Real-time observation of the dynamics of an individual rotaxane molecular shuttle using a single-molecule junction

Measurements on single molecules can sometimes reveal features that can be difficult to detect using techniques that probe the averaged properties of many molecules. Here, we report on the use of graphene-molecule-graphene single-molecule junctions (GMG-SMJs) to probe the shuttling dynamics of an individual [2]rotaxane molecule. The experiments show variations in the thermodynamic and kinetic shuttling parameters over a temperature range, and in different solvents, allowing the single-molecule data to be quantitatively related to simulation and ensemble experiments. The structural (∼1 nm) and temporal (∼17 μs) resolution of the GMG-SMJ enables direct observation of a previously unidentified weak-binding intermediate, arising from the formation of weak hydrogen bonds between the ring and triazole units. The results illustrate how GMG-SMJ measurements provide new opportunities for elucidating aspects of the structure, dynamics, and operational mechanisms of synthetic molecular machines that may be hidden to techniques that probe averaged behavior of an ensemble.