How many metals does it take to fix N2? A mechanistic overview of biological nitrogen fixation

Photocatalytic Dinitrogen Reduction to Ammonia over Biomimetic FeMoSx Nanosheets

Reduction of atmospheric dinitrogen (N2) to ammonia (NH3) using water and sunlight in the absence of sacrificial reducing reagents at room temperature is very challenging and is considered an eco-friendly approach to meet the rapidly increasing demand for nitrogen storage, fertilizers, and a sustainable society. Currently, ammonia production via the energy-intensive Haber-Bosch process causes ∼350 million tons of carbon dioxide (CO2) emission per year. Interestingly, natural N2 fixation by the nitrogenase enzyme occurs under ambient conditions. Unfortunately, N2 fixation on biomimetic catalysts has rarely been studied. To mimic biological nitrogen fixation, herein, we synthesized the novel iron molybdenum sulfide (FeMoSx) micro-/nanosheets via a simple hydrothermal approach for the first time. Further, we successfully demonstrated the photochemical conversion of N2 to NH3 over a biomimetic FeMoSx photocatalyst. The estimated yield is around 99.79 ± 6.0 μmol/h/g photocatalyst with a quantum efficiency of ∼0.028% at 532 nm visible-light wavelength. Besides, we also systematically studied the influence of key factors to further improve NH3 yields. Overall, this study paves a new pathway to fabricate carbon-free, photochemical N2 fixation materials for future applications.

Nitrogen Reduction to Ammonia on a Fe16 Nanocluster: A Computational Study of Catalysis

The sequence of elementary steps leading to reductive ammonia formation from N2 and H2 catalyzed by a Fe16 cluster is studied using generalized gradient approximation density functional theory and an all-electron basis set of triple-ζ quality. The computational methods are validated by comparison to experimental data such as binding energies where possible. First, the associative and dissociative attachment of N2 to Fe16 is considered, followed by exploration of the pathways leading to distal (Fe16-N-NH2) and enzymatic (NFe16-NH2) formation of an amino group. Next, the pathways leading to NH3 formation in both distal and enzymatic cases are examined. Two mechanisms for NH3 detachment have been discovered. An interesting peculiarity of the pathways is that they often proceed with total spin fluctuations, which are related to the rupture and formation of bonds on the surface of the catalyst over the course of the reactions. The reaction Fe16 + N2 + 2H2 → Fe16NH + NH3 is found to be exothermic by 1.02 eV (93.8 kJ/mol).

Thiobacillus spp. and Anaeromyxobacter spp. mediate arsenite oxidation-dependent biological nitrogen fixation in two contrasting types of arsenic-contaminated soils

As(III) oxidation-dependent biological nitrogen fixing (As-dependent BNF) bacteria use a novel biogeochemical process observed in tailings recently. However, our understanding of microorganisms responsible for As-dependent BNF is limited and whether such a process occurs in As-contaminated soils is still unknown. In this study, two contrasting types of soils (surface soils versus river sediments) heavily contaminated by As were selected to study the occurrence of As-dependent BNF. BNF was observed in sediments and soils amended with As(III), whereas no apparent BNF was found in the cultures without As(III). The increased abundances of the nitrogenase gene (nifH) and As(III) oxidation gene (aioA) suggest that an As-dependent BNF process was catalyzed by microorganisms harboring nifH and aioA. In addition, DNA-SIP demonstrated that Thiobacillus spp. and Anaeromyxobacter spp. were putative As-dependent BNF bacteria in As-contaminated soils and sediments, respectively. Metagenomic analysis further suggested that these taxa contained genes responsible for BNF, As(III) oxidation, and CO₂ fixation, demonstrating their capability for serving as As-dependent BNF. These results indicated the occurrence of As-dependent BNF in various As-contaminated habitats. The contrasting geochemical conditions in different types of soil suggested that these conditions may enrich different As-dependent BNF bacteria (Thiobacillus spp. for soils and Anaeromyxobacter spp. for sediments).

A Rearrangement Reaction to Yield a NH4 + Ion Driven by Polyoxometalate Formation

Triethylamine is a volatile liquid and exists in the atmosphere in the gas phase. It is a hazardous air pollutant and identified as a toxic air contaminant. Thus, producing ammonia (a vital chemical for fertilizer production) from the vapor state of this toxic substance is a challenging task. Diffusion of the vapor of triethylamine, (C₂H₅)₃N, into an acidified aqueous solution of sodium molybdate results in the formation of single crystals of compound [(C₂H₅)₃NH]₂[(C₂H₅)₄N][NaMo₈O₂₆] (1). Notably, compound 1 includes a [(C₂H₅)₄N]⁺ cation, even though the concerned reaction mixture was not treated with any tetraethylammonium salt. The formation of the [(C₂H₅)₄N]⁺ cation from (C₂H₅)₃N in an acidic aqueous medium is logically possible only when an ammonium cation (NH₄ ⁺) is formed in the overall reaction: 4(C₂H₅)₃N + 4H⁺ = 3[(C₂H₅)₄N]⁺ + [NH₄]⁺. Although the resulting NH₄ ⁺ cation (identified by Nessler's reagent test) is not included in the crystals of compound 1 as a cation, it can be made associated with a crown ether in the isolation of single crystals of compound [NH₄⊂B15C5]₃[PMo₁₂O₄₀]·B15C5 (2), (B15C5 = benzo-15-crown-5). Crystal structure analysis and ¹H NMR studies of compound 2 have established the presence of an H-bonded NH₄ ⁺ ion in compound 2, thereby established the rearrangement reaction.

