Alumni Dissertations

 

Alumni Dissertations

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  • Design of Well-Defined Mesoporous Silicas via Surfactant Templating Method Enhanced by the Use of Swelling Agents

    Author:
    Tiffany Man
    Year of Dissertation:
    2014
    Program:
    Chemistry
    Advisor:
    Michal Kruk
    Abstract:

    Surfactant-templated ordered mesoporous materials continue to attract tremendous attention as these materials are characterized by reproducibility and predictability of their synthesis as well as their wide range of potential applications, which serve as future opportunities for additional advancement. The main purpose of this dissertation is to advance the understanding how to control the structural features and properties in the synthesis of well-defined porous materials via surfactant templating method, while keeping in mind that the uniformity of pore size and structural ordering are essential characteristics for these well-defined materials. The work was primarily focused on the issue of the unit-cell size and pore size adjustment in the large-pore domain (that is, for pore diameters above 12 nm) for two-dimensional hexagonal silica structures with cylindrical pores (referred to as SBA-15 silicas). The use of common poly(ethylene oxide)-poly(propylene oxide)-poly(ethylene oxide), PEO-PPO-PEO, surfactants, commercially known as Pluronics® in combination with appropriate hydrophobic micelle swelling agents was pursued. The main hypothesis was that it is possible to judiciously select surfactant/swelling agent pairs to achieve optimal structural adjustment capabilities. Moreover, it was hypothesized that different surfactant/swelling agent pairs may work most effectively in certain temperature intervals. The choice of Pluronic tri-block copolymer as main templating agent, the selection of micelle expanders, the adjustment of initial synthesis temperature (including room temperature conditions), and the adjustment of the amount of silica precursor (tetraethylorthosilicate) can systematically affect the structure of porous silica materials formed via the surfactant-micelle-templating synthesis approach. The advancement in pore size tailoring discussed in this dissertation focuses on the above aspects. In particular, considerations based on the extent of solubilization of organic compounds in Pluronic surfactants paved the way to the identification of new excellent swelling agent for the synthesis of large-pore SBA-15. Ordered SBA-15 silica with d100 interplanar spacing of up to about 30 nm has been successfully synthesized. Modifications in the synthesis approach in terms of shortening the duration of the synthesis to as little as six hours and eliminating the need for temperature control to carry out the SBA-15 synthesis were found effective for the synthesis around room temperature. Highly ordered face-center-cubic silica materials have also been synthesized using surfactants with moderate content of the hydrophilic PPO domains challenging our current understanding of viable selections of surfactants for the synthesis of materials with spherical mesopores. These materials exhibited increased mesopore volumes when compared to the silicas obtained via the traditional synthesis of materials with spherical pores involving block copolymers with a high fraction of the hydrophilic PEO domains. Overall, the dissertation demonstrates that the synthesis mixture composition and synthesis conditions can be predictively selected to achieve particular structural properties (such as unit-cell size) or to observe formation of material under particular conditions. Moreover, some additional opportunities emerge as we explore the predictability of the synthesis pathways.

  • Ultra-Large-Pore Ordered Mesoporous Organosilicas and Related Hollow Nanoparticles

    Author:
    Manik Mandal
    Year of Dissertation:
    2010
    Program:
    Chemistry
    Advisor:
    Michal Kruk
    Abstract:

    My dissertation describes the synthesis of ultra-large-pore ordered mesoporous organosilicas and related hollow nanoparticles. In the first part, we developed a versatile approach through which a series of periodic mesoporous organosilicas (PMOs) with 2-dimensional hexagonal structure and different bridging groups can be synthesized. The bridging groups are methylene (-CH2-), ethylene (-CH2CH2-), ethenylene (-CH=CH-), and phenylene (-C6H4-). For this purpose, a combination of a commercially available triblock copolymer Pluronic P123 (EO20PO70EO20) with judiciously chosen micelle swelling agent (cyclohexane, or 1,3,5-triisopropylbenzene) was used as a miceller template, and the initial step of the synthesis was performed at temperature between 10 and 18 oC, followed by hydrothermal treatment at 100-150 oC. The PMOs were characterized using small-angle X-ray scattering (SAXS), nitrogen adsorption, transmission electron microscopy, and solid-state 29Si NMR. For all PMO compositions, the formation of 2-D hexagonal structures with (100) interplanar spacing, d100, up to 21-26 nm was achieved, which is at least seven nanometers larger than d100 reported earlier for any PMO with 2-D hexagonal structure. The nominal (BJH) pore diameters up to 20-27 nm were achieved for the considered compositions of PMOs with with 2-D hexagonal ordering, while even larger pore sizes were sometimes attained for disordered or weakly ordered structures. The mesopores exhibited constrictions or narrow entrances that were widened by increasing the hydrothermal treatment temperature. The pore diameter tended to increase as an initial synthesis temperature decreased, allowing for the pore size adjustment, but the useful temperature range depended on the bridging groups. The present work suggests that the low-temperature micelle-templated synthesis with judicious selected swelling agents is a general pathway to ultra-large-pore 2-D hexagonal PMOs with both aliphatic and aromatic bridging groups. In the second part, we have demonstrated the synthesis of large-pore ethylene-bridged periodic mesoporous organosilica with face-centered-cubic structure. This was achieved by the use of judiciously chosen swelling agents and Pluronic F127 block copolymers at sub-ambient temperature (~ 15 oC). While our work confirmed that 1,3,5-trimethylbenzene (TMB) which was already employed by other researchers, is a facile swelling agent for Pluronic F127-templated ethylene-bridged PMOs with cubic Fm3m structure and our optimization of the synthesis afforded hitherto unreported unit-cell size and pore size for this PMO, it was also demonstrated that swelling agent predicted to have a higher extent of solubilization in Pluronics than TMB provide vast new opportunities. In particular, xylene was found to afford highly ordered materials with large unit-cell size and pore diameter, and a wide range of moderately or weakly ordered materials with very large unit-cell parameters (up to ~ 50 nm) and some with very large pore diameters (up to ~ 20 nm). In this case, the pore size and unit-cell size was tunable by adjusting the amount of inorganic salt (KCl) in the synthesis mixture. The use toluene allowed for the increase in the primary mesopore volume and also afforded large-pore PMOs in the absence of an inorganic salt. The use of the latter was also not required when benzene was used as a swelling agent. The identification of new swelling agents for ethylene-bridged PMO with spherical mesopores is likely to be extendable on PMOs of other framework compositions and for other related materials. In the third part, based on understanding of the condition for the formation of ordered mesoporous organosilicas, we were able to synthesize hollow nanoparticles with different organic bridging groups. Different organic bridging groups such as methylene, ethylene, ethenylene, and phenylene were incorporated in the organosilica walls of the hollow nanoparticles. Further, we were able to synthesize hollow nanotubules comprising of these bridging groups in the walls.

  • Aqueous Solvation of Protein Secondary Structures: Density Functional Theory Study

    Author:
    Mateusz Marianski
    Year of Dissertation:
    2013
    Program:
    Chemistry
    Advisor:
    Joseph Dannenberg
    Abstract:

    In recent years, van der Waals forces have received considerable attention among the scientific community. It is hard to overestimate the significance of dispersion forces which are thought to play important roles in the energetics of biological molecules, such as DNA and peptides. However, the weakest of interactions is also the most difficult to approach by theoretical methods and has been troubling computational chemists for at least last two decades. In my thesis I will answer how well recently developed density functionals deal with the dispersion in the case study of dispersion-enhanced induction complexes, relative stability of pi-stacking and hydrogen bonded dimers, and protein secondary structures. The presented results undermine the belief that recent widely-parametrized and/or dispersion-corrected functionals outperforms older well-established functionals, like famous B3LYP. In the second part of my thesis I will focus on the influence of aqueous solvent on protein structures. Water is present in all biological systems, where it is not only a static medium of the reaction, but also an active part of the process called life, and it requires careful treatment. I compare models of implicit and explicit solvation for beta-turns, alpha-helices, and beta-sheets. I find that solvation by small water clusters can alter the molecular properties of gas phase molecules and continuous methods are not able to model all effects.

