T, Borgstahl GEO. The role of Tyr34 in proton-coupled electron transfer of human manganese superoxide dismutase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.29.596464. [PMID: 38853997 PMCID: PMC11160768 DOI: 10.1101/2024.05.29.596464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Human manganese superoxide dismutase (MnSOD) plays a crucial role in controlling levels of reactive oxygen species (ROS) by converting superoxide (O 2 •- ) to molecular oxygen (O 2 ) and hydrogen peroxide (H 2 O 2 ) with proton-coupled electron transfers (PCETs). The reactivity of human MnSOD is determined by the state of a key catalytic residue, Tyr34, that becomes post-translationally inactivated by nitration in various diseases associated with mitochondrial dysfunction. We previously reported that Tyr34 has an unusual pK a due to its proximity to the Mn metal and undergoes cyclic deprotonation and protonation events to promote the electron transfers of MnSOD. To shed light on the role of Tyr34 MnSOD catalysis, we performed neutron diffraction, X-ray spectroscopy, and quantum chemistry calculations of Tyr34Phe MnSOD in various enzymatic states. The data identifies the contributions of Tyr34 in MnSOD activity that support mitochondrial function and presents a thorough characterization of how a single tyrosine modulates PCET catalysis.
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6
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Malik DD, Ryu W, Kim Y, Singh G, Kim JH, Sankaralingam M, Lee YM, Seo MS, Sundararajan M, Ocampo D, Roemelt M, Park K, Kim SH, Baik MH, Shearer J, Ray K, Fukuzumi S, Nam W. Identification, Characterization, and Electronic Structures of Interconvertible Cobalt-Oxygen TAML Intermediates. J Am Chem Soc 2024; 146:13817-13835. [PMID: 38716885 PMCID: PMC11216523 DOI: 10.1021/jacs.3c14346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2024]
Abstract
The reaction of Li[(TAML)CoIII]·3H2O (TAML = tetraamido macrocyclic tetraanionic ligand) with iodosylbenzene at 253 K in acetone in the presence of redox-innocent metal ions (Sc(OTf)3 and Y(OTf)3) or triflic acid affords a blue species 1, which is converted reversibly to a green species 2 upon cooling to 193 K. The electronic structures of 1 and 2 have been determined by combining advanced spectroscopic techniques (X-band electron paramagnetic resonance (EPR), electron nuclear double resonance (ENDOR), X-ray absorption spectroscopy/extended X-ray absorption fine structure (XAS/EXAFS), and magnetic circular dichroism (MCD)) with ab initio theoretical studies. Complex 1 is best represented as an S = 1/2 [(Sol)(TAML•+)CoIII---OH(LA)]- species (LA = Lewis/Brønsted acid and Sol = solvent), where an S = 1 Co(III) center is antiferromagnetically coupled to S = 1/2 TAML•+, which represents a one-electron oxidized TAML ligand. In contrast, complex 2, also with an S = 1/2 ground state, is found to be multiconfigurational with contributions of both the resonance forms [(H-TAML)CoIV═O(LA)]- and [(H-TAML•+)CoIII═O(LA)]-; H-TAML and H-TAML•+ represent the protonated forms of TAML and TAML•+ ligands, respectively. Thus, the interconversion of 1 and 2 is associated with a LA-associated tautomerization event, whereby H+ shifts from the terminal -OH group to TAML•+ with the concomitant formation of a terminal cobalt-oxo species possessing both singlet (SCo = 0) Co(III) and doublet (SCo = 1/2) Co(IV) characters. The reactivities of 1 and 2 at different temperatures have been investigated in oxygen atom transfer (OAT) and hydrogen atom transfer (HAT) reactions to compare the activation enthalpies and entropies of 1 and 2.
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Affiliation(s)
- Deesha D Malik
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
| | - Wooyeol Ryu
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Yujeong Kim
- Western Seoul Center, Korea Basic Science Institute, Seoul 03759, Korea
| | - Gurjot Singh
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489 Berlin, Germany
| | - Jun-Hyeong Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
- Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science, Daejeon 34141, Korea
| | | | - Yong-Min Lee
- 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
| | - Mahesh Sundararajan
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
- Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science, Daejeon 34141, Korea
- Theoretical Chemistry Section, Chemistry Division, Bhabha Atomic Research Centre, Mumbai 400 085, India
| | - Daniel Ocampo
- Department of Chemistry, Trinity University, San Antonio, Texas 78212-7200, United States
| | - Michael Roemelt
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489 Berlin, Germany
| | - Kiyoung Park
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Sun Hee Kim
- Western Seoul Center, Korea Basic Science Institute, Seoul 03759, Korea
- Department of Chemistry, Chung-Ang University, Seoul 06974, Korea
| | - Mu-Hyun Baik
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
- Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science, Daejeon 34141, Korea
| | - Jason Shearer
- Department of Chemistry, Trinity University, San Antonio, Texas 78212-7200, United States
| | - Kallol Ray
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489 Berlin, Germany
| | - 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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7
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Barlow K, Phelps R, Eng J, Katayama T, Sutcliffe E, Coletta M, Brechin EK, Penfold TJ, Johansson JO. Tracking nuclear motion in single-molecule magnets using femtosecond X-ray absorption spectroscopy. Nat Commun 2024; 15:4043. [PMID: 38744877 PMCID: PMC11094174 DOI: 10.1038/s41467-024-48411-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 04/30/2024] [Indexed: 05/16/2024] Open
Abstract
The development of new data storage solutions is crucial for emerging digital technologies. Recently, all-optical magnetic switching has been achieved in dielectrics, proving to be faster than traditional methods. Despite this, single-molecule magnets (SMMs), which are an important class of magnetic materials due to their nanometre size, remain underexplored for ultrafast photomagnetic switching. Herein, we report femtosecond time-resolved K-edge X-ray absorption spectroscopy (TR-XAS) on a Mn(III)-based trinuclear SMM. Exploiting the elemental specificity of XAS, we directly track nuclear dynamics around the metal ions and show that the ultrafast dynamics upon excitation of a crystal-field transition are dominated by a magnetically active Jahn-Teller mode. Our results, supported by simulations, reveal minute bond length changes from 0.01 to 0.05 Å demonstrating the sensitivity of the method. These geometrical changes are discussed in terms of magneto-structural relationships and consequently our results illustrate the importance of TR-XAS for the emerging area of ultrafast molecular magnetism.
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Affiliation(s)
- Kyle Barlow
- EaStCHEM School of Chemistry, University of Edinburgh, David Brewster Road, EH9 3FJ, Edinburgh, UK
| | - Ryan Phelps
- EaStCHEM School of Chemistry, University of Edinburgh, David Brewster Road, EH9 3FJ, Edinburgh, UK
| | - Julien Eng
- Chemistry, School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Tetsuo Katayama
- Japan Synchrotron Radiation Research Institute, Kouto 1-1-1, Sayo, Hyogo, 679-5198, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan
| | - Erica Sutcliffe
- EaStCHEM School of Chemistry, University of Edinburgh, David Brewster Road, EH9 3FJ, Edinburgh, UK
| | - Marco Coletta
- EaStCHEM School of Chemistry, University of Edinburgh, David Brewster Road, EH9 3FJ, Edinburgh, UK
| | - Euan K Brechin
- EaStCHEM School of Chemistry, University of Edinburgh, David Brewster Road, EH9 3FJ, Edinburgh, UK
| | - Thomas J Penfold
- Chemistry, School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK.
| | - J Olof Johansson
- EaStCHEM School of Chemistry, University of Edinburgh, David Brewster Road, EH9 3FJ, Edinburgh, UK.
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8
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Porte V, Milunovic MNM, Knof U, Leischner T, Danzl T, Kaiser D, Gruene T, Zalibera M, Jelemenska I, Bucinsky L, Jannuzzi SAV, DeBeer S, Novitchi G, Maulide N, Arion VB. Chemical and Redox Noninnocence of Pentane-2,4-dione Bis( S-methylisothiosemicarbazone) in Cobalt Complexes and Their Application in Wacker-Type Oxidation. JACS AU 2024; 4:1166-1183. [PMID: 38559722 PMCID: PMC10976605 DOI: 10.1021/jacsau.4c00005] [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: 01/02/2024] [Revised: 02/09/2024] [Accepted: 02/15/2024] [Indexed: 04/04/2024]
Abstract
Cobalt complexes with multiproton- and multielectron-responsive ligands are of interest for challenging catalytic transformations. The chemical and redox noninnocence of pentane-2,4-dione bis(S-methylisothiosemicarbazone) (PBIT) in a series of cobalt complexes has been studied by a range of methods, including spectroscopy [UV-vis, NMR, electron paramagnetic resonance (EPR), X-ray absorption spectroscopy (XAS)], cyclic voltammetry, X-ray diffraction, and density functional theory (DFT) calculations. Two complexes [CoIII(H2LSMe)I]I and [CoIII(LSMe)I2] were found to act as precatalysts in a Wacker-type oxidation of olefins using phenylsilane, the role of which was elucidated through isotopic labeling. Insights into the mechanism of the catalytic transformation as well as the substrate scope of this selective reaction are described, and the essential role of phenylsilane and the noninnocence of PBIT are disclosed. Among the several relevant species characterized was an unprecedented Co(III) complex with a dianionic diradical PBIT ligand ([CoIII(LSMe••)I]).
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Affiliation(s)
- Vincent Porte
- University
of Vienna, Institute of Organic Chemistry, Währinger Strasse 38, A-1090 Vienna, Austria
| | - Miljan N. M. Milunovic
- University
of Vienna, Institute of Inorganic Chemistry, Währinger Strasse 42, A-1090 Vienna, Austria
| | - Ulrich Knof
- Novartis
Pharma AG, CH-4056 Basel, Switzerland
| | - Thomas Leischner
- University
of Vienna, Institute of Organic Chemistry, Währinger Strasse 38, A-1090 Vienna, Austria
| | - Tobias Danzl
- University
of Vienna, Institute of Organic Chemistry, Währinger Strasse 38, A-1090 Vienna, Austria
| | - Daniel Kaiser
- University
of Vienna, Institute of Organic Chemistry, Währinger Strasse 38, A-1090 Vienna, Austria
| | - Tim Gruene
- University
of Vienna, Institute of Inorganic Chemistry, Währinger Strasse 42, A-1090 Vienna, Austria
| | - Michal Zalibera
- Institute
of Physical Chemistry and Chemical Physics, Faculty of Chemical and
Food Technology, Slovak University of Technology
in Bratislava, Radlinského 9, SK-81237 Bratislava, Slovak Republic
| | - Ingrid Jelemenska
- Institute
of Physical Chemistry and Chemical Physics, Faculty of Chemical and
Food Technology, Slovak University of Technology
in Bratislava, Radlinského 9, SK-81237 Bratislava, Slovak Republic
| | - Lukas Bucinsky
- Institute
of Physical Chemistry and Chemical Physics, Faculty of Chemical and
Food Technology, Slovak University of Technology
in Bratislava, Radlinského 9, SK-81237 Bratislava, Slovak Republic
| | - Sergio A. V. Jannuzzi
- 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
| | | | - Nuno Maulide
- University
of Vienna, Institute of Organic Chemistry, Währinger Strasse 38, A-1090 Vienna, Austria
| | - Vladimir B. Arion
- University
of Vienna, Institute of Inorganic Chemistry, Währinger Strasse 42, A-1090 Vienna, Austria
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9
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Borgstahl G, Azadmanesh J, Slobodnik K, Struble L, Lutz W, Coates L, Weiss K, Myles D, Kroll T. Revealing the atomic and electronic mechanism of human manganese superoxide dismutase product inhibition. RESEARCH SQUARE 2024:rs.3.rs-3880128. [PMID: 38405788 PMCID: PMC10889052 DOI: 10.21203/rs.3.rs-3880128/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Human manganese superoxide dismutase (MnSOD) is a crucial oxidoreductase that maintains the vitality of mitochondria by converting O 2 ∙ - to O 2 and H 2 O 2 with proton-coupled electron transfers (PCETs). Since changes in mitochondrial H 2 O 2 concentrations are capable of stimulating apoptotic signaling pathways, human MnSOD has evolutionarily gained the ability to be highly inhibited by its own product, H 2 O 2 . A separate set of PCETs is thought to regulate product inhibition, though mechanisms of PCETs are typically unknown due to difficulties in detecting the protonation states of specific residues that coincide with the electronic state of the redox center. To shed light on the underlying mechanism, we combined neutron diffraction and X-ray absorption spectroscopy of the product-bound, trivalent, and divalent states to reveal the all-atom structures and electronic configuration of the metal. The data identifies the product-inhibited complex for the first time and a PCET mechanism of inhibition is constructed.
