X-ray emission spectroscopy evidences a central carbon in the nitrogenase iron-molybdenum cofactor

Single-Step Sulfur Insertions into Iron Carbide Carbonyl Clusters: Unlocking the Synthetic Door to FeMoco Analogues

The one-step syntheses, X-ray structures, and spectroscopic characterization of synthetic iron clusters, bearing either inorganic sulfides or thiolate with interstitial carbide motifs, are reported. Treatment of iron carbide carbonyl clusters [Fe_n (μ_n -C)(CO)_m ]^x (n=5,6; m=15,16; x=0,-2) with electrophilic sulfur sources (S₂ Cl₂ , S₈ ) results in the formation of several μ₄ -S dimers of clusters, and moreover, iron-sulfide-(sulfocarbide) clusters. The core sulfocarbide unit {C-S}^4- serves as a structural model for a proposed intermediate in the radical S-adenosyl-L-methionine biogenesis of the M-cluster. Furthermore, the electrophilic sulfur strategy has been extended to provide the first ever thiolato-iron-carbide complex: an analogous reaction with toluylsulfenyl chloride affords the cluster [Fe₅ (μ₅ -C)(SC₇ H₇ )(CO)₁₃ ]^- . The strategy described herein provides a breakthrough towards developing syntheses of biomimetic iron-sulfur-carbide clusters like FeMoco.

Molybdenum-Containing Metalloenzymes and Synthetic Catalysts for Conversion of Small Molecules

The energy deficiency and environmental problems have motivated researchers to develop energy conversion systems into a sustainable pathway, and the development of catalysts holds the center of the research endeavors. Natural catalysts such as metalloenzymes have maintained energy cycles on Earth, thus proving themselves the optimal catalysts. In the previous research results, the structural and functional analogs of enzymes and nano-sized electrocatalysts have shown promising activities in energy conversion reactions. Mo ion plays essential roles in natural and artificial catalysts, and the unique electrochemical properties render its versatile utilization as an electrocatalyst. In this review paper, we show the current understandings of the Mo-enzyme active sites and the recent advances in the synthesis of Mo-catalysts aiming for high-performing catalysts.

Synthesis and Reactivity of Iron Complexes with a Biomimetic SCS Pincer Ligand

Recent experimental evidence suggests that the FeMoco of nitrogenase undergoes structural rearrangement during N₂ reduction, which may result in the generation of coordinatively unsaturated iron sites with two sulfur donors and a carbon donor. In an effort to synthesize and study small-molecule model complexes with a one-carbon/two-sulfur coordination environment, we have designed two new SCS pincer ligands containing a central NHC donor accompanied by thioether- or thiolate-functionalized aryl groups. Metalation of the thioether ligand with Fe(OTf)₂ gives 6-coordinate complexes in which the SCS ligand binds meridionally. In contrast, metalation of the thiolate ligand with Fe(HMDS)₂ gives a four-coordinate pseudotetrahedral amide complex in which the ligand binds facially, illustrating the potential structural flexibility of these ligands. Reaction of the amide complex with a bulky monothiol gives a four-coordinate complex with a one-carbon/three-sulfur coordination environment that resembles the resting state of nitrogenase. Reaction of the amide complex with phenylhydrazine gives a product with a rare κ¹-bound phenylhydrazido group which undergoes N-N cleavage to give a phenylamido complex.

Preparation and spectroscopic characterization of lyophilized Mo nitrogenase

Mo nitrogenase is the primary source of biologically fixed nitrogen, making this system highly interesting for developing new, energy efficient ways of ammonia production. Although heavily investigated, studies of the active site of this enzyme have generally been limited to spectroscopic methods that are compatible with the presence of water and relatively low protein concentrations. One method of overcoming this limitation is through lyophilization, which allows for measurements to be performed on solvent free, high concentration samples. This method also has the potential for allowing efficient protein storage and solvent exchange. To investigate the viability of this preparatory method with Mo nitrogenase, we employ a combination of electron paramagnetic resonance, Mo and Fe K-edge X-ray absorption spectroscopy, and acetylene reduction assays. Our results show that while some small distortions in the metallocofactors occur, oxidation and spin states are maintained through the lyophilization process and that reconstitution of either lyophilized protein component into buffer restores acetylene reducing activity.

