Theses and Dissertations - Department of Chemistry & Biochemistry

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Anionic polymerization of activated aziridines
(University of Alabama Libraries, 2018) Mbarushimana, Pierre Canisius C.; Rupar, Paul A.; University of Alabama Tuscaloosa
Polyethyleneimine, also referred to as polyaziridine, is a polymer that has a repeat unit of (-CH2CH2NH-). Due to its high amine density, PEI finds application in several domains including gene transfection, antimicrobial/antibacterial medicine, CO2 capture, thin film metal deposition, industrial wastewater treatments, and more. Commercially, PEI is obtained via the uncontrolled polymerization of aziridine and the cationic ring opening polymerization (CROP) of oxazolines. However, the available cationic polymerization techniques of aziridines are poorly controlled. In order to synthesize well-defined PEIs, recent literature approaches have used the anionic ring opening polymerization (AROP) of various N-substituted aziridines. The present research, done at The University of Alabama, has focused on the synthesis and AROP of N-substituted aziridines, without the substitution at the 2-position of the aziridine ring. The studied monomers include three tert-butylcarboxy-protected aziridine monomers, specifically tert-butyl aziridine-1-carboxylate, tert-butyl 2-methylaziridine-1-carboxylate, tert-butyl 2-decylaziridine, and six 1-(alkylsulfonylsulfonyl) aziridine monomers, i.e. 1-(methylsulfonyl)aziridine, 1-(toluenesulfonyl)aziridine, 1-(octylsulfonyl)aziridine, 1-(sec-butylsulfonyl)aziridine, 1-((2-nitrophenyl)sulfonyl)aziridine, and 1-((4-nitrophenyl)sulfonyl)aziridine. After characterization, the synthesized monomers were homopolymerized by AROP using various nucleophilic initiators. Except for BOCDecAz, all the synthesized monomers were successfully converted into the corresponding polymers. However, only short oligomers of the resulting homopolymers were formed, as high molecular weight polymer chains were insoluble. The synthesized polymers can potentially be used as precursor to pure linear polyamines A single sulfonyl aziridine, namely1-((ortho-nitrophenyl)sulfonyl)aziridine (oNsAz) was found to produce high molecular weight poly(oNsAz) that was soluble in DMF and DMSO. This is significant as it is the first example of a soluble poly(1-sulfonylaziridine) homopolymer; prior examples were limited to random copolymer. The deprotection of poly(oNsAz) was also attempted in effort to synthesize linear PEI. Although evidence was found for the formation of linear PEI, satisfactory purification of the linear PEI was not achievable.
Borafluorenes and polyborafluorenes boron doped varients of fluorene
(University of Alabama Libraries, 2017) Adams, Ian; Rupar, Paul A.; University of Alabama Tuscaloosa
A series of novel boron containing variants of fluorene were synthesized. Boron was incorporated synthetically via lithium halogen exchange and Grignard reaction pathways. Once incorporated, the borafluorene could be polymerized or undergo further functionalization via Yamamoto and Stille coupling reactions. This incorporation of boron into a conjugated system imparted Lewis acidic and electron deficient properties into a conjugated system. It is our hope that this will dope fluorene and create novel n-type semiconductors. A novel polymer of borafluorene, poly(9-borafluorene) (P9BF) was synthesized. HOMO and LUMO levels of P9BF were estimated by cyclic voltammetry. As predicted in prior DFT studies, P9BF has a reduced band gap and a lower lying LUMO compared with polyfluorene. To examine how the HOMO and LUMO levels of borafluorene systems could be tuned, copolymers of 9-borafluorene were synthesized. Four of the copolymers were a series of donor-acceptor (DA) type copolymers. A borafluorene-fluorene (P9BF-OF) copolymer and borafluorene-diketopyrrolopyrrole (P9BF-DPP), as an acceptor-acceptor (AA) copolymer were also synthesized. The series of DA copolymers showed higher energy HOMO and LUMO levels in correlation with the relative donating ability of the donor monomer. P9BF-OF has a reduced LUMO level in comparison with P9BF. P9BF-DPP has a very low band gap (1.8eV), with absorption well into the near-IR region. To examine ways to make borafluorene more air stable, a series of borafluorenes bearing bismethylmethoxyphenyl (BMMP) ligands were investigated. Interestingly, ii bismethylmethoxyphenyl-borafluorene (BMMP-BF) exhibits an exceptionally large Stokes shift of 16000 cm-1. To extend the conjugation and change the Stokes shift, thiophene containing derivatives BMMP-BF-T, BMMP-BF-2T, and BMMP-BF-3T were synthesized. These thiophene containing compounds exhibited anomalous two wavelength fluorescence. During our fluoride titration experiments, we noticed spectral impurities when using tetrabutylammonium fluoride (TBAF) as our fluoride source. Examining this more closely, we found that commercial samples of TBAF were found to absorb light at 295 and 370 nm and fluoresce as 435 nm. This was not expected for analytically pure TBAF, so we concluded that there must be an impurity present in commercial TBAF. The source of this impurity was found to be I3- which occurs from the oxidation of I-.
