Chemistry Commons^™

Fluorescent Lifetimes Of Oils And Oil Distillates In Artificial Seawater, Warren J. De Bruyn, Aaron Harrison, Emma Kocik, Dhivya Manickam, Ethan Truong, Catherine D. Clark

Chemistry Faculty and Staff Publications

Supporting data associated with a study of the fluorescent lifetimes of eleven oil and oil distillates in artificial seawater are given. The table is a list of the oil and oil distillate names along with the associated sample numbers used in this study and their API densities.

The excel data file contains lifetimes as a function of emission wavelength for different oils and oil products shown by sample number. The lifetimes were measured with a Horiba DeltaFlex Lifetime System that uses pulsed diode light sources. There is a separate sheet for each excitation source: 268, 285 and 348 nm. Lifetimes …

Blood Coagulation Factor Ix: Purification, Activation, Crystallization, Juliet Mcgill

WWU Honors College Senior Projects

This paper presents readers with an optimized procedure for the purification, activation, and crystallization of selected blood coagulation Factor IX double mutant (FIX_2). Through the completion of this work, we aim to enhance future biochemical and structural studies by providing an easier means for the FIX_2 production, in order to increase understanding of the protein’s function within the blood coagulation cascade. The initiation of the blood coagulation cascade is brought on by activation of inactive Factor VIII (FVIII) protein though contact with tissue factor, the FVIII protein then binds to an activated platelet surface where it must wait for its …

Supporting Data For Impact Of The Macrophyte Nymphaea Odorata (Lily Pads) On Dissolved Organic Matter (Dom) In A Lake, Kyle Juetten, Warren J. De Bruyn, Zachary Landram, Aaron Harrison, Angela Strecker, Catherine D. Clark

Chemistry Faculty and Staff Publications

(Files are available for download below.)

This is supporting data for a publication on the role of lily pads in contributing to the dissolved organic matter pool in Lake Louise, a small lake in the Pacific Northwest region of the USA. Specifically, this data includes the absorbance and fluorescence spectra of the Lake Louise water samples (taken weekly over the course of 2018). These files include large spreadsheets with raw and corrected absorbance and fluorescence intensity data as a function of wavelength, as well as the raw and corrected absorbance and fluorescence 3D excitation-emission matrix spectra (EEMs). These files are …

Investigations On The Active Catalyst In Pd Catalyzed Organic Reactions, Riley Mcgraw

WWU Honors College Senior Projects

Cross coupling and C-H functionalization reactions are valuable tools in the synthesis of pharmaceuticals, natural products, fine chemicals, and electronics. Molecular precatalysts are frequently used in both reactions but because the reactions use conditions like those employed in intentional preparation of nanoparticles, the presence of nanoparticles is highly likely for both systems. In the case of the cross-coupling reaction, nanoparticles have been shown to have catalytic relevance, but C-H functionalization reactions are widely thought to occur by means of a homogenous catalyst. To better understand the state of the active catalyst, a method of homogeneity analysis by centrifuge is proposed. …

Synthesis And Characterization Of Hydroxy-Functionalized Copper Indium Disulfide Quantum Dots, Julia Schexnayder

WWU Honors College Senior Projects

Quantum dots offer tunable electronic and optical properties due to the quantum confinement effect, making them desirable for various applications. However, their native hydrophobic form requires surface chemistry modification for certain applications. This research explores the method of ligand exchange using 11-mercapto-1-undecanol for improving the stability of copper indium disulfide (CIS) quantum dot (QD) nanoparticles in polar environments. The effects of this ligand exchange on QD chemical composition, optical properties, hydroxy-reactivity, and hydrodynamic radius are characterized. Analysis of characterization results indicates successful surface modification through hydroxyfunctionalization, as confirmed by 1H-NMR and IR spectroscopy. The desired optical properties of the QDs …

Class A Sortases: Structures And Alternative Substrate Binding And Cleavage, Brandon Vogel

WWU Graduate School Collection

Sortases, consisting of classes A-F, are cysteine transpeptidases found in the cell wall of Gram-positive bacteria. They play a crucial role in ligating proteins to the cell wall that are responsible for cell adhesion, immune evasion, host cell invasion, and nutrient acquisition through a transpeptidation reaction. Consequently, they are an attractive therapeutic target. Class A sortases are also utilized in protein engineering applications such as sortase-mediated ligations and sortagging. Despite extensive research in the past two decades, gaps persist in understanding how class A sortases recognize their substrates, primarily due to a lack of structural information on sortases non-covalently bound …

