Binding modes for the first coupled electron and proton addition to FeMoco of nitrogenase

Catalysis and structure of nitrogenases

In providing bioavailable nitrogen as building blocks for all classes of biomacromolecules, biological nitrogen fixation is an essential process for all organismic life. Only a single enzyme, nitrogenase, performs this task at ambient conditions and with ATP as an energy source. The assembly of the complex iron-sulfur enzyme nitrogenase and its catalytic mechanism remains a matter of intense study. Recent progress in the structural analysis of the three known isoforms of nitrogenase-differentiated primarily by the heterometal in their active site cofactor-has revealed a degree of structural plasticity of these clusters that suggest two distinct binding sites for substrates and reaction intermediates. A mechanistic proposal based on this finding integrates most of the available experimental data. Furthermore, the first applications of high-resolution cryo-electron microscopy have highlighted further dynamic conformational changes. Structures obtained under turnover conditions support the proposed alternating half-site reactivity in the C2-symmetric nitrogenase complex.

Nitrogenase FeMoco investigated by spatially resolved anomalous dispersion refinement

The [Mo:7Fe:9S:C] iron-molybdenum cofactor (FeMoco) of nitrogenase is the largest known metal cluster and catalyses the 6-electron reduction of dinitrogen to ammonium in biological nitrogen fixation. Only recently its atomic structure was clarified, while its reactivity and electronic structure remain under debate. Here we show that for its resting S=3/2 state the common iron oxidation state assignments must be reconsidered. By a spatially resolved refinement of the anomalous scattering contributions of the 7 Fe atoms of FeMoco, we conclude that three irons (Fe1/3/7) are more reduced than the other four (Fe2/4/5/6). Our data are in agreement with the recently revised oxidation state assignment for the molybdenum ion, providing the first spatially resolved picture of the resting-state electron distribution within FeMoco. This might provide the long-sought experimental basis for a generally accepted theoretical description of the cluster that is in line with available spectroscopic and functional data.

The [Mo:7Fe:9S:C] iron-molybdenum cofactor (FeMoco) of nitrogenase is a large metal cluster with an important role in biological nitrogen fixation. Here, the authors use spatially resolved refinement of the anomalous scattering contributions of the iron atoms to determine the resting-state electron distribution of FeMoco.

The discovery of Mo(III) in FeMoco: reuniting enzyme and model chemistry

Biological nitrogen fixation is enabled by molybdenum-dependent nitrogenase enzymes, which effect the reduction of dinitrogen to ammonia using an Fe₇MoS₉C active site, referred to as the iron molybdenum cofactor or FeMoco. In this mini-review, we summarize the current understanding of the molecular and electronic structure of FeMoco. The advances in our understanding of the active site structure are placed in context with the parallel evolution of synthetic model studies. The recent discovery of Mo(III) in the FeMoco active site is highlighted with an emphasis placed on the important role that model studies have played in this finding. In addition, the reactivities of synthetic models are discussed in terms of their relevance to the enzymatic system.

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

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.

Involvement of thiolate ligands in binding substrates to Fe-S clusters

Kinetic studies on reactions between [Fe4S4(SR)4]2- (R = Et or But) and 4-YC6H4COCl (Y = MeO, H or Cl) to form [Fe4S4Cl4]2- and 4-YC6H4COSR indicate that the terminal thiolate ligand is involved in the initial binding of the acid chloride to the cluster.

Binding nucleophiles to [Fe4Y4Cl4](2-) (Y = S or Se) can increase or suppress the rate of proton transfer to the cluster

In the proton transfer reactions between [Fe 4Y 4Cl 4] (2-) (Y = S or Se) and [pyrH] (+) (pyr = pyrrolidine) in the presence of a variety of nucleophiles (L = I (-), Br (-), PhS (-), EtS (-) or ButNC), initial binding of the nucleophile can occur to generate [Fe 4Y 4Cl 4(L)] ( n- ). The subsequent rate of proton transfer depends markedly on the nature of L. Stopped-flow kinetic studies show that proton transfer from [pyrH] (+) to [Fe 4Y 4Cl 4] (2-) { (S) k 4 = (2.1 +/- 0.5) x 10 (4) dm (3) mol (-1) s (-1); (Se) k 4 = (8.0 +/- 0.5) x 10 (3) dm (3) mol (-1) s (-1)} is increased by prior binding of L = PhS (-) or Bu ( t )NC to form [Fe 4Y 4Cl 4(L)] (n-) ( (S) k 7 (L) approximately 1 x 10 (6) dm (3) mol (-1) s (-1)), but prior binding of L = I (-), Br (-), or EtS (-) to the clusters inhibits the rate of proton transfer {e.g. (S) k 7 (I) = (6.0 +/- 0.8) x 10 (2) dm (3) mol (-1) s (-1); (Se) k 7 (I) = (4.5 +/- 0.5) x 10 (2) dm (3) mol (-1) s (-1)}. This behavior is correlated with the bonding characteristics of L and the effect this has on bond length reorganization within the cluster upon proton transfer.

