Physical Sciences and Mathematics Commons^™

Ph-Dependent Fluorescent Probe That Can Be Tuned For Cysteine Or Homocysteine, Yongkang Yue, Fangjun Huo, Xiaoqi Li, Ying Wen, Tao Yi, James C. Salamanca, Jorge O. Escobedo, Robert Strongin, Caixia Yin

Chemistry Faculty Publications and Presentations

The very close structural similarities between cysteine and homocysteine present a great challenge to achieve their selective detection using regular fluorescent probes, limiting the biological and pathological studies of these two amino thiols. A coumarin-based fluorescent probe was designed featuring pH-promoted distinct turn-on followed by ratiometric fluorescence responses for Cys and turn-on fluorescence response for Hcy through two different reaction paths. These specific responses demonstrate the activity differences between Cys and Hcy qualitatively for the first time. The probe could also be used for Cys and Hcy imaging in living cells.

Formulation Of Colloidal Suspensions Of 3-Mercaptopropionic Acid Capped Pbs Quantum Dots As Solution Processable Qd "Inks" For Optoelectronic Applications, Chase Collier Reinhart

Dissertations and Theses

The use of colloidal quantum dots (QDs) for photovoltaic energy conversion is a nascent field that has been dominated for well over a decade by the use of 3-mercaptopropionic acid (3-MPA) capped PbS QDs. These QDs are routinely deposited via an in situ solid state ligand exchange process that displaces the native oleate ligand on the PbS QD surface. This ligand exchange procedure is wasteful of material and has been demonstrated to leave numerous impurities that limit electronic performance of the as-deposited QD devices. Until the last few years there was very little understanding in chemical literature as to many …

Investigations Into The Effects Of Water Exchange And The Structure Of Lanthanide Chelates, Katherine Marie Payne

Dissertations and Theses

Lanthanide chelates are effective agents for improving contrast in MR images. Optimizing the relaxation of inner sphere water molecules is a common focus of research in this field. However, the efforts to design an optimal contrast agent have commonly over-looked the relationship of water position and water exchange kinetics. This work explores structural conformation, the impact of very fast water exchange kinetics on hydration, and differing tumbling rates for regioisomers of a number of lanthanide chelates. We have grown crystals of LnDOTMA and obtained structural data by X-ray diffraction that provide a picture of the chelate during water exchange and …

The Application Of Electrochemical Impedance Spectroscopy To Immediately Diagnose The Protective Quality Of Coatings On Artistic And Architectural Metalwork, Kathryn Nicole Hosbein

Dissertations and Theses

Corrosion is a spontaneous process that causes irreversible damage to nearly all metals, which has world-wide implications for architectural and artistic metalwork, such as bridges, buildings, airplanes and sculptures. Protective coatings such as wax, paint, or polymeric clear coatings are used to prolong the lifetime of metals such as steel and bronze. Unfortunately, these coatings fail over time due to oxidative damage by UV rays and by failure to exclude water that can carry salts and pollutants that cause corrosion of the underlying substrate. The current method of coating assessment is visual inspection but when coating failure is detected at …

Assessing The Protective Quality Of Wax Coatings On Bronze Sculptures Using Hydrogel Patches In Impedance Measurements, Alice H. England, Kathryn N. Hosbein, Capri A. Price, Morgan K. Wylder, Kenna S. Miller, Tami Lasseter Clare

Chemistry Faculty Publications and Presentations

In this work, we used chemically cross-linked acrylamide-based hydrogel patches that have been specifically developed for use as solid electrolytes in Electrochemical Impedance Spectroscopy to measure the impedance of two waxed bronze sculptures at the Seattle Art Museum’s (SAM) Olympic Sculpture Park (OSP) and compare those results to laboratory test panels. We determined that the impedance response in the frequency range in which measurements may be taken (10 kHz to 1 MHz) is mostly capacitive and that a freshly applied wax coating should ideally be less than 1 nF·cm⁻²for optimal protective performance.

