Value of Temporal Information When Analyzing Reaction Coordinates.

Area of Science:

• Computational Chemistry
• Chemical Kinetics
• Molecular Dynamics

Background:

• Reaction coordinates are crucial for visualizing chemical reaction pathways from reactants to products.
• Determining reaction coordinates from molecular trajectory ensembles is a key area of research.
• The committor function, a probability-based metric, is a widely used reaction coordinate.

Purpose of the Study:

• To investigate alternative reaction coordinates beyond the standard committor function.
• To incorporate mechanistic information using mean first passage time and exit time.
• To establish relationships between these different reaction coordinate functions.

Main Methods:

• Analysis of molecular trajectories to determine reaction pathways.
• Derivation of mathematical relationships between committor, mean first passage time, and exit time functions.
• Application of toy models and a protein-DNA search model for illustration.

Main Results:

• Identified mean first passage time and exit time as valuable alternatives to the committor function.
• Derived a simple analytical relationship connecting these different reaction coordinate metrics.
• Demonstrated the ability of alternative coordinates to reveal diverse reaction mechanisms.

Conclusions:

• Alternative reaction coordinates provide richer mechanistic details than the committor function alone.
• The derived relationships facilitate a unified understanding of different pathway descriptors.
• These methods offer powerful tools for analyzing complex molecular processes, such as protein-DNA interactions.