Vanadium K-edge X-ray-absorption spectroscopy of the functioning and thionine-oxidized forms of the VFe-protein of the vanadium nitrogenase from Azotobacter chroococcum

Characterizing Polyoxovanadate-Alkoxide Clusters Using Vanadium K-Edge X-Ray Absorption Spectroscopy

A number of technologies would benefit from developing inorganic compounds and materials with specific electronic and magnetic exchange properties. Unfortunately, designing compounds with these properties is difficult because metal⋅⋅⋅metal coupling schemes are hard to predict and control. Fully characterizing communication between metals in existing compounds that exhibit interesting properties could provide valuable insight and advance those predictive capabilities. One such class of molecules are the series of Lindqvist iron-functionalized and hexavanadium polyoxovanadate-alkoxide clusters, which we characterized here using V K-edge X-ray absorption spectroscopy. Substantial changes in the pre-edge peak intensities were observed that tracked with the V 3d-electron count. The data also suggested substantial delocalization between the vanadium cations. Meanwhile, the Fe^III cations were electronically isolated from the polyoxovanadate core.

Quantum Mechanics/Molecular Mechanics Study of Resting-State Vanadium Nitrogenase: Molecular and Electronic Structure of the Iron-Vanadium Cofactor

The nitrogenase enzymes are responsible for all biological nitrogen reduction. How this is accomplished at the atomic level, however, has still not been established. The molybdenum-dependent nitrogenase has been extensively studied and is the most active catalyst for dinitrogen reduction of the nitrogenase enzymes. The vanadium-dependent form, on the other hand, displays different reactivity, being capable of CO and CO2 reduction to hydrocarbons. Only recently did a crystal structure of the VFe protein of vanadium nitrogenase become available, paving the way for detailed theoretical studies of the iron-vanadium cofactor (FeVco) within the protein matrix. The crystal structure revealed a bridging 4-atom ligand between two Fe atoms, proposed to be either a CO32- or NO3- ligand. Using a quantum mechanics/molecular mechanics model of the VFe protein, starting from the 1.35 Å crystal structure, we have systematically explored multiple computational models for FeVco, considering either a CO32- or NO3- ligand, three different redox states, and multiple broken-symmetry states. We find that only a [VFe7S8C(CO3)]2- model for FeVco reproduces the crystal structure of FeVco well, as seen in a comparison of the Fe-Fe and V-Fe distances in the computed models. Furthermore, a broken-symmetry solution with Fe2, Fe3, and Fe5 spin-down (BS7-235) is energetically preferred. The electronic structure of the [VFe7S8C(CO3)]2- BS7-235 model is compared to our [MoFe7S9C]- BS7-235 model of FeMoco via localized orbital analysis and is discussed in terms of local oxidation states and different degrees of delocalization. As previously found from Fe X-ray absorption spectroscopy studies, the Fe part of FeVco is reduced compared to FeMoco, and the calculations reveal Fe5 as locally ferrous. This suggests resting-state FeVco to be analogous to an unprotonated E1 state of FeMoco. Furthermore, V-Fe interactions in FeVco are not as strong compared to Mo-Fe interactions in FeMoco. These clear differences in the electronic structures of otherwise similar cofactors suggest an explanation for distinct differences in reactivity.

The Spectroscopy of Nitrogenases

Nitrogenases are responsible for biological nitrogen fixation, a crucial step in the biogeochemical nitrogen cycle. These enzymes utilize a two-component protein system and a series of iron-sulfur clusters to perform this reaction, culminating at the FeMco active site (M = Mo, V, Fe), which is capable of binding and reducing N2 to 2NH3. In this review, we summarize how different spectroscopic approaches have shed light on various aspects of these enzymes, including their structure, mechanism, alternative reactivity, and maturation. Synthetic model chemistry and theory have also played significant roles in developing our present understanding of these systems and are discussed in the context of their contributions to interpreting the nature of nitrogenases. Despite years of significant progress, there is still much to be learned from these enzymes through spectroscopic means, and we highlight where further spectroscopic investigations are needed.

