This thesis outlines two projects that examine interactions between DNA and cyanine dyes: 1) Investigation of monomethine cyanine dye through the synthesis and optical characteristics with a goal to synthetically manipulate these systems to develop a fluorescent biological probe. Several asymmetric and one symmetrical monomethine cyanine dyes were synthetically prepared and their optical properties versus structural changes were explored. Representative dyes were selected for spectroscopically investigating DNA binding to enhance existing probe designs. 2) Early stage development of a non-metalated photosensitizer for photodynamic therapy (PDT) by screening experimentally derived cleavage activities of a number of polymethine cyanine dyes with various adjoining heterocycles. Structural characteristics of these dyes which promoted cleavage in the dark were identified and eliminated to allow for more selective photo-induced cleavage to enhance the candidacy of these compounds as photosensitizing agents. All compounds were purified through recrystallization or column chromatography and were characterized via 1H and 13C nuclear magnetic resonance (NMR). Compounds from the first chapter were further characterized using mass spectrometry.

Carbocyanine dyes are organic compounds containing chains of conjugated methine groups with electron-donating and electron-withdrawing substituents at the terminal heterocycles of the general formula [R1-(CH)n-R2]+X-. The synthetic methodology and optical properties of carbocyanines will be discussed. This thesis consists of two parts: (A) synthesis and optical properties of novel carbocyanine dyes substituted with various amines and the synthesis of unsymmetrical carbocyanine dyes containing monofunctional groups for bioconjugation. (B) synthesis of heptamethine carbocyanine dyes to be used for image-guided surgery. In part A, the synthesis of carbocyanine dyes functionalized with various amines and studies of their optical properties with respect to absorbance, fluorescence, quantum yield and extinction coefficient will be presented. These property studies will aid in designing efficient dyes for future biomedical applications. Part A will also include a one pot synthesis of unsymmetrical carbocyanine dyes functionalized with mono carboxylic acid chains, useful for biomolecule (i.e. proteins, amino acids, etc.) conjugation. Part B will describe the synthesis of novel carbocyanine dyes to be used for cancer image-guided surgery. Cancers are thus far incurable diseases, i.e. there are no drugs currently available to cure cancer; however, by designing a dye to visualize tumor cells will greatly increase the efficiency of cancer removal and hopefully increase the survival rate of cancer patients. The dyes reported in this thesis are superior to commercially available dyes used to visualize and identify various tumors invisible to the naked eye of surgeons with regards to biodistribution and clearance through kidney filtration.

Demonstration of ultrafast all-optical signal processing (AOSP) using silicon as the active material has been limited by large two-photon absorption loss and long lifetimes of the resulting free carriers. For AOSP at speeds in the terahertz, an order of magnitude faster than that the fastest current electronic counterpart, a class of π-conjugated organic molecules called polymethines provides a promising alternative to silicon as they possess large third-order nonlinearities, and ultrafast polarization response to an incident field. The challenge in the application of polymethines as active nonlinear optical materials for AOSP is in translating their promising molecular properties into bulk material properties. The large linear polarizability and charged nature of the polymethines molecules strongly promote aggregation and phase-separation in solid blends, offsetting their advantageous molecular optical properties. In this work, polymethines’ resistance to deleterious spontaneous symmetry breaking and aggregation was enhanced by substitutions of metal- and chalcogen- containing terminal groups, and rigid steric groups above and below the π-conjugated plane of polymethine chain. The resulting polymethines/amorphous polycarbonate (APC) blend films demonstrated an unprecedentedly high two-photon figure-of-merit, |Re(χ(3))/Im(χ(3))| and low linear loss. The optical quality of the polymethines/APC films was also improved by replacing the commonly-used alkyl ammonium counterions with more polarizable aryl phosphonium counterions with moderate ground state dipole moment. The resulting dye-polymer blend films showed an enhanced near-infrared transparency while its magnitude of the third-order susceptibility, |χ(3)|, showed a good agreement with that extrapolated from the molecular third-order polarizability, γ. For facile integration of these promising organic materials into SOH, the substrate surface was functionalized using silane coupling chemistry for the reduction of surface energy mismatch between the polymer films and the waveguide containing substrates. The optical and SEM micrographs showed vastly improved coverage and infiltration of the microfeatures. Furthermore, to enable the precise engineering of waveguide cross-sectional dimensions for single-mode propagation in the organic cladding, the dispersion curves of the polymethines/polymer blends were generated using prism coupling and ellipsometry. The combined efforts in the development of molecules and materials discussed in the thesis have culminated into a successful identification and optimization of the polymethines dyes and their polymer blends for imminent demonstrations of on-chip AOSP at terahertz speed.

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