Satheesan Babu C, Yang Pei-Kun, Lim Carmay
Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529 Taiwan R 0.C.
J Biol Phys. 2002 Jun;28(2):95-113. doi: 10.1023/A:1019978119707.
Solvent-induced electrostatic potentials and field components at thesolute sites of model Na(+q)-Cs(-q) molecules were computed bysumming over either solvent charges (q-summation) or solventmolecular centers (M-summation) from molecular dynamics simulations.These were compared with values obtained by solving Poisson equation withthe dielectric boundary defined by R(eff) = (R(atom)+R(gmax) )/2.q-summation using cut-offs that are ≤ 10 Å generallyunderestimates or overestimates the magnitude of (a) the potentials and field components atNa(+q) and Cs(-q) relative to the theoretical values and (b)electrostatic solvation free energies of the dipolar solutes assuminglinear solvent response relative to the respective values from free energysimulations. Furthermore, the q-summed electric potentials showedsignificant oscillations even beyond the second hydration shell. Incontrast, the corresponding M-summed potentials plateaued after thefirst hydration shell. Although the different water molecular centersyielded different converged potential values, the dipole center producedvalues in remarkable agreement with the theoretical values for solutecharges ranging from 1 to 0.1e, indicating the existence of an a convenient molecular center for computing these quantities. In contrast to theM-summed potentials, the electrostatic field components andelectrostatic solvation free energies from linear response relationshipswere found not to be sensitive to the choice of the molecular centerfor typical cut-off distances (8 to 12 Å) used in most simulations.
通过对分子动力学模拟中的溶剂电荷（q 求和）或溶剂分子中心（M 求和）进行求和，计算了模型 Na(+q)-Cs(-q)分子溶质位点处的溶剂诱导静电势和场分量。将这些结果与通过求解泊松方程得到的值进行比较，泊松方程的介电边界由 R(eff) = (R(atom)+R(gmax) )/2 定义。一般来说，使用≤10 Å 的截止值进行 q 求和会低估或高估：(a) Na(+q)和 Cs(-q)处的势和场分量相对于理论值的大小；(b) 假设线性溶剂响应时，偶极溶质的静电溶剂化自由能相对于自由能模拟中各自值的大小。此外，即使在第二个水合壳层之外，q 求和的电势也显示出显著的振荡。相比之下，相应的 M 求和电势在第一个水合壳层之后趋于平稳。尽管不同的水分子中心产生了不同的收敛电势值，但偶极中心产生的值与溶质电荷从 1 到 0.1e 的理论值非常一致，这表明存在一个方便计算这些量的分子中心。与 M 求和电势不同，发现对于大多数模拟中使用的典型截止距离（8 到 12 Å），线性响应关系中的静电场分量和静电溶剂化自由能对分子中心的选择不敏感。