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10
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Azadmanesh J, Slobodnik K, Struble LR, Lutz WE, Coates L, Weiss KL, Myles DAA, Kroll T, Borgstahl GEO. Revealing the atomic and electronic mechanism of human manganese superoxide dismutase product inhibition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.26.577433. [PMID: 38328249 PMCID: PMC10849630 DOI: 10.1101/2024.01.26.577433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Human manganese superoxide dismutase (MnSOD) is a crucial oxidoreductase that maintains the vitality of mitochondria by converting O 2 ●- to O 2 and H 2 O 2 with proton-coupled electron transfers (PCETs). Since changes in mitochondrial H 2 O 2 concentrations are capable of stimulating apoptotic signaling pathways, human MnSOD has evolutionarily gained the ability to be highly inhibited by its own product, H 2 O 2 . A separate set of PCETs is thought to regulate product inhibition, though mechanisms of PCETs are typically unknown due to difficulties in detecting the protonation states of specific residues that coincide with the electronic state of the redox center. To shed light on the underlying mechanism, we combined neutron diffraction and X-ray absorption spectroscopy of the product-bound, trivalent, and divalent states to reveal the all-atom structures and electronic configuration of the metal. The data identifies the product-inhibited complex for the first time and a PCET mechanism of inhibition is constructed.
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11
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Chrysina M, Drosou M, Castillo RG, Reus M, Neese F, Krewald V, Pantazis DA, DeBeer S. Nature of S-States in the Oxygen-Evolving Complex Resolved by High-Energy Resolution Fluorescence Detected X-ray Absorption Spectroscopy. J Am Chem Soc 2023; 145:25579-25594. [PMID: 37970825 PMCID: PMC10690802 DOI: 10.1021/jacs.3c06046] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 10/13/2023] [Accepted: 10/13/2023] [Indexed: 11/19/2023]
Abstract
Photosystem II, the water splitting enzyme of photosynthesis, utilizes the energy of sunlight to drive the four-electron oxidation of water to dioxygen at the oxygen-evolving complex (OEC). The OEC harbors a Mn4CaO5 cluster that cycles through five oxidation states Si (i = 0-4). The S3 state is the last metastable state before the O2 evolution. Its electronic structure and nature of the S2 → S3 transition are key topics of persisting controversy. Most spectroscopic studies suggest that the S3 state consists of four Mn(IV) ions, compared to the Mn(III)Mn(IV)3 of the S2 state. However, recent crystallographic data have received conflicting interpretations, suggesting either metal- or ligand-based oxidation, the latter leading to an oxyl radical or a peroxo moiety in the S3 state. Herein, we utilize high-energy resolution fluorescence detected (HERFD) X-ray absorption spectroscopy to obtain a highly resolved description of the Mn K pre-edge region for all S-states, paying special attention to use chemically unperturbed S3 state samples. In combination with quantum chemical calculations, we achieve assignment of specific spectroscopic features to geometric and electronic structures for all S-states. These data are used to confidently discriminate between the various suggestions concerning the electronic structure and the nature of oxidation events in all observable catalytic intermediates of the OEC. Our results do not support the presence of either peroxo or oxyl in the active configuration of the S3 state. This establishes Mn-centered storage of oxidative equivalents in all observable catalytic transitions and constrains the onset of the O-O bond formation until after the final light-driven oxidation event.
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Affiliation(s)
- Maria Chrysina
- Max-Planck-Institut
für Chemische Energiekonversion, Stiftstr. 34-36, Mülheim
an der Ruhr 45470, Germany
- Institute
of Nanoscience & Nanotechnology, NCSR “Demokritos”, Athens 15310, Greece
| | - Maria Drosou
- Max-Planck-Institut
für Kohlenforschung, Kaiser-Wilhelm-Platz 1, Mülheim an der Ruhr 45470, Germany
| | - Rebeca G. Castillo
- Max-Planck-Institut
für Chemische Energiekonversion, Stiftstr. 34-36, Mülheim
an der Ruhr 45470, Germany
- Laboratory
of Ultrafast Spectroscopy (LSU) and Lausanne Centre for Ultrafast
Science, École Polytechnique Fédérale
de Lausanne (EPFL), Lausanne CH-1015, Switzerland
| | - Michael Reus
- Max-Planck-Institut
für Chemische Energiekonversion, Stiftstr. 34-36, Mülheim
an der Ruhr 45470, Germany
| | - Frank Neese
- Max-Planck-Institut
für Kohlenforschung, Kaiser-Wilhelm-Platz 1, Mülheim an der Ruhr 45470, Germany
| | - Vera Krewald
- Department
of Chemistry, Technical University of Darmstadt, Peter-Grünberg-Str. 4, Darmstadt 64287, Germany
| | - Dimitrios A. Pantazis
- Max-Planck-Institut
für Kohlenforschung, Kaiser-Wilhelm-Platz 1, Mülheim an der Ruhr 45470, Germany
| | - Serena DeBeer
- Max-Planck-Institut
für Chemische Energiekonversion, Stiftstr. 34-36, Mülheim
an der Ruhr 45470, Germany
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12
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Herbert JM, Zhu Y, Alam B, Ojha AK. Time-Dependent Density Functional Theory for X-ray Absorption Spectra: Comparing the Real-Time Approach to Linear Response. J Chem Theory Comput 2023; 19:6745-6760. [PMID: 37708349 DOI: 10.1021/acs.jctc.3c00673] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/16/2023]
Abstract
We simulate X-ray absorption spectra at elemental K-edges using time-dependent density functional theory (TDDFT) in both its conventional linear-response implementation and its explicitly time-dependent or "real-time" formulation. Real-time TDDFT simulations enable broadband spectra calculations without the need to invoke frozen occupied orbitals ("core/valence separation"), but we find that these spectra are often contaminated by transitions to the continuum that originate from lower-energy core and semicore orbitals. This problem becomes acute in triple-ζ basis sets, although it is sometimes sidestepped in double-ζ basis sets. Transitions to the continuum acquire surprisingly large dipole oscillator strengths, leading to spectra that are difficult to interpret. Meaningful spectra can be recovered by means of a filtering technique that decomposes the spectrum into contributions from individual occupied orbitals, and the same procedure can be used to separate L- and K-edge spectra arising from different elements within a given molecule. In contrast, conventional linear-response TDDFT requires core/valence separation but is free of these artifacts. It is also significantly more efficient than the real-time approach, even when hundreds of individual states are needed to reproduce near-edge absorption features and even when Padé approximants are used to reduce the real-time simulations to just 2-4 fs of time propagation. Despite the cost, the real-time approach may be useful to examine the validity of the core/valence separation approximation.
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Affiliation(s)
- John M Herbert
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
- Chemical Physics Graduate Program, The Ohio State University, Columbus, Ohio 43210, United States
| | - Ying Zhu
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
- Chemical Physics Graduate Program, The Ohio State University, Columbus, Ohio 43210, United States
| | - Bushra Alam
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Avik Kumar Ojha
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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13
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Alayoglu P, Chang T, Lorenzo Ocampo MV, Murray LJ, Chen YS, Mankad NP. Metal Site-Specific Electrostatic Field Effects on a Tricopper(I) Cluster Probed by Resonant Diffraction Anomalous Fine Structure (DAFS). Inorg Chem 2023; 62:15267-15276. [PMID: 37651726 DOI: 10.1021/acs.inorgchem.3c02472] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
Studies of multinuclear metal complexes are greatly enhanced by resonant diffraction measurements, which probe X-ray absorption profiles of crystallographically independent metal sites within a cluster. In particular, X-ray diffraction anomalous fine structure (DAFS) analysis provides data that can be interpreted akin to site-specific XANES, allowing for differences in metal K-edge resonances to be deconvoluted even for different metal sites within a homometallic system. Despite the prevalence of Cu-containing clusters in biology and energy science, DAFS has yet to be used to analyze multicopper complexes of any type until now. Here, we report an evaluation of trends using a series of strategically chosen Cu(I) and Cu(II) complexes to determine how energy dependencies of anomalous scattering factors are impacted by coordination geometry, ligand shell, cluster nuclearity, and oxidation state. This calibration data is used to analyze a formally tricopper(I) complex that was found by DAFS to be site-differentiated due to the unsymmetrical influence on different Cu sites of the electrostatic field from a proximal K+ cation.
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Affiliation(s)
- Pinar Alayoglu
- Department of Chemistry, University of Illinois at Chicago, 845 W. Taylor St., Chicago, Illinois 60607, United States
| | - Tieyan Chang
- ChemMatCARS, The University of Chicago, Argonne, Illinois 60439, United States
| | - M Victoria Lorenzo Ocampo
- Center for Catalysis and Florida Center for Heterocyclic Chemistry, Department of Chemistry, University of Florida, Gainesville, Florida 32611 United States
| | - Leslie J Murray
- Center for Catalysis and Florida Center for Heterocyclic Chemistry, Department of Chemistry, University of Florida, Gainesville, Florida 32611 United States
| | - Yu-Sheng Chen
- ChemMatCARS, The University of Chicago, Argonne, Illinois 60439, United States
| | - Neal P Mankad
- Department of Chemistry, University of Illinois at Chicago, 845 W. Taylor St., Chicago, Illinois 60607, United States
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14
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Jana S, Herbert JM. Fractional-Electron and Transition-Potential Methods for Core-to-Valence Excitation Energies Using Density Functional Theory. J Chem Theory Comput 2023; 19:4100-4113. [PMID: 37312236 DOI: 10.1021/acs.jctc.3c00202] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Methods for computing X-ray absorption spectra based on a constrained core hole (possibly containing a fractional electron) are examined. These methods are based on Slater's transition concept and its generalizations, wherein core-to-valence excitation energies are determined using Kohn-Sham orbital energies. Methods examined here avoid promoting electrons beyond the lowest unoccupied molecular orbital, facilitating robust convergence. Variants of these ideas are systematically tested, revealing a best-case accuracy of 0.3-0.4 eV (with respect to experiment) for K-edge transition energies. Absolute errors are much larger for higher-lying near-edge transitions but can be reduced below 1 eV by introducing an empirical shift based on a charge-neutral transition-potential method, in conjunction with functionals such as SCAN, SCAN0, or B3LYP. This procedure affords an entire excitation spectrum from a single fractional-electron calculation, at the cost of ground-state density functional theory and without the need for state-by-state calculations. This shifted transition-potential approach may be especially useful for simulating transient spectroscopies or in complex systems where excited-state Kohn-Sham calculations are challenging.
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Affiliation(s)
- Subrata Jana
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - John M Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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15
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Sension RJ, McClain TP, Lamb RM, Alonso-Mori R, Lima FA, Ardana-Lamas F, Biednov M, Chollet M, Chung T, Deb A, Dewan PA, Gee LB, Huang Ze En J, Jiang Y, Khakhulin D, Li J, Michocki LB, Miller NA, Otte F, Uemura Y, van Driel TB, Penner-Hahn JE. Watching Excited State Dynamics with Optical and X-ray Probes: The Excited State Dynamics of Aquocobalamin and Hydroxocobalamin. J Am Chem Soc 2023. [PMID: 37327324 DOI: 10.1021/jacs.3c04099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Femtosecond time-resolved X-ray absorption (XANES) at the Co K-edge, X-ray emission (XES) in the Co Kβ and valence-to-core regions, and broadband UV-vis transient absorption are combined to probe the femtosecond to picosecond sequential atomic and electronic dynamics following photoexcitation of two vitamin B12 compounds, hydroxocobalamin and aquocobalamin. Polarized XANES difference spectra allow identification of sequential structural evolution involving first the equatorial and then the axial ligands, with the latter showing rapid coherent bond elongation to the outer turning point of the excited state potential followed by recoil to a relaxed excited state structure. Time-resolved XES, especially in the valence-to-core region, along with polarized optical transient absorption suggests that the recoil results in the formation of a metal-centered excited state with a lifetime of 2-5 ps. This combination of methods provides a uniquely powerful tool to probe the electronic and structural dynamics of photoactive transition-metal complexes and will be applicable to a wide variety of systems.
