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价键理论对细胞色素P450中氢原子提取屏障的见解。

Valence Bond Insights into the H-Abstraction Barrier in Cytochrome P450.

作者信息

Zhang Enhua, Hirao Hajime

机构信息

Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China.

出版信息

Molecules. 2025 May 21;30(10):2242. doi: 10.3390/molecules30102242.

Abstract

The valence bond (VB) framework is widely recognized as a powerful tool for elucidating the electronic origins of activation energy barriers in chemical reactions. We employed ab initio VB calculations to investigate the hydrogen abstraction (H-abstraction) barrier in cytochrome P450 enzymes (P450s), using a simplified model in which an oriented external electric field (OEEF) was applied to efficiently capture the electronic effects of the equatorial porphyrin and proximal thiolate ligands on the iron(IV)-oxo unit in compound I (Cpd I). Methane (CH) was used as the model substrate. The VB-calculated barrier height, evaluated with this simplified model, qualitatively reproduced the barrier predicted by density functional theory (DFT) calculations using a more complete active-site model. Additionally, by examining the weights and diagonal elements of the Hamiltonian matrix for different VB structures along the reaction coordinate, we identified key VB structures-including covalent and ionic configurations representing the C-H and O-H bonds-that contribute significantly to the electronic origin of the barrier height. The mixing of these distinct VB structures leads to resonance stabilization, which is maximized at the transition state.

摘要

价键(VB)框架被广泛认为是阐明化学反应中活化能垒电子起源的有力工具。我们采用从头算VB计算来研究细胞色素P450酶(P450s)中的氢提取(H-提取)能垒,使用了一个简化模型,其中施加了定向外部电场(OEEF),以有效捕捉赤道卟啉和近端硫醇盐配体对化合物I(Cpd I)中铁(IV)-氧单元的电子效应。甲烷(CH)用作模型底物。用这个简化模型评估的VB计算能垒高度定性地重现了使用更完整活性位点模型的密度泛函理论(DFT)计算预测的能垒。此外,通过检查沿反应坐标不同VB结构的哈密顿矩阵的权重和对角元素,我们确定了关键的VB结构,包括代表C-H和O-H键的共价和离子构型,它们对能垒高度的电子起源有显著贡献。这些不同VB结构的混合导致共振稳定,在过渡态达到最大化。

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