Mechanism of nitrogen fixation by nitrogenase: the next stage

Hydrogen overproducing nitrogenases obtained by random mutagenesis and high-throughput screening

When produced biologically, especially by photosynthetic organisms, hydrogen gas (H₂) is arguably the cleanest fuel available. An important limitation to the discovery or synthesis of better H₂-producing enzymes is the absence of methods for the high-throughput screening of H₂ production in biological systems. Here, we re-engineered the natural H₂ sensing system of Rhodobacter capsulatus to direct the emission of LacZ-dependent fluorescence in response to nitrogenase-produced H₂. A lacZ gene was placed under the control of the hupA H₂-inducible promoter in a strain lacking the uptake hydrogenase and the nifH nitrogenase gene. This system was then used in combination with fluorescence-activated cell sorting flow cytometry to screen large libraries of nitrogenase Fe protein variants generated by random mutagenesis. Exact correlation between fluorescence emission and H₂ production levels was found for all automatically selected strains. One of the selected H₂-overproducing Fe protein variants lacked 40% of the wild-type amino acid sequence, a surprising finding for a protein that is highly conserved in nature. We propose that this method has great potential to improve microbial H₂ production by allowing powerful approaches such as the directed evolution of nitrogenases and hydrogenases.

Activation and reduction of carbon dioxide by nitrogenase iron proteins

The iron (Fe) proteins of molybdenum (Mo) and vanadium (V) nitrogenases mimic carbon monoxide (CO) dehydrogenase in catalyzing the interconversion between CO₂ and CO under ambient conditions. Catalytic reduction of CO₂ to CO is achieved in vitro and in vivo upon redox changes of the Fe-protein-associated [Fe₄S₄] clusters. These observations establish the Fe protein as a model for investigation of CO₂ activation while suggesting its biotechnological adaptability for recycling the greenhouse gas into useful products.

Hydrogenated Bismuth Molybdate Nanoframe for Efficient Sunlight-Driven Nitrogen Fixation from Air

Sunlight-driven dinitrogen fixation can lead to a novel concept for the production of ammonia under mild conditions. However, the efficient artificial photosynthesis of ammonia from ordinary air (instead of high pure N₂ ) has never been implemented. Here, we report for the first time the intrinsic catalytic activity of Bi₂ MoO₆ catalyst for direct ammonia synthesis under light irradiation. The edge-exposed coordinatively unsaturated Mo atoms in an Mo-O coordination polyhedron can act as activation centers to achieve the chemisorption, activation, and photoreduction of dinitrogen efficiently. Using that insight as a starting point, through rational structure and defect engineering, the optimized Bi₂ MoO₆ sunlight-driven nitrogen fixation system, which simultaneously possesses robust nitrogen activation ability, excellent light-harvesting performance, and efficient charge transmission was successfully constructed. As a surprising achievement, this photocatalytic system demonstrated for the first time ultra-efficient (1.3 mmol g^-1  h^-1 ) and stable sunlight-driven nitrogen fixation from air in the absence of any organic scavengers.

Enzymatic Bioelectrosynthetic Ammonia Production: Recent Electrochemistry of Nitrogenase, Nitrate Reductase, and Nitrite Reductase

As an essential component of amino acids and nucleic acids, nitrogen (N) is a key element of life. For atmospheric (dinitrogen, N₂ ) and environmental (nitrate and nitrite, NO₃ ^- and NO₂ ^- ) sources of N to be utilized in amino acid synthesis in various forms of life, it must first be reduced to ammonia (NH₃ ). The Haber-Bosch process, in which N₂ is reduced to NH₃ at elevated temperature and pressure, represents a major NH₃ production process that has had a great impact on the agricultural crop industry. This Minireview discusses the recent electrochemistry of three key enzymes of the global biogeochemical N cycle (nitrogenase, nitrate reductase, and nitrite reductase), in view of moving toward the creation of alternative NH₃ production biotechnologies.

The Mechanism of N-N Double Bond Cleavage by an Iron(II) Hydride Complex

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.