Activity And Selectivity Of Class B Sortase Enzymes, Sophie Jackson

WWU Graduate School Collection

Gram-positive bacteria attach many proteins to their cell walls via sortase enzymes. Sortases are cysteine transpeptidases and are grouped into 6 classes, A-F. Sortase enzymes, particularly sortase A from Staphylococcus aureus, have been used extensively for in vitro protein ligations. Here, we investigate substrate-binding in sortase A from Streptococcus pyogenes. In addition, class B sortases are typically overlooked for research and development due to low in vitro activity and incomplete knowledge of substrate specificity. Here, we investigate the activity of class B sortases from Bacillus anthracis (baSrtB), Clostridioides difficile (cdSrtB), Listeria monocytogenes (lmSrtB), and Staphylococcus aureus (saSrtB). Of these, …

Selectivity And Structure Of Chimeric Loop Swaps In Sh2 Domains, Sarah N. Smith

WWU Graduate School Collection

SH2 (Src Homology 2) domains are protein domains that bind to phosphorylated tyrosine residues within cell signaling cascades. They have been found to play a role in certain cancers and immunological disorders. Despite their importance in cell signaling and medical relevance, the structural basis of the various selectivity classes of SH2 domains is only partially understood. Previous research found that the EF and BG loops of the domains contribute to forming the peptide binding pocket, and thus impact their selectivity. To further understand the role of these loops in selectivity, we engineered chimeric SH2 domains by swapping the EF and …

Tuned Gold Layer Growth Onto Plasmonic Sensing Silver Nanocubes Via Synthetic Control Of Reduction Potentials., Nicolas Hall

WWU Graduate School Collection

Metallic nanoparticles (mNPs) are commonly employed as sensors and detection tools due to their unique plasmonic properties. Silver NPs exhibit these properties in heightened capacity in comparison to other metals. However, Ag NPs are susceptible to oxidation, degradation over time and are biotoxic. These issues are commonly addressed by creating Ag-alloy NPs or by adding additional layers to Ag NPs. This work improves upon these methods by focusing on the growth of an Au layer onto Ag nanocubes (AgNCs), resulting in a layered Au-Ag NC (Au@AgNC). The resulting morphology of these Au@AgNCs are dependent on the synthetic pathway taken and …

Kinetic Analysis Of The Grafting Thermal Ring-Opening Polymerization Reaction Of Benzoxazine With Sulfonyl-Ester Functionalized Polymers, Tawakalt Adetoun Akinjobi

WWU Graduate School Collection

This project will explore the fundamental mechanistic details and kinetics of a grafting polymerization reaction that occurs with blended benzoxazine monomers (or resins) and polymers functionalized with reactive sulfonyl-ester leaving groups [such as tosylate (Ts), nosylate (Ns) or mesylate (Ms) groups]. Isoconversional analysis (ICA) is one of the most important methods for establishing the kinetics of the complex reactions associated with curing thermosets. In the case of ICA, activation energy is measured at fixed values of reaction conversion.²⁶ For thermosets the data are typically based on differential scanning calorimetry (DSC). The combinatorial approach not only provides uncertainty associated with …

Stereoselective Synthesis Of (+)- And (-)-Cananodine, Haley Holliday

WWU Graduate School Collection

Natural products are an important class of molecules utilized in traditional medicine and inspire drug design in medicinal chemistry. Cananga odorata, a tree commonly known as ylang-ylang, contains natural products known to positively benefit health, and specifically promote liver health. One alkaloid isolated from Cananga odorata, cananodine, possesses cytotoxic properties, specifically against hepatocellular carcinoma (HCC). HCC is the most common type of liver cancer, with one million diagnoses projected by 2025 globally. Cananodine is a member of the guaipyridine alkaloid family, a class of compounds that feature a substituted pyridine bonded to a seven-membered ring. The first enantiomer …

Structural, Mutational, And Kinetic Characterization Of Ura4, An Isocytosine Deaminase, Ashlee Hoffman

WWU Graduate School Collection

Cytosine Deaminases (CD) are a class of enzymes found in prokaryotes and fungi that have been studied in the past due to their ability to deaminate the prodrug 5-fluorocytosine (5-FC) producing 5-fluorouracil (5-FU). 5-FU is a common anti-cancer drug that can inhibit DNA synthesis leading to cancer cell death. 5-fluorocytosine can interact with digestive bacteria leading to unwanted side effects for cancer patients. Isocytosine Deaminases (ICD) are enzymes that are of interest in the treatment of cancers using Gene Directed Enzyme Prodrug Therapy (GDEPT). ICDs can deaminate the prodrug 5-fluoroisocytosine (5-FIC) also producing the drug 5-FU.  5-FIC will likely not …