Reactivity, Mechanism, and Assembly of the Alternative Nitrogenases

Biological nitrogen fixation is catalyzed by the enzyme nitrogenase, which facilitates the cleavage of the relatively inert triple bond of N₂. Nitrogenase is most commonly associated with the molybdenum-iron cofactor called FeMoco or the M-cluster, and it has been the subject of extensive structural and spectroscopic characterization over the past 60 years. In the late 1980s and early 1990s, two "alternative nitrogenase" systems were discovered, isolated, and found to incorporate V or Fe in place of Mo. These systems are regulated by separate gene clusters; however, there is a high degree of structural and functional similarity between each nitrogenase. Limited studies with the V- and Fe-nitrogenases initially demonstrated that these enzymes were analogously active as the Mo-nitrogenase, but more recent investigations have found capabilities that are unique to the alternative systems. In this review, we will discuss the reactivity, biosynthetic, and mechanistic proposals for the alternative nitrogenases as well as their electronic and structural properties in comparison to the well-characterized Mo-dependent system. Studies over the past 10 years have been particularly fruitful, though key aspects about V- and Fe-nitrogenases remain unexplored.

Synthesis, characterization, DFT calculations, and reactivity study of a nitrido-bridged dimeric vanadium(iv) complex

Two vanadium(iii) complexes, Cz^tBu(Pyr^iPr)₂VCl₂ (1) and Cz^tBu(Pyr^iPr)₂V(N₃)₂ (2), were synthesized and characterized. Chemical reduction of both 1 and 2 gives the thermally stable nitrido-bridged vanadium(iv) dimer complex, [{Cz^tBu(Pyr^iPr)₂}V]₂(μ-N)₂ (3), which is a rare example of a dimeric vanadium(iv) complex bridged by two nitrido ligands. The nitride ligands of 3 are unreactive due to the well-protected environment provided by the pincer ligand and its substituents, as is supported by its X-ray crystal structure and further described by DFT calculations.

Nitrogenases

Biological nitrogen fixation, the conversion of dinitrogen (N₂) into ammonia (NH₃), stands as a particularly challenging chemical process. As the entry point into a bioavailable form of nitrogen, biological nitrogen fixation is a critical step in the global nitrogen cycle. In Nature, only one enzyme, nitrogenase, is competent in performing this reaction. Study of this complex metalloenzyme has revealed a potent substrate reduction system that utilizes some of the most sophisticated metalloclusters known. This chapter discusses the structure and function of nitrogenase, covers methods that have proven useful in the elucidation of enzyme properties, and provides an overview of the three known nitrogenase variants.

Iron L2,3-Edge X-ray Absorption and X-ray Magnetic Circular Dichroism Studies of Molecular Iron Complexes with Relevance to the FeMoco and FeVco Active Sites of Nitrogenase

Herein, a systematic study of a series of molecular iron model complexes has been carried out using Fe L_2,3-edge X-ray absorption (XAS) and X-ray magnetic circular dichroism (XMCD) spectroscopies. This series spans iron complexes of increasing complexity, starting from ferric and ferrous tetrachlorides ([FeCl₄]^−/2–), to ferric and ferrous tetrathiolates ([Fe(SR)₄]^−/2–), to diferric and mixed-valent iron–sulfur complexes [Fe₂S₂R₄]^2–/3–. This test set of compounds is used to evaluate the sensitivity of both Fe L_2,3-edge XAS and XMCD spectroscopy to oxidation state and ligation changes. It is demonstrated that the energy shift and intensity of the L_2,3-edge XAS spectra depends on both the oxidation state and covalency of the system; however, the quantitative information that can be extracted from these data is limited. On the other hand, analysis of the Fe XMCD shows distinct changes in the intensity at both L₃ and L₂ edges, depending on the oxidation state of the system. It is also demonstrated that the XMCD intensity is modulated by the covalency of the system. For mononuclear systems, the experimental data are correlated with atomic multiplet calculations in order to provide insights into the experimental observations. Finally, XMCD is applied to the tetranuclear heterometal–iron–sulfur clusters [MFe₃S₄]^3+/2+ (M = Mo, V), which serve as structural analogues of the FeMoco and FeVco active sites of nitrogenase. It is demonstrated that the XMCD data can be utilized to obtain information on the oxidation state distribution in complex clusters that is not readily accessible for the Fe L_2,3-edge XAS data alone. The advantages of XMCD relative to standard K-edge and L_2,3-edge XAS are highlighted. This study provides an important foundation for future XMCD studies on complex (bio)inorganic systems.

