Alumni Dissertations

 

Alumni Dissertations

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  • PHOTOPHYSICS AND CATALYSIS OF PORPHYRINOIDS

    Author:
    Amit Aggarwal
    Year of Dissertation:
    2011
    Program:
    Chemistry
    Advisor:
    Charles Drain
    Abstract:

    Organic nanoparticles (ONP) of metalloporphyrins can be versatile catalysts for the selective oxidation of alkenes and other hydrocarbons. Herein, we report the catalytic activity of ONP of 5,10,15,20-tetrakis-[4-(1'H,1'H,2'H,2'H-heptadecafluorodecane-1-thiol)-2,3,5,6-tetrafluorophenyl] porphyrinato iron(III), Fe(III)TPPF84, and 5,10,15,20-tetakis-(2,3,4,5,6-pentafluorophenyl) porphyrinato manganese(III), Mn(III)TPPF20, for cyclohexene oxidation using molecular oxygen as an oxidant in water under ambient conditions. While the solvated metalloporphyrins catalytically oxidize alkenes to the corresponding epoxide in halogenated solvent with a modest turn-over numbers (TON), 10-30 nm ONP of these metalloporphyrins have enhanced catalytic activity with up to a 4-fold greater TON and yields only allylic oxidation products. These ONP catalytic systems facilitate a greener reaction since ca. 89% of the reaction medium is water, molecular oxygen is used in place of man-made oxidants, and the ambient reaction conditions require less energy. The enhanced catalytic activity of these ONP is unexpected because the metalloporphyrins in the nanoaggregates are in the close proximity and the TON should diminish by self-oxidative degradation. The fluorous alkanes in Fe(III)TPPF84 stabilize the ONP towards self-oxidative degradation. Sequential dipping of indium-tin-oxide electrodes into solutions of tetra cationic porphyrins and tetra anionic polyoxometalates results in the controlled formation of nm thick films. The potential applications of these robust films on electrodes range from catalysts to sensors. This chapter focuses on the electrochemistry of the multilayered films where it is found that the oxidation and reduction potentials of each species remain largely the same as found in solution. Photophysical properties of Porphyrinoids bearing four rigid hydrogen bonding motifs on the meso positions, self-assembled into a cofacial cage with four complementary bis(decyl)melamine units in dry solvents are presented here. Self-assembly was investigated by NMR spectroscopy, dynamic light scattering, and atomic force microscopy. The phototphysical properties of the cage formation involve the measurement of their absorption and emission spectra and the fluorescence life time in dry THF. The hydrocarbon chains on the bis(decyl)melamine mediate the formation of nanofilms on surfaces as the solvent slowly evaporates. A systematic study of the photophysical properties of a series of porphyrinoids is presented. The role of the location of a heavy atom in shunting the excited state from the singlet to the triplet manifolds is compared for three cases. It is well known that Pt(II) metalloporphyrins do not fluoresce. For meso pyridyl porphyrins, the fluorescence quantum yield decreases as the number of coordinatively attached Pt(II) complexes increase from 0-4, but the tetracoordinated species retains about 30% of the fluorescence. Covalently attaching a heavy metal complex e.g.Pt(II) complex to the macrocycle by an organometalic bond at the peripheral meso position causes greater than a 20-fold decrease in fluorescence quantum yield and may enhance some internal conversion to the ground state. For comparison, the fluorescence quantum yield decreases somewhat as the number of pyridyl groups on the meso positions increase 0-4. We also evaluate the photophysical properties of a series of porphyrins with nitro groups on the β pyrrole position and on the meso phenyl group, which also quenches the fluorescence. These studies bear on the use of metal ions to enhance the photophysical properties of these dyes as photodynamic therapeutics and for supramolecular systems, while the nitrated macrocycles have potential application in non linear optics. The photophysical properties of non-hydrolysable tetra- thioglycosylated conjugates of chlorin (CGlc4), isobacteriochlorin (IGlc4) and bacteriochlorin (BGlc4) and core F20 platforms are reported here. These studies involve the measurement of absorption and emission spectra, fluorescence quantum yield, singlet oxygen quantum yield, and singlet state life time in three different solvents: phosphate buffer saline (PBS), ethanol, and ethylacetate. Compared to the porphyrin in PBS, CGlc4 has a markedly greater absorbance of red light near 650 nm and a 6-fold increase in fluorescence quantum yield; whereas IGlc4 has broad Q bands and a 12-fold increase in fluorescence quantum yield. Since IGlc4 CGlc4 very slowly bleach, these properties may enable their use as fluorescent tags to track biological processes. BGlc4 has a similar fluorescence quantum yield to PGlc4, (<10%), but the lowest energy absorption/emission peaks of BGlc4 are considerably red shifted to near 730 nm with a nearly 50-fold greater absorbance, which may allow this conjugate to be an effective PDT agent. The excited state life time of these conjugates ranges from 3-11 ns. The radiative time constant for IGlc4 is 20 fold less while non-radiative time constant is 2 fold more than BGlc4, indicates that IGlc4 has greater potential to form triplet state via inter system crossing, and so can serves as a better PDT agent. The uptake of CGlc4, IGlc4 and BGlc4 derivatives into cells such as human breast cancer cells MDA-MB-231 and K:Molv NIH 3T3 mouse fibroblast cells can be observed at nM concentrations. Photobleaching under these conditions is minimal.

