  For a detailed understanding of chemical processes in nature and industry, we
need accurate models of chemical reactions in complex environments. While
Eyring transition state theory is commonly used for modeling chemical
reactions, it is most accurate for small molecules in the gas phase. A wide
range of alternative rate theories exist that can better capture reactions
involving complex molecules and environmental effects. However, they require
that the chemical reaction is sampled by molecular dynamics simulations. This
is a formidable challenge since the accessible simulation timescales are many
orders of magnitude smaller than typical timescales of chemical reactions. To
overcome these limitations, rare event methods involving enhanced molecular
dynamics sampling are employed. In this work, thermal isomerization of retinal
is studied using tight-binding density functional theory. Results from
transition state theory are compared to those obtained from enhanced sampling.
Rates obtained from dynamical reweighting using infrequent metadynamics
simulations were in close agreement with those from transition state theory.
Meanwhile, rates obtained from application of Kramers rate equation to a
sampled free energy profile along a torsional dihedral reaction coordinate were
found to be up to three orders of magnitude higher. This discrepancy raises
concerns about applying rate methods to one-dimensional reaction coordinates in
chemical reactions.
