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Area of Science:

  • Computational chemistry
  • Molecular dynamics
  • Host-guest chemistry

Background:

  • Ligand residence time computation is challenging due to long timescales.
  • Factors influencing residence times, such as solvation and steric hindrance, are not fully understood.
  • Accurate computation of residence times is crucial for drug discovery and materials science.

Purpose of the Study:

  • To demonstrate the utility of Gaussian mixture based enhanced sampling for computing ligand residence times.
  • To elucidate the unbinding mechanism of guests from host systems.
  • To investigate the role of solvation, specifically water molecules, in guest unbinding and residence times.

Main Methods:

  • Utilized a recently developed Gaussian mixture based enhanced sampling method.
  • Applied the method to a set of model host-guest systems.
  • Analyzed guest unbinding pathways and correlated residence times with water trapping times.

Main Results:

  • Successfully computed ligand residence times in model host-guest systems.
  • Identified a series of intermediate states during guest unbinding, characterized by the number of water molecules in the binding cavity.
  • Observed a correlation between ligand residence times and water trapping times within the binding cavity.

Conclusions:

  • Gaussian mixture based enhanced sampling is an effective method for computing ligand residence times.
  • Guest unbinding is often a multi-step process influenced by solvation.
  • Water molecules in the binding cavity play a significant role in determining ligand residence times.