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Dance I. The activating capture of N 2 at the active site of Mo-nitrogenase. Dalton Trans 2024; 53:14193-14211. [PMID: 39140218 DOI: 10.1039/d4dt01866d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2024]
Abstract
Dinitrogen is inherently inert. This report describes detailed density functional calculations (with a 485+ atom model) of mechanistic steps by which the enzyme nitrogenase activates unreactive N2 at the intact active site FeMo-co, to form a key intermediate with bound HNNH. This mechanism does not bind N2 first and then add H atoms, but rather captures N2 ('N2-ready') that diffuses in through the substrate channel and enters a strategic gallery of H atom donors in the reaction zone, between Fe2 and Fe6. This occurs at the E4 stage of the complete mechanism. Exploration of possible reactions of N2 in this space leads to the conclusion that the first reaction step is transfer of H on Fe7 to one end of N2-ready, soon followed by Fe-N bond formation, and then a second H transfer from bridging S2BH to the other N. Two H-N bonds and one or two N-Fe bonds are formed, in some cases with a single transition state. The variable positions and orientations of N2-ready lead to various reaction trajectories and products. The favourable products resulting from this capture, judged by the criteria of reaction energies, reaction barriers, and mechanistic competence for further hydrogenation reactions in the nitrogenase cycle, have Fe2-NH-NH bonding. The trajectory of one N2 capture reaction is described in detail, and calculations that separate the H atom component and the 'heavy atom' components of the classical activation energy are described, in the context of possible H atom tunneling in the activation of N2-ready. I present arguments for the activation of N2 by the pathway of concerted hydrogenation and binding of N2-ready, alternative to the commonly assumed pathway of binding N2 first, with subsequent hydrogenation. The active site of nitrogenase is well primed for the thermodynamic and kinetic advantages of N2 capture.
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Affiliation(s)
- Ian Dance
- School of Chemistry, UNSW Sydney, NSW 2052, Australia.
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2
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Siegbahn PEM. Sulfide release and rebinding in the mechanism for nitrogenase. J Comput Chem 2024. [PMID: 39189512 DOI: 10.1002/jcc.27494] [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: 07/01/2024] [Revised: 08/09/2024] [Accepted: 08/13/2024] [Indexed: 08/28/2024]
Abstract
Nitrogenases are the only enzymes that activate the strong triple bond in N2. The mechanism for the activation has been very difficult to determine in spite of decades of work. In previous modeling studies it has been suggested that the mechanism for nitrogen activation starts out by four pre-activation steps (A0-A4) before catalysis. That suggestion led to excellent agreement with experimental Elecrtron Paramagnetic Resonance (EPR) observations in the step where N2 becomes protonated (E4). An important part of the pre-activation is that a sulfide is released. In the present paper, the details of the pre-activation are modeled, including the release of the sulfide. Several possible transition states for the release have been obtained. An A4(E0) state is reached which is very similar to the E4 state. For completeness, the steps going back from A4(E0) to A0 after catalysis are also modeled, including the insertion of a sulfide.
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Affiliation(s)
- Per E M Siegbahn
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden
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3
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Jiang H, Ryde U. Reaction Mechanism for CO Reduction by Mo-Nitrogenase Studied by QM/MM. Inorg Chem 2024; 63:15951-15963. [PMID: 39141025 DOI: 10.1021/acs.inorgchem.4c02323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2024]
Abstract
We have studied the conversion of two molecules of carbon monoxide to ethylene catalyzed by nitrogenase. We start from a recent crystal structure showing the binding of two carbon monoxide molecules to nitrogenase and employ the combined quantum mechanics and molecular mechanics approach. Our results indicate that the reaction is possible only if S2B dissociates as H2S (i.e., the charge of the FeMo cluster remains the same as in the E0 state, indicating that the Fe ions are formally reduced two steps when CO binds). Eight electrons and protons are needed for the reaction, and our mechanism suggests that the first four bind alternatively to the two carbon atoms. The C-C bond formation takes place already after the first protonation (in the E3 state). The next two protons bind to the same O atom, which then dissociates as water. In the same state (E8), the second C-O bond is cleaved, forming the ethylene product. The last two electrons and protons are used to form a water molecule that can be exchanged by S2B or by two CO molecules to start a new reaction cycle.
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Affiliation(s)
- Hao Jiang
- Department of Computational Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Ulf Ryde
- Department of Computational Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
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4
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Wang J, Jing X, Yang Y, Xu B, Jia R, Duan C. Enzymatic Activation and Continuous Electrochemical Production of Methane from Dilute CO 2 Sources with a Self-Healing Capsule. J Am Chem Soc 2024; 146:19951-19961. [PMID: 38963753 DOI: 10.1021/jacs.4c03367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2024]
Abstract
Converting dilute CO2 source into value-added chemicals and fuels is a promising route to reduce fossil fuel consumption and greenhouse gas emission, but integrating electrocatalysis with CO2 capture still faced marked challenges. Herein, we show that a self-healing metal-organic macrocycle functionalized as an electrochemical catalyst to selectively produce methane from flue gas and air with the lowest applied potential so far (0.06 V vs reversible hydrogen electrode, RHE) through an enzymatic activation fashion. The capsule emulates the enzyme' pocket to abstract one in situ-formed CO2-adduct molecule with the commercial amino alcohols, forming an easy-to-reduce substrate-involving clathrate to combine the CO2 capture with electroreduction for a thorough CO2 reduction. We find that the self-healing system exhibited enzymatic kinetics for the first time with the Michaelis-Menten mechanism in the electrochemical reduction of CO2 and maintained a methane Faraday efficiency (FE) of 74.24% with a selectivity of over 99% for continuous operation over 200 h. A consecutive working lab at 50 mA·cm-2, in an eleven-for-one (10 h working and 1 h healing) electrolysis manner, gives a methane turnover number (TON) of more than 10,000 within 100 h. The integrated electrolysis with CO2 capture facilitates the thorough reduction of flue gas (ca. 13.0% of CO2) and first time of air (ca. 400 ppm of CO2 to 42.7 mL CH4 from 1.0 m3 air). The new self-healing strategy of molecular electrocatalyst with an enzymatic activation manner and anodic shifting of the applied potentials provided a departure from the existing electrochemical catalytic techniques.
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Affiliation(s)
- Jinfeng Wang
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, China
| | - Xu Jing
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, China
| | - Yang Yang
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, China
| | - Baijie Xu
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, China
| | - Ruiming Jia
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, China
| | - Chunying Duan
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, China
- State Key Laboratory of Coordination Chemistry, Nanjing University, Nanjing 210008, China
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5
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Escomel L, Martins FF, Vendier L, Coffinet A, Queyriaux N, Krewald V, Simonneau A. Coordination of Al(C 6F 5) 3 vs. B(C 6F 5) 3 on group 6 end-on dinitrogen complexes: chemical and structural divergences. Chem Sci 2024; 15:11321-11336. [PMID: 39055009 PMCID: PMC11268509 DOI: 10.1039/d4sc02713b] [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: 04/24/2024] [Accepted: 06/14/2024] [Indexed: 07/27/2024] Open
Abstract
The coordination of the Lewis superacid tris(pentafluorophenyl)alane (AlCF) to phosphine-supported, group 6 bis(dinitrogen) complexes [ML2(N2)2] is explored, with M = Cr, Mo or W and L = dppe (1,2-bis(diphenylphosphino)ethane), depe (1,2-bis(diethylphosphino)ethane), dmpe (1,2-bis(dimethylphosphino)ethane) or 2 × PMe2Ph. Akin to tris(pentafluorophenyl)borane (BCF), AlCF can form 1 : 1 adducts by coordination to one distal nitrogen of general formula trans-[ML2(N2){(μ-η1:η1-N2)Al(C6F5)3}]. The boron and aluminium adducts are structurally similar, showing a comparable level of N2 push-pull activation. A notable exception is a bent (BCF adducts) vs. linear (AlCF adducts) M-N-N-LA motif (LA = Lewis acid), explained computationally as the result of steric repulsion. A striking difference arose when the formation of two-fold adducts was conducted. While in the case of BCF the 2 : 1 Lewis pairs could be observed in equilibrium with the 1 : 1 adduct and free borane but resisted isolation, AlCF forms robust 2 : 1 adducts trans-[ML2{(μ-η1:η1-N2)Al(C6F5)3}2] that isomerise into a more stable cis configuration. These compounds could be isolated and structurally characterized, and represent the first examples of trinuclear heterometallic complexes formed by Lewis acid-base interaction exhibiting p and d elements. Calculations also demonstrate that from the bare complex to the two-fold aluminium adduct, substantial decrease of the HOMO-LUMO gap is observed, and, unlike the trans adducts (1 : 1 and 1 : 2) for which the HOMO was computed to be a pure d orbital, the one of the cis-trinuclear compounds mixes a d orbital with a π* one of each N2 ligands. This may translate into a more favourable electrophilic attack on the N2 ligands instead of the metal centre, while a stabilized N2-centered LUMO should ease electron transfer, suggesting Lewis acids could be co-activators for electro-catalysed N2 reduction. Experimental UV-vis spectra for the tungsten family of compounds were compared with TD-DFT calculations (CAM-B3LYP/def2-TZVP), allowing to assign the low extinction bands found in the visible spectrum to unusual low-lying MLCT involving N2-centered orbitals. As significant red-shifts are observed upon LA coordination, this could have important implications for the development of visible light-driven nitrogen fixation.
