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

Understanding non-reducible N2 in the mechanism of Mo-nitrogenase

In my proposed mechanism of Mo-nitrogenase there are two roles for separate N2 molecules. One N2 diffuses into the reaction zone between Fe2 and Fe6 where a strategic gallery of H atoms can capture N2 to form the Fe-bound HNNH intermediate which is then progressively hydrogenated through intermediates containing HNNH2, NH and NH2 entities and then two NH3 in sequence. The second N2 can be parked in an N2-pocket about 3.2 Å from Fe2 or bind end-on at the exo coordination site of Fe2. This second N2 is outside the reaction zone, not exposed to H atom donors, and so is 'non-reducible'. Here density functional calculations using a 485+ atom model describe the thermodynamics for non-reducible N2 moving between the N2-pocket and the exo-Fe2 position, for the resting state and 19 intermediates in the mechanism. The entropy component is estimated and included. The result is that for all intermediates with ligation by H or NHx at the endo-Fe2 position the free energy for association of non-reducible N2 at exo-Fe2 is negative. There remains some uncertainty about the status of exo-Fe2-N2 during the step in which H2 exchanges with the incoming reducible N2, where at least two unbound molecules are present. At Fe2 it is evident that attainment of octahedral coordination stereochemistry dominates the binding thermodynamics for non-reducible N2. Possibilities for experimental support of these computational conclusions are discussed.

The mechanism of Mo-nitrogenase: from N2 capture to first release of NH3

Mo-nitrogenase hydrogenates N2 to NH3. This report continues from the previous paper [I. Dance, Dalton Trans., 2024, 53, 14193-14211] that described how the active site FeMo-co of the enzyme is uniquely able to capture and activate N2, forming a key intermediate with Fe-bound HNNH. Density functional simulations with a 485+ atom model of the active site and its surroundings are used to describe here the further reactions of this HNNH intermediate. The first step is hydrogenation to form HNNH2 bridging Fe2 and Fe6. Then a single-step reaction breaks the N-N bond, generating an Fe2-NH-Fe6 bridge and forming NH3 bound to Fe6. Then NH3 dissociates from Fe6. Reaction potential energies and kinetic barriers for all steps are reported for the most favourable electronic states of the system. The steps that follow the Fe2-NH-Fe6 intermediate, forming and dissociating the second NH3, and regenerating the resting state of the enzyme, are outlined. These results provide an interpretation of the recent steady-state kinetics data and analysis by Harris et al., [Biochemistry, 2022, 61, 2131-2137] who found a slow step after the formation of the HNNH intermediate. The calculated potential energy barriers for the HNNH2 → NH + NH3 reaction (30-36 kcal mol-1) are larger than the potential energy barriers for the N2 → HNNH reaction (19-29 kcal mol-1). I propose that the post-HNNH slow step identified kinetically is the key HNNH2 → NH + NH3 reaction described here. This step and the N2-capture step are the most difficult in the conversion of N2 to 2NH3. The steps in the complete mechanism still to be computationally detailed are relatively straightforward.

Structural evolution of nitrogenase states under alkaline turnover

Biological nitrogen fixation, performed by the enzyme nitrogenase, supplies nearly 50% of the bioavailable nitrogen pool on Earth, yet the structural nature of the enzyme intermediates involved in this cycle remains ambiguous. Here we present four high resolution cryoEM structures of the nitrogenase MoFe-protein, sampled along a time course of alkaline reaction mixtures under an acetylene atmosphere. This series of structures reveals a sequence of salient changes including perturbations to the inorganic framework of the FeMo-cofactor; depletion of the homocitrate moiety; diminished density around the S2B belt sulfur of the FeMo-cofactor; rearrangements of cluster-adjacent side chains; and the asymmetric displacement of the FeMo-cofactor. We further demonstrate that the nitrogenase associated factor T protein can recognize and bind an alkaline inactivated MoFe-protein in vitro. These time-resolved structures provide experimental support for the displacement of S2B and distortions of the FeMo-cofactor at the E0-E3 intermediates of the substrate reduction mechanism, prior to nitrogen binding, highlighting cluster rearrangements potentially relevant to nitrogen fixation by biological and synthetic clusters.

