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

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.

Computational Design of Transition Metal Single-Atom Electrocatalysts on PtS2 for Efficient Nitrogen Reduction

Electrocatalytic nitrogen reduction is promising to serve as a sustainable and environmentally friendly strategy to achieve ammonia production. Single-atom catalysts (SACs) hold great promise to convert N₂ into NH₃ because of the unique molecular catalysis property and ultrahigh atomic utilization ratio. Here, we demonstrate a universal computational design principle to assess the N₂ reduction reaction (NRR) performance of SACs anchored on a monolayer PtS₂ substrate (SACs-PtS₂). Our density functional theory simulations unveil that the barriers of the NRR limiting potential step on different SAC centers are observed to be linearly correlated to the integral of unoccupied d states (UDSs) of SACs. As a result, the Ru SAC-PtS₂ catalyst with the largest number of UDSs exhibits a much lower barrier of the limiting step than those of other SACs-PtS₂ catalysts and the Ru(0001) benchmark. Our work bridges the apparent NRR activity and intrinsic electronic structure of SAC centers and offers effective guidance to screen and design efficient SACs for the electrochemical NRR process.

Jahn-Teller Distorted Effects To Promote Nitrogen Reduction over Keggin-Type Phosphotungstic Acid Catalysts: Insight from Density Functional Theory Calculations

Molecular geometry, electronic structure, and possible reaction mechanism of a series of mono-transition-metal-substituted Keggin-type polyoxometalate (POM)-dinitrogen complexes [PW₁₁O₃₉M(N₂)] ^n- (M = Cr, Mn, Fe, Co, Ni, Cu, Zn, Mo, Tc, Ru, Rh, Pd, Ag, Cd, W, Re, Os, Ir, Pt, Au, and Hg) have been investigated by using density functional theory (DFT) calculations with M06L functional. The calculated adsorption energy of N₂ molecule, N-N bond length, N-N stretching frequency, and the NBO charge on the coordinated N₂ moiety indicate that Mo^II-, Tc^II-, W^II-, Re^II-, and Os^II-POM complexes are significant for binding and activation of the inert N₂ molecule. The degree of the N₂ activation can be classified into the "moderately activated" category according to Tuczek's sense [ J. Comput. Chem. 2006 , 27 , 1278 ]. Electronic structure and NBO analysis indicate that the terminal N atom of the coordinated N₂ molecule in these POM-dinitrogen complexes possesses more negative charge relative to the bridge N atom because Jahn-Teller distorted effects lead to an effective orbital mixture between σ_2s* orbital of N₂ and d _z² orbital of transition metal center. And the mono-lacunary Keggin-type POM ligand with five oxygen donor atoms serves as a strong electron donor to the bivalent metal center. Meanwhile, a catalytic cycle for direct conversion of N₂ into NH₃ has been systematically investigated based on a Re-POM complex along distal, alternating, and enzymatic pathways. The calculated free energy profile of the three catalytic cycles indicates that the distal mechanism is the favorable pathway in the presence of proton and electron donors.

The mechanism for nitrogenase including all steps

Nitrogen in the air is turned into biologically useful ammonia by the nitrogenase enzyme. The leading member of this group has a cofactor with one molybdenum and seven irons linked together by sulfurs. The structure that binds N₂ has a triply protonated carbide and a rotated homocitrate. Both these structural changes are necessary for the activation.

A single boron atom doped boron nitride edge as a metal-free catalyst for N2 fixation

The first-principle theory has been used to predict a new metal-free single atom electrocatalyst for N₂ reduction.

Structural characterization of CO-inhibited Mo-nitrogenase by combined application of nuclear resonance vibrational spectroscopy, extended X-ray absorption fine structure, and density functional theory: new insights into the effects of CO binding and the role of the interstitial atom

