1
|
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.
Collapse
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
| |
Collapse
|
2
|
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.
Collapse
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.
| |
Collapse
|
3
|
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] [MESH Headings] [Grants] [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.
Collapse
Affiliation(s)
- Ian Dance
- School of ChemistryUNSWSydneyAustralia
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Jiang H, Svensson OKG, Cao L, Ryde U. Proton Transfer Pathways in Nitrogenase with and without Dissociated S2B. Angew Chem Int Ed Engl 2022; 61:e202208544. [PMID: 35920055 PMCID: PMC9804283 DOI: 10.1002/anie.202208544] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Indexed: 01/05/2023]
Abstract
Nitrogenase is the only enzyme that can convert N2 to NH3 . Crystallographic structures have indicated that one of the sulfide ligands of the active-site FeMo cluster, S2B, can be replaced by an inhibitor, like CO and OH- , and it has been suggested that it may be displaced also during the normal reaction. We have investigated possible proton transfer pathways within the FeMo cluster during the conversion of N2 H2 to two molecules of NH3 , assuming that the protons enter the cluster at the S3B, S4B or S5A sulfide ions and are then transferred to the substrate. We use combined quantum mechanical and molecular mechanical (QM/MM) calculations with the TPSS and B3LYP functionals. The calculations indicate that the barriers for these reactions are reasonable if the S2B ligand remains bound to the cluster, but they become prohibitively high if S2B has dissociated. This suggests that it is unlikely that S2B reversibly dissociates during the normal reaction cycle.
Collapse
Affiliation(s)
- Hao Jiang
- Theoretical ChemistryLund UniversityChemical CentreP. O. Box 12422100LundSweden
| | | | - Lili Cao
- Theoretical ChemistryLund UniversityChemical CentreP. O. Box 12422100LundSweden
| | - Ulf Ryde
- Theoretical ChemistryLund UniversityChemical CentreP. O. Box 12422100LundSweden
| |
Collapse
|
6
|
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.
Collapse
Affiliation(s)
- Ian Dance
- School of Chemistry, UNSW Sydney, NSW 2051, Australia.
| |
Collapse
|
7
|
Jiang H, Svensson OKG, Cao L, Ryde U. Proton Transfer Pathways in Nitrogenase with and without Dissociated S2B. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202208544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Hao Jiang
- Lund University: Lunds Universitet Theoretical Chemistry P. O. Box 124 22100 Lund SWEDEN
| | - Oskar K. G. Svensson
- Lund University: Lunds Universitet Theoretical Chemistry P. O. Box 124 22100 Lund SWEDEN
| | - Lili Cao
- Lund University: Lunds Universitet Theoretical Chemistry P. O. Box 124 Lund SWEDEN
| | - Ulf Ryde
- Lund university Theoretical Chemistry P. O. Box 124 S-221 00 Lund SWEDEN
| |
Collapse
|
8
|
Novel bidentate oxovanadium(IV) glycolate, α-hydroxybutyrate and citrate with terpyridine and their conversions to nitrosyl products. J Inorg Biochem 2020; 208:111086. [PMID: 32353582 DOI: 10.1016/j.jinorgbio.2020.111086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 04/02/2020] [Accepted: 04/07/2020] [Indexed: 11/23/2022]
Abstract
A series of monomeric α-hydroxycarboxylato oxovanadium(IV) complexes [VO(H2cit)(tpy)]·H2O (1) (H4cit = citric acid, tpy = 2,2':6',2-terpyridine), [VO(glyc)(tpy)]·5.5H2O (2) (H2glyc = glycolic acid) and [VO(α-hbut)(tpy)]·3H2O (3) (α-H2hbut = α-hydroxybutyratic acid) have been obtained from the reactions of vanadyl sulfate with α-hydroxycarboxylates and terpyridine in acidic solutions. These complexes feature bidentate citrate, glycolate or α-hydroxybutyrate respectively. The ligand chelates to vanadium atom through α-hydroxy (in 1) or α-alkoxy (in 2 and 3) and α-carboxy groups, while β-carboxy groups of citrate in 1 are free to participate strong hydrogen bonds with neighboring citrate. With comparable chelation, 1 shares a similar V-Oα-hydroxy distance [2.168(1) Å] with that observed in FeV-cofactor [2.17 Å] [1]. Moreover, nitrosyl vanadium complexes [V(NO)(glyc)(tpy)]·3H2O (4) and [V(NO)(α-hbut)(tpy)]·4H2O (5) were obtained via reductions of synthetic solutions of 2 and 3 with hydroxylamine respectively. The terminal oxygen atoms were substituted by linear nitrosyl groups in 4 and 5. They were fully characterized by UV-vis, IR, EPR spectra, X-ray structural analyses and theoretical bond valence calculations.
Collapse
|
9
|
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
| |
Collapse
|
10
|
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.