  • PHOTOPHYSICS AND CATALYSIS OF PORPHYRINOIDS

    Author:
    Amit Aggarwal
    Year of Dissertation:
    2011
    Program:
    Chemistry
    Advisor:
    Charles Drain
    Abstract:

    Organic nanoparticles (ONP) of metalloporphyrins can be versatile catalysts for the selective oxidation of alkenes and other hydrocarbons. Herein, we report the catalytic activity of ONP of 5,10,15,20-tetrakis-[4-(1'H,1'H,2'H,2'H-heptadecafluorodecane-1-thiol)-2,3,5,6-tetrafluorophenyl] porphyrinato iron(III), Fe(III)TPPF84, and 5,10,15,20-tetakis-(2,3,4,5,6-pentafluorophenyl) porphyrinato manganese(III), Mn(III)TPPF20, for cyclohexene oxidation using molecular oxygen as an oxidant in water under ambient conditions. While the solvated metalloporphyrins catalytically oxidize alkenes to the corresponding epoxide in halogenated solvent with a modest turn-over numbers (TON), 10-30 nm ONP of these metalloporphyrins have enhanced catalytic activity with up to a 4-fold greater TON and yields only allylic oxidation products. These ONP catalytic systems facilitate a greener reaction since ca. 89% of the reaction medium is water, molecular oxygen is used in place of man-made oxidants, and the ambient reaction conditions require less energy. The enhanced catalytic activity of these ONP is unexpected because the metalloporphyrins in the nanoaggregates are in the close proximity and the TON should diminish by self-oxidative degradation. The fluorous alkanes in Fe(III)TPPF84 stabilize the ONP towards self-oxidative degradation. Sequential dipping of indium-tin-oxide electrodes into solutions of tetra cationic porphyrins and tetra anionic polyoxometalates results in the controlled formation of nm thick films. The potential applications of these robust films on electrodes range from catalysts to sensors. This chapter focuses on the electrochemistry of the multilayered films where it is found that the oxidation and reduction potentials of each species remain largely the same as found in solution. Photophysical properties of Porphyrinoids bearing four rigid hydrogen bonding motifs on the meso positions, self-assembled into a cofacial cage with four complementary bis(decyl)melamine units in dry solvents are presented here. Self-assembly was investigated by NMR spectroscopy, dynamic light scattering, and atomic force microscopy. The phototphysical properties of the cage formation involve the measurement of their absorption and emission spectra and the fluorescence life time in dry THF. The hydrocarbon chains on the bis(decyl)melamine mediate the formation of nanofilms on surfaces as the solvent slowly evaporates. A systematic study of the photophysical properties of a series of porphyrinoids is presented. The role of the location of a heavy atom in shunting the excited state from the singlet to the triplet manifolds is compared for three cases. It is well known that Pt(II) metalloporphyrins do not fluoresce. For meso pyridyl porphyrins, the fluorescence quantum yield decreases as the number of coordinatively attached Pt(II) complexes increase from 0-4, but the tetracoordinated species retains about 30% of the fluorescence. Covalently attaching a heavy metal complex e.g.Pt(II) complex to the macrocycle by an organometalic bond at the peripheral meso position causes greater than a 20-fold decrease in fluorescence quantum yield and may enhance some internal conversion to the ground state. For comparison, the fluorescence quantum yield decreases somewhat as the number of pyridyl groups on the meso positions increase 0-4. We also evaluate the photophysical properties of a series of porphyrins with nitro groups on the β pyrrole position and on the meso phenyl group, which also quenches the fluorescence. These studies bear on the use of metal ions to enhance the photophysical properties of these dyes as photodynamic therapeutics and for supramolecular systems, while the nitrated macrocycles have potential application in non linear optics. The photophysical properties of non-hydrolysable tetra- thioglycosylated conjugates of chlorin (CGlc4), isobacteriochlorin (IGlc4) and bacteriochlorin (BGlc4) and core F20 platforms are reported here. These studies involve the measurement of absorption and emission spectra, fluorescence quantum yield, singlet oxygen quantum yield, and singlet state life time in three different solvents: phosphate buffer saline (PBS), ethanol, and ethylacetate. Compared to the porphyrin in PBS, CGlc4 has a markedly greater absorbance of red light near 650 nm and a 6-fold increase in fluorescence quantum yield; whereas IGlc4 has broad Q bands and a 12-fold increase in fluorescence quantum yield. Since IGlc4 CGlc4 very slowly bleach, these properties may enable their use as fluorescent tags to track biological processes. BGlc4 has a similar fluorescence quantum yield to PGlc4, (<10%), but the lowest energy absorption/emission peaks of BGlc4 are considerably red shifted to near 730 nm with a nearly 50-fold greater absorbance, which may allow this conjugate to be an effective PDT agent. The excited state life time of these conjugates ranges from 3-11 ns. The radiative time constant for IGlc4 is 20 fold less while non-radiative time constant is 2 fold more than BGlc4, indicates that IGlc4 has greater potential to form triplet state via inter system crossing, and so can serves as a better PDT agent. The uptake of CGlc4, IGlc4 and BGlc4 derivatives into cells such as human breast cancer cells MDA-MB-231 and K:Molv NIH 3T3 mouse fibroblast cells can be observed at nM concentrations. Photobleaching under these conditions is minimal.

