Chemistry Commons^™

Small Island Taphonomy In Western Australia, Courtney J. Newberry

Honors Theses

Forensic death investigations rely on postmortem interval estimations to establish a timeline surrounding a decedent’s death. Several methods are used, often together, to make such estimations. One of the main methods is the evaluation of the stage of decomposition; although decomposition follows the same general steps, the length of the process can vary by location and environmental factors. Animal scavenging can also impact decomposition by consuming flesh and impacting insect activity on the remains.

This study investigates the scavenging guilds and rate of decomposition of pig (Sus scrofa) legs on Rottnest Island, Australia. Three sites with unique environments were selected …

Hplc Detection Of Organic Gunshot Residues With Silicone Wristbands, Yelyzaveta Zuy

Honors Theses

The analysis of gunshot residue (GSR) is frequently used to aid in investigating firearm-related crimes. Typically, Scanning Electron Microscopy (SEM) is applied for inorganic analysis of elements such as lead, barium, and antimony to study GSR. However, heavy metal-free ammunition creates the need for a different type of approach. This research focuses on studying the potential of detecting organic gunshot residue (OGSR) collected with silicone wristbands through passive sampling. This study has been directed towards the development of an optimal High Performance Liquid Chromatography (HPLC) procedure for the detection and separation of five selected compounds typically found in OGSR. The …

Discriminating Azo Dyes: Conjugated Polymers, The Inner Filter Effect, And Array Sensors, Erin Crater

Honors Theses

Azo dyes are abundant pollutants that contaminate water supplies and threaten humans, biota, and ecosystem health. Their detection and discrimination are an incredible challenge due to the structural, chemical, and optical similarities between dyes, the complexity of the wastewater environment in which they are found, and their low environmental concentrations. In this work, the inner filter effect (IFE), combined with conjugated polymer array-based sensing, is utilized for the quantitative profiling of these pollutants. The array was constructed using three fluorescent, anionic conjugated polyelectrolytes whose varying spectroscopic properties led to distinct IFE patterns in the presence of the dyes. The unique …

Molecular Dynamics Simulations Of Apolipoprotein A1 In Ionic Liquids, Benjamin Smith

Honors Theses

High-density lipoprotein function is essential for the healthy processing of fats in the blood. The function of these proteins is determined by their conformational structure of chains of amino acids. Certain ionic liquids have been shown to interact with individual amino acids to affect the tertiary shape of the protein. These interactions can disrupt the native hydrogen bonds between amino acids which can either promote folding or denaturing of the protein. Our work focused on apoA-1, a high-density lipoprotein that binds to cholesterol for efflux from the body. We studied this protein in different ion-based liquids with sodium, chloride, and …

Gold Nanoparticles: Core Conversion Of Au144(Sch2ch2ph)60 To Au99(Sph-Ch3)42 Using Aromatic Thiolate Ligands And Crystallization Of Au99(Sph-Ch3)42, Elizabeth Turnage

Honors Theses

The purpose of this thesis is to synthesize Au₁₄₄(SCH₂CH₂Ph)₆₀ using a two-step synthesis reaction, and then using this product to conduct a core conversion from Au₁₄₄(SCH₂CH₂Ph)₆₀ to Au₉₉(SPh-CH₃)₄₂. The Au₉₉(SPh-CH₃)₄₂ product will then be used to attempt to form crystals using five different crystal set-up methods. Au₁₄₄(SCH₂CH₂Ph)₆₀ is made with aliphatic thiolate ligands, and when it is placed in a mixture containing excess para-methyl benzenethiol, it undergoes a …

Raman Spectroscopic And Quantum Chemical Investigation Of The Effects Of Tri-Methylamine N-Oxide (Tmao) On Hydrated Urea, Hydrated Guanidinium, And Hydrogen Bonded Networks, Genevieve Verville

Honors Theses

Trimethylamine N-Oxide (TMAO), guanidinium, and urea are three important

osmolytes with their main significance to the biophysical field being in how they

uniquely interact with proteins. TMAO is known to stabilize and counteract the

destabilizing effects of both urea and guanidinium. The exact mechanisms by which