Organometallic μ-Nitridodiiron Complexes in Oxidation States Ranging from (III/III) to (IV/IV)

Iron complexes with nitrido ligands are of interest as molecular analogues of key intermediates during N₂-to-NH₃ conversion in industrial or enzymatic processes. Dinuclear iron complexes with a bridging nitrido unit are mostly known in relatively high oxidation states (III/IV or IV/IV), originating from the decomposition of azidoiron precursors via high-valent Fe≡N intermediates. The use of a tetra-NHC macrocyclic scaffold ligand (NHC = N-heterocyclic carbene) has now allowed for the isolation of a series of organometallic μ-nitridodiiron complexes ranging from the mid-valent Fe^III-N-Fe^III (1) via mixed-valent Fe^III-N-Fe^IV (type 4) to the high-valent Fe^IV-N-Fe^IV (type 5) species that are interconverted at moderate potentials, accompanied by axial ligand binding at the Fe^IV sites. Magnetic measurements and electron paramagnetic resonance spectroscopy showed the homovalent complexes to be diamagnetic and the mixed-valent system to feature an S = 1/2 ground state due to very strong antiferromagnetic coupling. The bonding in the Fe-N-Fe moiety has been further probed by crystallographic structure determination, ⁵⁷Fe Mössbauer and UV-vis spectroscopies, as well as density functional theory computations, which revealed high covalency and nearly identical Fe-N distances across this redox series. The latter has been rationalized in terms of the nonbonding nature of the combination of Fe d_z² atomic orbitals from which electrons are successively removed upon oxidation, and these redox processes are best described as being metal-centered. The tetra-NHC-ligated μ-nitridodiiron series complements a set of related complexes with single-atom μ-oxido and μ-phosphido bridges, but the Fe-N-Fe core exhibits a comparatively high stability over several oxidation states. This promises interesting applications in view of the manifold catalytic uses of μ-nitridodiiron complexes based on macrocyclic N-donor porphinato(2-) or phthalocyaninato(2-) ligands.

Complete genome sequence of a nitrate reducing bacteria, Algoriphagus sp. Y33 isolated from the water of the Indian Ocean

Algoriphagus sp. Y33, is a nitrate-reducing bacterium isolated from the water of Indian Ocean. Here, we present the complete genome sequence of strain Y33. The genome has one circular chromosome of 6,378,979 bp, with an average GC content of 41.86%, and 5757 coding sequences. According to the annotation analysis, strain Y33 encodes 32 proteins related to nitrogen metabolism. To our knowledge, this is the first report of Algoriphagus sp. isolated from the Indian Ocean with the capacity of nitrate reduction, which will provide insights into regulatory mechanisms of nitrate uptake by heterotrophic bacteria and the global nitrogen cycling.

Photocatalyst-enzyme hybrid systems for light-driven biotransformation

Enzymes catalyse target reactions under mild conditions with high efficiency, as well as excellent regional-, stereo-, and enantiomeric selectivity. Photocatalysis utilises sustainable and environment-friendly light power to realise efficient chemical conversion. By combining the interdisciplinary advantages of photo- and enzymatic catalysis, the photocatalyst-enzyme hybrid systems have proceeded various light-driven biotransformation with high efficiency under environmentally benign conditions, thus, attracting unparalleled focus during the last decades. It has also been regarded as a promising pathway towards green chemistry utilising ubiquitous solar energy. This systematic review gives insight into this research field by classifying the existing photocatalyst-enzyme hybrid systems into three sections based on different hybridizing modes between photo- and enzymatic catalysis. Furthermore, existing challenges and proposed strategies are discussed within this context. The first system summarised is the cofactor-mediated hybrid system, in which natural/artificial cofactors act as reducing equivalents that connect photocatalysts with enzymes for light-driven enzymatic biotransformation. Second, the direct contact-based photocatalyst-enzyme hybrid systems are described, including two different kinds of electron exchange sites on the enzyme molecules. Third, some cases where photocatalysts and enzymes are integrated into a reaction cascade with specific intermediates will be discussed in the following chapter. Finally, we provide perspective concerning the future of this field.