Collapse
|
11
|
Dance I. How feasible is the reversible S-dissociation mechanism for the activation of FeMo-co, the catalytic site of nitrogenase? Dalton Trans 2019; 48:1251-1262. [PMID: 30607401 DOI: 10.1039/c8dt04531c] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The active site of the enzyme nitrogenase (N2→ NH3) is a Fe7MoS9C cluster that contains three doubly-bridging μ-S atoms around a central belt. A vanadium nitrogenase variant has a slightly different cluster, containing two μ-S atoms. Recent crystal structures have revealed substitution of one μ-S (S2B, bridging Fe2 and Fe6), by CO in Mo-nitrogenase and an uncertain light atom in V-nitrogenase. These systems retained catalytic activity, and were able to recover the lost μ-S atom. Electron density attributed to the dissociated S is displaced by 7 Å in the crystal structure of the non-standard V-protein. The hypothesis arising from these observations is that the chemical mechanism of nitrogenase involves reversible dissociation of S2B, leaving Fe2 and Fe6 seriously under-coordinated and reactive in trapping N2 and binding reaction intermediates. Accumulated experimental evidence points to the Fe2-S2B-Fe6 domain as the centre of catalytic hydrogenation of N2. Using DFT simulations of a large model (>488 atoms) containing all relevant surrounding protein residues, I have investigated the chemical steps that could allow dissociation of S2B. The participation of H atoms is crucial, as is involvement of the nearby side chain of His195 that can function as proton donor to S2B and hydrogen-bonding supporter of displaced S2B. A significant result is that after ingress and binding of N2 at Fe2 the breaking of the Fe2-S2B bond can be strongly exergonic with negligible kinetic barrier. Subsequent extension of the Fe6-S2B bond and dissociation as H2S (or SH-) is endergonic by 20-25 kcal mol-1, partly because the separating H2S is restricted by surrounding amino-acids. I present a number of reaction sequences and energy landscapes, and derive thirteen chemical principles relevant to the postulated S-dissociation mechanism. A key conclusion is that unhooking of S2BH or S2BH2 from Fe2 is favourable, likely, and propitious for subsequent H transfer to bound N2 or reaction intermediates. The space between Fe2 and Fe6 supports two bridging ligands, and another H atom on Fe6 can move without kinetic barrier to occupy the bridging position vacated by S2B.
Collapse
Affiliation(s)
- Ian Dance
- School of Chemistry, UNSW Sydney, Sydney 2000, Australia.
| |
Collapse
|
12
|
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
| |
Collapse
|
13
|
Arnet NA, McWilliams SF, DeRosha DE, Mercado BQ, Holland PL. Synthesis and Mechanism of Formation of Hydride-Sulfide Complexes of Iron. Inorg Chem 2017; 56:9185-9193. [PMID: 28726395 DOI: 10.1021/acs.inorgchem.7b01230] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Iron-sulfide complexes with hydride ligands provide an experimental precedent for spectroscopically detected hydride species on the iron-sulfur MoFe7S9C cofactor of nitrogenase. In this contribution, we expand upon our recent synthesis of the first iron sulfide hydride complex from an iron hydride and a sodium thiolate ( Arnet, N. A.; Dugan, T. R.; Menges, F. S.; Mercado, B. Q.; Brennessel, W. W.; Bill, E.; Johnson, M. A.; Holland, P. L., J. Am. Chem. Soc. 2015 , 137 , 13220 - 13223 ). First, we describe the isolation of an analogous iron sulfide hydride with a smaller diketiminate supporting ligand, which benefits from easier preparation of the hydride precursor and easier isolation of the product. Second, we describe mechanistic studies on the C-S bond cleavage through which the iron sulfide hydride product is formed. In a key experiment, use of cyclopropylmethanethiolate as the sulfur precursor leads to products from cyclopropane ring opening, implicating an alkyl radical as an intermediate. Combined with the results of isotopic labeling studies, the data are consistent with a mechanism in which homolytic C-S bond cleavage is followed by rebound of the alkyl radical to abstract a hydrogen atom from iron to give the observed alkane and iron-sulfide products.
Collapse
Affiliation(s)
- Nicholas A Arnet
- Department of Chemistry, Yale University , 225 Prospect Street, New Haven, Connecticut 06511, United States
| | - Sean F McWilliams
- Department of Chemistry, Yale University , 225 Prospect Street, New Haven, Connecticut 06511, United States
| | - Daniel E DeRosha
- Department of Chemistry, Yale University , 225 Prospect Street, New Haven, Connecticut 06511, United States
| | - Brandon Q Mercado
- Department of Chemistry, Yale University , 225 Prospect Street, New Haven, Connecticut 06511, United States
| | - Patrick L Holland
- Department of Chemistry, Yale University , 225 Prospect Street, New Haven, Connecticut 06511, United States
| |
Collapse
|
14
|
Dance I. New insights into the reaction capabilities of His195 adjacent to the active site of nitrogenase. J Inorg Biochem 2017; 169:32-43. [DOI: 10.1016/j.jinorgbio.2017.01.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 12/01/2016] [Accepted: 01/03/2017] [Indexed: 01/22/2023]
|
15
|
Bellows SM, Arnet NA, Gurubasavaraj PM, Brennessel WW, Bill E, Cundari TR, Holland PL. The Mechanism of N-N Double Bond Cleavage by an Iron(II) Hydride Complex. J Am Chem Soc 2016; 138:12112-23. [PMID: 27598037 PMCID: PMC5499983 DOI: 10.1021/jacs.6b04654] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The use of hydride species for substrate reductions avoids strong reductants, and may enable nitrogenase to reduce multiple bonds without unreasonably low redox potentials. In this work, we explore the N═N bond cleaving ability of a high-spin iron(II) hydride dimer with concomitant release of H2. Specifically, this diiron(II) complex reacts with azobenzene (PhN═NPh) to perform a four-electron reduction, where two electrons come from H2 reductive elimination and the other two come from iron oxidation. The rate law of the H2 releasing reaction indicates that diazene binding occurs prior to H2 elimination, and the negative entropy of activation and inverse kinetic isotope effect indicate that H-H bond formation is the rate-limiting step. Thus, substrate binding causes reductive elimination of H2 that formally reduces the metals, and the metals use the additional two electrons to cleave the N-N multiple bond.
