1
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Heidinger L, Perez K, Spatzal T, Einsle O, Weber S, Rees DC, Schleicher E. Analysis of early intermediate states of the nitrogenase reaction by regularization of EPR spectra. Nat Commun 2024; 15:4041. [PMID: 38740794 DOI: 10.1038/s41467-024-48271-8] [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: 06/28/2023] [Accepted: 04/25/2024] [Indexed: 05/16/2024] Open
Abstract
Due to the complexity of the catalytic FeMo cofactor site in nitrogenases that mediates the reduction of molecular nitrogen to ammonium, mechanistic details of this reaction remain under debate. In this study, selenium- and sulfur-incorporated FeMo cofactors of the catalytic MoFe protein component from Azotobacter vinelandii are prepared under turnover conditions and investigated by using different EPR methods. Complex signal patterns are observed in the continuous wave EPR spectra of selenium-incorporated samples, which are analyzed by Tikhonov regularization, a method that has not yet been applied to high spin systems of transition metal cofactors, and by an already established grid-of-error approach. Both methods yield similar probability distributions that reveal the presence of at least four other species with different electronic structures in addition to the ground state E0. Two of these species were preliminary assigned to hydrogenated E2 states. In addition, advanced pulsed-EPR experiments are utilized to verify the incorporation of sulfur and selenium into the FeMo cofactor, and to assign hyperfine couplings of 33S and 77Se that directly couple to the FeMo cluster. With this analysis, we report selenium incorporation under turnover conditions as a straightforward approach to stabilize and analyze early intermediate states of the FeMo cofactor.
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Affiliation(s)
- Lorenz Heidinger
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Kathryn Perez
- Howard Hughes Medical Institute (HHMI), California Institute of Technology, Division of Chemistry and Chemical Engineering, Pasadena, CA, USA
| | - Thomas Spatzal
- Howard Hughes Medical Institute (HHMI), California Institute of Technology, Division of Chemistry and Chemical Engineering, Pasadena, CA, USA
| | - Oliver Einsle
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Stefan Weber
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Douglas C Rees
- Howard Hughes Medical Institute (HHMI), California Institute of Technology, Division of Chemistry and Chemical Engineering, Pasadena, CA, USA.
| | - Erik Schleicher
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany.
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2
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Hooper RX, Wertz AE, Shafaat HS, Holland PL. Evaluating Diazene to N 2 Interconversion at Iron-Sulfur Complexes. Chemistry 2024; 30:e202304072. [PMID: 38376370 PMCID: PMC11045311 DOI: 10.1002/chem.202304072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 02/19/2024] [Accepted: 02/20/2024] [Indexed: 02/21/2024]
Abstract
Biological N2 reduction occurs at sulfur-rich multiiron sites, and an interesting potential pathway is concerted double reduction/ protonation of bridging N2 through PCET. Here, we test the feasibility of using synthetic sulfur-supported diiron complexes to mimic this pathway. Oxidative proton transfer from μ-η1 : η1-diazene (HN=NH) is the microscopic reverse of the proposed N2 fixation pathway, revealing the energetics of the process. Previously, Sellmann assigned the purple metastable product from two-electron oxidation of [{Fe2+(PPr3)L1}2(μ-η1 : η1-N2H2)] (L1=tetradentate SSSS ligand) at -78 °C as [{Fe2+(PPr3)L1}2(μ-η1 : η1-N2)]2+, which would come from double PCET from diazene to sulfur atoms of the supporting ligands. Using resonance Raman, Mössbauer, NMR, and EPR spectroscopies in conjunction with DFT calculations, we show that the product is not an N2 complex. Instead, the data are most consistent with the spectroscopically observed species being the mononuclear iron(III) diazene complex [{Fe(PPr3)L1}(η2-N2H2)]+. Calculations indicate that the proposed double PCET has a barrier that is too high for proton transfer at the reaction temperature. Also, PCET from the bridging diazene is highly exergonic as a result of the high Fe3+/2+ redox potential, indicating that the reverse N2 protonation would be too endergonic to proceed. This system establishes the "ground rules" for designing reversible N2/N2H2 interconversion through PCET, such as tuning the redox potentials of the metal sites.
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Affiliation(s)
- Reagan X Hooper
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, CT-06511
| | - Ashlee E Wertz
- Department of Chemistry and Biochemistry, The Ohio State University, 100 W 18th Ave, Columbus, OH-43210
| | - Hannah S Shafaat
- Department of Chemistry and Biochemistry, The Ohio State University, 100 W 18th Ave, Columbus, OH-43210
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, CA-90095
| | - Patrick L Holland
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, CT-06511
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3
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Warmack RA, Rees DC. Nitrogenase beyond the Resting State: A Structural Perspective. Molecules 2023; 28:7952. [PMID: 38138444 PMCID: PMC10745740 DOI: 10.3390/molecules28247952] [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: 11/06/2023] [Revised: 11/30/2023] [Accepted: 12/01/2023] [Indexed: 12/24/2023] Open
Abstract
Nitrogenases have the remarkable ability to catalyze the reduction of dinitrogen to ammonia under physiological conditions. How does this happen? The current view of the nitrogenase mechanism focuses on the role of hydrides, the binding of dinitrogen in a reductive elimination process coupled to loss of dihydrogen, and the binding of substrates to a binuclear site on the active site cofactor. This review focuses on recent experimental characterizations of turnover relevant forms of the enzyme determined by cryo-electron microscopy and other approaches, and comparison of these forms to the resting state enzyme and the broader family of iron sulfur clusters. Emerging themes include the following: (i) The obligatory coupling of protein and electron transfers does not occur in synthetic and small-molecule iron-sulfur clusters. The coupling of these processes in nitrogenase suggests that they may involve unique features of the cofactor, such as hydride formation on the trigonal prismatic arrangement of irons, protonation of belt sulfurs, and/or protonation of the interstitial carbon. (ii) Both the active site cofactor and protein are dynamic under turnover conditions; the changes are such that more highly reduced forms may differ in key ways from the resting-state structure. Homocitrate appears to play a key role in coupling cofactor and protein dynamics. (iii) Structural asymmetries are observed in nitrogenase under turnover-relevant conditions by cryo-electron microscopy, although the mechanistic relevance of these states (such as half-of-sites reactivity) remains to be established.
