Chemistry Commons^™

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 …

Redox-Active Coordination Complexes For Small Molecule Activation With Environmental Applications, Hanalei Lewine

WWU Honors College Senior Projects

Nitrate and nitrate are harmful pollutants resulting from the overuse of nitrogen fertilizers in agriculture. The pyridinediimine ligand scaffold with a hemilabile pendant phosphine shows reactivity towards these species to selectively reduce them to NO on a mononitrosyl iron complex (MNIC). Experimental work is supported by DFT broken symmetry calculations.

Insulin: Roles And Functions In Biochemistry And U.S. Healthcare, Mia Brinkley

WWU Honors College Senior Projects

I will be researching insulin through a variety of academic perspectives, utilizing both my biochemistry major and history minor, as well as my passion for healthcare and goals for my future career in medicine. I will begin by researching the history of the discovery of the hormone and the start of its use as a drug for diabetes. I will go into the biochemistry of the insulin protein and its interaction with the insulin receptor protein. I will then go into the problems it poses for those receiving it, regarding cost and access to low-income populations in the US. I …

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 …

Spike Protein Antibody Interactions Elicited By The Sars-Cov-2 Vaccine, Meghan Quinlan

WWU Honors College Senior Projects

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) arose as a novel virus in Wuhan China in December 2019. Then, as it rapidly spread across the world, it was declared a global health emergency by the World Health Organization in March 2020. SARS-CoV-2, the causative agent of coronavirus disease 2019 (COVID-19), has dramatically disrupted both normal life and the economy. In the past year and a half, there have been over 175 million cases globally1 (as of June 15, 2021). High death rates, disruption to education, and widespread job loss has necessitated the desperate need for a vaccine against SARS-CoV-2. A …

Multifunctional Polymer-Nanoparticle Composites For Surface-Enhanced Raman Scattering Applications, Aliandra E. Pierce, Samantha A. Patrick, Steven R. Emory

WWU Honors College Senior Projects

To create a multifunctional nanoparticle-based optical sensor, a pH-responsive microgel consisting of 20% polystyrene (PS) and 80% poly(2-vinylpyridine) (P2VP) surface-coated with gold nanoparticle (NP) seeds was synthesized. The pH-responsive microgel serves as a size-tunable scaffold for the assembly of the surface-enhanced Raman scatter active (SERS-active) metal, gold. The random copolymer of PS and P2VP (PS20P2VP80) is sterically stabilized by poly(ethyleneglycol) methyl ether methacrylate (PEGMA) and lightly crosslinked with divinylbenzene (DVB) to allow for reversible pH-swelling over multiple cycles of acid-base titration. The ability to swell and de-swell in response to changes in pH allows for the tuning of gold NP …

Demystifying Denitrification: Coordination Complexes Give Valuable Insight Into The Reduction Of Nitrogen Oxides, Walker R. Marks

WWU Graduate School Collection

Increasing human population is driving the need to produce increasing amounts of food without the ability to dramatically increase farmland area. This has been accomplished by the application of increasing amounts of nitrogen containing fertilizers onto croplands. Nitrogen fertilizer overuse is causing imbalance in the natural nitrogen cycle via excessive amounts of high oxidation-state nitrogen entering both the atmosphere and aquatic ecosystems, which are major contributors to global warming and environmental damage. There is a need to explore synthetic systems which are capable of the reduction of these pollutants through pathways such as denitrification. This thesis will explore the functionalization …

Enhancing Plasmonic Nanomaterials: Colorimetric Sensing And Sers, John Crockett

WWU Graduate School Collection

Nanomaterials, materials with at least one dimension on the nanoscale have become an area of extreme scientific interest due to their many unique properties with applications in catalysis, optics, and sensing, just to name a few. Metal nanoparticles are particularly interesting because of the interactions between light and surface electrons in the metal’s conduction band, called localized surface plasmons. In anisotropic metal nanoparticles these plasmons are especially exciting due to the highly responsive quality of the plasmonic resonance associated with their varied nano dimensions. Gold nanorods and nano dendrites in particular exhibit electromagnetic effects which are specifically associated to the …

Structural And Mutational Characterization Of The Blood Coagulation Factor Viii C Domain Lipid Binding Interface, Shaun C. Peters

WWU Graduate School Collection

Blood coagulation factor VIII (fVIII) functions as a cofactor in the blood coagulation cascade for proteolytic activation of factor X by factor IXa. During coagulation, fVIII is activated and subsequently binds to activated platelet surfaces by coordination of the fVIII C1 and C2 domains to the exposed phosphatidylserine of activated platelet membranes. Structural and mutational studies have suggested that both hydrophobic and electrostatic interactions occur between the two tandem C domains and activated lipid surfaces, but models of C domain phospholipid binding propose conflicting regions that directly interact with the membrane surface. This thesis reports the determination of the molecular …