Development Of Silk Microparticles Capable Of Bioluminescence, Monique Berg

WWU Graduate School Collection

The use of silk microparticles (µPs) as drug delivery devices has gained attention due to slow degradation properties, mild preparation conditions, and advantageous biocompatibility. However, little research has been done on where these particles go once injected. To expand these studies, the goal for this work is to create bioluminescent silk µPs that can be tracked in vivo. Here several methods are demonstrated for preparing bioluminescent silk µPs containing Nanoluciferase (NLuc) and/or its substrate furimazine (FZ). In this study, silk µPs were formed using a salting-out procedure. The first method involved non-specific adsorption of NLuc and non-specific adsorption of FZ …

New Synthetic Methods Based On Silicon-Tethered Nucleophilic Addition Reactions, Alexie W. Clover

WWU Graduate School Collection

With the recent discovery of an iodine mediated rearrangement of diallylsilanes, we set out to investigate a similar fluorine mediated rearrangement, aimed at introducing a new method for synthesizing organofluorine compounds. Interest in incorporating fluorine into organic molecules has grown significantly in recent years, primarily for medicinal applications. Since certain fluorination methods require the use of mCPBA, a common epoxidizing reagent, control experiments were performed on the reaction of several diallylsilanes with mCPBA, anticipating that a competing epoxidation of the diallylsilanes might occur. It was found that the formation of the hydroxy ester occurred through a regioselective epoxide opening from …

Regio- And Diastereoselective Samarium-Mediated Allylic Sulfone Reductions, Cody Schwans

WWU Graduate School Collection

A series of allylic sulfones were synthesized containing a stereodirecting group and chelating element and subjected to samarium diiodide reductions in the presence of a proton donor. The resulting products could be obtained with high regioselectivity (no less than 95:5) and high diastereoselectivity (>10:1) that correlated with the size of the stereodirecting group. A mechanism is proposed that includes loss of the sulfone and formation of a chelated organosamarium intermediate followed by intramolecular protonation by a samarium-bound proton source. In this way, both the regioselectivity and absolute stereochemistry of the resulting products are explained.

Using Qm/Mm Methods To Explore Sortase Enzyme Intermediates, Kinetics, And Stability, Kyle Whitham

WWU Graduate School Collection

Biochemistry has seen advancements in methods and understanding of the inner workings of proteins, yet biochemists struggle to see real time reaction pathways of protein intermediates. This is where computational chemistry comes in and fills in the holes in knowledge through the use of Quantum Mechanical (QM) models. QM chemistry alone does not give results in a reasonable timescale to predict protein chemistry in a reasonable amount of time. Computational chemistry methods such as Quantum mechanical (QM)/ Molecular Mechanical (MM) (QM/MM), allow us to split the in-silico system into two regions that utilize a fast MM force field region and …

Structural And Thermodynamic Studies Of Antibody Binding To Blood Coagulation Factor Viii, Jordan Vaughan

WWU Graduate School Collection

Blood coagulation factor VIII (FVIII) is a 2332 residue glycoprotein expressed in endothelial cells and plays a significant role in the formation of blood clots. Structurally, FVIII’s domains are organized as A1-A2-B-A3-C1-C2. The absence or deficiency of FVIII in the bloodstream gives rise to Hemophilia A; an X-linked bleeding disorder affecting 1 in 5000 males worldwide. To combat this deficiency, patients undergo FVIII replacement therapy which involves frequent injections of FVIII into the bloodstream in the form of blood, plasma, or protein concentrates. Although effective, this treatment commonly results in the development of anti-FVIII inhibitory antibodies in approximately 20-30% of …

Supporting Information For Chromophoric Dissolved Organic Matter (Cdom) Across An Elevational Gradient From Sea Level To Mountain Lakes In The Pacific Northwest, Kyle Juetten, Angela L. Strecker, Aaron Harrison, Zachary Landram, Warren J. De Bruyn, Catherine D. Clark

Chemistry Faculty and Staff Publications

This dataset is in support of Juetten et al., which has been submitted to the Journal of Geophysical Research Biogeosciences for consideration for publication. Chromophoric dissolved organic matter (CDOM) in lakes across elevation gradients is a complex function of topography, climate, vegetation coverage, land use, and lake properties. To examine sources and processing of CDOM from sea level to mountain lakes (3 to 1574 m), we measured CDOM optical properties, lake characteristics, and water quality parameters in 62 freshwater lakes in the Pacific Northwest, USA. Higher elevation lakes had lower dissolved organic carbon (DOC) and absorbance. These lakes had higher …