Carbohydrate sensing using boronic acid modified polymers
(University of Alabama Libraries, 2019) Liang, Xiaoli; Bonizzoni, Marco; University of Alabama Tuscaloosa
Polyelectrolytes have attained a more prominent role in the design of supramolecular systems in recent years. In particular, commercially available poly(amidoamine) (PAMAM) dendrimers have been widely used because they have high loading capacities and good solubility in water. We focus here on using optical spectroscopy to investigate the application of PAMAM dendrimer derivatives as receptors in carbohydrate sensing, and to study the multivalent behavior of receptors covalently appended to the surface of these macromolecules. We then extended the design principles obtained from this work to linear water-soluble anionic polyelectrolytes developed in collaboration with the Kharlampieva group at the University of Alabama at Birmingham (UAB), using polymethacrylate-acrylamide co-polymers synthesized by their group. In chapters 2 and 3, we describe a carbohydrate sensing system that can operate in neutral water, using covalently modified polyelectrolytes as receptors, and common commercially available dyes as optical signaling units. Particularly, in chapter 2, boronic acid modified PAMAM dendrimers were used as receptors to differentiate common monosaccharides in water at millimolar concentration. This is a significant improvement in affinity and sensitivity over simple boronic acid receptors, particularly for work in aqueous environment, which is considered a challenging medium for carbohydrate detection. In chapter 3, these design concepts were also extended to using boronic acid modified polymethacrylate-acrylamide copolymers synthesized at UAB. Binding affinity trends of carbohydrates to boronic acid moieties were then investigated from a fundamental perspective. In chapter 4, the multivalent behavior of boronic acid moieties on surface-modified PAMAM dendrimers was characterized in detail to determine the factors influencing the onset of multivalent behavior, including the surface density of receptor sites and the overall size of the polymeric scaffold.
Characterization and catalytic applications of silver nanoparticles supported on hierarchically porous SiO_2 and Co_3O_4 monoliths
(University of Alabama Libraries, 2017) Yildirim, Yasemin; Bakker, Martin G.; University of Alabama Tuscaloosa
Hierarchically porous materials are of great interest in such applications as catalysis, drug delivery, chromatography, and electrochemical sensor arrays due to properties such as high surface area, large void volume, and tunable surface chemistry. In this study, we give the detailed report of the synthesis of supported Ag nanoparticles by nanocasting on to hierarchically porous SiO2 (silica) and Co3O4 (cobalt oxide) monoliths, as well as the use of these materials as heterogeneous catalysts for the hydrogenation and oxidation reactions. In the preliminary work, we investigated the synthesis of Ag supported on hierarchically porous SiO2 and Co3O4 monoliths, and the catalytic activity of these monoliths for the hydrogenation of MB (methylene blue) and MO (methyl orange) dyes in the presence of NaBH4 (sodium borohydride). The SiO2 monoliths were synthesized using a sol-gel technique. The Co3O4 monoliths were prepared by nanocasting, using the SiO2 monoliths as a template. The loading of Ag nanoparticles on the SiO2 and Co3O4 monoliths was done by a solution infiltration method using aqueous AgNO3 (silver nitrate) solution followed by reduction with ethylene glycol and hydrazine hydrate. Such monoliths also were used as continuous flow monolithic microreactors for the catalytic activity and stability studies for the hydrogenation of EO (eosin-Y) dye in the presence of NaBH4. Finally, the use of these monoliths for the oxidation of cyclohexene was investigated including the effects of temperature, oxidant, catalyst loading, and substrate to oxidant ratio. All these studies are presented in different sections depending on the different synthesis, procedures, and catalytic activity occurring in each heterogeneous catalyst.
Characterization and thermoelectric performance of polymer/inorganic hybrid films using spectroscopic and microscopic techniques
(University of Alabama Libraries, 2019) Sutch, Tabitha Patricia; Szulczewski, Greg J.; University of Alabama Tuscaloosa
The main goal of this dissertation was to investigate the thermoelectric performance of films of silver telluride (Ag2Te), bismuth sulfide (Bi2S3) and bismuth telluride (Bi2Te3) nanowires (NWs) dispersed in P(NDI2OD-T2). We hypothesize that the electrical properties of the films made with Ag2Te, Bi2S3, and Bi2Te3 will be n-type and behave like composite materials. Ag2Te was synthesized to make three different lengths of NWs. Powder x-ray diffraction (XRD) and energy dispersive x-ray spectroscopy (EDS) confirmed that β-Ag2Te was synthesized with the anticipated stoichiometry. Scanning electron microscopy (SEM) of Ag2Te NWs in P(NDI2OD-T2) revealed that the longest Ag2Te NWs produced homogeneous composites whereas the shorter Ag2Te NWs phase-separated. Electrical conductivity and Seebeck coefficients for each composite film were determined and theoretical models were used to investigate charge-transport behavior. Seebeck coefficients confirmed that all composites were n-type. The longest Ag2Te NWs produced the highest electrical conductivities with parallel transport behavior and are promising to the field of thermoelectrics. Bi2S3 and Bi2Te3 NWs were synthesized, and their stoichiometry and structures were confirmed using XRD and EDS. SEM images of the NW/P(NDI2OD-T2) films revealed that both Bi2S3 and Bi2Te3 phase-separated. The electrical conductivity for each composite film was determined and theoretical models were applied. The electrical conductivity of the Bi2S3 and Bi2Te3 composites were slightly higher than pristine P(NDI2OD-T2), further indicating that the NWs phase-separated. Seebeck coefficients for both systems confirmed that the composites were n-type. Despite the various strategies for improving the film morphology, composites made with Bi2Te3 and Bi2S3 NWs did not produce promising results. The spin-dynamics of P(NDI2OD-T2) doped with cobaltocene were studied with continuous-wave electron paramagnetic resonance (EPR). Additionally, the electrical conductivity of cobaltocene doped P(NDI2OD-T2) films increased several orders of magnitude compared to pristine P(NDI2OD-T2). A sputter depth profile in conjunction with x-ray photoelectron spectroscopy was used to analyze how the dopant dispersed in the polymer matrix. Temperature-dependent pulsed EPR of two different doping concentrations suggested two different relaxation rates. Overall, this study investigated the temperature-dependent spin dynamics of cobaltocene doped P(NDI2OD-T2) films and lays the foundation for further investigations on n-doped polymer system.