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Affiliation(s)
- Rebeccah A. Warmack
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - Douglas C. Rees
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA
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4
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Rutledge HL, Cook BD, Nguyen HPM, Herzik MA, Tezcan FA. Structures of the nitrogenase complex prepared under catalytic turnover conditions. Science 2022; 377:865-869. [PMID: 35901182 PMCID: PMC9949965 DOI: 10.1126/science.abq7641] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The enzyme nitrogenase couples adenosine triphosphate (ATP) hydrolysis to the multielectron reduction of atmospheric dinitrogen into ammonia. Despite extensive research, the mechanistic details of ATP-dependent energy transduction and dinitrogen reduction by nitrogenase are not well understood, requiring new strategies to monitor its structural dynamics during catalytic action. Here, we report cryo-electron microscopy structures of the nitrogenase complex prepared under enzymatic turnover conditions. We observe that asymmetry governs all aspects of the nitrogenase mechanism, including ATP hydrolysis, protein-protein interactions, and catalysis. Conformational changes near the catalytic iron-molybdenum cofactor are correlated with the nucleotide-hydrolysis state of the enzyme.
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Affiliation(s)
- Hannah L. Rutledge
- Department of Chemistry and Biochemistry, University of California San Diego, San Diego, CA 92093, USA
| | - Brian D. Cook
- Department of Chemistry and Biochemistry, University of California San Diego, San Diego, CA 92093, USA
| | - Hoang P. M. Nguyen
- Department of Chemistry and Biochemistry, University of California San Diego, San Diego, CA 92093, USA
| | - Mark A. Herzik
- Department of Chemistry and Biochemistry, University of California San Diego, San Diego, CA 92093, USA,Corresponding author. (FAT), (MAH)
| | - F. Akif Tezcan
- Department of Chemistry and Biochemistry, University of California San Diego, San Diego, CA 92093, USA,Corresponding author. (FAT), (MAH)
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5
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Henthorn JT, DeBeer S. Selenium Valence-to-Core X-ray Emission Spectroscopy and Kβ HERFD X-ray Absorption Spectroscopy as Complementary Probes of Chemical and Electronic Structure. Inorg Chem 2022; 61:2760-2767. [PMID: 35113562 PMCID: PMC8848279 DOI: 10.1021/acs.inorgchem.1c02802] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
![]()
Selenium X-ray absorption
spectroscopy (XAS) has found widespread
use in investigations of Se-containing materials, geochemical processes,
and biologically active sites. In contrast to sulfur Kβ X-ray
emission spectroscopy (XES), which has been found to contain electronic
and structural information complementary to S XAS, Se Kβ XES
remains comparatively underexplored. Herein, we present the first
Se Valence-to-Core (VtC) XES studies of reduced Se-containing compounds
and FeSe dimers. Se VtC XES is found to be sensitive to changes in
covalent Se bonding interactions (Se–Se/Se–C/Se–H
bonding) while being relatively insensitive to changes in Fe oxidation
states as selenide bridges in FeSe dimers ([Fe2Se2]2+ vs [Fe2Se2]+). In
contrast, Se Kβ HERFD XAS is demonstrated to be quite sensitive
to changes in the Fe oxidation state with Se Kβ HERFD XAS demonstrating
experimental resolution equivalent to Kα HERFD XAS. Additionally,
computational studies reveal both Se VtC XES and XAS to be sensitive
to selenium protonation in FeSe complexes. Selenium is a trace element that plays
vital roles in biological
and geochemical cycles, energy storage, photovoltaics, and nanomaterials.
Herein, selenium Valence-to-Core X-ray emission spectroscopy is explored
as a new method of probing the chemical and electronic structure in
selenium-containing compounds, demonstrating sensitivity to selenium
bonding interactions. When paired with high-resolution Se X-ray absorption
spectroscopy (HERFD XAS), these two methods have the potential to
reveal greater insight into protonation and redox changes of Se-substituted
FeS clusters.
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Affiliation(s)
- Justin T Henthorn
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Serena DeBeer
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
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6
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Yuan C, Jin WT, Zhou ZH. Statistical analysis of PN clusters in Mo/VFe protein crystals using a bond valence method toward their electronic structures. RSC Adv 2022; 12:5214-5224. [PMID: 35425536 PMCID: PMC8981338 DOI: 10.1039/d1ra08507g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 01/26/2022] [Indexed: 11/21/2022] Open
Abstract
Iron valences of 129 P-clusters from FeMo/V proteins were analyzed using a bond valence method, supposing the existence of Fe3+ in a generally considered all-ferrous PN cluster in solution with excess reducing agent.
