Alumni Dissertations

 

Alumni Dissertations

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  • Genetically Modified Collagen-like Triple helix Protein as Biomimetic Template to Fabricate Metal/Semiconductor Nanowires

    Author:
    Hanying Bai
    Year of Dissertation:
    2011
    Program:
    Chemistry
    Advisor:
    Hiroshi Matsui
    Abstract:

    Various metal and semiconductor nanowires have been developed as building blocks for electronics, optics, and sensors devices. Among these, new nanowires developed on biomolecular templates got more attention since the molecular recognition functions of these biomolecules with specific ligands can be employed to immobilize nanowires onto specific locations to establish desired device geometries. In order for their application in electronics, optics, and sensors device fabrications, after configuring device geometries with nanowires by the biomolecular recognition, we focused upon the biomineralization function of peptides on the nanotemplate sidewall to develop various material coatings such as metals and semiconductors for electronics and sensor applications. It should be noted that the coating morphology such as particle-domain size and inter-particle distance on the nanotemplates could be tuned by peptide sequences and conformations. We launched the genetically modified recombinant collagen-like triple helix proteins as a biorecognition, size-controlling and rigid biotemplate. This collagen-like triple helix is the genetically engineered polypeptide assembly that contains a fragment from the natural collagen sequence and has attractive features in hybrid nanomaterials. The length of the protein nanowire is uniform since it is determined by the number of amino acids. The length can be flexible if we genetically modify the sequence, which can also add chemical functionality by the genetic engineering procedure. Genetic engineering is more advantageous than the chemical synthesis for the functionalization /deritivization of peptide nanowire because only the desired specific residue of the peptide is functionalized by the genetic approach. The specific sequence can also increase stability so that the mechanical property can be tuned to be suitable for device application in harsh environment. By using the recombinant technology, it is possible to design and amplify a collagen-like triple helix that is monodisperse, easily mineralized with metal/ semiconductor precursors, and therefore can be applied as a rigid biomolecular template for metal/semiconductor nanowire fabrications. Moreover the production of triple helix can be large scaled up by means of the cell multiplication. As continued work based on previous study of the application of C7 glycylglycine bolaamphiphilic peptide, the self-assembly of doughnut-shaped nanoreactors from monomer peptides with silica precursors was studied, and uniform size silica (SiO2) nanoparticles were obtained. Possible mechanism in terms of chelating and catalysis functions of the peptide was formulated.

  • INTERACTIONS OF EUKARYOTIC TRANSLATION INITIATION FACTORS AND 3' UNTRANSLATED REGION OF BARLEY YELLOW DWARF VIRUS mRNA DURING PROTEIN SYNTHESIS: A STUDY OF EQUILIBRIUM BINDING, KINETICS AND THERMODYNAMICS

    Author:
    Bidisha Banerjee
    Year of Dissertation:
    2014
    Program:
    Chemistry
    Advisor:
    Dixie Goss
    Abstract:

    Eukaryotic initiation factor (eIF) 4F binding to mRNA is the first committed step in cap-dependent protein synthesis. Barley Yellow Dwarf Virus (BYDV) employs a cap-independent mechanism of translation initiation which is mediated by a structural element BTE (BYDV translation element) located in the 3' UTR of its mRNA. eIF4F bound the BTE and a translational inactive mutant with high affinity; thus questioning the role of eIF4F in translation of BYDV. To examine the effects of eIF4F in BYDV translation initiation, BTE mutants with widely different in vitro translation efficiencies ranging from 5-164% compared to WT were studied. Using fluorescence anisotropy to obtain quantitative data, we show 1) the equilibrium binding affinity (complex stability) correlated well with translation efficiency, whereas the "on" rate of binding did not. 2) other unidentified proteins or small molecules in wheat germ extract (WGE) prevented eIF4F binding to mutant BTE but not WT BTE. 3) BTE mutants-eIF4F interactions were found to be both enthalpically and entropically favorable with an enthalpic contribution of 52-90% to delta G° at 25°C suggesting hydrogen bonding contributes to stability and 4) in contrast to cap-dependent and tobacco etch virus (TEV) Internal Ribosome Entry Site (IRES) interaction with eIF4F, PABP did not increase eIF4F binding. Further, the eIF4F bound to the 3' BTE with higher affinity than for either m7G cap or TEV IRES, suggesting that the 3' BTE may play a role in sequestering host cell initiation factors and possibly regulating the switch from replication to translation. In another project, we studied the interaction of a deletion mutant of wheat eukaryotic initiation factor 4B (eIF4B320-527) with zinc using the biophysical technique of circular dichroism. eIF4B is suspected to be a metalloprotein and it is known that zinc stimulates eIF4B self-association at physiological concentrations . It was found that in the presence of zinc there is significant change in the secondary structure of eIF4B320-527. There was approximately a 70% change in the presence of 500 &muM zinc and around 38% change in the presence of 500 &muM magnesium in alpha content as compared to native protein. There was a change observed in beta sheet content. The changes in secondary structure caused by zinc may be the one of the causes for the eIF4B self-association or enhanced eIF4B-PABP interaction. These results enhance our understanding of the molecular mechanisms by which cell controls translation initiation which is the rate limiting step of cellular protein synthesis.

  • Europium Complexes as Probes for Biological and Materials applications

    Author:
    Laurence Bensaid-Geyer
    Year of Dissertation:
    2009
    Program:
    Chemistry
    Advisor:
    Lynn Francesconi
    Abstract:

    Europium is a widely used lanthanide due to its emission in the visible region and its long life time. It is often complexed with ligands in order to serve different purposes in various domains: these complexes can be used as photostable biological probes but also as photoelectronic devices. This thesis interest will lie on both aspects. In chapter 2, we focused on europium phosphonates for targeting bone cancer. As we look at the adsorption of europium phosphonate to bone, possible scenario can take place: the complex can adsorb to the bone and/or the europium can transchelate from the ligand. If the europium transchelate, we looked at the possibility of a europium incorporation into the hydroxyapatite (HA) structure. We prove the presence of europium within the HA structure using various analytical and spectroscopic methods such as elemental analysis, X&ndashray diffraction (XRD), Infra-red (IR), luminescence studies, X&ndashray absorption fine structure (XAFS), and other spectroscopic analysis (SEM, BSE and EDS). In another part, the actual adsorption of europium phosphonate onto HA surface was studied. The adsorption was demonstrated based on luminescence studies showing a change of europium environment. In chapter 3, solution behavior of lanthanide complexes of the &alpha2&ndashP2W17O6110- ligand was reported to identify trends that will facilitate rational synthesis of hybrid organic lanthanide polyoxometalate complexes. Based on 31P NMR studies, the equilibrium between the 1:1 and the 1:2 species, that was observed by Pope for the Ce(III) analog is prevalent for the early-mid lanthanides. This equilibrium is slightly dependent on pH but seems to be very much influenced by larger poorly hydrated cations which appear to favor the 1:2 species for the early to mid lanthanides while they do not appear to influence the equilibrium for the later lanthanides. For all counterions, we found the 1:1 species stable with no trace of the 1:2 species. Finally, in chapter 4, we investigated Eu&alpha1&ndashP2W17O617- (EuPOM) for a layer by layer deposition application with Zn(phen)32+ (Zn(phen)) and its potential as a electroluminescence device. The depositions were monitored by UV-vis. We successfully fabricated multilayer film via electrostatic interaction between the polyanion EuPOM7- and the polycation Zn(phen)32+ until reaching four bilayers when the layers appeared to strip off. Also luminescence studies showed that the multilayer film demonstrated an effective luminescence activity due to the energy transfer through space from the phenanthroline to the europium ion.

