There are currently three known crystal packing motifs of boronsubphthalocyanine derivatives. Each motif is associated with a particular class of BsubPc derivatives, and none are ideal for organic electronic applications according to the criteria we defined for evaluation: having a continuous pathway for charge-carrier conduction in the solid-state, resistance to hydrolysis, good electrochemical and optical properties, and possession of a robust crystal form. In this thesis, we present five methods for altering the crystal packing structure of phenoxy-BsubPc derivatives in order to meet the above four criteria. We find that neither addition of steric bulk to the axial derivative nor changing the symmetry of the compounds is sufficient for creating a new crystal packing motif. We do find that reducing the symmetry of the axial group does increase the solubility greatly, however. We identify a new motif for BsubPc crystals that occurs when the intermolecular interactions between the axial phenoxy segment and the BsubPc ligand are increased. We present two methods for achieving this new motif, one is through addition of a π-Br interaction and the other is through creation of a strong π-acid/ π-base stacking by making the axial phenoxy more π-electron rich. Unfortunately, the p-bromophenoxy-BsubPc forms this new motif as a kinetic product, isolation of which is unreliable. Attaching a naphthol fragment axially to the BsubPc creates a stable version of this new motif. We also synthesized a new class of BsubPc pseudohalides based on sulfonate derivatives. Of the derivatives in this new class, we found that mesylate-BsubPc forms into a crystal packing structure that possesses a one-dimensional pathway for charge carrier mobility, but is still resistant to hydrolysis under the conditions tested. Overall, we show four compounds that meet the criteria for further study as organic electronic materials: p-methoxyphenoxy-BsubPc, α-naphthoxy-BsubPc, β-naphthoxy-BsubPc, and mesylate-BsubPc.

There are currently three known crystal packing motifs of boronsubphthalocyanine derivatives. Each motif is associated with a particular class of BsubPc derivatives, and none are ideal for organic electronic applications according to the criteria we defined for evaluation: having a continuous pathway for charge-carrier conduction in the solid-state, resistance to hydrolysis, good electrochemical and optical properties, and possession of a robust crystal form. In this thesis, we present five methods for altering the crystal packing structure of phenoxy-BsubPc derivatives in order to meet the above four criteria. We find that neither addition of steric bulk to the axial derivative nor changing the symmetry of the compounds is sufficient for creating a new crystal packing motif. We do find that reducing the symmetry of the axial group does increase the solubility greatly, however. We identify a new motif for BsubPc crystals that occurs when the intermolecular interactions between the axial phenoxy segment and the BsubPc ligand are increased. We present two methods for achieving this new motif, one is through addition of a π-Br interaction and the other is through creation of a strong π-acid/ π-base stacking by making the axial phenoxy more π-electron rich. Unfortunately, the p-bromophenoxy-BsubPc forms this new motif as a kinetic product, isolation of which is unreliable. Attaching a naphthol fragment axially to the BsubPc creates a stable version of this new motif. We also synthesized a new class of BsubPc pseudohalides based on sulfonate derivatives. Of the derivatives in this new class, we found that mesylate-BsubPc forms into a crystal packing structure that possesses a one-dimensional pathway for charge carrier mobility, but is still resistant to hydrolysis under the conditions tested. Overall, we show four compounds that meet the criteria for further study as organic electronic materials: p-methoxyphenoxy-BsubPc, α-naphthoxy-BsubPc, β-naphthoxy-BsubPc, and mesylate-BsubPc.

