Since chromatographic separation is a dynamic process, with the
interactions between the drug and the chiral stationary phase mediated
by the solvent, no single interacting structure, such as could be found
by minimizing the energy, could possibly describe and account for the
ratio of residence times in the chromatographic column for the
enantiomeric pair. We describe the use of explicit-solvent fully
atomistic molecular dynamics simulations, permitting all the
interactions between the atoms constituting the chiral stationary phase,
solvent molecules and the drug molecule. This allows us to better
understand the molecular dynamic chiral recognition that provides the
discrimination which results in the separation of enantiomers by high
performance liquid chromatography. It also provides a means of
predicting, for a given set of conditions, which enantiomer elutes first
and an estimate of the expected separation factor. In this review we
consider the use of molecular dynamics towards this understanding and
prediction.