Putative reaction mechanism of nitrogenase with a half-dissociated S2B ligand

We have studied whether dissociation of the S2B sulfide ligand from one of its two coordinating Fe ions may affect the later parts of the reaction mechanism of nitrogenase. Such dissociation has been shown to be favourable for the E2-E4 states in the reaction mechanism, but previous studies have assumed that S2B either remains bridging or has fully dissociated from the active-site FeMo cluster. We employ combined quantum mechanical and molecular mechanical (QM/MM) calculations with two density-functional theory methods, r2SCAN and TPSSh. To make dissociation of S2B possible, we have added a proton to this group throughout the reaction. We study the reaction starting from the E4 state with N2H2 bound to the cluster. Our results indicate that half-dissociation of S2B is unfavourable in most steps of the reaction mechanism. We observe favourable half-dissociation of S2B only when NH or NH2 is bound to the cluster, bridging Fe2 and Fe6. However, the former state is most likely not involved in the reaction mechanism and the latter state is only an intermittent intermediate of the E7 state. Therefore, half-dissociation of S2B seems to play only a minor role in the later parts of the reaction mechanism of nitrogenase. Our suggested mechanism with a protonated S2B is alternating (the two N atoms of the substrate is protonated in an alternating manner) and the substrate prefers to bind to Fe2, in contrast to the preferred binding to Fe6 observed when S2B is unprotonated and bridging Fe2 and Fe6.

What triggers the coupling of proton transfer and electron transfer at the active site of nitrogenase?

In converting N2 to NH3 the enzyme nitrogenase utilises 8 electrons and 8 protons in the complete catalytic cycle. The source of the electrons is an Fe4S4 reductase protein (Fe-protein) which temporarily docks with the MoFe-protein that contains the catalytic active cofactor, FeMo-co, and an electron transfer cluster called the P cluster. The overall mechanism involves 8 repetitions of a cycle in which reduced Fe-protein docks with the MoFe-protein, one electron transfers to the P-cluster, and then to FeMo-co, followed by dissociation of the two proteins and re-reduction of the Fe-protein. Protons are supplied serially to FeMo-co by a Grotthuss proton translocation mechanism from the protein surface along a conserved chain of water molecules (a proton wire) that terminates near S atoms of the FeMo-co cluster [CFe7S9Mo(homocitrate)] where the multiple steps of the chemical conversions are effected. It is assumed that the chemical mechanisms use proton-coupled electron-transfer (PCET) and that H atoms (e- + H+) are involved in each of the hydrogenation steps. However there is neither evidence for, or mechanism proposed, for this coupling. Here I report calculations of cluster charge distribution upon electron addition, revealing that the added negative charge is on the S atoms of FeMo-co, which thereby become more basic, and able to trigger proton transfer from H3O+ waiting at the near end of the proton wire. This mechanism is supported by calculations of the dynamics of the proton transfer step, in which the barrier is reduced by ca. 3.5 kcal mol-1 and the product stabilised by ca. 7 kcal mol-1 upon electron addition. H tunneling is probable in this step. In nitrogenase it is electron transfer that triggers proton transfer.

Accessing a synthetic FeIIIMnIV core to model biological heterobimetallic active sites