The activating capture of N2 at the active site of Mo-nitrogenase

Dinitrogen is inherently inert. This report describes detailed density functional calculations (with a 485+ atom model) of mechanistic steps by which the enzyme nitrogenase activates unreactive N2 at the intact active site FeMo-co, to form a key intermediate with bound HNNH. This mechanism does not bind N2 first and then add H atoms, but rather captures N2 ('N2-ready') that diffuses in through the substrate channel and enters a strategic gallery of H atom donors in the reaction zone, between Fe2 and Fe6. This occurs at the E4 stage of the complete mechanism. Exploration of possible reactions of N2 in this space leads to the conclusion that the first reaction step is transfer of H on Fe7 to one end of N2-ready, soon followed by Fe-N bond formation, and then a second H transfer from bridging S2BH to the other N. Two H-N bonds and one or two N-Fe bonds are formed, in some cases with a single transition state. The variable positions and orientations of N2-ready lead to various reaction trajectories and products. The favourable products resulting from this capture, judged by the criteria of reaction energies, reaction barriers, and mechanistic competence for further hydrogenation reactions in the nitrogenase cycle, have Fe2-NH-NH bonding. The trajectory of one N2 capture reaction is described in detail, and calculations that separate the H atom component and the 'heavy atom' components of the classical activation energy are described, in the context of possible H atom tunneling in the activation of N2-ready. I present arguments for the activation of N2 by the pathway of concerted hydrogenation and binding of N2-ready, alternative to the commonly assumed pathway of binding N2 first, with subsequent hydrogenation. The active site of nitrogenase is well primed for the thermodynamic and kinetic advantages of N2 capture.

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.

The HD Reaction of Nitrogenase: a Detailed Mechanism

Nitrogenase is the enzyme that converts N2 to NH3 under ambient conditions. The chemical mechanism of this catalysis at the active site FeMo-co [Fe7 S9 CMo(homocitrate)] is unknown. An obligatory co-product is H2 , while exogenous H2 is a competitive inhibitor. Isotopic substitution using exogenous D2 revealed the N2 -dependent reaction D2 +2H+ +2e- →2HD (the 'HD reaction'), together with a collection of additional experimental characteristics and requirements. This paper describes a detailed mechanism for the HD reaction, developed and elaborated using density functional simulations with a 486-atom model of the active site and surrounding protein. First D2 binds at one Fe atom (endo-Fe6 coordination position), where it is flanked by H-Fe6 (exo position) and H-Fe2 (endo position). Then there is synchronous transfer of these two H atoms to bound D2 , forming one HD bound to Fe2 and a second HD bound to Fe6. These two HD dissociate sequentially. The final phase is recovery of the two flanking H atoms. These H atoms are generated, sequentially, by translocation of a proton from the protein surface to S3B of FeMo-co and combination with introduced electrons. The first H atom migrates from S3B to exo-Fe6 and the second from S3B to endo-Fe2. Reaction energies and kinetic barriers are reported for all steps. This mechanism accounts for the experimental data: (a) stoichiometry; (b) the N2 -dependence results from promotional N2 bound at exo-Fe2; (c) different N2 binding Km for the HD reaction and the NH3 formation reaction results from involvement of two different sites; (d) inhibition by CO; (e) the non-occurrence of 2HD→H2 +D2 results from the synchronicity of the two transfers of H to D2 ; (f) inhibition of HD production at high pN2 is by competitive binding of N2 at endo-Fe6; (g) the non-leakage of D to solvent follows from the hydrophobic environment and irreversibility of proton introduction.