  • Oxocarbenium Ion and Alkene Metathesis Strategies for the Synthesis of Complex Cyclohexanes

    Author:
    CLAYTON MATTIS
    Year of Dissertation:
    2014
    Program:
    Chemistry
    Advisor:
    David Mootoo
    Abstract:

    ABSTRACT Oxocarbenium Ion and Alkene Metathesis Strategies for the Synthesis of Complex Cyclohexanes. by Clayton Mattis Mentor: Professor David R. Mootoo Highly oxygenated cyclohexanes comprise the structures of a number of pharmacologically interesting molecules, including potently bioactive natural products and carbapyranosides. The latter, which are unnatural analogues of carbohydrates in which the ring oxygen of the parent sugar is replaced with a methylene group, have attracted interest as hydrolytically stable mimetics of their parent O-glycosides. This research reports the development of two general methodologies for the synthesis of highly oxygenated cyclohexanes: (1) Oxocarbenium Ion Cyclization (OCC) and (2) Ring Closing Metathasis (RCM). Chapter one gives a review of the literature on the synthesis for highly oxygenated cyclohexanes. Previous results from this laboratory have shown that OCCs on cyclic oxocarbeniums derived from 1-thio-1,2-O-isopropylidene precursotrs are highly stereoselective for cyclohexanes and tetrahydropyrans with cis 3,4-diols. To expand the scope of the OCC methodology, the goal was to evaluate the OCCs on non-cyclic oxocarbenium ions derived from mixed thioacetal precursors. Chapter two describes reactions with alkene nucleophiles. In particular, the OCC on an alkene-mixed thioacetal precursor aimed at the cyclohexane core of the immunosuppressive agent FR65814, was examined. This study revealed that OCCs on non-cyclic oxocarbenium ions could deliver cyclohexanes with trans 3,4-diols in high stereoselectivety. As for the previous observations on OCCs with cyclic oxocarbenium ions, these results can be explained in terms of conformational arguments. Chapter three discusses OCCs for non-cyclic oxocarbenium ions and enol-ether nucleophiles. These reactions were expected to give highly oxygenated cyclic enol ether precursors for carba- and C- pyranosides with trans 3,4-diols. However, in all cases, complex mixtures of products that suggested multiple deleterious pathways from the initial formed cyclization intermediates, was observed. This result contrasts to the successful OCCs involving cyclic oxocarbenium ions and enol ethers, and suggests that conformational rigidity is an important requirement for OCCs involving enol ether nucleophiles. Therefore, the OCC strategy appears to be limited to the synthesis of carba- and C- pyranosides with cis-3,4-vicinal diols. Chapter four describes a more general synthesis of carbapyranosides, which is based on the RCM of an enol ether - alkene substrate. This reaction delivers a six-membered cyclic enol ether in which the enol ether oxygen is exocyclic, and contrasts with a related cyclization from the Postema group that provides C-1-substituted glycals, i.e. cyclic enol ethers with an endocyclic enol ether oxygen. This RCM strategy for carbapyranosides was applied to the carba-arabinose and carba-xylose analogues of the sugar residues in the potent antitumor steroidal glycoside OSW-1.