Characterization of the carotenoid cis-bixin
(University of Alabama Libraries, 2018) Tay-Agbozo, Sefadzi; Street, Shane C.; Bowman, Michael K.; University of Alabama Tuscaloosa
Bixin, a carotenoid found in annatto, Bixa orellana, is unique among natural carotenoids by being sparingly water-soluble. Bixin free radicals have been stabilized on the surface of silica alumina and TiO2 and characterized by pulsed electron nuclear double resonance (ENDOR). Least-square fitting of experimental ENDOR spectra calculated from density functional theory (DFT) calculations hyperfine couplings characterized the radicals trapped on silica alumina and TiO2. DFT predicts that the trans bixin radical cation is more stable than the cis bixin radical cation by 1.26 kcal/mol. While this small energy difference is consistent with the 26% trans and 23% cis radical cations in the ENDOR spectrum for silica alumina, the TiO2 spectrum could not be fitted due to poor signal. The ENDOR spectrum for silica alumina shows several neutral radicals formed by loss of a H+ ion from the 9, 9′, 13, or 13′ methyl group, a common occurrence in all water-insoluble carotenoids studied in literature. In addition, the continuous wave (CW) electron paramagnetic resonance (EPR) spectroscopy signal of bixin on silica alumina was intense prior to irradiation. Upon irradiation, the intensity is reduced 4-fold. On the other hand, unlike on TiO2 there was no signal prior to irradiation but signal was observed upon irradiation. The extinction coefficient bixin in chloroform is determined to be 1.1 x 105 ± 0.49 and 1.0 x 105 M-1cm-1 ±0.05 at 472 and 503 nm, respectively, while the redox potential in THF is found to be 0.94 ± 0.01V by cyclic voltammogram (CV) measurements. Based on the irreversibility of the CV, the bixin radical cation is estimated to have a short lifetime and decay rapidly at ambient temperature.
The effect of fluoride on the crystallinity and photoactivity of titania
(University of Alabama Libraries, 2012) Brauer, Jonathan Isaac; Szulczewski, Gregory J.; University of Alabama Tuscaloosa
This dissertation describes the synthesis and characterization of fluorinated N-doped TiO_2 nanoparticles under ambient conditions. Samples were synthesized by sol-gel methods that utilized the controlled hydrolysis of titanium(IV) tetra-isopropoxide in acidic solutions. Nitrogen doping was achieved by two different methods. In one scheme triethylamine (TEA) was added post-synthesis to the nanoparticle formation. In the other scheme, ammonium chloride (NH_4 Cl) was added during the acid catalyzed hydrolysis reaction. A freeze-drying process of the sol-gel was used to prevent aggregation during dehydration and was found to retain the high surface area of the powder. Post-synthesis the hydroxyl groups on the surface were exchanged with fluoride by stirring the powders in acidic solution of NaF. Using this synthetic approach the amount of nitrogen and fluoride could be independently controlled. The nanoparticles were characterized by numerous spectroscopic techniques including DRS, FTIR, Raman, and XPS. Vibrational spectroscopy shows that the particles contain significant amounts of organic impurities after doping with TEA. In contrast, particles synthesized with NH_4 Cl showed much less contamination. XPS analysis revealed that a single nitrogen species with a binding energy of 400.6 eV when using TEA as the N precursor. In contrast, when NH_4 Cl was used as the nitrogen precursor two nitrogen species were observed with binding energies at 402.6 and 401.2 eV. These latter peaks are assigned to interstitial nitrogen in the N^(1+) and N^0 oxidation states. The as-synthesized nanoparticles also show a significant differences in their optical properties. In general, the particles doped from TEA and NH_4 Cl were yellow and white, respectively, despite containing approximately the same amount of nitrogen (~5% with respect to Ti). The difference is attributed to a high fraction of oxygen-vacancies in the TEA doped nanoparticles. XRD and Raman measurements determined that the as-synthesized samples were amorphous, but could be converted to the anatase phase by two different methods. Thermal annealing was shown to convert the amorphous particles to the anatase polymorph. The presence of surface fluoride was found to significantly lower the temperature to observe the amorphous to anatase transition. In the second method, stirring the powders in acidic solutions of NaF at room temperature for 12-168 hours produced the anatase phase with an average crystallite size of 4 nm. It was found that the phase transition only occurs when the pH is below the point of zero charge of the particles. The photoactivity of the nitrogen and nitrogen / fluoride-doped particles was tested for their ability to degrade methylene blue (MB) with visible light (> 400 nm). In general the particles with a surface fluoride were more photoactive that those without. In addition, particles with nitrogen were more photoactive than pure TiO_2 . By analyzing the decomposition products with electrospray ionization mass spectrometry and UV-Vis spectroscopy, it was possible to elucidate a different decomposition pathway for the nitrogen-doped samples. When TEA was the dopant precursor, MB primarily decomposed by a ring-cleavage pathway using superoxide. In contrast, when NH_4 Cl was the dopant precursor, MB decomposed through demethylation pathway induced by hydroxyl radicals. The as-synthesized particles were found to be more photoactive those thermally annealed. The loss of photoactivity could be ascribed to two main factors: (1) loss of nitrogen and fluoride and (2) loss of surface area by sintering.