Engineering Segmentally Labeled Intrinsically Disordered Proteins, Erin Rosenkranz

WWU Graduate School Collection

It has long been accepted that a protein’s fold informs its function, but for the vital proteins that don’t adopt one specified fold, this is uninformative. Intrinsically disordered proteins have non-folded regions (IDRs) in their native functional state, which make up 30% of eukaryotic proteins, perform vital cellular processes and contribute to a multitude of disease states. Yet, IDR’s function, interactions and dynamics remain unknown due to their unstable, dynamic, lengthy and solvent-exposed nature. This, along with their tendency for insolubility and aggregation provide formidable challenges to not only their analysis, but their purification, requiring lengthy optimizations. NMR is valuable …

Signaling And Trafficking In Choanoflagellates And Humans: A Study Of Conserved Peptide-Binding Domains, Haley Wofford

WWU Graduate School Collection

Many crucial cellular processes are regulated by signaling and trafficking pathways, which are largely dependent on protein interactions in the cell. These networks are thought to play a crucial role in the evolution of multicellular organisms from their unicellular ancestors. Choanoflagellates are unicellular organisms that can adopt a multicellular state, called a rosette. Though they evolved independently from and prior to the diversification of metazoans, they are the closest extant nonmetazoan ancestor to animals, making them a compelling model for the study of early multicellularity. Here, we look at two structurally conserved peptide-binding domains that both play important roles in …

Synthesis Of Guaipyridine Alkaloids Rupestines C, D And K With Studies Toward The Synthesis Of Rupestines B, J, L And M, Briana J. Mulligan

WWU Graduate School Collection

Hepatocellular carcinoma (HCC) is a type of primary liver cancer that is responsible for roughly 700,000 deaths around the world each year. While invasive treatment methods for HCC have proven to be limited, there are drug treatments available that show promising features. The structural elements of these drugs have given rise to an interest in guaipyridine alkaloids, specifically a family of naturally occurring guaipyridine alkaloids known as the rupestines. The rupestines have previously been isolated from the flowers of the plant Artemisia rupestris. This plant has been known for its reported antitumor, antiviral and antibacterial properties when used in traditional …

Pyridinediimine Complexes With Coordination Sphere Interactions Relevant To Copper And Non-Heme Iron Enzymes, Pui Man Audrey Cheung

WWU Graduate School Collection

Primary and secondary coordination sphere interactions with proximal Brønsted-Lowry acid/base sites were investigated using a family of pyridinediimine (PDI) complexes. The PDI ligands used in this project could be easily prepared by the Schiff base reactions with commercially available diamines as proton relays. Upon activation, the pendant Bronsted site and accessible electrons were arranged in a single scaffold that allowed the transportation of both protons and electrons to occur.

Two new PDI complexes with morpholine and pyrrolidine derivatives were introduced to the pendant PDI family. Their proton dissociation constant in acetonitrile were 17.1 and 18.3, respectively. The PDI complexes were …

Computational Design Of Novel Materials For Solar Energy Conversion And Catalysis, Corey Teply

WWU Graduate School Collection

As synthetic chemists and materials scientists increasingly gain the ability to precisely arrange the atoms in solids, computation can provide guiding insight toward designing materials for a variety of applications. This work focuses on two distinct projects: 1) the use of biaxial strain in all crystallographic directions to tune the structural and electronic properties of perovskites for solar energy conversion, and 2) the extension of the concept of single-atom alloys to design stable motifs of multiple catalyst atoms on metal surfaces.

Perovskite solar cells have been shown to have band gap tunability when compressive or tensile-biaxial strain is enacted on …

Organic Crystal Nucleation In Ultrathin Liquid Films: Applications Of Computational And Experimental Methods For The Exploration Of Dynamic Spatial Relationships And Controlled Growth, Haley Doran

WWU Graduate School Collection

The advancement of semiconducting materials is paramount to the future of electronics. Organic semiconducting materials are of particular interest due to their significantly lower processing cost compared to traditional inorganic semiconducting materials, such as silicon. However, the present toolkit for solution-based controlled growth of polycrystalline thin films is lacking. Therefore, the purpose of this research is to build such a toolkit, wherein tunable parameter relationships of organic thin-film growth are evaluated and compared both experimentally and computationally. A multi-scale model has been developed, which combines mean field rate equations with a self-consistent treatment of the critical stable monomer cluster size, …

