The Use of Molecular Dynamics to Predict the Stability of Squaraine Rotaxanes

Squaraine rotaxanes are fluorescent molecules comprised of two parts—a dumbbell-shaped squaraine dye threaded through a ring-shaped macrocycle—that are held together by hydrogen bonding, hydrophobic effects, and the size of the opening in the macrocycle1. Since the squaraine is an extremely electrophilic species3, nucleophilic attack by water is possible when it slips out of the macrocycle. This results in a loss of fluorescence. These near-IR dyes have many applications, including effective labeling of bacterial cells4. Previous studies have shown that the unprotected squaraine dye is unstable, and the adamantyl rotaxane degrades over time while the isophthalamidyl and pyridinyl rotaxanes remain stable2(Fig. 2). In this study, we aim to determine if molecular dynamics (MD) is an effective method of ascertaining the relative stabilities of squaraine rotaxanes in solution