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Affiliation(s)
- Chang Yuan
- State Key Laboratory for Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Wan-Ting Jin
- State Key Laboratory for Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Zhao-Hui Zhou
- State Key Laboratory for Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
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7
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Yan M, Jasin Arachchige L, Dong A, Zhang XL, Dai Z, Sun C. Rational Design of Graphene-Supported Single-Atom Catalysts for Electroreduction of Nitrogen. Inorg Chem 2021; 60:18314-18324. [PMID: 34787407 DOI: 10.1021/acs.inorgchem.1c02946] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Critically, the central metal atoms along with their coordination environment play a significant role in the catalytic performance of single-atom catalysts (SACs). Herein, 12 single Fe, Mo, and Ru atoms supported on defective graphene are theoretically deigned for investigation of their structural and electronic properties and catalytic nitrogen reduction reaction (NRR) performance using first-principles calculations. Our results reveal that graphene with vacancies can be an ideal anchoring site for stabilizing isolated metal atoms owing to the strong metal-support interaction, forming stable TMCx or TMNx active centers (x = 3 or 4). Six SACs are screened as promising NRR catalyst candidates with excellent activity and selectivity during NRR, and RuN3 is identified as the optimal one with an overpotential of ≥0.10 V via the distal mechanism.
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Affiliation(s)
- Min Yan
- Science & Technology Innovation Institute, Dongguan University of Technology, Dongguan 523808, China
| | - Lakshitha Jasin Arachchige
- School of Chemical Engineering and Energy Technology, Dongguan University of Technology, Dongguan 523808, China.,Department of Chemistry and Biotechnology and Center for Translational Atomaterials, Swinburne University of Technology, Hawthorn, Victoria 3122, Australia
| | - Ani Dong
- Department of Computer and Information Science, City College of Dongguan University of Technology, Dongguan 523419, China
| | - Xiao Li Zhang
- State Centre for International Cooperation on Designer Low-Carbon & Environmental Materials, School of Materials Science and Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Zhongxu Dai
- College of Materials and Chemical Engineering, Key Laboratory of Inorganic Nonmetallic Crystalline and Energy Conversion Materials, China Three Gorges University, Yichang 443002, China
| | - Chenghua Sun
- School of Chemical Engineering and Energy Technology, Dongguan University of Technology, Dongguan 523808, China.,Department of Chemistry and Biotechnology and Center for Translational Atomaterials, Swinburne University of Technology, Hawthorn, Victoria 3122, Australia
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8
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Thorhallsson AT, Bjornsson R. The E 2 state of FeMoco: Hydride Formation versus Fe Reduction and a Mechanism for H 2 Evolution. Chemistry 2021; 27:16788-16800. [PMID: 34541722 PMCID: PMC9293435 DOI: 10.1002/chem.202102730] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Indexed: 11/27/2022]
Abstract
The iron‐molybdenum cofactor (FeMoco) is responsible for dinitrogen reduction in Mo nitrogenase. Unlike the resting state, E0, reduced states of FeMoco are much less well characterized. The E2 state has been proposed to contain a hydride but direct spectroscopic evidence is still lacking. The E2 state can, however, relax back the E0 state via a H2 side‐reaction, implying a hydride intermediate prior to H2 formation. This E2→E0 pathway is one of the primary mechanisms for H2 formation under low‐electron flux conditions. In this study we present an exploration of the energy surface of the E2 state. Utilizing both cluster‐continuum and QM/MM calculations, we explore various classes of E2 models: including terminal hydrides, bridging hydrides with a closed or open sulfide‐bridge, as well as models without. Importantly, we find the hemilability of a protonated belt‐sulfide to strongly influence the stability of hydrides. Surprisingly, non‐hydride models are found to be almost equally favorable as hydride models. While the cluster‐continuum calculations suggest multiple possibilities, QM/MM suggests only two models as contenders for the E2 state. These models feature either i) a bridging hydride between Fe2 and Fe6 and an open sulfide‐bridge with terminal SH on Fe6 (E2‐hyd) or ii) a double belt‐sulfide protonated, reduced cofactor without a hydride (E2‐nonhyd). We suggest both models as contenders for the E2 redox state and further calculate a mechanism for H2 evolution. The changes in electronic structure of FeMoco during the proposed redox‐state cycle, E0→E1→E2→E0, are discussed.