Ray-finned fish from a diversity of distantly related lineages have remarkably large visual opsin repertoires. Starry flounder (Platichthys stellatus) development, morphology, life history, and behavior make this species especially suitable for experiments designed to determine why fish have so many opsins. Human and bird colour vision uses three and five opsins, respectively. Fish often have many more opsins. We sequenced an eye transcriptome to determine the starry flounder opsin repertoire, and used high performance liquid chromatography to determine the chromophore content of the retina. We found eight visual opsins that utilize only 11-cis-retinal (vitamin A1). This species’ entire visual opsin toolkit appears to be functional. The number of distinct cone and rod cell absorbance profiles determined using microspectrophotomery are consistent with the number of visual opsins in the transcriptome. RH2 transcripts were more abundant and SWS1 and SWS2 transcripts were less abundant in the dorsal retina, where cone density was highest, outer segments the longest, and where we observed double cones with outer segments that differed in their wavelength of maximum absorbance. Regions of fish retinas appear to be specialized and I predict that this fine-tuning is enhanced by photoreceptor plasticity and opsin gene duplication and divergence. Studies that compare opsin expression patterns among individuals, populations, or species typically assume that the differences observed influence vision. Direct connections between opsin expression and quantitative behaviours are rare. This thesis aimed to test whether varying opsin expression affects vision by modifying opsin expression and characterizing vision in starry flounder. We held starry flounder in aquaria exposed to either broad spectrum sunlight or green-filtered light. We tested vision by quantifying the visually-mediated camouflage response and we measured opsin expression using digital-PCR. Granularity analysis of photographs of the camouflage response revealed higher overall pattern energy at each of the seven spatial frequency bands in fish exposed to broad spectrum sunlight compared to the green-filtered fish. However, no statistical difference in typical measurements of pattern or contrast (e.g., maximum filter size, the standard deviation of pattern energy, and the proportional power) was observed between the two groups. Opsin expression was different between fish held in the green light environment compared to those exposed to broad spectrum light. SWS1 (UV sensitive) and SWS2B (blue sensitive) were significantly down regulated in response to the green light environment. Surprisingly, this difference was lost after only three hours under a white LED light, suggesting rapid changes in opsin expression in response to the light environment. We found tantalizing, albeit not statistically significant evidence that fish with higher expression of UV- and blue-wavelength sensitive opsins could see more contrast in colour on blue-green checkerboards. / Graduate

Coral reefs are in decline worldwide and coral disease is a significant contributing factor. However, etiologies of coral diseases are still not well understood. In contrast with the Caribbean, extremely little is known about coral diseases in the Philippines. In 2005, off Southeast Negros Island, Philippines, I investigated relationships between environmental parameters and prevalence of the two most common coral diseases, ulcerative white spot (UWS) and massive Porites growth anomalies (MPGAs). Samples were collected along a disease prevalence gradient 40.5 km long. Principal component analyses showed prevalence of MPGAs was positively correlated with water column nitrogen, organic carbon of surface sediments, and colony density. UWS was positively correlated with water column phosphorus. This is the first quantitative evidence linking anthropogenically-impacted water and sediment to a higher prevalence of these diseases. Histological and cytological alterations were investigated by comparing tissues from two distinct types of MPGA lesions (types 1 and 2) and healthy coral using light and electron microscopy. Skeletal abnormalities and sloughing, swelling, thinning, and loss of tissues in MPGAs resembled tissues exposed to bacterial or fungal toxins. Both lesion types had decreases in symbiotic zooxanthellae, which supply nutrients to corals. Notable alterations included migrations of chromophore cells (amoebocytes) (1) nocturnally to outer epithelia to perform wound-healing, including plugging gaps and secreting melanin in degraded tissues, and (2) diurnally to the interior of the tissue possibly to prevent shading zooxanthellae in order to maximize photosynthate production. Depletion of melanin (active in wound healing) in type 2 lesions suggested type 2 tissues were overtaxed and less stable. MPGAs contained an abundance of endolithic fungi and virus-like particles, which may result from higher nutrient levels and play roles in disease development. Swollen cells and mucus frequently blocked gastrovascular canals (GVCs) in MPGAs. Type 1 lesions appeared to compensate for impeded flow of wastes and nutrients through these canals with proliferation of new GVCs, which were responsible for the observed thickened tissues. In contrast, type 2 tissues were thin and more degraded. Dysplasia and putative neoplasia were also observed in MPGAs which may result from the tissue regeneration capacity being overwhelmed.