TMAO stabilizes and both guanidinium and urea destabilize folded proteins continue

to be debated in the literature. Some studies suggest that solvent interactions do not

play a large role in TMAO’s stabilizing effects and therefore advocate direct

stabilization, whereas others suggest that TMAO counteracts denaturation primarily

through an indirect effect of strong solvent interactions. …

Assessing Amino Acid Racemization In Avian Eggshells Through Reverse Phase Liquid Chromatography, Nikitha Nelapudi

Honors Theses

The extent of amino acid racemization (AAR) observed in organic material offers insight into geochronology. Within the scope of AAR research, Avian eggshells are reliable sources of data due to retention of indigenous amino acids through calcification. This project develops a robust quantification methodology for up to 9 D/L amino acids using reverse-phase HPLC (RP-HPLC) with precolumn derivatization. Reliable quantitation is established via statistical assessment of detectability and calibration curves. Progress has focused on obtaining adequate enantioseparation and reproducible data of single D/L amino acids.

Design Of A Novel Isoxazoline Class Drug For The Suppressive Treatment Of Malaria, Peyton Ware

Honors Theses

Design of a novel isoxazoline class drug for the suppressive treatment of erythrocytic malaria through the inhibition of Plasmodium Falciparum Gylceraldehyde-3-phosphate Dehydrogenase (PfGAPDH) gave rise to creation of a synthetic plan for the proposed target molecule α-amino- 3-bromo-4,5-dihydroisoxazol-5-yl propionic acid. A literature-based analysis of the moieties targeting the PfGADPH active site led to the design of the target molecule. Subsequently, an exploration of the literature yielded a possible bifold synthetic plan. Attempts at a model epoxidation reaction using mCPBA and further efforts towards the synthesis of a 3- bromoisoxazoline were shown to be successful using GCMS analysis.

Spectroscopic And Computational Studies Of The Agricultural Active Ingredient Dicamba, James Johnson

Honors Theses

3,6-dichloro-2-methoxy benzoic acid, more commonly known as Dicamba, is the active ingredient in an array of pesticides used on farmlands across the globe. Dicamba’s mode of action works by mimicking the plant hormone auxin, which is synonymous to growth hormones in mammals. The mimicking of auxin results in excessive elongation and growing, which is eventually fatal for plants when the rate of growth can no longer be sustained. Dicamba has risen in prominence in recent years due to drift damage as a result of Dicamba’s high volatility. Having the ability to identify Dicamba is crucial for the agricultural industry. The …

Biological Evaluation Of Fda-Approved Drugs As Mirna-31 Inhibitors Using Real Time Qrt-Pcr And A Luciferase Assay, Nicholas Sienkiewicz

Honors Theses

MicroRNAs (miRNAs) are a group of post-transcriptional, negative regulators of gene expression, consisting of ~19-24 nucleotides. Since their discovery in 1993, miRNAs have been found to be involved in a diverse amount of cellular and disease pathways, including certain types of cancer. Overexpression of certain oncogenic miRNAs, including miRNA-31, have been shown to play a role in cancer cell development. Recent findings have suggested that miRNAs play a significant role in every stage of colorectal cancer (CRC) initiation, progression, and development, as well as induce resistance to chemotherapy drugs like 5-FU. In particular, research has shown that increased levels of …

Synthesis Of Novel Temozolomide-Fatty Acid Imide Hybrid Compounds For The Chemotherapeutic Treatment Of Glioblastoma Multiforme, Janice Pakkianathan

Honors Theses

Glioblastoma multiforme (GBM) is an aggressive form of brain cancer that originates from glial cells, which make up the supportive tissue surrounding neurons. Temozolomide (TMZ) is the current chemotherapeutic drug administered to treat GBM as it works to inhibit the growth of the cancer cells. This research study focused on developing a method for synthesizing novel hybrid compounds that combines TMZ with various fatty acids known to have anticancer properties, forming a series of imide compounds with potential chemotherapeutic effects. Before synthesizing the compounds, various methods for synthesizing an imide from a primary amide were tested to ensure that TMZ …

