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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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2
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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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3
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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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4
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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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5
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Guo B, Cheng X, Tang Y, Guo W, Deng S, Wu L, Fu X. Dehydrated UiO-66(SH) 2 : The Zr-O Cluster and Its Photocatalytic Role Mimicking the Biological Nitrogen Fixation. Angew Chem Int Ed Engl 2022; 61:e202117244. [PMID: 35083838 DOI: 10.1002/anie.202117244] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Indexed: 12/20/2022]
Abstract
This work reports the dehydrated Zr-based MOF UiO-66(SH)2 as a visible-light-driven photocatalyst to mimic the biological N2 fixation process. The 15 N2 and other control experiments demonstrated that the new photocatalyst is highly efficient in converting N2 to ammonia. In-situ TGA, XPS, and EXAFS as well as first-principles simulations were used to demonstrate the role of the thermal treatment and the changes of the local structures around Zr due to the dehydration. It was shown that the dehydration opened a gate for the entry of N2 molecules into the [Zr6 O6 ] cluster where the strong N≡N bond was broken stepwise by μ-N-Zr type interactions driven by the photoelectrons aided by the protonation. This mechanism was discussed in comparison with the Lowe-Thorneley mechanism proposed for the MoFe nitrogenase, and with emphasis on the [Zr6 O6 ] cluster effect and the leading role of photoelectrons over the protonation. The results shed new light on understanding the catalytic mechanism of biological N2 fixation and open a new way to fix N2 under mild conditions.
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Affiliation(s)
- Binbin Guo
- State Key Laboratory of Photocatalysis on Energy and Environment, Fuzhou University, Fuzhou, Fujian 350116, China.,State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, P.R. China
| | - Xiyue Cheng
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, P.R. China
| | - Yu Tang
- State Key Laboratory of Photocatalysis on Energy and Environment, Fuzhou University, Fuzhou, Fujian 350116, China
| | - Wei Guo
- State Key Laboratory of Photocatalysis on Energy and Environment, Fuzhou University, Fuzhou, Fujian 350116, China
| | - Shuiquan Deng
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, P.R. China
| | - Ling Wu
- State Key Laboratory of Photocatalysis on Energy and Environment, Fuzhou University, Fuzhou, Fujian 350116, China.,State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, P.R. China
| | - Xianzhi Fu
- State Key Laboratory of Photocatalysis on Energy and Environment, Fuzhou University, Fuzhou, Fujian 350116, China
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6
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Guo B, Cheng X, Tang Y, Guo W, Deng S, Wu L, Fu X. Dehydrated UiO‐66(SH)
2
: The Zr−O Cluster and Its Photocatalytic Role Mimicking the Biological Nitrogen Fixation. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202117244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Binbin Guo
- State Key Laboratory of Photocatalysis on Energy and Environment Fuzhou University Fuzhou Fujian 350116 China
- State Key Laboratory of Structural Chemistry Fujian Institute of Research on the Structure of Matter Chinese Academy of Sciences Fuzhou Fujian 350002 P.R. China
| | - Xiyue Cheng
- State Key Laboratory of Structural Chemistry Fujian Institute of Research on the Structure of Matter Chinese Academy of Sciences Fuzhou Fujian 350002 P.R. China
| | - Yu Tang
- State Key Laboratory of Photocatalysis on Energy and Environment Fuzhou University Fuzhou Fujian 350116 China
| | - Wei Guo
- State Key Laboratory of Photocatalysis on Energy and Environment Fuzhou University Fuzhou Fujian 350116 China
| | - Shuiquan Deng
- State Key Laboratory of Structural Chemistry Fujian Institute of Research on the Structure of Matter Chinese Academy of Sciences Fuzhou Fujian 350002 P.R. China
| | - Ling Wu
- State Key Laboratory of Photocatalysis on Energy and Environment Fuzhou University Fuzhou Fujian 350116 China
- State Key Laboratory of Structural Chemistry Fujian Institute of Research on the Structure of Matter Chinese Academy of Sciences Fuzhou Fujian 350002 P.R. China
| | - Xianzhi Fu
- State Key Laboratory of Photocatalysis on Energy and Environment Fuzhou University Fuzhou Fujian 350116 China
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Luxem KE, Leavitt WD, Zhang X. Large Hydrogen Isotope Fractionation Distinguishes Nitrogenase-Derived Methane from Other Methane Sources. Appl Environ Microbiol 2020; 86:e00849-20. [PMID: 32709722 PMCID: PMC7499036 DOI: 10.1128/aem.00849-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 07/16/2020] [Indexed: 02/01/2023] Open
