Physical Sciences and Mathematics Commons^™

Mathematical Modeling And Examination Into Existing And Emerging Parkinson’S Disease Treatments: Levodopa And Ketamine, Gabrielle Riddlemoser

Undergraduate Honors Theses

Parkinson’s disease (PD) is the second most common neurodegenerative disease across the world, affecting over 6 million people worldwide. This disorder is characterized by the progressive loss of dopaminergic neurons within the substantia nigra pars compacta (SNpc) due to the aggregation of α-synuclein within the brain. Patients with PD develop motor symptoms such as tremors, bradykinesia, and postural instability, as well as a host of non-motor symptoms such as behavioral changes, sleep difficulties, and fatigue. The reduction of dopamine within the brain is the primary cause of these symptoms. The main form of treatment for PD is levodopa, a precursor …

Process Modeling The Neuroprotective Effects Of A Plant-Based Diet On Parkinson's Disease, Julia Mitchell

Undergraduate Honors Theses

Parkinson's disease (PD) is a progressive neurodegenerative disorder characterized by motor symptoms such as tremors, bradykinesia, rigidity, and postural instability. Recent research suggests an avenue for potential neuroprotection through dietary intervention, specifically the adoption of a plant-based diet. A plant-based diet predominantly comprises foods derived from plants, emphasizing fruits, vegetables, grains, legumes, and nuts while minimizing or excluding animal products. This thesis aims to explore the biochemical pathways implicated in PD progression and the potential impact of dietary choices on these pathways. The investigation focuses on several key pathways: alpha-synuclein aggregation, the blood-brain barrier crossing of levodopa, oxidative stress, ferroptosis, …

Use Of Molecular Logic Gates For The Tuning Of Chemosensor Dynamic Range, Orhan Acikgoz

Undergraduate Honors Theses

The first molecular logic gates were created in the 1990s; integrating such logic gates into fluorescent chemosensors allowed for the detection of different types of ions in solution. In this study, we have developed a new use of molecular logic gates by having two of the same type of binding site. The two binding sites on a fluorophore that both detect Na⁺ ions led to an increase in the detection limit compared with the chemosensor with a single binding site. Since the two sodium binding sites create an AND logic gate, two sodium ions are needed to generate a …

Modeling Group 3 Medulloblastoma: Describing The Interconnected Pathway Of The Most Common Pediatric Brain Cancer, Amber Cantú

Undergraduate Honors Theses

Group 3 medulloblastoma is one of the most common pediatric brain cancers. Affecting infants and children, this cancer has the worst prognosis of the medulloblastoma group. Current treatments use surgical resection, radiation, and chemotherapy to afflict the cancer, however no cure has been found. This project aims to model one of the many pathways being investigated in Group 3 medulloblastoma which may be used to synthesize future treatments. Specifically, showing the interconnections between various precursors of BCL-xL, an antiapoptotic protein, and how these factors influence the progression of the disease. Scientific databases were used to find previous research articles which …

Harnessing The Power Of Virtual Reality For Organic Chemistry Education, Jungmin Shin

Undergraduate Honors Theses

Understanding organic chemistry concepts heavily relies on visualization of the geometry of molecules and spatial arrangement of molecules during mechanisms. 2D textbook depictions have their limitations in visualizing the three-dimensionality of organic chemistry. Student learning outcomes could be greatly improved from 3D visualizations of these topics. This project explores the potential of an emerging technology, Virtual Reality (VR), being incorporated as a teaching resource for organic chemistry.

This paper discusses two trials for evaluating the potential of VR as a teaching resource for organic chemistry in select topics of the Diels-Alder reaction and R/S configurations and stereoisomers. The Diels-Alder reaction …

Spectroscopy And Dynamics Of Atmospherically And Combustion-Relevant Collision Complexes, John Patrick Davis

Dissertations, Theses, and Masters Projects

Potential energy surfaces describing bimolecular collisions sensitively depend on the chemical functionality and the relative orientation of colliding partners, thus defining the accessibly reactive and nonreactive pathways. Herein, we investigate the peculiar product outcomes arising from Jahn-Teller distortion of the nitric oxide and methane complex (NO-CH4). We have reported an in-depth spectroscopic and dynamics study of NO-CH4 by utilizing conformation-specific and action spectroscopy, as well as velocity map imaging, to understand the fundamental dissociative mechanisms at play. Ultimately, we have gained information about how the Jahn Teller effect possibly impacts the potential product energy transfer pathways. There is a translationally …