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Affiliation(s)
- Albert Th Thorhallsson
- Science Institute, University of Iceland, Dunhagi 3, 107, Reykjavik, Iceland.,Department of Inorganic Spectroscopy, Max-Planck-Institut für Chemische Energiekonversion, Stiftstrasse 34-36, 45470, Mülheim an der Ruhr, Germany
| | - Ragnar Bjornsson
- Science Institute, University of Iceland, Dunhagi 3, 107, Reykjavik, Iceland.,Department of Inorganic Spectroscopy, Max-Planck-Institut für Chemische Energiekonversion, Stiftstrasse 34-36, 45470, Mülheim an der Ruhr, Germany
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9
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Guo J, Wang M, Xu L, Li X, Iqbal A, Sterbinsky GE, Yang H, Xie M, Zai J, Feng Z, Cheng T, Qian X. Bioinspired Activation of
N
2
on Asymmetrical Coordinated Fe Grafted
1T MoS
2
at Room Temperature
†. CHINESE J CHEM 2021. [DOI: 10.1002/cjoc.202000675] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Jiaojiao Guo
- School of Chemistry and Chemical Engineering and State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University Shanghai 200240 China
| | - Maoyu Wang
- School of Chemical, Biological, and Environmental Engineering, Oregon State University Corvallis OR 97331 USA
| | - Liang Xu
- Institute of Functional Nano and Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon‐Based Functional Materials and Devices, Soochow University Suzhou Jiangsu 215123 China
| | - Xiaomin Li
- School of Chemistry and Chemical Engineering and State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University Shanghai 200240 China
- Instrumental Analysis Center, Shanghai Jiao Tong University Shanghai 200240 China
| | - Asma Iqbal
- School of Chemistry and Chemical Engineering and State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University Shanghai 200240 China
| | | | - Hao Yang
- Institute of Functional Nano and Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon‐Based Functional Materials and Devices, Soochow University Suzhou Jiangsu 215123 China
| | - Miao Xie
- Institute of Functional Nano and Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon‐Based Functional Materials and Devices, Soochow University Suzhou Jiangsu 215123 China
| | - Jiantao Zai
- School of Chemistry and Chemical Engineering and State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University Shanghai 200240 China
| | - Zhenxing Feng
- School of Chemical, Biological, and Environmental Engineering, Oregon State University Corvallis OR 97331 USA
| | - Tao Cheng
- Institute of Functional Nano and Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon‐Based Functional Materials and Devices, Soochow University Suzhou Jiangsu 215123 China
| | - Xuefeng Qian
- School of Chemistry and Chemical Engineering and State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University Shanghai 200240 China
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10
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Arnett CH, Bogacz I, Chatterjee R, Yano J, Oyala PH, Agapie T. Mixed-Valent Diiron μ-Carbyne, μ-Hydride Complexes: Implications for Nitrogenase. J Am Chem Soc 2020; 142:18795-18813. [PMID: 32976708 DOI: 10.1021/jacs.0c05920] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Binding of N2 by the FeMo-cofactor of nitrogenase is believed to occur after transfer of 4 e- and 4 H+ equivalents to the active site. Although pulse EPR studies indicate the presence of two Fe-(μ-H)-Fe moieties, the structural and electronic features of this mixed valent intermediate remain poorly understood. Toward an improved understanding of this bioorganometallic cluster, we report herein that diiron μ-carbyne complex (P6ArC)Fe2(μ-H) can be oxidized and reduced, allowing for the first time spectral characterization of two EPR-active Fe(μ-C)(μ-H)Fe model complexes linked by a 2 e- transfer which bear some resemblance to a pair of En and En+2 states of nitrogenase. Both species populate S = 1/2 states at low temperatures, and the influence of valence (de)localization on the spectroscopic signature of the μ-hydride ligand was evaluated by pulse EPR studies. Compared to analogous data for the {Fe2(μ-H)}2 state of FeMoco (E4(4H)), the data and analysis presented herein suggest that the hydride ligands in E4(4H) bridge isovalent (most probably FeIII) metal centers. Although electron transfer involves metal-localized orbitals, investigations of [(P6ArC)Fe2(μ-H)]+1 and [(P6ArC)Fe2(μ-H)]-1 by pulse EPR revealed that redox chemistry induces significant changes in Fe-C covalency (-50% upon 2 e- reduction), a conclusion further supported by X-ray absorption spectroscopy, 57Fe Mössbauer studies, and DFT calculations. Combined, our studies demonstrate that changes in covalency buffer against the accumulation of excess charge density on the metals by partially redistributing it to the bridging carbon, thereby facilitating multielectron transformations.
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Affiliation(s)
- Charles H Arnett
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Isabel Bogacz
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Ruchira Chatterjee
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Paul H Oyala
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Theodor Agapie
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
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11
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Anderson GA, Behera RN, Gomatam R. Calculation of higher protonation states and of a new resting state for vanadium chloroperoxidase using QM/MM, with an Atom-in-Molecules analysis. J Mol Graph Model 2020; 99:107624. [PMID: 32388271 DOI: 10.1016/j.jmgm.2020.107624] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 03/12/2020] [Accepted: 04/16/2020] [Indexed: 12/18/2022]
Abstract
Earlier QM/MM studies of the resting state of vanadium chloroperoxidase (VCPO) focused on the diprotonated states of the vanadate cofactor. Herein, we report a new extensive QM/MM study that includes the tri- and quadprotonated states of VCPO at neutral pH. We identify certain di- and triprotonated states as being candidates for the resting state based on a comparison of relative energies. The quadprotonated states as well as some of the triprotonated states are ruled out as the resting state. An Atoms-in-Molecules (AIM) analysis of the complex hydrogen bonding around the vanadate cofactor helps to explain the relative energies of the protonation states considered herein, and it also indicates new hydrogen bonding which has not been recognized previously. A Natural Bond Orbital (NBO) study is presented to give a better understanding of the electronic structure of the vanadate co-factor.
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Affiliation(s)
| | - Raghu Nath Behera
- Department of Chemistry, Birla Institute of Technology and Science, Pilani - Goa Campus, Zuarinagar, Goa, 403726, India.