Distribution, Quantification And Toxicity Of Cinnamaldehyde In Electronic Cigarette Refill Fluids And Aerosols, Rachel Z. Behar, Wentai Luo, Sabrina C. Lin, Yuhuan Wang, Jackelyn Valle, James F. Pankow, Prue Talbot

Chemistry Faculty Publications and Presentations

Objective The aim of this study was to evaluate the distribution, concentration and toxicity of cinnamaldehyde in electronic cigarette (e-cigarette) refill fluids and aerosols.

Methods The distribution and concentration of cinnamaldehyde were determined in 39 e-cigarette refill fluids plus 6 duplicates using gas chromatography and mass spectrometry (GC/MS). A cinnamaldehyde toxicity profile was established for embryonic and adult cells using a live cell imaging assay, immunocytochemistry, the comet assay and a recovery assay.

Results Twenty of the 39 refill fluids contained cinnamaldehyde at concentrations that are cytotoxic to human embryonic and lung cells in the MTT assay. Cinnamon Ceylon aerosol …

Quef And Quef-Like: Diverse Chemistries In A Common Fold, Adriana Bon Ramos

Dissertations and Theses

The tunneling fold (T-Fold) superfamily is a small superfamily of enzymes found in organisms encompassing all kingdoms of life. Seven members have been identified thus far. Despite sharing a common three-dimensional structure these enzymes perform very diverse chemistries.

QueF is a bacterial NADPH-dependent oxidoreductase that catalyzes the reduction of the nitrile group of 7-cyano-7-deazaguanine (preQ₀) to a primary amine (preQ₁) in the queuosine biosynthetic pathway. Previous work on this enzyme has revealed the mechanism of reaction but the cofactor binding residues remain unknown. The experiments discussed herein aim to elucidate the role of residues lysine 80, …

Thermal Decomposition Of Electronic Cigarette Liquids, Robert Paul Jensen

Dissertations and Theses

Electronic cigarette liquid (e-liquid) is a solution of propylene glycol and/or glycerol with varying concentrations of nicotine and flavorants. Inhalation of vaporized e-liquid is a method of nicotine delivery that is growing in popularity and is commonly regarded as safe relative to smoking traditional tobacco products. The thermal decomposition of glycerol and propylene glycol is typical of alcohols and has been investigated, although not exhaustively. In this work, samples of propylene glycol and glycerol were vaporized using an electronic cigarette (e-cigarette) and were analyzed for evidence of decomposition using nuclear magnetic resonance (NMR) spectroscopy. E-cigarettes are shown to degrade glycerol …

Molecular Probes For Pancreatic Cancer Imaging, Lei Wang

Dissertations and Theses

Pancreatic ductal adenocarcinoma (PDAC) has the poorest five-year survival rate of any cancer. Currently, there are no effective diagnostics or chemotherapeutics. Surgical resection is the only curative therapy. However, most patients experience recurrence due largely to challenges in assessing tumor margin status in the operating room. Molecular probes that selectively highlight pancreatic cancer tissue, having the potential to improve PDAC margin assessment intraoperatively, are urgently needed. In this work, a series of red and near-infrared fluorescent probes is reported. Two were found to distribute to normal pancreas following systemic administration. One selectively accumulates in genetically modified mouse models of PDAC, …

Relative Sensitivities Of Dce-Mri Pharmacokinetic Parameters To Arterial Input Function (Aif) Scaling, Xin Li, Yu Cai, Brendan Moloney, Yiyi Chen, Wei Huang, Mark Woods, Fergus V. Coakley, William D. Rooney, Mark G. Garzotto, Charles S. Springer Jr.

