Chemistry Commons^™

Raw Nmr Data For Tripeptides, David J. Michaelis, Scott R. Burt, Mariur Rodriguez Moreno, Nye C. Johnson, Christopher B. Stewart, Mary L. Setelin, Adam X. Wayment, Braxton M. Felix

ScholarsArchive Data

This data set contains primary data for 50 tripeptides that were generated as part of an advanced undergraduate laboratory experience in solid phase peptide synthesis. The raw data can be processed sing NMR interpretation software and can be used as problems for exams and quizzes or as supplementary materials for a laboratory experience

Stemficohort1preinterviewdata, Rebecca L. Sansom, Bryn Stclair, Jamie Jensen, Richard West

ScholarsArchive Data

The science, technology, engineering, and mathematics faculty institute (STEMFI) is a National Science Foundation funded project designed to provide support, measurement, and training to BYU faculty developing their own student-centered curriculum.

This PDF file contains pre-institute participation interview data from the first cohort of faculty involved in the STEM faculty institute (2018).

Quantifying Protein Quality To Understand Protein Homeostasis (Supplemental Data), Hsien-Jung Lavender Lin

ScholarsArchive Data

This data set includes the supplementary data for chpaters 3 and 4 in the dissertation Quantifying Protein Quality to Understand Protein Homeostasis. It includes various excel worksheets that were used to generate the data reported in the dissertation. We make this data available to the public so anyone who wants to reproduce the results has the resources and access to other perspectives that weren't discussed in depth in the dissertation. Chapter 3 used mass-spectrometry to quantify the surface accessibility differences in human serum albumin (HSA)between patients with and without rheumatoid arthritis (RA). We found certain residues are less reactive …

The Regulation Of Atg9a-Mediated Aggrephagy By An Ulk1-Independent Atg13-Atg101 Complex, Joshua Youngs

Undergraduate Honors Theses

Aggrephagy, a type of autophagy, is an essential cellular process by which protein aggregates are collected and broken down in the lysosome. Protein aggregates are implicated in several diseases including Alzheimer’s disease, diabetes, and cancer. Here, we investigate the ATG13-ATG101 protein complex, a sub-complex of the canonical ULK1 complex whose regulatory role in aggrephagy is not completely understood. We also develop a protein fragment complementation (PFC) assay using the biotin ligase TurboID to study the functions of the ATG13-ATG101 complex with increased specificity. We demonstrate that ATG13 is required for optimal degradation of p62-ubiquitin condensates. We also show that a …

Encirclement Of Moving Targets Using Noisy Range And Bearing Measurements, Cammy Peterson, Puneet Jain, Randal Beard

Faculty Publications

This paper presents theoretically justified controllers that use relative range and bearing measurements to steer a team of autonomous vehicles, operating without inertial position information, to circular trajectories around a constant-acceleration, constant-velocity, or stationary target. An extended Kalman filter is used to improve the noisy relative measurements and estimate the velocity of the moving target. These estimated values are used in the control laws to encircle constant-velocity moving targets. Lyapunov techniques are utilized to show that the vehicle will converge to the desired circular formations. Additionally, cooperating vehicles are shown to converge to a circular formation with equal temporal spacing …

Sd2 Ptov1 Interactomics, Joshua Andersen

ScholarsArchive Data

PTOV1 interactome data

Sd3 Ptov1 Ptms, Joshua Andersen

ScholarsArchive Data

MS data on PTOV1 PTMs

Sd1 14-3-3 Interactome For Ptov1 Manuscript, Joshua Andersen

ScholarsArchive Data

14-3-3 interactome

Tp-5801 In Vitro Kinase Screen Data, Joshua Andersen

ScholarsArchive Data

In vitro kinase screen data for TP-5801 to accompany Chan and Egbert et al., Nature Communications, 2021 (in press)

A Fret Flow Cytometry-Based Screening Assay For Multiplex Analysis Of Metabolites In T. Brucei, Ronald A. Zegarra

Undergraduate Honors Theses

Kinetoplastid parasites are a significant public health issue in some tropical and subtropical regions of the world. Kinetoplastid parasites all require glycolysis for survival, with host glucose key for ATP production. One such parasite, Trypanosoma brucei, exclusively metabolizes glucose in its bloodstream form. Trypanosomal glycolysis is unique because it displays unconventional structural features. Hence, glucose metabolism has been studied extensively in T. brucei and is a therapeutic target in kinetoplastid parasites.The lack of in vivo analytical techniques for measuring vital glycolytic metabolites in situ has restricted the ability of researchers to test, with high sensitivity and specificity, the essential roles …

Exploration Of Fluorinated Α,Β-Dehydroamino Acids And Their Structure, Austin Lesueur

Undergraduate Honors Theses

This thesis explores the synthesis of fluorinated α,β-dehydroamino acids, specifically a fluorinated dehydrovaline derivative. Previous work has been done on the equivalent dehydrovaline derivative without fluorine present and this work builds toward the fluorinated version with the goal of comparing the two structurally. The synthesis presented here pulls from previous synthetic strategies employed for dehydrovaline while also exploring the synthetic impact of the electronegative fluorine atoms.

