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Description
Water-soluble, adenosine triphosphate (ATP)-stabilized palladium nanoparticles have been synthesized by reduction of palladium salt in the presence of excess ATP. They have been characterized by electron microscopy, energy dispersive X-ray spectroscopy, ultraviolet-visible (UV-Vis) spectroscopy, and X-ray diffraction in order to determine particle size, shape, composition and crystal structure. The particles were then subsequently attached to a glassy carbon electrode (GCE) in order to explore their electrochemical properties with regard to hydrogen insertion in 1 M sodium hydroxide. The particles were found to be in the size range 2.5 to 4 nm with good size dispersion. The ATP capping ligand allowed the particles to be air-stable and re-dissolved without agglomeration. It was found that the NPs could be firmly attached to the working electrode via cycling the voltage repeatedly in a NP/phosphate solution. Further electrochemical experiments were conducted to investigate the adsorption and absorption of hydrogen in the NPs in 1 M sodium hydroxide. Results for cyclic voltammetry experiments were consistent with those for nanostructured and thin-film palladium in basic solution. Absorbed hydrogen content was analyzed as a function of potential. The maximum hydrogen:Pd ratio was found to be ~0.7, close the theoretical maximum value for β phase palladium hydride.
ContributorsLamb, Timothy (Author) / Buttry, Daniel A (Thesis advisor) / Yarger, Jeffery (Committee member) / Ros, Alexandra (Committee member) / Arizona State University (Publisher)
Created2013
Description
Thiol functionalization is one potentially useful way to tailor physical and chemical properties of graphene oxides (GOs) and reduced graphene oxides (RGOs). Despite the ubiquitous presence of thiol functional groups in diverse chemical systems, efficient thiol functionalization has been challenging for GOs and RGOs, or for carbonaceous materials in general. In this work, thionation of GOs has been achieved in high yield through two new methods that also allow concomitant chemical reduction/thermal reduction of GOs; a solid-gas metathetical reaction method with boron sulfides (BxSy) gases and a solvothermal reaction method employing phosphorus decasulfide (P4S10). The thionation products, called "mercapto reduced graphene oxides (m-RGOs)", were characterized by employing X-ray photoelectron spectroscopy, powder X-ray diffraction, UV-Vis spectroscopy, FT-IR spectroscopy, Raman spectroscopy, electron probe analysis, scanning electron microscopy, (scanning) transmission electron microscopy, nano secondary ion mass spectrometry, Ellman assay and atomic force microscopy. The excellent dispersibility of m-RGOs in various solvents including alcohols has allowed fabrication of thin films of m-RGOs. Deposition of m-RGOs on gold substrates was achieved through solution deposition and the m-RGOs were homogeneously distributed on gold surface shown by atomic force microscopy. Langmuir-Blodgett (LB) films of m-RGOs were obtained by transferring their Langmuir films, formed by simple drop casting of m-RGOs dispersion on water surface, onto various substrates including gold, glass and indium tin oxide. The m-RGO LB films showed low sheet resistances down to about 500 kΩ/sq at 92% optical transparency. The successful results make m-RGOs promising for applications in transparent conductive coatings, biosensing, etc.
ContributorsJeon, Kiwan (Author) / Seo, Dong-Kyun (Thesis advisor) / Jones, Anne K (Committee member) / Yarger, Jeffery (Committee member) / Arizona State University (Publisher)
Created2013
Characterization of a Lipid Coating on the Surface of Silk Produced by the Embiid Antipaluria urichi
Description
Insects of the order Embiidina spin sheets of very thin silk fibers from their forelimbs to build silken shelters on bark and in leaf litter in tropical climates. Their shelters are very stiff and hydrophobic to keep out predators and rain. In this study, the existence of an outer lipid coating on silk produced by the embiid Antipaluria urichi is shown using scanning and transmission electron microscopy, FT-IR, and water drop contact angle analysis. Subsequently, the composition of the lipid layer is then characterized by 1H NMR and GC-MS.
