Quantum Mechanics/Molecular Mechanics Study of Resting-State Vanadium Nitrogenase: Molecular and Electronic Structure of the Iron-Vanadium Cofactor.,Inorganic Chemistry

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Quantum Mechanics/Molecular Mechanics Study of Resting-State Vanadium Nitrogenase: Molecular and Electronic Structure of the Iron-Vanadium Cofactor.
Inorganic Chemistry ( IF 4.3 ) Pub Date : 2020-08-05 , DOI: 10.1021/acs.inorgchem.0c01320
Bardi Benediktsson ₁ , Ragnar Bjornsson _{1,

2}

Affiliation

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 CO₂ 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 CO₃^2– or NO₃^– 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 CO₃^2– or NO₃^– ligand, three different redox states, and multiple broken-symmetry states. We find that only a [VFe₇S₈C(CO₃)]^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 [VFe₇S₈C(CO₃)]^2– BS7-235 model is compared to our [MoFe₇S₉C]⁻ 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 E₁ 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.

中文翻译：

静息态钒固氮酶的量子力学/分子力学研究：铁钒辅因子的分子和电子结构。

固氮酶负责所有生物氮还原。然而，如何在原子水平上实现这一点尚未确定。钼依赖性固氮酶已被广泛研究，并且是固氮酶二氮还原最活跃的催化剂。另一方面，钒依赖性形式表现出不同的反应性，能够将CO和CO ₂还原为碳氢化合物。直到最近，钒固氮酶的 VFe 蛋白的晶体结构才变得可用，这为蛋白质基质内铁钒辅因子 (FeVco) 的详细理论研究铺平了道路。晶体结构揭示了两个 Fe 原子之间的桥接 4 原子配体，被认为是 CO ₃ ^2–或 NO ₃ ^–配体。使用 VFe 蛋白的量子力学/分子力学模型，从 1.35 Å 晶体结构开始，我们系统地探索了 FeVco 的多种计算模型，考虑 CO ₃ ^2–或 NO ₃ ^–配体、三种不同的氧化还原态，以及多个破缺对称态。我们发现，只有 FeVco 的 [VFe ₇ S ₈ C(CO ₃ )] ^2–模型能够很好地再现 FeVco 的晶体结构，如计算模型中 Fe-Fe 和 V-Fe 距离的比较所示。此外，Fe2、Fe3 和 Fe5 自旋下降的对称破缺解 (BS7-235) 在能量上是优选的。通过局域轨道分析将 [VFe ₇ S ₈ C(CO ₃ )] ^2– BS7-235 模型的电子结构与 FeMoco 的 [MoFe ₇ S ₉ C] ⁻ BS7-235 模型进行比较，并根据以下方面进行讨论局部氧化态和不同程度的离域。正如之前从 Fe X 射线吸收光谱研究中发现的那样，与 FeMoco 相比，FeVco 中的 Fe 部分有所减少，并且计算表明 Fe5 为局部亚铁。这表明静息态 FeVco 类似于 FeMoco 的非质子化 E ₁态。此外，FeVco 中的 V-Fe 相互作用不如 FeMoco 中的 Mo-Fe 相互作用那么强。其他相似的辅助因子的电子结构的这些明显差异表明了反应性明显差异的解释。

更新日期：2020-08-17

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