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Binding of N 2 by the FeMo-cofactor of nitrogenase is believed to occur after transfer of 4 e - and 4 H + equivalents to the active site. Although pulse EPR studies indicate the presence of two Fe-(μ-H)-Fe moieties, the structural and electronic features of this mixed valent intermediate remain poorly understood. Toward an improved understanding of this bioorganometallic cluster, we report herein that diiron μ-carbyne complex (P 6 ArC)Fe 2 (μ-H) can be oxidized and reduced, allowing for the first time spectral characterization of two EPR-active Fe(μ-C)(μ-H)Fe model complexes linked by a 2 e - transfer which bear some resemblance to a pair of E n and E n +2 states of nitrogenase. Both species populate S = 1/2 states at low temperatures, and the influence of valence (de)localization on the spectroscopic signature of the μ-hydride ligand was evaluated by pulse EPR studies. Compared to analogous data for the {Fe 2 (μ-H)} 2 state of FeMoco (E 4 (4H)), the data and analysis presented herein suggest that the hydride ligands in E 4 (4H) bridge isovalent (most probably Fe III ) metal centers. Although electron transfer involves metal-localized orbitals, investigations of [(P 6 ArC)Fe 2 (μ-H)] +1 and [(P 6 ArC)Fe 2 (μ-H)] -1 by pulse EPR revealed that redox chemistry induces significant changes in Fe-C covalency (-50% upon 2 e - reduction), a conclusion further supported by X-ray absorption spectroscopy, 57 Fe Mössbauer studies, and DFT calculations. Combined, our studies demonstrate that changes in covalency buffer against the accumulation of excess charge density on the metals by partially redistributing it to the bridging carbon, thereby facilitating multielectron transformations.

X-ray crystallography is the main source of atomistic information on the structure of proteins. Normal crystal structures are obtained as a compromise between the X-ray scattering data and a set of empirical restraints that ensure chemically reasonable bond lengths and angles. However, such restraints are not always available or accurate for nonstandard parts of the structure, for example substrates, inhibitors and metal sites. The method of quantum refinement, in which these empirical restraints are replaced by quantum-mechanical (QM) calculations, has previously been suggested for small but interesting parts of the protein. Here, this approach is extended to allow for multiple conformations in the QM region by performing separate QM calculations for each conformation. This approach is shown to work properly and leads to improved structures in terms of electron-density maps and real-space difference density Z-scores. It is also shown that the quality of the structures can be gauged using QM strain energies. The approach, called ComQumX-2QM, is applied to the P-cluster in two different crystal structures of the enzyme nitrogenase, i.e. an Fe 8 S 7 Cys 6 cluster, used for electron transfer. One structure is at a very high resolution (1.0 Å) and shows a mixture of two different oxidation states, the fully reduced P N state (Fe 8 2+ , 20%) and the doubly oxidized P 2+ state (80%). In the original crystal structure the coordinates differed for only two iron ions, but here it is shown that the two states also show differences in other atoms of up to 0.7 Å. The second structure is at a more modest resolution, 2.1 Å, and was originally suggested to show only the one-electron oxidized state, P 1+ . Here, it is shown that it is rather a 50/50% mixture of the P 1+ and P 2+ states and that many of the Fe-Fe and Fe-S distances in the original structure were quite inaccurate (by up to 0.8 Å). This shows that the new ComQumX-2QM approach can be used to sort out what is actually seen in crystal structures with dual conformations and to give locally improved coordinates., (open access.)

Biological nitrogen fixation is catalyzed by the enzyme nitrogenase. Two forms of this metalloenzyme, the vanadium (V)- and iron (Fe)-only nitrogenases, were recently found to reduce small amounts of carbon dioxide (CO 2 ) into the potent greenhouse gas methane (CH 4 ). Here, we report carbon ( 13 C/ 12 C) and hydrogen ( 2 H/ 1 H) stable isotopic compositions and fractionations of methane generated by V- and Fe-only nitrogenases in the metabolically versatile nitrogen fixer Rhodopseudomonas palustris The stable carbon isotope fractionation imparted by both forms of alternative nitrogenase are within the range observed for hydrogenotrophic methanogenesis ( 13 α CO2/CH4 = 1.051 ± 0.002 for V-nitrogenase and 1.055 ± 0.001 for Fe-only nitrogenase; values are means ± standard errors). In contrast, the hydrogen isotope fractionations ( 2 α H2O/CH4 = 2.071 ± 0.014 for V-nitrogenase and 2.078 ± 0.018 for Fe-only nitrogenase) are the largest of any known biogenic or geogenic pathway. The large 2 α H2O/CH4 shows that the reaction pathway nitrogenases use to form methane strongly discriminates against 2 H, and that 2 α H2O/CH4 distinguishes nitrogenase-derived methane from all other known biotic and abiotic sources. These findings on nitrogenase-derived methane will help constrain carbon and nitrogen flows in microbial communities and the role of the alternative nitrogenases in global biogeochemical cycles. IMPORTANCE All forms of life require nitrogen for growth. Many different kinds of microbes living in diverse environments make inert nitrogen gas from the atmosphere bioavailable using a special enzyme, nitrogenase. Nitrogenase has a wide substrate range, and, in addition to producing bioavailable nitrogen, some forms of nitrogenase also produce small amounts of the greenhouse gas methane. This is different from other microbes that produce methane to generate energy. Until now, there was no good way to determine when microbes with nitrogenases are making methane in nature. Here, we present an isotopic fingerprint that allows scientists to distinguish methane from microbes making it for energy versus those making it as a by-product of nitrogen acquisition. With this new fingerprint, it will be possible to improve our understanding of the relationship between methane production and nitrogen acquisition in nature., (Copyright © 2020 Luxem et al.)

We report an organic redox-polymer-based electroenzymatic nitrogen fixation system using a metal-free redox polymer, namely neutral-red-modified poly(glycidyl methacrylate-co-methylmethacrylate-co-poly(ethyleneglycol)methacrylate) with a low redox potential of -0.58 V vs. SCE. The stable and efficient electric wiring of nitrogenase within the redox polymer matrix enables mediated bioelectrocatalysis of N 3 - , NO 2 - and N 2 to NH 3 catalyzed by the MoFe protein via the polymer-bound redox moieties distributed in the polymer matrix in the absence of the Fe protein. Bulk bioelectrosynthetic experiments produced 209±30 nmol NH 3  nmol MoFe -1  h -1 from N 2 reduction. 15 N 2 labeling experiments and NMR analysis were performed to confirm biosynthetic N 2 reduction to NH 3 ., (© 2020 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.)

Recently, a crystal structure of V-nitrogenase was presented, showing that one of the µ 2 sulphide ions in the active site (S2B) is replaced by a lighter atom, suggested to be NH or NH 2 , i.e. representing a reaction intermediate. Moreover, a sulphur atom is found 7 Å from the S2B site, suggested to represent a storage site for this ion when it is displaced. We have re-evaluated this structure with quantum refinement, i.e. standard crystallographic refinement in which the empirical restraints (employed to ensure that the final structure makes chemical sense) are replaced by more accurate quantum-mechanical calculations. This allows us to test various interpretations of the structure, employing quantum-mechanical calculations to predict the ideal structure and to use crystallographic measures like the real-space Z-score and electron-density difference maps to decide which structure fits the crystallographic raw data best. We show that the structure contains an OH - -bound state, rather than an N 2 -derived reaction intermediate. Moreover, the structure shows dual conformations in the active site with ~ 14% undissociated S2B ligand, but the storage site seems to be fully occupied, weakening the suggestion that it represents a storage site for the dissociated ligand.