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Affiliation(s)
- Léon Escomel
- LCC-CNRS, Université de Toulouse, CNRS UPS 205 Route de Narbonne, BP44099 F-31077 Toulouse Cedex 4 France
| | - Frederico F Martins
- Department of Chemistry, Quantum Chemistry, TU Darmstadt Peter-Grünberg-Str. 4, 6 4287 Darmstadt Germany
| | - Laure Vendier
- 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
| | - Nicolas Queyriaux
- LCC-CNRS, Université de Toulouse, CNRS UPS 205 Route de Narbonne, BP44099 F-31077 Toulouse Cedex 4 France
| | - Vera Krewald
- Department of Chemistry, Quantum Chemistry, TU Darmstadt Peter-Grünberg-Str. 4, 6 4287 Darmstadt Germany
| | - Antoine Simonneau
- LCC-CNRS, Université de Toulouse, CNRS UPS 205 Route de Narbonne, BP44099 F-31077 Toulouse Cedex 4 France
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6
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Jiang H, Ryde U. Putative reaction mechanism of nitrogenase with a half-dissociated S2B ligand. Dalton Trans 2024; 53:11500-11513. [PMID: 38916132 DOI: 10.1039/d4dt00937a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
We have studied whether dissociation of the S2B sulfide ligand from one of its two coordinating Fe ions may affect the later parts of the reaction mechanism of nitrogenase. Such dissociation has been shown to be favourable for the E2-E4 states in the reaction mechanism, but previous studies have assumed that S2B either remains bridging or has fully dissociated from the active-site FeMo cluster. We employ combined quantum mechanical and molecular mechanical (QM/MM) calculations with two density-functional theory methods, r2SCAN and TPSSh. To make dissociation of S2B possible, we have added a proton to this group throughout the reaction. We study the reaction starting from the E4 state with N2H2 bound to the cluster. Our results indicate that half-dissociation of S2B is unfavourable in most steps of the reaction mechanism. We observe favourable half-dissociation of S2B only when NH or NH2 is bound to the cluster, bridging Fe2 and Fe6. However, the former state is most likely not involved in the reaction mechanism and the latter state is only an intermittent intermediate of the E7 state. Therefore, half-dissociation of S2B seems to play only a minor role in the later parts of the reaction mechanism of nitrogenase. Our suggested mechanism with a protonated S2B is alternating (the two N atoms of the substrate is protonated in an alternating manner) and the substrate prefers to bind to Fe2, in contrast to the preferred binding to Fe6 observed when S2B is unprotonated and bridging Fe2 and Fe6.
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Affiliation(s)
- Hao Jiang
- Department of Computational Chemistry, Lund University, Chemical Centre, P. O. Box 124, SE-221 00 Lund, Sweden.
| | - Ulf Ryde
- Department of Computational Chemistry, Lund University, Chemical Centre, P. O. Box 124, SE-221 00 Lund, Sweden.
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7
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Yang D, Wang B, Qu J. Construction and Function of Thiolate-Bridged Diiron N xH y Nitrogenase Model Complexes. Acc Chem Res 2024; 57:1761-1776. [PMID: 38861704 DOI: 10.1021/acs.accounts.4c00068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2024]
Abstract
ConspectusBiological nitrogen fixation mediated by nitrogenases has garnered significant research interest due to its critical importance to the development of efficient catalysts for mild ammonia synthesis. Although the active center of the most studied FeMo-nitrogenases has been determined to be a complicated [Fe7S9MoC] hetero-multinuclear metal-sulfur cluster known as the FeMo-cofactor, the exact binding site and reduction pathway of N2 remain a subject of debate. Over the past decades, the majority of studies have focused on mononuclear molybdenum or iron centers as potential reaction sites. In stark contrast, cooperative activation of N2 through bi- or multimetallic centers has been largely overlooked and underexplored, despite the renewed interest sparked by recent biochemical and computational studies. Consequently, constructing bioinspired bi- or multinuclear metallic model complexes presents an intriguing yet challenging prospect. In this Account, we detail our long-standing research on the design and synthesis of novel thiolate-bridged diiron complexes as nitrogenase models and their application to chemical simulations of potential biological N2 reduction pathways.Inspired by the structural and electronic features of the potential diiron active center in the belt region of the FeMo-cofactor, we have designed and synthesized a series of new thiolate-bridged diiron nitrogenase model complexes, wherein iron centers with +2 or +3 oxidation states are coordinated by Cp* as carbon-based donors and thiolate ligands as sulfur donors. Through the synergistic interaction between the two iron centers, unstable diazene (NH═NH) species can be trapped to generate the first example of a [Fe2S2]-type complex bearing a cis-μ-η1:η1-NH═NH subunit. Significantly, this species can not only catalyze the reductive N-N bond cleavage of hydrazine to ammonia but also trigger a stepwise reduction sequence NH═NH → [NH2-NH]- → [NH]2-(+NH3) → [NH2]- → NH3. Furthermore, an unprecedented thiolate-bridged diiron μ-nitride featuring a bent Fe-N-Fe moiety was successfully isolated and structurally characterized. Importantly, this diiron μ-nitride can undergo successive proton-coupled electron transfer processes to efficiently release ammonia in the presence of separate protons and electrons and can even be directly hydrogenated using H2 as a combination of protons and electrons for high-yield ammonia formation. Based on combined experimental and computational studies, we proposed two distinct reductive transformation sequences on the diiron centers, which involve a series of crucial NxHy intermediates. Moreover, we also achieved catalytic N2 reduction to silylamines with [Fe2S2]-type complexes by ligand modulation.Our bioinspired diiron cooperative scaffold may provide a suitable model for probing the potential N2 stepwise reduction pathways from the molecular level. Different from the traditional alternating and distal pathways dominated by mononuclear iron or molybdenum complexes, our proposed alternating transformation route based on the diiron centers may not involve the N2H4 intermediate, and the convergence point of the alternating and terminal pathways is imide, not amide. Our research strategy could inform the design and development of new types of bioinspired catalysts for mild and efficient nitrogen reduction in the future.
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Affiliation(s)
- Dawei Yang
- State Key Laboratory of Fine Chemicals, Frontier Science Center for Smart Materials, Dalian University of Technology, Dalian 116024, P. R. China
| | - Baomin Wang
- State Key Laboratory of Fine Chemicals, Frontier Science Center for Smart Materials, Dalian University of Technology, Dalian 116024, P. R. China
| | - Jingping Qu
- State Key Laboratory of Fine Chemicals, Frontier Science Center for Smart Materials, Dalian University of Technology, Dalian 116024, P. R. China
- State Key Laboratory of Bioreactor Engineering, Collaborative Innovation Centre for Biomanufacturing, Frontiers Science Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, Shanghai 200237, P. R. China
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8
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Warmack RA, Wenke BB, Spatzal T, Rees DC. Anaerobic cryoEM protocols for air-sensitive nitrogenase proteins. Nat Protoc 2024; 19:2026-2051. [PMID: 38575747 DOI: 10.1038/s41596-024-00973-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 01/11/2024] [Indexed: 04/06/2024]
Abstract
Single-particle cryo-electron microscopy (cryoEM) provides an attractive avenue for advancing our atomic resolution understanding of materials, molecules and living systems. However, the vast majority of published cryoEM methodologies focus on the characterization of aerobically purified samples. Air-sensitive enzymes and microorganisms represent important yet understudied systems in structural biology. We have recently demonstrated the success of an anaerobic single-particle cryoEM workflow applied to the air-sensitive nitrogenase enzymes. In this protocol, we detail the use of Schlenk lines and anaerobic chambers to prepare samples, including a protein tag for monitoring sample exposure to oxygen in air. We describe how to use a plunge freezing apparatus inside of a soft-sided vinyl chamber of the type we routinely use for anaerobic biochemistry and crystallography of oxygen-sensitive proteins. Manual control of the airlock allows for introduction of liquid cryogens into the tent. A custom vacuum port provides slow, continuous evacuation of the tent atmosphere to avoid accumulation of flammable vapors within the enclosed chamber. These methods allowed us to obtain high-resolution structures of both nitrogenase proteins using single-particle cryoEM. The procedures involved can be generally subdivided into a 4 d anaerobic sample generation procedure, and a 1 d anaerobic cryoEM sample preparation step, followed by conventional cryoEM imaging and processing steps. As nitrogen is a substrate for nitrogenase, the Schlenk lines and anaerobic chambers described in this procedure are operated under an argon atmosphere; however, the system and these procedures are compatible with other controlled gas environments.
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Affiliation(s)
- Rebeccah A Warmack
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA.
- Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, USA.
| | - Belinda B Wenke
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Thomas Spatzal
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Douglas C Rees
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA.
- Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, USA.
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9
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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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10
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Beagan DM, Rivera C, Szymczak NK. Appended Lewis Acids Enable Dioxygen Reactivity and Catalytic Oxidations with Ni(II). J Am Chem Soc 2024; 146:12375-12385. [PMID: 38661576 PMCID: PMC11148854 DOI: 10.1021/jacs.3c12399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
We disclose a suite of Ni(II) complexes featuring secondary sphere Lewis acids of varied Lewis acidity and tether lengths. Several of these complexes feature atypical behavior of Ni(II): reactivity with O2 that occurs only in the presence of a tethered Lewis acid. In situ UV-vis spectroscopy revealed that, although adducts are stable at -40 °C, complexes containing 9-borabicyclo[3.3.1]nonane (9-BBN) Lewis acids underwent irreversible oxidative deborylation when warmed to room temperature. We computationally and experimentally identified that oxidative instability of appended 9-BBN moieties can be mitigated using weaker Lewis acids such as pinacolborane (BPin). These insights enabled the realization of catalytic reactions: hydrogen atom abstraction from phenols and room temperature oxygen atom transfer to PPh3.
