Abstract
Squaraine dyes are a unique class of near-infrared fluorophores that have fascinated researchers because of their interesting donor-acceptor structure and their electron deficient aromatic core. While these moieties make them interesting to study, they produce an inherent weakness: the electron deficient core is readily attacked by nucleophiles. This deficiency should preclude them from use as in vivo fluorescent probes, an area where they could be very effective. This topic was addressed in 2005 by a publication from our group which placed the squaraine dye inside a phenylene tetralactam macrocyclic receptor in a low yielding five component assembly process. While steric protection of the dye enabled it to survive for prolonged periods of time in serum and solutions of cysteine, the synthetic clipping process resulted in a loss of 70% of the starting dye. To overcome this limitation, a second generation anthracene based tetralactam macrocyle was designed which posessed greater solubility, allowing a ``two component slipping process' to be the key synthetic step. In this disertaiton, data is presented which shows the remarkable supramolecular complementarity of this dye-macrocycle system, which allows for self assembly in highly cometitive environemnts, including the interior of a living cell. Also presented are synthetic methods for functionalizing the rotaxane with different ``stopper group' in quantitive coupling reactions. The macrocycle shows interesting supramolecular directing effects, producing Diels-Alder products at the 1,4 carbons with N-ethylmaleimide. As a rotaxanated structure, the dyes encapsulated by the anthracene macrocycle show interesting strain mediated reactivity with singlet molecular oxygen and an interesting fluorescent molecular shuttle that uses an aniline derived tetralactam macrocycle which responds to chloride is presented.
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