Synthetic Development Of Carbodiimide-Containing Polymers As Precursors To Guanidine-Based Covalent Adaptable Networks, Hayden Houck

WWU Honors College Senior Projects

Covalent adaptable networks (CANs) are a newly emerging class of polymers that uniquely bridge the gap between traditional thermosets and thermoplastics. The distinguishing characteristic of these polymer networks is that they contain reversible crosslink bonds that allows these materials to be recycled. Two of the currently best-understood CAN systems include those based on Diels-Alder1 and transesterification2 reactions, both of which involve dissociative exchange mechanisms. Our group aimed to create a novel CAN system based on the thermal guanidine metathesis (TGM) reaction3 by using a guanidine functional group as a crosslinker. In order to create a guanidine-crosslinked network, our research took …

Chemical And Physical Tailoring Of Guanidine-Based Covalent Adaptable Networks, Kate A. Mcconnell, Michael B. Larsen

WWU Honors College Senior Projects

We present the synthesis of two different guanidine-based CAN materials which, unlike traditional thermoset polymer networks, can undergo an exchange reaction called thermal guanidine metathesis (TGM) and be reprocessed. Thermosets, which are polymer networks characterized by permanent covalent crosslinks between chains, have a myriad of commercial applications. However, a major drawback to thermosets is their inability to be reprocessed. To develop a more sustainable thermoset-like material, CANs exhibit breaking and reforming of crosslinks under certain conditions that enable reprocessing. To elucidate the effects of varied guanidine structure on the rheological and mechanical properties of these dissociative CANs, we synthesized two …

Blood Coagulation Factor Ix: Purification, Isolation, Activation, Alex Macneil

WWU Honors College Senior Projects

This paper attempts to provide an optimized strategy for the purification, activation, and isolation of blood coagulation Factor IX mutants. The goal of this work is to enable future biochemical and structural studies of Factor IX to a gain a better understanding of the structural-functional role this protein plays in the blood coagulation cascade. The orchestration and amplification of the blood coagulation cascade requires the binding of Factor VIII (FVIII) to an activated platelet surface, where it serves as a cofactor to a serine protease, Factor IX (FIX). Factor IX circulates the bloodstream as a catalytically silent multidomain protein1. Like …

Nickel Phosphide Photothermal Catalyst Development For Co2-Derived Solar Fuels, Hannah K. Hennig

WWU Graduate School Collection

Converting CO2 to CO via the photocatalyzed reverse water gas shift (RWGS) reaction satisfies a critical step in the production of C1 solar fuels (e.g., CH4, CH3OH) and longer hydrocarbons via the Fischer-Tropsch process. Oxide-supported nickel phosphides (NixPy) are an emerging class of photocatalysts with a number of accessible crystalline phases. Additionally, the broad-spectrum absorption of NixPy materials affords photo-induced local heating to drive catalytic processes at mild operating temperatures. In the current project, NixPy with different P/Ni molar ratios were investigated as RWGS catalysts on two types of support materials: 1) silica (SiO2) as a relatively inert support, and …

The Curious Case Of Concept: A Nation-Wide Survey Of Faculty Beliefs About Quantum Mechanics Concept Inventories Uncovers New Details Regarding Physical Chemistry Experts’ Understanding Of Conceptual Knowledge., Matt Smiley

WWU Graduate School Collection

According to the chemistry education literature, physical chemistry educators strongly believe developing students’ conceptual understanding is important; however, the vast majority of educators (84%) were found to assess students predominantly on mathematical knowledge. To better serve students of physical chemistry, the cause of misalignment between stated learning goals and assessment needs to be elucidated. To this end, the Faculty Perceptions of Published Quantum Mechanics Assessments Survey (FPPQMA) was developed. The FPPQMA is designed to probe physical chemistry educators’ beliefs regarding the dichotomy between conceptual and mathematical knowledge. In addition to free response questions that ask respondents to define conceptual and …

Blood Replacement Therapy By Generation Of Polymeric Recombinant Hemoglobin Using “Click Chemistry” And Circular Tandem Repeat Proteins, Johanna Hamilton Urbach

WWU Graduate School Collection

Our work with hemoglobin-based oxygen carriers (HBOCs) is focused on developing a hemoglobin (Hb) polymer that can be used as a blood replacement in critical care at an affordable cost. For medical use, the Hb must be polymeric since cell-free Hb has multiple adverse side effects when it is not encapsulated in a red blood cell. These include kidney damage and heme-induced toxicity, which is due to cell-free Hb’s ability to extravasate. Challenges in making HBOCs, that have been observed in the past, are low protein expression yields and heterogeneity in polymeric Hb products produced by chemical crosslinking. In conducting …

