Self-Assembly of\nV‑Shaped Polyaromatic Amphiphiles\nStudied by Molecular Dynamics Simulation

V-shaped polyaromatic amphiphiles (<b>VPAA</b>s)\nform micelle-like\nnonbonded self-assemblies in aqueous solution and feature prominent\nproperties of encapsulation and solubilization for various types of\nhydrophobic molecules. To understand microscopic molecular characteristics\nunderlying the wide capability of solubilization, the atomic-level\nmolecular structures of the self-assemblies of <b>VPAA</b>s\nwere investigated by microsecond molecular dynamics (MD) simulations.\nThe MD simulations showed that <b>VPAA</b>s spontaneously formed\nquasi-stable self-assemblies, in close agreement with experimental\nobservations. To characterize the nanosized structures of the assemblies\nand their microscopic conformational changes, we developed a root-mean-square\ndisplacement (RMSD)-based structural similarity metric applicable\nto molecular assemblies. Through conformational classification by\nan unsupervised clustering, highly stable conformations depending\non the number of constituent molecules in the assemblies were identified.\nThe analysis revealed that the stable conformations of the <b>VPAA</b> assemblies flexibly reorganized depending on the number of constituent\nmolecules, well explaining the wide capability of solubilization of\nhydrophobic molecules of various sizes and shapes.