1
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Le LN, Joyce JP, Oyala PH, DeBeer S, Agapie T. Highly Activated Terminal Carbon Monoxide Ligand in an Iron-Sulfur Cluster Model of FeMco with Intermediate Local Spin State at Fe. J Am Chem Soc 2024; 146:5045-5050. [PMID: 38358932 PMCID: PMC10910499 DOI: 10.1021/jacs.3c12025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/17/2024]
Abstract
Nitrogenases, the enzymes that convert N2 to NH3, also catalyze the reductive coupling of CO to yield hydrocarbons. CO-coordinated species of nitrogenase clusters have been isolated and used to infer mechanistic information. However, synthetic FeS clusters displaying CO ligands remain rare, which limits benchmarking. Starting from a synthetic cluster that models a cubane portion of the FeMo cofactor (FeMoco), including a bridging carbyne ligand, we report a heterometallic tungsten-iron-sulfur cluster with a single terminal CO coordination in two oxidation states with a high level of CO activation (νCO = 1851 and 1751 cm-1). The local Fe coordination environment (2S, 1C, 1CO) is identical to that in the protein making this system a suitable benchmark. Computational studies find an unusual intermediate spin electronic configuration at the Fe sites promoted by the presence the carbyne ligand. This electronic feature is partly responsible for the high degree of CO activation in the reduced cluster.
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Affiliation(s)
- Linh N.
V. Le
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Justin P. Joyce
- Max
Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Paul H. Oyala
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Serena DeBeer
- Max
Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Theodor Agapie
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
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2
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Specklin D, Boegli MC, Coffinet A, Escomel L, Vendier L, Grellier M, Simonneau A. An orbitally adapted push-pull template for N 2 activation and reduction to diazene-diide. Chem Sci 2023; 14:14262-14270. [PMID: 38098710 PMCID: PMC10718075 DOI: 10.1039/d3sc04390h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 11/19/2023] [Indexed: 12/17/2023] Open
Abstract
A Lewis superacidic bis(borane) C6F4{B(C6F5)2}2 was reacted with tungsten N2-complexes [W(N2)2(R2PCH2CH2PR2)2] (R = Ph or Et), affording zwitterionic boryldiazenido W(ii) complexes trans-[W(L)(R2PCH2CH2PR2)2(N2{B(C6F5)2(C6F4B(C6F5)3})] (L = ø, N2 or THF). These compounds feature only one N-B linkage of the covalent type, as a result of intramolecular boron-to-boron C6F5 transfer. Complex trans-[W(THF)(Et2PCH2CH2PEt2)2(N2{B(C6F5)2C6F4B(C6F5)3})] (5) was shown to split H2, leading to a seven-coordinate complex [W(H)2(Et2PCH2CH2PEt2)2(N2{B(C6F5)2}2C6F4)] (7). Interestingly, hydride storage at the metal triggers backward C6F5 transfer. This reverts the bis(boron) moiety to its bis(borane) state, now doubly binding the distal N, with structural parameters and DFT computations pointing to dative N→B bonding. By comparison with an N2 complex [W(H)2(Et2PCH2CH2PEt2)2(N2{B(C6F5)3}] (10) differing only in the Lewis acid (LA), namely B(C6F5)3, coordinated to the distal N, we demonstrate that two-fold LA coordination imparts strong N2 activation up to the diazene-diide (N22-) state. To the best of our knowledge, this is the first example of a neutral LA coordination that induces reduction of N2.
