Mechanism of nitrogen fixation by nitrogenase: the next stage

Easily reduced bis-pincer (NS2)2molybdenum(iv) to (NHS2)2Mo(ii) by alcohols vs. redox-inert (NS2)(NHS2)iron(iii) complexes

Iron and molybdenum complexes supported by a pincer-type dianionic [NS₂]²⁻ donor were prepared to compare their structural, spectroscopic, and electrochemical properties.

An arene-tethered silylene ligand enabling reversible dinitrogen binding to iron and catalytic silylation

A silylene–iron(0) dinitrogen complex enabled the catalytic silylation of N₂ with high activity.

The integration of experiment and computational modelling in heterogeneously catalysed ammonia synthesis over metal nitrides

The integration of experimental studies and computational modelling is a powerful approach for the enhanced understanding of ammonia synthesis mechanisms and for the design of new catalysts.

Cooperative bimetallic reactivity of a heterodinuclear molybdenum–copper model of Mo–Cu CODH

Modeling the reactivity of Mo–Cu CODH: Cu(i) brings the substrate close to Mo–oxo and develops electrophilic character in CO carbon.

Comparison of hydroxycarboxylato imidazole molybdenum(iv) complexes and nitrogenase protein structures: indirect evidence for the protonation of homocitrato FeMo-cofactors

Glycolato and lactato imidazole molybdenum(iv) complexes are used for structural comparison with FeMo-cofactors of MoFe-protein structures.

Triply bridged dinuclear ruthenium complexes bearing alkylbis(2-pyridylmethyl)amine in the mixed-valence state of Ru(ii)–Ru(iii)

Five diruthenium complexes in the mixed-valence state of Ru(ii)–Ru(iii), triply bridged by halogeno and methoxido ligands, were newly synthesized and compared.

On the possibility of an Eley–Rideal mechanism for ammonia synthesis on Mn6N5+x (x = 1)-(111) surfaces

A complete pathway for ammonia synthesis via an Eley–Rideal mechanism has been calculated with DFT.

Triphos–Fe dinitrogen and dinitrogen–hydride complexes: relevance to catalytic N2 reductions

Mechanistic investigations of the catalyzed reduction of N₂ with a rare (tridentate phosphine)Fe(0) bis dinitrogen complex.

Impact of H-termination on the nitrogen reduction reaction of molybdenum carbide as an electrochemical catalyst

H-Terminals can remarkably affect the performance of catalysts in nitrogen reduction.

Dinitrogen photoactivation: status quo and future perspectives

New perspectives for dinitrogen activation: an overview of photochemical pathways to cleave the strong N–N bond.

Surface Single-Cluster Catalyst for N2-to-NH3 Thermal Conversion

The ammonia synthesis from N₂ is of vital importance, with imitating biological nitrogen fixation attracted much interest. Herein, we investigate the catalytic mechanisms of N₂-to-NH₃ thermal conversion on the singly dispersed bimetallic catalyst Rh₁Co₃/CoO(011), and find that the preferred pathway is an associative mechanism analogous to the biological process, in which alternating hydrogenations of the N₂ occur, with H₂ activation on both metal sites. We propose that the singly dispersed bimetallic M₁A_n catalyst, in which the doped metal atom M substitutes an oxygen atom on the oxide surface of metal A, serves as a new surface single-cluster catalyst (SCC) design platform for the biomimetic N₂-to-NH₃ thermal conversion. The catalytic ability of M₁A_n catalyst is attributed to both the charge buffer capacity of doped metal M and the complementary role of synergic metal A in catalysis. Our work provides insights and guidelines for further optimizing the M₁A_n catalyst.

Robust Production, Crystallization, Structure Determination, and Analysis of [Fe-S] Proteins: Uncovering Control of Electron Shuttling and Gating in the Respiratory Metabolism of Molybdopterin Guanine Dinucleotide Enzymes

