Protonation of Homocitrate and the E1 State of Fe-Nitrogenase Studied by QM/MM Calculations

Nitrogenase is the only enzyme that can cleave the strong triple bond in N2, making nitrogen available for biological life. There are three isozymes of nitrogenase, differing in the composition of the active site, viz., Mo, V, and Fe-nitrogenase. Recently, the first crystal structure of Fe-nitrogenase was presented. We have performed the first combined quantum mechanical and molecular mechanical (QM/MM) study of Fe-nitrogenase. We show with QM/MM and quantum-refinement calculations that the homocitrate ligand is most likely protonated on the alcohol oxygen in the resting E0 state. The most stable broken-symmetry (BS) states are the same as for Mo-nitrogenase, i.e., the three Noodleman BS7-type states (with a surplus of β spin on the eighth Fe ion), which maximize the number of nearby antiferromagnetically coupled Fe-Fe pairs. For the E1 state, we find that protonation of the S2B μ2 belt sulfide ion is most favorable, 14-117 kJ/mol more stable than structures with a Fe-bound hydride ion (the best has a hydride ion on the Fe2 ion) calculated with four different density-functional theory methods. This is similar to what was found for Mo-nitrogenase, but it does not explain the recent EPR observation that the E1 state of Fe-nitrogenase should contain a photolyzable hydride ion. For the E1 state, many BS states are close in energy, and the preferred BS state differs depending on the position of the extra proton and which density functional is used.

Protonated and deprotonated vanadyl imidazole tartrates for the mimics of the vanadium coordination in the FeV-cofactor of V-nitrogenase

Chiral imidazole-based oxidovanadium tartrates (H2im)2[Δ,Λ-VIV2O2(R,R-H2tart)(R,R-tart)(Him)2]·Him (1, H4tart = tartaric acid, Him = imidazole) and [Λ,Λ-VIV2O2(R,R-tart)(Him)6]·4H2O (2) and their corresponding enantiomers (H2im)2[Λ,Δ-VIV2O2(S,S-H2tart)(S,S-tart)(Him)2]·Him (3) and [Δ,Δ-VIV2O2(S,S-tart)(Him)6]·4H2O (4) were obtained in alkaline solutions. Interestingly, the tartrates chelate with vanadium bidentately through α-alkoxy/α-hydroxy and α-carboxy groups and imidazole coordinates monodentately through nitrogen atom. It is worth noting that complexes 1 and 3 contain both protonated α-hydroxy and deprotonated α-alkoxy groups simultaneously, which have short V-Oα-alkoxy distances [1.976(4)av Å in 1-4] and long V-Oα-hydroxy distances [2.237(3)av Å in 1 and 2.230(2)av Å in 3]. There is an interesting strong intramolecular hydrogen bond [O(11)⋯O(1) 2.731(5) Å] between the two parts in 1 and 3. The protonated V-O distances are closer to the average bond distance in reported FeV-cofactors (FeV-cos, V-Oα-alkoxy 2.156av Å) in VFe proteins, which corresponds to the feasible protonation of coordinated α-hydroxy in R-homocitrate in V-nitrogenase, showing the homocitrate in the mechanistic model for nitrogen reduction as a secondary proton donor. Furthermore, vibrational circular dichroism (VCD) and IR spectra of 1-4 pointed out the disparity between the characteristic vibrations of the C-O and C-OH groups clearly. EPR experiment and theoretical calculations support +4 oxidation states for vanadium in 1-4. Solution 13C {1H} NMR spectra and CV analyses exhibited the solution properties for 1 and 2, respectively, which indicates that there should be a rapid exchange equilibrium between the protonated and deprotonated species in solutions.

Electrochemical and X-ray structural evidence of multiple molybdenum precursor candidates from a reported non-aqueous electrodeposition of molybdenum disulfide

