Tillack Andreas F, Johnson Lewis E, Eichinger Bruce E, Robinson Bruce H
Department of Chemistry, University of Washington , Seattle, Washington 98195-1700, United States.
J Chem Theory Comput. 2016 Sep 13;12(9):4362-74. doi: 10.1021/acs.jctc.6b00219. Epub 2016 Aug 8.
We have developed an approach to coarse-grained (CG) modeling of the van der Waals (vdW) type of interactions among molecules by representing groups of atoms within those molecules in terms of ellipsoids (rather than spheres). Our approach systematically translates an arbitrary underlying all-atom (AA) representation of a molecular system to a multisite ellipsoidal potential within the family of Gay-Berne type potentials. As the method enables arbitrary levels of coarse-graining, or even multiple levels of coarse-graining within a single simulation, we describe the method as a Level of Detail (LoD) model. The LoD model, as integrated into our group's Metropolis Monte Carlo computational package, is also capable of reducing the complexity of the molecular electrostatics by means of a multipole expansion of charges obtained from an AA force field (or directly from electronic structure calculations) of the charges within each ellipsoid. Electronic polarizability may additionally be included. The present CG representation does not include transformation of bonded interactions; ellipsoids are connected at the fully atomistic bond sites by freely rotating links that are constrained to maintain a constant distance. The accuracy of the method is demonstrated for three distinct types of self-assembling or self-organizing molecular systems: (1) the interaction between benzene and perfluorobenzene (dispersion interactions), (2) linear hydrocarbon chains (a system with large conformational flexibility), and (3) the self-organization of ethylene carbonate (a highly polar liquid). Lastly, the method is applied to the interaction of large (∼100 atom) molecules, which are typical of organic nonlinear optical chromophores, to demonstrate the effect of different CG models on molecular assembly.
我们已经开发出一种对分子间范德华（vdW）相互作用进行粗粒度（CG）建模的方法，该方法通过用椭球体（而非球体）来表示分子中的原子基团。我们的方法系统地将分子系统的任意基础全原子（AA）表示转换为盖伊 - 伯尔尼型势函数族中的多位点椭球势。由于该方法能够实现任意程度的粗粒度，甚至在单个模拟中实现多个层次的粗粒度，我们将该方法描述为细节层次（LoD）模型。集成到我们团队的 metropolis 蒙特卡罗计算软件包中的 LoD 模型，还能够通过对每个椭球体内从 AA 力场（或直接从电子结构计算）获得的电荷进行多极展开，来降低分子静电学的复杂性。此外，还可以考虑电子极化率。目前的 CG 表示不包括键合相互作用的转换；椭球体通过自由旋转的链接在全原子键位点处相连，这些链接被约束以保持恒定距离。该方法的准确性在三种不同类型的自组装或自组织分子系统中得到了证明：（1）苯和全氟苯之间的相互作用（色散相互作用），（2）线性烃链（具有大构象灵活性的系统），以及（3）碳酸亚乙酯的自组织（一种高极性液体）。最后，该方法被应用于大型（约 100 个原子）分子的相互作用，这些分子是有机非线性光学发色团的典型代表，以展示不同 CG 模型对分子组装的影响。
