Chemistry Commons^™

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 …

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 …

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 …

New 4-Aminoquinoline Compounds To Reverse Drug Resistance In P. Falciparum Malaria, And A Survey Of Early European Antimalarial Treatments, Katherine May Liebman

Dissertations and Theses

Intermittent fevers caused by Plasmodium parasites have been known for millennia, and have caused untold human suffering. Today, millions of people are afflicted by malaria each year, and hundreds of thousands die. Historically, the most successful synthetic antimalarial drug was chloroquine, as it was safe, inexpensive, and highly efficacious. However, plasmodial resistance to chloroquine now greatly limits its utility. Previously in our laboratories it has been shown that attachment of a "reversal agent moiety" to the side chain of chloroquine can result in the restoration of activity against chloroquine-resistant strains of P. falciparum malaria. In the first part of the …

Empirical Demonstration Of Environmental Sensing In Catalytic Rna: Evolution Of Interpretive Behavior At The Origins Of Life, Niles Lehman, Tess Bernhard, Brian C. Larson, Andrew J.N. Robinson, Christopher C.B. Southgate

Chemistry Faculty Publications and Presentations

Background: The origins of life on the Earth required chemical entities to interact with their environments in ways that could respond to natural selection. The concept of interpretation, where biotic entities use signs in their environment as proxy for the existence of other items of selective value in their environment, has been proposed on theoretical grounds to be relevant to the origins and early evolution of life. However this concept has not been demonstrated empirically.

Results: Here, we present data that certain catalytic RNA sequences have properties that would enable interpretation of divalent cation levels in their environment. …

Human Whole-Blood (1)H2o Longitudinal Relaxation With Normal And High-Relaxivity Contrast Reagents: Influence Of Trans-Cell-Membrane Water Exchange, Gregory J. Wilson, Mark Woods, Charles S. Springer Jr., Sarah Bastawrous, Puneet Bhargava, Jeffrey H. Maki

Chemistry Faculty Publications and Presentations

PURPOSE: Accurate characterization of contrast reagent (CR) longitudinal relaxivity in whole blood is required to predict arterial signal intensity in contrast-enhanced MR angiography (CE-MRA). This study measured the longitudinal relaxation rate constants (R₁ ) over a concentration range for non-protein-binding and protein-binding CRs in ex vivo whole blood and plasma at 1.5 and 3.0 Tesla (T) under physiologic arterial conditions.

METHODS: Relaxivities of gadoteridol, gadobutrol, gadobenate, and gadofosveset were measured for [CR] from 0 to 18 mM [mmol(CR)/L(blood)]: the latter being the upper limit of what may be expected in CE-MRA.

RESULTS: In plasma, the ¹H2 O R …

Selective Indicators For Optical Determination Of Disease Biomarkers, Lovemore Hakuna

Dissertations and Theses

The most abundant biological thiols, homocysteine (Hcy), cysteine (Cys) and glutathione (GSH) have been the subject of intense research due to their association with a wide range of diseases. They play a key role in maintaining the redox status of biological systems. Selective detection methods for these thiols are challenging due to their similar structures and properties. Current commercially available detection methods use separations, fragile and expensive enzymatic or immunogenic materials and complex instrumentation. This has led to a global effort towards developing simple and inexpensive optical probes and indicators selective for specific biological thiols.

Highly selective chemical probes and …

Mimicking Metabolism Of A Reversed Chloroquine Antimalarial, Kelsie Lynn Kendrick

Dissertations and Theses

The aim of this study was to elucidate the oxidation products of a candidate antimalarial drug, PL69, using a porphyrin system and to determine the accuracy of the oxidation products produced, as compared to what is expected in metabolism. PL69 is a reversed chloroquine (RCQ) that is active against chloroquine resistant malaria. Porphyrin oxidation systems have been shown to mimic in vitro enzymatic metabolism reactions. PL69 and its known metabolite, PL16, were incubated with the porphyrin system, and then the oxidation products were collected and separated by HPLC. The oxidation products were characterized by NMR and mass spectrometry and compared …

Reducing The Effects Of Shot Noise Using Nanoparticles, Moshood K. Morakinyo, Shankar B. Rananavare

Chemistry Faculty Publications and Presentations

We present a hybrid nano-lithographic approach to minimizes the effects of line edge roughness and shot noise in nano-hole patterning by reflowing photoresist polymers around the nanoparticles deposited using self-assembly and simple etch chemistries. The method extends the transistor contact holes patterning limits to below 20 nm.

