Marine biofouling is the accumulation of marine species on surfaces submerged in seawater leading to unwanted problems for man-made surfaces such as hulls of ships and aquaculture nets. Historically, the amount of biofouling was regulated using metal based coatings whose usage have been disused lately due to adverse toxic effects. Alternative environmentally friendly coatings are currently avidly being pursued. Nanopatterned polymer thin films were investigated as potential candidates for marine antifouling coatings. Polystyrene-block-poly(2-vinyl pyridine) and polystyrene-block-poly(methyl methacrylate) diblock copolymer thin films self-assembled using vapor solvent annealing into cylinders perpendicular to the substrate composed of poly(2-vinyl pyridine) or poly(methyl methacrylate) respectively with diameters between 30 nm to 82 nm and center-to-center spacing between 46 nm to 113 nm in a polystyrene matrix on various substrates such as silicon or nylon. Polystyrene-block-poly(2-vinyl pyridine) copolymers were also mixed with the photoinitiator benzophenone and irradiated with ultraviolet light to crosslink the polymer chains and decrease the surface hydrophobicity. In the case of polystyrene-block-poly(methyl methacrylate), the yield of these nanopatterned films increased with the modification of the vapor annealing method. A low temperature vapor annealing technique was developed in which the annealing occurs at 2 °C. In another strategy, polystyrene and poly(2-vinyl pyridine) homopolymers were nanopatterned with alternating lines and grooves with widths between 200 nm and 900 nm and depths between 15 nm to 100 nm using Thermal Nanoimprint Lithography. Poly(2-vinyl pyridine) films were synthesized as brushes using surface initiated Atom Transfer Radical Polymerization to produce robust polymer films. The chemical and/or the topographical heterogeneity of the polymer surfaces influenced the settlement of Ulva linza algae zoospores. Overall, the incorporation of nanoscale features enhanced the antifouling properties of the samples. Further exploration of these types of coatings is highly encouraged.

Marine biofouling is the accumulation of marine species on surfaces submerged in seawater leading to unwanted problems for man-made surfaces such as hulls of ships and aquaculture nets. Historically, the amount of biofouling was regulated using metal based coatings whose usage have been disused lately due to adverse toxic effects. Alternative environmentally friendly coatings are currently avidly being pursued. Nanopatterned polymer thin films were investigated as potential candidates for marine antifouling coatings. Polystyrene-block-poly(2-vinyl pyridine) and polystyrene-block-poly(methyl methacrylate) diblock copolymer thin films self-assembled using vapor solvent annealing into cylinders perpendicular to the substrate composed of poly(2-vinyl pyridine) or poly(methyl methacrylate) respectively with diameters between 30 nm to 82 nm and center-to-center spacing between 46 nm to 113 nm in a polystyrene matrix on various substrates such as silicon or nylon. Polystyrene-block-poly(2-vinyl pyridine) copolymers were also mixed with the photoinitiator benzophenone and irradiated with ultraviolet light to crosslink the polymer chains and decrease the surface hydrophobicity. In the case of polystyrene-block-poly(methyl methacrylate), the yield of these nanopatterned films increased with the modification of the vapor annealing method. A low temperature vapor annealing technique was developed in which the annealing occurs at 2 °C. In another strategy, polystyrene and poly(2-vinyl pyridine) homopolymers were nanopatterned with alternating lines and grooves with widths between 200 nm and 900 nm and depths between 15 nm to 100 nm using Thermal Nanoimprint Lithography. Poly(2-vinyl pyridine) films were synthesized as brushes using surface initiated Atom Transfer Radical Polymerization to produce robust polymer films. The chemical and/or the topographical heterogeneity of the polymer surfaces influenced the settlement of Ulva linza algae zoospores. Overall, the incorporation of nanoscale features enhanced the antifouling properties of the samples. Further exploration of these types of coatings is highly encouraged.