Chemistry Faculty Publications and Presentations

Dynamic-Contrast-Enhanced Magnetic Resonance Imaging (DCE-MRI) has been used widely for clinical applications. Pharmacokinetic modeling of DCE-MRI data that extracts quantitative contrast reagent/tissue-specific model parameters is the most investigated method. One of the primary challenges in pharmacokinetic analysis of DCE-MRI data is accurate and reliable measurement of the arterial input function (AIF), which is the driving force behind all pharmacokinetics. Because of effects such as inflow and partial volume averaging, AIF measured from individual arteries sometimes require amplitude scaling for better representation of the blood contrast reagent (CR) concentration time-courses. Empirical approaches like blinded AIF estimation or reference tissue AIF derivation …

Multiple New-Particle Growth Pathways Observed At The Us Doe Southern Great Plains Field Site, Anna L. Hodshire, Michael J. Lawler, Jun Zhao, John Ortega, Coty Jen, Taina Yli-Juuti, Jared F. Brewer, Jack K. Kodros, Kelley C. Barsanti, Dave R. Hanson, Peter H. Mcmurry, James N. Smith, Jeffery R. Pierce

Civil and Environmental Engineering Faculty Publications and Presentations

New-particle formation (NPF) is a significant source of aerosol particles into the atmosphere. However, these particles are initially too small to have climatic importance and must grow, primarily through net uptake of low volatility species, from diameters ∼ 1 to 30–100 nm in order to potentially impact climate. There are currently uncertainties in the physical and chemical processes associated with the growth of these freshly formed particles that lead to uncertainties in aerosol-climate modeling. Four main pathways for new-particle growth have been identified: condensation of sulfuric-acid vapor (and associated bases when available), condensation of organic vapors, uptake of organic acids …

Minimizing Corrosion Of Outdoor Metalworks Using Dispersed Chemically Stabilized Nanoclays In Polyvinylidene Fluoride Latex Coatings, Natasja Alexandria Swartz, Capri A. Price, Tami Lasseter Clare

Chemistry Faculty Publications and Presentations

Nanoclays are small enough to appear optically transparent, yet they have large surface-to-volume and high aspect ratios that can significantly inhibit water diffusion when incorporated into protective coatings. Clear coatings, which minimally affect the aesthetics of metalworks, are commonly applied to outdoor metalworks, such as sculptures, to prevent and slow corrosion. In recent years, waterborne clear coatings, rather than solvent-based clear coatings, are increasingly used in many applications to reduce the quantity of volatile organic components in the formulation, yet the performance of dry films produced from waterborne colloidal suspensions is generally poorer. In this work, we aim to improve …

Expanding The Versatility Of Nano Assembled Capsules As Platform Of Potential High Payload Mri Contrast Agents, Annah Farashishiko

Dissertations and Theses

Magnetic resonance imaging (MRI) has become a powerful clinical modality in diagnostic medicine. It is non-invasive and offers high spatial and temporal resolution. The goal of molecular imaging is to reveal the pathophysiology underlying the observed anatomy and diagnose diseases. The detection of pathological biomarkers can lead to early recognition of diseases and improved monitoring for recurrence. Clinically available contrast agents are limited in their discrimination of contrast between tissues and they tend to have very high detection limits. Because biomarkers are very low in concentration there is a need for high payload deposition of contrast agent (CA) and targeted …

Discovery And Characterization Of The Proteins Involved In The Synthesis Of N⁶-Threonylcarbamoyl Adenosine, A Nucleoside Modification Of Trna, Christopher Wayne Deutsch

Dissertations and Theses

N6-threonylcarbamoyl adenosine (t⁶A) is a universally conserved tRNA modification found at position 37 of tRNAs which decode ANN codons. Structural studies have implicated its presence as a requirement for the disruption of a U-turn motif in certain tRNAs, leading to the formation of properly structured anticodon stem loop. This structure is proposed to enhance the base pairing between U₃₆ of tRNA and A₁ of the codon which aids in translational frame maintenance.

