Alumni Dissertations

 

Alumni Dissertations

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  • SYNTHESE OF POLYMER-SUPPORTED AMIDE-TYPE LIGANDS AND COMPLEXATION OF LANTHANIDE IONS

    Author:
    Yijia Yang
    Year of Dissertation:
    2011
    Program:
    Chemistry
    Advisor:
    Spiro Alexandratos
    Abstract:

    The complexation of lanthanide ions from acidic solutions was studied with cross-linked polystyrene modified with amide-type ligands: N,N,N',N'-tetramethylmalonamide (TMMA), monoamidated malonate and urea. The TMMA resin showed preference towards Tb, Dy and Eu from highly acidic solutions. Ionic recognition is achieved through a mechanism in which two opposing processes--electrostatic attraction of M(H2O)xCl4- or M(H2O)x(NO3)your4- by the protonated ligand and (partial) loss of the waters of hydration--dominate at different points along the lanthanide series. The proposed complexation mechanism consists of protonation of one of the carbonyls, which is stabilized by hydrogen bonding to the neighboring carbonyl oxygen, formation of iminium site and ion exchange by exchanging the chloride ion with the lanthanide chloro or nitro complex. The importance of the substituents at amide nitrogen was probed with immobilized malonate ligands monoamidated with diethylenetriamine (DETA-MAm) and immobilized diethylenetriamine ligands with one amine nitrogen converted to urea (Urea-3). The comparison of the lanthanides complexation by the TMMA, DETA-MAm and Urea-3, was carried out under conditions in which each resin has its best performance: 6 M HCl for TMMA and 8 M HCl for DETA-MAm and Urea-3. The protonated TMMA, with two electron-donating methyl groups at the iminium nitrogen to attenuate the (+) charge (=NR2(+)), is the weakest ligand with ionic recognition properties towards the lanthanides in the middle of the series. The reduced ligand strength makes it more responsive towards changes between the electrostatic attraction and the enthalpy of dehydration. The protonated Urea-3 showed much higher lanthanide affinities than the TMMA and DETA-MAm, and its affinity trend paralleled the trend of lanthanides ionization potentials due to the absence of methyl group to attenuate the (+) charge (=NH2(+)). The DETA-Mam is somewhere in between the TMMA and Urea-3 because its iminium has only one −CH2− moiety attenuating the (+) charge (=NHR(+)) and it is also a two-site interaction with the ammonium group probably contributing to the electrostatic stabilization of the chlorocomplex.

  • EUKARYOTIC INITIATION FACTOR 4F (elF4F) ENHANCES HIGH AFFINITY BINDING OF 40S RIBOSOMAL SUBUNIT TO TOBACCO ETCH VIRUS (TEV) INTERNAL RIBOSOME ENTRY SITE (IRES)

    Author:
    Sumeyra Yumak
    Year of Dissertation:
    2010
    Program:
    Chemistry
    Advisor:
    Dixie Goss
    Abstract:

    Many viruses and some eukaryotic mRNAs employ a cap-independent pathway in which an RNA element called the internal ribosome entry site (IRES), drives preinitiation complex formation by positioning the ribosome on the message, either at or just upstream of the start site. We have studied binding of wheat germ 40S subunit of wheat germ ribosome to wild type PK1 RNA, which shows 100 % translation activity. To explore the specificity of the IRES RNA*40S interaction, we also measured the affinity for IRES RNA mutants, S2-3 RNA and to S1-3 RNA that have been previously characterized in terms of in vitro translation initiation activity (1). The level of expression from each mutant is calculated relative to the corresponding wild-type sequence, which is set at 100%.S2-3 RNA shows about 30% translation activity while S1-3 RNA shows about 7% translation activity. While ribosome binding to eukaryotic mRNAs requires the participation of eukaryotic initiation factors eIF4A, eIF4B, and eIF4F and the hydrolysis of ATP, our results suggest that the 40S ribosomal subunit binds directly to the PK1 RNA with dissociation constant (Kd) of 67 nM. While 40S ribosome bound to S2-3 RNA with Kd of 138 nM; significant binding to S1-3 RNA was not observed. Direct binding measurements of both wild type and mutant TEV IRES RNAs suggest that TEV message is driven through a high affinity TEV RNA*40S interaction, involving a novel strategy of ribosome recruitment distinct from eukaryotic cap-dependent mechanisms. Fluorescence anisotropy data showed that eIF4F increased 40S Ribosome binding affinity to PK1 RNA by approximately 2.6 fold. To determine the effects of initiation factor mediated RNA unwinding in cap independent initiation, we determined RNA binding activity of elF4A, elF4B and 40S Ribosome with TEV RNAs. The fluorescence anisotropy data revealed that in the presence of eIF4A, eIF4B, and hydrolysis of ATP, binding affinity of 40S ribosome to PK1 RNA increased 4 fold; giving Kd of 17 nM. Under the same conditions, while binding affinity of 40S ribosome to S2-3 RNA increased 2 fold, there was no significant change in S1-3 RNA binding to 40S.These data correlate well with the observed translational data and provide more detailed information on the translational strategy of tobacco etch virus.