ContributorsOsborn Popp, Thomas Michael (Author) / Yarger, Jeffery (Thesis director) / Holland, Gregory (Committee member) / Barrett, The Honors College (Contributor) / Department of Chemistry and Biochemistry (Contributor)
Created2014-05
Description
A novel small metal-binding protein (SmbP), with only 93 residues and no similarity to other known proteins, has been isolated from the periplasm of Nitrosomonas europaea. It is characterized by its high percentage (17%) of histidines, a motif of ten repeats of seven residues, a four α-helix bundle structure, and a high binding affinity to about six equivalents of Cu2+. The goal of this study is to investigate the Cu2+ binding sites in SmbP and to understand how Cu2+ stabilizes the protein. Preliminary folding experiments indicated that Cu2+ greatly stabilizes SmbP. In this study, protein folding data from circular dichroism (CD) spectroscopy was used to elucidate the role of Cu2+ in stabilizing SmbP structure against unfolding induced by decreased pH, increased temperature, and chemical denaturants. The significant stabilization effects of Cu2+ were demonstrated by the observation that Cu2+-SmbP remained fully folded under extreme environmental conditions, such as acidic pH, 96 °C, and 8 M urea. Also, it was shown that Cu2+ is able to induce the refolding of unfolded SmbP in acidic solutions. These findings imply that the coordination of Cu2+ to histidine residues is responsible for the stabilization effects. The crystal structure of SmbP without Cu2+ has been determined. However, attempts to crystallize Cu2+-SmbP have not been successful. In this study, multidimensional NMR experiments were conducted in order to gain additional information regarding the Cu2+-SmbP structure, in particular its metal binding sites. Unambiguous resonance assignments were successfully made. Cα secondary chemical shifts confirmed that SmbP has a four α-helical structure. A Cu2+-protein titration experiment monitored by NMR indicated a top-to-bottom, sequential metal binding pattern for SmbP. In addition, several bioinformatics tools were used to complement the experimental approach and identity of the ligands in Cu2+-binding sites in SmbP is proposed.
ContributorsYan, Qin (Author) / Francisco, Wilson A (Thesis advisor) / Allen, James (Committee member) / Ghirlanda, Giovanna (Committee member) / Arizona State University (Publisher)
Created2010
Description
ABSTRACT Peptide microarrays may prove to be a powerful tool for proteomics research and clinical diagnosis applications. Fodor et al. and Maurer et al. have shown proof-of-concept methods of light- and electrochemically-directed peptide microarray fabrication on glass and semiconductor microchips respectively. In this work, peptide microarray fabrication based on the abovementioned techniques were optimized. In addition, MALDI mass spectrometry based peptide synthesis characterization on semiconductor microchips was developed and novel applications of a CombiMatrix (CBMX) platform for electrochemically controlled synthesis were explored. We have investigated performance of 2-(2-nitrophenyl)propoxycarbonyl (NPPOC) derivatives as photo-labile protecting group. Specifically, influence of substituents on 4 and 5 positions of phenyl ring of NPPOC group on the rate of photolysis and the yield of the amine was investigated. The results indicated that substituents capable of forming a π-network with the nitro group enhanced the rate of photolysis and yield. Once such properly substituted NPPOC groups were used, the rate of photolysis/yield depended on the nature of protected amino group indicating that a different chemical step during the photo-cleavage process became the rate limiting step. We also focused on electrochemically-directed parallel synthesis of high-density peptide microarrays using the CBMX technology referred to above which uses electrochemically generated acids to perform patterned chemistry. Several issues related to peptide synthesis on the CBMX platform were studied and optimized, with emphasis placed on the reactions of electro-generated acids during the deprotection step of peptide synthesis. We have developed a MALDI mass spectrometry based method to determine the chemical composition of microarray synthesis, directly on the feature. This method utilizes non-diffusional chemical cleavage from the surface, thereby making the chemical characterization of high-density microarray features simple, accurate, and amenable to high-throughput. CBMX Corp. has developed a microarray reader which is based on electro-chemical detection of redox chemical species. Several parameters of the instrument were studied and optimized and novel redox applications of peptide microarrays on CBMX platform were also investigated using the instrument. These include (i) a search of metal binding catalytic peptides to reduce overpotential associated with water oxidation reaction and (ii) an immobilization of peptide microarrays using electro-polymerized polypyrrole.