Metalloproteins with dinuclear cores are known to bind and activate dioxygen, with a subclass of these proteins having active sites containing FeMn cofactors and activities ranging from long-range proton-coupled electron transfer (PCET) to post-translational peptide modification. While mechanistic studies propose that these metallocofactors access FeIIIMnIV intermediates, there is a dearth of related synthetic analogs. Herein, the first well-characterized synthetic FeIII-(μ-O)-MnIV complex is reported; this complex shows similar spectroscopic features as the catalytically competent FeIIIMnIV intermediate X found in Class Ic ribonucleotide reductase and demonstrates PCET function towards phenolic substrates. This complex is prepared from the oxidation of the isolable FeIII-(μ-O)-MnIII species, whose stepwise assembly is facilitated by a tripodal ligand containing phosphinic amido groups. Structural and spectroscopic studies found proton movement involving the FeIIIMnIII core, whereby the initial bridging hydroxido ligand is converted to an oxido ligand with concomitant protonation of one phosphinic amido group. This series of FeMn complexes allowed us to address factors that may dictate the preference of an active site for a heterobimetallic cofactor over one that is homobimetallic: comparisons of the redox properties of our FeMn complexes with those of the di-Fe analogs suggested that the relative thermodynamic ease of accessing an FeIIIMnIV core can play an important role in determining the metal ion composition when the key catalytic steps do not require an overly potent oxidant. Moreover, these complexes allowed us to demonstrate the effect of the hyperfine interaction from non-Fe nuclei on 57Fe Mössbauer spectra which is relevant to MnFe intermediates in proteins.

Nitrogenase beyond the Resting State: A Structural Perspective

Nitrogenases have the remarkable ability to catalyze the reduction of dinitrogen to ammonia under physiological conditions. How does this happen? The current view of the nitrogenase mechanism focuses on the role of hydrides, the binding of dinitrogen in a reductive elimination process coupled to loss of dihydrogen, and the binding of substrates to a binuclear site on the active site cofactor. This review focuses on recent experimental characterizations of turnover relevant forms of the enzyme determined by cryo-electron microscopy and other approaches, and comparison of these forms to the resting state enzyme and the broader family of iron sulfur clusters. Emerging themes include the following: (i) The obligatory coupling of protein and electron transfers does not occur in synthetic and small-molecule iron-sulfur clusters. The coupling of these processes in nitrogenase suggests that they may involve unique features of the cofactor, such as hydride formation on the trigonal prismatic arrangement of irons, protonation of belt sulfurs, and/or protonation of the interstitial carbon. (ii) Both the active site cofactor and protein are dynamic under turnover conditions; the changes are such that more highly reduced forms may differ in key ways from the resting-state structure. Homocitrate appears to play a key role in coupling cofactor and protein dynamics. (iii) Structural asymmetries are observed in nitrogenase under turnover-relevant conditions by cryo-electron microscopy, although the mechanistic relevance of these states (such as half-of-sites reactivity) remains to be established.

The role of ion solvation in lithium mediated nitrogen reduction

Since its verification in 2019, there have been numerous high-profile papers reporting improved efficiency of lithium-mediated electrochemical nitrogen reduction to make ammonia. However, the literature lacks any coherent investigation systematically linking bulk electrolyte properties to electrochemical performance and Solid Electrolyte Interphase (SEI) properties. In this study, we discover that the salt concentration has a remarkable effect on electrolyte stability: at concentrations of 0.6 M LiClO₄ and above the electrode potential is stable for at least 12 hours at an applied current density of -2 mA cm^-2 at ambient temperature and pressure. Conversely, at the lower concentrations explored in prior studies, the potential required to maintain a given N₂ reduction current increased by 8 V within a period of 1 hour under the same conditions. The behaviour is linked more coordination of the salt anion and cation with increasing salt concentration in the electrolyte observed via Raman spectroscopy. Time of flight secondary ion mass spectrometry and X-ray photoelectron spectroscopy reveal a more inorganic, and therefore more stable, SEI layer is formed with increasing salt concentration. A drop in faradaic efficiency for nitrogen reduction is seen at concentrations higher than 0.6 M LiClO₄, which is attributed to a combination of a decrease in nitrogen solubility and diffusivity as well as increased SEI conductivity as measured by electrochemical impedance spectroscopy.