A published report of electrodeposited molybdenum(iv) disulfide microflowers at 100 °C in the ionic liquid N-methyl-N-propylpiperidinium bis(trifluoromethane)sulfonimide (PP13-TFSI) from 1,4-butanedithiol and the concentrated filtrate from a reaction mixture of molybdenum(vi) trioxide and ethylene glycol could not be reproduced reliably, affording numerous uniquely coloured reaction mixtures that precipitated a variety of crystalline molybdenum coordination complexes. Further attempts to use the same two of these filtrates to electrodeposit molybdenum(iv) disulfide from 0.1 M PP13-TFSI in tetrahydrofuran with 1,4-butanedithiol at room temperature were unsuccessful. Various crude reaction mixtures grew crystals of different identity from eight attempts to synthesize the reported molybdenum-precursor. Single crystal X-ray diffraction (SC-XRD) offered insight into a wide range of structural features from four candidate paramagnetic precursor compounds, including a novel organomolybdenum cluster. Electrochemical studies of the various molybdenum-precursor filtrates, ethylene glycol, and 1,4-butanedithiol were conducted in 0.1 M PP13-TFSI in tetrahydrofuran, offering insight into differences between preparations of the molybdenum-precursor and interference between ethylene glycol and 1,4-butanedithiol on platinum working electrodes. Molybdenum(iv) disulfide electrodeposition attempts included cyclic voltammetry and chronoamperometry on platinum and glassy carbon working electrodes, which led to either no deposited material, or molybdenum, carbon, oxygen, and sulfur containing amorphous and non-homogenous deposits, as indicated by SEM-EDS analysis.

Binuclear, tetranuclear and hexadecanuclear thio-oxomolybdenum(V/IV) glycolates with selective adsorptions of gases

By adjusting the pH values of the solutions, binuclear, tetranuclear and hexadecanuclear glycolato thio- and oxomolybdenum(V/IV) complexes [MoV2O₂(μ₂-O)(μ₂-S)(Hglyc)₂(Hpz)₂]·H₂O (1, H₂glyc = glycolic acid, Hpz = pyrazole), (Hdpa)[MoV2O₂(μ₂-S)₂(Hglyc)(glyc)(H₂O)] (2, dpa = 2,2'-dipyridylamine), (Hdpa)₄[MoV4O₄(μ₃-O)₂(μ₂-S)₂(glyc)₂(S₂O₃)₂] (3) and Na₂[MoIV4MoV12O₁₂(μ₂-O)₆(μ₂-OH)₂(μ₃-O)₁₂(glyc)₄(Hpz)₄(pz)₈]·28H₂O (4) have been obtained successfully. Here the glycolates existed in varying aggregates with different degrees of protonation and deprotonation in 1-4. The stable formations of 1 and 2 are attributed to strong hydrogen bonds formed between the molecules. In particular, the asymmetric unit in 2 is a tetramer linked by hydrogen bonding [2.574(9) Å] between α-hydroxy and α-alkoxy groups for further construction of unsaturated penta-coordination environments. Moreover, deprotonated glycolates act as bridging ligands to form tetra- and hexadecanuclear compounds 3 and 4, respectively. The smallest unit in 4 exhibits mixed valences of 4+ and 5+ simultaneously, where its gas adsorption experiments manifest that 4 is obviously beneficial for O₂ and CO₂ compared with no adsorption of N₂, CH₄ and H₂ at different pressures.

Chiral Supramolecular Microporous Thio-Oxomolybdenum(V) Tartrates for the Selective Adsorptions of Gases

Two pairs of enantiomerically pure hexanuclear and tetranuclear microporous molybdenum(V) d/l-tartrates, (H₂trz)₃[Mo₆O₆(μ₂-O)₃(μ₂-S)₃(d/l-Htart)₃(Htrz)₆]·8H₂O (abbreviated as d-1 and l-1; H₄tart = tartaric acid, Htrz = 1,2,4-triazole) and (H₂2-mim)₈[Mo₄O₄(μ₂-S)₄(d/l-tart)₂]₂·4H₂O (d-2/l-2; H2-mim = 2-methylimidazole), have been isolated in reduced media and well characterized. These enantiomers are observed to finish self-assemblies with single chiral configurations. Structural analyses indicate that tartrates adopt different coordination modes with α-carboxy and/or α-alkoxy groups in 1 and 2, which are further completed with nitrogen-containing ligands. There are two types of micropores that exist in 1 and 2, separately, which are all formed by the isolated molecules themselves. The significant roles of hydrogen bonding among lattice molecules, tartrates, and multi-azoles are suggested, where 1 and 2 exhibited interesting supramolecular networks only through intramolecular self-sorts. Adsorption tests show that 1 has good affinities toward CO₂ and O₂, while 2 is the most potential O₂ adsorbent compared with other common gases CO₂, H₂, CH₄, and N₂ under different pressures. In addition, IR, UV-vis, CD (circular dichroism), and solid-state ¹³C NMR spectroscopies have demonstrated the special chemical properties of these novel molybdenum d/l-tartrates.

