This thesis presents the design and synthesis of compounds that can be utilized as bioimaging agents to detect various targets. A squaraine rotaxane core was selected because of its ability to be detected using infrared microscopy. Squaraine rotaxanes have been developed previously, but here I present work toward creating a squaraine rotaxane core that can easily be functionalized using "click" chemistry, which has been shown to form products quickly and in high yields. The first section deals with the design and synthesis of squaraine rotaxanes that were functionalized with a glucose derivative so that it might be used to target tumor cells. In the final section, the squaraine rotaxane was derivatized with various compounds to show its ability to react in various "click" reactions. One example used azide-functionalized polyamidoamine (PAMAM) derivatives.