1
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Jenney FE, Wang H, George SJ, Xiong J, Guo Y, Gee LB, Marizcurrena JJ, Castro-Sowinski S, Staskiewicz A, Yoda Y, Hu MY, Tamasaku K, Nagasawa N, Li L, Matsuura H, Doukov T, Cramer SP. Temperature-dependent iron motion in extremophile rubredoxins - no need for 'corresponding states'. Sci Rep 2024; 14:12197. [PMID: 38806591 PMCID: PMC11133467 DOI: 10.1038/s41598-024-62261-2] [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: 12/15/2023] [Accepted: 05/15/2024] [Indexed: 05/30/2024] Open
Abstract
Extremophile organisms are known that can metabolize at temperatures down to - 25 °C (psychrophiles) and up to 122 °C (hyperthermophiles). Understanding viability under extreme conditions is relevant for human health, biotechnological applications, and our search for life elsewhere in the universe. Information about the stability and dynamics of proteins under environmental extremes is an important factor in this regard. Here we compare the dynamics of small Fe-S proteins - rubredoxins - from psychrophilic and hyperthermophilic microorganisms, using three different nuclear techniques as well as molecular dynamics calculations to quantify motion at the Fe site. The theory of 'corresponding states' posits that homologous proteins from different extremophiles have comparable flexibilities at the optimum growth temperatures of their respective organisms. Although 'corresponding states' would predict greater flexibility for rubredoxins that operate at low temperatures, we find that from 4 to 300 K, the dynamics of the Fe sites in these homologous proteins are essentially equivalent.
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Affiliation(s)
- Francis E Jenney
- Georgia Campus, Philadelphia College of Osteopathic Medicine, Suwanee, GA, 30024, USA
| | | | | | - Jin Xiong
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Yisong Guo
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Leland B Gee
- LCLS, SLAC National Laboratory, Stanford, CA, 94025, USA
| | | | | | - Anna Staskiewicz
- Georgia Campus, Philadelphia College of Osteopathic Medicine, Suwanee, GA, 30024, USA
| | - Yoshitaka Yoda
- Precision Spectroscopy Division, SPring-8/JASRI, Sayo, Hyogo, 679-5198, Japan
| | - Michael Y Hu
- Advanced Photon Source, Argonne National Laboratory, Lemont, IL, 60439, USA
| | | | - Nobumoto Nagasawa
- Precision Spectroscopy Division, SPring-8/JASRI, Sayo, Hyogo, 679-5198, Japan
| | - Lei Li
- Synchrotron Radiation Research Center, Hyogo, 679-5165, Japan
| | | | - Tzanko Doukov
- SSRL, SLAC National Laboratory, Stanford, CA, 94025, USA
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2
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Heppe N, Gallenkamp C, Snitkoff-Sol RZ, Paul SD, Segura-Salas N, Haak H, Moritz DC, Kaiser B, Jaegermann W, Potapkin V, Jafari A, Schünemann V, Leupold O, Elbaz L, Krewald V, Kramm UI. Applying Nuclear Forward Scattering as In Situ and Operando Tool for the Characterization of FeN 4 Moieties in the Hydrogen Evolution Reaction. J Am Chem Soc 2024; 146:12496-12510. [PMID: 38630640 PMCID: PMC11082898 DOI: 10.1021/jacs.4c00436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 03/24/2024] [Accepted: 03/26/2024] [Indexed: 04/19/2024]
Abstract
Nuclear forward scattering (NFS) is a synchrotron-based technique relying on the recoil-free nuclear resonance effect similar to Mössbauer spectroscopy. In this work, we introduce NFS for in situ and operando measurements during electrocatalytic reactions. The technique enables faster data acquisition and better discrimination of certain iron sites in comparison to Mössbauer spectroscopy. It is directly accessible at various synchrotrons to a broad community of researchers and is applicable to multiple metal isotopes. We demonstrate the power of this technique with the hydrogen evolution mechanism of an immobilized iron porphyrin supported on carbon. Such catalysts are often considered as model systems for iron-nitrogen-carbon (FeNC) catalysts. Using in situ and operando NFS in combination with theoretical predictions of spectroscopic data enables the identification of the intermediate that is formed prior to the rate-determining step. The conclusions on the reaction mechanism can be used for future optimization of immobilized molecular catalysts and metal-nitrogen-carbon (MNC) catalysts.
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Affiliation(s)
- Nils Heppe
- Catalysts
and Electrocatalysts, Eduard-Zintl-Institute of Inorganic and Physical
Chemistry, Department of Chemistry, Technical
University Darmstadt, Otto-Berndt-Str. 3, 64287 Darmstadt, Germany
| | - Charlotte Gallenkamp
- Catalysts
and Electrocatalysts, Eduard-Zintl-Institute of Inorganic and Physical
Chemistry, Department of Chemistry, Technical
University Darmstadt, Otto-Berndt-Str. 3, 64287 Darmstadt, Germany
- Quantum
Chemistry, Eduard-Zintl-Institute of Inorganic and Physical Chemistry,
Department of Chemistry, Technical University
Darmstadt, Peter-Grünberg-Str.
4, 64287 Darmstadt, Germany
| | - Rifael Z. Snitkoff-Sol
- Bar-Ilan
Center for Nanotechnology and Advanced Materials and the Department
of Chemistry, Bar-Ilan University, Ramat-Gan 529002, Israel
| | - Stephen D. Paul
- Catalysts
and Electrocatalysts, Eduard-Zintl-Institute of Inorganic and Physical
Chemistry, Department of Chemistry, Technical
University Darmstadt, Otto-Berndt-Str. 3, 64287 Darmstadt, Germany
| | - Nicole Segura-Salas
- Catalysts
and Electrocatalysts, Eduard-Zintl-Institute of Inorganic and Physical
Chemistry, Department of Chemistry, Technical
University Darmstadt, Otto-Berndt-Str. 3, 64287 Darmstadt, Germany
| | - Hendrik Haak
- Catalysts
and Electrocatalysts, Eduard-Zintl-Institute of Inorganic and Physical
Chemistry, Department of Chemistry, Technical
University Darmstadt, Otto-Berndt-Str. 3, 64287 Darmstadt, Germany
| | - Dominik C. Moritz
- Surface
Science Division, Institute of Materials Science, Department of Materials
and Earth Sciences, Technical University
Darmstadt, Otto-Berndt-Str.
3, 64287 Darmstadt, Germany
| | - Bernhard Kaiser
- Surface
Science Division, Institute of Materials Science, Department of Materials
and Earth Sciences, Technical University
Darmstadt, Otto-Berndt-Str.
3, 64287 Darmstadt, Germany
| | - Wolfram Jaegermann
- Surface
Science Division, Institute of Materials Science, Department of Materials
and Earth Sciences, Technical University
Darmstadt, Otto-Berndt-Str.
3, 64287 Darmstadt, Germany
| | - Vasily Potapkin
- Catalysts
and Electrocatalysts, Eduard-Zintl-Institute of Inorganic and Physical
Chemistry, Department of Chemistry, Technical
University Darmstadt, Otto-Berndt-Str. 3, 64287 Darmstadt, Germany
| | - Atefeh Jafari
- Deutsches
Elektronen-Synchrotron, Notkestraße 85, 22607 Hamburg, Germany
| | - Volker Schünemann
- Department
of Physics, University of Kaiserslautern-Landau, Erwin-Schrödinger Straße
56, 67663 Kaiserslautern, Germany
| | - Olaf Leupold
- Deutsches
Elektronen-Synchrotron, Notkestraße 85, 22607 Hamburg, Germany
| | - Lior Elbaz
- Bar-Ilan
Center for Nanotechnology and Advanced Materials and the Department
of Chemistry, Bar-Ilan University, Ramat-Gan 529002, Israel
| | - Vera Krewald
- Quantum
Chemistry, Eduard-Zintl-Institute of Inorganic and Physical Chemistry,
Department of Chemistry, Technical University
Darmstadt, Peter-Grünberg-Str.
4, 64287 Darmstadt, Germany
| | - Ulrike I. Kramm
- Catalysts
and Electrocatalysts, Eduard-Zintl-Institute of Inorganic and Physical
Chemistry, Department of Chemistry, Technical
University Darmstadt, Otto-Berndt-Str. 3, 64287 Darmstadt, Germany
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3
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Ansari M, Bhattacharjee S, Pantazis DA. Correlating Structure with Spectroscopy in Ascorbate Peroxidase Compound II. J Am Chem Soc 2024; 146:9640-9656. [PMID: 38530124 PMCID: PMC11009960 DOI: 10.1021/jacs.3c13169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 03/15/2024] [Accepted: 03/15/2024] [Indexed: 03/27/2024]
Abstract
Structural and spectroscopic investigations of compound II in ascorbate peroxidase (APX) have yielded conflicting conclusions regarding the protonation state of the crucial Fe(IV) intermediate. Neutron diffraction and crystallographic data support an iron(IV)-hydroxo formulation, whereas Mössbauer, X-ray absorption (XAS), and nuclear resonance vibrational spectroscopy (NRVS) studies appear consistent with an iron(IV)-oxo species. Here we examine APX with spectroscopy-oriented QM/MM calculations and extensive exploration of the conformational space for both possible formulations of compound II. We establish that irrespective of variations in the orientation of a vicinal arginine residue and potential reorganization of proximal water molecules and hydrogen bonding, the Fe-O distances for the oxo and hydroxo forms consistently fall within distinct, narrow, and nonoverlapping ranges. The accuracy of geometric parameters is validated by coupled-cluster calculations with the domain-based local pair natural orbital approach, DLPNO-CCSD(T). QM/MM calculations of spectroscopic properties are conducted for all structural variants, encompassing Mössbauer, optical, X-ray absorption, and X-ray emission spectroscopies and NRVS. All spectroscopic observations can be assigned uniquely to an Fe(IV)═O form. A terminal hydroxy group cannot be reconciled with the spectroscopic data. Under no conditions can the Fe(IV)═O distance be sufficiently elongated to approach the crystallographically reported Fe-O distance. The latter is consistent only with a hydroxo species, either Fe(IV) or Fe(III). Our findings strongly support the Fe(IV)═O formulation of APX-II and highlight unresolved discrepancies in the nature of samples used across different experimental studies.
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Affiliation(s)
- Mursaleem Ansari
- Max-Planck-Institut für
Kohlenforschung, Kaiser-Wilhelm-Platz
1, Mülheim an der Ruhr 45470, Germany
| | - Sinjini Bhattacharjee
- Max-Planck-Institut für
Kohlenforschung, Kaiser-Wilhelm-Platz
1, Mülheim an der Ruhr 45470, Germany
| | - Dimitrios A. Pantazis
- Max-Planck-Institut für
Kohlenforschung, Kaiser-Wilhelm-Platz
1, Mülheim an der Ruhr 45470, Germany
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4
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Gallenkamp C, Kramm UI, Krewald V. FeN 4 Environments upon Reduction: A Computational Analysis of Spin States, Spectroscopic Properties, and Active Species. JACS AU 2024; 4:940-950. [PMID: 38559729 PMCID: PMC10976608 DOI: 10.1021/jacsau.3c00714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/08/2024] [Accepted: 01/09/2024] [Indexed: 04/04/2024]
Abstract
FeN4 motifs, found, for instance, in bioinorganic chemistry as heme-type cofactors, play a crucial role in man-made FeNC catalysts for the oxygen reduction reaction. Such single-atom catalysts are a potential alternative to platinum-based catalysts in fuel cells. Since FeNC catalysts are prepared via pyrolysis, the resulting materials are amorphous and contain side phases and impurities. Therefore, the geometric and electronic nature of the catalytically active FeN4 site remains to be clarified. To further understand the behavior of FeN4 centers in electrochemistry and their expected spectroscopic behavior upon reduction, we investigate two FeN4 environments (pyrrolic and pyridinic). These are represented by the model complexes [Fe(TPP)Cl] and [Fe(phen2N2)Cl], where TPP = tetraphenylporphyrin and phen = 1,10-phenanthroline. We predict their Mössbauer, UV-vis, and NRV spectral data using density functional theory as windows into their electronic structure differences. By varying the axial ligand, we further show how well small chemical changes in both complexes can be discerned. We find that the differences in ligand field strength in pyrrolic and pyridinic coordination result in different spin ground states, which in turn leads to distinct Mössbauer spectroscopic properties. As a result, pyrrolic nitrogen donors with a weaker ligand field are predicted to show more pronounced spectroscopic differences under in situ and operando conditions, while pyridinic nitrogen donors are expected to show less pronounced spectroscopic changes upon reduction and/or ligand loss. We therefore suggest that a weaker ligand field leads to better detectability of catalytic intermediates in in situ and operando experiments.