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Affiliation(s)
- David Specklin
- LCC-CNRS, Université de Toulouse, CNRS, UPS 205 route de Narbonne BP44099 F-31077 Toulouse Cedex 4 France
| | - Marie-Christine Boegli
- LCC-CNRS, Université de Toulouse, CNRS, UPS 205 route de Narbonne BP44099 F-31077 Toulouse Cedex 4 France
| | - Anaïs Coffinet
- LCC-CNRS, Université de Toulouse, CNRS, UPS 205 route de Narbonne BP44099 F-31077 Toulouse Cedex 4 France
| | - Léon Escomel
- LCC-CNRS, Université de Toulouse, CNRS, UPS 205 route de Narbonne BP44099 F-31077 Toulouse Cedex 4 France
| | - Laure Vendier
- LCC-CNRS, Université de Toulouse, CNRS, UPS 205 route de Narbonne BP44099 F-31077 Toulouse Cedex 4 France
| | - Mary Grellier
- LCC-CNRS, Université de Toulouse, CNRS, UPS 205 route de Narbonne BP44099 F-31077 Toulouse Cedex 4 France
| | - Antoine Simonneau
- LCC-CNRS, Université de Toulouse, CNRS, UPS 205 route de Narbonne BP44099 F-31077 Toulouse Cedex 4 France
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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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Pang Y, Bjornsson R. The E3 state of FeMoco: one hydride, two hydrides or dihydrogen? Phys Chem Chem Phys 2023; 25:21020-21036. [PMID: 37522223 DOI: 10.1039/d3cp01106b] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/01/2023]
Abstract
Hydrides are present in the reduced states of the iron-molybdenum cofactor (FeMoco) of Mo nitrogenase and are believed to play a key mechanistic role in the dinitrogen reduction reaction catalyzed by the enzyme. Two hydrides are present in the E4 state according to 1H ENDOR and there is likely a single hydride in the E2 redox state. The 2-hydride E4 state has been experimentally observed to bind N2 and it has been speculated that E3 may bind N2 as well. However, the E3 state has not been directly observed and very little is known about its molecular and electronic structure or reactivity. In recent computational studies, we have explored the energy surfaces of the E2 and E4 by QM/MM modelling, and found that the most stable hydride isomers contain bridging or partially bridging hydrides with an open protonated belt sulfide-bridge. In this work we systematically explore the energy surface of the E3 redox state, comparing single hydride and two-hydride isomers with varying coordination and bridging vs. terminal sulfhydryl groups. We also include a model featuring a triply protonated carbide. The results are only mildly dependent on the QM-region size. The three most stable E3 isomers at the r2SCAN level of theory have in common: an open belt sulfide-bridge (terminal sulfhydryl group on Fe6) and either 2 bridging hydrides (between Fe2 and Fe6), 1 bridging-1-terminal hydride (around Fe2 and Fe6) or a dihydrogen ligand bound at the Fe2 site. Analyzing the functional dependency of the results, we find that functionals previously found to predict accurate structures of spin-coupled Fe/Mo dimers and FeMoco (TPSSh, B97-D3, r2SCAN, and B3LYP*) are in generally good agreement about the stability of these 3 E3 isomers. However, B3LYP*, similar to its parent B3LYP method, predicts a triply protonated carbide isomer as the most stable isomer, an unlikely scenario in view of the lack of experimental evidence for carbide protonation occurring in reduced FeMoco states. Distinguishing further between the 3 hydride isomers is difficult and this flexible coordination nature of hydrides suggests that multiple hydride isomers could be present during experimental conditions. N2 binding was explored and resulted in geometries with 2 bridging hydrides and N2 bound to either Fe2 or Fe6 with a local low-spin state on the Fe. N2 binding is predicted to be mildly endothermic, similar to the E2 state, and it seems unlikely that the E3 state is capable of binding N2.
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Affiliation(s)
- Yunjie Pang
- College of Chemistry, Beijing Normal University, 100875, Beijing, China
- Max-Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Ragnar Bjornsson
- Max-Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
- Univ. Grenoble Alpes, CNRS, CEA, IRIG, Laboratoire de Chimie et Biologie des Métaux, 17 Rue des Martyrs, F-38054 Grenoble, Cedex, France.
