Chemistry Commons^™

New Strategies To Reveal Protein Candidates In Protein-Protein Interactome Study, Meng-Chieh Chen

Open Access Theses

Comprehensive protein-protein interaction network analysis can help reveal protein functions in a system-wide manner. A reliable knowledgebase of interaction networks is not only important for selecting the candidates for drug therapies, but also for evaluating the disease risk. In current interaction databases, 322579 interactions comprised of 56460 proteins have been reported (statistical analysis from APID: Agile Protein Interaction DataAnalyzer; http://bioinfow.dep.usal.es/apid/index.htm). The huge datasets are contributed mainly by yeast -two -hybrid (Y2H) screening and affinity-purification followed by mass spectrometry (AP-MS). High false positive rates and failing to cover certain interaction categories are the limitations of these two methods. Here, we developed …

Reverse-Phase Liquid Chromatography Of Small Molecules Using Silica Colloidal Crystals, Natalya Khanina

Open Access Theses

Capillaries packed with a silica colloidal crystal (SCC) of 470 nm nonporous particles have recently been shown to offer significant improvements in the peak width, resolution, and speed of protein analysis due to the reduction of the A and C term broadening contributions of the Van Deemter equation. While protein separations using this technology have shown vast improvements, small molecules remain largely unexplored. As the SCC allows for an approximately diffusion limited system, extremely high plate numbers are expected for small molecule separations. The research presented herein studies the feasibility of pressure-driven small molecule separation using SCCs and commercial instrumentation. …

High-Purity Gallium Analysis By Inductively Coupled Plasma Mass Spectrometry, Kyungjean Min

Open Access Theses

The mobility of Two-dimensional Electron Gas in AlGaAs/GaAs heterostructures that are grown in the Molecular Beam Epitaxy (MBE) can be increased by purification of the gallium used to grow the films. To attain 200 million cm2/Vs mobility, the impurity concentration of gallium should be reduced to below 1 ppb. The commercial 7N (99.99999%) gallium with 100 ppb total impurity is currently used in the MBE at Purdue University and is being purified by zone refining. To evaluate the commercial 7N gallium and establish the methodology for the impurity measurement after zone refining, germanium, iron, and zinc in 6N and 7N …

Identifying Conditions To Optimize Lactic Acid Production From Food Waste, Raymond M. Redcorn

Open Access Theses

There is an increased demand for lactic acid for the production of biopolymers and to aid nutrient removal in wastewater treatment. Food waste offers a source of soluble sugars to produce lactic acid, which does not increase land demand, but digestion conditions have yet to be optimized when co-digested with primary sludge. Food waste was collected from cafeteria waste bins, homogenized and seeded with primary sludge. A Box Behnken Response surface design was used to optimize lactic acid production based on pH, temperature, loading rate, and retention time. Subsequent experiments verified and refined those conditions to optimize for both yield …

Elucidating The Mechanism Of Phenylpropanoid Regulation By The Arabidopsis Mediator Complex, Wenjie Zeng

Open Access Theses

The Mediator complex is a multi-protein co-regulator of eukaryotic transcription which plays a role in the expression of many, if not most, genes of the cell. Two Mediator subunits, REF4 and RFR1, were demonstrated to be important for the normal regulation of phenylpropanoid metabolism in Arabidopsis. Phenylpropanoids are a family of specialized plant metabolites derived from the amino acid phenylalanine and are involved in defense against pathogens, UV protection and structural support. In order to understand how Mediator regulates phenylpropanoid metabolism through REF4 and RFR1, a better basic understanding of this protein complex is required. Here I provide data on …

Impact Of Nanostructure On Polymer-Based Nonvolatile Memory Devices, Seung Hyun Sung

Open Access Theses

Memory functionality is essential for many high-end electronic applications (e.g. , smart phones, personal computers). Particularly, organic nonvolatile memory devices based on polymer ferroelectric materials are a promising approach toward the development of low-cost memory due to the ease of processing and flexibility associated with the device. Here, we will focus on a memory device with a two-component active layer and a diode structure. This ferroelectric diode (FeD) has a nanostructured active layer, composed of ferroelectric and semiconducting polymers, and it can provide easy access to high-performance polymer-based memory devices. In order to create these nanostructured active layers, we …

Gas-Phase Ion/Ion Reactions Of Biomolecules: An Examination Of Carboxylate Reactivity And Arginine Based Non-Covalent Complexes, Nathan Zachary Barefoot

