Chemistry Commons^™

Methodological Improvements In The Mrna Profiling Assays For Incorporation Into Dna Casework Workflows, Paris Volk

Electronic Theses and Dissertations

Currently, DNA profiling is the gold standard to identify an individual. However, determining body fluid origin is important in criminal investigations, offering additional information surrounding the circumstances of a crime. However, crime labs can only definitively identify blood and semen and presumptively saliva using techniques that consume time and sample and do not simultaneously identify all forensically relevant body fluids. This causes many crime labs to want to bypass body fluid identification altogether. Therefore, advances into more definitive molecular-based body fluid methods are necessary. One such technique is mRNA profiling because it provides a highly sensitive and specific approach to …

Deposition Of Platinum Particles On Surface-Modified Carbon Ultramicroelectrodes, Caitlin Millsaps

Undergraduate Honors Theses

Nanoparticles are used as electrocatalysts due to their large surface area-to-volume ratios. Most studies of nanoparticle electrocatalysis are performed on collections of particles on a support, which represent ensemble average behavior influenced by spatial distribution of the nanoparticles. Therefore, recent emphasis has been placed on analyzing electrocatalytic behavior of single particles. The focus here is to develop carbon ultramicro- and nanoelectrode platforms for studying the electrocatalytic properties of single metal nanoparticles. Ultramicroelectrodes were prepared using chemical vapor deposition of carbon in pulled quartz capillaries. Electrode diameters were determined by cyclic voltammetry. Electrodes were modified using a soft nitriding technique to …

Examining Electrochemical Properties Of O-Quinone And Sulfur Adducts Using Bisphenol A-3,4-Quinone Platform, Barbara Mullen

Theses/Capstones/Creative Projects

o-Quinones are toxic electrophiles that can disrupt cellular macromolecules. Whether endogenous or xenobiotic, o-quinones are reactive compounds that are difficult to isolate. This work uses the o-quinone of bisphenol(BPA), bisphenol A-3,4-quinone(BPAQ), which can be efficiently synthesized and isolated, to study the electrochemical properties of o-quinones and their sulfur adducts in order to understand their metabolic fate. Cyclic voltammetry and equilibrium analysis were used to determine the relative oxidation potential of the BPA catechol and adducts, formed by reacting glutathione(GSH) and N-acetylcysteine(NAC) with BPAQ. BPAQ-sulfur adducts with 5-position substitution displayed lower oxidation potentials when compared to the …

Gas Chromatography Analysis Of Co2 Reduction Photocatalysis With Zinc Dipyrrin Complexes, Alex Day

Undergraduate Honors Theses

Bis(1,3,7,9-tetramethyl-5-mesityldipyrrinato)zinc(II) (ZnDPY) was synthesized in the lab by the McCusker group and a procedure was created to analyze its ability as a photosensitizer, a molecule that provides the energy for the reaction to occur by capturing light energy and turning it into a form that can be used by the photocatalyst. While more work is needed, preliminary steps have been made to create a process that can analyze the amount of carbon monoxide produced by a photocatalytic CO₂ reduction reaction with ZnDPY as the photosensitizer. Progress has been made via the setup of a reaction apparatus, targeted gas chromatography …

Structure Modeling And Property Calculations Of Amorphous Materials, Ilia Ponomarev

Chemistry & Biochemistry Dissertations - Archive

The demand in discovery of novel materials for a seemingly infinite list of applications is growing year by year. Even though it’s not uncommon to find the application for the material after its discovery upon experimentally studying its properties, it can be essential to be able to build the material to satisfy the specific need. This kind of targeted development for a specific application requires deep understanding of the “synthesis => structure => properties” sequence, and this is why insights into the mechanisms of the synthesis, structure formation and structure vs. properties relations are highly desired. Structural insights can be …

Synthesis And Reactivity Of Π-Conjugated Triazenes, Horacio Enrique Barragan Peyrani