| | - Ravi Gomatam
- Bhaktivedanta Institute and Institute of Semantic Information Sciences and Technology, Juhu Road, Juhu, Mumbai, 400049, India
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12
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Chica B, Ruzicka J, Kallas H, Mulder DW, Brown KA, Peters JW, Seefeldt LC, Dukovic G, King PW. Defining Intermediates of Nitrogenase MoFe Protein during N 2 Reduction under Photochemical Electron Delivery from CdS Quantum Dots. J Am Chem Soc 2020; 142:14324-14330. [PMID: 32787260 DOI: 10.1021/jacs.0c06343] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Coupling the nitrogenase MoFe protein to light-harvesting semiconductor nanomaterials replaces the natural electron transfer complex of Fe protein and ATP and provides low-potential photoexcited electrons for photocatalytic N2 reduction. A central question is how direct photochemical electron delivery from nanocrystals to MoFe protein is able to support the multielectron ammonia production reaction. In this study, low photon flux conditions were used to identify the initial reaction intermediates of CdS quantum dot (QD):MoFe protein nitrogenase complexes under photochemical activation using EPR. Illumination of CdS QD:MoFe protein complexes led to redox changes in the MoFe protein active site FeMo-co observed as the gradual decline in the E0 resting state intensity that was accompanied by an increase in the intensity of a new "geff = 4.5" EPR signal. The magnetic properties of the geff = 4.5 signal support assignment as a reduced S = 3/2 state, and reaction modeling was used to define it as a two-electron-reduced "E2" intermediate. Use of a MoFe protein variant, β-188Cys, which poises the P cluster in the oxidized P+ state, demonstrated that the P cluster can function as a site of photoexcited electron delivery from CdS to MoFe protein. Overall, the results establish the initial steps for how photoexcited CdS delivers electrons into the MoFe protein during reduction of N2 to ammonia and the role of electron flux in the photochemical reaction cycle.
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Affiliation(s)
- Bryant Chica
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Jesse Ruzicka
- Department of Chemistry, University of Colorado-Boulder, Boulder, Colorado 80309, United States
| | - Hayden Kallas
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
| | - David W Mulder
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Katherine A Brown
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - John W Peters
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99163, United States
| | - Lance C Seefeldt
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
| | - Gordana Dukovic
- Department of Chemistry, University of Colorado-Boulder, Boulder, Colorado 80309, United States
| | - Paul W King
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
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13
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Affiliation(s)
- Oliver Einsle
- Institute for Biochemistry, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Douglas C. Rees
- Division of Chemistry and Chemical Engineering, Howard Hughes Medical Institute, California Institute of Technology, Pasadena California 91125, United States
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14
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Jin WT, Yang M, Zhu SS, Zhou ZH. Bond-valence analyses of the crystal structures of FeMo/V cofactors in FeMo/V proteins. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2020; 76:428-437. [PMID: 32355039 DOI: 10.1107/s2059798320003952] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 03/18/2020] [Indexed: 12/15/2022]
Abstract
The bond-valence method has been used for valence calculations of FeMo/V cofactors in FeMo/V proteins using 51 crystallographic data sets of FeMo/V proteins from the Protein Data Bank. The calculations show molybdenum(III) to be present in MoFe7S9C(Cys)(HHis)[R-(H)homocit] (where H4homocit is homocitric acid, HCys is cysteine and HHis is histidine) in FeMo cofactors, while vanadium(III) with a more reduced iron complement is obtained for FeV cofactors. Using an error analysis of the calculated valences, it was found that in FeMo cofactors Fe1, Fe6 and Fe7 can be unambiguously assigned as iron(III), while Fe2, Fe3, Fe4 and Fe5 show different degrees of mixed valences for the individual Fe atoms. For the FeV cofactors in PDB entry 5n6y, Fe4, Fe5 and Fe6 correspond to iron(II), iron(II) and iron(III), respectively, while Fe1, Fe2, Fe3 and Fe7 exhibit strongly mixed valences. Special situations such as CO-bound and selenium-substituted FeMo cofactors and O(N)H-bridged FeV cofactors are also discussed and suggest rearrangement of the electron configuration on the substitution of the bridging S atoms.
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Affiliation(s)
- Wan Ting Jin
- State Key Laboratory for Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People's Republic of China
| | - Min Yang
- State Key Laboratory for Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People's Republic of China
| | - Shuang Shuang Zhu
- State Key Laboratory for Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People's Republic of China
| | - Zhao Hui Zhou
- State Key Laboratory for Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People's Republic of China
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Buscagan TM, Rees DC. Rethinking the Nitrogenase Mechanism: Activating the Active Site. JOULE 2019; 3:2662-2678. [PMID: 32864580 PMCID: PMC7451245 DOI: 10.1016/j.joule.2019.09.004] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Metalloenzymes called nitrogenases (N2ases) harness the reactivity of transition metals to reduce N2 to NH3. Specifically, N2ases feature a multimetallic active site, called a cofactor, which binds and reduces N2. The seven Fe centers and one additional metal center (Mo, V, or Fe) that make up the cofactor are all potential substrate binding sites. Unraveling the mechanism by which the cofactor binds N2 and reduces N2 to NH3 represents a multifaceted challenge because cofactor activation is required for N2 binding and functionalization to NH3. Despite decades of fascinating contributions, the nature of N2 binding to the active site and the structure of the activated cofactor remain unknown. Herein, we discuss the challenges associated with N2 reduction and how transition metal complexes facilitate N2 functionalization by coordinating N2. We also review the activation and/or reaction mechanisms reported for small molecule catalysts and the Haber-Bosch catalyst and discuss their potential relevance to biological N2 fixation. Finally, we survey what is known about the mechanism of N2ase and highlight recent X-ray crystallographic studies supporting Fe-S bond cleavage at the active site to generate reactive Fe centers as a potential, underexplored route for cofactor activation. We propose that structural rearrangements, beyond electron and proton transfers, are key in generating the catalytically active state(s) of the cofactor. Understanding the mechanism of activation will be key to understanding N2 binding and reduction.