Despite significant effort since its discovery in the 1970s the enzymes involved in its biosynthesis remained undiscovered. Bioinformatic analysis identified two proteins as likely …

Communication: Visualization And Spectroscopy Of Defects Induced By Dehydrogenation In Individual Silicon Nanocrystals, Dmitry A. Kislitsyn, Jon M. Mills, Vancho Kocevski, Sheng-Kuei Chiu, William J.I. Debenedetti, Christian F. Gervasi, Benjamen N. Taber, Ariel E. Rosenfield, Olle Eriksson, Ján Rusz, Andrea Mitchell Goforth, George V. Nazin

Chemistry Faculty Publications and Presentations

We present results of a scanning tunneling spectroscopy (STS) study of the impact of dehydrogenation on the electronic structures of hydrogen-passivated silicon nanocrystals (SiNCs) supported on the Au(111)surface. Gradual dehydrogenation is achieved by injecting high-energy electrons into individual SiNCs, which results, initially, in reduction of the electronic bandgap, and eventually produces midgap electronic states. We use theoretical calculations to show that the STS spectra of midgap states are consistent with the presence of silicon dangling bonds, which are found in different charge states. Our calculations also suggest that the observed initial reduction of the electronic bandgap is attributable to the …

Biomimetic Tools In Oxidative Metabolism: Characterization Of Reactive Metabolites From Antithyroid Drugs, Kudzanai Chipiso

Dissertations and Theses

Toxicities of sulfur-based drugs have been attributed to formation of highly reactive sulfur oxo-acids and depletion of glutathione by the formation of reactive metabolites. Metabolic activation of these sulfur centers to conceivably toxic reactive metabolites (RMs) that can covalently modify proteins is considered the initial step in drug-induced toxicity. Despite considerable effort and research, detection and characterization of these RMs during drug development and therapy remains a challenge. Methimazole (MMI) and 6-propyl-2-thiouracil (PTU) are two commonly used antithyroid, sulfur-based drugs. Though effective, these drugs are associated with idiosyncratic toxicity. PTU has acquired a black box warning and physicians are calling …

The Effects Of Phosphonic Acids In Dye-Sensitized Solar Cells, Keith Edward James

Dissertations and Theses

Novel methods for the construction of dye-sensitized solar cells (DSSCs) were developed. A thin dense underlayer of TiO₂ was applied on fluorine-doped tin oxide (FTO) glass using as a precursor Tyzor AA-105. Subsequently a mesoporous film of P-25 TiO₂ was applied by spreading a suspension uniformly over the surface of the underlayer and allowing the plate to slowly dry while resting on a level surface. After sintering at 500° C slides were treated with TCPP as a sensitizing dye and assembled into DSSCs. A novel method was used to seal the cells; strips of Parafilm® were used as …

The Foundations Of Network Dynamics In An Rna Recombinase System, Jessica Anne Mellor Yeates

Dissertations and Theses

How life originated from physical and chemical processes is one of the great questions still unanswered today. Studies towards this effort have transitioned from the notion of a single self-replicating entity to the idea that a network of interacting molecules made this initial biological leap. In order to understand the chemical kinetic and thermodynamic mechanisms that could engender pre-life type networks we present an empirical characterization of a network of RNA recombinase molecules. We begin with 1-, 2-, and 3-molecular ensembles and provide a game theoretic analysis to describe the frequency dependent dynamics of competing and cooperating RNA genotypes. This …

Thiophene Based Molecular Sensors Towards Mercury Detection, Austin K. Shigemoto, Carolyn N. Virca, Sam Underwood, Lauren Shetterly, Theresa M. Mccormick

Student Research Symposium

Toxic heavy metals such as mercury have increased in concentration in the environment due to pollution. Inorganic mercury in the environment can be later converted to a more toxic form: methylmercury. Regular consumption of fish containing methylmercury can lead to several cognitive and motor disorders as well as Minamata disease. The current methods used to detect both methylmercury and inorganic mercury in sea life and drinking water involve long sample preparation and cost. In order to more efficiently track this toxic metal in the environment and identify contaminated food and water sources, a cheaper and faster method of detection is …

Understanding The Optical Properties Of Ambient Sub-And Supermicron Particulate Matter: Results From The Cares 2010 Field Study In Northern California, Christopher D. Cappa, Katheryn R. Kolesar, Xiaolu Zhang, Dean B. Atkinson, Mikhail S. Pekour, Rahul A. Zaveri, Alla Zelenyuk, Qi Zhang