Vegetative cells may perform nitrogen fixation function under nitrogen deprivation in Anabaena sp. strain PCC 7120 based on genome-wide differential expression analysis

Nitrogen assimilation is strictly regulated in cyanobacteria. In an inorganic nitrogen-deficient environment, some vegetative cells of the cyanobacterium Anabaena differentiate into heterocysts. We assessed the photosynthesis and nitrogen-fixing capacities of heterocysts and vegetative cells, respectively, at the transcriptome level. RNA extracted from nitrogen-replete vegetative cells (NVs), nitrogen-deprived vegetative cells (NDVs), and nitrogen-deprived heterocysts (NDHs) in Anabaena sp. strain PCC 7120 was evaluated by transcriptome sequencing. Paired comparisons of NVs vs. NDHs, NVs vs. NDVs, and NDVs vs. NDHs revealed 2,044 differentially expressed genes (DEGs). Kyoto Encyclopedia of Genes and Genomes enrichment analysis of the DEGs showed that carbon fixation in photosynthetic organisms and several nitrogen metabolism-related pathways were significantly enriched. Synthesis of Gvp (Gas vesicle synthesis protein gene) in NVs was blocked by nitrogen deprivation, which may cause Anabaena cells to sink and promote nitrogen fixation under anaerobic conditions; in contrast, heterocysts may perform photosynthesis under nitrogen deprivation conditions, whereas the nitrogen fixation capability of vegetative cells was promoted by nitrogen deprivation. Immunofluorescence analysis of nitrogenase iron protein suggested that the nitrogen fixation capability of vegetative cells was promoted by nitrogen deprivation. Our findings provide insight into the molecular mechanisms underlying nitrogen fixation and photosynthesis in vegetative cells and heterocysts at the transcriptome level. This study provides a foundation for further functional verification of heterocyst growth, differentiation, and water bloom control.

Probing the All-Ferrous States of Methanogen Nitrogenase Iron Proteins

The Fe protein of nitrogenase reduces two C1 substrates, CO₂ and CO, under ambient conditions when its [Fe₄S₄] cluster adopts the all-ferrous [Fe₄S₄]⁰ state. Here, we show disparate reactivities of the nifH- and vnf-encoded Fe proteins from Methanosarcina acetivorans (designated MaNifH and MaVnfH) toward C1 substrates in the all-ferrous state, with the former capable of reducing both CO₂ and CO to hydrocarbons, and the latter only capable of reducing CO to hydrocarbons at substantially reduced yields. EPR experiments conducted at varying solution potentials reveal that MaVnfH adopts the all-ferrous state at a more positive reduction potential than MaNifH, which could account for the weaker reactivity of the MaVnfH toward C1 substrates than MaNifH. More importantly, MaVnfH already displays the g = 16.4 parallel-mode EPR signal that is characteristic of the all-ferrous [Fe₄S₄]⁰ cluster at a reduction potential of -0.44 V, and the signal reaches 50% maximum intensity at a reduction potential of -0.59 V, suggesting the possibility of this Fe protein to access the all-ferrous [Fe₄S₄]⁰ state under physiological conditions. These results bear significant relevance to the long-lasting debate of whether the Fe protein can utilize the [Fe₄S₄]^0/2+ redox couple to support a two-electron transfer during substrate turnover which, therefore, is crucial for expanding our knowledge of the reaction mechanism of nitrogenase and the cellular energetics of nitrogenase-based processes.

The Medicago truncatula Vacuolar iron Transporter-Like proteins VTL4 and VTL8 deliver iron to symbiotic bacteria at different stages of the infection process

The symbiotic relationship between legumes and rhizobium bacteria in root nodules has a high demand for iron, and questions remain regarding which transporters are involved. Here, we characterize two nodule-specific Vacuolar iron Transporter-Like (VTL) proteins in Medicago truncatula. Localization of fluorescent fusion proteins and mutant studies were carried out to correlate with existing RNA-seq data showing differential expression of VTL4 and VTL8 during early and late infection, respectively. The vtl4 insertion lines showed decreased nitrogen fixation capacity associated with more immature nodules and less elongated bacteroids. A mutant line lacking the tandemly-arranged VTL4-VTL8 genes, named 13U, was unable to develop functional nodules and failed to fix nitrogen, which was almost fully restored by expression of VTL8 alone. Using a newly developed lux reporter to monitor iron status of the bacteroids, a moderate decrease in luminescence signal was observed in vtl4 mutant nodules and a strong decrease in 13U nodules. Iron transport capability of VTL4 and VTL8 was shown by yeast complementation. These data indicate that VTL8, the closest homologue of SEN1 in Lotus japonicus, is the main route for delivering iron to symbiotic rhizobia. We propose that a failure in iron protein maturation leads to early senescence of the bacteroids.

Reduction of Substrates by Nitrogenases

Nitrogenase is the enzyme that catalyzes biological N₂ reduction to NH₃. This enzyme achieves an impressive rate enhancement over the uncatalyzed reaction. Given the high demand for N₂ 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 N₂ 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 CO₂, is also discussed, and remaining challenges in understanding nitrogenase substrate reduction are considered.

Ammonia Synthesis through Hydrolysis of a Trianionic Pincer Ligand-Supported Molybdenum-Nitride Complex

Reported is the hydrolysis of a homogeneous Mo-nitride complex bearing a trianionic pincer-type ligand to produce ammonia. Treating the anionic [(ONO)]Mo≡N(OtBu)]Ph₃ PCH₃ with two equivalents of water produces ammonia and the dioxo complex [(ONO)]MoO₂ ]Ph₃ PCH₃ . X-Ray crystal structures of the starting nitrido complex and product dioxo complex are presented. Evidence for ammonia release comes from GC-MS and deuterium-labelling studies. The reaction is presented in the context of a two-stage solar thermochemical dinitrogen fixation process as the solid-state nitride hydrolysis step.

