Abstract: Hydrophobicity can either be determined experimentally or predicted by means of commercially available programmes. In the studies concerning biological activities of pyrazine analogues of chalcones, 3-(2-hydroxyphenyl)-1-pyrazin-2-ylpropen-1-ones were more potent than the corresponding 3-(4-hydroxyphenyl)-1-pyrazin-2-ylpropen-1-ones. As the difference in lipohilicity may be a factor responsible for the difference in the potency, RM values of the compounds were determined by RP-TLC and compared with logP values calculated by various commercially available programmes. Important discrepancies were found between experimental and computational lipophilicity data. Therefore, we have tried to find a reliable method for calculating RM values from in silico derived molecular parameters. The RM values obtained with the chromatographic system consisting of Silufol UV 254 plates impregnated with silicon oil as the stationary phase and acetone-citrate buffer (pH = 3) 50:50 (V/V) as the mobile phase correlated well with van der Waals volumes (VW) and hydration energies ( Δ GH2O ) derived of molecular models calculated on RHF/AM1 level.