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Affiliation(s)
- Roseanne J Sension
- Department of Chemistry, University of Michigan, 930 N University Avenue, Ann Arbor, Michigan 48109-1055, United States
- Department of Physics, University of Michigan, 450 Church Street, Ann Arbor, Michigan 48109-1040, United States
| | - Taylor P McClain
- Department of Biophysics, University of Michigan, 930 N University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Ryan M Lamb
- Department of Chemistry, University of Michigan, 930 N University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Roberto Alonso-Mori
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Frederico Alves Lima
- Femtosecond X-ray Experiments Group, European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Fernando Ardana-Lamas
- Femtosecond X-ray Experiments Group, European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Mykola Biednov
- Femtosecond X-ray Experiments Group, European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Matthieu Chollet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Taewon Chung
- Department of Chemistry, University of Michigan, 930 N University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Aniruddha Deb
- Department of Chemistry, University of Michigan, 930 N University Avenue, Ann Arbor, Michigan 48109-1055, United States
- Department of Biophysics, University of Michigan, 930 N University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Paul A Dewan
- Department of Biophysics, University of Michigan, 930 N University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Leland B Gee
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Joel Huang Ze En
- Department of Chemistry, University of Michigan, 930 N University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Yifeng Jiang
- Femtosecond X-ray Experiments Group, European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Dmitry Khakhulin
- Femtosecond X-ray Experiments Group, European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Jianhao Li
- Department of Chemistry, University of Michigan, 930 N University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Lindsay B Michocki
- Department of Chemistry, University of Michigan, 930 N University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Nicholas A Miller
- Department of Chemistry, University of Michigan, 930 N University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Florian Otte
- Femtosecond X-ray Experiments Group, European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Yohei Uemura
- Femtosecond X-ray Experiments Group, European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Tim B van Driel
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - James E Penner-Hahn
- Department of Chemistry, University of Michigan, 930 N University Avenue, Ann Arbor, Michigan 48109-1055, United States
- Department of Biophysics, University of Michigan, 930 N University Avenue, Ann Arbor, Michigan 48109-1055, United States
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16
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Cutsail III GE, DeBeer S. Challenges and Opportunities for Applications of Advanced X-ray Spectroscopy in Catalysis Research. ACS Catal 2022. [DOI: 10.1021/acscatal.2c01016] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- George E. Cutsail III
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
- Institute of Inorganic Chemistry, University of Duisburg-Essen, Universitätsstr. 5-7, 45117 Essen, Germany
| | - Serena DeBeer
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
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17
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Epifanovsky E, Gilbert ATB, Feng X, Lee J, Mao Y, Mardirossian N, Pokhilko P, White AF, Coons MP, Dempwolff AL, Gan Z, Hait D, Horn PR, Jacobson LD, Kaliman I, Kussmann J, Lange AW, Lao KU, Levine DS, Liu J, McKenzie SC, Morrison AF, Nanda KD, Plasser F, Rehn DR, Vidal ML, You ZQ, Zhu Y, Alam B, Albrecht BJ, Aldossary A, Alguire E, Andersen JH, Athavale V, Barton D, Begam K, Behn A, Bellonzi N, Bernard YA, Berquist EJ, Burton HGA, Carreras A, Carter-Fenk K, Chakraborty R, Chien AD, Closser KD, Cofer-Shabica V, Dasgupta S, de Wergifosse M, Deng J, Diedenhofen M, Do H, Ehlert S, Fang PT, Fatehi S, Feng Q, Friedhoff T, Gayvert J, Ge Q, Gidofalvi G, Goldey M, Gomes J, González-Espinoza CE, Gulania S, Gunina AO, Hanson-Heine MWD, Harbach PHP, Hauser A, Herbst MF, Hernández Vera M, Hodecker M, Holden ZC, Houck S, Huang X, Hui K, Huynh BC, Ivanov M, Jász Á, Ji H, Jiang H, Kaduk B, Kähler S, Khistyaev K, Kim J, Kis G, Klunzinger P, Koczor-Benda Z, Koh JH, Kosenkov D, Koulias L, Kowalczyk T, Krauter CM, Kue K, Kunitsa A, Kus T, Ladjánszki I, Landau A, Lawler KV, Lefrancois D, Lehtola S, Li RR, Li YP, Liang J, Liebenthal M, Lin HH, Lin YS, Liu F, Liu KY, Loipersberger M, Luenser A, Manjanath A, Manohar P, Mansoor E, Manzer SF, Mao SP, Marenich AV, Markovich T, Mason S, Maurer SA, McLaughlin PF, Menger MFSJ, Mewes JM, Mewes SA, Morgante P, Mullinax JW, Oosterbaan KJ, Paran G, Paul AC, Paul SK, Pavošević F, Pei Z, Prager S, Proynov EI, Rák Á, Ramos-Cordoba E, Rana B, Rask AE, Rettig A, Richard RM, Rob F, Rossomme E, Scheele T, Scheurer M, Schneider M, Sergueev N, Sharada SM, Skomorowski W, Small DW, Stein CJ, Su YC, Sundstrom EJ, Tao Z, Thirman J, Tornai GJ, Tsuchimochi T, Tubman NM, Veccham SP, Vydrov O, Wenzel J, Witte J, Yamada A, Yao K, Yeganeh S, Yost SR, Zech A, Zhang IY, Zhang X, Zhang Y, Zuev D, Aspuru-Guzik A, Bell AT, Besley NA, Bravaya KB, Brooks BR, Casanova D, Chai JD, Coriani S, Cramer CJ, Cserey G, DePrince AE, DiStasio RA, Dreuw A, Dunietz BD, Furlani TR, Goddard WA, Hammes-Schiffer S, Head-Gordon T, Hehre WJ, Hsu CP, Jagau TC, Jung Y, Klamt A, Kong J, Lambrecht DS, Liang W, Mayhall NJ, McCurdy CW, Neaton JB, Ochsenfeld C, Parkhill JA, Peverati R, Rassolov VA, Shao Y, Slipchenko LV, Stauch T, Steele RP, Subotnik JE, Thom AJW, Tkatchenko A, Truhlar DG, Van Voorhis T, Wesolowski TA, Whaley KB, Woodcock HL, Zimmerman PM, Faraji S, Gill PMW, Head-Gordon M, Herbert JM, Krylov AI. Software for the frontiers of quantum chemistry: An overview of developments in the Q-Chem 5 package. J Chem Phys 2021; 155:084801. [PMID: 34470363 PMCID: PMC9984241 DOI: 10.1063/5.0055522] [Citation(s) in RCA: 466] [Impact Index Per Article: 155.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
This article summarizes technical advances contained in the fifth major release of the Q-Chem quantum chemistry program package, covering developments since 2015. A comprehensive library of exchange-correlation functionals, along with a suite of correlated many-body methods, continues to be a hallmark of the Q-Chem software. The many-body methods include novel variants of both coupled-cluster and configuration-interaction approaches along with methods based on the algebraic diagrammatic construction and variational reduced density-matrix methods. Methods highlighted in Q-Chem 5 include a suite of tools for modeling core-level spectroscopy, methods for describing metastable resonances, methods for computing vibronic spectra, the nuclear-electronic orbital method, and several different energy decomposition analysis techniques. High-performance capabilities including multithreaded parallelism and support for calculations on graphics processing units are described. Q-Chem boasts a community of well over 100 active academic developers, and the continuing evolution of the software is supported by an "open teamware" model and an increasingly modular design.
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Affiliation(s)
- Evgeny Epifanovsky
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | | | | | - Joonho Lee
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Yuezhi Mao
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | | | - Pavel Pokhilko
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Alec F. White
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Marc P. Coons
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Adrian L. Dempwolff
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Zhengting Gan
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | - Diptarka Hait
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Paul R. Horn
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Leif D. Jacobson
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | | | - Jörg Kussmann
- Department of Chemistry, Ludwig Maximilian University, Butenandtstr. 7, D-81377 München, Germany
| | - Adrian W. Lange
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Ka Un Lao
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Daniel S. Levine
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | | | - Simon C. McKenzie
- Research School of Chemistry, Australian National University, Canberra, Australia
| | | | - Kaushik D. Nanda
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | | | - Dirk R. Rehn
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Marta L. Vidal
- Department of Chemistry, Technical University of Denmark, Kemitorvet Bldg. 207, DK-2800 Kgs Lyngby, Denmark
| | | | - Ying Zhu
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Bushra Alam
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Benjamin J. Albrecht
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | | | - Ethan Alguire
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Josefine H. Andersen
- Department of Chemistry, Technical University of Denmark, Kemitorvet Bldg. 207, DK-2800 Kgs Lyngby, Denmark
| | - Vishikh Athavale
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Dennis Barton
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg, Luxembourg
| | - Khadiza Begam
- Department of Physics, Kent State University, Kent, Ohio 44242, USA
| | - Andrew Behn
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Nicole Bellonzi
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Yves A. Bernard
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | | | - Hugh G. A. Burton
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Abel Carreras
- Donostia International Physics Center, 20080 Donostia, Euskadi, Spain
| | - Kevin Carter-Fenk
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | | | - Alan D. Chien
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | | | - Vale Cofer-Shabica
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Saswata Dasgupta
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Marc de Wergifosse
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Jia Deng
- Research School of Chemistry, Australian National University, Canberra, Australia
| | | | - Hainam Do
- School of Chemistry, University of Nottingham, Nottingham, United Kingdom
| | - Sebastian Ehlert
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Beringstr. 4, 53115 Bonn, Germany
| | - Po-Tung Fang
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
| | | | - Qingguo Feng
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44240, USA
| | - Triet Friedhoff
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - James Gayvert
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
| | - Qinghui Ge
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Gergely Gidofalvi
- Department of Chemistry and Biochemistry, Gonzaga University, Spokane, Washington 99258, USA
| | - Matthew Goldey
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Joe Gomes
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | | | - Sahil Gulania
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Anastasia O. Gunina
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | | | - Phillip H. P. Harbach
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Andreas Hauser
- Institute of Experimental Physics, Graz University of Technology, Graz, Austria
| | | | - Mario Hernández Vera
- Department of Chemistry, Ludwig Maximilian University, Butenandtstr. 7, D-81377 München, Germany
| | - Manuel Hodecker
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Zachary C. Holden
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Shannon Houck
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, USA
| | - Xunkun Huang
- Department of Chemistry, Xiamen University, Xiamen 361005, China
| | - Kerwin Hui
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
| | - Bang C. Huynh
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Maxim Ivanov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Ádám Jász
- Stream Novation Ltd., Práter utca 50/a, H-1083 Budapest, Hungary
| | - Hyunjun Ji
- Graduate School of Energy, Environment, Water and Sustainability (EEWS), Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Hanjie Jiang
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Benjamin Kaduk
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Sven Kähler
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Kirill Khistyaev
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Jaehoon Kim
- Graduate School of Energy, Environment, Water and Sustainability (EEWS), Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Gergely Kis
- Stream Novation Ltd., Práter utca 50/a, H-1083 Budapest, Hungary
| | | | - Zsuzsanna Koczor-Benda
- Department of Chemistry, Ludwig Maximilian University, Butenandtstr. 7, D-81377 München, Germany
| | - Joong Hoon Koh
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Dimitri Kosenkov
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Laura Koulias
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, USA
| | | | - Caroline M. Krauter
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Karl Kue
- Institute of Chemistry, Academia Sinica, 128, Academia Road Section 2, Nangang District, Taipei 11529, Taiwan
| | - Alexander Kunitsa
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
| | - Thomas Kus
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | | | - Arie Landau
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Keith V. Lawler
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Daniel Lefrancois
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | | | - Run R. Li
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, USA
| | - Yi-Pei Li
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Jiashu Liang
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Marcus Liebenthal
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, USA
| | - Hung-Hsuan Lin
- Institute of Chemistry, Academia Sinica, 128, Academia Road Section 2, Nangang District, Taipei 11529, Taiwan
| | - You-Sheng Lin
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
| | - Fenglai Liu
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | | | | | - Arne Luenser
- Department of Chemistry, Ludwig Maximilian University, Butenandtstr. 7, D-81377 München, Germany
| | - Aaditya Manjanath
- Institute of Chemistry, Academia Sinica, 128, Academia Road Section 2, Nangang District, Taipei 11529, Taiwan
| | - Prashant Manohar
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Erum Mansoor
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Sam F. Manzer
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Shan-Ping Mao
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
| | | | - Thomas Markovich
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Stephen Mason
- School of Chemistry, University of Nottingham, Nottingham, United Kingdom
| | - Simon A. Maurer
- Department of Chemistry, Ludwig Maximilian University, Butenandtstr. 7, D-81377 München, Germany
| | - Peter F. McLaughlin
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | | | - Jan-Michael Mewes
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Stefanie A. Mewes
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Pierpaolo Morgante
- Department of Chemistry, Florida Institute of Technology, Melbourne, Florida 32901, USA
| | - J. Wayne Mullinax
- Department of Chemistry, Florida Institute of Technology, Melbourne, Florida 32901, USA
| | | | | | - Alexander C. Paul
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Suranjan K. Paul
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Fabijan Pavošević
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Zheng Pei
- School of Electrical and Computer Engineering, University of Oklahoma, Norman, Oklahoma 73019, USA
| | - Stefan Prager
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Emil I. Proynov
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | - Ádám Rák
- Stream Novation Ltd., Práter utca 50/a, H-1083 Budapest, Hungary
| | - Eloy Ramos-Cordoba
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Bhaskar Rana
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Alan E. Rask
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Adam Rettig
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Ryan M. Richard
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Fazle Rob
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | - Elliot Rossomme
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Tarek Scheele
