Self-Assembly of V-Shaped Polyaromatic Amphiphiles Studied by Molecular Dynamics Simulation.

V-shaped polyaromatic amphiphiles (VPAAs) form micelle-like nonbonded self-assemblies in aqueous solution and feature prominent properties of encapsulation and solubilization for various types of hydrophobic molecules. To understand microscopic molecular characteristics underlying the wide capability of solubilization, the atomic-level molecular structures of the self-assemblies of VPAAs were investigated by microsecond molecular dynamics (MD) simulations. The MD simulations showed that VPAAs spontaneously formed quasi-stable self-assemblies, in close agreement with experimental observations. To characterize the nanosized structures of the assemblies and their microscopic conformational changes, we developed a root-mean-square displacement (RMSD)-based structural similarity metric applicable to molecular assemblies. Through conformational classification by an unsupervised clustering, highly stable conformations depending on the number of constituent molecules in the assemblies were identified. The analysis revealed that the stable conformations of the VPAA assemblies flexibly reorganized depending on the number of constituent molecules, well explaining the wide capability of solubilization of hydrophobic molecules of various sizes and shapes.