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Affiliation(s)
- Daniel M Beagan
- University of Michigan, 930 N. University Ave., Ann Arbor, Michigan 48109, United States
| | - Carolina Rivera
- University of Michigan, 930 N. University Ave., Ann Arbor, Michigan 48109, United States
| | - Nathaniel K Szymczak
- University of Michigan, 930 N. University Ave., Ann Arbor, Michigan 48109, United States
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11
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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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12
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Xie ZL, Jin WT, Zhou ZH. Analyses of the electronic structures of FeFe-cofactors compared with those of FeMo- and FeV-cofactors and their P-clusters. Dalton Trans 2024; 53:6529-6536. [PMID: 38299993 DOI: 10.1039/d3dt04126c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2024]
Abstract
The electronic structures of FeFe-cofactors (FeFe-cos) in resting and turnover states, together with their PN clusters from iron-only nitrogenases, have been calculated using the bond valence method, and their crystallographic data were reported recently and deposited in the Protein Data Bank (PDB codes: 8BOQ and 8OIE). The calculated results have also been compared with those of their homologous Mo- and V-nitrogenases. For FeFe-cos in the resting state, Fe1/2/4/5/6/7/8 atoms are prone to Fe3+, while the Fe3 atom shows different degrees of mixed valences. The results support that the Fe8 atom at the terminal positions of FeFe-cos possesses the same oxidation states as the Mo3+/V3+ atoms of FeMo-/FeV-cos. In the turnover state, the overall oxidation state of FeFe-co is slightly reduced than those in the resting species, and its electronic configuration is rearranged after the substitution of S2B with OH, compatible with those found in CO-bound FeV-co. Moreover, the calculations give the formal oxidation states of 6Fe2+-2Fe3+ for the electronic structures of PN clusters in Fe-nitrogenases. By the comparison of Mo-, V- and Fe-nitrogenases, the overall oxidation levels of 7Fe atoms (Fe1-Fe7) for both FeFe- and FeMo-cos in resting states are found to be higher than that of FeV-co. For the PN clusters in MoFe-, VFe- and FeFe-proteins, they all exhibit a strong reductive character.
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Affiliation(s)
- Zhen-Lang Xie
- State Key Laboratory of Physical Chemistry of Solid Surfaces and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China.
| | - Wan-Ting Jin
- College of Chemical and Material Engineering, Quzhou University, Quzhou, 324000, China
| | - Zhao-Hui Zhou
- State Key Laboratory of Physical Chemistry of Solid Surfaces and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China.
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13
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Siegbahn PEM, Wei WJ. The energetics of N 2 reduction by vanadium containing nitrogenase. Phys Chem Chem Phys 2024; 26:1684-1695. [PMID: 38126534 DOI: 10.1039/d3cp04698b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
The main class of nitrogenases has a molybdenum in its cofactor. A mechanism for Mo-nitrogenase has recently been described. In the present study, another class of nitrogenases has been studied, the one with a vanadium instead of a molybdenum in its cofactor. It is generally believed that these classes use the same general mechanism to activate nitrogen. The same methodology has been used here as the one used for Mo-nitrogenase. N2 activation is known to occur after four reductions in the catalytic cycle, in the E4 state. The main features of the mechanism for Mo-nitrogenase found in the previous study are an activation process in four steps prior to catalysis, the release of a sulfide during the activation steps and the formation of H2 from two hydrides in E4, just before N2 is activated. The same features have been found here for V-nitrogenase. A difference is that five steps are needed in the activation process, which explains why the ground state of V-nitrogenase is a triplet (even number) and the one for Mo-nitrogenase is a quartet (odd number). The reason an additional step is needed for V-nitrogenase is that V3+ can be reduced to V2+, in contrast to the case for Mo3+ in Mo-nitrogenase. The fact that V3+ is Jahn-Teller active has important consequences. N2H2 is formed in E4 with reasonably small barriers.
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Affiliation(s)
- Per E M Siegbahn
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91, Stockholm, Sweden.
| | - Wen-Jie Wei
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91, Stockholm, Sweden.
- 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, China
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14
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Jiang H, Ryde U. H 2 formation from the E 2-E 4 states of nitrogenase. Phys Chem Chem Phys 2024; 26:1364-1375. [PMID: 38108422 DOI: 10.1039/d3cp05181a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Nitrogenase is the only enzyme that can cleave the strong triple bond in N2, making nitrogen available for biological lifeforms. The active site is a MoFe7S9C cluster (the FeMo cluster) that binds eight electrons and protons during one catalytic cycle, giving rise to eight intermediate states E0-E7. It is experimentally known that N2 binds to the E4 state and that H2 is a compulsory byproduct of the reaction. However, formation of H2 is also an unproductive side reaction that should be avoided, especially in the early steps of the reaction mechanism (E2 and E3). Here, we study the formation of H2 for various structural interpretations of the E2-E4 states using combined quantum mechanical and molecular mechanical (QM/MM) calculations and four different density-functional theory methods. We find large differences in the predictions of the different methods. B3LYP strongly favours protonation of the central carbide ion and H2 cannot form from such structures. On the other hand, with TPSS, r2SCAN and TPSSh, H2 formation is strongly exothermic for all structures and En and therefore need strict kinetic control to be avoided. For the E2 state, the kinetic barriers for the low-energy structures are high enough to avoid H2 formation. However, for both the E3 and E4 states, all three methods predict that the best structure has two hydride ions bridging the same pair of Fe ions (Fe2 and Fe6) and these two ions can combine to form H2 with an activation barrier of only 29-57 kJ mol-1, corresponding to rates of 7 × 102 to 5 × 107 s-1, i.e. much faster than the turnover rate of the enzyme (1-5 s-1). We have also studied H-atom movements within the FeMo cluster, showing that the various protonation states can quite freely be interconverted (activation barriers of 12-69 kJ mol-1).
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Affiliation(s)
- Hao Jiang
- Department of Computational Chemistry, Lund University, Chemical Centre, P. O. Box 124, SE-221 00 Lund, Sweden.
| | - Ulf Ryde
- Department of Computational Chemistry, Lund University, Chemical Centre, P. O. Box 124, SE-221 00 Lund, Sweden.
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15
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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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16
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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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17
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Einsle O. On the Shoulders of Giants-Reaching for Nitrogenase. Molecules 2023; 28:7959. [PMID: 38138449 PMCID: PMC10745432 DOI: 10.3390/molecules28247959] [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: 10/08/2023] [Revised: 11/14/2023] [Accepted: 11/27/2023] [Indexed: 12/24/2023] Open
Abstract
Only a single enzyme system-nitrogenase-carries out the conversion of atmospheric N2 into bioavailable ammonium, an essential prerequisite for all organismic life. The reduction of this inert substrate at ambient conditions poses unique catalytic challenges that strain our mechanistic understanding even after decades of intense research. Structural biology has added its part to this greater tapestry, and in this review, I provide a personal (and highly biased) summary of the parts of the story to which I had the privilege to contribute. It focuses on the crystallographic analysis of the three isoforms of nitrogenases at high resolution and the binding of ligands and inhibitors to the active-site cofactors of the enzyme. In conjunction with the wealth of available biochemical, biophysical, and spectroscopic data on the protein, this has led us to a mechanistic hypothesis based on an elementary mechanism of repetitive hydride formation and insertion.
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Affiliation(s)
- Oliver Einsle
- Institute of Biochemistry, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104 Freiburg im Breisgau, Germany
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18
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Einsle O. Catalysis and structure of nitrogenases. Curr Opin Struct Biol 2023; 83:102719. [PMID: 37802004 DOI: 10.1016/j.sbi.2023.102719] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 09/03/2023] [Accepted: 09/06/2023] [Indexed: 10/08/2023]
Abstract
In providing bioavailable nitrogen as building blocks for all classes of biomacromolecules, biological nitrogen fixation is an essential process for all organismic life. Only a single enzyme, nitrogenase, performs this task at ambient conditions and with ATP as an energy source. The assembly of the complex iron-sulfur enzyme nitrogenase and its catalytic mechanism remains a matter of intense study. Recent progress in the structural analysis of the three known isoforms of nitrogenase-differentiated primarily by the heterometal in their active site cofactor-has revealed a degree of structural plasticity of these clusters that suggest two distinct binding sites for substrates and reaction intermediates. A mechanistic proposal based on this finding integrates most of the available experimental data. Furthermore, the first applications of high-resolution cryo-electron microscopy have highlighted further dynamic conformational changes. Structures obtained under turnover conditions support the proposed alternating half-site reactivity in the C2-symmetric nitrogenase complex.
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Affiliation(s)
- Oliver Einsle
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104 Freiburg im Breisgau, Germany.
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19
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Zhu SS, Xie ZL, Deng L, Wang SY, Ni LB, Zhou ZH. Protonated and deprotonated vanadyl imidazole tartrates for the mimics of the vanadium coordination in the FeV-cofactor of V-nitrogenase. Dalton Trans 2023; 52:16849-16857. [PMID: 37910198 DOI: 10.1039/d3dt02903d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023]
Abstract
Chiral imidazole-based oxidovanadium tartrates (H2im)2[Δ,Λ-VIV2O2(R,R-H2tart)(R,R-tart)(Him)2]·Him (1, H4tart = tartaric acid, Him = imidazole) and [Λ,Λ-VIV2O2(R,R-tart)(Him)6]·4H2O (2) and their corresponding enantiomers (H2im)2[Λ,Δ-VIV2O2(S,S-H2tart)(S,S-tart)(Him)2]·Him (3) and [Δ,Δ-VIV2O2(S,S-tart)(Him)6]·4H2O (4) were obtained in alkaline solutions. Interestingly, the tartrates chelate with vanadium bidentately through α-alkoxy/α-hydroxy and α-carboxy groups and imidazole coordinates monodentately through nitrogen atom. It is worth noting that complexes 1 and 3 contain both protonated α-hydroxy and deprotonated α-alkoxy groups simultaneously, which have short V-Oα-alkoxy distances [1.976(4)av Å in 1-4] and long V-Oα-hydroxy distances [2.237(3)av Å in 1 and 2.230(2)av Å in 3]. There is an interesting strong intramolecular hydrogen bond [O(11)⋯O(1) 2.731(5) Å] between the two parts in 1 and 3. The protonated V-O distances are closer to the average bond distance in reported FeV-cofactors (FeV-cos, V-Oα-alkoxy 2.156av Å) in VFe proteins, which corresponds to the feasible protonation of coordinated α-hydroxy in R-homocitrate in V-nitrogenase, showing the homocitrate in the mechanistic model for nitrogen reduction as a secondary proton donor. Furthermore, vibrational circular dichroism (VCD) and IR spectra of 1-4 pointed out the disparity between the characteristic vibrations of the C-O and C-OH groups clearly. EPR experiment and theoretical calculations support +4 oxidation states for vanadium in 1-4. Solution 13C {1H} NMR spectra and CV analyses exhibited the solution properties for 1 and 2, respectively, which indicates that there should be a rapid exchange equilibrium between the protonated and deprotonated species in solutions.