- Institute for Physical and Theoretical Chemistry, University of Bremen, Bremen, Germany
| | - Maximilian Scheurer
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Matthias Schneider
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Nickolai Sergueev
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44240, USA
| | - Shaama M. Sharada
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Wojciech Skomorowski
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - David W. Small
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Christopher J. Stein
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Yu-Chuan Su
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
| | - Eric J. Sundstrom
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Zhen Tao
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Jonathan Thirman
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Gábor J. Tornai
- Stream Novation Ltd., Práter utca 50/a, H-1083 Budapest, Hungary
| | - Takashi Tsuchimochi
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Norm M. Tubman
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | | | - Oleg Vydrov
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Jan Wenzel
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Jon Witte
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Atsushi Yamada
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44240, USA
| | - Kun Yao
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Sina Yeganeh
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Shane R. Yost
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Alexander Zech
- Department of Physical Chemistry, University of Geneva, 30, Quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
| | - Igor Ying Zhang
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Xing Zhang
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Yu Zhang
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | - Dmitry Zuev
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Alán Aspuru-Guzik
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Alexis T. Bell
- Department of Chemical Engineering, University of California, Berkeley, California 94720, USA
| | - Nicholas A. Besley
- School of Chemistry, University of Nottingham, Nottingham, United Kingdom
| | - Ksenia B. Bravaya
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
| | - Bernard R. Brooks
- Laboratory of Computational Biophysics, National Institute of Health, Bethesda, Maryland 20892, USA
| | - David Casanova
- Donostia International Physics Center, 20080 Donostia, Euskadi, Spain
| | | | - Sonia Coriani
- Department of Chemistry, Technical University of Denmark, Kemitorvet Bldg. 207, DK-2800 Kgs Lyngby, Denmark
| | | | | | - A. Eugene DePrince
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, USA
| | - Robert A. DiStasio
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Andreas Dreuw
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Barry D. Dunietz
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44240, USA
| | - Thomas R. Furlani
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, New York 14260, USA
| | - William A. Goddard
- Materials and Process Simulation Center, California Institute of Technology, Pasadena, California 91125, USA
| | | | - Teresa Head-Gordon
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | | | | | | | - Yousung Jung
- Graduate School of Energy, Environment, Water and Sustainability (EEWS), Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Andreas Klamt
- COSMOlogic GmbH & Co. KG, Imbacher Weg 46, D-51379 Leverkusen, Germany
| | - Jing Kong
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | - Daniel S. Lambrecht
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | | | | | - C. William McCurdy
- Department of Chemistry, University of California, Davis, California 95616, USA
| | - Jeffrey B. Neaton
- Department of Physics, University of California, Berkeley, California 94720, USA
| | - Christian Ochsenfeld
- Department of Chemistry, Ludwig Maximilian University, Butenandtstr. 7, D-81377 München, Germany
| | - John A. Parkhill
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Roberto Peverati
- Department of Chemistry, Florida Institute of Technology, Melbourne, Florida 32901, USA
| | - Vitaly A. Rassolov
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, USA
| | | | | | | | - Ryan P. Steele
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City, Utah 84112, USA
| | - Joseph E. Subotnik
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Alex J. W. Thom
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Alexandre Tkatchenko
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg, Luxembourg
| | - Donald G. Truhlar
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Troy Van Voorhis
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Tomasz A. Wesolowski
- Department of Physical Chemistry, University of Geneva, 30, Quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
| | - K. Birgitta Whaley
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - H. Lee Woodcock
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, USA
| | - Paul M. Zimmerman
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Shirin Faraji
- Zernike Institute for Advanced Materials, University of Groningen, 9774AG Groningen, The Netherlands
| | | | - Martin Head-Gordon
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - John M. Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Anna I. Krylov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA,Author to whom correspondence should be addressed:
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18
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Kroll T, Baker ML, Wilson SA, Lundberg M, Juhin A, Arrio MA, Yan JJ, Gee LB, Braun A, Weng TC, Sokaras D, Hedman B, Hodgson KO, Solomon EI. Effect of 3d/4p Mixing on 1s2p Resonant Inelastic X-ray Scattering: Electronic Structure of Oxo-Bridged Iron Dimers. J Am Chem Soc 2021; 143:4569-4584. [PMID: 33730507 PMCID: PMC8018712 DOI: 10.1021/jacs.0c11193] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
1s2p resonant inelastic X-ray scattering (1s2p RIXS) has proven successful in the determination of the differential orbital covalency (DOC, the amount of metal vs ligand character in each d molecular orbital) of highly covalent centrosymmetric iron environments including heme models and enzymes. However, many reactive intermediates have noncentrosymmetric environments, e.g., the presence of strong metal-oxo bonds, which results in the mixing of metal 4p character into the 3d orbitals. This leads to significant intensity enhancement in the metal K-pre-edge and as shown here, the associated 1s2p RIXS features, which impact their insight into electronic structure. Binuclear oxo bridged high spin Fe(III) complexes are used to determine the effects of 4p mixing on 1s2p RIXS spectra. In addition to developing the analysis of 4p mixing on K-edge XAS and 1s2p RIXS data, this study explains the selective nature of the 4p mixing that also enhances the analysis of L-edge XAS intensity in terms of DOC. These 1s2p RIXS biferric model studies enable new structural insight from related data on peroxo bridged biferric enzyme intermediates. The dimeric nature of the oxo bridged Fe(III) complexes further results in ligand-to-ligand interactions between the Fe(III) sites and angle dependent features just above the pre-edge that reflect the superexchange pathway of the oxo bridge. Finally, we present a methodology that enables DOC to be obtained when L-edge XAS is inaccessible and only 1s2p RIXS experiments can be performed as in many metalloenzyme intermediates in solution.
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Affiliation(s)
- Thomas Kroll
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
| | - Michael L Baker
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Department of Chemistry, The University of Manchester, Manchester M13 9PL, United Kingdom
| | - Samuel A Wilson
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Marcus Lundberg
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Department of Chemistry - Ångström Laboratory, Uppsala University, SE-751 20 Uppsala, Sweden
| | - Amélie Juhin
- CNRS, Sorbonne Université, UMR7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC) Univ Paris 06, Muséum National d'Histoire Naturelle, IRD UMR206, 4 Place Jussieu, F-75005 Paris, France
| | - Marie-Anne Arrio
- CNRS, Sorbonne Université, UMR7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC) Univ Paris 06, Muséum National d'Histoire Naturelle, IRD UMR206, 4 Place Jussieu, F-75005 Paris, France
| | - James J Yan
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Leland B Gee
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Augustin Braun
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Tsu-Chien Weng
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
| | - Dimosthenis Sokaras
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
| | - Britt Hedman
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
| | - Keith O Hodgson
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
| | - Edward I Solomon
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
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19
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Arnett CH, Bogacz I, Chatterjee R, Yano J, Oyala PH, Agapie T. Mixed-Valent Diiron μ-Carbyne, μ-Hydride Complexes: Implications for Nitrogenase. J Am Chem Soc 2020; 142:18795-18813. [PMID: 32976708 DOI: 10.1021/jacs.0c05920] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Binding of N2 by the FeMo-cofactor of nitrogenase is believed to occur after transfer of 4 e- and 4 H+ equivalents to the active site. Although pulse EPR studies indicate the presence of two Fe-(μ-H)-Fe moieties, the structural and electronic features of this mixed valent intermediate remain poorly understood. Toward an improved understanding of this bioorganometallic cluster, we report herein that diiron μ-carbyne complex (P6ArC)Fe2(μ-H) can be oxidized and reduced, allowing for the first time spectral characterization of two EPR-active Fe(μ-C)(μ-H)Fe model complexes linked by a 2 e- transfer which bear some resemblance to a pair of En and En+2 states of nitrogenase. Both species populate S = 1/2 states at low temperatures, and the influence of valence (de)localization on the spectroscopic signature of the μ-hydride ligand was evaluated by pulse EPR studies. Compared to analogous data for the {Fe2(μ-H)}2 state of FeMoco (E4(4H)), the data and analysis presented herein suggest that the hydride ligands in E4(4H) bridge isovalent (most probably FeIII) metal centers. Although electron transfer involves metal-localized orbitals, investigations of [(P6ArC)Fe2(μ-H)]+1 and [(P6ArC)Fe2(μ-H)]-1 by pulse EPR revealed that redox chemistry induces significant changes in Fe-C covalency (-50% upon 2 e- reduction), a conclusion further supported by X-ray absorption spectroscopy, 57Fe Mössbauer studies, and DFT calculations. Combined, our studies demonstrate that changes in covalency buffer against the accumulation of excess charge density on the metals by partially redistributing it to the bridging carbon, thereby facilitating multielectron transformations.
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Affiliation(s)
- Charles H Arnett
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Isabel Bogacz
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Ruchira Chatterjee
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Paul H Oyala
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Theodor Agapie
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
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20
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DiMucci IM, MacMillan SN, Walroth RC, Lancaster KM. Scrutinizing "Ligand Bands" via Polarized Single-Crystal X-ray Absorption Spectra of Copper(I) and Copper(II) Bis-2,2'-bipyridine Species. Inorg Chem 2020; 59:13416-13426. [PMID: 32871080 DOI: 10.1021/acs.inorgchem.0c01800] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
High-energy resolution fluorescence-detected Cu K-edge X-ray absorption spectroscopy (XAS) and single-crystal polarized XAS data are presented toward refining the assignments of bands assigned as excitations from Cu 1s to ligand-localized molecular orbitals. These have been previously dubbed "XAS-metal-ligand charge transfer" (XAS-MLCT) bands. Data are presented for a series of [Cu(xbpy)2]n+ complexes (xbpy = 2,2'-bipyridine (1n+), 4,4'-bisamino-2,2'-bipyridine (2n+), and 4,4'-dimethoxy-2,2'-bipyridine (3n+); n = 1 and 2). Dipolar dependencies of these "XAS-MLCT" bands in both Cu1+ and Cu2+ species lead to reassignment of these features as owing their intensities primarily to Cu 1s → Cu 4p excitations. The transition densities are Cu-localized, highlighting that XAS-MLCT features in Cu XAS spectra are not "charge transfer" transitions but rather quasi-atomic transitions. Although scrutiny of the acceptor orbitals supports assignment as Cu 1s → ligand π* transitions, it ultimately appears that while the ligand orbital energetics govern the positions of these bands the intensity is conferred through a small degree of metal 4p mixing into otherwise ligand-dominated acceptor molecular orbitals.
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Affiliation(s)
- Ida M DiMucci
- Cornell Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853, United States
| | - Samantha N MacMillan
- Cornell Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853, United States
| | - Richard C Walroth
- Stanford Synchrotron Radiation Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Kyle M Lancaster
- Cornell Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853, United States
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21
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Neese F, Wennmohs F, Becker U, Riplinger C. The ORCA quantum chemistry program package. J Chem Phys 2020; 152:224108. [DOI: 10.1063/5.0004608] [Citation(s) in RCA: 697] [Impact Index Per Article: 174.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Frank Neese
- Max Planck Institut für Kohlenforschung, Kaiser-Wilhelm Platz 1, D-45470 Mülheim an der Ruhr, Germany
- FAccTs GmbH, Rolandstr. 67, 50677 Köln, Germany
| | - Frank Wennmohs
- Max Planck Institut für Kohlenforschung, Kaiser-Wilhelm Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Ute Becker
- Max Planck Institut für Kohlenforschung, Kaiser-Wilhelm Platz 1, D-45470 Mülheim an der Ruhr, Germany
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22
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Rupp S, Plasser F, Krewald V. Multi‐Tier Electronic Structure Analysis of Sita's Mo and W Complexes Capable of Thermal or Photochemical N
2
Splitting. Eur J Inorg Chem 2020. [DOI: 10.1002/ejic.201901304] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Severine Rupp
- Fachbereich Chemie Theoretische Chemie Technische Universität Darmstadt Alarich‐Weiss‐Str. 4 64287 Darmstadt Germany
| | - Felix Plasser
- Department of Chemistry Loughborough University Loughborough LE11 3TU United Kingdom
| | - Vera Krewald
- Fachbereich Chemie Theoretische Chemie Technische Universität Darmstadt Alarich‐Weiss‐Str. 4 64287 Darmstadt Germany
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23
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Chen WT, Hsu CW, Lee JF, Pao CW, Hsu IJ. Theoretical Analysis of Fe K-Edge XANES on Iron Pentacarbonyl. ACS OMEGA 2020; 5:4991-5000. [PMID: 32201785 PMCID: PMC7081404 DOI: 10.1021/acsomega.9b03887] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 02/21/2020] [Indexed: 05/21/2023]
Abstract
Iron pentacarbonyl (Fe(CO)5) is a versatile material that is utilized as an inhibitor of flame, shows soot suppressibility, and is used as a precursor for focused electron-beam-induced deposition (FEBID). X-ray absorption near-edge structure (XANES) of the K edge, which is a powerful technique for monitoring the oxidation states and coordination environment of metal sites, can be used to gain insight into Fe(CO)5-related reaction mechanisms in in situ experiments. We use a finite difference method (FDM) and molecular-orbital-based time-dependent density functional theory (TDDFT) calculations to clarify the Fe K-edge XANES features of Fe(CO)5. The two pre-edge peaks P1 and P2 are mainly the Fe(1s) → Fe-C(σ*) and Fe(1s) → Fe-C(π*) transitions, respectively. When the geometry transformed from D 3h to C 4v symmetry, a ∼30% decrease of the pre-edge P2 intensity was observed in the simulated spectra. This implies that the π bonding of Fe and CO is sensitive to changes in geometry. The following rising edge and white line regions are assigned to the Fe(1s) → Fe(4p)(mixing C(2p)) transitions. Our results may provide useful information to interpret XANES spectra variations of in situ reactions of metal-CO or similar compounds with π acceptor ligandlike metal-CN complexes.
