Dissecting the intimate mechanism of cyanation of {2Fe3S} complexes related to the active site of all-iron hydrogenases by DFT analysis of energetics, transition states, intermediates and products in the carbonyl substitution pathway

被引:43
作者
Zampella, G
Bruschi, M
Fantucci, P
Razavet, M
Pickett, CJ [1 ]
De Gioia, L
机构
[1] John Innes Ctr, Dept Biol Chem, Norwich NR4 7UH, Norfolk, England
[2] Univ Milano Bicocca, Dept Environm Sci, I-20126 Milan, Italy
[3] Univ Milano Bicocca, Dept Biosci & Biotechnol, I-20126 Milan, Italy
关键词
bioinorganic chemistry; carbonyl ligands; density functional calculations; hydrogenases; iron;
D O I
10.1002/chem.200400442
中图分类号
O6 [化学];
学科分类号
0703 ;
摘要
A bridging carbonyl intermediate with key structural elements of the diiron sub-site of all-iron hydrogenase has been experimentally observed in the CN/CO substitution pathway of the {2Fe3S} carbonyl precursor, [Fe-2(CO)(5){MeSCH2C(Me)(CH2S)(2)}]. Herein we have used density functional theory (DFT) to dissect the overall substitution pathway in terms of the energetics and the structures of transition states, intermediates and products. We show that the formation of bridging CO transitions states is explicitly involved in the intimate mechanism of dicyanation. The enhanced rate of monocyanation of {2Fe3S} over the {2Fe2S} species [Fe-2(CO)(6){CH2(CH2S)(2)}] is found to rest with the ability of the thioether ligand to both stabilise a mu-CO transition state and act as a good leaving group. In contrast, the second cyanation step of the {2Fe3S} species is kinetically slower than for the {2Fe2S} monocyanide because the Fe2 atom is deactivated by coordination of the electron-donating thioether group. In addition, hindered rotation and the reaction coordinate of the approaching CN- group, are other factors which explain reactivity differences in {2Fe2S} and {2Fe3S} systems. The intermediate species formed in the second cyanation step of {2Fe3S} species is a mu-CO species, confirming the structural assignment made on the basis of FT-IR data (S. J. George, Z. Cui, M. Razavet, C. J. Pickett, Chem. Eur. J. 2002, 8, 40374046). In support of this we find that computed and experimental IR frequencies of structurally characterised {2Fe3S} species and those of the bridging carbonyl intermediate are in excellent agreement. In a wider context, the study may provide some insight into the reactivity of dinuclear systems in which neighbouring group on-off coordination plays a role in substitution pathways.
引用
收藏
页码:509 / 520
页数:12
相关论文
共 62 条
[1]   ELECTRONIC-STRUCTURE CALCULATIONS ON WORKSTATION COMPUTERS - THE PROGRAM SYSTEM TURBOMOLE [J].
AHLRICHS, R ;
BAR, M ;
HASER, M ;
HORN, H ;
KOLMEL, C .
CHEMICAL PHYSICS LETTERS, 1989, 162 (03) :165-169
[2]   DENSITY-FUNCTIONAL THERMOCHEMISTRY .1. THE EFFECT OF THE EXCHANGE-ONLY GRADIENT CORRECTION [J].
BECKE, AD .
JOURNAL OF CHEMICAL PHYSICS, 1992, 96 (03) :2155-2160
[3]   DENSITY-FUNCTIONAL THERMOCHEMISTRY .3. THE ROLE OF EXACT EXCHANGE [J].
BECKE, AD .
JOURNAL OF CHEMICAL PHYSICS, 1993, 98 (07) :5648-5652
[4]   DENSITY-FUNCTIONAL EXCHANGE-ENERGY APPROXIMATION WITH CORRECT ASYMPTOTIC-BEHAVIOR [J].
BECKE, AD .
PHYSICAL REVIEW A, 1988, 38 (06) :3098-3100
[5]   DFT investigation of structural, electronic, and catalytic properties of diiron complexes related to the [2Fe]H subcluster of Fe-only hydrogenases [J].
Bruschi, M ;
Fantucci, P ;
De Gioia, L .
INORGANIC CHEMISTRY, 2002, 41 (06) :1421-1429
[6]   Density functional theory investigation of the active site of [Fe]-hydrogenases:: Effects of redox state and ligand characteristics on structural, electronic, and reactivity properties of complexes related to the [2Fe]H subcluster [J].
Bruschi, M ;
Fantucci, P ;
De Gioia, L .
INORGANIC CHEMISTRY, 2003, 42 (15) :4773-4781
[7]   Density functional theory investigation of the active site of Fe-hydrogenases.: Systematic study of the effects of redox state and ligands hardness on structural and electronic properties of complexes related to the [2Fe]H subcluster [J].
Bruschi, M ;
Fantucci, P ;
De Gioia, L .
INORGANIC CHEMISTRY, 2004, 43 (12) :3733-3741
[8]   Modeling the active sites in metalloenzymes. 3. Density functional calculations on models for [Fe]-hydrogenase: Structures and vibrational frequencies of the observed redox forms and the reaction mechanism at the diiron active center [J].
Cao, ZX ;
Hall, MB .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2001, 123 (16) :3734-3742
[9]   Infrared studies of the CO-inhibited form of the Fe-only hydrogenase from Clostridium pasteurianum I:: Examination of its light sensitivity at cryogenic temperatures [J].
Chen, ZJ ;
Lemon, BJ ;
Huang, S ;
Swartz, DJ ;
Peters, JW ;
Bagley, KA .
BIOCHEMISTRY, 2002, 41 (06) :2036-2043
[10]   Structural variability of the active site of Fe-only hydrogenase and its hydrogenated forms [J].
Dance, I .
CHEMICAL COMMUNICATIONS, 1999, (17) :1655-1656