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Affiliation(s)
- Shuang-Shuang Zhu
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China.
| | - Zhen-Lang Xie
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China.
| | - Lan Deng
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China.
| | - Si-Yuan Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China.
| | - Lu-Bin Ni
- School of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou 225002, Jiangsu, China
| | - Zhao-Hui Zhou
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China.
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20
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Brown AC, Suess DLM. An Iron-Sulfur Cluster with a Highly Pyramidalized Three-Coordinate Iron Center and a Negligible Affinity for Dinitrogen. J Am Chem Soc 2023; 145:20088-20096. [PMID: 37656961 PMCID: PMC10824254 DOI: 10.1021/jacs.3c07677] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/03/2023]
Abstract
Attempts to generate open coordination sites for N2 binding at synthetic Fe-S clusters often instead result in cluster oligomerization. Recently, it was shown for Mo-Fe-S clusters that such oligomerization reactions can be prevented through the use of sterically protective supporting ligands, thereby enabling N2 complex formation. Here, this strategy is extended to Fe-only Fe-S clusters. One-electron reduction of (IMes)3Fe4S4Cl (IMes = 1,3-dimesitylimidazol-2-ylidene) forms the transiently stable edge-bridged double cubane (IMes)6Fe8S8, which loses two IMes ligands to form the face-bridged double-cubane, (IMes)4Fe8S8. The finding that the three supporting IMes ligands do not confer sufficient protection to curtail cluster oligomerization prompted the design of a new N-heterocyclic carbene, SIArMe,iPr (1,3-bis(3,5-diisopropyl-2,6-dimethylphenyl)-2-imidazolidinylidene; abbreviated as SIAr), that features bulky groups strategically placed in remote positions. When the reduction of (SIAr)3Fe4S4Cl or [(SIAr)3Fe4S4(THF)]+ is conducted in the presence of SIAr, the formation of (SIAr)4Fe8S8 is indeed suppressed, permitting characterization of the reduced [Fe4S4]0 product. Surprisingly, rather than being an N2 complex, the product is simply (SIAr)3Fe4S4: a cluster with a three-coordinate Fe site that adopts an unusually pyramidalized geometry. Although (SIAr)3Fe4S4 does not coordinate N2 to any appreciable extent under the surveyed conditions, it does bind CO to form (SIAr)3Fe4S4(CO). This finding demonstates that the binding pocket at the unique Fe is not too small for N2; instead, the exceptionally weak affinity for N2 can be attributed to weak Fe-N2 bonding. The differences in the N2 coordination chemistry between sterically protected Mo-Fe-S clusters and Fe-only Fe-S clusters are discussed.
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Affiliation(s)
- Alexandra C Brown
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Daniel L M Suess
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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21
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Santos MFA, Pessoa JC. Interaction of Vanadium Complexes with Proteins: Revisiting the Reported Structures in the Protein Data Bank (PDB) since 2015. Molecules 2023; 28:6538. [PMID: 37764313 PMCID: PMC10536487 DOI: 10.3390/molecules28186538] [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: 07/27/2023] [Revised: 09/04/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
The structural determination and characterization of molecules, namely proteins and enzymes, is crucial to gaining a better understanding of their role in different chemical and biological processes. The continuous technical developments in the experimental and computational resources of X-ray diffraction (XRD) and, more recently, cryogenic Electron Microscopy (cryo-EM) led to an enormous growth in the number of structures deposited in the Protein Data Bank (PDB). Bioinorganic chemistry arose as a relevant discipline in biology and therapeutics, with a massive number of studies reporting the effects of metal complexes on biological systems, with vanadium complexes being one of the relevant systems addressed. In this review, we focus on the interactions of vanadium compounds (VCs) with proteins. Several types of binding are established between VCs and proteins/enzymes. Considering that the V-species that bind may differ from those initially added, the mentioned structural techniques are pivotal to clarifying the nature and variety of interactions of VCs with proteins and to proposing the mechanisms involved either in enzymatic inhibition or catalysis. As such, we provide an account of the available structural information of VCs bound to proteins obtained by both XRD and/or cryo-EM, mainly exploring the more recent structures, particularly those containing organic-based vanadium complexes.
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Affiliation(s)
- Marino F. A. Santos
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- UCIBIO—Applied Molecular Biosciences Unit, Chemistry Department, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- Centro de Química Estrutural, Departamento de Engenharia Química, Institute of Molecular Sciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - João Costa Pessoa
- Centro de Química Estrutural, Departamento de Engenharia Química, Institute of Molecular Sciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
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22
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Brinck T, Sahoo SK. Anomalous π-backbonding in complexes between B(SiR 3) 3 and N 2: catalytic activation and breaking of scaling relations. Phys Chem Chem Phys 2023; 25:21006-21019. [PMID: 37519222 DOI: 10.1039/d3cp00248a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/01/2023]
Abstract
Chemical transformations of molecular nitrogen (N2), including the nitrogen reduction reaction (NRR), are difficult to catalyze because of the weak Lewis basicity of N2. In this study, it is shown that Lewis acids of the types B(SiR3)3 and B(GeR3)3 bind N2 and CO with anomalously short and strong B-N or B-C bonds. B(SiH3)3·N2 has a B-N bond length of 1.48 Å and a complexation enthalpy of -15.9 kcal mol-1 at the M06-2X/jun-cc-pVTZ level. The selective binding enhancement of N2 and CO is due to π-backbonding from Lewis acid to Lewis base, as demonstrated by orbital analysis and density difference plots. The π-backbonding is found to be a consequence of constructive orbital interactions between the diffuse and highly polarizable B-Si and B-Ge bond regions and the π and π* orbitals of N2. This interaction is strengthened by electron donating substituents on Si or Ge. The π-backbonding interaction is predicted to activate N2 for chemical transformation and reduction, as it decreases the electron density and increases the length of the N-N bond. The binding of N2 and CO by the B(SiR3)3 and B(GeR3)3 types of Lewis acids also has a strong σ-bonding contribution. The relatively high σ-bond strength is connected to the highly positive surface electrostatic potential [VS(r)] above the B atom in the tetragonal binding conformation, but the σ-bonding also has a significant coordinate covalent (dative) contribution. Electron withdrawing substituents increase the potential and the σ-bond strength, but favor the binding of regular Lewis acids, such as NH3 and F-, more strongly than binding of N2 and CO. Molecules of the types B(SiR3)3 and B(GeR3)3 are chemically labile and difficult to synthesize. Heterogenous catalysts with the wanted B(Si-)3 or B(Ge-)3 bonding motif may be prepared by boron doping of nanostructured silicon or germanium compounds. B-doped and hydrogenated silicene is found to have promising properties as catalyst for the electrochemical NRR.
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Affiliation(s)
- Tore Brinck
- Department of Chemistry, CBH, KTH Royal Institute of Technology, SE-100 44 Stockholm, Sweden.
| | - Suman Kalyan Sahoo
- Department of Chemistry, CBH, KTH Royal Institute of Technology, SE-100 44 Stockholm, Sweden.
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23
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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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24
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Jin H, Kim SS, Venkateshalu S, Lee J, Lee K, Jin K. Electrochemical Nitrogen Fixation for Green Ammonia: Recent Progress and Challenges. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2300951. [PMID: 37289104 PMCID: PMC10427382 DOI: 10.1002/advs.202300951] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 05/08/2023] [Indexed: 06/09/2023]
Abstract
Ammonia, a key feedstock used in various industries, has been considered a sustainable fuel and energy storage option. However, NH3 production via the conventional Haber-Bosch process is costly, energy-intensive, and significantly contributing to a massive carbon footprint. An electrochemical synthetic pathway for nitrogen fixation has recently gained considerable attention as NH3 can be produced through a green process without generating harmful pollutants. This review discusses the recent progress and challenges associated with the two relevant electrochemical pathways: direct and indirect nitrogen reduction reactions. The detailed mechanisms of these reactions and highlight the recent efforts to improve the catalytic performances are discussed. Finally, various promising research strategies and remaining tasks are presented to highlight future opportunities in the electrochemical nitrogen reduction reaction.
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Affiliation(s)
- Haneul Jin
- Department of Energy and Materials EngineeringDongguk University‐SeoulSeoul04620Republic of Korea
| | - Suyeon S. Kim
- Department of Chemistry and Research Institute of Natural ScienceKorea UniversitySeoul02841Republic of Korea
| | - Sandhya Venkateshalu
- Department of Chemistry and Research Institute of Natural ScienceKorea UniversitySeoul02841Republic of Korea
| | - Jeseok Lee
- Department of Chemistry and Research Institute of Natural ScienceKorea UniversitySeoul02841Republic of Korea
| | - Kwangyeol Lee
- Department of Chemistry and Research Institute of Natural ScienceKorea UniversitySeoul02841Republic of Korea
| | - Kyoungsuk Jin
- Department of Chemistry and Research Institute of Natural ScienceKorea UniversitySeoul02841Republic of Korea
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25
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Zheng J, Zhang H, Lv J, Zhang M, Wan J, Gerrits N, Wu A, Lan B, Wang W, Wang S, Tu X, Bogaerts A, Li X. Enhanced NH 3 Synthesis from Air in a Plasma Tandem-Electrocatalysis System Using Plasma-Engraved N-Doped Defective MoS 2. JACS AU 2023; 3:1328-1336. [PMID: 37234124 PMCID: PMC10207100 DOI: 10.1021/jacsau.3c00087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 04/12/2023] [Accepted: 04/13/2023] [Indexed: 05/27/2023]
Abstract
We have developed a sustainable method to produce NH3 directly from air using a plasma tandem-electrocatalysis system that operates via the N2-NOx-NH3 pathway. To efficiently reduce NO2- to NH3, we propose a novel electrocatalyst consisting of defective N-doped molybdenum sulfide nanosheets on vertical graphene arrays (N-MoS2/VGs). We used a plasma engraving process to form the metallic 1T phase, N doping, and S vacancies in the electrocatalyst simultaneously. Our system exhibited a remarkable NH3 production rate of 7.3 mg h-1 cm-2 at -0.53 V vs RHE, which is almost 100 times higher than the state-of-the-art electrochemical nitrogen reduction reaction and more than double that of other hybrid systems. Moreover, a low energy consumption of only 2.4 MJ molNH3-1 was achieved in this study. Density functional theory calculations revealed that S vacancies and doped N atoms play a dominant role in the selective reduction of NO2- to NH3. This study opens up new avenues for efficient NH3 production using cascade systems.