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 CO 2 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 CO 3 2- or NO 3 - 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 CO 3 2- or NO 3 - ligand, three different redox states, and multiple broken-symmetry states. We find that only a [VFe 7 S 8 C(CO 3 )] 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 [VFe 7 S 8 C(CO 3 )] 2- BS7-235 model is compared to our [MoFe 7 S 9 C] - 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 E 1 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.

Nitrogen (N) is used in many of life's fundamental biomolecules, and it is also a participant in environmental redox chemistry. Biogeochemical processes control the amount and form of N available to organisms ("fixed" N). These interacting processes result in N acting as the proximate limiting nutrient in most surface environments. Here, we review the global biogeochemical cycle of N and its anthropogenic perturbation. We introduce important reservoirs and processes affecting N in the environment, focusing on the ocean, in which N cycling is more generalizable than in terrestrial systems, which are more heterogeneous. Particular attention is given to processes that create and destroy fixed N because these comprise the fixed N input/output budget, the most universal control on environmental N availability. We discuss preindustrial N budgets for terrestrial and marine systems and their modern-day alteration by N inputs from human activities. We summarize evidence indicating that the simultaneous roles of N as a required biomass constituent and an environmental redox intermediate lead to stabilizing feedbacks that tend to blunt the impact of N cycle perturbations at larger spatiotemporal scales, particularly in marine systems. As a result of these feedbacks, the anthropogenic "N problem" is distinct from the "carbon dioxide problem" in being more local and less global, more immediate and less persistent.

Nitrogenase is the enzyme that catalyzes biological N 2 reduction to NH 3 . This enzyme achieves an impressive rate enhancement over the uncatalyzed reaction. Given the high demand for N 2 fixation to support food and chemical production and the heavy reliance of the industrial Haber-Bosch nitrogen fixation reaction on fossil fuels, there is a strong need to elucidate how nitrogenase achieves this difficult reaction under benign conditions as a means of informing the design of next generation synthetic catalysts. This Review summarizes recent progress in addressing how nitrogenase catalyzes the reduction of an array of substrates. New insights into the mechanism of N 2 and proton reduction are first considered. This is followed by a summary of recent gains in understanding the reduction of a number of other nitrogenous compounds not considered to be physiological substrates. Progress in understanding the reduction of a wide range of C-based substrates, including CO and CO 2 , is also discussed, and remaining challenges in understanding nitrogenase substrate reduction are considered.

Biological nitrogen fixation is catalyzed by the enzyme nitrogenase, which facilitates the cleavage of the relatively inert triple bond of N 2 . 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.

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 N 2 to 2NH 3 . 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.

The reduction of dinitrogen to ammonia by nitrogenase reflects a complex choreography involving two component proteins, MgATP and reductant. At center stage of this process resides the active site cofactor, a complex metallocluster organized around a trigonal prismatic arrangement of iron sites surrounding an interstitial carbon. As a consequence of the choreography, electrons and protons are delivered to the active site for transfer to the bound N 2 . While the detailed mechanism for the substrate reduction remains enigmatic, recent developments highlight the role of hydrides and the privileged role for two irons of the trigonal prism in the binding of exogenous ligands. Outstanding questions concern the precise nature of the intermediates between N 2 and NH 3 , and whether the cofactor undergoes significant rearrangement during turnover; resolution of these issues will require the convergence of biochemistry, structure, spectroscopy, computation, and model chemistry.

Nitrogenase is the only enzyme capable of reducing N 2 to NH 3 . This challenging reaction requires the coordinated transfer of multiple electrons from the reductase, Fe-protein, to the catalytic component, MoFe-protein, in an ATP-dependent fashion. In the last two decades, there have been significant advances in our understanding of how nitrogenase orchestrates electron transfer (ET) from the Fe-protein to the catalytic site of MoFe-protein and how energy from ATP hydrolysis transduces the ET processes. In this review, we summarize these advances, with focus on the structural and thermodynamic redox properties of nitrogenase component proteins and their complexes, as well as on new insights regarding the mechanism of ET reactions during catalysis and how they are coupled to ATP hydrolysis. We also discuss recently developed chemical, photochemical, and electrochemical methods for uncoupling substrate reduction from ATP hydrolysis, which may provide new avenues for studying the catalytic mechanism of nitrogenase.

Transition metal-sulfur (M-S) compounds are an indispensable means for biological systems to convert N 2 into NH 3 (biological N 2 fixation), and these may have emerged by chemical evolution from a prebiotic N 2 fixation system. With a main focus on synthetic species, this article provides a comprehensive review of the chemistry of M-S compounds related to the conversion of N 2 and the structures/functions of the nitrogenase cofactors. Three classes of M-S compounds are highlighted here: multinuclear M-S clusters structurally or functionally relevant to the nitrogenase cofactors, mono- and dinuclear transition metal complexes supported by sulfur-containing ligands in N 2 and N 2 H x ( x = 2, 4) chemistry, and metal sulfide-based solid materials employed in the reduction of N 2 . Fair assessments on these classes of compounds revealed that our understanding is still limited in N 2 reduction and related substrate reductions. Our aims of this review are to compile a collection of studies performed at atomic to mesoscopic scales and to present potential opportunities for elucidating the roles of metal and sulfur atoms in the biological N 2 fixation that might be helpful for the development of functional materials.

Three different types of electron-transferring metallo-ATPases are able to couple ATP hydrolysis to the reduction of low-potential metal sites, thereby energizing an electron. Besides the Fe-protein known from nitrogenase and homologous enzymes, two other kinds of ATPase with different scaffolds and cofactors are used to achieve a unidirectional, energetic, uphill electron transfer to either reduce inactive Co-corrinoid-containing proteins (RACE-type activators) or a second iron-sulfur cluster-containing enzyme of a unique radical enzymes family (archerases). We have found a new cofactor in the latter enzyme family, that is, a double-cubane cluster with two [4Fe4S] subclusters bridged by a sulfido ligand. An enzyme containing this cofactor catalyzes the ATP-dependent reduction of small molecules, including acetylene. Thus, enzymes containing the double-cubane cofactor are analogous in function and share some structural features with nitrogenases., (© 2020 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.)

The active site of the nitrogen-fixing enzyme Mo-nitrogenase is the M cluster ([MoFe 7 S 9 C⋅R-homocitrate]), also known as the FeMo cofactor or FeMoco. The biosynthesis of this highly complex metallocluster involves a series of proteins. Among them, NifB, a radical-SAM enzyme, is instrumental in the assembly of the L cluster ([Fe 8 S 9 C]), a precursor and all-iron core of the M cluster. In the absence of sulfite, NifB assembles a precursor form of the L cluster called the L* cluster ([Fe 8 S 8 C]), which lacks the final ninth sulfur. EPR and MCD spectroscopies are used to probe the electronic structures of the paramagnetic, oxidized forms of both the L and L* clusters, labeled L Ox and [L*] Ox . This study shows that both L Ox and [L*] Ox have nearly identical EPR and MCD spectra, thus suggesting that the two clusters have identical structures upon oxidation; in other words, a sulfur migrates away from L Ox following oxidation, thereby rendering the cluster identical to [L*] Ox . It is proposed that a similar migration could occur to the M cluster upon oxidation, and that this is an instrumental part of both M cluster formation and nitrogenase substrate/inhibitor binding., (© 2019 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.)

