Alumni Dissertations and Theses

 
 

Alumni Dissertations and Theses

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  • Fabrication and Assembly of Patchy Particles with Uniform Patches

    Author:
    Zhenping He
    Year of Dissertation:
    2014
    Program:
    Chemistry
    Advisor:
    Ilona Kretzschmar
    Abstract:

    Patchy colloidal particles have been widely studied as the self-assembly building blocks to illustrate their potential for forming complex structures. The parameters affecting the final assembly structures include (i) patch size, shape, and number per particle, (ii) their relative positions, and (iii) the surface properties of the patch material. Recent computational studies have highlighted the impact of patch shape on assembly structure; however, there are only a limited number of methods that can provide control over patch shape and size. In this thesis, a template is introduced to the Glancing Angle Vapor Deposition method (GLAD) to create surface anisotropy on colloidal particles with uniform and controlled patch size and shape. Further, a mathematical model is derived that instructs the patchy particle fabrication process and also assists in the quantitative description of patch area. The template-assisted GLAD method is used to fabricate patchy particles, i.e., colloidal particles with a predefined patch on their surface. The patch size is controlled by varying the incident angle and rotation angle when particle size and template dimension are fixed. Due to the shadowing effect of the template and adjacent particles, a large variety of patch shapes can be achieved, including but not limited to symmetric semi-spherical caps and asymmetric crescent moon and triangular-shaped patches. A second vapor deposition enables the addition of another patch, which partly overlaps with the first patch. The mathematical model provides instruction on selecting adequate parameters to achieve a specific patch shape. In addition, it can also be used to calculate the patch size. In the model, the patch shape is defined in a three-dimensional space thereby enabling the description of various patch shapes obtained from the different fabrication parameters. Last but not least, the model also predicts patch position and calculates the size of the overlapping region of two patches. Overall, the template-assisted GLAD method is illustrated to be a powerful tool for the control of patch size, shape and uniformity, while providing the opportunity for scalability and reduced occurrence of defects. Such patchy particles with a specific patch shape and/or multiple patches made of different materials have great potential to provide more intricate assembly structures and potential applications.

  • DEVELOPMENT AND APPLICATIONS OF MASS SPECTROMETRIC METHODS FOR PHOSPHORYLATION ANALYSIS

    Author:
    Hsin-Pin Ho
    Year of Dissertation:
    2014
    Program:
    Chemistry
    Advisor:
    Emmanuel Chang
    Abstract:

    Protein phosphorylation modification regulates numerous cellular functions by a reversible and selective control of kinases and phosphatases. To understand the entire dynamic network of phosphorylation requires sensitive and reliable quantification of phosphorylation, measurements that can be achieved by mass spectrometry. In this research, we established efficient MALDI-mass spectrometric methods as strategies for single- or multi-site phosphorylation quantification without the use of isotopes, chromatography and calibration curves. The methods were assessed by analyzing peptide standards with different single-multiple phosphorylation sites, showing a wide dynamic range, good accuracy and reproducibility. This is the first label-free MALDI method without using a calibration methodology proposed for quantification of in vitro phosphorylation in a kinase assay. Moreover, advanced mass spectrometry empowers identification of a highly conserved Cdk2 phosphorylation site of HIV-1 reverse transcriptase (RT) at Thr 261 across thousands of HIV-1 strains. We demonstrated phosphorylation on HIV-1 RT peptides and protein in in vitro assays, and confirmed phosphorylation in vivo with antibodies and mutation studies. Blocking this phosphorylation by p21, a naturally occurring Cdk inhibitor, defines a potential Cdk2-mediated cell-intrinsic mechanism for restricting HIV-replication in a clinically significant way.