Telsam-Target Protein Fusions Can Form Diffraction-Quality Crystals Without Direct Inter-Polymer Contacts, Moriah Longhurst

Undergraduate Honors Theses

X-ray diffraction is a robust method for determining the detailed 3D structures of specific proteins. However, this requires the formation of well-ordered protein crystals, a process that is time-consuming, expensive, and only has about a 10-30% success rate. New methods are needed to enable the efficient crystallization of challenging proteins. One such technique is explored here, which utilizes a protein polymer (the sterile alpha motif domain of the human protein translocation Ets leukemia, or TELSAM) as a crystallization chaperone to form a more ordered crystal lattice of target proteins and drive crystallization. This method was successfully used to crystallize, collect …

In Vitro Screening Of Tp5801 Against Kinases For Nature Communications Publication, Joshua Andersen

ScholarsArchive Data

Data from screen of TP-5801 against in vitro kinases

Kinase Screen Data For Nature Communications Publication, Joshua Andersen

ScholarsArchive Data

A TNK1 peptide encompassing S502 was screened against 245 Ser/Thr kinases. This file contains kinase activity values (against S502) from an n=1 experiment. These data support a manuscript to be published in Nature Communications (Chan and Egbert et al.)

Building An Ins-1 Cdna Library For A Genome-Wide Crispr-Cas9 Screen, Idongesit Ekpo

Undergraduate Honors Theses

By the year 2040, an estimated 642 million people are expected to have diabetes globally. Diabetes results from an elevation of metabolic stressors, such as glucotoxicity, lipotoxicity, oxidative stress and apoptosis. In type 2 diabetes, these stressful conditions contribute to the malfunction and loss of functional insulin-producing β-cells. Current treatment methods for diabetes include insulin therapy, islet transplant and anti-diabetes medication. These treatments are not curative and ignore other factors that contribute to the pathogenesis of diabetes beyond insulin resistance and islet β-cell failure. Previous research on β-cells has focused on ways to replace functional β-cell mass, trigger β-cell proliferation, …

Preparation And Detailed X-Ray Photoelectron Spectroscopy And Spectroscopic Ellipsometryanalysis Of Ultrathin Protective Coatings, Brian Ivins Johnson

Theses and Dissertations

Ultra-thin films (UTFs) are important in many applications, seen in the semiconductor industry, in chromatography, in sensing, in microfluidics, in aerospace, and in robotics. They also protect materials from corrosion, change surface energies, limit water intrusion into materials, allow material self-cleaning and self-healing, provide scratch resistance, and impart other specific chemical properties. In many cases, UTFs drastically alter surface properties and therefore their applications. It is imperative that proper and consistent characterization be performed on coatings to confirm and understand their desired properties. In Chapter two, Al oxidation under MgF2 protective layers is studied using real time X-ray photoelectron spectroscopy …

Preparation, Functionalization, And/Or Characterization By X-Ray Photoelectron Spectroscopy Of Carbon Surfaces For Biosensors And Other Materials, Varun Jain

Theses and Dissertations

My dissertation is primarily divided into two parts. The first deals with the preparation, functionalization, and characterization of carbon surfaces prepared by direct current magnetron sputtering (DCMS) and high power impulse magnetron sputtering (HiPIMS) as substrates for bioarrays. Part two discusses applications of XPS peak fitting in surface chemical analysis. Chapter 1, the introduction, includes (i) a discussion of the construction of bioarrays and the preparation of sputtered surfaces, e.g., by DCMS and HiPIMS, and also functionalization (bioconjugate) chemistry with special emphasis on the importance of covalent functionalization of surfaces, and (ii) a discussion of the surface characterization techniques and …

Computational Studies Of High-Oxidation State Main-Group Metal Hydrocarbon C-H Functionalization, Clinton R. King