Bioinspired Framework Catalysts: From Enzyme Immobilization to Biomimetic Catalysis

Enzymatic catalysis has fueled considerable interest from chemists due to its high efficiency and selectivity. However, the structural complexity and vulnerability hamper the application potentials of enzymes. Driven by the practical demand for chemical conversion, there is a long-sought quest for bioinspired catalysts reproducing and even surpassing the functions of natural enzymes. As nanoporous materials with high surface areas and crystallinity, metal-organic frameworks (MOFs) represent an exquisite case of how natural enzymes and their active sites are integrated into porous solids, affording bioinspired heterogeneous catalysts with superior stability and customizable structures. In this review, we comprehensively summarize the advances of bioinspired MOFs for catalysis, discuss the design principle of various MOF-based catalysts, such as MOF-enzyme composites and MOFs embedded with active sites, and explore the utility of these catalysts in different reactions. The advantages of MOFs as enzyme mimetics are also highlighted, including confinement, templating effects, and functionality, in comparison with homogeneous supramolecular catalysts. A perspective is provided to discuss potential solutions addressing current challenges in MOF catalysis.

Near ambient N2 fixation on solid electrodes versus enzymes and homogeneous catalysts

The Mo/Fe nitrogenase enzyme is unique in its ability to efficiently reduce dinitrogen to ammonia at atmospheric pressures and room temperature. Should an artificial electrolytic device achieve the same feat, it would revolutionize fertilizer production and even provide an energy-dense, truly carbon-free fuel. This Review provides a coherent comparison of recent progress made in dinitrogen fixation on solid electrodes, homogeneous catalysts and nitrogenases. Specific emphasis is placed on systems for which there is unequivocal evidence that dinitrogen reduction has taken place. By establishing the cross-cutting themes and synergies between these systems, we identify viable avenues for future research.

Biological nitrogen fixation in theory, practice, and reality: a perspective on the molybdenum nitrogenase system

Nitrogenase is the sole enzyme responsible for the ATP-dependent conversion of atmospheric dinitrogen into the bioavailable form of ammonia (NH₃ ), making this protein essential for the maintenance of the nitrogen cycle and thus life itself. Despite the widespread use of the Haber-Bosch process to industrially produce NH₃ , biological nitrogen fixation still accounts for half of the bioavailable nitrogen on Earth. An important feature of nitrogenase is that it operates under physiological conditions, where the equilibrium strongly favours ammonia production. This biological, multielectron reduction is a complex catalytic reaction that has perplexed scientists for decades. In this review, we explore the current understanding of the molybdenum nitrogenase system based on experimental and computational research, as well as the limitations of the crystallographic, spectroscopic, and computational techniques employed. Finally, essential outstanding questions regarding the nitrogenase system will be highlighted alongside suggestions for future experimental and computational work to elucidate this essential yet elusive process.

Proton Transfer Pathways in Nitrogenase with and without Dissociated S2B

Nitrogenase is the only enzyme that can convert N₂ to NH₃ . Crystallographic structures have indicated that one of the sulfide ligands of the active-site FeMo cluster, S2B, can be replaced by an inhibitor, like CO and OH^- , and it has been suggested that it may be displaced also during the normal reaction. We have investigated possible proton transfer pathways within the FeMo cluster during the conversion of N₂ H₂ to two molecules of NH₃ , assuming that the protons enter the cluster at the S3B, S4B or S5A sulfide ions and are then transferred to the substrate. We use combined quantum mechanical and molecular mechanical (QM/MM) calculations with the TPSS and B3LYP functionals. The calculations indicate that the barriers for these reactions are reasonable if the S2B ligand remains bound to the cluster, but they become prohibitively high if S2B has dissociated. This suggests that it is unlikely that S2B reversibly dissociates during the normal reaction cycle.