Open Access Theses

The advent of Electrospray Ionization with the ability to generate multiply charges ions has contributed significantly to the study of gas-phase ion/ion reactions. With the tools available in mass spectrometry it has been shown that these reactions are effective at transforming one type of gaseous ion into another through a series of reactions. This work examines some of these reactions and their application to field of proteomics specifically focusing on the amino acids of arginine and lysine. NHS reagents have been shown to react to both of these molecules with in the gas-phase under different conditions but have relies on …

Correlating Molecular Architecture Of A Radical Polymer Based Copolymer With Its Electrical Transport Properties, Holly Chan

Open Access Theses

The design and synthesis of electrically-conductive macromolecules can lead to significant improvements in the performance of polymer-based energy conversion devices (e.g., thermoelectric devices). For these organic electronic devices, conjugated polymers have dominated the area of conductive polymers; however, these materials are usually synthesized using conditions that lead to poorly-defined polymers. Furthermore, in these increasingly-standard polymers, the charge transport ability of the polymer thin films is largely affected by the degree of crystallinity, which is a difficult property to control in a reproducible fashion. Therefore, we seek to explore a new class of amorphous, non-conjugated polymers containing a stable radical …

Separation Of On-Column Labeled Model Proteins With Packed Capillary Electrophoresis, Yingxu Hao

Open Access Theses

Protein drugs are increasingly developed in the pharmaceutical company. Under the regulation of FDA, high purity of therapeutic proteins needs to be maintained. Before putting those drugs in the market, fast and efficient method is in need to achieve homogeneity. Traditionally, polyacrylamide gel electrophoresis (PAGE), capillary electrophoresis (CE), and size-exclusion chromatography (SEC) are used for the purification process. These methods have the disadvantages of low time and cost efficiency, and this quality assurance process has become the bottleneck of production. In our group, sub-micron silica colloidal particles with polyacrylamide layer on the surface are packed inside capillaries to increase the …

Cloning And Characterization Of Ef-Tu And Ef-Ts From Streptococcus Pneumoniae, Carlos Eduardo Rivera

Theses and Dissertations - UTB/UTPA

Antibiotic resistance is a prevalent threat to public health around the world, and resistance among strains of Streptococcus pneumoniae is growing rapidly. This increasing resistance elevates the demand for new drug discoveries. This research attempts to develop a means to combat S. pneumoniae by targeting protein synthesis for the discovery of new antibacterial agents. Protein synthesis components, elongation factor Tu (EF-Tu) and elongation factor Ts (EF-Ts) facilitate many steps in the biosynthesis of proteins and are therefore essential proteins involved in protein synthesis. EF-Tu and EF-Ts were cloned, expressed, purified, and enzymatically characterized to help develop a screening system that …

A Screening Platform For Identification Of Compounds That Inhibit Protein Synthesis In Pseudomonas Aeruginosa, Yanmei Hu

Theses and Dissertations - UTB/UTPA

Pseudomonas aeruginosa is a Gram-negative pathogenic bacteria and a common cause of nosocomial infections. This pathogen has recently garnered attention due to its pan-resistance. We have developed a poly(U) mRNA-directed aminoacylation/translation (A/T) protein synthesis system from P. aeruginosa. The concentration of each component of the system has been arrived at through multiple rounds of optimization. Poly-phenylalanine synthesis in the system was monitored using scintillation proximity assays (SPA). This system has been used to screen two natural compound libraries (>1100) and a number of the compounds that inhibit greater than 50% of the activity of the system have been identified. …

Metal Oxide Nanostructures For Energy Conversion And Storage, Xing Sun

Theses and Dissertations - UTB/UTPA

With the depletion of non-renewable resources and the related problems such as environmental pollutions and global warming effect, the society urgently needs more efficient and controllable energy conversion and storage systems. Three-dimensional ZnO nanoforests were prepared and morphology-tunable, which benefits both of energy conversion and storage systems. Willow-like ZnO nanoforests led the highest conversion efficiency of photoelectrochemical water splitting in reported pure ZnO nanostructures. Compared with nanowire arrays, ZnO@MnO2 nanoforests delivered 5 times higher specific capacitances within the same footprint area. V2O5@PPy exhibited higher specific capacitance and better rate stability than pure V2O5 nanofibers. This work lays the foundation for …

Monitoring Citrus Nutrition In The Rio Grande Valley For Fertilizer Recommendations, Iram Lopez