Effects of transition metal cationization on peptide dissociation by mass spectrometry
(University of Alabama Libraries, 2011) Watson, Heather Malone; Cassady, Carolyn J.; University of Alabama Tuscaloosa
Peptide sequencing is fundamental to understanding a protein's structure and function. The field of proteomics is dedicated to how these aspects relate to human health and disease. Unfortunately, the majority of peptides and proteins are not fully sequenced. In mass spectrometry, this is often due to spectral complications and incomplete fragmentation. There is a need to develop new sample preparation techniques or dissociation methods to increase sequence information. The dissociation of transition metal-cationized peptides by collision-induced dissociation (CID), electron-transfer dissociation (ETD), and electron-transfer collisionally activated dissociation (ETcaD) has been investigated in a quadrupole ion trap (QIT). The resulting mass spectra provide a wealth of information about the primary structures of the peptides. Using transition metal ions as cationizing reagents proves beneficial to peptide sequencing by CID and, in some cases, is better than the analysis of protonated species. For instance, spectra obtained from CID of singly and doubly charged Cu(II)-heptaalanine ions, [M + Cu - H]^+ and [M + Cu]^2, are complementary and together provide cleavage at every residue and no neutral losses. This contrasts with protonated heptaalanine, [M + H]^+, which results in fewer backbone cleavages by CID and does not allow sequencing of the first three residues. Multiply charged precursor ions are required in order to carry out ETD and ETcaD. This can be problematic for acidic or neutral peptides. This work demonstrates that addition of transition metals as a cationizing reagent allows peptides to be submitted to ETD and ETcaD that do not otherwise form multiply charged precursors. ETD spectra were less complex than those produced by CID. ETcaD increases backbone cleavages for all samples studied relative to ETD. In addition, complexes that result in very few cleavages by CID are cleaved at every residue when submitted to ETcaD. Evidence for macrocyclic metallated a- and b-ions is found in ETD and ETcaD spectra in the form of nonsequential product ions. The sequence (pEEEEGDD) of the peptide component of biologically derived low-molecular-weight chromium binding substance (LMWCr) is obtained as a result of extensive mass spectrometric studies. LMWCr is proposed to be involved in carbohydrate metabolism. The sequencing of the peptide component of LMWCr by MS represents a potentially significant milestone towards understanding the pharmacological role of chromium at a molecular level.
Electrochemical and spectroscopic studies of bodipy dyes and nanostructured electrodes for solar energy harvesting and conversion
(University of Alabama Libraries, 2018) Kaneza, Nelly; Pan, Shanlin; University of Alabama Tuscaloosa
The use of fossil fuel-based technologies has contributed to the increase in the concentration of greenhouse gases, especially CO2, causing global climate change. To achieve the global energy demand, advanced energy technologies for renewable and sustainability applications have been gaining much attention. Among several promising approaches, stable organic chromophores and nanostructured materials have provided new opportunities in their application in solar energy harvesting and conversion and storage. This dissertation explores the emerging technologies to harvest solar energy to generate (1) electricity using boron dipyrromethene (BODIPY)-thiophene- triphenylamine (TPA) dye-sensitized solar cells, (2) hydrogen fuel using an unbiased Z-scheme tandem cell, and (3) carbon-free fuels by reducing atmospheric CO2 in the presence of water. Nanostructured electrode materials are used for all these three major projects described in this dissertation because of their surface to volume ratios, tunable light absorption, and enhanced charge transport and transfer. By engineering the structural properties of the proposed functional nanomaterials with respect to increasing solar energy conversion and at a low cost, earth abundant and environmental friendly, metal oxide nanomaterials were synthesized and characterized using different analytical techniques. Firstly, this study investigated a series of BODIPY-based dye-sensitized solar cells (DSSCs). Due to their promising potential as efficient photosensitizers, the synthesized BODIPY-based dyes (Dyes 1-5) containing thiophene and/or triphenylamine as electron donors were studied using optical and electrochemical techniques. Although the highest power efficiency achieved was low, correlation between the BODIPY dye structure and properties were established. Secondly, inspired by nature’s photosynthesis, a Z-scheme solar water splitting system comprised of carbon-modified cuprous oxide (C /Cu2O) nanoneedles and oxygen-deficient titanium dioxide (TiO2-x) nanorods in tandem cell was established to enhance charge carrier-separation for unassisted solar water splitting. Although the overall tandem performance is still limited by the C/Cu2O NNs performance, the proposed tandem cell exhibited a photo-induced catalytic activity of 64.7 µA cm-2 that unfortunately gradually decreases over time. Lastly, a photocatalytic anode material, cobalt-doped WO3/BiVO4, was combined with CuO-based nanoneedles to demonstrate a low cost approach to reduce CO2 selectively and water oxidation under sunlight. In addition to highlighting the optical, electrochemical, and spectroscopic advantages of the proposed nanostructured materials, their limitations and challenges were also addressed.
Electron transfer dissociation and collision-induced dissociation mass spectrometry of metallated oligosaccharides
(University of Alabama Libraries, 2019) Duke, Ranelle Marie; Cassady, Carolyn J.; University of Alabama Tuscaloosa
Investigations of metallated glycans through tandem mass spectrometry (MS/MS) can further the field of glycomics, the sequencing of the human glycome. The field is hindered by the lack of an analytical technique that can determine all the stereo-diverse features of carbohydrates. In this dissertation, electron transfer dissociation (ETD) and collision-induced dissociation (CID) are utilized with metal-adducted oligosaccharides to explore the potential of these techniques to sequence glycans. The resulting mass spectra provide significant insight and information about the structure of oligosaccharides and how to distinguish between these complicated isomeric species. Using univalent, divalent, and trivalent transition metal adducts is valuable to glycan analysis. The ETD process requires multiply charged ions, which do not form via protonation for neutral glycans, and CID of protonated glycans produces uninformative glycosidic bond cleavage. The univalent and trivalent metals investigated did not produce ions sufficient for ETD studies, but CID of the trivalent metal adducts showed significant fragmentation. Dissociation of [M + Met]²⁺ from the divalent metals formed various fragment ions with ETD producing more cross-ring and internal cleavages, which are necessary for structural analysis. The two dissociation techniques are complementary. For both ETD and CID of all glycans studied, [M + Co]²⁺ provided the most uniform structurally informative dissociation. Permethylation is a common derivatization technique used in the study of glycans. Permethylation reduces the hydrophilicity of oligosaccharides by replacing all hydrogen atoms on oxygen and nitrogen atoms with methyl groups. Permethylation increases ion intensity in electrospray ionization (ESI) and prevents rearrangements of certain monosaccharides. In this study, permethylation reduced the fragmentation by both ETD and CID for the metallated glycans. The spectra for non-derivatized metallated oligosaccharides was more structurally informative, especially with ETD. For some exact mass ions, permethylation reduced the ambiguity in the spectra. The trivalent lanthanide metal series was investigated as metal adducts. ESI on mixtures of trivalent metals and tetrasaccharides produced [M + Met-H]²⁺, [M + Met + NO3]²⁺, and [M + Met-2H]⁺. For the larger heptasaccharide, both [M + Met-H]²⁺ and [M + Met]³⁺ formed. Dissociation of these ions by both ETD and CID yields extensive sequence information. All trivalent lanthanide cations are suitable for sequencing glycans, and the fragmentation did not vary by metal identity.