Quantification of Ni-N-O Bond Angles and NO Activation by X-ray Emission Spectroscopy

A series of β-diketiminate Ni-NO complexes with a range of NO binding modes and oxidation states were studied by X-ray emission spectroscopy (XES). The results demonstrate that XES can directly probe and distinguish end-on vs side-on NO coordination modes as well as one-electron NO reduction. Density functional theory (DFT) calculations show that the transition from the NO 2s2s σ* orbital has higher intensity for end-on NO coordination than for side-on NO coordination, whereas the 2s2s σ orbital has lower intensity. XES calculations in which the Ni-N-O bond angle was fixed over the range from 80° to 176° suggest that differences in NO coordination angles of ∼10° could be experimentally distinguished. Calculations of Cu nitrite reductase (NiR) demonstrate the utility of XES for characterizing NO intermediates in metalloenzymes. This work shows the capability of XES to distinguish NO coordination modes and oxidation states at Ni and highlights applications in quantifying small molecule activation in enzymes.

Expression, Isolation, and Characterization of Vanadium Nitrogenase from Azotobacter vinelandii

Nitrogenases are the sole enzymes known to mediate biological nitrogen fixation, an essential process for sustaining life on earth. Among the three known variants, molybdenum nitrogenase is the best-studied to date. Recent work on the alternative vanadium nitrogenase provided important insights into the mechanism of nitrogen fixation since this enzyme differs from its molybdenum counterpart in some important aspects. Here, we present a protocol to obtain unmodified vanadium nitrogenase in high yield and purity from the paradigmatic diazotroph Azotobacter vinelandii, including procedures for cell cultivation, purification, and protein characterization.

A quantum chemical approach for the mechanisms of redox-active metalloenzymes

During the past 20 years, quantum chemistry has grown to be a significant part in the investigation of mechanisms for redox-active enzymes. In our group we have developed an approach that has been applied to a large number of such systems. Hybrid density functional theory (hybrid DFT) has from the start of these investigations been the leading electronic structure tool. An understanding of how the method works in practice has significantly improved the accuracy and applicability. During the past ten years, it has been found that the results for redox enzymes mainly depend on the chosen fraction of exact exchange in the functional, and that a choice of 15% has worked best. The idea has therefore been to vary that fraction over a reasonable range and study the relative energy dependence. For modeling the enzymes, a cluster approach has been developed. In the present review the development of the method we used is described from its start in work on photosystem II, fifteen years ago. Examples from a few recent applications are described, where the metals have been iron, nickel, copper, cobalt or manganese. The results are in excellent agreement with available experiments, and a large number of new predictions have been made.

During the past 20 years, quantum chemistry has grown to be a significant part in the investigation of mechanisms for redox-active enzymes.

CO Binding to the FeV Cofactor of CO-Reducing Vanadium Nitrogenase at Atomic Resolution

Nitrogenases reduce N2 , the most abundant element in Earth's atmosphere that is otherwise resistant to chemical conversions due to its stable triple bond. Vanadium nitrogenase stands out in that it additionally processes carbon monoxide, a known inhibitor of the reduction of all substrates other than H+ . The reduction of CO leads to the formation of hydrocarbon products, holding the potential for biotechnological applications in analogy to the industrial Fischer-Tropsch process. Here we report the most highly resolved structure of vanadium nitrogenase to date at 1.0 Å resolution, with CO bound to the active site cofactor after catalytic turnover. CO bridges iron ions Fe2 and Fe6, replacing sulfide S2B, in a binding mode that is in line with previous reports on the CO complex of molybdenum nitrogenase. We discuss the structural consequences of continued turnover when CO is removed, which involve the replacement of CO possibly by OH- , the movement of Q176D and K361D , the return of sulfide and the emergence of two additional water molecules that are absent in the CO-bound state.

Kβ X-ray Emission Spectroscopy as a Probe of Cu(I) Sites: Application to the Cu(I) Site in Preprocessed Galactose Oxidase

Cu(I) active sites in metalloproteins are involved in O₂ activation, but their O₂ reactivity is difficult to study due to the Cu(I) d¹⁰ closed shell which precludes the use of conventional spectroscopic methods. Kβ X-ray emission spectroscopy (XES) is a promising technique for investigating Cu(I) sites as it detects photons emitted by electronic transitions from occupied orbitals. Here, we demonstrate the utility of Kβ XES in probing Cu(I) sites in model complexes and a metalloprotein. Using Cu(I)Cl, emission features from double-ionization (DI) states are identified using varying incident X-ray photon energies, and a reasonable method to correct the data to remove DI contributions is presented. Kβ XES spectra of Cu(I) model complexes, having biologically relevant N/S ligands and different coordination numbers, are compared and analyzed, with the aid of density functional theory (DFT) calculations, to evaluate the sensitivity of the spectral features to the ligand environment. While the low-energy Kβ_2,5 emission feature reflects the ionization energy of ligand np valence orbitals, the high-energy Kβ_2,5 emission feature corresponds to transitions from molecular orbitals (MOs) having mainly Cu 3d character with the intensities determined by ligand-mediated d-p mixing. A Kβ XES spectrum of the Cu(I) site in preprocessed galactose oxidase (GO_pre) supports the 1Tyr/2His structural model that was determined by our previous X-ray absorption spectroscopy and DFT study. The high-energy Kβ_2,5 emission feature in the Cu(I)-GO_pre data has information about the MO containing mostly Cu 3d_x²-y² character that is the frontier molecular orbital (FMO) for O₂ activation, which shows the potential of Kβ XES in probing the Cu(I) FMO associated with small-molecule activation in metalloproteins.