Calculating the chemical mechanism of nitrogenase: new working hypotheses

The enzyme nitrogenase converts N₂ to NH₃ with stoichiometry N₂ + 8H⁺ + 8e^- → 2NH₃ + H₂. The mechanism is chemically complex with multiple steps that must be consistent with much accumulated experimental information, including exchange of H₂ and N₂ and the N₂-dependent hydrogenation of D₂ to HD. Previous investigations have developed a collection of working hypotheses that guide ongoing density functional investigations of mechanistic steps and sequences. These include (i) hypotheses about the serial provision of protons and their conversion to H atoms bonded to S and Fe atoms of the FeMo-co catalytic site, (ii) the migration of H atoms over the surface of FeMo-co, (iii) the roles of His195, (iv) identification of three protein channels, one for the ingress of N₂, a separate pathway for the passage of exogenous H₂ (D₂) and product H₂ (HD), and a hydrophilic pathway for egress of product NH₃. Two additional working hypotheses are described in this paper. N₂ passing along the N₂ channel approaches and binds end-on to the exo coordination position of Fe2, with favourable energetics when FeMo-co is pre-hydrogenated. This exo-Fe2-N₂ is apparently not reduced but has a promotional role by expanding the reaction zone. A second N₂ can enter via the N₂ ingress channel and bind at the endo-Fe6 position, where it is surrounded by H atom donors suitable for the N₂ → NH₃ conversion. It is proposed that this endo-Fe6 position is also the binding site for H₂ (generated or exogenous), accounting for the competitive inhibition of N₂ reduction by H₂. The HD reaction occurs at the endo-Fe6 site, promoted by N₂ at the exo-Fe2 site. The second hypothesis concerns the most stable electronic states of FeMo-co with ligands bound at Fe2 and Fe6, and provides a protocol for management of electronic states in mechanism calculations.

Thermodynamically Favourable States in the Reaction of Nitrogenase without Dissociation of any Sulfide Ligand

We have used combined quantum mechanical and molecular mechanical (QM/MM) calculations to study the reaction mechanism of nitrogenase, assuming that none of the sulfide ligands dissociates. To avoid the problem that there is no consensus regarding the structure and protonation of the E₄ state, we start from a state where N₂ is bound to the cluster and is protonated to N₂H₂, after dissociation of H₂. We show that the reaction follows an alternating mechanism with HNNH (possibly protonated to HNNH₂) and H₂NNH₂ as intermediates and the two NH₃ products dissociate at the E₇ and E₈ levels. For all intermediates, coordination to Fe6 is preferred, but for the E₄ and E₈ intermediates, binding to Fe2 is competitive. For the E₄, E₅ and E₇ intermediates we find that the substrate may abstract a proton from the hydroxy group of the homocitrate ligand of the FeMo cluster, thereby forming HNNH₂, H₂NNH₂ and NH₃ intermediates. This may explain why homocitrate is a mandatory component of nitrogenase. All steps in the suggested reaction mechanism are thermodynamically favourable compared to protonation of the nearby His‐195 group and in all cases, protonation of the NE2 atom of the latter group is preferred.

Iron Complexes of a Proton-Responsive SCS Pincer Ligand with a Sensitive Electronic Structure

Sulfur/carbon/sulfur pincer ligands have an interesting combination of strong-field and weak-field donors, a coordination environment that is also present in the nitrogenase active site. Here, we explore the electronic structures of iron(II) and iron(III) complexes with such a pincer ligand, bearing a monodentate phosphine, thiolate S donor, amide N donor, ammonia, or CO. The ligand scaffold features a proton-responsive thioamide site, and the protonation state of the ligand greatly influences the reduction potential of iron in the phosphine complex. The N-H bond dissociation free energy, derived from the Bordwell equation, is 56 ± 2 kcal/mol. Electron paramagnetic resonance (EPR) spectroscopy and superconducting quantum interference device (SQUID) magnetometry measurements show that the iron(III) complexes with S and N as the fourth donors have an intermediate spin (S = 3/2) ground state with a large zero field splitting, and X-ray absorption spectra show a high Fe-S covalency. The Mössbauer spectrum changes drastically with the position of a nearby alkali metal cation in the iron(III) amido complex, and density functional theory calculations explain this phenomenon through a change between having the doubly occupied orbital as dz2 or dyz, as the former is more influenced by the nearby positive charge.