The properties of CO-inhibited Azotobacter vinelandii (Av) Mo-nitrogenase (N2ase) have been examined by the combined application of nuclear resonance vibrational spectroscopy (NRVS), extended X-ray absorption fine structure (EXAFS), and density functional theory (DFT). Dramatic changes in the NRVS are seen under high-CO conditions, especially in a 188 cm(-1) mode associated with symmetric breathing of the central cage of the FeMo-cofactor. Similar changes are reproduced with the α-H195Q N2ase variant. In the frequency region above 450 cm(-1), additional features are seen that are assigned to Fe-CO bending and stretching modes (confirmed by (13)CO isotope shifts). The EXAFS for wild-type N2ase shows evidence for a significant cluster distortion under high-CO conditions, most dramatically in the splitting of the interaction between Mo and the shell of Fe atoms originally at 5.08 Å in the resting enzyme. A DFT model with both a terminal -CO and a partially reduced -CHO ligand bound to adjacent Fe sites is consistent with both earlier FT-IR experiments, and the present EXAFS and NRVS observations for the wild-type enzyme. Another DFT model with two terminal CO ligands on the adjacent Fe atoms yields Fe-CO bands consistent with the α-H195Q variant NRVS. The calculations also shed light on the vibrational "shake" modes of the interstitial atom inside the central cage, and their interaction with the Fe-CO modes. Implications for the CO and N2 reactivity of N2ase are discussed.

Synthesis, spectral, and structural characterizations of imidazole oxalato molybdenum(IV/V/VI) complexes

Substitutions of trans-Na(Him)[Mo(2)O(4)(ox)(2)(H(2)O)(2)]·H(2)O (1) and trans-(Him)(2)[Mo(2)O(4)(ox)(2)(H(2)O)(2)] (2) with imidazole result in the formation of the mixed-ligand molybdenum complexes cis-Na(2)[Mo(2)O(4)(ox)(2)(im)(2)]·4.5H(2)O (3), cis-K(2)[Mo(2)O(4)(ox)(2)(im)(2)]·3H(2)O (4), respectively (H(2)ox = oxalic acid; im = imidazole). Further reduction of cis-K(2)[Mo(2)O(4)(ox)(2)(im)(2)]·3H(2)O (4) gives a trinuclear molybdenum(IV) complex K(Him)[Mo(3)O(4)(ox)(3)(im)(3)]·3H(2)O (5), which contains an incomplete cubane cluster [Mo(IV)(3)O(4)](4+). Two novel trinuclear mixed-valence imidazole compounds [Mo(3)O(8)(im)(4)](im)·H(2)O (6) and [Mo(3)O(8)(im)(4)]·H(2)O (7) were obtained by the reduction of (Him)(4)[Mo(8)O(26)(im)(2)] (8). Both 6 and 7 contain a novel Mo(VI)O(4)(Mo(V)(2)O(4)) center, where the [Mo(V)(2)O(4)](2+) unit is linked by [Mo(VI)O(4)](2-) anion. The Mo-Mo bond distances in 1-7 decrease with the decrease of oxidation state of molybdenum. Solid and solution NMR spectra show that imidazole molybdenum compounds 6-8 fully dissociate in solution, where solvated imidazole and imidazolium groups in 6 and 8 could be served as internal references in their solid (13)C NMR spectra. Furthermore, mixed-ligand molybdenum species 3 and 4 are stable in water. Stabilities of 3 and 4 in solution may be attributed to the strong coordination of bidentate oxalate and the formation of hydrogen bond. Dimers 2 and 4 display quasi-reversible redox process, while trimer 6 is irreversible. Bond valence calculations for 1-8 are consistent with their oxidation states of molybdenum atoms. Calculation of the oxidation state in recent structure of iron molybdenum cofactor [MoFe(7)S(9)C(R-homocit)] (FeMo-co) is 3.318.

Site-isolated redox reactivity in a trinuclear iron complex

The symmetric, high-spin triiron complex ((Ph)L)Fe(3)(THF)(3) reacts with mild chemical oxidants (e.g., Ph(3)C-X, I(2)) to afford an asymmetric core, where one iron bears the halide ligand ((Ph)L)Fe(3)X(L) and the hexadentate ((Ph)L = MeC(CH(2)NPh-o-NPh)(3)) ligand has undergone significant rearrangement. In the absence of a suitable trapping ligand, the chlorine and bromine complexes form (μ-X)(2)-bridged structures of the type [((Ph)L)Fe(3)(μ-X)](2). In the trinuclear complexes, the halide-bearing iron site sits in approximate trigonal-bipyramidal (tbp) geometry, formed by two ((Ph)L) anilides and an exogenous solvent molecule. The two distal iron atoms reside in distorted square-planar sites featuring a short Fe-Fe separation at 2.301 Å, whereas the distance to the tbp site is substantially elongated (2.6-2.7 Å). Zero-field, (57)Fe Mössbauer analysis reveals the diiron unit as the locus of oxidation, while the tbp site bearing the halide ligand remains divalent. Magnetic data acquired for the series reveal that the oxidized diiron unit comprises a strongly coupled S = (3)/(2) unit that is weakly ferromagnetically coupled to the high-spin (S = 2) ferrous site, giving an overall S = (7)/(2) ground state for the trinuclear units.