The nitrogenase superfamily constitutes a large and diverse ensemble of two-component metalloenzymes. These systems couple the hydrolysis of ATP to the reduction of disparate substrates from diatomic gases (Mo and alternative nitrogenases) to photosynthetic pigments (protochlorophyllide and chlorophyllide oxidoreductases). Only very recently have the activities of the highly divergent and paraphyletic Group IV nitrogenases begun to be uncovered. This review highlights the first characterized member of this group, which was found to catalyze an unprecedented reaction in the coenzyme F430 biosynthetic pathway, and the catalytic potential of a superfamily that has yet to be fully explored., (© 2020 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.)

The chemical mechanism of nitrogenase, catalysing N 2 +8 e+8 H + →2 NH 3 +H 2 , occurs at a large multi-metal cluster (FeMo-co) with composition CFe 7 MoS 9 (homocitrate). More than 20 steps are required. Experimental elucidation of this mechanism is elusive, for various reasons, and computational approaches have a valuable role. This review critically surveys recent density functional calculations of the coordination chemistry and relevant reactions of FeMo-co within the protein surrounds. Topics covered include the accuracies and validation of the density functionals, the treatment of electronic structure, and the chemical models used. The components of mechanism are described, including the input of N 2 , proton supply, the egress of NH 3 , and the roles of surrounding protein. This leads to descriptions and evaluations of the overall mechanistic cycles proposed on the basis of density functional calculations. Finally, I discuss some current issues, and consider the outlook for further work., (© 2019 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Early work with viologen-mediated nitrogenase bio-electrochemistry focused on bio-electrocatalysis with the enzyme in solution, but biocatalyst immobilization at electrode surfaces is favorable as it provides a high effective concentration of biocatalyst at the electrode surface. We have used a pyrene-peptide linker as a method for immobilizing nitrogenase on carbon electrode surfaces for nitrogenase bio-electrocatalysis., (© 2019 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.)

The nitrogenase superfamily comprises homologous enzyme systems that carry out fundamentally important processes, including the reduction of N 2 and CO, and the biosynthesis of bacteriochlorophyll and coenzyme F430. This special issue provides a cross-disciplinary overview of the ongoing research in this highly diverse and unique research area of metalloprotein biochemistry., (© 2020 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Nitrogenases catalyze the ambient reduction of N 2 and CO at its cofactor site. Herein we present a biochemical and spectroscopic characterization of an Azotobacter vinelandii V nitrogenase variant expressing a citrate-substituted cofactor. Designated VnfDGK Cit , the catalytic component of this V nitrogenase variant has an αβ 2 (δ) subunit composition and carries an 8Fe P* cluster and a citrate-substituted V cluster analogue in the αβ dimer, as well as a 4Fe cluster in the "orphaned" β-subunit. Interestingly, when normalized based on the amount of cofactor, VnfDGK Cit shows a shift of N 2 reduction from H 2 evolution toward NH 3 formation and an opposite shift of CO reduction from hydrocarbon formation toward H 2 evolution. These observations point to a role of the organic ligand in proton delivery during catalysis and imply the use of different reaction sites/mechanisms by nitrogenase for different substrate reductions. Moreover, the increased NH 3 /H 2 ratio upon citrate substitution suggests the possibility to modify the organic ligand for improved ammonia synthesis in the future., (© 2019 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.)

The engineering of transgenic organisms with the ability to fix nitrogen is an attractive possibility. However, oxygen sensitivity of nitrogenase, mainly conferred by the reductase component (NifH) 2 , is an imminent problem. Nitrogenase-like enzymes involved in coenzyme F 430 and chlorophyll biosynthesis utilize the highly homologous reductases (CfbC) 2 and (ChlL) 2 , respectively. Chimeric protein-protein interactions of these reductases with the catalytic component of nitrogenase (MoFe protein) did not support nitrogenase activity. Nucleotide-dependent association and dissociation of these complexes was investigated, but (CfbC) 2 and wild-type (ChlL) 2 showed no modulation of the binding affinity. By contrast, the interaction between the (ChlL) 2 mutant Y127S and the MoFe protein was markedly increased in the presence of ATP (or ATP analogues) and reduced in the ADP state. Upon formation of the octameric (ChlL) 2 MoFe(ChlL) 2 complex, the ATPase activity of this variant is triggered, as seen in the homologous nitrogenase system. Thus, the described reductase(s) might be an attractive tool for further elucidation of the diverse functions of (NifH) 2 and the rational design of a more robust reductase., (© 2020 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.)

The nitrogenase metalloenzyme family, essential for supplying fixed nitrogen to the biosphere, is one of life's key biogeochemical innovations. The three forms of nitrogenase differ in their metal dependence, each binding either a FeMo-, FeV-, or FeFe-cofactor where the reduction of dinitrogen takes place. The history of nitrogenase metal dependence has been of particular interest due to the possible implication that ancient marine metal availabilities have significantly constrained nitrogenase evolution over geologic time. Here, we reconstructed the evolutionary history of nitrogenases, and combined phylogenetic reconstruction, ancestral sequence inference, and structural homology modeling to evaluate the potential metal dependence of ancient nitrogenases. We find that active-site sequence features can reliably distinguish extant Mo-nitrogenases from V- and Fe-nitrogenases and that inferred ancestral sequences at the deepest nodes of the phylogeny suggest these ancient proteins most resemble modern Mo-nitrogenases. Taxa representing early-branching nitrogenase lineages lack one or more biosynthetic nifE and nifN genes that both contribute to the assembly of the FeMo-cofactor in studied organisms, suggesting that early Mo-nitrogenases may have utilized an alternate and/or simplified pathway for cofactor biosynthesis. Our results underscore the profound impacts that protein-level innovations likely had on shaping global biogeochemical cycles throughout the Precambrian, in contrast to organism-level innovations that characterize the Phanerozoic Eon., (© 2020 The Authors. Geobiology Published by John Wiley & Sons Ltd.)

We have made a systematic combined quantum mechanical and molecular mechanical (QM/MM) investigation of possible structures of the N 2 bound state of nitrogenase. We assume that N 2 is immediately protonated to a N 2 H 2 state, thereby avoiding the problem of determining the position of the protons in the cluster. We have systematically studied both end-on and side-on structures, as well as both HNNH and NNH 2 states. Our results indicate that the binding of N 2 H 2 is determined more by interactions and steric clashes with the surrounding protein than by the intrinsic preferences of the ligand and the cluster. The best binding mode with both the TPSS and B3LYP density-functional theory methods has trans-HNNH terminally bound to Fe2. It is stabilised by stacking of the substrate with His-195 and Ser-278. However, several other structures come rather close in energy (within 3-35 kJ/mol) at least in some calculations: The corresponding cis-HNNH structure terminally bound to Fe2 is second best with B3LYP. A structure with HNNH 2 terminally bound to Fe6 is second most stable with TPSS (where the third proton is transferred to the substrate from the homocitrate ligand). Structures with trans-HNNH, bound to Fe4 or Fe6, or cis-HNNH bound to Fe6 are also rather stable. Finally, with the TPSS functional, a structure with cis-HNNH side-on binding to the Fe3-Fe4-Fe5-Fe7 face of the cluster is also rather low in energy, but all side-on structures are strongly disfavoured by the B3LYP method.

