Molecular Dynamics Simulations Of Shuttling Of Daisy Chain And Rotaxane

As a new type of supramolecular, mechanically interlocked molecules（MIMs） have the properties of shuttling movement. These molecular configurations can be altered according to an external stimulus, which make it have great application value for molecular machine, molecular switches and drug delivery and so on. However, a few problems need to be solved for the protonatedly and deprotonatedly driven MIMs.These problems include switching structure—effects of structural changes on the molecular motion of the ring; swtiching rate—effects of temperature on the shuttling speed, and shuttling barrier—the energy required to shuttle or the thermodynamic stable point.This research investigates the shuttling behavior of daisy chain and rotaxanes by classical molecular dynamics simulations. The rotaxane is composed of a dibenzo[24]crown-8 ether（DB24C8） macrocycle and main chain. The main chain has two recognition sites or “stations”—a secondary ammonium（NH₂⁺）/amine（NH） unit and a 4,4’-bipyridinium（bipy2+）unit. The daisy chain consists of pseudorotaxanes which have alkyl ether site and- NH₂⁺- sites. Each molecule has four configurations: stable rotaxane 5A and 6A, unstable rotaxane 5B and 6B, stable daisy chain 1A and 2A, unstable daisy chain 1B and 2B. The shuttling configuration, swtiching rate and shuttling barrier are studied by the molecular dynamics simulation（MD） in vacuum at 298 K, 338 K, 378 K. From the result of the molecular dynamics simulation, the change of the distance between ring and the station of the MIMs and the change of energy of the MIMs in the process of switching are obtained. the PMF curve of PMF are also obtained by constraint MD.The result shows that the ring in the stable molecule does not switch during the shuttling process. The distance between ring and the site or the structural energy of the molecule has been at a fixed value with a slight fluctuatuation. The configurational energy increases with the increase of temperature. The planes of conjugate groups are mutually parallel due to Ï€-Ï€ electron interaction. The ring in the unstable rotaxane 5B can not switch because of main chain bending. The ring in the unstable rotaxane 6B moves to the N+ in the 4,4’-bipyridinium unit.Free energy barriers and themodynamic stable site can be obtained from the PMF curve. The secondary ammonium or the N atom in the 4,4-bipyridinium are the thermodynamic stable points under different conditions. The shuttling barrier is 40 kcal/mol in 5B while it is 10.79 kcal/mol in 6B. Rotaxane 5B switches only in 338 K. For the unstable the daisy chain 1B, the ring moves from alkyl ether site to- NH₂⁺- site at each temperature. Shuttling speed V changes with the temperature: V_{378 K}>V_{298 K}>V_{338 K}. The molecular constraction and stretch extension percent W also changes with temperature: W_{298 K}>W_{338 K}=W_{378 K}. The unstable daisy chain 2B can not switch because the small energy difference between two points.