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Affiliation(s)
- Wei-Ting Chen
- Department
of Molecular Science and Engineering, National
Taipei University of Technology, Taipei 10608, Taiwan
| | - Che-Wei Hsu
- Department
of Molecular Science and Engineering, National
Taipei University of Technology, Taipei 10608, Taiwan
| | - Jyh-Fu Lee
- National
Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
| | - Chih-Wen Pao
- National
Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
| | - I-Jui Hsu
- Department
of Molecular Science and Engineering, National
Taipei University of Technology, Taipei 10608, Taiwan
- Research
and Development Center for Smart Textile Technology, National Taipei University of Technology, Taipei 10608, Taiwan
- E-mail: .
Tel: +886-2-27712171#2420
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24
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Chala SA, Tsai MC, Su WN, Ibrahim KB, Thirumalraj B, Chan TS, Lee JF, Dai H, Hwang BJ. Hierarchical 3D Architectured Ag Nanowires Shelled with NiMn-Layered Double Hydroxide as an Efficient Bifunctional Oxygen Electrocatalyst. ACS NANO 2020; 14:1770-1782. [PMID: 32003975 DOI: 10.1021/acsnano.9b07487] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Herein, we report hierarchical 3D NiMn-layered double hydroxide (NiMn-LDHs) shells grown on conductive silver nanowire (Ag NWs) cores as efficient, low-cost, and durable oxygen reduction reaction (ORR)/oxygen evolution reaction (OER) bifunctional electrocatalysts for metal-air batteries. The hierarchical 3D architectured Ag NW@NiMn-LDH catalysts exhibit superb OER/ORR activities in alkaline conditions. The outstanding bifunctional activities of Ag NW@NiMn-LDHs are essentially attributed to increasing both site activity and site populations. The synergistic contributions from the hierarchical 3D open-pore structure of the LDH shells, improved electrical conductivity, and small thickness of the LDHs shells are associated with more accessible site populations. Moreover, the charge transfer between Ag cores and metals of LDH shells and the formation of defective and distorted sites (less coordinated Ni and Mn sites) strongly enhance the site activity. Thus, Ag NW@NiMn-LDH hybrids exhibit a 0.75 V overvoltage difference between ORR and OER with excellent durability for 30 h, demonstrating the distinguished bifunctional electrocatalyst reported to date. Interestingly, the homemade rechargeable Zn-air battery using the hybrid Ag NW@NiMn-LDHs (1:2) catalyst as the air electrode exhibits a charge-discharge voltage gap of ∼0.77 V at 10 mA cm-2 and shows excellent cycling stability. Thus, the concept of the hierarchical 3D architecture of Ag NW@NiMn-LDHs considerably advances the practice of LDHs toward metal-air batteries and oxygen electrocatalysts.
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Affiliation(s)
- Soressa Abera Chala
- NanoElectrochemistry Laboratory, Department of Chemical Engineering , National Taiwan University of Science and Technology , Taipei 106 , Taiwan
- Sustainable Energy Development Center , National Taiwan University of Science and Technology , Taipei 106 , Taiwan
| | - Meng-Che Tsai
- NanoElectrochemistry Laboratory, Graduate Institute of Applied Science and Technology , National Taiwan University of Science and Technology , Taipei 106 , Taiwan
- Sustainable Energy Development Center , National Taiwan University of Science and Technology , Taipei 106 , Taiwan
| | - Wei-Nien Su
- NanoElectrochemistry Laboratory, Graduate Institute of Applied Science and Technology , National Taiwan University of Science and Technology , Taipei 106 , Taiwan
- Sustainable Energy Development Center , National Taiwan University of Science and Technology , Taipei 106 , Taiwan
| | - Kassa Belay Ibrahim
- NanoElectrochemistry Laboratory, Graduate Institute of Applied Science and Technology , National Taiwan University of Science and Technology , Taipei 106 , Taiwan
| | - Balamurugan Thirumalraj
- NanoElectrochemistry Laboratory, Department of Chemical Engineering , National Taiwan University of Science and Technology , Taipei 106 , Taiwan
- Sustainable Energy Development Center , National Taiwan University of Science and Technology , Taipei 106 , Taiwan
| | - Ting-Shan Chan
- National Synchrotron Radiation Research Center , Hsin-Chu 30076 , Taiwan
| | - Jyh-Fu Lee
- National Synchrotron Radiation Research Center , Hsin-Chu 30076 , Taiwan
| | - Hongjie Dai
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | - Bing-Joe Hwang
- NanoElectrochemistry Laboratory, Department of Chemical Engineering , National Taiwan University of Science and Technology , Taipei 106 , Taiwan
- NanoElectrochemistry Laboratory, Graduate Institute of Applied Science and Technology , National Taiwan University of Science and Technology , Taipei 106 , Taiwan
- Sustainable Energy Development Center , National Taiwan University of Science and Technology , Taipei 106 , Taiwan
- National Synchrotron Radiation Research Center , Hsin-Chu 30076 , Taiwan
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25
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Yi J, Nakatani N, Nomura K, Hada M. Time-dependent DFT study of the K-edge spectra of vanadium and titanium complexes: effects of chloride ligands on pre-edge features. Phys Chem Chem Phys 2020; 22:674-682. [DOI: 10.1039/c9cp05891e] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
X-ray absorption near edge structures (XANES) of vanadium and titanium complexes were investigated with time-dependent density functional theory (TDDFT).
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Affiliation(s)
- Jun Yi
- Department of Chemistry
- Faculty and Graduate School of Science
- Tokyo Metropolitan University
- Hachioji
- Japan
| | - Naoki Nakatani
- Department of Chemistry
- Faculty and Graduate School of Science
- Tokyo Metropolitan University
- Hachioji
- Japan
| | - Kotohiro Nomura
- Department of Chemistry
- Faculty and Graduate School of Science
- Tokyo Metropolitan University
- Hachioji
- Japan
| | - Masahiko Hada
- Department of Chemistry
- Faculty and Graduate School of Science
- Tokyo Metropolitan University
- Hachioji
- Japan
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26
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Aðalsteinsson HM, Lima FA, Galuppo C, Abbehausen C. Evaluation of cobalt complexes with tripod ligands for zinc finger targeting. Dalton Trans 2020; 49:16143-16153. [DOI: 10.1039/d0dt00067a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We report the ability of CoII and CoIII complexes of tri(2-pyridylmethyl)amine and N,N-di(2-pyridylmethyl)glycinate to disrupt zinc fingers.
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Affiliation(s)
| | - Frederico A. Lima
- European X-Ray Free-Electron Laser Facility GmbH
- 22869 Schenefeld
- Germany
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27
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Bergmann TG, Welzel MO, Jacob CR. Towards theoretical spectroscopy with error bars: systematic quantification of the structural sensitivity of calculated spectra. Chem Sci 2019; 11:1862-1877. [PMID: 34123280 PMCID: PMC8148348 DOI: 10.1039/c9sc05103a] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Molecular spectra calculated with quantum-chemical methods are subject to a number of uncertainties (e.g., errors introduced by the computational methodology) that hamper the direct comparison of experiment and computation. Judging these uncertainties is crucial for drawing reliable conclusions from the interplay of experimental and theoretical spectroscopy, but largely relies on subjective judgment. Here, we explore the application of methods from uncertainty quantification to theoretical spectroscopy, with the ultimate goal of providing systematic error bars for calculated spectra. As a first target, we consider distortions of the underlying molecular structure as one important source of uncertainty. We show that by performing a principal component analysis, the most influential collective distortions can be identified, which allows for the construction of surrogate models that are amenable to a statistical analysis of the propagation of uncertainties in the molecular structure to uncertainties in the calculated spectrum. This is applied to the calculation of X-ray emission spectra of iron carbonyl complexes, of the electronic excitation spectrum of a coumarin dye, and of the infrared spectrum of alanine. We show that with our approach it becomes possible to obtain error bars for calculated spectra that account for uncertainties in the molecular structure. This is an important first step towards systematically quantifying other relevant sources of uncertainty in theoretical spectroscopy. Uncertainty quantification is applied in theoretical spectroscopy to obtain error bars accounting for the structural sensitivity of calculated spectra.![]()
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Affiliation(s)
- Tobias G Bergmann
- Technische Universität Braunschweig, Institute of Physical and Theoretical Chemistry Gaußstraße 17 38106 Braunschweig Germany
| | - Michael O Welzel
- Technische Universität Braunschweig, Institute of Physical and Theoretical Chemistry Gaußstraße 17 38106 Braunschweig Germany
| | - Christoph R Jacob
- Technische Universität Braunschweig, Institute of Physical and Theoretical Chemistry Gaußstraße 17 38106 Braunschweig Germany
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28
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Paradisi A, Johnston EM, Tovborg M, Nicoll CR, Ciano L, Dowle A, McMaster J, Hancock Y, Davies GJ, Walton PH. Formation of a Copper(II)-Tyrosyl Complex at the Active Site of Lytic Polysaccharide Monooxygenases Following Oxidation by H 2O 2. J Am Chem Soc 2019; 141:18585-18599. [PMID: 31675221 PMCID: PMC7007232 DOI: 10.1021/jacs.9b09833] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Indexed: 01/14/2023]
Abstract
Hydrogen peroxide is a cosubstrate for the oxidative cleavage of saccharidic substrates by copper-containing lytic polysaccharide monooxygenases (LPMOs). The rate of reaction of LPMOs with hydrogen peroxide is high, but it is accompanied by rapid inactivation of the enzymes, presumably through protein oxidation. Herein, we use UV-vis, CD, XAS, EPR, VT/VH-MCD, and resonance Raman spectroscopies, augmented with mass spectrometry and DFT calculations, to show that the product of reaction of an AA9 LPMO with H2O2 at higher pHs is a singlet Cu(II)-tyrosyl radical species, which is inactive for the oxidation of saccharidic substrates. The Cu(II)-tyrosyl radical center entails the formation of significant Cu(II)-(●OTyr) overlap, which in turn requires that the plane of the d(x2-y2) SOMO of the Cu(II) is orientated toward the tyrosyl radical. We propose from the Marcus cross-relation that the active site tyrosine is part of a "hole-hopping" charge-transfer mechanism formed of a pathway of conserved tyrosine and tryptophan residues, which can protect the protein active site from inactivation during uncoupled turnover.
