CUP Undergraduate Research


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

Date of Award


Document Type

Restricted Access Thesis


College of Theology, Arts, & Sciences


Math & Science

Degree Name

Chemistry, BA

First Advisor

Andrew T. Johnson


Squaraine rotaxanes are fluorescent molecules comprised of two parts—a dumbbell-shaped squaraine dye threaded through a ring-shaped macrocycle—that are held together non-covalently by hydrogen bonding, hydrophobic effects, and the size of the opening in the macrocycle (Arunkumar, et al., 2005, p. 3288). Since the squaraine is an extremely electrophilic species, nucleophilic attack by solvent is possible when it slips out of the macrocycle (Ros-Lis, et al., 2004, p. 4064, White, et al., 2010, p. 1297, Fu, et al., 2008, p. 118, 120). This results in a loss of fluorescence. These near-IR dyes have many applications, including effective labeling of bacterial and cancer cells (White, et al., 2010, p. 1297, Smith, et al., 2010, p. 67). Previous studies have shown that the unprotected squaraine dye is unstable, and a series of macrocycles were synthesized to test their protective qualities. The adamantyl rotaxane proved to be unstable and started to degrade within a couple hours. However, the isophthalamidyl and pyridinyl rotaxanes remained stable, seemingly indefinitely (Collins, et al., 2014, p. 3). In this study, we use molecular dynamics (MD) to compare the relative stabilities of squaraine rotaxanes in solution, and elucidate the structural basis for the instability of the adamantyl rotaxane system in solution. In addition, scans of the potential energy surface at the B3LYP/6-311+G** level of theory shed light on the dynamics of the amide-squaraine hydrogen bond which stabilizes these complexes. See Figure 1, below, for a diagram of each rotaxane studied.

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