Chemistry & Biochemistry Dissertations - Archive

The triazene functional group has found numerous applications in organic and medicinal chemistry, with several important chemotherapeutic drugs containing this functionality. In spite of this, the reactivity of π-conjugated triazenes has been scarcely explored. The work described in this dissertation investigates the synthesis and new reactions of π-conjugated triazenes developed in our group, demonstrating the versatility of these molecules that allow access to several functionalities which can serve as building blocks for more complex structures. Chapter 1 surveys the prior literature of π-conjugated triazenes, describing their known synthesis and reactivity . In Chapter 2, new oxidation and substitution reactions of …

Advances In Liquid Chromatography And Liquid Chromatography Mass Spectrometry For The Analysis Of Biologically Important Pharmaceuticals, Glycosaminoglycans And Amino Acids, Yadi Wang

Chemistry & Biochemistry Dissertations - Archive

The use of high-performance liquid chromatography (HPLC) and liquid chromatography-mass spectrometry (LC-MS) is now commonplace among pharmaceutical laboratories. They are major analytical tools in the drug discovery process. They are used to check the identity and the purity of newly synthesized compounds as well as to follow the reaction processes. They are also utilized to monitor the concentration of a drug in different biological matrices. In this thesis, fundamental contributions to HPLC and LC-MS bioanalysis work are discussed. The goal of the HPLC work is to develop a hydrolytically stable hydrophilic interaction liquid chromatography (HILIC) stationary phase. A carboxylate modified …

Determination Of Tobacco Alkaloid Enantiomers Using Reversed Phase Uplc/Ms/Ms, Huihua Ji, Ying Wu, Franklin Fannin, Lowell P. Bush

Kentucky Tobacco Research and Development Center Faculty Publications

Nʹ-Nitrosonornicotine (NNN), a carcinogenic tobacco-specific Nʹ-nitrosamine (TSNA), is on the FDA list of harmful and potentially harmful constituents (HPHCs). Nornicotine, a product of the demethylation of nicotine, is the immediate alkaloid precursor for NNN formation. Nicotine, nornicotine and NNN are optically active. The accumulation of the isomers of nicotine, nornicotine, and NNN impacts their biological activity. In this paper, we report the determination of tobacco alkaloid enantiomers (including nicotine, nornicotine, anabasine, and anatabine) in samples of different tobacco lines using a reversed phase ultra-performance liquid chromatography-tandem mass spectrometer (UPLC/MS/MS) method. Current method demonstates excellent detection capability for all alkaloid enantiomers, …

The Effects Of The Stereochemistry Of Ruthenium (Ii) Polypyridyl Complexes On Microtubules As Targets For Chemotherapy, Radhiyah Himawan

Chemistry & Biochemistry Theses - Archive

Ruthenium polypyridyl complexes (RPCs) are promising anticancer agents due to their robustness and tunability of their polypyridyl ligands. Their axial chirality generally allows for more selective binding to biological molecules. The ruthenium complexes [Ru(phen)3]Cl2 (RPC 1), [Ru(DIP)3]Cl2 (RPC 2), [(phen)2Ru(tatpp)]Cl2 (RPC 3), [(phen)2Ru(tatpp)Ru(phen)2]Cl4 (RPC 4), and [(phen)2Ru(dppz)]Cl2 (RPC 5) have all been investigated, and RPCs 2, 3, and 4 have shown lower micromolar cytotoxicity against malignant cell lines without irradiation. Herein we show that microtubules (MTs) may be the target of some RPCs in cells and all these RPCs 1-5 promote tubulin polymerization in vitro. How they interact with MTs …

Probing Inter-Subunit Communication Of F₄₂₀ Nadp Oxidoreductase: A Kinetic Analysis, Denzel L. Pugh

