Molecular Dynamics Study on the Structure–Property Relationship of Self-Assembled Gear-Shaped Amphiphile Molecules with/without Methyl Groups

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Gaining insight into the encapsulation mechanism is important for controlling the encapsulation rate toward the self-assembly of gear-shaped amphiphile molecules (GSAs). To this aim, we conducted molecular dynamics (MD) simulations for three different hexameric nanocubes ( 1 6 12+, 2 6 12+, and 3 6 12+ ) of GSAs ( 1 2+, 2 2+, and 3 2+, respectively) to elucidate the quantitative structure–property relationship between the stability of the nanocubes and the rate of encapsulation of a guest molecule. The 1 2+, 2 2+, and 3 2+ monomers differ from each other in the number of methyl groups, having three, zero, and two methyl groups, respectively. The 3 6 12+ hexamer has methyl groups only on the equatorial region. In the cases of the simulations of 1 6 12+ and 3 6 12+, the cubic structures are maintained due to a tight triple-π stacking around the equator region. Meanwhile, 2 6 12+ deforms easily due to the occurrence of a large fluctuation. These results indicate that the methyl groups on the equator are crucial to stabilize the nanocubes. The encapsulation of an iodide ion as a guest molecule is revealed to occur through the pole region via a gap that is easily formed in the nanocubes without methyl groups on the poles. Our study clearly suggests that self-assembled nanocubes can be designed to attain a specific stability and encapsulation efficiency simultaneously.