  • Europium Complexes as Probes for Biological and Materials applications

    Author:
    Laurence Bensaid-Geyer
    Year of Dissertation:
    2009
    Program:
    Chemistry
    Advisor:
    Lynn Francesconi
    Abstract:

    Europium is a widely used lanthanide due to its emission in the visible region and its long life time. It is often complexed with ligands in order to serve different purposes in various domains: these complexes can be used as photostable biological probes but also as photoelectronic devices. This thesis interest will lie on both aspects. In chapter 2, we focused on europium phosphonates for targeting bone cancer. As we look at the adsorption of europium phosphonate to bone, possible scenario can take place: the complex can adsorb to the bone and/or the europium can transchelate from the ligand. If the europium transchelate, we looked at the possibility of a europium incorporation into the hydroxyapatite (HA) structure. We prove the presence of europium within the HA structure using various analytical and spectroscopic methods such as elemental analysis, X&ndashray diffraction (XRD), Infra-red (IR), luminescence studies, X&ndashray absorption fine structure (XAFS), and other spectroscopic analysis (SEM, BSE and EDS). In another part, the actual adsorption of europium phosphonate onto HA surface was studied. The adsorption was demonstrated based on luminescence studies showing a change of europium environment. In chapter 3, solution behavior of lanthanide complexes of the &alpha2&ndashP2W17O6110- ligand was reported to identify trends that will facilitate rational synthesis of hybrid organic lanthanide polyoxometalate complexes. Based on 31P NMR studies, the equilibrium between the 1:1 and the 1:2 species, that was observed by Pope for the Ce(III) analog is prevalent for the early-mid lanthanides. This equilibrium is slightly dependent on pH but seems to be very much influenced by larger poorly hydrated cations which appear to favor the 1:2 species for the early to mid lanthanides while they do not appear to influence the equilibrium for the later lanthanides. For all counterions, we found the 1:1 species stable with no trace of the 1:2 species. Finally, in chapter 4, we investigated Eu&alpha1&ndashP2W17O617- (EuPOM) for a layer by layer deposition application with Zn(phen)32+ (Zn(phen)) and its potential as a electroluminescence device. The depositions were monitored by UV-vis. We successfully fabricated multilayer film via electrostatic interaction between the polyanion EuPOM7- and the polycation Zn(phen)32+ until reaching four bilayers when the layers appeared to strip off. Also luminescence studies showed that the multilayer film demonstrated an effective luminescence activity due to the energy transfer through space from the phenanthroline to the europium ion.

  • Synthesis and characterization of Lanthanide Aluminotungstates and Rhenium Polyoxometalates: Potential Application in Molecular Information Storage Devices

    Author:
    Fang Bian
    Year of Dissertation:
    2011
    Program:
    Chemistry
    Advisor:
    Lynn Francesconi
    Abstract:

    Abstract Synthesis, speciation, and application of Polyoxometalates: Redox Molecular Information Storage Device Pre-research and Rhenium Chemistry By Fang Bian Adviser: Professor Lynn C. Francesconi Polyoxometalates (abbreviated as POMs) are metal-oxide clusters with frameworks built from group 5 or 6 transition metals linked by shared oxide ions. The Keggin structure is one of the most famous structural forms of POMs. Keggin anions have a general formula of [XM12O40]n-, where X is a p-block atom and M is a transition metal atom such as W or Mo. Upon removal of one MO4+ unit from the Keggin anion, the monovacant structure [XM11O39]n- is formed. Those POMs that have lost one or more metal center are called lacunary POMs, which are very nice building blocks for the fabrication of coordination polymers. My research focuses on two facets of POM chemistry: 1) Lanthanide chemistry of aluminum tungstate monovacant Keggin and 2) Rhenium chemistry of aluminum tungstate Keggin and Wells-Dawson POM a1-P2W17O61. In lanthanide POM research area, we obtained the following results: 1) The starting material aluminum tungstate monovacant Keggin α-K9AlW12O39 was synthesized. Its single crystal was firstly identified by multinuclear NMR and X-ray crystallography. Its redox properties on the nano-scale solid state were determined by Conducting Electrostatic Force Mode (EFM) probes. It is well known that for POMs, a number of varies redox states are normally stable and reversible. Thus we estimated that POMs can potentially be used in molecular information storage applications, which we refer to as "redox disk drives". 2) Eight lanthanide aluminum tungstate Keggin complexes were synthesized. In their molecular structures (identified by multinuclear NMR and X-ray crystallography), each α-AlW11O39 is connected by lanthanide (III) cations to form 1D and 2D networks. All AlW11O39 Keggin POMs are regularly aligning on a flat plane. Microscopic data also verified that there is layer-by-layer morphology in this series of compounds. Overall, we postulate that aluminum tungstate Keggin POMs are a very promising materials for making future information storage device because they have several stable redox states and can be reduced by adding voltage in solid state, The Keggin POMs can be regularly aligned on a flat plane, 3) In rhenium chemistry research area, we successfully synthesized rhenium complexes of the [a1-P2W17O61]10- and α-K9AlW13O39. The structure info of [ReVO(a1-P2W17O61)]7- was identified by multinuclear NMR and X-ray crystallography. The cyclic-voltammetry of [ReVO(a1-P2W17O61)]7- has also been measured and compared to the [ReVO(a2-P2W17O61)]7- isomer. A rhenium derivative of α-K9AlW11O39 also has been synthesized. Multinuclear NMR gives structure information. After oxidation in air, this compound can aggregate to form insoluble nanoparticles.