Chemistry & Biochemistry Theses - Archive

F₄₂₀-dependent enzymes are important in a number of organisms, which play vital roles in methane production, NADPH regulation, nucleic acid biosynthesis, folate biosynthesis and carbon cycling. Until our recent publications on F₄₂₀:NADP+ Oxidoreductase (Fno) and F₄₂₀-dependent glucose-6-phosphate dehydrogenase (FGD), these enzymes, in general, had not been subjected to rigorous enzymological investigation. Our work has provided valuable new mechanistic and functional insights into the enzymes that use this unique cofactor. Our previous kinetic studies on Fno, which is the focus of this proposal, indicated half-site reactivity in only one of the active sites in a functional dimer. These data suggest that …

N-Heterocyclic Carbene And Bis(Pyrazolyl)Methane Supported Copper(I) And Silver(I) Complexes Of Organotrifluoroborates, Adway Ouseph Zacharias

Chemistry & Biochemistry Theses - Archive

Organotrifluoroborates have gone from capturing the imagination of the scientific community to being used extensively in a host of applications ranging from being employed to study boron intermediates to being used as a means of introducing trifluoroborate moieties on molecules for custom chemical synthesis. There has been a lot of research done on the application of these molecules as reagents in carbon-carbon coupling reactions such as the Suzuki-Miyaura cross coupling reaction. Despite all of these efforts to understand the versatility of organotrifluoroborates, the possibility of using these molecules as potential ligands in transition metal complexes has not been extensively studied. …

Undergraduate Research Experiences Reports On Acne Treatment, Heavy Metal In Water, And Measurement Of The Heat Reaction Of Isosorbide Methacrylate, Jaida Lewis

Honor’s College Freeman Research Journal

This thesis reports on three significant science projects I have done during my undergraduate years. The first part is on the effect of Benzoyl Peroxide and Salicylic, two active ingredients in face wash for acne control, on MCF-7, epithelial cells. My assays suggested that salicylic acid lowered the viability of the MCF-7 cells, meaning it is more likely to decrease the viability of acne cells, while benzoyl peroxide did not seem to have any effect at all, meaning it is safer to use on the skin. My second research involved measurement of heavy metals, such as aluminum, nickel, cadmium, lead, …

Nanomaterials-Based Electrodes For Lithium-Ion Batteries And Alcohol Fuel Cells, Lakshman K. Ventrapragada

All Dissertations

This dissertation describes my research on surfactant-free synthesis of nanomaterials with applications for alcohol fuel-cell electrodes, and design and fabrication of nanomaterials-based current collectors that improve the performance of lithium-ion batteries (LIBs) by replacing existing current collectors.

Chapter 1 provides a background on the electroanalytical tools used in this research, and an introduction to fuel cells and LIBs.

Chapter 2 describes a novel synthesis method for fabricating gold-graphene composites by laser ablation of a gold strip in water. A well-known limitation in the fabrication of a metal-graphene composite is the use of surfactants that strongly adsorb on the metal surface …

Molecular Machines: Synthesis, Modeling, And Applications, Syd Kotar

Student Scholar Symposium Abstracts and Posters

While some of the smallest, most useful machines known to science are the biological molecules that keep living organisms alive, there is a growing advancement of the creation of artificial molecules that have the same function and are more efficient. Molecular machines were invented in 1983 when scientists in France created a machine formed of two interlinked molecular rings. In 2016, the Nobel prize in chemistry was awarded to Feringa, Stoddart, and Sauvage who finally documented molecular machines and put them into energy‐filled states in which their movements could be controlled. From this, molecular machines became known as a group …

Molecular Packing Control Enables Excellent Performance And Mechanical Property Of Blade-Cast All-Polymer Solar Cells, Baojun Lin, Lin Zhang, Heng Zhao, Xianbin Xu, Ke Zhou, Song Zhang, Lu Guo, Baobing Fan, Lei Zhang, Hongping Yan, Xiaodan Gu, Lei Ying, Fei Huang, Yong Cao, Wei Ma