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Affiliation(s)
- Alessandro Paradisi
- Department
of Chemistry, Centre of Excellence of Mass Spectrometry, Technology
Facility, and Department of Physics, University of York, Heslington, York YO10
5DD, United Kingdom
| | - Esther M. Johnston
- Department
of Chemistry, Centre of Excellence of Mass Spectrometry, Technology
Facility, and Department of Physics, University of York, Heslington, York YO10
5DD, United Kingdom
| | | | - Callum R. Nicoll
- Department
of Chemistry, Centre of Excellence of Mass Spectrometry, Technology
Facility, and Department of Physics, University of York, Heslington, York YO10
5DD, United Kingdom
| | - Luisa Ciano
- Department
of Chemistry, Centre of Excellence of Mass Spectrometry, Technology
Facility, and Department of Physics, University of York, Heslington, York YO10
5DD, United Kingdom
| | - Adam Dowle
- Department
of Chemistry, Centre of Excellence of Mass Spectrometry, Technology
Facility, and Department of Physics, University of York, Heslington, York YO10
5DD, United Kingdom
| | - Jonathan McMaster
- School
of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Y. Hancock
- Department
of Chemistry, Centre of Excellence of Mass Spectrometry, Technology
Facility, and Department of Physics, University of York, Heslington, York YO10
5DD, United Kingdom
- York
Cross-Disciplinary Centre for Systems Analysis, University of York, Heslington,
York YO10 5GE, United Kingdom
| | - Gideon J. Davies
- Department
of Chemistry, Centre of Excellence of Mass Spectrometry, Technology
Facility, and Department of Physics, University of York, Heslington, York YO10
5DD, United Kingdom
| | - Paul H. Walton
- Department
of Chemistry, Centre of Excellence of Mass Spectrometry, Technology
Facility, and Department of Physics, University of York, Heslington, York YO10
5DD, United Kingdom
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29
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High-resolution iron X-ray absorption spectroscopic and computational studies of non-heme diiron peroxo intermediates. J Inorg Biochem 2019; 203:110877. [PMID: 31710865 DOI: 10.1016/j.jinorgbio.2019.110877] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 09/05/2019] [Accepted: 10/01/2019] [Indexed: 11/20/2022]
Abstract
Ferritin-like carboxylate-bridged non-heme diiron enzymes activate O2 for a variety of difficult reactions throughout nature. These reactions often begin by abstraction of hydrogen from strong CH bonds. The enzymes activate O2 at their diferrous cofactors to form canonical diferric peroxo intermediates, with a range of possible coordination modes. Herein, we explore the ability of high-energy resolution fluorescence detected X-ray absorption spectroscopy (HERFD XAS) to provide insight into the nature of peroxo level intermediates in non-heme diiron proteins. Freeze quenched (FQ) peroxo intermediates from p-aminobenzoate N-oxygenase (AurF), aldehyde-deformylating oxygenase (ADO), and the β subunit of class Ia ribonucleotide reductase from Escherichia coli (Ecβ) are investigated. All three intermediates are proposed to adopt different peroxo binding modes, and each exhibit different Fe Kα HERFD XAS pre-edge features and intensities. As these FQ-trapped samples consist of multiple species, deconvolution of HERFD XAS spectra based on speciation, as determined by Mössbauer spectroscopy, is also necessitated - yielding 'pure' diferric peroxo HERFD XAS spectra from dilute protein samples. Finally, the impact of a given peroxo coordination mode on the HERFD XAS pre-edge energy and intensity is evaluated through time-dependent density functional theory (TDDFT) calculations of the XAS spectra on a series of hypothetical model complexes, which span a full range of possible peroxo coordination modes to a diferric core. The utility of HERFD XAS for future studies of enzymatic intermediates is discussed.
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30
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McGale J, Cutsail GE, Joseph C, Rose MJ, DeBeer S. Spectroscopic X-ray and Mössbauer Characterization of M 6 and M 5 Iron(Molybdenum)-Carbonyl Carbide Clusters: High Carbide-Iron Covalency Enhances Local Iron Site Electron Density Despite Cluster Oxidation. Inorg Chem 2019; 58:12918-12932. [PMID: 31553598 PMCID: PMC6784818 DOI: 10.1021/acs.inorgchem.9b01870] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The present study
employs a suite of spectroscopic techniques to
evaluate the electronic and bonding characteristics of the interstitial
carbide in a set of iron-carbonyl-carbide clusters, one of which is
substituted with a molybdenum atom. The M6C and M5C clusters are the dianions (Et4N)2[Fe6(μ6-C)(μ2-CO)2(CO)14] (1),
[K(benzo-18-crown-6)]2[Fe5(μ5-C)(μ2-CO)1(CO)13] (2), and [K(benzo-18-crown-6)]2[Fe5Mo(μ6-C)(μ2-CO)2(CO)15] (3). Because 1 and 2 have the same overall cluster charge (2−) but different numbers
of iron sites (1: 6 sites → 2: 5
sites), the metal atoms of 2 are formally oxidized compared
to those in 1. Despite this, Mössbauer studies
indicate that the iron sites in 2 possess significantly
greater electron density (lower spectroscopic oxidation state)
compared with those in 1. Iron K-edge X-ray absorption
and valence-to-core X-ray emission spectroscopy measurements, paired
with density functional theory spectral calculations, revealed the
presence of significant metal-to-metal and carbide 2p-based character
in the filled valence and low-lying unfilled electronic manifolds.
In all of the above experiments, the presence of the molybdenum atom
in 3 (Fe5Mo) results in somewhat unremarkable
spectroscopic properties that are essentially a “hybrid”
of 1 (Fe6) and 2 (Fe5). The overall electronic portrait that emerges illustrates that
the central inorganic carbide ligand is essential for distributing
charge and maximizing electronic communication throughout the cluster.
It is evident that the carbide coordination environment is quite flexible
and adaptive: it can drastically modify the covalency of individual
Fe–C bonds based on local structural changes and redox manipulation
of the clusters. In light of these findings, our data and calculations
suggest a potential role for the central carbon atom in FeMoco, which
likely performs a similar function in order to maintain cluster integrity
through multiple redox and ligand binding events. An in-depth
spectroscopic investigation of a series of iron-carbonyl
carbide complexes: [Fe6C] (1), [Fe5C] (2), and [Fe5CMo] (3) is
described. Using Mössbauer spectroscopy, valence-to-core X-ray
emission spectroscopy, and high-energy-resolution fluorescence-detected
X-ray absorption spectroscopy, we detail the ability of the conserved
central carbon atom in maintaining cluster stability despite dramatic
geometric rearrangements. Our study suggests a potential role for
the interstitial carbide in FeMoco as an electronic modulator, allowing
for charge and ligand accumulation under turnover conditions.
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Affiliation(s)
- Jeremy McGale
- Department of Inorganic Spectroscopy , Max Planck Institute for Chemical Energy Conversion , Stiftstrasse 34-36 , D-45470 , Mülheim an der Ruhr , Germany
| | - George E Cutsail
- Department of Inorganic Spectroscopy , Max Planck Institute for Chemical Energy Conversion , Stiftstrasse 34-36 , D-45470 , Mülheim an der Ruhr , Germany
| | - Chris Joseph
- Department of Chemistry , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - Michael J Rose
- Department of Chemistry , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - Serena DeBeer
- Department of Inorganic Spectroscopy , Max Planck Institute for Chemical Energy Conversion , Stiftstrasse 34-36 , D-45470 , Mülheim an der Ruhr , Germany
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31
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Krewald V, Neese F, Pantazis DA. Implications of structural heterogeneity for the electronic structure of the final oxygen-evolving intermediate in photosystem II. J Inorg Biochem 2019; 199:110797. [PMID: 31404888 DOI: 10.1016/j.jinorgbio.2019.110797] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 07/18/2019] [Accepted: 08/01/2019] [Indexed: 10/26/2022]
Abstract
Heterogeneity in intermediate catalytic states of the oxygen-evolving complex (OEC) of Photosystem II is known from a wide range of experimental and theoretical data, but its potential implications for the mechanism of water oxidation remain unexplored. We delineate the consequences of structural heterogeneity for the final step of the catalytic cycle by tracing the evolution of three spectroscopically relevant and structurally distinct components of the last metastable S3 state to the transient O2-evolving S4 state of the OEC. Using quantum chemical calculations, we show that each S3 isomer leads to a different electronic structure formulation for the active S4 state. Crucially, in addition to previously hypothesized Mn(IV)-oxyl species, we establish for the first time, how a genuine Mn(V)-oxo can be obtained in the catalytically active S4 state: this takes the form of a five-coordinate and locally high-spin (SMn = 1) Mn(V) site. This formulation for the S4 state evolves naturally from a preceding S3-state structural intermediate that contains a quasi-trigonal-bipyramidal Mn(IV) ion. The results strongly suggest that water binding in the S3 state is not prerequisite for reaching the oxygen-evolving S4 state of the complex, supporting the notion that both substrates are preloaded at the beginning of the catalytic cycle. This scenario allows true four-electron metal-centered hole accumulation to precede OO bond formation and hence the latter can proceed via a genuine even-electron mechanism. This can occur as intramolecular nucleophilic coupling of two oxo units synchronously with the binding of a water substrate for the next catalytic cycle.
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Affiliation(s)
- Vera Krewald
- Theoretische Chemie, Fachbereich Chemie, Technische Universität Darmstadt, Alarich-Weiss-Str. 4, 64287 Darmstadt, Germany
| | - Frank Neese
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Dimitrios A Pantazis
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany.
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32
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Matson BD, McLoughlin EA, Armstrong KC, Waymouth RM, Sarangi R. Effect of Redox Active Ligands on the Electrochemical Properties of Manganese Tricarbonyl Complexes. Inorg Chem 2019; 58:7453-7465. [PMID: 31117629 DOI: 10.1021/acs.inorgchem.9b00652] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The synthesis, structural characterization, and electrochemical behavior of the neutral Mn(azpy)(CO)3(Br) 4 (azpy = 2-phenylazopyridine) complex is reported and compared with its structural analogue Mn(bipy)(CO)3(Br) 1 (bipy = 2,2'-bipyridine). 4 exhibits reversible two-electron reduction at a mild potential (-0.93 V vs Fc+/0 in acetonitrile) in contrast to 1, which exhibits two sequential one-electron reductions at -1.68 V and -1.89 V vs Fc+/0 in acetonitrile. The key electronic structure differences between 1 and 4 that lead to disparate electrochemical properties are investigated using a combination of Mn-K-edge X-ray absorption spectroscopy (XAS), Mn-Kβ X-ray emission spectroscopy (XES), and density functional theory (DFT) on 1, 4, their debrominated analogues, [Mn(L)(CO)3(CH3CN)][CF3SO3] (L = bipy 2, azpy 5), and two-electron reduced counterparts [Mn(bipy)(CO)3][K(18-crown-6)] 3 and [Mn(azpy)(CO)3][Cp2Co] 6. The results reveal differences in the distribution of electrons about the CO and bidentate ligands (bipy and azpy), particularly upon formation of the highly reduced, formally Mn(-1) species. The data show that the degree of ligand noninnocence and resulting redox-activity in Mn(L)(CO)3 type complexes impacts not only the reducing power of such systems, but the speciation of the reduced complexes via perturbation of the monomer-dimer equilibrium in the singly reduced Mn(0) state. This study highlights the role of redox-active ligands in tuning the reactivity of metal centers involved in electrocatalytic transformations.
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Affiliation(s)
- Benjamin D Matson
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States.,Stanford Synchrotron Radiation Lightsource , SLAC National Accelerator Laboratory , Menlo Park , California , United States
| | - Elizabeth A McLoughlin
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | - Keith C Armstrong
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | - Robert M Waymouth
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | - Ritimukta Sarangi
- Stanford Synchrotron Radiation Lightsource , SLAC National Accelerator Laboratory , Menlo Park , California , United States
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33
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Lim H, Thomas KE, Hedman B, Hodgson KO, Ghosh A, Solomon EI. X-ray Absorption Spectroscopy as a Probe of Ligand Noninnocence in Metallocorroles: The Case of Copper Corroles. Inorg Chem 2019; 58:6722-6730. [PMID: 31046257 PMCID: PMC6644708 DOI: 10.1021/acs.inorgchem.9b00128] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The question of ligand noninnocence in Cu corroles has long been a topic of discussion. Presented herein is a Cu K-edge X-ray absorption spectroscopy (XAS) study, which provides a direct probe of the metal oxidation state, of three Cu corroles, Cu[TPC], Cu[Br8TPC], and Cu[(CF3)8TPC] (TPC = meso-triphenylcorrole), and the analogous Cu(II) porphyrins, Cu[TPP], Cu[Br8TPP], and Cu[(CF3)8TPP] (TPP = meso-tetraphenylporphyrin). The Cu K rising-edges of the Cu corroles were found to be about 0-1 eV upshifted relative to the analogous porphyrins, which is substantially lower than the 1-2 eV shifts typically exhibited by authentic Cu(II)/Cu(III) model complex pairs. In an unusual twist, the Cu K pre-edge regions of both the Cu corroles and the Cu porphyrins exhibit two peaks split by 0.8-1.3 eV. Based on time-dependent density functional theory calculations, the lower- and higher-energy peaks were assigned to a Cu 1s → 3d x2- y2 transition and a Cu 1s → corrole/porphyrin π* transition, respectively. From the Cu(II) porphyrins to the corresponding Cu corroles, the energy of the Cu 1s → 3d x2- y2 transition peak was found to upshift by 0.6-0.8 eV. This shift is approximately half that observed between Cu(II) to Cu(III) states for well-defined complexes. The Cu K-edge XAS spectra thus show that although the metal sites in the Cu corroles are more oxidized relative to those in their Cu(II) porphyrin analogues, they are not oxidized to the Cu(III) level, consistent with the notion of a noninnocent corrole. The relative importance of σ-donation versus corrole π-radical character is discussed.