Nitrogenase is the only enzyme that can cleave the strong triple bond in N 2 . The active site contains a complicated MoFe 7 S 9 C cluster. It is believed that it needs to accept four protons and electrons, forming the E 4 state, before it can bind N 2 . However, there is no consensus on the atomic structure of the E 4 state. Experimental studies indicate that it should contain two hydride ions bridging two pairs of Fe ions, and it has been suggested that both hydride ions as well as the two protons bind on the same face of the cluster. On the other hand, density functional theory (DFT) studies have indicated that it is energetically more favorable with either three hydride ions or with a triply protonated carbide ion, depending on the DFT functional. We have performed a systematic combined quantum mechanical and molecular mechanical (QM/MM) study of possible E 4 states with two bridging hydride ions. Our calculations suggest that the most favorable structure has hydride ions bridging the Fe2/6 and Fe3/7 ion pairs. In fact, such structures are 14 kJ/mol more stable than structures with three hydride ions, showing that pure DFT functionals give energetically most favorable structures in agreement with experiments. An important reason for this finding is that we have identified a new type of broken-symmetry state that involves only two Fe ions with minority spin, in contrast to the previously studied states with three Fe ions with minority spin. The energetically best structures have the two hydride ions on different faces of the FeMo cluster, whereas better agreement with ENDOR data is obtained if they are on the same face; such structures are only 6-22 kJ/mol less stable.

The fixation of atmospheric dinitrogen to ammonia by industrial technologies (such as the Haber Bosch process) has revolutionized humankind. In contrast to industrial technologies, a single enzyme is known for its ability to reduce or "fix" dinitrogen: nitrogenase. Nitrogenase is a complex oxidoreductase enzymatic system that includes a catalytic protein (where dinitrogen is reduced) and an electron-transferring reductase protein (termed the Fe protein) that delivers the electrons necessary for dinitrogen fixation. The catalytic protein most commonly contains a FeMo cofactor (called the MoFe protein), but it can also contain a VFe or FeFe cofactor. Besides their ability to fix dinitrogen to ammonia, these nitrogenases can also reduce substrates such as carbon dioxide to formate. Interestingly, the VFE nitrogenase can also form carbon-carbon bonds. The vast majority of research surrounding nitrogenase employs the Fe protein to transfer electrons, which is also associated with the rate-limiting step of nitrogenase catalysis and also requires the hydrolysis of adenosine triphosphate. Thus, there is significant interest in artificially transferring electrons to the catalytic nitrogenase proteins. In this Account, we review nitrogenase electrocatalysis whereby electrons are delivered to nitrogenase from electrodes. We first describe the use of an electron mediator (cobaltocene) to transfer electrons from electrodes to the MoFe protein. The reduction of protons to molecular hydrogen was realized, in addition to azide and nitrite reduction to ammonia. Bypassing the rate-limiting step within the Fe protein, we also describe how this approach was used to interrogate the rate-limiting step of the MoFe protein: metal-hydride protonolysis at the FeMo-co. This Account next reviews the use of cobaltocene to mediate electron transfer to the VFe protein, where the reduction of carbon dioxide and the formation of carbon-carbon bonds (yielding the formation of ethene and propene) was realized. This approach also found success in mediating electron transfer to the FeFe catalytic protein, which exhibited improved carbon dioxide reduction in comparison to the MoFe protein. In the final example of mediated electron transfer to the catalytic protein, this Account also reviews recent work where the coupling of infrared spectroscopy with electrochemistry enabled the potential-dependent binding of carbon monoxide to the FeMo-co to be studied. As an alternative to mediated electron transfer, recent work that has sought to transfer electrons to the catalytic proteins in the absence of electron mediators (by direct electron transfer) is also reviewed. This approach has subsequently enabled a thermodynamic landscape to be proposed for the cofactors of the catalytic proteins. Finally, this Account also describes nitrogenase electrocatalysis whereby electrons are first transferred from an electrode to the Fe protein, before being transferred to the MoFe protein alongside the hydrolysis of adenosine triphosphate. In this way, increased quantities of ammonia can be electrocatalytically produced from dinitrogen fixation. We discuss how this has led to the further upgrade of electrocatalytically produced ammonia, in combination with additional enzymes (diaphorase, alanine dehydrogenase, and transaminase), to selective production of chiral amine intermediates for pharmaceuticals. This Account concludes by discussing current and future research challenges in the field of electrocatalytic nitrogen fixation by nitrogenase.

The electronic structure of the nitrogenase metal cofactors is central to nitrogen fixation. However, the P-cluster and FeMo cofactor, each containing eight Fe atoms, have eluded detailed characterization of their electronic properties. We report on the low-energy electronic states of the P-cluster in three oxidation states through exhaustive many-electron wavefunction simulations enabled by new theoretical methods. The energy scales of orbital and spin excitations overlap, yielding a dense spectrum with features that we trace to the underlying atomic states and recouplings. The clusters exist in superpositions of spin configurations with non-classical spin correlations, complicating interpretation of magnetic spectroscopies, whereas the charges are mostly localized from reorganization of the cluster and its surroundings. On oxidation, the opening of the P-cluster substantially increases the density of states, which is intriguing given its proposed role in electron transfer. These results demonstrate that many-electron simulations stand to provide new insights into the electronic structure of the nitrogenase cofactors.

Nitrogenase enzymes are the only biological catalysts able to convert N 2 to NH 3 . Molybdenum-dependent nitrogenase consists of two proteins and three metallocofactors that sequentially shuttle eight electrons between three distinct metallocofactors during the turnover of one molecule of N 2 . While the kinetics of isolated nitrogenase has been extensively studied, little is known about the thermodynamics of its cofactors under catalytically relevant conditions. Here, we employ a recently described pyrene-modified linear poly(ethylenimine) hydrogel to immobilize the catalytic protein of nitrogenase onto an electrode surface. The resulting electroenzymatic interface enabled direct measurement of reduction potentials associated with each metallocofactor of the nitrogenase complex, illuminating the role of nitrogenase reductase in altering the potential landscape in the active site of nitrogenase and revealing the endergonic nature of electron-transfer steps associated with the conversion of N 2 to NH 3 under physiological conditions.

Nitrogenase is activated for N 2 reduction through the accumulation of four reducing equivalents at the active-site FeMo-cofactor (FeMo-co: Fe7S9MoC; homocitrate) to form the key Janus intermediate, denoted E 4 (4H), whose lowest-energy structure contains two [Fe-H-Fe] bridging hydrides and two protons bound to the sulfurs that also bridge the Fe pairs. In the critical step of catalysis, a H 2 complex transiently produced by reductive elimination ( re ) of the hydrides of E 4 (4H), denoted E 4 (H 2 ;2H), undergoes H 2 displacement by N 2 , which then undergoes the otherwise energetically unfavorable cleavage of the N≡N triple bond. In pursuing the study of the re activation process, we have employed a photochemical approach to obtaining its atomic-level details. Continuous 450 nm irradiation of the ground state of the dihydride Janus intermediate, denoted E 4 (4H) a , in an EPR cavity at cryogenic temperatures causes photoinduced re of H 2 to generate E 4 (H 2 ;2H). We here extend this photochemical approach with time-resolved EPR studies of the photolysis process on the ns time scale. These studies reveal an additional intermediate in the catalytic reductive elimination process, an isomer of the E 4 (4H) FeMo-co metal-ion core that is formed prior to E 4 (H 2 ;2H) and is thought to be created by breaking an Fe-SH bond, thus further integrating the calculational and structural studies into the experimentally determined mechanism by which nitrogenase is activated to cleave the N≡N triple bond.