Chemistry Faculty Publications and Presentations

Measurements of the optical properties (absorption, scattering and extinction) of PM1, PM2.5 and PM10 made at two sites around Sacramento, CA, during the June 2010 Carbonaceous Aerosols and Radiative Effects Study (CARES) are reported. These observations are used to establish relationships between various intensive optical properties and to derive information about the dependence of the optical properties on photochemical aging and sources. Supermicron particles contributed substantially to the total light scattering at both sites, about 50 % on average. A strong, linear relationship is observed between the scattering Ångström exponent for PM10 and the fraction of the scattering that is …

The Biomolecule Sequencer Project: Nanopore Sequencing As A Dual-Use Technology For Crew Health And Astrobiology Investigations, K. K. John, D. S. Botkin, A. S. Burton, S. L. Castro-Wallace, J. D. Chaput, J. P. Dworkin, Niles Lehman, M. L. Lupisella, C. E. Mason, D. J. Smith, S. Stahl, C. Switzer

Chemistry Faculty Publications and Presentations

Human missions to Mars will fundamentally transform how the planet is explored, enabling new scientific discoveries through more sophisticated sample acquisition and processing than can currently be implemented in robotic exploration. The presence of humans also poses new challenges, including ensuring astronaut safety and health and monitoring contamination. Because the capability to transfer materials to Earth will be extremely limited, there is a strong need for in situ diagnostic capabilities. Nucleotide sequencing is a particularly powerful tool because it can be used to: (1) mitigate microbial risks to crew by allowing identification of microbes in water, in air, and on …

One-Dimensional Nanostructure And Sensing Applications: Tin Dioxide Nanowires And Carbon Nanotubes, Hoang Anh Tran

Dissertations and Theses

The key challenge for a nanomaterial based sensor is how to synthesize in bulk quantity and fabricate an actual device with insightful understanding of operational mechanisms during performance. I report here effective, controllable methods that exploit the concepts of the "green approach" to synthesize two different one-dimensional nanostructures, including tin oxide nanowires and carbon nanotubes. The syntheses are followed by product characterization and sensing device fabrications as well as sensor performance understanding at the molecular level. Sensor-analyte response and recovery kinetics are also presented.

The first part of the thesis describes bulk-scale synthesis and characterization of tin oxide nanowires by …

Characterization And Comparative Analysis Of 2,4-Toluene Diisocyanate And 1,6-Hexamethylene Diisocyanate Haptenated Human Serum Albumin And Hemoglobin, Morgen Mhike, Ita Chipinda, Brandon F. Law, Toni A. Bledsoe, Angela R. Lemons, Ajay P. Nayak, Brett J. Green, Donald H. Beezhold, Reuben H. Simoyi, Paul D. Siegel

Chemistry Faculty Publications and Presentations

Diisocyanates (dNCOs) are lowmolecularweight chemical sensitizers that reactwith autologous proteins to produce neoantigens. dNCO-haptenated proteins have been used as immunogens for generation of dNCO-specific antibodies and as antigens to screen for dNCO-specific antibodies in exposed individuals. Detection of dNCOspecific antibodies in exposed individuals for diagnosis of dNCO asthma has been hampered by poor sensitivities of the assay methods in that specific IgE can only be detected in approximately 25% of the dNCO asthmatics. Apart from characterization of the conjugates used for these immunoassays, the choice of the carrier protein and the dNCO used are important parameters that can influence the …

The Elusive Quest For Rna Knots, Aaron S. Burton, Marco Di Stefano, Niles Lehman, Henri Orland, Cristian Micheletti

Chemistry Faculty Publications and Presentations

Physical entanglement, and particularly knots arise spontaneously in equilibrated polymers that are sufficiently long and densely packed. Biopolymers are no exceptions: knots have long been known to occur in proteins as well as in encapsidated viral DNA. The rapidly growing number of RNA structures has recently made it possible to investigate the incidence of physical knots in this type of biomolecule, too. Strikingly, no knots have been found to date in the known RNA structures. In this Point of View Article we discuss the absence of knots in currently available RNAs and consider the reasons why knots in RNA have …