EXAFS and NRVS reveal a conformational distortion of the FeMo-cofactor in the MoFe nitrogenase propargyl alcohol complex

We have used EXAFS and NRVS spectroscopies to examine the structural changes in the FeMo-cofactor active site of the α-70(Ala) variant of Azotobacter vinelandii nitrogenase on binding and reduction of propargyl alcohol (PA). The Mo K-edge near-edge and EXAFS spectra are very similar in the presence and absence of PA, suggesting PA does not bind at Mo. By contrast, Fe EXAFS spectra show a clear and reproducible change in the long Fe-Fe interaction at ~3.7 Å on PA binding with the apparent appearance of a new Fe-Fe interaction at 3.99 Å. An analogous change in the long Mo-Fe 5.1 Å interaction is not seen. The NRVS spectra exclude the possibility of large-scale structural change of the FeMo-cofactor involving breaking the μ(2) Fe-S-Fe bonds of the Fe(6)S(9)X core. The simplest chemically consistent structural change is that the bound form of PA is coordinated at Fe atoms (Fe6 or Fe7) adjacent to the Mo terminus, with a concomitant movement of the Fe away from the central atom X and along the Fe-X bond by about 0.35 Å. This study comprises the first experimental evidence of the conformational changes of the FeMo-cofactor active site on binding a substrate or product.

DENSITY FUNTIONAL STUDY OF THE STRUCTURE OF THE FeMo COFACTOR WITH AN INTERSTITIAL ATOM AND HOMOCITRATE LIGAND RING OPENING

The structure of the FeMo cofactor with the central X ligand ( X = C 4-, C 2-, N 3-, N -, or O 2-) has been determined by the density functional approach. The FeMo cluster with one of the proposed central atoms C 4-, C 2-, N 3-, or N - has an optimized geometry, comparable with the high-resolution X-Ray crystallographic structure of the nitrogenase FeMo cofactor. When the O 2- species is present, the FeMo cofactor has an expanded cage. Calculations in the gas phase show that an >Fe 4 facet of the FeMo cluster binds NO and CO in end-on coordination with an exothermicity of 25 and 8 kcal mol-1, respectively, while the singlet O 2 coordinates to the FeMo cluster with an endothermicity of 12 kcal mol-1. Deoxygenization of the bound NO and CO by the proton-electron addition is favored energetically, which leads to penetration of the C or N atom into the FeMo cage and yields the FeMo (μ6- X ) cluster. Antiferromagnetic coupling between the Fe sites and vibrational properties of the FeMo (μ6- X ) cluster, as well as the Mo-bound homocitrate ligand ring opening, have been explored theoretically. Present results suggest that O 2- is unlikely as a central anion and the central ligands are identifiable by their IR spectra. Predicted energetics indicates that the protonation opening of the homocitrate ligand ring at the Mo site is feasible.

Multi-site reactivity: reduction of six equivalents of nitrite to give an Fe6(NO)6 cluster with a dramatically expanded octahedral core

Reaction of NO(2)(-) with the octahedral cluster ((H)L)(2)Fe(6) in the presence of a proton source affords the hexanitrosyl cluster ((H)L)(2)Fe(6)(NO)(6). This species forms via a proton-induced reduction of six nitrite molecules per cluster, utilizing each site available on the polynuclear core. Formation of the hexanitrosyl cluster is accompanied by a near 2-fold expansion of the ((H)L)(2)Fe(6) core volume, where intracore Fe-Fe interactions are overcome by strong π-bonding between Fe centers and NO ligands. A core volume of this magnitude is rare in octahedral metal clusters not supported by interstitial atoms. Moreover, the structural flexibility afforded by the ((H)L)(2)Fe(6) platform highlights the potential for other reaction chemistry involving species with metal-ligand multiple bonds. Carrying out the reaction of the cluster [((H)L)(2)Fe(6)(NCMe)(6)](4+) with nitrite in the absence of a proton source serves to forestall the nitrite reduction and enables clean isolation of the intermediate hexanitro cluster [((H)L)(2)Fe(6)(NO(2))(6)](2-).