ContributorsKumar, Pallav (Author) / Woodbury, Neal (Thesis advisor) / Allen, James (Committee member) / Johnston, Stephen (Committee member) / Arizona State University (Publisher)
Created2013
Description
Transition metal oxides are used for numerous applications, includingsemiconductors, batteries, solar cells, catalysis, magnetic devices, and are commonly
observed in interstellar media. However, the atomic-scale properties which dictate the
overall bulk material activity is still lacking fundamental details. Most importantly, how
the electron shells of metals and O atoms mix is inherently significant to reactivity. This
thesis compares the binding and excited state properties of highly correlated first-row
transition metal oxides using four separate transition metal systems of Ti, Cr, Fe and Ni.
Laser ablation coupled with femtosecond pump-probe spectroscopy is utilized to resolve
the time-dependent excited state relaxation dynamics of atomically precise neutral
clusters following 400 nm (3.1 eV) photoexcitation. All transition metal oxides form
unique stable stoichiometries with excited state dynamics that evolve due to oxidation,
size, or geometry. Theoretical calculations assist in experimental analysis, showing
correlations between charge transfer characteristics, electron and hole localization, and
magnetic properties to the experimentally determined excited state lifetimes.
This thesis finds that neutral Ti and Cr form stable stoichiometries of MO2 (M =
Ti, Cr) which easily lose up to two O atoms, while neutral Fe and Ni primarily form MO
(M = Fe, Ni) geometries with suboxides also produced. TiO2 clusters possess excited
state lifetimes that increase with additional cluster units to ~600 fs, owing to a larger
delocalization of excited charge carriers with cluster size. CrO2 clusters show a unique
inversed metallic behavior with O content, where the fast (~30 fs) metallic relaxation
component associated with electron scattering increases with higher O content, connected
to the percent of ligand-to-metal charge transfer (LMCT) character and higher density of
states. FeO clusters show a decreased lifetime with size, reaching a plateau of ~150 fs at
the size of (FeO)5 related to the density of states as clusters form 3D geometries. Finally,
neutral (NiO)n clusters all have similar fast lifetimes (~110 fs), with suboxides possessing
unexpected electronic transitions involving s-orbitals, increasing excited state lifetimes
up to 80% and causing long-lived states lasting over 2.5 ps. Similarities are drawn
between each cluster system, providing valuable information about each metal oxide
species and the evolution of excited state dynamics as a result of the occupied d-shell.
The work presented within this thesis will lead to novel materials of increased reactivity
while facilitating a deeper fundamental understanding on the effect of electron
interactions on chemical properties.
ContributorsGarcia, Jacob M. (Author) / Sayres, Scott G (Thesis advisor) / Yarger, Jeffery (Committee member) / Steimle, Timothy (Committee member) / Arizona State University (Publisher)
Created2021
Description
The ability to manipulate the interaction between small molecules and biological macromolecules towards the study of disease pathogenesis has become a very important part of research towards treatment options for various diseases. The work described here shows both the use of DNA oligonucleotides as carriers for a nicotine hapten small molecule, and the use of microsomes to study the stability of compounds derived to treat mitochondrial diseases.
Nicotine addiction is a worldwide epidemic because nicotine is one of the most widely used addictive substances. It is linked to early death, typically in the form of heart or lung disease. A new vaccine conjugate against nicotine held within a DNA tetrahedron delivery system has been studied. For this purpose, several strands of DNA, conjugated with a modified dTpT having three or six carbon atom alkynyl linkers, have been synthesized. These strands have later been conjugated to three separate hapten small molecules to analyze which conjugates formed would be optimal for further testing in vivo.