[Fe-S] clusters are essential cofactors in all domains of life. They play many biological roles due to their unique abilities for electron transfer and conformational control. Yet, producing and analyzing Fe-S proteins can be difficult and even misleading if not done anaerobically. Due to unique redox properties of [Fe-S] clusters and their oxygen sensitivity, they pose multiple challenges and can lose enzymatic activity or cause their component proteins to be structurally disordered due to [Fe-S] cluster oxidation and loss in air. Here we highlight tested protocols and strategies enabling efficient and stable [Fe-S] protein production, purification, crystallization, X-ray diffraction data collection, and structure determination. From multiple high-resolution anaerobic crystal structures, we furthermore analyze exemplary data defining [Fe-S] clusters, substrate entry, and product exit for the functional oxidation states of type II molybdo-bis(molybdopterin guanine dinucleotide) (Mo-bisMGD) enzymes. Notably, these enzymes perform electron shuttling between quinone pools and specific substrates to catalyze respiratory metabolism. The identified structure-activity relationships for this enzyme class have broad implications germane to perchlorate environments on Earth and Mars extending to an alternative mechanism underlying metabolic origins for the evolution of the oxygen atmosphere. Integrated structural analyses of type II Mo-bisMGD enzymes unveil novel distinctive shared molecular mechanisms for dynamic control of substrate entry and product release gated by hydrophobic residues. Collective findings support a prototypic model for type II Mo-bisMGD enzymes including insights for a fundamental molecular mechanistic understanding of selectivity and regulation by a conformationally gated channel with general implications for [Fe-S] cluster respiratory enzymes.

Succinate Transport Is Not Essential for Symbiotic Nitrogen Fixation by Sinorhizobium meliloti or Rhizobium leguminosarum

Symbiotic nitrogen fixation (SNF) is an energetically expensive process performed by bacteria during endosymbiotic relationships with plants. The bacteria require the plant to provide a carbon source for the generation of reductant to power SNF. While C₄-dicarboxylates (succinate, fumarate, and malate) appear to be the primary, if not sole, carbon source provided to the bacteria, the contribution of each C₄-dicarboxylate is not known. We address this issue using genetic and systems-level analyses. Expression of a malate-specific transporter (MaeP) in Sinorhizobium meliloti Rm1021 dct mutants unable to transport C₄-dicarboxylates resulted in malate import rates of up to 30% that of the wild type. This was sufficient to support SNF with Medicago sativa, with acetylene reduction rates of up to 50% those of plants inoculated with wild-type S. melilotiRhizobium leguminosarum bv. viciae 3841 dct mutants unable to transport C₄-dicarboxylates but expressing the maeP transporter had strong symbiotic properties, with Pisum sativum plants inoculated with these strains appearing similar to plants inoculated with wild-type R. leguminosarum This was despite malate transport rates by the mutant bacteroids being 10% those of the wild type. An RNA-sequencing analysis of the combined P. sativum-R. leguminosarum nodule transcriptome was performed to identify systems-level adaptations in response to the inability of the bacteria to import succinate or fumarate. Few transcriptional changes, with no obvious pattern, were detected. Overall, these data illustrated that succinate and fumarate are not essential for SNF and that, at least in specific symbioses, l-malate is likely the primary C₄-dicarboxylate provided to the bacterium.IMPORTANCE Symbiotic nitrogen fixation (SNF) is an economically and ecologically important biological process that allows plants to grow in nitrogen-poor soils without the need to apply nitrogen-based fertilizers. Much research has been dedicated to this topic to understand this process and to eventually manipulate it for agricultural gains. The work presented in this article provides new insights into the metabolic integration of the plant and bacterial partners. It is shown that malate is the only carbon source that needs to be available to the bacterium to support SNF and that, at least in some symbioses, malate, and not other C₄-dicarboxylates, is likely the primary carbon provided to the bacterium. This work extends our knowledge of the minimal metabolic capabilities the bacterium requires to successfully perform SNF and may be useful in further studies aiming to optimize this process through synthetic biology approaches. The work describes an engineering approach to investigate a metabolic process that occurs between a eukaryotic host and its prokaryotic endosymbiont.

Nitrogen Reduction to Ammonia on a Biomimetic Mononuclear Iron Centre: Insights into the Nitrogenase Enzyme

Nitrogenases catalyse nitrogen fixation to ammonia on a multinuclear Fe‐Mo centre, but their mechanism and particularly the order of proton and electron transfer processes that happen during the catalytic cycle is still unresolved. Recently, a unique biomimetic mononuclear iron model was developed using tris(phosphine)borate (TPB) ligands that was shown to convert N₂ into NH₃. Herein, we present a computational study on the [(TPB)FeN₂]⁻ complex and describe its conversion into ammonia through the addition of electrons and protons. In particular, we tested the consecutive proton transfer on only the distal nitrogen atom or alternated protonation of the distal/proximal nitrogen. It is found that the lowest energy pathway is consecutive addition of three protons to the same site, which forms ammonia and an iron‐nitrido complex. In addition, the proton transfer step of complexes with the metal in various oxidation and spin states were tested and show that the pK_a values of biomimetic mononuclear nitrogenase intermediates vary little with iron oxidation states. As such, the model gives several possible NH₃ formation pathways depending on the order of electron/proton transfer, and all should be physically accessible in the natural system. These results may have implications for enzymatic nitrogenases and give insight into the catalytic properties of mononuclear iron centres.

