Alumni Dissertations and Theses

 
 

Alumni Dissertations and Theses

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  • Probing Reaction Dynamics in Complex Gas-Phase Systems Using Guided-Ion-Beam Scattering and Computational Methods

    Author:
    Yigang Fang
    Year of Dissertation:
    2013
    Program:
    Chemistry
    Advisor:
    Jianbo Liu
    Abstract:

    An electrospray ionization (ESI) guided-ion-beam tandem mass spectrometer was developed in our research lab, including vacuum systems, electronics and instrument control and data acquisition (DAQ) systems using LabVIEW programming. Capitalizing on this instrument, two experimental projects have been accomplished as described below. In project 1, formation and characterization of multiply positively and negatively charged sodium bis(2-ethylhexyl)sulfosuccinate (NaAOT) aggregates were studied in the gas phase. Mass spectra show the compositions of [(NaAOT)nNaz]z+ for positively charged aggregates and [Nan-zAOTn]z- for negatively charged aggregates, with various aggregation numbers (n) and charges (z). Collision-induced dissociation (CID) of mass-selected micellar ions with Xe was performed to probe structures of gas-phase micellar assemblies, identify effects of charge states, solute-surfactant interactions, and determine preferential incorporation sites of different amino acids. Gas-phase NaAOT surfactants are able to assemble into a reverse micelle-like structure in positive ion mode and a direct micelle-like structure in negative ion mode, respectively. Both direct and reverse micelles are able to incorporate amino acids. Driving forces for amino acid solubilization in gas-phase micelles come from hydrophobic and/or electrostatic interactions, which strongly depend on amino acid hydrophobicity and charge states. In project 2, the reaction of deprotonated cysteine ([Cys-H]-) with singlet molecular oxygen (O2[a1?g]) has been studied, including the measurement of effects of collision energy (Ecol) on reaction cross sections. [Cys-H]- has a carboxylate anionic structure (HSCH2CH(NH2)CO2-) in the gas phase. Density functional theory (DFT) calculations were employed to examine the properties of various complexes, transition states and products. Three product channels were observed, corresponding to the formation of NH2CH2CO2- with remaining neutral products, OSCH2CH(NH2)CO2- via elimination of OH from an intermediate complex, and HSCH2C(NH)CO2- + H2O2 via abstraction of two hydrogen atoms from HSCH2CH(NH2)CO2- by 1O2, respectively. Quasi-classical direct dynamics trajectory simulations were carried out at Ecol = 0.2 eV using B3LYP/4-31G(d) level of theory. Trajectory results were used to guide the construction of the reaction coordinate, discriminate between different mechanisms, and provide additional mechanistic insights. Analysis of trajectories highlights the importance of complex mediation at the early stage of all reactions, and suggests a partially concerted mechanism for the H2O2 elimination reaction.

  • Heterolytic Activation of Hydrogen Promoted by Ruthenium Nanoparticles immobilized on Basic Supports and Hydrogenation of Aromatic Compounds

    Author:
    Minfeng Fang
    Year of Dissertation:
    2013
    Program:
    Chemistry
    Advisor:
    Roberto Sánchez-Delgado
    Abstract:

    Despite the aggressive development and deployment of new renewable and nuclear technologies, petroleum-derived transportation fuels--gasoline, diesel and jet fuels-- will continue to dominate the markets for decades. Environmental legislation imposes severe limits on the tolerable proportion of aromatics, sulfur and nitrogen contents in transportation fuels, which is difficult to achieve with current refining technologies. Catalytic hydrogenation plays an important role in the production of cleaner fuels, both as a direct means to reduce the aromatics and as a key step in the hydrodenitrogenation (HDN) and hydrodesulfurization (HDS) processes. However, conventional catalysts require drastic conditions and/or are easily poisoned by S or N aromatics. Therefore, there is still a need for new efficient catalysts for hydrogenation reactions relevant to the production of cleaner fossil fuels. Our catalyst design involves metallic nanoparticles intimately associated with a basic support, with the aim of creating a nanostructure capable of promoting the heterolytic activation of hydrogen and ionic hydrogenation mechanisms, as a strategy to avoid catalyst poisoning and enhance catalytic activity. We have designed and prepared a new nanostructured catalytic material composed of RuNPs immobilized on the basic polymer P4VPy. We have demonstrated that the Ru/P4VPy catalyst can promote heterolytic hydrogen activation and a unique surface ionic hydrogenation mechanism for the efficient hydrogenation of N-aromatics. This is the first time these ionic hydrogenation pathways have been demonstrated on solid surfaces. For the RuNPs surfaces without basic sites in close proximity, the conventional homolytic H2 splitting is otherwise involved. Using the mechanistic concepts from Ru/P4VPy, we have designed and prepared the Ru/MgO catalyst, with the aim to improve the catalytic efficiency for the hydrogenation of heteroatom aromatics operating by the ionic hydrogenation mechanism. The Ru/MgO catalyst significantly improves the catalytic efficiency for hydrogenation of a variety of N-/S-heteroaromatics and mono-/polycyclic aromatic hydrocarbons representative of components of petroleum-derived fuels. The catalyst is superior to the few other known supported noble metal catalysts for these reactions. Mechanistic studies also point to the ionic hydrogenation mechanism on the Ru/MgO surfaces. In addition, the Ru/MgO catalyst is highly recyclable and long-lived.