Inhalable Constituents Of Thirdhand Tobacco Smoke: Chemical Characterization And Health Impact Considerations, Mohamad Sleiman, Jennifer M. Logue, Wentai Luo, James F. Pankow, Lara A. Gundel, Hugo Destaillats

Chemistry Faculty Publications and Presentations

Tobacco smoke residues lingering in the indoor environment, also termed thirdhand smoke (THS), can be a source of long-term exposure to harmful pollutants. THS composition is affected by chemical transformations and by air–surface partitioning over time scales of minutes to months. This study identified and quantified airborne THS pollutants available for respiratory exposure, identified potential environmental tracers, and estimated health impacts to nonsmokers. In a ventilated 18 m3 laboratory chamber, six cigarettes were machine-smoked, and levels of particulate matter (PM2.5) and 58 volatile organic compounds (VOCs) were monitored during an aging period of 18 h. Results were compared with field …

Translational Fidelity Of A Eukaryotic Glutaminyl-Trna Synthetase With An N-Terminal Domain Appendage, Aaron Bethea Rogers

Dissertations and Theses

Several Saccharomyces cerevisiae mutant tRNA^Q2 species (glutamine isoacceptor, CUG anticodon) were synthesized and assayed for aminoacylation activity with Saccharomyces cerevisiae glutaminyl-tRNA synthetase. The derived steady state parameters were compared to similar datasets from the literature. The mutants behaved analogously to similar mutant species based on tRNA from Escherichia coli, but with slightly relaxed specificity as revealed by comparison of k_cat/K_M values relative to wild type in vitro transcribed tRNA. Additionally the eukaryotic N-terminal domain appendage, as found in Sce glutaminyl-tRNA synthetase, is considered in light of the discovery of non-canonical aminoacyl-tRNA synthetase functions, including …

The Atmosphere Can Be A Source Of Certain Water Soluble Volatile Organic Compounds In Urban Streams, Scott J. Kenner, David A. Bender, James F. Pankow, John S. Zogorski

Chemistry Faculty Publications and Presentations

Surface water and air volatile organic compound (VOC) data from 10 U. S. Geological Survey monitoring sites were used to evaluate the potential for direct transport of VOCs from the atmosphere to urban streams. Analytical results of 87 VOC compounds were screened by evaluating the occurrence and detection levels in both water and air, and equilibrium concentrations in water (C-w(s)) based on the measured air concentrations. Four compounds (acetone, methyl tertiary butyl ether, toluene, and m- & p-xylene) were detected in more than 20% of water samples, in more than 10% of air samples, and more than 10% of detections …

Optical Injection Unlocking For Cavity Ringdown Spectroscopy, Gregory A. Bostrom, Andrew L. Rice, Dean B. Atkinson

Physics Faculty Publications and Presentations

Continuous wave cavity ringdown spectroscopy requires a rapid termination of the injection of light into the cavity to initiate the decay (i.e., ringdown) event. We demonstrate a technique that accomplishes this through pulsed optical injection of a second laser into the main laser, resulting in 20-100 MHz frequency shifts in the otherwise cavity-locked main laser sufficient to create ringdown events at 3.5 kHz. Data on the frequency shift as a function of both main laser current and relative wavelength are presented, 88 well 88 a demonstration that single exponential decays are maintained in the process.

