Chemistry Commons^™

Self-Assembling Rna Nanostructures Are Highly Sensitive To Environmental Conditions, Jordan Aposhian, Surya Pratap S. Deopa, Scott Horowitz, Joseph D. Yesselman

Chemistry and Biochemistry: Faculty Scholarship

Recent developments in RNA nanotechnology have led to an increase in the design of specific, higher-order RNA structures, which will ultimately be used in drug delivery and immunomodulation applications. As researchers create RNA nanostructures with the intention of making them a standard tool in molecular biologists' toolkits, further investigation is required into the robustness of RNA designs. Primarily, in what different molecular contexts are the designed and intended nanostructures stable? In this work, we show that RNA nanostructure self-assembly is highly sensitive to environmental conditions by using second-order right-angle light scattering. While a test RNA hexagonal grid nanostructure forms correctly …

N-Aryl Phenoxazines As Polymer Supported Photocatalysts, Mary Kathryn Hall

Master's Theses

In photosynthesis, the energy of sunlight is perfectly harnessed to facilitate the production of small molecules that are essential for plant life on earth. Inspired by this model of energy efficiency and simplicity, this work seeks to mimic that ability to use the energy in visible light to perform new and more efficient chemistries. Just like in photosynthesis, photocatalysts can act as chromophores absorbing light to excite electrons opening new pathways for previously untapped reactivity. Recent research has provided a wide range of small molecule reactions that are made possible or easier by the use of a photocatalyst. However, these …

An Experiment In Electron Paramagnetic Resonance Spectroscopy For Undergraduate Labs In Physical Chemistry Or Physical Biochemistry, Evan A. Old, Matthew C. Rehak, Jefferson C. Thompson, Herbert J. Sipe Jr.

TeachEPR Submissions

We report a biochemically based EPR experiment for undergraduate laboratories that will serve as instruction for learning EPR sample preparation, spectral observation, and spectral analysis. There is a current lack of EPR instructional experiments that present complex spectra in which computational analysis may be required. The biochemical oxidation system of horse radish peroxidase (HRP) activated by H₂O₂ acts on 2,6-di-t-butyl-4-hydroxyanisole (DTBHA) to form phenoxyl radicals. This experiment produces moderately complex spectra of moderately long-lived radicals using relatively small amounts of readily available reactants. Spectrum analysis and simulation is accomplished using software freely available on-line. If desired, EPR …

Characterization Of L-Band Resonators And Relaxation Times Of Soₓ- Radicals At X-Band, Georgina Naa Odey Amassah

Electronic Theses and Dissertations

Electron Paramagnetic Resonance (EPR) analysis requires resonators optimized for specific experimental challenges. Volume resonators enclose samples, while surface coil resonators allow imaging of larger subjects. For in vivo studies, L-band frequencies are commonly used because they offer a good balance between signal-to-noise ratio (S/N) and the ability to penetrate tissue. Rapid Scan (RS) EPR at L-band frequencies was chosen for my studies of resonators because of this balance but presents a challenge for sensitivity.

The spatial position dependence of signal intensity was evaluated for selected paramagnetic samples using 10 mm and 30 mm surface coils. The 10 mm coil, with …

Extreme Value Theory View Of High Emitter Diesel Vehicles In The Us From 1991 To 2021, M. Matti Maricq, Gary A. Bishop

Fuel Efficiency Automobile Test Publications

Extreme value theory (EVT) is a statistical method to characterize the tails of distributions, such as high emitter vehicle emissions. The present work addresses the United States (US) diesel fleet. EVT confirms that high emitters contribute disproportionately to adverse air quality. It further reveals that high emitter emissions have responded differently to progressively tighter emissions standards compared to fleet averages. Carbon monoxide (CO) and hydrocarbons (HC) high emitter emissions fell in concert with the fleet average after widespread implementation of the diesel oxidation catalyst to meet US Environmental Protection Agency (EPA) Tier 1 emissions standards, but remained unchanged after introduction …

Investigating The Influence Of Experimental Parameters On The Formation Of Gold Nanoparticles: A Green Synthesis And Design Of Experiments Approach, Isaac Opeyemi Subuloye