Abstract
Biological nitrogen fixation is catalyzed by the enzyme nitrogenase. Two forms of this metalloenzyme, the vanadium (V)- and iron (Fe)-only nitrogenases, were recently found to reduce small amounts of carbon dioxide (CO2) into the potent greenhouse gas methane (CH4). Here, we report carbon (13C/12C) and hydrogen (2H/1H) stable isotopic compositions and fractionations of methane generated by V- and Fe-only nitrogenases in the metabolically versatile nitrogen fixer Rhodopseudomonas palustris The stable carbon isotope fractionation imparted by both forms of alternative nitrogenase are within the range observed for hydrogenotrophic methanogenesis (13αCO2/CH4 = 1.051 ± 0.002 for V-nitrogenase and 1.055 ± 0.001 for Fe-only nitrogenase; values are means ± standard errors). In contrast, the hydrogen isotope fractionations (2αH2O/CH4 = 2.071 ± 0.014 for V-nitrogenase and 2.078 ± 0.018 for Fe-only nitrogenase) are the largest of any known biogenic or geogenic pathway. The large 2αH2O/CH4 shows that the reaction pathway nitrogenases use to form methane strongly discriminates against 2H, and that 2αH2O/CH4 distinguishes nitrogenase-derived methane from all other known biotic and abiotic sources. These findings on nitrogenase-derived methane will help constrain carbon and nitrogen flows in microbial communities and the role of the alternative nitrogenases in global biogeochemical cycles.IMPORTANCE All forms of life require nitrogen for growth. Many different kinds of microbes living in diverse environments make inert nitrogen gas from the atmosphere bioavailable using a special enzyme, nitrogenase. Nitrogenase has a wide substrate range, and, in addition to producing bioavailable nitrogen, some forms of nitrogenase also produce small amounts of the greenhouse gas methane. This is different from other microbes that produce methane to generate energy. Until now, there was no good way to determine when microbes with nitrogenases are making methane in nature. Here, we present an isotopic fingerprint that allows scientists to distinguish methane from microbes making it for energy versus those making it as a by-product of nitrogen acquisition. With this new fingerprint, it will be possible to improve our understanding of the relationship between methane production and nitrogen acquisition in nature.
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Affiliation(s)
- Katja E Luxem
- Department of Geosciences, Princeton University, Princeton, New Jersey, USA
- Princeton Environmental Institute, Princeton University, Princeton, New Jersey, USA
| | - William D Leavitt
- Department of Earth Sciences, Dartmouth College, Hanover, New Hampshire, USA
- Department of Chemistry, Dartmouth College, Hanover, New Hampshire, USA
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, USA
| | - Xinning Zhang
- Department of Geosciences, Princeton University, Princeton, New Jersey, USA
- Princeton Environmental Institute, Princeton University, Princeton, New Jersey, USA
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8
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Dance I. Computational Investigations of the Chemical Mechanism of the Enzyme Nitrogenase. Chembiochem 2020; 21:1671-1709. [DOI: 10.1002/cbic.201900636] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Indexed: 12/15/2022]
Affiliation(s)
- Ian Dance
- School of Chemistry UNSW Sydney Sydney 2052 Australia
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9
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Survey of the Geometric and Electronic Structures of the Key Hydrogenated Forms of FeMo-co, the Active Site of the Enzyme Nitrogenase: Principles of the Mechanistically Significant Coordination Chemistry. INORGANICS 2019. [DOI: 10.3390/inorganics7010008] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The enzyme nitrogenase naturally hydrogenates N2 to NH3, achieved through the accumulation of H atoms on FeMo-co, the Fe7MoS9C(homocitrate) cluster that is the catalytically active site. Four intermediates, E1H1, E2H2, E3H3, and E4H4, carry these hydrogen atoms. I report density functional calculations of the numerous possibilities for the geometric and electronic structures of these poly-hydrogenated forms of FeMo-co. This survey involves more than 100 structures, including those with bound H2, and assesses their relative energies and most likely electronic states. Twelve locations for bound H atoms in the active domain of FeMo-co, including Fe–H–Fe and Fe–H–S bridges, are studied. A significant result is that transverse Fe–H–Fe bridges (transverse to the pseudo-threefold axis of FeMo-co and shared with triply-bridging S) are not possible geometrically unless the S is hydrogenated to become doubly-bridging. The favourable Fe–H–Fe bridges are shared with doubly-bridging S. ENDOR data for an E4H4 intermediate trapped at low temperature, and interpretations in terms of the geometrical and electronic structure of E4H4, are assessed in conjunction with the calculated possibilities. The results reported here yield a set of 24 principles for the mechanistically significant coordination chemistry of H and H2 on FeMo-co, in the stages prior to N2 binding.