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Affiliation(s)
- Jiageng Zheng
- State
Key Laboratory of Clean Energy Utilization, College of Energy and
Engineering, Academy of Ecological Civilization, Zhejiang University, Hangzhou 310027, China
| | - Hao Zhang
- State
Key Laboratory of Clean Energy Utilization, College of Energy and
Engineering, Academy of Ecological Civilization, Zhejiang University, Hangzhou 310027, China
| | - Jiabao Lv
- State
Key Laboratory of Clean Energy Utilization, College of Energy and
Engineering, Academy of Ecological Civilization, Zhejiang University, Hangzhou 310027, China
| | - Meng Zhang
- College
of Optical Science and Engineering, Zhejiang
University, Hangzhou 310027, China
| | - Jieying Wan
- State
Key Laboratory of Clean Energy Utilization, College of Energy and
Engineering, Academy of Ecological Civilization, Zhejiang University, Hangzhou 310027, China
| | - Nick Gerrits
- Research
Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, BE-2610 Wilrijk, Belgium
| | - Angjian Wu
- State
Key Laboratory of Clean Energy Utilization, College of Energy and
Engineering, Academy of Ecological Civilization, Zhejiang University, Hangzhou 310027, China
| | - Bingru Lan
- State
Key Laboratory of Clean Energy Utilization, College of Energy and
Engineering, Academy of Ecological Civilization, Zhejiang University, Hangzhou 310027, China
| | - Weitao Wang
- Department
of Electrical Engineering and Electronics, University of Liverpool, Liverpool L69 3GJ, U.K.
| | - Shuangyin Wang
- State
Key Laboratory of Chem/Bio-Sensing and Chemometrics, College of Chemistry
and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Xin Tu
- Department
of Electrical Engineering and Electronics, University of Liverpool, Liverpool L69 3GJ, U.K.
| | - Annemie Bogaerts
- Research
Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, BE-2610 Wilrijk, Belgium
| | - Xiaodong Li
- State
Key Laboratory of Clean Energy Utilization, College of Energy and
Engineering, Academy of Ecological Civilization, Zhejiang University, Hangzhou 310027, China
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26
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Abstract
The Fischer-Tropsch (FT) process converts a mixture of CO and H2 into liquid hydrocarbons as a major component of the gas-to-liquid technology for the production of synthetic fuels. Contrary to the energy-demanding chemical FT process, the enzymatic FT-type reactions catalyzed by nitrogenase enzymes, their metalloclusters, and synthetic mimics utilize H+ and e- as the reducing equivalents to reduce CO, CO2, and CN- into hydrocarbons under ambient conditions. The C1 chemistry exemplified by these FT-type reactions is underscored by the structural and electronic properties of the nitrogenase-associated metallocenters, and recent studies have pointed to the potential relevance of this reactivity to nitrogenase mechanism, prebiotic chemistry, and biotechnological applications. This review will provide an overview of the features of nitrogenase enzymes and associated metalloclusters, followed by a detailed discussion of the activities of various nitrogenase-derived FT systems and plausible mechanisms of the enzymatic FT reactions, highlighting the versatility of this unique reactivity while providing perspectives onto its mechanistic, evolutionary, and biotechnological implications.
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Affiliation(s)
- Yilin Hu
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine 92697-3900, USA
| | - Chi Chung Lee
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine 92697-3900, USA
| | - Mario Grosch
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine 92697-3900, USA
| | - Joseph B. Solomon
- Department of Chemistry, University of California, Irvine, CA 92697-2025, USA
| | - Wolfgang Weigand
- Institute of Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Markus W. Ribbe
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine 92697-3900, USA
- Department of Chemistry, University of California, Irvine, CA 92697-2025, USA
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27
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Wang H, Cheng C, Du K, Xu Z, Zhao E, Lan N, Yin PF, Ling T. A Plasmon Resonance Enhanced Photo-Electrode to Promote NH 3 Yield in Sustainable N 2 Conversion. Chemistry 2023; 29:e202300204. [PMID: 36941243 DOI: 10.1002/chem.202300204] [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: 01/20/2023] [Indexed: 03/23/2023]
Abstract
A key challenge for electrochemical nitrogen reduction reactions (NRR) is the difficulty for conventional catalysts to achieve high currents at low H* coverage to produce appreciable NH3 . Herein, we specially designed an Au nanoparticle-embedded ZnSe photo-electrode to solve the problem. As-designed photo-electrode achieves excellent NRR performance with a high NH3 yield (12.2 μg cm-2 h-1 ) and Faradaic efficiency (27.3 %). Our work reveals that the unique plasmon resonance effect of embedded Au nanoparticles plays a key role in increasing catalytic current when the H* coverage is decreased. Moreover, we successfully established a correlation between H* coverage and NRR performance based on theoretical calculations and experimental observations. This work paves the path for the future design of catalytic materials to overcome the selectivity and yield challenge of sustainable NH3 production.
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Affiliation(s)
- Haonan Wang
- Key Laboratory for Advanced Ceramics and, Machining Technology of Ministry of Education, Institute of New-Energy, School of Materials Science and Engineering, Tianjin University, Tianjin, 300072, P. R. China
| | - Chuanqi Cheng
- Key Laboratory for Advanced Ceramics and, Machining Technology of Ministry of Education, Institute of New-Energy, School of Materials Science and Engineering, Tianjin University, Tianjin, 300072, P. R. China
| | - Kun Du
- Key Laboratory for Advanced Ceramics and, Machining Technology of Ministry of Education, Institute of New-Energy, School of Materials Science and Engineering, Tianjin University, Tianjin, 300072, P. R. China
| | - Zongwei Xu
- School of Precision Instruments and, Optoelectronics Engineering Tianjin University, Tianjin, 300072, P. R. China
| | - Erling Zhao
- Key Laboratory for Advanced Ceramics and, Machining Technology of Ministry of Education, Institute of New-Energy, School of Materials Science and Engineering, Tianjin University, Tianjin, 300072, P. R. China
| | - Ning Lan
- Key Laboratory for Advanced Ceramics and, Machining Technology of Ministry of Education, Institute of New-Energy, School of Materials Science and Engineering, Tianjin University, Tianjin, 300072, P. R. China
| | - Peng-Fei Yin
- Key Laboratory for Advanced Ceramics and, Machining Technology of Ministry of Education, Institute of New-Energy, School of Materials Science and Engineering, Tianjin University, Tianjin, 300072, P. R. China
| | - Tao Ling
- Key Laboratory for Advanced Ceramics and, Machining Technology of Ministry of Education, Institute of New-Energy, School of Materials Science and Engineering, Tianjin University, Tianjin, 300072, P. R. China
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28
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Beagan DM, Kiernicki JJ, Zeller M, Szymczak NK. A Bidentate Ligand Featuring Ditopic Lewis Acids in the Second Sphere for Selective Substrate Capture and Activation. Angew Chem Int Ed Engl 2023; 62:e202218907. [PMID: 36720708 PMCID: PMC10023486 DOI: 10.1002/anie.202218907] [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: 12/21/2022] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/02/2023]
Abstract
We present a ligand platform featuring appended ditopic Lewis acids to facilitate capture/activation of diatomic substrates. We show that incorporation of two 9-borabicyclo[3.3.1]nonane (9-BBN) units on a single carbon tethered to a pyridine pyrazole scaffold maintains a set of unquenched nitrogen donors available to coordinate FeII , ZnII , and NiII . Using hydride ion affinity and competition experiments, we establish an additive effect for ditopic secondary sphere boranes, compared to the monotopic analogue. These effects are exploited to achieve high selectivity for binding NO2 - in the presence of competitive anions such as F- and NO3 - . Finally, we demonstrate hydrazine capture within the second-sphere of metal complexes, followed by unique activation pathways to generate hydrazido and diazene ligands on Zn and Fe, respectively.
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Affiliation(s)
- Daniel M Beagan
- Department of Chemistry, University of Michigan, 930 N. University, Ann Arbor, MI 48109, USA
| | - John J Kiernicki
- Department of Chemistry, University of Michigan, 930 N. University, Ann Arbor, MI 48109, USA
- Present address: Drury University, Department of Chemistry and Physics, 900 North Benton Ave., Springfield, MO 65802, USA
| | - Matthias Zeller
- H.C. Brown Laboratory, Department of Chemistry, Purdue University, 560 Oval Dr., West Lafayette, IN 47907, USA
| | - Nathaniel K Szymczak
- Department of Chemistry, University of Michigan, 930 N. University, Ann Arbor, MI 48109, USA
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29
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Lycus P, Einsle O, Zhang L. Structural biology of proteins involved in nitrogen cycling. Curr Opin Chem Biol 2023; 74:102278. [PMID: 36889028 DOI: 10.1016/j.cbpa.2023.102278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/31/2023] [Accepted: 02/02/2023] [Indexed: 03/08/2023]
Abstract
Microbial metabolic processes drive the global nitrogen cycle through sophisticated and often unique metalloenzymes that facilitate difficult redox reactions at ambient temperature and pressure. Understanding the intricacies of these biological nitrogen transformations requires a detailed knowledge that arises from the combination of a multitude of powerful analytical techniques and functional assays. Recent developments in spectroscopy and structural biology have provided new, powerful tools for addressing existing and emerging questions, which have gained urgency due to the global environmental implications of these fundamental reactions. The present review focuses on the recent contributions of the wider area of structural biology to understanding nitrogen metabolism, opening new avenues for biotechnological applications to better manage and balance the challenges of the global nitrogen cycle.
