Programed dynamical ordering in self-organization processes of a nanocube: a molecular dynamics study

Abstract

Self-organization processes of a gear-shaped amphiphile molecule (1) to form a hexameric structure (nanocube, 1₆) were inferred from sequential dissociation processes by using molecular dynamics (MD) simulations. Our MD study unveiled that programed dynamic ordering exists in the dissociation processes of 1₆. According to the dissociation processes, it is proposed that triple π-stacking among three 3-pyridyl groups and other weak molecular interactions such as CH–π and van der Waals interactions, some of which arise from the solvophobic effect, were sequentially formed in stable and transient oligomeric states in the self-organization processes, i.e.1₂, 1₃, 1₄, and 1₅. By subsequent analyses on structural stabilities, it was found that 1₃ and 1₄ are stable intermediate oligomers, whereas 1₂ and 1₅ are transient ones. Thus, the formation of 1₃ from three monomers and of 1₆ from 1₄ and two monomers via corresponding transients is time consuming in the self-assembly process.