Squaraine dyes have been the subject of intensive studies due their unusual electronic properties that make them good candidates for a wide range of applications in various technological fields. They are particularly promising in nonlinear optics, bioimaging for labeling and sensing of biomolecules, as sensitizers for solar energy harvesting in solar cells and organic photovoltaics, two-photon absorbing materials, near-infrared (NIR) emitting fluorescent probes, second harmonic generation organic dyes, and sensitizers for photodynamic therapy among others. In this dissertation, the aggregation behaviors and features of several squaraine dye derivatives in solid state thin films were studied and reported. In the first chapter of the dissertation, three squaraine dye derivatives with two and four hydroxy groups and with different N-alkyl amino donor substituents were synthesized and used as models to study aggregation behavior. Their UV-vis absorption, thermal properties, and photoluminescence properties were determined. The models with four hydroxy substituents exhibited higher thermal stability and melt at higher temperature compared to the dye with only two hydroxy substituents due to increased hydrogen bonding. The UV-vis absorption and photoluminescence properties in liquid solution at room temperature were found to be similar. In the second chapter, the squaraine dyes, 2,4-bis [4-(N,N-di-n-pentylamino)-2-hydroxyphenyl] squaraine [SQC5(OH)2], 2,4-bis [4-(N,N-di-n-pentylamino)-2,4-hydroxyphenyl] squaraine [SQC5(OH)4 n], and 2,4-bis [4-(N,N-di-isopentylamino)-2,4-hydroxyphenyl] squaraine [SQC5(OH)4 b], where "n" and "b" stand for normal or linear and branched alkyl groups, respectively, were investigated to study their aggregation in solid state thin film form using UV-vis absorption spectroscopy. The investigation revealed significant differences in aggregation behaviors and features. The dye SQC5(OH)2 mainly exhibited J-type aggregation with an intense absorption band in the NIR region. In contrast, the SQC5(OH)4 n and SQC5(OH)4 b compounds mainly exhibited H-type aggregation, characterized by less intense and blue shifted absorption bands. The third chapter presents the kinetic study conducted on the squaraine dye derivative 2,4-bis [4-(N,N-di-n-pentylamino)-2-hydroxyphenyl] squaraine [SQC5(OH)2] in solid state spin-coated thin films. The study revealed the formation of J-aggregates with bands at 767 nm at room temperature. This aggregate was temperature dependent. It was transformed into H-aggregates as the temperature increased. The activation energy of the decay (transformation) process was found to be 91.2 kJ. The values of ΔH and ΔS are 88.4 kJ/mol and 48.2 J/K.mol, respectively, indicating the J-aggregate of SQC5(OH)2 was a kinetic product while the H-aggregate was thermondynamically more stable.

This dissertation contains the synthesis and characterization of squaraine based new functional materials. In the first part of this thesis work, a water soluble benzothiazolium squaraine dye was synthesized with pyridium pendents, and controlled aggregation properties were achieved. After formation of partially reversible J-aggregation on a polyelectrolyte (poly(acryl acid) sodium salt) template, the nonlinear, two-photon absorption cross section per repeat unit was found to be above 30-fold enhanced compared with nonaggregate and/or low aggregates. Using a similar strategy, sulfonate anions were introduced into the squaraine structure, and the resulting compounds exhibited good water solubilities. A ‘turn on’ fluorescence was discovered when these squaraine dyes interacted with bovine serum albumin (BSA), titration studies by BSA site selective reagents show these squaraine dyes can bind to both site I and II of BSA, with a preference of site II. Introduction of these squaraine dyes to BSA nanoparticles generated near-IR protein nano fabricates, and cell images were collected. Metal sensing properties were also studied using the sulfonates containing a benzoindolium squaraine dye, and the linear response of the absorption of the squaraine dye to the concentration of Hg2+ makes it a good heavy metal-selective sensing material that can be carried out in aqueous solution. Later, a squaraine scaffold was attached to deoxyribonucleosides by Sonogashira coupling reactions, in which the reaction conditions were modified. Iodo-deoxyuridine and bromo-deoxyadenosine were used as the deoxyribonucleosides building blocks, and the resulting squaraine dye-modified deoxyribonucleosides exhibited near-IR absorption and emission properties due to the squaraine chromophore. Interestingly, these non-natural deoxyribonucleosdies showed viscosity dependent photophysical properties, which make them nice candidates for fluorescence viscosity sensors at the cellular level. After incubation with cells, these iv viscosity sensors were readily uptaken by cell, and images were obtained showing regions of high viscosity in cells.

A new Laser Induced Fluorescence Capillary Zone Electrophoresis (LIF-CZE) bioassay to detect and study the catalytic activity of the sulfur assimilating enzyme commonly found in E. coli species; alkanesulfonate monooxygenase (EC 1.14.14.5) is described for the first time. This technique enables the possibility for direct injection onto a capillary for detection without the need for pre-concentration of sample and with minimal sample preparative steps prior to analysis. In this bioassay, a group of Fischer based cyanine dyes and two Oxazine (Nile red) derivatives were designed for further optimization as key Vis-NIR fluorescent substrate. In developing this technique, the test dyes were first assessed for their photophysical properties, based on four criteria; (1) photostable (2) solvatochromism (3) binding affinity towards both the monooxygenase active site and serum albumin and (4) chemical stability in strong electric field strength. Applying key dye characterization procedures including; molar absorptivity determination, quantum yield determination, photostability, solvatochromism and protein interaction studies it was determined that the Fischer indolium cyanine dyes were most suitable for the method development. The data revealed that under the test conditions, reduced flavin, the oxidative monooxygenase catalytically specifically converts the alkylsulfonate substituted cyanine dyes to the corresponding aldehyde. This new bioassay has proven to be quick, portable, sensitive, reliable and the exhibit the possibility of ‘on-the-spot’ detection; advantages not readily realized with other commonly applied techniques such as PCR, SPR, ELISA and GC used to study bacterial sulfur assimilation processes. In addition, recent literature results proposed by other research groups developing similar techniques showed strong reliance on GC analyses. Those assays involve the use of low molecular weight straight chain non-emissive alkanesulfonate substrates. Once enzyme catalysis occurs the aldehyde is formed becomes rather volatile and requires complex and tedious headspace sampling for GC analyses. This feature limits the in vitro applicability and eliminated the possibility in vivo development. Our goal is to further develop, optimize and present this CZE based bioassay as a suitable alternative to the current trends in the field while creating a more robust and sensitive in vitro monooxygenase detection method with the possibilities of in vivo application.