Reactivity of [Fe4S4] Clusters toward C1 Substrates: Mechanism, Implications, and Potential Applications

FeS proteins are metalloproteins prevalent in the metabolic pathways of most organisms, playing key roles in a wide range of essential cellular processes. A member of this protein family, the Fe protein of nitrogenase, is a homodimer that contains a redox-active [Fe₄S₄] cluster at the subunit interface and an ATP-binding site within each subunit. During catalysis, the Fe protein serves as the obligate electron donor for its catalytic partner, transferring electrons concomitant with ATP hydrolysis to the cofactor site of the catalytic component to enable substrate reduction. The effectiveness of Fe protein in electron transfer is reflected by the unique reactivity of nitrogenase toward small-molecule substrates. Most notably, nitrogenase is capable of catalyzing the ambient reduction of N₂ and CO into NH₄⁺ and hydrocarbons, respectively, in reactions that parallel the important industrial Haber-Bosch and Fischer-Tropsch processes. Other than participating in nitrogenase catalysis, the Fe protein also functions as an essential factor in nitrogenase assembly, which again highlights its capacity as an effective, ATP-dependent electron donor. Recently, the Fe protein of a soil bacterium, Azotobacter vinelandii, was shown to act as a reductase on its own and catalyze the ambient conversion of CO₂ to CO at its [Fe₄S₄] cluster either under in vitro conditions when a strong reductant is supplied or under in vivo conditions through the action of an unknown electron donor(s) in the cell. Subsequently, the Fe protein of a mesophilic methanogenic organism, Methanosarcina acetivorans, was shown to catalyze the in vitro reduction of CO₂ and CO into hydrocarbons under ambient conditions, illustrating an impact of protein scaffold on the redox properties of the [Fe₄S₄] cluster and the reactivity of the cluster toward C1 substrates. This reactivity was further traced to the [Fe₄S₄] cluster itself, as a synthetic [Fe₄S₄] compound was shown to catalyze the reduction of CO₂ and CO to hydrocarbons in solutions in the presence of a strong reductant. Together, these observations pointed to an inherent ability of the [Fe₄S₄] clusters and, possibly, the FeS clusters in general to catalyze C1-substrate reduction. Theoretical calculations have led to the proposal of a plausible reaction pathway that involves the formation of hydrocarbons via aldehyde-like intermediates, providing an important framework for further mechanistic investigations of FeS-based activation and reduction of C1 substrates. In this Account, we summarize the recent work leading to the discovery of C1-substrate reduction by protein-bound and free [Fe₄S₄] clusters as well as the current mechanistic understanding of this FeS-based reactivity. In addition, we briefly discuss the evolutionary implications of this discovery and potential applications that could be developed to enable FeS-based strategies for the ambient recycling of unwanted C1 waste into useful chemical commodities.

Characterization of the Earliest Intermediate of Fe-N2 Protonation: CW and Pulse EPR Detection of an Fe-NNH Species and Its Evolution to Fe-NNH2

Iron diazenido species (Fe(NNH)) have been proposed as the earliest intermediates of catalytic N₂-to-NH₃ conversion (N₂RR) mediated by synthetic iron complexes and relatedly as intermediates of N₂RR by nitrogenase enzymes. However, direct identification of such iron species, either during or independent of catalysis, has proven challenging owing to their high degree of instability. The isolation of more stable silylated diazenido analogues, Fe(NNSiR₃), and also of further downstream intermediates (e.g., Fe(NNH₂)), nonetheless points to Fe(NNH) as the key first intermediate of protonation in synthetic systems. Herein we show that low-temperature protonation of a terminally bound Fe-N₂^- species, supported by a bulky trisphosphinoborane ligand (^ArP₃^B), generates an S = 1/2 terminal Fe(NNH) species that can be detected and characterized by continuous-wave (CW) and pulse EPR techniques. The ¹H-hyperfine for ^ArP₃^BFe(NNH) derived from the presented ENDOR studies is diagnostic for the distally bound H atom ( a_iso = 16.5 MHz). The Fe(NNH) species evolves further to cationic [Fe(NNH₂)]⁺ in the presence of additional acid, the latter being related to a previously characterized [Fe(NNH₂)]⁺ intermediate of N₂RR mediated by a far less encumbered iron tris(phosphine)borane catalyst. While catalysis is suppressed in the present sterically very crowded system, N₂-to-NH₃ conversion can nevertheless be demonstrated. These observations in sum add support to the idea that Fe(NNH) plays a central role as the earliest intermediate of Fe-mediated N₂RR in a synthetic system.

