This project aims to use computational chemistry to better understand the interactions in mechanically interlocked molecules (MIMs), which are comprised of multiple physically entangled components held together by mechanical bonds, like how each pair of links in a chain are joined together in space. Such molecules have a large degree of conformational freedom and movement intrinsic to their structure, in addition to non-covalent interactions holding the supramolecules together. Rotaxanes are a type of MIM which we study in our group, consisting of a thread encircled by a macrocycle (which cannot be removed from the thread without breakage of a bond). The thread is typically quite long and flexible, so it can take on many different conformations due to different twisting and rotating modes of freedom. Additionally, the macrocyclic ring can interact with different functional group “stations” situated along the thread, characterised by non-covalent interactions through space, and giving rise to many more conformations of the same molecule. Understandably, such complex systems are ambitious to simulate computationally, and will require a lot of computing power. By use of initial semi-empirical calculations followed by density functional theory calculations, this project will lead to a better understanding of the MIMs, including their conformational freedom, the non-covalent interactions holding them together, and the reaction mechanisms that form these interesting compounds. Furthermore, we will investigate MIMs that will be able to interact in complex environments, including multiple solvents, acid/bases environment, materials chemistry (i.e. polymers) and biological environments (i.e. protein docking). The MIMs that we investigate will be experimentally prepared in the lab alongside our computational work, so that we can verify our experimental findings with theoretical data and use the computations to increase our understanding of the molecules we synthesise.