  • Arylboronic Acid-Catalyzed Hydrolyses of Salicylaldehyde Imines

    Author:
    Sheuli Zakia
    Year of Dissertation:
    2011
    Program:
    Chemistry
    Advisor:
    Manfred Philipp
    Abstract:

    ABSTRACT Arylboronic Acid-Catalyzed Hydrolyses of Salicylaldehyde Imines By Sheuli Zakia Adviser: Prof. Manfred Philipp Boronic acids accelerate hydrolyses of the Schiff's bases derived from salicylaldehyde and primary amines. The accelerations of Schiff's base hydrolyses are due to the formation of a complex between the boronic acid and the imine followed by the break-down of the complex to products. The formation of a reversible complex between arylboronic acids and imines allows the rate of hydrolysis to display typical Michaelis-Menten enzyme-substrate kinetics, including situations where the imine is completely saturated with the boronic acid. This thesis focuses on the ability of different arylboronic/benzeneboronic acids(BBAs) to catalyze the hydrolysis of different imines, most of them being salicylaldehyde imines made using primary amines or amino acids, an example being salicylidene-threonine. In order to better understand the mechanism involved in the imine hydrolysis by arylboronic acids, I studied structure-activity relationships(SAR) for different substituted BBAs and of different imine substrates undergoing hydrolyses. Herein, I present the most important aspects of these SAR studies on both the catalysts(BBAs) and on their imine substrates. I hypothesized that electron withdrawing groups would enable BBAs to be more easily ionized, thus becoming better hydrogen bond donors and making it easier to have higher affinities for the imine substrates. SAR experiments conducted with different fluoro-substituted benzeneboronic acids showed that all fluoro-BBAs have higher catalytic efficiencies of imine hydrolysis than the un-substituted boronic acid except for the catalysts with two fluorine atoms substituted in the ortho- position with respect to the boron atom. The latter presumably induced steric hindrance. SAR on BBAs enabled me to discover novel catalysts for the hydrolysis of salicylidene-3-hydroxyaniline imine. The best ones are with 2,3,5-trifluoroBBA and 2,3,4,5-tetrafluoroBBA and their kcat/KM values go over 1000 fold higher than with the unsubstituted BBA. Furthermore, SAR of different imine substrates highlights the most important structural determinants of the enhanced catalytic efficiency. The most important contribution to the efficiency of imine hydrolysis are shown to be the hydrogen bonding donors or acceptors (hydroxy or amino groups) in the imine substrates which are demonstrated to activate the catalytic turn-over (kcat) of the arylboronic acid catalyst. The pH dependencies for BBA catalyzed hydrolysis of salicylaldehyde-3-hydroxyaniline shows that rate constants are maximal at lower pH values and decrease with increasing pH. The kinetics shows single proton ionizations, demonstrating that there is no other ionization event related to the imine itself which could affect catalytic efficiency. Moreover, the kcat, KM and kcat/ KM dependencies with pH shows that kcat is independent of pH. This indicates the absence of hydroxide or hydronium ion involvement in the hydrolysis. The plots of Log10 (KM), Log10 (kcat), Log10 (kcat/KM), vs. Hammett sigma substituent constants indicate that kcat, KM and kcat/KM all dependent on electron withdrawing substituent groups present in the benzeneboronic acids. The hydrogen bonding network provided by the hydroxyl or amino groups in the imine substrates during the hydrolysis could assist the BBA catalysts in binding tighter to the substrate, which in turn, are reflected in higher catalytic efficiencies. The presence of hydroxyl and amino groups in imine substrates of 2,3,4,5-tetrafluoroBBA resulted in 5- to over 100-fold increases in kcat/KM values. Thus the 2,3,4,5-tetrafluoroBBA-catalyzed kcat/KM value for salicylidene-threonine is 33 M-1sec-1 and for salicylidene-lysine is 17 M-1sec-1 whereas for salicylidene-valine, without an amino acid side chain hydroxyl or amino group, it is only 8 M-1sec-1. The relative stabilities of the complexes between BBAs and imines are predicted through docking experiments with the software SCULPT provided by MDL. NMR spectroscopy experiments are performed to confirm the structures. This thesis highlights the importance of the hydroxyl group substituted to the benzene ring in aniline or benzylamine based imines in inducing better catalytic efficiencies for their hydrolyses by fluoro-substituted BBAs. Examples are shown in the kcat/KM values for the hydrolysis of salicylidene-3-hydroxyaniline with 2,3,5-trifluoroBBA (232 M-1sec-1), and 2,3,4,5-tetrafluoroBBA (175 M-1sec-1).