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Affiliation(s)
- Hyeongtaek Lim
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Kolle E. Thomas
- Department of Chemistry, UiT — The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Britt Hedman
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
| | - Keith O. Hodgson
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
| | - Abhik Ghosh
- Department of Chemistry, UiT — The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Edward I. Solomon
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
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34
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Burkhardt L, Mueller C, Groß OA, Sun Y, Sitzmann H, Bauer M. The Bonding Situation in the Dinuclear Tetra-Hydrido Complex [{ 5CpFe} 2(μ-H) 4] Revisited by Hard X-Ray Spectroscopy. Inorg Chem 2019; 58:6609-6618. [PMID: 30596494 DOI: 10.1021/acs.inorgchem.8b03032] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
High energy resolution fluorescence detected XANES (HERFD-XANES) and valence-to-core X-ray emission spectroscopy (VtC-XES) are introduced as powerful tools to investigate hydride-iron interaction, the possible iron-iron bond, and iron spin state of the dinuclear tetra-hydrido complex [{5CpFe}2(μ-H)4] (1H, 5Cp = η5-C5 iPr5) by thoroughly accessing the geometric and electronic structure of this complex in comparison to the nonhydride reference [5CpCpFe] (1, Cp = C5H5). The so far observed most intense hydride induced signals in the pre-edge feature of the HERFD-XANES and in the VtC-XES spectra at the iron K-edge allow a precise analysis of the LUMO and HOMO states, respectively, by application of time-dependent density function theory (TD-DFT) and density functional theory (DFT) calculations. The results of these calculations are further employed to understand the oxidation state, spin states, and potential Fe-Fe bonds in this complex.
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Affiliation(s)
- Lukas Burkhardt
- Faculty of Science , Paderborn University , Warburger Straße 100 , 33098 Paderborn , Germany
| | - Carsten Mueller
- Department of Chemistry , University of Kaiserslautern , Erwin-Schrödinger-Straße 54 , 67663 Kaiserslautern , Germany
| | - Oliver A Groß
- Faculty of Science , Paderborn University , Warburger Straße 100 , 33098 Paderborn , Germany
| | - Yu Sun
- Department of Chemistry , University of Kaiserslautern , Erwin-Schrödinger-Straße 54 , 67663 Kaiserslautern , Germany
| | - Helmut Sitzmann
- Department of Chemistry , University of Kaiserslautern , Erwin-Schrödinger-Straße 54 , 67663 Kaiserslautern , Germany
| | - Matthias Bauer
- Faculty of Science , Paderborn University , Warburger Straße 100 , 33098 Paderborn , Germany.,Center for Sustainable Systems Design (CSSD) , Paderborn University , Warburger Straße 100 , 33098 Paderborn , Germany
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35
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36
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Magherusan AM, Kal S, Nelis DN, Doyle LM, Farquhar ER, Que L, McDonald AR. A Mn II Mn III -Peroxide Complex Capable of Aldehyde Deformylation. Angew Chem Int Ed Engl 2019; 58:5718-5722. [PMID: 30830996 DOI: 10.1002/anie.201900717] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 02/27/2019] [Indexed: 11/07/2022]
Abstract
Ribonucleotide reductases (RNRs) are essential enzymes required for DNA synthesis. In class Ib Mn2 RNRs superoxide (O2 .- ) was postulated to react with the MnII 2 core to yield a MnII MnIII -peroxide moiety. The reactivity of complex 1 ([MnII 2 (O2 CCH3 )2 (BPMP)](ClO4 ), where HBPMP=2,6-bis{[(bis(2-pyridylmethyl)amino]methyl}-4-methylphenol) towards O2 .- was investigated at -90 °C, generating a metastable species, 2. The electronic absorption spectrum of 2 displayed features (λmax =440, 590 nm) characteristic of a MnII MnIII -peroxide species, representing just the second example of such. Electron paramagnetic resonance and X-ray absorption spectroscopies, and mass spectrometry supported the formulation of 2 as a MnII MnIII -peroxide complex. Unlike all other previously reported Mn2 -peroxides, which were unreactive, 2 proved to be a capable oxidant in aldehyde deformylation. Our studies provide insight into the mechanism of O2 -activation in Class Ib Mn2 RNRs, and the highly reactive intermediates in their catalytic cycle.
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Affiliation(s)
- Adriana M Magherusan
- School of Chemistry, Trinity College Dublin, The University of Dublin, College Green, Dublin 2, Ireland
| | - Subhasree Kal
- Department of Chemistry and Centre for Metals in Biocatalysis, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN, 55455, USA
| | - Daniel N Nelis
- School of Chemistry, Trinity College Dublin, The University of Dublin, College Green, Dublin 2, Ireland
| | - Lorna M Doyle
- School of Chemistry, Trinity College Dublin, The University of Dublin, College Green, Dublin 2, Ireland
| | - Erik R Farquhar
- Case Western Reserve University Centre for Synchrotron Biosciences, National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Lawrence Que
- Department of Chemistry and Centre for Metals in Biocatalysis, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN, 55455, USA
| | - Aidan R McDonald
- School of Chemistry, Trinity College Dublin, The University of Dublin, College Green, Dublin 2, Ireland
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37
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McLoughlin EA, Giles LJ, Waymouth RM, Sarangi R. X-ray Absorption Spectroscopy and Theoretical Investigation of the Reductive Protonation of Cyclopentadienyl Cobalt Compounds. Inorg Chem 2019; 58:1167-1176. [DOI: 10.1021/acs.inorgchem.8b02475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Logan J. Giles
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Robert M. Waymouth
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Ritimukta Sarangi
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
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38
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de Arruda EGR, Rocha BA, Barrionuevo MVF, Aðalsteinsson HM, Galdino FE, Loh W, Lima FA, Abbehausen C. The influence of ZnII coordination sphere and chemical structure over the reactivity of metallo-β-lactamase model compounds. Dalton Trans 2019; 48:2900-2916. [DOI: 10.1039/c8dt03905d] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The first coordination sphere influences the reactivity of metallo-β-lactamase monozinc model complexes.
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39
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Zimmer P, Burkhardt L, Schepper R, Zheng K, Gosztola D, Neuba A, Flörke U, Wölper C, Schoch R, Gawelda W, Canton SE, Bauer M. Towards Noble-Metal-Free Dyads: Ground and Excited State Tuning by a Cobalt Dimethylglyoxime Motif Connected to an Iron N-Heterocyclic Carbene Photosensitizer. Eur J Inorg Chem 2018. [DOI: 10.1002/ejic.201800946] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Peter Zimmer
- Faculty of science; Paderborn University; Warburger Straße 100 33098 Paderborn Germany
| | - Lukas Burkhardt
- Faculty of science; Paderborn University; Warburger Straße 100 33098 Paderborn Germany
| | - Rahel Schepper
- Faculty of science; Paderborn University; Warburger Straße 100 33098 Paderborn Germany
| | - Kaibo Zheng
- Department of Chemistry; Technical University of Denmark; -2800 Kongens Lyngby Denmark
- Department of Chemical Physics and NanoLund; Lund University; Box 124 22100 Lund Sweden
| | - David Gosztola
- Argonne National Laboratory; Center for Nanoscale Materials; 9700 S. Cass Avenue 60439 Lemont, Illinois United States
| | - Adam Neuba
- Faculty of science; Paderborn University; Warburger Straße 100 33098 Paderborn Germany
| | - Ulrich Flörke
- Faculty of science; Paderborn University; Warburger Straße 100 33098 Paderborn Germany
| | - Christoph Wölper
- Institute for Inorganic Chemistry and Center for Nanointegration Duisburg-Essen (Cenide); University of Duisburg-Essen; Universitätsstraße 5-7 -45117 Essen Germany
| | - Roland Schoch
- Faculty of science; Paderborn University; Warburger Straße 100 33098 Paderborn Germany
| | - Wojciech Gawelda
- European XFEL, Holzkoppel 4; 22869 Schenefeld Germany
- Faculty of Physics; Adam Mickiewicz University, Umultowska 85, 61-614 Poznań; Poland
| | - Sophie E. Canton
- ELI-ALPS, ELI-HU Non-Profit Ltd., Dugonics ter 13, Szeged 6720, Hungary & Attosecond Science Group, Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85; Germany
| | - Matthias Bauer
- Faculty of science; Paderborn University; Warburger Straße 100 33098 Paderborn Germany
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40
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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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41
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Denler MC, Wijeratne GB, Rice DB, Colmer HE, Day VW, Jackson TA. Mn III-Peroxo adduct supported by a new tetradentate ligand shows acid-sensitive aldehyde deformylation reactivity. Dalton Trans 2018; 47:13442-13458. [PMID: 30183042 PMCID: PMC6176719 DOI: 10.1039/c8dt02300j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The new tetradentate L7BQ ligand (L7BQ = 1,4-di(quinoline-8-yl)-1,4-diazepane) has been synthesized and shown to support MnII and MnIII-peroxo complexes. X-ray crystallography of the [MnII(L7BQ)(OTf)2] complex shows a monomeric MnII center with the L7BQ ligand providing four donor nitrogen atoms in the equatorial field, with two triflate ions bound in the axial positions. When this species is treated with H2O2 and Et3N at -40 °C, a MnIII-peroxo adduct, [MnIII(O2)(L7BQ)]+ is formed. The formation of this new intermediate is supported by a variety of spectroscopic techniques, including electronic absorption, Mn K-edge X-ray absorption and electron paramagnetic resonance methods. Evaluation of extended X-ray absorption fine structure data for [MnIII(O2)(L7BQ)]+ resolved Mn-O bond distances of 1.85 Å, which are on the short end of those previously reported for crystallographically characterized MnIII-peroxo adducts. An analysis of the X-ray pre-edge region of [MnIII(O2)(L7BQ)]+ revealed a large pre-edge area of 20.8 units. Time-dependent density functional theory computations indicate that the pre-edge intensity is due to Mn 4p-3d mixing caused by geometric distortions from centrosymmetry induced by both the peroxo and L7BQ ligands. The reactivity of [MnIII(O2)(L7BQ)]+ towards aldehydes was assessed through reaction with cyclohexanecarboxaldehyde and 2-phenylpropionaldehyde. From these experiments, it was determined that [MnIII(O2)(L7BQ)]+ only reacts with aldehydes in the presence of acid. Specifically, the addition of cyclohexanecarboxylic acid to [MnIII(O2)(L7BQ)]+ converts the MnIII-peroxo adduct to a new intermediate that could be responsible for the observed aldehyde deformylation activity. These observations underscore the challenges in identifying the reactive metal species in aldehyde deformylation reactions.
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Affiliation(s)
- Melissa C Denler
- The University of Kansas, Department of Chemistry and Center for Environmentally Beneficial Catalysis, 1251 Wescoe Hall Drive, Lawrence, KS 66045, USA.
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42
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Rudolph J, Jacob CR. Revisiting the Dependence of Cu K-Edge X-ray Absorption Spectra on Oxidation State and Coordination Environment. Inorg Chem 2018; 57:10591-10607. [PMID: 30113840 DOI: 10.1021/acs.inorgchem.8b01219] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
X-ray absorption spectroscopy (XAS) at the Cu K-edge is an important tool for probing the properties of copper centers in transition-metal chemistry and catalysis. However, the interpretation of experimental XAS spectra requires a detailed understanding of the dependence of spectroscopic features on the local geometric and electronic structure, which can be established by theoretical X-ray spectroscopy. Here, we present a systematic computational study of the Cu K-edge XAS spectra of selected Cu complexes based on time-dependent density-functional theory in combination with a molecular orbital analysis of the relevant transitions. For a series of Cu ammine model complexes as well as a comprehensive test set of 12 Cu(I) and 5 Cu(II) complexes, we revisit the dependence of the pre-edge region in Cu K-edge XAS spectra on oxidation state and coordination geometry. While our calculations confirm earlier experimental assignments, we can also reveal additional signatures of the ligand orbitals and identify the underlying orbital interactions. The comprehensive picture revealed by this study will provide a reliable basis for the interpretation of in situ Cu K-edge XAS spectra of catalytic intermediates.