Quantum Mechanical Calculations of Redox Potentials of the Metal Clusters in Nitrogenase

We have calculated redox potentials of the two metal clusters in Mo-nitrogenase with quantum mechanical (QM) calculations. We employ an approach calibrated for iron-sulfur clusters with 1-4 Fe ions, involving QM-cluster calculations in continuum solvent and large QM systems (400-500 atoms), based on structures from combined QM and molecular mechanics (QM/MM) geometry optimisations. Calculations on the P-cluster show that we can reproduce the experimental redox potentials within 0.33 V. This is similar to the accuracy obtained for the smaller clusters, although two of the redox reactions involve also proton transfer. The calculated P1+/PN redox potential is nearly the same independently of whether P1+ is protonated or deprotonated, explaining why redox titrations do not show any pH dependence. For the FeMo cluster, the calculations clearly show that the formal oxidation state of the cluster in the resting E0 state is MoIIIFe3IIFe4III , in agreement with previous experimental studies and QM calculations. Moreover, the redox potentials of the first five E0-E4 states are nearly constant, as is expected if the electrons are delivered by the same site (the P-cluster). However, the redox potentials are insensitive to the formal oxidation states of the Fe ion (i.e., whether the added protons bind to sulfide or Fe ions). Finally, we show that the later (E4-E8) states of the reaction mechanism have redox potential that are more positive (i.e., more exothermic) than that of the E0/E1 couple.

13C ENDOR Characterization of the Central Carbon within the Nitrogenase Catalytic Cofactor Indicates That the CFe6 Core Is a Stabilizing "Heart of Steel"

Substrates and inhibitors of Mo-dependent nitrogenase bind and react at Fe ions of the active-site FeMo-cofactor [7Fe-9S-C-Mo-homocitrate] contained within the MoFe protein α-subunit. The cofactor contains a CFe6 core, a carbon centered within a trigonal prism of six Fe, whose role in catalysis is unknown. Targeted 13C labeling of the carbon enables electron-nuclear double resonance (ENDOR) spectroscopy to sensitively monitor the electronic properties of the Fe-C bonds and the spin-coupling scheme adopted by the FeMo-cofactor metal ions. This report compares 13CFe6 ENDOR measurements for (i) the wild-type protein resting state (E0; α-Val70) to those of (ii) α-Ile70, (iii) α-Ala70-substituted proteins; (iv) crystallographically characterized CO-inhibited "hi-CO" state; (v) E4(4H) Janus intermediate, activated for N2 binding/reduction by accumulation of 4[e-/H+]; (vi) E4(2H)* state containing a doubly reduced FeMo-cofactor without Fe-bound substrates; and (vii) propargyl alcohol reduction intermediate having allyl alcohol bound as a ferracycle to FeMo-cofactor Fe6. All states examined, both S = 1/2 and 3/2 exhibited near-zero 13C isotropic hyperfine coupling constants, Ca = [-1.3 ↔ +2.7] MHz. Density functional theory computations and natural bond orbital analysis of the Fe-C bonds show that this occurs because a (3 spin-up/3 spin-down) spin-exchange configuration of CFe6 Fe-ion spins produces cancellation of large spin-transfers to carbon in each Fe-C bond. Previous X-ray diffraction and DFT both indicate that trigonal-prismatic geometry around carbon is maintained with high precision in all these states. The persistent structure and Fe-C bonding of the CFe6 core indicate that it does not provide a functionally dynamic (hemilabile) "beating heart"─instead it acts as "a heart of steel", stabilizing the structure of the FeMo-cofactor-active site during nitrogenase catalysis.