Comparisons of bond valences and distances for CO- and N2-bound clusters of FeMo-cofactors

By comparisons of N2 and isoelectronic substrate CO bound FeMo-cofactors (FeMo-cos) in nitrogenases, we have used a classical bond valence method to calculate the oxidation states of the iron and molybdenum atoms in FeMo-cos.

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

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

Spontaneous conversions of glutamine, histidine and arginine into α-hydroxycarboxylates with NH4VO3 or V2O5

Glutamine gets transformed to 2-hydroxy-5-oxoproline with NH₄VO₃ in a neutral solution as a product of 2,2'-bipyridine oxidovanadium(v) 2-hydroxy-5-oxoproline [V^V₂O₃(hop)₂(bpy)₂]·7H₂O [1, H₂hop = 2-hydroxy-5-oxoproline] with yields of 65.6%. Similarly, histidine and arginine are converted into the corresponding α-hydroxycarboxylates as 2,2'-bipyridine oxidovanadium(iv) 3-(1H-imidazolyl-5-yl)-2-hydroxyacrylate [V^IV₂O₂(imha)₂(bpy)₂]·bpy [2, H₂imha = 3-(1H-imidazolyl-5-yl)-2-hydroxyacrylic acid] and guanidinium oxidovanadium(v) 1-(aminoiminomethyl)-2-hydroxyproline (CN₃H₆)[V^VO₂(Haimhp)₂]·2H₂O [3, H₂aimhp = 1-(aminoiminomethyl)-2-hydroxyproline] with V₂O₅ in low yields respectively, where an aggregate of oxidovanadium(v) arginine (H₂arg)_n(V^VO₃)_n·½nH₂O (4, Harg = arginine) has been isolated preferentially in an initial experiment for 3. α-Hydroxycarboxylates chelate bidentately with vanadium viaα-alkoxy and α-carboxy groups in 1-3, as observed from structural analyses. Their racemizations have been observed after the conversions. There is no coordination in 4 based on solid-state ¹³C NMR spectra, and only strong hydrogen bonds exist in the anion chains (V^VO₃)^- and protonated arginines. 1 and 4 were fully characterized by elemental analysis, UV-vis, IR and solid-state ¹³C NMR spectroscopies, TG and X-ray structural analyses, and theoretical bond valence calculations (BVS). The conversions of glutamine, histidine and arginine occur spontaneously in a solution under ambient conditions.

Isolated Mixed-Valence Iron Vanadium Malate and Its Metal Hydrates (M = Fe2+, Cu2+, Zn2+) with Reversible and Irreversible Adsorptions for Oxygen

Isolated octanuclear iron-vanadium malate (NH₄)₃(CH₃NH₃)₃[Fe^III₂V^IV₂V^V₄O₁₁(mal)₆]·7.5H₂O (1; H₃mal = malic acid) and its family of metal hydrates M'_3n[M^II(H₂O)₂]_1.5n[Fe^III₂V^IV₂V^V₄O₁₁(mal)₆]_n·xnH₂O (2 or 2-Fe, M' = NH₄⁺, M = Fe, x = 7.5; 3 or 3-Cu, M' = K⁺, M = Cu, x = 10; 4 or 4-Zn, M' = K⁺, M = Zn, x = 6.5) have been obtained by self-assembly in water. The cluster anion [Fe₂V₆O₁₁(mal)₆]^6- (1a) shows an interesting iron bicapped-triangular-prismatic structure, which is bridged by M²⁺ hydrates (M = Fe, Cu, Zn) to construct isostructural metal organic frameworks (MOFs) 2-4. The mixed-valence vanadium systems in 1-4 were determined by theoretical bond valence calculations (BVS) and charge balance. The magnetic susceptibilities are further elucidated as high spin for Fe³⁺ in 1a and bridging Fe²⁺ in 2-Fe, respectively. A strong ferromagnetic interaction was also observed for 2-Fe at 3 K. 2-Fe, 3-Cu, and 4-Zn have similar hydrophilic channels with diameters of 6.8, 6.5, and 6.6 Å, respectively, which show obvious affinity for O₂ in comparison with no adsorption of N₂, H₂, CO₂, and CH₄ at room temperature under different pressures. Moreover, 2-Fe and 4-Zn exhibit irreversible O₂ absorptions, which may be attributed to charge transfer between O₂ and open metal sites (OMSs) formed during vacuum heating pretreatment. UV-vis and EPR spectra show a change in electronic structure of 2-Fe after O₂ adsorption. The reversible adsorption observed in 3-Cu suggests a weak interaction between O₂ and Cu²⁺ due to the Jahn-Teller effect. The properties of gas adsorption provide an insight into the performances of small molecules in the channels constructed by synthetic octanuclear model compounds, which are related to the interactions between the gas substrate and the heterometal cluster in biology.