Electron transfer dissociation mass spectromerty studies of peptides
(University of Alabama Libraries, 2014) Feng, Changgeng; Cassady, Carolyn J.; University of Alabama Tuscaloosa
Electron transfer dissociation (ETD) is an important tandem mass spectrometry technique in peptide and protein sequencing. In the past, ETD experiments have primarily involved basic peptides. A limitation of ETD is the requirement that analytes be at least doubly cationized by electrospray ionization (ESI). In this research, a method has been developed for enhancing protonation of acidic and neutral peptides. This has allowed doubly protonated ions, [M+2H]2+, to be produced from peptides without basic residues and has enabled their study by ETD. This dissertation includes the first extensive study of non-basic peptides by ETD. The effects of a basic residue on ETD were investigated using a series of heptapeptides with one lysine, histidine, or arginine residue. The spectra contain primarily c"- and z'-ions, which result from cleavage of N-C_α bonds along the backbone. Almost all of product ions include the basic residue. Enhanced fragmentation occurs on the C-terminal side of the basic residue. Also, cn-1 formation is enhanced, where n is the number of residues in the peptide. Addition of Cr(III) nitrate to a solution of the neutral peptide heptaalanine yields abundant [M+2H]2+ formation by ESI. Eleven metal ions were tested and Cr(III) gave by far the most intense supercharging of peptides. In contrast, Cr(III) does not increase protonation of proteins. Experiments were performed to explore the supercharging mechanism. Addition of Cr(III) to the sample solution was used to produce [M+2H]2+ in the remainder of this research. Neutral peptides with alkyl side chains were studied by ETD and found to produce b- and c-ions. Two mechanisms are proposed for b-ion formation, which involves cleavage of backbone amide (O=C)-N bonds. The length of peptide chain affects ETD fragmentation, but the identity of the alkyl residue has minimal effect. Acidic peptides with one or two aspartic or glutamic acid residues produce b-, c- and zOe-ions. The mechanism of b-ion formation is probably the same as that for neutral peptides, while c- and zOe-ions result from a radical mechanism involving oxygen atoms on the acidic side chains. For highly acidic heptapeptides, c- and zOe-ions are the major products, which supports a radical mechanism.
Enhancing energy harvesting and conversion efficiencies of heterogeneous photocatalysts for solar water splitting using surface plasmon resonance and cathodic reduction methods
(University of Alabama Libraries, 2015) Wang, Jue; Pan, Shanlin; University of Alabama Tuscaloosa
This dissertation presents surface enhanced photocatalytic characteristics of heterogeneous catalysts (e.g., α-Fe2O3 and CdS) for solar water splitting. The enhancement can be obtained by either incorporating plasmonic metallic nanostructures, such as Au nanorods (NRs), or cathodic reduction of catalytic materials. This dissertation also presents various electrochemical methods for large-scale synthesis of plasmonic structures (e.g., vertically aligned NRs) for surface enhanced photoelectrochemistry. Four major aspects of the dissertation are described briefly. First, surface-enhanced light absorption and photoelectrochemical characteristics of α-Fe2O3 thin film modified with Au NRs in a top configuration are studied. The photoelectrochemical reaction of the plasmon active substrates for water oxidation is performed and compared at various α-Fe2O3 thicknesses. The photocurrent increase in the surface plasmon region is attributed to the enhanced visible light absorption of α-Fe2O3 in the presence of Au NRs. Second, a template-free technique is invented for a facile fabrication of vertically standing metal NRs and nanowires (NWs). The growth mechanism of NRs and NWs is explored through investigating their morphological changes as the electrodeposition proceeds. Because of their large specific surface area, one direction alignment, stability, and wide tunability over the diameter, length, and coverage, these NRs and NWs will have broad applications in surface enhanced photoelectrochemical reaction and optical spectroscopy. Third, cathodic reduction methods are introduced and they are capable of improving the photoelectrochemical performance of α-Fe2O3 photoanode. The morphology and photoelectrochemical responses of α-Fe2O3 thin-film photoanode are presented before and after the cathodic reduction. The photocurrent of ~20 nm α-Fe2O3 thin film is enhanced by about 7 times after the cathodic reduction. The enhancement is attributed to the conductivity improvement. Finally, vertical-aligned Ag nanoplates and NWs are presented at the outlet of this dissertation. These nanostructures are electrochemically deposited on Indium Tin Oxide (ITO) substrates with the assistance of sacrificial templates such as anodic aluminum oxide (AAO) templates. Ag nanostructures obtained using this method have minimum contamination because no surfactant is adopted for the synthesis; therefore they are suitable for surface modifications for applications in surface-enhanced Raman scattering, surface-enhanced photocatalyst, and metal-enhanced fluorescence.