Construction of Synthetic Models for Nitrogenase-Relevant NifB Biogenesis Intermediates and Iron-Carbide-Sulfide Clusters

The family of nitrogenase enzymes catalyzes the reduction of atmospheric dinitrogen (N2) to ammonia under remarkably benign conditions of temperature, pressure, and pH. Therefore, the development of synthetic complexes or materials that can similarly perform this reaction is of critical interest. The primary obstacle for obtaining realistic synthetic models of the active site iron-sulfur-carbide cluster (e.g., FeMoco) is the incorporation of a truly inorganic carbide. This review summarizes the present state of knowledge regarding biological and chemical (synthetic) incorporation of carbide into iron-sulfur clusters. This includes the Nif cluster of proteins and associated biochemistry involved in the endogenous biogenesis of FeMoco. We focus on the chemical (synthetic) incorporation portion of our own efforts to incorporate and modify C1 units in iron/sulfur clusters. We also highlight recent contributions from other research groups in the area toward C1 and/or inorganic carbide insertion.

Structural insight into [Fe-S2-Mo] motif in electrochemical reduction of N2 over Fe1-supported molecular MoS2

The catalytic synthesis of NH₃ from the thermodynamically challenging N₂ reduction reaction under mild conditions is currently a significant problem for scientists. Accordingly, herein, we report the development of a nitrogenase-inspired inorganic-based chalcogenide system for the efficient electrochemical conversion of N₂ to NH₃, which is comprised of the basic structure of [Fe-S₂-Mo]. This material showed high activity of 8.7 mg_NH3 mg_Fe ^-1 h^-1 (24 μg_NH3 cm^-2 h^-1) with an excellent faradaic efficiency of 27% for the conversion of N₂ to NH₃ in aqueous medium. It was demonstrated that the Fe₁ single atom on [Fe-S₂-Mo] under the optimal negative potential favors the reduction of N₂ to NH₃ over the competitive proton reduction to H₂. Operando X-ray absorption and simulations combined with theoretical DFT calculations provided the first and important insights on the particular electron-mediating and catalytic roles of the [Fe-S₂-Mo] motifs and Fe₁, respectively, on this two-dimensional (2D) molecular layer slab.

Mixed-Valent Diiron μ-Carbyne, μ-Hydride Complexes: Implications for Nitrogenase

Binding of N₂ 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 (P₆ArC)Fe₂(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 {Fe₂(μ-H)}₂ state of FeMoco (E₄(4H)), the data and analysis presented herein suggest that the hydride ligands in E₄(4H) bridge isovalent (most probably Fe^III) metal centers. Although electron transfer involves metal-localized orbitals, investigations of [(P₆ArC)Fe₂(μ-H)]⁺¹ and [(P₆ArC)Fe₂(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, ⁵⁷Fe 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.

Assignment of protonated R-homocitrate in extracted FeMo-cofactor of nitrogenase via vibrational circular dichroism spectroscopies

Protonation of FeMo-cofactor is important for the process of substrate hydrogenation. Its structure has been clarified as Δ-Mo*Fe₇S₉C(R-homocit*)(cys)(Hhis) for the efforts of nearly 30 years, while it remains controversial whether FeMo-cofactor is protonated or deprotonated with chelated ≡C-O(H) homocitrate. We have used protonated molybdenum(V) lactates 1 and its enantiomer as model compounds for R-homocitrate in FeMo-cofactor of nitrogenase. Vibrational circular dichroism (VCD) spectrum of 1 at 1051 cm^-1 is attributed to ≡C-O_H vibration, and molybdenum(VI) R-lactate at 1086 cm^-1 is assigned as ≡C-O _α-alkoxy vibration. These vibrations set up labels for the protonation state of coordinated α-hydroxycarboxylates. The characteristic VCD band of NMF-extracted FeMo-cofactor is assigned to ν(C-O_H), which is based on the comparison of molybdenum(VI) R-homocitrate. Density Functional Theory calculations are in consistent with these assignments. To the best of our knowledge, this is the first time that protonated R-homocitrate in FeMo-cofactor is confirmed by VCD spectra.