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Affiliation(s)
- Julian Rudolph
- Institute of Physical and Theoretical Chemistry , TU Braunschweig , Gaußstraße 17 , 38106 Braunschweig , Germany
| | - Christoph R Jacob
- Institute of Physical and Theoretical Chemistry , TU Braunschweig , Gaußstraße 17 , 38106 Braunschweig , Germany
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43
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Chantzis A, Kowalska JK, Maganas D, DeBeer S, Neese F. Ab Initio Wave Function-Based Determination of Element Specific Shifts for the Efficient Calculation of X-ray Absorption Spectra of Main Group Elements and First Row Transition Metals. J Chem Theory Comput 2018; 14:3686-3702. [DOI: 10.1021/acs.jctc.8b00249] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Agisilaos Chantzis
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Joanna K. Kowalska
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Dimitrios Maganas
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Serena DeBeer
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Frank Neese
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
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44
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Moonshiram D, Garrido‐Barros P, Gimbert‐Suriñach C, Picón A, Liu C, Zhang X, Karnahl M, Llobet A. Elucidating the Nature of the Excited State of a Heteroleptic Copper Photosensitizer by using Time‐Resolved X‐ray Absorption Spectroscopy. Chemistry 2018; 24:6464-6472. [DOI: 10.1002/chem.201800330] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Indexed: 11/06/2022]
Affiliation(s)
- Dooshaye Moonshiram
- Max Planck Institute for Chemical Energy Conversion Stiftstrasse 34–36 Mülheim an der Ruhr 45470 Germany
- Institute of Chemical Research of Catalonia (ICIQ) Avinguda Països Catalans 16 43007 Tarragona Spain
| | - Pablo Garrido‐Barros
- Institute of Chemical Research of Catalonia (ICIQ) Avinguda Països Catalans 16 43007 Tarragona Spain
- Departament de Química Física i Inorganica Universitat Rovira i Virgili Campus Sescelades, C/Marcellí Domingo, s/n 43007 Tarragona Spain
| | - Carolina Gimbert‐Suriñach
- Institute of Chemical Research of Catalonia (ICIQ) Avinguda Països Catalans 16 43007 Tarragona Spain
| | - Antonio Picón
- Grupo de Investigacion en Aplicaciones del Laser y Fotonica Universidad de Salamanca 37008 Salamanca Spain
- Departamento de Química, Modulo 13 Universidad Autónoma de Madrid Cantoblanco 28049 Madrid Spain
| | - Cunming Liu
- X-ray Science Division Argonne National Laboratory 9700 S. Cass Avenue Lemont IL 60439 USA
| | - Xiaoyi Zhang
- X-ray Science Division Argonne National Laboratory 9700 S. Cass Avenue Lemont IL 60439 USA
| | - Michael Karnahl
- University of Stuttgart Institute of Organic Chemistry Pfaffenwaldring 55 70569 Stuttgart Germany
| | - Antoni Llobet
- Institute of Chemical Research of Catalonia (ICIQ) Avinguda Països Catalans 16 43007 Tarragona Spain
- Departament de Química Universitat Autonoma de Barcelona 08193 Cerdanyola del Valles Barcelona Spain
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45
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Wilkin OM, Harris N, Rooms JF, Dixon EL, Bridgeman AJ, Young NA. How Inert, Perturbing, or Interacting Are Cryogenic Matrices? A Combined Spectroscopic (Infrared, Electronic, and X-ray Absorption) and DFT Investigation of Matrix-Isolated Iron, Cobalt, Nickel, and Zinc Dibromides. J Phys Chem A 2018; 122:1994-2029. [DOI: 10.1021/acs.jpca.7b09734] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Owen M. Wilkin
- Department
of Chemistry, The University of Hull, Kingston upon Hull HU6
7RX, U.K
| | - Neil Harris
- Department
of Chemistry, The University of Hull, Kingston upon Hull HU6
7RX, U.K
| | - John F. Rooms
- Department
of Chemistry, The University of Hull, Kingston upon Hull HU6
7RX, U.K
| | - Emma L. Dixon
- Department
of Chemistry, The University of Hull, Kingston upon Hull HU6
7RX, U.K
| | - Adam J. Bridgeman
- School
of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
| | - Nigel A. Young
- Department
of Chemistry, The University of Hull, Kingston upon Hull HU6
7RX, U.K
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46
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Parham JD, Wijeratne GB, Rice DB, Jackson TA. Spectroscopic and Structural Characterization of Mn(III)-Alkylperoxo Complexes Supported by Pentadentate Amide-Containing Ligands. Inorg Chem 2018; 57:2489-2502. [DOI: 10.1021/acs.inorgchem.7b02793] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Joshua D. Parham
- Department of Chemistry and Center for Environmentally Beneficial Catalysis, University of Kansas, Lawrence, Kansas 66045, United States
| | - Gayan B. Wijeratne
- Department of Chemistry and Center for Environmentally Beneficial Catalysis, University of Kansas, Lawrence, Kansas 66045, United States
| | - Derek B. Rice
- Department of Chemistry and Center for Environmentally Beneficial Catalysis, University of Kansas, Lawrence, Kansas 66045, United States
| | - Timothy A. Jackson
- Department of Chemistry and Center for Environmentally Beneficial Catalysis, University of Kansas, Lawrence, Kansas 66045, United States
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47
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Castillo RG, Banerjee R, Allpress CJ, Rohde GT, Bill E, Que L, Lipscomb JD, DeBeer S. High-Energy-Resolution Fluorescence-Detected X-ray Absorption of the Q Intermediate of Soluble Methane Monooxygenase. J Am Chem Soc 2017; 139:18024-18033. [PMID: 29136468 PMCID: PMC5729100 DOI: 10.1021/jacs.7b09560] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Kα high-energy-resolution fluorescence detected X-ray absorption spectroscopy (HERFD XAS) provides a powerful tool for overcoming the limitations of conventional XAS to identify the electronic structure and coordination environment of metalloprotein active sites. Herein, Fe Kα HERFD XAS is applied to the diiron active site of soluble methane monooxygenase (sMMO) and to a series of high-valent diiron model complexes, including diamond-core [FeIV2(μ-O)2(L)2](ClO4)4] (3) and open-core [(O═FeIV-O-FeIV(OH)(L)2](ClO4)3 (4) models (where, L = tris(3,5-dimethyl-4-methoxypyridyl-2-methyl)amine) (TPA*)). Pronounced differences in the HERFD XAS pre-edge energies and intensities are observed for the open versus closed Fe2O2 cores in the model compounds. These differences are reproduced by time-dependent density functional theory (TDDFT) calculations and allow for the pre-edge energies and intensity to be directly correlated with the local active site geometric and electronic structure. A comparison of the model complex HERFD XAS data to that of MMOHQ (the key intermediate in methane oxidation) is supportive of an open-core structure. Specifically, the large pre-edge area observed for MMOHQ may be rationalized by invoking an open-core structure with a terminal FeIV═O motif, though further modulations of the core structure due to the protein environment cannot be ruled out. The present study thus motivates the need for additional experimental and theoretical studies to unambiguously assess the active site conformation of MMOHQ.
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Affiliation(s)
- Rebeca G. Castillo
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34, D-45470 Mülheim an der Ruhr, Germany
| | - Rahul Banerjee
- Department of Biochemistry, Molecular Biology and Biophysics, 321 Church St. SE, Minneapolis, MN 55455
| | - Caleb J. Allpress
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, MN 55455
| | - Gregory T. Rohde
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, MN 55455
| | - Eckhard Bill
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34, D-45470 Mülheim an der Ruhr, Germany
| | - Lawrence Que
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, MN 55455
| | - John D. Lipscomb
- Department of Biochemistry, Molecular Biology and Biophysics, 321 Church St. SE, Minneapolis, MN 55455
| | - Serena DeBeer
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34, D-45470 Mülheim an der Ruhr, Germany
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48
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Zimmer P, Burkhardt L, Friedrich A, Steube J, Neuba A, Schepper R, Müller P, Flörke U, Huber M, Lochbrunner S, Bauer M. The Connection between NHC Ligand Count and Photophysical Properties in Fe(II) Photosensitizers: An Experimental Study. Inorg Chem 2017; 57:360-373. [DOI: 10.1021/acs.inorgchem.7b02624] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Peter Zimmer
- Department
Chemie, Universität Paderborn, Warburger Straße 100, 33098 Paderborn, Germany
| | - Lukas Burkhardt
- Department
Chemie, Universität Paderborn, Warburger Straße 100, 33098 Paderborn, Germany
| | - Aleksej Friedrich
- Institute
of Physics, University of Rostock, Albert-Einstein-Str. 23, 18059 Rostock, Germany
| | - Jakob Steube
- Department
Chemie, Universität Paderborn, Warburger Straße 100, 33098 Paderborn, Germany
| | - Adam Neuba
- Department
Chemie, Universität Paderborn, Warburger Straße 100, 33098 Paderborn, Germany
| | - Rahel Schepper
- Department
Chemie, Universität Paderborn, Warburger Straße 100, 33098 Paderborn, Germany
| | - Patrick Müller
- Department
Chemie, Universität Paderborn, Warburger Straße 100, 33098 Paderborn, Germany
| | - Ulrich Flörke
- Department
Chemie, Universität Paderborn, Warburger Straße 100, 33098 Paderborn, Germany
| | - Marina Huber
- Department
Chemie, Universität Paderborn, Warburger Straße 100, 33098 Paderborn, Germany
| | - Stefan Lochbrunner
- Institute
of Physics, University of Rostock, Albert-Einstein-Str. 23, 18059 Rostock, Germany
| | - Matthias Bauer
- Department
Chemie, Universität Paderborn, Warburger Straße 100, 33098 Paderborn, Germany
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49
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Abbehausen C, de Paiva REF, Bjornsson R, Gomes SQ, Du Z, Corbi PP, Lima FA, Farrell N. X-ray Absorption Spectroscopy Combined with Time-Dependent Density Functional Theory Elucidates Differential Substitution Pathways of Au(I) and Au(III) with Zinc Fingers. Inorg Chem 2017; 57:218-230. [DOI: 10.1021/acs.inorgchem.7b02406] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Camilla Abbehausen
- Institute of Chemistry, University of Campinas—UNICAMP, P.O. Box 6154, CEP, 13083-970 Campinas, São Paulo, Brazil
| | | | - Ragnar Bjornsson
- Science Institute, University of Iceland, Dunhagi 3,
IS-107 Reykjavik, Iceland
| | - Saulo Quintana Gomes
- Institute of Chemistry, University of Campinas—UNICAMP, P.O. Box 6154, CEP, 13083-970 Campinas, São Paulo, Brazil
| | - Zhifeng Du
- Department of Chemistry, Virginia Commonwealth University, 1001 W. Main Street, Richmond, Virginia 23284-2006, United States
| | - Pedro Paulo Corbi
- Institute of Chemistry, University of Campinas—UNICAMP, P.O. Box 6154, CEP, 13083-970 Campinas, São Paulo, Brazil
| | - Frederico Alves Lima
- Centro Nacional de Pesquisa em Energia
e Materiais, Brazilian Synchrotron Light Laboratory—LNLS, CP 6192, 13084-971 Campinas, São Paulo, Brazil
| | - Nicholas Farrell
- Department of Chemistry, Virginia Commonwealth University, 1001 W. Main Street, Richmond, Virginia 23284-2006, United States
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50
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Burkhardt L, Holzwarth M, Plietker B, Bauer M. Detection and Characterization of Hydride Ligands in Iron Complexes by High-Resolution Hard X-ray Spectroscopy and Implications for Catalytic Processes. Inorg Chem 2017; 56:13300-13310. [PMID: 29058447 DOI: 10.1021/acs.inorgchem.7b02063] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Two hydride catalysts [Fe(CO)(dppp)H(NO)] (dppp = 1,3-bis(diphenylphosphino)propane) and [Fe(CO)H(NO)(PPh3)2] in comparison with nonhydride analogues [Fe(dppe)(NO)2] (dppe = 1,3-bis(diphenylphosphino)ethane) and [Fe(NO)2(PPh3)2] are investigated with a combination of valence-to-core X-ray emission spectroscopy (VtC-XES) and high-energy resolution fluorescence detected X-ray absorption near-edge structure (HERFD-XANES). To fully understand the experiments and to obtain precise information about molecular levels being involved in the spectral signals, time-dependent density functional theory (TD-DFT) calculations and ground state density functional theory (DFT) calculations are necessary. An excellent agreement between experiment and theory allows the identification of particular spectral signals of the Fe-H group. Antibonding Fe-H interactions clearly contribute to pre-edge signals in HERFD-XANES spectra, while bonding Fe-H interactions cause characteristic signatures in the VtC-XES spectra. The sensitivity of both methods with respect to the Fe-H distance is demonstrated by a scanning simulation approach. The results open the way to study metal hydride complexes in situ, their formation, and their fate during catalytic reactions, using high-resolution XANES and valence-to-core X-ray emission spectroscopy.
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Affiliation(s)
- Lukas Burkhardt
- Department Chemie, Universität Paderborn , Warburger Straße 100, D-33098 Paderborn, Germany
| | - Michael Holzwarth
- Institut für Organische Chemie, Universität Stuttgart , Pfaffenwaldring 55, D-70569 Stuttgart, Germany
| | - Bernd Plietker
- Institut für Organische Chemie, Universität Stuttgart , Pfaffenwaldring 55, D-70569 Stuttgart, Germany
| | - Matthias Bauer
- Department Chemie, Universität Paderborn , Warburger Straße 100, D-33098 Paderborn, Germany
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