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Dance I. Evaluations of the accuracies of DMol3 density functionals for calculations of experimental binding enthalpies of N2, CO, H2, C2H2 at catalytic metal sites. MOLECULAR SIMULATION 2017. [DOI: 10.1080/08927022.2017.1413711] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Ian Dance
- School of Chemistry, UNSW Sydney, Sydney, Australia
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11
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Dance I. Mechanisms of the S/CO/Se interchange reactions at FeMo-co, the active site cluster of nitrogenase. Dalton Trans 2016; 45:14285-300. [PMID: 27534727 DOI: 10.1039/c6dt03159e] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The active site of the N2 fixing enzyme nitrogenase is a C-centred Fe7MoS cluster (FeMo-co) containing a trigonal prism of six Fe atoms connected by a central belt of three doubly-bridging S atoms. The trigonal faces of the prism are capped via triply-bridging S atoms to Fe1 at one end and Mo at the other end. One of the central belt atoms, S2B, considered to be important in the chemical mechanism of the enzyme, has been shown by Spatzal, Rees et al. to undergo substitution by CO, and also substitution by Se in the presence of SeCN(-), under turnover conditions. Further, when turning over under C2H2 or N2/CO there is migration of Se to the other two belt bridging positions. These reactions are extraordinary, and unprecedented in metal chalcogenide cluster chemistry. Using density functional simulations, mechanisms for all of these reactions have been developed, involving the small molecules SCO, SeCO, C2H2S, C2H2Se, SeCN(-), SCN(-) functioning as carriers of S and Se atoms. The possibility that the S2B bridge position is vacant is discounted, because the barrier to formation of a bridge-void intermediate with two contiguous three-coordinate Fe atoms is too large. A bridging ligand is retained throughout the proposed mechanisms. Intermediates with Fe-C(O)-S/Se-Fe cycles and with SCO/SeCO C-bound to Fe are predicted. The energetics of the reaction trajectories show them to be feasible and easily reversible, consistent with experiment. Alternative mechanisms involving intramolecular differential rotatory rearrangements of the cluster to scramble the Se bridges are also examined, and shown to be very unlikely. The implications of these new facets of the reactivity of the FeMo-co cluster are discussed: it is considered that they are unlikely to be part of the mechanism of the physiological reactions of nitrogenase.
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Affiliation(s)
- Ian Dance
- School of Chemistry, UNSW Australia, Sydney 2052, Australia.
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12
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Moha V, Leitner W, Hölscher M. NH3 Synthesis in the N2/H2 Reaction System using Cooperative Molecular Tungsten/Rhodium Catalysis in Ionic Hydrogenation: A DFT Study. Chemistry 2016; 22:2624-8. [PMID: 26711865 DOI: 10.1002/chem.201504660] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Indexed: 11/10/2022]
Abstract
The ionic hydrogenation of N2 with H2 to give NH3 is investigated by means of density functional theory (DFT) computations using a cooperatively acting catalyst system. In this system, N2 binds to a neutral tungsten pincer complex of the type [(PNP)W(N2)3] (PNP=pincer ligand) and is reduced to NH3. The protons and hydride centers necessary for the reduction are delivered by heterolytic cleavage of H2 between the N2-tungsten complex and the cationic rhodium complex [Cp*Rh{2-(2-pyridyl)phenyl}(CH3 CN)](+). Successive transfer of protons and hydrides to the bound N2, as well as all Nx Hy units that occur during the reaction, enable the computation of closed catalytic cycles in the gas and in the solvent phase. By optimizing the pincer ligands of the tungsten complex, energy spans as low as 39.3 kcal mol(-1) could be obtained, which is unprecedented in molecular catalysis for the N2/H2 reaction system.
