Alumni Dissertations

 

Alumni Dissertations

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  • Development of Mesoporous Silicas, Responsive Polymer Microgels, and Related Nanocomposites

    Author:
    Yingyu Li
    Year of Dissertation:
    2014
    Program:
    Chemistry
    Advisor:
    Michal Kruk
    Abstract:

    This dissertation covers research on polymer-templated nanoporous materials and functional soft materials, and it consists of four major parts. The first part is on introduction. The next part (Chapters 2-3) describes the research work on the synthesis of silicas with spherical mesopores. Chapter 2 is focused on the synthesis of large-pore FDU-12 silicas at room temperature by using surfactants with large hydrophilic blocks and relatively small hydrophobic blocks (such as Pluronic F108 (EO132PO50EO132)) as the template. Chapter 3 discusses an interesting mesopore structure, which is the hollow silica nanosphere (HSN). The single-micelle-templating strategy provides a general approach for the synthesis of HSNs at room temperature, and the judicious choice of the framework precursor and synthesis conditions allows for the synthesis of HSNs with pore void diameter tunable from ~ 10 nm to ~ 44 nm. In addition, the one-pot room-temperature synthetic approach can be employed to the construction of hybrid organic/inorganic hollow spheres. The third part involved the preparation of glucose-responsive polymer microgels (Chapter 4-6). In Chapter 4 and 5, two kinds of dye-composited microgel sensors have been developed, and they exhibited good stability, high selectivity, and good reproducibility for detection of glucose. In Chapter 6, a glucose responsive core-shell structured microgel was designed and developed for insulin release at proper physiologically needed glucose levels. The last part of this dissertation (Chapter 7, 8) was about the synthesis of inorganic particle/polymer hybrid materials. In Chapter 7, the stimuli-responsive polymer brushes were successfully grafted from the surface of hollow silica nanospheres via surface-initiated atom transfer radical polymerization with activators regenerated by electron transfer (SI-ARGET ATRP), and the polymer loading was well controlled. Besides, the core-shell-structured nanocomposites were successfully fabricated in Chapter 8. Magnetite nanoparticles were adopted as the core, and the multifunctional polymer layer was coated on their surface. They demonstrated significant adsorption capacity towards cobalt ions, and suitability for magnetic separation, making it an excellent absorbent for waste water treatment.

  • Atomic and Molecular Low-n Rydberg States in Supercritical Fluids

    Author:
    Luxi Li
    Year of Dissertation:
    2009
    Program:
    Chemistry
    Advisor:
    Cherice Evans
    Abstract:

    The structure of low-n Rydberg states doped into supercritical fluids represents an important probe to investigate solvation effects, especially near the solvent (or perturber) critical point. We have investigated the solvation of excited atomic and molecular dopants in various perturbing fluids (both atomic and molecular). This systematic study was performed from low perturber number densities to the density of the triple point liquid, at both non-critical temperatures and on an isotherm near the critical isotherm. Dopant low-n Rydberg states were investigated using vacuum ultraviolet photoabsorption spectroscopy. The absorption spectra of these states were then simulated using a semi-classical statistical line shape function. With accurate line shape simulations, the perturber induced energy shift of the primary transition was obtained using a standard moment analysis. The moment analysis indicated that the dopant low-n Rydberg state energy blue shifts as a function of perturber number density without a significant temperature effect (except near the critical isotherm). A significant critical point effect was observed in all dopant/pertuber systems investigated here. This critical point effect is caused by a large increase in the dopant/perturber radial distribution function near the critical temperature of the perturber. Since the first perturber solvent shell shields the cationic core, the binding energy of the optical electron decreases. This acts to increase the dopant low-n Rydberg state excitation energy. However, the overall blue shift and critical point effect varies from atomic to molecular perturber systems due to the structure of the perturber. These differences are also discussed in more detail in this work.