  • SYNTHESIS, CRYSTAL GROWTH AND CHARACTERIZATION OF PHOSPHIDES, SELENIDES, SULFIDES AND OXIDES

    Author:
    Chun-Min Feng
    Year of Dissertation:
    2010
    Program:
    Chemistry
    Advisor:
    Glen Kowach
    Abstract:

    The desire to build smaller, faster, inexpensive electronics has prompted researchers to exploit electron "spin" in transistors. Spin in semiconductors offers a pathway towards integration of storage and processing in a single material. These "spintronic" transistors could be highly energy-efficient and perform more computations than traditional transistors in a smaller space. In addition, in optoelectronic applications, lasers and lightemitting diodes that take advantage of electron spin could increase the data-carrying capacity of light. But one of the key hurdles in this emerging field is that the magnetic and semiconducting materials needed to make a spintronic device are notoriously incompatible. We have focused on different oxides, phosphides and sulfides to study crystal growth and properties of spintronics. We have reported the synthesis of pure ZnO and Mn substituted ZnO crystals from sodium hydroxide and potassium hydroxide flux for the first time. Various oxides, including boron oxide (B2O3), vanadium oxide (V2O5), tungsten oxide (WO3) and vmolybdenum oxide (MoO3), were also used for crystal growth. A non-uniform distribution of Mn substitution was found in ZnO single crystals, and 3 at.% Mn concentration was identified. In addition, polycrystalline Mn-substituted ZnO powder samples exhibited solubility of Mn in the ZnO lattice. SQUID magnetic propertiesinvestigation of Mn-substituted polycrystalline samples indicated paramagnetism down to 5 K. We have also investigated phosphides, selenides, and sulfides for spintronic applications, based on the well-studied spintronic material, gallium arsenide (GaAs), with a Curie temperature of 110 . GaAs has the zincblende structure with Ga in tetrahedral coordination. ZnSiP2, CdSiP2, KGaS2 and KGaSe2 have metal atoms in tetrahedral coordination with no localized spin. Localized spin will be present if transition metals are substituted in. The synthesis of single phase ZnSiP2 and CdSiP2 were grown from two different heat treatments. Also, potassium gallium selenide (KGaSe2) and potassium gallium sulfide (KGaS2) were reported. Temperature dependence susceptibility data revealed a ferromagnetic transition near 300 K followed by an antiferromagnetic transition near 50 K. Hysteresis loops at room temperature were present in all Mn substituted samples. Magnetic properties of Mn substituted samples are comparable with the crystalline MnP sample; they remain unidentified in X-ray diffraction data.

  • SYNTHESIS, CRYSTAL GROWTH AND CHARACTERIZATION OF PHOSPHIDES, SELENIDES, SULFIDES AND OXIDES

    Author:
    Chun-Min Feng
    Year of Dissertation:
    2010
    Program:
    Chemistry
    Advisor:
    Glen Kowach
    Abstract:

    The desire to build smaller, faster, inexpensive electronics has prompted researchers to exploit electron "spin" in transistors. Spin in semiconductors offers a pathway towards integration of storage and processing in a single material. These "spintronic" transistors could be highly energy-efficient and perform more computations than traditional transistors in a smaller space. In addition, in optoelectronic applications, lasers and lightemitting diodes that take advantage of electron spin could increase the data-carrying capacity of light. But one of the key hurdles in this emerging field is that the magnetic and semiconducting materials needed to make a spintronic device are notoriously incompatible. We have focused on different oxides, phosphides and sulfides to study crystal growth and properties of spintronics. We have reported the synthesis of pure ZnO and Mn substituted ZnO crystals from sodium hydroxide and potassium hydroxide flux for the first time. Various oxides, including boron oxide (B2O3), vanadium oxide (V2O5), tungsten oxide (WO3) and vmolybdenum oxide (MoO3), were also used for crystal growth. A non-uniform distribution of Mn substitution was found in ZnO single crystals, and 3 at.% Mn concentration was identified. In addition, polycrystalline Mn-substituted ZnO powder samples exhibited solubility of Mn in the ZnO lattice. SQUID magnetic propertiesinvestigation of Mn-substituted polycrystalline samples indicated paramagnetism down to 5 K. We have also investigated phosphides, selenides, and sulfides for spintronic applications, based on the well-studied spintronic material, gallium arsenide (GaAs), with a Curie temperature of 110 . GaAs has the zincblende structure with Ga in tetrahedral coordination. ZnSiP2, CdSiP2, KGaS2 and KGaSe2 have metal atoms in tetrahedral coordination with no localized spin. Localized spin will be present if transition metals are substituted in. The synthesis of single phase ZnSiP2 and CdSiP2 were grown from two different heat treatments. Also, potassium gallium selenide (KGaSe2) and potassium gallium sulfide (KGaS2) were reported. Temperature dependence susceptibility data revealed a ferromagnetic transition near 300 K followed by an antiferromagnetic transition near 50 K. Hysteresis loops at room temperature were present in all Mn substituted samples. Magnetic properties of Mn substituted samples are comparable with the crystalline MnP sample; they remain unidentified in X-ray diffraction data.

  • GROUND- AND EXCITED-STATE CHEMISTRY OF [BIS(2,2'-BIPYRIDINE)(2-(2-PYRIDYL)PYRAZINE) RUTHENIUM(II)]: PROTONATION AND COORDINATION

    Author:
    Elena Ferloni
    Year of Dissertation:
    2012
    Program:
    Chemistry
    Advisor:
    Harry Gafney
    Abstract:

    Ruthenium(II) diimines have been extensively studied for their notable photo physical properties. Of particular interest are compounds with ligands with peripheral base sites, where the metal-to-ligand charge transfer shifts electron density onto the ligand yielding an emissive state of increased in basicity. One well known example of such complexes, (bis(2,2'-bipyridine) (2-3-bis(2-pyridyl) pyrazine) ruthenium(II), [Ru(bpy)2dpp]2+, has been studied extensively, yet questions remained regarding the sequence of protonation steps at the two peripheral dpp nitrogens in the ground and excited states and the magnitude of the photo-induced change in acid-base properties at each site. In order to reach a deeper understanding of the kinetic and thermodynamic steps involved in its protonation and coordination, a similar complex was synthesized and studied, (bis(2,2'-bipyridine) (2-(2-pyridyl) pyrazine) ruthenium(II), [(bpy)2Ru(pypz)]2+. The alternative ligand is identical in almost every respect to dpp except for the absence of the free pyridyl ring and the fact that it has only one possible protonation site instead of two. The pypz ligand, thus, represents an ideal candidate to elucidate how the pyrazinyl nitrogen on the coordinated dpp would behave if the additional pyridyl ring on dpp was not present. The differences and similarities in the properties of [(bpy)2Ru(pypz)]2+ and [Ru(bpy)2dpp]2+ in the same environment are highlighted here, describing the peculiar behavior of the acid-base sites of each complex upon excitation and their role in protonation reactions and coordination reactions to d10 metals, namely zinc.

  • Synthesis and Evaluation of Sensitizer Drug Photorelease Chemistry: Micro-Optic Method Applied to Singlet Oxygen Generation and Drug Delivery

    Author:
    Goutam Ghosh
    Year of Dissertation:
    2014
    Program:
    Chemistry
    Advisor:
    Alexander Greer
    Abstract:

    This thesis summarizes a new micro-optic method for singlet oxygen generation and sensitizer drug delivery, which include i) synthesis and evaluation of a first generation device for drug delivery from native and fluorinated silica probe tips, ii) synthesis of PEG conjugated sensitizers to study phototoxicity in ovarian cancer cells, and iii) synthesis and evaluation of tris-PEGylated chlorin conjugated fluorinated silica for its future integration into the device to use as a 2nd generation device. A first generation micro-optic device was developed that works by sparging O2 gas and light generating cytotoxic singlet oxygen that cleaves the covalently attached drug (sensitizer) from the probe tip at the distal end of the fiber. The aim is to develop a 1st and 2nd generation device for site specific delivery of photosensitizer and singlet oxygen to overcome the challenges involved in systemic administration of the sensitizer. Synthesis and evaluation of drug (pheophorbide-a) delivery applying micro-optic method from native and fluorinated silica probe tip was achieved. The amount of sensitizer photocleavage depends on the loading level of sensitizer onto the probe tips. We also found that photorelease efficiency depends on the nature of the solvents where sensitizer is photocleaved. For example, no photorelease was observed in an aqueous solvent where sensitizer remained adsorbed to the native silica probe-tip. But, 90% photocleavage was obtained in octanol. A significant amount of photosensitizer (formate ester of pyropheophorbide-a) diffused into the liposome when photocleavage study was carried out in liposome. Substantial increase of photorelease was observed in organic solvent when pyropheophorbide-a (PPa) sensitizer was attached to the partially fluorinated porous Vycor glass. We also explored sensitizer photorelease from the fluorinated silica surface at various temperatures and we found that autocatalytic photorelease happened at room temperature and above. No photorelease was observed at low temperature. Chlorin e6 and its one, two and three short chain methoxy triethylene glycol (PEG) conjugated derivatives were synthesized. A comparative study of photocytotoxicity and cellular uptake between each showed that 173,152,131- chlorin e6 methoxy triethylene glycol triester has the highest photocytotoxic activity and uptake by ovarian OVCAR-5 cancer cells. Therefore, we decided to load three short chain PEG conjugated chlorin e6 onto the silica surface through spacer alkene for delivery via a fiber-optic probe tip. In order to load chlorin e6-triPEG ester conjugate, in chapter 4, we explored different synthetic strategies. We have been successful in synthesizing spacer alkene succinate linker conjugated chlorin e6-tri PEG ester, which was attached to the fiber-optic probe tip. Reactions were carried out in mild conditions to avoid detachment of the PEG ester from the carboxylic acid sites of chlorin. Photocleavage of the triPEG modified fluorinated probe tip system was studied in n-butanol.

  • BIOPHYSICAL STUDIES OF MOLECULAR RECOGNITION IN PERIPHERAL AND INTEGRAL MEMBRANE PROTEINS

    Author:
    Xudong Guan
    Year of Dissertation:
    2012
    Program:
    Chemistry
    Advisor:
    Ruth Stark
    Abstract:

    The molecular interactions of peripheral and integral membrane proteins with ligands and model biological membranes play important roles in the regulation of human nutrition, cell signaling, and other physiological processes. In the current study, we have used solution- and solid-state nuclear magnetic resonance (NMR) and computational modeling methods to study the interactions of fatty acid-binding proteins (FABPs) with ligands and membrane mimetics, and to examine the conformation of a transmembrane peptide fragment of the Ste2p G protein-coupled receptor (GPCR) in lipids. Computational docking with NMR-derived restraints has been used to identify critical ligand-protein electrostatic interactions in both an intermediate singly-liganded state and the double-liganded liver fatty acid-binding protein (LFABP). The model structure for a R122L/S124A LFABP mutant reveals that two charged residues are required to ensure that the first oleate ligand adopts an orientation and conformation favoring binding of the second ligand within the protein cavity. A detailed model for the ligand binding process is proposed based on the analysis of these docked structures and solution-state NMR structures determined previously. A new isotropically tumbling bilayered micelle (bicelle) system composed of dimyristoylphosophatidylcholine (DMPC) and 1,2-di-O-hexyl-sn-glycero-3-phosphocholine (DIOHPC) has been assessed as a membrane-mimetic medium and used to probe molecular interactions with two FABPs. Rat intestinal fatty acid-binding protein (IFABP) and LFABP were titrated with the bicelles, with site-specific changes monitored by chemical shift perturbations. Contrasting transfer mechanisms for fatty acids between FABPs and membranes were differentiated based on their respective chemical shift perturbations, and site-specific information was deduced about the IFABP-membrane interaction. Additionally, both solution- and solid-state NMR have been utilized to investigate a double transmembrane peptide (TM1TM2) from the Ste2p GPCR in phospholipid environments. A solution-state NMR interaction study of the 15N alanine-labeled peptide with DMPC-sodium docecylsulfate detergent mixtures demonstrated successful reconstitution into a helical conformation, whereas solid-state NMR experiments on TM1TM2 in DMPC multilayers permitted assignment of some signals by residue type.

