Theoretical Spectroscopy of the NiII Intermediate States in the Catalytic Cycle and the Activation of [NiFe] Hydrogenases
Theoretical Spectroscopy of the NiII Intermediate States in the Catalytic Cycle and the Activation of [NiFe] Hydrogenases
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DOI：
10.1002/cbic.201300104
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发表时间：
2013-09-23
期刊：
影响因子：
3.2
通讯作者：
Neese, Frank
中科院分区：
文献类型：
--
作者：
Kraemer, Tobias;Kamp, Mario;Neese, Frank
氢化酶催化二氢的可逆氧化。相应的催化循环涉及大量的Ni-Fe活性位点的氧化还原态；它们可以通过与铁配位的CN和CO配体的红外拉伸频率进行实验区分。这些光谱指纹作为金属芯的固有电子结构的敏感探针，间接地用于活性位点的结构组成。本研究采用密度泛函理论（DFT）计算含二价金属中心的epr沉默中间态的振动频率。以表征良好的Ni-C和Ni-B态为参考，我们通过将预测的相对频移与实验结果相匹配，确定了Ni-SIr、Ni-SIa和Ni-R态的候选态。Ni-SIr态和Ni-SIa态的特征是水分子松散地与镍结合，并形成一个空桥。这两个态通过质子化平衡相互连接；也就是说，在Ni-SIa状态中，一端的硫酸盐是质子化的，而在Ni-SIr状态中，这个硫酸盐是未质子化的。对于还原的Ni-R态，出现了两种可行的模型：一种是H-2座标侧对镍，另一种是氢化物桥和质子化硫酸盐。Ni-SU状态仍然难以捉摸，因为实验数据和模型计算频率之间没有明确的对应关系，因此表明从Ni-A还原为Ni-SU时可能发生更大的结构重排，并且桥接配体可能解离。
[NiFe] hydrogenases catalyze the reversible oxidation of dihydrogen. The corresponding catalytic cycle involves a formidable number of redox states of the Ni-Fe active site; these can be distinguished experimentally by the IR stretching frequencies of their CN and CO ligands coordinated to iron. These spectroscopic fingerprints serve as sensitive probes for the intrinsic electronic structure of the metal core and, indirectly, for the structural composition of the active site. In this study, density functional theory (DFT) was used to calculate vibrational frequencies, by focusing on the EPR-silent intermediate states that contain divalent metal centers. By using the well-characterized Ni-C and Ni-B states as references, we identified candidates for the Ni-SIr, Ni-SIa, and Ni-R states by matching the predicted relative frequency shifts with experimental results. The Ni-SIr and Ni-SIa states feature a water molecule loosely bound to nickel and a formally vacant bridge. Both states are connected to each other through protonation equilibria; that is, in the Ni-SIa state one of the terminal thiolates is protonated, whereas in Ni-SIr this thiolate is unprotonated. For the reduced Ni-R state two feasible models emerged: in one, H-2 coordinates side-on to nickel, and the second features a hydride bridge and a protonated thiolate. The Ni-SU state remains elusive as no unequivocal correspondence between the experimental data and calculated frequencies of the models was found, thus indicating that a larger structural rearrangement might occur upon reduction from Ni-A to Ni-SU and that the bridging ligand might dissociate.