N-Heterocyclic Carbenes in Materials Chemistry

N-Heterocyclic carbenes (NHCs) have become one of the most widely studied class of ligands in molecular chemistry and have found applications in fields as varied as catalysis, the stabilization of reactive molecular fragments, and biochemistry. More recently, NHCs have found applications in materials chemistry and have allowed for the functionalization of surfaces, polymers, nanoparticles, and discrete, well-defined clusters. In this review, we provide an in-depth look at recent advances in the use of NHCs for the development of functional materials.

Breaking Molecular Nitrogen under Mild Conditions with an Atomically Clean Lanthanide Surface

A route to break molecular nitrogen (N₂) under mild conditions is demonstrated by N₂ gas cracking on, and incorporation into, lanthanide films. Successful growth of lanthanide nitride thin films, made by evaporation of lanthanides in a partial N₂ atmosphere at room temperature and pressure as low as 10^-4 Torr, is confirmed using X-ray diffraction. In situ conductance measurements of pure lanthanide thin films exposed to N₂ gas show an immediate surface reaction and a slower bulk reaction. Finally, we report partial reversal of the nitrogen incorporation in a lanthanide nitride by cycling vacuum and nitrogen conditions in the sample chamber.

Site-Specific Oxidation State Assignments of the Iron Atoms in the [4Fe:4S]2+/1+/0 States of the Nitrogenase Fe-Protein

The nitrogenase iron protein (Fe-protein) contains an unusual [4Fe:4S] iron-sulphur cluster that is stable in three oxidation states: 2+, 1+, and 0. Here, we use spatially resolved anomalous dispersion (SpReAD) refinement to determine oxidation assignments for the individual irons for each state. Additionally, we report the 1.13-Å resolution structure for the ADP bound Fe-protein, the highest resolution Fe-protein structure presently determined. In the dithionite-reduced [4Fe:4S]1+ state, our analysis identifies a solvent exposed, delocalized Fe2.5+ pair and a buried Fe2+ pair. We propose that ATP binding by the Fe-protein promotes an internal redox rearrangement such that the solvent-exposed Fe pair becomes reduced, thereby facilitating electron transfer to the nitrogenase molybdenum iron-protein. In the [4Fe:4S]0 and [4Fe:4S]2+ states, the SpReAD analysis supports oxidation states assignments for all irons in these clusters of Fe2+ and valence delocalized Fe2.5+ , respectively.

Requirements for Lewis Acid-Mediated Capture and N-N Bond Cleavage of Hydrazine at Iron

An iron complex bearing a pyridine(dicarbene) pincer was designed to probe the requirements of Lewis acid-enabled N2H4 capture and subsequent N-N bond cleavage. Appended boron Lewis acids were installed by two methods to circumvent the incompatibilities associated with Lewis acid/base quenching of free carbenes and boranes. N2H4 capture by borane Lewis acids is dependent on both the Lewis acidity and the steric profile about boron. A substitutionally inert primary coordination sphere at iron prevents an Fe-N2H4 interaction as well as N-N bond homolysis upon reduction.

How feasible is the reversible S-dissociation mechanism for the activation of FeMo-co, the catalytic site of nitrogenase?

The active site of the enzyme nitrogenase (N₂→ NH₃) is a Fe₇MoS₉C 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 N₂ and binding reaction intermediates. Accumulated experimental evidence points to the Fe2-S2B-Fe6 domain as the centre of catalytic hydrogenation of N₂. 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 N₂ 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 H₂S (or SH^-) is endergonic by 20-25 kcal mol^-1, partly because the separating H₂S 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 S2BH₂ from Fe2 is favourable, likely, and propitious for subsequent H transfer to bound N₂ 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.

Crystallization of Nitrogenase Proteins

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 N₂ 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.

Plant-soil feedbacks on free-living nitrogen fixation over geological time

Free-living heterotrophic nitrogen fixation (FNF) is a widespread nitrogen input pathway in terrestrial ecosystems. However, questions remain over the relative influence of co-occurring controls on patterns of heterotrophic FNF activity, especially across generalized stages of primary succession, from biomass accumulation to retrogressive phases. Here, we experimentally test two alternative hypotheses regarding FNF rates during ecosystem development: (H1) site (i.e., changes in soil fertility during succession) is the primary driver of leaf-litter FNF rates, vs. (H2) leaf-litter chemistry is the primary determinant of FNF activity across a broad range of ecosystem conditions. We evaluated these hypotheses across a well-studied soil chronosequence in California (i.e., the Ecological Staircase), which spans ~1 million years of ecosystem development and displays extreme ranges in plant-soil nutrient conditions, culminating in the nutrient depleted and stunted Pygmy forest. Across this successional gradient, we implemented a reciprocal leaf-litter transplant and a common garden litter bag decomposition experiment with senesced needles of Pinus muricata. Our results support H1: rates of FNF were similar for all leaf-litter types decomposed at the same site regardless of initial leaf-litter C and nutrient contents. FNF rates sharply declined from the maximal to retrogressive stage of succession. Trends in P dynamics during decomposition suggest an important role of P in regulating FNF. For example, P. muricata litter collected from the infertile Pygmy site displayed substantially higher FNF rates when decomposed at the fertile site, in part by immobilizing significant quantities of P from the soil at the fertile site. Conversely, P. muricata litter collected from the fertile site decomposed more slowly at the Pygmy site, with concomitant declines in FNF rates that matched those of Pygmy site litter decomposed in situ. These results are consistent with the idea that, over millennia, long-term declines in P availability feedback to constrain FNF rates, in part explaining the emergence of extremely nutrient-poor and retrograded ecosystems.

