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<p>In this study, we investigate the encapsulation mechanism of small alkane molecules<b>,</b> <i>cyclo-</i>pentane and <i>neo-</i>pentane, within the supramolecular host cucurbit-[6]-uril. Using a combination of computational methodologies, including molecular docking, molecular dynamics simulations, and well-tempered metadynamics, we evaluated structures and computed the energetic barrier associated with the encapsulation/decapsulation processes. Our findings indicate that the guest binding at the cavity requires prior removal of water molecules, leading to high energetic barriers. Nevertheless, the hydrophobic nature of the ligand stabilizes the encapsulated state significantly, making the binding feasible at the cavity. The free energy surface reveals that <i>neo-</i>pentane experiences a slightly higher energy barrier to exit the cucurbit-[6]-uril cavity compared to <i>cyclo-</i>pentane, possibly due to the higher molecular volume causing greater hindrance at the portal.</p> Graphical abstract <p></p>

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Multi-scale modelling of encapsulation mechanism of simple alkanes to cucurbituril

  • 期刊论文

  • 发表日期：

    2026年1月13日

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  • NAMAN K BHARTI,
  • BISWAJIT SADHU,
  • CHANDRA N PATRA,
  • MAHESH SUNDARARAJAN

摘要

In this study, we investigate the encapsulation mechanism of small alkane molecules, cyclo-pentane and neo-pentane, within the supramolecular host cucurbit-[6]-uril. Using a combination of computational methodologies, including molecular docking, molecular dynamics simulations, and well-tempered metadynamics, we evaluated structures and computed the energetic barrier associated with the encapsulation/decapsulation processes. Our findings indicate that the guest binding at the cavity requires prior removal of water molecules, leading to high energetic barriers. Nevertheless, the hydrophobic nature of the ligand stabilizes the encapsulated state significantly, making the binding feasible at the cavity. The free energy surface reveals that neo-pentane experiences a slightly higher energy barrier to exit the cucurbit-[6]-uril cavity compared to cyclo-pentane, possibly due to the higher molecular volume causing greater hindrance at the portal.

Graphical abstract