光合释氧机理的ABEEM/MM/MD和BS-DFT理论研究  

Theoretical Study on the Mechanism of Photosynthetic Oxygen Evolution by ABEEM/MM/MD and BS-DFT

作　　者：郭宇[1] 姚远 李慧 赫兰兰[1] 朱尊伟[1] 杨忠志[1] 宫利东[1] 刘翠[1] 赵东霞[1] Guo Yu Yao Yuan Li Hui He Lanlan Zhu Zunwei Yang Zhongzhi Gong Lidong Liu Cui Zhao Dongxia＊(School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029)

机构地区：[1]辽宁师范大学化学化工学院,大连116029

出　　处：《化学学报》2017年第9期903-913,共11页Acta Chimica Sinica

基　　金：中国国家自然科学基金(Nos.21473083;21133005);辽宁省自然科学基金(No.2014020150)资助~~

摘　　要：建立了S_2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,S_2态Mn_4CaO_5的双向异构化过程伴随Ca上的水分子W3转移至Mn1(Ⅲ)/Mn_4(Ⅲ),它很可能作为底物水之一,与O_5在S4态结合产生O_2.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.Charge parameters of atom-bond electronegativity equalization method（ABEEMσπ） for the oxygen-evolving complex（OEC） in the S_2 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 Mn_4 Ca O_5 cluster accompany by the transfer of Ca-bound water molecule W3 to pentacoordinate Mn1（Ⅲ）/Mn_4（Ⅲ）. For the g=2 to g=4.1 form, W3 leaves for Mn_4（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 O_5 may imply W3 could be the fast-exchanging substrate water（Wf） in the S_2 state, which makes O_2 with O_5 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 O_2 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 Mn_4（Ⅳ） lowers the barr

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 

分 类 号：O644.1[理学—物理化学] TQ116.14[理学—化学]