Faculty Publications

All-polymer solar cells (all-PSCs) are the most promising power generators for flexible and portable devices due to excellent morphology stability and outstanding mechanical property. Previous work indicates high crystallinity is beneficial to device performance but detrimental to mechanical property, therefore identifying the optimized ratio between crystalline and amorphous domains becomes important. In this work, we demonstrated highly efficient and mechanically robust all-PSCs by blade-coating technology in ambient environment based on PTzBI:N2200 system. By controlling the aggregation in solution state and ultrafast film formation process, a weakly ordered molecular packing morphology as well as small phase separation is obtained, which leads …

Using Green Emitting Ph-Responsive Nanogels To Report Environmental Changes Within Hydrogels: A Nanoprobe For Versatile Sensing, Mingning Zhu, Dongdong Lu, Shanglin Wu, Qing Lian, Wenkai Wang, L. Andrew Lyon, Weiguang Wang, Paulo Bártolo, Brian R. Saunders

Engineering Faculty Articles and Research

Remotely reporting the local environment within hydrogels using inexpensive laboratory techniques has excellent potential to improve our understanding of the nanometer-scale changes that cause macroscopic swelling or deswelling. Whilst photoluminescence (PL) spectroscopy is a popular method for such studies this approach commonly requires bespoke and time-consuming synthesis to attach fluorophores which may leave toxic residues. A promising and more versatile alternative is to use a pre-formed nanogel probe that contains a donor/acceptor pair and then “dope” that into the gel during gel assembly. Here, we introduce green-emitting methacrylic acid-based nanogel probe particles and use them to report the local environment …

A Break In Communication: The Synthesis, Characterization, Dna Binding And Photocleavage Of A Novel Ruthenium Polypyridyl Complex Containing An Electronically Isolated Pyrene Group, Samantha Klein

Bryn Mawr College Dissertations and Theses

A novel complex [Ru(bpy)2bpy-py]2+ (where bpy= 2,2’-bipyridine and bpy-py=N-(6-(4-(pyren-1-yl) butanamido) hexyl)-[2,2'-bipyridine]-5-carboxamide))) has been synthesized. The effect of electronically isolating the pyrene from the metal core on the complex’s ability to bind to and photocleave DNA was studied. Other molecules such as 1-pyreneacetic acid and [Ru(bpy)2dep]2+ (where dep= N-(6-aminohexyl)-[2,2'-bipyridine]-5-carboxamide), which share structural similarities to [Ru(bpy)2bpy-py]2+, were also studied to help determine which areas of the [Ru(bpy)2bpy-py]2+ molecule may be responsible for interacting with DNA. Spectroscopic experiments including isothermal and competitive binding titrations in addition to the hydrodynamic technique of viscometry were used to show that [Ru(bpy)2bpy-py]2+ binds to DNA with a …

The Characterization Of A New Metabolite From A Trichodesmium Bloom, Kelly M. Mcmanus

Senior Honors Projects

Our laboratory has been investigating blooms of Trichodesmium, a genus of ecologically important, nitrogen-fixing cyanobacteria, collected from Padre Island in the Gulf of Mexico. Trichodesmium species are an underexplored biological source of cyanobacteria – a taxa that has been shown to produce chemically diverse secondary metabolites. With our focus on the isolation and structure characterization of new bioactive marine natural products, our research group has discovered over 25 new-to-science compounds over the past three years from these blooms. UV and mass spectrometry-guided isolation of Trichodesmium chromatography fractions were utilized to isolate a new metabolite. Isolation of this metabolite was …

Determining The Interference Of Lactate And Lactate Dehydrogenase In An Ethanol Enzyme Assay, Julia Liebl

Master's Theses

Enzymatic ethanol assays are widely used to determine blood alcohol content for individuals admitted to a hospital. In some instances, this hospital data is later used as evidence in a court of law, most commonly in DUI cases. As the enzymatic assay targets, but does not exclusively measure ethanol, it is theoretically possible that interference could occur and produce a falsely elevated result, leading to wrongful convictions or other consequences. This project examined the potential of clinically relevant levels of one potential interferant, lactate and the hepatic enzyme lactate dehydrogenase (LDH) to cause significant and falsely elevated results. Threshold levels …

Light Addressable Electrode For Neurotransmitter Sensing, Irina Michelle Terrero Rodríguez

Theses, Dissertations and Culminating Projects

Electrochemical sensors are important for a variety of applications. However, they suffer from physical constraints, as each electrode requires a dedicated wire. Although arrays of 500 electrodes have been reported, achieving high-density electrochemical measurements is still difficult.