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Affiliation(s)
- Pawel Lycus
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104, Freiburg im Breisgau, Germany; Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Oliver Einsle
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104, Freiburg im Breisgau, Germany.
| | - Lin Zhang
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104, Freiburg im Breisgau, Germany.
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30
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Dance I. The binding of reducible N 2 in the reaction domain of nitrogenase. Dalton Trans 2023; 52:2013-2026. [PMID: 36691966 DOI: 10.1039/d2dt03599e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The binding of N2 to FeMo-co, the catalytic site of the enzyme nitrogenase, is central to the conversion to NH3, but also has a separate role in promoting the N2-dependent HD reaction (D2 + 2H+ + 2e- → 2HD). The protein surrounding FeMo-co contains a clear channel for ingress of N2, directly towards the exo-coordination position of Fe2, a position which is outside the catalytic reaction domain. This led to the hypothesis [I. Dance, Dalton Trans., 2022, 51, 12717] of 'promotional' N2 bound at exo-Fe2, and a second 'reducible' N2 bound in the reaction domain, specifically the endo-coordination position of Fe2 or Fe6. The range of possibilities for the binding of reducible N2 in the presence of bound promotional N2 is described here, using density functional simulations with a 486 atom model of the active site and surrounding protein. The pathway for ingress of the second N2 through protein, past the first N2 at exo-Fe2, and tumbling into the binding domain between Fe2 and Fe6, is described. The calculations explore 24 structures involving 6 different forms of hydrogenated FeMo-co, including structures with S2BH unhooked from Fe2 but tethered to Fe6. The calculations use the most probable electronic states. End-on (η1) binding of N2 at the endo position of either Fe2 or Fe6 is almost invariably exothermic, with binding potential energies ranging up to -18 kcal mol-1. Many structures have binding energies in the range -6 to -14 kcal mol-1. The relevant entropic penalty for N2 binding from a diffusible position within the protein is estimated to be 4 kcal mol-1, and so the binding free energies for reducible N2 are suitably negative. N2 binding at endo-Fe2 is stronger than at endo-Fe6 in three of the six structure categories. In many cases the reaction domain containing reducible N2 is expanded. These results inform computational simulation of the subsequent steps in which surrounding H atoms transfer to reducible N2.
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Affiliation(s)
- Ian Dance
- School of Chemistry, UNSW Sydney, Australia.
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31
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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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32
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Near ambient N2 fixation on solid electrodes versus enzymes and homogeneous catalysts. Nat Rev Chem 2023; 7:184-201. [PMID: 37117902 DOI: 10.1038/s41570-023-00462-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/31/2022] [Indexed: 02/04/2023]
Abstract
The Mo/Fe nitrogenase enzyme is unique in its ability to efficiently reduce dinitrogen to ammonia at atmospheric pressures and room temperature. Should an artificial electrolytic device achieve the same feat, it would revolutionize fertilizer production and even provide an energy-dense, truly carbon-free fuel. This Review provides a coherent comparison of recent progress made in dinitrogen fixation on solid electrodes, homogeneous catalysts and nitrogenases. Specific emphasis is placed on systems for which there is unequivocal evidence that dinitrogen reduction has taken place. By establishing the cross-cutting themes and synergies between these systems, we identify viable avenues for future research.
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33
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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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34
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Rehder D. Vanadium in biological systems and medicinal applications. Inorganica Chim Acta 2023. [DOI: 10.1016/j.ica.2023.121387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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35
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Activation of unsaturated small molecules by bio-relevant multinuclear metal-sulfur clusters. Coord Chem Rev 2023. [DOI: 10.1016/j.ccr.2022.214838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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36
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Threatt SD, Rees DC. Biological nitrogen fixation in theory, practice, and reality: a perspective on the molybdenum nitrogenase system. FEBS Lett 2023; 597:45-58. [PMID: 36344435 PMCID: PMC10100503 DOI: 10.1002/1873-3468.14534] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 10/30/2022] [Accepted: 10/31/2022] [Indexed: 11/09/2022]
Abstract
Nitrogenase is the sole enzyme responsible for the ATP-dependent conversion of atmospheric dinitrogen into the bioavailable form of ammonia (NH3 ), making this protein essential for the maintenance of the nitrogen cycle and thus life itself. Despite the widespread use of the Haber-Bosch process to industrially produce NH3 , biological nitrogen fixation still accounts for half of the bioavailable nitrogen on Earth. An important feature of nitrogenase is that it operates under physiological conditions, where the equilibrium strongly favours ammonia production. This biological, multielectron reduction is a complex catalytic reaction that has perplexed scientists for decades. In this review, we explore the current understanding of the molybdenum nitrogenase system based on experimental and computational research, as well as the limitations of the crystallographic, spectroscopic, and computational techniques employed. Finally, essential outstanding questions regarding the nitrogenase system will be highlighted alongside suggestions for future experimental and computational work to elucidate this essential yet elusive process.
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Affiliation(s)
- Stephanie D Threatt
- Division of Chemistry and Chemical Engineering, Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, USA
| | - Douglas C Rees
- Division of Chemistry and Chemical Engineering, Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, USA
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37
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Lee CH, Lin DJ, Pan HR, Wu J, Liu HK, Hsu HF. Reversible Conversion of Disulfide/Dithiolate Occurring at a Vanadium(IV) Center: A Biomimetic System for Redox Exchange in Vanabin. Inorg Chem 2022; 61:19882-19889. [PMID: 36441974 DOI: 10.1021/acs.inorgchem.2c03115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ascidians use a class of cysteine-rich proteins generally referred to as vanabins to reduce vanadium ions, one of the many biological processes that involve the redox conversion between disulfide and dithiolate mediated by transition-metal ions. To further understand the nature of disulfide/dithiolate exchange facilitated by a vanadium center, we report herein a six-coordinate non-oxido VIV complex containing an unbound disulfide moiety, [VIV(PS3″)(PS1″S-S)] (1) (PS3″ = [P(C6H3-3-Me3Si-2-S)3]3-, where PS1″S-S is a disulfide form of PS3″). Complex 1 is obtained from a reaction of previously reported [VV(PS3″)(PS2″SH)] (2) (PS2″SH = [P(C6H3-3-Me3Si-2-SH)(C6H3-3-Me3Si-2-S)2] with TEMPO (TEMPO = 2,2,6,6-tetramethylpiperidin-1-yl)oxyl) via hydrogen atom transfer. Importantly, complex 1 can be reduced by two electrons to form an eight-coordinate VIV complex, [VIV(PS3″)2]2- (4). The reaction can be reversed through a two-electron oxidation process to regenerate complex 1. The redox pathways both proceed through a common intermediate, [V(PS3″)2]- (3), that has been previously reported as a resonance form of VV-dithiolate and a VIV-(thiolate)(thiyl-radical) species. This work demonstrates an unprecedented example of reversible disulfide/dithiolate interconversion mediated by a VIV center, as well as provides insights into understanding the function of VV reductases in vanabins.
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Affiliation(s)
- Cheng-Hsun Lee
- Department of Chemistry, National Cheng Kung University, Tainan 701, Taiwan
| | - Ding-Jyun Lin
- Department of Chemistry, National Cheng Kung University, Tainan 701, Taiwan
| | - Hung-Ruei Pan
- Department of Chemistry, National Cheng Kung University, Tainan 701, Taiwan
| | - John Wu
- Department of Chemistry, National Cheng Kung University, Tainan 701, Taiwan
| | - Hsin-Kuan Liu
- Core Facility Center, National Cheng Kung University, Tainan 701, Taiwan
| | - Hua-Fen Hsu
- Department of Chemistry, National Cheng Kung University, Tainan 701, Taiwan
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38
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Rutledge HL, Field MJ, Rittle J, Green MT, Akif Tezcan F. Role of Serine Coordination in the Structural and Functional Protection of the Nitrogenase P-Cluster. J Am Chem Soc 2022; 144:22101-22112. [PMID: 36445204 PMCID: PMC9957664 DOI: 10.1021/jacs.2c09480] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Nitrogenase catalyzes the multielectron reduction of dinitrogen to ammonia. Electron transfer in the catalytic protein (MoFeP) proceeds through a unique [8Fe-7S] cluster (P-cluster) to the active site (FeMoco). In the reduced, all-ferrous (PN) state, the P-cluster is coordinated by six cysteine residues. Upon two-electron oxidation to the P2+ state, the P-cluster undergoes conformational changes in which a highly conserved oxygen-based residue (a Ser or a Tyr) and a backbone amide additionally ligate the cluster. Previous studies of Azotobacter vinelandii (Av) MoFeP revealed that when the oxygen-based residue, βSer188, was mutated to a noncoordinating residue, Ala, the P-cluster became redox-labile and reversibly lost two of its eight Fe centers. Surprisingly, the Av strain with a MoFeP variant that lacked the serine ligand (Av βSer188Ala MoFeP) displayed the same diazotrophic growth and in vitro enzyme turnover rates as wild-type Av MoFeP, calling into question the necessity of this conserved ligand for nitrogenase function. Based on these observations, we hypothesized that βSer188 plays a role in protecting the P-cluster under nonideal conditions. Here, we investigated the protective role of βSer188 both in vivo and in vitro by characterizing the ability of Av βSer188Ala cells to grow under suboptimal conditions (high oxidative stress or Fe limitation) and by determining the tendency of βSer188Ala MoFeP to be mismetallated in vitro. Our results demonstrate that βSer188 (1) increases Av cell survival upon exposure to oxidative stress in the form of hydrogen peroxide, (2) is necessary for efficient Av diazotrophic growth under Fe-limiting conditions, and (3) may protect the P-cluster from metal exchange in vitro. Taken together, our findings suggest a structural adaptation of nitrogenase to protect the P-cluster via Ser ligation, which is a previously unidentified functional role of the Ser residue in redox proteins and adds to the expanding functional roles of non-Cys ligands to FeS clusters.