Conformationally Gated Electron Transfer in Nitrogenase. Isolation, Purification, and Characterization of Nitrogenase From Gluconacetobacter diazotrophicus

Nitrogenase is a complex, bacterial enzyme that catalyzes the ATP-dependent reduction of dinitrogen (N₂) to ammonia (NH₃). In its most prevalent form, it consists of two proteins, the catalytic molybdenum-iron protein (MoFeP) and its specific reductase, the iron protein (FeP). A defining feature of nitrogenase is that electron and proton transfer processes linked to substrate reduction are synchronized by conformational changes driven by ATP-dependent FeP-MoFeP interactions. Yet, despite extensive crystallographic, spectroscopic, and biochemical information on nitrogenase, the structural basis of the ATP-dependent synchronization mechanism is not understood in detail. In this chapter, we summarize some of our efforts toward obtaining such an understanding. Experimental investigations of the structure-function relationships in nitrogenase are challenged by the fact that it cannot be readily expressed heterologously in nondiazotrophic bacteria, and the purification protocols for nitrogenase are only known for a small number of diazotrophic organisms. Here, we present methods for purifying and characterizing nitrogenase from a new model organism, Gluconacetobacter diazotrophicus. We also describe procedures for observing redox-dependent conformational changes in G. diazotrophicus nitrogenase by X-ray crystallography and electron paramagnetic resonance spectroscopy, which have provided new insights into the redox-dependent conformational gating processes in nitrogenase.

Electrocatalytic CO2 reduction catalyzed by nitrogenase MoFe and FeFe proteins

Nitrogenases catalyze biological dinitrogen (N₂) reduction to ammonia (NH₃), and also reduce a number of non-physiological substrates, including carbon dioxide (CO₂) to formate (HCOO^-) and methane (CH₄). Three versions of nitrogenase are known (Mo-, V-, and Fe-nitrogenase), each showing different reactivities towards various substrates. Normally, electrons for substrate reduction are delivered by the Fe protein component of nitrogenase, with energy coming from the hydrolysis of 2 ATP to 2 ADP+2 Pi for each electron transferred. Recently, it has been demonstrated that energy and electrons can be delivered from an electrode to the catalytic nitrogenase MoFe-protein without the need for Fe protein or ATP hydrolysis. Here, it is demonstrated that both the MoFe- and FeFe-protein can be immobilized as a polymer layer on an electrode and that electron transfer mediated by cobaltocene can drive CO₂ reduction to formate in this system. It was also found that the FeFe-protein diverts a greater percentage of electrons to CO₂ reduction versus proton reduction compared to the MoFe-protein. Quantification of electron flow to products exhibited Faradaic efficiencies of CO₂ conversion to formate of 9% for MoFe protein and 32% for FeFe-protein, with the remaining electrons going to proton reduction to make H₂.

Carbon-Heteroatom Bond Formation by an Ultrasonic Chemical Reaction for Energy Storage Systems

The direct formation of CN and CO bonds from inert gases is essential for chemical/biological processes and energy storage systems. However, its application to carbon nanomaterials for improved energy storage remains technologically challenging. A simple and very fast method to form CN and CO bonds in reduced graphene oxide (RGO) and carbon nanotubes (CNTs) by an ultrasonic chemical reaction is described. Electrodes of nitrogen- or oxygen-doped RGO (N-RGO or O-RGO, respectively) are fabricated via the fixation between N₂ or O₂ carrier gas molecules and ultrasonically activated RGO. The materials exhibit much higher capacitance after doping (133, 284, and 74 F g^-1 for O-RGO, N-RGO, and RGO, respectively). Furthermore, the doped 2D RGO and 1D CNT materials are prepared by layer-by-layer deposition using ultrasonic spray to form 3D porous electrodes. These electrodes demonstrate very high specific capacitances (62.8 mF cm^-2 and 621 F g^-1 at 10 mV s^-1 for N-RGO/N-CNT at 1:1, v/v), high cycling stability, and structural flexibility.

