The natural alkaloid quinine (QN) was immobilized on porous silica particles, and part of the material was subsequently endcapped with n-hexyl hydrocarbon chains. Two synthetic strategies for silanization of the support were first compared. These columns were thoroughly evaluated in order to study the influence of endcapping in the enantiorecognition features. Enantioseparations of twenty N-derivatized 2,4-dinitrophenyl α-amino acids (DNP-amino acids) were studied by changing mobile phase pH, buffer concentration, type of organic solvent in the mobile phase, and column temperature. Maximum retention factors were observed at pH ≈6, at this intermediate pH the tertiary amine of the quinine is protonated to a high degree and therefore available for strong electrostatic interactions with unprotonated anionic DNP-amino acids. The enantioselectivity factors, however, increased as the pH did in the range between 5 and 7. The increase in ionic strength had influence on retention, but not on enantioselectivity, allowing the use of this variable for optimization of retention factors. Finally, the thermodynamic transfer parameters of the enantiomers from the mobile to both CSPs (with and without endcapping, QN-CSP(EC) and QN-CSP, respectively) were estimated from van’t Hoff plots within the range of 10–40 °C. Thus, the differences in the transfer enthalpy, Δ(Δ H°), and transfer entropy, Δ(Δ S°), enabled an investigation of the origin of the differences in interaction energies.