Theses and Dissertations - UTB/UTPA

Soil fertility and plant nutrition is crucial for a better yield and consistent harvest in the Rio Grande Valley for local farmers growing citrus trees. A field of oranges and a field of grapefruits were monitored and nutrition deficiencies were noticed that played an important role during fruit set. Soil samples that were taken throughout the year were analyzed via a carbon dioxide extraction method that mimics the way plants naturally take up nutrients or extract nutrients from every soil type. Macronutrients such as the N, P, K, Na, Ca, Mg and some of the micronutrients (Zn, Fe, Mn, and …

Effect Of Multivalent Ions On The Swelling And Mechanical Behavior Of Superabsorbent Polymers (Saps) For Mitigation Of Mortar Autogenous Shrinkage, Qian Zhu

Open Access Theses

The chemical and physical structure-property relationships of model superabsorbent polymer (SAP) hydrogels were characterized with respect to swelling behavior and mechanical properties in different ionic solutions (Na+ , Ca2+ , and Al3+ ). The model hydrogels were composed of poly(sodium acrylate-acrylamide) (PANa-PAM) copolymer with varying concentrations of PANa (0, 17, 33, 67, and 83 wt.%) and covalent crosslinking densities of 1, 1.5, and 2 wt.%. By synthesizing the hydrogels in-house, systems with independently tunable amounts of covalent crosslinking and anionic functional groups were created, allowing for the relative effects of covalent and ionic crosslinking on the properties of the hydrogels …

The Development Of 6.7% Efficient Copper Zinc Indium Selenide Devices From Copper Zinc Indium Sulfide Nanocrystal Inks, Brian Kemp Graeser

Open Access Theses

As solar cell absorber materials, alloys of CuIn(S,Se)2 and Zn(S,Se) provide an opportunity to reduce the usage of indium along with the ability to tune the band gap. Here we report successful synthesis of alloyed (CuInS2 )0.5(ZnS)0.5 nanocrystals by a method that solely uses oleylamine as the liquid medium for synthesis. The reactive sintering of a thin film of these nanocrystals via selenization at 500 °C results in a uniform composition alloy (CuIn(S,Se)2 )0.5 (Zn(S,Se)) 0.5 layer with micron size grains. Due to the large amount of zinc in the film, the sintered grains exhibit the zinc blende structure instead …

Investigation Of Isotope Effects Of Ozone As A Function Of Temperature, Daniel J. Mcmahon

Open Access Theses

Ozone is an important oxidizer in the atmosphere and plays a crucial role as a cleanser, removing various compounds such NOx and SOx. It also is intriguing to those that study stable isotopes as it has a unique signature found in no other oxygen containing molecule. Ozone is observed to fractionate mass independently, which means it does not follow the typical δ 17 O /δ18 O = 0.52 ratio expected for molecules enriched with 17 O and 18 O. The magnitude of ozone's mass independent enrichment has been studied in laboratory experiments and atmospheric observations but its explanation is still …

Applications Of Calculated Second Harmonic Generation Tensors On Monomolecular And Bimolecular Systems, Gregory R. Snyder

Open Access Theses

The field of nonlinear optics (NLO) has proven itself as a relatively recent and powerful area of science in the areas of microscopy and high-sensitivity quantification measurements. In particular, symmetry selective NLO processes such as second harmonic generation (SHG) take advantage of symmetry rules to cancel background noise almost completely, leading to both high resolution images and limits of detection (LOD) in the photon counting range. Background noise in SHG is negated as result of signal cancellation in systems containing inversion symmetry; generally isotropic sources. Quantum mechanical computational chemistry has enriched the field of NLO by enabling studies on hypothetical …

Protein Affinity Extraction Of Prostate Specific Antigen (Psa) Using Submicron Spheres, Yao Wang

Open Access Theses

PSA has been used as a biomarker for prostate cancer for a long time. To characterize different glycoforms of PSA using techniques like UHPLC and cIEF, concentration and purification of PSA from complex samples becomes necessary. Our group has developed submicron silica spheres based affinity beads to extract PSA through immunoprecipitation. This study focuses on measuring the bead performance when antibody type/amount was varied and PSA concentration was lowered for clinical use. To better satisfy the requirement of large-scale extraction, several attempts were made to increase the bead capacity. The results will be presented and future directions of the project …

Biological Compatibility And Cytotoxicity Studies Of Hepa-1c1c7, Hepg2, And Mcf-7 Cancer Cell Lines Upon Exposure To Silver, Palladium, And Gold Nanoparticles, M. Esther Salinas

