Host-rotaxanes as binding agents: the effects of wheel dynamics


Institution: University of Cincinnati
Department: Arts and Sciences : Chemistry
Degree: PhD
Year: 2008
Keywords: Chemistry; rotaxane
Record ID: 1820559
Full text PDF: http://rave.ohiolink.edu/etdc/view?acc_num=ucin1214400642


Many protein-binding domains have a Hot Spot of 3-5 amino acids and an O-Ring of 20-30 amino acids. The O-ring surrounds the hot spot. To simplify the investigation of protein binding domains, synthetic mimics of proteins are created and investigated. Our host-rotaxanes split a binding domain into two components. A rotaxane contains a linear molecule (axle) threaded through a circular molecule (DB24C8 ring) with bulky molecules (blocking groups) on the ends of the axle to keep the wheel from dethreading. A calixarene, cyclophane or cleft was used as one of the blocking groups to provide a binding pocket, mimicking the hot spot. A ditert-butyl aromatic ring acted as the other blocking group. Functional groups were attached to the DB24C8 ring for guest recognition. The axle contains a positively charged amine group that can interact with the partial negatively charged oxygen atoms on the wheel. This unique arrangement not only provides the opportunity of investigating the relationship between the hot spot and O-ring, but it also simplifies the process of studying the dynamic motion in molecular recognition. To more fully explore the dynamics in molecular recognition, two new cleft-rotaxanes were constructed with very long axles. One axle is a polyether chain, and the other is a polyalkyl chain. The differences in the dynamical motion of these cleft-rotaxanes result in different binding strengths of complexes.