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Affiliation(s)
- Trixia M. Buscagan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125 USA
| | - Douglas C. Rees
- to whom correspondence concerning the manuscript may be addressed, , telephone: 1-626-395-8393
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16
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Zanello P. Structure and electrochemistry of proteins harboring iron-sulfur clusters of different nuclearities. Part V. Nitrogenases. Coord Chem Rev 2019. [DOI: 10.1016/j.ccr.2019.07.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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17
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Wang SY, Dai JW, Chen HB, Zhou ZH. 2,2′-Bipyridine or 1,10-phenanthroline chelated oxomolybdenum(V) complexes with glycolate, lactate and malate in acidic media. Inorganica Chim Acta 2019. [DOI: 10.1016/j.ica.2019.03.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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18
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Wang SY, Zhou ZH. Molybdenum imidazole citrate and bipyridine homocitrate in different oxidation states – balance between coordinated α-hydroxy and α-alkoxy groups. RSC Adv 2019; 9:519-528. [PMID: 35521591 PMCID: PMC9059298 DOI: 10.1039/c8ra09134j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Accepted: 12/11/2018] [Indexed: 01/28/2023] Open
Abstract
Oxo and thiomolybdenum(iv/vi) imidazole hydrocitrates K2{MoIV3O4(im)3[MoVIO3(Hcit)]2}·3im·4H2O (1), (Him)2{MoIV3SO3(im)3[MoVIO3(Hcit)]2}·im·6H2O (2), molybdenum(v) bipyridine homocitrate trans-[(MoVO)2O(H2homocit)2(bpy)2]·4H2O (3) and molybdenum(vi) citrate (Et4N)[MoVIO2Cl(H2cit)]·H2O (4) (H4cit = citric acid, H4homocit = homocitric acid, im = imidazole and bpy = 2,2′-bipyridine) with different oxidation states were prepared. 1 and 2 are the coupling products of [MoVIO3(Hcit)]3− anions and incomplete cubane units [MoIV3O4]4+ ([MoIV3SO3]4+) with monodentate imidazoles, respectively, where tridentate citrates coordinate with α-hydroxy, α-carboxy and β-carboxy groups, forming pentanuclear skeleton structures. The molybdenum atoms in 1 and 2 show unusual +4 and +6 valences based on charge balances, theoretical bond valence calculations and Mo XPS spectrum. The coordinated citrates in 1 and 2 are protonated with α-hydroxy groups, while 3 and 4 with higher oxidation states of +5 and +6 are deprotonated with α-alkoxy group even under strong acidic condition, respectively. This shows the relationship between the oxidation state and protonation of the α-alkoxy group in citrate or homocitrate, which is related to the protonation state of homocitrate in FeMo-cofactor of nitrogenase. The homocitrate in 3 chelates to molybdenum(v) with bidentate α-alkoxy and monodentate α-carboxy groups. Molybdenum(vi) citrate 4 is only protonated with coordinated and uncoordinated β-carboxy groups. The solution behaviours of 1 and 2 are discussed based on 1H and 13C NMR spectroscopies and cyclic voltammograms, showing no decomposition of the species. Oxo and thiomolybdenum(iv/vi) citrates, molybdenum(v) homocitrate and molybdenum(vi) citrate were obtained, showing the influence of coordinated α-hydroxy and α-alkoxy groups with different oxidation states.![]()
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Affiliation(s)
- Si-Yuan Wang
- State Key Laboratory for Physical Chemistry of Solid Surfaces
- College of Chemistry and Chemical Engineering
- Xiamen University
- Xiamen
- China
| | - Zhao-Hui Zhou
- State Key Laboratory for Physical Chemistry of Solid Surfaces
- College of Chemistry and Chemical Engineering
- Xiamen University
- Xiamen
- China
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Critical computational analysis illuminates the reductive-elimination mechanism that activates nitrogenase for N 2 reduction. Proc Natl Acad Sci U S A 2018; 115:E10521-E10530. [PMID: 30355772 DOI: 10.1073/pnas.1810211115] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Recent spectroscopic, kinetic, photophysical, and thermodynamic measurements show activation of nitrogenase for N2 → 2NH3 reduction involves the reductive elimination (re) of H2 from two [Fe-H-Fe] bridging hydrides bound to the catalytic [7Fe-9S-Mo-C-homocitrate] FeMo-cofactor (FeMo-co). These studies rationalize the Lowe-Thorneley kinetic scheme's proposal of mechanistically obligatory formation of one H2 for each N2 reduced. They also provide an overall framework for understanding the mechanism of nitrogen fixation by nitrogenase. However, they directly pose fundamental questions addressed computationally here. We here report an extensive computational investigation of the structure and energetics of possible nitrogenase intermediates using structural models for the active site with a broad range in complexity, while evaluating a diverse set of density functional theory flavors. (i) This shows that to prevent spurious disruption of FeMo-co having accumulated 4[e -/H+] it is necessary to include: all residues (and water molecules) interacting directly with FeMo-co via specific H-bond interactions; nonspecific local electrostatic interactions; and steric confinement. (ii) These calculations indicate an important role of sulfide hemilability in the overall conversion of E 0 to a diazene-level intermediate. (iii) Perhaps most importantly, they explain (iiia) how the enzyme mechanistically couples exothermic H2 formation to endothermic cleavage of the N≡N triple bond in a nearly thermoneutral re/oxidative-addition equilibrium, (iiib) while preventing the "futile" generation of two H2 without N2 reduction: hydride re generates an H2 complex, but H2 is only lost when displaced by N2, to form an end-on N2 complex that proceeds to a diazene-level intermediate.