  • Two Types of Protein Salt Bridges Studied by Quantum Calculation

    Author:
    Sing Liao
    Year of Dissertation:
    2009
    Program:
    Chemistry
    Advisor:
    Michael Green
    Abstract:

    Abstract Two types of protein salt bridges in an aqueous environment, the arginine-acid salt bridge and the lysine-acid salt bridge, are studied here. The former is modeled by propionic acid and ethylguanidine, the latter by propionic acid and propyl amine. Both have been investigated by quantum calculations for the purpose of obtaining improved salt bridge potentials in an aqueous environment with constraints on the distances between the two functional groups, which are defined as the bridge lengths in this report, designed for applications to molecular dynamics simulations of ion channels. For the arginine-acid salt bridge, we perform optimization calculations on 13 molecular clusters corresponding to the salt bridge with 0 to 12 water molecules. For the lysine-acid salt bridge, we perform optimization calculations on 2 molecular clusters for the salt bridge with 0 or 1 water molecule. To each of the model systems, after obtaining its optimized geometry, we slowly vary the bridge lengths and bridge angles in three dimensions, and subsequently we perform COSMO, frequency and NBO calculations on the contracted and expanded model systems. COSMO calculations give the dielectric constant dependence, and the frequency provides the thermodynamic properties of the system while the NBO provides the electronic distributions and bonding information. We found: (1) there is a fill-in mechanism for water molecules to enter into the salt bridge systems; such a fill-in order may have periodicity in energy, as a function of number of water molecules. (2) we show that the salt bridge systems have both hydrophilic and hydrophobic properties; (3) we look into the proton ionization process from several new aspects in terms of comparison between potentials in two different salt bridge systems and the rates of Wiberg bond order change; (4) we have an in-depth look at effects that can cause large variations to system potentials, and we take note of effects that resulted from environments of limited amounts of local waters and that may have been missed by classical treatments; (5) we look into a new aspect in the applications of Wiberg bond order that are closely associated with the electron density in predicting the formation and disruption of bonding in the systems; (6) in regard to applications to simulations of ion channels, we discuss a possible method to formulate system potentials in specific environments.

  • Development of Highly Efficient Transition Metal-Catalyzed Addition Reactions

    Author:
    Yuanxi Liao
    Year of Dissertation:
    2011
    Program:
    Chemistry
    Advisor:
    Qiaosheng Hu
    Abstract:

    Development of new and efficient reactions as powerful tools for synthetic chemistry is one of the most important tasks in modern chemistry. Transition metal-catalyzed carbon-carbon bond-forming reactions including addition reactions are some of the most powerful transformations in organic synthesis. My research is on developing highly efficient transition metal-catalyzed addition reactions as powerful tools for organic synthesis. There are two parts of my Ph. D. dissertation research projects. In the first part, based on our understanding on transmetalation and reductive elimination of palladium catalysis, we minimized the decomposition of catalysts and developed a series of new, highly efficient Pt(II), Pd(II), Rh(I) and Cu(II)-catalyzed addition reactions of organoboron reagents with carbonyl-containing compounds. Since Pt complexes can undergo reductive elimination very reluctantly, we explored the platinacycle-catalyzed addition reaction of arylboronic acids with aldehydes with low catalyst loadings. However, the low catalyst loading catalysis with platinacycles as catalysts was achieved at the expense of the catalyst catalytic activity. In order to minimize the decomposition of catalyst as well as keep the catalytic activity, a new anhydrous condition of addition reactions was established and a novel non-transmetalation mechanism of the Pd-catalyzed addition reaction was proposed and demonstrated. Under the guidance of the new reaction mechanism, we pinpointed that some addition reactions which are thought to be hardly achievable before may be accomplished now. By using the anhydrous condition, we explored Cu-catalyzed addition reactions of arylboroxines with carbonyl-containing compounds and Rh-catalyzed addition reactions of arylboroxines with ketones. In the second part, to make the addition reactions we developed in the first part be more powerful, we explored new tandem/sequential reactions involved such addition reactions as one of bond-forming reactions. Specifically, we combined Pt(II)-catalyzed 1,2-addition reactions of arylboronic acids and aldehydes with the secondary alcohol oxidation process in a tandem fashion to synthesis aryl ketones from readily available aldehydes and arylboronic acids. We also developed the synthesis of â-arylated ketones via the aldol condensation of aldehydes with methyl ketones followed by transition metal-catalyzed addition reaction in a sequential and tandem fashion. Such sequential/tandem protocols offer us rapid entry to synthesize complex materials or biological active compounds from simple precursors.