An Unsymmetric Ligand Framework for Noncoupled Homo- and Heterobimetallic Complexes

We introduce a new unsymmetric ligand, PDIpCy (PDI = pyridyldiimine; Cy = cyclam), that offers two distinct, noncoupled coordination sites. A series of homo- and heterobimetallic complexes, [Zn₂(PDIpCy)(THF)(OTf)₄] (1; THF = tetrahydrofuran and OTf = triflate), [Ni₂(PDIpCy)(THF)(OTf)₂](OTf)₂ (2), and [NiZn(PDIpCy)(THF)(OTf)₄] (3), are described. The one-electron-reduced compounds, [Zn₂(PDIpCy)(OTF)₃] (4), [Ni₂(PDIpCy)(OTf)](OTf)₂ (5), and [NiZn(PDIpCy)(OTf)₃] (6), were isolated, and their electronic structures were characterized. The reduced compounds are charge-separated species, with electron storage at either the PDI ligand (4) or at the PDI-bound metal ion (5 and 6).

Nitrogen Fixation Genes and Nitrogenase Activity of the Non-Heterocystous Cyanobacterium Thermoleptolyngbya sp. O-77

Cyanobacteria are widely distributed in marine, aquatic, and terrestrial ecosystems, and play an important role in the global nitrogen cycle. In the present study, we examined the genome sequence of the thermophilic non-heterocystous N₂-fixing cyanobacterium, Thermoleptolyngbya sp. O-77 (formerly known as Leptolyngbya sp. O-77) and characterized its nitrogenase activity. The genome of this cyanobacterial strain O-77 consists of a single chromosome containing a nitrogen fixation gene cluster. A phylogenetic analysis indicated that the NifH amino acid sequence from strain O-77 was clustered with those from a group of mesophilic species: the highest identity was found in Leptolyngbya sp. KIOST-1 (97.9% sequence identity). The nitrogenase activity of O-77 cells was dependent on illumination, whereas a high intensity of light of 40 μmol m⁻² s⁻¹ suppressed the effects of illumination.

Synthesis and reactivity of thiolate-bridged multi-iron complexes supported by cyclic (alkyl)(amino)carbene

The combined utilization of Me₂-cAAC (Me₂-cAAC = :C(CH₂)(CMe₂)₂N-2,6-ⁱPr₂C₆H₃) and thiolates as supporting ligands enables the access of unprecedented carbene coordinated thiolate-bridged diiron(ii) complexes [(Me₂-cAAC)Fe(μ-SR)(Br)]₂ (R = Me, 3; R = Et, 4). The coordination environment of each tetrahedral iron(ii) center in complexes 3 and 4 is composed of one terminal bromide atom, one carbene carbon atom and two thiolate sulfur atoms, which is similar to the carbide-containing sulfur-rich environment of iron centers in the belt region of the FeMo-cofactor. Interestingly, when NaSCPh₃ was chosen as the thiolate ligand, C-S bond homolysis occurred to form a rare [3 : 1] site-differentiated cubane-type cluster [(Me₂-cAAC)Fe₄S₄(Br)₃][Me₂-cAACH] (5). Furthermore, complexes 3 and 4 exhibit good exchange reactivity toward the azide anion to give novel thiolate-bridged diiron complexes with two azido ligands in a trans arrangement.

Catalytic Nitrogen-to-Ammonia Conversion by Osmium and Ruthenium Complexes

Despite the critical role Ru and Os complexes have played in the development of transition metal dinitrogen chemistry, they have not been shown to mediate catalytic N2-to-NH3 conversion (N2RR), nor have M-NxHy complexes been derived from protonation of their M-N2 precursors. To help delineate factors for N2RR catalysis, we report on isostructural tris(phosphino)silyl Ru and Os complexes that mediate catalytic N2RR, and compare their activities with an isostructural Fe complex. The Os system is most active, and liberates more than 120 equiv NH3 per Os center in a single batch experiment using Cp*2Co and [H2NPh2][OTf] as reductant and acid source. Isostructural Ru and Fe complexes generate little NH3 under the same conditions. Protonation of Os-N2- affords a structurally characterized Os=NNH2+ hydrazido species that mediates NH3 generation, suggesting it is a plausible intermediate of the catalysis. Inactive Os hydrides are characterized that form during catalysis.