  • The Development Of New Organocatalysts and New Organocatalytic Cascade Reactions

    Author:
    Patrick McGarraugh
    Year of Dissertation:
    2012
    Program:
    Chemistry
    Advisor:
    Stacey Brenner-Moyer
    Abstract:

    Organocatalysis is the use of small organic molecules to catalyze chemical reactions. They are generally cheaper, less toxic, and easier to handle on a laboratory and industrial scale than more traditional metal-based catalysts. This dissertation discusses the development of new organocatalysts and organocatalytic methods for the asymmetric synthesis of useful small molecules. The research conducted has specifically focused on the use of chiral diarylprolinol silyl ether organocatlysts and their ability to catalyze a variety of useful cascade reactions through iminium and enamine catalysis. Cascade reactions are useful in that a great deal of molecular complexity may be generated in a one-pot process using simple, readily available building blocks. Herein, is provided a comprehensive background on the use of diarylprolinol silyl ethers in the catalysis of iminium-initiated cascade reactions. The research conducted has focused on three main topics: 1.) The development of a novel class of bifunctional bissulfonamide organocatalysts for the asymmetric conjugate addition of dicarbonyls to nitroolefins. 2.) The use of diarylprolinol silyl ether organocatalysts to catalyze a novel Michael-Michael cascade reaction which generates fused carbocycles. 3.) The discovery and development of a novel organocascade kinetic resolution reaction using diarylprolinol silyl ether organocatalysts, which can be used for the synthesis of chiral 2,6-disubstituted tetrahydropyrans and chiral 2,5-disubstituted tetrahydrofurans.

  • SPECIATION OF TECHNETIUM-99 INCORPORATED INTO METAL OXIDE MATRICES: A MOLECULAR LEVEL UNDERSTANDING OF Tc-99 REDUCTION AND ITS COMPLEXATION INTO POLYOXOMETALATES

    Author:
    DONNA MCGREGOR
    Year of Dissertation:
    2009
    Program:
    Chemistry
    Advisor:
    Lynn Francesconi
    Abstract:

    Technetium-99 (99Tc) is a long-lived (T1/2 = 2.13 x 105 years) β-emitting (Emax = 294 KeV) radionuclide formed during the fission of 235U and fallout from nuclear weapons testing. It exists in relatively high concentrations in nuclear waste tanks, and the pertechnetate (TcO4-) anion has been shown to leach into surrounding subsurface soils and groundwaters. Due to its long half-life and the high mobility of the pertechnetate (TcO4-) anion, 99) Tc management is an issue for both waste characterization and long-term storage. A better understanding of both its extensive redox chemistry and the parameters that affect the speciation and coordination environment of Tc will promote the development of more appropriate methods for the separation of Tc from nuclear waste tanks as well as more fitting mediums for storage. Polyoxometalates (POMs) are early transition metal oxide clusters that are chemically robust. They have homogeneous crystalline structures and are known to be good model systems for metal oxide solid-state materials such as the glasses and ceramics used to house nuclear waste. The synthesis of pure 99Tc-POM compounds, however, is complicated by both the unwanted hydrolysis of the Tc(V) starting material and difficulties with the separation of the free POM ligand from the desired 99Tc-POM complex. We have developed methods for the clean synthesis of the 99Tc - (α1-P2W17O61)10-) and (α2-P2W17O61)10-) Wells-Dawson POM compounds (as both organic and aqueous soluble complexes) and characterized them using various spectroscopic techniques. POMs also have unique, tunable, electron transfer abilities and can be reduced, both electrochemically and photochemically in the presence of a sacrificial electron donor, by multiple electrons while maintaining their structural integrity. To this end we have investigated a number of POMs; Keggin ions, (XW12O40n-), X=P, n=3; Si, n=4; Al, n=5), the Wells-Dawson lacunary isomer (α2-P2W17O61) 10-), and a "wheel" POM, P8W48O18440-), for their ability to reduce pertechnetate and sequester low valent 99Tc. The resulting low valent Tc species have been characterized by physical methods including multinuclear NMR and electrochemistry.

