Molecular dynamics simulations study of [5]rotaxane in bulk and at interfaces

Abstract

Rotaxanes are a class mechanically interlocked molecular architectures that exhibit quasi-mechanical movement in response to specific stimuli. [5]Rotaxane is a complex rotaxane structure that is reported to show extraordinary cyctotoxic properties with light stimuli. By using all-atom classical molecular dynamics simulations, we study equilibrium and kinetics properties of various charge states of [5]Rotaxane in salt-free water as well as [5]Rotaxane network derivatives at the interface of water and chloroform. By analyzing molecular configurations, hydrogen bonding and size, energy based metrics of individual molecules both in bulk and water-chloroform interfaces, we demonstrate that charge-state of [5]Rotaxane directly influences the molecular conformation and solvation properties. While charge-neutral and negatively charges molecules often tend to collapse in a way that they expose their porphyrin core, positively charged moieties tend to take more extended molecular configuration screening the core. Further, sudden changes in the charge states emulating the pH alterations in solution conditions leads to gradual, 1000-ps level, changes in molecular conformation of [5]Rotaxane via shuttling motion of CB6 rings along [5]Rotaxane axles. Finally, simulations with 2D networks of [5]Rotaxane confirm the possibility of molecular film formation at hydrophobic-hydrophilic interfaces. Overall, our results suggest that [5]Rotaxane can exhibit a rich spectrum of molecular configurations and assembly properties depending on the ionic strengths of the solution or external stimuli.