Pentanuclear Scaffold: A Molecular Platform for Small-Molecule Conversions

Small-molecule conversions involving multielectron transfer processes enable the conversion of earth-abundant materials into valuable chemicals and are regarded as a solution for environmental and energy shortage problems. In this context, the development of artificial catalysts that promote these reactions is an important research target. In nature, metalloenzymes that contain multinuclear metal complexes as active sites are known to efficiently catalyze reactions under mild conditions. Therefore, using multinuclear metal complexes as artificial catalysts can be an attractive strategy for small-molecule conversions involving multielectron transfer processes. However, multinuclear-metal-complex-based catalysts for these reactions have not been well established. In this Account, we describe our recent advances in the development of multinuclear metal complexes as catalysts for small-molecule conversion, mainly focusing on water oxidation. As small-molecule conversions involving multielectron transfer processes consists of two essential processes, (1) the transfer of multiple electrons and (2) the formation/cleavage of covalent bond(s), catalysts for these reactions should facilitate both steps. Therefore, we assumed that the assembly of redox-active metal ions and the cooperative effect of neighboring coordinatively unsaturated metal ions can promote these processes. On the basis of this assumption, we employed a pentanuclear metal complex as a molecular scaffold for the catalyst. The scaffold has a pentanuclear structure with quasi-D₃ symmetry and consists of a [M₃(μ₃-X)] core (X = O^2- or OH^-) wrapped by two [M(μ-bpp)₃] units (Hbpp = 3,5-bis(2-pyridyl)pyrazole). The metal ions in the triangular core are coordinatively unsaturated, whereas the metal ions at the apical positions are coordinatively saturated. In other words, the pentanuclear scaffold possesses multiple redox-active centers and coordinatively unsaturated sites. It should also be noted that the electron transfer ability of the complex changes dramatically depending on the identity of the constituent metal ions. The iron derivative of the pentanuclear scaffold was found to serve as an electrocatalyst for water oxidation (2H₂O → O₂ + 4e^- + 4H⁺) with a high reaction rate and excellent robustness. The substitution of metal ions in the pentanuclear scaffold to cobalt ions resulted in the development of a catalyst for CO₂ reduction. Furthermore, we investigated the effect of substituents on the ligands of the pentanuclear iron complex and succeeded in precisely manipulating the electron transfer possess. These results clearly demonstrate that the pentanuclear scaffold is an attractive platform for catalysts for small-molecule conversions. Additionally, the intrinsic features of the multinuclear catalytic system, which are totally different from those of conventional mononuclear-metal-complex-based catalysts, are disclosed. In reactions mediated by multinuclear complexes, the multinuclear core can initially accumulate the charge required for catalysis to reach the catalytically active state. Subsequently, the catalyst in the active state reacts with the substrate, initiating electron transfer to the substrate and rearrangement of covalent bonds in the substrate to afford the product. In such a mechanism, the desired number of electrons can be transferred to the substrates in an on-demand fashion, and the formation of undesired chemical species in the targeted catalysis may be prevented. This feature of multinuclear-metal-complex-based catalysts will achieve demanding small-molecule conversions with a high reaction rate, selectivity, and durability.

Revealing a role for the G subunit in mediating interactions between the nitrogenase component proteins

Azotobacter vinelandii contains three forms of nitrogenase known as the Mo-, V-, and Fe-nitrogenases. They are all two-component enzyme systems, where the catalytic component, referred to as NifDK, VnfDGK, and AnfDGK, associates with the reductase component, the Fe protein or NifH, VnfH, and AnfH respectively. AnfDGK and VnfDGK have an additional subunit compared to NifDK, termed gamma or AnfG and VnfG, whose role is unknown. The expression of each nitrogenase is tightly regulated by metal availability, however it is known that there is crosstalk between the Mo- and V‑nitrogenases but the Fe‑nitrogenase components cannot support substrate reduction with its Mo‑nitrogenase counterparts. Here, docking models for the nitrogenase complexes were generated in ClusPro 2.0 based on the crystal structure of the Mo‑nitrogenase and refined using the HADDOCK 2.2 refinement interface to identify structural determinants that enable crosstalk between the Mo- and V‑nitrogenase but not the Fe‑nitrogenase. Differing salt bridge interactions were identified at the binding interface of each complex. Specifically, positively charged residues of VnfG enable complementary interactions with NifH and VnfH but not AnfH. Similarly, negatively charged residues of AnfG enable interactions with AnfH but not NifH or VnfH. A role for the G subunit is revealed where VnfG could be mediating crosstalk between the Mo- and V‑nitrogenases while the AnfG subunit on AnfDGK makes interactions with NifH and VnfH unfavorable, reducing competition with NifDK and funneling electrons to the most efficient nitrogenase.