CO2 Reduction Catalyzed by Nitrogenase: Pathways to Formate, Carbon Monoxide, and Methane

The reduction of N2 to NH3 by Mo-dependent nitrogenase at its active-site metal cluster FeMo-cofactor utilizes reductive elimination of Fe-bound hydrides with obligatory loss of H2 to activate the enzyme for binding/reduction of N2. Earlier work showed that wild-type nitrogenase and a nitrogenase with amino acid substitutions in the MoFe protein near FeMo-cofactor can catalytically reduce CO2 by two or eight electrons/protons to carbon monoxide (CO) and methane (CH4) at low rates. Here, it is demonstrated that nitrogenase preferentially reduces CO2 by two electrons/protons to formate (HCOO(-)) at rates >10 times higher than rates of CO2 reduction to CO and CH4. Quantum mechanical calculations on the doubly reduced FeMo-cofactor with a Fe-bound hydride and S-bound proton (E2(2H) state) favor a direct reaction of CO2 with the hydride ("direct hydride transfer" reaction pathway), with facile hydride transfer to CO2 yielding formate. In contrast, a significant barrier is observed for reaction of Fe-bound CO2 with the hydride ("associative" reaction pathway), which leads to CO and CH4. Remarkably, in the direct hydride transfer pathway, the Fe-H behaves as a hydridic hydrogen, whereas in the associative pathway it acts as a protic hydrogen. MoFe proteins with amino acid substitutions near FeMo-cofactor (α-70(Val→Ala), α-195(His→Gln)) are found to significantly alter the distribution of products between formate and CO/CH4.

Experimental and theoretical correlations between vanadium K-edge X-ray absorption and Kβ emission spectra

A series of vanadium compounds was studied by K-edge X-ray absorption (XAS) and K[Formula: see text] X-ray emission spectroscopies (XES). Qualitative trends within the datasets, as well as comparisons between the XAS and XES data, illustrate the information content of both methods. The complementary nature of the chemical insight highlights the success of this dual-technique approach in characterizing both the structural and electronic properties of vanadium sites. In particular, and in contrast to XAS or extended X-ray absorption fine structure (EXAFS), we demonstrate that valence-to-core XES is capable of differentiating between ligating atoms with the same identity but different bonding character. Finally, density functional theory (DFT) and time-dependent DFT calculations enable a more detailed, quantitative interpretation of the data. We also establish correction factors for the computational protocols through calibration to experiment. These hard X-ray methods can probe vanadium ions in any oxidation or spin state, and can readily be applied to sample environments ranging from solid-phase catalysts to biological samples in frozen solution. Thus, the combined XAS and XES approach, coupled with DFT calculations, provides a robust tool for the study of vanadium atoms in bioinorganic chemistry.

Mechanisms of the S/CO/Se interchange reactions at FeMo-co, the active site cluster of nitrogenase

The active site of the N2 fixing enzyme nitrogenase is a C-centred Fe7MoS cluster (FeMo-co) containing a trigonal prism of six Fe atoms connected by a central belt of three doubly-bridging S atoms. The trigonal faces of the prism are capped via triply-bridging S atoms to Fe1 at one end and Mo at the other end. One of the central belt atoms, S2B, considered to be important in the chemical mechanism of the enzyme, has been shown by Spatzal, Rees et al. to undergo substitution by CO, and also substitution by Se in the presence of SeCN(-), under turnover conditions. Further, when turning over under C2H2 or N2/CO there is migration of Se to the other two belt bridging positions. These reactions are extraordinary, and unprecedented in metal chalcogenide cluster chemistry. Using density functional simulations, mechanisms for all of these reactions have been developed, involving the small molecules SCO, SeCO, C2H2S, C2H2Se, SeCN(-), SCN(-) functioning as carriers of S and Se atoms. The possibility that the S2B bridge position is vacant is discounted, because the barrier to formation of a bridge-void intermediate with two contiguous three-coordinate Fe atoms is too large. A bridging ligand is retained throughout the proposed mechanisms. Intermediates with Fe-C(O)-S/Se-Fe cycles and with SCO/SeCO C-bound to Fe are predicted. The energetics of the reaction trajectories show them to be feasible and easily reversible, consistent with experiment. Alternative mechanisms involving intramolecular differential rotatory rearrangements of the cluster to scramble the Se bridges are also examined, and shown to be very unlikely. The implications of these new facets of the reactivity of the FeMo-co cluster are discussed: it is considered that they are unlikely to be part of the mechanism of the physiological reactions of nitrogenase.