Understanding the tethered unhooking and rehooking of S2B in the reaction domain of FeMo-co, the active site of nitrogenase

The active site of the nitrogen fixing enzyme nitrogenase is an Fe₇MoS₉C cluster, and investigations of the enigmatic chemical mechanism of the enzyme have focussed on a pair of Fe atoms, Fe2 and Fe6, and the S2B atom that bridges them. There are three proposals for the status of the Fe2-S2B-Fe6 bridge during the catalytic cycle: one that it remains intact, another that it is completely labile and absent during catalysis, and a third that S2B is hemilabile, unhooking one of its bonds to Fe2 or Fe6. This report examines the tethered unhooking of S2B and factors that affect it, using DFT calculations of 50 geometric/electronic possibilities with a 485 atom model including all relevant parts of surrounding protein. The outcomes are: (a) unhooking the S2B-Fe2 bond is feasible and favourable, but alternative unhooking of the S2B-Fe6 bond is unlikely for steric reasons, (b) energy differences between hooked and unhooked isomers are generally <10 kcal mol^-1, usually with unhooked more stable, (c) ligation at the exo-Fe6 position inhibits unhooking, (d) unhooking of hydrogenated S2B is more favourable than that of bare S2B, (e) hydrogen bonding from the NεH function of His195 to S2B occurs in hooked and unhooked forms, and possibly stabilises unhooking, (f) unhooking is reversible with kinetic barriers ranging 10-13 kcal mol^-1. The conclusion is that energetically accessible reversible unhooking of S2B or S2BH, as an intrinsic property of FeMo-co, needs to be considered in the formulation of mechanisms for the reactions of nitrogenase.

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.

Analysis of the Geometric and Electronic Structure of Spin-Coupled Iron-Sulfur Dimers with Broken-Symmetry DFT: Implications for FeMoco

The open-shell electronic structure of iron-sulfur clusters presents considerable challenges to quantum chemistry, with the complex iron-molybdenum cofactor (FeMoco) of nitrogenase representing perhaps the ultimate challenge for either wavefunction or density functional theory. While broken-symmetry density functional theory has seen some success in describing the electronic structure of such cofactors, there is a large exchange-correlation functional dependence in calculations that is not fully understood. In this work, we present a geometric benchmarking test set, FeMoD11, of synthetic spin-coupled Fe-Fe and Mo-Fe dimers, with relevance to the molecular and electronic structure of the Mo-nitrogenase FeMo cofactor. The reference data consists of high-resolution crystal structures of metal dimer compounds in different oxidation states. Multiple density functionals are tested on their ability to reproduce the local geometry, specifically the Fe-Fe/Mo-Fe distance, for both antiferromagnetically coupled and ferromagnetically coupled dimers via the broken-symmetry approach. The metal-metal distance is revealed not only to be highly sensitive to the amount of exact exchange in the functional but also to the specific exchange and correlation functionals. For the antiferromagnetically coupled dimers, the calculated metal-metal distance correlates well with the covalency of the bridging metal-ligand bonds, as revealed via the corresponding orbital analysis, Hirshfeld S/Fe charges, and Fe-S Mayer bond order. Superexchange via bridging ligands is expected to be the dominant interaction in these dimers, and our results suggest that functionals that predict accurate Fe-Fe and Mo-Fe distances describe the overall metal-ligand covalency more accurately and in turn the superexchange of these systems. The best performing density functionals of the 16 tested for the FeMoD11 test set are revealed to be either the nonhybrid functionals r2SCAN and B97-D3 or hybrid functionals with 10-15% exact exchange: TPSSh and B3LYP*. These same four functionals are furthermore found to reproduce the high-resolution X-ray structure of FeMoco well according to quantum mechanics/molecular mechanics (QM/MM) calculations. Almost all nonhybrid functionals systematically underestimate Fe-Fe and Mo-Fe distances (with r2SCAN and B97-D3 being the sole exceptions), while hybrid functionals with >15% exact exchange (including range-separated hybrid functionals) overestimate them. The results overall suggest r2SCAN, B97-D3, TPSSh, and B3LYP* as accurate density functionals for describing the electronic structure of iron-sulfur clusters in general, including the complex FeMoco cluster of nitrogenase.

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.