Fundamental and applied studies of organic photovoltaic systems
(University of Alabama Libraries, 2014) Hill, Caleb M.; Pan, Shanlin; University of Alabama Tuscaloosa
Presented here are applied and fundamental studies of model organic photovoltaic (OPV) systems. Graphene oxide (GO) nanosheets were investigated as a potential electron acceptor in bulk heterojunction organic solar cells which employed poly[3-hexylthiophene] (P3HT) as an electron donor. GO nanosheets were transferred into organic solution through a surfactant-assisted phase transfer method. Electron transfer from P3HT to GO in solutions and thin films was established through fluorescence spectroscopy. Bulk heterojunction solar cells containing P3HT, P3HT-GO, and P3HT-phenyl-C₆₁-butyric acid methyl ester (PCBM, a prototypical elector acceptor employed in polymer solar cells) were constructed and evaluated. Single molecule fluorescence spectroscopy was employed to study charge transfer between conjugated polymers and TiO₂ at the single molecule level. The fluorescence of individual chains of the conjugated polymer poly[2-methoxy-5-(2-ethylhexyloxy)-1,4-phenylenevinylene] (MEH-PPV) at TiO₂ surfaces was shown to exhibit increased intermittent (on/off "blinking") behavior compared to molecules on glass substrates. Single molecule fluorescence excitation anisotropy measurements showed the conformation of the polymer molecules did not differ appreciably between glass and TiO₂ substrates. The similarities in molecular conformation suggest that the observed differences in blinking activity are due to charge transfer between MEH-PPV and TiO₂, which provides additional pathways between states of high and low fluorescence quantum efficiency. The electrodeposition of individual Ag nanoparticles (NPs), which can be used to enhance light harvesting in organic photovoltaic systems, was studied in situ via dark field scattering (DFS) microscopy. The scattering at the surface of an indium tin oxide (ITO) working electrode was measured during a potential sweep. Utilizing Mie scattering theory and high resolution scanning electron microscopy (SEM), the scattering data were used to calculate current-potential curves depicting the electrodeposition of individual Ag NPs. The oxidation of individual presynthesized and electrodeposited Ag NPs was also investigated using fluorescence and DFS microscopies.
The importance of the backbone and C-terminus to mass spectrometry studies of peptides: gas-phase dissociation and acidity studies
(University of Alabama Libraries, 2012) Bokatzian-Johnson, Samantha S.; Cassady, Carolyn J.; University of Alabama Tuscaloosa
The work described in this dissertation shows the importance of the C-terminus and the backbone in dissociation and deprotonation of peptides. Characteristic dissociative behavior can be extremely valuable in proteomic applications and for mechanistic interpretation of mass spectra. Identification of the deprotonation site of a peptide is also important to the development of mechanisms for mass spectrometry, as dissociation is often charge-directed. Collsion-induced dissociation (CID) and electron transfer dissociation (ETD) have been used to discover distinguishing features of peptide dissociation related to the presence of an amidated C-terminus (-CONH_2) compared with the standard acid C-terminus (-COOH). Protonated peptide acids and amides are found to produce practically identical spectra, except for increased ammonia loss from the precursor for the peptide amide. ETD of multiply-protonated peptide acids and amides also produce similar spectra, although dissociation trends related to the basic amino acid residues (e.g. Arg, His, Lys) are observed for the peptide pairs. Deprotonated peptide acids and amides produced several unique product ions that differentiated the analogs. In CID experiments, abundant c_m-2^- (m = the number of amino acid residues in the peptide) formed for many of the peptide amides and c_m-3^- formed for many of the peptide acids. Supporting computational work by Michele Stover of the Dixon Group shows that the process leading to c_m-2^- from peptide amides is less endothermic than the same process for peptide acids. Gas-phase acidities (GA) have been determined for tyrosine, phenylalanine, their amino acid amides and 4-(4-hydroxyphenyl)-2-butanone using bracketing ion/molecule reactions. Two deprotonated species of tyrosine are observed, corresponding to deprotonation at the carboxylic acid -OH and the phenolic -OH. The two GAs determined for tyrosine are: GA(1) = 332.4 ± 2.2 kcal/mol and GA(2) = 333.5 ± 2.4 kcal/mol. Tyrosine amide has an experimental GA of 336.4 ± 2.7 kcal/mol, phenylalanine has a GA of 332.5 ± 2.2 kcal/mol, phenylalanine amide has a GA of 345.8 ± 3.8 kcal/mol, and 4-(4-hydroxyphenyl)-2-butanone has a GA of 339.6 ± 3.0 kcal/mol. The GAs of six tripeptides (with alkyl or H- side chains) have been determined. All of the experimental GAs fall within a 1.2 kcal/mol range, which is consistent with the C-terminus being the most acidic site on the peptides. The GAs of three methyl esters have been determined, demonstrating the ability of peptides to deprotonate on the backbone. The peptide methyl ester GAs are all very similar and fall within a 1.4 kcal/mol range. Computational results indicate that these methyl esters are deprotonating at the central amide NH. Three other methyl esters could not be deprotonated by ESI, because of conformation and steric hindrance to the deprotonation site.
Ionic liquids platform for biomass dissolution leading to advanced biocomposite materials
(University of Alabama Libraries, 2012) Maxim, Mirela Liliana; Rogers, Robin D.; University of Alabama Tuscaloosa
The focus on biomass as a renewable resource has been triggered by the increasing demand for non-renewable supplies and the distress of imminent depletion of petroleum reserves. The term "biorefinery" has been defined in analogy to fuel and petrochemical refineries, and has the purpose to process raw biomass for fuel production, but also a variety of platform chemicals and materials that would complement the current chemical refineries. The ability of ionic liquids (ILs) to serve as non-derivative solvents for biomass facilitates the preparation of chemicals and materials from biorenewable feedstocks. This window of opportunity allows the research community to explore and develop the next generation of materials, products and processes. This dissertation focuses on the development of novel functional materials using ILs technology initiated in 2002. A tunable approach was developed which allows the preparation of composite materials with added functionality for specific applications. Throughout the studies, we were able to understand the interactions among polymers, additives, and ILs, and also evaluate the properties of biocomposite materials processed from ILs/biopolymers solutions embedded with various functional additives. By adjusting one or more of the ILs process variables (ILs' basicity, concentration of the biopolymer, the additive's load in the biopolymer matrix, additive's particle size, regeneration solvent, etc.), we were able to influence the fundamental and specific properties of the composites. It was determined that the ILs' capability for biopolymer dissolution increases with anion's basicity and decrease of the cation's side chain. The molecular weight and concentrations of the biopolymer are factors that influence the morphology and strength of the fibers. Using high molecular weight cellulose the strength of the fibers was increased, but the surface texture of the fibers became wrinkled compared to smooth cellulose fibers obtained from small molecular weight polymers. The addition of micron size inorganic particles such as TiO2 and magnetite to the IL/cellulose solutions can bring functionality to the prepared composite cellulosic material, but can also generate stress failure of the fibers. However, after changing the additive's particle size from micron to nano size and using ultrasonic dispersion for homogeneity enhancement of the IL/additive mixture, the functionality of the particles was retained in the composite and the mechanical properties were significantly improved. ILs also facilitate the preparation of composite materials with swelling capacity and flame-retardant properties through combination of alginic acid and structural polymers like cellulose. These materials can be successfully used as reinforced wound care dressings in the medical field. Chitin nanobeads (~ 25 nm) have been prepared directly from shrimp shells powder and IL solution through the electrospinning process. The nanosize of the chitinous materials provides a large surface area for potential applications such as selective metal extraction media or support for drug delivery systems. In conclusion, the ILs process overall facilitates the preparation of biocomposite materials in various shapes that can retain both biopolymer and additive particular properties (such as flexibility, biocompatibility, and magnetic or antimicrobial properties) after regeneration from IL/biopolymer/additive blends and can be easily used for specific applications.