  • Design of Ultra-large-pore Ordered Mesoporous Silicas and Grafting of Organic Groups on Their Surfaces

    Author:
    Liang Huang
    Year of Dissertation:
    2012
    Program:
    Chemistry
    Advisor:
    Michal Kruk
    Abstract:

    Developing novel methods to synthesize ordered mesoporous silicas with ultra-large pores and exploring robust approaches to functionalize their surfaces are two attractive topics in material science. Focused on these two aspects, this dissertation includes the selection of swelling agents for the synthesis of ordered mesoporous silicas templated by commercially available surfactants, and the development of diverse surface modification strategies to graft functional molecules on the surface of ordered mesoporous silicas. In chapter 2, the synthesis of FDU-12 silicas with face-centered cubic structure of ultra-large mesopores was described. Xylene was identified as a superior swelling agent, which worked perfectly with Pluronic F127 (EO106PO70EO106). The unit-cell parameter of FDU-12 silicas was expanded up to 56 nm, and the pore diameter reached 36 nm without the loss of structural ordering. The acid treatment effectively suppressed the structural shrinkage. Ethylbezene was proven to be another powerful swelling agent comparable with xylene. Highly ordered closed-pore FDU-12 silicas were prepared via a simple thermally-induced pore closure process at temperatures as low as 400-450 °C. In chapter 3, grafting of organic groups on surfaces of ordered mesoporous silicas was discussed. Polymers were grafted either by growing from the initiation sites on the surface of the solid support ("grafting from") or attached to the surface by forming covalent bond between the chain ends and the functional groups on the surface ("grafting to"). Polymer/FDU-12 silica composites were obtained by surface-initiated atom transfer radical polymerization (SI-ATRP) or surface-initiated atom transfer radical polymerization with activators regenerated by electron transfer (SI-ARGET ATRP). Good control of the polymerizations was observed in organic and protic media. The Huisgen azide-alkyne cycloaddition "click" reaction and thiol-ene "click" reaction were employed for grafting organic groups to the surfaces of SBA-15 silicas. The alkyne-azide "click" reaction was highly effective for grafting various azide molecules including low-molecular weight polymers to the inner surface of mesopores. The thiol-ene "click" was found less effective but still suitable for the "grafting to" method in nanopores.

  • SUGAR ALCOHOLS: A NOVEL PLATFORM FOR FUNCTIONAL MOLECULAR GELS

    Author:
    Swapnil Jadhav
    Year of Dissertation:
    2012
    Program:
    Chemistry
    Advisor:
    George John
    Abstract:

    The rise in interest in molecular gels is evident from the ample variety of molecular gelators (MGrs) being developed for diverse applications, ranging from medicinal to electronic devices. MGrs, typically amphiphiles, exhibit high biocompatibility and biodegradability, accounting for their emergence as potential successors to polymeric gelators. However, most of these gelators have been discovered serendipitously. Therefore there is a strong impetus to probe: (i) the process of gelation; and (ii) structural requirements for a molecule to be a successful gelator. Such systematic investigation rationalizes the relationship between the gelator structure and properties of gels. In this research work, this challenge is addressed for a new class of gelators: sugar alcohol-fatty acid conjugates. The natural abundance and vast structural diversity of sugar alcohols and fatty acids make them ideal candidates for use in the synthesis of new MGrs. Mannitol, sorbitol and xylitol were chosen as representative entities to study the effect of subtle structural variation in sugar alcohols on the gelation mechanism. Lipase-mediated regioselective transesterification was employed to quantitatively conjugate sugar alcohols with fatty acids. The hydrophobicity of the amphiphiles was fine tuned by varying fatty acid chain length from C4 to C14. The gelation tendency (or self-assembly) of sugar alcohol-based amphiphiles was investigated in water and organic liquids. Several techniques such as XRD, microscopy (optical, SEM and TEM) and spectroscopy (FT-IR) were used to characterize the gels and to decipher the self-assembly mechanism responsible for gelation. The characterization techniques collectively helped in elucidating the relationship between the gelation efficiency and amphiphilic structure (stereochemistry of sugars or chain length of fatty acid). These non-toxic and readily biodegradable amphiphiles exhibited unprecedented gelation in crude oil fractions, edible oil and liquid pheromones. Their utility was successfully demonstrated by developing: (i) oil spill recovery materials (Chapter 3); (ii) controlled release devices for pheromones and biopesticides (Chapter 4); and (iii) healthy vegetable oil structuring agents (Chapter 5). This entire study successfully demonstrates the prudent utilization of biobased resources and biocatalysis for developing multifunctional amphiphiles. Such value-added chemicals developed through the biorefinery concept may have an impact on industrial applications and new products.