A systematic Fe L_2,3-edge X-ray absorption (XAS) and X-ray magnetic circular dichroism (XMCD) study of iron tetrachlorides ([FeCl₄]^−/2−), iron tetrathiolates ([Fe(SR)₄]^−/2−), diferric and mixed-valent iron−sulfur dimers [Fe₂S₂R₄]^2−/3− and heterometal−iron−sulfur tetramers [MFe₃S₄]^3+/2+ (M = Mo, V) is reported. The changes in XAS and XMCD energies and intensities across this set of complexes are presented together with atomic multiplet calculations. The advantages of XMCD as an electronic structure probe of complex clusters are highlighted.

Comparative electronic structures of nitrogenase FeMoco and FeVco

An investigation of the active site cofactors of the molybdenum and vanadium nitrogenases (FeMoco and FeVco) was performed using high-resolution X-ray spectroscopy. Synthetic heterometallic iron-sulfur cluster models and density functional theory calculations complement the study of the MoFe and VFe holoproteins using both non-resonant and resonant X-ray emission spectroscopy. Spectroscopic data show the presence of direct iron-heterometal bonds, which are found to be weaker in FeVco. Furthermore, the interstitial carbide is found to perturb the electronic structures of the cofactors through highly covalent Fe-C bonding. The implications of these conclusions are discussed in light of the differential reactivity of the molybdenum and vanadium nitrogenases towards various substrates. Possible functional roles for both the heterometal and the interstitial carbide are detailed.

Nitrogenase and homologs

Nitrogenase catalyzes biological nitrogen fixation, a key step in the global nitrogen cycle. Three homologous nitrogenases have been identified to date, along with several structural and/or functional homologs of this enzyme that are involved in nitrogenase assembly, bacteriochlorophyll biosynthesis and methanogenic process, respectively. In this article, we provide an overview of the structures and functions of nitrogenase and its homologs, which highlights the similarity and disparity of this uniquely versatile group of enzymes.

Binding affinity of alkynes and alkenes to low-coordinate iron

We report the synthesis, spectroscopy, and structural characterization of iron-alkyne and -alkene complexes of the type L(Me)Fe(ligand) [L(Me) = bulky beta-diketiminate, ligand = HCCPh, EtCCEt, CH2CHPh, EtCHCHEt, HCC(p-C6H4OCH3), HCC(p-C6H4CF3)]. The neutral ligand exchanges rapidly at room temperature, and the equilibrium constants have been measured or estimated. The binding affinity toward the low-coordinate Fe follows the trend HCCPh > EtCCEt > CH2CHPh > EtCHCHEt approximately PPh3 > benzene >> N2. This trend is consistent with a model in which pi back-bonding from the formally Fe(I) center is the dominant interaction in determining the relative binding affinities. In nitrogenase, alkynes are reduced while alkenes are unreactive, and this work suggests that the different binding affinities to low-coordinate Fe might explain the differential activity of the enzyme toward these two substrates.

Catalytic reduction of dinitrogen to ammonia at well-defined single metal sites

Dinitrogen (N2) is reduced to ammonia at room temperature and 1atm with molybdenum catalysts that contain tetradentate [HIPTN3N]3- triamidoamine ligands {[HIPTN3N]3-=[{3,5-(2,4,6-i-Pr3C6H2)2C6H3NCH2CH2}3N]3-, an example being [HIPTN3N]Mo(N2)} in heptane. Slow addition of the proton source ({2,6-lutidinium}{BAr'4}; Ar'=3,5-(CF3)2C6H3) and reductant (decamethyl chromocene) assure a high yield of ammonia (63-65% in four turnovers) versus dihydrogen formation. Numerous X-ray studies, along with isolation and characterization of seven intermediates in the proposed catalytic reaction (under noncatalytic conditions), suggest that N2 is being reduced at a sterically protected, single Mo centre that cycles between states Mo(III), Mo(IV), Mo(V) and Mo(VI).

