Many pharmaceutical drugs are chiral and may interact differently with biological molecules in vivo. According to current FDA rules, each enantiomer of these chiral drugs has to be tested separately before its approval to the market. Chiral chromatography plays a key role in the pharmaceutical industry for obtaining pure enantiomers from racemic mixtures. Phenylcarbamate derivatives of polysaccharides show higher resolution for chiral molecules when used in chromatography columns as stationary phases. The chiral recognition mechanism of these biopolymers is still not clear. In the present study, the molecular structure of one of these derivatives was probed in detail with IR spectroscopy, and with x-ray diffraction. In one example, interactions of phenylpropanolamine (PPA) enantiomers in methanol with this stationary phase were probed in detail. It was found that the two PPA enantiomers are first absorbed inside the solid polymer structure, and subsequently are selectively adsorbed in the nanostructured polymer cavities. There they bind and selectively interact with the polymer amide groups. The methanol also interacts with the polymer amide groups, but less intensely than the PPA enantiomers. The detailed PPA enantiomer recognition mechanism is also studied via molecular mechanics simulations and via ONIOM DFT calculations, which are more accurate for some portions of the chiral cavities. The simulation results can provide further qualitatively molecular insights, and predict the key features of the amide bands of IR spectra. The current study provides a detailed insight into how these polymers interact with chiral molecules.