  • Development of Highly Efficient Transition Metal-Catalyzed Addition Reactions

    Author:
    Yuanxi Liao
    Year of Dissertation:
    2011
    Program:
    Chemistry
    Advisor:
    Qiaosheng Hu
    Abstract:

    Development of new and efficient reactions as powerful tools for synthetic chemistry is one of the most important tasks in modern chemistry. Transition metal-catalyzed carbon-carbon bond-forming reactions including addition reactions are some of the most powerful transformations in organic synthesis. My research is on developing highly efficient transition metal-catalyzed addition reactions as powerful tools for organic synthesis. There are two parts of my Ph. D. dissertation research projects. In the first part, based on our understanding on transmetalation and reductive elimination of palladium catalysis, we minimized the decomposition of catalysts and developed a series of new, highly efficient Pt(II), Pd(II), Rh(I) and Cu(II)-catalyzed addition reactions of organoboron reagents with carbonyl-containing compounds. Since Pt complexes can undergo reductive elimination very reluctantly, we explored the platinacycle-catalyzed addition reaction of arylboronic acids with aldehydes with low catalyst loadings. However, the low catalyst loading catalysis with platinacycles as catalysts was achieved at the expense of the catalyst catalytic activity. In order to minimize the decomposition of catalyst as well as keep the catalytic activity, a new anhydrous condition of addition reactions was established and a novel non-transmetalation mechanism of the Pd-catalyzed addition reaction was proposed and demonstrated. Under the guidance of the new reaction mechanism, we pinpointed that some addition reactions which are thought to be hardly achievable before may be accomplished now. By using the anhydrous condition, we explored Cu-catalyzed addition reactions of arylboroxines with carbonyl-containing compounds and Rh-catalyzed addition reactions of arylboroxines with ketones. In the second part, to make the addition reactions we developed in the first part be more powerful, we explored new tandem/sequential reactions involved such addition reactions as one of bond-forming reactions. Specifically, we combined Pt(II)-catalyzed 1,2-addition reactions of arylboronic acids and aldehydes with the secondary alcohol oxidation process in a tandem fashion to synthesis aryl ketones from readily available aldehydes and arylboronic acids. We also developed the synthesis of â-arylated ketones via the aldol condensation of aldehydes with methyl ketones followed by transition metal-catalyzed addition reaction in a sequential and tandem fashion. Such sequential/tandem protocols offer us rapid entry to synthesize complex materials or biological active compounds from simple precursors.

  • Two Types of Protein Salt Bridges Studied by Quantum Calculation

    Author:
    Sing Liao
    Year of Dissertation:
    2009
    Program:
    Chemistry
    Advisor:
    Michael Green
    Abstract:

    Abstract Two types of protein salt bridges in an aqueous environment, the arginine-acid salt bridge and the lysine-acid salt bridge, are studied here. The former is modeled by propionic acid and ethylguanidine, the latter by propionic acid and propyl amine. Both have been investigated by quantum calculations for the purpose of obtaining improved salt bridge potentials in an aqueous environment with constraints on the distances between the two functional groups, which are defined as the bridge lengths in this report, designed for applications to molecular dynamics simulations of ion channels. For the arginine-acid salt bridge, we perform optimization calculations on 13 molecular clusters corresponding to the salt bridge with 0 to 12 water molecules. For the lysine-acid salt bridge, we perform optimization calculations on 2 molecular clusters for the salt bridge with 0 or 1 water molecule. To each of the model systems, after obtaining its optimized geometry, we slowly vary the bridge lengths and bridge angles in three dimensions, and subsequently we perform COSMO, frequency and NBO calculations on the contracted and expanded model systems. COSMO calculations give the dielectric constant dependence, and the frequency provides the thermodynamic properties of the system while the NBO provides the electronic distributions and bonding information. We found: (1) there is a fill-in mechanism for water molecules to enter into the salt bridge systems; such a fill-in order may have periodicity in energy, as a function of number of water molecules. (2) we show that the salt bridge systems have both hydrophilic and hydrophobic properties; (3) we look into the proton ionization process from several new aspects in terms of comparison between potentials in two different salt bridge systems and the rates of Wiberg bond order change; (4) we have an in-depth look at effects that can cause large variations to system potentials, and we take note of effects that resulted from environments of limited amounts of local waters and that may have been missed by classical treatments; (5) we look into a new aspect in the applications of Wiberg bond order that are closely associated with the electron density in predicting the formation and disruption of bonding in the systems; (6) in regard to applications to simulations of ion channels, we discuss a possible method to formulate system potentials in specific environments.