Collapse
Affiliation(s)
- Sarina M. Bellows
- Department of Chemistry, University of Rochester, Rochester, NY 14627
| | | | | | | | - Eckhard Bill
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, Mülheim an der Ruhr, Germany
| | - Thomas R. Cundari
- Department of Chemistry and CASCaM, University of North Texas, Denton, TX 76203
| | - Patrick L. Holland
- Department of Chemistry, University of Rochester, Rochester, NY 14627
- Department of Chemistry, Yale University, New Haven, CT 06520
| |
Collapse
|
16
|
Čorić I, Holland PL. Insight into the Iron-Molybdenum Cofactor of Nitrogenase from Synthetic Iron Complexes with Sulfur, Carbon, and Hydride Ligands. J Am Chem Soc 2016; 138:7200-11. [PMID: 27171599 PMCID: PMC5508211 DOI: 10.1021/jacs.6b00747] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Nitrogenase enzymes are used by microorganisms for converting atmospheric N2 to ammonia, which provides an essential source of N atoms for higher organisms. The active site of the molybdenum-dependent nitrogenase is the unique carbide-containing iron-sulfur cluster called the iron-molybdenum cofactor (FeMoco). On the FeMoco, N2 binding is suggested to occur at one or more iron atoms, but the structures of the catalytic intermediates are not clear. In order to establish the feasibility of different potential mechanistic steps during biological N2 reduction, chemists have prepared iron complexes that mimic various structural aspects of the iron sites in the FeMoco. This reductionist approach gives mechanistic insight, and also uncovers fundamental principles that could be used more broadly for small-molecule activation. Here, we discuss recent results and highlight directions for future research. In one direction, synthetic iron complexes have now been shown to bind N2, break the N-N triple bond, and produce ammonia catalytically. Carbon- and sulfur-based donors have been incorporated into the ligand spheres of Fe-N2 complexes to show how these atoms may influence the structure and reactivity of the FeMoco. Hydrides have been incorporated into synthetic systems, which can bind N2, reduce some nitrogenase substrates, and/or reductively eliminate H2 to generate reduced iron centers. Though some carbide-containing iron clusters are known, none yet have sulfide bridges or high-spin iron atoms like the FeMoco.
Collapse
Affiliation(s)
- Ilija Čorić
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Patrick L. Holland
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| |
Collapse
|
17
|
McKee ML. A New Nitrogenase Mechanism Using a CFe8S9 Model: Does H2 Elimination Activate the Complex to N2 Addition to the Central Carbon Atom? J Phys Chem A 2016; 120:754-64. [PMID: 26821350 DOI: 10.1021/acs.jpca.5b10384] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A truncated model of the FeMo cofactor is used to explore a new mechanism for the conversion of N2 to NH3 by the nitrogenase enzyme. After four initial protonation/reduction steps, the H4CFe8S9 cluster has two hydrogen atoms attached to sulfur, one hydrogen bridging two iron centers and one hydrogen bonded to carbon. The loss of the CH and FeHFe hydrogens as molecular hydrogen activates the cluster to addition of N2 to the carbon center. This unique step takes place at a nearly planar four-coordinate carbon center and leads to an intermediate with a significantly weakened N-N bond. A hydrogen attached to a sulfur atom is then transferred to the distal nitrogen atom. Additional prontonation/reduction steps are modeled by adding a hydrogen atom to sulfur and locating the transition states for transfer to nitrogen. The first NH3 is lost in a thermal neutral step, while the second step is endothermic. The loss of H2 activates the complex by reducing the barrier for N2 addition by 3.5 kcal/mol. Since this is the most difficult step in the mechanism, reducing the barrier for this step justifies the "extra expense" of H2 production.
Collapse
Affiliation(s)
- Michael L McKee
- Department of Chemistry and Biochemistry, Auburn University , Auburn, Alabama 36849, United States
| |
Collapse
|
18
|
Arnet NA, Dugan TR, Menges FS, Mercado BQ, Brennessel WW, Bill E, Johnson MA, Holland PL. Synthesis, Characterization, and Nitrogenase-Relevant Reactions of an Iron Sulfide Complex with a Bridging Hydride. J Am Chem Soc 2015; 137:13220-3. [PMID: 26457740 PMCID: PMC4818001 DOI: 10.1021/jacs.5b06841] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
![]()
The
FeMoco of nitrogenase is an iron–sulfur cluster with
exceptional bond-reducing abilities. ENDOR studies have suggested
that E4, the state that binds and reduces N2, contains bridging hydrides as part of the active-site iron-sulfide
cluster. However, there are no examples of any isolable iron-sulfide
cluster with a hydride, which would test the feasibility of such a
species. Here, we describe a diiron sulfide hydride complex that is
prepared using a mild method involving C–S cleavage of added
thiolate. Its reactions with nitrogenase substrates show that the
hydride can act as a base or nucleophile and that reduction can cause
the iron atoms to bind N2. These results add experimental
support to hydride-based pathways for nitrogenase.