  • Fabrication of Quantum Dot Encoded Silica Beads for High-throughput Screening Applications

    Author:
    Gerson Aguirre
    Year of Dissertation:
    2011
    Program:
    Chemistry
    Advisor:
    Alex Couzis
    Abstract:

    The focus of this research is on the development of optically barcoded silica gel microbeads, synthesized to be used in high throughput screening platforms, using suspension methods for bead synthesis developed specifically for rapid gelation. In suspension methods for particle manufacture, precursor droplets are first formed in a continuous phase immiscible with the droplet phase. The droplets are then solidified into particles. Silica is chosen as the bead material because it can very easily be functionalized to anchor probe molecules which is necessary to function as a capture element in high throughput screening applications. The optical code embedded into the microbeads consists of the spectral signature (the emission spectrum) of a collection of luminescent species. In particular, for this study, multicolor semiconductor nanocrystals or quantum dots (QDs) are used. Each type of QD emits electromagnetic waves at a set wavelength (color), and sets of QDs will be incorporated in differing quantities to form the code. The encoding QDs are dispersed in the pre-gel droplet phase, and are surface functionalized so as not to partition in the continuous phase. In this way, the QDs are effectively trapped in the droplets as they gel to microbeads, which allows for a quantitative loading necessary for optical coding. In this study, the suspension process for encoded silica bead production is implemented using a batch stirring method for forming the emulsion, and a flow-focusing microfluidic device. The later is used to generate uniformally sized droplets of the pre-gel phase, thus insuring a monodisperse size distribution that is useful for high throughput screening platforms. The gelation of the silica precursor droplets uses an amine catalyst as an accelerant, and thus eliminates the post-production necessary in existing methodologies for obtaining silica beads. Confocal laser scanning microscopy (CLSM) is used to record the spatial distribution of the nanocrystal fluorescence in the beads and the emission spectra (the barcode). Two colors of QDs were used to create a prototype barcode, and Forster Resonance Energy Transfer (FRET) between these colors was used in addition to the spatial distribution of the fluorescence to infer the aggregation of the nanocrystals in their new silica gel environment. A comparison of the photoluminescence (PL) profiles of the barcoded silica beads demonstrate that indeed resonant energy transfer is occurring, and the crystals do aggregate. FRET shifts in the PL profiles can be attributed to poor dispersability issues in the precursor solution and can in some instances- due to extent of unfavorable conditions for the surface molecules of QDs with the solvent- limit our ability to generate a full compliment of barcodes. Untimely ionization of catalyst, and degree of which, and poor solvability of hydrophylically surface functionalized nanocrystals leads to their poor performance as entrapped luminescing signals.

