Optimizing reaction coordinate by flux maximization in the transition path ensemble.

Area of Science:

• Computational Chemistry
• Chemical Dynamics
• Molecular Modeling

Background:

• The transition path ensemble contains crucial information for identifying reaction coordinates.
• Previous methods utilized full position and momentum coordinates to determine reaction coordinates.
• A simplified approach using only positional data is desirable for efficient analysis.

Purpose of the Study:

• To develop a method for obtaining a one-dimensional reaction coordinate using only conformational coordinates from the transition path ensemble.
• To identify optimal reaction coordinates by maximizing the flux through a dividing surface.
• To assess the correlation of identified reaction coordinates with the committor function.

Main Methods:

• Utilized the transition path ensemble, focusing solely on conformational (position) coordinates.
• Employed a flux maximization criterion to identify meaningful one-dimensional reaction coordinates.
• Applied the method to alanine dipeptide in vacuum, analyzing dihedral angles and pairwise distances.

Main Results:

• Dihedral angles ϕ and θ were identified as significant reaction coordinates for alanine dipeptide, consistent with prior studies.
• A linear combination of dihedral angles yielded a superior reaction coordinate highly correlated with the committor.
• A linear combination of pairwise heavy atom distances also showed strong correlation with the committor, achieving a low committor standard deviation (0.08).

Conclusions:

• Conformational coordinates alone are sufficient for identifying meaningful reaction coordinates.
• The flux maximization method effectively determines reaction coordinates that accurately represent the reaction pathway.
• The developed approach provides a robust and efficient way to analyze complex chemical reactions.