This thesis describes studies of rotaxanes which are interlocked molecules with a dumbbell shaped thread component surrounded by a macrocycle. The macrocycle pirouetting motion in xanthone rotaxanes was studied using variable temperature NMR. The surrounding tetralactam macrocycle contained either 2,6-pyridine dicarboxamide or isophthalamide bridging units. Rotaxanes with macrocycle containing 2,6-pyridine dicarboxamide bridges exhibited higher rotational barriers due to a cavity contraction effect which disfavors macrocycle breathing. Chapter two discusses the influence of metal cation binding to a squaraine rotaxane endoperoxide with a 2,2'dipicolylamine stopper group. Metal cations bind strongly and decrease the rate of singlet oxygen release due to cycloreversion by about a factor of two. Binding of Feå_⁺ induced Fenton-type reaction with endoperoxide, causing the macrocycle cleavage and desctruction of the rotaxane molecule. Chapter three describes experiments that help elucidate the mechanisms for the chemiluminescence, and highlight the key role of singlet oxygen as a mediator of energy transfer to the encapsulated squaraine dye.