光合释氧机理的ABEEM/MM/MD和BS-DFT理论研究

doi:10.6023/A17040151

摘要/Abstract

建立了S₂态光合释氧络合物（OEC）的原子-键电负性均衡模型（ABEEMσπ）的电荷参数，并使用ABEEM/MM/MD可极化力场的分子动力学模拟和对称性破损的DFT研究了光合作用制造氧气的微观机制.HF/STO-3G（采用此基组的原因请见引用文献）水平下的电荷拟合结果证明了ABEEMσπ模型计算电荷分布的合理性和高效性.MD模拟显示，S₂态Mn₄CaO₅的双向异构化过程伴随Ca上的水分子W3转移至Mn1（III）/Mn4（III），它很可能作为底物水之一，与O5在S₄态结合产生O₂.基于此，考察了全自旋态下两种异构体形式中O－O键形成的自由基耦合机理.BS-DFT计算结果表明，开立方结构的释氧活性大大优于闭立方结构，金属锰和氧自由基的自旋耦合方式也是反应性的决定性因素，同时，OEC的结构灵活性对于S态循环和光合水分解至关重要.

关键词: 光合释氧络合物, 原子-键电负性均衡模型, 分子动力学模拟, 对称性破损密度泛函理论, 异构化, 底物水结合, 释氧机理, 自旋态

Charge parameters of atom-bond electronegativity equalization method (ABEEMσπ) for the oxygen-evolving complex (OEC) in the S₂ state were established, which were applied to molecular dynamic (MD) simulation based on ABEEM/MM polarizable force field in order to study the mechanism of photosynthetic oxygen evolution, in combination with broken-symmetry density functional theory (BS-DFT). Charge fitting results at HF/STO-3G level (the reason why the basis set is adopted is shown in the cited literatures) show good linear correlation, proving the rationality and efficiency of the ABEEMσπ model in calculating charge distributions. It can be seen from MD simulations that bidirectional isomerizations of the Mn₄CaO₅ cluster accompany by the transfer of Ca-bound water molecule W3 to pentacoordinate Mn1(Ⅲ)/Mn4(Ⅲ). For the g=2 to g=4.1 form, W3 leaves for Mn4(Ⅲ), while W3 moves to Mn1(Ⅲ) for the inverse course. Both processes involve motions to the original positions of W4 to W3, W588 to W4, and local rearrangements of the water environment, which may indicate the importance of hydrogen bond network to biocatalysis. The observation of W3 coordination to the vacant site of Mn(Ⅲ) as the sixth ligand proximal to O5 may imply W3 could be the fast-exchanging substrate water (W_f) in the S₂ state, which makes O₂ with O5 in the S₄ state. Based on the inference, we investigate O-O bond formation in all the possible spin states for the two isomeric structures under the framework of oxo-oxyl radical coupling mechanism. It is demonstrated from BS-DFT calculations that O₂ formation activity is significantly advantageous for the open-cubane structure than the closed-cubane form, i.e. the differences of barriers and driving forces are beyond 20 kcal/mol and 25 kcal/mol, respectively. For the open-cubane structure, the antiferromagnetic coupling of Mn1(IV)-O^· stabilizes the reactants, and the spin-parallel feature between O· radical and Mn4(IV) lowers the barriers, and ferromagnetic coupling of Mn1-Mn3 ensures the release of triplet O₂. For the closed-cubane structure, the antiferromagnetic coupled Mn4(IV)-O^· changes to more stabilized Mn4(Ⅲ)-oxo, losing the radical character of the ligand oxygen, which greatly increases the barriers. The ferromagnetic coupled Mn4(IV)-O^· does not belong to the relatively stable electronic configuration of reactants, and cannot be formed by spin frustration from the stable spin states, for their large energy differences above 20 kcal/mol. Thus it cannot be accepted as the accesses of effective reaction channels. Our work expounds the exclusive role of the open-cubane OEC in oxo-oxyl coupling mechanism of O₂ creation. It also reveals that the oxygen evolution reactivity is extremely dependent on the spin coupling ways of manganeses and oxygen radical, meanwhile, the structural flexibility of the OEC is essential to the S-state cycle and photosynthetic water splitting.

Key words: oxygen-evolving complex (OEC), atom-bond electronegativity equalization method (ABEEM), molecular dynamic (MD) simulation, broken-symmetry density functional theory (BS-DFT), isomerization, substrate water binding, oxygen evolution, spin state

引用此文

郭宇, 姚远, 李慧, 赫兰兰, 朱尊伟, 杨忠志, 宫利东, 刘翠, 赵东霞. 光合释氧机理的ABEEM/MM/MD和BS-DFT理论研究[J]. 化学学报, 2017, 75(9): 903-913.

Guo Yu, Yao Yuan, Li Hui, He Lanlan, Zhu Zunwei, Yang Zhongzhi, Gong Lidong, Liu Cui, Zhao Dongxia. Theoretical Study on the Mechanism of Photosynthetic Oxygen Evolution by ABEEM/MM/MD and BS-DFT[J]. Acta Chim. Sinica, 2017, 75(9): 903-913.

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