Structures and reaction dynamics of N2 and H2 binding at FeMo-co, the active site of nitrogenase

The chemical reactions occurring at the Fe₇MoS₉C(homocitrate) cluster, FeMo-co, the active site of the enzyme nitrogenase (N₂ → NH₃), are enigmatic. Experimental information collected over a long period reveals aspects of the roles of N₂ and H₂, each with more than one type of reactivity. This paper reports investigations of the binding of H₂ and N₂ at intact FeMo-co, using density functional simulations of a large 486 atom relevant portion of the protein, resulting in 27 new structures containing H₂ and/or N₂ bound at the exo and endo coordination sites of the participating Fe atoms, Fe2 and Fe6. Binding energies and transition states for association/dissociation are determined, and trajectories for the approach, binding and separation of H₂/N₂ are described, including diffusion of these small molecules through proximal protein. Influences of surrounding amino acids are identified. FeMo-co deforms geometrically when binding H₂ or N₂, and a procedure for calculating the energy cost involved, the adaptation energy, is introduced here. Adaptation energies, which range from 7 to 36 kcal mol^-1 for the reported structures, are influenced by the protonation state of the His195 side chain. Seven N₂ structures and three H₂ structures have negative binding free energies, which include the estimated entropy penalties for binding of N₂, H₂ from proximal protein. These favoured structures have N₂ bound end-on at exo-Fe2, exo-Fe6 and endo-Fe2 positions of FeMo-co, and H₂ bound at the endo-Fe2 position. Various postulated structures with N₂ bridging Fe2 and Fe6 revert to end-on-N₂ at endo positions. The structures are also assessed via the calculated potential energy barriers for association and dissociation. Barriers to the binding of H₂ range from 1 to 20 kcal mol^-1 and barriers to dissociation of H₂ range from 3 to 18 kcal mol^-1. Barriers to the binding of N₂, in either side-on or end-on mode, range from 2 to 18 kcal mol^-1, while dissociation of bound N₂ encounters barriers of 3 to 8 kcal mol^-1 for side-on bonding and 7 to 18 kcal mol^-1 for end-on bonding. These results allow formulation of mechanisms for the H₂/N₂ exchange reaction, and three feasible mechanisms for associative exchange and three for dissociative exchange are identified. Consistent electronic structures and potential energy surfaces are maintained throughout. Changes in the spin populations of Fe2 and Fe6 connected with cluster deformation and with metal-ligand bond formation are identified.

Characterization of a Mo-Nitrogenase Variant Containing a Citrate-Substituted Cofactor

Nitrogenase converts N₂ to NH₃ , and CO to hydrocarbons, at its cofactor site. Herein, we report a biochemical and spectroscopic characterization of a Mo-nitrogenase variant expressed in an Azotobacter vinelandii strain containing a deletion of nifV, the gene encoding the homocitrate synthase. Designated NifDK^Cit , the catalytic component of this Mo-nitrogenase variant contains a citrate-substituted cofactor analogue. Activity analysis of NifDK^Cit reveals a shift of CO reduction from H₂ evolution toward hydrocarbon formation and an opposite shift of N₂ reduction from NH₃ formation toward H₂ evolution. Consistent with a shift in the Mo K-edge energy of NifDK^Cit relative to that of its wild-type counterpart, EPR analysis demonstrates a broadening of the line-shape and a decrease in the intensity of the cofactor-originated S=3/2 signal, suggesting a change in the spin properties of the cofactor upon citrate substitution. These observations point to a crucial role of homocitrate in substrate reduction by nitrogenase and the possibility to tune product profiles of nitrogenase reactions via organic ligand substitution.

What Is the Structure of the E4 Intermediate in Nitrogenase?