  • Electronic spectroscopy and computational studies of GSCbl, H2OCbl, and MeCbl

    Author:
    Iya Likhtina
    Year of Dissertation:
    2011
    Program:
    Chemistry
    Advisor:
    RONALD BIRKE
    Abstract:

    In the present study we are interested in the electronic and geometric structure of GS-Cbl and the chemical nature of its Co(III)-S bond in comparison with aquo- and methyl- axial ligand bonds to Co(III) in cobalamins. We examine the structures with DFT calculations of truncated models of the entire molecule. Furthermore, we compare the electronic spectroscopy (UV-VIS and CD) of GS-Cbl(III) with H2O-Cbl(III) and CH3-Cbl(III) using both experimental spectra and TD-DFT calculated spectra. The AOMIX program was used to analyze molecular orbital, MO, compositions, partial density of states, DOS, between molecular fragments, and generalized Wiberg and Mayer bond orders, Charge Decomposition Analysis, CDA, and Energy Decomposition Analysis, EDA. Natural Bond Order (NBO) analysis as implement in G03 and G09 was made on gas phase and aqueous ground state structures.

  • Electronic spectroscopy and computational studies of GSCbl, H2OCbl, and MeCbl

    Author:
    Iya Likhtina
    Year of Dissertation:
    2011
    Program:
    Chemistry
    Advisor:
    RONALD BIRKE
    Abstract:

    In the present study we are interested in the electronic and geometric structure of GS-Cbl and the chemical nature of its Co(III)-S bond in comparison with aquo- and methyl- axial ligand bonds to Co(III) in cobalamins. We examine the structures with DFT calculations of truncated models of the entire molecule. Furthermore, we compare the electronic spectroscopy (UV-VIS and CD) of GS-Cbl(III) with H2O-Cbl(III) and CH3-Cbl(III) using both experimental spectra and TD-DFT calculated spectra. The AOMIX program was used to analyze molecular orbital, MO, compositions, partial density of states, DOS, between molecular fragments, and generalized Wiberg and Mayer bond orders, Charge Decomposition Analysis, CDA, and Energy Decomposition Analysis, EDA. Natural Bond Order (NBO) analysis as implement in G03 and G09 was made on gas phase and aqueous ground state structures.

  • Polymerization in a small droplet on a superhydrophobic surface

    Author:
    Fang-Ju Lin
    Year of Dissertation:
    2013
    Program:
    Chemistry
    Advisor:
    Alan Lyons
    Abstract:

    Droplets of fluids have been used as small volume reactors in microfluidic applications, including polymerase chain reaction, as well as synthesis of small-molecules, polymers, and gel particles. More recently, reactions within individual droplets on superhydrophobic surfaces have been studied. However, the fundamentals of polymerization reactions in a droplet on a superhydrophobic surface have not been reported. To address this issue, firstly, a temperature- and atmosphere-controlled environmental chamber was designed to maintain a constant volume of the droplet on superhydrophobic surface by insuring an equilibrium solvent vapor pressure, eliminating extraneous evaporation or condensation of water. A new technique, micro-dilatometry, was developed to measure the change in volume of the droplet in real-time as a function of photopolymerization conditions. Experimental parameters include photoinitiator concentration, UV light intensity and surface type. In this way, polymerization rate could be calculated in isolated 10 uL droplets. Droplets on a superhydrophobic surface can be easily and completely lifted off the surface with a syringe because of the weak interactions between liquid and solid surface. Because of this unique aspect of superhydrophobic surfaces, small droplets could be easily analyzed in an external instrument such as NMR or GPC. The percent conversion of monomer to polymer, calculated by micro-dilatometry, was verified by NMR for the same droplet. The molecular weight of the formed polymer could also be measured by injecting the droplet into a GPC. These results demonstrated good correlation between micro-dilatometry and NMR for percent conversions ranging from 5 - 18%. Above 18% conversion, experiments demonstrated significant deviations between micro-dilatometry and NMR. Main reason of these discrepancies is proofed to be changes in the vapor pressure of water within the droplet as the concentration of solute molecules decreased significantly during polymerization. Using the micro-dilatometry technique, the kinetics of polymerization of acrylamide was studied. The polymerization rate within isolated 10 uL droplets was found to be significantly higher than in a well-stirred vial. In addition, the molecular weight of polymers formed in droplets was found to be larger than in the well-stirred system. A hypothesis is presented to explain the higher polymerization rate and molecular weight in small isolated droplets.