Chromophore is a molecule or a part of a molecule which is responsible for its appearance color. This definition has been evolving over time with the progress of science. Contemporary scientific advances have expanded its meaning: to an inclusive level, chromophore is an irreducible collective of fundamental particles, which can represent the photophysical (optical physical) properties of the macroscopic matter. Previous studies have already found that the same molecule can have different photophysical properties under different condensed states. Therefore, it is straight forward to conclude that the definition of chromophore should take such extrinsic influencing interactions of this given molecule into consideration, thus simply taking the smallest unit such as a molecule is not accurate. A good example is quantum dots. Same species of quantum dots possess the identical smallest chemical unit but can emit very differently due to quantum confinement effect, thus defining the smallest unit as the chromophore is apparently fallacious. In solid polymeric compositions, the chemical unit or building blocks may differ from the spectroscopic unit depending on how these chemical units interacts within their ensemble to evolve new properties such as a new transition dipole. As thus, understanding the evolution of photophysical behaviors between the targeted unit and neighbors is of much importance to determine whether they should be considered as one chromophore or many. This requires a thorough understanding towards the evolution of photophysical properties of a collective, and the construction of such collective will need to pay extra attention to, as any structural factor could have changed some photophysical interactions of the collective. The introductory chapter discusses the material platform and fundamental photophysics investigated in this dissertation. Chromophore assembly (CA) as a sylloge of several classes of self-assembled materials, including metal-organic frameworks (MOFs), covalent-organic frameworks (COFs), porous organic polymers (POPs). Among them, MOF-based CAs (MOF-CAs) featuring with the ease of synthesis, demonstrate incomparable promises to construct such collective with several appealing characteristics, including component diversity, chemical stability, structural porosity, and post-synthetic versatility (Chapter 1.1). As for here, the main target to achieve using these assemblies is to understand the interaction between adjacent chemical monomeric units, therefore their spatial arrangements are of the paramount importance. As modern theory discovered, both ordered and random systems can be very important for novel quantum material developments. Both crystalline and amorphous arrangements of monomeric units can be achieved by adopting different classes of materials. MOF-CAs could achieve the precise control of spatial arrangement including distance, direction, and dihedral angle by its crystalline structures, whereas porous organic polymer-based CAs (POP-CAs) could feature a total randomness. Photophysics, as the research topic targeting the firsthand knowledge gained by interrogating the information provided by the propagating light after its interaction with matters, could provide crucial knowledge of the targeted matter. Hence, photophysical properties could provide fundamental understanding of the targeted matter (Chapter 1.2). State-of-the-art spectroscopic methods and instrumentation have made it possible to critically examine new structures to correlate photophysics with the chemical structure of their assemblies. By combining multiple spectroscopic techniques along with theoretical study, several correlations between the electronic properties of the matter, such as structural features, have been investigated. To illustrate, some unique topology-dependent photophysical behaviors found in chromophore assemblies are introduced (Chapter 1.3). In this dissertation, the feasibility of using specific types of MOF-CAs to conduct unique photophysical studies has been carefully chosen and verified (Chapter 2). Next, with the help of first principles computations, the nature of several electronic excited states as a function of different extent of Van der Waals or electronic interaction in MOF-CAs is unveiled, and experimentally studied with several environmental variates (Chapter 3). The knowledge was then articulated to devise a strategy to improve resonance energy transfer process in MOF-CAs. Here, low electronic symmetry of linker and directionally aligned transition dipoles of their collective ensembled are found beneficial to improve such photophysical process in a bottom-up manner (Chapter 4). Then, a series of MOFs were rationally designed to examine the feasibility and extent of a nonlinear excitonic process, singlet fission, to promote the generation of carriers usable for many applications including light-harvesting applications. The outcome demonstrated MOF-CA is a powerful tool to design such materials and is more capable in terms of its tunability (Chapter 5). At last, a set of randomly oriented CAs in POP were examined for underlying excited state dynamic process that highlights a thermal activated delayed fluorescence (TADF) involving S1 and low-lying T2 excited states (Chapter 6). This dissertation has highlighted unique yet tunable excited-state features and photophysical processes within the well-defined molecular ensemble realized via porous frameworks. These photophysical properties differ from those of their respective molecular system in their solubilized forms. Studies in this dissertation demonstrates a reliable platform to investigate multibody chromophore systems and suggested several valuable discoveries and lights the way for the study of novel chromophore assembly systems.