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

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

Novel bidentate oxovanadium(IV) glycolate, α-hydroxybutyrate and citrate with terpyridine and their conversions to nitrosyl products

A series of monomeric α-hydroxycarboxylato oxovanadium(IV) complexes [VO(H₂cit)(tpy)]·H₂O (1) (H₄cit = citric acid, tpy = 2,2':6',2-terpyridine), [VO(glyc)(tpy)]·5.5H₂O (2) (H₂glyc = glycolic acid) and [VO(α-hbut)(tpy)]·3H₂O (3) (α-H₂hbut = α-hydroxybutyratic acid) have been obtained from the reactions of vanadyl sulfate with α-hydroxycarboxylates and terpyridine in acidic solutions. These complexes feature bidentate citrate, glycolate or α-hydroxybutyrate respectively. The ligand chelates to vanadium atom through α-hydroxy (in 1) or α-alkoxy (in 2 and 3) and α-carboxy groups, while β-carboxy groups of citrate in 1 are free to participate strong hydrogen bonds with neighboring citrate. With comparable chelation, 1 shares a similar V-O_α-hydroxy distance [2.168(1) Å] with that observed in FeV-cofactor [2.17 Å] [1]. Moreover, nitrosyl vanadium complexes [V(NO)(glyc)(tpy)]·3H₂O (4) and [V(NO)(α-hbut)(tpy)]·4H₂O (5) were obtained via reductions of synthetic solutions of 2 and 3 with hydroxylamine respectively. The terminal oxygen atoms were substituted by linear nitrosyl groups in 4 and 5. They were fully characterized by UV-vis, IR, EPR spectra, X-ray structural analyses and theoretical bond valence calculations.

α-Lys424 Participates in Insertion of FeMoco to MoFe Protein and Maintains Nitrogenase Activity in Klebsiella oxytoca M5al

Our previous investigation of substrates reduction catalyzed by nitrogenase suggested that α-Ile⁴²³ of MoFe protein possibly functions as an electron transfer gate to Mo site of active center-“FeMoco”. Amino acid residue α-Lys⁴²⁴ connects directly to α-Ile⁴²³, and they are located in the same α-helix (α423-431). In the present study, function of α-Lys⁴²⁴ was investigated by replacing it with Arg (alkaline, like Lys), Gln (neutral), Glu (acidic), and Ala (neutral) through site-directed mutagenesis and homologous recombination. The mutants were, respectively, termed 424R, 424Q, 424E, and 424A. Studies of diazotrophic cell growth, cytological, and enzymatic properties indicated that none of the substitutions altered the secondary structure of MoFe protein, or normal expression of nifA, nifL, and nifD. Substitution of alkaline amino acid (i.e., 424R) maintained acetylene (C₂H₂) and proton (H⁺) reduction activities at normal levels similar to that of wild-type (WT), because its FeMoco content did not reduce. In contrast, substitution of acidic or neutral amino acid (i.e., 424Q, 424E, 424A) impaired the catalytic activity of nitrogenase to varying degrees. Combination of MoFe protein structural simulation and the results of a series of experiments, the function of α-Lys⁴²⁴ in ensuring insertion of FeMoco to MoFe protein was further confirmed, and the contribution of α-Lys⁴²⁴ in maintaining low potential of the microenvironment causing efficient catalytic activity of nitrogenase was demonstrated.