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5
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Yogendra S, Wilson DWN, Hahn AW, Weyhermüller T, Van Stappen C, Holland P, DeBeer S. Sulfur-Ligated [2Fe-2C] Clusters as Synthetic Model Systems for Nitrogenase. Inorg Chem 2023; 62:2663-2671. [PMID: 36715662 PMCID: PMC9930126 DOI: 10.1021/acs.inorgchem.2c03693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Indexed: 01/31/2023]
Abstract
Metal clusters featuring carbon and sulfur donors have coordination environments comparable to the active site of nitrogenase enzymes. Here, we report a series of di-iron clusters supported by the dianionic yldiide ligands, in which the Fe sites are bridged by two μ2-C atoms and four pendant S donors.The [L2Fe2] (L = {[Ph2P(S)]2C}2-) cluster is isolable in two oxidation levels, all-ferrous Fe2II and mixed-valence FeIIFeIII. The mixed-valence cluster displays two peaks in the Mössbauer spectra, indicating slow electron transfer between the two sites. The addition of the Lewis base 4-dimethylaminopyridine to the Fe2II cluster results in coordination with only one of the two Fe sites, even in the presence of an excess base. Conversely, the cluster reacts with 8 equiv of isocyanide tBuNC to give a monometallic complex featuring a new C-C bond between the ligand backbone and the isocyanide. The electronic structure descriptions of these complexes are further supported by X-ray absorption and resonant X-ray emission spectroscopies.
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Affiliation(s)
- Sivathmeehan Yogendra
- Max
Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Daniel W. N. Wilson
- Department
of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, United States
| | - Anselm W. Hahn
- Max
Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Thomas Weyhermüller
- Max
Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Casey Van Stappen
- Max
Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Patrick Holland
- Department
of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, United States
| | - Serena DeBeer
- Max
Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
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6
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Dance I. The HD Reaction of Nitrogenase: a Detailed Mechanism. Chemistry 2023; 29:e202202502. [PMID: 36274057 PMCID: PMC10099629 DOI: 10.1002/chem.202202502] [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: 08/11/2022] [Indexed: 11/06/2022]
Abstract
Nitrogenase is the enzyme that converts N2 to NH3 under ambient conditions. The chemical mechanism of this catalysis at the active site FeMo-co [Fe7 S9 CMo(homocitrate)] is unknown. An obligatory co-product is H2 , while exogenous H2 is a competitive inhibitor. Isotopic substitution using exogenous D2 revealed the N2 -dependent reaction D2 +2H+ +2e- →2HD (the 'HD reaction'), together with a collection of additional experimental characteristics and requirements. This paper describes a detailed mechanism for the HD reaction, developed and elaborated using density functional simulations with a 486-atom model of the active site and surrounding protein. First D2 binds at one Fe atom (endo-Fe6 coordination position), where it is flanked by H-Fe6 (exo position) and H-Fe2 (endo position). Then there is synchronous transfer of these two H atoms to bound D2 , forming one HD bound to Fe2 and a second HD bound to Fe6. These two HD dissociate sequentially. The final phase is recovery of the two flanking H atoms. These H atoms are generated, sequentially, by translocation of a proton from the protein surface to S3B of FeMo-co and combination with introduced electrons. The first H atom migrates from S3B to exo-Fe6 and the second from S3B to endo-Fe2. Reaction energies and kinetic barriers are reported for all steps. This mechanism accounts for the experimental data: (a) stoichiometry; (b) the N2 -dependence results from promotional N2 bound at exo-Fe2; (c) different N2 binding Km for the HD reaction and the NH3 formation reaction results from involvement of two different sites; (d) inhibition by CO; (e) the non-occurrence of 2HD→H2 +D2 results from the synchronicity of the two transfers of H to D2 ; (f) inhibition of HD production at high pN2 is by competitive binding of N2 at endo-Fe6; (g) the non-leakage of D to solvent follows from the hydrophobic environment and irreversibility of proton introduction.