Mitochondrial diseases are hard to treat, given that there are so many different variations to treat. There is no one compound that can treat all mitochondrial and neurodegenerative diseases; however, improvements can be made to compounds currently under study to improve the conditions of those afflicted. A significant issue leading to compounds failing in clinical trials is insufficient metabolic stability. Many compounds have good biological activity, but once introduced to an animal, are not stable enough to have any effect. Here, several synthesized compounds have been evaluated for metabolic stability, and several showed improved stability, while maintaining biological activity.
Nicotine addiction is a worldwide epidemic because nicotine is one of the most widely used addictive substances. It is linked to early death, typically in the form of heart or lung disease. A new vaccine conjugate against nicotine held within a DNA tetrahedron delivery system has been studied. For this purpose, several strands of DNA, conjugated with a modified dTpT having three or six carbon atom alkynyl linkers, have been synthesized. These strands have later been conjugated to three separate hapten small molecules to analyze which conjugates formed would be optimal for further testing in vivo.
Mitochondrial diseases are hard to treat, given that there are so many different variations to treat. There is no one compound that can treat all mitochondrial and neurodegenerative diseases; however, improvements can be made to compounds currently under study to improve the conditions of those afflicted. A significant issue leading to compounds failing in clinical trials is insufficient metabolic stability. Many compounds have good biological activity, but once introduced to an animal, are not stable enough to have any effect. Here, several synthesized compounds have been evaluated for metabolic stability, and several showed improved stability, while maintaining biological activity.
ContributorsSchmierer, Margaret (Author) / Hecht, Sidney M. (Thesis advisor) / Allen, James (Committee member) / Gould, Ian (Committee member) / Arizona State University (Publisher)
Created2016
Description
Glycosaminoglycans (GAGs) are a class of complex biomolecules comprised of linear, sulfated polysaccharides whose presence on cell surfaces and in the extracellular matrix involve them in many physiological phenomena as well as in interactions with pathogenic microbes. Decorin binding protein A (DBPA), a Borrelia surface lipoprotein involved in the infectivity of Lyme disease, is responsible for binding GAGs found on decorin, a small proteoglycan present in the extracellular matrix. Different DBPA strains have notable sequence heterogeneity that results in varying levels of GAG-binding affinity. In this dissertation, the structures and GAG-binding mechanisms for three strains of DBPA (B31 and N40 DBPAs from B. burgdorferi and PBr DBPA from B. garinii) are studied to determine why each strain has a different affinity for GAGs. These three strains have similar topologies consisting of five α-helices held together by a hydrophobic core as well as two long flexible segments: a linker between helices one and two and a C-terminal tail. This structural arrangement facilitates the formation of a basic pocket below the flexible linker which is the primary GAG-binding epitope. However, this GAG-binding site can be occluded by the flexible linker, which makes the linker a negative regulator of GAG-binding. ITC and NMR titrations provide KD values that show PBr DBPA binds GAGs with higher affinity than B31 and N40 DBPAs, while N40 binds with the lowest affinity of the three. Work in this thesis demonstrates that much of the discrepancies seen in GAG affinities of the three DBPAs can be explained by the amino acid composition and conformation of the linker. Mutagenesis studies show that B31 DBPA overcomes the pocket obstruction with the BXBB motif in its linker while PBr DBPA has a retracted linker that exposes the basic pocket as well as a secondary GAG-binding site. N40 DBPA, however, does not have any evolutionary modifications to its structure to enhance GAG binding which explains its lower affinity for GAGs. GMSA and ELISA assays, along with NMR PRE experiments, confirm that structural changes in the linker do affect GAG-binding and, as a result, the linker is responsible for regulating GAG affinity.
