Molecular dynamics simulation of self-assembled nanocubes in methanol

Abstract

Molecular dynamics simulations were performed for the hexameric nanocubes of methylated (1₆) and demethylated (2₆) gear-shaped amphiphiles in pure methanol to reveal the difference in structural fluctuation between 1₆ and 2₆. Within our simulation time of 2.0 ns, the cubic structure of 1₆ in methanol is maintained, whereas that of 2₆ is collapsed. We found that the triple π-stacking moieties consisting of the three 3-pyridyl groups in 2₆ are more fluctuated than those in 1₆. This suggests that methyl groups serve to reduce structural fluctuation for nanocubes. We also found that the existence of the solvent molecules near the nanocube is an important factor for the collapse of the 2₆ structure.

Keywords::

• molecular dynamics simulation
• nanocube
• methanol solvent
• self-assembly
• gear-shaped amphiphile molecule

Additional information

Funding

This study was supported by the Grant-in-Aid for Scientific Research by the Ministry of Education, Culture, Sports, Science and Technology, Japan (Kakenhi).