Perfluorinated carboxylates (PFCAs) are persistent and ubiquitous in the environment. Humans are exposed to PFCAs through direct and indirect sources, although the relative importance of each is uncertain. Direct sources of PFCAs have been attributed to two primary fluorochemical manufacturing processes: electrochemical fluorination (ECF) and telomerization. A focus of this thesis was to elucidate an additional direct source of PFCAs resulting from the direct fluorination of polyolefin materials. High density polyethylene bottles with varying levels of fluorination were observed to contain significant amounts of PFCAs, particularly those with carbon chain-lengths ≤ C6, marking an unexplored source of PFCA exposure. PFCAs are also produced indirectly from the biotransformation of fluorotelomer-based compounds, such as polyfluoroalkyl phosphate esters (PAPs) and fluorotelomer alcohols (FTOHs). During this transformation process, two predominant classes of metabolic intermediates are formed: the fluorotelomer unsaturated aldehydes (FTUALs) and the fluorotelomer unsaturated carboxylic acids (FTUCAs). Another focus of this thesis was to examine the reactivity of FTUALs and FTUCAs with endogenous nucleophiles such as glutathione (GSH), select amino acids, and model proteins. FTUALs formed adducts with all nucleophiles examined, where those having shorter carbon chain lengths (i.e. 6:2 and 8:2 FTUAL) were more reactive than longer carbon chains (i.e. 10:2 FTUAL). By contrast, FTUCAs had comparably limited reactivity; although FTUCAs showed mild reactivity with GSH, they did not react with any other nucleophiles. In vitro and in vivo experiments were carried out to determine the extent of protein binding formed from the biotransformation of fluorotelomer-based compounds, including the 8:2 FTOH and the 6:2 PAP diester. A significant portion of these biotransformations yielded covalent protein binding at nmol/mg protein concentrations. Protein adducts were observed predominantly in rat liver and also in plasma and kidney. The formation of reactive intermediates may be toxicologically important through protein deactivation. Cellular toxicity of FTUALs was significantly higher compared to PFCAs and the acid metabolic intermediates (i.e. FTUCAs). The EC50 values calculated from dose-response incubations were dependant on chain length and functional group. The work in this thesis examined an unexplored consequence of indirect exposure to PFCAs, potentially impacting the relative importance of PFCA exposure sources.

Perfluorinated carboxylates (PFCAs) are persistent and ubiquitous in the environment. Humans are exposed to PFCAs through direct and indirect sources, although the relative importance of each is uncertain. Direct sources of PFCAs have been attributed to two primary fluorochemical manufacturing processes: electrochemical fluorination (ECF) and telomerization. A focus of this thesis was to elucidate an additional direct source of PFCAs resulting from the direct fluorination of polyolefin materials. High density polyethylene bottles with varying levels of fluorination were observed to contain significant amounts of PFCAs, particularly those with carbon chain-lengths ≤ C6, marking an unexplored source of PFCA exposure. PFCAs are also produced indirectly from the biotransformation of fluorotelomer-based compounds, such as polyfluoroalkyl phosphate esters (PAPs) and fluorotelomer alcohols (FTOHs). During this transformation process, two predominant classes of metabolic intermediates are formed: the fluorotelomer unsaturated aldehydes (FTUALs) and the fluorotelomer unsaturated carboxylic acids (FTUCAs). Another focus of this thesis was to examine the reactivity of FTUALs and FTUCAs with endogenous nucleophiles such as glutathione (GSH), select amino acids, and model proteins. FTUALs formed adducts with all nucleophiles examined, where those having shorter carbon chain lengths (i.e. 6:2 and 8:2 FTUAL) were more reactive than longer carbon chains (i.e. 10:2 FTUAL). By contrast, FTUCAs had comparably limited reactivity; although FTUCAs showed mild reactivity with GSH, they did not react with any other nucleophiles. In vitro and in vivo experiments were carried out to determine the extent of protein binding formed from the biotransformation of fluorotelomer-based compounds, including the 8:2 FTOH and the 6:2 PAP diester. A significant portion of these biotransformations yielded covalent protein binding at nmol/mg protein concentrations. Protein adducts were observed predominantly in rat liver and also in plasma and kidney. The formation of reactive intermediates may be toxicologically important through protein deactivation. Cellular toxicity of FTUALs was significantly higher compared to PFCAs and the acid metabolic intermediates (i.e. FTUCAs). The EC50 values calculated from dose-response incubations were dependant on chain length and functional group. The work in this thesis examined an unexplored consequence of indirect exposure to PFCAs, potentially impacting the relative importance of PFCA exposure sources.