Reductive Elimination of H2 Activates Nitrogenase to Reduce the N≡N Triple Bond: Characterization of the E4(4H) Janus Intermediate in Wild-Type Enzyme

We proposed a reductive elimination/oxidative addition (re/oa) mechanism for reduction of N2 to 2NH3 by nitrogenase, based on identification of a freeze-trapped intermediate of the α-70(Val→Ile) MoFe protein as the Janus intermediate that stores four reducing equivalents on FeMo-co as two [Fe-H-Fe] bridging hydrides (denoted E4(4H)). The mechanism postulates that obligatory re of the hydrides as H2 drives reduction of N2 to a state (denoted E4(2N2H)) with a moiety at the diazene (HN═NH) reduction level bound to the catalytic FeMo-co. EPR/ENDOR/photophysical measurements on wild type (WT) MoFe protein now establish this mechanism. They show that a state freeze-trapped during N2 reduction by WT MoFe is the same Janus intermediate, thereby establishing the α-70(Val→Ile) intermediate as a reliable guide to mechanism. Monitoring the Janus state in WT MoFe during N2 reduction under mixed-isotope condition, H2O buffer/D2, and the converse, establishes that the bridging hydrides/deuterides do not exchange with solvent during enzymatic turnover, thereby solving longstanding puzzles. Relaxation of E4(2N2H) to the WT resting-state is shown to occur via oa of H2 and release of N2 to form Janus, followed by sequential release of two H2, demonstrating the kinetic reversibility of the re/oa equilibrium. Relative populations of E4(2N2H)/E4(4H) freeze-trapped during WT turnover furthermore show that the reversible re/oa equilibrium between [E4(4H) + N2] and [E4(2N2H) + H2] is ∼ thermoneutral (ΔreG(0) ∼ -2 kcal/mol), whereas, by itself, hydrogenation of N2(g) is highly endergonic. These findings demonstrate that (i) re/oa accounts for the historical Key Constraints on mechanism, (ii) that Janus is central to N2 reduction by WT enzyme, which (iii) indeed occurs via the re/oa mechanism. Thus, emerges a picture of the central mechanistic steps by which nitrogenase carries out one of the most challenging chemical transformations in biology.

The DUF59 Containing Protein SufT Is Involved in the Maturation of Iron-Sulfur (FeS) Proteins during Conditions of High FeS Cofactor Demand in Staphylococcus aureus

Proteins containing DUF59 domains have roles in iron-sulfur (FeS) cluster assembly and are widespread throughout Eukarya, Bacteria, and Archaea. However, the function(s) of this domain is unknown. Staphylococcus aureus SufT is composed solely of a DUF59 domain. We noted that sufT is often co-localized with sufBC, which encode for the Suf FeS cluster biosynthetic machinery. Phylogenetic analyses indicated that sufT was recruited to the suf operon, suggesting a role for SufT in FeS cluster assembly. A S. aureus ΔsufT mutant was defective in the assembly of FeS proteins. The DUF59 protein Rv1466 from Mycobacterium tuberculosis partially corrected the phenotypes of a ΔsufT mutant, consistent with a widespread role for DUF59 in FeS protein maturation. SufT was dispensable for FeS protein maturation during conditions that imposed a low cellular demand for FeS cluster assembly. In contrast, the role of SufT was maximal during conditions imposing a high demand for FeS cluster assembly. SufT was not involved in the repair of FeS clusters damaged by reactive oxygen species or in the physical protection of FeS clusters from oxidants. Nfu is a FeS cluster carrier and nfu displayed synergy with sufT. Furthermore, introduction of nfu upon a multicopy plasmid partially corrected the phenotypes of the ΔsufT mutant. Biofilm formation and exoprotein production are critical for S. aureus pathogenesis and vancomycin is a drug of last-resort to treat staphylococcal infections. Defective FeS protein maturation resulted in increased biofilm formation, decreased production of exoproteins, increased resistance to vancomycin, and the appearance of phenotypes consistent with vancomycin-intermediate resistant S. aureus. We propose that SufT, and by extension the DUF59 domain, is an accessory factor that functions in the maturation of FeS proteins. In S. aureus, the involvement of SufT is maximal during conditions of high demand for FeS proteins.