Covalent Modifications As Targets And Means For Research In Intrinsically Disordered Proteins, Derek Mccaffery

WWU Graduate School Collection

A reported 33% of eukaryotic proteins are predicted to contain intrinsically disordered regions (IDRs) over 30 residues in length. IDRs are regions of protein which natively exist in an unfolded conformation. Due to their highly dynamic nature, many common methods of inquiry such as crystallography and NMR can be thwarted. As a result, valuable analysis such as probing function, dynamics and binding interfaces are unable to be performed. To minimize these problems, researchers typically study shorter IDRs. We probed fragments of plant protein villin 4 (VLN4) for covalent modifications to explore its regulation and degradation. Disordered regions of proteins have …

Sortase-Mediated Ligation To Investigate Large Idr-Containing Cytoskeletal Regulators, Melissa Oueld Es Cheikh

WWU Graduate School Collection

About 43% of eukaryotic proteins contain intrinsically disordered regions (IDRs) of 40 residues or longer. These proteins modulate key cellular functions such as transcription, translation, and signal transduction. Despite their vital roles, little is known about the properties of large disordered proteins due to the difficulties encountered studying them. Solution nuclear magnetic resonance (NMR) spectroscopy is a unique tool allowing for their analysis but traditionally requires uniform protein labeling with 15N and 13C isotopesresulting in convoluted spectra which obscure any meaningful information on their structures and interactions. To remedy this issue, we aim at developing a procedure to segmentally label …

Synthesis And Characterization Of Plga Capped Gold Nanoparticles For Use In Cancer Therapeutics, Tara Chin

WWU Graduate School Collection

This research project aims to create gold nanoparticles (AuNPs) functionalized with PLGA (poly(lactic co-glycolic acid)) polymers for generating reactive oxygen species (ROS) by way of Xray irradiation for use in cancer therapies. The current methods of cancer treatment rely on drugs and/or chemotherapy depending on the type of cancer present; these methods come with varying success rates which are also dependent on how severe the condition has become (the lower the severity, the higher chance of success). The latest method of cancer treatment is proton beam radiation therapy (PBRT) which can be specific in its targeting but not very cost …

Structural Characterization Of Factor Viii-Inhibitor Complexes And Factor Viii Lipid Binding Mechanics, Corbin Mitchell

WWU Graduate School Collection

Blood coagulation factor VIII (FVIII) is a crucial protein cofactor within the blood coagulation cascade and facilitates the proteolytic activation of factor X by activated factor IX. During coagulation FVIII is activated and binds, via its C1 and C2 domains, to activated platelet membranes coordinated by interactions with exposed phosphatidylserine on the membrane surface. A deficiency of functional FVIII within a patient's bloodstream leads to the blood disorder hemophilia A, which results in prolonged bleeding episodes. Current treatment for hemophilia A relies on FVIII replacement therapy via the injection of exogenous FVIII. The main complication which arises from FVIII replacement …

Indium Oxide-Based Catalysts For Solar Fuel Generation, Ryan Hagmann

WWU Honors College Senior Projects

The need to pursue renewable, carbon neutral forms of energy has led to a far reaching-research effort to generate and store solar energy. It has been shown that indium oxide-based catalysts have the potential to reduce carbon dioxide to carbon monoxide or even continue reduction to methanol. Recent advances and current challenges in further developing indium oxide catalysis as a means of producing a sustainable liquid fuel supply will be addressed. This project will give an overview of the research in indium oxide catalysts for solar fuels generation and the immediate relevance of recent work within the Bussell Research Group …

Structure Of Blood Coagulation Factor Viii In Complex With Anti-C2 Domain Inhibitory Antibody, Estelle K. Ronayne, Shaun C. Peters, Joseph Gish, Celena Wilson, H. Trent Spencer, Christopher B. Doering, Pete Lollar, P. Clint Spiegel Jr., Kenneth C. Childers

WWU Honors College Senior Projects

Factor VIII (fVIII) is a procoagulant protein that binds to activated factor IX (fIXa) on platelet surfaces to form the intrinsic tenase complex. Due to the high immunogenicity of fVIII, generation of antibody inhibitors is a common occurrence in patients during hemophilia A treatment and spontaneously occurs in acquired hemophilia A patients. Non-classical antibody inhibitors, which block fVIII activation by thrombin and formation of the tenase complex, are the most common anti-C2 domain pathogenic inhibitors in hemophilia A murine models and have been identified in patient plasmas. In this study, we report on the X-ray crystal structure of a B …