  • Chemistry of 6-Monobrominated Indigo, MBI

    Author:
    Hiroko Ajiki
    Year of Dissertation:
    2014
    Program:
    Chemistry
    Advisor:
    Lou Massa
    Abstract:

    6-monobrominated indigo, MBI, is a component of a historically important and the most expensive colorant, Tyrian Purple. The colorant is remarkably stable under the sun, in the air and after extensive washing with water. The color is still vivid after thousands of years. Even though it has such a high stability, MBI and Tyrian Purple have color changes from purple to blue upon temperature changes. This color change has been known for long to certain people, but the mechanism of the color change was unknown. Tyrian Purple also has recently attracted interests for applications towards semiconducting material due to its ambipolar property and high stacking structure and towards its biomedical applications. Though other chemicals in the colorant have been studied and analyzed well, MBI is the least studied and understood chemical. The full investigation of the chemistry of MBI has been conducted and reported in this study.

  • Nickel-catalyzed cross-coupling reactions involving secondary and tertiary alkyl nucleophiles

    Author:
    Amruta Ajit Joshi
    Year of Dissertation:
    2014
    Program:
    Chemistry
    Advisor:
    Mark Biscoe
    Abstract:

    NICKEL-CATALYZED CROSS-COUPLING REACTIONS INVOLVING SECONDARY AND TERTIARY ALKYL NUCLEOPHILES by Amruta Ajit Joshi Advisor: Prof. Mark R. Biscoe In the first chapter, introduction of transition metal-catalyzed cross-coupling reactions has been given. These transition metal-catalyzed C-C bond forming reactions have been used extensively in organic synthesis. Among them, C(sp2)-C(sp2) bond forming reactions have been widely studied over decades. More recently, some reports have demonstrated the use of C(sp3) nucleophiles and electrophiles in cross-coupling reactions. However, use of secondary and tertiary alkyl nucleophiles has remained a challenge due to competitive β-hydride elimination and slow transmetallation of bulky secondary and tertiary alkyl organometallic nucleophiles. In the second chapter, the first general nickel-catalyzed Negishi reaction for the cross-coupling of unactivated, acyclic secondary alkylzinc halides and aryl and hetero-aryl iodides has been reported. This process is the first to overcome the β-hydride elimination problem inherent to the use of the analogous palladium-catalyzed processes. This method is very general and tolerates a wide range of functional groups. A detailed study of the effect of salt additives on these reactions has also been presented. In the third chapter, this work has been extended to the use of tertiary alkyl nucleophiles and the first metal-catalyzed Kumada cross-coupling reaction of tertiary alkylmagnesium halides and aryl bromides/triflates has been reported. This reaction has very wide substrate scope, and vinyl bromides and vinyl chlorides can also be employed as electrophiles. Here, the effect of catalyst hydration on the reaction yield and selectivity has been demonstrated. In the fourth chapter, a mild palladium-catalyzed reaction for the monoborylation of primary alkyl halides using bis(pinacolato)diboron as the boron source has been reported. This reaction is very general and can accommodate a wide range of functional groups. To increase the utility of this process, the crude borylation product has been converted into the corresponding boronic acid, trifluoroborate salt and another boronic ester. Aditionally, bis(neopentylglycolato)diboron has also been employed as the boron source.