Collapse
Affiliation(s)
- Nicholas A Arnet
- Department of Chemistry, Yale University , New Haven, Connecticut 06520, United States
| | - Thomas R Dugan
- Department of Chemistry, University of Rochester , Rochester, New York 14627, United States
| | - Fabian S Menges
- Department of Chemistry, Yale University , New Haven, Connecticut 06520, United States
| | - Brandon Q Mercado
- Department of Chemistry, Yale University , New Haven, Connecticut 06520, United States
| | - William W Brennessel
- Department of Chemistry, University of Rochester , Rochester, New York 14627, United States
| | - Eckhard Bill
- Max-Planck-Institut für Chemische Energiekonversion , Mülheim an der Ruhr, Germany
| | - Mark A Johnson
- Department of Chemistry, Yale University , New Haven, Connecticut 06520, United States
| | - Patrick L Holland
- Department of Chemistry, Yale University , New Haven, Connecticut 06520, United States
| |
Collapse
|
19
|
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.
Collapse
Affiliation(s)
- Ian Dance
- School of Chemistry
- University of New South Wales
- Sydney 2052
- Australia
| |
Collapse
|
20
|
Chen CY, Chen ML, Chen HB, Wang H, Cramer SP, Zhou ZH. α-Hydroxy coordination of mononuclear vanadyl citrate, malate and S-citramalate with N-heterocycle ligand, implying a new protonation pathway of iron-vanadium cofactor in nitrogenase. J Inorg Biochem 2014; 141:114-120. [PMID: 25240212 PMCID: PMC5065718 DOI: 10.1016/j.jinorgbio.2014.08.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 08/04/2014] [Accepted: 08/04/2014] [Indexed: 11/17/2022]
Abstract
Unlike the most of α-alkoxy coordination in α-hydroxycarboxylates to vanadium, novel α-hydroxy coordination to vanadium(IV) has been observed for a series of chiral and achiral monomeric α-hydroxycarboxylato vanadyl complexes [VO(H2cit)(bpy)]·2H2O (1), [VO(Hmal)(bpy)]·H2O (2), [VO(H2cit)(phen)]·1.5H2O (3), [VO(Hmal)(phen)]·H2O (4), and [(Δ)VO(S-Hcitmal)(bpy)]·2H2O (5), [VO(H2cit)(phen)]2·6.5H2O (6), which were isolated from the reactions of vanadyl sulfate with α-hydroxycarboxylates and N-heterocycle ligands in acidic solution. The complexes feature a tridentate citrate, malate or citramalate that chelates to vanadium atom through their α-hydroxy, α-carboxy and β-carboxy groups; while the other β-carboxylic acidic group of citrate is free to participate strong hydrogen bonds with lattice water molecule. The neutral α-hydroxy group also forms strong intermolecular hydrogen bonds with water molecule and the negatively-charged α-carboxy group in the environment. The inclusion of a hydrogen ion in α-alkoxy group results in the formation of a series of neutral complexes with one less positive charge. There are two different configurations of citrate with respect to the trans-position of axial oxo group, where the complex with trans-hydroxy configuration seems more stable with less hindrance. The average bond distances of V-Ohydroxy and V-Oα-carboxy are 2.196 and 2.003Å respectively, which are comparable to the VO distance (2.15Å) of homocitrate in FeV-cofactor of V-nitrogenase. A new structural model is suggested for R-homocitrato iron vanadium cofactor as VFe7S9C(R-Hhomocit) (H4homocit=homocitric acid) with one more proton in homocitrate ligand.
Collapse
Affiliation(s)
- Can-Yu Chen
- State Key Laboratory for Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China; College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou 310036, China
| | - Mao-Long Chen
- State Key Laboratory for Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Hong-Bin Chen
- State Key Laboratory for Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Hongxin Wang
- Department of Chemistry, University of California, Davis, CA 95616, United States
| | - Stephen P Cramer
- Department of Chemistry, University of California, Davis, CA 95616, United States.
| | - Zhao-Hui Zhou
- State Key Laboratory for Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China; Department of Chemistry, University of California, Davis, CA 95616, United States.
| |
Collapse
|
21
|
Gilbert-Wilson R, Field LD, Bhadbhade M. Ruthenium Hydrides Containing the Superhindered Polydentate Polyphosphine Ligand P(CH2CH2PtBu2)3. Inorg Chem 2014; 53:12469-79. [DOI: 10.1021/ic501895s] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Ryan Gilbert-Wilson
- School
of Chemistry, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Leslie D. Field
- School
of Chemistry, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Mohan Bhadbhade
- Mark
Wainwright Analytical Centre, The University of New South Wales, Sydney, NSW 2052, Australia
| |
Collapse
|
22
|
Fisher K, Hare ND, Newton WE. Another Role for CO with Nitrogenase? CO Stimulates Hydrogen Evolution Catalyzed by Variant Azotobacter vinelandii Mo-Nitrogenases. Biochemistry 2014; 53:6151-60. [DOI: 10.1021/bi500546k] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Karl Fisher
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
| | - Nathan D. Hare
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
| | - William E. Newton
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
| |
Collapse
|
23
|
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.