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Affiliation(s)
- Charlotte Gallenkamp
- Theoretische
Chemie, Technische Universität Darmstadt, Peter-Grünberg-Str. 4, 64287 Darmstadt, Germany
| | - Ulrike I. Kramm
- Anorganische
Chemie, Technische Universität Darmstadt, Otto-Berndt-Str. 3, 64287 Darmstadt, Germany
| | - Vera Krewald
- Theoretische
Chemie, Technische Universität Darmstadt, Peter-Grünberg-Str. 4, 64287 Darmstadt, Germany
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5
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Babicz JT, Rogers MS, DeWeese DE, Sutherlin KD, Banerjee R, Böttger LH, Yoda Y, Nagasawa N, Saito M, Kitao S, Kurokuzu M, Kobayashi Y, Tamasaku K, Seto M, Lipscomb JD, Solomon EI. Nuclear Resonance Vibrational Spectroscopy Definition of Peroxy Intermediates in Catechol Dioxygenases: Factors that Determine Extra- versus Intradiol Cleavage. J Am Chem Soc 2023; 145:15230-15250. [PMID: 37414058 PMCID: PMC10804917 DOI: 10.1021/jacs.3c02242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Abstract
The extradiol dioxygenases (EDOs) and intradiol dioxygenases (IDOs) are nonheme iron enzymes that catalyze the oxidative aromatic ring cleavage of catechol substrates, playing an essential role in the carbon cycle. The EDOs and IDOs utilize very different FeII and FeIII active sites to catalyze the regiospecificity in their catechol ring cleavage products. The factors governing this difference in cleavage have remained undefined. The EDO homoprotocatechuate 2,3-dioxygenase (HPCD) and IDO protocatechuate 3,4-dioxygenase (PCD) provide an opportunity to understand this selectivity, as key O2 intermediates have been trapped for both enzymes. Nuclear resonance vibrational spectroscopy (in conjunction with density functional theory calculations) is used to define the geometric and electronic structures of these intermediates as FeII-alkylhydroperoxo (HPCD) and FeIII-alkylperoxo (PCD) species. Critically, in both intermediates, the initial peroxo bond orientation is directed toward extradiol product formation. Reaction coordinate calculations were thus performed to evaluate both the extra- and intradiol O-O cleavage for the simple organic alkylhydroperoxo and for the FeII and FeIII metal catalyzed reactions. These results show the FeII-alkylhydroperoxo (EDO) intermediate undergoes facile extradiol O-O bond homolysis due to its extra e-, while for the FeIII-alkylperoxo (IDO) intermediate the extradiol cleavage involves a large barrier and would yield the incorrect extradiol product. This prompted our evaluation of a viable mechanism to rearrange the FeIII-alkylperoxo IDO intermediate for intradiol cleavage, revealing a key role in the rebinding of the displaced Tyr447 ligand in this rearrangement, driven by the proton delivery necessary for O-O bond cleavage.
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Affiliation(s)
- Jeffrey T. Babicz
- Department of Chemistry, Stanford University, 380 Roth Way, Stanford, California 94305, United States
| | - Melanie S. Rogers
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55391, United States
| | - Dory E. DeWeese
- Department of Chemistry, Stanford University, 380 Roth Way, Stanford, California 94305, United States
| | - Kyle D. Sutherlin
- Department of Chemistry, Stanford University, 380 Roth Way, Stanford, California 94305, United States
| | - Rahul Banerjee
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55391, United States
| | - Lars H. Böttger
- Department of Chemistry, Stanford University, 380 Roth Way, Stanford, California 94305, United States
| | - Yoshitaka Yoda
- Japan Synchrotron Radiation Research Institute, Hyogo 679-5198, Japan
| | - Nobumoto Nagasawa
- Japan Synchrotron Radiation Research Institute, Hyogo 679-5198, Japan
| | - Makina Saito
- Department of Physics, Tohoku University, Sendai, Miyagi 980-8578, Japan
| | - Shinji Kitao
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Osaka 590-0494, Japan
| | - Masayuki Kurokuzu
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Osaka 590-0494, Japan
| | - Yasuhiro Kobayashi
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Osaka 590-0494, Japan
| | - Kenji Tamasaku
- RIKEN SPring-8 Center, RIKEN, Sayo, Hyogo 679-5148, Japan
| | - Makoto Seto
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Osaka 590-0494, Japan
| | - John D. Lipscomb
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55391, United States
| | - Edward I. Solomon
- Department of Chemistry, Stanford University, 380 Roth Way, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
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6
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Auerbach H, Faus I, Rackwitz S, Wolny JA, Chumakov AI, Knipp M, Walker FA, Schünemann V. Heme protonation affects iron-NO binding in the NO transport protein nitrophorin. J Inorg Biochem 2023; 246:112281. [PMID: 37352657 DOI: 10.1016/j.jinorgbio.2023.112281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 04/26/2023] [Accepted: 05/30/2023] [Indexed: 06/25/2023]
Abstract
The nitrophorins (NPs) comprise an unusual group of heme proteins with stable ferric heme iron nitric oxide (Fe-NO) complexes. They are found in the salivary glands of the blood-sucking kissing bug Rhodnius prolixus, which uses the NPs to transport the highly reactive signaling molecule NO. Nuclear resonance vibrational spectroscopy (NRVS) of both isoform NP2 and a mutant NP2(Leu132Val) show, after addition of NO, a strong structured vibrational band at around 600 cm-1, which is due to modes with significant Fe-NO bending and stretching contribution. Based on a hybrid calculation method, which uses density functional theory and molecular mechanics, it is demonstrated that protonation of the heme carboxyl groups does influence both the vibrational properties of the Fe-NO entity and its electronic ground state. Moreover, heme protonation causes a significant increase of the gap between the highest occupied and lowest unoccupied molecular orbital by almost one order of magnitude leading to a stabilization of the Fe-NO bond.
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Affiliation(s)
- Hendrik Auerbach
- Department of Physics, RPTU Kaiserslautern-Landau, 67663 Kaiserslautern, Germany
| | - Isabelle Faus
- Department of Physics, RPTU Kaiserslautern-Landau, 67663 Kaiserslautern, Germany
| | - Sergej Rackwitz
- Department of Physics, RPTU Kaiserslautern-Landau, 67663 Kaiserslautern, Germany
| | - Juliusz A Wolny
- Department of Physics, RPTU Kaiserslautern-Landau, 67663 Kaiserslautern, Germany
| | | | - Markus Knipp
- Max Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, 45470 Mülheim an der Ruhr, Germany; Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Universitätsstraße 150, 44780 Bochum, Germany
| | - F Ann Walker
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, AZ 85721-0041, United States
| | - Volker Schünemann
- Department of Physics, RPTU Kaiserslautern-Landau, 67663 Kaiserslautern, Germany.
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7
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Heppe N, Gallenkamp C, Paul S, Segura-Salas N, von Rhein N, Kaiser B, Jaegermann W, Jafari A, Sergueev I, Krewald V, Kramm UI. Substituent Effects in Iron Porphyrin Catalysts for the Hydrogen Evolution Reaction. Chemistry 2023; 29:e202202465. [PMID: 36301727 DOI: 10.1002/chem.202202465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 10/27/2022] [Accepted: 10/27/2022] [Indexed: 11/07/2022]
Abstract
For a future hydrogen economy, non-precious metal catalysts for the water splitting reactions are needed that can be implemented on a global scale. Metal-nitrogen-carbon (MNC) catalysts with active sites constituting a metal center with fourfold coordination of nitrogen (MN4 ) show promising performance, but an optimization rooted in structure-property relationships has been hampered by their low structural definition. Porphyrin model complexes are studied to transfer insights from well-defined molecules to MNC systems. This work combines experiment and theory to evaluate the influence of porphyrin substituents on the electronic and electrocatalytic properties of MN4 centers with respect to the hydrogen evolution reaction (HER) in aqueous electrolyte. We found that the choice of substituent affects their utilization on the carbon support and their electrocatalytic performance. We propose an HER mechanism for supported iron porphyrin complexes involving a [FeII (P⋅)]- radical anion intermediate, in which a porphinic nitrogen atom acts as an internal base. While this work focuses on the HER, the limited influence of a simultaneous interaction with the support and an aqueous electrolyte will likely be transferrable to other catalytic applications.
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Affiliation(s)
- Nils Heppe
- Catalysts and Electrocatalysts, Department of Chemistry, Eduard-Zintl-Insitute for Inorganic and Physical Chemistry, Technical University Darmstadt, Otto-Berndt-Str. 3, 64287, Darmstadt, Germany
| | - Charlotte Gallenkamp
- Catalysts and Electrocatalysts, Department of Chemistry, Eduard-Zintl-Insitute for Inorganic and Physical Chemistry, Technical University Darmstadt, Otto-Berndt-Str. 3, 64287, Darmstadt, Germany.,Department of Chemistry, Theoretical Chemistry, Technical University Darmstadt, Alarich-Weiss-Str. 4, 64287, Darmstadt, Germany
| | - Stephen Paul
- Catalysts and Electrocatalysts, Department of Chemistry, Eduard-Zintl-Insitute for Inorganic and Physical Chemistry, Technical University Darmstadt, Otto-Berndt-Str. 3, 64287, Darmstadt, Germany
| | - Nicole Segura-Salas
- Catalysts and Electrocatalysts, Department of Chemistry, Eduard-Zintl-Insitute for Inorganic and Physical Chemistry, Technical University Darmstadt, Otto-Berndt-Str. 3, 64287, Darmstadt, Germany
| | - Niklas von Rhein
- Department of Chemistry, Theoretical Chemistry, Technical University Darmstadt, Alarich-Weiss-Str. 4, 64287, Darmstadt, Germany
| | - Bernhard Kaiser
- Institute of Materials Science, Surface Science Division, Technical University Darmstadt, Otto-Berndt-Str. 3, 64287, Darmstadt, Germany
| | - Wolfram Jaegermann
- Institute of Materials Science, Surface Science Division, Technical University Darmstadt, Otto-Berndt-Str. 3, 64287, Darmstadt, Germany
| | - Atefeh Jafari
- Deutsches Elektronen-Synchrotron, Notkestraße 85, 22607, Hamburg, Germany
| | - Ilya Sergueev
- Deutsches Elektronen-Synchrotron, Notkestraße 85, 22607, Hamburg, Germany
| | - Vera Krewald
- Department of Chemistry, Theoretical Chemistry, Technical University Darmstadt, Alarich-Weiss-Str. 4, 64287, Darmstadt, Germany
| | - Ulrike I Kramm
- Catalysts and Electrocatalysts, Department of Chemistry, Eduard-Zintl-Insitute for Inorganic and Physical Chemistry, Technical University Darmstadt, Otto-Berndt-Str. 3, 64287, Darmstadt, Germany
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8
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Podgorski MN, Coleman T, Churchman LR, Bruning JB, De Voss JJ, Bell SG. Investigating the Active Oxidants Involved in Cytochrome P450 Catalyzed Sulfoxidation Reactions. Chemistry 2022; 28:e202202428. [PMID: 36169207 PMCID: PMC10100219 DOI: 10.1002/chem.202202428] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Indexed: 12/30/2022]
Abstract
Cytochrome P450 (CYP) heme-thiolate monooxygenases catalyze the hydroxylation of the C-H bonds of organic molecules. This reaction is initiated by a ferryl-oxo heme radical cation (Cpd I). These enzymes can also catalyze sulfoxidation reactions and the ferric-hydroperoxy complex (Cpd 0) and the Fe(III)-H2 O2 complex have been proposed as alternative oxidants for this transformation. To investigate this, the oxidation of 4-alkylthiobenzoic acids and 4-methoxybenzoic acid by the CYP199A4 enzyme from Rhodopseudomonas palustris HaA2 was compared using both monooxygenase and peroxygenase pathways. By examining mutants at the mechanistically important, conserved acid alcohol-pair (D251N, T252A and T252E) the relative amounts of the reactive intermediates that would form in these reactions were disturbed. Substrate binding and X-ray crystal structures helped to understand changes in the activity and enabled an attempt to evaluate whether multiple oxidants can participate in these reactions. In peroxygenase reactions the T252E mutant had higher activity towards sulfoxidation than O-demethylation but in the monooxygenase reactions with the WT enzyme the activity of both reactions was similar. The peroxygenase activity of the T252A mutant was greater for sulfoxidation reactions than the WT enzyme, which is the reverse of the activity changes observed for O-demethylation. The monooxygenase activity and coupling efficiency of sulfoxidation and oxidative demethylation were reduced by similar degrees with the T252A mutant. These observations infer that while Cpd I is required for O-dealkylation, another oxidant may contribute to sulfoxidation. Based on the activity of the CYP199A4 mutants it is proposed that this is the Fe(III)-H2 O2 complex which would be more abundant in the peroxide-driven reactions.