  • MICROSTRUCTURAL ENVIRONMENTS AND REDOX STATES OF IRON IN RANDOM AND ORDERED POROUS SILICA MATRICES

    Author:
    Don Anton Amarasinghe
    Year of Dissertation:
    2009
    Program:
    Chemistry
    Advisor:
    Harry Gafney
    Abstract:

    In our previous studies we have shown that the refractive index of porous Vycor glass can be changed by doping with iron and at the lower end of the iron loading, the refractive index shows a fairly linear increase with the loading. This allows us to create refractive index patterns in porous Vycor glass. The exact mechanisms regarding image formation in the Vycor glass and the factors that affect the image quality are still being investigated. In this study we analyzed the cross-sectional distribution of iron and the lateral diffusion of iron during the heat treatment in order to understand the contrast variations. The study also focused on microstructural changes of iron particles from the surface to the interior of the porous Vycor glass. The other objective of the study is to understand microstructural variations of iron in regular pore structured materials such as MCM-41 and random pore networks such as xerogel and PVG. Results show that the maximum effective lateral diffusion length of iron in PVG is <10 μm at 650C. We conclude that the particle growth which occurs at 650C is due to a less than 10 μm diffusion length within the matrix. XANES results show that elemental iron found in the PVG immediately after photolysis is concentrated in the interior of the glass. Although some elemental iron is found on the surface of the glass they are covered with a protective layer of Fe(III) oxides. This protective layer seems to be robust enough to prevent further oxidation of elemental iron particles during the annealing process at 6500C but the elemental iron found in the interior of the glass did oxidize during the annealing process until the protective layer of Fe(III) oxide is formed. The results suggest that once the Fe(III) / Fe(0) ratio reach a critical value further oxidation is prevented. EXAFS data analysis along with EPR confirmed that the chemical nature of iron oxides formed on the surface and the interior of the PVG are identical and Fe(III) is in an octahedral environment. The Mössbauer data suggest that the Fe(0) particles in the PVG substrate are randomly oriented whereas Fe(III) has some orientation suggesting that particles are attached to the silica substrate through the oxide envelope. Unlike Fe(CO)5 doped PVG, when Fe(CO)5 doped MCM-41 is photolyzed, it leads to formation of octahedrally and tetrahedrally coordinated iron sites within the silica matrix. Mossbauer study shows that with the increasing temperature, iron migrates from octahedral sites to tetrahedral sites. Iron in xerogel behaves differently than iron in PVG or MCM-41. Iron migration into tetrahedral sites initiates at 650C and the number of tetrahedral sites increase with temperature. Neither xerogel nor MCM-41 shows any evidence of elemental iron before or after heat treatments. The Fe(0) formation in PVG seems to be a unique phenomenon.

  • MICROSTRUCTURAL ENVIRONMENTS AND REDOX STATES OF IRON IN RANDOM AND ORDERED POROUS SILICA MATRICES

    Author:
    Don Anton Amarasinghe
    Year of Dissertation:
    2009
    Program:
    Chemistry
    Advisor:
    Harry Gafney
    Abstract:

    In our previous studies we have shown that the refractive index of porous Vycor glass can be changed by doping with iron and at the lower end of the iron loading, the refractive index shows a fairly linear increase with the loading. This allows us to create refractive index patterns in porous Vycor glass. The exact mechanisms regarding image formation in the Vycor glass and the factors that affect the image quality are still being investigated. In this study we analyzed the cross-sectional distribution of iron and the lateral diffusion of iron during the heat treatment in order to understand the contrast variations. The study also focused on microstructural changes of iron particles from the surface to the interior of the porous Vycor glass. The other objective of the study is to understand microstructural variations of iron in regular pore structured materials such as MCM-41 and random pore networks such as xerogel and PVG. Results show that the maximum effective lateral diffusion length of iron in PVG is <10 μm at 650C. We conclude that the particle growth which occurs at 650C is due to a less than 10 μm diffusion length within the matrix. XANES results show that elemental iron found in the PVG immediately after photolysis is concentrated in the interior of the glass. Although some elemental iron is found on the surface of the glass they are covered with a protective layer of Fe(III) oxides. This protective layer seems to be robust enough to prevent further oxidation of elemental iron particles during the annealing process at 6500C but the elemental iron found in the interior of the glass did oxidize during the annealing process until the protective layer of Fe(III) oxide is formed. The results suggest that once the Fe(III) / Fe(0) ratio reach a critical value further oxidation is prevented. EXAFS data analysis along with EPR confirmed that the chemical nature of iron oxides formed on the surface and the interior of the PVG are identical and Fe(III) is in an octahedral environment. The Mössbauer data suggest that the Fe(0) particles in the PVG substrate are randomly oriented whereas Fe(III) has some orientation suggesting that particles are attached to the silica substrate through the oxide envelope. Unlike Fe(CO)5 doped PVG, when Fe(CO)5 doped MCM-41 is photolyzed, it leads to formation of octahedrally and tetrahedrally coordinated iron sites within the silica matrix. Mossbauer study shows that with the increasing temperature, iron migrates from octahedral sites to tetrahedral sites. Iron in xerogel behaves differently than iron in PVG or MCM-41. Iron migration into tetrahedral sites initiates at 650C and the number of tetrahedral sites increase with temperature. Neither xerogel nor MCM-41 shows any evidence of elemental iron before or after heat treatments. The Fe(0) formation in PVG seems to be a unique phenomenon.