Diversity and Functional Analysis of the FeMo-Cofactor Maturase NifB

One of the main hurdles to engineer nitrogenase in a non-diazotrophic host is achieving NifB activity. NifB is an extremely unstable and oxygen sensitive protein that catalyzes a low-potential SAM-radical dependent reaction. The product of NifB activity is called NifB-co, a complex [8Fe-9S-C] cluster that serves as obligate intermediate in the biosyntheses of the active-site cofactors of all known nitrogenases. Here we study the diversity and phylogeny of naturally occurring NifB proteins, their protein architecture and the functions of the distinct NifB domains in order to understand what defines a catalytically active NifB. Focus is on NifB from the thermophile Chlorobium tepidum (two-domain architecture), the hyperthermophile Methanocaldococcus infernus (single-domain architecture) and the mesophile Klebsiella oxytoca (two-domain architecture), showing in silico characterization of their nitrogen fixation (nif) gene clusters, conserved NifB motifs, and functionality. C. tepidum and M. infernus NifB were able to complement an Azotobacter vinelandii (ΔnifB) mutant restoring the Nif⁺ phenotype and thus demonstrating their functionality in vivo. In addition, purified C. tepidum NifB exhibited activity in the in vitro NifB-dependent nitrogenase reconstitution assay. Intriguingly, changing the two-domain K. oxytoca NifB to single-domain by removal of the C-terminal NifX-like extension resulted in higher in vivo nitrogenase activity, demonstrating that this domain is not required for nitrogen fixation in mesophiles.

Pairwise H2/D2 Exchange and H2 Substitution at a Bimetallic Dinickel(II) Complex Featuring Two Terminal Hydrides

A compartmental ligand scaffold HL with two β-diketiminato binding sites spanned by a pyrazolate bridge gave a series of dinuclear nickel(II) dihydride complexes M[LNi₂(H)₂], M = Na (Na·2) and K (K·2), which were isolated after reacting the precursor complex [LNi₂(μ-Br)] (1) with MHBEt₃ (M = Na and K). Crystallographic characterization showed the two hydride ligands to be directed into the bimetallic pocket, closely interacting with the alkali metal cation. Treatment of K·2 with dibenzo(18-crown-6) led to the separated ion pair [LNi₂(H)₂][K(DB18C6)] (2[K(DB18C6)]). Reaction of Na·2 or K·2 with D₂ was investigated by a suite of ¹H and ²H NMR experiments, revealing an unusual pairwise H₂/D₂ exchange process that synchronously involves both Ni-H moieties without H/D scrambling. A mechanistic picture was provided by DFT calculations which suggested facile recombination of the two terminal hydrides within the bimetallic cleft, with a moderate enthalpic barrier of ∼62 kJ/mol, to give H₂ and an antiferromagnetically coupled [LNi^I₂]^- species. This was confirmed by SQUID monitoring during H₂ release from solid 2[K(DB18C6)]. Interaction with the Lewis acid cation (Na⁺ or K⁺) significantly stabilizes the dihydride core. Kinetic data for the M[L(Ni-H)₂] → H₂ transition derived from 2D ¹H EXSY spectra confirmed first-order dependence of H₂ release on M·2 concentration and a strong effect of the alkali metal cation M⁺. Treating [LNi₂(D)₂]^- with phenylacetylene led to D₂ and dinickel(II) complex 3^- with a twice reduced styrene-1,2-diyl bridging unit in the bimetallic pocket. Complexes [LNi^II₂(H)₂]^- having two adjacent terminal hydrides thus represent a masked version of a highly reactive dinickel(I) core. Storing two reducing equivalents in adjacent metal hydrides that evolve H₂ upon substrate binding is reminiscent of the proposed N₂ binding step at the FeMo cofactor of nitrogenase, suggesting the use of the present bimetallic scaffold for reductive bioinspired activation of a range of inert small molecules.

Interplay of hemilability and redox activity in models of hydrogenase active sites