Fischer-Tropsch chemistry at room temperature?

The unique catalytic activity of vanadium nitrogenase suggests a new direction for the direct production of biofuels from CO with either synthetic catalysts or nitrogenase-containing bacteria. The reduction of CO by V nitrogenase to light hydrocarbons shows striking similarities to the established Fischer-Tropsch process; however, the enzyme does not use H(2) directly for this reaction. ADP=adenosine diphosphate, ATP= adenosine triphosphate.

Comparative assessment of the composition and charge state of nitrogenase FeMo-cofactor

A significant limitation in our understanding of the molecular mechanism of biological nitrogen fixation is the uncertain composition of the FeMo-cofactor (FeMo-co) of nitrogenase. In this study we present a systematic, density functional theory-based evaluation of spin-coupling schemes, iron oxidation states, ligand protonation states, and interstitial ligand composition using a wide range of experimental criteria. The employed functionals and basis sets were validated with molecular orbital information from X-ray absorption spectroscopic data of relevant iron-sulfur clusters. Independently from the employed level of theory, the electronic structure with the greatest number of antiferromagnetic interactions corresponds to the lowest energy state for a given charge and oxidation state distribution of the iron ions. The relative spin state energies of resting and oxidized FeMo-co already allowed exclusion of certain iron oxidation state distributions and interstitial ligand compositions. Geometry-optimized FeMo-co structures of several models further eliminated additional states and compositions, while reduction potentials indicated a strong preference for the most likely charge state of FeMo-co. Mössbauer and ENDOR parameter calculations were found to be remarkably dependent on the employed training set, density functional, and basis set. Overall, we found that a more oxidized [Mo(IV)-2Fe(II)-5Fe(III)-9S(2-)-C(4-)] composition with a hydroxyl-protonated homocitrate ligand satisfies all of the available experimental criteria and is thus favored over the currently preferred composition of [Mo(IV)-4Fe(II)-3Fe(III)-9S(2-)-N(3-)] from the literature.

Theoretical studies of homogeneous catalysts mimicking nitrogenase

The conversion of molecular nitrogen to ammonia is a key biological and chemical process and represents one of the most challenging topics in chemistry and biology. In Nature the Mo-containing nitrogenase enzymes perform nitrogen 'fixation' via an iron molybdenum cofactor (FeMo-co) under ambient conditions. In contrast, industrially, the Haber-Bosch process reduces molecular nitrogen and hydrogen to ammonia with a heterogeneous iron catalyst under drastic conditions of temperature and pressure. This process accounts for the production of millions of tons of nitrogen compounds used for agricultural and industrial purposes, but the high temperature and pressure required result in a large energy loss, leading to several economic and environmental issues. During the last 40 years many attempts have been made to synthesize simple homogeneous catalysts that can activate dinitrogen under the same mild conditions of the nitrogenase enzymes. Several compounds, almost all containing transition metals, have been shown to bind and activate N₂ to various degrees. However, to date Mo(N₂)(HIPTN)₃N with (HIPTN)₃N= hexaisopropyl-terphenyl-triamidoamine is the only compound performing this process catalytically. In this review we describe how Density Functional Theory calculations have been of help in elucidating the reaction mechanisms of the inorganic compounds that activate or fix N₂. These studies provided important insights that rationalize and complement the experimental findings about the reaction mechanisms of known catalysts, predicting the reactivity of new potential catalysts and helping in tailoring new efficient catalytic compounds.

Modeling the MoFe nitrogenase system with broken symmetry density functional theory

Density functional theory (DFT) represents a unified framework for gaining molecular level insight into molybdenum-iron (MoFe) nitrogenase. However, accurately describing the electronic structure of the spin-polarized and spin-coupled iron-molybdenum cofactor (FeMo-co) where N(2) reduction occurs within MoFe nitrogenase is challenging. Therefore, the enhancement of DFT to include broken symmetry (BS-DFT) plus approximate spin projection has proven valuable because it provides a procedure to compute reliable geometries, energies, redox potentials, and quantities relevant to Mössbauer and ENDOR spectroscopies. After describing the theoretical tools necessary to obtain this information, we show by way of examples how BS-DFT is a very powerful partner to experiment. We expect that quantitative quantum chemical theory of this type will play an ever-increasing role in helping to decipher complex bioinorganic systems like those found in MoFe nitrogenase.

