Dong Geng, Phung Quan Manh, Hallaert Simon D, Pierloot Kristine, Ryde Ulf
Department of Theoretical Chemistry, Lund University, Chemical Centre, P. O. Box 124, SE-221 00 Lund, Sweden.
Phys Chem Chem Phys. 2017 Apr 19;19(16):10590-10601. doi: 10.1039/c7cp01331k.
[NiFe] hydrogenases catalyse the reversible conversion of molecular hydrogen to protons and electrons. This seemingly simple reaction has attracted much attention because of the prospective use of H as a clean fuel. In this paper, we have studied how H binds to the active site of this enzyme. Combined quantum mechanical and molecular mechanics (QM/MM) optimisation was performed to obtain the geometries, using both the TPSS and B3LYP density-functional theory (DFT) methods and considering both the singlet and triplet states of the Ni(ii) ion. To get more accurate energies and obtain a detailed account of the surroundings, we performed calculations with 819 atoms in the QM region. Moreover, coupled-cluster calculations with singles, doubles, and perturbatively treated triples (CCSD(T)) and cumulant-approximated second-order perturbation theory based on the density-matrix renormalisation group (DMRG-CASPT2) were carried out using three models to decide which DFT methods give the most accurate structures and energies. Our calculations show that H binding to Ni in the singlet state is the most favourable by at least 47 kJ mol. In addition, the TPSS functional gives more accurate energies than B3LYP for this system.
[镍铁]氢化酶催化分子氢与质子和电子的可逆转化。由于氢有望作为一种清洁燃料，这个看似简单的反应引起了广泛关注。在本文中，我们研究了氢如何与这种酶的活性位点结合。采用量子力学和分子力学相结合（QM/MM）的方法进行优化以获得几何结构，使用TPSS和B3LYP密度泛函理论（DFT）方法，并考虑了Ni（ii）离子的单重态和三重态。为了获得更精确的能量并详细了解周围环境，我们在QM区域对819个原子进行了计算。此外，使用三种模型进行了含单、双激发和微扰处理的三激发的耦合簇计算（CCSD(T)）以及基于密度矩阵重整化群的累积量近似二阶微扰理论（DMRG-CASPT2），以确定哪种DFT方法能给出最精确的结构和能量。我们的计算表明，氢以单重态与镍结合最为有利，至少比其他情况高出47 kJ/mol。此外，对于该体系，TPSS泛函比B3LYP能给出更精确的能量。