The hydrogen evolution reaction, as catalyzed by two electrocatalysts [M(N₂S₂)·Fe(NO)₂]⁺, [Fe-Fe]⁺ (M = Fe(NO)) and [Ni-Fe]⁺ (M = Ni) was investigated by computational chemistry. As nominal models of hydrogenase active sites, these bimetallics feature two kinds of actor ligands: Hemilabile, MN₂S₂ ligands and redox-active, nitrosyl ligands, whose interplay guides the H₂ production mechanism. The requisite base and metal open site are masked in the resting state but revealed within the catalytic cycle by cleavage of the MS-Fe(NO)₂ bond from the hemilabile metallodithiolate ligand. Introducing two electrons and two protons to [Ni-Fe]⁺ produces H₂ from coupling a hydride temporarily stored on Fe(NO)₂ (Lewis acid) and a proton accommodated on the exposed sulfur of the MN₂S₂ thiolate (Lewis base). This Lewis acid-base pair is initiated and preserved by disrupting the dative donation through protonation on the thiolate or reduction on the thiolate-bound metal. Either manipulation modulates the electron density of the pair to prevent it from reestablishing the dative bond. The electron-buffering nitrosyl's role is subtler as a bifunctional electron reservoir. With more nitrosyls as in [Fe-Fe]⁺, accumulated electronic space in the nitrosyls' π*-orbitals makes reductions easier, but redirects the protonation and reduction to sites that postpone the actuation of the hemilability. Additionally, two electrons donated from two nitrosyl-buffered irons, along with two external electrons, reduce two protons into two hydrides, from which reductive elimination generates H₂.

A Terminal Iron(IV) Nitride Supported by a Super Bulky Guanidinate Ligand and Examination of Its Electronic Structure and Reactivity

Utilizing the bulky guanidinate ligand [L^Ar*]^- (L^Ar* = (Ar*N)₂C(R), Ar* = 2,6-bis(diphenylmethyl)-4-tert-butylphenyl, R = NC^tBu₂) for kinetic stabilization, the synthesis of a rare terminal Fe(IV) nitride complex is reported. UV irradiation of a pyridine solution of the Fe(II) azide [L^Ar*]FeN₃(py) (3-py) at 0 °C cleanly generates the Fe(IV) nitride [L^Ar*]FeN(py) (1). The ¹⁵N NMR spectrum of the 1^15N (50% Fe≡¹⁵N) isotopomer shows a resonance at 1016 ppm (vs externally referenced CH₃NO₂ at 380 ppm), comparable to that known for other terminal iron nitrides. Notably, the computed structure of 1 reveals an iron center with distorted tetrahedral geometry, τ₄ = 0.72, featuring a short Fe≡N bond (1.52 Å). Inspection of the frontier orbital ordering of 1 shows a relatively small HOMO/LUMO gap with the LUMO comprised by Fe(d_xz,yz)N(p_x,y) π*-orbitals, a splitting that is manifested in the electronic absorption spectrum of 1 (λ = 610 nm, ε = 1375 L·mol^-1·cm^-1; λ = 613 nm (calcd)). Complex 1 persists in low-temperature solutions of pyridine but becomes unstable at room temperature, gradually converting to the Fe(II) hydrazide product [κ²-(^tBu₂CN)C(η⁶-NAr*)(N-NAr*)]Fe (4) upon standing via intramolecular N-atom insertion. This reactivity of the Fe≡N moiety was assessed through molecular orbital analysis, which suggests electrophilic character at the nitride functionality. Accordingly, treatment of 1 with the nucleophiles PMe₂Ph and Ar-N≡C (Ar = 2,6-dimethylphenyl) leads to partial N-atom transfer and formation of the Fe(II) addition products [L^Ar*]Fe(N═PMe₂Ph)(py) (5) and [L^Ar*]Fe(N═C═NAr)(py) (6). Similarly, 1 reacts with PhSiH₃ to give [L^Ar*]Fe[N(H)(SiH₂Ph)](py) (7) which Fukui analysis shows to proceed via electrophilic insertion of the nitride into the Si-H bond.

Influence of surface chemistry of carbon materials on their interactions with inorganic nitrogen contaminants in soil and water

Inorganic nitrogen contaminants (INC) (NH₄⁺, NO₃^-, NO₂^-, NH₃, NO, NO₂, and N₂O) pose a growing risk to the environment, and their remediation methods are highly sought after. Application of carbon materials (CM), such as biochar and activated carbon, to remediate INC from agricultural fields and wastewater treatment plants has gained a significant interest since past few years. Understanding the role of surface chemistry of CM in adsorption of various INC is highly critical to increase adsorption efficiency as well as to assess the long term impact of using these highly recalcitrant CM for remediation of INC. Critical reviews of adsorption studies related to INC have revealed that carbon surface chemistry (surface functional groups, pH, Eh, elemental composition, and mineral content) has significant influence on adsorption of INC. Compared to basic functional groups, oxygen containing surface functional groups have been found to be more influential for adsorption of INC. However, basic sites on carbon materials still play an important role in chemisorption of anionic INC. Apart from surface functional groups, pH, Eh and pH_zpc of CM and elemental and mineral composition of its surface are important properties capable of altering INC interactions with CM. This review summarizes our current understanding of INC interactions with CM's surface through the known chemisorption mechanisms: electrostatic interaction, hydrogen bonding, electron donor-acceptor mechanism, hydrophobic and hydrophilic interaction, chemisorption aided by minerals, and interactions influenced by pH and elemental composition. Change in surface chemistry of CM in soil during aging is also discussed.