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Affiliation(s)
- Matthew N Podgorski
- Department of Chemistry, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Tom Coleman
- Department of Chemistry, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Luke R Churchman
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Qld, 4072, Australia
| | - John B Bruning
- School of Biological Sciences, University of Adelaide, Adelaide, SA, 5005, Australia
| | - James J De Voss
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Qld, 4072, Australia
| | - Stephen G Bell
- Department of Chemistry, University of Adelaide, Adelaide, SA, 5005, Australia
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9
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Ren W, Schulz CE, Shroyer MH, Xu W, Xi S, An P, Guo W, Li J. Electronic Configurations and the Effect of Peripheral Substituents of (Nitrosyl)iron Corroles. Inorg Chem 2022; 61:20385-20396. [DOI: 10.1021/acs.inorgchem.2c03026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Wanjie Ren
- College of Materials Science and Optoelectronic Technology and Chinese Academy of Sciences Center for Excellence in Topological Quantum Computation, University of Chinese Academy of Sciences, Yanqi Lake, Huairou District, Beijing101408, P. R. China
| | - Charles E. Schulz
- Department of Physics and Astronomy, Knox College, Galesburg, Illinois61401, United States
| | - Mark H. Shroyer
- Department of Physics and Astronomy, Knox College, Galesburg, Illinois61401, United States
| | - Wei Xu
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences (CAS), Beijing100049, P. R. China
- RICMASS, Rome International Center for Materials Science Superstripes, Via dei Sabelli 119A, Rome00185, Italy
| | - Shibo Xi
- Institute of Chemical and Engineering Sciences, Agency for Science, Technology and Research, 1 Pesek Road, Jurong Island, Singapore627833, Singapore
| | - Pengfei An
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences (CAS), Beijing100049, P. R. China
| | - Wenping Guo
- National Energy Center for Coal to Clean Fuels, Synfuels China Co., Ltd., Huairou District, Beijing101400, P. R. China
| | - Jianfeng Li
- College of Materials Science and Optoelectronic Technology and Chinese Academy of Sciences Center for Excellence in Topological Quantum Computation, University of Chinese Academy of Sciences, Yanqi Lake, Huairou District, Beijing101408, P. R. China
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10
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Wang H, Huang SD, Yan L, Hu MY, Zhao J, Alp EE, Yoda Y, Petersen CM, Thompson MK. Europium-151 and iron-57 nuclear resonant vibrational spectroscopy of naturally abundant KEu(III)Fe(II)(CN) 6 and Eu(III)Fe(III)(CN) 6 complexes. Dalton Trans 2022; 51:17753-17761. [PMID: 36346270 PMCID: PMC9933908 DOI: 10.1039/d2dt02600g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have performed and analyzed the first combined 151Eu and 57Fe nuclear resonant vibrational spectroscopy (NRVS) for naturally abundant KEu(III)[Fe(II)(CN)6] and Eu(III)[Fe(III)(CN)6] complexes. Comparison of the observed 151Eu vs.57Fe NRVS spectroscopic features confirms that Eu(III) in both KEu(III)[Fe(II)(CN)6] and Eu(III)[Fe(III)(CN)6] occupies a position outside the [Fe(CN)6] core and coordinates to the N atoms of the CN- ions, whereas Fe(III) or Fe(II) occupies the site inside the [Fe(CN)6]4- core and coordinates to the C atoms of the CN- ions. In addition to the spectroscopic interest, the results from this study provide invaluable insights for the design and evaluation of the nanoparticles of such complexes as potential cellular contrast agents for their use in magnetic resonance imaging. The combined 151Eu and 57Fe NRVS measurements are also among the first few explorations of bi-isotopic NRVS experiments.
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Affiliation(s)
| | - Songping D Huang
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA.
| | - Lifen Yan
- SETI Institute, Mountain View, CA 94043, USA.
| | - Michael Y Hu
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Jiyong Zhao
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Ercan E Alp
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Yoshitaka Yoda
- Precision Spectroscopy Division, SPring-8/JASRI, Sayo, Hyogo 679-5198, Japan
| | - Courtney M Petersen
- Department of Chemistry and Biochemistry, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - Matthew K Thompson
- Department of Chemistry and Biochemistry, The University of Alabama, Tuscaloosa, AL 35487, USA
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11
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Chatterjee S, Harden I, Bistoni G, Castillo RG, Chabbra S, van Gastel M, Schnegg A, Bill E, Birrell JA, Morandi B, Neese F, DeBeer S. A Combined Spectroscopic and Computational Study on the Mechanism of Iron-Catalyzed Aminofunctionalization of Olefins Using Hydroxylamine Derived N-O Reagent as the "Amino" Source and "Oxidant". J Am Chem Soc 2022; 144:2637-2656. [PMID: 35119853 PMCID: PMC8855425 DOI: 10.1021/jacs.1c11083] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
![]()
Herein, we study
the mechanism of iron-catalyzed direct synthesis
of unprotected aminoethers from olefins by a hydroxyl amine derived
reagent using a wide range of analytical and spectroscopic techniques
(Mössbauer, Electron Paramagnetic Resonance, Ultra-Violet Visible
Spectroscopy, X-ray Absorption, Nuclear Resonance Vibrational Spectroscopy,
and resonance Raman) along with high-level quantum chemical calculations.
The hydroxyl amine derived triflic acid salt acts as the “oxidant”
as well as “amino” group donor. It activates the high-spin
Fe(II) (St = 2) catalyst [Fe(acac)2(H2O)2] (1) to generate
a high-spin (St = 5/2) intermediate (Int I), which decays to a second intermediate (Int II) with St = 2. The analysis of spectroscopic
and computational data leads to the formulation of Int I as [Fe(III)(acac)2-N-acyloxy] (an alkyl-peroxo-Fe(III)
analogue). Furthermore, Int II is formed by N–O
bond homolysis. However, it does not generate a high-valent
Fe(IV)(NH) species (a Fe(IV)(O) analogue), but instead a high-spin
Fe(III) center which is strongly antiferromagnetically coupled (J = −524 cm–1) to an iminyl radical,
[Fe(III)(acac)2-NH·], giving St = 2. Though Fe(NH) complexes as isoelectronic surrogates
to Fe(O) functionalities are known, detection of a high-spin Fe(III)-N-acyloxy intermediate (Int I), which undergoes
N–O bond cleavage to generate the active iron–nitrogen
intermediate (Int II), is unprecedented. Relative to
Fe(IV)(O) centers, Int II features a weak elongated Fe–N
bond which, together with the unpaired electron density along the
Fe–N bond vector, helps to rationalize its propensity for N-transfer reactions onto styrenyl olefins, resulting in
the overall formation of aminoethers. This study thus demonstrates
the potential of utilizing the iron-coordinated nitrogen-centered
radicals as powerful reactive intermediates in catalysis.
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Affiliation(s)
- Sayanti Chatterjee
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany.,Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Ingolf Harden
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Giovanni Bistoni
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Rebeca G Castillo
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Sonia Chabbra
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Maurice van Gastel
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Alexander Schnegg
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Eckhard Bill
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - James A Birrell
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Bill Morandi
- ETH Zürich, Vladimir-Prelog-Weg 3, HCI, 8093 Zürich, Switzerland.,Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Frank Neese
- 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, 45470 Mülheim an der Ruhr, Germany
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12
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Zhao B, Tang M, Lv Y. Shear stress regulates the migration of suspended breast cancer cells by nuclear lamina protein A/C and large tumor suppressor through yes-associated protein. Hum Cell 2022; 35:583-598. [PMID: 34984662 DOI: 10.1007/s13577-021-00666-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 12/22/2021] [Indexed: 12/30/2022]
Abstract
Breast cancer is life threatening among women because its migration by hematogenous metastasis, where, besides biochemical cues, breast circulating tumor cells (CTCs) expose to suspension state and shear stress. However, the combined effects of these mechanical factors on CTCs migration were unclear. Here, suspension state and shear stress were loaded to breast tumor cells (BTCs) to mimic two mechanical cues in the mechanical environment of breast CTCs and the mechanobiological mechanism of suspension state and shear stress regulating the migration of (BTCs) was investigated. The migration and nuclear lamina protein A/C (Lamin A/C) accumulation were enhanced in MDA-MB-231 and SK-BR-3 BTCs exposed to shear stress though lower than that of suspended cells with different yes-associated protein (YAP) subcellular localization. Knockdown of LMNA downregulated and upregulated YAP targets in suspended BTCs and BTCs exposed to shear stress, respectively, which inhibited MDA-MB-231 BTCs migration in vitro and in vivo. Large tumor suppressor (LATS) responded to suspension state and shear stress, knockdown of which decreased the migration of MDA-MB-231 BTCs. These findings uncover the mechanobiological mechanism that suspension state and shear stress antagonistically promote BTCs migration by Lamin A/C and LATS through YAP and the potential for targeting YAP in CTCs prognosis. Shear stress regulates suspended breast cancer cells migration by Lamin A/C and LATS through YAP.
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Affiliation(s)
- Boyuan Zhao
- Mechanobiology and Regenerative Medicine Laboratory, Bioengineering College, Chongqing University, Chongqing, 400044, People's Republic of China
| | - Mei Tang
- Mechanobiology and Regenerative Medicine Laboratory, Bioengineering College, Chongqing University, Chongqing, 400044, People's Republic of China
| | - Yonggang Lv
- State Key Laboratory of New Textile Materials and Advanced Processing Technologies, Wuhan Textile University, Jiangxia District, No. 1 Sunshine Avenue, Wuhan, 430200, Hubei Province, People's Republic of China.
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13
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Lehnert N, Kim E, Dong HT, Harland JB, Hunt AP, Manickas EC, Oakley KM, Pham J, Reed GC, Alfaro VS. The Biologically Relevant Coordination Chemistry of Iron and Nitric Oxide: Electronic Structure and Reactivity. Chem Rev 2021; 121:14682-14905. [PMID: 34902255 DOI: 10.1021/acs.chemrev.1c00253] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Nitric oxide (NO) is an important signaling molecule that is involved in a wide range of physiological and pathological events in biology. Metal coordination chemistry, especially with iron, is at the heart of many biological transformations involving NO. A series of heme proteins, nitric oxide synthases (NOS), soluble guanylate cyclase (sGC), and nitrophorins, are responsible for the biosynthesis, sensing, and transport of NO. Alternatively, NO can be generated from nitrite by heme- and copper-containing nitrite reductases (NIRs). The NO-bearing small molecules such as nitrosothiols and dinitrosyl iron complexes (DNICs) can serve as an alternative vehicle for NO storage and transport. Once NO is formed, the rich reaction chemistry of NO leads to a wide variety of biological activities including reduction of NO by heme or non-heme iron-containing NO reductases and protein post-translational modifications by DNICs. Much of our understanding of the reactivity of metal sites in biology with NO and the mechanisms of these transformations has come from the elucidation of the geometric and electronic structures and chemical reactivity of synthetic model systems, in synergy with biochemical and biophysical studies on the relevant proteins themselves. This review focuses on recent advancements from studies on proteins and model complexes that not only have improved our understanding of the biological roles of NO but also have provided foundations for biomedical research and for bio-inspired catalyst design in energy science.
