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Abstract: Highly stereoselective, uniformly sized molecularly imprinted polymers (MIPs) for cinchona alkaloids, cinchonine (CN) and cinchonidine (CD), were prepared using methacrylic acid (MAA) as a functional monomer and ethylene glycol dimethacrylate (EDMA) as a cross-linker. The MIPs were evaluated using a mixture of phosphate buffer and acetonitrile as the mobile phase. The CN- and CD-imprinted MAA-co-EDMA polymers can recognize the respective template molecule more than the other diastereomer, and afford an excellent diastereomer separation of CN and CD. In addition, the MIPs gave diastereomer separations of structurally related compounds, quinidine and quinine. The retentive and stereoselective properties of those compounds on the MIPs suggest that electrostatic and hydrophobic interactions can work to recognize these compounds. Furthermore, thermodynamic studies reveal that the entropy- driven effect is significant at mobile-phase pH 5.4, while the enthalpy-driven interactions seem to be dominant at mobile- phase pH 9.6