In a light-addressable electrode, electrochemical processes occur only when the electrode is illuminated. Light-addressable electrodes could potentially solve many of the drawbacks of traditional electrode arrays, as light is used to spatially confine the redox process to only a small part of the electrode and only one connection is needed. It could also allow for new imaging techniques.

Light-addressable electrodes require a semiconductor …

Fingerprint Analysis: Moving Toward Multiattribute Determination Via Individual Markers, Morgan Eldridge

Chemistry

Forensic science will be forever revolutionized if law enforcement can identify personal attributes of a person of interest solely from a fingerprint. For the past five years, the goal of the Halamek Lab has been to establish a way to identify originator attributes. Specifically, biological sex has been accomplished and the ultimate goal is to continue to accomplish this using a single analyte for each. To date, an enzymatic assay and two chemical assays have been developed for the analysis of multiple analytes. In this thesis, an additional enzymatic assay has been developed. This time, however, the assay utilizes only …

Raman Spectroscopic Examination Of Bloodstains For Forensic Purposes : Background And Race Determination, Ewelina M. Mistek

Legacy Theses & Dissertations (2009 - 2024)

Chapter 1 of this thesis critically overviews recent developments in forensic trace evidence analysis since 2016. It covers improvements to existing techniques as well as new methods for the analysis of fibers, hair, paint, glass, gunshot residue (GSR), and explosives.

Unravel Allostery Mechanism Through Molecular Dynamic Simulations With Machine Learning Approaches, Hongyu Zhou

Chemistry Theses and Dissertations

Allostery is referred to as protein function changes due to external perturbations, and ubiquitous in the living cells. Investigation of the allosteric mechanism is essential for developing drugs or assisting protein engineering. Recently, the population shift model has been proposed to explain the allosteric mechanism. This model emphasizes the importance of conformational distribution in the allostery. In the past several years, I have been continuously working on developing computational methods to explore and quantify protein allostery mechanism. By fully utilizing protein simulation results, several machine learning related methods have been applied to protein systems to investigate the underlying conformational changes …

Dom Control Of Mercury Methylation In The Water Column Of A Meromictic Lake, Madalyn Bozinski

Renée Crown University Honors Thesis Projects - All

The trophic transfer and bioaccumulation of methyl mercury (MeHg) in aquatic ecosystems is a substantial concern, resulting in fish consumption advisories worldwide. Aquatic ecosystems have been identified as the critical environments that breed production of MeHg and low levels of initial accumulation in biota. MeHg production is a microbially-mediated process, occurring primarily at the transition between oxic and anoxic environments. This research aimed to assess the extent to which dissolved organic matter (DOM) affects methylation of mercury in the oligotrophic meromictic lake, Green Lake, in Fayetteville, NY and the warm monomictic lake, Seneca Lake, in Geneva, NY. General physical parameters …

Anthocyanin Stability In Food Products Made With Freeze-Dried Blueberry Powder, Samantha Findley

Food Science Undergraduate Honors Theses

This study evaluated the stability of anthocyanins in six blueberry products (gummy, graham bar, oatmeal bar, rice krispy bar, ice pop and juice) prepared with freeze-dried wild blueberry powder during processing and over eight weeks storage. Total anthocyanins were determined by HPLC before processing and at day 0 and 2, 4, 6, and 8 weeks of storage. Thermal processing of gummy and graham bar products resulted in significant losses of anthocyanins (50% and 31%, respectively). An eight-week storage time also resulted in a significant decrease in anthocyanins (7% to 51%) in products stored at ambient temperature. The ice pop, which …