Theses and Dissertations

High-oxidation state main-group metal complexes are potential alternatives to transition metals for electrophilic C-H functionalization reactions. However, there is little known about how selection of the p-block, main-group metal and ligand impact C-H activation and functionalization thermodynamics and reactivity. Chapter 2 reports density functional theory (DFT) calculations used to determine qualitative and quantitative features of C-H activation and metal-methyl functionalization energy landscapes for reaction between high-oxidation state d10s0 InIII, TlIII, SnIV, and PbIV carboxylate complexes with methane. While the main-group metal influences the C-H activation barrier height in a periodic manner, the carboxylate ligand has a much larger quantitative impact …

The Investigation Of Secondary Particle Formation Initiated By Non-Prototypical Sources And The Role Of Amines In The Atmosphere, Emily Burrell

Theses and Dissertations

This dissertation is a collection of works that investigate non-prototypical sources leading to new particle formation in the atmosphere. Particles play a major role in atmospheric chemistry. For example, particles are a component of smog and are commonly found in high concentrations under conditions of atmospheric inversions. In order to reconcile the difference between measured and modeled particle concentrations new mechanisms from non-prototypical sources for particle formation need to be determined. Formation of particles has frequently been modeled using classical nucleation theory (CNT). The first step in CNT is the nucleation step where molecular clusters form. In a second step, …

The Development Of Individualized Anemia Treatments Using Point Of Care Diagnostics To Distinguish Anemia Caused By Infection Or Chronic Inflammation, Dr. Richard Watt

Journal of Undergraduate Research

Background: Anemia that accompanies inflammation is associated with negative outcomes for patients. Early intervention to treat anemia is an important step in improving the quality of life for anemic patients. Our lab proposed to develop simple diagnostic tests using a Lateral Flow Immunoassays (LFIs) to measure the presence of a hormone called hepcidin because hepcidin is the master regulator of iron homeostasis in the body and elevated hepcidin levels lead to anemia.

Rational Design Of Multifunctional Enzyme-Like Catalysts For Assembly-Line Chemical Synthesis, David Michaelis

Journal of Undergraduate Research

The main objectives of this proposal was to publish our preliminary findings in peptide catalysis and then submit applications for external funding. Both of these objectives were accomplished during the grant period. In the Fall of 2017, we published our first paper on the development of our new enzyme-like catalysts (ACS Catal. 2017, 7, 7704–7708). This publication should serve as a springboard for additional publications in the area (on which we are currently working) and help ensure external funding for this project. During 2017-2018, we submitted 3 grant applications to the NIH to help support this project. These submissions have …

Cyclic Peptide Catalyst Design, Millicent Campbell, David Michaelis

Journal of Undergraduate Research

Enzymes found in nature are more efficient catalysts than those used in organic chemistry labs. However, natural enzymes are not ideal for organic synthesis because they only make one product and only work in specific conditions. The Michaelis lab designed a catalyst capable of mimicking enzyme-like reactivity in the lab. This catalyst consists of an alpha helix with an imidazolidinone catalyst and a thiourea catalyst (see figure 1). The imidazolidinone catalyst and thiourea catalysts are attached adjacent to each other on the alpha helix, which acts as a rigid scaffold that can mimic the proximity effects seen in natural enzymes. …

Modeling Main Group Metal Alkane Functionalization Reactions In Highly Acidic Carboxylic And Sulfuric Acid Solvents, Lily H. Carlson, Daniel H. Ess

Journal of Undergraduate Research

Our group is interested in identifying the unknown mechanisms of main-group C-H functionalization reactions. In the long term, our goal is to use computational chemistry tools to develop general principles on mechanisms, intermediates, reactivity, and selectivity for hydrocarbon C-H functionalization reactions by p-block main-group compounds as well as provide prediction of new catalysts and reactions. However, in providing these predictions, it remains unclear if different mechanistic pathways and intermediates will be predicted if examined in a complete solvent sphere (see Figure 1 for technical details). This is especially important for non-aqueous solvents such as carboxylic acids and sulfuric acid. To …

Heterodinuclear Co-Zr Compound Shows Increased Reactivity In Kumada Coupling, James Coombs, Daniel Ess

Journal of Undergraduate Research

Heterodinuclear compounds containing a metal–metal bond represent a potentially useful subclass of catalyst in organic synthesis. Heterodinuclear compounds offer the possibility of increased reactivity due to interactions between metal centers (Scheme 1A). These so-called cooperative effects can enhance reactivity by changing the electronic density, increasing nucleophilicity/electrophilicity of the reactive metal, and by lowering the energy barriers for changes in oxidation state. These changes in reactivity can allow a heterodinuclear compound to be an effective catalyst for many chemical reactions that would be unfeasible with a mononuclear analogue.