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20
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Singh AK, Singh PP, Tripathi V, Verma H, Singh SK, Srivastava AK, Kumar A. Distribution of cyanobacteria and their interactions with pesticides in paddy field: A comprehensive review. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2018; 224:361-375. [PMID: 30059934 DOI: 10.1016/j.jenvman.2018.07.039] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 07/13/2018] [Accepted: 07/14/2018] [Indexed: 06/08/2023]
Abstract
Cyanobacteria, also known as blue green algae are one of the important ubiquitous oxygen evolving photosynthetic prokaryotes and ultimate source of nitrogen for paddy fields since decades. In past two decades, indiscriminated use of pesticides led to biomagnification that intensively harm the structure and soil functions of soil microbes including cyanobacteria. Cyanobacterial abundance biomass, short generation, water holding capacity, mineralizing capacity and more importantly nitrogen fixing have enormous potential to abate the negative effects of pesticides. Therefore, investigation of the ecotoxicological effects of pesticides on the structure and function of the tropical paddy field associated cyanobacteria is urgent and need to estimate the fate of interaction of pesticides over nitrogen fixations and other attributes. In this regard, comprehensive survey over cyanobacterial distribution patterns and their interaction with pesticides in Indian context has been deeply reviewed. In addition, the present paper also deals the molecular docking pattern of pesticides with the nitrogen fixing proteins, which helps in revealing the functional interpretation over nitrogen fixation process.
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Affiliation(s)
| | - Prem Pratap Singh
- Center of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Vijay Tripathi
- Jacob Institute of Biotechnology and Bioengineering, Sam Higginbottom University of Agriculture, Technology and Sciences, Allahabad, 211007, India
| | - Hariom Verma
- Center of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Sandeep Kumar Singh
- Center of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | | | - Ajay Kumar
- Center of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India.
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21
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Deegan MM, Peters JC. Electrophile-promoted Fe-to-N 2 hydride migration in highly reduced Fe(N 2)(H) complexes. Chem Sci 2018; 9:6264-6270. [PMID: 30123481 PMCID: PMC6063139 DOI: 10.1039/c8sc02380h] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 06/26/2018] [Indexed: 11/21/2022] Open
Abstract
An emerging challenge in nitrogen fixation catalysis is the formation of hydride species, which can play a role in catalyst deactivation and unproductive hydrogen evolution. A new pathway for productive N–H bond formation from an iron hydride precursor is described.
One of the emerging challenges associated with developing robust synthetic nitrogen fixation catalysts is the competitive formation of hydride species that can play a role in catalyst deactivation or lead to undesired hydrogen evolution reactivity (HER). It is hence desirable to devise synthetic systems where metal hydrides can migrate directly to coordinated N2 in reductive N–H bond-forming steps, thereby enabling productive incorporation into desired reduced N2-products. Relevant examples of this type of reactivity in synthetic model systems are limited. In this manuscript we describe the migration of an iron hydride (Fe-H) to Nα of a disilylhydrazido(2-) ligand (Fe
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NNR2) derived from N2via double-silylation in a preceding step. This is an uncommon reactivity pattern in general; well-characterized examples of hydride/alkyl migrations to metal heteroatom bonds (e.g., (R)M
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NR′ → M–N(R)R′) are very rare. Mechanistic data establish the Fe-to-Nα hydride migration to be intramolecular. The resulting disilylhydrazido(1-) intermediate can be isolated by trapping with CNtBu, and the disilylhydrazine product can then be liberated upon treatment with an additional acid equivalent, demonstrating the net incorporation of an Fe-H equivalent into an N-fixed product.
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Affiliation(s)
- Meaghan M Deegan
- Division of Chemistry and Chemical Engineering , California Institute of Technology , Pasadena , CA 91125 , USA .
| | - Jonas C Peters
- Division of Chemistry and Chemical Engineering , California Institute of Technology , Pasadena , CA 91125 , USA .
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22
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Slater JW, Marguet SC, Monaco HA, Shafaat HS. Going beyond Structure: Nickel-Substituted Rubredoxin as a Mechanistic Model for the [NiFe] Hydrogenases. J Am Chem Soc 2018; 140:10250-10262. [PMID: 30016865 DOI: 10.1021/jacs.8b05194] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Jeffrey W. Slater
- The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Sean C. Marguet
- The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Haleigh A. Monaco
- The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Hannah S. Shafaat
- The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
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23
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Dance I. What is the role of the isolated small water pool near FeMo‐co, the active site of nitrogenase? FEBS J 2018; 285:2972-2986. [DOI: 10.1111/febs.14519] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Revised: 05/02/2018] [Accepted: 05/22/2018] [Indexed: 01/14/2023]
Affiliation(s)
- Ian Dance
- School of Chemistry UNSW Sydney NSW Australia
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24
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Gu NX, Oyala PH, Peters JC. An S = 1/ 2 Iron Complex Featuring N 2, Thiolate, and Hydride Ligands: Reductive Elimination of H 2 and Relevant Thermochemical Fe-H Parameters. J Am Chem Soc 2018; 140:6374-6382. [PMID: 29684269 DOI: 10.1021/jacs.8b02603] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Believed to accumulate on the Fe sites of the FeMo-cofactor (FeMoco) of MoFe-nitrogenase under turnover, strongly donating hydrides have been proposed to facilitate N2 binding to Fe and may also participate in the hydrogen evolution process concomitant to nitrogen fixation. Here, we report the synthesis and characterization of a thiolate-coordinated FeIII(H)(N2) complex, which releases H2 upon warming to yield an FeII-N2-FeII complex. Bimolecular reductive elimination of H2 from metal hydrides is pertinent to the hydrogen evolution processes of both enzymes and electrocatalysts, but well-defined examples are uncommon and usually observed from diamagnetic second- and third-row transition metals. Kinetic data obtained on the HER of this ferric hydride species are consistent with a bimolecular reductive elimination pathway, arising from cleavage of the Fe-H bond with a computationally determined BDFE of 55.6 kcal/mol.