Hydrogenase Enzymes and Their Synthetic Models: The Role of Metal Hydrides

Hydrogenase enzymes efficiently process H2 and protons at organometallic FeFe, NiFe, or Fe active sites. Synthetic modeling of the many H2ase states has provided insight into H2ase structure and mechanism, as well as afforded catalysts for the H2 energy vector. Particularly important are hydride-bearing states, with synthetic hydride analogues now known for each hydrogenase class. These hydrides are typically prepared by protonation of low-valent cores. Examples of FeFe and NiFe hydrides derived from H2 have also been prepared. Such chemistry is more developed than mimicry of the redox-inactive monoFe enzyme, although functional models of the latter are now emerging. Advances in physical and theoretical characterization of H2ase enzymes and synthetic models have proven key to the study of hydrides in particular, and will guide modeling efforts toward more robust and active species optimized for practical applications.

Tyrosine-Coordinated P-Cluster in G. diazotrophicus Nitrogenase: Evidence for the Importance of O-Based Ligands in Conformationally Gated Electron Transfer

The P-cluster is a unique iron-sulfur center that likely functions as a dynamic electron (e(-)) relay site between the Fe-protein and the catalytic FeMo-cofactor in nitrogenase. The P-cluster has been shown to undergo large conformational changes upon 2-e(-) oxidation which entail the coordination of two of the Fe centers to a Ser side chain and a backbone amide N, respectively. Yet, how and if this 2-e(-) oxidized state (P(OX)) is involved in catalysis by nitrogenase is not well established. Here, we present the crystal structures of reduced and oxidized MoFe-protein (MoFeP) from Gluconacetobacter diazotrophicus (Gd), which natively possesses an Ala residue in the position of the Ser ligand to the P-cluster. While reduced Gd-MoFeP is structurally identical to previously characterized counterparts around the FeMo-cofactor, oxidized Gd-MoFeP features an unusual Tyr coordination to its P-cluster along with ligation by a backbone amide nitrogen. EPR analysis of the oxidized Gd-MoFeP P-cluster confirmed that it is a 2-e(-) oxidized, integer-spin species. Importantly, we have found that the sequence positions corresponding to the Ser and Tyr ligands are almost completely covariant among Group I nitrogenases. These findings strongly support the possibility that the P(OX) state is functionally relevant in nitrogenase catalysis and that a hard, O-based anionic ligand serves to stabilize this state in a switchable fashion.

Exploring Electron/Proton Transfer and Conformational Changes in the Nitrogenase MoFe Protein and FeMo-cofactor Through Cryoreduction/EPR Measurements

We combine cryoreduction/annealing/EPR measurements of nitrogenase MoFe protein with results of earlier investigations to provide a detailed view of the electron/proton transfer events and conformational changes that occur during early stages of [e^-/H⁺] accumulation by the MoFe protein. This includes reduction of (i) the non-catalytic state of the iron-molybdenum cofactor (FeMo-co) active site that is generated by chemical oxidation of the resting-state cofactor (S = 3/2)) within resting MoFe (E₀), and (ii) the catalytic state that has accumulated n =1 [e^-/H⁺] above the resting-state level, denoted E₁(1H) (S ≥ 1) in the Lowe-Thorneley kinetic scheme. FeMo-co does not undergo a major change of conformation during reduction of oxidized FeMo-co. In contrast, FeMo-co undergoes substantial conformational changes during the reduction of E₀ to E₁(1H), and of E₁(1H) to E₂(2H) (n = 2; S = 3/2). The experimental results further suggest that the E₁(1H) → E₂(2H) step involves coupled delivery of a proton and electron (PCET) to FeMo-co of E₁(H) to generate a non-equilibrium S = ½ form E₂(2H)*. This subsequently undergoes conformational relaxation and attendant change in FeMo-co spin state, to generate the equilibrium E₂(2H) (S = 3/2) state. Unexpectedly, these experiments also reveal conformational coupling between FeMo-co and P-cluster, and between Fe protein binding and FeMo-co, which might play a role in gated ET from reduced Fe protein to FeMo-co.

Is Trehalose an Effective Quenching Agent of Azotobacter vinelandii Mo-Nitrogenase Turnover?