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Affiliation(s)
- Nicolai Lehnert
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Eunsuk Kim
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Hai T Dong
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Jill B Harland
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Andrew P Hunt
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Elizabeth C Manickas
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Kady M Oakley
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - John Pham
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Garrett C Reed
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Victor Sosa Alfaro
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
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14
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Cook EN, Machan CW. Bioinspired mononuclear Mn complexes for O 2 activation and biologically relevant reactions. Dalton Trans 2021; 50:16871-16886. [PMID: 34730590 DOI: 10.1039/d1dt03178c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A general interest in harnessing the oxidizing power of dioxygen (O2) continues to motivate research efforts on bioinspired and biomimetic complexes to better understand how metalloenzymes mediate these reactions. The ubiquity of Fe- and Cu-based enzymes attracts significant attention and has resulted in many noteworthy developments for abiotic systems interested in direct O2 reduction and small molecule activation. However, despite the existence of Mn-based metalloenzymes with important O2-dependent activity, there has been comparatively less focus on the development of these analogues relative to Fe- and Cu-systems. In this Perspective, we summarize important contributions to the development of bioinspired mononuclear Mn complexes for O2 activation and studies on their reactivity, emphasizing important design parameters in the primary and secondary coordination spheres and outlining mechanistic trends.
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Affiliation(s)
- Emma N Cook
- Department of Chemistry, University of Virginia, PO Box 400319, Charlottesville, VA 22904-4319, USA.
| | - Charles W Machan
- Department of Chemistry, University of Virginia, PO Box 400319, Charlottesville, VA 22904-4319, USA.
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15
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Tung CY, Tseng YT, Lu TT, Liaw WF. Insight into the Electronic Structure of Biomimetic Dinitrosyliron Complexes (DNICs): Toward the Syntheses of Amido-Bridging Dinuclear DNICs. Inorg Chem 2021; 60:15846-15873. [PMID: 34009960 DOI: 10.1021/acs.inorgchem.1c00566] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The ubiquitous function of nitric oxide (NO) guided the biological discovery of the natural dinitrosyliron unit (DNIU) [Fe(NO)2] as an intermediate/end product after Fe nitrosylation of nonheme cofactors. Because of the natural utilization of this cofactor for the biological storage and delivery of NO, a bioinorganic study of synthetic dinitrosyliron complexes (DNICs) has been extensively explored in the last 2 decades. The bioinorganic study of DNICs involved the development of synthetic methodology, spectroscopic discrimination, biological application of NO-delivery reactivity, and translational application to the (catalytic) transformation of small molecules. In this Forum Article, we aim to provide a systematic review of spectroscopic and computational insights into the bonding nature within the DNIU [Fe(NO)2] and the electronic structure of different types of DNICs, which highlights the synchronized advance in synthetic methodology and spectroscopic tools. With regard to the noninnocent nature of a NO ligand, spectroscopic and computational tools were utilized to provide qualitative/quantitative assignment of oxidation states of Fe and NO in DNICs with different redox levels and ligation modes as well as to probe the Fe-NO bonding interaction modulated by supporting ligands. Besides the strong antiferromagnetic coupling between high-spin Fe and paramagnetic NO ligands within the covalent DNIU [Fe(NO)2], in polynuclear DNICs, the effects of the Fe···Fe distance, nature of the bridging ligands, and type of bridging modes on the regulation of the magnetic coupling among paramagnetic DNIU [Fe(NO)2] are further reviewed. In the last part of this Forum Article, the sequential reaction of {Fe(NO)2}10 DNIC [(NO)2Fe(AMP)] (1-red) with NO(g), HBF4, and KC8 establishes a synthetic cycle, {Fe(NO)2}9-{Fe(NO)2}9 DNIC [(NO)2Fe(μ-dAMP)2Fe(NO)2] (1) → {Fe(NO)2}9 DNIC [(NO2)Fe(AMP)][BF4] (1-H) → {Fe(NO)2}10 DNIC 1-red → DNIC 1, for the transformation of NO into HNO/N2O. Of importance, the NO-induced transformation of {Fe(NO)2}10 DNIC 1-red and [(NO)2Fe(DTA)] (2-red; DTA = diethylenetriamine) unravels a synthetic strategy for preparation of the {Fe(NO)2}9-{Fe(NO)2}9 DNICs [(NO)2Fe(μ-NHR)2Fe(NO)2] containing amido-bridging ligands, which hold the potential to feature distinctive physical properties, chemical reactivities, and biological applications.
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Affiliation(s)
- Chi-Yen Tung
- Department of Chemistry, National Tsing Hua University (NTHU), Hsinchu 30013 Taiwan
| | - Yu-Ting Tseng
- Department of Chemistry, National Tsing Hua University (NTHU), Hsinchu 30013 Taiwan
| | - Tsai-Te Lu
- Institute of Biomedical Engineering, National Tsing Hua University (NTHU), Hsinchu 30013, Taiwan
| | - Wen-Feng Liaw
- Department of Chemistry, National Tsing Hua University (NTHU), Hsinchu 30013 Taiwan
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16
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Ledray AP, Mittra K, Green MT. NRVS investigation of ascorbate peroxidase compound II: Observation of Iron(IV)oxo stretching. J Inorg Biochem 2021; 224:111548. [PMID: 34481347 DOI: 10.1016/j.jinorgbio.2021.111548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 07/07/2021] [Accepted: 07/13/2021] [Indexed: 11/18/2022]
Abstract
The protonation state of ascorbate peroxidase compound II (APX-II) has been a subject of debate. A combined X-ray/neutron crystallographic study reported that APX-II is best described as an iron(IV)hydroxide species with an FeO distance of 1.88 Å (Kwon, et al. Nat Commun2016, 7, 13,445), while X-ray absorption spectroscopy (XAS) experiments (utilizing extended X-ray absorption fine structure (EXAFS) and pre-edge analyses) indicate APX-II is an authentic iron(IV)oxo species with an FeO distance 1.68 Å (Ledray, et al. Journal of the American Chemical Society2020,142, 20,419). Previous debates concerning ferryl protonation states have been resolved through the application of Badger's rule, which correlates FeO bond distances with FeO vibrational frequencies. To obtain the required vibrational data, we have collected Nuclear Resonance Vibrational Spectroscopy (NRVS) data for APX-II. We observe a broad vibrational feature in the range associated with iron(IV)oxo stretching (700-800 cm-1). This feature appears to have two peaks at 732 cm-1 and 770 cm-1, corresponding to FeO distances of 1.69 and 1.67 Å, respectively. The broad vibrational envelope and the presence of multiple resonances could reflect a distribution of hydrogen bonding interactions within the active-site pocket.
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Affiliation(s)
- Aaron P Ledray
- Department of Chemistry, University of California, Irvine, CA 92697, USA; Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA
| | - Kaustuv Mittra
- Department of Chemistry, University of California, Irvine, CA 92697, USA; Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA
| | - Michael T Green
- Department of Chemistry, University of California, Irvine, CA 92697, USA; Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA.
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17
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Wang H, Braun A, Cramer SP, Gee LB, Yoda Y. Nuclear Resonance Vibrational Spectroscopy: A Modern Tool to Pinpoint Site-Specific Cooperative Processes. Catalysts 2021; 11:909. [PMID: 35582460 PMCID: PMC9109880 DOI: 10.3390/cryst11080909] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2023] Open
Abstract
Nuclear resonant vibrational spectroscopy (NRVS) is a synchrotron radiation (SR)-based nuclear inelastic scattering spectroscopy that measures the phonons (i.e., vibrational modes) associated with the nuclear transition. It has distinct advantages over traditional vibration spectroscopy and has wide applications in physics, chemistry, bioinorganic chemistry, materials sciences, and geology, as well as many other research areas. In this article, we present a scientific and figurative description of this yet modern tool for the potential users in various research fields in the future. In addition to short discussions on its development history, principles, and other theoretical issues, the focus of this article is on the experimental aspects, such as the instruments, the practical measurement issues, the data process, and a few examples of its applications. The article concludes with introduction to non-57Fe NRVS and an outlook on the impact from the future upgrade of SR rings.
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Affiliation(s)
| | - Artur Braun
- Laboratory for High Performance Ceramics, Empa. Swiss Federal Laboratories for Materials Science and Technology, Überlandstrasse 129, CH-8600 Dübendorf, Switzerland
| | | | - Leland B. Gee
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Yoshitaka Yoda
- Precision Spectroscopy Division, SPring-8/JASRI, Sayo 679-5198, Japan
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18
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Lorent C, Pelmenschikov V, Frielingsdorf S, Schoknecht J, Caserta G, Yoda Y, Wang H, Tamasaku K, Lenz O, Cramer SP, Horch M, Lauterbach L, Zebger I. Exploring Structure and Function of Redox Intermediates in [NiFe]-Hydrogenases by an Advanced Experimental Approach for Solvated, Lyophilized and Crystallized Metalloenzymes. Angew Chem Int Ed Engl 2021; 60:15854-15862. [PMID: 33783938 PMCID: PMC8360142 DOI: 10.1002/anie.202100451] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/20/2021] [Indexed: 01/28/2023]
Abstract
To study metalloenzymes in detail, we developed a new experimental setup allowing the controlled preparation of catalytic intermediates for characterization by various spectroscopic techniques. The in situ monitoring of redox transitions by infrared spectroscopy in enzyme lyophilizate, crystals, and solution during gas exchange in a wide temperature range can be accomplished as well. Two O2 -tolerant [NiFe]-hydrogenases were investigated as model systems. First, we utilized our platform to prepare highly concentrated hydrogenase lyophilizate in a paramagnetic state harboring a bridging hydride. This procedure proved beneficial for 57 Fe nuclear resonance vibrational spectroscopy and revealed, in combination with density functional theory calculations, the vibrational fingerprint of this catalytic intermediate. The same in situ IR setup, combined with resonance Raman spectroscopy, provided detailed insights into the redox chemistry of enzyme crystals, underlining the general necessity to complement X-ray crystallographic data with spectroscopic analyses.
