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采用大规模多参考从头算计算研究 Δ⁹ 去饱和酶双核非血红素铁活性中心的反应性。

Reactivity of the binuclear non-heme iron active site of Δ⁹ desaturase studied by large-scale multireference ab initio calculations.

机构信息

Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo náměstí 2, 166 10 Praha 6, Czech Republic.

出版信息

J Am Chem Soc. 2014 Nov 12;136(45):15977-91. doi: 10.1021/ja506934k. Epub 2014 Oct 31.

DOI:10.1021/ja506934k
PMID:25313991
Abstract

The results of density matrix renormalization group complete active space self-consistent field (DMRG-CASSCF) and second-order perturbation theory (DMRG-CASPT2) calculations are presented on various structural alternatives for the O-O and first C-H activating step of the catalytic cycle of the binuclear nonheme iron enzyme Δ(9) desaturase. This enzyme is capable of inserting a double bond into an alkyl chain by double hydrogen (H) atom abstraction using molecular O2. The reaction step studied here is presumably associated with the highest activation barrier along the full pathway; therefore, its quantitative assessment is of key importance to the understanding of the catalysis. The DMRG approach allows unprecedentedly large active spaces for the explicit correlation of electrons in the large part of the chemically important valence space, which is apparently conditio sine qua non for obtaining well-converged reaction energetics. The derived reaction mechanism involves protonation of the previously characterized 1,2-μ peroxy Fe(III)Fe(III) (P) intermediate to a 1,1-μ hydroperoxy species, which abstracts an H atom from the C10 site of the substrate. An Fe(IV)-oxo unit is generated concomitantly, supposedly capable of the second H atom abstraction from C9. In addition, several popular DFT functionals were compared to the computed DMRG-CASPT2 data. Notably, many of these show a preference for heterolytic C-H cleavage, erroneously predicting substrate hydroxylation. This study shows that, despite its limitations, DMRG-CASPT2 is a significant methodological advancement toward the accurate computational treatment of complex bioinorganic systems, such as those with the highly open-shell diiron active sites.

摘要

密度矩阵重整化群完全活性空间自洽场 (DMRG-CASSCF) 和二级微扰理论 (DMRG-CASPT2) 计算的结果被呈现于双核非血红素铁酶 Δ(9) 去饱和酶催化循环的 O-O 和第一个 C-H 激活步骤的各种结构替代物上。这种酶能够通过使用分子 O2 对双氢 (H) 原子进行双重提取,将双键插入烷基链中。这里研究的反应步骤被认为与完整途径中最高的活化势垒相关联;因此,对其进行定量评估对于理解催化作用至关重要。DMRG 方法允许在重要的化学价空间的大部分中对电子进行前所未有的大的活性空间关联,这显然是获得良好收敛反应能量的必要条件。所得的反应机制涉及到对先前表征的 1,2-μ 过氧 Fe(III)Fe(III) (P) 中间体的质子化,形成 1,1-μ 过氧物种,从底物的 C10 位提取一个 H 原子。同时生成一个 Fe(IV)-氧单位,据称能够从 C9 中再次提取 H 原子。此外,还比较了几种流行的 DFT 泛函与计算的 DMRG-CASPT2 数据。值得注意的是,其中许多泛函都显示出对异裂 C-H 断裂的偏好,错误地预测了底物的羟化。本研究表明,尽管存在局限性,但 DMRG-CASPT2 是对复杂生物无机体系(如具有高度开壳双核铁活性中心的体系)进行准确计算处理的重要方法学进展。

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