Efficient Nitrogen Fixation via a Redox-Flexible Single-Iron Site with Reverse-Dative Iron → Boron σ Bonding

Model systems of the FeMo cofactor of nitrogenase have been explored extensively in catalysis to gain insights into their ability for nitrogen fixation that is of vital importance to the human society. Here we investigate the trigonal pyramidal borane-ligand Fe complex by first-principles calculations, and find that the variation of oxidation state of Fe along the reaction path correlates with that of the reverse-dative Fe → B bonding. The redox-flexibility of the reverse-dative Fe → B bonding helps to provide an electron reservoir that buffers and stabilizes the evolution of Fe oxidation state, which is essential for forming the key intermediates of N₂ activation. Our work provides insights for understanding and optimizing homogeneous and surface single-atom catalysts with reverse-dative donating ligands for efficient dinitrogen fixation. The extension of this kind of molecular catalytic active center to heterogeneous catalysts with surface single-clusters is also discussed.

Mechanism of N2 Reduction Catalyzed by Fe-Nitrogenase Involves Reductive Elimination of H2

Of the three forms of nitrogenase (Mo-nitrogenase, V-nitrogenase, and Fe-nitrogenase), Fe-nitrogenase has the poorest ratio of N2 reduction relative to H2 evolution. Recent work on the Mo-nitrogenase has revealed that reductive elimination of two bridging Fe-H-Fe hydrides on the active site FeMo-cofactor to yield H2 is a key feature in the N2 reduction mechanism. The N2 reduction mechanism for the Fe-nitrogenase active site FeFe-cofactor was unknown. Here, we have purified both component proteins of the Fe-nitrogenase system, the electron-delivery Fe protein (AnfH) plus the catalytic FeFe protein (AnfDGK), and established its mechanism of N2 reduction. Inductively coupled plasma optical emission spectroscopy and mass spectrometry show that the FeFe protein component does not contain significant amounts of Mo or V, thus ruling out a requirement of these metals for N2 reduction. The fully functioning Fe-nitrogenase system was found to have specific activities for N2 reduction (1 atm) of 181 ± 5 nmol NH3 min-1 mg-1 FeFe protein, for proton reduction (in the absence of N2) of 1085 ± 41 nmol H2 min-1 mg-1 FeFe protein, and for acetylene reduction (0.3 atm) of 306 ± 3 nmol C2H4 min-1 mg-1 FeFe protein. Under turnover conditions, N2 reduction is inhibited by H2 and the enzyme catalyzes the formation of HD when presented with N2 and D2. These observations are explained by the accumulation of four reducing equivalents as two metal-bound hydrides and two protons at the FeFe-cofactor, with activation for N2 reduction occurring by reductive elimination of H2.

Fe-mediated HER vs N2RR: Exploring Factors that Contribute to Selectivity in P3 EFe(N2) (E = B, Si, C) Catalyst Model Systems

Mitigation of the hydrogen evolution reaction (HER) is a key challenge in selective small molecule reduction catalysis. This is especially true of catalytic nitrogen (N₂) and carbon dioxide (CO₂) reduction reactions (N₂RR and CO₂RR, respectively) using H⁺/e^- currency. Here we explore, via DFT calculations, three iron model systems, P₃ ^EFe (E = B, Si, C), known to mediate both N₂RR and HER, but with different selectivity depending on the identity of the auxiliary ligand. It is suggested that the respective efficiencies of these systems for N₂RR trend with the predicted N-H bonds strengths of two putative hydrazido intermediates of the proposed catalytic cycle, P₃ ^EFe(NNH₂)⁺ and P₃ ^EFe(NNH₂). Further, a mechanism is presented for undesired HER consistent with DFT studies, and previously reported experimental data, for these systems; bimolecular proton-coupled-electron-transfer (PCET) from intermediates with weak N-H bonds is posited as an important source of H_2' instead of more traditional scenarios that proceed via metal hydride intermediates and proton transfer/electron transfer (PT/ET) pathways. Wiberg bond indices provide additional insight into key factors related to the degree of stabilization of P₃ ^EFe(NNH₂) species, factors that trend with overall product selectivity.

Hydrazine Capture and N-N Bond Cleavage at Iron Enabled by Flexible Appended Lewis Acids

Incorporation of two 9-borabicyclo[3.3.1]nonyl substituents within the secondary coordination sphere of a pincer-based Fe(II) complex provides Lewis acidic sites capable of binding 1 or 2 equiv of N₂H₄. Reduction of the 1:1 Fe:N₂H₄ species affords a rare Fe(NH₂)₂ complex in which the amido ligands are stabilized through interactions with the appended boranes. The NH₂ units can be released as NH₃ upon protonation and exchanged with exogenous N₂H₄.