Introduction: Currently, there are no objective techniques to assess burn depth. An early assessment of burn depth would enable accurate management decisions, which would improve patient outcomes. Near infrared (NIR) technology has shown promise as a non-invasive monitor of oxygenation and perfusion, and its potential to assess the depth of burn injuries has been investigated clinically over the past five years. The purpose of the thesis was to determine the capacity of NIR technology to differentiate acute thermal injuries. Methods: Burn sites (n=5) and control sites (n=5) were created on the dorsum of sixteen animals with brass rods held at constant pressure and heated to 100°C and 37.5°C respectively. NIR data was collected from the burns and control sites pre-burn, immediately post-burn, and 1, 12, 24, 36, 48 and 96 hours after the burn injury. Biopsies of the burn and control sites were acquired at each time point and used to confirm the depth of injury. NIR data was processed for the content of water, oxy-, deoxy- and methemoglobin. Results: Oxyhemoglobin and total hemoglobin decreased as burn depth increased. The proportion of oxy- and deoxyhemoglobin to total hemoglobin showed that the ratio of oxy- to deoxyhemoglobin decreased as burn injury increased. Methemoglobin levels as a ratio of total hemoglobin also showed that as the severity of injury increased the proportion of methemoglobin also increased. Finally, superficial partial thickness injuries (3 s and 12 s) showed early peak levels of water, which rapidly declined towards baseline. The deep partial thickness injuries (20 s and 30 s) do not experience peak levels and retain water over the course of the experiment. The full thickness injuries water levels remain close or below baseline levels throughout the experiment. Conclusion: NIR spectroscopy could distinguish burn depth using water, oxy-, met- and total hemoglobin as separate entities. The presence of methemoglobin in the burn wounds is a novel finding that has not been described previously in burn literature.

Master of Science / Department of Grain Science and Industry / Praveen V. Vadlani / Large quantities of byproducts are generated during the biomass processing, which leads to under-utilization of resources and concomitant waste disposal problem. Typically, these byproducts still contain considerable amounts of high-value compounds that have important industrial applications. However, in current time, most of these byproducts are used for low-value applications, including as boiler fuel. These byproducts are potential sources for many valuable chemicals such as antioxidants, flavors, colorants, preservatives, and biocides. Therefore, the reuse and recycle of these biomass residues is very important for the bioeconomy. By some additional and necessary processing steps, we can transfer those biomass residues from a low-value level to a higher value status and apply the final products to various fields such as food industry, and pharmaceutical industry, etc. Till date, limited research has been reported in the production of important specialty chemicals from biomass residues. This thesis is focused on the solvent extraction and isolation of valuable chemicals from bioprocessing byproducts. While choosing different solvents and techniques, “environmental friendly” green solvents were also evaluated. Also some new techniques, such as thin-layer chromatography plates making and laboratory-made lignin are developed to make the research more economically feasible. Even though conventional extraction method such as solid-liquid extraction was evaluated, we tried to minimize the solvent/biomass ratio and also augmented additional processes to the conventional process to obtain higher yield of compounds of interest (COI). In this research, different biomass resources were evaluated for valuable specialty chemicals. These resources include: lignocellulosic biomass and raw biomass. Lignocellulosic biomass is a sustainable feedstock for the production of biofuels and chemicals. The potential chemicals from the resources were extracted using various organic solvents and analyzed by gas chromatography-mass spectrometry (GC-MS). The results indicated that the selected biomass residues contain relatively higher amounts of three valuable compounds: vanillin, apocynin, and phytol. Different types of organic solvents and extraction techniques were tested to optimize the extraction process. Ultra-sonication was considered as an efficient extraction method and ethanol was chosen as the final solvent. Commercially viable isolation methods such as thin-layer chromatography (TLC) and column chromatography were also studied in this research. A solvent system of hexane, dichloromethane, ethyl acetate, and chloroform with 1:1:1:0.1 v/v ratio gave us a good separation of the COI. Biomass-derived lignin was made in the laboratory to compare with commercially available lignin. The results show that the laboratory-made lignin contains similar bioactive compounds and gives us a good quantity of target compounds. In conclusion, instead of letting the byproducts being discarded or used as low-value applications or become a threat to the environment, the decision to select them as raw materials to produce valuable specialty targeted compounds for industries has been demonstrated in our research. The future research will focus on optimization and scale-up study of the extraction process. In addition, the application and production of bioactive compounds will be further evaluated.

