'Dynamic Distance' Reaction Coordinate for Competing Bonds:  Applications in Classical and Ab Initio Simulations

Area of Science:

• Computational Chemistry
• Molecular Dynamics
• Biophysics

Background:

• Studying complex chemical reactions requires robust reaction coordinates.
• Existing methods may struggle with multiple bond formations/ruptures.
• Accurate reaction pathway analysis is crucial for understanding molecular processes.

Purpose of the Study:

• Introduce and validate a versatile
• dynamic distance
• reaction coordinate.
• Demonstrate its utility in analyzing complex chemical reactions and molecular events.
• Facilitate the calculation of free energy profiles for activated processes.

Main Methods:

• Development of the
• dynamic distance
• as a mass-weighted mean of selected distances.
• Implementation as a generalized constraint in molecular dynamics simulations.
• Application within Car-Parrinello molecular dynamics and classical mechanics frameworks.

Main Results:

• The
• dynamic distance
• effectively drives activated processes and unambiguously defines reaction pathways.
• Successfully applied to double proton transfer in formic acid dimer.
• Analyzed the guanine-cytosine DNA base pair photocycle and rubisco enzyme binding pocket opening.

Conclusions:

• The
• dynamic distance
• is a powerful and versatile tool for studying diverse chemical and biological processes.
• Enables straightforward free energy profile determination from simulation data.
• Offers a unified approach for analyzing reactions involving multiple bond changes.