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Affiliation(s)
- Verena Moha
- Institut für Technische und Makromolekulare Chemie, RWTH Aachen, University, Worringerweg 1, 52074, Aachen, Germany
| | - Walter Leitner
- Institut für Technische und Makromolekulare Chemie, RWTH Aachen, University, Worringerweg 1, 52074, Aachen, Germany
| | - Markus Hölscher
- Institut für Technische und Makromolekulare Chemie, RWTH Aachen, University, Worringerweg 1, 52074, Aachen, Germany.
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13
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Jia HP, Gouré E, Solans-Monfort X, Llop Castelbou J, Chow C, Taoufik M, Eisenstein O, Quadrelli EA. Hydrazine N–N Bond Cleavage over Silica-Supported Tantalum-Hydrides. Inorg Chem 2015; 54:11648-59. [DOI: 10.1021/acs.inorgchem.5b01541] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hong-Peng Jia
- Laboratoire C2P2
(équipe COMS), UMR 5265 CNRS−Université de Lyon 1−CPE Lyon, 43, Bvd du 11 Novembre 1918, 69616 Villeurbanne, France
| | - Eric Gouré
- Laboratoire C2P2
(équipe COMS), UMR 5265 CNRS−Université de Lyon 1−CPE Lyon, 43, Bvd du 11 Novembre 1918, 69616 Villeurbanne, France
| | | | - Jessica Llop Castelbou
- Laboratoire C2P2
(équipe COMS), UMR 5265 CNRS−Université de Lyon 1−CPE Lyon, 43, Bvd du 11 Novembre 1918, 69616 Villeurbanne, France
| | - Catherine Chow
- Laboratoire C2P2
(équipe COMS), UMR 5265 CNRS−Université de Lyon 1−CPE Lyon, 43, Bvd du 11 Novembre 1918, 69616 Villeurbanne, France
| | - Mostafa Taoufik
- Laboratoire C2P2
(équipe COMS), UMR 5265 CNRS−Université de Lyon 1−CPE Lyon, 43, Bvd du 11 Novembre 1918, 69616 Villeurbanne, France
| | - Odile Eisenstein
- Institut Charles Gerhardt, UMR 5253 CNRS Université de Montpellier, cc 1501, Place E. Bataillon, 34095 Montpellier, France
| | - Elsje Alessandra Quadrelli
- Laboratoire C2P2
(équipe COMS), UMR 5265 CNRS−Université de Lyon 1−CPE Lyon, 43, Bvd du 11 Novembre 1918, 69616 Villeurbanne, France
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14
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Dance I. Misconception of reductive elimination of H2, in the context of the mechanism of nitrogenase. Dalton Trans 2015; 44:9027-37. [DOI: 10.1039/c5dt00771b] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Calculated atom partial charges reveal misconceptions of reductive elimination of H2.
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Affiliation(s)
- Ian Dance
- School of Chemistry
- University of New South Wales
- Sydney 2052
- Australia
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15
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Dance I. What is the trigger mechanism for the reversal of electron flow in oxygen-tolerant [NiFe] hydrogenases? Chem Sci 2014; 6:1433-1443. [PMID: 29560232 PMCID: PMC5811149 DOI: 10.1039/c4sc03223c] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 12/08/2014] [Indexed: 11/21/2022] Open
Abstract
A new mechanistic model is developed for the sequence of events by which oxygen-tolerant [NiFe] hydrogenase enzymes respond to O2.
