Alumni Dissertations and Theses

 
 

Alumni Dissertations and Theses

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  • 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.

  • 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.

  • 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.

  • STRUCTURAL STUDIES OF BIOPOLYMERS USING COMPUTER SIMULATIONS, OPTICAL AND MAGNETIC SPECTROSCOPY

    Author:
    Subhasish Chatterjee
    Year of Dissertation:
    2009
    Program:
    Chemistry
    Advisor:
    RUTH STARK
    Abstract:

    Biopolymers are essential components of numerous natural and synthetic macromolecular assemblies. In the present study, the structural properties of biopolymers ranging from fungal melanins to synthetic nucleic acids were investigated using spectroscopic methods and theoretical modeling. (1) Computational modeling and molecular dynamics simulations were used to study the structural properties of a short single-stranded (ss) DNA. The dependence of the conformational stability and flexibility of the ssDNA on the thermodynamic conditions of the system was demonstrated. (2) Time-resolved fluorescence spectroscopy involving an organic donor-quencher pair was utilized to study the conformational properties of Y-shaped DNA. Results highlighted the different distances between the arms of the Y-DNA and indicated the overall structural stability of the Y-DNA system. Time-resolved fluorescence techniques were applied to investigate the distance dependence of the non-radiative energy transfer process between an organic donor (fluorescein) and a gold nanoparticle quencher connected by double stranded (ds) DNA. (3) Synthesis of phospholipid-conjugated gold nanoparticles and their self-assembly onto an aqueous subphase were tested. The resulting lipid-capped nanoparticles were characterized by optical methods such as UV-Vis absorption spectroscopy and dynamic light scattering. The effects of bio-functionalization on the size of biotin-capped gold nanoparticles were investigated using optical techniques. (4) Solid-state nuclear magnetic resonance (NMR) spectroscopy was utilized to elucidate the structural characteristics of fungal melanins. Various spinning speeds, temperatures, magnetic field strengths, and isotopic labels were utilized with 1D and 2D 13C MAS NMR, revealing distinctive structural fingerprints of the fungal melanins generated biosynthetically with L-dopa, methyldopa, epinephrine, and norepinephrine. These pigments exhibited differences in their aromatic and aliphatic structures and probable biosynthetic pathways, and it was possible to delineate proximities between particular melanin and membrane-related molecular groups.

  • I. The RCM Approach Towards 1,6-methano-bridged[12] & [14]Annulenes and their Bisdehydro-derivatives II. 1,5-bisdehydro[10]Annulene Revisited

    Author:
    Yor-Yu Chen
    Year of Dissertation:
    2010
    Program:
    Chemistry
    Advisor:
    Klaus Grohmann
    Abstract:

    Part I of my dissertation presents a new efficient synthesis of 3,4-benzo-1,6-methano[12]annulene (3). This novel synthetic approach involves a grignard addition to 3,4-benzo-cycloheptatriene-1,6-dialdehyde followed by a ring closing olefin metathesis (RCM) reaction giving the bridged 12-menber ring of 3,4-benzo-1,6-methano[12]annulene (3) was obstained in six steps and an overall yield 44%. This allowed the complete structural and spectroscopic characterization as a paratropic ethano-bridged benzo[12]annulene with a 28% reduction of the paramagnetic ring current relative to the non-benzannulated molecule. A careful comparison of the 1H NMR of (3) with its 9,10-dihydro derivative (104) suggests an extended paratropic 16π system. The RCM approach is general and thus formally presents a 6 steps route to the parent 1,6-methano[12]annulene, previously reported by E. Vogel et al. Combination of cis-selective Wittig reaction of (36) with the ylide derived from 4-bromo-1-butene followed by RCM reaction yielded the 9,12-dihydro-3,4-benzo-1,6-methano[14]annulene (35). Attempts to convert this molecular in to the expectedly diatropic 14π system did not succeed so far. In course of this investigation, an efficient synthesis for 3,4-benzo-1,6-ethynylcycloheptatriene was developed. Diketone (37) obtained through Jones oxidation of the diasteromeric alcohols (26) was converted into the 3,4-benzo-1,6-methano-7,12-bis(dibromomethylene)-8,11-dihydro[12]annulene (38). Treatment of this molecule with two moles of n-butyllithium did not yield the anticipated diacetylene (39). From diketone (37) a series of 7,12-disubstituted bridged [12]annulene can be synthesized, this illustrating the generality of this approach. In part II of my dissertation, approaches toward 1,5-bisdehydro[10]annulenes were investigated with the goal to increase the activation energy for the known Bergmann rearrangement or even mark it impossible for the molecule to undergo it. This would enable us to investigate the expected 10π aromaticity of the 1,5-bisdehydro[10]annulene system. An initial approach utilizing the Ramberg Bakelund rearrangement failed due to the irreproducibility of the formation of the cyclic sulfide (70). Elimination was the major pathway even at pH8, most likely due to the very acidic propargylic hydrogens. The second approach started with the 10 menber ring diyneacetals (78), (85), (91). In course of this investigation a new reaction sequence was discovered as outline on scheme 3-9. This valuable fragmentation deprotection of stable cyclic benzylidene acetals leads directly to allylic alcohols such as compound (86). The introduction of the last double bond via the mesylate followed by treatment with potassium t-butoxide gave unexpectedly Benz(a)anthacene (89) and tetracene (88) in a ratio of 40:1. This result is being interpreted as an initial acetylene-allene isomerization followed by an allene-acetylene cyclization (Myers-Saito cyclization), hydrogen abstraction and aromatization as shown on scheme 3-14. Treatment of the mesylate (93) derived from the allylic alcohol with potassium t-butoxide gave phenanthrene and anthracene in a ratio of 2:3. Treatment of the mesylate with triethylamine gave only anthracene, the expected product of the Bergmann rearrangement.

