We have made a systematic combined quantum mechanical and molecular mechanical (QM/MM) investigation of possible structures of the N₂ bound state of nitrogenase. We assume that N₂ is immediately protonated to a N₂H₂ state, thereby avoiding the problem of determining the position of the protons in the cluster. We have systematically studied both end-on and side-on structures, as well as both HNNH and NNH₂ states. Our results indicate that the binding of N₂H₂ is determined more by interactions and steric clashes with the surrounding protein than by the intrinsic preferences of the ligand and the cluster. The best binding mode with both the TPSS and B3LYP density-functional theory methods has trans-HNNH terminally bound to Fe2. It is stabilised by stacking of the substrate with His-195 and Ser-278. However, several other structures come rather close in energy (within 3–35 kJ/mol) at least in some calculations: The corresponding cis-HNNH structure terminally bound to Fe2 is second best with B3LYP. A structure with HNNH₂ terminally bound to Fe6 is second most stable with TPSS (where the third proton is transferred to the substrate from the homocitrate ligand). Structures with trans-HNNH, bound to Fe4 or Fe6, or cis-HNNH bound to Fe6 are also rather stable. Finally, with the TPSS functional, a structure with cis-HNNH side-on binding to the Fe3–Fe4–Fe5–Fe7 face of the cluster is also rather low in energy, but all side-on structures are strongly disfavoured by the B3LYP method.

中文翻译：

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通过QM / MM方法研究了N2H2与固氮酶FeMo簇的结合。

我们已经进行了系统的结合的量子力学和分子力学（QM / MM）研究的N ₂ N结合状态的固氮酶的结构。我们假设N ₂立即质子化为N ₂ H ₂状态，从而避免了确定质子在簇中的位置的问题。我们已经系统地研究了端对端和侧对端结构，以及HNNH和NNH ₂态。我们的结果表明，N ₂ H ₂的结合与配体和簇的内在偏好相比，更多地由与周围蛋白质的相互作用和空间冲突决定。TPSS和B3LYP密度泛函理论方法的最佳结合方式是反式HNNH最终与Fe2结合。通过将底物与His-195和Ser-278堆叠在一起可以使其稳定。但是，至少在一些计算中，其他一些结构的能量相当接近（在3–35 kJ / mol之内）：最终与Fe2结合的顺式-HNNH结构在B3LYP中次之。具有HNNH ₂的结构末端连接到Fe6上的TPSS稳定度第二高（第三质子从纯柠檬酸盐配体转移到底物上）。具有与Fe4或Fe6结合的反式-HNNH或与Fe6结合的顺式-HNNH的结构也相当稳定。最后，通过TPSS功能，具有顺式-HNNH侧面结合在簇的Fe3-Fe4-Fe5-Fe7面上的结构的能量也相当低，但是B3LYP方法强烈反对所有侧面结构。