H₂-evolution assays, plus EPR and FTIR spectroscopies, using CO-inhibited Azotobacter vinelandii Mo-nitrogenase have shown that the disaccharide trehalose is an effective quenching agent of enzymatic turnover and also stabilizes the reaction intermediates formed. Complete inhibition of H₂-evolution activity was achieved at 1.5 M trehalose, which compares favorably to the requirement for 10 M ethylene glycol to achieve similar inhibition. Reaction-intermediate stabilization was demonstrated by monitoring the EPR spectrum of the 'hi-CO' form of CO-inhibited N₂ase, which did not change during 1 hr after trehalose quenching. Similarly, in situ photolysis with FTIR monitoring of 'hi-CO' resulted in the same 1973 and 1681 cm^-1 signals as observed previously in ethylene glycol-quenched systems. [a] These results clearly show that 1.5 M trehalose is an effective quench and stabilization agent for Mo-N₂ase studies. Possible applications are discussed.

Catalytic transformation of dinitrogen into ammonia and hydrazine by iron-dinitrogen complexes bearing pincer ligand

Synthesis and reactivity of iron-dinitrogen complexes have been extensively studied, because the iron atom plays an important role in the industrial and biological nitrogen fixation. As a result, iron-catalyzed reduction of molecular dinitrogen into ammonia has recently been achieved. Here we show that an iron-dinitrogen complex bearing an anionic PNP-pincer ligand works as an effective catalyst towards the catalytic nitrogen fixation, where a mixture of ammonia and hydrazine is produced. In the present reaction system, molecular dinitrogen is catalytically and directly converted into hydrazine by using transition metal-dinitrogen complexes as catalysts. Because hydrazine is considered as a key intermediate in the nitrogen fixation in nitrogenase, the findings described in this paper provide an opportunity to elucidate the reaction mechanism in nitrogenase.

Converting dinitrogen into other nitrogen compounds such as ammonia is a difficult task, especially under mild conditions. Here, the authors report a molecular iron complex capable of reducing dinitrogen to both ammonia and hydrazine in a catalytic process.

Evidence That the Pi Release Event Is the Rate-Limiting Step in the Nitrogenase Catalytic Cycle

Nitrogenase reduction of dinitrogen (N2) to ammonia (NH3) involves a sequence of events that occur upon the transient association of the reduced Fe protein containing two ATP molecules with the MoFe protein that includes electron transfer, ATP hydrolysis, Pi release, and dissociation of the oxidized, ADP-containing Fe protein from the reduced MoFe protein. Numerous kinetic studies using the nonphysiological electron donor dithionite have suggested that the rate-limiting step in this reaction cycle is the dissociation of the Fe protein from the MoFe protein. Here, we have established the rate constants for each of the key steps in the catalytic cycle using the physiological reductant flavodoxin protein in its hydroquinone state. The findings indicate that with this reductant, the rate-limiting step in the reaction cycle is not protein-protein dissociation or reduction of the oxidized Fe protein, but rather events associated with the Pi release step. Further, it is demonstrated that (i) Fe protein transfers only one electron to MoFe protein in each Fe protein cycle coupled with hydrolysis of two ATP molecules, (ii) the oxidized Fe protein is not reduced when bound to MoFe protein, and (iii) the Fe protein interacts with flavodoxin using the same binding interface that is used with the MoFe protein. These findings allow a revision of the rate-limiting step in the nitrogenase Fe protein cycle.

Insight into the Iron-Molybdenum Cofactor of Nitrogenase from Synthetic Iron Complexes with Sulfur, Carbon, and Hydride Ligands

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.

Stepwise N-H Bond Formation From N2-Derived Iron Nitride, Imide and Amide Intermediates to Ammonia

Reduction of N₂ to ammonia in nature and in electrocatalysis takes place through 1-proton/1-electron steps, motivating efforts to experimentally study the steps during proton/electron transfer to well-characterized N₂-derived species with bridging nitrides. We report here the protonation and reduction reactions of an N₂-derived iron bis(nitride) complex (Rodriguez et al., Science, 2011, 334, 780). We isolate and definitively characterize triiron imido and amido intermediates that lie along the path to ammonia formation, and Mössbauer spectroscopy shows the oxidation level of iron atoms in these mixed-valence clusters. The first two H atoms add to one of the two nitrides of the bis(nitride) complex, and the proton-coupled electron transfer in the second step can be concerted or stepwise depending on the sources of protons and electrons. The characterization of partially protonated nitrides and their mechanisms of formation are expected to guide efforts to convert N₂ to ammonia with mild acids.