  • MULTIFERROIC AND CORE-SHELL NANOSTRUCTURES - ADVANCES IN PREPARATIONS AND NOVEL PROPERTIES

    Author:
    I-Wei Chu
    Year of Dissertation:
    2010
    Program:
    Chemistry
    Advisor:
    Nan-Loh Yang
    Abstract:

    This dissertation reports the research findings in two nanoscience areas: (i) facile methods for the preparation of multiferroic bismuth ferrites nanoparticles and the observation of room temperature magnetoelectric coupling and optically induced magnetic and electric orderings in BiFeO3 (BFO) thin film; (ii) preparation and characterization of core-shell nanomaterials based on conducting polymer as components for shell and core. Controlled cargo release from the core as well as from the shell surface was examined for nanospheres with conjugate polymer shell. An unusual enhanced electric polarization was observed for nanospheres with high-k strontium titanate (STO) nanocrystals embedded in conductive polyaniline (PANI) matrix. Multiferroics represent a class of new materials having potential applications for design and preparation of multifunctional material due to the coupling of their coexisting electric and magnetic orderings. Previously, the syntheses of thin film multiferroic materials involve multi-steps in various high temperatures or specific demanding environment. We discovered that nanocrystal thin film and powder of multiferroic BFO could be prepared using new facile procedures: spin-casting and autoclave methods. The room temperature magnetoelectric coupling in nanocrystal BFO was established using scanning probe microscopy, including magnetic force microscopy (MFM) and Kelvin probe force microscopy (KPFM). Magnetic and electrical orderings induced by irradiation 300 to 560 nm were observed. Thus, the "magnetic-electric-optic" coupling at room temperature was observed for the first time in BFO nanocrystal thin film. Core-shell nanospheres of conducting polymer poly(3, 4-ethylenedioxythiophene), PEDOT, with soft template (1-butyl-3-methyimidazolium hexafluorophosphate, bmimPF6) were prepared using interfacial polymerization on the shell surface of the micelle stabilized by surfactant (Triton X-100). The diameter of nanospheres was controlled by bmimPF6-to-surfacnt ratio. The release of cargo from the core and shell of the spheres was trigged by pH control and observed by photometric measurement. Aspect ratio and crystallinity of PEDOT shell increases in high pH value (above 10). In addition, the interaction of electronic polarization with atomic polarization was studied for core-shell nanosphere of PANI matrix with STO nanoparticles embedded. This nanosystem represents the first encapsulated nanospheres with extensive interfacial interaction within the core due to atomic polarizable isolated nano-domains embedded in an electronic polarizable continuous matrix.

  • Development of Cell-Active Inhibitors and Activity-Based Probe of Cysteine Cathepsins

    Author:
    Dibyendu Dana
    Year of Dissertation:
    2014
    Program:
    Chemistry
    Advisor:
    SANJAI KUMAR
    Abstract:

    Cysteine cathepsins are an important class of enzymes that coordinate a variety of important cellular processes, and are implicated in various types of human diseases. Still however, many of their cellular function remain poorly understood. Chemical biology approaches employing small molecules can be utilized for this purpose. Unfortunately small molecule probes that are cell-permeable and non-peptidyl in nature are scarcely available. In this work, first a library of sulfonyloxiranes is synthesized. From this library, 2-(2-ethylphenylsulfonyl)oxirane is identified as a selective inhibitor of cysteine cathepsins. Cell-based study reveals that 2-(2-ethylphenylsulfonyl)oxirane is a cell-permeable, covalent, and irreversible inhibitor of cathepsin B with modest efficacy. Next, a hybrid-design approach is undertaken to develop a highly potent and selective peptidyl vinylsulfonates inhibitor (KD-1) of human cathepsin L. Studies involving human breast carcinoma MDA-MB-231 cells establishes that this inhibitor can successfully block intracellular cathepsin L activity, and retards the cell-migratory potential of these highly metastatic cells. This work has been further extended to develop an activity-based probe (KDP-1) of cathepsin L by suitable modification of KD-1 inhibitory scaffold. KDP-1 has been found to be so far the most potent activity-based probe of cathepsin L. Cell-based studies are currently underway to demonstrate the cellular efficacy of KDP-1. Further, KDP-1 is anticipated to find extensive applications in proteome-wide analysis of cathepsin L activity in both normal and diseased cells.