Physical Sciences and Mathematics Commons^™

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 …

Development Of An Optical Method For The Detection Of Homocysteine As A Disease Biomarker Using Fluorescein-Aldehydes, Aabha Barve

Dissertations and Theses

Homocysteine is a natural occurring aminothiol. It is an intermediate product in the metabolism of methionine. Methionine is an essential amino acid required for protein synthesis. Metabolic irregularities disrupt homocysteine levels in plasma. Elevated homocysteine levels are directly linked to folate and cobalamin (vitamin B12) deficiencies, and are an independent risk factor for cardiovascular diseases. High homocysteine levels have also been associated with Alzheimer's, osteoporosis, renal failure, cancer, birth defects and pregnancy complications. The association of elevated homocysteine levels with cardiovascular disease and other diseases has generated great interest in the detection of homocysteine.

An optical method for the detection …

Facile Methods For The Analysis Of Lysophosphatidic Acids In Human Plasma, Jialu Wang

Dissertations and Theses

Lysophosphatidic acid (LPA) influences many physiological processes, such as brain and vascular development. It is associated with several diseases including ovarian cancer, breast cancer, prostate cancer, colorectal cancer, hepatocellular carcinoma, multiple myeloma atherosclerotic diseases, cardiovascular diseases, pulmonary inflammatory diseases and renal diseases. LPA plasma and serum levels have been reported to be important values in diagnosing ovarian cancer and other diseases. However, the extraction and quantification of LPA in plasma are very challenging because of the low physiological concentration and similar structures of LPA to other phospholipids. Many previous studies have not described the separation of LPA from other phospholipids, …

Spectroscopy, Nmr, And Electrochemistry Studies Of Protonated Aminophenyl/Pyridyl Porphyrins And Their Application In Hydrogen Evolution, Chenyi Wang

Dissertations and Theses

Spectrophotometric titrations for a full series of 4-aminophenyl/4-pyridyl meso-substituted porphyrins were carried out using methanesulfonic acid in DMSO to study the hyperporphyrin effect across different substitution patterns. The series included zero, one, two (cis and trans), three, and four meso(4-aminophenyl) groups, with the remaining meso substituents being 4-pyridyl groups. The peripheral pyridyl groups consistently protonate before the interior porphyrin pyrrole nitrogens, which protonate before the aminophenyl groups. Aminophenyl substituents increase the basicity of the pyrrole nitrogens and lead to distinctive hyperporphyrin spectra with a broad Soret band and a strong red absorption. The structure proposed to give rise to these …

Delay Line As A Chemical Reaction Network, Josh Moles, Peter Banda, Christof Teuscher

Computer Science Faculty Publications and Presentations

Chemistry as an unconventional computing medium presently lacks a systematic approach to gather, store, and sort data over time. To build more complicated systems in chemistries, the ability to look at data in the past would be a valuable tool to perform complex calculations. In this paper we present the first implementation of a chemical delay line providing information storage in a chemistry that can reliably capture information over an extended period of time. The delay line is capable of parallel operations in a single instruction, multiple data (SIMD) fashion.

Using Michaelis-Menten kinetics, we describe the chemical delay line implementation …

Analysis Of The Surface Density And Reactivity Of Perfluorophenylazide And The Impact On Ligand Immobilization, Gilad Zorn, David G. Castner, Anuradha Tyagi, Xin Wang, Hui Wang, Mingdi Yan

Chemistry Faculty Publications and Presentations

Perfluorophenylazide (PFPA) chemistry is a novel method for tailoring the surface properties of solid surfaces and nanoparticles. It is general and versatile, and has proven to be an efficient way to immobilize graphene, proteins, carbohydrates, and synthetic polymers. The main thrust of this work is to provide a detailed investigation on the chemical composition and surface density of the PFPA tailored surface. Specifically, gold surfaces were treated with PFPA-derivatized (11-mercaptoundecyl) tetra(ethylene glycol) (PFPA-MUTEG) mixed with 2-[2-(2-mercaptoethoxy)ethoxy]ethanol (MDEG) at varying solution mole ratios. Complementary analytical techniques were employed to characterize the resulting films including Fourier transform infrared spectroscopy to detect fingerprints …

Hidden Formaldehyde In E-Cigarette Aerosols, R. Paul Jensen, Wentai Luo, James F. Pankow, Robert M. Strongin, David H. Peyton

Chemistry Faculty Publications and Presentations

This letter reports a chemical analysis of vapor from electronic cigarettes that shows high levels of formaldehyde, a known carcinogen. The authors project that the associated incremental lifetime risk of cancer could be higher than that from long-term smoking.