ContributorsMorgan, Ashli M (Author) / Wang, Xu (Thesis advisor) / Allen, James (Committee member) / Yarger, Jeffery (Committee member) / Arizona State University (Publisher)
Created2015
Description
An evolving understanding of elastomeric polymer nanocomposites continues to expand commercial, defense, and industrial products and applications. This work explores the thermomechanical properties of elastomeric nanocomposites prepared from bisphenol A diglycidyl ether (BADGE) and three amine-terminated poly(propylene oxides) (Jeffamines). The Jeffamines investigated include difunctional crosslinkers with molecular weights of 2,000 and 4,000 g/mol and a trifunctional crosslinker with a molecular weight of 3,000 g/mol. Additionally, carbon nanotubes (CNTs) were added, up to 1.25 wt%, to each thermoset. The findings indicate that the Tg and storage modulus of the polymer nanocomposites can be controlled independently within narrow concentration windows, and that effects observed following CNT incorporation are dependent on the crosslinker molecular weight.
Polymer matrix composites (PMCs) offer design solutions to produce smart sensing, conductive, or high performance composites for a number of critical applications. Nanoparticle additives, in particular, carbon nanotubes and metallic quantum dots, have been investigated for their ability to improve the conductivity, thermal stability, and mechanical strength of traditional composites. Herein we report the use of quantum dots (QDs) and fluorescently labeled carbon nanotubes (CNTs) to modify the thermomechanical properties of PMCs. Additionally, we find that pronounced changes in fluorescence emerge following plastic deformation, indicating that in these polymeric materials the transduction of mechanical force into the fluorescence occurs in response to mechanical activation.
Segmented ionenes are a class of thermoplastic elastomers that contain a permanent charged group within the polymer backbone and a spacer segment with a low glass transition temperature (Tg) to provide flexibility. Ionenes are of interest because of their synthetic versatility, unique morphologies, and ionic nature. Using phase changing ionene-based nanocomposites could be extended to create reversible mechanically, electrically, optically, and/or thermally responsive materials depending on constituent nanoparticles and polymers. This talk will discuss recent efforts to utilize the synthetic versatility of ionenes (e.g., spacer composition of PTMO or PEG) to prepare percolated ionic domains in microphase separated polymers that display a range of thermomechanical properties. Furthermore, by synthesizing two series of ionene copolymers with either PEG or PTMO spacers at various ratios with 1,12-dibromododecane will yield a range of ion contents (hard contents) and will impact nanoparticle dispersion.
Polymer matrix composites (PMCs) offer design solutions to produce smart sensing, conductive, or high performance composites for a number of critical applications. Nanoparticle additives, in particular, carbon nanotubes and metallic quantum dots, have been investigated for their ability to improve the conductivity, thermal stability, and mechanical strength of traditional composites. Herein we report the use of quantum dots (QDs) and fluorescently labeled carbon nanotubes (CNTs) to modify the thermomechanical properties of PMCs. Additionally, we find that pronounced changes in fluorescence emerge following plastic deformation, indicating that in these polymeric materials the transduction of mechanical force into the fluorescence occurs in response to mechanical activation.
Segmented ionenes are a class of thermoplastic elastomers that contain a permanent charged group within the polymer backbone and a spacer segment with a low glass transition temperature (Tg) to provide flexibility. Ionenes are of interest because of their synthetic versatility, unique morphologies, and ionic nature. Using phase changing ionene-based nanocomposites could be extended to create reversible mechanically, electrically, optically, and/or thermally responsive materials depending on constituent nanoparticles and polymers. This talk will discuss recent efforts to utilize the synthetic versatility of ionenes (e.g., spacer composition of PTMO or PEG) to prepare percolated ionic domains in microphase separated polymers that display a range of thermomechanical properties. Furthermore, by synthesizing two series of ionene copolymers with either PEG or PTMO spacers at various ratios with 1,12-dibromododecane will yield a range of ion contents (hard contents) and will impact nanoparticle dispersion.
