Thermal isomerization rates in retinal analogues using Ab-Initio molecular dynamics

Area of Science:

• Computational Chemistry
• Chemical Dynamics
• Molecular Modeling

Background:

• Eyring transition state theory is limited for complex molecules and environments.
• Molecular dynamics simulations are crucial for accurate rate theories but face timescale limitations.
• Rare event methods enhance sampling for computationally expensive chemical processes.

Purpose of the Study:

• To investigate thermal isomerization of retinal using advanced computational methods.
• To compare the accuracy of transition state theory with enhanced sampling techniques.
• To evaluate the applicability of Kramers' rate equation in complex chemical reactions.

Main Methods:

• Tight-binding density functional theory for electronic structure calculations.
• Infrequent metadynamics for enhanced molecular dynamics sampling.
• Dynamical reweighting and Kramers' rate equation for rate calculations.

Main Results:

• Rates from dynamical reweighting closely matched transition state theory predictions.
• Kramers' rate equation applied to a 1D reaction coordinate yielded rates up to three orders of magnitude higher.
• Discrepancies highlight potential issues with simplified reaction coordinate models.

Conclusions:

• Enhanced sampling methods can provide accurate reaction rates for complex systems.
• The choice of reaction coordinate and rate theory is critical for reliable results.
• Further research is needed to refine methods for modeling chemical reactions in complex environments.