Metal substitution in the active site of nitrogenase MFe(7)S(9) (M = Mo(4+), V(3+), Fe(3+))

The unifying view that molybdenum is the essential component in nitrogenase has changed over the past few years with the discovery of a vanadium-containing nitrogenase and an iron-only nitrogenase. The principal question that has arisen for the alternative nitrogenases concerns the structures of their corresponding cofactors and their metal-ion valence assignments and whether there are significant differences with that of the more widely known molybdenum-iron cofactor (FeMoco). Spin-polarized broken-symmetry (BS) density functional theory (DFT) calculations are used to assess which of the two possible metal-ion valence assignments (4Fe(2+)4Fe(3+) or 6Fe(2+)2Fe(3+)) for the iron-only cofactor (FeFeco) best represents the resting state. For the 6Fe(2+)2Fe(3+) oxidation state, the spin coupling pattern for several spin state alignments compatible with S = 0 were generated and assessed by energy criteria. The most likely BS spin state is composed of a 4Fe cluster with spin S(a) = (7)/(2) antiferromagnetically coupled to a 4Fe' cluster with spin S(b) = (7)/(2). This state has the lowest DFT energy for the isolated FeFeco cluster and displays calculated Mössbauer isomer shifts consistent with experiment. Although the S = 0 resting state of FeFeco has recently been proposed to have metal-ion valencies of 4Fe(2+)4Fe(3+) (derived from experimental Mössbauer isomer shifts), our isomer shift calculations for the 4Fe(2+)4Fe(3+) oxidation state are in poorer agreement with experiment. Using the Mo(4+)6Fe(2+)Fe(3+) oxidation level of the cofactor as a starting point, the structural consequences of replacement of molybdenum (Mo(4+)) with vanadium (V(3+)) or iron (Fe(3+)) in the cofactor have been investigated. The size of the cofactor cluster shows a dependency on the nature of the heterometal and increases in the order FeMoco < FeVco < FeFeco.

High-nuclearity sulfide-rich molybdenum[bond]iron[bond]sulfur clusters: reevaluation and extension

High-nuclearity Mo[bond]Fe[bond]S clusters are of interest as potential synthetic precursors to the MoFe(7)S(9) cofactor cluster of nitrogenase. In this context, the synthesis and properties of previously reported but sparsely described trinuclear [(edt)(2)M(2)FeS(6)](3-) (M = Mo (2), W (3)) and hexanuclear [(edt)(2)Mo(2)Fe(4)S(9)](4-) (4, edt = ethane-1,2-dithiolate; Zhang, Z.; et al. Kexue Tongbao 1987, 32, 1405) have been reexamined and extended. More accurate structures of 2-4 that confirm earlier findings have been determined. Detailed preparations (not previously available) are given for 2 and 3, whose structures exhibit the C(2) arrangement [[(edt)M(S)(mu(2)-S)(2)](2)Fe(III)](3-) with square pyramidal Mo(V) and tetrahedral Fe(III). Oxidation states follow from (57)Fe Mössbauer parameters and an S = (3)/(2) ground state from the EPR spectrum. The assembly system 2/3FeCl(3)/3Li(2)S/nNaSEt in methanol/acetonitrile (n = 4) affords (R(4)N)(4)[4] (R = Et, Bu; 70-80%). The structure of 4 contains the [Mo(2)Fe(4)(mu(2)-S)(6)(mu(3)-S)(2)(mu(4)-S)](0) core, with the same bridging pattern as the [Fe(6)S(9)](2-) core of [Fe(6)S(9)(SR)(2)](4-) (1), in overall C(2v) symmetry. Cluster 4 supports a reversible three-member electron transfer series 4-/3-/2- with E(1/2) = -0.76 and -0.30 V in Me(2)SO. Oxidation of (Et(4)N)(4)[4] in DMF with 1 equiv of tropylium ion gives [(edt)(2)Mo(2)Fe(4)S(9)](3-) (5) isolated as (Et(4)N)(3)[5].2DMF (75%). Alternatively, the assembly system (n = 3) gives the oxidized cluster directly as (Bu(4)N)(3)[5] (53%). Treatment of 5 with 1 equiv of [Cp(2)Fe](1+) in DMF did not result in one-electron oxidation but instead produced heptanuclear [(edt)(2)Mo(2)Fe(5)S(11)](3-) (6), isolated as the Bu(4)N(+)salt (38%). Cluster 6 features the previously unknown core Mo(2)Fe(5)(mu(2)-S)(7)(mu(3)-S)(4) in molecular C(2) symmetry. In 4-6, the (edt)MoS(3) sites are distorted trigonal bipramidal and the FeS(4) sites are distorted tetrahedral with all sulfide ligands bridging. Mössbauer spectroscopic data for 2 and 4-6 are reported; (mean) iron oxidation states increase in the order 4 < 5 approximately 1 < 6 approximately 2. Redox and spectroscopic data attributed earlier to clusters 2 and 4 are largely in disagreement with those determined in this work. The only iron and molybdenum[bond]iron clusters with the same sulfide content as the iron[bond]molybdenum cofactor of nitrogenase are [Fe(6)S(9)(SR)(2)](4-) and [(edt)(2)Mo(2)Fe(4)S(9)](3-)(,4-).

