Molecular boxes derived from crown ethers and nucleotide bases: Probes for Hoogsteen vs Watson-Crick H-bonding and other base-base interactions in self-assembly processes

Article abstract of DOI:10.1021/ja00093a005

Bibracchial lariat ethers based upon 4,13-diaza-18-crown-6 having -(CH₂)₃- sidearms terminated in adenine or thymine have been prepared and characterized. The three structures are as follows: adenine-(CH₂)₃-〈N18N〉- (CH₂)₃-adenine (A-O-A), thymine-(CH₂)₃-〈N18N〉-(CH₂) ₃-thymine (T-O-T), and adenine-(CH₂)₃-〈N18N〉- (CH₂)₃-thymine (A-O-T). Association of the nucleotide bases was expected to afford molecular boxes or other aggregates that would be stabilized by interactions between or among the nucleotide bases. These compounds have been studied in solution by ¹H-NMR spectroscopy and by vapor pressure osmometry to determine the extent of association as well as what interactions occur between the bases. The ¹H-NMR solution studies involved both temperature and concentration dependence and NOE studies. Several lines of evidence make clear that association does occur in CDCl₃ with an association constant for A-O-A with T-O-T of 855 M^-1. Both intra- and intermolecular H-bonding interactions are detected. Hoogsteen binding modes appear to play a very important role in these flexible systems. The A-O- A·T-O-T box may also comprise a ditopic receptor system in which the sides of the box are Ade::Thy pairs and the ends are crown ethers. We have studied such systems in the presence of decanediyldiammonium and dodecanediyldiammonium salts and report evidence for a ternary induced-fit receptor complex.