Synthesis, Characterization, And Reactivity Of Palladium Proazaphosphatrane Complexes, Adrian D. Matthews

Honors Theses

Palladium-catalyzed cross-coupling reactions provide an efficient pathway to a wide variety of otherwise inaccessible compounds. In this study, the synthesis and reactivity of novel palladium proazaphosphatrane complexes that are believed to be intermediates in C–N cross-coupling reactions are described. Both the fundamental reactivity of these complexes and elementary steps involved in a catalytic process are demonstrated. The catalytic viability of palladium proazaphosphatrane complexes is shown through stoichiometric and catalytic cross-coupling reactions. Our findings support the long-standing hypothesis that proazaphosphatranes are conformationally flexible ligands that stabilize a number of catalytic intermediates.

Nanoparticles As Alternative Ceramic Glaze Colorants, Nathan Dinh

Honors Theses

Metallic nanoparticles, including gold and silver, have been used in wide-ranging applications due to their versatile characteristics. These include catalysis, biosensing, imaging, cancer treatments, and art. Due to the phenomenon called surface plasmon resonance, metallic particles change optical properties when sized in the nanoscale based on their composition, shape, diameters, or aspect ratios. In study, these robust nanoparticle systems are applied as an alternative to traditional bulk metal colorants in ceramic glazes.

In this study, the research goals are two-fold: to understand firing mechanism on the gold nanoparticle size and to develop these processes for wider use by regular artisans. …

Aldol Condensations And Nitrile Aldol Reactions Mediated By Trimethylsilyl Trifluoromethanesulfonate, Samuel R. Bottum

Honors Theses

In the presence of excess trimethylsilyl trifluoromethanesulfonate (TMSOTf), ketones and esters undergo aldol addition and dehydration to yield chalcones and cinnamates. This one-pot reaction proceeds through in situ enol silane formation, avoiding the need to pre-form and purify the nucleophile in the Mukaiyama aldol reaction. The stoichiometry of the TMSOTf controls whether the reaction proceeds with simple addition or addition-dehydration. When (trimethylsilyl) acetonitrile is stirred with an aldehyde and TMSOTf, nitrile aldol addition is observed.

Design Of New Ruthenium Complexes For Photoactivated Chemotherapy, Lindsey Paul

Honors Theses

Photoactivated chemotherapy (PACT) offers a targeted approach to cancer treatment through selective drug activation. Substitutionally labile ruthenium-based prodrugs undergo ligand-loss when irradiated, producing an unbound ligand and a Ru-aqua complex. We report the synthesis and cytotoxicity of several new ruthenium-centered complexes and their irradiation products for use in PACT. A series of complexes were synthesized in order to study the effects of structural differences on cell viability. Cell viability was tested on T47D human breast cancer cells in the presence of compound to determine cytotoxicity and dose-response. While neither the Rucomplexes nor their ligands demonstrated cytotoxicity, their Ru-aqua dissociation complexes …

Towards The Synthesis Of An Artificial Fluorescent Siderophore, Ashley Burns

Honors Theses

Siderophores are molecules capable of binding ferric ions with high affinity (Ka = 1052). This thesis outlines our attempts to synthesize an artificial siderophore, which incorporates a signaling group to help monitor the uptake of ferric ions. The artificial siderophore is a tripodal molecular receptor synthesized in a five-step procedure with a proposed final sixth step. Rhodamine 6G azide (95.0% yield) was formed from rhodamine 6G and the synthesis of 2-azidoethanamine was modified from the literature. The tripodal arm portion of the sensor was successfully synthesized by protecting the catechol of 2,3-dihydroxybenzaldehyde to form 3-formyl-1,2-phenylene dimethanesulfonate (98.8% yield). The reduction …