Master's Theses

This thesis examines the green synthesis of gold nanoparticles using catechin, a naturally occurring plant-derived compound, as both a reducing and capping agent. The synthesis process was guided by a structured Design of Experiments (DOE) methodology to ensure systematic investigation and optimization. A two-phase experimental approach was adopted. First, a full factorial screening design was used to evaluate the effects of catechin concentration, NaOH concentration, and pre-reaction time. This was followed by an optimization phase using a face-centered composite design to identify conditions that produce nanoparticles with ideal characteristics. The nanoparticles were analyzed using UV-visible spectroscopy and dynamic light scattering …

Photochemistry Of Quinones And Combustion-Derived Particles, Desiree J. Sarmiento

Electronic Theses and Dissertations

Quinones are ubiquitous species that can be produced from the photochemical aging of combustion-derived particles (CDPs). Polycyclic aromatic hydrocarbons (PAHs) are a major component of CDPs and are precursors to quinones and other oxidized products (OPAHs). My work first expanded on the PAH and OPAH photochemistry research of Dr. John Haynes, who showed that anthracene (ANT) oxidizes into 1,4-naphthoquinone (1,4-NAPQ), 1,4-anthraquinone (1,4-ANTQ), and 9,10-anthraquinone (9,10-ANTQ), and of Dr. Heather Runberg, who demonstrated the ability of ANT and these quinones to generate reactive oxygen species (ROS). Then at the Pacific Northwest National Laboratory (PNNL), I was given the opportunity to investigate …

Synthetic Protein Mimetic Based Therapies For Neurodegeneration, Nicholas H. Stillman

Electronic Theses and Dissertations

Protein-protein interactions (PPIs) are crucial for the regulation of a majority of, if not every fundamental cellular process. Despite their role in regular biological processes, dysregulated and/or aberrant protein-protein interactions (aPPIs) are often related to the onset of disease including cancer, viral infection, and amyloid diseases. aPPIs have historically been deemed ‘undruggable’ due to their large surface area and lack of a binding cavity; however, today, more than 40 disease-related aPPIs have been targeted with small molecules and several of those have reached clinical trials.

A class of synthetic protein mimetics called oligopyridylamides (OPs) has been shown to inhibit disease-related …

Epr Imaging Workshop: From Theory And Practice To Applications, Arthur H. Heiss, Ralph T. Weber, Sandra S. Eaton, Gareth R. Eaton

TeachEPR Submissions

Methods of imaging and insights from imaging are described. Practical aspects of sample type and dimensions are described.

Workshop presented at the 27th International EPR Symposium, sponsored by Bruker BioSpin EPR Division and the University of Denver, in Denver, Colorado on August 1, 2004.

Workshop On The Epr Of Aqueous Samples, Gareth R. Eaton

TeachEPR Submissions

The problem with water and other materials that absorb microwave energy are described. Dielectric properties are described as a function of frequency.

Workshop presented at the 25th International EPR Symposium on July 28, 2002.

Special Purpose Epr Resonators, Gareth R. Eaton

TeachEPR Submissions

Many types of EPR resonators are described.

Special applications that use various resonators are mentioned.

Lab Practical: Cw Basics, Gareth R. Eaton

TeachEPR Submissions

1. How do you position the sample in the resonator?
2. How do you select the center field for a spectrum?
3. How do you select the modulation amplitude?
4. How do you select the microwave power?

Lab Practical: Transition Metals: Epr Of A Vanadyl Complex, Gareth R. Eaton

TeachEPR Submissions

1. What information can you obtain from a spectrum of one orientation of a single crystal that is wide enough to encompass all of the vanadium hyperfine lines?

2. How does the spectrum change when you rotate the crystal? Look at both the position of the center of the spectrum and the hyperfine splitting.

How To Measure B1, Gareth R. Eaton

TeachEPR Submissions

• CW Methods
• Pulsed EPR Methods

Lab Practical: Nitroxides, Gareth R. Eaton

TeachEPR Submissions

1. How do you fill a capillary tube with an aqueous solution? How are capillaries positioned in the resonator?
2. How does the spectrum of a nitroxide change when the viscosity of a solution is increased?
3. How do you determine the concentration of the radical in the solution?

