Atomistic description of molecular binding processes based on returning probability theory.

Area of Science:

• Chemical Kinetics
• Computational Chemistry
• Molecular Dynamics

Background:

• Molecular binding efficiency is typically assessed using kinetics, specifically rate coefficients.
• Calculating overall binding rates requires considering reactant diffusion and barrier crossing.
• Host-guest binding, crucial in various chemical processes, necessitates accurate kinetic evaluation.

Purpose of the Study:

• To develop a novel methodology for quantifying molecular binding rate coefficients.
• To apply returning probability (RP) theory combined with molecular dynamics simulations.
• To validate the method using host-guest binding systems like beta-cyclodextrin.

Main Methods:

• Utilizing molecular dynamics (MD) simulations to capture molecular motion and interactions.
• Applying returning probability (RP) theory to derive a tractable formula for rate coefficients.
• Defining the interaction energy between reactants as the reaction coordinate for a 1D analysis.
• Investigating the thermodynamic stability and kinetics of intermediate states.

Main Results:

• Successfully quantified binding rate coefficients for host-guest systems.
• Demonstrated consistency between calculated and experimentally observed rate coefficients.
• Validated the effectiveness of using interaction energy as a reaction coordinate.

Conclusions:

• The developed methodology provides an accurate and efficient way to determine molecular binding rates.
• RP theory, integrated with MD simulations and interaction energy as a reaction coordinate, is a powerful tool for kinetic studies.
• This approach offers valuable insights into the kinetics of host-guest complexation and other molecular binding events.