Collapse
Affiliation(s)
- Ian Dance
- School of Chemistry, University of New South Wales, Sydney 2052, Australia
| |
Collapse
|
24
|
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
| |
Collapse
|
25
|
|
26
|
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]
|
27
|
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]
|
28
|
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]
|
29
|
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.
Collapse
Affiliation(s)
- Travis V Harris
- Department of Chemistry and Biochemistry, Astrobiology Biogeochemistry Research Center, Montana State University, Bozeman, MT 59717, USA.
| | | |
Collapse
|
30
|
|
31
|
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
| |
Collapse
|
32
|
Tanaka H, Ohsako F, Seino H, Mizobe Y, Yoshizawa K. Theoretical Study on Activation and Protonation of Dinitrogen on Cubane-Type MIr3S4 Clusters (M = V, Cr, Mn, Fe, Co, Ni, Cu, Mo, Ru, and W). Inorg Chem 2010; 49:2464-70. [DOI: 10.1021/ic902414n] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hiromasa Tanaka
- Institute for Materials Chemistry and Engineering, Kyushu University, Fukuoka 819-0395, Japan
| | - Fumihiro Ohsako
- Institute for Materials Chemistry and Engineering, Kyushu University, Fukuoka 819-0395, Japan
| | - Hidetake Seino
- Institute of Industrial Science, The University of Tokyo, Tokyo 153-8505, Japan
| | - Yasushi Mizobe
- Institute of Industrial Science, The University of Tokyo, Tokyo 153-8505, Japan
| | - Kazunari Yoshizawa
- Institute for Materials Chemistry and Engineering, Kyushu University, Fukuoka 819-0395, Japan
| |
Collapse
|
33
|
|
34
|
Dance I. The chemical mechanism of nitrogenase: hydrogen tunneling and further aspects of the intramolecular mechanism for hydrogenation of eta(2)-N(2) on FeMo-co to NH(3). Dalton Trans 2008:5992-8. [PMID: 19082055 DOI: 10.1039/b806103c] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The preceding paper (Dalton Trans., 2008, DOI: 10.1039/b806100a) describes the logical development of a chemical mechanism for the catalysis of hydrogenation of N(2) to 2NH(3) that occurs at the Fe(7)MoS(9)N(c)(homocitrate) cofactor (FeMo-co) of the enzyme nitrogenase. The mechanism uses a single replenishable path for serial supply of protons which become H atoms on FeMo-co, migrating to become S-H and Fe-H donors to N(2) and to the intermediates that follow. This chemical catalysis at FeMo-co is distinctly intramolecular: transition states and reaction profiles for the preferred 21 step pathway were presented. This paper describes a number of alternative intermediates and pathways that were considered in developing the mechanism. These results reveal further relevant principles of the reactivity of hydrogenated FeMo-co, and the reasons why these pathways are less likely to be part of the mechanism. The intramolecular character of the mechanism, and the relatively small distances over which H atoms transfer, lead to expectations of extensive quantum mechanical hydrogen tunneling as part of the catalytic rate enhancement. This possibility is supported by comparisons of reaction profiles with those for enzyme reactions for which tunneling is established.
Collapse
Affiliation(s)
- Ian Dance
- School of Chemistry, University of New South Wales, Sydney 2052, Australia.
| |
Collapse
|
35
|
Xie H, Wu R, Zhou Z, Cao Z. Exploring the Interstitial Atom in the FeMo Cofactor of Nitrogenase: Insights from QM and QM/MM Calculations. J Phys Chem B 2008; 112:11435-9. [DOI: 10.1021/jp803616z] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Hujun Xie
- Department of Chemistry and State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Ruibo Wu
- Department of Chemistry and State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Zhaohui Zhou
- Department of Chemistry and State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Zexing Cao
- Department of Chemistry and State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| |
Collapse
|
36
|
Pelmenschikov V, Case DA, Noodleman L. Ligand-bound S = 1/2 FeMo-cofactor of nitrogenase: hyperfine interaction analysis and implication for the central ligand X identity. Inorg Chem 2008; 47:6162-72. [PMID: 18578487 DOI: 10.1021/ic7022743] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Broken symmetry density functional theory (BS-DFT) has been used to address the hyperfine parameters of the single atom ligand X, proposed to be coordinated by six iron ions in the center of the paramagnetic FeMo-cofactor (FeMoco) of nitrogenase. Using the X = N alternative, we recently found that any hyperfine signal from X would be small (calculated A(iso)(X = (14)N) = 0.3 MHz) due to both structural and electronic symmetry properties of the [Mo-7Fe-9S- X] FeMoco core in its resting S = 3/2 state. Here, we extend our BS-DFT approach to the 2e(-) reduced S = 1/2 FeMoco state. Alternative substrates coordinated to this FeMoco state effectively perturb the electronic and/or structural symmetry properties of the cofactor. Using an example of an allyl alcohol (H2C=CH-CH2-OH) product ligand, we consider three different binding modes at single iron site and three different BS-DFT spin state structures and show that this binding would enhance the key hyperfine signal A(iso)(X) by at least 1 order of magnitude (3.8 < or = A(iso)(X = (14)N) < or = 14.7 MHz), and this result should not depend strongly on the exact identity of X (nitrogen, carbon, or oxygen). The interstitial atom, when the nucleus has a nonzero magnetic moment, should therefore be observable by ESR methods for some ligand-bound FeMoco states. In addition, our results illustrate structural details and likely spin-coupling patterns for models for early intermediates in the catalytic cycle.
