Silica gels based on Silokhrom S-120 chemically modified with malonic ester chelates are studied using a set of physicochemical analytical techniques. The effect that a grafted layer of nickel, cobalt, or copper malonates has on the thermodynamic properties of adsorption of organic compounds from different classes on silica gel is investigated via gas chromatography. The test compounds are n-alkanes (C6–C9), chlorinated alkanes, alkenes, and adsorptives whose molecules exhibit different electron-donating and electron-withdrawing properties. Values for differential molar heat of adsorption change in standard differential molar entropy , and contributions to the energies of dispersive and specific interactions are calculated from experimental retention data for the considered adsorptives. The effect the metal ion of modifying malonate has on the parameters of thermodynamic retention is demonstrated.