Coarse-grained modeling of nanocube self-assembly system and transition network analyses

K Imamura and T Yamamoto and H Sato, CHEMICAL PHYSICS LETTERS, 742, 137135 (2020).

DOI: 10.1016/j.cplett.2020.137135

An implicit-solvent coarse-grained (CG) model of a self-assembling molecular capsule called nanocube is developed based on all-atom molecular dynamics (MD) simulations and the iterative Boltzmann inversion method. The present model well describes the chemical specificity of constituent monomers (gear-shaped amphiphiles) and effective intermonomer interactions in aqueous methanol. Standard and replica exchange CG-MD simulations are performed and it is confirmed that the CG model can reproduce a highly ordered self-assembled structure similar to the AA model. Furthermore, the transition network is studied based on a cluster analysis, which suggests several major routes for the assembly via metastable bipyramidal states.

Return to Publications page