A Synthesis And Analysis Of Anhydrous Hydroxide Ion Conducting Polymer Electrolytes, Stanton Heydinger

Honors Theses

This project investigates the synthesis and physical properties of polyethylene glycol monomethyl ether (MePEGn where n=3 or 7) based polymer electrolytes. The two polymer electrolytes explored in the experiments were designed from two different MePEG chains that varied in their overall length and degree of polymerization. The first MePEG backbone contained three polymerized ethoxy groups and the second contained seven. Both MePEGn polymers were modified by substituting an imidazolium group in place of the alcohol functional group at the end of the PEG chain. This modification was made to create a polymer electrolyte with an attached positive charge that could …

Blocking Recombinations In Dscs Through Mgo And Pfts Surface Treatments, Kayla Foell

Honors Theses

High voltage dye-sensitized solar cells (DSCs) are becoming novel sources in the production of various fuel precursors, such as carbon monoxide and hydrogen, by powering carbon dioxide reduction, water oxidation, and proton reduction catalysts via sunlight. An important task in order to increase overall efficiency of DSC devices is to minimize recombination (electron flow in an undesirable direction) while increasing photovoltage. Surface treatment modifications can be applied to the TiO2 electrodes within DSC devices in an effort to block recombination without negatively effecting the other device performance metrics: fill factor (FF), short-circuit current density (Jsc), and open-circuit photovoltage (Voc). In …

Theoretical And Experimental Vibrational Modes Of The Borane Pyridine Complex, Benjamin Stratton

Honors Theses

Benjamin Wade Stratton: Theoretical and Experimental Vibrational Modes of the Borane Pyridine Complex (Under the direction of Dr. Nathan Hammer) The Borane Pyridine complex is a molecule that contains a dative bond between the boron and nitrogen atoms. A dative bond is a type of covalent bonding that occurs when both electrons come from the same atom. The B-N bond has been studied in several other molecules such as ammonia borane and determining the frequency at which this bond vibrates has been a topic of interest studied in these molecules as well as several others. This complex has another factor …

Structures, Energetics, And Vibrational Frequencies Of Microhydrated Hexafluorophosphate, Pf6−(H2o)N=1,2 From Dft And Ab Initio Computations, Yasmeen Abdo

Honors Theses

This study systematically examines an anion commonly used in room temperature ionic liquids, hexafluorophosphate PF6−, and its non-covalent interactions with up to two explicit water molecules (PF6 − (H2 O)n where n = 1, 2). Initial low-energy configurations are identified via a set of relaxed angular scans across the edges and faces of the PF6− octahedron using the global hybrid M06-2X density functional with a triple-ζ correlation consistent basis set augmented with diffuse functions on all non- hydrogen atoms (cc-pVTZ for H and aug-cc-pVTZ for P, O, F; denoted haTZ). Full geometry optimizations are performed on these initial structures using …

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. …

Preparation Of Organometallic Cobalt(Iii) Complexes Containing Bidentate Chiral Amine Ligands As Potential Transfer Hydrogenation Catalysts, Luccas C. Do Carmo

Honors Theses

Mixed coordination sphere cobalt(III) complexes containing a chiral bidentate amine ligand and an organic carbocyclic ligand have been prepared and characterized. The integration of this mixed ligand environment involving an organometallic and Werner-type ligand along with the earth abundant metal in a high oxidation state has the potential for interesting reactivity. Complexes of the type [Co(CpR)(X-DPEN)(I)](I), where CpR = cyclopentadienyl (Cp, R = H) or pentamethylcyclopentadienyl (Cp*, R = Me) and X = meso-1,2-, 1R,2R-, and 1S,2S-, have been prepared by ligand substitution from [Co(CpR)(I)2(CO)] with 1,2-diphenyletheylenediamine (DPEN). The outer sphere iodide is readily exchangeable with sodium tetrakis[3,5-bis(trifluoromethyl)phenyl]borate (NaBArF) or …