Lab Practical: Pulse Epr, Gareth R. Eaton

TeachEPR Submissions

1. How do you over-couple the resonator for a pulse experiment?
2. How do you find a 2-pulse echo?
3. How do you select the microwave attenuation?

How To Measure Q, Gareth R. Eaton

TeachEPR Submissions

•Frequency bandwidth
–Using spectrometer frequency sweep
–Using a network analyzer

•Ring down following a pulse

Motion Of Nitroxide Radicals, Gareth R. Eaton

TeachEPR Submissions

A brief outline is presented of how motion of a nitroxide radical can be estimated from the continuous wave (CW) EPR line shape.

Lab Practical: Rapid Scan Epr, Gareth R. Eaton

TeachEPR Submissions

• To develop an understanding of the rapid scan experiment relative to other EPR methods.
• To observe the effects of scan rate on samples with differing T₂ relaxation times.

Workshop On Quantitative Epr, Dave Barr, Sandra S. Eaton, Gareth R. Eaton, Ralph T. Weber, Patrick Carl, Peter Höfer, Richard W. Quine, George A. Rinard, Colin Mailer

TeachEPR Submissions

Presentations on quantitative EPR at the workshop that preceded the writing of our text, Quantitative EPR.

Presented at the 31^st Annual EPR Symposium in Breckenridge, Colorado on July 27, 2008.

Types Of Epr Resonators, Gareth R. Eaton

TeachEPR Submissions

Fundamental properties of resonators are described with photographs of a variety of actual EPR resonators.

Distances Between Spins, Gareth R. Eaton

TeachEPR Submissions

• Distance measurement by measuring T₁ and T_2.
• Relation to DEER and CW simulation and half-field intensity.
• Dipolar and exchange interactions.
• The dynamic NMR spectral collapse picture.

Epr Workshop: Lab Practicals Summary, Gareth R. Eaton

TeachEPR Submissions

• Basics – nitroxide and trityl
• Nitroxides
• Metals - vanadyl
• Pulse
• Rapid scan

Vanadium Line Shapes, Gareth R. Eaton

TeachEPR Submissions

VO²⁺ complexed with water, acetylacetonate, and/or other ligands yields a well-resolved 8-line spectrum (I = 7/2 for V) in solution. Powder spectra show that the hyperfine couplings are anisotropic.

Introduction To Epr, Gareth R. Eaton

TeachEPR Submissions

A very brief introduction to the scope of EPR at the beginning of a workshop in 2019.

Anisotropy Of Nitroxide Radicals, Gareth R. Eaton

TeachEPR Submissions

The special utility of nitroxide radicals for probing orientation and motion depends on the anisotropy of g-values and hyperfine values, especially the ¹⁴N hyperfine.

Workshop On Rapid Scan Epr, Gareth R. Eaton, Arthur H. Heiss, Deborah Gale Mitchell, Joshua R. Biller, Richard W. Quine, George A. Rinard, Mark Tseitlin, Sandra S. Eaton

TeachEPR Submissions

An introduction to the method of rapid scan EPR is given with emphasis on the design of rapid scan coils, selection of scan parameters, and the reasons that the method improves signal to noise per unit time.

Concentration Effects On Nitroxides, Gareth R. Eaton

TeachEPR Submissions

We need to distinguish line broadening due to restricted motion from line broadening due to concentration of the same or other paramagnetic species. For example, if you increase the concentration of nitroxyl to get better S/N, the lines will broaden due to collisions with other nitroxyl molecules.

Copper Line Shapes, Gareth R. Eaton

TeachEPR Submissions

The spectrum of Cu²⁺ has 4 lines, since I = 3/2. Cu has two major isotopes, ⁶³Cu (69.2%) and ⁶⁵Cu (30.8%). The magnetic moment of ⁶⁵Cu is 7% larger than that for ⁶³Cu, so the hyperfine coupling is 7% larger. If the lines are narrow enough, one can observe superposition of spectra due to complexes of the two isotopes.

Workshop On Selecting An Epr Resonator, Gareth R. Eaton

TeachEPR Submissions

Guidance is presented to help select a resonator to optimize a measurement. Different resonator types are described with information about resonator Q and microwave power efficiency.

Workshop presented at the 28th International EPR Symposium on July 31, 2005.