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The enantioselective binding of optical analytes on chiral stationary phases used in column chromatography is investigated with molecular modeling techniques. By rolling the analytes over the van der Waals surface of the phase, configurations are sampled and free energies of transient diastereomeric complexes are computed. These free energies allow us to compute chromatographic separability factors and a linear relationship between computed and observed values is found. The intermolecular potential energy surfaces of these diastereomeric complexes are flat with gentle rolling hills and multiple minima. The binding sites are ill-defined and the analytes are found to freely slide over the chiral stationary phases. An energy partitioning algorithm is used to determine how much of the total binding energy is attributable to a given molecular fragment on the phase. It is found that the fragments of the phase bearing the stereogenic carbons are the least cognizant of differences between optical antipodes.

Molecular recognition in Fkbeks cleft was studied with the MM2 force field. A new computational protocol was used t.o determine the free energies of substrate binding to this topologically unique model receptor. The energies and structural features of substrate-receptor complexes reveal that molecular recognition involves ammonium ion binding to the interior of the cleft and aromatic n-stacking on the exterior of the cleft.

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