Abiotic variables affect STX concentration in a meso-oligotrophic subtropical coastal lake dominated by Cylindrospermopsis raciborskii (Cyanophyceae)

The cyanobacterium Cylindrospermopsis raciborskii is capable of producing toxins including saxitoxin (STX). Few studies have verified the influence of environmental variables on the production of STX and most have only been studied in the laboratory. The goal of this work was to identify the abiotic variables related to STX concentration in situ. The relationship among STX concentration and the physical variables, nutrients and chlorophyll-a (chl-a) concentration was examined in a meso-oligotrophic subtropical coastal lake dominated by C. raciborskii. A generalized linear model was developed, incorporating all variables measured monthly over a 45-month monitoring period. Conductivity and dissolved inorganic nitrogen (DIN) concentration provided the greatest explanatory power for STX concentration in situ. Previous studies suggested that C. raciborskii cells exposed to stress associated with higher ionic concentrations appear to activate the biosynthesis of STX suggesting that STX can elicit changes cell permeability and may contribute to the homeostasis of this organism. An increase of DIN concentration results in a higher concentration of STX which may be related to a reduced metabolic demand, since the uptake of inorganic nitrogen requires less energy than N₂-fixation. Thus, increased DIN can favor the growth of C. raciborskii population or improve cellular homeostasis, both potentially increasing STX concentration in the aquatic system, which was observed through a delayed response pattern. The developed model, while providing only a moderate predictive power, can assist in the understanding of the environmental variables associated with increases in STX concentration, and in monitoring and minimizing the risks of toxic blooms.

Nitrogenases-A Tale of Carbon Atom(s)

Named after its ability to catalyze the reduction of nitrogen to ammonia, nitrogenase has a surprising rapport with carbon-both through the interstitial carbide that resides in the central cavity of its cofactor and through its ability to catalyze the reductive carbon-carbon coupling of small carbon compounds into hydrocarbon products. Recently, a radical-SAM-dependent pathway was revealed for the insertion of carbide, which signifies a novel biosynthetic route to complex bridged metalloclusters. Moreover, a sulfur-displacement mechanism was proposed for the activation of carbon monoxide by nitrogenase, which suggests an essential role of the interstitial carbide in maintaining the stability while permitting a certain flexibility of the cofactor structure during substrate turnover.

Mass Spectrometric-Based Selected Reaction Monitoring of Protein Phosphorylation during Symbiotic Signaling in the Model Legume, Medicago truncatula

Unlike the major cereal crops corn, rice, and wheat, leguminous plants such as soybean and alfalfa can meet their nitrogen requirement via endosymbiotic associations with soil bacteria. The establishment of this symbiosis is a complex process playing out over several weeks and is facilitated by the exchange of chemical signals between these partners from different kingdoms. Several plant components that are involved in this signaling pathway have been identified, but there is still a great deal of uncertainty regarding the early events in symbiotic signaling, i.e., within the first minutes and hours after the rhizobial signals (Nod factors) are perceived at the plant plasma membrane. The presence of several protein kinases in this pathway suggests a mechanism of signal transduction via posttranslational modification of proteins in which phosphate is added to the hydroxyl groups of serine, threonine and tyrosine amino acid side chains. To monitor the phosphorylation dynamics and complement our previous untargeted 'discovery' approach, we report here the results of experiments using a targeted mass spectrometric technique, Selected Reaction Monitoring (SRM) that enables the quantification of phosphorylation targets with great sensitivity and precision. Using this approach, we confirm a rapid change in the level of phosphorylation in 4 phosphosites of at least 4 plant phosphoproteins that have not been previously characterized. This detailed analysis reveals aspects of the symbiotic signaling mechanism in legumes that, in the long term, will inform efforts to engineer this nitrogen-fixing symbiosis in important non-legume crops such as rice, wheat and corn.