  • Synthesis, Characterization and Chemistry of Platinum and Iridium Nanoparticles in Solution and Nanoporous Silicas

    Author:
    Parbatee Jagassar
    Year of Dissertation:
    2012
    Program:
    Chemistry
    Advisor:
    Harry Gafney
    Abstract:

    This project focuses on the synthesis of catalytically-active, transition-metal nanoparticles, their adsorption into porous Vycor glass (PVG), the removal of the poly(vinylpyrrolidone) (PVP) surfactant employed in their synthesis and their chemistry with Ru(II) diimine complexes. Platinum and iridium nanoparticles with a narrow size distribution were prepared by the alcohol reduction method with poly(vinylpyrrolidone) (PVP) as the size limiting surfactant. PVP/Pt nanoparticles adsorb into PVG and as much as 46 ± 4% of the PVP can be removed without further nanoparticle aggregation. XANES spectra show that removal of the PVP surfactant occurs without oxidation of the Pt nanoparticle. EXAFS of the adsorbed Pt nanoparticles after removal of the PVP yield a Pt-Pt bond length of 2.74 ± 0.01 Å which is slightly shorter than the Pt-Pt bond length measured in Pt foil, 2.78 Å. We have shown that the Pt nanoparticles, both the stripped and the unstripped of PVP in porous Vycor glass, does not influence their reactivity with either the [Ru(bpy)2dpp]2+ or the [Ru(bpy)2ppz]2+ complexes. The addition of PVP/Pt or PVP/Ir nanoparticles to aqueous-ethanol solutions of [Ru(bpy)2ppz]2+ (ppz denotes 4,7-phenanthro-lino-5:6,5'6'pyrazine) leads to the spontaneous aggregation of the nanoparticles about the complex. A comparison of the aggregation about different Ru(II) diimines indicates aggregation initiates at the heteroleptic ligand. Although initiating at the ppz ligand, continued aggregation of the nanoparticles about the complex dilutes the specificity of the initial interaction leading to larger aggregates of differing shape. TEM analyses of the aggregates indicate the volume occupied by the individual nanoparticles is a small fraction of the total volume of the aggregate suggesting a somewhat open structure interlaced with the solvent. Correlating TEM analyses of the aggregation with the electronic spectra of the solutions reveals a new absorption assigned to the formation of the [Ru(bpy)2(ppz)2+-PVP/Pt] and [Ru(bpy)2(ppz)2+-PVP/Ir] aggregates. Analysis of the latter absorption as a function of the concentration of PVP/Pt nanoparticles indicates step-wise formation of the [Ru(bpy)2(ppz)2+-PVP/Pt] aggregates. Consistent with the self-assembly of the aggregates, intensity and lifetime quenching of the complex by the PVP/Pt nanoparticles shows that ≥ 80% of the quenching occurs by a static mechanism, i.e., the self-assembly of the [Ru(bpy)2(ppz)2+-PVP/Pt] aggregates.

  • EUROPIUM REDUCTION AND LANTHANIDE COORDINATION IN POLYOXOMETALATES

    Author:
    Jing Jing
    Year of Dissertation:
    2010
    Program:
    Chemistry
    Advisor:
    Lynn Francesconi
    Abstract:

    Polyoxometalates (POMs) are a unique class of metal-oxygen cluster anions in which the early transition metals are in their highest oxidation states. POMs have applications in quite diverse disciplines including catalysis, medicine and material sciences, many of which are based upon their reduction-oxidation (redox) properties. The variation of metal coordination environments and metal-oxygen framework architectures influences redox properties of POMs, and the extent of that influence depends on the nature of the incorporated metal ion. When combined with lanthanide (Ln) ions, Ln-POMs form new structures, exhibit catalytic properties, and offer unique functionality, such as the creation of luminescent and Lewis acid catalytic centers. Because of this, Ln-POM derivatives have attracted increasing attention in recent years. The first project focused on Europium (Eu) and Wells-Dawson Heteropolytungstates because of their prospects in electroanalytical chemistry. Eu is redox-active. Wells-Dawson Heteropolytungstates contain electroactive, lacunary P-W-O anions that, upon reduction in aqueous and organic media, form heteropoly blue species that retain the same structures as the parent anions. The combination of the electrochemical properties of both the Eu and the ligands in one molecule produces a two-center, multielectron redox. We wish to investigate multi-electron redox processes so as to derive some information about the interaction between the Ln f orbitals and the tungsten d-band LUMO. To this end, electrochemical techniques (cyclic voltammetry and bulk electrolysis), in situ XAFS (X-ray absorption fine structure) spectroelectrochemistry, NMR spectroscopy and optical luminescence were used. The cyclic voltammograms show concentration dependence. The reduced form of K7[(H2O)4Eu(α-1- P2W17O61)] was probed by Eu LIII edge XANES and confirmed that Eu(III) is reduced to Eu(II). EXAFS data for the reduced Eu(II)-POM shows the average Eu-O bond length is 2.55(4) Å, which is 0.17 Å longer than that for the oxidized anion, and consistent with the 0.184 difference between the Eu(II) and Eu(III) ionic radii. In the second project, the Nd3+, Sm3+, Eu3+, Tb3+, Dy3+, and Yb3+ complexes with α-1- [P2W17O61]7- of 1:1 Ln:α-1-ligand stoichiometries, [(H2O)nLn(α-1-P2W17O61)]7-, as the tetra-n-butylammonium solid salts as well as their solutions in dry and wet acetonitrile were probed through use of voltammetry, electrolysis, and EXAFS. The comparative metrical data obtained about the inner-sphere Eu coordination environments in the solid salt of TBA+-Eu-α-1 and upon its dissolution in dry MeCN with a 0.1 M TBAPF6 electrolyte suggest that MeCN binds to Eu(III) in part (0 < δ < 4) and in exchange with H2O, forming a mixed H2O-MeCN solvate. These results, in combination with the EXAFS results for the TBA+-Ln-α-1 systems across the 4f period provide a fresh perspective on the variation of Ln(III) coordination in MeCN, including the effects of the lanthanoid contraction as well as known variations of MeCN and H2O residence times. The third project, the SAXS measurements for potassium salts of [α-1-P2W17O61]10-, [Eu(α-1-P2W17O61)]7- and [Yb(α-1-P2W17O61))]7- at different concentrations, is presented in Appendix. The Guinier plots showing linear and parallel response suggest that the cluster size for each compound is independent of concentration and the clusters remain monodisperse without aggregation at high concentrations. The Rgs obtained from the Guinier fit over the low Q range and P(r) analysis over the entire Q rang exhibit good consistence with each other, which again indicates that the clusters remain intact and monodisperse with no interparticle interactions and no aggregation at high concentrations.

  • New Materials for Supramolecular Nanoscale Devices

    Author:
    Matthew Jurow
    Year of Dissertation:
    2013
    Program:
    Chemistry
    Advisor:
    Charles Drain
    Abstract:

    The projects reported here seek to employ the very small - molecules, nanoparticles, films of materials far thinner than a human hair - to create diverse useful systems. We have focused our attention of a class of molecules which strongly absorb light and can be induced to interact with other materials to create devices which can harvest the energy in sunlight, change the way they respond to external stimulus based on the way they are being illuminated, and hopefully in the future make electronic devices more efficient, sustainable, smaller and broadly better. The majority of our most advanced current technologies are made by "top down" fabrication. Large portions of materials which do not demonstrate any of the strange properties which emerge when physical dimensions are severely limited, called bulk materials, are whittled down and painstakingly arranged sometimes one molecule at a time to make microchips and the screens in our cell phones. Another driving force of the research described here is to advance the idea of "self assembly" by which molecules can be designed to interact with each other in such a way that they arrange into a precise manner without needing to be moved one at a time. By advancing our knowledge of self assembled systems, especially those which interact with light, we have strived to make real progress towards new highly applicable functional technologies across many disciplines.

  • RADICAL FORMATION AND FUNCTIONS IN MYCOBACTERIUM TUBERCULOSIS CATALASE-PEROXIDASE (KatG) AND IN CRYPTOCOCCUS NEOFORMANS MELANIN

    Author:
    Abdelahad Khajo
    Year of Dissertation:
    2012
    Program:
    Chemistry
    Advisor:
    Richard Magliozzo
    Abstract:

    The dual-function heme enzyme catalase-peroxidase, KatG, is found in many microorganisms but in the human pathogen M. tuberculosis it is the only catalase (2H2O2 → O2 + 2H2O) and plays an important role in protecting this organism against oxidative stress. The structural and functional origins of its high catalase activity are therefore of special interest. KatG also exhibits a broad-spectrum peroxidase activity (ROOH + 2AH → 2ROH + 2A·) and in M. tuberculosis it is responsible for peroxidative activation of the pro-drug isoniazid used to treat tuberculosis infection. Previous studies have shown that the catalase activity of KatG depends upon a unique adduct structure consisting of three conserved amino acids (Met255, Tyr229 and Trp107, M-Y-W) on the distal side of the heme pocket and that this adduct enables formation of a unique radical intermediate required for efficient turnover of H2O2. Here, EPR measurements along with site-directed mutagenesis and isotope labeling experiments allowed assignment of the `narrow doublet' radical signal found during catalase turnover to Tyr229 of the M-Y-W adduct, explained the operation of this radical in KatG using optical and stopped-flow spectrometry, and elucidated a function for this unique cofactor and a role for neighboring residues in the enzyme's catalase activity. Based on these findings, a new radical-dependent catalase reaction mechanism in KatG could be proposed. Previous studies also showed formation of other amino acid-based radicals in KatG upon reaction with alkyl peroxides. Gaining insights into the poorly-understood peroxidase reaction mechanism in KatG through identifying the location and the possible function of the `wide doublet' radical signal was among the goals of this thesis. Mutagenesis and rapid freeze-quench EPR experiments revealed the involvement of several residues in an electron transfer pathway including Tyr229, Tyr597, Tyr678, Trp90, Trp135, and Trp149. Other important aspects regarding the peroxidase function of KatG such as the electronic structure of its initial hypervalent heme species and the role of proximal Trp321 were studied. While details of the peroxidase reaction in KatG are far from being resolved, a mechanism was presented based on the available data. The second part of this work was devoted to studying another biologically-relevant free radical, which occurs in eumelanin from the fungus C. neoformans. With the application of EPR spectroscopy, UV-Vis spectrometry, chemical analyses, and other physico-chemical techniques to investigate how high-dose gamma irradiation under aqueous aerobic conditions interacts with the semiquinone radical and affects the physical and chemical properties of natural and synthetic melanins, the studies aimed to gain insights into a radioprotective role of melanin in fungal cells. Findings here revealed a shielding function for melanin in live fungal cells from high-dose ionizing radiation by attenuating the destructive effects of radiolysis-induced hydroxyl radicals and serving as a sacrificial barrier in the cell wall. Chemical analysis of irradiated samples showed that hydroxyl radical attack on susceptible sites in melanin subunits lead to C-C bond cleavage and the release of low molecular weight aldehydes.

  • BIMOLECULAR ENCOUNTERS: ACID-BASE AND/OR ELECTRON TRANSFER IN RUTHENIUM (II) COMPLEXES. EXPERIMENT AND THEORY.

    Author:
    Marta Kowalczyk
    Year of Dissertation:
    2013
    Program:
    Chemistry
    Advisor:
    Harry Gafney
    Abstract:

    This work correlates experimental and theoretical studies of ruthenium diimines, [Ru(bpy)2L]2+ where L = bpy, or dpp. Experimental research concentrates on excited state acid-base and electron transfer properties. Although the driving force for reduction of Fe(III) and Ag(I) are essentially equivalent, data presented here show that the bimolecular encounter between bis(2,2'-bipyridine)(2,3-bis(2-pyridyl)pyrazine)ruthenium(II), [Ru(bpy)2(dpp)]2+ in its dpp localized MLCT state, leads to coordination of Ag+, but electron transfer to Fe3+. Several redox reactions were performed between [Ru(bpy)2dpp]2+ and a strong oxidizing agents to analyze the spectroscopic signature of the oxidized form of the complex, [Ru(bpy)2dpp]3+ . The experiments confirm electron transfer between excited state of bis(2,2'-bipyridine(2,3-bis(2pyridyl)pyrazine)ruthenium(II), [Ru(bpy)2dpp]2+ and iron(III) in aqueous and buffered solutions. Electron transfer has been confirmed by trapping Fe(II), one of the products of excited state electron transfer. The efficiency of excited electron transfer is influenced by solvent cage, where redox pair products form by competition between back reaction and diffusion process. Two molecules of ruthenium complexes, [Ru(bpy)3]n+ and [Ru(bpy)2dpp]n+ , where n = 2+, 3+, have been investigated theoretically with a particular attention to their changes in electron density. Structural optimizations and energy calculations were performed by the Density Functional Theory (DFT) method in the Gaussian09 package including the effective core potentials (Los - Alamos ECP) for the ruthenium(II) ion. Electronic absorption spectra have been calculated and compared with experimental data. Computation of spectroscopic properties and electrochemical energies agree with experimental findings and provide a rationale for the spectroscopic properties of the oxidized form of [Ru(bpy)2dpp]3+. The possibility of proton-coupled electron transfer (PCET) reaction was investigated by examining the energetics and pKa's of all possible forms of [Ru(bpy)2dpp]2+, which suggested that the quenching by iron(III) is an electron transfer process. Theoretical electron transfer rates between iron(III) and excited state of [Ru(bpy)2dpp]2+ calculated with Marcus cross-relation are in good agreement with experimental findings.