The Fe protein of nitrogenase catalyzes the ambient reduction of CO 2 when its cluster is present in the all-ferrous, [Fe 4 S 4 ] 0 oxidation state. Here, we report a combined structural and theoretical study that probes the unique reactivity of the all-ferrous Fe protein toward CO 2 . Structural comparisons of the Azotobacter vinelandii Fe protein in the [Fe 4 S 4 ] 0 and [Fe 4 S 4 ] + states point to a possible asymmetric functionality of a highly conserved Arg pair in CO 2 binding and reduction. Density functional theory (DFT) calculations provide further support for the asymmetric coordination of O by the "proximal" Arg and binding of C to a unique Fe atom of the all-ferrous cluster, followed by donation of protons by the proximate guanidinium group of Arg that eventually results in the scission of a C-O bond. These results provide important mechanistic and structural insights into CO 2 activation by a surface-exposed, scaffold-held [Fe 4 S 4 ] cluster., (© 2019 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Nitrogenases catalyze the reduction of N 2 to NH 4 + at its cofactor site. Designated the M-cluster, this [MoFe 7 S 9 C(R-homocitrate)] cofactor is synthesized via the transformation of a [Fe 4 S 4 ] cluster pair into an [Fe 8 S 9 C] precursor (designated the L-cluster) prior to insertion of Mo and homocitrate. We report the characterization of an eight-iron cofactor precursor (designated the L*-cluster), which is proposed to have the composition [Fe 8 S 8 C] and lack the "9 th sulfur" in the belt region of the L-cluster. Our X-ray absorption and electron spin echo envelope modulation (ESEEM) analyses strongly suggest that the L*-cluster represents a structural homologue to the l-cluster except for the missing belt sulfur. The absence of a belt sulfur from the L*-cluster may prove beneficial for labeling the catalytically important belt region, which could in turn facilitate investigations into the reaction mechanism of nitrogenases., (© 2019 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Simple synthetic compounds with only S and C donors offer a ligation environment similar to the active site of nitrogenase (FeMoco) and thus demonstrate reasonable mechanisms and geometries for N 2 binding and reduction in nature. We recently reported the first example of N 2 binding at a mononuclear iron site supported by only S and C donors. In this work, we report experiments that examine the mechanism of N 2 binding in this system. The reduction of an iron(II) tris(thiolate) complex with 1 equiv of KC 8 leads to a thermally unstable intermediate, and a combination of Mössbauer, EPR, and X-ray absorption spectroscopies identifies it as a high-spin ( S = 3/2) iron(I) species that maintains coordination of all three sulfur atoms. DFT calculations suggest that this iron(I) intermediate has a pseudotetrahedral geometry that resembles the S 3 C iron coordination environment of the belt iron sites in the resting state of the FeMoco. Further reduction to the iron(0) oxidation level under argon causes the dissociation of one of the thiolate donors and gives an η 6 -arene species which reacts with N 2 . Thus, in this system the loss of thiolate and binding of N 2 require reduction beyond the iron(I) level to the iron(0) level. Further reduction of the iron(0)-N 2 complex gives a reactive, formally iron(-I) species. Treatment of the putative iron(-I) complex with weak acids gives low yields of ammonia and hydrazine, demonstrating that these nitrogenase products can be generated from N 2 at a synthetic Fe-S-C site. Catalytic N 2 reduction is not observed, which is attributed to protonation of the supporting ligand and degradation of the complex via ligand dissociation. Identification of the challenges in this system gives insight into the design features needed for functional biomimetic complexes.

We have studied the geometry and electronic structure of the P-cluster in nitrogenase in four oxidation states: P N , P 1+ , P 2+ , and P 3+ . We have employed combined quantum mechanical and molecular mechanical (QM/MM) calculations, using two different density-functional theory methods, TPSS and B3LYP. The calculations confirm that the side chain of Ser-188 is most likely deprotonated in the partly oxidized P 1+ state, thereby forming a bond to Fe6. Likewise, the backbone amide group of Cys-88 is deprotonated in the doubly oxidized P 2+ state, forming a bond to Fe5. The calculations also confirm the two conformations of the P-cluster in the atomic-resolution crystal structure of the enzyme, representing the P N and P 2+ states, but show that the finer differences between the two structures are not fully reflected in the crystal structure, because the coordinates of only two atoms differ between the two conformations. However, the recent crystal structure of the P 1+ state seems to be of lower quality with many dubious Fe-Fe and Fe-S distances. Quantum refinement of this structure indicates that it is a mixture of the P 1+ and P 2+ states but confirms that the side chain of Ser-188 is most likely deprotonated in both states. TPSS gives structures that are appreciably closer to the crystal structures than does B3LYP. In addition, we have studied all 16-48 possible broken-symmetry states of the four oxidation states of the P-cluster with DFT in the one or two observed spin states. For the reduced P N state, we can settle the most likely state from the calculated energies and geometries. However, for the more oxidized states there are large differences in the predictions obtained with the two DFT methods.

We have shown that the key state in N 2 reduction to two NH 3 molecules by the enzyme nitrogenase is E 4 (4H), the "Janus" intermediate, which has accumulated four [e - /H + ] and is poised to undergo reductive elimination of H 2 coupled to N 2 binding and activation. Initial 1 H and 95 Mo ENDOR studies of freeze-trapped E 4 (4H) revealed that the catalytic multimetallic cluster (FeMo-co) binds two Fe-bridging hydrides, [Fe-H-Fe]. However, the analysis failed to provide a satisfactory picture of the relative spatial relationships of the two [Fe-H-Fe]. Our recent density functional theory (DFT) study yielded a lowest-energy form, denoted as E 4 (4H) (a) , with two parallel Fe-H-Fe planes bridging pairs of "anchor" Fe on the Fe2,3,6,7 face of FeMo-co. However, the relative energies of structures E 4 (4H) (b) , with one bridging and one terminal hydride, and E 4 (4H) (c) , with one pair of anchor Fe supporting two bridging hydrides, were not beyond the uncertainties in the calculation. Moreover, a structure of V-dependent nitrogenase resulted in a proposed structure analogous to E 4 (4H) (c) , and additional structures have been proposed in the DFT studies of others. To resolve the nature of hydride binding to the Janus intermediate, we performed exhaustive, high-resolution CW-stochastic 1 H-ENDOR experiments using improved instrumentation, Mims 2 H ENDOR, and a recently developed pulsed-ENDOR protocol ("PESTRE") to obtain absolute hyperfine interaction signs. These measurements are coupled to DFT structural models through an analytical point-dipole Hamiltonian for the hydride electron-nuclear dipolar coupling to its "anchoring" Fe ions, an approach that overcomes limitations inherent in both experimental interpretation and computational accuracy. The result is the freeze-trapped, lowest-energy Janus intermediate structure, E 4 (4H) (a) .