Preliminary Assignment of Protonated and Deprotonated Homocitrates in Extracted FeMo-Cofactors by Comparisons with Molybdenum(IV) Lactates and Oxidovanadium Glycolates

A similar pair of protonated and deprotonated mononuclear oxidovanadium glycolates [VO(Hglyc)(phen)(H₂O)]Cl·2H₂O (1) and [VO(glyc)(bpy)(H₂O)] (2) and a mixed-(de)protonated oxidovanadium triglycolate (NH₄)₂[VO(Hglyc)₂(glyc)]·H₂O (3) were isolated and examined. The ≡C-O(H) (≡C-OH or ≡C-O) groups coordinated to vanadium were spectroscopically and structurally identified. The glycolate in 1 features a bidentate chelation through protonated α-hydroxy and α-carboxy groups, whereas the glycolate in 2 coordinates through deprotonated α-alkoxy and α-carboxy groups. The glycolates in 3 coordinate to vanadium through α-alkoxy or α-hydroxy and α-carboxy groups and thus have both protonated ≡C-OH and deprotonated ≡C-O bonds simultaneously. Structural investigations revealed that the longer protonated V-O_α-hydroxy bonds [2.234(2) Å and 2.244(2) Å] in 1 and 3 are close to those of FeV-cofactor (FeV-co) 2.17 Ź (FeMo-co 2.17 Ų), while deprotonated V-O_α-alkoxy bonds [2, 1.930(2); 3, 1.927(2) Å] were obviously shorter. This shows a similar elongated trend as the Mo-O distances in the previously reported deprotonated vs protonated molybdenum lactates (Wang, S. Y. et al. Dalton Trans. 2018, 47, 7412-7421) and these vanadium and molybdenum complexes have the same local V/Mo-homocitrate structures as those of FeV/Mo-cos of nitrogenases. The IR spectra of these oxidovanadium and the previously synthesized molybdenum complexes including different substituted ≡C-O(H) model compounds show red-shifts for ≡C-OH vs ≡C-O alternation, which further assign the two IR bands of extracted FeMo-co at 1084 and 1031 cm^-1 to ≡C-O and ≡C-OH vibrations, respectively. Although the structural data or IR spectra for some of the previously synthesized Mo/V complexes and extracted FeMo-co were measured earlier, this is the first time that the ≡C-O(H) coordinated peaks are assigned. The overall structural and IR results well suggest the coexistence of homocitrates coordinated with α-alkoxy (deprotonated) and α-hydroxy (protonated) groups in the extracted FeMo-co.

Molybdenum imidazole citrate and bipyridine homocitrate in different oxidation states – balance between coordinated α-hydroxy and α-alkoxy groups

Oxo and thiomolybdenum(iv/vi) imidazole hydrocitrates K₂{Mo^IV₃O₄(im)₃[Mo^VIO₃(Hcit)]₂}·3im·4H₂O (1), (Him)₂{Mo^IV₃SO₃(im)₃[Mo^VIO₃(Hcit)]₂}·im·6H₂O (2), molybdenum(v) bipyridine homocitrate trans-[(Mo^VO)₂O(H₂homocit)₂(bpy)₂]·4H₂O (3) and molybdenum(vi) citrate (Et₄N)[Mo^VIO₂Cl(H₂cit)]·H₂O (4) (H₄cit = citric acid, H₄homocit = homocitric acid, im = imidazole and bpy = 2,2′-bipyridine) with different oxidation states were prepared. 1 and 2 are the coupling products of [Mo^VIO₃(Hcit)]³⁻ anions and incomplete cubane units [Mo^IV₃O₄]⁴⁺ ([Mo^IV₃SO₃]⁴⁺) with monodentate imidazoles, respectively, where tridentate citrates coordinate with α-hydroxy, α-carboxy and β-carboxy groups, forming pentanuclear skeleton structures. The molybdenum atoms in 1 and 2 show unusual +4 and +6 valences based on charge balances, theoretical bond valence calculations and Mo XPS spectrum. The coordinated citrates in 1 and 2 are protonated with α-hydroxy groups, while 3 and 4 with higher oxidation states of +5 and +6 are deprotonated with α-alkoxy group even under strong acidic condition, respectively. This shows the relationship between the oxidation state and protonation of the α-alkoxy group in citrate or homocitrate, which is related to the protonation state of homocitrate in FeMo-cofactor of nitrogenase. The homocitrate in 3 chelates to molybdenum(v) with bidentate α-alkoxy and monodentate α-carboxy groups. Molybdenum(vi) citrate 4 is only protonated with coordinated and uncoordinated β-carboxy groups. The solution behaviours of 1 and 2 are discussed based on ¹H and ¹³C NMR spectroscopies and cyclic voltammograms, showing no decomposition of the species.

Oxo and thiomolybdenum(iv/vi) citrates, molybdenum(v) homocitrate and molybdenum(vi) citrate were obtained, showing the influence of coordinated α-hydroxy and α-alkoxy groups with different oxidation states.