Abstract: Small organic dyes are used in many applications, such as heat absorbers, solar cells, biological imaging, and photodynamic therapies for cancers. Xanthene-based dyes exhibit unique structural features and photophysical properties, and good water solubility, allowing them to be used as biological sensory materials. Conventional xanthene dyes (eg: fluorescein and rhodamine) have their absorptions and emissions in the visible region, which limits their use in cellular imaging. Absorptions and emissions at longer wavelengths allow for low background cellular autofluorescence, deep tissue penetration, and minimum cell damage. Chapter I discusses the background of fluorescent dyes and the importance of near-infrared (NIR) emissive dyes for biological applications. Chapter II is based on the design and synthesis of new xanthene-based NIR I dyes using simple and short synthetic routes. This study used pyrrole and indole as donor molecules and combined them to the xanthene core by the Suzuki cross-coupling reaction to prepare the new dyes. After the treatment with trifluoroacetic acid, these new dyes transformed from their non-fluorescent to fluorescent forms and exhibited excellent red shifts in their maximum absorption and emission wavelengths. The novel pyrrole-based xanthene dye was used to investigate the efficacy of the dye as a probe for fluoride ions. We were able to modify this dye with a silyl ester receptor and develop a probe as a colorimetric turn-off fluoride ion sensor. In chapter III, we describe the synthesis of different NIR emissive xanthene dyes using the donor-acceptor-donor concept. New xanthene-based dyes were designed with five-membered heterocycles and fused heteronuclear molecules. Additionally, xanthene-based dyes containing an alkyne spacer were synthesized using the D-pi-A model to extend the pi-conjugation through the alkyne spacer. All of the dyes exhibited absorption and emission maxima in the visible to NIR I region, between 500-850 nm. In chapter IV, we discussed the synthesis of xanthene-based electrochromic materials. These compounds used xanthene as the chromophore and ferrocene as the electrophore units. Novel rhodamine-based symmetric and unsymmetric dyes were synthesized by attaching the ferrocene unit through the lactam ring. The compounds were then investigated as an electrochromic probe using UV-vis , cyclic voltammetry, and spectroelectrochemical analysis.
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