Three genetically distinct, but structurally similar, isozymes of nitrogenase catalyze biological N 2 reduction to 2NH 3 : Mo-, V-, and Fe-nitrogenase, named respectively for the metal ( M ) in their active site metallocofactors (metal-ion composition, M Fe 7 ). Studies of the Mo-enzyme have revealed key aspects of its mechanism for N 2 binding and reduction. Central to this mechanism is accumulation of four electrons and protons on its active site metallocofactor, called FeMo-co, as metal bound hydrides to generate the key E 4 (4H) ("Janus") state. N 2 binding/reduction in this state is coupled to reductive elimination ( re ) of the two hydrides as H 2 , the forward direction of a reductive-elimination/oxidative-addition ( re/oa ) equilibrium. A recent study demonstrated that Fe-nitrogenase follows the same re/oa mechanism, as particularly evidenced by HD formation during turnover under N 2 /D 2 . Kinetic analysis revealed that Mo- and Fe-nitrogenases show similar rate constants for hydrogenase-like H 2 formation by hydride protonolysis ( k HP ) but significant differences in the rate constant for H 2 re with N 2 binding/reduction ( k re ). We now report that V-nitrogenase also exhibits HD formation during N 2 /D 2 turnover (and H 2 inhibition of N 2 reduction), thereby establishing the re/oa equilibrium as a universal mechanism for N 2 binding and activation among the three nitrogenases. Kinetic analysis further reveals that differences in catalytic efficiencies do not stem from significant differences in the rate constant ( k HP ) for H 2 production by the hydrogenase-like side reaction but directly arise from the differences in the rate constant ( k re ) for the re of H 2 coupled to N 2 binding/reduction, which decreases in the order Mo > V > Fe.

The catalytic cofactor of the most common form of nitrogenase contains seven irons and one molybdenum bound together by sulfide bonds. Surprisingly, a central carbide has been demonstrated by experiments. Another noteworthy structural component is a large homocitrate ligand. In recent theoretical studies it has been shown that the central carbide is needed as a place for the incoming protons that are necessary parts of a reduction process. It has also been shown that a role for the homocitrate ligand could be that it may be rotated to release one bond to molybdenum. In the present study, the carbide protonation steps are reinvestigated with similar results to those reported before. The actual activation of N2 in the E4 state is an extremely complicated process. It has been found experimentally that two hydrides should leave as H2, in a reductive elimination process, to allow N2 activation in E4 in an easily reversible step. It is here suggested that after H2 is released, it is necessary for the metal cofactor to get rid of one proton. This is achieved by protonating the homocitrate and then rotating it to release one of the bonds to Mo. After this rotation, N2 can bind. In the E5 step, the homocitrate is rotated back to its original position and remains that way until the end of the catalytic process. The N2 protonation steps are energetically easy. Since a protonated carbide has never been observed experimentally, it is necessary to also have a mechanism for deprotonating the carbon at the end of the catalytic cycles. Such a mechanism is suggested here.

Nitrogenase iron (Fe) proteins reduce CO 2 to CO and/or hydrocarbons under ambient conditions. Here, we report a 2.4-Å crystal structure of the Fe protein from Methanosarcina acetivorans ( Ma NifH), which is generated in the presence of a reductant, dithionite, and an alternative CO 2 source, bicarbonate. Structural analysis of this methanogen Fe protein species suggests that CO 2 is possibly captured in an unactivated, linear conformation near the [Fe 4 S 4 ] cluster of Ma NifH by a conserved arginine (Arg) pair in a concerted and, possibly, asymmetric manner. Density functional theory calculations and mutational analyses provide further support for the capture of CO 2 on Ma NifH while suggesting a possible role of Arg in the initial coordination of CO 2 via hydrogen bonding and electrostatic interactions. These results provide a useful framework for further mechanistic investigations of CO 2 activation by a surface-exposed [Fe 4 S 4 ] cluster, which may facilitate future development of FeS catalysts for ambient conversion of CO 2 into valuable chemical commodities. IMPORTANCE This work reports the crystal structure of a previously uncharacterized Fe protein from a methanogenic organism, which provides important insights into the structural properties of the less-characterized, yet highly interesting archaeal nitrogenase enzymes. Moreover, the structure-derived implications for CO 2 capture by a surface-exposed [Fe 4 S 4 ] cluster point to the possibility of developing novel strategies for CO 2 sequestration while providing the initial insights into the unique mechanism of FeS-based CO 2 activation., (Copyright © 2019 Rettberg et al.)

Nitrogenase enzymes catalyze the reduction of atmospheric dinitrogen to ammonia utilizing a Mo-7Fe-9S-C active site, the so-called FeMoco cluster. FeMoco and an analogous small-molecule (Et 4 N)[(Tp)MoFe 3 S 4 Cl 3 ] cubane have both been proposed to contain unusual spin-coupled Mo III sites with an S(Mo)=1/2 non-Hund configuration at the Mo atom. Herein, we present Fe and Mo L 3 -edge X-ray magnetic circular dichroism (XMCD) spectroscopy of the (Et 4 N)[(Tp)MoFe 3 S 4 Cl 3 ] cubane and Fe L 2,3 -edge XMCD spectroscopy of the MoFe protein (containing both FeMoco and the 8Fe-7S P-cluster active sites). As the P-clusters of MoFe protein have an S=0 total spin, these are effectively XMCD-silent at low temperature and high magnetic field, allowing for FeMoco to be selectively probed by Fe L 2,3 -edge XMCD within the intact MoFe protein. Further, Mo L 3 -edge XMCD spectroscopy of the cubane model has provided experimental support for a local S(Mo)=1/2 configuration, demonstrating the power and selectivity of XMCD., (© 2019 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Molybdenum nitrogenase catalyzes the reduction of dinitrogen into ammonia, which requires the coordinated transfer of eight electrons to the active site cofactor (FeMoco) through the intermediacy of an [8Fe-7S] cluster (P-cluster), both housed in the molybdenum-iron protein (MoFeP). Previous studies on MoFeP from two different organisms, Azotobacter vinelandii ( Av) and Gluconacetobacter diazotrophicus ( Gd), have established that the P-cluster is conformationally flexible and can undergo substantial structural changes upon two-electron oxidation to the P OX state, whereby a backbone amidate and an oxygenic residue (Ser or Tyr) ligate to two of the cluster's Fe centers. This redox-dependent change in coordination has been implicated in the conformationally gated electron transfer in nitrogenase. Here, we have investigated the role of the oxygenic ligand in Av MoFeP, which natively contains a Ser ligand (βSer188) to the P-cluster. Three variants were generated in which (1) the oxygenic ligand was eliminated (βSer188Ala), (2) the P-cluster environment was converted to the one in Gd MoFeP (βPhe99Tyr/βSer188Ala), and (3) two oxygenic ligands were simultaneously included (βPhe99Tyr). Our studies have revealed that the P-cluster can become compositionally labile upon oxidation and reversibly lose one or two Fe centers in the absence of the oxygenic ligand, while still retaining wild-type-like dinitrogen reduction activity. Our findings also suggest that Av and Gd MoFePs evolved with specific preferences for Ser and Tyr ligands, respectively, and that the structural control of these ligands must extend beyond the primary and secondary coordination spheres of the P-cluster. The P-cluster adds to the increasing number of examples of inherently labile Fe-S clusters whose compositional instability may be an obligatory feature to enable redox-linked conformational changes to facilitate multielectron redox reactions.