  • Property Enhancements of Dielectric Nanoparticles via Surface Functionalization

    Author:
    Andrew Byro
    Year of Dissertation:
    2014
    Program:
    Chemistry
    Advisor:
    Stephen O'Brien
    Abstract:

    This thesis describes the surface modification of barium strontium titanate nanoparticles for use in polymer/ceramic composite thin film capacitors with resultant improved dielectric and film-making properties. Phosphonic acid-type ligands proved to be most effective for surface conjugation to the surface of the barium strontium titanate nanoparticles. Amine-terminated ligands proved to be effective at removing surface adsorbed water before being almost entirely removed during the sample washing stage. Carboxylic acid terminated ligands proved to adhere less well to the nanoparticle than the phosphonic acid, but resulted in thin films with a higher dielectric constant, which was more stable in the measured frequency range than the phosphonic acid. This is seen via a systematic change in thin film variables, including ligand length, ligand reactive head, presence of polymer composite, and concentration of ligand. The nanoparticles were synthesized, ligands attached, then a series of thin film capacitors were fabricated to study the chang in dielectric properties. The results show a stabilized dielectric constant over a wide frequency range, a dramatically decreased loss, and better film-making properties. The new materials presented in this study are potentially useful as dielectrics for low-energy-density/low-loss capacitors.

  • Design of Large Pore Ordered Mesoporous Silicas, Related Silica/Polymer Composites and Carbon Replicas

    Author:
    Liang Cao
    Year of Dissertation:
    2010
    Program:
    Chemistry
    Advisor:
    Michal Kruk
    Abstract:

    This dissertation includes four chapters, namely, the introduction to development and current research interests in mesoporous materials, the "soft-templating" synthesis of large pore 2-D hexagonal ordered mesoporous silicas, the synthesis of mesoporous polymer/silica composites via surface-initiated controlled polymerization, and the "hard-templating" method to fabricate ordered mesoporous carbons. In Chapter 2, the synthesis of SBA-15 silica with 2-D hexagonal structure of large and ultra-large cylindrical mesopores is outlined. Our work on hexane and 1,3,5-triisopropylbenzene, as suitable micelle expanders, allowed us to tailor SBA-15 pore diameter up to ~15 nm and ~30 nm, respectively. Silica precursors tetraethylorthosilicate (TEOS) and tetramethylorthosilicate were both found suitable, but TEOS was preferred. We also developed a facile and rapid method to synthesize SBA-15 and other mesoporous silicas (FDU-12) in a few hours instead of at least 2 days as originally reported. We also found that the use of static conditions can induce formation of large-pore SBA-15 with platelet morphology. In Chapter 3, the synthesis of well-defined mesoporous polymer/silica composites via surface-initiated atom transfer radical polymerization (ATRP) was described. 2-(4-chlorosulfonylphenyl)ethyltrichlorosilane was successfully proven as a cost-effective and powerful initiator to initiate polymerizations of various monomers from SBA-15 silicas. We further demonstrated the ATRP with activators regenerated by electron transfer (ARGET) as a more convenient and more environmentally friendly pathway to synthesize polymer/silica composites under mild conditions with hundred ppm levels of copper catalyst and tolerance of limited initial amount of air. In both methods, tunable surface properties, such as adjustable polymer loadings and polymer film thicknesses, can be achieved. In Chapter 4, high quality ordered mesoporous carbons were synthesized using mesophase pitch or grafted polyacrylonitrile (PAN) as carbon precursors. The infiltration of mesophase pitch into the silica host was effective for synthesis of semi-graphitic carbons with different framework geometries, such as 2-D hexagonal array of nano-rods or cubic carbon structures, even at low carbonization temperature (850 oC). After stabilization and carbonization of silica/PAN composites, and removal of silica templates, mesoporous carbon materials had ordered structures with hollow nanoscale features, nanopipes or nanospheres from replication of SBA-15 or FDU-12 silicas, respectively.