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Affiliation(s)
- Christian Lorent
- Department of ChemistryTechnische Universität BerlinStrasse des 17. Juni 13510623BerlinGermany
| | - Vladimir Pelmenschikov
- Department of ChemistryTechnische Universität BerlinStrasse des 17. Juni 13510623BerlinGermany
| | - Stefan Frielingsdorf
- Department of ChemistryTechnische Universität BerlinStrasse des 17. Juni 13510623BerlinGermany
| | - Janna Schoknecht
- Department of ChemistryTechnische Universität BerlinStrasse des 17. Juni 13510623BerlinGermany
| | - Giorgio Caserta
- Department of ChemistryTechnische Universität BerlinStrasse des 17. Juni 13510623BerlinGermany
| | - Yoshitaka Yoda
- Japan Synchrotron Radiation Research InstituteSPring-81-1-1 Kouto, Mikazuki-choSayo-gunHyogo679-5198Japan
| | - Hongxin Wang
- SETI Institute189 Bernardo AvenueMountain ViewCalifornia94043USA
| | - Kenji Tamasaku
- RIKEN SPring-8 center1-1-1 Kouto, Sayo-choSayo-gunHyogo679-5148Japan
| | - Oliver Lenz
- Department of ChemistryTechnische Universität BerlinStrasse des 17. Juni 13510623BerlinGermany
| | | | - Marius Horch
- Department of ChemistryTechnische Universität BerlinStrasse des 17. Juni 13510623BerlinGermany
- Department of PhysicsFreie Universität BerlinArnimallee 1414195BerlinGermany
| | - Lars Lauterbach
- Department of ChemistryTechnische Universität BerlinStrasse des 17. Juni 13510623BerlinGermany
| | - Ingo Zebger
- Department of ChemistryTechnische Universität BerlinStrasse des 17. Juni 13510623BerlinGermany
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19
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Lorent C, Pelmenschikov V, Frielingsdorf S, Schoknecht J, Caserta G, Yoda Y, Wang H, Tamasaku K, Lenz O, Cramer SP, Horch M, Lauterbach L, Zebger I. Ein neuer Aufbau zur Untersuchung der Struktur und Funktion von solvatisierten, lyophilisierten und kristallinen Metalloenzymen – veranschaulicht anhand von [NiFe]‐Hydrogenasen. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202100451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Christian Lorent
- Department of Chemistry Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Deutschland
| | - Vladimir Pelmenschikov
- Department of Chemistry Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Deutschland
| | - Stefan Frielingsdorf
- Department of Chemistry Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Deutschland
| | - Janna Schoknecht
- Department of Chemistry Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Deutschland
| | - Giorgio Caserta
- Department of Chemistry Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Deutschland
| | - Yoshitaka Yoda
- Japan Synchrotron Radiation Research Institute SPring-8 1-1-1 Kouto, Mikazuki-cho Sayo-gun Hyogo 679-5198 Japan
| | - Hongxin Wang
- SETI Institute 189 Bernardo Avenue Mountain View California 94043 USA
| | - Kenji Tamasaku
- RIKEN SPring-8 center 1-1-1 Kouto, Sayo-cho Sayo-gun Hyogo 679-5148 Japan
| | - Oliver Lenz
- Department of Chemistry Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Deutschland
| | - Stephen P. Cramer
- SETI Institute 189 Bernardo Avenue Mountain View California 94043 USA
| | - Marius Horch
- Department of Chemistry Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Deutschland
- Department of Physics Freie Universität Berlin Arnimallee 14 14195 Berlin Deutschland
| | - Lars Lauterbach
- Department of Chemistry Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Deutschland
| | - Ingo Zebger
- Department of Chemistry Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Deutschland
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20
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Pelmenschikov V, Birrell JA, Gee LB, Richers CP, Reijerse EJ, Wang H, Arragain S, Mishra N, Yoda Y, Matsuura H, Li L, Tamasaku K, Rauchfuss TB, Lubitz W, Cramer SP. Vibrational Perturbation of the [FeFe] Hydrogenase H-Cluster Revealed by 13C 2H-ADT Labeling. J Am Chem Soc 2021; 143:8237-8243. [PMID: 34043346 DOI: 10.1021/jacs.1c02323] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[FeFe] hydrogenases are highly active catalysts for the interconversion of molecular hydrogen with protons and electrons. Here, we use a combination of isotopic labeling, 57Fe nuclear resonance vibrational spectroscopy (NRVS), and density functional theory (DFT) calculations to observe and characterize the vibrational modes involving motion of the 2-azapropane-1,3-dithiolate (ADT) ligand bridging the two iron sites in the [2Fe]H subcluster. A -13C2H2- ADT labeling in the synthetic diiron precursor of [2Fe]H produced isotope effects observed throughout the NRVS spectrum. The two precursor isotopologues were then used to reconstitute the H-cluster of [FeFe] hydrogenase from Chlamydomonas reinhardtii (CrHydA1), and NRVS was measured on samples poised in the catalytically crucial Hhyd state containing a terminal hydride at the distal Fe site. The 13C2H isotope effects were observed also in the Hhyd spectrum. DFT simulations of the spectra allowed identification of the 57Fe normal modes coupled to the ADT ligand motions. Particularly, a variety of normal modes involve shortening of the distance between the distal Fe-H hydride and ADT N-H bridgehead hydrogen, which may be relevant to the formation of a transition state on the way to H2 formation.
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Affiliation(s)
| | - James A Birrell
- Max Planck Institute for Chemical Energy Conversion, 45470 Mülheim an der Ruhr, Germany
| | - Leland B Gee
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Casseday P Richers
- School of Chemical Sciences, University of Illinois, Urbana, Illinois 61801, United States
| | - Edward J Reijerse
- Max Planck Institute for Chemical Energy Conversion, 45470 Mülheim an der Ruhr, Germany
| | - Hongxin Wang
- SETI Institute, Mountain View, California 94043, United States
| | - Simon Arragain
- IFP Energies nouvelles, 92852 Rueil-Malmaison, France.,Department of Chemistry, University of California, Davis, California 95616, United States
| | - Nakul Mishra
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - Yoshitaka Yoda
- Precision Spectroscopy Division, SPring-8/JASRI, Sayo, Hyogo 679-5198, Japan
| | - Hiroaki Matsuura
- Life Science Research Infrastructure Group, Advanced Photon Technology Division, RIKEN/SPring-8 Center, Sayo, Hyogo 679-5148, Japan
| | - Lei Li
- Hyogo Science and Technology Association, Synchrotron Radiation Research Center, Tatsuno-shi, Hyogo 679-5165, Japan
| | - Kenji Tamasaku
- Research and Utilization Division, SPring-8/JASRI, Sayo, Hyogo 679-5198, Japan
| | - Thomas B Rauchfuss
- School of Chemical Sciences, University of Illinois, Urbana, Illinois 61801, United States
| | - Wolfgang Lubitz
- Max Planck Institute for Chemical Energy Conversion, 45470 Mülheim an der Ruhr, Germany
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21
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Chiang MH, Pelmenschikov V, Gee LB, Liu YC, Hsieh CC, Wang H, Yoda Y, Matsuura H, Li L, Cramer SP. High-Frequency Fe-H and Fe-H 2 Modes in a trans-Fe(η 2-H 2)(H) Complex: A Speed Record for Nuclear Resonance Vibrational Spectroscopy. Inorg Chem 2021; 60:555-559. [PMID: 33356182 PMCID: PMC7886317 DOI: 10.1021/acs.inorgchem.0c03006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nuclear resonance vibrational spectroscopy (NRVS) and density functional theory (DFT) are complementary tools for studying the vibrational and geometric structures of specific isotopically labeled molecular systems. Here we apply NRVS and DFT to characterize the trans-[57Fe(η2-H2)(H)(dppe)2][BPh4] [dppe = 1,2-bis(diphenylphosphino)ethane] complex. Heretofore, most NRVS observations have centered on the spectral region below 1000 cm-1, where the 57Fe signal is strongest. In this work, we show that state-of-the-art synchrotron facilities can extend the observable region to 2000 cm-1 and likely beyond, in measurements that require less than 1 day. The 57Fe-H stretch was revealed at 1915 cm-1, along with the asymmetric 57Fe-H2 stretch at 1774 cm-1. For a small fraction of the H2-dissociated product, the 57Fe-H stretch was detected at 1956 cm-1. The unique sensitivity to 57Fe motion and the isolated nature of the Fe-H/H2 stretching modes enabled NRVS to quantitatively analyze the sample composition.
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Affiliation(s)
- Ming-Hsi Chiang
- Institute of Chemistry, Academia Sinica, Nankang, Taipei 115, Taiwan and Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Vladimir Pelmenschikov
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Leland B. Gee
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Yu-Chiao Liu
- Institute of Chemistry, Academia Sinica, Nankang, Taipei 115, Taiwan and Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Chang-Chih Hsieh
- Institute of Chemistry, Academia Sinica, Nankang, Taipei 115, Taiwan and Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Hongxin Wang
- SETI Institute, Mountain View, California 94043, United States
| | - Yoshitaka Yoda
- Precision Spectroscopy Division, SPring-8/JASRI, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Hiroaki Matsuura
- RIKEN/SPring-8 Center, Advanced Photon Technology Division, Life Science Research Infrastructure Group, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Lei Li
- Synchrotron Radiation Research Center, Hyogo Science and Technology Association, 1-490-2, Kouto, Singu-cho, Tatsuno-shi, Hyogo 679-5165, Japan
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22
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Scherthan L, Pfleger RF, Auerbach H, Hochdörffer T, Wolny JA, Bi W, Zhao J, Hu MY, Alp EE, Anson CE, Diller R, Powell AK, Schünemann V. Exploring the Vibrational Side of Spin-Phonon Coupling in Single-Molecule Magnets via 161 Dy Nuclear Resonance Vibrational Spectroscopy. Angew Chem Int Ed Engl 2020; 59:8818-8822. [PMID: 32181552 PMCID: PMC7317570 DOI: 10.1002/anie.201914728] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 02/14/2020] [Indexed: 11/06/2022]
Abstract
Synchrotron-based nuclear resonance vibrational spectroscopy (NRVS) using the Mössbauer isotope 161 Dy has been employed for the first time to study the vibrational properties of a single-molecule magnet (SMM) incorporating DyIII , namely [Dy(Cy3 PO)2 (H2 O)5 ]Br3 ⋅2 (Cy3 PO)⋅2 H2 O ⋅2 EtOH. The experimental partial phonon density of states (pDOS), which includes all vibrational modes involving a displacement of the DyIII ion, was reproduced by means of simulations using density functional theory (DFT), enabling the assignment of all intramolecular vibrational modes. This study proves that 161 Dy NRVS is a powerful experimental tool with significant potential to help to clarify the role of phonons in SMMs.
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Affiliation(s)
- Lena Scherthan
- Department of PhysicsTechnische Universität KaiserslauternErwin-Schrödinger-Str. 4667663KaiserslauternGermany
| | - Rouven F. Pfleger
- Institute of Inorganic ChemistryKarlsruhe Institute of TechnologyEngesserstr. 1576131KarlsruheGermany
| | - Hendrik Auerbach
- Department of PhysicsTechnische Universität KaiserslauternErwin-Schrödinger-Str. 4667663KaiserslauternGermany
| | - Tim Hochdörffer
- Department of PhysicsTechnische Universität KaiserslauternErwin-Schrödinger-Str. 4667663KaiserslauternGermany
| | - Juliusz A. Wolny
- Department of PhysicsTechnische Universität KaiserslauternErwin-Schrödinger-Str. 4667663KaiserslauternGermany
| | - Wenli Bi
- Advanced Photon SourceArgonne National Laboratory9700 South Cass AvenueArgonneIL60439USA
- Department of PhysicsUniversity of Alabama at BirminghamBirminghamAL35294USA
| | - Jiyong Zhao
- Advanced Photon SourceArgonne National Laboratory9700 South Cass AvenueArgonneIL60439USA
| | - Michael Y. Hu
- Advanced Photon SourceArgonne National Laboratory9700 South Cass AvenueArgonneIL60439USA
| | - E. Ercan Alp
- Advanced Photon SourceArgonne National Laboratory9700 South Cass AvenueArgonneIL60439USA
| | - Christopher E. Anson
- Institute of Inorganic ChemistryKarlsruhe Institute of TechnologyEngesserstr. 1576131KarlsruheGermany
| | - Rolf Diller
- Department of PhysicsTechnische Universität KaiserslauternErwin-Schrödinger-Str. 4667663KaiserslauternGermany
| | - Annie K. Powell
- Institute of Inorganic ChemistryKarlsruhe Institute of TechnologyEngesserstr. 1576131KarlsruheGermany
- Institute of NanotechnologyKarlsruhe Institute of Technology76021KarlsruheGermany
| | - Volker Schünemann
- Department of PhysicsTechnische Universität KaiserslauternErwin-Schrödinger-Str. 4667663KaiserslauternGermany
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23
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Gee LB, Pelmenschikov V, Wang H, Mishra N, Liu YC, Yoda Y, Tamasaku K, Chiang MH, Cramer SP. Vibrational characterization of a diiron bridging hydride complex - a model for hydrogen catalysis. Chem Sci 2020; 11:5487-5493. [PMID: 34094075 PMCID: PMC8159291 DOI: 10.1039/d0sc01290d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 05/01/2020] [Indexed: 11/21/2022] Open
Abstract
A diiron complex containing a bridging hydride and a protonated terminal thiolate of the form [(μ,κ2-bdtH)(μ-PPh2)(μ-H)Fe2(CO)5]+ has been investigated through 57Fe nuclear resonance vibrational spectroscopy (NRVS) and interpreted using density functional theory (DFT) calculations. We report the Fe-μH-Fe wagging mode, and indications for Fe-μD stretching vibrations in the D-isotopologue, observed by 57Fe-NRVS. Our combined approach demonstrates an asymmetric sharing of the hydride between the two iron sites that yields two nondegenerate Fe-μH/D stretching vibrations. The studied complex provides an important model relevant to biological hydrogen catalysis intermediates. The complex mimics proposals for the binuclear metal sites in [FeFe] and [NiFe] hydrogenases. It is also an appealing prototype for the 'Janus intermediate' of nitrogenase, which has been proposed to contain two bridging Fe-H-Fe hydrides and two protonated sulfurs at the FeMo-cofactor. The significance of observing indirect effects of the bridging hydride, as well as obstacles in its direct observation, is discussed in the context of biological hydrogen intermediates.