Collapse
Affiliation(s)
- Vladimir Pelmenschikov
- The Scripps Research Institute, Department of Molecular Biology TPC-15, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.
| | | | | |
Collapse
|
37
|
Tanaka H, Mori H, Seino H, Hidai M, Mizobe Y, Yoshizawa K. DFT Study on Chemical N2 Fixation by Using a Cubane-Type RuIr3S4 Cluster: Energy Profile for Binding and Reduction of N2 to Ammonia via Ru−N−NHx (x = 1−3) Intermediates with Unique Structures. J Am Chem Soc 2008; 130:9037-47. [DOI: 10.1021/ja8009567] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Hiromasa Tanaka
- Institute for Materials Chemistry and Engineering, Kyushu University, Fukuoka 819-0395, Japan, Institute of Industrial Science, The University of Tokyo, Tokyo 153-8505, Japan, and Department of Materials Science and Technology, Faculty of Industrial Science and Technology, Tokyo University of Science, Noda, Chiba 278-8510, Japan
| | - Hiroyuki Mori
- Institute for Materials Chemistry and Engineering, Kyushu University, Fukuoka 819-0395, Japan, Institute of Industrial Science, The University of Tokyo, Tokyo 153-8505, Japan, and Department of Materials Science and Technology, Faculty of Industrial Science and Technology, Tokyo University of Science, Noda, Chiba 278-8510, Japan
| | - Hidetake Seino
- Institute for Materials Chemistry and Engineering, Kyushu University, Fukuoka 819-0395, Japan, Institute of Industrial Science, The University of Tokyo, Tokyo 153-8505, Japan, and Department of Materials Science and Technology, Faculty of Industrial Science and Technology, Tokyo University of Science, Noda, Chiba 278-8510, Japan
| | - Masanobu Hidai
- Institute for Materials Chemistry and Engineering, Kyushu University, Fukuoka 819-0395, Japan, Institute of Industrial Science, The University of Tokyo, Tokyo 153-8505, Japan, and Department of Materials Science and Technology, Faculty of Industrial Science and Technology, Tokyo University of Science, Noda, Chiba 278-8510, Japan
| | - Yasushi Mizobe
- Institute for Materials Chemistry and Engineering, Kyushu University, Fukuoka 819-0395, Japan, Institute of Industrial Science, The University of Tokyo, Tokyo 153-8505, Japan, and Department of Materials Science and Technology, Faculty of Industrial Science and Technology, Tokyo University of Science, Noda, Chiba 278-8510, Japan
| | - Kazunari Yoshizawa
- Institute for Materials Chemistry and Engineering, Kyushu University, Fukuoka 819-0395, Japan, Institute of Industrial Science, The University of Tokyo, Tokyo 153-8505, Japan, and Department of Materials Science and Technology, Faculty of Industrial Science and Technology, Tokyo University of Science, Noda, Chiba 278-8510, Japan
| |
Collapse
|
38
|
Wander MCF, Kubicki JD, Schoonen MAA. Reduction of N2 by Fe2+ via homogeneous and heterogeneous reactions Part 2: the role of metal binding in activating N2 for reduction; a requirement for both pre-biotic and biological mechanisms. ORIGINS LIFE EVOL B 2008; 38:195-209. [PMID: 18452061 DOI: 10.1007/s11084-008-9133-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2007] [Accepted: 03/16/2008] [Indexed: 10/22/2022]
Abstract
Nitrogen reduction by ferrous iron has been suggested as an important mechanism in the formation of ammonia on pre-biotic Earth. This paper examines the effects of adsorption of ferrous iron onto a goethite (alpha-FeOOH) substrate on the thermodynamic driving force and rate of a ferrous iron-mediated reduction of N2 as compared with the homogeneous aqueous reaction. Utilizing density functional theory and Marcus Theory of proton coupled electron transfer reactions, the following two reactions were studied: Fe2+aq + N2aq + H2Oaq --> N2H* + FeOH2+aq and triple bond Fe2+ads + N2aq + 2H2Oaq --> N2H* + alpha-FeOOHs + 2H+aq. Although the rates of both reactions were calculated to be approximately zero at 298 K, the model results suggest that adsorption alters the thermodynamic driving force for the reaction but has no other effect on the direct electron transfer kinetics. Given that simply altering the thermodynamic driving force will not reduce dinitrogen, we can make mechanistic connections between possible prebiotic pathways and biological N2 reduction. The key to reduction in both cases is N2 adsorption to multiple transition metal centers with competitive H2 production.
