Faculty of Chemistry, University of Gdańsk, ul. Sobieskiego 18, 80-952 Gdańsk, Poland.
J Phys Chem B. 2010 Jan 21;114(2):993-1003. doi: 10.1021/jp907794h.
The potentials of mean force (PMFs) were determined, in both water with the TIP3P water model and in vacuo, for systems involving formation of nonpolar dimers composed of bicyclooctane, adamantane (both an all-atom model and a sphere with the radius of 3.4 A representing adamantane), and fullerene, respectively. A series of umbrella-sampling molecular dynamics simulations with the AMBER force field were carried out for each pair under both environmental conditions. The PMFs were calculated by using the weighted histogram analysis method. The results were compared with our previously determined PMF for neopentane. The shape of the PMFs for dimers of all four nonpolar molecules is characteristic of hydrophobic interactions with contact and solvent-separated minima and desolvation maxima. The positions of all these minima and maxima change with the size of the nonpolar molecule; for larger molecules they shift toward larger distances. Comparison of the PMFs of the bicyclooctane, adamantane, and fullerene dimers in water and in vacuo shows that hydrophobic interactions in each dimer are different from that for the dimer of neopentane. Interactions in the bicyclooctane, adamantane, and fullerene dimers are stronger in vacuo than in water. These dimers cannot be treated as classical, spherical, hydrophobic objects. The solvent contribution to the PMF was also computed by subtracting the PMF determined in vacuo from that in explicit solvent. The solvent contribution to the PMFs of bicyclooctane, adamantane, and fullerene is positive, as opposed to that of neopentane. The water molecules in the first solvation sphere of both adamantane and neopentane dimers are more ordered as compared to bulk water, with their dipole moments pointing away from the surface of the dimers. The average number of hydrogen bonds per water molecule in the first hydration shell of adamantane is smaller compared to that in bulk water, but this shell is thicker for all-atom adamantane than for neopentane or a spherical model of adamantane. In the second hydration shell, the average number of hydrogen bonds is greater compared to that in bulk water only for neopentane and a spherical model of adamantane but not for the all-atom model. The strength of the hydrophobic interactions shows a linear dependence on the number of carbon atoms both in water and in vacuo. Smaller nonpolar particles interact more strongly in water than in vacuo. For larger molecules, such as bicyclooctane, adamantane and fullerene, the reversed tendency is observed.
我们测定了分别由双环辛烷、金刚烷（全原子模型和 3.4Å 半径的球体代表）和富勒烯形成的非极性二聚体在水中（使用 TIP3P 水模型）和真空中的形成势能（PMFs）。在这两种环境条件下，我们分别使用 AMBER 力场对每一对体系进行了一系列伞状采样分子动力学模拟。通过加权直方图分析方法计算了 PMFs。我们将结果与之前确定的新戊烷 PMF 进行了比较。所有这四个非极性分子的二聚体的 PMF 形状均具有疏水性相互作用的特征，具有接触和溶剂分离的最小值和去溶剂化的最大值。所有这些最小值和最大值的位置随非极性分子的大小而变化；对于较大的分子，它们向更大的距离移动。将双环辛烷、金刚烷和富勒烯二聚体在水中和真空中的 PMFs 进行比较表明，每个二聚体中的疏水性相互作用与新戊烷二聚体的疏水性相互作用不同。在真空中，二聚体的相互作用强于在水中。这些二聚体不能被视为经典的、球形的、疏水性的物体。我们还通过从真空中确定的 PMF 中减去在显溶剂中确定的 PMF 来计算溶剂对 PMF 的贡献。与新戊烷相比，双环辛烷、金刚烷和富勒烯的溶剂对 PMF 的贡献为正值。与双环辛烷和新戊烷二聚体的第一溶剂化壳层中的水分子相比，水分子的有序性更高，其偶极矩指向二聚体表面。与新戊烷相比，金刚烷全原子模型的第一水合壳层中每个水分子的氢键平均数较小，但该壳层比新戊烷或金刚烷的球形模型更厚。在第二水合壳层中，只有新戊烷和金刚烷的球形模型的氢键平均数大于水，而全原子模型的氢键平均数则没有。在水中和真空中，疏水性相互作用的强度都与碳原子数呈线性关系。较小的非极性粒子在水中的相互作用比在真空中更强。对于较大的分子，如双环辛烷、金刚烷和富勒烯，观察到相反的趋势。