Nitrogenase is the only enzyme that can cleave the strong triple bond in N₂. The active site contains a complicated MoFe₇S₉C cluster. It is believed that it needs to accept four protons and electrons, forming the E₄ state, before it can bind N₂. However, there is no consensus on the atomic structure of the E₄ state. Experimental studies indicate that it should contain two hydride ions bridging two pairs of Fe ions, and it has been suggested that both hydride ions as well as the two protons bind on the same face of the cluster. On the other hand, density functional theory (DFT) studies have indicated that it is energetically more favorable with either three hydride ions or with a triply protonated carbide ion, depending on the DFT functional. We have performed a systematic combined quantum mechanical and molecular mechanical (QM/MM) study of possible E₄ states with two bridging hydride ions. Our calculations suggest that the most favorable structure has hydride ions bridging the Fe2/6 and Fe3/7 ion pairs. In fact, such structures are 14 kJ/mol more stable than structures with three hydride ions, showing that pure DFT functionals give energetically most favorable structures in agreement with experiments. An important reason for this finding is that we have identified a new type of broken-symmetry state that involves only two Fe ions with minority spin, in contrast to the previously studied states with three Fe ions with minority spin. The energetically best structures have the two hydride ions on different faces of the FeMo cluster, whereas better agreement with ENDOR data is obtained if they are on the same face; such structures are only 6–22 kJ/mol less stable.

Controlling dinitrogen functionalization at rhenium through alkali metal ion pairing

The rhenium(i) salt Na[Re(η⁵-Cp)(BDI)] can be cooled in solution under a dinitrogen atmosphere to selectively access complexes containing rhenium(iii) centers bound to direduced, doubly-bonded N₂ (i.e. diazenide) fragments. We demonstrate this reactivity is critically dependent on ion pairing involving the Na⁺ ion in the starting material, as N₂ binding by Na[Re(η⁵-Cp)(BDI)] proved to be much less favorable when the Na⁺ was sequestered by benzo-12-crown-4. The analogous chemistry of Na[Re(η⁵-Cp)(BDI)] with carbon monoxide (CO) and 2,6-xylylisocyanide (XylNC) was also investigated, which provided structural and spectroscopic bases for determining the impact of ion pairing on π-acid activation in this system.

Electrostatic polarization of nonpolar substrates: a study of interactions between simple cations and Mo-bound N2

Although a great deal of catalytic studies have focused on covalent interactions between substrates and catalyst centers, recognition of the importance of noncovalent and ionic interactions is driving new approaches to catalyst design. Electrostatic interactions with simple cations (those with little covalency, such as alkali metals) play crucial roles in many catalytic processes, but these effects are challenging to study due to their complicated solvation and speciation behaviour. These effects are particularly difficult to study during cation-mediated reactions with weakly-polar or non-polar substrates. Dinitrogen is one of the most nonpolar substrates known to be affected by electrostatic interactions in both heterogeneous and homogeneous reactions but understanding the significance of these effects requires further exploration. To examine these effects systematically, a new multidentate ligand framework bearing pendent crown ethers has been developed and incorporated into a series of Mo(0)-based dinitrogen complexes. Prepared via both reduction and ligand substitution routes, the strength and impact of cation-N₂ interactions have been studied experimentally (IR spectroscopy) and computationally. Although the smallest cation (Li⁺) has the largest impact on the ground-state heterobimetallic activation of N₂, solvation interactions are highly competitive and result in low Li⁺-(N₂)Mo binding affinities. Thus, although smaller cations can have the largest electronic impact on substrates, these interactions are also the least persistent.

Survey of the Geometric and Electronic Structures of the Key Hydrogenated Forms of FeMo-co, the Active Site of the Enzyme Nitrogenase: Principles of the Mechanistically Significant Coordination Chemistry

The enzyme nitrogenase naturally hydrogenates N2 to NH3, achieved through the accumulation of H atoms on FeMo-co, the Fe7MoS9C(homocitrate) cluster that is the catalytically active site. Four intermediates, E1H1, E2H2, E3H3, and E4H4, carry these hydrogen atoms. I report density functional calculations of the numerous possibilities for the geometric and electronic structures of these poly-hydrogenated forms of FeMo-co. This survey involves more than 100 structures, including those with bound H2, and assesses their relative energies and most likely electronic states. Twelve locations for bound H atoms in the active domain of FeMo-co, including Fe–H–Fe and Fe–H–S bridges, are studied. A significant result is that transverse Fe–H–Fe bridges (transverse to the pseudo-threefold axis of FeMo-co and shared with triply-bridging S) are not possible geometrically unless the S is hydrogenated to become doubly-bridging. The favourable Fe–H–Fe bridges are shared with doubly-bridging S. ENDOR data for an E4H4 intermediate trapped at low temperature, and interpretations in terms of the geometrical and electronic structure of E4H4, are assessed in conjunction with the calculated possibilities. The results reported here yield a set of 24 principles for the mechanistically significant coordination chemistry of H and H2 on FeMo-co, in the stages prior to N2 binding.