The [NiFe] hydrogenases use an electron transfer relay of three FeS clusters – proximal, medial and distal – to release the electrons from the principal reaction, H2 → 2H+ + 2e–, that occurs at the Ni–Fe catalytic site. This site is normally inactivated by O2, but the subclass of O2-tolerant [NiFe] hydrogenases are able to counter this inactivation through the agency of an unusual and unprecedented proximal cluster, with composition [Fe4S3(Scys)6], that is able to transfer two electrons back to the Ni–Fe site and effect crucial reduction of O2-derived species and thereby reactivate the Ni–Fe site. This proximal cluster gates both the direction and the number of electrons flowing through it, and can reverse the normal flow during O2 attack. The unusual structures and redox potentials of the proximal cluster are known: a structural change in the proximal cluster causes changes in its electron-transfer potentials. Using protein structure analysis and density functional simulations, this paper identifies a closed protonic system comprising the proximal cluster, some contiguous residues, and a proton reservoir, and proposes that it is activated by O2-induced conformational change at the Ni–Fe site. This change is linked to a key histidine residue which then causes protonation of the proximal cluster, and migration of this proton to a key μ3-S atom. The resulting SH group causes the required structural change at the proximal cluster, modifying its redox potentials, and leads to the reversed electron flow back to the Ni–Fe site. This cycle is reversible, and the protons involved are independent of those used or produced in reactions at the active site. Existing experimental support for this model is cited, and new testing experiments are suggested.
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Affiliation(s)
- Ian Dance
- School of Chemistry , University of New South Wales , Sydney 2052 , Australia .
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16
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Hölscher M, Leitner W. Low Activation Barriers in N2Reduction with H2at Ruthenium Pincer Complexes Induced by Ligand Cooperativity: A Computational Study. Eur J Inorg Chem 2014. [DOI: 10.1002/ejic.201402706] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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17
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Reduction of Metal Coordinated N2to NH3with H2by Heterolytic Hydrogen Cleavage induced by External Lewis Bases - a DFT Study. Z Anorg Allg Chem 2014. [DOI: 10.1002/zaac.201400337] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Dance I. A molecular pathway for the egress of ammonia produced by nitrogenase. Sci Rep 2013; 3:3237. [PMID: 24241241 PMCID: PMC3831235 DOI: 10.1038/srep03237] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 11/01/2013] [Indexed: 01/19/2023] Open
Abstract
Nitrogenase converts N2 to NH3, at one face of an Fe-Mo-S cluster (FeMo-co) buried in the protein. Through exploration of cavities in the structures of nitrogenase proteins, a pathway for the egress of ammonia from its generation site to the external medium is proposed. This pathway is conserved in the three species Azotobacter vinelandii, Klebsiella pneumoniae and Clostridium pasteurianum. A molecular mechanism for the translocation of NH3 by skipping through a sequence of hydrogen bonds involving eleven water molecules and surrounding aminoacids has been developed. The putative mechanism requires movement aside of some water molecules by up to ~ 1Å. Consistent with this, the surrounding protein is comprised of different chains and has little secondary structure: protein fluctuations are part of the mechanism. This NH3 pathway is well separated from the water chain and embedded proton wire that have been proposed for serial supply of protons to FeMo-co. Verification procedures are suggested.
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Affiliation(s)
- Ian Dance
- School of Chemistry, University of New South Wales, Sydney 2052, Australia
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20
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Dance I. The Stereochemistry and Dynamics of the Introduction of Hydrogen Atoms onto FeMo-co, the Active Site of Nitrogenase. Inorg Chem 2013; 52:13068-77. [DOI: 10.1021/ic401818k] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ian Dance
- School of Chemistry, University of New South Wales, Sydney 2052, Australia
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21
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Heiden ZM, Chen S, Mock MT, Dougherty WG, Kassel WS, Rousseau R, Bullock RM. Protonation of Ferrous Dinitrogen Complexes Containing a Diphosphine Ligand with a Pendent Amine. Inorg Chem 2013; 52:4026-39. [DOI: 10.1021/ic4000704] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Zachariah M. Heiden
- Center for Molecular Electrocatalysis,
Physical Sciences Division, Pacific Northwest National Laboratory,
Richland, Washington 99352, United States
| | - Shentan Chen
- Center for Molecular Electrocatalysis,
Physical Sciences Division, Pacific Northwest National Laboratory,
Richland, Washington 99352, United States
| | - Michael T. Mock
- Center for Molecular Electrocatalysis,
Physical Sciences Division, Pacific Northwest National Laboratory,
Richland, Washington 99352, United States
| | - William G. Dougherty
- Department of Chemistry, Villanova
University, Villanova, Pennsylvania 19085, United States
| | - W. Scott Kassel
- Department of Chemistry, Villanova
University, Villanova, Pennsylvania 19085, United States
| | - Roger Rousseau
- Center for Molecular Electrocatalysis,