No description available.

Ionically self-assembled monolayer (ISAM) films are typically an assemblage of oppositely charged polymers built layer by layer through Coulombic attraction utilizing an environmentally friendly process to form ordered structures that are uniform, molecularly smooth and physically robust. ISAM films have been shown to be capable of the noncentrosymmetric order requisite for a second-order nonlinear optical response with excellent temporal and thermal stability. However, such films fabricated with a nonlinear optical (NLO) polyanion result in significant cancellation of the chromophore orientations. This cancellation occurs by two mechanisms: competitive orientation due to the ionic bonding of the polymer chromophore with the subsequent polycation layer, and random orientation of the chromophores within the bulk of each polyanion layer. A reduction in film thickness accompanied by an increase in net polar ordering is one possible avenue to obtain the second-order susceptibility chi(2) necessary for practical application in electro-optic devices. In this thesis, we discuss the structural characteristics of ISAM films and explore a novel approach to obtain the desired characteristics for nonlinear optical response. This approach involves a hybrid covalent / ionic self-assembly technique which affords improved net dipole alignment and concentration of monomer chromophores in the film. This technique yields a substantial increase in chi(2) due to the preferential chromophore orientation being locked in place by a covalent bond to the preceding polycation layer. The films fabricated in this manner yield a chi(2) that substantially exceeds that of any known polymer-polymer ISAM film. This covalent-hybrid ionically self-assembled multilayer (CHISAM) technique is demonstrated to result in films suitable for electro-optic devices, with measured electro-optic coefficient (14 pm/V) comparable to that of the inorganic crystal lithium niobate (30 pm/V). Thermal and temporal stability are important properties of electro-optic device implementation, and are demonstrated for CHISAM films. CHISAM films have remained stable at room temperature for more than 420 days, and suffered no loss of chi(2) when held at 80 C for 36 hours, followed by 150 C for 24 hours. Studies are also presented that demonstrate the ability to produce ISAM chi(2) films that are nearly one micron thick, and exhibit no evidence of a thickness limitation to the polar order. Analytical considerations for second-order NLO characterization of thick films are addressed in detail. The effect of absorption of the second harmonic wavelength and resonant enhancement of chi(2) are investigated, and it is demonstrated that accurate determination of chi(2) may be made for thick films and for films that absorb the second harmonic. The temporal and thermal stability of a variety of ISAM and CHISAM NLO films are examined in detail. In some cases, a decrease in the NLO response is observed at elevated temperature that is completely restored upon cooling. Studies are presented that suggest this effect is a result of thermally induced trans-to-cis isomerization of azo linkages in the NLO chromophores. / Ph. D.

