Metastructure Analysis of Self-Assembled Nanocubes with Different Equatorial Methyl Groups Based on Molecular Dynamics Simulations

Nanocubes are self-assembled structures composed of six gear-shaped amphiphiles. They have attracted significant attention for their symmetric architecture and ability to encapsulate guest molecules. Their conformational behavior is strongly influenced by methyl groups located in the equatorial region. To elucidate the effects of these methyl groups, molecular dynamics (MD) simulations were performed on several nanocube models. During the simulations, the nanocubes deform continuously, adopting different conformations that can be classified into four metastructure types based on (i) the number of opened cation-π interactions and (ii) the distance between the equatorial atoms. Here, the metastructures are used to describe dynamically recurring deformation motifs observed during the simulations, rather than thermodynamically equilibrated metastable states. A metastructure-based analysis revealed the preservation of the adopted metastructures, with transitions occurring infrequently and reversibly. Transition frequencies increased as the number of equatorial methyl groups decreased; their positional arrangement significantly affected the structural dynamics. Atomic-level analysis further demonstrated that equatorial methyl groups located near cation-π interactions restrict their motion, potentially stabilizing the cubic structure.