Doctor of Philosophy / Department of Chemistry / Duy H. Hua / The first chapter of this dissertation introduces and discusses the syntheses of a series of substituted quinolines as glycogen synthase kinase-3[beta] (GSK-3[beta]) inhibitors. GSK-3[beta] is highly associated with Alzheimer’s disease (AD), and it is suggested that inhibition of this enzyme could alleviate the symptoms of AD. Total 16 novel substituted quinolines were designed and synthesized, and their bio-activities were evaluated on MC65 cell protection assay. Four of the most active compounds were selected to test their enzyme inhibitory activities on GSK-3[beta] and protein kinase C assays. Among these compounds, 4-{[6-methoxy-4-methyl-5-(3-(trifluoromethyl)phenoxy)quinolin-8-ylamino]methyl} phenol (1.5) shows the highest MC65 cell protection and GSK-3[beta] enzyme inhibitory activities and potential enzyme specificity. Structure-activity relationship (SAR) was built as well, and the binding mode was simulated via computational method to interpret the observed SAR. Although additional bio-evaluation is needed, compound 1.5 is a promising lead compound for the development of more active and less toxic drug for the conteraction of AD. The second chapter introduces the progress on the total synthesis of myriceric acid A. Myriceric acid A is a triterpene-type natural product which was isolated from the young twigs of Myrica cerifera. It is a non-peptide endotheline-1 (ET-1) receptor antagonist. The total synthesis of this natural product started from the stereoselective synthesis of bicyclic intermediate (R)-5,8a-dimethyl-3,4,8,8a-tetrahydronaphthalene-1,6(2H,7H)-dione [(-)-2.28]. Then a new method was developed to enatioselectively synthesize the tricyclic intermediate (4aR,8R,8aR)-8-(tertbutyldimethylsilyloxy)-1,4a,8a-trimethyl-4,4a,4b,5,6,7,8,8a,9,10-decahydro phenanthren-2(3H)-one [(+)-2.72] which used the synthesized optically-pure (4aR,5R)-5-(tertbutyldimethylsilyloxy)-1,4a-dimethyl-4,4a,5,6,7,8-hexahydronaphthalen-2(3H)-one [(-)-2.53] derived from (-)-2.28 and [alpha]-trimethylsilylvinyl ethyl ketone via a cascade reductive Michael addition – aldol condensation reaction. After functional group inter-conversion, the desired tricyclic intermediate (4a'S,8a'R)-1',1',4a',8a'-tetramethyldecahydro-1'H-spiro[[1,3]dioxolane-2,2'-phenanthren]-8'(3'H)-one [(-)-2.33] was synthesized. An intramolecular cascade Michael addition-aldol condensation reaction was designed to construct the triterpene-skeleton of myriceric acid A, and the desired starting material for this reaction was prepared with the trimethyl{(4a'R,8a'R)-1',1',4a',8a'-tetramethyl-3',4',4a',4b',5',6',8a',9',10',10a'-decahydro-1'Hspiro[(1,3)dioxolane-2,2'-phenanthrene]-8'-yloxy}silane [(-)-2.81] and 3,3-dimethyl-7-oxooctanal (2.46) via Mukaiyama aldol condensation reaction. The resulting pentacyclic compound was further transformed to the desired ester (6a'R,8a'R,12a'S,12b'R,14b'R)-ethyl 4',4',6a',11',11',14b'-hexamethyl-8'-oxo-2',4',4a',5',6',6a',8',8a',9',10',11',12',12a',12b',13',14',14a',14b'-octadecahydro-1'H-spiro[(1,3) dioxolane - 2, 3 '- picene]-8a'-carboxylate (-)-2.106. The further investigation on total synthesis of myriceric acid A will be pursued in future.

Doctor of Philosophy / Department of Chemistry / Stefan Bossmann / My thesis is divided into two parts. The first part is focused on studies of N-heterocyclic carbene (NHC) palladium(IV) intermediates, which are involved in oxidative addition mediated C-C, and C-O bond formation processes as well as in C-Cl bond forming reactions via a reductive elimination process. Bis-NHC-Pd(II) complexes have been reported as effective catalysts to mediate direct conversion of methane into methanol. However, a H-D exchange study revealed that the bis-NHC-Pd(II) complexes are not the active species responsible for the C-H bond activation reaction. This unexpected result implies that the high oxidation state bis- NHC-Pd(IV) species may be the real catalyst! The oxidative addition of methyl iodide to the bis- NHC-Pd(II)-Me2 complex led to the successful observation of the formation of a transient trimethyl bis-NHC-Pd(IV) intermediate by both 1H-NMR and 13C-NMR spectroscopy. Different oxidants such as O2, PhI(OAc)2, PhI(OTFA)2 and Cl2 reacted with the bis-NHC-Pd(II)-Me2 complex, and competitive C-C and C-O bond formations, as well as C-C and C-Cl bond formations were observed. Dioxygen triggered C-C bond formation under dry condition and both C-C and C-O bond formation in the presence of H2O gave strong indications that the bis-NHCPd( II)-Me2 complex can be oxidized to a bis-NHC-Pd(IV) intermediate by dioxygen. The reaction between the hypervalent iodine regents PhI(OAc)2 and PhI(OTFA)2 and the bis-NHCPd( II)-Me2 complex gave only reductive elimination products. Therefore, this system can act as a model system, which is able to providing valuable information of the product forming (functionalization) step of the C-H bond activation system. The reaction between chlorine and the bis-NHC-Pd(II)-Me2 complex resulted in a relatively stable bis-NHC-Pd(IV)-Cl4 complex, which was characterized by 1H-NMR spectroscopy and mass spectroscopy. The structure of bis- NHC-Pd(IV)-Cl4 was unambiguously established by X-ray crystallography. The second part of this thesis describes the synthesis of functionalized bimagnetic core/shell iron/iron oxide nanoparticles for the treatment of cancer. Biocompatible dopamineoligoethylene glycol functionalized bimagnetic core/shell Fe/Fe3O4 nanoparticles were prepared via ligand exchange, and purified by repeated dispersion/magneto-precipitation cycles. A porphyrin (TCPP) has been tethered to the stealth nanoparticles to enhance their uptake by tumor cells and (neural) stem cells. The stealth nanoparticles have been delivered in a mouse model to tumor sites intravenously by using the EPR (enhanced permeation and retention) effect. Magnetic hyperthermia proved to be very effective against B16-F10 mouse melanomas in Charles River black mice. After hyperthermia, the nanoparticles have shown a significant effect on the growth of tumor (up to 78% growth inhibition).