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Affiliation(s)
- Nina X Gu
- Division of Chemistry and Chemical Engineering , California Institute of Technology , Pasadena , California 91125 , United States
| | - Paul H Oyala
- Division of Chemistry and Chemical Engineering , California Institute of Technology , Pasadena , California 91125 , United States
| | - Jonas C Peters
- Division of Chemistry and Chemical Engineering , California Institute of Technology , Pasadena , California 91125 , United States
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25
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Lukoyanov DA, Khadka N, Yang ZY, Dean DR, Seefeldt LC, Hoffman BM. Hydride Conformers of the Nitrogenase FeMo-cofactor Two-Electron Reduced State E 2(2H), Assigned Using Cryogenic Intra Electron Paramagnetic Resonance Cavity Photolysis. Inorg Chem 2018; 57:6847-6852. [PMID: 29575898 PMCID: PMC6008734 DOI: 10.1021/acs.inorgchem.8b00271] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Early studies in which nitrogenase was freeze-trapped during enzymatic turnover revealed the presence of high-spin ( S = 3/2) electron paramagnetic resonance (EPR) signals from the active-site FeMo-cofactor (FeMo-co) in electron-reduced intermediates of the MoFe protein. Historically denoted as 1b and 1c, each of the signals is describable as a fictitious spin system, S' = 1/2, with anisotropic g' tensor, 1b with g' = [4.21, 3.76, ?] and 1c with g' = [4.69, ∼3.20, ?]. A clear discrepancy between the magnetic properties of 1b and 1c and the kinetic analysis of their appearance during pre-steady-state turnover left their identities in doubt, however. We subsequently associated 1b with the state having accumulated 2[e-/H+], denoted as E2(2H), and suggested that the reducing equivalents are stored on the catalytic FeMo-co cluster as an iron hydride, likely an [Fe-H-Fe] hydride bridge. Intra-EPR cavity photolysis (450 nm; temperature-independent from 4 to 12 K) of the E2(2H)/1b state now corroborates the identification of this state as storing two reducing equivalents as a hydride. Photolysis converts E2(2H)/1b to a state with the same EPR spectrum, and thus the same cofactor structure as pre-steady-state turnover 1c, but with a different active-site environment. Upon annealing of the photogenerated state at temperature T = 145 K, it relaxes back to E2(2H)/1b. This implies that the 1c signal comes from an E2(2H) hydride isomer of E2(2H)/1b that stores its two reducing equivalents either as a hydride bridge between a different pair of iron atoms or an Fe-H terminal hydride.
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Affiliation(s)
- Dmitriy A Lukoyanov
- Departments of Chemistry and Molecular Biosciences , Northwestern University , Evanston , Illinois 60208 , United States
| | - Nimesh Khadka
- Department of Chemistry and Biochemistry , Utah State University , Logan , Utah 84322 , United States
| | - Zhi-Yong Yang
- Department of Chemistry and Biochemistry , Utah State University , Logan , Utah 84322 , United States
| | - Dennis R Dean
- Department of Biochemistry , Virginia Polytechnic Institute and State University , Blacksburg , Virginia 24061 , United States
| | - Lance C Seefeldt
- Department of Chemistry and Biochemistry , Utah State University , Logan , Utah 84322 , United States
| | - Brian M Hoffman
- Departments of Chemistry and Molecular Biosciences , Northwestern University , Evanston , Illinois 60208 , United States
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26
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Wang SY, Jin WT, Chen HB, Zhou ZH. Comparison of hydroxycarboxylato imidazole molybdenum(iv) complexes and nitrogenase protein structures: indirect evidence for the protonation of homocitrato FeMo-cofactors. Dalton Trans 2018; 47:7412-7421. [DOI: 10.1039/c8dt00278a] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Glycolato and lactato imidazole molybdenum(iv) complexes are used for structural comparison with FeMo-cofactors of MoFe-protein structures.
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Affiliation(s)
- Si-Yuan Wang
- State Key Laboratory for Physical Chemistry of Solid Surfaces
- College of Chemistry and Chemical Engineering
- Xiamen University
- Xiamen
- China
| | - Wan-Ting Jin
- State Key Laboratory for Physical Chemistry of Solid Surfaces
- College of Chemistry and Chemical Engineering
- Xiamen University
- Xiamen
- China
| | - Hong-Bin Chen
- State Key Laboratory for Physical Chemistry of Solid Surfaces
- College of Chemistry and Chemical Engineering
- Xiamen University
- Xiamen
- China
| | - Zhao-Hui Zhou
- State Key Laboratory for Physical Chemistry of Solid Surfaces
- College of Chemistry and Chemical Engineering
- Xiamen University
- Xiamen
- China
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27
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Benediktsson B, Bjornsson R. QM/MM Study of the Nitrogenase MoFe Protein Resting State: Broken-Symmetry States, Protonation States, and QM Region Convergence in the FeMoco Active Site. Inorg Chem 2017; 56:13417-13429. [DOI: 10.1021/acs.inorgchem.7b02158] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Bardi Benediktsson
- Science Institute, University of Iceland, Dunhagi 3, 107 Reykjavik, Iceland
| | - Ragnar Bjornsson
- Science Institute, University of Iceland, Dunhagi 3, 107 Reykjavik, Iceland
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