Theses and Dissertations - UTB/UTPA

The field of nanomedicine has recently explored potential applications for cancer treatment ranging from drug delivery methods to cancer imaging techniques. Due to potential risks of nanomaterials affecting non-cancerous cells in the body, in vitro toxicity studies are being conducted. The nanoparticles (NPs) were synthesized from potassium tetrachloroaurate (III) hydrate, potassium tetrabromoaurate (III) dihydrate, potassium tetrachloropalladate (II), and silver nitrate. NPs were synthesized using the Turkevich method or through the sodium borohydride reduction. Particles synthesized using sodium borohydride were stabilized with cetyltrimethylammonium bromide (CTAB). The NPs under investigation were used to treat three cancer cell lines. The treated cells were …

Oxidation Of Dibenzothiophene To Dibenzothiophene Sulfone Using Tungsten (Vi) Oxide, Alejandrina Rivera

Theses and Dissertations - UTB/UTPA

The oxidation of dibenzothiophene (DBT) to dibenzothiophene-sulfone has been considered as an alternate method to remove sulfur from crude oil. This study demonstrates that the oxidative desulfurization (ODS) of DBT to DBT-sulfone occurs using WO3 as a catalyst. WO3 was synthesized and characterized using X-ray diffraction to determine the phase of WO3. Each reaction was refluxed and run for four hours using WO3 as a catalyst, dibenzothiphene, and four different solvents: decahydronapthalene, n-dodecane, decalin, and dodecane. The reactions were performed at temperatures ranging from 120 oC to 150 oC. Aliquots were taken at 30 minutes for up to four hours …

Microfluidics Guided By Redox-Magnetohydrodynamics (Mhd) For Lab-On-A-Chip Applications, Vishal Sahore

Graduate Theses and Dissertations

Unique microfluidic control actuated by simply turning off and on microfabricated electrodes in a small-volume system was investigated for lab-on-a-chip applications. This was accomplished using a relatively new pumping technique of redox-magnetohydrodynamics (MHD), which as shown in this dissertation generated the important microfluidic features of flat flow profile and fluid circulation. MHD is driven by the body force, FB = j × B, which is the magnetic part of the Lorentz force equation, and its direction is given by the right hand rule. The ionic current density, j, was generated in an equimolar solution of potassium ferri/ferro cyanide by applying …

Monodentate, Bidentate And Photocrosslinkable Thiol Ligands For Improving Aqueous Biocompatible Quantum Dots, Hiroko Takeuchi

Graduate Theses and Dissertations

Water-soluble Quantum Dots (QDs) are highly sensitive fluorescent probes that are often used to study biological species. One of the most common ways to render QDs water-soluble for such applications is to apply hydrophilic thiolated ligands to the QD surface. However, these ligands are labile and can be easily exchanged on the QD surface, which can severely limit their application. As one way to overcome this limitation while maintaining a small colloidal size of QDs, we developed a method to stabilize hydrophilic thiolated ligands on the surface of QDs through the formation of a crosslinked shell using a photocrosslinking approach. …

Electrospinning Polymer Blends For Biomimetic Scaffolds For Acl Tissue Engineering, Vanessa Lizeth Garcia

Theses and Dissertations - UTB/UTPA

The anterior cruciate ligament (ACL) rupture is one of the most common knee injuries. Current ACL reconstructive strategies consist of using an autograft or an allograft to replace the ligament. However, limitations have led researchers to investigate tissue engineered grafts, known as scaffolds, through electrospinning. Scaffolds made of natural and synthetic polymer blends have the potential to promote cell adhesion while having strong mechanical properties. However, enzymes found in the knee are known to degrade tissues and affect the healing of intra-articular injuries. Results suggest that the natural polymers used in this study modify the thermal properties and tensile strength …

Remediation Of Copper(Ii) And Lead(Ii) From Aqueous Solution Using Engineered Iron Oxide And Manganese Oxide Nanomaterials, Carlos Tamez Jr.

Theses and Dissertations - UTB/UTPA

Nano-sized Fe3O4, Fe2O3, Mn3O4, and MnO2 were synthesized by titration/precipitation and characterized using powder XRD. pH assays determined that optimum binding occurred at pH 4 for Fe3O4 and Fe2O3 and pH 3 for Mn3O4 and MnO2. Maximum adsorption of Cu(II) and Pb(II) occurred within 20 min or less of contact with the nanomaterials. The synthesized nanomaterials showed a binding preference for Pb(II) over Cu(II) at concentrations above 50 ppm. Batch studies also showed no significant reduction in the binding of copper and lead to either Fe3O4, Fe2O3, Mn3O4, or MnO2 in the presence of Na+ , K+ , Mg2+ or …

Reduction Of Nitroaromatic Compounds With Sodium Borohydride Using Transition Metal Sulfides, Samuel Pina Jr.