Electrochemical and structural characterization of Azotobacter vinelandii flavodoxin II

Azotobacter vinelandii flavodoxin II serves as a physiological reductant of nitrogenase, the enzyme system mediating biological nitrogen fixation. Wildtype A. vinelandii flavodoxin II was electrochemically and crystallographically characterized to better understand the molecular basis for this functional role. The redox properties were monitored on surfactant-modified basal plane graphite electrodes, with two distinct redox couples measured by cyclic voltammetry corresponding to reduction potentials of -483 ± 1 mV and -187 ± 9 mV (vs. NHE) in 50 mM potassium phosphate, 150 mM NaCl, pH 7.5. These redox potentials were assigned as the semiquinone/hydroquinone couple and the quinone/semiquinone couple, respectively. This study constitutes one of the first applications of surfactant-modified basal plane graphite electrodes to characterize the redox properties of a flavodoxin, thus providing a novel electrochemical method to study this class of protein. The X-ray crystal structure of the flavodoxin purified from A. vinelandii was solved at 1.17 Å resolution. With this structure, the native nitrogenase electron transfer proteins have all been structurally characterized. Docking studies indicate that a common binding site surrounding the Fe-protein [4Fe:4S] cluster mediates complex formation with the redox partners Mo-Fe protein, ferredoxin I, and flavodoxin II. This model supports a mechanistic hypothesis that electron transfer reactions between the Fe-protein and its redox partners are mutually exclusive.

Reversible Protonated Resting State of the Nitrogenase Active Site

Protonated states of the nitrogenase active site are mechanistically significant since substrate reduction is invariably accompanied by proton uptake. We report the low pH characterization by X-ray crystallography and EPR spectroscopy of the nitrogenase molybdenum iron (MoFe) proteins from two phylogenetically distinct nitrogenases (Azotobacter vinelandii, Av, and Clostridium pasteurianum, Cp) at pHs between 4.5 and 8. X-ray data at pHs of 4.5–6 reveal the repositioning of side chains along one side of the FeMo-cofactor, and the corresponding EPR data shows a new S = 3/2 spin system with spectral features similar to a state previously observed during catalytic turnover. The structural changes suggest that FeMo-cofactor belt sulfurs S3A or S5A are potential protonation sites. Notably, the observed structural and electronic low pH changes are correlated and reversible. The detailed structural rearrangements differ between the two MoFe proteins, which may reflect differences in potential protonation sites at the active site among nitrogenase species. These observations emphasize the benefits of investigating multiple nitrogenase species. Our experimental data suggest that reversible protonation of the resting state is likely occurring, and we term this state “E₀H⁺”, following the Lowe–Thorneley naming scheme.

Testing the Push-Pull Hypothesis: Lewis Acid Augmented N2 Activation at Iron

We present a systematic investigation of the structural and electronic changes that occur in an Fe(0)-N2 unit (Fe(depe)2(N2); depe = 1,2-bis(diethylphosphino)ethane) upon the addition of exogenous Lewis acids. Addition of neutral boranes, alkali metal cations, and an Fe2+ complex increases the N-N bond activation (Δ νNN up to 172 cm-1), decreases the Fe(0)-N2 redox potential, polarizes the N-N bond, and enables -N protonation at uncommonly anodic potentials. These effects were rationalized using combined experimental and theoretical studies.

Exploring secondary-sphere interactions in Fe-N x H y complexes relevant to N2 fixation

Hydrogen bonding and other types of secondary-sphere interactions are ubiquitous in metalloenzyme active sites and are critical to the transformations they mediate. Exploiting secondary sphere interactions in synthetic catalysts to study the role(s) they might play in biological systems, and to develop increasingly efficient catalysts, is an important challenge. Whereas model studies in this broad context are increasingly abundant, as yet there has been relatively little progress in the area of synthetic catalysts for nitrogen fixation that incorporate secondary sphere design elements. Herein we present our first study of Fe-N x H y complexes supported by new tris(phosphine)silyl ligands, abbreviated as [SiPNMe3] and [SiPiPr2PNMe], that incorporate remote tertiary amine hydrogen-bond acceptors within a tertiary phosphine/amine 6-membered ring. These remote amine sites facilitate hydrogen-bonding interactions via a boat conformation of the 6-membered ring when certain nitrogenous substrates (e.g., NH3 and N2H4) are coordinated to the apical site of a trigonal bipyramidal iron complex, and adopt a chair conformation when no H-bonding is possible (e.g., N2). Countercation binding at the cyclic amine is also observed for anionic {Fe-N2}- complexes. Reactivity studies in the presence of proton/electron sources show that the incorporated amine functionality leads to rapid generation of catalytically inactive Fe-H species, thereby substantiating a hydride termination pathway that we have previously proposed deactivates catalysts of the type [EPR3]FeN2 (E = Si, C).