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Affiliation(s)
- Ian Dance
- School of Chemistry, UNSW, Sydney, Australia
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7
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Dance I. Understanding the tethered unhooking and rehooking of S2B in the reaction domain of FeMo-co, the active site of nitrogenase. Dalton Trans 2022; 51:15538-15554. [PMID: 36168836 DOI: 10.1039/d2dt02571j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The active site of the nitrogen fixing enzyme nitrogenase is an Fe7MoS9C cluster, and investigations of the enigmatic chemical mechanism of the enzyme have focussed on a pair of Fe atoms, Fe2 and Fe6, and the S2B atom that bridges them. There are three proposals for the status of the Fe2-S2B-Fe6 bridge during the catalytic cycle: one that it remains intact, another that it is completely labile and absent during catalysis, and a third that S2B is hemilabile, unhooking one of its bonds to Fe2 or Fe6. This report examines the tethered unhooking of S2B and factors that affect it, using DFT calculations of 50 geometric/electronic possibilities with a 485 atom model including all relevant parts of surrounding protein. The outcomes are: (a) unhooking the S2B-Fe2 bond is feasible and favourable, but alternative unhooking of the S2B-Fe6 bond is unlikely for steric reasons, (b) energy differences between hooked and unhooked isomers are generally <10 kcal mol-1, usually with unhooked more stable, (c) ligation at the exo-Fe6 position inhibits unhooking, (d) unhooking of hydrogenated S2B is more favourable than that of bare S2B, (e) hydrogen bonding from the NεH function of His195 to S2B occurs in hooked and unhooked forms, and possibly stabilises unhooking, (f) unhooking is reversible with kinetic barriers ranging 10-13 kcal mol-1. The conclusion is that energetically accessible reversible unhooking of S2B or S2BH, as an intrinsic property of FeMo-co, needs to be considered in the formulation of mechanisms for the reactions of nitrogenase.
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Affiliation(s)
- Ian Dance
- School of Chemistry, UNSW Sydney, Australia.
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8
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Stripp ST, Duffus BR, Fourmond V, Léger C, Leimkühler S, Hirota S, Hu Y, Jasniewski A, Ogata H, Ribbe MW. Second and Outer Coordination Sphere Effects in Nitrogenase, Hydrogenase, Formate Dehydrogenase, and CO Dehydrogenase. Chem Rev 2022; 122:11900-11973. [PMID: 35849738 PMCID: PMC9549741 DOI: 10.1021/acs.chemrev.1c00914] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Gases like H2, N2, CO2, and CO are increasingly recognized as critical feedstock in "green" energy conversion and as sources of nitrogen and carbon for the agricultural and chemical sectors. However, the industrial transformation of N2, CO2, and CO and the production of H2 require significant energy input, which renders processes like steam reforming and the Haber-Bosch reaction economically and environmentally unviable. Nature, on the other hand, performs similar tasks efficiently at ambient temperature and pressure, exploiting gas-processing metalloenzymes (GPMs) that bind low-valent metal cofactors based on iron, nickel, molybdenum, tungsten, and sulfur. Such systems are studied to understand the biocatalytic principles of gas conversion including N2 fixation by nitrogenase and H2 production by hydrogenase as well as CO2 and CO conversion by formate dehydrogenase, carbon monoxide dehydrogenase, and nitrogenase. In this review, we emphasize the importance of the cofactor/protein interface, discussing how second and outer coordination sphere effects determine, modulate, and optimize the catalytic activity of GPMs. These may comprise ionic interactions in the second coordination sphere that shape the electron density distribution across the cofactor, hydrogen bonding changes, and allosteric effects. In the outer coordination sphere, proton transfer and electron transfer are discussed, alongside the role of hydrophobic substrate channels and protein structural changes. Combining the information gained from structural biology, enzyme kinetics, and various spectroscopic techniques, we aim toward a comprehensive understanding of catalysis beyond the first coordination sphere.
