Supramolecular Chemistry of Amide Containing Molecules

Amide-based synthetic molecules have been prepared and examined in four separate research projects which investigate conformational isomerization, anion binding, phospholipid translocation and rotaxane formation. It was found that N-(pyrimidin-2-yl)pentafluorobenzamide adopts a cis conformation in the solid state with a nitrogen of the pyrimidine ring pointing toward the center of the perfluorinated ring. In solution the compound is a mixture of cis and trans isomers. The conformational equilibrium is strongly solvent dependent, and the cis conformation is entropically favored. A disulfide macrocyclic compound possessing an isophthalamide moiety, which is a known hydrogen bond donor, was shown to bind chloride, acetate and dihydrogen phosphate anions with binding constants of 30, 137, and 151 M-1 respectively. The binding ability of the isophthalamide moiety was also used to construct rotaxane architectures around fumaramide and squaraine bearing thread molecules. The investigation into squaraine-based rotaxanes shows significant enhancement in chemical stability of the parent squaraine dye molecule with only minimal changes in quantum yield of fluorescence. These results represent a new method of protecting squaraine dyes from harsh chemical environments. Bolaamphiphilic fumaramide-based rotaxanes and amide-based bolaamphiphilic thread molecules that are long enough to span a phospholipid bilayer membrane were shown to induce the translocation of phospholipid probes across vesicle membranes. The mechanism of translocase activity is theorized to be a 'slip-pop' mechanism involving local perturbations of the membrane headgroup region.