  • Benzophenone photoprobes for chemical proteomics and drug target identification

    Author:
    Doina Mihai
    Year of Dissertation:
    2011
    Program:
    Chemistry
    Advisor:
    Akira Kawamura
    Abstract:

    Benzophenone photoprobes are widely used in photoaffinity-labeling studies, especially for the characterization of ligand-receptor interaction. Photolabeling studies using benzophenone, however, are by no means routine experiments. It is not uncommon that carefully designed photoligands fail to label target proteins. In order to get insights into the important factors that affect the photolabeling efficiency, we conducted a structure-activity relationship study (SAR) on adenine-benzophenone photoligands. The study suggested that conformational flexibility was the determining factor that controls the photolabeling efficiency by benzophenone photoprobes. In theory, photoaffinity-labeling can also be used for target identification of small molecules. However, the complexity of proteins in biological samples, such as cell lysate, tissue homogenates and serum samples, limits the use of benzophenone photoprobes in drug target identification and chemical proteomics. By using so called "blocking strategy" we were able to systematically classify the list of proteins identified from photoaffinity-labeling studies using benzophenone. The findings of this study enabled us to refine the experimental protocol for drug target identification and chemical proteomics using benzophenone photoprobes. During the affinity purification of phochemically biotinylated proteins, we discovered that monomeric avidin resin can selectively enrich heat shock proteins (Hsps) from complex proteomes. Although such serum Hsps or circulating Hsps, has been linked to various diseases, including cancer and cardiovascular diseases, their characterization have been hampered be the abundant proteins in serum such as albumin and immunoglobulings. The development of simple and reproducible method for Hsp enrichment opens a new opportunity to define the roles of circulating Hsps in various diseases.

  • Chiral Sulfurization For Synthesis Of Antisense Oligonucleotides

    Author:
    Joshua Mukhlall
    Year of Dissertation:
    2010
    Program:
    Chemistry
    Advisor:
    William Hersh
    Abstract:

    Chapter 1: Antisense and RNA interference (RNAi) reagents are two of the most widely studied oligonucleotide-based therapeutics. Phosphorothioate oligonucleotide, an antisense reagent, has a stereogenic center at the phosphorothioate linkage and in the absence of enantioselective synthesis, a mixture of diastereomers results. Stereodefined phosphorothioates have shown greater antisense activity; however, only a few research groups have successfully designed methods for enantioselective synthesis of phosphorothioates with >98% de, albeit in low yields. This dissertation presents a conceptually different method for enantioselective synthesis of phosphorothioate oligonucleotides via a Curtin-Hammett system that requires epimerization of the phosphite triester on the reaction time scale and selective sulfurization of one of the equilibrating epimers with a chiral sulfurizing reagent. Chapter 2: 2-Cyanoethyl[5'-O-acetyl-2'-deoxythymylyl]-(3',5')-3'-O-(acetyl)-2'-deoxythymidine phosphite triester was found to invert at 150 ºC with ΔG = 33.0 ± 0.2 kcal/mol. Separation of the two diastereomers of the phosphite triester was successfully achieved via its 2-cyanoethyl[5'-O-(p,p'-dimethoxytrityl)-2'-deoxythymylyl]-(3',5')-3'-O-(tert-butyldimethylsilyl)-2'-deoxythymidine boranophosphate analogue. For the inversion study the p,p'-dimethoxytrityl and tert-butyldimethylsilyl groups were substituted with acetyl groups to reduce decomposition during heating. Attempts to induce inversion at lower temperature with acidic and radical species failed. Chapter 3: Chiral analogues of phenylacetyl disulfide (PADS) and 5-methyl-3H-1,2,4-dithiazol-3-one (MEDITH) were synthesized from the same α-alkylated carboxylic acids to give products with enantiomeric purities of 99.0 to >99.9% and 86.1-99.4%, respectively. X-ray diffraction results for one pair of enantiomers unequivocally establish the absolute configurations of two disulfides, and density functional theory (DFT) calculations suggest that the observed high specific rotations could be due to preferred retention of helicity about the S-S bond in solution. Chapter 4: Phosphite triesters with varying degrees of steric hindrance around the phosphorus atom (β-cyanoethyl, TMS, TBDMS, and TPS derivatives) were screened against chiral analogues of PADS and MEDITH. The RPS:SPS diastereomeric ratios of the resulting phosphite sulfides or phosphorothioates were determined by reverse-phase HPLC, and a numerical procedure was developed to express the diastereoselectivity of the reactions. The best selectivities to give RPS enriched and SPS enriched phosphorothioates were achieved with MEDITH analogues (S)-6d (naproxen derivative) (14.7% de) and (S)-6c (isopropyl group at the α position) (-7.9% de), respectively, when reacted with the phosphite triester bearing the TMS group.