  • SYNTHESIS AND CHARACTERIZATION OF CARBON NANOFILMS FOR CHEMICAL SENSING

    Author:
    Vivek Kumar
    Year of Dissertation:
    2012
    Program:
    Chemistry
    Advisor:
    Alexander Zaitsev
    Abstract:

    Carbon nanofilms obtained by high temperature graphitization of diamond surface in inert atmospheres or vacuum are modified by treatment in plasma of different precursor gases. At temperatures above 1000 oC, a stable conductive film of thickness between 10 - 100 nm and specific resistivity 10-3-10-4 ohm.m, depending upon the heating conditions and the growth atmosphere, is formed on diamond surface. A gray, thin film of high surface resistivity is obtained in high vacuum, while at low vacuum (below 10-4 mbar), a thick black film of low surface resistivity forms. It is observed that the exposure to plasma reduces the surface conductance of carbon nanofilms as result of a partial removal of carbon and the plasma-stimulated amorphization. The rate of the reduction of conductance and hence the etching ability of plasma depends on the type of precursor gas. Hydrogen reveals the strongest etching ability, followed by oxygen and argon, whereas SF6 is ineffective. The carbon nanofilms show significant sensitivity of their electrical conductance to temperature and exposure to the vapors of common organic compounds. The oxygen plasma treated films exhibit selective response to acetone and water vapors. The fast response and recovery of the conductance are the features of the carbon nanofilms. The plasma-treated carbon nanofilm on graphitized diamond surface is discussed as a promising sensing material for development of all-carbon chemical sensors, which may be suitable for biological and medical applications. An alternative approach of fabrication of temperature and chemical sensitive carbon nanofilms on insulating substrates is proposed. The films are obtained by direct deposition of sputtered carbon on highly polished quartz substrates followed by subsequent annealing at temperatures above 400 oC. It is observed that the as-deposited films are essentially amorphous, while the heating induces irreversible structural ordering and gradual conversion of amorphous carbon in disordered graphite. This evolution is confirmed by Raman spectroscopy and electrical measurements. The carbon nanofilms grown on diamond and deposited on quartz both show similar exponential dependence of their conductance on temperature, which is essentially different from the usual behavior of the thermally activated conduction and the conduction due to variable range hopping of charge carriers. The observed exponential dependence of conductance is explained by a model based on the thermally vibrating energy barriers. The as-grown nanofilms on diamond surface show a negative response (decrease in conductance) to the vapors of acetone, toluene and hexane, and a positive response (increase in conductance) to the water vapor. Sensitivity (relative change in conductance) to toluene is greater than to water, acetone, and hexane, in that order. Plasma exposure alters the sensitivity to positive for all the organic vapors. Overall, an increase in sensitivity is observed with the plasma exposure time. For acetone and water, an increased exponential dependence on vapor concentration is also observed. The exposure to oxygen plasma renders the carbon films on diamond selectively sensitive to acetone and water vapors. The hydrogen plasma exposure makes the films selectively sensitive to toluene vapor. It is found that the carbon nanofilms on quartz have p-type conductivity, as indicated by the opposite response to NO2 and NH3 analytes. NO2, a known electron acceptor, increases the conductance. NH3, a known electron donor, decreases the conductance. The phenomenological description of the chemical sensitivity of the carbon nanofilms σ = β/τ is proposed as a function of two main parameters: the time constant τ and the maximum relative change in conductance β. τ and β are described as the parameters related to the surface and bulk material properties of the films, respectively.