In the present study a hydrophilic or a lipophilic alkylated barbituric acid derivative was allowed to interact in the melt and in solution with a complementary series of alkylated diamidopyridine derivatives, both hydrophilic or lipophilic. The interaction between the molecules was mainly studied by FT-IR spectroscopy. Phase transitions of reaction mixtures were studied with polarized optical microscopy and differential scanning calorimetry. It was found that the molecular recognition of the interacting components is only effective between the molecularly compatible ones. Specifically, employing Methods I and II, (see text) the short chain derivatives form 1:1 complexes whereas the long-chain derivatives are only partially complexed. Derivatives of dissimilar lipophilicity do not form complexes employing the same methods. However, comparing the two methods, complexation is more effective employing Method II. The induction of molecular recognition in the presence of an apolar solvent is enhanced in solution, Method III. The equilibrium which was established in solution is shifted to different directions during the evaporation step (Method II), leading either to the formation of complexes or to self-association.