Why is a proton transformed into a hydride by [NiFe] hydrogenases? An intrinsic reactivity analysis based on conceptual DFT

被引:13
作者
Qiu, Siyao [1 ]
Azofra, Luis Miguel [1 ,2 ]
MacFarlane, Douglas R. [1 ,2 ]
Sun, Chenghua [1 ,2 ]
机构
[1] Monash Univ, Fac Sci, Sch Chem, Clayton, Vic 3800, Australia
[2] Monash Univ, Fac Sci, Sch Chem, ARC Ctr Excellence Electromat Sci ACES, Clayton, Vic 3800, Australia
基金
澳大利亚研究理事会;
关键词
DENSITY-FUNCTIONAL THEORY; VULGARIS MIYAZAKI-F; ACTIVE-SITE MODELS; CATALYTIC CYCLE; OXIDIZED STATES; ELECTRONIC-STRUCTURE; ENERGY; ACTIVATION; EPR; CLASSIFICATION;
D O I
10.1039/c6cp00948d
中图分类号
O64 [物理化学(理论化学)、化学物理学];
学科分类号
070304 ; 081704 ;
摘要
The hydrogen evolution reaction (HER) catalysed by [NiFe] hydrogenases entails a series of chemical events involving great mechanistic interest. In an attempt to understand and delve into the question about 'Why does nature work in that way?', an in-depth intrinsic reactivity analysis based on conceptual DFT has been carried out focusing on the so-called I1 to Ni-C step, i.e. our work tries to answer how and why the proton attached to the reactive sulphur atom from one of the exo-cyclic cysteine residues is transformed into a bridging hydride to be shared between the Ni/Fe metals in the active site of [NiFe] hydrogenases, which involves not only H migration, but also a change of the charge state on Ni from Ni(I) to Ni(III). Our DFT results suggest that the transformation is motivated by spontaneous rearrangements of the electron density, and stabilisation comes from the decrease of both electronic activity and electrophilicity index from Ni.
引用
收藏
页码:15369 / 15374
页数:6
相关论文
共 57 条
[21]  
Glendening E. D., 2018, NBO 70
[22]   REACTION-PATH FOLLOWING IN MASS-WEIGHTED INTERNAL COORDINATES [J].
GONZALEZ, C ;
SCHLEGEL, HB .
JOURNAL OF PHYSICAL CHEMISTRY, 1990, 94 (14) :5523-5527
[23]   Removal of the bridging ligand atom at the Ni-Fe active site of [NiFe] hydrogenase upon reduction with H2, as revealed by X-ray structure analysis at 1.4 Å resolution [J].
Higuchi, Y ;
Ogata, H ;
Miki, K ;
Yasuoka, N ;
Yagi, T .
STRUCTURE WITH FOLDING & DESIGN, 1999, 7 (05) :549-556
[24]   Computational study of the electronic structure and magnetic properties of the Ni-C state in [NiFe] hydrogenases including the second coordination sphere [J].
Kampa, Mario ;
Lubitz, Wolfgang ;
van Gastel, Maurice ;
Neese, Frank .
JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY, 2012, 17 (08) :1269-1281
[25]  
Koopmans TA., 1933, Physica, V1, P104, DOI [https://doi.org/10.1016/S0031-8914(34)90011-2, DOI 10.1016/S0031-8914(34)90011-2, 10.1016/S0031-8914(34)90011-2]
[26]   Theoretical Spectroscopy of the NiII Intermediate States in the Catalytic Cycle and the Activation of [NiFe] Hydrogenases [J].
Kraemer, Tobias ;
Kamp, Mario ;
Lubitz, Wolfgang ;
van Gastel, Maurice ;
Neese, Frank .
CHEMBIOCHEM, 2013, 14 (14) :1898-1905
[27]   A black-box self-consistent field convergence algorithm:: One step closer [J].
Kudin, KN ;
Scuseria, GE ;
Cancès, E .
JOURNAL OF CHEMICAL PHYSICS, 2002, 116 (19) :8255-8261
[28]   Modeling the active sites of metalloenzymes.: 4.: Predictions of the unready states of [NiFe] Desulfovibrio gigas hydrogenase from density functional theory [J].
Li, SH ;
Hall, MB .
INORGANIC CHEMISTRY, 2001, 40 (01) :18-24
[29]   [NiFe] and [FeFe] hydrogenases studied by advanced magnetic resonance techniques [J].
Lubitz, Wolfgang ;
Reijerse, Eduard ;
van Gastel, Maurice .
CHEMICAL REVIEWS, 2007, 107 (10) :4331-4365
[30]   Hydrogenases [J].
Lubitz, Wolfgang ;
Ogata, Hideaki ;
Ruediger, Olaf ;
Reijerse, Edward .
CHEMICAL REVIEWS, 2014, 114 (08) :4081-4148