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Affiliation(s)
- Hannah L. Rutledge
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Mackenzie J. Field
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Jonathan Rittle
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Michael T. Green
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States.,Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, California 92697, United States
| | - F. Akif Tezcan
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States.,Corresponding Author:
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39
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Papanikolaou MG, Simaioforidou AV, Drouza C, Tsipis AC, Miras HN, Keramidas AD, Louloudi M, Kabanos TA. A Combined Experimental and Theoretical Investigation of Oxidation Catalysis by cis-[V IV(O)(Cl/F)(N 4)] + Species Mimicking the Active Center of Metal-Enzymes. Inorg Chem 2022; 61:18434-18449. [PMID: 36357045 PMCID: PMC9682486 DOI: 10.1021/acs.inorgchem.2c02526] [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: 11/12/2022]
Abstract
![]()
Reaction
of VIVOCl2 with the nonplanar
tetradentate
N4 bis-quinoline ligands yielded four oxidovanadium(IV)
compounds of the general formula cis-[VIV(O)(Cl)(N4)]Cl. Sequential treatment of the two nonmethylated
N4 oxidovanadium(IV) compounds with KF and NaClO4 resulted in the isolation of the species with the general formula cis-[VIV(O)(F)(N4)]ClO4. In marked contrast, the methylated N4 oxidovanadium(IV)
derivatives are inert toward KF reaction due to steric hindrance,
as evidenced by EPR and theoretical calculations. The oxidovanadium(IV)
compounds were characterized by single-crystal X-ray structure analysis,
cw EPR spectroscopy, and magnetic susceptibility. The crystallographic
characterization showed that the vanadium compounds have a highly
distorted octahedral coordination environment and the d(VIV–F) = 1.834(1) Å is the shortest to be
reported for (oxido)(fluorido)vanadium(IV) compounds. The experimental
EPR parameters of the VIVO2+ species deviate
from the ones calculated by the empirical additivity relationship
and can be attributed to the axial donor atom trans to the oxido group
and the distorted VIV coordination environment. The vanadium
compounds act as catalysts toward alkane oxidation by aqueous H2O2 with moderate ΤΟΝ up to 293
and product yields of up to 29% (based on alkane); the vanadium(IV)
is oxidized to vanadium(V), and the ligands remain bound to the vanadium
atom during the catalysis, as determined by 51V and 1H NMR spectroscopies. The cw X-band EPR studies proved that
the mechanism of the catalytic reaction is through hydroxyl radicals.
The chloride substitution reaction in the cis-[VIV(O)(Cl)(N4)]+ species by fluoride and
the mechanism of the alkane oxidation were studied by DFT calculations. Highly distorted N4−oxidovanadium(IV), cis-[VIV(=O)(Cl/F)(N4)]+, compounds mimicking the distorted coordination environment of the
metal-ion in metal-enzymes’ active center catalyze oxidation
of alkanes. The structural distortion results in significant deviation
of the cw EPR parameters from the expected ones and equilibrium between
six- and five- coordinate species in solution. DFT studies show that
distortion, steric hindrance, and the coordinated halogen define the
catalytic mechanism of oxidation of alkanes by cis-[VIV(=O)(Cl/F)(N4)]+ compounds.
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Affiliation(s)
- Michael G. Papanikolaou
- Section of Inorganic and Analytical Chemistry, Department of Chemistry, University of Ioannina, Ioannina45110, Greece
- Department of Chemistry, University of Cyprus, Nicosia1678, Cyprus
| | - Anastasia V. Simaioforidou
- Section of Inorganic and Analytical Chemistry, Department of Chemistry, University of Ioannina, Ioannina45110, Greece
| | - Chryssoula Drouza
- Department of Agricultural Production, Biotechnology and Food Science, Cyprus University of Technology, 3036Limassol, Cyprus
| | - Athanassios C. Tsipis
- Section of Inorganic and Analytical Chemistry, Department of Chemistry, University of Ioannina, Ioannina45110, Greece
| | | | | | - Maria Louloudi
- Section of Inorganic and Analytical Chemistry, Department of Chemistry, University of Ioannina, Ioannina45110, Greece
| | - Themistoklis A. Kabanos
- Section of Inorganic and Analytical Chemistry, Department of Chemistry, University of Ioannina, Ioannina45110, Greece
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40
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Lukoyanov DA, Yang ZY, Pérez-González A, Raugei S, Dean DR, Seefeldt LC, Hoffman BM. 13C ENDOR Characterization of the Central Carbon within the Nitrogenase Catalytic Cofactor Indicates That the CFe 6 Core Is a Stabilizing "Heart of Steel". J Am Chem Soc 2022; 144:18315-18328. [PMID: 36166637 DOI: 10.1021/jacs.2c06149] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Substrates and inhibitors of Mo-dependent nitrogenase bind and react at Fe ions of the active-site FeMo-cofactor [7Fe-9S-C-Mo-homocitrate] contained within the MoFe protein α-subunit. The cofactor contains a CFe6 core, a carbon centered within a trigonal prism of six Fe, whose role in catalysis is unknown. Targeted 13C labeling of the carbon enables electron-nuclear double resonance (ENDOR) spectroscopy to sensitively monitor the electronic properties of the Fe-C bonds and the spin-coupling scheme adopted by the FeMo-cofactor metal ions. This report compares 13CFe6 ENDOR measurements for (i) the wild-type protein resting state (E0; α-Val70) to those of (ii) α-Ile70, (iii) α-Ala70-substituted proteins; (iv) crystallographically characterized CO-inhibited "hi-CO" state; (v) E4(4H) Janus intermediate, activated for N2 binding/reduction by accumulation of 4[e-/H+]; (vi) E4(2H)* state containing a doubly reduced FeMo-cofactor without Fe-bound substrates; and (vii) propargyl alcohol reduction intermediate having allyl alcohol bound as a ferracycle to FeMo-cofactor Fe6. All states examined, both S = 1/2 and 3/2 exhibited near-zero 13C isotropic hyperfine coupling constants, Ca = [-1.3 ↔ +2.7] MHz. Density functional theory computations and natural bond orbital analysis of the Fe-C bonds show that this occurs because a (3 spin-up/3 spin-down) spin-exchange configuration of CFe6 Fe-ion spins produces cancellation of large spin-transfers to carbon in each Fe-C bond. Previous X-ray diffraction and DFT both indicate that trigonal-prismatic geometry around carbon is maintained with high precision in all these states. The persistent structure and Fe-C bonding of the CFe6 core indicate that it does not provide a functionally dynamic (hemilabile) "beating heart"─instead it acts as "a heart of steel", stabilizing the structure of the FeMo-cofactor-active site during nitrogenase catalysis.
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Affiliation(s)
- Dmitriy A Lukoyanov
- Departments of Chemistry and Molecular Biosciences, Northwestern University, Evanston, Illinois60208, United States
| | - Zhi-Yong Yang
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah84322, United States
| | - Ana Pérez-González
- Biochemistry Department, Virginia Tech, Blacksburg, Virginia24061, United States
| | - Simone Raugei
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington99352, United States
| | - Dennis R Dean
- Biochemistry Department, Virginia Tech, Blacksburg, Virginia24061, United States
| | - Lance C Seefeldt
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah84322, United States
| | - Brian M Hoffman
- Departments of Chemistry and Molecular Biosciences, Northwestern University, Evanston, Illinois60208, United States
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41
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Tanifuji K, Jasniewski AJ, Lee CC, Solomon JB, Nagasawa T, Ohki Y, Tatsumi K, Hedman B, Hodgson KO, Hu Y, Ribbe MW. Incorporation of an Asymmetric Mo-Fe-S Cluster as an Artificial Cofactor into Nitrogenase. Chembiochem 2022; 23:e202200384. [PMID: 35925843 PMCID: PMC9547968 DOI: 10.1002/cbic.202200384] [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: 07/07/2022] [Revised: 08/03/2022] [Indexed: 11/07/2022]
Abstract
Nitrogenase employs a sophisticated electron transfer system and a Mo-Fe-S-C cofactor, designated the M-cluster [(cit)MoFe7 S9 C]), to reduce atmospheric N2 to bioaccessible NH3 . Previously, we have shown that the cofactor-free form of nitrogenase can be repurposed as a protein scaffold for the incorporation of a synthetic Fe-S cluster [Fe6 S9 (SEt)2 ]4- . Here, we demonstrate the utility of an asymmetric Mo-Fe-S cluster [Cp*MoFe5 S9 (SH)]3- as an alternative artificial cofactor upon incorporation into the cofactor-free nitrogenase scaffold. The resultant semi-artificial enzyme catalytically reduces C2 H2 to C2 H4 , and CN- into short-chain hydrocarbons, yet it is clearly distinct in activity from its [Fe6 S9 (SEt)2 ]4- -reconstituted counterpart, pointing to the possibility to employ molecular design and cluster synthesis strategies to further develop semi-artificial or artificial systems with desired catalytic activities.