Efficient Bimolecular Mechanism Of Photochemical Hydrogen Production Using Halogenated Boron-Dipyrromethene (Bodipy) Dyes And A Bis(Dimethylglyoxime) Cobalt(Iii) Complex, Randy Pat Sabatini, Brian M. Lindley, Theresa M. Mccormick, Theodore Lazarides, William Brennessel, David W. Mccamant, Richard Eisenberg

Chemistry Faculty Publications and Presentations

A series of Boron-­dipyrromethene (Bodipy) dyes were used as photosensitizers for photochemical hydrogen production in conjunction with [Co^III(dmgH)2pyCl] (where dmgH = dimethylglyoximate, py = pyridine) as the catalyst and triethanolamine (TEOA) as the sacrificial electron donor. The Bodipy dyes are fully characterized by electrochemistry, x-­‐ray crystallography, quantum chemistry calculations, femtosecond transient absorption and time-­‐resolved fluorescence, as well as in long-­‐term hydrogen production assays. Consistent with other recent reports, only systems containing halogenated chromophores were active for hydrogen production, as the long-­‐lived triplet state is necessary for efficient bimolecular electron transfer. Here, it is shown that the photostability of …

Reactivity Measurement In Estimation Of Benzoquinone And Benzoquinone Derivatives’ Allergenicity, Wilbes Mbiya, Ita Chipinda, Reuben H. Simoyi, Paul D. Siegel

Chemistry Faculty Publications and Presentations

Benzoquinone (BQ) and benzoquinone derivatives (BQD) are used in the production of dyes and cosmetics. While BQ, an extreme skin sensitizer, is an electrophile known to covalently modify proteins via Michael Addition (MA) reaction whilst halogen substituted BQD undergo nucleophilic vinylic substitution (SNV) mechanism onto amine and thiol moieties on proteins, the allergenic effects of adding substituents on BQ have not been reported. The effects of inserting substituents on the BQ ring has not been studied in animal assays. However, mandated reduction/elimination of animals used in cosmetics testing in Europe has led to an increased need for alternatives for the …

Oxyhalogen-Sulfur Chemistry: Kinetics And Mechanism Of Oxidation Of N-Acetylthiourea By Aqueous Bromate And Acidified Bromate, Kudzanai Chipiso, Wilbes Mbiya, Thai Tran, Reuben H. Simoyi

Chemistry Faculty Publications and Presentations

The oxidation of N-acetylthiourea (ACTU) by acidic bromate has been studied by observing formation of bromine in excess bromate conditions. The reaction displays an induction period before formation of bromine. The stoichiometry of the reaction was determined to be 4:3: 4BrO 3 – +3(CH 3 CO)NH(NH 2 )C=S+3H 2 O®4Br – +3(CH 3 CO)NH(NH 2 )C=O+3SO 4 2– +6H + (A) with a complete desulfurization of ACTU to its urea analogue. In excess bromate conditions the stoichiometry was 8:5: 8BrO 3 – + 5(CH 3 CO)NH(NH 2 )C=S + H 2 O ® 4Br 2 + 5(CH 3 CO)NH(NH 2 …

Electrochemistry-Coupled To Mass Spectrometry In Simulation Of Metabolic Oxidation Of Methimazole: Identification And Characterization Of Metabolites, Kudzanai Chipiso, Reuben H. Simoyi

Chemistry Faculty Publications and Presentations

Methimazole (MMI), an antithyroid drug, is associated with idiosyncratic toxicity. Reactive metabolites resulting from bioactivation of the drug have been implicated in these adverse drug reactions. Mimicry of enzymatic oxidation of MMI was carried out by electrochemically oxidizing MMI using a coulometric flow-through cell equipped with a porous graphite working electrode. The cell was coupled on-line to electrospray ionization mass spectrometry (EC/ESI-MS). ESI spectra were acquired in both negative and positive modes. In acidic medium, ESI spectral analysis showed that the dimer was the main product, while in neutral and basic media, methimazole sulfenic acid, methimazole sulfinic acid and methimazole …