Chemistry Commons^™

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 …

Dynamics Of Prebiotic Rna Reproduction Illuminated By Chemical Game Theory, Jessica Anne Mellor Yeates, Christian Hilbe, Martin Zwick, Martin. A. Nowak, Niles Lehman

Chemistry Faculty Publications and Presentations

Many origins-of-life scenarios depict a situation in which there are common and potentially scarce resources needed by molecules that compete for survival and reproduction. The dynamics of RNA assembly in a complex mixture of sequences is a frequency-dependent process and mimics such scenarios. By synthesizing Azoarcus ribozyme genotypes that differ in their single-nucleotide interactions with other genotypes, we can create molecules that interact among each other to reproduce. Pairwise interplays between RNAs involve both cooperation and selfishness, quantifiable in a 2 × 2 payoff matrix. We show that a simple model of differential equations based on chemical kinetics accurately predicts …

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 …

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 …

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 …

Polymeric Porphyrins As Solar Photocatalysts, Nicholas Upton Day

Dissertations and Theses

Research concentrated on the absorption, transformation, and storage of light energy is useful for the energy challenges faced by humanity. In particular, photocatalysis using solar energy to generate useful fuels has become a primary research goal in the drive to replace fossil fuels for the future. In this dissertation it is shown that poly-tetra(4-aminophenyl)porphyrin (pTAPP) can be oxidatively polymerized using a variety of methods, including electropolymerization, chemical oxidation, and interfacial polymerization and that pTAPP has photocatalytic ability to reduce O₂ to H₂O₂ for a storable fuel.

Organic conductive polymers such as pTAPP are attractive catalysts because …

Design And Synthesis Of Novel Chloroquine-Based Antimalarials, Kevin Vincent Murphy

Dissertations and Theses

Malaria is an infectious, often fatal disease that afflicts nearly 200 million people every year. The disease, characterized by recurring and extreme flu-like symptoms, is caused by the protozoan parasite Plasmodium falciparum. Victims usually contract the disease through a mosquito vector. Chloroquine is a chemotherapeutic that was introduced in the 1940s. For many years the drug was the foremost treatment of malaria, being effective and producing few side effects. Unfortunately, tolerance to chloroquine developed when the parasite evolved a resistance mechanism. Newer drugs have been developed and implemented, but these medicines also show a decreasing effect with continued administration. …

The Rna World: 4,000,000,050 Years Old, Niles Lehman

Chemistry Faculty Publications and Presentations

The notion that molecular systems such as RNA can display a wide range of evolutionary processes in the absence of fully formed cellular life continues to gain support. Understanding how RNA can behave in an abiotic context is a key piece of our picture of how life developed and expanded on the Earth, and by proxy, elsewhere. We can study how RNA behaves in this regard through a combination of in vivo work (with small regulatory RNAs and larger catalytic RNAs alike), experimental work in the laboratory, and through powerful analytical and simulation studies. These efforts will not only grant …

Phase Considerations In The Gas/Particle Partitioning Of Organic Amines In The Atmosphere, James F. Pankow

Chemistry Faculty Publications and Presentations

Amines in the atmosphere are of interest because of their likely role in new particle formation, and because of anthropogenic emissions of amines at post-combustion carbon capture (PCCC) facilities. A conceptual framework for considering the partitioning of a monobasic amine (Am = unprotonated "free-base form) from the gas phase to atmospheric particulate matter (PM) is presented for cases when the PM may be composed of multiple liquid phases. Three types of liquid phases are considered as being individually or simultaneously possible for absorptive uptake of atmospheric amines: w) a mostly water phase; α ) a mostly (by mass) organic phase …

Antimalarial Drug Discovery Using Triazoles To Overcome Chloroquine Resistance, Elias Sibhatu Tesfaselassie

Dissertations and Theses

Malaria is considered as one of the most prevalent and debilitating diseases affecting humans. Plasmodium falciparum is the most virulent form of the parasite which developed resistance to several antimalarial drugs. Chloroquine is one of the most successful antimalarials developed that is safe, effective, and cheap. However, its use has been limited due to the emergence of drug resistance. Click chemistry, particularly, the copper(I)-catalyzed reaction between azides and alkynes has shown to have a cutting-edge advantage in medicinal chemistry by its reliability, selectivity and biocompatibility.

Triazole-based antimalarials were synthesized via copper(I)-catalyzed alkyne-azide cycloaddition reaction by modifying the aliphatic chains terminal …

Formaldehyde From E-Cigarettes - It's Not As Simple As Some Suggest, James F. Pankow, Robert M. Strongin, David H. Peyton

Chemistry Faculty Publications and Presentations

The Authors address critics of a previously published letter to the Editor in The New England Journal of Medicine, pertaining to hidden formaldehyde in E-Cigarette aerosols and the need for future testing of their safety.