Transcriptional Analysis of an Ammonium-Excreting Strain of Azotobacter vinelandii Deregulated for Nitrogen Fixation

Biological nitrogen fixation is accomplished by a diverse group of organisms known as diazotrophs and requires the function of the complex metalloenzyme nitrogenase. Nitrogenase and many of the accessory proteins required for proper cofactor biosynthesis and incorporation into the enzyme have been characterized, but a complete picture of the reaction mechanism and key cellular changes that accompany biological nitrogen fixation remain to be fully elucidated. Studies have revealed that specific disruptions of the antiactivator-encoding gene nifL result in the deregulation of the nif transcriptional activator NifA in the nitrogen-fixing bacterium Azotobacter vinelandii, triggering the production of extracellular ammonium levels approaching 30 mM during the stationary phase of growth. In this work, we have characterized the global patterns of gene expression of this high-ammonium-releasing phenotype. The findings reported here indicated that cultures of this high-ammonium-accumulating strain may experience metal limitation when grown using standard Burk's medium, which could be amended by increasing the molybdenum levels to further increase the ammonium yield. In addition, elevated levels of nitrogenase gene transcription are not accompanied by a corresponding dramatic increase in hydrogenase gene transcription levels or hydrogen uptake rates. Of the three potential electron donor systems for nitrogenase, only the rnf1 gene cluster showed a transcriptional correlation to the increased yield of ammonium. Our results also highlight several additional genes that may play a role in supporting elevated ammonium production in this aerobic nitrogen-fixing model bacterium.IMPORTANCE The transcriptional differences found during stationary-phase ammonium accumulation show a strong contrast between the deregulated (nifL-disrupted) and wild-type strains and what was previously reported for the wild-type strain under exponential-phase growth conditions. These results demonstrate that further improvement of the ammonium yield in this nitrogenase-deregulated strain can be obtained by increasing the amount of available molybdenum in the medium. These results also indicate a potential preference for one of two ATP synthases present in A. vinelandii as well as a prominent role for the membrane-bound hydrogenase over the soluble hydrogenase in hydrogen gas recycling. These results should inform future studies aimed at elucidating the important features of this phenotype and at maximizing ammonium production by this strain.

Mechanism of Nitrogenase H2 Formation by Metal-Hydride Protonation Probed by Mediated Electrocatalysis and H/D Isotope Effects

Nitrogenase catalyzes the reduction of dinitrogen (N₂) to two ammonia (NH₃) at its active site FeMo-cofactor through a mechanism involving reductive elimination of two [Fe-H-Fe] bridging hydrides to make H₂. A competing reaction is the protonation of the hydride [Fe-H-Fe] to make H₂. The overall nitrogenase rate-limiting step is associated with ATP-driven electron delivery from Fe protein, precluding isotope effect measurements on substrate reduction steps. Here, we use mediated bioelectrocatalysis to drive electron delivery to the MoFe protein allowing examination of the mechanism of H₂ formation by the metal-hydride protonation reaction. The ratio of catalytic current in mixtures of H₂O and D₂O, the proton inventory, was found to change linearly with the D₂O/H₂O ratio, revealing that a single H/D is involved in the rate-limiting step of H₂ formation. Kinetic models, along with measurements that vary the electron/proton delivery rate and use different substrates, reveal that the rate-limiting step under these conditions is the H₂ formation reaction. Altering the chemical environment around the active site FeMo-cofactor in the MoFe protein, either by substituting nearby amino acids or transferring the isolated FeMo-cofactor into a different peptide matrix, changes the net isotope effect, but the proton inventory plot remains linear, consistent with an unchanging rate-limiting step. Density functional theory predicts a transition state for H₂ formation where the S-H⁺ bond breaks and H⁺ attacks the Fe-hydride, and explains the observed H/D isotope effect. This study not only reveals the nitrogenase mechanism of H₂ formation by hydride protonation, but also illustrates a strategy for mechanistic study that can be applied to other oxidoreductase enzymes and to biomimetic complexes.

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.