Carbon-Metal Bonds: Rare and Primordial in Metabolism

Submarine hydrothermal vents are rich in hydrogen (H₂), an ancient source of electrons and chemical energy for life. Geochemical H₂ stems from serpentinization, a process in which rock-bound iron reduces water to H₂. Reactions involving H₂ and carbon dioxide (CO₂) in hydrothermal systems generate abiotic methane and formate; these reactions resemble the core energy metabolism of methanogens and acetogens. These organisms are strict anaerobic autotrophs that inhabit hydrothermal vents and harness energy via H₂-dependent CO₂ reduction. Serpentinization also generates native metals, which can reduce CO₂ to formate and acetate in the laboratory. The enzymes that channel H₂, CO₂, and dinitrogen (N₂) into methanogen and acetogen metabolism are the backbone of the most ancient metabolic pathways. Their active sites share carbon-metal bonds which, although rare in biology, are conserved relics of primordial biochemistry present at the origin of life.

Reactivity of Neutral Tantalum Sulfide Clusters Ta3Sn (n = 0-4) with N2

Nitrogen (N₂) fixation is a challenging and vital issue in chemistry. Inspired by the fact that the active sites of nitrogenases are polynuclear metal sulfide clusters, the reactivity of gas-phase metal sulfide clusters toward N₂ has received considerable attention to gain fundamental insights into nitrogen fixation. Herein, neutral tantalum sulfide clusters have been prepared and their reactivity toward N₂ has been investigated by mass spectrometry in conjunction with density functional theory (DFT) calculations. The experimental results showed that Ta₃S_n (n = 0-3) could adsorb N₂, while Ta₃S₄ was inert to N_2. The DFT calculations revealed that the complete cleavage of the N≡N bond on the trinuclear metal center in the Ta₃S_0-3/N₂ reaction systems was overall barrierless under thermal collision conditions. The sulfur ligands can facilitate the approaching of N₂ toward the metal center but weaken the electron-donating ability of the metal center. The inertness of Ta₃S₄ is ascribed to the electron-deficient state of Ta₃ in Ta₃S₄ and the least effective orbital interaction in the Ta₃S₄/N₂ couple. This study provides new insights into the ligand effect on the interaction of the metal clusters with N_2.

Chemical Sensitivity of Kβ and Kα X-ray Emission from a Systematic Investigation of Iron Compounds

K-fluorescence X-ray emission spectroscopy (XES) is receiving growing interest in all fields of natural sciences to investigate the local spin. The spin sensitivity in Kβ (Kα) XES stems from the exchange interaction between the unpaired 3p (2p) and the 3d electrons, which is greater for Kβ than for Kα. We present a thorough investigation of a large number of iron-bearing compounds. The experimental spectra were analyzed in terms of commonly used quantitative parameters (Kβ_1,3-first moment, Kα₁-full width at half-maximum, and integrated absolute difference -IAD-), and we carefully examined the difference spectra. Multiplet calculations were also performed to elucidate the underlying mechanisms that lead to the chemical sensitivity. Our results confirm a strong influence of covalency on both Kβ and Kα lines. We establish a reliable spin sensitivity of Kβ XES as it is dominated by the exchange interaction, whose variations can be quantified by either Kβ_1,3-first moment or Kβ-IAD and result in a systematic difference signal line shape. We find an exception in the Kβ XES of Fe³⁺ and Fe²⁺ in water solution, where a new difference spectrum is identified that cannot be reproduced by scaling the exchange integrals. We explain this by strong differences in orbital mixing between the valence orbitals. This result calls for caution in the interpretation of Kβ XES spectral changes as due to spin variations without a careful analysis of the line shape. For Kα XES, the smaller exchange interaction and the influence of other electron-electron interactions make it difficult to extract a quantity that directly relates to the spin.

