One-dimensional reaction coordinate and the corresponding potential of mean force from commitment probability...

Area of Science:

• Computational Chemistry
• Physical Chemistry
• Chemical Kinetics

Background:

• Studying high-dimensional systems is complex.
• One-dimensional representations simplify kinetic analysis.
• Existing methods have limitations.

Purpose of the Study:

• To develop a novel method for obtaining a one-dimensional representation of high-dimensional kinetics.
• To create a reaction coordinate whose mean force potential reproduces the commitment probability distribution.
• To demonstrate the method's utility in predicting system dynamics.

Main Methods:

• Calculating a relevant one-dimensional representation from equilibrium distribution of commitment probabilities.
• Utilizing simulations to obtain equilibrium distributions.
• Comparing the new method with a previous approach based on quadratic approximation of the potential energy surface.

Main Results:

• The proposed method yields a one-dimensional representation that accurately reproduces the commitment probability distribution.
• The new representation is complementary to existing methods.
• Dynamics in a two-dimensional system showed the method can predict intermediates and path switching without prior knowledge of the surface morphology.

Conclusions:

• The developed method offers a powerful tool for simplifying and analyzing complex kinetic systems.
• This approach has potential applications in studying complex reactions like protein folding.
• The method provides insights into system behavior, including intermediate states and pathway transitions.