Dynamics of Molecular Machines

Rotaxanes are an example of a molecular machine designed to mimic machines at a molecular level. In this thesis, I will discuss the dynamics of rotaxanes, focusing on the influence of components on these motions. A deep understanding of how components govern the motions of molecular machines can aid in their design process.

This need to understand the basic motions of our rotaxanes had us apply an advanced array of NMR experiments. Historically used for biological molecular machines, we used these experiments to study artificial molecular machines. These experiments highlighted differences in a switchable rotaxane which led to our macrocyclic breathing model for the free pirouetting form of [3]rotaxane 1. This model was found through our relaxation dispersion studies, where we detected chemical exchange at critical points on the macrocyclic wheel.

We continued these studies with another form of [3]rotaxane with a different axle structure which provided the impact of the axle component on the wheel components. We see the effect of the change in the axle structure on the cyclodextrin through our relaxation studies. We did not detect the exchange process that led to our macrocyclic breathing model for the alternate rotaxane, [3]rotaxane 8, indicating a change of dynamics due to the axle.

We ran molecular dynamics simulations in association with the NMR experiment work to provide further information on the relationships between components. A shuttling motion was detected where interactions between the cyclodextrins are possibly mediated by inter hydrogen bonding.

The impact of the axle on the cyclodextrin and the dynamics between the cyclodextrin show the importance of these studies on future molecular machines. The properties detected in our macrocyclic breathing model of rotaxane may be specific to a particular rotaxane, as this thesis showed the importance of individual components on function. Future work will provide the basic motions that govern all rotaxanes.