Promiscuous And Adaptable Enzymes Fill “Holes” In The Tetrahydrofolate Pathway In Chlamydia Species, Nancy E. Adams, Jennifer J. Thiaville, James Proestos, Ana L. Juárez-Vázquez, Andrea J. Mccoy, Francisco Barona-Gómez, Dirk Iwata-Reuyl, Valérie De Crécy-Lagard, Anthony T. Maurelli

Chemistry Faculty Publications and Presentations

Folates are tripartite molecules comprising pterin, para-aminobenzoate (PABA), and glutamate moieties, which are essential cofactors involved in DNA and amino acid synthesis. The obligately intracellular Chlamydia species have lost several biosynthetic pathways for essential nutrients which they can obtain from their host but have retained the capacity to synthesize folate. In most bacteria, synthesis of the pterin moiety of folate requires the FolEQBK enzymes, while synthesis of the PABA moiety is carried out by the PabABC enzymes. Bioinformatic analyses reveal that while members of Chlamydia are missing the genes for FolE (GTP cyclohydrolase) and FolQ, which catalyze the initial …

Characterization Of Methylene Diphenyl Diisocyanate Protein Conjugates, Morgen Mhike

Dissertations and Theses

Diisocyanates (dNCO) such as methylene diphenyl diisocyanate (MDI) are used primarily as cross-linking agents in the production of polyurethane products such as paints, elastomers, coatings and adhesives, and are the most frequently reported cause of chemically induced immunologic sensitization and occupational asthma (OA). Immune mediated hypersensitivity reactions to dNCOs include allergic rhinitis, asthma, hypersensitivity pneumonitis and allergic contact dermatitis.

There is currently no simple diagnosis for the identification of dNCO asthma due to the variability of symptoms and uncertainty regarding the underlying mechanisms. Immunological sensitization due to dNCO exposure is traditionally thought to require initial conjugation of the dNCO to …

Candy Flavorings In Tobacco, Jessica E. Brown, Wentai Luo, Lorne M. Isabelle, James F. Pankow

Chemistry Faculty Publications and Presentations

Professor James F. Pankow reveals striking similarities between the patterns in the flavoring chemicals used in flavored tobacco products and those in popular candy and Kool-Aid products. The authors analyzed 12 artificially flavored candy and fruit drink products and compared them to 15 widely-available flavored tobacco products. They found significant overlap in the chemical signatures of the flavor chemicals. Several of the tobacco products contained flavor chemicals at much higher concentrations than in the non-tobacco products.

The Impact Of Surface Ligands And Synthesis Method On The Toxicity Of Glutathione-Coated Gold Nanoparticles, Bryan Harper, Federico Sinche, Meenambika Gowrishankar, Grant Marquart, Marilyn R. Mackiewicz, Stacey L. Harper

Chemistry Faculty Publications and Presentations

Gold nanoparticles (AuNPs) are increasingly used in biomedical applications, hence understanding the processes that affect their biocompatibility and stability are of significant interest. In this study, we assessed the stability of peptide-capped AuNPs and used the embryonic zebrafish (Danio rerio) as a vertebrate system to investigate the impact of synthesis method and purity on their biocompatibility. Using glutathione (GSH) as a stabilizer, Au-GSH nanoparticles with identical core sizes were terminally modified with Tryptophan (Trp), Histidine (His) or Methionine (Met) amino acids and purified by either dialysis or ultracentrifugation. Au-GSH-(Trp)2 purified by dialysis elicited significant morbidity and mortality at …

A Facile Route To Tailoring Peptide-Stabilized Gold Nanoparticles Using Glutathione As A Synthon, Rosina Ho Wu, Tan P. Nguyen, Grant W. Marquart, Thomas J. Miesen, Theresa Mau, Marilyn R. Mackiewicz

Chemistry Faculty Publications and Presentations

The preparation of gold nanoparticles (AuNPs) of high purity and stability remains a major challenge for biological applications. This paper reports a simple synthetic strategy to prepare water-soluble peptide-stabilized AuNPs. Reduced glutathione, a natural tripeptide, was used as a synthon for the growth of two peptide chains directly on the AuNP surface. Both nonpolar (tryptophan and methionine) and polar basic (histidine and dansylated arginine) amino acids were conjugated to the GSH-capped AuNPs. Ultracentrifugation concentrators with polyethersulfone (PES) membranes were used to purify precursor materials in each stage of the multi-step synthesis to minimize side reactions. Thin layer chromatography, transmission electron …