Nitrogenase Assembly: Strategies and Procedures

Nitrogenase is a metalloenzyme system that plays a critical role in biological nitrogen fixation, and the study of how its metallocenters are assembled into functional entities to facilitate the catalytic reduction of dinitrogen to ammonia is an active area of interest. The diazotroph Azotobacter vinelandii is especially amenable to culturing and genetic manipulation, and this organism has provided the basis for many insights into the assembly of nitrogenase proteins and their respective metallocofactors. This chapter will cover the basic procedures necessary for growing A. vinelandii cultures and subsequent recombinant transformation and protein expression techniques. Furthermore, protocols for nitrogenase protein purification and substrate reduction activity assays are described. These methods provide a solid framework for the assessment of nitrogenase assembly and catalysis.

Unraveling the interactions of the physiological reductant flavodoxin with the different conformations of the Fe protein in the nitrogenase cycle

Nitrogenase reduces dinitrogen (N₂) to ammonia in biological nitrogen fixation. The nitrogenase Fe protein cycle involves a transient association between the reduced, MgATP-bound Fe protein and the MoFe protein and includes electron transfer, ATP hydrolysis, release of P_i, and dissociation of the oxidized, MgADP-bound Fe protein from the MoFe protein. The cycle is completed by reduction of oxidized Fe protein and nucleotide exchange. Recently, a kinetic study of the nitrogenase Fe protein cycle involving the physiological reductant flavodoxin reported a major revision of the rate-limiting step from MoFe protein and Fe protein dissociation to release of P_i Because the Fe protein cannot interact with flavodoxin and the MoFe protein simultaneously, knowledge of the interactions between flavodoxin and the different nucleotide states of the Fe protein is critically important for understanding the Fe protein cycle. Here we used time-resolved limited proteolysis and chemical cross-linking to examine nucleotide-induced structural changes in the Fe protein and their effects on interactions with flavodoxin. Differences in proteolytic cleavage patterns and chemical cross-linking patterns were consistent with known nucleotide-induced structural differences in the Fe protein and indicated that MgATP-bound Fe protein resembles the structure of the Fe protein in the stabilized nitrogenase complex structures. Docking models and cross-linking patterns between the Fe protein and flavodoxin revealed that the MgADP-bound state of the Fe protein has the most complementary docking interface with flavodoxin compared with the MgATP-bound state. Together, these findings provide new insights into the control mechanisms in protein-protein interactions during the Fe protein cycle.

Synthesis and Mechanism of Formation of Hydride-Sulfide Complexes of Iron

Iron-sulfide complexes with hydride ligands provide an experimental precedent for spectroscopically detected hydride species on the iron-sulfur MoFe₇S₉C cofactor of nitrogenase. In this contribution, we expand upon our recent synthesis of the first iron sulfide hydride complex from an iron hydride and a sodium thiolate ( Arnet, N. A.; Dugan, T. R.; Menges, F. S.; Mercado, B. Q.; Brennessel, W. W.; Bill, E.; Johnson, M. A.; Holland, P. L., J. Am. Chem. Soc. 2015 , 137 , 13220 - 13223 ). First, we describe the isolation of an analogous iron sulfide hydride with a smaller diketiminate supporting ligand, which benefits from easier preparation of the hydride precursor and easier isolation of the product. Second, we describe mechanistic studies on the C-S bond cleavage through which the iron sulfide hydride product is formed. In a key experiment, use of cyclopropylmethanethiolate as the sulfur precursor leads to products from cyclopropane ring opening, implicating an alkyl radical as an intermediate. Combined with the results of isotopic labeling studies, the data are consistent with a mechanism in which homolytic C-S bond cleavage is followed by rebound of the alkyl radical to abstract a hydrogen atom from iron to give the observed alkane and iron-sulfide products.

How Plant Root Exudates Shape the Nitrogen Cycle

Although the global nitrogen (N) cycle is largely driven by soil microbes, plant root exudates can profoundly modify soil microbial communities and influence their N transformations. A detailed understanding is now beginning to emerge regarding the control that root exudates exert over two major soil N processes - nitrification and N2 fixation. We discuss recent breakthroughs in this area, including the identification of root exudates as nitrification inhibitors and as signaling compounds facilitating N-acquisition symbioses. We indicate gaps in current knowledge, including questions of how root exudates affect newly discovered microbial players and N-cycle components. A better understanding of these processes is urgent given the widespread inefficiencies in agricultural N use and their links to N pollution and climate change.

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.