In this work, the effect of IL’s functionalization of the interaction of IL with organic solutes and water at infinite dilution has been investigated. Based on the experimental activity coefficients at infinite dilution, (γ13∞) the possibility of using ionic liquids (ILs) in different separation processes, such as aliphatic from aromatic hydrocarbon (heptane/benzene, or cyclohexane/benzene), desulfurization and denitrification of model fuel (heptane/thiophene and heptane/pyridine) were investigated based on the experimental study of the activity coefficients at infinite dilution. The (γ13∞) values were determined for more than fifty different solutes including alkanes, cycloalkanes, alkenes, alkynes, aromatic hydrocarbons, alcohols, ethers, ketones, thiophene, acetonitrile, pyridine, 1-nitropropane and water in two ionic liquids: 4-(3-cyanopropyl)-4-methylmorpholinium tricyanomethanide, [Mo1,3CN][TCM] and 4-(3-hydroxypropyl)-4-methylmorpholinium tricyanomethanide, [Mo1,3OH][TCM]. The experiment was performed using inverse gas–liquid chromatography at a wide temperature range from T = (308.15 to 358.15) K. From the experimental data, the partial molar excess Gibbs energy (ΔG1E,∞), enthalpy (ΔH1E,∞) and entropy (Tref ΔS1E,∞) at infinite dilution were determined. The gas–liquid partition coefficients of the solutes, KL were also calculated. Finally, two the values of two factors important from separation point of view: selectivity (S12∞) and capacity (k2) at infinite dilution for few separation problems as hexane/benzene, cyclohexane/benzene, heptane/thiophene, and heptane/pyridine were calculated from γ13∞ and compared to literature values for other ionic liquids taken from available literature. Moreover, physicochemical properties of pure IL including liquid density and dynamic viscosity data, important from the technological point of view was determined at a wide temperature range.