Kβ X-Ray Emission Spectroscopic Study of a Second-Row Transition Metal (Mo) and Its Application to Nitrogenase-Related Model Complexes

In recent years, X-ray emission spectroscopy (XES) in the Kβ (3p-1s) and valence-to-core (valence-1s) regions has been increasingly used to study metal active sites in (bio)inorganic chemistry and catalysis, providing information about the metal spin state, oxidation state and the identity of coordinated ligands. However, to date this technique has been limited almost exclusively to first-row transition metals. In this work, we present an extension of Kβ XES (in both the 4p-1s and valence-to-1s [or VtC] regions) to the second transition row by performing a detailed experimental and theoretical analysis of the molybdenum emission lines. It is demonstrated in this work that Kβ2 lines are dominated by spin state effects, while VtC XES of a 4d transition metal provides access to metal oxidation state and ligand identity. An extension of Mo Kβ XES to nitrogenase-relevant model complexes shows that the method is sufficiently sensitive to act as a spectator probe for redox events that are localized at the Fe atoms. Mo VtC XES thus has promise for future applications to nitrogenase, as well as a range of other Mo-containing biological cofactors. Further, the clear assignment of the origins of Mo VtC XES features opens up the possibility of applying this method to a wide range of second-row transition metals, thus providing chemists with a site-specific tool for the elucidation of 4d transition metal electronic structure.

NH3 formation from N2 and H2 mediated by molecular tri-iron complexes

Living systems carry out the reduction of N₂ to ammonia (NH₃) through a series of protonation and electron transfer steps under ambient conditions using the enzyme nitrogenase. In the chemical industry, the Haber-Bosch process hydrogenates N₂ but requires high temperatures and pressures. Both processes rely on iron-based catalysts, but molecular iron complexes that promote the formation of NH₃ on addition of H₂ to N₂ have remained difficult to devise. Here, we isolate the tri(iron)bis(nitrido) complex [(Cp'Fe)₃(μ₃-N)₂] (in which Cp' = η⁵-1,2,4-(Me₃C)₃C₅H₂), which is prepared by reduction of [Cp'Fe(μ-I)]₂ under an N₂ atmosphere and comprises three iron centres bridged by two μ₃-nitrido ligands. In solution, this complex reacts with H₂ at ambient temperature (22 °C) and low pressure (1 or 4 bar) to form NH₃. In the solid state, it is converted into the tri(iron)bis(imido) species, [(Cp'Fe)₃(μ₃-NH)₂], by addition of H₂ (10 bar) through an unusual solid-gas, single-crystal-to-single-crystal transformation. In solution, [(Cp'Fe)₃(μ₃-NH)₂] further reacts with H₂ or H⁺ to form NH₃.

Biosynthesis of Nitrogenase Cofactors

Nitrogenase harbors three distinct metal prosthetic groups that are required for its activity. The simplest one is a [4Fe-4S] cluster located at the Fe protein nitrogenase component. The MoFe protein component carries an [8Fe-7S] group called P-cluster and a [7Fe-9S-C-Mo-R-homocitrate] group called FeMo-co. Formation of nitrogenase metalloclusters requires the participation of the structural nitrogenase components and many accessory proteins, and occurs both in situ, for the P-cluster, and in external assembly sites for FeMo-co. The biosynthesis of FeMo-co is performed stepwise and involves molecular scaffolds, metallochaperones, radical chemistry, and novel and unique biosynthetic intermediates. This review provides a critical overview of discoveries on nitrogenase cofactor structure, function, and activity over the last four decades.

Electron Transfer in Nitrogenase

Nitrogenase is the only enzyme capable of reducing N2 to NH3. 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.

Reactivity, Mechanism, and Assembly of the Alternative Nitrogenases

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

The Spectroscopy of Nitrogenases

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

Direct transformation of dinitrogen: synthesis of N-containing organic compounds via N−C bond formation

N-containing organic compounds are of vital importance to lives. Practical synthesis of valuable N-containing organic compounds directly from dinitrogen (N₂), not through ammonia (NH₃), is a holy-grail in chemistry and chemical industry. An essential step for this transformation is the functionalization of the activated N₂ units/ligands to generate N−C bonds. Pioneering works of transition metal-mediated direct conversion of N₂ into organic compounds via N−C bond formation at metal-dinitrogen [N₂-M] complexes have generated diversified coordination modes and laid the foundation of understanding for the N−C bond formation mechanism. This review summarizes those major achievements and is organized by the coordination modes of the [N₂-M] complexes (end-on, side-on, end-on-side-on, etc.) that are involved in the N−C bond formation steps, and each part is arranged in terms of reaction types (N-alkylation, N-acylation, cycloaddition, insertion, etc.) between [N₂-M] complexes and carbon-based substrates. Additionally, earlier works on one-pot synthesis of organic compounds from N₂ via ill-defined intermediates are also briefed. Although almost all of the syntheses of N-containing organic compounds via direct transformation of N₂ so far in the literature are realized in homogeneous stoichiometric thermochemical reaction systems and are discussed here in detail, the sporadically reported syntheses involving photochemical, electrochemical, heterogeneous thermo-catalytic reactions, if any, are also mentioned. This review aims to provide readers with an in-depth understanding of the state-of-the-art and perspectives of future research particularly in direct catalytic and efficient conversion of N₂ into N-containing organic compounds under mild conditions, and to stimulate more research efforts to tackle this long-standing and grand scientific challenge.

