Nucleobase Recognition by Artificial Receptors Possessing a Ferrocene Skeleton as a Novel Modular Unit for Hydrogen Bonding and Stacking Interactions

Abstract

Novel ferrocene-modified artificial nucleobase receptors were designed and synthesized. The nucleobase receptors possess hydrogen-bonding and pi-stacking interaction sites that act simultaneously for binding to 1-butylthymine utilizing the pivot character of the ferrocene skeleton. Diamidopyridine was chosen for the hydrogen-bonding moiety, and various polynuclear aromatics were used for pi-stacking one. The two components were tethered to the cyclopentadienyl rings via ethynediyl and oxymethylene spacers. The binding affinity of the receptors to 1-butylthymine was found to be dependent on the aromatic structures. Thus, the association constants for perylene-linked receptors were approximately doubled compared to those of aromatic-free ones, an energy difference of approximately 0.5 kcal/mol. Detailed comparisons between the 10 receptors clarified the value of the pivot character of the ferrocene for construction of the intermolecular interaction site.