Thermodynamic quantitative structure-activity relationships (QSAR) for chymotrypsin-ligand binding is developed, and the results are compared for the effects of organic solvent on the substrate specificity of the enzymes to those in aqueous phosphate buffer. This is the first of such analysis utilizing thermodynamic QSAR. A possible explanation for the difference describing the effects of organic solvent for the binding of substituted phenyl esters of N-benzoyl L-alanine analogues [PhCONHCH(Me)COOC(6)H(4)-p-X, I] observed in both the classical and the thermodynamic QSAR is presented.