Catalytic NH3 Synthesis using N2 /H2 at Molecular Transition Metal Complexes: Concepts for Lead Structure Determination using Computational Chemistry

While industrial NH₃ synthesis based on the Haber-Bosch-process was invented more than a century ago, there is still no molecular catalyst available which reduces N₂ in the reaction system N₂ /H₂ to NH₃ . As the many efforts of experimentally working research groups to develop a molecular catalyst for NH₃ synthesis from N₂ /H₂ have led to a variety of stoichiometric reductions it seems justified to undertake the attempt of systematizing the various approaches of how the N₂ molecule might be reduced to NH₃ with H₂ at a transition metal complex. In this contribution therefore a variety of intuition-based concepts are presented with the intention to show how the problem can be approached. While no claim for completeness is made, these concepts intend to generate a working plan for future research. Beyond this, it is suggested that these concepts should be evaluated with regard to experimental feasibility by checking barrier heights of single reaction steps and also by computation of whole catalytic cycles employing density functional theory (DFT) calculations. This serves as a tool which extends the empirically driven search process and expands it by computed insights which can be used to rationalize the various challenges which must be met.

Can boron antisites of BNNTs be an efficient metal-free catalyst for nitrogen fixation? – A DFT investigation

Nitrogen fixation is a challenging reaction under ambient conditions.

Activation and reduction of carbon dioxide by nitrogenase iron proteins

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

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

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

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

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

Plant-Microbiota Interactions as a Driver of the Mineral Turnover in the Rhizosphere

A major challenge facing agriculture in the 21st century is the need to increase the productivity of cultivated land while reducing the environmentally harmful consequences of mineral fertilization. The microorganisms thriving in association and interacting with plant roots, the plant microbiota, represent a potential resource of plant probiotic function, capable of conjugating crop productivity with sustainable management in agroecosystems. However, a limited knowledge of the organismal interactions occurring at the root-soil interface is currently hampering the development and use of beneficial plant-microbiota interactions in agriculture. Therefore, a comprehensive understanding of the recruitment cues of the plant microbiota and the molecular basis of nutrient turnover in the rhizosphere will be required to move toward efficient and sustainable crop nutrition. In this chapter, we will discuss recent insights into plant-microbiota interactions at the root-soil interface, illustrate the processes driving mineral dynamics in soil, and propose experimental avenues to further integrate the metabolic potential of the plant microbiota into crop management and breeding strategies for sustainable agricultural production.

Waltzing around cofactors

The metallocofactor involved in fixing nitrogen is not a rigid scaffold, as was previously thought.

Facet-dependent solar ammonia synthesis of BiOCl nanosheets via a proton-assisted electron transfer pathway

Under the pressure of a fossil fuels shortage and global climate change, solar ammonia synthesis and the need to develop N2 fixation under mild conditions is becoming more urgent need; however, their intrinsic mechanisms still remain unclear. Herein, we demonstrate that the kinetic inertia of N2 can be overcome using oxygen vacancies (OVs) of BiOCl as the catalytic centers to create lower energy molecular steps, which are amendable for the solar light driven N-N triple bond cleavage via a proton-assisted electron transfer pathway. Moreover, the distinct structures of OVs on different BiOCl facets strongly determine the N2 fixation pathways by influencing both the adsorption structure and the activation level of N2. The fixation of terminal end-on bound N2 on the OVs of BiOCl {001} facets follows an asymmetric distal mode by selectively generating NH3, while the reduction of side-on bridging N2 on the OVs of BiOCl {010} facets is more energetically favorable in a symmetric alternating mode to produce N2H4 as the main intermediate.

Exploring excited state properties of 7-hydroxy and 7-methoxy 4-methycoumarin: a combined time-dependent density functional theory/effective fragment potential study

Hydrogen bond dynamics, C–OH bond contracting, O–H bond stretching and O–H⋯O HB strengthening reveal the ESHT in 4MU at the S₁state.

A Conformational Switch Triggers Nitrogenase Protection from Oxygen Damage by Shethna Protein II (FeSII)

The two-component metalloprotein nitrogenase catalyzes the reductive fixation of atmospheric dinitrogen into bioavailable ammonium in diazotrophic prokaryotes. The process requires an efficient energy metabolism, so that although the metal clusters of nitrogenase rapidly decompose in the presence of dioxygen, many free-living diazotrophs are obligate aerobes. In order to retain the functionality of the nitrogen-fixing enzyme, some of these are able to rapidly "switch-off" nitrogenase, by shifting the enzyme into an inactive but oxygen-tolerant state. Under these conditions the two components of nitrogenase form a stable, ternary complex with a small [2Fe:2S] ferredoxin termed FeSII or the "Shethna protein II". Here we have produced and isolated Azotobacter vinelandii FeS II and have determined its three-dimensional structure to 2.1 Å resolution by X-ray diffraction. In the crystals, the dimeric protein was present in two distinct states that differ in the conformation of an extended loop in close proximity to the iron-sulfur cluster. We show that this rearrangement is redox-dependent and forms the molecular basis for oxygen-dependent conformational protection of nitrogenase. Protection assays highlight that FeSII binds to a preformed complex of MoFe and Fe protein upon activation, primarily through electrostatic interactions. The surface properties and known complexes of nitrogenase component proteins allow us to propose a model of the conformationally protected ternary complex of nitrogenase.