Title

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

Author

Ruth Nelson, Concordia University - Portland
Jeffrey Baumes, University of Notre Dame
Richard D. Connell, University of Notre Dame
Ivan Murgu, University of Notre Dame
Allen Oliver, University of Notre Dame
Bradley Smith, University of Notre Dame
Andrew Johnson, Concordia University - PortlandFollow

Date of Award

1-1-2013

Document Type

Poster

College

College of Arts & Sciences

Department

Math & Science

Abstract

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.

Recommended Citation

Nelson, R., Baumes, J., Connell, R. D., Murgu, I., Oliver, A., Smith, B., & Johnson, A. (2013). The Use of Molecular Dynamics to Predict the Stability of Squaraine Rotaxanes (Thesis, Concordia University, St. Paul). Retrieved from https://digitalcommons.csp.edu/cup_commons_undergrad/222