Single- and double-cubane clusters in the multiple oxidation states [VFe(3)S(4)](3+,2+,1+)

A new series of cubane-type [VFe(3)S(4)](z)() clusters (z = 1+, 2+, 3+) has been prepared as possible precursor species for clusters related to those present in vanadium-containing nitrogenase. Treatment of [(HBpz(3))VFe(3)S(4)Cl(3)](2)(-) (2, z = 2+), protected from further reaction at the vanadium site by the tris(pyrazolyl)hydroborate ligand, with ferrocenium ion affords the oxidized cluster [(HBpz(3))VFe(3)S(4)Cl(3)](1)(-) (3, z = 3+). Reaction of 2 with Et(3)P results in chloride substitution to give [(HBpz(3))VFe(3)S(4)(PEt(3))(3)](1+) (4, z = 2+). Reaction of 4 with cobaltocene reduced the cluster with formation of the edge-bridged double-cubane [(HBpz(3))(2)V(2)Fe(6)S(8)(PEt(3))(4)] (5, z = 1+, 1+), which with excess chloride underwent ligand substitution to afford [(HBpz(3))(2)V(2)Fe(6)S(8)Cl(4)](4)(-) (6, z = 1+, 1+). X-ray structures of (Me(4)N)[3], [4](PF(6)), 5, and (Et(4)N)(4)[6] x 2MeCN are described. Cluster 5 is isostructural with previously reported [(Cl(4)cat)(2)(Et(3)P)(2)Mo(2)Fe(6)S(8)(PEt(3))(4)] and contains two VFe(3)S(4) cubanes connected across edges by a Fe(2)S(2) rhomb in which the bridging Fe-S distances are shorter than intracubane Fe-S distances. Mössbauer (2-5), magnetic (2-5), and EPR (2, 4) data are reported and demonstrate an S = 3/2 ground state for 2 and 4 and a diamagnetic ground state for 3. Analysis of (57)Fe isomer shifts based on an empirical correlation between shift and oxidation state and appropriate reference shifts results in two conclusions. (i) The oxidation 2 --> 3 + e(-) results in a change in electron density localized largely or completely on the Fe(3) subcluster and associated sulfur atoms. (ii) The most appropriate charge distributions are [V(3+)Fe(3+)Fe(2+)(2)S(4)](2+) (Fe(2.33+)) for 1, 2, and 4 and [V(3+)Fe(3+)(2)Fe(2+)S(4)](3+) (Fe(2.67+)) for 3 and [V(2)Fe(6)S(8)(SEt)(9)](3+). Conclusion i applies to every MFe(3)S(4) cubane-type cluster thus far examined in different redox states at parity of cluster ligation. The formalistic charge distributions are regarded as the best current approximations to electron distributions in these delocalized species. The isomer shifts require that iron atoms are mixed-valence in each cluster.