Enzymatic Control Of The Related Pathways Of Fatty Acid And Undecylprodiginine Biosynthesis In Streptomyces Coelicolor, Renu Singh

Dissertations and Theses

Streptomyces coelicolor produces fatty acids for both primary metabolism and for production of the components of natural products such as undecylprodiginine. Primary metabolism makes the longer and predominantly branched-chain fatty acids, while undecylprodiginine utilizes shorter and almost exclusively straight chain fatty acids. The first step in fatty acid biosynthetic process is catalyzed by FabH (β-ketoacyl synthase III), which catalyzes a decarboxylative condensation of an acyl-CoA primer with malonyl-acyl carrier protein (ACP). The resulting 3-ketoacyl-ACP product is reduced by NADPH-dependent FabG into 3-hydroxyacyl-ACP, which is dehydrated by FabA to form enoyl-ACP. The NADH-dependent FabI (InhA) completes the cycle. Subsequent rounds of …

Analyzing Free-Base Nicotine Content In The Particulate Matter Of Mainstream Tobacco Smoke Using A Headpace Solid-Phase Microextraction Gc/Ms Method, Christopher S. Motti

Civil and Environmental Engineering Master's Project Reports

The acid/base chemistry of cigarette smoke allows nicotine, the primary drug in mainstream tobacco smoke, to exist in protonated and free-base forms. Evidence suggests that most of the nicotine present in mainstream tobacco smoke is in the particle phase. α_fb is the fraction of particle-phase nicotine in the free-base form. The magnitude and rate of nicotine deposition in the respiratory tract is dependent on α_fb because only the free-base form of nicotine can volatilize from the particle phase of an inhaled aerosol and, once gaseous, rapidly deposit. This study develops a headspace solid-phase microextraction technique coupled with gas …

Phthalimide-Based Π-Conjugated Small Molecules With Tailored Electronic Energy Levels For Use As Acceptors In Organic Solar Cells, Arthur D. Hendsbee, Seth M. Mcafee, Jon-Paul Sun, Theresa M. Mccormick, Ian G. Hill, Gregory C. Welch

Chemistry Faculty Publications and Presentations

The design, synthesis, and characterization of seven phthalimide-based organic π-conjugated small molecules are reported. The new materials are based on a phthalimide–thiophene–CORE–thiophene–phthalimide architecture. The CORE units utilized were phthalimide (M2), diketopyrrolopyrrole (M3), isoindigo (M4), naphthalene diimide (M5), perylene diimide (M6), and difluorobenzothiadiazole (M7); they were specifically selected to progressively increase the electron affinity of the resulting compound. A small molecule with no core (M1) was synthesized for comparison. Each material was synthesized through optimized direct heteroarylation cross-coupling procedures using bench top solvents in air. Combinations of …

Controlled Deposition Of Tin Oxide And Silver Nanoparticles Using Microcontact Printing, Joo C. Chan, Nicole Hannah-Moore, Shankar B. Rananavare

Chemistry Faculty Publications and Presentations

This report describes extensive studies of deposition processes involving tin oxide (SnO_x) nanoparticles on smooth glass surfaces. We demonstrate the use of smooth films of these nanoparticles as a platform for spatially-selective electroless deposition of silver by soft lithographic stamping. The edge and height roughness of the depositing metallic films are 100 nm and 20 nm, respectively, controlled by the intrinsic size of the nanoparticles. Mixtures of alcohols as capping agents provide further control over the size and shape of nanoparticles clusters. The distribution of cluster heights obtained by atomic force microscopy (AFM) is modeled through a modified …