Physical Sciences Division, Pacific Northwest National Laboratory,
Richland, Washington 99352, United States
| | - R. Morris Bullock
- Center for Molecular Electrocatalysis,
Physical Sciences Division, Pacific Northwest National Laboratory,
Richland, Washington 99352, United States
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22
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23
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Chen XD, Zhang W, Duncan JS, Lee SC. Iron–Amide–Sulfide and Iron–Imide–Sulfide Clusters: Heteroligated Core Environments Relevant to the Nitrogenase FeMo Cofactor. Inorg Chem 2012; 51:12891-904. [DOI: 10.1021/ic301868m] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Xu-Dong Chen
- Department of Chemistry, University of Waterloo, Waterloo, Ontario, Canada N2L
3G1
| | - Wei Zhang
- Department of Chemistry, University of Waterloo, Waterloo, Ontario, Canada N2L
3G1
| | - Jeremiah S. Duncan
- Department of Chemistry, University of Waterloo, Waterloo, Ontario, Canada N2L
3G1
| | - Sonny C. Lee
- Department of Chemistry, University of Waterloo, Waterloo, Ontario, Canada N2L
3G1
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24
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Asatryan R, Bozzelli JW, Ruckenstein E. Dihydrogen Catalysis: A Degradation Mechanism for N2-Fixation Intermediates. J Phys Chem A 2012; 116:11618-42. [DOI: 10.1021/jp303692v] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Rubik Asatryan
- Department of Chemical and Biological
Engineering, State University of New York, Buffalo, New York 14260, United States
- Department of Chemistry and
Environmental Science, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
| | - Joseph W. Bozzelli
- Department of Chemistry and
Environmental Science, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
| | - Eli Ruckenstein
- Department of Chemical and Biological
Engineering, State University of New York, Buffalo, New York 14260, United States
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25
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Hölscher M, Leitner W. Heterolytische Outer-Sphere-Spaltung von H2 zur Reduktion von N2 in der Koordinationssphäre von Übergangsmetallen - eine DFT-Studie. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201202025] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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26
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Hölscher M, Leitner W. Heterolytic outer-sphere cleavage of H2 for the reduction of N2 in the coordination sphere of transition metals--a DFT study. Angew Chem Int Ed Engl 2012; 51:8225-9. [PMID: 22782940 DOI: 10.1002/anie.201202025] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Revised: 05/31/2012] [Indexed: 11/08/2022]
Affiliation(s)
- Markus Hölscher
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany.
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27
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Gimbert-Suriñach C, Bhadbhade M, Colbran SB. Bridgehead Hydrogen Atoms Are Important: Unusual Electrochemistry and Proton Reduction at Iron Dimers with Ferrocenyl-Substituted Phosphido Bridges. Organometallics 2012. [DOI: 10.1021/om201126w] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Carolina Gimbert-Suriñach
- School of Chemistry and ‡Mark Wainwright Analytical Centre, University of New South Wales, Sydney,
New South Wales 2052, Australia
| | - Mohan Bhadbhade
- School of Chemistry and ‡Mark Wainwright Analytical Centre, University of New South Wales, Sydney,
New South Wales 2052, Australia
| | - Stephen B. Colbran
- School of Chemistry and ‡Mark Wainwright Analytical Centre, University of New South Wales, Sydney,
New South Wales 2052, Australia
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28
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Dance I. The controlled relay of multiple protons required at the active site of nitrogenase. Dalton Trans 2012; 41:7647-59. [DOI: 10.1039/c2dt30518f] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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29
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Dance I. Ramifications of C-centering rather than N-centering of the active site FeMo-co of the enzyme nitrogenase. Dalton Trans 2012; 41:4859-65. [DOI: 10.1039/c2dt00049k] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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30
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31
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Field LD, Guest RW, Turner P. Mixed-valence dinitrogen-bridged Fe(0)/Fe(II) complex. Inorg Chem 2011; 49:9086-93. [PMID: 20815362 DOI: 10.1021/ic101646p] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The reactions of a dinitrogen-bridged Fe(II)/Fe(II) complex [(FeH(PP(3)))(2)(μ-N(2))](2+) (3) (PP(3) = P(CH(2)CH(2)PMe(2))(3)) with base were investigated using (15)N labeling techniques to enhance characterization. In the presence of base, 3 is initially deprotonated to the Fe(II)/Fe(0) dinitrogen-bridged complex [(FeH(PP(3)))(μ-N(2))(Fe(PP(3)))](+) (4) and then to the symmetrical Fe(0)/Fe(0) dinitrogen-bridged complex (Fe(PP(3)))(2)(μ-N(2)) (5). [(FeH(PP(3)))(μ-N(2))(Fe(PP(3)))](+) (4) exhibits unusual long-range (31)P-(31)P NMR coupling through the bridging dinitrogen ligand from the phosphines at the Fe(0) center and those at the Fe(II) center. Reaction of 4 with base under an atmosphere of argon resulted in the known dinitrogen Fe(0) complex Fe(N(2))(PP(3)) (6) and a solvent C-H activation product. Complexes 3, 4, and 5 were fully characterized by multinuclear NMR spectroscopy, and complexes 3 and 4 by X-ray crystallography.