Probing Sulfur Chemical and Electronic Structure with Experimental Observation and Quantitative Theoretical Prediction of Kα and Valence-to-Core Kβ X-ray Emission Spectroscopy

An extensive experimental and theoretical study of the Kα and Kβ high-resolution X-ray emission spectroscopy (XES) of sulfur-bearing systems is presented. This study encompasses a wide range of organic and inorganic compounds, including numerous experimental spectra from both prior published work and new measurements. Employing a linear-response time-dependent density functional theory (LR-TDDFT) approach, strong quantitative agreement is found in the calculation of energy shifts of the core-to-core Kα as well as the full range of spectral features in the valence-to-core Kβ spectrum. The ability to accurately calculate the sulfur Kα energy shift supports the use of sulfur Kα XES as a bulk-sensitive tool for assessing sulfur speciation. The fine structure of the sulfur Kβ spectrum, in conjunction with the theoretical results, is shown to be sensitive to the local electronic structure including effects of symmetry, ligand type and number, and, in the case of organosulfur compounds, to the nature of the bonded organic moiety. This agreement between theory and experiment, augmented by the potential for high-access XES measurements with the latest generation of laboratory-based spectrometers, demonstrates the possibility of broad analytical use of XES for sulfur and nearby third-row elements. The effective solution of the forward problem, i.e., successful prediction of detailed spectra from known molecular structure, also suggests future use of supervised machine learning approaches to experimental inference, as has seen recent interest for interpretation of X-ray absorption near-edge structure (XANES).

Special Issue on Nitrogenases and Homologous Systems

The nitrogenase superfamily comprises homologous enzyme systems that carry out fundamentally important processes, including the reduction of N2 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.

Ruthenium 4d-to-2p X-ray Emission Spectroscopy: A Simultaneous Probe of the Metal and the Bound Ligands

Ruthenium 4d-to-2p X-ray emission spectroscopy (XES) was systematically explored for a series of Ru²⁺ and Ru³⁺ species. Complementary density functional theory calculations were utilized to allow for a detailed assignment of the experimental spectra. The studied complexes have a range of different coordination spheres, which allows the influence of the ligand donor/acceptor properties on the spectra to be assessed. Similarly, the contributions of the site symmetry and the oxidation state of the metal were analyzed. Because the 4d-to-2p emission lines are dipole-allowed, the spectral features are intense. Furthermore, in contrast with K- or L-edge X-ray absorption of 4d transition metals, which probe the unoccupied levels, the observed 4p-to-2p XES arises from electrons in filled-ligand- and filled-metal-based orbitals, thus providing simultaneous access to the ligand and metal contributions to bonding. As such, 4d-to-2p XES should be a promising tool for the study of a wide range of 4d transition-metal compounds.

Ruthenium 4d-to-2p XES was applied to a series of molecular Ru complexes with varied coordination environment, oxidation state and site symmetry. Through correlations to calculations, it is demonstrated the Ru 4d-to-2p XES provides a unique probe of both the filled ligand np and filled metal 4d orbitals, providing a promising new tool for the study of a wide range of 4d transition metals.

Bond-valence analyses of the crystal structures of FeMo/V cofactors in FeMo/V proteins

The bond-valence method has been used for valence calculations of FeMo/V cofactors in FeMo/V proteins using 51 crystallographic data sets of FeMo/V proteins from the Protein Data Bank. The calculations show molybdenum(III) to be present in MoFe₇S₉C(Cys)(HHis)[R-(H)homocit] (where H₄homocit is homocitric acid, HCys is cysteine and HHis is histidine) in FeMo cofactors, while vanadium(III) with a more reduced iron complement is obtained for FeV cofactors. Using an error analysis of the calculated valences, it was found that in FeMo cofactors Fe1, Fe6 and Fe7 can be unambiguously assigned as iron(III), while Fe2, Fe3, Fe4 and Fe5 show different degrees of mixed valences for the individual Fe atoms. For the FeV cofactors in PDB entry 5n6y, Fe4, Fe5 and Fe6 correspond to iron(II), iron(II) and iron(III), respectively, while Fe1, Fe2, Fe3 and Fe7 exhibit strongly mixed valences. Special situations such as CO-bound and selenium-substituted FeMo cofactors and O(N)H-bridged FeV cofactors are also discussed and suggest rearrangement of the electron configuration on the substitution of the bridging S atoms.

