Dynamic nanogates let longer molecules pass faster

Longer molecules move faster through dynamic molecular gates
A research team led by Professor Shuichi Hiraoka at the University of Tokyo and Professor Masanori Tachikawa at Yokohama City University has quantitatively analyzed how molecules pass through dynamic nanoscale pores using self-assembled molecular “nanocubes” in water.
The researchers discovered an unexpected phenomenon: for linear alkane molecules, longer molecules passed through the molecular gates faster than shorter ones. The study further revealed that transport rates are determined not only by pore size but also by the dynamic flexibility of the gate and weak transient interactions at the outer pore surface.
Transport through nanoscale pores is fundamental to many biological processes, including ion channels and aquaporins in cell membranes. However, unlike rigid artificial filters, biological pores constantly fluctuate and change shape because of thermal motion. Understanding how molecules pass through such dynamic gates at the molecular level has remained challenging.
To investigate this problem, the researchers used cube-shaped molecular assemblies formed by the self-assembly of amphiphilic molecules in water. These “nanocubes” contain hydrophobic inner cavities connected to the outside through small flexible pores. By preparing three nanocubes with different flexibilities, the team systematically examined how pore dynamics influence molecular transport.
Using time-resolved luminescence measurements, the researchers analyzed the uptake rates of various hydrocarbon molecules. They found that linear alkanes entered the nanocubes much faster than branched alkanes of the same carbon number, demonstrating that the dynamic pores discriminate molecular shape rather than simply molecular size.
More surprisingly, transport rates increased as the hydrocarbon chain became longer. This trend is opposite to ordinary macroscopic intuition, where longer objects are generally expected to pass through narrow openings more slowly. The researchers also found that introducing double or triple bonds at the ends of molecules accelerated transport, whereas incorporating oxygen atoms slowed it down.
To explain these observations, the team proposed a two-step transport mechanism. Molecules first form a transient “encounter complex” at the outer surface of the nanocube before passing through the fluctuating pore. Molecules that interact more strongly with the outer surface remain there longer, increasing the probability of entering when the gate temporarily opens. Molecular dynamics simulations directly visualized pore opening and molecular passage events, supporting the proposed mechanism.
The findings provide a new kinetic principle for molecular transport through dynamic nanoscale gates and may contribute to the future design of selective artificial channels, molecular recognition systems, and separation materials inspired by biological transport processes.

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