  • Design of Large Pore Ordered Mesoporous Silicas, Related Silica/Polymer Composites and Carbon Replicas

    Author:
    Liang Cao
    Year of Dissertation:
    2010
    Program:
    Chemistry
    Advisor:
    Michal Kruk
    Abstract:

    This dissertation includes four chapters, namely, the introduction to development and current research interests in mesoporous materials, the "soft-templating" synthesis of large pore 2-D hexagonal ordered mesoporous silicas, the synthesis of mesoporous polymer/silica composites via surface-initiated controlled polymerization, and the "hard-templating" method to fabricate ordered mesoporous carbons. In Chapter 2, the synthesis of SBA-15 silica with 2-D hexagonal structure of large and ultra-large cylindrical mesopores is outlined. Our work on hexane and 1,3,5-triisopropylbenzene, as suitable micelle expanders, allowed us to tailor SBA-15 pore diameter up to ~15 nm and ~30 nm, respectively. Silica precursors tetraethylorthosilicate (TEOS) and tetramethylorthosilicate were both found suitable, but TEOS was preferred. We also developed a facile and rapid method to synthesize SBA-15 and other mesoporous silicas (FDU-12) in a few hours instead of at least 2 days as originally reported. We also found that the use of static conditions can induce formation of large-pore SBA-15 with platelet morphology. In Chapter 3, the synthesis of well-defined mesoporous polymer/silica composites via surface-initiated atom transfer radical polymerization (ATRP) was described. 2-(4-chlorosulfonylphenyl)ethyltrichlorosilane was successfully proven as a cost-effective and powerful initiator to initiate polymerizations of various monomers from SBA-15 silicas. We further demonstrated the ATRP with activators regenerated by electron transfer (ARGET) as a more convenient and more environmentally friendly pathway to synthesize polymer/silica composites under mild conditions with hundred ppm levels of copper catalyst and tolerance of limited initial amount of air. In both methods, tunable surface properties, such as adjustable polymer loadings and polymer film thicknesses, can be achieved. In Chapter 4, high quality ordered mesoporous carbons were synthesized using mesophase pitch or grafted polyacrylonitrile (PAN) as carbon precursors. The infiltration of mesophase pitch into the silica host was effective for synthesis of semi-graphitic carbons with different framework geometries, such as 2-D hexagonal array of nano-rods or cubic carbon structures, even at low carbonization temperature (850 oC). After stabilization and carbonization of silica/PAN composites, and removal of silica templates, mesoporous carbon materials had ordered structures with hollow nanoscale features, nanopipes or nanospheres from replication of SBA-15 or FDU-12 silicas, respectively.

