Theoretical Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden.
J Am Chem Soc. 2010 Apr 7;132(13):4512-3. doi: 10.1021/ja909194f.
The active site of the [FeFe] hydrogenases contains two Fe ions bound to one Cys ligand, three CO molecules, two CN(-) ions, and a dithiolate ligand. The nature of the last of these has been much discussed, and it has been suggested that it contains C, N, or O as the bridgehead atom. Most experimental studies indicate a N atom, whereas a recent density functional theory (DFT) study of a crystal structure indicated an O atom. Here, we performed quantum refinement on the same crystal structure with five different models of the dithiolate ligand X(CH(2)S(-))(2), with X = CH(2), NH(2)(+), NH (two conformations), or O; we found that structures with a N bridgehead atom actually provide the best fit to the raw crystallographic data. Quantum refinement is standard crystallographic refinement in which the molecular mechanics force field normally used to supplement the experimental raw data to give a more chemical structure is replaced by more accurate DFT calculations for the active site. Thereby, we obtain structures that are an ideal compromise between DFT and crystallography.
[FeFe]氢化酶的活性部位含有两个与一个 Cys 配体结合的 Fe 离子、三个 CO 分子、两个 CN(-)离子和一个二硫代羧酸配体。关于最后一个配体的性质有很多讨论，有人认为它含有桥原子的 C、N 或 O。大多数实验研究表明是 N 原子，而最近对晶体结构的密度泛函理论（DFT）研究表明是 O 原子。在这里，我们对同一个晶体结构进行了量子精修，使用了五种不同的二硫代羧酸配体 X(CH(2)S(-))(2)的模型，其中 X = CH(2)、NH(2)(+)、NH（两种构象）或 O；我们发现，具有 N 桥原子的结构实际上与原始晶体学数据最吻合。量子精修是标准的晶体学精修，其中通常用于补充实验原始数据以获得更化学结构的分子力学力场被用于活性部位的更准确的 DFT 计算所取代。因此，我们获得了在 DFT 和晶体学之间的理想折衷结构。