Theoretical Studies Of Naphthoquinone Reactivity Toward Amines, Kevin Lee

Honors Theses

Quinones are a class of organic compounds containing a six-membered unsaturated cyclic ring with two carbonyl groups and are biologically relevant due to their ability to participate in redox reactions. Experiments have showed that quinones can induce protein modifications including oligomerization and polymerization by binding to proteins. To complement these experimental studies, theoretical studies of naphthoquinone reactivity toward an amino group were conducted. The reactions between three naphthoquinones, 1,2-naphthoquinone (ONQ), 1,4-naphthoquinone (PNQ), and 2-hydroxy-1,4-naphthoquinone (HNQ), and methylamine, a N-containing nucleophile, were investigated. For each naphthoquinone, the first step of both 1,2- and 1,4-additions at all possible C=O positions were examined. …

Active Colloid Behavior Exhibiting Soft-Sphere Characteristics For Non-Newtonian Solvent, Courtney Baier

Honors Theses

The purpose of analyzing soft-sphere Brownian particles with varying velocities and densities is to be able to predict their interaction behavior once a force has been applied. The particles portray different behaviors depending on if the particles are passive or active Brownian particles. The data studied was collected from simulations, and there are no attractive forces involved in the particles’ interactions. Mean square displacement graphs, radial distribution graphs, structure factor graphs, and viscosity as a function of density and velocity were used to examine and compare the data generated. Experimental data was analyzed by a program to be interpreted into …

Best Organic Chemistry Practices In The Midwest, Claire Van Der Bosch

Honors Theses

Organic Chemistry is a gateway course to a handful of courses in higher chemical education. Unfortunately, it is notorious for its high-fail, high-withdrawal, and high-drop rate and has a reputation for being time-consuming, with difficult concepts that are oftentimes new to students. It is often taught in a two-semester sequence, with the courses named Organic I and Organic II, and both courses have a lab component. At Western Michigan University, the fail rate for these two courses are 53.5% and 36.9%, respectively. Most higher education institutions are certified with the American Chemical Society (ACS) and given a skeleton of a …

The Effects Of Climate Change And Forest Disturbances On Terpene Production Of White Pine (Pinus Strobus) And Red Pine (Pinus Resinosa) In Northern Michigan, Troy Dehagen

Honors Theses

The secondary impacts that climate change may have on the interactions between forests and the atmosphere through forest disturbances is of increasing interest as the climate continues to change. Anthropogenic climate change, which is a direct result of coal and fossil fuel emissions, is likely to impact forest ecology through increased temperatures and extreme precipitation events, thus increasing the frequency and severity of climate-induced forest disturbances. Forest disturbances may have a secondary impact on the production and emission of biogenic volatile organic compounds (BVOC) within forests. In the presence of oxides of nitrogen (NO_x) produced from fossil fuel …

Design And Synthesis Of A Novel Lsoxazoline As A Potential Pam-Agonist, Josselyn Roosenberg

Honors Theses

Progression of Alzheimer's disease is associated with a loss of Ml receptor activation in the brain. However, a lack of clinical success following attempts to activate the Ml receptor at the orthosteric site has contributed to a transition towards the allosteric pocket of the receptor. Here, positive allosteric modulators (PAMs) interact to potentiate the acetylcholine response. Recent research proposes that optimization of PAM activity at the expense of intrinsic agonism may posit a means to limit adverse side effects. Therefore, this project proposes a design and synthesis of a novel isoxazoline as a potent PAM agent with weak intrinsic agonism.

Analysis Of Dl-Amino Acid Ratios In Eggshells Using Reverse Phase-High Pressure Liquid Chromatography, Gergana Milkova

Honors Theses

HPLC methodology was developed to determine the concentrations and ratios of D to L amino acids in emu and ostrich eggshells treated with heat at different temperatures . We aimed to determine an internal standard and how ratios were affected under different conditions. An HPLC method was determined that gave consistent retention times and satisfactory enantioseparation . Calibration curves for each amino acid were developed from single and multi-amino acid containing dilution series producing a model that most closely replicates the eggshell-extracted amino acids.