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Affiliation(s)
- Leland B Gee
- Department of Chemistry, Stanford University 333 Campus Drive Stanford CA 94305 USA
| | - Vladimir Pelmenschikov
- Institut für Chemie, Technische Universität Berlin Strasse des 17 Juni 135 10623 Berlin Germany
| | - Hongxin Wang
- SETI Institute 189 Bernardo Avenue Mountain View CA 94043 USA
| | - Nakul Mishra
- Department of Chemistry, University of California, Davis One Shields Ave Davis CA 95616 USA
| | - Yu-Chiao Liu
- Institute of Chemistry, Academia Sinica Nankang Taipei 115 Taiwan
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University Kaohsiung 807 Taiwan
| | - Yoshitaka Yoda
- Japan Synchrotron Radiation Research Institute (JASRI), SPring-8 1-1-1 Kouto, Sayo-gun Hyogo 679-5198 Japan
| | - Kenji Tamasaku
- RIKEN SPring-8 Center 1-1-1 Kouto, Sayo-cho, Sayo-gun Hyogo 679-5148 Japan
| | - Ming-Hsi Chiang
- Institute of Chemistry, Academia Sinica Nankang Taipei 115 Taiwan
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University Kaohsiung 807 Taiwan
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24
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Scherthan L, Pfleger RF, Auerbach H, Hochdörffer T, Wolny JA, Bi W, Zhao J, Hu MY, Alp EE, Anson CE, Diller R, Powell AK, Schünemann V. Untersuchung von Schwingungen in Bezug auf Spin‐Phonon‐Kopplung in Einzelmolekülmagneten mittels nuklearer inelastischer Streuung am
161
Dy‐Kern. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201914728] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Lena Scherthan
- Department of Physics Technische Universität Kaiserslautern Erwin-Schrödinger-Str. 46 67663 Kaiserslautern Deutschland
| | - Rouven F. Pfleger
- Institute of Inorganic Chemistry Karlsruhe Institute of Technology Engesserstr. 15 76131 Karlsruhe Deutschland
| | - Hendrik Auerbach
- Department of Physics Technische Universität Kaiserslautern Erwin-Schrödinger-Str. 46 67663 Kaiserslautern Deutschland
| | - Tim Hochdörffer
- Department of Physics Technische Universität Kaiserslautern Erwin-Schrödinger-Str. 46 67663 Kaiserslautern Deutschland
| | - Juliusz A. Wolny
- Department of Physics Technische Universität Kaiserslautern Erwin-Schrödinger-Str. 46 67663 Kaiserslautern Deutschland
| | - Wenli Bi
- Advanced Photon Source Argonne National Laboratory 9700 S. Cass Avenue Argonne IL 60439 USA
- Department of Physics University of Alabama at Birmingham Birmingham AL 35294 USA
| | - Jiyong Zhao
- Advanced Photon Source Argonne National Laboratory 9700 S. Cass Avenue Argonne IL 60439 USA
| | - Michael Y. Hu
- Advanced Photon Source Argonne National Laboratory 9700 S. Cass Avenue Argonne IL 60439 USA
| | - E. Ercan Alp
- Advanced Photon Source Argonne National Laboratory 9700 S. Cass Avenue Argonne IL 60439 USA
| | - Christopher E. Anson
- Institute of Inorganic Chemistry Karlsruhe Institute of Technology Engesserstr. 15 76131 Karlsruhe Deutschland
| | - Rolf Diller
- Department of Physics Technische Universität Kaiserslautern Erwin-Schrödinger-Str. 46 67663 Kaiserslautern Deutschland
| | - Annie K. Powell
- Institute of Inorganic Chemistry Karlsruhe Institute of Technology Engesserstr. 15 76131 Karlsruhe Deutschland
- Institute of Nanotechnology Karlsruhe Institute of Technology 76021 Karlsruhe Deutschland
| | - Volker Schünemann
- Department of Physics Technische Universität Kaiserslautern Erwin-Schrödinger-Str. 46 67663 Kaiserslautern Deutschland
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25
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Kramm UI, Ni L, Wagner S. 57 Fe Mössbauer Spectroscopy Characterization of Electrocatalysts. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2019; 31:e1805623. [PMID: 30773742 DOI: 10.1002/adma.201805623] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 01/11/2019] [Indexed: 05/06/2023]
Abstract
This work addresses the importance of Mössbauer spectroscopy for the characterization of iron-containing electrocatalysts. The most important aspects of electrocatalysis and Mössbauer spectroscopy are summarized. Next, Fe-N-C catalysts and important conclusions made by this technique on preparation, active site identification and degradation are summarized. Furthermore, recent highlights derived for other iron-containing electrocatalysts are summarized.
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Affiliation(s)
- Ulrike I Kramm
- TU Darmstadt, Department of Chemistry and Department of Materials- and Earth Sciences, Otto-Berndt-Str. 3, 64287, Darmstadt, Germany
| | - Lingmei Ni
- TU Darmstadt, Department of Chemistry and Department of Materials- and Earth Sciences, Otto-Berndt-Str. 3, 64287, Darmstadt, Germany
| | - Stephan Wagner
- TU Darmstadt, Department of Chemistry and Department of Materials- and Earth Sciences, Otto-Berndt-Str. 3, 64287, Darmstadt, Germany
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26
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Li A, Nicolae SA, Qiao M, Preuss K, Szilágyi PA, Moores A, Titirici M. Homogenous Meets Heterogenous and Electro‐Catalysis: Iron‐Nitrogen Molecular Complexes within Carbon Materials for Catalytic Applications. ChemCatChem 2019. [DOI: 10.1002/cctc.201900910] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Alain Li
- Centre for Green Chemistry and Catalysis Department of ChemistryMcGill University 801 Sherbrooke St West Montreal H3A 0B8 Canada
| | - Sabina A. Nicolae
- Queen Mary University of LondonSchool of Engineering and Materials Science Mile End Road London E1 4NS UK
| | - Mo Qiao
- Queen Mary University of LondonMaterials Research Institute Mile End Road London E1 4NS UK
| | - Kathrin Preuss
- Queen Mary University of LondonSchool of Engineering and Materials Science Mile End Road London E1 4NS UK
- Queen Mary University of LondonMaterials Research Institute Mile End Road London E1 4NS UK
| | - Petra A. Szilágyi
- Queen Mary University of LondonSchool of Engineering and Materials Science Mile End Road London E1 4NS UK
- Queen Mary University of LondonMaterials Research Institute Mile End Road London E1 4NS UK
| | - Audrey Moores
- Centre for Green Chemistry and Catalysis Department of ChemistryMcGill University 801 Sherbrooke St West Montreal H3A 0B8 Canada
| | - Maria‐Magdalena Titirici
- Queen Mary University of LondonSchool of Engineering and Materials Science Mile End Road London E1 4NS UK
- Queen Mary University of LondonMaterials Research Institute Mile End Road London E1 4NS UK
- Department of Chemical Engineering Imperial College LondonSouth Kensington Campus London SE7 2AZ UK
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27
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Wagner S, Auerbach H, Tait CE, Martinaiou I, Kumar SCN, Kübel C, Sergeev I, Wille H, Behrends J, Wolny JA, Schünemann V, Kramm UI. Elucidating the Structural Composition of an Fe–N–C Catalyst by Nuclear‐ and Electron‐Resonance Techniques. Angew Chem Int Ed Engl 2019; 58:10486-10492. [DOI: 10.1002/anie.201903753] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 05/15/2019] [Indexed: 11/06/2022]
Affiliation(s)
- Stephan Wagner
- TU DarmstadtGraduate School Energy Science and Engineering Otto-Berndt-Str. 3 64287 Darmstadt Germany
- TU DarmstadtDepartment of Material and Earth Sciences Otto-Berndt-Str. 3 64287 Darmstadt Germany
| | - Hendrik Auerbach
- TU KaiserslauternDepartment of Physics, Biophysics and Medical Physics Erwin-Schrödinger-Strasse 46 67663 Kaiserslautern Germany
| | - Claudia E. Tait
- Freie Universität BerlinBerlin Joint EPR Lab, Department of Physics Arnimallee 14 14195 Berlin Germany
| | - Ioanna Martinaiou
- TU DarmstadtGraduate School Energy Science and Engineering Otto-Berndt-Str. 3 64287 Darmstadt Germany
- TU DarmstadtDepartment of Chemistry Otto-Berndt-Str. 3 64287 Darmstadt Germany
| | - Shyam C. N. Kumar
- Karlsruhe Institute of Technology (KIT)Institute for NanotechnologyCampus North Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Germany
| | - Christian Kübel
- TU DarmstadtDepartment of Material and Earth Sciences Otto-Berndt-Str. 3 64287 Darmstadt Germany
- Karlsruhe Institute of Technology (KIT)Institute for NanotechnologyCampus North Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Germany
- Karlsruhe Institute of Technology (KIT)Nano Micro FacilityCampus North Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Germany
| | - Ilya Sergeev
- Deutsches Elektronen-Synchrotron Notkestraße 85 22607 Hamburg Germany
| | | | - Jan Behrends
- Freie Universität BerlinBerlin Joint EPR Lab, Department of Physics Arnimallee 14 14195 Berlin Germany
| | - Juliusz A. Wolny
- TU KaiserslauternDepartment of Physics, Biophysics and Medical Physics Erwin-Schrödinger-Strasse 46 67663 Kaiserslautern Germany
| | - Volker Schünemann
- TU KaiserslauternDepartment of Physics, Biophysics and Medical Physics Erwin-Schrödinger-Strasse 46 67663 Kaiserslautern Germany
| | - Ulrike I. Kramm
- TU DarmstadtGraduate School Energy Science and Engineering Otto-Berndt-Str. 3 64287 Darmstadt Germany
- TU DarmstadtDepartment of Material and Earth Sciences Otto-Berndt-Str. 3 64287 Darmstadt Germany
- TU DarmstadtDepartment of Chemistry Otto-Berndt-Str. 3 64287 Darmstadt Germany
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28
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Wagner S, Auerbach H, Tait CE, Martinaiou I, Kumar SCN, Kübel C, Sergeev I, Wille H, Behrends J, Wolny JA, Schünemann V, Kramm UI. Elucidating the Structural Composition of an Fe–N–C Catalyst by Nuclear‐ and Electron‐Resonance Techniques. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201903753] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Stephan Wagner
- TU DarmstadtGraduate School Energy Science and Engineering Otto-Berndt-Str. 3 64287 Darmstadt Germany
- TU DarmstadtDepartment of Material and Earth Sciences Otto-Berndt-Str. 3 64287 Darmstadt Germany
| | - Hendrik Auerbach
- TU KaiserslauternDepartment of Physics, Biophysics and Medical Physics Erwin-Schrödinger-Strasse 46 67663 Kaiserslautern Germany
| | - Claudia E. Tait
- Freie Universität BerlinBerlin Joint EPR Lab, Department of Physics Arnimallee 14 14195 Berlin Germany
| | - Ioanna Martinaiou
- TU DarmstadtGraduate School Energy Science and Engineering Otto-Berndt-Str. 3 64287 Darmstadt Germany
- TU DarmstadtDepartment of Chemistry Otto-Berndt-Str. 3 64287 Darmstadt Germany
| | - Shyam C. N. Kumar
- Karlsruhe Institute of Technology (KIT)Institute for NanotechnologyCampus North Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Germany
| | - Christian Kübel
- TU DarmstadtDepartment of Material and Earth Sciences Otto-Berndt-Str. 3 64287 Darmstadt Germany
- Karlsruhe Institute of Technology (KIT)Institute for NanotechnologyCampus North Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Germany
- Karlsruhe Institute of Technology (KIT)Nano Micro FacilityCampus North Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Germany
| | - Ilya Sergeev
- Deutsches Elektronen-Synchrotron Notkestraße 85 22607 Hamburg Germany
| | | | - Jan Behrends
- Freie Universität BerlinBerlin Joint EPR Lab, Department of Physics Arnimallee 14 14195 Berlin Germany
| | - Juliusz A. Wolny
- TU KaiserslauternDepartment of Physics, Biophysics and Medical Physics Erwin-Schrödinger-Strasse 46 67663 Kaiserslautern Germany
| | - Volker Schünemann
- TU KaiserslauternDepartment of Physics, Biophysics and Medical Physics Erwin-Schrödinger-Strasse 46 67663 Kaiserslautern Germany
| | - Ulrike I. Kramm
- TU DarmstadtGraduate School Energy Science and Engineering Otto-Berndt-Str. 3 64287 Darmstadt Germany
- TU DarmstadtDepartment of Material and Earth Sciences Otto-Berndt-Str. 3 64287 Darmstadt Germany
- TU DarmstadtDepartment of Chemistry Otto-Berndt-Str. 3 64287 Darmstadt Germany
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29
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Wittkamp F, Mishra N, Wang H, Wille HC, Steinbrügge R, Kaupp M, Cramer SP, Apfel UP, Pelmenschikov V. Insights from 125Te and 57Fe nuclear resonance vibrational spectroscopy: a [4Fe-4Te] cluster from two points of view. Chem Sci 2019; 10:7535-7541. [PMID: 31588304 PMCID: PMC6761874 DOI: 10.1039/c9sc02025j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 06/22/2019] [Indexed: 11/21/2022] Open
Abstract
Can sulfur-to-tellurium exchange serve as a method to understand iron–sulfur clusters of enzymatic systems?