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Affiliation(s)
- Leslie D Field
- School of Chemistry, The University of New South Wales, NSW 2052, Australia.
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32
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Sgrignani J, Franco D, Magistrato A. Theoretical studies of homogeneous catalysts mimicking nitrogenase. Molecules 2011; 16:442-65. [PMID: 21221062 PMCID: PMC6259282 DOI: 10.3390/molecules16010442] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2010] [Revised: 12/27/2010] [Accepted: 01/05/2011] [Indexed: 11/16/2022] Open
Abstract
The conversion of molecular nitrogen to ammonia is a key biological and chemical process and represents one of the most challenging topics in chemistry and biology. In Nature the Mo-containing nitrogenase enzymes perform nitrogen 'fixation' via an iron molybdenum cofactor (FeMo-co) under ambient conditions. In contrast, industrially, the Haber-Bosch process reduces molecular nitrogen and hydrogen to ammonia with a heterogeneous iron catalyst under drastic conditions of temperature and pressure. This process accounts for the production of millions of tons of nitrogen compounds used for agricultural and industrial purposes, but the high temperature and pressure required result in a large energy loss, leading to several economic and environmental issues. During the last 40 years many attempts have been made to synthesize simple homogeneous catalysts that can activate dinitrogen under the same mild conditions of the nitrogenase enzymes. Several compounds, almost all containing transition metals, have been shown to bind and activate N₂ to various degrees. However, to date Mo(N₂)(HIPTN)₃N with (HIPTN)₃N= hexaisopropyl-terphenyl-triamidoamine is the only compound performing this process catalytically. In this review we describe how Density Functional Theory calculations have been of help in elucidating the reaction mechanisms of the inorganic compounds that activate or fix N₂. These studies provided important insights that rationalize and complement the experimental findings about the reaction mechanisms of known catalysts, predicting the reactivity of new potential catalysts and helping in tailoring new efficient catalytic compounds.
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Affiliation(s)
- Jacopo Sgrignani
- CNR-IOM-DEMOCRITOS National Simulation Center at SISSA, via Bonomea 265, Trieste, Italy
| | - Duvan Franco
- International School for Advanced Studies (SISSA/ISAS), via Bonomea 265, Trieste, Italy
| | - Alessandra Magistrato
- CNR-IOM-DEMOCRITOS National Simulation Center at SISSA, via Bonomea 265, Trieste, Italy
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33
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Chen Y, Liu L, Peng Y, Chen P, Luo Y, Qu J. Unusual thiolate-bridged diiron clusters bearing the cis-HN═NH ligand and their reactivities with terminal alkynes. J Am Chem Soc 2011; 133:1147-9. [PMID: 21218814 DOI: 10.1021/ja105948r] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
A series of well-defined thiolate-bridged diiron clusters bearing the cis-HN═NH ligand, [Cp(†)Fe(μ-SEt)(2)(μ-η(1):η(1)-HN═NH)FeCp(†)][PF(6)] (Cp(†) = η(5)-C(5)Me(4)H or η(5)-C(5)Me(5)), are successfully prepared in high yields and fully characterized by spectroscopy and X-ray crystallography. Under moderate conditions, these new Fe/S clusters exhibit high activity, not only for the catalytic cleavage of the N-N bond of hydrazines but also for the activation and coupling of terminal alkynes.
