Quantum Mechanics/Molecular Mechanics Study of Resting-State Vanadium Nitrogenase: Molecular and Electronic Structure of the Iron–Vanadium Cofactor

Abstract

The nitrogenase enzymes are responsible for all biological nitrogen reduction. How this is accomplished at the atomic level, however, has still not been established. The molybdenum-dependent nitrogenase has been extensively studied and is the most active catalyst for dinitrogen reduction of the nitrogenase enzymes. The vanadium-dependent form, on the other hand, displays different reactivity, being capable of CO and CO 2 reduction to hydrocarbons. Only recently did a crystal structure of the VFe protein of vanadium nitrogenase become available, paving the way for detailed theoretical studies of the iron–vanadium cofactor (FeVco) within the protein matrix. The crystal structure revealed a bridging 4-atom ligand between two Fe atoms, proposed to be either a CO 3 2– or NO 3 – ligand. Using a quantum mechanics/molecular mechanics model of the VFe protein, starting from the 1.35 Å crystal structure, we have systematically explored multiple computational models for FeVco, considering either a CO 3 2– or NO 3 – ligand, three different redox states, and multiple broken-symmetry states. We find that only a [VFe 7 S 8 C(CO 3 )] 2– model for FeVco reproduces the crystal structure of FeVco well, as seen in a comparison of the Fe–Fe and V–Fe distances in the computed models. Furthermore, a broken-symmetry solution with Fe2, Fe3, and Fe5 spin-down (BS7-235) is energetically preferred. The electronic structure of the [VFe 7 S 8 C(CO 3 )] 2– BS7-235 model is compared to our [MoFe 7 S 9 C] − BS7-235 model of FeMoco via localized orbital analysis and is discussed in terms of local oxidation states and different degrees of delocalization. As previously found from Fe X-ray absorption spectroscopy studies, the Fe part of FeVco is reduced compared to FeMoco, and the calculations reveal Fe5 as locally ferrous. This suggests resting-state FeVco to be analogous to an unprotonated E 1 state of FeMoco. Furthermore, V–Fe interactions in FeVco are not as strong compared to Mo–Fe interactions in FeMoco. These clear differences in the electronic structures of otherwise similar cofactors suggest an explanation for distinct differences in reactivity.

The influences of carbon donor ligands on biomimetic multi-iron complexes for N2reduction

“…67 From this analysis, the Mayer bond order 68 (MBO) provides a convenient method to sum all of the contributions to the bond; it has been applied to FeMoco and related systems to understand the magnitude of bonding between two atoms. 68,69 The MBOs for the Fe-C interactions are similar between 3 (0.87) and 1 (0.90). Upon the introduction of a sulde ligand and oxidation of the iron centers, the Fe-C interactions of the bridging alkylidene in 2 display a similar MBO of 0.86.…”

The electronic structure of FeV-cofactor in vanadium-dependent nitrogenase

“…62 The finding that 51 V hyperfine coupling of E 1,3 (1,3H) is fully isotropic then identifies the vanadium of E 1,3 (1,3H) as V 3+ (d 2 , S = 1). 35,42,43 The isotropic 51 V hyperfine coupling observed in the E 1,3 (1,3H) intermediate, a iso = 110 MHz, is much smaller than that of an isolated V 3+ , a V un ~ 300 MHz, and furthermore, the intermediate signal is from an S = ½ (Kramers) center, not that of an isolated V 3+ (non-Kramers) S = 1 center. These observations together confirm that the observed signal comes not from an isolated V 3+ (d 2 , S = 1) complex produced by cofactor degradation, but from a spin-coupled multi-metallic cluster, a state of spin-coupled FeV-cofactor itself, and thus indeed from a VFe intermediate.…”

“…This broad feature ranges from g5. 6,42,43 However, there are several important observations that contradict assignment of an S = 3/2 state to the resting FeV-cofactor: (i) unlike the quantitative FeMo-cofactor EPR signal of MoFe protein, the g-4.3 S = 3/2 signal of VFe protein has always been observed with low, and varying intensity, 5,13,19,41,45,50,51 being absent in some isolations; 12,44,57,58 and (ii) the different redox responses of the two S = 3/2 spin systems seen with VFe protein toward the oxidation by IDS 45 and methylene blue described here demonstrate that the two S = 3/2 signals do not originate from the catalytically relevant FeV-cofactor. Thus, as described above (Table 1, Figures 3 and 4…”

“…31,32 These findings are consistent with the electronic similarities suggested by iron-selective Mӧssbauer study of V-dependent nitrogenase, 37 but contradict the suggestion of electronic structure differences of the Fe 7 subclusters in FeMo-cofactor and FeV-cofactor based on XAS and DFT studies. 6,42,43…”

“…35,42 Combined with the assignment of FeV-cofactor as EPR-active in the resting state, this implies there must be one more ferrous (Fe 2+ ) ion in the Fe 7 subcluster of FeV-cofactor (Figure 1) compared to FeMo-cofactor. 6,42,43 Considering the uncertainties in assigning the origins of the resting-state EPR signal for VFe protein, the electronic structures derived from these spectroscopic and theoretical studies, as summarized in Figure 1, remained likewise uncertain. Moreover, a proposed assignment of the low spin (S = ½) EPR signal for resting-state VFe protein to the oxidized P-cluster has been debated.…”