ContributorsWang, Meng, Ph.D (Author) / Green, Matthew D (Thesis advisor) / Green, Alexander (Committee member) / Yarger, Jeffery (Committee member) / Arizona State University (Publisher)
Created2019
Description
Serial crystallography (SX) is a relatively new structural biology technique that collects X-ray diffraction data from microcrystals via femtosecond pulses produced by an X-ray free electron laser (X-FEL) or by synchrotron radiation, allowing for challenging protein structures to be solved from microcrystals at room temperature. Because of the youth of this technique, method development is necessary for it to achieve its full potential.
Most serial crystallography experiments have relied on delivering sample in the mother liquor focused into a stream by compressed gas. This liquid stream moves at a fast rate, meaning that most of the valuable sample is wasted. For this reason, the liquid jet can require 10-100 milligrams of sample for a complete data set. Agarose has been developed as a slow moving microcrystal carrier to decrease sample consumption and waste. The agarose jet provides low background, no Debye-Sherrer rings, is compatible for sample delivery in vacuum environments, and is compatible with a wide variety of crystal systems. Additionally, poly(ethylene oxide) which is amenable for data collection in atmosphere has been developed for synchrotron experiments. Thus this work allows sample limited proteins of difficult to crystallize systems to be investigated by serial crystallography.
Time-resolved serial X-ray crystallography (TR-SX) studies have only been employed to study light-triggered reactions in photoactive systems. While these systems are very important, most proteins in Nature are not light-driven. However, fast mixing of two liquids, such as those containing enzyme protein crystals and substrates, immediately before being exposed to an X-ray beam would allow conformational changes and /or intermediates to be seen by diffraction. As a model, 3-deoxy-D-manno-2-octulosonate-8-phosphate synthase (KDO8PS), has been developed for TR-SX. This enzyme initializes the first step of lipopolysaccharide synthesis by a net aldol condensation between arabinose-5-phosphate, phosphoenol pyruvate, and water. During this reaction, a short lived intermediate is formed and has been observed on a millisecond timescale using other methods. Thus KDO8PS is an ideal model protein for studying diffusion times into a crystal and short mixing times (<10 ms). For these experiments, microcrystals diffracting to high resolution have been developed and characterized.
Most serial crystallography experiments have relied on delivering sample in the mother liquor focused into a stream by compressed gas. This liquid stream moves at a fast rate, meaning that most of the valuable sample is wasted. For this reason, the liquid jet can require 10-100 milligrams of sample for a complete data set. Agarose has been developed as a slow moving microcrystal carrier to decrease sample consumption and waste. The agarose jet provides low background, no Debye-Sherrer rings, is compatible for sample delivery in vacuum environments, and is compatible with a wide variety of crystal systems. Additionally, poly(ethylene oxide) which is amenable for data collection in atmosphere has been developed for synchrotron experiments. Thus this work allows sample limited proteins of difficult to crystallize systems to be investigated by serial crystallography.
Time-resolved serial X-ray crystallography (TR-SX) studies have only been employed to study light-triggered reactions in photoactive systems. While these systems are very important, most proteins in Nature are not light-driven. However, fast mixing of two liquids, such as those containing enzyme protein crystals and substrates, immediately before being exposed to an X-ray beam would allow conformational changes and /or intermediates to be seen by diffraction. As a model, 3-deoxy-D-manno-2-octulosonate-8-phosphate synthase (KDO8PS), has been developed for TR-SX. This enzyme initializes the first step of lipopolysaccharide synthesis by a net aldol condensation between arabinose-5-phosphate, phosphoenol pyruvate, and water. During this reaction, a short lived intermediate is formed and has been observed on a millisecond timescale using other methods. Thus KDO8PS is an ideal model protein for studying diffusion times into a crystal and short mixing times (<10 ms). For these experiments, microcrystals diffracting to high resolution have been developed and characterized.
ContributorsConrad, Chelsie E (Author) / Fromme, Petra (Thesis advisor) / Ros, Alexandra (Committee member) / Allen, James (Committee member) / Arizona State University (Publisher)
Created2016