Recent developments of the quantum chemical cluster approach for modeling enzyme reactions

被引:240
作者
Siegbahn, Per E. M. [1 ,2 ]
Himo, Fahmi [3 ]
机构
[1] Univ Stockholm, Dept Phys, ALBA NOVA, Arrhenius Lab, S-10691 Stockholm, Sweden
[2] Univ Stockholm, Dept Biochem & Biophys, Arrhenius Lab, S-10691 Stockholm, Sweden
[3] Royal Inst Technol, Dept Theoret Chem, Sch Biotechnol, S-10691 Stockholm, Sweden
来源
JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY | 2009年 / 14卷 / 05期
关键词
Computational chemistry; Density functional theory; Molecularmodeling; Photosynthesis; SITE ARGININE RESIDUES; 4-OXALOCROTONATE TAUTOMERASE; HALOHYDRIN DEHALOGENASE; PHOTOSYSTEM-II; QM/MM METHODS; MECHANISM; RESOLUTION; COMPLEX; EPOXIDES; POLARIZATION;
D O I
10.1007/s00775-009-0511-y
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
The quantum chemical cluster approach for modeling enzyme reactions is reviewed. Recent applications have used cluster models much larger than before which have given new modeling insights. One important and rather surprising feature is the fast convergence with cluster size of the energetics of the reactions. Even for reactions with significant charge separation it has in some cases been possible to obtain full convergence in the sense that dielectric cavity effects from outside the cluster do not contribute to any significant extent. Direct comparisons between quantum mechanics (QM)-only and QM/molecular mechanics (MM) calculations for quite large clusters in a case where the results differ significantly have shown that care has to be taken when using the QM/MM approach where there is strong charge polarization. Insights from the methods used, generally hybrid density functional methods, have also led to possibilities to give reasonable error limits for the results. Examples are finally given from the most extensive study using the cluster model, the one of oxygen formation at the oxygen-evolving complex in photosystem II.
引用
收藏
页码:643 / 651
页数:9
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