2D Electrocatalysts for Converting Earth-Abundant Simple Molecules into Value-Added Commodity Chemicals: Recent Progress and Perspectives

The electrocatalytic conversion of earth-abundant simple molecules into value-added commodity chemicals can transform current chemical production regimes with enormous socioeconomic and environmental benefits. For these applications, 2D electrocatalysts have emerged as a new class of high-performance electrocatalyst with massive forward-looking potential. Recent advances in 2D electrocatalysts are reviewed for emerging applications that utilize naturally existing H₂ O, N₂ , O₂ , Cl^- (seawater) and CH₄ (natural gas) as reactants for nitrogen reduction (N₂ → NH₃ ), two-electron oxygen reduction (O₂ → H₂ O₂ ), chlorine evolution (Cl^- → Cl₂ ), and methane partial oxidation (CH₄ → CH₃ OH) reactions to generate NH₃ , H₂ O₂ , Cl₂ , and CH₃ OH. The unique 2D features and effective approaches that take advantage of such features to create high-performance 2D electrocatalysts are articulated with emphasis. To benefit the readers and expedite future progress, the challenges facing the future development of 2D electrocatalysts for each of the above reactions and the related perspectives are provided.

Catalytic N2-to-NH3 (or -N2H4) Conversion by Well-Defined Molecular Coordination Complexes

Nitrogen fixation, the six-electron/six-proton reduction of N₂, to give NH₃, is one of the most challenging and important chemical transformations. Notwithstanding the barriers associated with this reaction, significant progress has been made in developing molecular complexes that reduce N₂ into its bioavailable form, NH₃. This progress is driven by the dual aims of better understanding biological nitrogenases and improving upon industrial nitrogen fixation. In this review, we highlight both mechanistic understanding of nitrogen fixation that has been developed, as well as advances in yields, efficiencies, and rates that make molecular alternatives to nitrogen fixation increasingly appealing. We begin with a historical discussion of N₂ functionalization chemistry that traverses a timeline of events leading up to the discovery of the first bona fide molecular catalyst system and follow with a comprehensive overview of d-block compounds that have been targeted as catalysts up to and including 2019. We end with a summary of lessons learned from this significant research effort and last offer a discussion of key remaining challenges in the field.

Natural and Engineered Electron Transfer of Nitrogenase

As the only enzyme currently known to reduce dinitrogen (N2) to ammonia (NH3), nitrogenase is of significant interest for bio-inspired catalyst design and for new biotechnologies aiming to produce NH3 from N2. In order to reduce N2, nitrogenase must also hydrolyze at least 16 equivalents of adenosine triphosphate (MgATP), representing the consumption of a significant quantity of energy available to biological systems. Here, we review natural and engineered electron transfer pathways to nitrogenase, including strategies to redirect or redistribute electron flow in vivo towards NH3 production. Further, we also review strategies to artificially reduce nitrogenase in vitro, where MgATP hydrolysis is necessary for turnover, in addition to strategies that are capable of bypassing the requirement of MgATP hydrolysis to achieve MgATP-independent N2 reduction.

Identity and function of an essential nitrogen ligand of the nitrogenase cofactor biosynthesis protein NifB

NifB is a radical S-adenosyl-L-methionine (SAM) enzyme that is essential for nitrogenase cofactor assembly. Previously, a nitrogen ligand was shown to be involved in coupling a pair of [Fe₄S₄] clusters (designated K1 and K2) concomitant with carbide insertion into an [Fe₈S₉C] cofactor core (designated L) on NifB. However, the identity and function of this ligand remain elusive. Here, we use combined mutagenesis and pulse electron paramagnetic resonance analyses to establish histidine-43 of Methanosarcina acetivorans NifB (MaNifB) as the nitrogen ligand for K1. Biochemical and continuous wave electron paramagnetic resonance data demonstrate the inability of MaNifB to serve as a source for cofactor maturation upon substitution of histidine-43 with alanine; whereas x-ray absorption spectroscopy/extended x-ray fine structure experiments further suggest formation of an intermediate that lacks the cofactor core arrangement in this MaNifB variant. These results point to dual functions of histidine-43 in structurally assisting the proper coupling between K1 and K2 and concurrently facilitating carbide formation via deprotonation of the initial carbon radical.

NifB is a radical SAM enzyme involved in the biosynthesis of the Mo-nitrogenase cofactor, which is responsible for the ambient conversion of N₂ to NH₃. Here, the authors identify and uncover the function of a His43 residue as an essential nitrogen ligand of NifB in cofactor biosynthesis.