Computational Design And Analysis Of Molecular Ethylene Oligomerization Catalysts, Doo Hyun Kwon

Theses and Dissertations

Linear alpha olefins (LAOs) are key petrochemical precursors for the synthesis of larger polymers, detergents, plasticizers, and lubricants. Most catalytic ethylene oligomerization processes generate a wide distribution of LAO carbon chain lengths. A major ongoing industrial challenge is to develop homogeneous catalysts that result in selective and tunable ethylene oligomerization to 1-hexene and 1-octene alkenes. Quantum mechanical calculations coupled with rapidly advancing technology have enabled the ability to calculate small molecule systems with high accuracy. Employing computational models to advance from empirical to quantitative prediction of product selectivities has become an active area of exploration. In this work, we demonstrate …

The Investigation Of Nickel-Based Catalysts For The Oxidative Dehydrogenation Of Ethane, Justin Lane Park

Theses and Dissertations

The Investigation of Nickel-Based Catalysts for the Oxidative Dehydrogenation of Ethane Justin Lane ParkDepartment of Chemistry & Biochemistry, BYU Doctor of Philosophy Chemistry The advancement of creating ethylene from ethane via oxidative dehydrogenation (ODH) rather than the traditional direct dehydrogenation is right on the cusp of commercialization. The oxidative pathway provides a novel route that reduces the operating temperature of this reaction by 400-500°C. A variety of metals including Mo, V, and Ni that have redox properties suitable for the partial oxidation of small chain alkanes have been investigated. Currently, a MoVNbTe oxide is the most promising catalyst but it …

Multi-Instrument Surface Characterization Of Display Glass, Cody Vic Cushman

Theses and Dissertations

Flat panel displays (FPDs) are microfabricated devices that are often fabricated on specialized glass substrates known as display glass. The surface chemistry of the outer few nanometers of display glass can have an important influence on FPD performance and yield. Dsiplay glass surface characterization is difficult because (i) display glass surface composition varies significantly from its bulk composition; (ii) high-surface area forms of glass, such as fibers and powders, may not have the same surface composition as melt-formed planar surfaces, and (iii) the surface composition of display glass may be altered through exposure to chemical treatments commonly used during flat …

Selective Catalysis By Polymer-Supported Ruthenium Nanoparticlesand New Ligand Design For Cooperative And Bimetallic Catalysis, Seyed Hadi Nazari

Theses and Dissertations

The abstract is the summary of three different projects all centered around the generalidea of catalysis which is the general theme of research in the Michaelis laboratory. The firstproject focuses on development of a new heterogeneous catalyst for selective catalysis. In theMichaelis lab, we were interested in the potential of nanoparticle catalysts for regioselectivetransformations. We showed that polymer supported ruthenium nanoparticles performed as areliable catalyst for regioselective reduction of azide to amine. In our study of regioselectivereduction of multiple azide containing substrates, we observed that in presence of ourruthenium nanoparticle catalysts, the least sterically hindered azide group reduced to aminefunctional …

Applications Of Pattern Recognition Entropy (Pre) And Informatics To Data Analysis, Shiladitya Chatterjee

Theses and Dissertations

The primary focus of my work is the application of informatics methods to the fields of materials science and analytical chemistry. The statistical analysis of data has become increasingly important in understanding the properties of materials and analytes. Statistical methods like principal component analysis (PCA) and multivariate curve resolution (MCR) are widely used for analysis in chemistry and other fields given their ability to categorize spectra in an unsupervised way. PCA is relatively easy to apply and has appealing mathematical properties. However, the results can be challenging to interpret, even for experienced users. In contrast, MCR results can be more …

Nonlinear Optical Characterization Of Solids, Alex Farnsworth

Undergraduate Honors Theses

Vibrational Sum Frequency Generation (VSFG) and the similar Second Harmonic Generation (SHG) are both classified as nonlinear optical phenomena, with the hallmark trait being that the input and output frequencies are different. Both of these systems are remarkable tools due to their surface specific nature. Still, there is much that is not known about the response from these systems, especially the nonresonant SFG response. We have worked to better understand SFG signal, specifically the nonresonant temporal profile. We have also collected results that call into question some underlying assumptions about time-based suppression methods when working with single crystal substrates.

As …