Ligand-bound S = 1/2 FeMo-cofactor of nitrogenase: hyperfine interaction analysis and implication for the central ligand X identity

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.

Activation and protonation of dinitrogen at the FeMo cofactor of nitrogenase

The protonation of N2 bound to the active center of nitrogenase has been investigated using state-of-the-art density-functional theory calculations. Dinitrogen in the bridging mode is activated by forming two bonds to Fe sites, which results in a reduction of the energy for the first hydrogen transfer by 123 kJ/mol. The axial binding mode with open sulfur bridge is less reactive by 30 kJ/mol and the energetic ordering of the axial and bridged binding modes is reversed in favor of the bridging dinitrogen during the first protonation. Protonation of the central ligand is thermodynamically favorable but kinetically hindered. If the central ligand is protonated, the proton is transferred to dinitrogen following the second protonation. Protonation of dinitrogen at the Mo site does not lead to low-energy intermediates.

An Electronic Perspective on the Reduction of an N?N Double Bond at a Conserved Dimolybdenum Core

Density functional theory has been used to assess the role of the bimetallic core in supporting reductive cleavage of the N=N double bond in [Cp2Mo2(mu-SMe)3(mu-eta1:eta1-HN=NPh)]+. The HOMO of the complex, the Mo-Mo delta orbital, plays a key role as a source of high-energy electrons, available for transfer into the vacant orbitals of the N=N unit. As a result, the metal centres cycle between the Mo(III) and Mo(IV) oxidation states. The symmetry of the Mo-Mo delta "buffer" orbital has a profound influence on the reaction pathway, because significant overlap with the redox-active orbital on the N=N unit (pi* or sigma*) is required for efficient electron transfer. The orthogonality of the Mo-Mo delta and N-N sigma* orbitals in the eta1:eta1 coordination mode ensures that electron transfer into the N-N sigma bond is effectively blocked, and a rate-limiting eta1:eta1-->eta1 rearrangement is a necessary precursor to cleavage of the bond.

Density Functional Theory Calculations and Exploration of a Possible Mechanism of N2 Reduction by Nitrogenase

Density functional theory (DFT) calculations have been performed on the nitrogenase cofactor, FeMoco. Issues that have been addressed concern the nature of M-M interactions and the identity and origin of the central light atom, revealed in a recent crystallographic study of the FeMo protein of nitrogenase (Einsle, O.; et al. Science 2002, 297, 871). Introduction of Se in place of the S atoms in the cofactor and energy minimization results in an optimized structure very similar to that in the native enzyme. The nearly identical, short, lengths of the Fe-Fe distances in the Se and S analogues are interpreted in terms of M-M weak bonding interactions. DFT calculations with O or N as the central atoms in the FeMoco marginally support the assignment of the central atom as N rather than O. The assumption was made that the central atom is the N atom, and steps of a catalytic cycle were calculated starting with either of two possible states for the cofactor and maintaining the same charge throughout (by addition of equal numbers of H(+) and e(-)) between steps. The states were [(Cl)Fe(II)(6)Fe(III)Mo(IV)S(9)(H(+))(3)N(3-)(Gl)(Im)](2-), [I-N-3H](2-), and [(Cl)Fe(II)(4)Fe(III)(3)Mo(IV)S(9)(H(+))(3)N(3-)(Gl)(Im)], [I-N-3H](0) (Gl = deprotonated glycol; Im = imidazole). These are the triply protonated ENDOR/ESEEM [I-N](5-) and Mössbauer [I-N](3-) models, respectively. The proposed mechanism explores the possibilities that (a) redox-induced distortions facilitate insertion of N(2) and derivative substrates into the Fe(6) central unit of the cofactor, (b) the central atom in the cofactor is an exchangeable nitrogen, and (c) the individual steps are related by H(+)/e(-) additions (and reduction of substrate) or aquation/dehydration (and distortion of the Fe(6) center). The Delta E's associated with the individual steps of the proposed mechanism are small and either positive or negative. The largest positive Delta E is +121 kJ/mol. The largest negative Delta E of -333 kJ/mol is for the FeMoco with a N(3-) in the center (the isolated form) and an intermediate in the proposed mechanism.

Nitrogen Binding to the FeMo-Cofactor of Nitrogenase

Density functional calculations are presented to unravel the first steps of nitrogen fixation of nitrogenase. The individual steps leading from the resting state to nitrogen binding at the FeMo-cofactor with a central nitrogen ligand are characterized. The calculations indicate that the Fe-Mo cage opens as dinitrogen binds to the cluster. In the resting state, the central cage is overall neutral. Electrons and protons are transferred in an alternating manner. Upon dinitrogen binding, one protonated sulfur bridge is broken. An axial and a bridged binding mode of dinitrogen have been identified. Adsorption at the Mo site has been investigated but appears to be less favorable than binding at Fe sites.