  • Hybrid Fiber-Optic Device For Spatiotemporal Control of Photosensitizer Release and Singlet Oxygen Delivery

    Author:
    Matibur Zamadar
    Year of Dissertation:
    2011
    Program:
    Chemistry
    Advisor:
    Alexander Greer
    Abstract:

    Abstract: This thesis outlined the gradual progress towards the development of the first fiber-optic singlet-oxygen generator designed for releasing singlet oxygen locally, which can surmount the challenges associated with current photodynamic therapy and water disinfection. We developed a photochemical approach to clean generation of singlet oxygen in aqueous solution with a sensitizer (meso-tetra(N-methyl-4 pyridyl)porphine) adsorbed onto solid porous Vycor glass (PVG)]. Photophysical analysis revealed that oxygen collision onto the sensitizer adsorbed porous Vycor glass matrix converts ground-state oxygen into singlet oxygen (1O2) which diffuses into bulk aqueous solution. Singlet oxygen was detected in water by time-resolved methods and by chemical trapping with alkene, N-benzoyl methionine, and anthracene derivative to give hydroperoxide, N-benzoyl sulfoxide, and anthracene endoperoxide derivative. Based on this study, we developed a device that channels light and oxygen through a hollow core fiber optic into the sensitizer adsorbed Vycor glass which acts as a cap. Singlet oxygen was generated on a microscale at the fiber cap site selectively which then diffused out into the surrounding aqueous solution. A complete Escherichia coli inactivation was observed in 2 h when the fiber cap was immersed in 0.1 mL aqueous samples of 0.1-4.4 × 107 cells. The prototype device was further modified to enhance singlet oxygen diffusion in aqueous solution as singlet oxygen has lifetime's ranges from microseconds to milliseconds and the corresponding diffusion distances of singlet oxygen ranges from nanometers to millimeters. Our efforts included 1O2 generation by cleaving off sensitizer molecules away from the fiber optic probe to increase 1O2 formation at a distance from the probe tip. Synthetic methodology was developed to modify the glass probe to release photosensitizer molecules into the surrounding medium by an oxidative self-cleaving mechanism where 1O2 was used as a sole reagent. We successfully attached pyropheophorbide photosensitizer containing a photosensitive electron rich alkene covalently to porous Vycor glass which is triggered for release on-site by visible light irradiation, via dioxetane decomposition to give two carbonyl fragments. The cleaved photosensitizer diffuses into solution to produce singlet oxygen at a distance from the glass surface which also improves the photooxidation efficiency of the heterogenous photosensitizer. Finally, a review of the literature on `singlet oxygen as a reagent in organic synthesis' was accomplished, which represent the last chapter of the thesis.