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Affiliation(s)
- Sven T Stripp
- Freie Universität Berlin, Experimental Molecular Biophysics, Berlin 14195, Germany
| | | | - Vincent Fourmond
- Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Institut Microbiologie, Bioénergies et Biotechnologie, CNRS, Aix Marseille Université, Marseille 13402, France
| | - Christophe Léger
- Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Institut Microbiologie, Bioénergies et Biotechnologie, CNRS, Aix Marseille Université, Marseille 13402, France
| | - Silke Leimkühler
- University of Potsdam, Molecular Enzymology, Potsdam 14476, Germany
| | - Shun Hirota
- Nara Institute of Science and Technology, Division of Materials Science, Graduate School of Science and Technology, Nara 630-0192, Japan
| | - Yilin Hu
- Department of Molecular Biology & Biochemistry, University of California, Irvine, California 92697-3900, United States
| | - Andrew Jasniewski
- Department of Molecular Biology & Biochemistry, University of California, Irvine, California 92697-3900, United States
| | - Hideaki Ogata
- Nara Institute of Science and Technology, Division of Materials Science, Graduate School of Science and Technology, Nara 630-0192, Japan.,Hokkaido University, Institute of Low Temperature Science, Sapporo 060-0819, Japan.,Graduate School of Science, University of Hyogo, Hyogo 678-1297, Japan
| | - Markus W Ribbe
- Department of Molecular Biology & Biochemistry, University of California, Irvine, California 92697-3900, United States.,Department of Chemistry, University of California, Irvine, California 92697-2025, United States
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9
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Milton RD. Nitrogenase loosens its belt to fix dinitrogen. Nat Catal 2022. [DOI: 10.1038/s41929-022-00795-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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10
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Liu YA, Quechol R, Solomon JB, Lee CC, Ribbe MW, Hu Y, Hedman B, Hodgson KO. Radical SAM-dependent formation of a nitrogenase cofactor core on NifB. J Inorg Biochem 2022; 233:111837. [PMID: 35550498 PMCID: PMC9526504 DOI: 10.1016/j.jinorgbio.2022.111837] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 04/10/2022] [Accepted: 04/14/2022] [Indexed: 11/15/2022]
Abstract
Nitrogenase is a versatile metalloenzyme that reduces N2, CO and CO2 at its cofactor site. Designated the M-cluster, this complex cofactor has a composition of [(R-homocitrate)MoFe7S9C], and it is assembled through the generation of a unique [Fe8S9C] core prior to the insertion of Mo and homocitrate. NifB is a radical S-adenosyl-L-methionine (SAM) enzyme that is essential for nitrogenase cofactor assembly. This review focuses on the recent work that sheds light on the role of NifB in the formation of the [Fe8S9C] core of the nitrogenase cofactor, highlighting the structure, function and mechanism of this unique radical SAM methyltransferase.
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Affiliation(s)
- Yiling A Liu
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900, United States of America
| | - Robert Quechol
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900, United States of America
| | - Joseph B Solomon
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900, United States of America; Department of Chemistry, University of California, Irvine, CA 92697-2025, United States of America
| | - Chi Chung Lee
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900, United States of America
| | - Markus W Ribbe
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900, United States of America; Department of Chemistry, University of California, Irvine, CA 92697-2025, United States of America.
| | - Yilin Hu
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900, United States of America.
| | - Britt Hedman
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, United States of America.
| | - Keith O Hodgson
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, United States of America; Department of Chemistry, Stanford University, Stanford, CA 94305, United States of America.
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11
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Abstract
Nitrogenase is the only enzyme in nature that can fix N2 from the air. The active cofactor of the leading form of this enzyme contains seven irons and one molybdenum connected by sulfide bridges. In several recent experimental studies, it has been suggested that the cofactor is very flexible, and might lose one of its sulfides during catalysis. In this study, the possible loss of a sulfide has been investigated by model calculations. In previous studies, we have shown that there should be four activation steps before catalysis starts, and this study is based on that finding. It was found here that, after the four reductions in the activation steps, a sulfide will become very loosely bound and can be released in a quite exergonic step with a low barrier. The binding of N2 has no part in that release. In our previous studies, we suggested that the central carbide should be protonated three times after the four activation steps. With the new finding, there will instead be a loss of a sulfide, as the barrier for the loss is much lower than the ones for protonating the carbide. Still, it is suggested here that the carbide will be protonated anyway, but only with one proton, in the E3 to E4 step. A very complicated transition state for H2 formation involving a large structural change was obtained. The combined step, with a loss of H2 and binding of N2 , is calculated to be endergonic by +2.3 kcal mol-1 ; this is in excellent agreement with experiments in which an easily reversible step has been found.
