Hydrogen Bonding and π-Stacking Interactions as Organizing Elements in Lariat Ethers Containing Nucleotide Bases

Two new bibracchial lariat ethers have been prepared as flexible model systems for nucleotide H-bonding and π-stacking interactions. In both compounds, nucleotide bases terminate side arms attached at the nitrogen atoms of a diaza-18-crown-6 macroring. Each side arm is terminated by one or more nucleotide bases. The unsymmetrical structure is ade-CH 2 CH 2 CH 2 CH 2 CH 2 -thy-CH 2 CH 2 -ade (A−O−T−A). The symmetrical compound is ade-CH 2 CH 2 -thy-CH 2 CH 2 CH 2 CH 2 CH 2 CH 2 -thy-CH 2 CH 2 -ade (A−T−O−T−A). NMR studies show that the thy−ade side arm organizes by π-stacking in both A−O−T−A and A−T−O−T−A. Both compounds exhibit hydrogen bonding between the stacked base pair and the opposite adenine. A−O−T−A exhibits a stronger interaction resulting from the enforced interplay of noncovalent forces, as evidenced by one- and two-dimensional NMR experiments. This compound also presented the opportunity to detect and examine single hydrogen-bonded interactions between two adenine bases. The effects of conformational rigidity, side arm orientation, metal ion complexation, and variations in solvent were assessed for both compounds. The results presented here indicate that an increase in the medium's dielectric constant or complexation of metal cations appear to modulate the interplay between hydrogen bonding and stacking interactions.