Iron–sulfur clusters are common building blocks for electron transport and active sites of metalloproteins. Their comprehensive investigation is crucial for understanding these enzymes, which play important roles in modern biomimetic catalysis and biotechnology applications. We address this issue by utilizing (Et4N)3[Fe4Te4(SPh)4], a tellurium modified version of a conventional reduced [4Fe–4S]+ cluster, and performed both 57Fe- and 125Te-NRVS to reveal its characteristic vibrational features. Our analysis exposed major differences in the resulting 57Fe spectrum profile as compared to that of the respective [4Fe–4S] cluster, and between the 57Fe and 125Te profiles. DFT calculations are applied to rationalize structural, electronic, vibrational, and redox-dependent properties of the [4Fe–4Te]+ core. We herein highlight the potential of sulfur/tellurium exchange as a method to isolate the iron-only motion in enzymatic systems.
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Affiliation(s)
- Florian Wittkamp
- Department of Chemistry and Biochemistry , Inorganic Chemistry I , Ruhr-Universität Bochum , Universitätsstraße 150 , 44801 Bochum , Germany .
| | - Nakul Mishra
- Department of Chemistry , University of California , Davis, One Shields Avenue , Davis , California 95616 , USA .
| | - Hongxin Wang
- Department of Chemistry , University of California , Davis, One Shields Avenue , Davis , California 95616 , USA .
| | - Hans-Christian Wille
- Deutsches Elektronen-Synchrotron DESY , Notkestraße 85 , 22607 Hamburg , Germany
| | - René Steinbrügge
- Deutsches Elektronen-Synchrotron DESY , Notkestraße 85 , 22607 Hamburg , Germany
| | - Martin Kaupp
- Institute of Chemistry , Theoretical Chemistry/Quantum Chemistry , Technical University of Berlin , Sekr. C7, Straße des 17. Juni 135 , 10623 Berlin , Germany .
| | - Stephen P Cramer
- Department of Chemistry , University of California , Davis, One Shields Avenue , Davis , California 95616 , USA .
| | - Ulf-Peter Apfel
- Department of Chemistry and Biochemistry , Inorganic Chemistry I , Ruhr-Universität Bochum , Universitätsstraße 150 , 44801 Bochum , Germany . .,Fraunhofer UMSICHT , Osterfelder Straße 3 , 46047 Oberhausen , Germany
| | - Vladimir Pelmenschikov
- Institute of Chemistry , Theoretical Chemistry/Quantum Chemistry , Technical University of Berlin , Sekr. C7, Straße des 17. Juni 135 , 10623 Berlin , Germany .
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30
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Mebs S, Duan J, Wittkamp F, Stripp ST, Happe T, Apfel UP, Winkler M, Haumann M. Differential Protonation at the Catalytic Six-Iron Cofactor of [FeFe]-Hydrogenases Revealed by 57Fe Nuclear Resonance X-ray Scattering and Quantum Mechanics/Molecular Mechanics Analyses. Inorg Chem 2019; 58:4000-4013. [PMID: 30802044 DOI: 10.1021/acs.inorgchem.9b00100] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
[FeFe]-hydrogenases are efficient biological hydrogen conversion catalysts and blueprints for technological fuel production. The relations between substrate interactions and electron/proton transfer events at their unique six-iron cofactor (H-cluster) need to be elucidated. The H-cluster comprises a four-iron cluster, [4Fe4S], linked to a diiron complex, [FeFe]. We combined 57Fe-specific X-ray nuclear resonance scattering experiments (NFS, nuclear forward scattering; NRVS, nuclear resonance vibrational spectroscopy) with quantum-mechanics/molecular-mechanics computations to study the [FeFe]-hydrogenase HYDA1 from a green alga. Selective 57Fe labeling at only [4Fe4S] or [FeFe], or at both subcomplexes was achieved by protein expression with a 57Fe salt and in vitro maturation with a synthetic diiron site precursor containing 57Fe. H-cluster states were populated under infrared spectroscopy control. NRVS spectral analyses facilitated assignment of the vibrational modes of the cofactor species. This approach revealed the H-cluster structure of the oxidized state (Hox) with a bridging carbon monoxide at [FeFe] and ligand rearrangement in the CO-inhibited state (Hox-CO). Protonation at a cysteine ligand of [4Fe4S] in the oxidized state occurring at low pH (HoxH) was indicated, in contrast to bridging hydride binding at [FeFe] in a one-electron reduced state (Hred). These findings are direct evidence for differential protonation either at the four-iron or diiron subcomplex of the H-cluster. NFS time-traces provided Mössbauer parameters such as the quadrupole splitting energy, which differ among cofactor states, thereby supporting selective protonation at either subcomplex. In combination with data for reduced states showing similar [4Fe4S] protonation as HoxH without (Hred') or with (Hhyd) a terminal hydride at [FeFe], our results imply that coordination geometry dynamics at the diiron site and proton-coupled electron transfer to either the four-iron or the diiron subcomplex discriminate catalytic and regulatory functions of [FeFe]-hydrogenases. We support a reaction cycle avoiding diiron site geometry changes during rapid H2 turnover.
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Affiliation(s)
| | | | | | | | | | - Ulf-Peter Apfel
- Fraunhofer UMSICHT , Osterfelder Straße 3 , 46047 Oberhausen , Germany
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31
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Schiewer CE, Müller CS, Dechert S, Bergner M, Wolny JA, Schünemann V, Meyer F. Effect of Oxidation and Protonation States on [2Fe–2S] Cluster Nitrosylation Giving {Fe(NO)2}9 Dinitrosyl Iron Complexes (DNICs). Inorg Chem 2018; 58:769-784. [DOI: 10.1021/acs.inorgchem.8b02927] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Christine E. Schiewer
- Institut für Anorganische Chemie, Universität Göttingen, Tammannstrasse 4, D-37077 Göttingen, Germany
| | - Christina S. Müller
- Fachbereich Physik, Technische Universität Kaiserslautern, D-67663 Kaiserslautern, Germany
| | - Sebastian Dechert
- Institut für Anorganische Chemie, Universität Göttingen, Tammannstrasse 4, D-37077 Göttingen, Germany
| | - Marie Bergner
- Institut für Anorganische Chemie, Universität Göttingen, Tammannstrasse 4, D-37077 Göttingen, Germany
| | - Juliusz A. Wolny
- Fachbereich Physik, Technische Universität Kaiserslautern, D-67663 Kaiserslautern, Germany
| | - Volker Schünemann
- Fachbereich Physik, Technische Universität Kaiserslautern, D-67663 Kaiserslautern, Germany
| | - Franc Meyer
- Institut für Anorganische Chemie, Universität Göttingen, Tammannstrasse 4, D-37077 Göttingen, Germany
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32
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Zhang L, Zhou J, Ma F, Wang Q, Xu H, Ju H, Lei J. Single‐Sided Competitive Axial Coordination of G‐Quadruplex/Hemin as Molecular Switch for Imaging Intracellular Nitric Oxide. Chemistry 2018; 25:490-494. [DOI: 10.1002/chem.201804897] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 11/03/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Lei Zhang
- State Key Laboratory of Analytical Chemistry for Life ScienceSchool of Chemistry and Chemical EngineeringNanjing University Nanjing 210023 P.R. China
- School of Chemistry and Molecular Engineering, Institute of, Advanced SynthesisJiangsu National Synergetic Innovation Center for, Advanced MaterialsNanjing Tech University Nanjing 211816 P.R. China
| | - Jun Zhou
- State Key Laboratory of Analytical Chemistry for Life ScienceSchool of Chemistry and Chemical EngineeringNanjing University Nanjing 210023 P.R. China
| | - Fengjiao Ma
- State Key Laboratory of Analytical Chemistry for Life ScienceSchool of Chemistry and Chemical EngineeringNanjing University Nanjing 210023 P.R. China
| | - Quanbo Wang
- Laboratory of Immunology for Environment and HealthShandong Analysis and Test CenterShandong Academy of Sciences Jinan 250014 P.R. China
| | - Hui Xu
- School of Chemistry and Molecular Engineering, Institute of, Advanced SynthesisJiangsu National Synergetic Innovation Center for, Advanced MaterialsNanjing Tech University Nanjing 211816 P.R. China
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life ScienceSchool of Chemistry and Chemical EngineeringNanjing University Nanjing 210023 P.R. China
| | - Jianping Lei
- State Key Laboratory of Analytical Chemistry for Life ScienceSchool of Chemistry and Chemical EngineeringNanjing University Nanjing 210023 P.R. China
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33
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Sutherlin KD, Wasada-Tsutsui Y, Mbughuni MM, Rogers MS, Park K, Liu LV, Kwak Y, Srnec M, Böttger LH, Frenette M, Yoda Y, Kobayashi Y, Kurokuzu M, Saito M, Seto M, Hu M, Zhao J, Alp EE, Lipscomb JD, Solomon EI. Nuclear Resonance Vibrational Spectroscopy Definition of O 2 Intermediates in an Extradiol Dioxygenase: Correlation to Crystallography and Reactivity. J Am Chem Soc 2018; 140:16495-16513. [PMID: 30418018 DOI: 10.1021/jacs.8b06517] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The extradiol dioxygenases are a large subclass of mononuclear nonheme Fe enzymes that catalyze the oxidative cleavage of catechols distal to their OH groups. These enzymes are important in bioremediation, and there has been significant interest in understanding how they activate O2. The extradiol dioxygenase homoprotocatechuate 2,3-dioxygenase (HPCD) provides an opportunity to study this process, as two O2 intermediates have been trapped and crystallographically defined using the slow substrate 4-nitrocatechol (4NC): a side-on Fe-O2-4NC species and a Fe-O2-4NC peroxy bridged species. Also with 4NC, two solution intermediates have been trapped in the H200N variant, where H200 provides a second-sphere hydrogen bond in the wild-type enzyme. While the electronic structure of these solution intermediates has been defined previously as FeIII-superoxo-catecholate and FeIII-peroxy-semiquinone, their geometric structures are unknown. Nuclear resonance vibrational spectroscopy (NRVS) is an important tool for structural definition of nonheme Fe-O2 intermediates, as all normal modes with Fe displacement have intensity in the NRVS spectrum. In this study, NRVS is used to define the geometric structure of the H200N-4NC solution intermediates in HPCD as an end-on FeIII-superoxo-catecholate and an end-on FeIII-hydroperoxo-semiquinone. Parallel calculations are performed to define the electronic structures and protonation states of the crystallographically defined wild-type HPCD-4NC intermediates, where the side-on intermediate is found to be a FeIII-hydroperoxo-semiquinone. The assignment of this crystallographic intermediate is validated by correlation to the NRVS data through computational removal of H200. While the side-on hydroperoxo semiquinone intermediate is computationally found to be nonreactive in peroxide bridge formation, it is isoenergetic with a superoxo catecholate species that is competent in performing this reaction. This study provides insight into the relative reactivities of FeIII-superoxo and FeIII-hydroperoxo intermediates in nonheme Fe enzymes and into the role H200 plays in facilitating extradiol catalysis.
