Pandey Anshu, Datta Sambhu N
Department of Chemistry, Indian Institute of Technology, Bombay, Powai, Mumbai-400076, India.
J Phys Chem B. 2005 May 12;109(18):9066-72. doi: 10.1021/jp0446478.
QM/MM calculations were performed on ethyl chlorophyllide-a and its radical cation and anion, by using the density functional (DF) B3LYP method to determine the molecular characteristics, and a molecular mechanics (MM) method to simulate the solvating medium. The presence of the solvent was accounted for during the optimization of the geometry of the 85-atom chlorophyll-a system by using an ONIOM methodology. A total of 24 solvent molecules were explicitly considered during the optimization process, and these were treated by the universal force field (UFF) method. Initially, the split-valence 3-21G basis set was used for optimizing the geometry of the 85-atom species, neutral, cation and anion. Electronic energies were then determined for the optimized species by making use of the polarized 6-31G(d) basis set. The ionization energy calculated (6.0 eV) is in very good agreement with the observed one (6.1 eV). The MM+ force field was used to investigate the dynamics of the acetonitrile molecules around the neutral species as well as the radical ions of chlorophyll. The required atomic charges on all the atoms were obtained from calculations on all involved molecules at the DFT/6-31G(d) level. Randomly sampled configurations were used to determine the first solvation layer contribution to the free energy of solvation of various species. A truncated 46-atom model of ethyl chlorophyllide-a was used to evaluate the thermal energies of neutral chlorophyll molecule relative to its two radical ions in the gas phase. Born energy, Onsager energy, and the Debye-Huckel energy of the chlorophyll-solvent aggregate were added as perturbative corrections to the free energy of solvation that was initially obtained through molecular dynamics method for the same complex. These calculations yield the oxidation potential as 0.75 +/- 0.32 V and the reduction potential -1.18 +/- 0.31 V at 298.15 K. The calculated values are in good agreement with the experimental midpoint potentials of +0.76 and -1.04 V, respectively.
采用密度泛函（DF）B3LYP方法确定分子特征，并结合分子力学（MM）方法模拟溶剂化介质，对脱镁叶绿酸-a乙酯及其自由基阳离子和阴离子进行了QM/MM计算。在优化85原子叶绿素-a体系的几何结构时，通过ONIOM方法考虑了溶剂的存在。在优化过程中明确考虑了总共24个溶剂分子，并采用通用力场（UFF）方法对其进行处理。最初，使用分裂价3-21G基组优化85原子物种（中性、阳离子和阴离子）的几何结构。然后利用极化6-31G(d)基组确定优化物种的电子能量。计算得到的电离能（6.0 eV）与观测值（6.1 eV）非常吻合。使用MM+力场研究了乙腈分子围绕中性物种以及叶绿素自由基离子的动力学。所有原子所需的原子电荷是通过在DFT/6-31G(d)水平上对所有相关分子进行计算得到的。使用随机采样的构型来确定第一溶剂化层对各种物种溶剂化自由能的贡献。使用脱镁叶绿酸-a的截断46原子模型来评估中性叶绿素分子相对于其在气相中的两个自由基离子的热能。将叶绿素-溶剂聚集体的玻恩能、翁萨格能和德拜-休克尔能作为微扰校正项，添加到最初通过分子动力学方法获得的相同配合物的溶剂化自由能中。这些计算得出在298.15 K时氧化电位为0.75±0.32 V，还原电位为-1.18±0.31 V。计算值分别与实验中点电位+0.76 V和-1.04 V吻合良好。
