Supramolecular motifs showing chemoresponsive properties toward organic molecules are sought after. Their selectivity, however, may depend even on a small structural change. Here, we demonstrate the influence of isomerization of glycoluril molecular clips, equipped with N-(4-methoxyphenyl)isonicotinamide sidewalls, on the complexation of resorcinol. Concentration- and temperature-dependent 1H NMR and 1H–1H ROESY NMR experiments along with theoretical studies were employed to determine the detailed mechanisms and thermodynamic parameters of complexation for both isomers with resorcinol. This study shows that clip 1, equipped with N-(4-methoxyphenyl)isonicotinamide moieties oppositely directed along the glycoluril frame, is able to associate one resorcinol molecule within its cleft according to the “inner” mechanism with the equilibrium constant, K283K = 2340 M–1. Within the clip cleft, resorcinol forms hydrogen bonds via OH groups with oxygen atoms of clip’s urea moieties and interacts with clip aromatic sidewalls via π–π stacking. Clip 2, the isomer whose N-(4-methoxyphenyl)isonicotinamide moieties are oriented in the same direction along the glycoluril core, possesses two binding sites and complexes resorcinol according to 1:2 stoichiometry. One of the binding sites is located in the clip cleft analogous to clip 1, whereas the second one is created by the mutual arrangement of pyridinyl moieties. The distance between nitrogen groups of individual pyridine moieties matches the distance of resorcinol hydroxyl groups facilitating the formation of two hydrogen bonds according to the “outer” mechanism. Both mechanisms are spontaneous (ΔG11 and ΔG12 < 0); however, the association constant differs, that is, K11 = 2520 M–1 and K12 = 650 M–1 at 283 K. Both mechanisms are exothermic; however, the “outer” mechanism is more sensitive to the increase of temperature, as ΔH11 = −8.9 kcal/mol and ΔH12 = −19.8 kcal/mol. Clip 2 is a first unique example of the glycoluril clip, which is able to complex two resorcinol molecules, as generally, glycoluril clips interact with dihydroxyaromatics according to 1:1 stoichiometry.
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