Molecular View Modeling Of Atmospheric Organic Particulate Matter: Incorporating Molecular Structure And Co-Condensation Of Water, James F. Pankow, Marguerite Colasurdo Marks, Kelley C. Barsanti, Abdullah Mahmud, William E. Asher, Jingyi Li, Qi Ying, Shantanu H. Jathar, Michael J. Kleeman

Chemistry Faculty Publications and Presentations

Most urban and regional models used to predict levels of organic particulate matter (OPM) are based on fundamental equations for gas/particle partitioning, but make the highly simplifying, anonymized-view (AV) assumptions that OPM levels are not affected by either: a) the molecular. characteristics of the condensing organic compounds (other than simple volatility); or b) co-condensation of water as driven by non-zero relative humidity (RH) values. The simplifying assumptions have allowed parameterized chamber results for formation of secondary organic aerosol (SOA) (e.g., “two-product” (2p) coefficients) to be incorporated in chemical transport models. However, a return towards a less simplistic (and more computationally …

Synthesis And Structure−Activity Relationships Of Tambjamines And B‑Ring Functionalized Prodiginines As Potent Antimalarials, Papireddy Kancharla, Jane Xu Kelly, Kevin A. Reynolds

Chemistry Faculty Publications and Presentations

Synthesis and antimalarial activity of 94 novel bipyrrole tambjamines (TAs) and a library of B-ring functionalized tripyrrole prodiginines (PGs) against a panel of Plasmodium falciparum strains are described. The activity and structure–activity relationships demonstrate that the ring-C of PGs can be replaced by an alkylamine, providing for TAs with retained/enhanced potency. Furthermore, ring-B of PGs/TAs can be substituted with short alkyl substitutions at either 4-position (replacement of OMe) or 3- and 4-positions without impacting potency. Eight representative TAs and two PGs have been evaluated for antimalarial activity against multidrug-resistant P. yoelii in mice in the dose range of 5–100 mg/kg …

Rational Design Of Materials For The Protection Of Outdoor Metalworks, Natasja Alexandria Swartz

Dissertations and Theses

Protective coatings are commonly used to protect culturally significant works, such as outdoor sculptures and architectural elements. Given the valuable nature of such metalworks, there is a surprising lack of environmentally sustainable coatings available for their conservation. High performance clear coatings are not developed or thoroughly tested for compatibility and longevity on outdoor sculptures. This can make the implementation of both methods and materials, no matter how promising in a lab, a significant hurdle for the conservation science community. This dissertation work initially aims to replace high-VOC formulations such as acrylic lacquers and waxes currently used as protective coatings for …

The Influence Of Surface Chemistry On The Photoelectrochemical Properties Of Fes(2) Photoanodes, Qi Tong

Dissertations and Theses

The recurring theme of this dissertation is the correlation between FeS₂ surface chemistry and key electrical and electronic properties of FeS₂. Efforts have been made to identify and characterize the FeS₂ surface, investigate the photoelectrochemistry of FeS₂ photoanodes under anhydrous and anoxic conditions, and investigate the influence of deliberate surface chemistry on FeS₂ photoelectrochemistry.

Infrared reflection-absorption spectroscopy (IRRAS) was used to investigate a thin adsorbate layer on pyrite. The results showed that the combination of angle-dependent studies and computational efforts are a powerful tool for characterizing the pyrite surface.

The photoelectrochemistry of FeS_{2 …}

Nmr-Based Structural Analysis Of Threonylcarbamoyl-Amp Synthase And Its Substrate Interactions, Kimberly A. Harris, Benjamin G. Bobay, Kathryn L. Sarachan, Alexis F. Sims, Yann Bilbille, Christopher Deutsch, Dirk Iwata-Reuyl, Paul F. Agris

Chemistry Faculty Publications and Presentations

The hypermodified nucleoside N(6)-threonylcarbamoyladenosine (t(6)A37) is present in many distinct tRNA species and has been found in organisms in all domains of life. This post-transcriptional modification enhances translation fidelity by stabilizing the anticodon/codon interaction in the ribosomal decoding site. The biosynthetic pathway of t(6)A37 is complex and not well understood. In bacteria, the following four proteins have been discovered to be both required and sufficient for t(6)A37 modification: TsaC, TsaD, TsaB, and TsaE. Of these, TsaC and TsaD are members of universally conserved protein families. Although TsaC has been shown to catalyze the formation of L-threonylcarbamoyl-AMP, a key intermediate in …

Characterization, Dna Binding And Cleavage Activities Of New Prodigiosin And Tambjamine Analogues And Their Cu²⁺ And Zn²⁺ Complexes, Karen Chichetu