Nitrogenase-mimic iron-containing chalcogels for photochemical reduction of dinitrogen to ammonia

A nitrogenase-inspired biomimetic chalcogel system comprising double-cubane [Mo2Fe6S8(SPh)3] and single-cubane (Fe4S4) biomimetic clusters demonstrates photocatalytic N2 fixation and conversion to NH3 in ambient temperature and pressure conditions. Replacing the Fe4S4 clusters in this system with other inert ions such as Sb(3+), Sn(4+), Zn(2+) also gave chalcogels that were photocatalytically active. Finally, molybdenum-free chalcogels containing only Fe4S4 clusters are also capable of accomplishing the N2 fixation reaction with even higher efficiency than their Mo2Fe6S8(SPh)3-containing counterparts. Our results suggest that redox-active iron-sulfide-containing materials can activate the N2 molecule upon visible light excitation, which can be reduced all of the way to NH3 using protons and sacrificial electrons in aqueous solution. Evidently, whereas the Mo2Fe6S8(SPh)3 is capable of N2 fixation, Mo itself is not necessary to carry out this process. The initial binding of N2 with chalcogels under illumination was observed with in situ diffuse-reflectance Fourier transform infrared spectroscopy (DRIFTS). (15)N2 isotope experiments confirm that the generated NH3 derives from N2 Density functional theory (DFT) electronic structure calculations suggest that the N2 binding is thermodynamically favorable only with the highly reduced active clusters. The results reported herein contribute to ongoing efforts of mimicking nitrogenase in fixing nitrogen and point to a promising path in developing catalysts for the reduction of N2 under ambient conditions.

Interplay between Theory and Experiment for Ammonia Synthesis Catalyzed by Transition Metal Complexes

Nitrogen fixation is an essential chemical process both biologically and industrially. Since the discovery of the first transition-metal-dinitrogen complex in 1965, a great deal of effort has been devoted to the development of artificial nitrogen fixation systems that work under mild reaction conditions. However, the transformation of chemically inert dinitrogen using homogeneous catalysts is still challenging because of the difficulty in breaking the strong triple bond of dinitrogen, and a very limited number of transition metal complexes have exhibited the catalytic activity for the direct transformation of dinitrogen into ammonia with low turnover numbers. To develop more effective nitrogen fixation systems, it is necessary to retrieve as much information as possible from the limited successful examples. Computational chemistry will provide valuable insights in the understanding of the reaction mechanisms involving unstable intermediates that are hard to isolate or characterize. We have been applying it for clarifying detailed mechanisms of dinitrogen activation and functionalization by transition metal complexes as well as for designing new catalysts for more effective nitrogen fixation. This Account summarizes recent progress in the elucidation of catalytic mechanisms of nitrogen fixation by using mono- and dinuclear molybdenum complexes, as well as cubane-type metal-sulfido clusters from a theoretical point of view. First, we briefly introduce experimental and theoretical contributions to the elucidation of the reaction mechanism of nitrogen fixation catalyzed by a mononuclear Mo-triamidoamine complex. Special attention is paid to our recent studies on Mo-catalyzed nitrogen fixation using dinitrogen-bridged dimolybdenum complexes. A possible catalytic mechanism is proposed based on theoretical and experimental investigations. The catalytic mechanism involves the formation of a monuclear molybdenum-nitride (Mo≡N) intermediate, as well as the regeneration of a dimolybdenum intermediate with the Mo-N≡N-Mo moiety. Comparison of the reactivity of di- and monomolybdenum complexes suggests that the dimolybdenum structure is essential for the catalytic activity. Synergy between the two Mo cores connected with a bridging N2 ligand is observed in the protonation of coordinated N2. Intermetallic electron transfer through the bridging N2 ligand reductively activates the coordinated N2 to be protonated. On the basis of the proposed catalytic mechanism, we used DFT calculations for rational design of dimolybdenum complexes serving as more effective catalysts for nitrogen fixation. Newly prepared dimolybdenum complexes with modified PNP-type pincer ligands exhibit greater catalytic activity than the original one.

Light-driven dinitrogen reduction catalyzed by a CdS:nitrogenase MoFe protein biohybrid

The splitting of dinitrogen (N2) and reduction to ammonia (NH3) is a kinetically complex and energetically challenging multistep reaction. In the Haber-Bosch process, N2 reduction is accomplished at high temperature and pressure, whereas N2 fixation by the enzyme nitrogenase occurs under ambient conditions using chemical energy from adenosine 5'-triphosphate (ATP) hydrolysis. We show that cadmium sulfide (CdS) nanocrystals can be used to photosensitize the nitrogenase molybdenum-iron (MoFe) protein, where light harvesting replaces ATP hydrolysis to drive the enzymatic reduction of N2 into NH3 The turnover rate was 75 per minute, 63% of the ATP-coupled reaction rate for the nitrogenase complex under optimal conditions. Inhibitors of nitrogenase (i.e., acetylene, carbon monoxide, and dihydrogen) suppressed N2 reduction. The CdS:MoFe protein biohybrids provide a photochemical model for achieving light-driven N2 reduction to NH3.

