Mehta Nital, Datta Sambhu N
Department of Chemistry, Indian Institute of Technology-Bombay, Powai, Mumbai, India.
J Phys Chem B. 2007 Jun 28;111(25):7210-7. doi: 10.1021/jp067383t. Epub 2007 May 31.
Quantum mechanical/molecular mechanics (QM/MM) calculations were performed on the neutral, anionic, and dianionic forms of Pheophytin-a (Pheo-a) in N,N-dimethyl formamide (DMF) in order to calculate the absolute free energy of reduction of Pheo-a in solution. The geometry of the solvated species was optimized by restricted open-shell density functional treatment (ROB3LYP) using the 6-31G(d) basis set for the molecular species while the primary solvent shell consisting of 45 DMF molecules was treated by the MM method using the universal force field (UFF). Electronic energies of the neutral, anionic, and dianionic species were obtained by carrying out single point density functional theory (DFT) calculations using the 6-311+G(2d,2p) basis set on the respective ONIOM optimized geometries. The CHARMM27 force field was used to account for the dynamical nature of the primary solvation shell of 45 DMF molecules. In the calculations using solvent shells, the required atomic charges for each solvent molecule were obtained from ROB3LYP/6-31G(d) calculation on a single isolated DMF molecule. Randomly sampled configurations generated by the Monte Carlo (MC) technique were used to determine the contribution of the primary shell to the free energy of solvation of the three species. The dynamical nature of the primary shell significantly corrects the free energy of solvation. Frequency calculations at the ROB3LYP/6-31G(d) level were carried out on the optimized geometries of truncated 47-atom models of the neutral and ionic species in vacuum so as to determine the differences in thermal energy and molecular entropy. The Born energy of ion-dielectric interaction, the Onsager energy of dipole-dielectric interaction, and the Debye-Hückel energy of ion-ionic cloud interaction for the pheophytin-solvent aggregate were added as perturbative corrections. The Born interaction also makes a large contribution to the absolute free energy of reduction. An implicit solvation model (DPCM) was also employed for the calculation of standard reduction potentials in DMF. Both the models were successful in reproducing the standard reduction potentials. An explicit solvent treatment(QM/MM/MC + Born + Onsager + Debye corrections) yielded the one electron reduction potential of Pheo-a as -0.92 +/- 0.27 V and the two electron reduction potential as -1.34 +/- 0.25 V at 298.15 K, while the implicit solvent treatment yielded the corresponding values as -1.03 +/- 0.17 and -1.30 +/- 0.17 V, respectively. The calculated values more or less agree with the experimental midpoint potentials of -0.90 and -1.25 V, respectively. Moreover, a numerical finite difference Poisson-Boltzmann solver (FDPB) along with the DPCM methodology was employed to obtain the reduction potential of pheophytin in the thylakoid membrane. The calculated reduction potential value of -0.58 V is in excellent agreement with the reported value -0.61 V.
为了计算脱镁叶绿素-a（Pheo-a）在溶液中的绝对还原自由能，我们在N，N-二甲基甲酰胺（DMF）中对中性、阴离子和二价阴离子形式的Pheo-a进行了量子力学/分子力学（QM/MM）计算。使用6-31G(d)基组对分子物种进行受限开壳密度泛函处理（ROB3LYP），优化溶剂化物种的几何结构，而由45个DMF分子组成的主溶剂壳则使用通用力场（UFF）通过MM方法进行处理。中性、阴离子和二价阴离子物种的电子能量通过在各自的ONIOM优化几何结构上使用6-311+G(2d,2p)基组进行单点密度泛函理论（DFT）计算获得。使用CHARMM27力场来考虑45个DMF分子的主溶剂壳的动力学性质。在使用溶剂壳的计算中，每个溶剂分子所需的原子电荷是通过对单个孤立的DMF分子进行ROB3LYP/6-31G(d)计算获得的。由蒙特卡罗（MC）技术生成的随机采样构型用于确定主壳对这三种物种溶剂化自由能的贡献。主壳的动力学性质显著校正了溶剂化自由能。在真空下，对中性和离子物种的截断47原子模型的优化几何结构进行ROB3LYP/6-31G(d)水平的频率计算，以确定热能和分子熵的差异。作为微扰校正，添加了脱镁叶绿素-溶剂聚集体的离子-介电相互作用的玻恩能量、偶极-介电相互作用的昂萨格能量和离子-离子云相互作用的德拜-休克尔能量。玻恩相互作用对绝对还原自由能也有很大贡献。还采用了隐式溶剂模型（DPCM）来计算DMF中的标准还原电位。两种模型都成功地再现了标准还原电位。在298.15 K时，显式溶剂处理（QM/MM/MC + 玻恩 + 昂萨格 + 德拜校正）得到Pheo-a的单电子还原电位为-0.92 +/- 0.27 V，双电子还原电位为-1.34 +/- 0.25 V，而隐式溶剂处理得到的相应值分别为-1.03 +/- 0.17和-1.30 +/- 0.17 V。计算值或多或少分别与实验中点电位-0.90和-1.25 V一致。此外，使用数值有限差分泊松-玻尔兹曼求解器（FDPB）以及DPCM方法来获得类囊体膜中脱镁叶绿素的还原电位。计算得到的还原电位值-0.58 V与报道值-0.61 V非常吻合。