  • SYNTHESIS, CHARACTERIZATION, RAMAN, AND SURFACE ENHANCED RAMAN STUDIES OF SEMICONDUCTOR QUANTUM DOTS

    Author:
    Yi Pan
    Year of Dissertation:
    2012
    Program:
    Chemistry
    Advisor:
    John Lombardi
    Abstract:

    The major contributions and discoveries of the dissertation include: (1) Homogeneous nucleation processes for the formation of nanocrystals can occur at low temperature and do not need to proceed at high temperature to overcome a high energy barrier. Monodisperse PbS quantum dots (QDs) obtained with nucleation and growth at 45°C support this finding. (2) Monodisperse single elemental Se QDs can be produced by simple solution crystallization from TDE (1-tetradecene) or ODE (1-octadecene). (3) TDE is a better non-coordinating solvent compare to ODE. STDE (S dissolved in TDE) and SeTDE (Se dissolved in TDE) are stable reagents with long storage time. They can be used as universal precursors for S-containing and Se-containing QDs. (4) QDs synthesis can be carried out at low temperature and relatively short reaction time using the simple, non-injection, one-pot synthetic method. (5) The one-pot method can be extended for the synthesis of QDs and graphene oxide nanocomposites and metal and graphene oxide nanocomposites. (6) PbCl2-OLA (oleylamine) is a universal system for the synthesis of Pb-chaclogenides QDs. (7) Surface enhanced Raman spectroscopy (SERS) is used to probe both size and wave length dependent quantum confinement effects (QCEs) of PbS QDs. (8) Raman spectroscopy is a powerful tool to elucidate crystal structure of Se nanoclusters with size of 1-2 nm. Semiconductor QDs have attracted considerable attention due to their potential for energy-efficient materials in optoelectronic and solar cell applications. When the radius of a QD is decreased to that of the exciton Bohr radius, the valence and conduction bands are known to split into narrower bands due to QCEs. QCEs are both size and wave length dependent. We have developed, synthesized and characterized a series of Pb-chaclogenide QDs, which all the sizes of the QDs are monodisperse and smaller than their respective exciton Bohr radius, to study the QCEs of these QDs. SERS is used as a crucial tool to investigate these QCEs. The QCEs are due to any of the following three resonances or a combination among them: interband resonance, molecular state resonance, and charge-transfer resonance.

  • Applications of Bionanotechnology

    Author:
    Christophe Pejoux
    Year of Dissertation:
    2011
    Program:
    Chemistry
    Advisor:
    Hiroshi Matsui
    Abstract:

    The aim of nanotechnology is to devise technologies at the crossroads of chemistry, physics and biology to shape matter at the atomic scale to form nanosized functional objects and to arrange them into intricate assemblies to elaborate new devices. Today, its biological aspect is largely emphasized to tackle biomedical issues such as pathogen identification, disease diagnosis and treatment. In this respect, interdigitated electrodes were employed to monitor the presence of harmful bacteria, then to attempt to detect human PC3 carcinoma prostate cells as well as the size variation of stimulus-responsive hydrogel beads designed for drug delivery. Our second project aimed at demonstrating the potential use of TiO2-labeled antibodies as substitute for horse-radish peroxidase-labeled antibodies for Enzyme-Linked ImmunoSorbent Assays (ELISA). Our last project revolved around harnessing the enzymatic activity of urease to grow silver-sulfide nanoparticles.