  • COMPUTATIONAL STUDIES OF REACTIVE OXYGEN AND SULFUR SPECIES

    Author:
    Álvaro Castillo
    Year of Dissertation:
    2011
    Program:
    Chemistry
    Advisor:
    ALEXANDER GREER
    Abstract:

    In this thesis, we summarized the use of computational chemistry methods to provide insight into the chemistry of reactive intermediates species like singlet oxygen, thiozone, radical and diradicals of mercapto-quinones, and benzyl alkynyl sulfides anions. The theoretical methods used included Density Functional Theory, and hybrid [Molecular Orbital:Molecular Orbital] methods and the Conductor-like Polarizable Continuum Model for condensed phase calculations. The first chapter deals with carbon nanotubes as a class of host cavities to encapsulate the unstable molecule thiozone (S3). We computed single-walled carbon nanotube (SWNT)-thiozone pairs. Nanotube diameter selectivity for isomerization of the C2v form of S3 to the D3h form proved to be elusive. 1,2,3-Thiozonide formation took place on the convex side of nanotubes of low tube radii, such as the armchair (4,4) and (5,5) SWNTs. The second chapter focused on singlet oxygen release from a naphthalene endoperoxide which bears a flexible (CH2)22 polymethylene "lid". Monte Carlo and ONIOM calculations that incorporated semiempirical and density functional theory were used in the study. Interestingly, the polymethylene chain appears to function as a gatekeeper for the oxygen, where, instead of coming full circle, a semi-circle rotation of the polymethylene bridge protected the peroxide group, limiting the dissociation of 1O2 from the naphthalene site. The third chapter deals with condensed-phase calculations of the reaction of aryl substituted benzyl 1-alkynyl sulfides with potassium t-methoxide in acetonitrile. This reaction produces 2-aryl 2,3-dihydrothiophene products. Experimental evidence (from our collaborators) indicates that there is a rapid exchange of protons and tautomerism of the alkynyl unit prior to cyclization to the dihydro-thiophenes. The fourth and last chapter is devoted to DFT calculations of quinones, radicals and diradicals. Calculations on these reactive species arising from mercapto- and bismercaptocatechols were conducted seeking to provide insight into their relative stability.

  • COMPUTATIONAL STUDIES OF REACTIVE OXYGEN AND SULFUR SPECIES

    Author:
    Álvaro Castillo
    Year of Dissertation:
    2011
    Program:
    Chemistry
    Advisor:
    ALEXANDER GREER
    Abstract:

    In this thesis, we summarized the use of computational chemistry methods to provide insight into the chemistry of reactive intermediates species like singlet oxygen, thiozone, radical and diradicals of mercapto-quinones, and benzyl alkynyl sulfides anions. The theoretical methods used included Density Functional Theory, and hybrid [Molecular Orbital:Molecular Orbital] methods and the Conductor-like Polarizable Continuum Model for condensed phase calculations. The first chapter deals with carbon nanotubes as a class of host cavities to encapsulate the unstable molecule thiozone (S3). We computed single-walled carbon nanotube (SWNT)-thiozone pairs. Nanotube diameter selectivity for isomerization of the C2v form of S3 to the D3h form proved to be elusive. 1,2,3-Thiozonide formation took place on the convex side of nanotubes of low tube radii, such as the armchair (4,4) and (5,5) SWNTs. The second chapter focused on singlet oxygen release from a naphthalene endoperoxide which bears a flexible (CH2)22 polymethylene "lid". Monte Carlo and ONIOM calculations that incorporated semiempirical and density functional theory were used in the study. Interestingly, the polymethylene chain appears to function as a gatekeeper for the oxygen, where, instead of coming full circle, a semi-circle rotation of the polymethylene bridge protected the peroxide group, limiting the dissociation of 1O2 from the naphthalene site. The third chapter deals with condensed-phase calculations of the reaction of aryl substituted benzyl 1-alkynyl sulfides with potassium t-methoxide in acetonitrile. This reaction produces 2-aryl 2,3-dihydrothiophene products. Experimental evidence (from our collaborators) indicates that there is a rapid exchange of protons and tautomerism of the alkynyl unit prior to cyclization to the dihydro-thiophenes. The fourth and last chapter is devoted to DFT calculations of quinones, radicals and diradicals. Calculations on these reactive species arising from mercapto- and bismercaptocatechols were conducted seeking to provide insight into their relative stability.