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.

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.

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).

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.

A New Nitrogenase Mechanism Using a CFe8S9 Model: Does H2 Elimination Activate the Complex to N2 Addition to the Central Carbon Atom?

A truncated model of the FeMo cofactor is used to explore a new mechanism for the conversion of N2 to NH3 by the nitrogenase enzyme. After four initial protonation/reduction steps, the H4CFe8S9 cluster has two hydrogen atoms attached to sulfur, one hydrogen bridging two iron centers and one hydrogen bonded to carbon. The loss of the CH and FeHFe hydrogens as molecular hydrogen activates the cluster to addition of N2 to the carbon center. This unique step takes place at a nearly planar four-coordinate carbon center and leads to an intermediate with a significantly weakened N-N bond. A hydrogen attached to a sulfur atom is then transferred to the distal nitrogen atom. Additional prontonation/reduction steps are modeled by adding a hydrogen atom to sulfur and locating the transition states for transfer to nitrogen. The first NH3 is lost in a thermal neutral step, while the second step is endothermic. The loss of H2 activates the complex by reducing the barrier for N2 addition by 3.5 kcal/mol. Since this is the most difficult step in the mechanism, reducing the barrier for this step justifies the "extra expense" of H2 production.

Docking and migration of carbon monoxide in nitrogenase: the case for gated pockets from infrared spectroscopy and molecular dynamics

Evidence of a CO docking site near the FeMo cofactor in nitrogenase has been obtained by Fourier transform infrared spectroscopy-monitored low-temperature photolysis. We investigated the possible migration paths for CO from this docking site using molecular dynamics calculations. The simulations support the notion of a gas channel with multiple internal pockets from the active site to the protein exterior. Travel between pockets is gated by the motion of protein residues. Implications for the mechanism of nitrogenase reactions with CO and N2 are discussed.

Substrate pathways in the nitrogenase MoFe protein by experimental identification of small molecule binding sites

In the nitrogenase molybdenum-iron (MoFe) protein, we have identified five potential substrate access pathways from the protein surface to the FeMo-cofactor (the active site) or the P-cluster using experimental structures of Xe pressurized into MoFe protein crystals from Azotobacter vinelandii and Clostridium pasteurianum. Additionally, all published structures of the MoFe protein, including those from Klebsiella pneumoniae, were analyzed for the presence of nonwater, small molecules bound to the protein interior. Each pathway is based on identification of plausible routes from buried small molecule binding sites to both the protein surface and a metallocluster. Of these five pathways, two have been previously suggested as substrate access pathways. While the small molecule binding sites are not conserved among the three species of MoFe protein, residues lining the pathways are generally conserved, indicating that the proposed pathways may be accessible in all three species. These observations imply that there is unlikely a unique pathway utilized for substrate access from the protein surface to the active site; however, there may be preferred pathways such as those described here.

The pathway for serial proton supply to the active site of nitrogenase: enhanced density functional modeling of the Grotthuss mechanism

Proton translocation along a chain of eight waters to the active site of nitrogenase is described in detail, using density functional simulations with a 269 atom system that includes surrounding amino acids.

Misconception of reductive elimination of H2, in the context of the mechanism of nitrogenase

Calculated atom partial charges reveal misconceptions of reductive elimination of H₂.