Low-molecular-weight chromium-binding substance: advanced studies from aves to human
(University of Alabama Libraries, 2009) Chen, Yuan; Vincent, John B.; University of Alabama Tuscaloosa
Chromium has been observed to play a role in maintaining proper carbohydrate and lipid metabolism of mammals. One of the potentially biological active forms of chromium in vitro is low-molecular-weight chromium-binding substance (LMWCr), which has been proposed to amplify the insulin cascade by binding with insulin receptor. LWMCr is a small bio-molecule (<1500 Da) containing a carboxylate-rich polypeptide with four bound chromic ions. LMWCr's (according to its amino acid composition and mass spectrum) were successfully isolated from chicken and alligator livers, as well as from human urine, using a modified method. The extreme hydrophilicity of the peptide and the tightly bound Cr(III) are two major hurdles to produce a stable end-product for mass spectrometry (MS) or high-performance liquid chromatography (HPLC) analysis. Treating bovine LMWCr with trifluoroacetic acid and application to a graphite powder micro-column was used to generate a heptapeptide fragment, and the peptide sequence was analyzed by mass spectrometry (MS) and tandem MS (MS/MS). Two candidate sequences, EEEEGDD and EEEGEDD, were identified; the mass spectrum of the former sequence is more similar to that of the LMWCr fragment. Langmuir isotherm and Hill plots were used to analyze the binding constants of chromic ions to synthetic peptides similar in composition to LMWCr and apoLMWCr. The sequence pEEEEGDD can bind 4 chromic ions per peptide as apoLMWCr does, while the other sequences examined only bind two chromic ions. Studies to further elucidate the structure of LMWCr are ongoing.
Nanostructured silver for applications in surface enhanced Raman spectroscopy and photoelectrochemical reactions
(University of Alabama Libraries, 2014) Clayton, Daniel Adam; Pan, Shanlin; University of Alabama Tuscaloosa
Initial work focused on characterizing silver and its surface enhanced Raman spectroscopy (SERS) capabilities. Silver nanowires were chosen as an ideal material and scanning confocal microscopy studies were performed to identify hot spots. The silver nanowires were found to exhibit fluorescence blinking that was attributed to small silver clusters undergoing rapid interchange from Ag0 to Ag₂O. Control of this blinking was accomplished through the removal of oxygen and through electrochemical control of the system. SERS was also recorded from these nanowires. Deconvolution of the SERS signal from the fluorescence was accomplished either by increasing the SERS analyte concentration or increasing the total number of "hot spots" in the focus volume. Silver applications were studied by performing a SERS study of Rhodamine 6G (R6G) and Poly(3-hexylthiophene-2,5-diyl) (P3HT). A Tollens' silver substrate was utilized as the SERS substrate and similar blinking effects were found to arise. P3HT was cast from 4 different solvents:dichloromethane, chlorobenzene, THF, and toluene. The solvent effects were studied, with kinking of the polymer noted in the non-chlorinated solvents. Single molecule studies in conjunction with polarization control indicated that the P3HT formed in an overlapping manner with only partial charge transfer within the molecule. Finally silvers interactions with TiO₂ were studied. Micron scale single crystal anatase TiO₂ was synthesized by using HF in a hydrothermal process forming a truncated bipyramidal structure consisting of [101] and [001] faces. Fluorine was present in small amounts on the surface of the TiO₂ as confirmed by x-ray photoelectron spectroscopy (XPS). An annealing process was used to remove the fluorine. Nitrogen doping was attempted, but was not found to occur in significant amounts. Visible light sensitivity was noted in annealed samples but did not occur in the bulk as demonstrated through photoelectrochemical measurements. Silver photoreduction directly on the surface of the TiO₂ crystals revealed visible light sensitivity at surface defects. No facial preference was noted for the silver growth through energy-dispersive X-ray spectroscopy (EDX) images. A secondary method of silver attachment through a linker molecule showed that on-resonance silver structures provided greater SERS enhancement dependent upon the direction of the linker molecule.
