Rotaxanes are composed of a dumbbell shaped molecule threaded through a ring shaped macrocycle; see Figure1. Rotaxanes are used in molecular machines due to the thread’s ability to rotate (pirouette) within the macrocycle. This rotation is often coupled with a shuttling movement as well making them especially useful. Unfortunately, rotaxanes are extremely difficult to synthesize, making it a challenge to study them. By being able to study them using molecular dynamics, one can predict their conformational energies before having to create them. In a previous study, energy barrier values were found for three DAP based rotaxane pirouettes using NMR spectroscopy. Our study looked at two of the previous study’s DAP based rotaxanes (figures 2 and 3). We intend to show that molecular dynamics is a viable approach to calculating energy barriers of rotaxane pirouettes.
Bodzewski, Kentaro and Johnson, Andrew, "A Comprehensive Exploration of the Conformational and Energetic Landscape of a Rotaxane System: A Molecular Dynamics Study" (2016). Math & Science Department (SURI). 15.