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

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.

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.

Deprotonation from an OH on myo-Inositol Promoted by μ2-Bridges with Possible Regioselectivity/Chiral Selectivity

Single-crystal structures of myo-inositol complexes with erbium ([Er₂(C₆H₁₁O₆)₂(H₂O)₅Cl₂]Cl₂(H₂O)₄, denoted ErI hereafter) and strontium (Sr(C₆H₁₂O₆)₂(H₂O)₂Cl₂, denoted SrI hereafter) are described. In ErI, deprotonation occurs on an OH of myo-inositol, although the complex is synthesized in an acidic solution, and the pK_a values of all of the OHs in myo-inositol are larger than 12. The deprotonated OH is involved in a μ₂-bridge. The polarization from two Er³⁺ ions activates the chemically relatively inert OH and promotes deprotonation. In the stable conformation of myo-inositol, there are five equatorial OHs and one axial OH. The deprotonation occurs on the only axial OH, suggesting that the deprotonation possesses characteristics of regioselectivity/chiral selectivity. Two Er³⁺ ions in the μ₂-bridge are stabilized by five-membered rings formed by chelating Er³⁺ with an O-C-C-O moiety. As revealed by the X-ray crystallography study, the absolute values of the O-C-C-O torsion angles decrease from ∼60 to ∼45° upon chelating. Since the O-C-C-O moiety is within a six-membered ring, the variation of the torsion angle may exert distortion of the chair conformation. Quantum chemistry calculation results indicate that an axial OH flanked by two equatorial OHs (double ax-eq motif) is favorable for the formation of a μ₂-bridge, accounting for the selectivity. The double ax-eq motif may be used in a rational design of high-performance catalysts where deprotonation with high regioselectivity/chiral selectivity is carried out.

Unexpected Deprotonation from a Chemically Inert OH Group Promoted by Metal Ions in Lanthanide-Erythritol Complexes

Single-crystal structures of five lanthanide-erythritol complexes are reported. The analysis of the chemical compositions and scrutinization of structural features in the single-crystal data of the complexes led us to find that unexpected deprotonation occurs on the OH group of erythritol of three complexes. Considering these complexes were prepared in acidic environments, where spontaneous ionization on an OH group is suppressed, we suggest metal ions play an important role in promoting the proton transfer. To find out why the chemically inert OH is activated, the single-crystal structures of 63 rare-earth complexes containing organic ligands with multiple hydroxyl groups (OLMHs) were surveyed. The formation of μ₂-bridges turns out to be directly relevant to the occurrence of deprotonation. When an OH group from an OLMH molecule participates in the formation of a μ₂-bridge, the polarization ability of the metal ions becomes strong enough to promote the deprotonation on the OH group. The above structural characteristics may be useful in the rational design of catalysts that can activate the chemically inert OH group and promote the relevant chemical conversions.

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.

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.