Negative ion mass spectrometry studies of non-traditional deprotonation sites in peptides: gas-phase acidities of amino acid analogs and fragmentation of model phosphopeptides
(University of Alabama Libraries, 2016) Plummer, Chelsea Elizabeth; Cassady, Carolyn J.; University of Alabama Tuscaloosa
Studying biomolecule deprotonated anions (amino acids, amino acid amides, phosphorylated amino acids, phosphorylated amino acid amides, and phosphorylated peptides) can further negative ion mode mass spectrometry work in the field of proteomics, the sequencing of human proteins. Traditionally, amino acids are considered to have acidic sites on their C-terminus and carboxylic acid-containing side chains. However, several non- traditional sites capable of deprotonation should be considered when examining peptides and proteins by mass spectrometry. A new deprotonated tyrosine conformer was found by electrospraying (ESI) tyrosine from aprotic solvents. Ion/molecule (I/M) reactions determined that tyrosine made by ESI from protic solvents is less acidic. The gas-phase acidity (GA) value for the low-energy structure is 324.7 ± 3.6 kcal/mol experimentally and 330.4 kcal/mol computationally. The ESI conditions and hexapole trapping can affect the deprotonation site of tyrosine. The GAs for the common amino acid amides, phosphorylated amino acids, and phosphorylated amino acid amides were determined experimentally and computationally. Two ion populations were observed via I/M reactions for the amino acid amides deprotonating on the C-terminal amide group that vary in energy by ~5 kcal/mol . Tyrosine, cysteine, tryptophan, and histidine amides undergo side chain deprotonation and are more acidic. Phosphorylated amino acids and their amides were found to be ~20 kcal/mol more acidic than their non-phosphorylated counterparts. Phosphorylated compounds deprotonate on the phosphate side chain, except phosphotyrosine (pTyr), which deprotonates at the C-terminal carboxylic acid. The acidity of pTyr can be affected by ESI conditions. Collison-induced dissociation (CID) was used to examine model phosphorylated peptides in the negative ion mode. The CID of singly charged deprotonated precursor ions produced the least amount of sequence informative fragmentation when the phosphorylated residue was located centrally in the peptide. Diagnostic ions and losses were found indicating the phosphate group. Phosphothreonine (pThr) and phosphoserine (pSer) undergo the loss of the phosphate group and side chain aldehyde to produce unique marker ions. Fragmentation of doubly charged precursor anions yielded little sequence informative fragmentation, however; diagnostic product ions indicating loss of the phosphate group allowed for differentiation between pThr, pSer, and pTyr.
On the synthesis of copper-nickel binary alloy nanoparticles and binding silane coupling agents to magnetic ferrite nanoparticles
(University of Alabama Libraries, 2011) Pritchett, Jeremy Scott; Nikles, David E.; University of Alabama Tuscaloosa
This dissertation addresses the creation of a multifunctional nanoplatform for cancer targeting, imaging, and therapy. Magnetic oxide nanoparticles were labeled with silane coupling agents that could be used for targeting. The magnetic oxides have application as contrast enhancing agents for magnetic resonance imaging. Copper-nickel binary alloy nanoparticles were prepared for possible use in Curie temperature limited hyperthermia therapy. Spherical, single crystal iron oxide nanoparticles with average diameters of 4 nm, 6 nm, 8 nm, 11 nm, or 16 nm were prepared using published procedures. The iron oxide particle chemistry was extended to synthesize 13 nm diameter CoFe_2 O_4 , 9 nm diameter MnFe_2 O_ 4 , and 12 nm diameter NiFe_2 O_4 . The particles had a coating of oleic acid and oleylamine ligands. Silane coupling chemistry was used to displace these ligands with either β-aminoethyl-ϒ-aminopropyl-trimethoxysilane, triethoxysilane-PEG, or triethoxysilane-biotin. The silane ligands would allow the particles to be conjugated with a targeting group. New chemistry was developed to synthesize fcc CuNi nanoparticles with the objective of finding methods that give particles with an average size less than 50 nm, a narrow distribution of particle sizes, and control of particle composition. The particle synthesis involves the reduction of a mixture of copper(II) and nickel(II) and the reduction conditions included diol reduction, polyol synthesis, seeding by diol reduction, and oleate reduction. One of the main issues is the formation of hcp nickel particles as a containment in the method. The factors that avoided the formation of hcp nickel particles and allow only fcc particles to form were the choice of reducing agent, ratio of surfactants, and heating time. Both the oleate reduction and diol reduction gave a mixture of the hcp and fcc phases. By controlling certain reaction conditions, such as keeping the ratio of oleic acid to oleylamine 1:1 and slowly heating to reflux for 30 minutes, only fcc nanoparticles were formed. The method of making CuNi nanoparticles by diol reduction gave the best result and it consisted of a total amount of 1 mmol of Cu(acac)_2 and Ni(acac)_2 , 5 mmol of 1,2 hexadecanediol, 1.5 mL of oleic acid, 1.5 mL of oleylamine and 15 mL of benzyl ether. It made fcc CuNi, provided control of composition, and gave particles with average size smaller than 100 nm.
Pattern-based recognition in supramolecular sensing ensemble
(University of Alabama Libraries, 2015) Mallet, Alie Marie; Bonizzoni, Marco; University of Alabama Tuscaloosa
A great deal of attention in studying polyelectrolytes has arisen due to their wide industrial use. These polymers have not received as much attention within the supramolecular chemistry field; the work presented here aims at showcasing their power and applicability to this field. In this dissertation, we utilize optical spectroscopic techniques to elucidate how polyelectrolytes behave as molecular host in solution. Moreover, we apply this knowledge to the design of simple, yet powerful optical sensor arrays. Chapter 1 briefly introduces polyelectrolytes and the molecular recognition properties utilized to study these assemblies. Chapter 2 details research directed toward gaining insight into the binding properties of the linear polyelectrolyte polystyrene sulfonate as a potential molecular host for small molecules. The remaining chapters describe the use of our accumulated knowledge in the design and implementation of optical arrays employing commercially available components to target various analyte classes. We showcase the power of multivariate techniques in developing these sensor arrays. Chapters 3 and 4 discuss our efforts in targeting biological phosphates utilizing a dendritic polyelectrolyte and an indicator probe. Chapter 5 expands our work on multivariate array sensing and details a metal cation sensor capable of differentiating a series of ten divalent metal.

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Browsing Theses and Dissertations - Department of Chemistry & Biochemistry by Subject "Analytical chemistry"

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