Studying the intrinsic properties of molecules in the gas-phase is advantageous, since it reduces the complexity present in solution that arises from interactions between the molecule of interest and other species present in the local environment, including those with the solvent itself. In this report, the photophysical properties of gaseous cationic rhodamine B (RBH+) were determined and photodissociation reaction kinetics and power dependence of three prototropic forms of fluorescein; the cation ([F + H]+), monoanion ([F - H]-), and dianion ([F – 2H]-2), each of which possesses their own distinct spectral properties, were measured. The analyte ions of interest were formed via electrospray ionization, mass-selected and stored in a quadrupole ion trap mass spectrometer which has been customized to enable gas-phase spectroscopic studies. Knowledge of the intrinsic photophysical properties of such chromophores in the gas-phase will enable a better understanding of how the local environment of the molecule alters its properties.

Background: We report here early attempts of adapting a prototype fluorescence imaging system (PRODIGI™) to be used as a surgical guidance tool to improve margin-detection in breast cancer. Methods: 36 patients were recruited to study the autofluorescence characteristics of ex vivo specimens. 5-ALA (20 mg/kg) was used as a contrast agent in human breast cancer cell lines and xenograft tumour models to detect PpIX fluorescence. Results: Administrative approvals were obtained and a surgical drape was used for sterilization. PRODIGITM could differentiate between normal and tumour tissues based on autofluorescence alone in ex vivo samples. PpIX signal was detected in experimental mice, and absent in control mice. The threshold of detection was on the order of 10 nM. Conclusions: Autofluorescence alone with PRODIGI™ was not sufficient for margin assessment of ex vivo breast tumour surgical specimens. 5-ALA at an optimal dosage may be adopted as a contrast agent to enhance tumour signal.

The research presented in this thesis introduces design criteria for development of a new type of self-contained optical biosensor. The study begins with evaluation of a dual label, fluorescence resonance energy transfer (FRET) bioassay format, and then goes on to demonstrate a signalling platform that uses an immobilized fluorescent intercalating dye so as to avoid labelling of both the target and probe strands. An extensive survey of FRET pairs that can be used to monitor hybridization events in solution and at solid interfaces was conducted in solution to provide a set of calculated Förster distances for the extrinsic labels Cyanine 3 (Cy3), Cyanine 5 (Cy5), Carboxytetramethylrhodamine (TAMRA), Iowa Black Fluorescence Quencher (IabFQ) and Iowa Black RQ (IabRQ). FRET parameters using thiazole orange (TO) intercalating dye as a FRET donor for various acceptor dye-labelled DNA conjugates in solution were determined. Limitations associated with quenching mechanisms other than those mediated by FRET motivated the development of a molecular switch that contained intercalating dye. The four binding sites associated with Neutravidin served for assembly of the switch using biotin interactions. One binding site was used to immobilize an unlabelled oligonucleotide probe. The adjacent site was used to immobilize a novel biotinylated TO derivative that could physically reach the probe. On hybridization of the probe with target, the intercalating dye was captured by the hybrid, leading to a change of fluorescence. This reversible signalling mechanism offers a method without nucleic acid labelling to detect nucleic acid association at an interface. A SNP discrimination strategy involving TO and formamide was investigated, and SNP discrimination without the requirement of thermal denaturation was achieved for multiple target lengths, including a 141-base pair PCR amplicon in solution. It was determined that formamide could also provide improvements of signal-to-noise when using thiazole orange to detect hybridization.

While unprotected amino aldehydes are typically not isolable due to imine formation and consequent polymerization, stable unprotected aziridine aldehydes are useful and available reagents. Moreover, reversible hemiacetal and hemiaminal formation enable these compounds to reveal both their electrophilic and nucleophilic functional groups. This exceptional arrangement allows for aziridine aldehyde dimers to participate in and disrupt the mechanisms of an array of well-known organic reactions, including isocyanide-based multicomponent reactions. The scope and selectivity patterns of aziridine aldehyde induced amino acid or peptide macrocyclization have been investigated. A small library of constrained tri-, tetra-, and penta-peptide macrocycles – representing the most difficult cyclic peptides to synthesize – has been prepared. The scope of aziridine aldehyde participation in multicomponent reactions was also expanded to Ugi and Passerini reactions that do not employ tethered amine and acid functional groups. In order to facilitate cellular imaging of peptide macrocycles a fluorescent isocyanide reagent was prepared and applied to prepare mitochondrial targeting macrocycles. Thioester isocyanide reagents were synthesized to enable rapid assembly of cycle-tail peptides through ligation technology.

Studying the intrinsic properties of molecules in the gas-phase is advantageous, since it reduces the complexity present in solution that arises from interactions between the molecule of interest and other species present in the local environment, including those with the solvent itself. In this report, the photophysical properties of gaseous cationic rhodamine B (RBH+) were determined and photodissociation reaction kinetics and power dependence of three prototropic forms of fluorescein; the cation ([F + H]+), monoanion ([F - H]-), and dianion ([F – 2H]-2), each of which possesses their own distinct spectral properties, were measured. The analyte ions of interest were formed via electrospray ionization, mass-selected and stored in a quadrupole ion trap mass spectrometer which has been customized to enable gas-phase spectroscopic studies. Knowledge of the intrinsic photophysical properties of such chromophores in the gas-phase will enable a better understanding of how the local environment of the molecule alters its properties.