  • Synthesis of C-Glycoside Analogs of the Immunostimulatory Glycosphingolipid, alfa-Galactosylceramide

    Author:
    Zheng Liu
    Year of Dissertation:
    2011
    Program:
    Chemistry
    Advisor:
    Robert Bittman
    Abstract:

    This dissertation presents the asymmetric total synthesis of immunostimulatory &alpha-C-galactosylceramide (&alpha-C-GalCer) glycolipids and D-ribo-phytosphingosine. Also included in this dissertation is an improved two-step synthetic route to primary allylic alcohols from aldehydes and verification of configurations of three contiguous stereogenic centers in the phytosphingosine backbone of &alpha-1C-GalCer, the nonisosteric analog of &alpha-C-GalCer in which the glycosidic oxygen atom linking the sugar with phytosphingosine is deleted.. Chapter 1 presents an improved two-step synthetic route to primary allylic alcohols from aldehydes. A modification of the Horner-Wadsworth-Emmons (HWE) olefination reaction in H2O/2-propanol (1:1) and a convenient protocol to prepare AlH3 in tetrahydrofuran from LiAlH4 and n-butyl bromide are the key factors in the improvement. Chapter 2 presents an asymmetric synthesis of D-ribo-phytosphingosine. The synthesis was achieved by utilizing the ProPhenol-catalyzed alkynylation of an unsaturated aldehyde to afford an allylic propargylic alcohol followed by asymmetric epoxidation and opening of a propargylic epoxy alcohol with NaN3/NH4Cl. Deprotection and reduction of the resulting acyclic azide then gave D-ribo-phytosphingosine. The acyclic azide was also subjected to an intramolecular click reaction, generating a bicyclic triazole, whose diacetate derivative was found to have almost identical cis and trans vicinal coupling constants. The relative stereochemistry of the final product was assigned by NMR analysis of corresponding Mosher esters and amides, and confirmed by comparison of NMR spectra and specific rotations of its tetraacetate derivative with reported data. The stereochemical assignment based on comparing J values with reported data in bicyclic triazoles, generated by a copper-free intramolecular click reaction, was inconclusive. Alkynyl-azide, an efficient glycosyl acceptor in the synthesis of &alpha-galactosylceramide derivatives, was also readily prepared by this route. Chapter 3 presents (1) a modification of the first generation synthesis of &alpha-1C-galactosylceramide featuring the two-step HWE olefination and alane reduction protocol described in Chapter 1 and the ProPhenol-catalyzed asymmetric alkynylation reaction, and (2) a detailed verification of the configurations of three contiguous stereogenic centers in the phytosphingosine moiety. Given the possible intramolecular participation by the 2'-O-benzyl group of the galactosyl moiety in epoxide opening by the azide anion, an attempt was made to assign the relative stereochemistry of the azide-bearing carbon through the coupling constants (J4,5 and J5,6) in a bicyclic triazole, which was obtained via an intramolecular click reaction and acetylation of diol. The cis J4,5 and trans J5,6 displayed almost the same values, suggestive of possible retention in the opening of the epoxide; however, nOe analysis was inconclusive. Model compounds containing the same bicyclic triazole skeleton were prepared via the same reaction sequence, and their cis J4,5 and trans J5,6 coupling constants showed similar values as to those in the sugar counterpart. According to the systematical investigation of the model compounds described in Chapter 2, the epoxide-opening reaction did indeed proceed with inversion. These results exclude intramolecular participation by the 2'-O-benzyl group and emphasize the need for caution when coupling constants alone are used to judge the relative configuration in bicyclic triazoles and related systems. Chapter 4 presents stereocontrolled syntheses of &alpha-C-GalCer and its &alpha-C-acetylenic analog from 1-hexadecene and D-galactose. The key transformations include Sonogashira coupling, Sharpless asymmetric epoxidation, and Et2AlCl-catalyzed cyclization of an epoxytrichloroacetimidate to generate a protected dihydrooxazine synthon.