Dissertations and Theses

Prodigiosins and tambjamines are natural compounds from bacterial and marine sources belonging to a family containing a common 4-methoxy-2,2'-bipyrrole core. These compounds have received a lot of interest due to their promising biological activities. Studies have suggested DNA as a potential therapeutic target for the natural prodigiosin and tambjamine due to their ability to facilitate oxidative DNA cleavage in the presence of Cu²⁺. Based on this we sought to study the metal binding activity of new prodigiosin and tambjamine analogues. A new prodigiosin analogue was synthesized and complexed with Cu²⁺. This revealed 1:1 complex formation between …

Steps Towards Deciphering The Post-Polyketide Synthase Tailoring Steps In The Phoslactomycin Biosynthesis Pathway, Patience Marimo

Dissertations and Theses

Phoslactomycins (PLMs) are a group of natural products belonging to a polyketides class. These polyketides are synthesized by sequential reaction catalyzed by a collection of enzymes activities called polyketide synthases. A polyketide is a large class of diverse compounds that are characterized by more than two carbonyl groups connected by single intervening carbon atoms. In other words, a polyketide is a polymer whose monomer is a ketide. The PLMs are also known as phosphazomycins or phospholines. These compounds were isolated based on antifungal and antitumor activities. This array of promising biological activities has stimulated research into the field of PLMs …

Dft Analysis Into The Intermediates Of Nickel Pyridenthiolate Catalysed Proton Reduction, Carolyn N. Virca, Theresa M. Mccormick

Chemistry Faculty Publications and Presentations

Nickel pyridine 2-thiolate (Ni(PyS)₃ −) has shown good stability and activity as a H₂ generation catalyst for use in solar energy storage. The experimentally proposed catalytic pathway is explored using DFT calculations. Free energy changes along the reaction coordinate, spin states, localization of charge and geometry of the intermediates were explored. Calculations were performed using Gaussian 09 with a B3P86/ 6-31+G(d) basis set and a CPCM water solvation model. Of particular interest were our findings that the first reduction occurs at the nickel rather than through non-innocent ligands and that water coordination is not favourable although protonation of …

Hydrophobic Surfactant Proteins Strongly Induce Negative Curvature, Mariya Chavarha, Ryan W. Loney, Shankar B. Rananavare, Stephen B. Hall

Chemistry Faculty Publications and Presentations

The hydrophobic surfactant proteins SP-B and SP-C greatly accelerate the adsorption of vesicles containing the surfactant lipids to form a film that lowers the surface tension of the air/water interface in the lungs. Pulmonary surfactant enters the interface by a process analogous to the fusion of two vesicles. As with fusion, several factors affect adsorption according to how they alter the curvature of lipid leaflets, suggesting that adsorption proceeds via a rate-limiting structure with negative curvature, in which the hydrophilic face of the phospholipid leaflets is concave. In the studies reported here, we tested whether the surfactant proteins might promote …

Flavour Chemicals In Electronic Cigarette Fluids, Peyton A. Tierney, Clarissa D. Karpinski, Jessica E. Brown, Wentai Luo, James F. Pankow

Chemistry Faculty Publications and Presentations

Background: Most e-cigarette liquids contain flavour chemicals. Flavour chemicals certified as safe for ingestion by the Flavor Extracts Manufacturers Association may not be safe for use in e-cigarettes. This study identified and measured flavour chemicals in 30 e-cigarette fluids.

Methods: Two brands of single-use e-cigarettes were selected and their fluids in multiple flavour types analysed by gas chromatography/mass spectrometry. For the same flavour types, and for selected confectionary flavours (eg, bubble gum and cotton candy), also analysed were convenience samples of e-cigarette fluids in refill bottles from local ‘vape’ shops and online retailers.

Results: In many liquids, total flavour chemicals …

Aerosol Optical Hygroscopicity Measurements During The 2010 Cares Campaign, Dean B. Atkinson, James Gregory Radney, Janel Lum, Katheryn R. Kolesar, Daniel J. Cziczo, Mikhail Pekour, Qi Zhang, Ari Setyan, Alla Zelenyuk, Christopher D. Cappa

Chemistry Faculty Publications and Presentations

Measurements of the effect of water uptake on particulate light extinction or scattering made at two locations during the 2010 CARES study around Sacramento, CA are reported. The observed influence of water uptake, characterized through the dimensionless optical hygroscopicity parameter γ, is compared with calculations constrained by observed particle size distributions and size-dependent particle composition. A closure assessment has been carried out that allowed for determination of the average hygroscopic growth factors (GF) at 85% relative humidity and the dimensionless hygroscopicity parameter κ for oxygenated organic aerosol (OA) and for supermicron particles, yielding κ = 0.1–0.15 and 0.9–1.0, respectively. The …