Nitrogenase is the only enzyme that can cleave the triple bond in N2, making nitrogen avaiable for other organisms. It contains a complicated MoFe7S9C(homocitrate) cluster in its active site. Many computational studies with density-functional theory (DFT) of the nitrogenase enzyme have been presented, but they do not show any consensus - they do not even agree where the first four protons should be added, forming the central intermediate E4. We show that the prime reason for this is that different DFT methods give relative energies that differ by almost 600 kJ mol-1 for different protonation states. This is 4-30 times more than what is observed for other systems. The reason for this is that in some structures, the hydrogens bind to sulfide or carbide ions as protons, whereas in other structures they bind to the metals as hydride ions, changing the oxidation state of the metals, as well as the Fe-C, Fe-S and Fe-Fe distances. The energies correlate with the amount of Hartree-Fock exchange in the method, indicating a variation in the amount of static correlation in the structures. It is currently unclear which DFT method gives the best results for nitrogenase. We show that non-hybrid DFT functionals and TPSSh give the most accurate structures of the resting active site, whereas B3LYP and PBE0 give the best H2 dissociation energies. However, no DFT method indicates that a structure of E4 with two bridging hydride ions is lowest in energy, as spectroscopic experiments indicate.

The active site of the enzyme nitrogenase (N 2 → NH 3 ) is a Fe 7 MoS 9 C cluster that contains three doubly-bridging μ-S atoms around a central belt. A vanadium nitrogenase variant has a slightly different cluster, containing two μ-S atoms. Recent crystal structures have revealed substitution of one μ-S (S2B, bridging Fe2 and Fe6), by CO in Mo-nitrogenase and an uncertain light atom in V-nitrogenase. These systems retained catalytic activity, and were able to recover the lost μ-S atom. Electron density attributed to the dissociated S is displaced by 7 Å in the crystal structure of the non-standard V-protein. The hypothesis arising from these observations is that the chemical mechanism of nitrogenase involves reversible dissociation of S2B, leaving Fe2 and Fe6 seriously under-coordinated and reactive in trapping N 2 and binding reaction intermediates. Accumulated experimental evidence points to the Fe2-S2B-Fe6 domain as the centre of catalytic hydrogenation of N 2 . Using DFT simulations of a large model (>488 atoms) containing all relevant surrounding protein residues, I have investigated the chemical steps that could allow dissociation of S2B. The participation of H atoms is crucial, as is involvement of the nearby side chain of His195 that can function as proton donor to S2B and hydrogen-bonding supporter of displaced S2B. A significant result is that after ingress and binding of N 2 at Fe2 the breaking of the Fe2-S2B bond can be strongly exergonic with negligible kinetic barrier. Subsequent extension of the Fe6-S2B bond and dissociation as H 2 S (or SH - ) is endergonic by 20-25 kcal mol -1 , partly because the separating H 2 S is restricted by surrounding amino-acids. I present a number of reaction sequences and energy landscapes, and derive thirteen chemical principles relevant to the postulated S-dissociation mechanism. A key conclusion is that unhooking of S2BH or S2BH 2 from Fe2 is favourable, likely, and propitious for subsequent H transfer to bound N 2 or reaction intermediates. The space between Fe2 and Fe6 supports two bridging ligands, and another H atom on Fe6 can move without kinetic barrier to occupy the bridging position vacated by S2B.

A major hurdle in the studies of nitrogenase, one of the most complicated metalloenzymes known to date, is to obtain large amounts of intact, active proteins. Nitrogenase and related proteins are often multimeric and consist of metal centers that are critical for their activities. Most notably, the well-studied MoFe protein of Mo-nitrogenase is a heterotetramer that houses two of the most complicated metal clusters found in nature, the P-cluster and the FeMoco (or M-cluster). The structural complexity of these proteins and the oxygen sensitivity of their associated metal clusters, along with the demand for large amounts of high-quality proteins in most downstream analyses, make large-scale, high-yield purification of fully competent nitrogenase proteins a formidable task and yet, at the same time, a prerequisite for the success of nitrogenase research. This chapter highlights several methods that have been developed over the past few decades chiefly for the purification of naturally expressed nitrogenase in the diazotroph Azotobacter vinelandii. In addition, purification and Fe-S reconstitution strategies are also outlined for the heterologously expressed nitrogenase proteins in Escherichia coli.

Enzymes with homology to nitrogenase are essential for the reduction of chemically stable double bonds within the biosynthetic pathways of bacteriochlorophyll and coenzyme F 430 . These tetrapyrrole-based compounds are crucial for bacterial photosynthesis and the biogenesis of methane in methanogenic archaea. Formation of bacteriochlorophyll requires the unique ATP-dependent enzyme chlorophyllide oxidoreductase (COR) for the two-electron reduction of chlorophyllide to bacteriochlorophyllide. COR catalysis is based on the homodimeric protein subunit BchX 2 , which facilitates the transfer of electrons to the corresponding heterotetrameric catalytic subunit (BchY/BchZ) 2 . By analogy to the nitrogenase system, the dynamic switch protein BchX 2 contains a [4Fe-4S] cluster that triggers the ATP-driven transfer of electrons onto a second [4Fe-4S] cluster located in (BchY/BchZ) 2 . The subsequent substrate reduction and protonation is unrelated to nitrogenase catalysis, with no further involvement of a molybdenum-containing cofactor. The biosynthesis of the nickel-containing coenzyme F 430 includes the six-electron reduction of the tetrapyrrole macrocycle of Ni 2+ -sirohydrochlorin a,c-diamide to Ni 2+ -hexahydrosirohydrochlorin a,c-diamide catalyzed by CfbC/D. The homodimeric CfbC 2 subunit carrying a [4Fe-4S] cluster shows close homology to BchX 2 . Accordingly, parallelism for the initial ATP-driven electron transfer steps of CfbC/D was proposed. Electrons are received by the dimeric catalytic subunit CfbD 2 , which contains a second [4Fe-4S] cluster and carries out the saturation of an overall of three double bonds in a highly orchestrated spatial and regioselective process. Following a short introduction to nitrogenase catalysis, this chapter will focus on the recent progress toward the understanding of the nitrogenase-like enzymes COR and CfbC/D, with special emphasis on the underlying enzymatic mechanism(s).

Biological nitrogen fixation, the conversion of dinitrogen (N 2 ) into ammonia (NH 3 ), 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.

Nitrogenase is the only known enzymatic system capable of reducing atmospheric dinitrogen to ammonia. This unique reaction requires tightly choreographed interactions between the nitrogenase component proteins, the molybdenum-iron (MoFe)- and iron (Fe)-proteins, as well as regulation of electron transfer between multiple metal centers that are only found in these components. Several decades of research beginning in the 1950s yielded substantial information of how nitrogenase manages the task of N 2 fixation. However, key mechanistic steps in this highly oxygen-sensitive and ATP-intensive reaction have only recently been identified at an atomic level. A critical part in any mechanistic elucidation is the necessity to connect spectroscopic and functional properties of the component proteins to the detailed three-dimensional structures. Structural information derived from X-ray diffraction (XRD) methods has provided detailed atomic insights into the enzyme system and, in particular, its active site FeMo-cofactor. The following chapter outlines the general protocols for the crystallization of Azotobacter vinelandii (Av) nitrogenase component proteins, with a special emphasis on different applications, such as high-resolution XRD, single-crystal spectroscopy, and the structural characterization of bound inhibitors.