Extension Of Restricted Open-Shell Kohn-Sham Methodology To A Density-Functional Tight-Binding Framework, Reuben Szabo

WWU Graduate School Collection

The restricted open-shell Kohn-Sham (ROKS) approach for singlet excited states provides some advantages over the ∆-self-consistent-field (∆SCF) method, requiring only a single SCF procedure and avoiding the problem of variational collapse. While ROKS is a powerful tool for DFT, its application to density functional tight-binding (DFTB) could offer significant improvements in time complexity when compared to DFT, enabling excited-state simulations of extended molecular systems on longer timescales than ROKS. In this work we discuss the implementation of an RO-DFTB approach in the DFTB+ package, as well as its suitability for the study of organic dyes and photoactive compounds. For benchmarking, …

Implementation Of A Constraint And Configuration Interaction Methodology Into Density Functional Tight Binding, Gunnar J. Carlson

WWU Graduate School Collection

This research aims to implement a charge constraint in conjunction with a small configuration interaction scheme into a density-functional tight-binding (DFTB) method within the DFTB+ quantum mechanical software package. This method aims to model the electron transfer rate of chemical systems by calculating the electronic couplings between two constrained states more efficiently. Electronic couplings are directly proportional to electron transfer, making them important parameters to efficiently compute the optimal minimum or maximum of an electron transfer rate, for example, when screening chemical systems based on their ability as a conductor. Other methods such as constrained density-functional theory followed by a …

Synthesis And Reactions Of Medium-Ring Silyl Ethers, Inna A. Fomina

WWU Graduate School Collection

Olefin metathesis is a reaction that creates new carbon-carbon double bonds by rearranging two alkenes. The reaction has undergone significant development since its discovery in the 1950s, from first reports to new catalysts and industrial uses, culminating in the 2005 Nobel Prize in chemistry. Grubbs ruthenium-based catalysts are widely used for such reactions, including ring closing metathesis (RCM) that involves the rearrangement of two alkenes on a single molecule to form a ring. During the course of investigating RCM reactions to produce eight-membered ring silyl ethers, we observed double bond isomerization when using the second-generation Grubbs catalyst and the Hoveyda-Grubbs …

Exploring Biochemical Mechanisms With Hybrid Quantum Mechanics/Molecular Mechanics And Enhanced Sampling Methods, Edwin Enciso

WWU Graduate School Collection

In the field of molecular dynamics (MD), a long-standing issue is the time frame required in order to fully observe a chemical reaction. Enhanced sampling methods have been the primary way of overcoming this issue for the past 40 years. In this experiment our goal was to combine new and existing sampling methods in order to create an efficient and accurate way of retrieving kinetics data from simulations. In order to do this, we examined two test cases: the enzymes chorismate mutase and cytosine deaminase. We did this using hybrid quantum mechanics/molecular mechanics simulations coupled with enhanced sampling methods. The …

Structural Studies Of The Von Willebrand Factor D’ Domain And Its Binding Mechanism To Factor Viii, Ap Wang

WWU Graduate School Collection

Hemophilia A is an X-linked disorder that results in uncontrolled bleeding, which is caused by a lack of activity for blood coagulation factor VIII, an essential protein cofactor in the clotting cascade. Factor VIII consists of multiple domains, and binding disruptions between factor VIII and its circulatory partner, von Willebrand Factor, may cause von Willebrand disease. Von Willebrand Disease type 2N is an autosomal recessive disease, and it is caused by binding disruptions between the D’ domain (also known as TIL’E’) of von Willebrand Factor and a3 domain of factor VIII. A 2.9Å Cryoelectron microscopy structure of the FVIII:vWF complex …

Chemical Modification Of Silk Protein Via Palladium-Mediated Suzuki-Miyaura Reactions, Racine Santen

WWU Graduate School Collection

Suzuki-Miyaura cross-coupling reactions were used to modify the tyrosine residues on Bombyx mori silkworm silk proteins using a water-soluble palladium catalyst. Utilizing this cross-coupling reaction, molecules with specific functions can be introduced to silk in order to broaden the capabilities of silk proteins in biological systems. Model reactions using tyrosine derivatives were first screened to optimize reaction conditions. For these reactions, a variety of aryl boronic acids, solvents, buffers and temperature ranges were explored. Qualitative information on the reaction progress was collected via high performance liquid chromatography (HPLC), mass spectrometry (MS) and nuclear magnetic resonance (NMR). Reactions were then applied …