Master of Science / Department of Chemistry / Takashi Ito / Adsorption of a series of primarily substituted hydrocarbons (RX; C[subscript]18H[subscript]37PO(OH)[subscript]2 (ODPA), C[subscript]17H[subscript]35COOH, C[subscript]18H[subscript]37OH, C[subscript]18H[subscript]37NH[subscript]2 and C[subscript]18H[subscript]37SH) onto solid gallium substrates with and without UV/ozone treatment was studied using contact angle goniometry, spectroscopic ellipsometry and cyclic voltammetry (CV). UV/ozone treatment offered a hydrophilic surface (water contact angle ([theta][superscript]water) less than 10°), reflecting the formation of a surface oxide layer with the maximum thickness of ca. 1 nm and possibly the removal of surface contaminants. Upon immersion in a toluene solution of a RX, [theta][superscript]water increased due to adsorption of the RX onto gallium substrates. In particular, UV/ozone-treated gallium substrates (UV-Ga) immersed in an ODPA solution exhibited [theta][superscript]water close to 105°. The ellipsometric thickness of the adsorbed ODPA layer was ca. 2.4 nm and CV data measured in an acetonitrile solution showed significant inhibition of redox reaction on the substrate surface. These results indicate the formation of a densely-packed ODPA monolayer on UV-Ga. The coverage of a C[subscript]17H[subscript]35COOH layer adsorbed onto UV-Ga was lower, as shown by smaller [theta][superscript]water (ca. 99°), smaller ellipsometric thickness (ca. 1.3 nm) and smaller electrode reaction inhibition. Adsorption of the other RX onto UV-Ga was weaker, as indicated by smaller [theta][superscript]water (82-92°). ODPA did not strongly adsorb onto UV-untreated gallium substrates, suggesting that the ODPA adsorption mainly originates from hydrogen bond interaction of a phosphonate group with surface oxide. These results will provide a means for controlling the surface properties of oxide-coated gallium that play an essential role in monolayer conductivity measurements and electroanalytical applications.

Master of Science / Department of Chemistry / Duy H. Hua / Graphene oxide (GO) has attracted many researchers in the past years because of its unique electrical and chemical properties which showed the potential applications in many fields such as electronic materials and biology. Increasing research efforts in the biomedical field are bringing to light new discoveries in areas such as drug delivery, treatment of cancers, and biosensors, and are therefore attractive. The purpose of this work is to prepare GO and modify the surface of GO in order to achieve a new functionalized GO for biosensor applications in the future. GO was synthesized from the flake graphite by using a modified Hummer’s method to achieve higher quality and yield. The flake graphite was first exfoliated by using a microwave reactor. The exfoliated flake graphite then was oxidized by K[subscript]2S[subscript]2O[subscript]8, P[subscript]2O[subscript]5, and KMnO[subscript]4 under acidic conditions, followed by H[subscript]2O[subscript]2 to form GO. The following steps were to attach carboxylic acid and benzoic acid groups onto the surface of GO. Atomic force microscopy (AFM), Fourier transform infrared spectroscopy (FTIR), and Raman spectroscopy were used to identity the modified GO and determine the sizes of the materials after a sequence of reactions. The modified GO will be used in the study of electronic sensing of biomolecules in Hua’s laboratory.

Doctor of Philosophy / Department of Chemistry / Stefan H. Bossmann / Numerous proteases are known to be necessary for cancer development and progression including Matrix Metalloproteinases (MMPs), Tissue Serine Proteases, and Cathepsins. The goal of this research is to develop a Fe/Fe₃O₄ nanoparticle-based system for clinical diagnostics, which has the potential to measure the activity of cancer-associated proteases in biospecimens. Our nanoparticle-based “light switches” for measuring protease activity, consist of fluorescent cyanine dyes which are directly attached to Fe/Fe₃O₄ nanoparticles and porphyrins that are attached to Fe/Fe₃O₄ nanoparticles via consensus sequences. The consensus (cleavage) sequences can be cleaved in the presence of the correct protease, thus releasing a fluorescent dye from the Fe/Fe₃O₄ nanoparticle resulting in highly sensitive (down to 1 x 10⁻¹⁶ mol L⁻¹ for 12 proteases), selective, and fast nanoplatforms (required time: 60 min.). Upon escape, the emission intensity of the organic dye will significantly increase, which can be detected using fluorescence spectroscopy. In order to demonstrate the potential of this new technology of early recognition of various cancers several analysis types have been used. Blood and urine samples from human cancer patients and healthy volunteers, tissue and blood serum samples from human cancer patients, and canine urine and blood serum samples are some of those types. Blood samples from human cancer patients and healthy volunteers were used to demonstrate the potential of this new technology for the early recognition of breast and lung cancers. We were able to establish several proteases with diagnostic potential for breast cancer and non-small cell lung cancer. It is very likely that different cancers will feature different “protease signatures”, meaning that different proteases will be activated, depending on the origin of cancer. This permits the diagnosis of various solid tumors at different stages. Tissue samples were collected from normal tissues, from the boundary of the tumor and from the tumor of the same person. Performed fluorescence experiments clearly indicate that tissue samples from the tumor show the highest fluorescence indicating the highest concentration of the protease. Results can be used excellently in a diagnostic system for breast cancer. Based on our results measuring protease signatures offers an inexpensive and fast approach towards early cancer diagnostics.