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Affiliation(s)
- Kyle D Sutherlin
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | - Yuko Wasada-Tsutsui
- Department of Life Science and Applied Chemistry, Graduate School of Engineering , Nagoya Institute of Technology , Gokiso-cho, Showa-ku, Nagoya 466-8555 , Japan
| | - Michael M Mbughuni
- Department of Biochemistry, Molecular Biology, & Biophysics , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Melanie S Rogers
- Department of Biochemistry, Molecular Biology, & Biophysics , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Kiyoung Park
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | - Lei V Liu
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | - Yeonju Kwak
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | - Martin Srnec
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | - Lars H Böttger
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | - Mathieu Frenette
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | - Yoshitaka Yoda
- Japan Synchrotron Radiation Research Institute , Hyogo 679-5198 , Japan
| | | | - Masayuki Kurokuzu
- Research Reactor Institute, Kyoto University , Osaka 590-0494 , Japan
| | - Makina Saito
- Research Reactor Institute, Kyoto University , Osaka 590-0494 , Japan
| | - Makoto Seto
- Research Reactor Institute, Kyoto University , Osaka 590-0494 , Japan
| | - Michael Hu
- Advanced Photon Source , Argonne National Laboratory , Lemont , Illinois 60439 , United States
| | - Jiyong Zhao
- Advanced Photon Source , Argonne National Laboratory , Lemont , Illinois 60439 , United States
| | - E Ercan Alp
- Advanced Photon Source , Argonne National Laboratory , Lemont , Illinois 60439 , United States
| | - John D Lipscomb
- Department of Biochemistry, Molecular Biology, & Biophysics , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Edward I Solomon
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States.,SLAC National Accelerator Laboratory , Menlo Park , California 94025 , United States
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34
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Ohta T, Shibata T, Kobayashi Y, Yoda Y, Ogura T, Neya S, Suzuki A, Seto M, Yamamoto Y. A Nuclear Resonance Vibrational Spectroscopic Study of Oxy Myoglobins Reconstituted with Chemically Modified Heme Cofactors: Insights into the Fe-O 2 Bonding and Internal Dynamics of the Protein. Biochemistry 2018; 57:6649-6652. [PMID: 30422640 DOI: 10.1021/acs.biochem.8b00829] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The molecular mechanism of O2 binding to hemoglobin (Hb) and myoglobin (Mb) is a long-standing issue in the field of bioinorganic and biophysical chemistry. The nature of Fe-O2 bond in oxy Hb and Mb had been extensively investigated by resonance Raman spectroscopy, which assigned the Fe-O2 stretching bands at ∼570 cm-1. However, resonance Raman assignment of the vibrational mode had been elusive due to the spectroscopic selection rule and to the limited information available about the ground-state molecular structure. Thus, nuclear resonance vibrational spectroscopy was applied to oxy Mbs reconstituted with 57Fe-labeled native heme cofactor and two chemically modified ones. This advanced spectroscopy in conjunction with DFT analyses gave new insights into the nature of the Fe-O2 bond of oxy heme by revealing the effect of heme peripheral substitutions on the vibrational dynamics of heme Fe atom, where the main Fe-O2 stretching band of the native protein was characterized at ∼420 cm-1.
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Affiliation(s)
- Takehiro Ohta
- Picobiology Institute, Graduate School of Life Science , University of Hyogo, RSC-UH LP Center , Hyogo 679-5148 , Japan
| | - Tomokazu Shibata
- Department of Chemistry , University of Tsukuba , Tsukuba 305-8571 , Japan
| | - Yasuhiro Kobayashi
- Institute for Integrated Radiation and Nuclear Science , Kyoto University , Osaka 590-0494 , Japan
| | - Yoshitaka Yoda
- Japan Synchrotron Radiation Research Institute , Hyogo 679-5198 , Japan
| | - Takashi Ogura
- Picobiology Institute, Graduate School of Life Science , University of Hyogo, RSC-UH LP Center , Hyogo 679-5148 , Japan
| | - Saburo Neya
- Department of Physical Chemistry, Graduate School of Pharmaceutical Sciences , Chiba University , Chiba 260-8657 , Japan
| | - Akihiro Suzuki
- Department of Materials Engineering, National Institute of Technology , Nagaoka College , Nagaoka 940-8532 , Japan
| | - Makoto Seto
- Institute for Integrated Radiation and Nuclear Science , Kyoto University , Osaka 590-0494 , Japan.,Japan Atomic Energy Agency , Hyogo 679-5148 , Japan
| | - Yasuhiko Yamamoto
- Department of Chemistry , University of Tsukuba , Tsukuba 305-8571 , Japan
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Dauphas N, Hu MY, Baker EM, Hu J, Tissot FLH, Alp EE, Roskosz M, Zhao J, Bi W, Liu J, Lin JF, Nie NX, Heard A. SciPhon: a data analysis software for nuclear resonant inelastic X-ray scattering with applications to Fe, Kr, Sn, Eu and Dy. JOURNAL OF SYNCHROTRON RADIATION 2018; 25:1581-1599. [PMID: 30179200 PMCID: PMC6140397 DOI: 10.1107/s1600577518009487] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 07/02/2018] [Indexed: 06/01/2023]
Abstract
The synchrotron radiation technique of nuclear resonant inelastic X-ray scattering (NRIXS), also known as nuclear resonance vibrational spectroscopy or nuclear inelastic scattering, provides a wealth of information on the vibrational properties of solids. It has found applications in studies of lattice dynamics and elasticity, superconductivity, heme biochemistry, seismology, isotope geochemistry and many other fields. It involves probing the vibrational modes of solids by using the nuclear resonance of Mössbauer isotopes such as 57Fe, 83Kr, 119Sn, 151Eu and 161Dy. After data reduction, it provides the partial phonon density of states of the Mössbauer isotope that is investigated, as well as many other derived quantities such as the mean force constant of the chemical bonds and the Debye velocity. The data reduction is, however, not straightforward and involves removal of the elastic peak, normalization and Fourier-Log transformation. Furthermore, some of the quantities derived are highly sensitive to details in the baseline correction. A software package and several novel procedures to streamline and hopefully improve the reduction of the NRIXS data generated at sector 3ID of the Advanced Photon Source have been developed. The graphical user interface software is named SciPhon and runs as a Mathematica package. It is easily portable to other platforms and can be easily adapted for reducing data generated at other beamlines. Several tests and comparisons are presented that demonstrate the usefulness of this software, whose results have already been used in several publications. Here, the SciPhon software is used to reduce Kr, Sn, Eu and Dy NRIXS data, and potential implications for interpreting natural isotopic variations in those systems are discussed.
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Affiliation(s)
- Nicolas Dauphas
- Department of the Geophysical Sciences and Enrico Fermi Institute, The University of Chicago, 5734 South Ellis Avenue, Chicago, IL 60615, USA
| | - Michael Y. Hu
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA
| | - Erik M. Baker
- Department of the Geophysical Sciences and Enrico Fermi Institute, The University of Chicago, 5734 South Ellis Avenue, Chicago, IL 60615, USA
- Department of Earth and Planetary Sciences, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Justin Hu
- Department of the Geophysical Sciences and Enrico Fermi Institute, The University of Chicago, 5734 South Ellis Avenue, Chicago, IL 60615, USA
| | - Francois L. H. Tissot
- Department of the Geophysical Sciences and Enrico Fermi Institute, The University of Chicago, 5734 South Ellis Avenue, Chicago, IL 60615, USA
| | - E. Ercan Alp
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA
| | - Mathieu Roskosz
- IMPMC-UMR CNRS 7590, Sorbonne Universités, UPMC, IRD, MNHN, Muséum National d’Histoire Naturelle, 61 Rue Buffon, 75005 Paris, France
| | - Jiyong Zhao
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA
| | - Wenli Bi
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA
| | - Jin Liu
- Department of Geological Sciences, Stanford University, Stanford, CA, USA
| | - Jung-Fu Lin
- Department of Geological Sciences, Jackson School of Geosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Nicole X. Nie
- Department of the Geophysical Sciences and Enrico Fermi Institute, The University of Chicago, 5734 South Ellis Avenue, Chicago, IL 60615, USA
| | - Andrew Heard
- Department of the Geophysical Sciences and Enrico Fermi Institute, The University of Chicago, 5734 South Ellis Avenue, Chicago, IL 60615, USA
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36
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Peng Q, Sage JT, Liu Y, Wang Z, Hu MY, Zhao J, Alp EE, Scheidt WR, Li J. How Does a Heme Carbene Differ from Diatomic Ligated (NO, CO, and CN -) Analogues in the Axial Bond? Inorg Chem 2018; 57:8788-8795. [PMID: 30010336 DOI: 10.1021/acs.inorgchem.8b00574] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Compared to well studied diatomic ligands (NO, CN-, CO), the axial bonds of carbene hemes is much less known although its significance in biological chemistry. The unusually large quadrupole splitting (Δ EQ = +2.2 mm·s-1) and asymmetric parameter (η = 0.9) of the five-coordinate heme carbene [Fe(TTP)(CCl2)], which is the largest among all known low spin ferrohemes, has driven investigations by means of Mössbauer effect Nuclear Resonance Vibrational Spectroscopy (NRVS). Three distinct measurements on one single crystal (two in-plane and one out-of-plane) have demonstrated comprehensive vibrational structures including stretch (429) and bending modes (472 cm-1) of the axial Fe-CCl2, and revealed iron vibrational anisotropy in three orthogonal directions for the first time. Frontier orbital analysis especially comparisons with diatomic analogues (NO, CN-, CO) suggest that CCl2, similar to NO, has led to strong but anisotropic π bonding in a ligand-based "4C"-coordinate which induced the vibrational anisotropies and very large Mössbauer parameters. This is contrasted to CN- and CO complexes which possess a porphyrin-based "4N"-coordinate electronic and vibrational structures due to inherent on-axis linear ligation.
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Affiliation(s)
- Qian Peng
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry , Nankai University , Tianjin 300071 , China
| | - J Timothy Sage
- Department of Physics and Center for Interdisciplinary Research on Complex Systems , Northeastern University , Boston , Massachusetts 02115 , United States
| | - Yulong Liu
- College of Materials Science and Optoelectronic Technology , University of Chinese Academy of Sciences , Yanqi Lake, Huairou, Beijing 101408 , China
| | - Zijian Wang
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry , Nankai University , Tianjin 300071 , China
| | - Michael Y Hu
- Advanced Photon Source , Argonne National Laboratory , Argonne , Illinois 60439 , United States
| | - Jiyong Zhao
- Advanced Photon Source , Argonne National Laboratory , Argonne , Illinois 60439 , United States
| | - E Ercan Alp
- Advanced Photon Source , Argonne National Laboratory , Argonne , Illinois 60439 , United States
| | - W Robert Scheidt
- Department of Chemistry and Biochemistry , University of Notre Dame , Notre Dame , Indiana 46556 , United States
| | - Jianfeng Li
- College of Materials Science and Optoelectronic Technology , University of Chinese Academy of Sciences , Yanqi Lake, Huairou, Beijing 101408 , China
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