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Affiliation(s)
- Wen-Jie Wei
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, Hubei Key Laboratory of Materials Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China.,Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, 106 91, Stockholm, Sweden
| | - Per E M Siegbahn
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, 106 91, Stockholm, Sweden
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12
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Yuan C, Jin WT, Zhou ZH. Comparisons of bond valences and distances for CO- and N 2-bound clusters of FeMo-cofactors. NEW J CHEM 2022. [DOI: 10.1039/d2nj00754a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
By comparisons of N2 and isoelectronic substrate CO bound FeMo-cofactors (FeMo-cos) in nitrogenases, we have used a classical bond valence method to calculate the oxidation states of the iron and molybdenum atoms in FeMo-cos.
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Affiliation(s)
- Chang Yuan
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Wan-Ting Jin
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Zhao-Hui Zhou
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
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13
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Dance I. Structures and reaction dynamics of N 2 and H 2 binding at FeMo-co, the active site of nitrogenase. Dalton Trans 2021; 50:18212-18237. [PMID: 34860237 DOI: 10.1039/d1dt03548g] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The chemical reactions occurring at the Fe7MoS9C(homocitrate) cluster, FeMo-co, the active site of the enzyme nitrogenase (N2 → NH3), are enigmatic. Experimental information collected over a long period reveals aspects of the roles of N2 and H2, each with more than one type of reactivity. This paper reports investigations of the binding of H2 and N2 at intact FeMo-co, using density functional simulations of a large 486 atom relevant portion of the protein, resulting in 27 new structures containing H2 and/or N2 bound at the exo and endo coordination sites of the participating Fe atoms, Fe2 and Fe6. Binding energies and transition states for association/dissociation are determined, and trajectories for the approach, binding and separation of H2/N2 are described, including diffusion of these small molecules through proximal protein. Influences of surrounding amino acids are identified. FeMo-co deforms geometrically when binding H2 or N2, and a procedure for calculating the energy cost involved, the adaptation energy, is introduced here. Adaptation energies, which range from 7 to 36 kcal mol-1 for the reported structures, are influenced by the protonation state of the His195 side chain. Seven N2 structures and three H2 structures have negative binding free energies, which include the estimated entropy penalties for binding of N2, H2 from proximal protein. These favoured structures have N2 bound end-on at exo-Fe2, exo-Fe6 and endo-Fe2 positions of FeMo-co, and H2 bound at the endo-Fe2 position. Various postulated structures with N2 bridging Fe2 and Fe6 revert to end-on-N2 at endo positions. The structures are also assessed via the calculated potential energy barriers for association and dissociation. Barriers to the binding of H2 range from 1 to 20 kcal mol-1 and barriers to dissociation of H2 range from 3 to 18 kcal mol-1. Barriers to the binding of N2, in either side-on or end-on mode, range from 2 to 18 kcal mol-1, while dissociation of bound N2 encounters barriers of 3 to 8 kcal mol-1 for side-on bonding and 7 to 18 kcal mol-1 for end-on bonding. These results allow formulation of mechanisms for the H2/N2 exchange reaction, and three feasible mechanisms for associative exchange and three for dissociative exchange are identified. Consistent electronic structures and potential energy surfaces are maintained throughout. Changes in the spin populations of Fe2 and Fe6 connected with cluster deformation and with metal-ligand bond formation are identified.