Collapse
Affiliation(s)
- Matthew C F Wander
- PSARC, Department of Geosciences, Stony Brook University, Stony Brook, NY 11794-2100, USA.
| | | | | |
Collapse
|
39
|
Yu Y, Sadique AR, Smith JM, Dugan TR, Cowley RE, Brennessel WW, Flaschenriem CJ, Bill E, Cundari TR, Holland PL. The reactivity patterns of low-coordinate iron-hydride complexes. J Am Chem Soc 2008; 130:6624-38. [PMID: 18444648 PMCID: PMC2474859 DOI: 10.1021/ja710669w] [Citation(s) in RCA: 163] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
We report a survey of the reactivity of the first isolable iron-hydride complexes with a coordination number less than 5. The high-spin iron(II) complexes [(beta-diketiminate)Fe(mu-H)] 2 react rapidly with representative cyanide, isocyanide, alkyne, N 2, alkene, diazene, azide, CO 2, carbodiimide, and Brønsted acid containing substrates. The reaction outcomes fall into three categories: (1) addition of Fe-H across a multiple bond of the substrate, (2) reductive elimination of H 2 to form iron(I) products, and (3) protonation of the hydride to form iron(II) products. The products include imide, isocyanide, vinyl, alkyl, azide, triazenido, benzo[ c]cinnoline, amidinate, formate, and hydroxo complexes. These results expand the range of known bond transformations at iron complexes. Additionally, they give insight into the elementary transformations that may be possible at the iron-molybdenum cofactor of nitrogenases, which may have hydride ligands on high-spin, low-coordinate metal atoms.
Collapse
Affiliation(s)
- Ying Yu
- Department of Chemistry, University of Rochester, Rochester, New York, 14627
| | - Azwana R. Sadique
- Department of Chemistry, University of Rochester, Rochester, New York, 14627
| | - Jeremy M. Smith
- Department of Chemistry, University of Rochester, Rochester, New York, 14627
| | - Thomas R. Dugan
- Department of Chemistry, University of Rochester, Rochester, New York, 14627
| | - Ryan E. Cowley
- Department of Chemistry, University of Rochester, Rochester, New York, 14627
| | | | | | - Eckhard Bill
- Max-Planck-Institut für Bioanorganische Chemie, D-45470 Mülheim an der Ruhr, Germany
| | - Thomas R. Cundari
- Department of Chemistry and Center for Advanced Scientific Computing and Modeling (CASCaM), University of North Texas, Denton, Texas, 76203
| | - Patrick L. Holland
- Department of Chemistry, University of Rochester, Rochester, New York, 14627
| |
Collapse
|
40
|
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]
|
41
|
Abstract
How does the enzyme nitrogenase reduce the inert molecule N2 to NH3 under ambient conditions that are so different from the energy-expensive conditions of the best industrial practices? This review focuses on recent theoretical investigations of the catalytic site, the iron-molybdenum cofactor FeMo-co, and the way in which it is hydrogenated by protons and electrons and then binds N2. Density functional calculations provide reaction profiles and activation energies for possible mechanistic steps. This establishes a conceptual framework and the principles for the coordination chemistry of FeMo-co that are essential to the chemical mechanism of catalysis. The model advanced herein explains relevant experimental data.
Collapse
Affiliation(s)
- Ian Dance
- School of Chemistry, University of New South Wales, Sydney 2052, Australia.
| |
Collapse
|
42
|
McKee ML. Modeling hydrogen evolution from the Fe4S4and Fe8S9X (X = N, C) clusters. Can a FeS high-spin cluster serve as a surrogate for the FeMo cofactor? J Comput Chem 2007; 28:1796-808. [PMID: 17285558 DOI: 10.1002/jcc.20636] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
A high-spin model of nitrogenase with a Fe(8)S(9)X(+) cluster (X = nitrogen or carbon) is used to test a mechanism for molecular hydrogen production, which is known to accompany ammonia production. The reaction proceeds with a series of protonation-reduction (PR) steps which are considered to be spontaneous if the calculated hydrogen-cluster bond energy exceeds 35-40 kcal/mol. The novel features of this mechanism include the opening of the cluster when one of the bridging sulfides undergoes two PR steps and the direct participation of the central atom when it undergoes a PR step. After the sixth PR step, a cluster is formed which has a low barrier for loss of molecular hydrogen in an exothermic reaction step. The central atom (nitrogen or carbon) has only a minor effect on the reaction steps.
Collapse
Affiliation(s)
- Michael L McKee
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, USA.
| |
Collapse
|
43
|
Sadique AR, Gregory EA, Brennessel WW, Holland PL. Mechanistic insight into N=N cleavage by a low-coordinate iron(II) hydride complex. J Am Chem Soc 2007; 129:8112-21. [PMID: 17564444 PMCID: PMC2548314 DOI: 10.1021/ja069199r] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The reaction pathways of high-spin iron hydride complexes are relevant to the mechanism of N2 reduction by nitrogenase, which has been postulated to involve paramagnetic iron-hydride species. However, almost all known iron hydrides are low-spin, diamagnetic Fe(II) compounds. We have demonstrated that the first high-spin iron hydride complex, LtBuFeH (LtBu = bulky beta-diketiminate), reacts with PhN=NPh to completely cleave the N-N double bond, giving LtBuFeNHPh. Here, we disclose a series of experiments that elucidate the mechanism of this reaction. Crossover and kinetic experiments rule out common nonradical mechanisms, and support a radical chain mechanism mediated by iron(I) species including a rare eta2-azobenzene complex. Therefore, this high-spin iron(II) hydride can break N-N bonds through both nonradical and radical insertion mechanisms, a special feature that enables novel reactivity.