Background: We report here early attempts of adapting a prototype fluorescence imaging system (PRODIGI™) to be used as a surgical guidance tool to improve margin-detection in breast cancer. Methods: 36 patients were recruited to study the autofluorescence characteristics of ex vivo specimens. 5-ALA (20 mg/kg) was used as a contrast agent in human breast cancer cell lines and xenograft tumour models to detect PpIX fluorescence. Results: Administrative approvals were obtained and a surgical drape was used for sterilization. PRODIGITM could differentiate between normal and tumour tissues based on autofluorescence alone in ex vivo samples. PpIX signal was detected in experimental mice, and absent in control mice. The threshold of detection was on the order of 10 nM. Conclusions: Autofluorescence alone with PRODIGI™ was not sufficient for margin assessment of ex vivo breast tumour surgical specimens. 5-ALA at an optimal dosage may be adopted as a contrast agent to enhance tumour signal.

Color plays a vitally important role in the world we live in. It surrounds us everywhere we go. Achromatic life, restricted to black, white and grey, is extremely dull. Color fascinates artists, for it adds enormously to aesthetic appreciation, directly invoking thoughts, emotions and feelings. Color fascinates scientists. For decades, scientists in color imaging, printing and digital photography have striven to satisfy increasing demands for accuracy in color reproduc- tion. Fluorescence is a very common phenomenon observed in many objects such as gems and corals, writing paper, clothes, and even laundry detergent. Traditional color imaging algo- rithms exclude fluorescence by assuming that all objects have only an ordinary reflective com- ponent. The first part of the thesis shows that the color appearance of an object with both reflective and fluorescent components can be represented as a linear combination of the two components. A linear model allows us to separate the two components using independent component analysis (ICA). We can then apply different algorithms to each component, and combine the results to form images with more accurate color. Displaying color images accurately is as important as reproducing color images accurately. The second part of the thesis presents a new, practical model for displaying color images on self-luminous displays such as LCD monitors. It shows that the model accounts for human visual system’s mixed adaptation condition and produces results comparable to many existing algorithms.

Variable fluorescence of chlorophyll a (Fv/Fm), measured by pulse amplitude modulated (PAM) fluorometers, is an attractive target for phytoplankton-related water quality management. Lowered Fv/Fm is believed to reflect the magnitude of nutrient sufficiency or deficiency in phytoplankton. This rapid and specific metric is relevant to Lake Erie, which often experiences problematic Cyanobacteria blooms. It is unknown whether PAMs reliably measure phytoplankton nutrient status or if different PAMs provide comparable results. Water samples collected from Lake Erie and two Lake Ontario sites in July and September 2011 were analysed using alkaline phosphatase assay (APA), P-debt, and N-debt to quantify phytoplankton nutrient status and with three different PAM models (PhytoPAM, WaterPAM and DivingPAM) to determine Fv/Fm. The Lake Ontario, Lake Erie East and Central Basin sites were all N- and P-deficient in July, but only the East and Central Basin and one Lake Ontario site were P-deficient in September. The West Basin sites were P-deficient in July and one West Basin site and a river site were N-deficient in September. Between-instrument Fv/Fm comparisons did not show the expected 1:1 relationship. Fv/Fm from the PhytoPAM and WaterPAM were well-correlated with each other but not with nutrient deficiency. DivingPAM Fv/Fm did not correlate with the other PAM models, but correlated with P-deficiency. Spectral PAM fluorometers (PhytoPAM) can potentially resolve Fv/Fm down to phytoplankton group by additionally measuring accessory pigment fluorescence. The nutrient-induced fluorescent transient (NIFT) is the observation that Fv/Fm drops immediately and recovers when the limiting nutrient is reintroduced to nutrient-starved phytoplankton. A controlled laboratory experiment was conducted on a 2x2 factorial mixture design of P-deficient and P-sufficient Asterionella formosa and Microcystis aeruginosa cultures. Patterns consistent with published reports of NIFT were observed for P-deficient M. aeruginosa in mixtures; the pattern for A. formosa was less clear. This thesis showed that Fv/Fm by itself was not a reliable metric of N or P deficiency and care must be taken when interpreting results obtained by different PAM fluorometers. NIFT analysis using spectral PAM fluorometers may be able to discriminate P-deficiency in M. aeruginosa, and possibly other Cyanobacteria, in mixed communities.

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This thesis aims to provide a detailed understanding of side-chain functionalized polymers as emissive materials for OLEDs. The syntheses and photophysical properties of these solution-processable materials as well as the effects of metal types, polymer backbones, chain lengths, spacer types and lengths, host types, and concentrations of the metal complexes on the emission properties and device performance will be dicussed. The polymers were functionalized with host materials along with the metal complexes to enhance the charge transport and to obtain energy transfer from the host to the complex. The physical and photophysical properties of the polymers were tuned by changing the backbone and the metal complex. Poly(norbornene)s, poly(cyclooctene)s, and poly(styrene)s were studied. The differences in the glass transition temperatures and PDIs of the polymers indicated that device performances might be affected by the polymer type due to the differences in the processability of the polymers. In addition to the backbone, it was found that device performance is dependent on various parameters such as molecular weight, metal loading, spacer type, and spacer length. In each case, it was found that the polymer backbone does not interfere with the basic photopysical properties of the metal complexes. The two main classes of metal complexes studied in this thesis are metalloquinolates and iridium complexes. It was shown that the emission properties of poly(cyclooctene)s containing 8-hydroxyquinolines in their side-chains could be altered by simply changing the metal. Green- and near IR-emitting polymers were synthesized by employing aluminum and ytterbium, respectively. On the other hand, for the iridium complexes, changes in color were achieved by varying the ligands. Iridium containing polymers with emission spectra that span the entire visible spectrum were synthesized by employing the appropriate ligands. It was demonstrated that OLEDs with high efficiencies can be fabricated by using these polymers as the emissive layer.