Molecular Recognition of Thymine and Uracil in Water by an Amino-, Amido-, and Carboxymethyl-functionalized Pyridinophane

Abstract

A new water soluble 26-membered macrocyclic pyridinophane functionalized by amide and carboxymethyl groups has been synthesized in a single step reaction and characterized by elemental analysis, mass spectrometry (FAB⁺), UV-vis, fluorescence, and ¹H NMR spectroscopy as well as single-crystal X-ray diffraction analysis. Its complexation properties with the nucleobases thymine and uracil have been explored in aqueous media by performing ¹H NMR titration experiments and potentiometric studies. The binding constants of the 1:1 host-guest complexes were determined as 10³ M^− 1 by proton NMR and 10²–10³ M^− 1 by potentiometry. Semiempirical molecular modelling studies have shown that the nucleobases are included within the cavity of the macrocyclic receptor and that the complexes are stabilized by hydrogen bonding.

Keywords:

• Binding constant
• Cyclophanes
• Host-guest complex
• Molecular recognition
• NMR
• Thymine
• Uracil

Acknowledgements

We thank Professors A. K. Yatsimirsky and M. Inoue for the advice and fruitful discussion of the results. This work was supported by CONACyT, project 39574-Q.