Expression of a functional oxygen-labile nitrogenase component in the mitochondrial matrix of aerobically grown yeast

The extreme sensitivity of nitrogenase towards oxygen stands as a major barrier to engineer biological nitrogen fixation into cereal crops by direct nif gene transfer. Here, we use yeast as a model of eukaryotic cell and show that aerobically grown cells express active nitrogenase Fe protein when the NifH polypeptide is targeted to the mitochondrial matrix together with the NifM maturase. Co-expression of NifH and NifM with Nif-specific Fe-S cluster biosynthetic proteins NifU and NifS is not required for Fe protein activity, demonstrating NifH ability to incorporate endogenous mitochondrial Fe-S clusters. In contrast, expression of active Fe protein in the cytosol requires both anoxic growth conditions and co-expression of NifH and NifM with NifU and NifS. Our results show the convenience of using mitochondria to host nitrogenase components, thus providing instrumental technology for the grand challenge of engineering N2-fixing cereals.

A Synthetic Single-Site Fe Nitrogenase: High Turnover, Freeze-Quench (57)Fe Mössbauer Data, and a Hydride Resting State

The mechanisms of the few known molecular nitrogen-fixing systems, including nitrogenase enzymes, are of much interest but are not fully understood. We recently reported that Fe-N2 complexes of tetradentate P3(E) ligands (E = B, C) generate catalytic yields of NH3 under an atmosphere of N2 with acid and reductant at low temperatures. Here we show that these Fe catalysts are unexpectedly robust and retain activity after multiple reloadings. Nearly an order of magnitude improvement in yield of NH3 for each Fe catalyst has been realized (up to 64 equiv of NH3 produced per Fe for P3(B) and up to 47 equiv for P3(C)) by increasing acid/reductant loading with highly purified acid. Cyclic voltammetry shows the apparent onset of catalysis at the P3(B)Fe-N2/P3(B)Fe-N2(-) couple and controlled-potential electrolysis of P3(B)Fe(+) at -45 °C demonstrates that electrolytic N2 reduction to NH3 is feasible. Kinetic studies reveal first-order rate dependence on Fe catalyst concentration (P3(B)), consistent with a single-site catalyst model. An isostructural system (P3(Si)) is shown to be appreciably more selective for hydrogen evolution. In situ freeze-quench Mössbauer spectroscopy during turnover reveals an iron-borohydrido-hydride complex as a likely resting state of the P3(B)Fe catalyst system. We postulate that hydrogen-evolving reaction activity may prevent iron hydride formation from poisoning the P3(B)Fe system. This idea may be important to consider in the design of synthetic nitrogenases and may also have broader significance given that intermediate metal hydrides and hydrogen evolution may play a key role in biological nitrogen fixation.

X-ray Absorption and Emission Spectroscopic Studies of [L2Fe2S2](n) Model Complexes: Implications for the Experimental Evaluation of Redox States in Iron-Sulfur Clusters

Herein, a systematic study of [L2Fe2S2](n) model complexes (where L = bis(benzimidazolato) and n = 2-, 3-, 4-) has been carried out using iron and sulfur K-edge X-ray absorption (XAS) and iron Kβ and valence-to-core X-ray emission spectroscopies (XES). These data are used as a test set to evaluate the relative strengths and weaknesses of X-ray core level spectroscopies in assessing redox changes in iron-sulfur clusters. The results are correlated to density functional theory (DFT) calculations of the spectra in order to further support the quantitative information that can be extracted from the experimental data. It is demonstrated that due to canceling effects of covalency and spin state, the information that can be extracted from Fe Kβ XES mainlines is limited. However, a careful analysis of the Fe K-edge XAS data shows that localized valence vs delocalized valence species may be differentiated on the basis of the pre-edge and K-edge energies. These findings are then applied to existing literature Fe K-edge XAS data on the iron protein, P-cluster, and FeMoco sites of nitrogenase. The ability to assess the extent of delocalization in the iron protein vs the P-cluster is highlighted. In addition, possible charge states for FeMoco on the basis of Fe K-edge XAS data are discussed. This study provides an important reference for future X-ray spectroscopic studies of iron-sulfur clusters.