Vanadium nitrogenase

The topic, vanadium nitrogenase, is reviewed with respect to biological characteristics and findings on its structure and functions. Structural models (vanadium complexes containing ligands related to the active center in the iron-vanadium cofactor) and functional models for the reductive protonation of dinitrogen, the activation of alkynes and reductive C-C coupling of isocyanides are addressed.

In vitro synthesis of the iron-molybdenum cofactor and maturation of the nif-encoded apodinitrogenase. Effect of substitution of VNFH for NIFH

NIFH (the nifH gene product) has several functions in the nitrogenase enzyme system. In addition to reducing dinitrogenase during nitrogenase turnover, NIFH functions in the biosynthesis of the iron-molybdenum cofactor (FeMo-co), and in the processing of alpha2beta2 apodinitrogenase 1 (a catalytically inactive form of dinitrogenase 1 that lacks the FeMo-co) to the FeMo-co-activatable alpha2beta2gamma2 form. The molybdenum-independent nitrogenase 2 (vnf-encoded) has a distinct dinitrogenase reductase protein, VNFH. We investigated the ability of VNFH to function in the in vitro biosynthesis of FeMo-co and in the maturation of apodinitrogenase 1. VNFH can replace NIFH in both the biosynthesis of FeMo-co and in the maturation of apodinitrogenase 1. These results suggest that the dinitrogenase reductase proteins do not specify the heterometal incorporated into the cofactors of the respective nitrogenase enzymes. The specificity for the incorporation of molybdenum into FeMo-co was also examined using the in vitro FeMo-co synthesis assay system.

Oxidative titration of the nitrogenase VFe protein from Azotobacter vinelandii: an example of redox-gated electron flow

The nitrogenase VFe protein of Azotobacter vinelandii (Av1') has been shown to exist in two forms called Av1'A, which has a primary alpha beta 2 trimeric structure, and Av1'B, which has an alpha 2 beta 2 tetrameric structure [Blanchard, C. Z., & Hales, B. J. (1996) Biochemistry 35, 472-478]. Both forms exhibit S = 5/2 EPR signals in the as-isolated state that may be assigned to 1-equiv-oxidized P clusters (P+). These signals are abolished by enzymatic reduction with the component 2 protein (Av2'). Stepwise oxidative titrations of enzymatically reduced Av1'B result in the restoration of the S = 5/2 P+ signals and the concurrent decrease of the S = 3/2 vanadium cofactor signal. Further oxidation results in the appearance of an integer spin signal assigned to the 2-equiv-oxidized P cluster (P2+). Unlike the analogous signal previously observed in Mo nitrogenase component 1 (Av1), which arises from an excited state, the integer spin P2+ signal in Av1'B originates from a ground-state doublet. Similar oxidative titrations of enzymatically reduced Av1'A show redox behavior dramatically different from that of Av1'B, as monitored by EPR spectroscopy. We observed spectral evidence for a redox-induced intramolecular electron transfer between the reduced P cluster and the oxidized FeV cofactor cluster during the titrations.

Iron K-edge X-ray-absorption spectroscopy of the iron-vanadium cofactor of the vanadium nitrogenase from Azotobacter chroococcum

Iron K-edge e.x.a.f.s. data for the iron-vanadium cofactor (FeVaco) from Azotobacter chroococcum vanadium nitrogenase reported here provide further evidence for the structural similarity between this and the iron-molybdenum nitrogenase cofactor (FeMoco) from Klebsiella pneumoniae molybdenum nitrogenase [Arber, Flood, Garner, Gormal, Hasnain & Smith (1988) Biochem. J. 252, 421-425]. The e.x.a.f.s. data are consistent with the vanadium being present in a V-Fe-S cluster, thus confirming that the N-methylformamide extract of the VFe protein component of A. chroococcum vanadium nitrogenase does indeed contain a polynuclear metal-sulphur cluster. Additionally, a long Fe-Fe distance is observed as 0.369 nm, demonstrating the presence of a long-range order in the cluster.