Surface Immobilization Of Terpyridine Compounds, Elizabeth Hallett

Chemical Engineering Undergraduate Honors Theses

The deoxydehydration (DODH) of polyols to alkenes is a promising method of producing high-value chemical feedstocks from biomass-derived materials. Current catalytic systems for DODH require the use of costly reducing agents that generate stoichiometric amounts of chemical waste. Immobilizing catalysts on electrode surfaces using chemical linking groups eliminates the need for sacrificial reductants. In this work, glassy carbon electrodes were modified with 4’-(3,4-dihydroxyphenyl)-2,2’:6’,2’’-terpyridine to investigate o-benzoquinone as a potential linking group for DODH, and possibly for other reactions. Previous studies involving electrodes modified with quinone-containing compounds have primarily been focused on catalyzing the oxidation of NADH; the nature or …

Hartree-Fock Implementation For Pedagogical & Research Purposes, Gary Zeri, Jerry Larue

Student Scholar Symposium Abstracts and Posters

Often during the process of innovation and scientific advancement, experimentation is the key to increasing the current knowledge of body. Unfortunately, experimentation can often require extended periods of time as well as monetary resources to perform. The use of computational chemistry can increase the rate of scientific advancement by simulating experimental results, allowing researchers to focus on experiments whose computational counterparts show the greatest promise. Students new to the sciences are often not exposed to these methods due to their complexities. The purpose of this project is to implement the Hartree-Fock method, one type of computational chemistry method, whose programming …

The Use Of Heterocycles As Important Structures In Medicinal Chemistry, Sayre Weast

Honors Theses

Heterocycles have many applications in the discipline of medicinal chemistry. These structures are found in various natural products with relevant biological activity. Our research group, in collaboration with two others, is particularly interested in one heterocycle, quinoline, as a scaffold for HIV-1 integrase inhibitors. A synthetic route has been developed to produce a derivatized structure on small scale. One goal of this thesis was to expand the scale of this route to provide increased quantities of the quinoline scaffold. Procedures were adapted to accommodate the increase in scale to convert commercially available anthranilic acids to quinolines via the isatoic anhydride. …

A Study On The Modifications Of [2.2]Paracyclophane And Their Effects On The Enantioselectivity Of The Copper Catalyzed Cyclopropanation Reaction, Yousef Dawoud

Honors Theses

The use of chiral [2.2]paracyclophane Schiff-base ligands has been shown to induce enantioselectivity in the copper catalyzed cyclopropanation of styrene with diazoesters. ¹ Previous research by Dr. Masterson tested Schiff-base ligands based on 4- amino[2.2]paracyclophane with moderate enantioselectivity. In this project, the Schiff-base N- salicylidene-4-amino[2.2]paracyclophane, was modified by way of Grignard addition to the imine carbon and its enantioselective properties were explored with the copper catalyzed cyclopropanation. The methyl Grignard addition to N- salicylidene-4-amino[2.2]paracyclophane was successful in producing the amino alcohol and the amino alcohol was characterized. The amino alcohol was produced from the R enantiomer of the Schiff-base and …

Synthesis, Characterization, And Utilization Of Iron Ii Ion Sensing Fluorescent Probes For Detection Of Early Onset Anodic Corrosion, Dane N. Wedgeworth

Honors Theses

Corrosion effects can be seen in infrastructure all around the world. From rusted bridges, ships, and other steel surfaces, the price of corrosion adds up quickly with repairs, maintenance, and complete replacement. Common approaches to corrosion detection and prevention require slow, optical inspection to begin the repair and maintenance process, which can also be very slow and costly. However, recent literature suggests that metal chelating probes can yield new understanding of the processes of corrosion faster and with greater specificity in location and diversity in mechanisms for early onset of corrosion. Earlier corrosion detection can be characterized by several ways. …