Theses and Dissertations - UTB/UTPA

The following systems: NaBH4/Fe3S4, NaBH4/Co3S4, NaBH4/NiS, NaBH4/CuS, and NaBH4/ZnS, were investigated for their nitro reducing abilities. Quantitative conversions were observed for the reduction of nitrobenzene with NaBH4/Co3S4 and NaBH4/NiS systems as opposed to only 9% conversion without any catalyst, representing a ten-fold increase in the reducing ability of NaBH4. In ethanol, various nitroaromatic compounds were also successfully reduced in moderate to high yields with 3 molar equivalents of NaBH4, demonstrating a mild alternative for the effective reduction of nitroaromatic compounds to their corresponding aryl amines. Screening of catalysts was carried out using gas chromatography. All products were characterized using 1 …

Oxidation Of Dibenzothiophene To Dibenzothiophene Sulfone Using Tio2, Juan H. Leal

Theses and Dissertations - UTB/UTPA

The oxidation of dibenzothiophene (DBT) to dibenzothiophene-sulfone has been considered as an alternate method to remove sulfur from crude oil. This study demonstrates that the oxidative desulfurization (ODS) of DBT to DBT-sulfone occurs using rutile TiO2 as a catalyst with the aid of O2. In addition, anatase and brookite were synthesized and tested in the reaction. Particle size of the catalysts was calculated and morphology was explored using SEM. A kinetic study was performed to determine the catalytic effect and activation energy of TiO2. The oxidation reaction was carried out by refluxing TiO2 and DBT in decahydronapthalene while flowing O2 …

Developing A Presumptive Test For Select Synthetic Cannabinoids, Carrie Snyder

Graduate Theses and Dissertations

Synthetic cannabinoids (SC's) began to gain popularity around the world in 2009. Since then, many of the compounds have been outlawed and methods developed to detect them and their metabolites using mass spectrometry. Our work investigated the possibility of developing a colorimetric presumptive test. The SC JWH-019 was synthesized and its ketone targeted as a possible reaction site. Many SC's contain ketones and thus a reaction at this site would be applicable to many of the compounds. Since JWH-019 is costly and time consuming to synthesize, much of the experimental work was done using benzophenone (BP). BP contains a diaryl …

Towards The Total Synthesis Of Antascomicin B. Efforts To Construct The C1-C21 Fragment, Juliette Rivero-Castro

Graduate Theses and Dissertations

Antascomicin B is a macrolide isolated from a strain of Micromonospora. It possesses structural similarities to FK506 and rapamycin and exhibits potent binding ability to FKBP12. Recent reports suggest that small molecule ligands of FKBP12 possess potent neuroprotective and neurodegenerative properties in mouse models of Parkinson's disease. Our approach to the C1-21 fragment of antascomicin B involves an asymmetric amino-Claisen rearrangement originally developed by Tsunoda et al.35 report the scalability of the preparation and rearrangement of an allylic amide possessing a silyloxy group at the terminal position of the alkene. The Tsunoda-Claisen rearrangement uses inexpensive (S)-α-methylbenzylamine as the chiral …

Development Of A Field-Portable Miniature Mass Spectrometer Designed For In-Situ Analysis And Ion Trap Miniaturization, Paul Isaac Hendricks

Open Access Dissertations

Chemical analysis by mass spectrometry has become the gold standard due to the sensitivity, selectivity, and short analysis times that are afforded by the method. Advances in miniaturized vacuum systems, mass analyzers, electronics, and ionization sources have allowed for the development of field-portable mass spectrometers. The performance of portable instruments has received much attention for their utility in the detection of illicit drugs, explosives, environmental contaminants, therapeutic drugs, and more recently, biological tissues. Furthermore, detection of the aforementioned compounds can be completed at atmospheric pressures and in the presence of complex matrices and sample surfaces when used in conjunction with …

Construction And Demonstration Of A Tandem Mass Spectrometer Based Instrument For Cold Ion Spectroscopy, James Gerhardt Redwine

Open Access Dissertations

A new instrument incorporating ion trap based tandem mass spectrometry and cold ion UV and UV-IR double resonance spectroscopy has been developed at Purdue University for the study of gas phase, biologically relevant ions. The instrument incorporates multiple quadrupole linear ion trap mass analyzers to prepare and isolate the precursor ions as well as to analyze the resultant photofragments. A 22-pole ion trap cooled to 5 K via a closed cycle helium cryostat is used to cool the ions for spectroscopic interrogation. Results show the vibrational and rotational temperature of a wide assortment of ions to be 12±2 K.

The …