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Affiliation(s)
- Kazuki Tanifuji
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, 92697-3900, USA
- Institute for Chemical Research, Kyoto University Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Andrew J Jasniewski
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, 92697-3900, USA
| | - Chi Chung Lee
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, 92697-3900, USA
| | - Joseph B Solomon
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, 92697-3900, USA
- Department of Chemistry, University of California Irvine, Irvine, CA, 92697-2025, USA
| | - Takayuki Nagasawa
- Department of Chemistry Graduate School of Science and Research Center for Materials Science, Nagoya University, Furo-cho Chikusa-ku, Nagoya, 464-8602, Japan
| | - Yasuhiro Ohki
- Institute for Chemical Research, Kyoto University Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Kazuyuki Tatsumi
- Department of Chemistry Graduate School of Science and Research Center for Materials Science, Nagoya University, Furo-cho Chikusa-ku, Nagoya, 464-8602, Japan
| | - Britt Hedman
- Stanford Synchrotron Radiation Lightsource SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, 94025, USA
| | - Keith O Hodgson
- Stanford Synchrotron Radiation Lightsource SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, 94025, USA
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | - Yilin Hu
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, 92697-3900, USA
| | - Markus W Ribbe
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, 92697-3900, USA
- Department of Chemistry, University of California Irvine, Irvine, CA, 92697-2025, USA
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42
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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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43
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Kokubo Y, Igarashi I, Nakao K, Hachiya W, Kugimiya S, Ozawa T, Masuda H, Kajita Y. The Steric Effect in Preparations of Vanadium(II)/(III) Dinitrogen Complexes of Triamidoamine Ligands Bearing Bulky Substituents. Molecules 2022; 27:5864. [PMID: 36144600 PMCID: PMC9500765 DOI: 10.3390/molecules27185864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/06/2022] [Accepted: 09/07/2022] [Indexed: 11/16/2022] Open
Abstract
The reactions of newly designed lithiated triamidoamines Li3LR (R = iPr, Pen, and Cy2) with VCl3(THF)3 under N2 yielded dinitrogen-divanadium complexes with a μ-N2 between vanadium atoms [{V(LR)}2(μ-N2)] (R = iPr (1) and Pen (2)) for the former two, while not dinitrogen-divanadium complexes but a mononuclear vanadium complex with a vacant site, [V(LCy2)] (R = Cy2 (3)), were obtained for the third ligand. The V-NN2 and N-N distances were 1.7655(18) and 1.219(4) Å for 1 and 1.7935(14) and 1.226(3) Å for 2, respectively. The ν(14N-14N) stretching vibrations of 1 and 2, as measured using resonance Raman spectroscopy, were detected at 1436 and 1412 cm-1, respectively. Complex 3 reacted with potassium metal in the presence of 18-crown-6-ether under N2 to give a hetero-dinuclear vanadium complex with μ-N2 between vanadium and potassium, [VK(LCy2)(μ-N2)(18-crown-6)] (4). The N-N distance and ν(14N-14N) stretching for 4 were 1.152(3) Å and 1818 cm-1, respectively, suggesting that 4 is more activated than complexes 1 and 2. The complexes 1, 2, 3, and 4 reacted with HOTf and K[C10H8] to give NH3 and N2H4. The yields of NH3 and N2H4 (per V atom) were 47 and 11% for 1, 38 and 16% for 2, 77 and 7% for 3, and 80 and 5% for 4, respectively, and 3 and 4, which have a ligand LCy2, showed higher reactivity than 1 and 2.
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Affiliation(s)
- Yoshiaki Kokubo
- Faculty of Engineering, Aichi Institute of Technology, 1247 Yachigusa, Yakusa-cho, Toyota 470-0392, Japan
| | - Itsuki Igarashi
- Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | - Kenichi Nakao
- Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | - Wataru Hachiya
- Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | - Shinichi Kugimiya
- Faculty of Engineering, Aichi Institute of Technology, 1247 Yachigusa, Yakusa-cho, Toyota 470-0392, Japan
| | - Tomohiro Ozawa
- Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | - Hideki Masuda
- Faculty of Engineering, Aichi Institute of Technology, 1247 Yachigusa, Yakusa-cho, Toyota 470-0392, Japan
- Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | - Yuji Kajita
- Faculty of Engineering, Aichi Institute of Technology, 1247 Yachigusa, Yakusa-cho, Toyota 470-0392, Japan
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44
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Norwine EE, Kiernicki JJ, Zeller M, Szymczak NK. Distinct Reactivity Modes of a Copper Hydride Enabled by an Intramolecular Lewis Acid. J Am Chem Soc 2022; 144:15038-15046. [PMID: 35960993 PMCID: PMC10291504 DOI: 10.1021/jacs.2c02937] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We disclose a 1,4,7-triazacyclononane (TACN) ligand featuring an appended boron Lewis acid. Metalation with Cu(I) affords a series of tetrahedral complexes including a boron-capped cuprous hydride. We demonstrate distinct reactivity modes as a function of chemical oxidation: hydride transfer to CO2 in the copper(I) state and oxidant-induced H2 evolution as well as alkyne reduction.
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Affiliation(s)
- Emily E. Norwine
- University of Michigan, 930 N. University, Ann Arbor, MI 48109 (USA)
| | - John J. Kiernicki
- University of Michigan, 930 N. University, Ann Arbor, MI 48109 (USA)
| | - Matthias Zeller
- H. C. Brown Laboratory, Purdue University, 560 Oval Dr., West Lafayette, IN 47907 (USA)
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45
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Dance I. Calculating the chemical mechanism of nitrogenase: new working hypotheses. Dalton Trans 2022; 51:12717-12728. [PMID: 35946501 DOI: 10.1039/d2dt01920e] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The enzyme nitrogenase converts N2 to NH3 with stoichiometry N2 + 8H+ + 8e- → 2NH3 + H2. The mechanism is chemically complex with multiple steps that must be consistent with much accumulated experimental information, including exchange of H2 and N2 and the N2-dependent hydrogenation of D2 to HD. Previous investigations have developed a collection of working hypotheses that guide ongoing density functional investigations of mechanistic steps and sequences. These include (i) hypotheses about the serial provision of protons and their conversion to H atoms bonded to S and Fe atoms of the FeMo-co catalytic site, (ii) the migration of H atoms over the surface of FeMo-co, (iii) the roles of His195, (iv) identification of three protein channels, one for the ingress of N2, a separate pathway for the passage of exogenous H2 (D2) and product H2 (HD), and a hydrophilic pathway for egress of product NH3. Two additional working hypotheses are described in this paper. N2 passing along the N2 channel approaches and binds end-on to the exo coordination position of Fe2, with favourable energetics when FeMo-co is pre-hydrogenated. This exo-Fe2-N2 is apparently not reduced but has a promotional role by expanding the reaction zone. A second N2 can enter via the N2 ingress channel and bind at the endo-Fe6 position, where it is surrounded by H atom donors suitable for the N2 → NH3 conversion. It is proposed that this endo-Fe6 position is also the binding site for H2 (generated or exogenous), accounting for the competitive inhibition of N2 reduction by H2. The HD reaction occurs at the endo-Fe6 site, promoted by N2 at the exo-Fe2 site. The second hypothesis concerns the most stable electronic states of FeMo-co with ligands bound at Fe2 and Fe6, and provides a protocol for management of electronic states in mechanism calculations.
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Affiliation(s)
- Ian Dance
- School of Chemistry, UNSW Sydney, NSW 2051, Australia.
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46
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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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47
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McSkimming A, Thompson NB. Four-Coordinate Fe N 2 and Imido Complexes Supported by a Hemilabile NNC Heteroscorpionate Ligand. Inorg Chem 2022; 61:12318-12326. [PMID: 35895990 PMCID: PMC9367695 DOI: 10.1021/acs.inorgchem.2c01656] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Indexed: 11/29/2022]
Abstract
Inspired by mechanistic proposals for N2 reduction at the nitrogenase FeMo cofactor, we report herein a new, strongly σ-donating heteroscorpionate ligand featuring two weak-field pyrazoles and an alkyl donor. This ligand supports four-coordinate Fe(I)-N2, Fe(II)-Cl, and Fe(III)-imido complexes, which we have characterized using a variety of spectroscopic and computational methods. Structural and quantum mechanical analysis reveal the nature of the Fe-C bonds to be essentially invariant between the complexes, with conversion between the (formally) low-valent Fe-N2 and high-valent Fe-imido complexes mediated by pyrazole hemilability. This presents a useful strategy for substrate reduction at such low-coordinate centers and suggests a mechanism by which FeMoco might accommodate the binding of both π-acidic and π-basic nitrogenous substrates.
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Affiliation(s)
- Alex McSkimming
- Department
of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Niklas B. Thompson
- Chemical
Sciences and Engineering Division, Argonne
National Laboratory, Lemont, Illinois 60439, United States
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48
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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: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [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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Singstock NR, Musgrave CB. How the Bioinspired Fe 2Mo 6S 8 Chevrel Breaks Electrocatalytic Nitrogen Reduction Scaling Relations. J Am Chem Soc 2022; 144:12800-12806. [PMID: 35816127 DOI: 10.1021/jacs.2c03661] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The nitrogen reduction reaction (NRR) is a renewable alternative to the energy- and CO2-intensive Haber-Bosch NH3 synthesis process but is severely limited by the low activity and selectivity of studied electrocatalysts. The Chevrel phase Fe2Mo6S8 has a surface Fe-S-Mo coordination environment that mimics the nitrogenase FeMo-cofactor and was recently shown to provide state-of-the-art activity and selectivity for NRR. Here, we elucidate the previously unknown NRR mechanism on Fe2Mo6S8 via grand-canonical density functional theory (GC-DFT) that realistically models solvated and biased surfaces. Fe sites of Fe2Mo6S8 selectively stabilize the key *NNH intermediate via a narrow band of free-atom-like surface d-states that selectively hybridize with p-states of *NNH, which results in Fe sites breaking NRR scaling relationships. These sharp d-states arise from an Fe-S bond dissociation during N2 adsorption that mimics the mechanism of the nitrogenase FeMo-cofactor. Furthermore, we developed a new GC-DFT-based approach for calculating transition states as a function of bias (GC-NEB) and applied it to produce a microkinetic model for NRR at Fe2Mo6S8 that predicts high activity and selectivity, in close agreement with experiments. Our results suggest new design principles that may identify effective NRR electrocatalysts that minimize the barriers for *N2 protonation and *NH3 desorption and that may be broadly applied to the rational discovery of stable, multinary electrocatalysts for other reactions where narrow bands of surface d-states can be tuned to selectively stabilize key reaction intermediates and guide selectivity toward a target product. Furthermore, our results highlight the importance of using GC-DFT and GC-NEB to accurately model electrocatalytic reactions.
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Affiliation(s)
- Nicholas R Singstock
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80303, United States
| | - Charles B Musgrave
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80303, United States.,Materials Science and Engineering Program, University of Colorado Boulder, Boulder, Colorado 80303, United States.,Renewable and Sustainable Energy Institute, University of Colorado Boulder, Boulder, Colorado 80303, United States
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Synthetic molecular cluster hints at mechanism of nitrogen fixation. Nature 2022; 607:37-38. [DOI: 10.1038/d41586-022-01787-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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