  • ENHANCEMENT TO IMPLICIT SOLVENT MODELING OF PEPTIDES IN WATER AND IN LIPID BILAYERS

    Author:
    Huan Zhan
    Year of Dissertation:
    2013
    Program:
    Chemistry
    Advisor:
    Themis Lazaridis
    Abstract:

    In recent years implicit solvation models have been increasingly used in molecular dynamics (MD) simulations of proteins/peptides due to their computational efficiency. While these models can account for electrostatic interactions and hydrophobic effect of proteins/peptides in both water and lipid membranes, other properties of the solvent, such as the local dielectric screening effect at the binding sites of metalloproteins, the membrane dipole potential, and the membrane lateral pressure, have not yet been included. In this work, first the effective energy function (EEF1) is extended to simulate metalloproteins by neutralizing ligand carboxylates based on their exposure to solvent water. The new model is then applied to MD simulation of calcium-binding proteins calbindin d9k, calmodulin, troponin C, and parvalbumin. Although structures consistent with experiments are obtained, the model is limited by the fact that the selection of charges for carboxylates is arbitrary, and that the charges cannot be modified as the protein structure changes during the simulation. Second the implicit membrane mode (IMM1) is extended to include the membrane dipole potential, and the new model is applied to MD simulation of the helical peptides alamethicin, WALP23, influenza hemagglutinin fusion peptide, HIV fusion peptide, magainin, and the pre-sequence of cytochrome c oxidase subunit IV (p25). The results show that the orientation of the peptides in the membrane can be influenced by the dipole potential. In general peptides that tend to insert the N-terminus in the membrane and/or have positively charged side chains will lose binding affinity upon increase of the dipole potential. Finally, IMM1 is extended to include lateral pressure effects and tested by MD simulation of the peptides alamethicin, melittin, cyclotide kalata B1, 18A, and KKpL15. The simulations of alamethicin binding to pure DOPC bilayer show that increase in the peptide/lipid molar ratio favors the transmembrane orientation, which is explained by the difference in the cross-sectional area of the two orientations. The simulations of all peptides binding to mixed DOPC/DOPE bilayers show that the binding energy can increase, decrease, or not change as the molar fraction of DOPE increases, which is explained by the difference in the binding location of the peptides.

  • SYNTHESIS OF SILICA NANOSTRUCTURES BY USING WET-CHEMISTRY METHODS

    Author:
    Henan Zhang
    Year of Dissertation:
    2013
    Program:
    Chemistry
    Advisor:
    Daniel Akins
    Abstract:

    For the sol-gel synthesis of silica particles under high pH catalytic conditions (pH>12) in water/ethanol solvent, we have deduced that the competing dynamics of chemical etching and sol-gel formation can explain the types of silica particles formed and their morphologies. We have demonstrated that emulsion droplets that are generated by adding tetraethyl orthosilicate (TEOS) to a water-ethanol solution serve as soft templates for hollow spherical silica (1~2 µm). And if the emulsion is converted by the sol-gel process, one finds that suspended solid silica spheres of diameter of ~900 nm are formed. Moreover, several other factors are found to play fundamental roles in determining the final morphologies of silica particles, such as by variation of the pH (in our case, using OH¯) to a level where condensation dominates; by changing the volume ratios of water/ethanol; and using an emulsifier (specifically, CTAB). For a sol-gel process occurring in a water/oil (w/o) system, the self-assembly of silica nuclei can be controlled by close control of synthesis conditions. We have synthesized ellipsoidal or spherical silica particles by a template-free scheme that involves controlling surface tension on silica nuclei through via use of different volume ratios of a w/o micellar system. We have utilized wet-chemical etching of ellipsoidal silica nanoparticles to form silica nanoshells of a range of elliptical morphologies, with the thicknesses of the ellipsoidal silica nanoshells controlled through via variation of synthesis conditions. A mechanism has been proposed to explain how the nanoshells are formed, and we demonstrate that the porosity of the silica ellipsoid plays a role in generating silica shells. Moreover, silica materials with the unique structures might be adjusted to meet practical application requirements.

  • Molecular Structure Engineering of Semiconducting Perylene Monoanhydride Diesters

    Author:
    Hao Zhang
    Year of Dissertation:
    2013
    Program:
    Chemistry
    Advisor:
    Shi Jin
    Abstract:

    The last decade has witnessed a significant progress in the field of organic electronic materials and devices. Inspired by organic electronics' promising potential and wide applications, intensive research effort has been made to discover and design organic molecules which can give good performance in organic electronic devices. In this thesis, my research effort focused on two important fields of organic electronics: polyethylene oxide (PEO)-based conducting polymers and perylene monoanhydride diester (PEA)-based discotic columnar liquid crystalline (DCLC) materials. In Chapter 1, general background of PEO-based polymer electrolytes is introduced in part I. Different strategies to improve the polymer's conductivity, including block copolymers, graft copolymers and cross-linked polymers, are summarized. In part II of Chapter 1, it is the general background of DCLC materials. Representative DCLC materials based on a broad class of -conjugated materials such as hexabenzocoronenes (HBCs), porphyrins and perylene diimides (PDIs) are briefly reviewed. In Chapter 2, a new, efficient chemical modification method of poly (epichlorohydrin-co-ethylene oxide) (PECH-PEO) was proposed and executed. The PECH-PEO copolymer was successfully modified by oligo ethylene glycol (OEG) side chains via click chemistry. The high degree of modification and minimum chain degradation were achieved. The resulted PEO-based polymer demonstrated high room temperature (RT) ionic conductivity upon forming a lithium complex, which makes it useful as a solid electrolyte in lithium batteries. In Chapter 3, a mild, one-pot synthesis strategy to prepare PEAs containing labile functional groups is presented. Currently this is the only approach towards PEAs containing labile functional groups. Furthermore, using an asymmetrically substituted PEA as the intermediate, a tetraphilic perylene monoimide diester (PEI) that contains acid-labile functionalities was synthesized in good yield for the first time. And the fluorine-containing PEI showed highly interesting structure properties. In Chapter 4, a tert-butyl-based PEA was designed as the intermediate towards unsymmetric perylene derivatives. Unlike previous reported PEA intermediate, the tert-butyl-based PEA can be easily cyclized in an appreciably milder condition. This unique property makes it an ideal candidate for the synthesis of PEIs with acid-labile functional groups. In Chapter 5, a series of PEAs with bundled-stack discotic columnar liquid crystalline (BSDCLC) phase were synthesized and characterized. Compared to conventional DCLC materials, BSDCLC materials are structurally more robust to the occurrence of defects and therefore are expected to exhibit enhanced charge carrier characteristics. More importantly, perylene-based BSDCLC phase with single stacking mode is realized for the first time. Furthermore, our experimental data show that the self-assembly of a PEA can be effectively tuned not only by changing the branching unit, but also by changing the nature of flexible chains. Compared to alkyl chains, OEG chains can induce the BSDCLC phase of PEAs with much higher atom efficiency. Apart from synthesis and molecular design, characterization is critical to my dissertation research. A full scope of instrumentation techniques including Fourier transform infrared spectroscopy (FTIR), nuclear magnetic resonance (NMR), differential scanning calorimetry (DSC), polarized light microscopy (PLM), gel permeation chromatography (GPC), small-angle and wide-angle X-ray diffraction (XRD) have been employed. Additionally, molecular simulation has also been applied to predict and obtain details in molecular packing. To sum up, the achievements in this research contribute an advance in the field of developing perylene-based BSDCLC materials which can be potentially used for organic electronics; and PECH-PEO based polymer electrolytes have reasonable good dimensional stability and conductivity, which are important properties for the application in lithium battery industry.

  • Raman imaging and spectroscopy of individual single-wall carbon nanotubes

    Author:
    Li Zhang
    Year of Dissertation:
    2010
    Program:
    Chemistry
    Advisor:
    Zhonghua Yu
    Abstract:

    Single-wall carbon nanotubes (SWNT) are unique one-dimensional materials that are promising for many potential applications in various important areas. Their vibrational properties reflect the electron and phonon confinement as well as the structures of the tubes. Resonant Raman spectroscopy has been proven to be an exceedingly powerful tool for the characterization of the vibrational and electronic properties of SWNTs. This thesis focuses on the study of Raman spectroscopy of individual single carbon nanotubes. Single tube spectroscopy allows probing the structure dependent properties of SWNTs. A beam-scanning confocal Raman microscope system capable of large-area Raman imaging is first developed for characterizing SWNTs at the single tube level. Raman images and first-order Raman spectra of nanotubes, consisting of both semicoducting and metallic nanotubes, are systemically studied at room temperature in ambient air. The diameter of the nanotubes is determined from their radial breathing mode (RBM) frequency. A broad diameter distribution is observed for nanotubes synthesized by chemical vapor deposition. The tangential G mode Raman spectra of individual metallic nanotubes are found to exhibit a broad distribution of line shapes, which is attributed to shift of the Fermi level due to O2 adsorption. The doping dependence of Raman spectra of metallic tubes is further studied by both electrostatic gating and electrochemical gating. Significant changes in the G band Raman spectra of nanotubes are observed, suggesting the effect of doping on electron-phonon interaction. The observation of a gradual evolution of G band spectrum from a semiconducting type to the broad BWF type reveals evidence of phonon interaction between two G band modes. Raman imaging and Raman spectra of isolated SWNTs and single-layer graphenen are investigated at both room temperature and low temperature. The temperature-induced Raman spectral change of individual nanotubes is observed to be tube diameter dependent, which can be ascribed to the temperature dependence of carbon-carbon bond force constant in SWNTs and the nanotube curvature effect. At last, second-order Raman modes between 1650 and 2000 cm-1 of small-diameter SWNTs are characterized under different excitation wavelength. Excitation wavelength dependent Raman spectra of the same nanotube reveals that frequencies of the overtone M band and combination iTOLA mode of a single tube are insensitive to excitation energy, which is in contrast to the dispersive behavior observed in the ensemble measurement. It is also discovered that the relative intensity of these second-order modes depends on the chirality and family type of a nanotube.

  • Preparation of Mesoporous Silica and Its Applications in Hydrogen Storage Materials

    Author:
    Yu Zhao
    Year of Dissertation:
    2013
    Program:
    Chemistry
    Advisor:
    Daniel Akins
    Abstract:

    The present study investigated the synthesis of mesoporous silica nanospheres (MSNs) and the application of mesoporous silica in hydrogen storage applications. MSNs with particle sizes ranging from ca. 25 to 150 nm are synthesized via sol-gel chemistry with 80 °C isothermal water bath. Initial pH values of the reactant solution were used as control parameters to tune both the particles and pores size of the products. We modified the syntheses conditions and synthesized MSNs using a microwave-assisted heating approach. The introduction of microwave-assisted heating results in better crystallized MSNs. After enhanced hydrogen release properties of pretreated AB were study, some AB/MSN nanocomposites were prepared and the hydrogen release properties of these composites were evaluated. It was found that the AB/MSN nanocomposites had faster hydrogen release kinetics. A critical loading level of ca.0.15 (weigh ratio of AB to MSNs) was found. When the loading level of the nanocomposites is below the critical level, the first two moles hydrogen would be released simultaneously from AB at temperature below 90 °C. Additional, the critical loading level still exists in the AB/mesoporous silica nanocomposite materials of different mesopore sizes, and their critical loading level is affected by the total surface area of the mesopores.

  • EMERGING ORGANIC CONTAMINANTS IN SURFACE AND GROUND WATERS OF NEW YORK

    Author:
    Sherry Zhao
    Year of Dissertation:
    2010
    Program:
    Chemistry
    Advisor:
    Pengfei Zhang
    Abstract:

    The first study was about monitor estrogens (estrone, 17a-estradiol, 17b-estradiol, and estriol) in three headwater streams within a concentrated animal feed operation (CAFO) site on a monthly base for a year. In general, estrogen concentrations in the streams are low (<1 ng/l), and appeared to increase in spring, likely due to the mobilization of estrogens from soils upon snow melting/precipitation. Estrogens were detected in the streams during dry periods, indicating the contribution of estrogens from groundwater. The low concentrations of estrogens in stream water were probably the result of the long residence time (~8 months) of the manure in the lagoons where the majority of the estrogens were degraded during storage. The second study was designed to distinguish between unsewered areas and septic systems application as two possible sources of nitrogen to coastal groundwater by analyzing groundwater samples for pharmaceutical residuals. Groundwater samples were taken through piezometers at shoreline sites in unsewered areas in Northport Harbor and in sewered areas adjacent to Manhasset Bay, both in western Long Island Sound. The frequent detection of the anticonvulsant compound carbamazepine in groundwater samples of Northport (unsewered), together with the fact that few pesticides associated with lawn applications were detected, suggest that wastewater input and atmospheric input are the likely sources of nitrogen in Northport groundwater. High concentrations of nitrogen were also detected in Manhasset (unsewered) groundwater. The low detection frequency of carbamazepine, however suggests that the sewer system effectively intercept nitrogen from wastewater there.