[2]Rotaxanes are molecular compounds that contain a macrocycle surrounding a dumbbell-shaped thread. This thesis focuses on squaraine rotaxanes that contain a tetralactam macrocycle encapsulating a fluorescent squaraine dye. These rotaxanes exhibit excellent chemical stability, high photochemical stability, and favorable photophysical properties. In fact, squaraine rotaxanes are now commercially available for use in imaging applications.;This thesis begins with the synthesis of a novel, organic soluble, anthracene-containing tetralactam macrocycle that serves as a common rotaxane building block. The anthracene containing macrocycle can undergo chemical reactions with various dienophiles and can associate non-covalently with various guests including squaraine dyes. A synthetic capping methodology converts these complexes into squaraine rotaxanes in high yields.;In addition to synthesis, a major part of this thesis describes the response of these squaraine rotaxanes to various chemical environments. A cycloaddition reaction with singlet oxygen produces an endoperoxide that can undergo a cycloreverison. The rate of the cycloreversion and oxygen release can be altered through rationale design. In fact, steric strain in the [2]rotaxane scaffold provides a rate acceleration of ∼3,000-fold. Not only does the cycloreversion process release singlet oxygen, it also emits near-infrared light. This novel form of chemiluminescence can be utilized for deep tissue in vivo molecular imaging. Various structural and environmental factors are examined for their effect on the emission wavelength and emission intensity, and the work builds a mechanistic picture of the chemiluminescence process.;This thesis also describes the effect of metal cations on the cycloreversion rates of squaraine rotaxane endoperoxides that have been designed with metal binding pockets. The presence of some metal cations can alter rates by small amounts, whereas the presence of Fe(II) leads to Fenton chemistry and macrocycle cleavage. Lastly, the photophysical response of squaraine rotaxanes to acid is discussed. Large changes in the emission spectrum intensity are observed in rotaxanes that are easily protonated on the surrounding macrocycle.;The results in this thesis suggest that squaraine rotaxanes and their corresponding endoperoxides have potential utility in a wide-array of scientific areas; from molecular machines to molecular imaging probes.
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