Master of Science / Department of Chemistry / Mark D. Hollingsworth / Most urea inclusion compounds (UICs) are known to share a common packing arrangement in which the urea host forms helical ribbons held together by hydrogen bonds to form a series of linear, hexagonal tunnels. Because UICs can encapsulate a wide variety of linear guest molecules, they serve as useful model systems for probing mechanisms of crystal growth and molecular recognition. In this thesis, the syntheses (or attempts thereof) of six compounds that will serve as consequential guest molecules in studies of UICs are presented. These compounds are (5S,6S)-2,9-decanedione-d2, 1,6-dicyanohexane-1,1,6,6-d4, 1,11-undecanedioic acid, bis(3-oxobutyl) adipate, 2,16-heptadecanedione, and 2-eicosanone. With the exception of (5S,6S)-2,9-decanedione-d2, whose synthesis remains incomplete, detailed synthesis and crystal growth of the UICs of these compounds are discussed. Ongoing studies with the UICs containing these guests include the determination of the absolute configuration of UICs, the study of guest conformer population changes via solid-state NMR, the development and identification of novel ferroelastic UICs, and the classification of guest ordering in a series of alkanedione UICs.

Doctor of Philosophy / Department of Chemistry / Viktor Chikan / Doping quantum dots to increase conductivity is a crucial step towards being able to fabricate a new generation of electronic devices built on the “bottom-up” platform that are smaller and more efficient than currently available. Indium, tin, and gallium have been used to dope CdSe in both the bulk and thin film regimes and introduce n-type electron donation to the conduction band. CdSe quantum dots have been successfully doped with indium, tin, and gallium using the Li4[Cd10Se4(SPh16)] single source precursor combined with metal chloride compounds. Doping CdSe quantum dots is shown to effect particle growth dynamics in the “heterogeneous growth regime.” Doping with indium, tin, and gallium introduce donor levels 280, 100, and 50 meV below the conduction band minimum, respectively. Thin films of indium and tin doped quantum dots show improved conductivity over films of undoped quantum dots. Transient Absorption spectroscopy indicates that indium doping introduces a new electron energy level in the conduction band that results in a 70 meV blue shift in the 1Se absorption bleach position. Novel characterization methods such as in-situ fluorescence growth monitoring, single quantum dot EDS acquisition, static and time-resolved temperature dependant fluorescence spectroscopy were developed in the course of this work as well. These results show that doping CdSe quantum dots with indium, tin, and gallium has not only been successful but has introduced new electronic properties to the quantum dots that make them superior to traditional CdSe quantum dots.

Doctor of Philosophy / Department of Chemistry / Stefan H. Bossmann / This paper describes two methods for utilizing cancer associated proteases for targeting cancer therapy to the tumor. The first method is designing a drug delivery system based on liposomes that are sensitive to cancer associated proteases. Upon contact with the protease, the liposome releases its contents. The second method is designing a prodrug that is based on a porin isolated from Mycobacterium smegmatis. The porin is modified with protease consensus sequences, inhibiting its toxicity. Upon contact with the protease, the drug is activated. Protease sensitive liposomes were synthesized that were sensitive to urokinase plasminogen activator. This was done by synthesizing a cholesterol-anchored, uPA consensus – sequence-containing, acrylic acid block copolymer and using it to form a covalently bound polymer cage around the outside of a hypertonic liposome. Liposomes were synthesized that had a diameter of 136 nm. Upon addition of the polymer the diameter increased by 2.69 nm, indicating it had successfully embedded into the liposome membrane. After crosslinking with either a short peptide containing a lysine (so that it is a diamine) or ethylenediamine, the diameter increased between 5.33 nm and 14.1 nm (depending on the type and amount of the crosslinked). Fluorescence release assays showed that the polymer cage could add in excess of thirty atmospheres of osmotic pressure resistance, and, under isobaric conditions, would prevent release of much of the liposomal contents. Upon treatment with uPA, the polymer caged liposomes released a significantly larger amount of their contents making the liposomes protease sensitive. MspA was shown to be a very stable protein able to be imaged by AFM. AFM imaging demonstrated that MspA is able to form native pore structures in membranes making it a good imitator of the membrane attack complex. MspA was demonstrated to be highly cytotoxic, but poor at distinguishing between cells. Pro-MspA was synthesized by adding a hydrophilic peptide to MspA that prevents insertion. A uPA cleavage sequence embedded causes the MspA to become activated at the cancer site. This was demonstrated in tests against uPA and non-uPA producing cell lines.

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.

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.