Interpretation Of Chemical Environments By Rna And The Implications To The Origins Of Life, Brian Larson

Dissertations and Theses

We describe the initial realization of behavior in the biosphere, which we term behavioral chemistry. If molecules are complex enough to attain a stochastic element to their structural conformation in such a way as to radically affect their function in a biological (evolvable) setting, then they have the capacity to behave. This circumstance is described here as behavioral chemistry, unique in its definition from the colloquial chemical behavior. This transition between chemical behavior and behavioral chemistry need be explicit when discussing the root cause of behavior, which itself lies squarely at the origins of life and is the foundation of …

Serial Transfer Can Aid The Evolution Of Autocatalytic Sets, Wim Hordijk, Nilesh Vaidya, Niles Lehman

Chemistry Faculty Publications and Presentations

Background: The concept of an autocatalytic set of molecules has been posited theoretically and demonstrated empirically with catalytic RNA molecules. For this concept to have significance in a realistic origins-of-life scenario, it will be important to demonstrate the evolvability of such sets. Here, we employ a Gillespie algorithm to improve and expand on previous simulations of an empirical system of self-assembling RNA fragments that has the ability to spontaneously form autocatalytic networks. We specifically examine the role of serial transfer as a plausible means to allow time-dependent changes in set composition, and compare the results to equilibrium, or "batch" scenarios. …

Photocatalytic Hydrogen Production From A Noble Metal Free System Based On A Water Soluble Porphyrin Derivative And A Cobaloxime Catalyst, Theodore Lazarides, Milan Delor, Igor V. Sazanovich, Theresa M. Mccormick, Irene Georgakaki, Georgios Charalambidis, Julia A. Weinstein, Athanassios G. Coutsolelos

Chemistry Faculty Publications and Presentations

A combination of noble-metal free components, a water soluble porphyrin photosensitizer zincmeso-tetrakis(1-methylpyridinium-4-yl)porphyrin chloride [ZnTMPyP⁴⁺]Cl₄ (1) with cobaloxime complex [Co^III(dmgH)₂(py)Cl] (2) as a catalyst, creates an efficient system for photochemical hydrogen production acting under visible light with 280 TONs. This is the first example of a water soluble porphyrin acting as a photosensitizer for cobaloxime catalysed H₂ production.

The Confluence Of Structure And Dynamics In Lanthanide(Iii) Chelates: How Dynamics Help Define Structure In Solution, Benjamin Charles Webber, Mark Woods

Chemistry Faculty Publications and Presentations

Coordination exchange processes tend to dominate the solution state behaviour of lanthanide chelates and generally prohibit the study of small conformational changes. In this article we take advantage of coordinatively rigid Eu³⁺ chelates to examine the small conformational changes that occur in these chelates as water dissociatively exchanges in and out of the inner coordination sphere. The results show that the time-averaged conformation of the chelate alters as the water exchange rate increases. This conformational change reflects a change in the hydration state (q/r_LnH⁶) of the chelate. The hydration state has recently come …

Investigation Of The Structure And Dynamics Of Regioisomeric Eu³⁺ And Gd³⁺ Chelates Of Nb-Dotma: Implications For Mri Contrast Agent Design, Benjamin Charles Webber

Dissertations and Theses

The detection of disease and abnormal pathology by magnetic resonance imaging (MRI) has been aided significantly by the use of gadolinium (Gd³⁺)-based contrast agents (CAs) over the past three decades. MRI and MRI CAs play a critical role in diagnosing tumors and diseases of the central nervous system. The agents used clinically have been shown to safely increase MRI contrast despite the toxicity of Gd³⁺, owing to the high kinetic and thermodynamic stability of these chelates. However, current CAs enhance contrast at a small fraction of what is theoretically possible. This leads to the necessity of …