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.