Layer-by-layer deposition techniques were used to fabricate films with second order nonlinear optical (NLO) properties. These materials are key to the development of electro-optic modulators used in fiber optic communication systems. Performance benefits and lower manufacturing costs are driving the development of organic NLO materials as replacements for inorganic crystalline materials such as lithium niobate. The layer-by-layer deposition technique in which polyelectrolytes are deposited on a surface by electrostatic effects is called the Ionically Self-Assembled Monolayer or ISAM method. The role of the optically inactive polycation's structure on deposition and chromophore orientation was studied by fabricating films with several different polycations. While the specific interactions responsible for chromophore orientation in ISAM films remains unclear, hydrogen bonding and electrostatic effects are ruled out as the sole sources of orientation. The highest values of χ(2) were observed under pH conditions that resulted in flat and thin layers. The relationship between pH and the optical homogeneity of the film was also explored. Deposition of polymers under pH conditions in which the polymer chains were aggregated in solution results in films that are not suitable for use in devices. In this work, a new layer-by-layer deposition technique was developed. Coined hybrid deposition, it relies on covalent bonds and electrostatic interactions for film fabrication. Optically inactive polyamines were used as sources of positive charges and as binding sites with optically active low molecular weight chromophores functionalized with a reactive triazine ring and negative charged sulfonate groups. Polar ordering of the chromophores was obtained when the deposition was done under conditions in which covalent bonding was the preferred attachment mechanism for the chromophore molecules. pH conditions in which electrostatic attachment dominated resulted in poorer orientation. The effect of adding ionic salts to the dye solutions was studied, with hopes of increasing the chromophore density in the film by shielding inter-dye electrostatic repulsions. A linear relationship in deposited amount, as characterized by absorbance/bilayer, was observed as the salt concentration was increased. Little effect on χ;(2) was observed for films made with the as-received Procion Red MX-5B chromophore. However, films fabricated from purified Procion Brown MX-GRN showed a definite dependence on added salt. Exceptional χ(2) values were obtained for Procion Brown films deposited using 0.5 M NaCl and PAH. The importance of depositing from non-aggregated solutions was again highlighted, as films made with the less soluble Procion Orange were significantly less homogeneous than those made from Procion Red and Procion Brown which were highly soluble. The role of polycation structure on the deposition and orientation of Procion Brown and Red was examined. / Ph. D.

Ionically self-assembled monolayer (ISAM) films are typically an assemblage of oppositely charged polymers built layer by layer through coulombic attraction utilizing an environmentally friendly process to form ordered structures that are uniform, molecularly smooth, and physically robust. ISAM films have been shown to be capable of the noncentrosymmetric order requisite for a second-order nonlinear optical response. However, films fabricated with a nonlinear optical (NLO) polymer result in significant cancellation of the chromophore orientations. This cancellation occurs by two mechanisms: competitive orientation due to the ionic bonding of the polymer chromophore with the subsequent polycation layer, and random orientation of the chromophores within the bulk of each polyanion layer. A reduction in film thickness accompanied by an increase in net polar ordering is one possible avenue to obtain the second-order nonlinear optical susceptibility chi(2) necessary for electro-optic devices. In this thesis, we will discuss the structural characteristics of ISAM films and explore three novel approaches to obtain the desired characteristics for nonlinear optical response. One approach involves the variation of solution parameters of several different cationic polymers separately from the polyanion solution in order to reduce the competitive chromophore orientation at the layer interfaces and to reduce the thickness of the inactive polycation layer. We have found that the complexity of ISAM films does not allow large chi(2) values in polyion-based films, and that the selection of the polymer cation is vital to achieve second harmonic generation (SHG) at all. The second approach involves the incorporation of dianionic molecules into ISAM films in order to eliminate both competitive chromophore orientation and random chromophore orientation inherent with polymer chromophores. We have also studied the effects of complexing dianionic chromophores with beta-cyclodextrin in order to increase solubility and improve chromophore orientation. This approach fails because the outermost monolayer of dianionic chromophore is only tethered to the preceding polycation layer by a single ionic bond for each molecule, so each chromophore can by dissociated during the following immersion into the cation solution. Finally, we have introduced a novel approach of hybrid covalent / ionic self-assembly which overcomes these disadvantages and yields a substantial increase in chi(2) due to the chromophore being locked in place to the preceding polycation layer by a covalent bond. The films fabricated in this manner yield a chi(2) that rival any polymer-polymer films despite the very low first-order molecular hyperpolarizability beta of the incorporated monomer. This suggests that incorporation of high beta molecules may result in significant improvement of chi(2), holding high promise for the hybrid covalent / ionic self-assembly technique. / Master of Science

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