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Affiliation(s)
- Ian Dance
- School of Chemistry, UNSW Sydney, NSW 2051, Australia.
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14
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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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15
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Abstract
Carbide complexes remain a rare class of molecules. Their paucity does not reflect exceptional instability but is rather due to the generally narrow scope of synthetic procedures for constructing carbide complexes. The preparation of carbide complexes typically revolves around generating LnM-CEx fragments, followed by cleavage of the C-E bonds of the coordinated carbon-based ligands (the alternative being direct C atom transfer). Prime examples involve deoxygenation of carbonyl ligands and deprotonation of methyl ligands, but several other p-block fragments can be cleaved off to afford carbide ligands. This Review outlines synthetic strategies toward terminal carbide complexes, bridging carbide complexes, as well as carbide-carbonyl cluster complexes. It then surveys the reactivity of carbide complexes, covering stoichiometric reactions where the carbide ligands act as C1 reagents, engage in cross-coupling reactions, and enact Fischer-Tropsch-like chemistry; in addition, we discuss carbide complexes in the context of catalysis. Finally, we examine spectroscopic features of carbide complexes, which helps to establish the presence of the carbide functionality and address its electronic structure.
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Affiliation(s)
- Anders Reinholdt
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Jesper Bendix
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
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16
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Oehlmann NN, Rebelein JG. The Conversion of Carbon Monoxide and Carbon Dioxide by Nitrogenases. Chembiochem 2021; 23:e202100453. [PMID: 34643977 PMCID: PMC9298215 DOI: 10.1002/cbic.202100453] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/13/2021] [Indexed: 12/02/2022]
Abstract
Nitrogenases are the only known family of enzymes that catalyze the reduction of molecular nitrogen (N2) to ammonia (NH3). The N2 reduction drives biological nitrogen fixation and the global nitrogen cycle. Besides the conversion of N2, nitrogenases catalyze a whole range of other reductions, including the reduction of the small gaseous substrates carbon monoxide (CO) and carbon dioxide (CO2) to hydrocarbons. However, it remains an open question whether these ‘side reactivities’ play a role under environmental conditions. Nonetheless, these reactivities and particularly the formation of hydrocarbons have spurred the interest in nitrogenases for biotechnological applications. There are three different isozymes of nitrogenase: the molybdenum and the alternative vanadium and iron‐only nitrogenase. The isozymes differ in their metal content, structure, and substrate‐dependent activity, despite their homology. This minireview focuses on the conversion of CO and CO2 to methane and higher hydrocarbons and aims to specify the differences in activity between the three nitrogenase isozymes.
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Affiliation(s)
- Niels N Oehlmann
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043, Marburg, Germany
| | - Johannes G Rebelein
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043, Marburg, Germany
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17
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Gardner EJ, Marguet SC, Cobb CR, Pham DM, Beringer JAM, Bertke JA, Shafaat HS, Warren TH. Uncovering Redox Non-innocent Hydrogen-Bonding in Cu(I)-Diazene Complexes. J Am Chem Soc 2021; 143:15960-15974. [PMID: 34546737 DOI: 10.1021/jacs.1c04108] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The life-sustaining reduction of N2 to NH3 is thermoneutral yet kinetically challenged by high-energy intermediates such as N2H2. Exploring intramolecular H-bonding as a potential strategy to stabilize diazene intermediates, we employ a series of [xHetTpCu]2(μ-N2H2) complexes that exhibit H-bonding between pendant aromatic N-heterocycles (xHet) such as pyridine and a bridging trans-N2H2 ligand at copper(I) centers. X-ray crystallography and IR spectroscopy clearly reveal H-bonding in [pyMeTpCu]2(μ-N2H2) while low-temperature 1H NMR studies coupled with DFT analysis reveals a dynamic equilibrium between two closely related, symmetric H-bonded structural motifs. Importantly, the xHet pendant negligibly influences the electronic structure of xHetTpCuI centers in xHetTpCu(CNAr2,6-Me2) complexes that lack H-bonding as judged by nearly indistinguishable ν(CN) frequencies (2113-2117 cm-1). Nonetheless, H-bonding in the corresponding [xHetTpCu]2(μ-N2H2) complexes results in marked changes in ν(NN) (1398-1419 cm-1) revealed through resonance Raman studies. Due to the closely matched N-H BDEs of N2H2 and the pyH0 cation radical, the aromatic N-heterocyclic pendants may encourage partial H-atom transfer (HAT) from N2H2 to xHet through redox-non-innocent H-bonding in [xHetTpCu]2(μ-N2H2). DFT studies reveal modest thermodynamic barriers for concerted transfer of both H-atoms of coordinated N2H2 to the xHet pendants to generate tautomeric [xHetHTpCu]2(μ-N2) complexes, identifying metal-assisted concerted dual HAT as a thermodynamically favorable pathway for N2/N2H2 interconversion.
