Abstarct: Abstract Because many biological reactions are space-consuming. Therefore, most biological compounds such as enzymes have different reactions for their racemic forms. For this reason, the separation of pharmaceutical enantiomers has become an important issue in the pharmaceutical industry. In this research, the separation process of modafinil enantiomers as a racemic mixture drug was studied by chiral carbon nanotube adsorption process and molecular docking simulation method. Also, the structural and electronic properties of the enantiomers of modafinil in the gas phase and in the presence of water were investigated through quantum calculations using density functional theory at the B3LYP/6-31G theoretical level. The results of structural calculations show that the values of the length and bond angle in the left-round enantiomer have changed more under the influence of the interactions between the double bonds of the nanotube and the drug compared to the right-round enantiomer. Examination of binding energy values showed that its value for enantiomer R (position outside the nanotube) is lower than enantiomer S (position inside the carbon nanotube) and has a higher absorption power due to less repulsion between the non-bonding electron pair of drug oxygen and the non-bonding electron pair. The ring is related. Examination of electronic properties showed that oxygen and nitrogen heteroatoms have the highest electron density and S atom has the lowest charge density in both enantiomers. The values of the energy gap between the homo and lomo enantiomers of S and R in the absorption process have a significant reduction, which can be a reason for the higher reactivity and lower conductivity of the nanotube-complex compared to the state before absorption. The results of the dipole moment values of the studied enantiomers after the absorption process show that its value has decreased for the R enantiomer and for the S enantiomer compared to the state before absorption. Investigating the thermodynamic properties of enantiomers adsorption process in gaseous and aqueous phase showed that the interaction of both drug forms and nanotubes is exothermic and enantiomer R has stronger absorption on carbon nanotubes due to its more negative Gibbs free energy values. Examining the thermodynamic properties of the absorption process of R and S enantiomers shows that this process is exothermic and spontaneous for both forms of modafinil in gaseous and aqueous phases. The effect of gas phase and water solvent on the values of enthalpy and Gibbs free energy of two enantiomers R and S are different. In general, the results of this research show that due to the better interaction of R enantiomer with carbon nanotube than S enantiomer, carbon nanotube can be used to separate racemic mixture.