Dinitrogen chemistry from trigonally coordinated iron and cobalt platforms

This report establishes that trigonally coordinated "[PhBPiPr3]M" platforms (M = Fe, Co) will support both pi-acidic (N2) and pi-basic (NR) ligands at a fourth binding site. The N2 complexes of iron that are described are the first thoroughly characterized examples to exhibit a 4-coordinate geometry. Methylation of monomeric {Fe0(N2)-} and {Co0(N2)-} species successfully derivatizes the beta-N atom of the coordinated N2 ligand and affords the diazenido products {FeII(N2Me)} and {CoII(N2Me)}, respectively. One-electron oxidation of the mononuclear M0(N2)- species produces dinuclear and synthetically versatile MI(N2)MI complexes. These latter species provide clean access to the chemistry of the "[PhBPiPr3]MI" subunit. For example, addition of RN3 to MI(N2)MI results in oxidative nitrene transfer to generate [PhBPiPr3]MNR with concomitant N2 release.

Structural, spectroscopic, and redox consequences of a central ligand in the FeMoco of nitrogenase: a density functional theoretical study

Broken symmetry density functional and electrostatics calculations have been used to shed light on which of three proposed atoms, C, N, or O, is most likely to be present in the center of the FeMoco, the active site of nitrogenase. At the Mo(4+)4Fe(2+)3Fe(3+) oxidation level, a central N(3-) anion results in (1) calculated Fe-N bond distances that are in very good agreement with the recent high-resolution X-ray data of Einsle et al.; (2) a calculated redox potential of 0.19 eV versus the standard hydrogen electrode (SHE) for FeMoco(oxidized) + e(-) --> FeMoco(resting), in good agreement with the measured value of -0.042 V in Azotobacter vinelandii; and (3) average Mössbauer isomer shift values (IS(av) = 0.48 mm s(-1)) compatible with experiment (IS(av) = 0.40 mm s(-1)). At the more reduced Mo(4+)6Fe(2+)1Fe(3+) level, the calculated geometry around a central N(3-) anion still correlates well with the X-ray data, but the average Mössbauer isomer shift value (IS(av) = 0.54 mm s(-1)) and the redox potential of -2.21 eV show a much poorer agreement with experiment. These calculated structural, spectroscopic, and redox data indicate the most likely iron oxidation state for the resting FeMoco of nitrogenase to be 4Fe(2+)3Fe(3+). At this favored oxidation state, oxygen or carbon coordination leads to (1) Fe-O distances in poor agreement and Fe-C distances in good agreement with experiment and (2) calculated redox potentials of +0.97 eV for O(2-) and -1.31 eV for C(4-). The calculated structural parameters and/or redox data suggest either O(2-) or C(4-) is unlikely as a central anion.

Speculative synthetic chemistry and the nitrogenase problem

There exist a limited but growing number of biological metal centers whose properties lie conspicuously outside the realm of known inorganic chemistry. The synthetic analogue approach, broadly directed, offers a powerful exploratory tool that can define intrinsic chemical possibilities for these sites while simultaneously expanding the frontiers of fundamental inorganic chemistry. This speculative application of analogue study is exemplified here in the evolution of synthetic efforts inspired by the cluster chemistry of biological nitrogen fixation.

Proton-coupled electron transfer in Fe-superoxide dismutase and Mn-superoxide dismutase

Fe-containing superoxide dismutase (FeSOD) and MnSOD are widely assumed to employ the same catalytic mechanism. However this has not been completely tested. In 1985, Bull and Fee showed that FeSOD took up a proton upon reduction [J. Am. Chem. Soc. 107 (1985) 3295]. We now demonstrate that MnSOD incorporates the same crucial coupling between electron transfer and proton transfer. The redox-coupled H(+) acceptor has been presumed to be the coordinated solvent molecule, in both FeSOD and MnSOD, however this is very difficult to test experimentally. We have now examined the most plausible alternative: that Tyr34 accepts a proton upon SOD reduction. We report specific incorporation of 13C in the C(zeta) positions of Tyr residues, assignment of the C(zeta) signal of Tyr34 in each of oxidized FeSOD and MnSOD, and direct NMR observations showing that in both cases, Tyr34 is in the neutral protonated state. Thus Tyr34 cannot accept a proton upon SOD reduction, and coordinated solvent is concluded to be the redox-coupled H(+) acceptor instead, in both FeSOD and MnSOD. We have also confirmed by direct 13C observation that the pK of 8.5 of reduced FeSOD corresponds to deprotonation of Tyr34. This work thus provides experimental proof of important commonalities between the detailed mechanisms of FeSOD and MnSOD.

Insights into properties and energetics of iron-sulfur proteins from simple clusters to nitrogenase

Some of the principal physical features of iron-sulfur clusters in proteins are analyzed, including metal-ligand covalency, spin polarization, spin coupling, valence delocalization, valence interchange and small reorganization energies, with emphasis on recent spectroscopic and theoretical work. The current state of structural, spectroscopic, and computational knowledge for the iron-sulfur clusters in the nitrogenase iron and iron-molybdenum proteins is examined by comparison and contrast to 'simpler' ironclusters. The differing interactions of the nitrogenase iron and iron-molybdenum clusters compared with those of other iron-sulfur clusters with the protein and solvent environment are also explored.