The synthetic inorganic chemistry of metal-sulfur (M-S, M = metals) clusters has played an important, complementary role to the biochemical analyses of nitrogenase toward a better understanding of the enzyme active site. The active site of nitrogenase (designated the M-cluster) can be extracted from the protein in a solvent-stabilized form, [(cit)MoFe 7 S 9 C] (cit = (R)-homocitrate). One important finding of the extracted M-cluster is its catalytic activity toward the reduction of C 1 -substrates (CN - , CO, CO 2 ) into C 1 -C 5 hydrocarbons in solution. This catalytic property poses challenges for chemists to reproduce the function with synthetic mimics, not only because of the biochemical interests but also due to the potential significance in green chemistry and catalysis research. In this context, our successful synthesis of an asymmetric Mo-Fe-S cluster, [Cp*MoFe 5 S 9 (SH)] 3- , is one of the recent important achievements in synthetic M-S chemistry, as this cluster catalyzes the reduction of C 1 -substrates in a similar manner to the extracted M-cluster. Even though the synthetic protocol for this cluster has been described in the literature, there are plenty of pitfalls for researchers unfamiliar with synthetic M-S chemistry. In this chapter, we provide general precautionary statements and detailed protocols for the synthesis of [Cp*MoFe 5 S 9 (SH)] 3- , with a brief discussion of the experimental tips based on the authors' experience in both biochemical and synthetic chemical fields.

We have performed a systematic computational study of the relative energies of possible protonation states of the FeMo cluster in nitrogenase in the E 0 -E 4 states, i.e., the resting state and states with 1-4 electrons and protons added but before N 2 binds. We use the combined quantum mechanics and molecular mechanics (QM/MM) approach, including the complete solvated heterotetrameric enzyme in the calculations. The QM system consisted of 112 atoms, i.e., the full FeMo cluster, as well all groups forming hydrogen bonds to it within 3.5 Å. It was treated with either the TPSS-D3 or B3LYP-D3 methods with the def2-SV(P) or def2-TZVPD basis sets. For each redox state, we calculated relative energies of at least 50 different possible positions for the proton, added to the most stable protonation state of the level with one electron less. We show quite conclusively that the resting E 0 state is not protonated using quantum refinement and by comparing geometries to the crystal structure. The E 1 state is protonated on S2B, in agreement with most previous computational studies. However, for the E 2 -E 4 states, the two QM methods give diverging results, with relative energies that differ by over 300 kJ/mol for the most stable E 4 states. TPSS favors hydride ions binding to the Fe ions. The first bridges Fe2 and Fe6, whereas the next two bind terminally to either Fe4, Fe5, or Fe6 with nearly equal energies. On the other hand, B3LYP disfavors hydride ions and instead suggests that 1-3 protons bind to the central carbide ion.

The bacterial enzyme nitrogenase achieves the reduction of dinitrogen (N 2 ) to ammonia (NH 3 ) utilizing electrons, protons, and energy from the hydrolysis of ATP. Building on earlier foundational knowledge, recent studies provide molecular-level details on how the energy of ATP hydrolysis is utilized, the sequencing of multiple electron transfer events, and the nature of energy transduction across this large protein complex. Here, we review the state of knowledge about energy transduction in nitrogenase., (Copyright © 2018 Elsevier Ltd. All rights reserved.)

The enzyme nitrogenase catalyzes the reduction of N 2 to ammonia but also that of protons to H 2 . These reactions compete at the mechanistically central 'Janus' intermediate, denoted E 4 (4H), which has accumulated 4e - /4H + as two bridging Fe-H-Fe hydrides on the active-site cofactor. This state can lose e - /H + by hydride protonolysis (HP) or become activated by reductive elimination ( re) of the two hydrides and bind N 2 with H 2 loss, yielding an E 4 (2N2H) state that goes on to generate two NH 3 molecules. Thus, E 4 (4H) represents the key branch point for these competing reactions. Here, we present a steady-state kinetic analysis that precisely describes this competition. The analysis demonstrates that steady-state, high-electron flux turnover overwhelmingly populates the E 4 states at the expense of less reduced states, quenching HP at those states. The ratio of rate constants for E 4 (4H) hydride protonolysis ( k HP ) versus reductive elimination ( k re ) provides a sensitive measure of competition between these two processes and thus is a central parameter of nitrogenase catalysis. Analysis of measurements with the three nitrogenase variants (Mo-nitrogenase, V-nitrogenase, and Fe-nitrogenase) reveals that at a fixed N 2 pressure their tendency to productively react with N 2 to produce two NH 3 molecules and an accompanying H 2 , rather than diverting electrons to the side reaction, HP production of H 2 , decreases with their ratio of rate constants, k re / k HP : Mo-nitrogenase, 5.1 atm -1 ; V-nitrogenase, 2 atm -1 ; and Fe-nitrogenase, 0.77 atm -1 (namely, in a 1:0.39:0.15 ratio). Moreover, the lower catalytic effectiveness of the alternative nitrogenases, with more H 2 production side reaction, is not caused by a higher k HP but by a significantly lower k re .

Nitrogenases catalyze the biological fixation of inert N 2 into bioavailable ammonium. They are bipartite systems consisting of the catalytic dinitrogenase and a complementary reductase, the Fe protein that is also the site where ATP is hydrolyzed to drive the reaction forward. Three different subclasses of dinitrogenases are known, employing either molybdenum, vanadium or only iron at their active site cofactor. Although in all these classes the mode and mechanism of interaction with Fe protein is conserved, each one encodes its own orthologue of the reductase in the corresponding gene cluster. Here we present the 2.2 Å resolution structure of VnfH from Azotobacter vinelandii, the Fe protein of the alternative, vanadium-dependent nitrogenase system, in its ADP-bound state. VnfH adopts the same conformation that was observed for NifH, the Fe protein of molybdenum nitrogenase, in complex with ADP, representing a state of the functional cycle that is ready for reduction and subsequent nucleotide exchange. The overall similarity of NifH and VnfH confirms the experimentally determined cross-reactivity of both ATP-hydrolyzing reductases.

The biomimetic diiron complex 4-(N 2 ) 2 , featuring two terminally bound Fe-N 2 centers bridged by two hydrides, serves as a model for two possible states along the pathway by which the enzyme nitrogenase reduces N 2 . One is the Janus intermediate E 4 (4H), which has accumulated 4[e-/H+], stored as two [Fe-H-Fe] bridging hydrides, and is activated to bind and reduce N 2 through reductive elimination (RE) of the hydride ligands as H 2 . The second is a possible RE intermediate. 1 H and 14 N 35 GHz ENDOR measurements confirm that the formally Fe(II)/Fe(I) 4-(N 2 ) 2 complex exhibits a fully delocalized, Robin-Day type-III mixed valency. The two bridging hydrides exhibit a fully rhombic dipolar tensor form, T ≈ [- t, + t, 0]. The rhombic form is reproduced by a simple point-dipole model for dipolar interactions between a bridging hydride and its "anchor" Fe ions, confirming validity of this model and demonstrating that observation of a rhombic form is a convenient diagnostic signature for the identification of such core structures in biological centers such as nitrogenase. Furthermore, interpretation of the 1 H measurements with the anchor model maps the g tensor onto the molecular frame, an important function of these equations for application to nitrogenase. Analysis of the hyperfine and quadrupole coupling to the bound 14 N of N 2 provides a reference for nitrogen-bound nitrogenase intermediates and is of chemical significance, as it gives a quantitative estimate of the amount of charge transferred between Fe and coordinated N, a key element in N 2 activation for reduction.