Department of Theoretical Chemistry, Lund University, Chemical Centre, SE-221 00Lund, Sweden.
Inorg Chem. 2022 Nov 14;61(45):18067-18076. doi: 10.1021/acs.inorgchem.2c02488. Epub 2022 Oct 28.
Nitrogenase is the only enzyme that can cleave the triple bond in N, making nitrogen available for all lifeforms. Previous computational studies have given widely diverging results regarding the reaction mechanism of the enzyme. For example, some recent studies have suggested that one of the μ-bridging sulfide ligands (S2B) may dissociate from one of the Fe ions when protonated in the doubly reduced and protonated E state, whereas other studies indicated that such half-dissociated states are unfavorable. We have examined how the relative energies of 26 structures of the E state depend on details of combined quantum mechanical and molecular mechanical (QM/MM) calculations. We show that the selection of the broken-symmetry state, the basis set, relativistic effects, the size of the QM system, relaxation of the surroundings, and the conformations of the bound protons may affect the relative energies of the various structures by up to 12, 22, 9, 20, 37, and 33 kJ/mol, respectively. However, they do not change the preferred type of structures. On the other hand, the choice of the DFT functional strongly affects the preferences. The hybrid B3LYP functional strongly prefers doubly protonation of the central carbide ion, but such a structure is not consistent with experimental EPR data. Other functionals suggest structures with a hydride ion, in agreement with the experiments, and show that the ion bridges between Fe2 and Fe6. Moreover, there are two structures of the same type that are degenerate within 1-5 kJ/mol, in agreement with the observation of two EPR signals. However, the pure generalized gradient approximation (GGA) functional TPSS favors structures with a protonated S2B also bridging Fe2 and Fe6, whereas rSCAN (meta-GGA) and TPSSh (hybrid) prefer structures with S2B dissociated from Fe2 (but remaining bound to Fe6). The energy difference between the two types of structure is so small (7-18 kJ/mol) that both types need to be considered in future investigations of the mechanism of nitrogenase.
固氮酶是唯一能够切断 N 中三键的酶，使氮可供所有生命形式使用。以前的计算研究对于酶的反应机制给出了广泛不同的结果。例如，一些最近的研究表明，当在双还原和质子化的 E 态中质子化时，μ-桥接的硫化物配体（S2B）之一可能从一个 Fe 离子上解离，而其他研究表明这种半解离状态是不利的。我们已经检查了 E 态的 26 种结构的相对能量如何取决于组合量子力学和分子力学（QM/MM）计算的细节。我们表明，打破对称态的选择、基组、相对论效应、QM 系统的大小、环境的弛豫以及结合质子的构象，可能分别使各种结构的相对能量变化高达 12、22、9、20、37 和 33 kJ/mol。然而，它们并没有改变结构的首选类型。另一方面，DFT 函数的选择强烈影响偏好。混合 B3LYP 函数强烈偏向于中心碳化钙离子的双重质子化，但这种结构与实验 EPR 数据不一致。其他函数表明，与实验一致的是，具有氢化物离子的结构，并且表明离子桥接在 Fe2 和 Fe6 之间。此外，还有两种相同类型的结构在 1-5 kJ/mol 内是简并的，这与两个 EPR 信号的观察结果一致。然而，纯广义梯度近似（GGA）函数 TPSS 倾向于具有质子化 S2B 的结构，该 S2B 也桥接 Fe2 和 Fe6，而 rSCAN（元 GGA）和 TPSSh（混合）则倾向于 S2B 从 Fe2 上解离的结构（但仍与 Fe6 结合）。两种结构类型之间的能量差非常小（7-18 kJ/mol），因此在未来的固氮酶机制研究中需要考虑这两种类型。