Collapse
Affiliation(s)
- Azwana R. Sadique
- Department of Chemistry, University of Rochester, Rochester, New York 14627,
| | | | | | - Patrick L. Holland
- Department of Chemistry, University of Rochester, Rochester, New York 14627,
| |
Collapse
|
44
|
McKee ML. Modeling the nitrogenase FeMo cofactor with high-spin Fe8
S9
X+
(XN, C) clusters. Is the first step for N2
reduction to NH3
a concerted dihydrogen transfer? J Comput Chem 2007; 28:1342-56. [PMID: 17318945 DOI: 10.1002/jcc.20635] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
A high-spin Fe(8)S(9)X(+) (X=N, C) cluster is used to model the reduction of molecular nitrogen to ammonia by the nitrogenase FeMo cofactor at the B3LYP/6-311G(d,p)/ECP(Fe,SDD) level of theory. A total of seventy-three structures were optimized (including three transition state optimizations) to explore the structure and energetic of N(2), C(2)H(2), and CO coordination to the Fe(8)S(9)X(+) cluster. After three protonation-reduction (PR) steps (modeled by addition of hydrogen atoms), N(2), C(2)H(2), and CO are predicted to bind to a Fe atom in the exo (cage does not open) position with binding energies of 7.6, 14.7, and 11.7 kcal/mol. With additional PR steps the coordination number of the core nitrogen atom is reduced from six to five and the bridging thiol group becomes a terminal SH(2) group. The fifth and sixth PR steps occur on the core nitrogen and the open Fe site. Coordination of N(2) is enhanced after six PR steps to give an intermediate ideally suited for a concerted dihydrogen transfer from the Fe and core nitrogen atoms to the coordinated N(2). The identity of the central atom (nitrogen or carbon) has only a minor effect on the reaction steps.
Collapse
Affiliation(s)
- Michael L McKee
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, USA.
| |
Collapse
|
45
|
Dance I. The Mechanistically Significant Coordination Chemistry of Dinitrogen at FeMo-co, the Catalytic Site of Nitrogenase. J Am Chem Soc 2007; 129:1076-88. [PMID: 17263388 DOI: 10.1021/ja0644428] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Reported here is a comprehensive theoretical investigation of the binding of N(2) to the Fe(7)MoS(9)N(homocitrate)(cysteine)(histidine) active site (FeMo-co) of the enzyme nitrogenase, as a prerequisite to elucidation of the chemical mechanism of the catalyzed reduction to NH(3). The degree and type of hydrogenation of FeMo-co, with H atoms and possibly an H(2) molecule, are key variables, following the Thorneley-Lowe kinetic scheme. Ninety-four local energy minima were located for N(2) coordinated in eta(2) (side) and eta(1) (end) modes at the endo and exo coordination positions of Fe2 and Fe6. The stabilities of 57 representative structures are assessed by calculation of the reaction profiles and activation energies for the association and dissociation of N(2). Barriers to association of N(2) depend mainly on the location of the hydrogenation and the location of N(2) coordination, while dissociation barriers depend primarily on whether N(2) is eta(2)- and eta(1)-coordinated, and secondarily on the location of the hydrogenation. Increased negative charge on FeMo-co increases the barriers, while C in place of N at the center of FeMo-co has little effect. The interactions of the models of ligated FeMo-co with the surrounding protein, including proteins with mutations of key amino acids, are assessed by in silico cofactor transplantations and calculations of protein strain energies. From these results, which identify models involving contacts and interactions with the surrounding residues that have been shown by mutation to affect the N(2) activity of nitrogenase, and from the N(2) coordination profiles, it is concluded that endo-eta(1)-N(2) coordination at Fe6 is most probable. There is strong reason to believe that the mechanism of nitrogenase will involve one or more of the preferred models presented here, and a detailed foundation of structures and principles is now available for postulation and calculation of the profiles of the steps in which H atoms bound to FeMo-co are transferred to bound N(2).
Collapse
Affiliation(s)
- Ian Dance
- School of Chemistry, University of New South Wales, Sydney 2052, Australia.
| |
Collapse
|
46
|
Vela J, Cirera J, Smith JM, Lachicotte RJ, Flaschenriem CJ, Alvarez S, Holland PL. Quantitative geometric descriptions of the belt iron atoms of the iron-molybdenum cofactor of nitrogenase and synthetic iron(II) model complexes. Inorg Chem 2007; 46:60-71. [PMID: 17198413 PMCID: PMC2676240 DOI: 10.1021/ic0609148] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Six of the seven iron atoms in the iron-molybdenum cofactor of nitrogenase display an unusual geometry, which is distorted from the tetrahedral geometry that is most common in iron-sulfur clusters. This distortion pulls the iron along one C3 axis of the tetrahedron toward a trigonal pyramid. The trigonal pyramidal coordination geometry is rare in four-coordinate transition metal complexes. In order to document this geometry in a systematic fashion in iron(II) chemistry, we have synthesized a range of four-coordinate iron(II) complexes that vary from tetrahedral to trigonal pyramidal. Continuous shape measures are used for a quantitative comparison of the stereochemistry of the Fe atoms in the iron-molybdenum cofactor with those of the presently and previously reported model complexes, as well as with those in polynuclear iron-sulfur compounds. This understanding of the iron coordination geometry is expected to assist in the design of synthetic analogues for intermediates in the nitrogenase catalytic cycle.
Collapse
Affiliation(s)
- Javier Vela
- Department of Chemistry, University of Rochester, Rochester, New York 14627, USA
| | | | | | | | | | | | | |
Collapse
|