Nitrogenase structure and function relationships by density functional theory

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.

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.

The reactivity patterns of low-coordinate iron-hydride complexes

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.

Theoretical, spectroscopic, and mechanistic studies on transition-metal dinitrogen complexes: implications to reactivity and relevance to the nitrogenase problem

Dinitrogen complexes of transition metals exhibit different binding geometries of N2 (end-on terminal, end-on bridging, side-on bridging, side-on end-on bridging), which are investigated by spectroscopy and DFT calculations, analyzing their electronic structure and reactivity. For comparison, a bis(mu-nitrido) complex, where the N--N bond has been split, has been studied as well. Most of these systems are highly covalent, and have strong metal-nitrogen bonds. In the present review, particular emphasis is put on a consideration of the activation of the coordinated dinitrogen ligand, making it susceptible to protonation, reactions with electrophiles or cleavage. In this context, theoretical, structural, and spectroscopic data giving informations on the amount of charge on the N2 unit are presented. The orbital interactions leading to a charge transfer from the metals to the dinitrogen ligand and the charge distribution within the coordinated N2 group are analyzed. Correlations between the binding mode and the observed reactivity of N2 are discussed.

Modeling hydrogen evolution from the Fe4S4and Fe8S9X (X = N, C) clusters. Can a FeS high-spin cluster serve as a surrogate for the FeMo cofactor?

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.

Expression and association of group IV nitrogenase NifD and NifH homologs in the non-nitrogen-fixing archaeon Methanocaldococcus jannaschii

Using genomic analysis, researchers previously identified genes coding for proteins homologous to the structural proteins of nitrogenase (J. Raymond, J. L. Siefert, C. R. Staples, and R. E. Blankenship, Mol. Biol. Evol. 21:541-554, 2004). The expression and association of NifD and NifH nitrogenase homologs (named NflD and NflH for "Nif-like" D and H, respectively) have been detected in a non-nitrogen-fixing hyperthermophilic methanogen, Methanocaldococcus jannaschii. These homologs are expressed constitutively and do not appear to be directly involved with nitrogen metabolism or detoxification of compounds such as cyanide or azide. The NflH and NflD proteins were found to interact with each other, as determined by bacterial two-hybrid studies. Upon immunoisolation, NflD and NflH copurified, along with three other proteins whose functions are as yet uncharacterized. The apparent presence of genes coding for NflH and NflD in all known methanogens, their constitutive expression, and their high sequence similarity to the NifH and NifD proteins or the BchL and BchN/BchB proteins suggest that NflH and NflD participate in an indispensable and fundamental function(s) in methanogens.

Diazene (HN=NH) is a substrate for nitrogenase: insights into the pathway of N2 reduction

Nitrogenase catalyzes the sequential addition of six electrons and six protons to a N2 that is bound to the active site metal cluster FeMo-cofactor, yielding two ammonia molecules. The nature of the intermediates bound to FeMo-cofactor along this reduction pathway remains unknown, although it has been suggested that there are intermediates at the level of reduction of diazene (HN=NH, also called diimide) and hydrazine (H2N-NH2). Through in situ generation of diazene during nitrogenase turnover, we show that diazene is a substrate for the wild-type nitrogenase and is reduced to NH3. Diazene reduction, like N2 reduction, is inhibited by H2. This contrasts with the absence of H2 inhibition when nitrogenase reduces hydrazine. These results support the existence of an intermediate early in the N2 reduction pathway at the level of reduction of diazene. Freeze-quenching a MoFe protein variant with alpha-195His substituted by Gln and alpha-70Val substituted by Ala during steady-state turnover with diazene resulted in conversion of the S = 3/2 resting state FeMo-cofactor to a novel S = 1/2 state with g1 = 2.09, g2 = 2.01, and g3 approximately 1.98. 15N- and 1H-ENDOR establish that this state consists of a diazene-derived [-NHx] moiety bound to FeMo-cofactor. This moiety is indistinguishable from the hydrazine-derived [-NHx] moiety bound to FeMo-cofactor when the same MoFe protein is trapped during turnover with hydrazine. These observations suggest that diazene joins the normal N2-reduction pathway, and that the diazene- and hydrazine-trapped turnover states represent the same intermediate in the normal reduction of N2 by nitrogenase. Implications of these findings for the mechanism of N2 reduction by nitrogenase are discussed.