Master of Science / Department of Chemistry / Jun Li / This study is focused on exploring the mechanisms of DNA dynamics at carbon electrode surfaces under a strong electric field for the development of novel DNA hybridization sensors. Oligonucleotides with FAM6 attached at the distal end are covalently tethered on the carbon electrode surface. The fluorescence emission from the FAM6 is strongly quenched in close proximity to the electrode surface. The modulation to the fluorescence intensity is correlated with the reversible reorientation of the negatively charged DNA molecules under the electric field within the electric double layer. The orientation dynamics are apparently determined by the interplay of the electropotential, salt concentration, and stiffness of the DNA molecules. We have observed that dsDNAs switch with fast dynamics (in < 0.05 second) followed by relaxation at a slower rate (in > 0.1 second) when the electric field is altered by stepping the electropotential to a more positive or negative value. The DNA reorientation exhibits strong dependence on the PBS buffer concentration and electric double layer thickness. A preliminary calculation based on dipole-surface energy transfer theory indicates that the critical distance between FAM6 and glassy carbon surface is 10.95 nm. In connection with the fluorescence study, the effect of DNA hybridization on electrochemical impedance spectroscopy (EIS) has also been investigated by two methods in an attempt to develop a fast electronic detection method. First, EIS at high AC amplitude (141 mV rms) with DNA-modified glassy carbon electrodes before and after target DNA hybridization have shown notable change at high frequencies, likely related to the DNA reorientation processes. Second, reversible EIS detection of DNA hybridization has been demonstrated with patterned regular carbon nanofiber arrays at normal AC amplitude (10 mV rms). The combination of these two methods will be explored in future studies. The effects of the electric field on surface-tethered molecular beacons (MBs) have also been studied with fluorescence spectroscopy. An increase in fluorescence at negative bias is observed accompanying the opening of the MB stem, which leads to larger separation between fluorophore and quencher. At positive bias, the rehybridization of the MB stem leads to a decrease in fluorescence intensity.

Master of Science / Department of Chemistry / Daniel A. Higgins / Single molecule tracking (SMT) measurements have been applied to the study of molecular mobility in sol-gel-derived silica gradient films in this thesis. Such gradient films have broad potential applications in controlled adhesion and transport of cells, vesicles and polymers; separation of complex chemical mixtures and in the development of new catalysts. Silica films were prepared by “infusion-withdrawal dip-coating”. In this method, a suitable substrate is slowly withdrawn from a silica sol of time varying composition. The deposition reservoir is initially filled with a sol derived from one silica precursor (tetramethoxysilane). A second sol, prepared from a different precursor (methyltrimethoxysilane), is then infused into the deposition reservoir, as the mixed sol is withdrawn. Films thus prepared were initially characterized by bulk fluorescence spectroscopy, infrared (IR) microscopy, contact angle goniometry, spectroscopic ellipsometry and surface profilometry. The fluorescence, IR and contact angle data all demonstrate the presence of a gradient in the methyl content of the silica film. The primary objective of the work performed under this thesis was to investigate the diffusion of Nile Red molecules in and on these films, as a function of position along the gradient, by SMT methods. Histograms of the mean-square displacement of the molecules depict the presence of at least two distinct populations: one incorporating fixed (entrapped or adsorbed) molecules and the other clearly reflecting the presence of mobile molecules. The latter population was observed to vary along the gradient dimension and also changed as the films aged over the course of five days. Molecular mobility is attributed to the presence of liquid-like silica oligomers in the films. Spatial variations in the observed mobility are tentatively assigned to variations in oligomer viscosity along the gradient. Film viscosity also changes as the polymerization of the oligomers continues during film aging.