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Affiliation(s)
- Yanhui Chen
- The State Key Laboratory of Fine Chemicals, School of Chemical Engineering, Dalian University of Technology, 158 Zhongshan Road, Dalian, 116012, PR China
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34
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Dance I. Calculated vibrational frequencies for FeMo-co, the active site of nitrogenase, bearing hydrogen atoms and carbon monoxide. Dalton Trans 2011; 40:6480-9. [DOI: 10.1039/c1dt10505a] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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35
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Harris TV, Szilagyi RK. Nitrogenase structure and function relationships by density functional theory. Methods Mol Biol 2011; 766:267-291. [PMID: 21833874 DOI: 10.1007/978-1-61779-194-9_18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Modern density functional theory has tremendous potential with matching popularity in metalloenzymology to reveal the unseen atomic and molecular details of structural data, spectroscopic measurements, and biochemical experiments by providing insights into unobservable structures and states, while also offering theoretical justifications for observed trends and differences. An often untapped potential of this theoretical approach is to bring together diverse experimental structural and reactivity information and allow for these to be critically evaluated at the same level. This is particularly applicable for the tantalizingly complex problem of the structure and molecular mechanism of biological nitrogen fixation. In this chapter we provide a review with extensive practical details of the compilation and evaluation of experimental data for an unbiased and systematic density functional theory analysis that can lead to remarkable new insights about the structure-function relationships of the iron-sulfur clusters of nitrogenase.
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Affiliation(s)
- Travis V Harris
- Department of Chemistry and Biochemistry, Astrobiology Biogeochemistry Research Center, Montana State University, Bozeman, MT 59717, USA.
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36
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37
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Dance I. Electronic Dimensions of FeMo-co, the Active Site of Nitrogenase, and Its Catalytic Intermediates. Inorg Chem 2010; 50:178-92. [DOI: 10.1021/ic1015884] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Ian Dance
- School of Chemistry, University of New South Wales, Sydney 2052, Australia
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38
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Garrett B, Henderson RA. Protonation and substitution reactions of [{WFe₃S₄Cl₃}₂(μ-L)₃]³⁻ (L = SEt or OMe): quantifying how metal content and spectator ligands individually affect reactivity. Dalton Trans 2010; 39:4586-92. [PMID: 20386803 DOI: 10.1039/b925835c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Kinetic studies on the substitution reactions of the terminal chloro-ligands of [{WFe₃S₄Cl₃}₂(μ-L)₃]³⁻ (L = SEt or MeO) by PhS⁻ in the presence of [NHEt₃](+) or [pyrH](+) allow determination of the proton affinities and rates of PhS⁻ and proton binding to the clusters. The behaviours of both clusters are similar and follow the same general kinetic characteristics established in earlier work for other synthetic Fe-S-based clusters. Comparison of the results obtained with [{WFe₃S₄Cl₃}₂(μ-SEt)₃]³⁻ with those of the isostructural [{MoFe₃S₄Cl₃}₂(μ-SEt)₃]³⁻ shows that changing a Mo for W in the cuboidal cluster framework has a large effect on the rates of binding of PhS⁻ or a proton. In contrast, comparison of the results of [{WFe₃S₄Cl₃}₂(μ-SEt)₃]³⁻ with those of [{WFe₃S₄Cl₃}₂(μ-OMe)₃]³⁻ shows that changing the bridging ligands has only a small effect on the rates of binding of PhS⁻ or a proton. The reactivities of [{MFe₃S₄Cl₃}₂(μ-L)₃]³⁻ are inconsistent with the major influence of the metal or bridging ligands being electronic, and are more consistent with their modulating the ability of the cluster to undergo bond length reorganisation during binding of the nucleophile or proton.
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Affiliation(s)
- Brendan Garrett
- School of Chemistry, Newcastle University, Newcastle upon Tyne, UK
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39
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40
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Dance I. The chemical mechanism of nitrogenase: calculated details of the intramolecular mechanism for hydrogenation of η2-N2 on FeMo-co to NH3. Dalton Trans 2008:5977-91. [DOI: 10.1039/b806100a] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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