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.

This thesis describes the synthesis and assembly of metal and semiconductor nanoparticles (NPs). The two research topics include i) hetero-assembly of metal and semiconductor NPs, ii) effect of ionic strength on homo-assembly of gold nanorods (GNRs). First, we present hetero-assembly of GNRs and semiconductor quantum dots (QDs) in a chain using biotin-streptavidin interaction. We synthesized alloyed CdTeSe QDs and modified them with mercaptoundecanoic acid to render them water-soluble and to attach streptavidin. We synthesized GNRs by a seed-mediated method and selectively modified the ends with biotin. Hetero-assembly of QDs and GNRs depended on the size, ligands, and ratio of QDs and GNRs. Second, we controlled the rate of homo-assembly of GNRs by varying the ionic strength of the DMF/water solution. The solubility of polystyrene on the ends of GNRs depended on the ionic strength of the solution, which correlated with the rate of assembly of GNRs into chains.

The Escherichia coli transcription factor NikR is responsible for nickel-mediated repression of the nik operon. The crystal structure of NikR in complex with its operator sequence provided insight into the mechanistic details of nickel-activated NikR-DNA complex formation. The crystal structure revealed that the α3 helix and its preceding loop (residues 63-79) in two of the metal-binding domains—which become structurally ordered after high-affinity nickel binding—make non-specific contacts with the DNA phosphodiester backbone. The proposed mechanism of NikR binding to DNA suggests that the non-specific interactions between the DNA phosphodiester backbone and the positively-charged residues Lys64 and Arg65 anchor NikR to the DNA, thereby allowing the protein to initiate a one-dimensional search for its recognition sequence. The DNA-binding studies presented here strongly support an important role for Lys64 and Arg65 in NikR-DNA complex formation which is in agreement with the proposed model of NikR binding to DNA.

The Escherichia coli transcription factor NikR is responsible for nickel-mediated repression of the nik operon. The crystal structure of NikR in complex with its operator sequence provided insight into the mechanistic details of nickel-activated NikR-DNA complex formation. The crystal structure revealed that the α3 helix and its preceding loop (residues 63-79) in two of the metal-binding domains—which become structurally ordered after high-affinity nickel binding—make non-specific contacts with the DNA phosphodiester backbone. The proposed mechanism of NikR binding to DNA suggests that the non-specific interactions between the DNA phosphodiester backbone and the positively-charged residues Lys64 and Arg65 anchor NikR to the DNA, thereby allowing the protein to initiate a one-dimensional search for its recognition sequence. The DNA-binding studies presented here strongly support an important role for Lys64 and Arg65 in NikR-DNA complex formation which is in agreement with the proposed model of NikR binding to DNA.

This thesis describes the synthesis and assembly of metal and semiconductor nanoparticles (NPs). The two research topics include i) hetero-assembly of metal and semiconductor NPs, ii) effect of ionic strength on homo-assembly of gold nanorods (GNRs). First, we present hetero-assembly of GNRs and semiconductor quantum dots (QDs) in a chain using biotin-streptavidin interaction. We synthesized alloyed CdTeSe QDs and modified them with mercaptoundecanoic acid to render them water-soluble and to attach streptavidin. We synthesized GNRs by a seed-mediated method and selectively modified the ends with biotin. Hetero-assembly of QDs and GNRs depended on the size, ligands, and ratio of QDs and GNRs. Second, we controlled the rate of homo-assembly of GNRs by varying the ionic strength of the DMF/water solution. The solubility of polystyrene on the ends of GNRs depended on the ionic strength of the solution, which correlated with the rate of assembly of GNRs into chains.