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Affiliation(s)
- Evan J Gardner
- Department of Chemistry, Georgetown University, Box 51277-1227, Washington, D.C. 20057, United States
| | - Sean C Marguet
- The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Caitlyn R Cobb
- Department of Chemistry, Georgetown University, Box 51277-1227, Washington, D.C. 20057, United States
| | - Dominic M Pham
- Department of Chemistry, Georgetown University, Box 51277-1227, Washington, D.C. 20057, United States
| | - Josalyne A M Beringer
- Department of Chemistry, Georgetown University, Box 51277-1227, Washington, D.C. 20057, United States
| | - Jeffery A Bertke
- Department of Chemistry, Georgetown University, Box 51277-1227, Washington, D.C. 20057, United States
| | - Hannah S Shafaat
- The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Timothy H Warren
- Department of Chemistry, Georgetown University, Box 51277-1227, Washington, D.C. 20057, United States
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González-Cabaleiro R, Thompson JA, Vilà-Nadal L. Looking for Options to Sustainably Fixate Nitrogen. Are Molecular Metal Oxides Catalysts a Viable Avenue? Front Chem 2021; 9:742565. [PMID: 34595154 PMCID: PMC8476845 DOI: 10.3389/fchem.2021.742565] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 08/17/2021] [Indexed: 11/13/2022] Open
Abstract
Fast and reliable industrial production of ammonia (NH3) is fundamentally sustaining modern society. Since the early 20th Century, NH3 has been synthesized via the Haber-Bosch process, running at conditions of around 350-500°C and 100-200 times atmospheric pressure (15-20 MPa). Industrial ammonia production is currently the most energy-demanding chemical process worldwide and contributes up to 3% to the global carbon dioxide emissions. Therefore, the development of more energy-efficient pathways for ammonia production is an attractive proposition. Over the past 20 years, scientists have imagined the possibility of developing a milder synthesis of ammonia by mimicking the nitrogenase enzyme, which fixes nitrogen from the air at ambient temperatures and pressures to feed leguminous plants. To do this, we propose the use of highly reconfigurable molecular metal oxides or polyoxometalates (POMs). Our proposal is an informed design of the polyoxometalate after exploring the catabolic pathways that cyanobacteria use to fix N2 in nature, which are a different route than the one followed by the Haber-Bosch process. Meanwhile, the industrial process is a "brute force" system towards breaking the triple bond N-N, needing high pressure and high temperature to increase the rate of reaction, nature first links the protons to the N2 to later easier breaking of the triple bond at environmental temperature and pressure. Computational chemistry data on the stability of different polyoxometalates will guide us to decide the best design for a catalyst. Testing different functionalized molecular metal oxides as ammonia catalysts laboratory conditions will allow for a sustainable reactor design of small-scale production.
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Affiliation(s)
| | - Jake A Thompson
- School of Chemistry, University of Glasgow, Glasgow, United Kingdom
| | - Laia Vilà-Nadal
- School of Chemistry, University of Glasgow, Glasgow, United Kingdom
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