Protonation of bridging sulfur in cubanoid Fe4S4 clusters causes large geometric changes: the theory of geometric and electronic structure

Density functional calculations indicate that protonation of a μ₃-S atom in cubanoid clusters [Fe₄S₄X₄]²⁻ leads to a large extension of one Fe–S(H) bond such that the SH ligand is doubly-bridging, μ-SH.

Substrate channel in nitrogenase revealed by a molecular dynamics approach

Mo-dependent nitrogenase catalyzes the biological reduction of N2 to two NH3 molecules at FeMo-cofactor buried deep inside the MoFe protein. Access of substrates, such as N2, to the active site is likely restricted by the surrounding protein, requiring substrate channels that lead from the surface to the active site. Earlier studies on crystallographic structures of the MoFe protein have suggested three putative substrate channels. Here, we have utilized submicrosecond atomistic molecular dynamics simulations to allow the nitrogenase MoFe protein to explore its conformational space in an aqueous solution at physiological ionic strength, revealing a putative substrate channel. The viability of this observed channel was tested by examining the free energy of passage of N2 from the surface through the channel to FeMo-cofactor, resulting in the discovery of a very low energy barrier. These studies point to a viable substrate channel in nitrogenase that appears during thermal motions of the protein in an aqueous environment and that approaches a face of FeMo-cofactor earlier implicated in substrate binding.

A molecular pathway for the egress of ammonia produced by nitrogenase

Nitrogenase converts N2 to NH3, at one face of an Fe-Mo-S cluster (FeMo-co) buried in the protein. Through exploration of cavities in the structures of nitrogenase proteins, a pathway for the egress of ammonia from its generation site to the external medium is proposed. This pathway is conserved in the three species Azotobacter vinelandii, Klebsiella pneumoniae and Clostridium pasteurianum. A molecular mechanism for the translocation of NH3 by skipping through a sequence of hydrogen bonds involving eleven water molecules and surrounding aminoacids has been developed. The putative mechanism requires movement aside of some water molecules by up to ~ 1Å. Consistent with this, the surrounding protein is comprised of different chains and has little secondary structure: protein fluctuations are part of the mechanism. This NH3 pathway is well separated from the water chain and embedded proton wire that have been proposed for serial supply of protons to FeMo-co. Verification procedures are suggested.

Multiple amino acid sequence alignment nitrogenase component 1: insights into phylogenetics and structure-function relationships

Amino acid residues critical for a protein's structure-function are retained by natural selection and these residues are identified by the level of variance in co-aligned homologous protein sequences. The relevant residues in the nitrogen fixation Component 1 α- and β-subunits were identified by the alignment of 95 protein sequences. Proteins were included from species encompassing multiple microbial phyla and diverse ecological niches as well as the nitrogen fixation genotypes, anf, nif, and vnf, which encode proteins associated with cofactors differing at one metal site. After adjusting for differences in sequence length, insertions, and deletions, the remaining >85% of the sequence co-aligned the subunits from the three genotypes. Six Groups, designated Anf, Vnf , and Nif I-IV, were assigned based upon genetic origin, sequence adjustments, and conserved residues. Both subunits subdivided into the same groups. Invariant and single variant residues were identified and were defined as “core” for nitrogenase function. Three species in Group Nif-III, Candidatus Desulforudis audaxviator, Desulfotomaculum kuznetsovii, and Thermodesulfatator indicus, were found to have a seleno-cysteine that replaces one cysteinyl ligand of the 8Fe:7S, P-cluster. Subsets of invariant residues, limited to individual groups, were identified; these unique residues help identify the gene of origin (anf, nif, or vnf) yet should not be considered diagnostic of the metal content of associated cofactors. Fourteen of the 19 residues that compose the cofactor pocket are invariant or single variant; the other five residues are highly variable but do not correlate with the putative metal content of the cofactor. The variable residues are clustered on one side of the cofactor, away from other functional centers in the three dimensional structure. Many of the invariant and single variant residues were not previously recognized as potentially critical and their identification provides the bases for new analyses of the three-dimensional structure and for mutagenesis studies.