  • Gold and Zinc Oxide Nanoparticle Coated Peptide Nanotubes Fabrication and Their Electrical Transport Properties Study

    Author:
    Luona Anjia
    Year of Dissertation:
    2012
    Program:
    Chemistry
    Advisor:
    Hiroshi Matsui
    Abstract:

    There is a growing interest in attempts in using biomolecular as the 1D nanotube templates to grow inorganic nanoparticles (NPs) in controlled morphology and structure. One of the research motivations for this combination is to take advantage of the catalytic activity for the room-temperature material growth and the ability of self-assembly into controlled structures on a large scale. One approach to fabricate such nanotube is by using a glycine-based peptide nanotube as template, and on template sidewall immobilizing biomineralizing peptide, which can selectively bind to the target metal/semiconductor precursor and mediate the formation of the inorganic material on templates incorporating these peptides. By optimizing the experiment conditions, we successfully fabricated high yield of nanotubes with full coverage of high-density monodispersed Au and ZnO NPs coating. Using drop casting technique, we built electronic device with these nanotubes and found very interesting electrical transport properties: the temperature-dependent current-voltage characteristic of Au NPs nanotube; and the negative differential resistance property (current decreases with increasing bias voltage) of ZnO NPs coated nanotube. These results are of great impact on the future development of bio-nanoelectronic devices. Besides, a new biomimetic approach for one-pod synthesis of ZnO nanotube at neutral pH and room temperature is introduced; by self-assembling peptides which possess the catalytic mineralization function for the specific oxide metal, ZnO nanotube can be grown as the peptides are simultaneously assembled into a rod structure and template ZnO growth in gels formed by the peptides and Zn precursors. Traditionally, biomineralizing peptides are coated on 1D templates and then grow ZnO at room temperature, however this new method allows one to grow ZnO nanotubes in one step without using 1D templates since the Zn-mineralizing peptide itself can be assembled into the 1D structure.

  • Carbohydrates as Scaffolds for Bioactive Agents

    Author:
    Stewart Bachan
    Year of Dissertation:
    2012
    Program:
    Chemistry
    Advisor:
    David Mootoo
    Abstract:

    ABSTRACT Carbohydrates as Scaffolds for Bioactive Agents By Stewart Bachan Mentor: Professor David. R. Mootoo Carbohydrates are attractive templates for drug design because of their accessibility, highly functionalized structures and rich synthetic chemistry. The goal of this research was to design mimetics of two classes of biologically interesting molecules using carbohydrate scaffolds. These are beta-D-galactosylceramide (GalCer) and the tetrahydrofuran (THF) containing AAs. The emergence of multi-drug resistant (MDR) strains of HIV-1 has created a need for new therapeutic agents. The glycolipid GalCer has been shown to be a cofactor in HIV-1 infection as it mediates the binding of the HIV envelope protein gp120 in CD4+ cells. Mimics of GalCer can serve as potential entry inhibitors of HIV-1. 1,1-Linked galactose-mannose (Gal-Man) and glucose-mannose (Glu-Man) disaccharides with an ester on the Man subunit were found to bind to the V3 loop peptide of gp120 and inhibit HIV infectivity in single round infection assays with the TZM-b1 cell line (a derivative of the HeLa cell line that express CD4, CXCR4, and CCR5). IC50 values were in the 50 micromolar range with no toxicity to the cells at concentrations up to 200 micromolar. These compounds appear to inhibit virus entry at early steps in viral infection since they were inactive if added post viral entry. Although these compounds were found to bind to the V3 loop peptide of gp120, it is not clear that this interaction is responsible for their anti-HIV activity because the binding affinity of closely related analogs did not correlate with their antiviral behavior. The low cytotoxicity of these 1,1-linked disaccharide fatty acid esters, combined with their easy accessibility to structurally diverse analogs, make these molecules attractive leads for new anti-viral agents. The THF-containing AAs have drawn much attention because of their potent antitumor activities. Their mode of action involves the inhibition of the NADH: ubiquinone oxidoreductase, Complex 1, of the mitochondrial electron transport chain. Their generally high cytotoxicity to both normal and tumor cells has hampered their development as anti-cancer agents. Thus acetogenin analogs that show increased specificity towards cancer cells are of interest as new therapeutic agents. Acetogenin analogs in which the THF core was replaced with either a monosaccharide or disaccharide framework were synthesized and evaluated against various cancer cell lines. The monosaccharide analogs showed antitumor activity in the low micromolar range and were generally more active than their disaccharide counterparts. It is also noteworthy that varying the degree of oxygenation on the monosaccharide ring did not show any significant effect on cytotoxicity. These structure activity observations open up possibilities for the design of tumor selective monosaccharide analogs that target carbohydrate receptors that are overexpressed on tumor cells.

  • Conformational features of the human U2-U6 snRNA complex

    Author:
    Ravichandra Bachu
    Year of Dissertation:
    2014
    Program:
    Chemistry
    Advisor:
    Nancy Greenbaum
    Abstract:

    The splicing of precursor messenger (pre-m) RNA, during which noncoding intervening sequences are excised and flanking coding regions ligated, is an integral reaction of gene expression. In eukaryotes, it is carried out by a dynamic RNA-protein complex called the spliceosome, in which five small nuclear (sn) RNA components are actively involved in recognition and chemical aspects of the process. A complex formed between U2 and U6 snRNAs is implicated in the chemistry of pre-mRNA splicing. The catalytic activity of the U2-U6 snRNA complex is dependent on the presence of Mg2+ ions, and the complex has been shown to have several specifically bound Mg2+ binding sites in vitro. The overall goal of this research is to characterize the conformational changes of the human U2-U6 snRNA complex upon addition of Mg2+. In order to pursue this question, we attempted to characterize the lowest energy structure of the complex in the absence of spliceosomal proteins using a combination of biophysical and biochemical techniques in the solution state. We first used enzymatic structure probing to evaluate the secondary structural fold of protein-free human U2-U6 snRNA complex. Cleavage patterns resulting from probing reactions were consistent with formation of four stem regions surrounding the junction, therefore favoring the four-helix model consistent with previous results of in vivo studies of the human U2-U6 snRNA complex. However, 19F NMR studies from our laboratory also identified a lesser fraction (up to 14%) of a three- helix conformation. Upon addition of up to 100 mM Mg2+, a slight increase in cleavage by enzymes specific for both single-stranded and double-stranded regions was observed at the junction region, suggesting that this region is becoming more accessible, perhaps because of an increase in the fraction of the three-helix conformation. Analytical ultracentrifugation studies revealed that the Stokes radius of the RNA complex decreased slightly from 31.3 Å to 27.9 Å in the presence of 100 mM Mg2+, suggesting a slight compaction of the tertiary structure in the presence of divalent metal ions. Hydroxyl radical footprinting experiments on this complex showed signs of increased protection in some areas near and more distant from the junction upon addition of Mg2+, suggesting a change in three-dimensional conformation. Therefore, it appears that Mg2+ induces a small three-dimensional conformational change on human U2-U6 snRNA complex. In order to build a three-dimensional model for the four-helix conformation, we designed a mutant that favors the formation of four-helix conformation and performed SAXS experiments on it. The preliminary SAXS studies suggest that the human U2-U6 snRNA complex and the mutant complex may also be amenable to further study by SAXS. These results act as a good starting point to characterize further the overall global conformation of human U2-U6 snRNA complex and effects of spliceosomal proteins on it.