  • Synthesis of Biologically important C-glycoinositols

    Author:
    Sunej Hans
    Year of Dissertation:
    2009
    Program:
    Chemistry
    Advisor:
    David Mootoo
    Abstract:

    Glycosylinositol subunits comprise important glycoproteins on eurkayotic cell membranes and oligosaccharide components of the cell wall of mycobacteria. Glycosylinositols are also believed to function as secondary messengers in cellular processes, such as the mediation of insulin action. Analogues of glycoinositols in which the ring or glycosidic oxygen of the acetal residue is replaced with a methylene group (C- and carba- glycoside respectively), have attracted interest as mechanistic probes because of their greater hydrolytic stability and different conformational behavior compared with the native O-glycosides. Chapter 1 of this thesis presents an overview of selected biologically important glycoinositols, and of previous synthetic approaches to C- and carba- glycosides. Chapters 2, 3 and 4 describes the synthesis of the C-glycosides of 6-O- (a-mannosyl)-myo-inositol and 4-O- (2-amino-2-deoxy-b-D-galactopyranosyl)-3-O-methyl-D-chiro-inositol (also called INS-2), and the carba-glycoside of INS-2. The synthetic strategy for these complex C- and carba- glycosides centers on formulation of the "sugar" or "glycone" component from a highly oxygenated cyclic enol ether in which the enolic oxygen is endo- or exo- cyclic, respectively. A key innovative element in these syntheses is an oxocarbenium ion cyclization strategy wherein these enol ethers are produced with complete stereocontrol from highly substituted thioacetal-enol ether precursors. An appealing aspect of this plan is that the cyclization precursors may be accessed in a convergent fashion starting from the esterification of "glycone" and "aglycone" components, thereby allowing for the preparation of a variety of C- or carba- inositols with different sugar and inositol residues.

  • Synthesis of Biologically important C-glycoinositols

    Author:
    Sunej Hans
    Year of Dissertation:
    2009
    Program:
    Chemistry
    Advisor:
    David Mootoo
    Abstract:

    Glycosylinositol subunits comprise important glycoproteins on eurkayotic cell membranes and oligosaccharide components of the cell wall of mycobacteria. Glycosylinositols are also believed to function as secondary messengers in cellular processes, such as the mediation of insulin action. Analogues of glycoinositols in which the ring or glycosidic oxygen of the acetal residue is replaced with a methylene group (C- and carba- glycoside respectively), have attracted interest as mechanistic probes because of their greater hydrolytic stability and different conformational behavior compared with the native O-glycosides. Chapter 1 of this thesis presents an overview of selected biologically important glycoinositols, and of previous synthetic approaches to C- and carba- glycosides. Chapters 2, 3 and 4 describes the synthesis of the C-glycosides of 6-O- (a-mannosyl)-myo-inositol and 4-O- (2-amino-2-deoxy-b-D-galactopyranosyl)-3-O-methyl-D-chiro-inositol (also called INS-2), and the carba-glycoside of INS-2. The synthetic strategy for these complex C- and carba- glycosides centers on formulation of the "sugar" or "glycone" component from a highly oxygenated cyclic enol ether in which the enolic oxygen is endo- or exo- cyclic, respectively. A key innovative element in these syntheses is an oxocarbenium ion cyclization strategy wherein these enol ethers are produced with complete stereocontrol from highly substituted thioacetal-enol ether precursors. An appealing aspect of this plan is that the cyclization precursors may be accessed in a convergent fashion starting from the esterification of "glycone" and "aglycone" components, thereby allowing for the preparation of a variety of C- or carba- inositols with different sugar and inositol residues.

  • CHEMICAL, BIOLOGICAL AND ANALYTICAL STUDIES ON NATURAL PRODUCTS FROM CENTRAL NERVOUS SYSTEM- (CNS) ACTIVE PLANTS

    Author:
    Fang He
    Year of Dissertation:
    2013
    Program:
    Chemistry
    Advisor:
    Wayne Harding
    Abstract:

    Abstract CHEMICAL, BIOLOGICAL AND ANALYTICAL STUDIES ON NATURAL PRODUCTS FROM CENTRAL NERVOUS SYSTEM- (CNS) ACTIVE PLANTS by Fang He Adviser: Professor Wayne W. Harding There are several CNS activities, including analgesic, antidepressant, sedative, euphoric, stimulant, anxiolytic, psychedelic and oneirogenic activity. Investigation of CNS-active plants has the promise to identify new compounds that may be therapeutically useful or that may be useful as probes for CNS receptors. This thesis deals with three plants that have been reported to possess CNS activity: Leonotis leonurus, Silene capensis, and Ipomoea indica. Leonotis leonurus when smoked or consumed as a tea is reported to cause mild marijuana-like sedative effects. Our investigation has uncovered three new labdane diterpenes from an aqueous extract of a commercial source of the plant. The labdane diterpenes tested did not show any CNS receptor affinity at the sites we tested. These compounds are not likely (by themselves) to be responsible for the activity. Silene capensis known as African Dream Root has oneirogenic activity. Phytochemical isolation of our plant material resulted in the isolation of ten known compounds. Six of these ten compounds are withanolides or withanolide glycosides. No phytochemical investigations of Ipomoea indica have been reported to date. Eight known compounds were isolated during our investigation.