Gas-Phase Proton Affinities Of Proline- And Pipecolic Acid-Containing Dipeptides, Trinh Ton

Dissertations, Theses, and Masters Projects

Mass spectrometry (MS) is one of the most used techniques in proteomics because it allows for both high-throughput and quantitative analyses. Bottom-up MS-based proteomics involves breaking down proteins into smaller chains of amino acids called peptides, ionizing and fragmenting the peptides, and identifying the fragments using sequencing databases. These databases depend on the random fragmentation at the backbone peptide bond of the peptides, as predicted by the mobile proton model. Research has shown that peptides containing proline or pipecolic acid have selective fragmentations that could lead to incorrect identification in the sequencing algorithms. These selective cleavages are called “the proline …

Characterizing Molecular Environments In Acrylic Paint Via Single-Sided Nmr, Lyndi Kiple

Dissertations, Theses, and Masters Projects

Acrylic paint is a modern artistic material made of colored pigment and polymeric binder. Acrylic binder requires fundamental study at the molecular level to understand its physical properties for purposes of art conservation and general polymer chemistry. The research presented in this thesis uses single-sided nuclear magnetic resonance (NMR) as a non-invasive and non-destructive way to measure relaxation and self-diffusion, which provide insight to molecular mobility and physical properties of proton-containing samples. Specifically, this study relies on T2 relaxation to gain insight to regions within acrylic paint with different molecular mobilities. In both dry and wet paint, relaxometry data revealed …

Gas-Phase Proton Affinities For Twenty Of The Proline-Containing Dipeptides, Henry Cardwell

Undergraduate Honors Theses

Peptide fragmentation plays a crucial role in the analysis of proteins through mass spectrometry-based proteomics. Most proteomics experiments take place in the low-energy regime and are governed by the mobile proton model which predicts random cleavages along the peptide backbone; however, there sometimes arise circumstances where the mobile proton model fails causing sequencing algorithms to misidentify peptides. One such example is noted in the “proline effect” wherein proline-containing peptides preferentially fragment N-terminal. While it has been established that the “proline effect” is due to the rigidity and basicity of the proline N-terminus, a further understanding of the factors influencing the …

Chemical Analysis Of Organic Compounds In Dew Water, Monica Dibley

Undergraduate Honors Theses

Water films on outdoor surfaces, such as dew, can act as a reservoir for organic molecules deposited from the atmosphere and they present a potential reactive medium for chemical transformations. To better understand the flux of volatile organic compounds from evaporating films, the composition and reactivity of the complex mixture of dissolved organic material (DOM) found in these films need to be characterized. Previous studies have measured the salts and the small organic molecules in dew collected on clean Teflon surfaces or condensers. Here, we expand on this by probing the organic chemicals found on natural outdoor surfaces covered in …

Differential Protein Expression In Bacteriophages Crimd And Larva, Daria Moody

Undergraduate Honors Theses

Proteomics studies allow us to answer questions about differential protein expression across different systems. Mass spectrometry is a powerful tool in these studies due to the distinct masses of the amino acids that compose proteins. In our experiment, we used a bottom-up approach and focused on two bacteriophages found on the William & Mary campus, CrimD and Larva. The infection of Mycobacterium smegmatis, a nonpathogenic model for tuberculosis, by these two bacteriophages was frozen at five different timepoints, and our goal was to compare the differential protein expression across the samples in order to gain a greater understanding of …

Honey As A Biomonitor For Air Pollutant Deposition In The Eastern United States Using Ion Chromatography And Scanning Electron Microscopy, Cole Cochran

Undergraduate Honors Theses

Anthropogenic activities generate metal, acid, and particulate air pollutants which negatively impact human and ecological health. In the United States, power plant, industrial, and vehicle emissions are leading causes of air pollution, however, the measurement of air pollution at high-resolution spatial regimes remains a challenge. Honey has emerged as a powerful biomonitoring tool to effectively quantify contaminants without the need for a large array of monitoring instruments. I hypothesized that honey could be used to effectively measure and map modern air pollutant spatiotemporal relationships over the Eastern U.S. Using ion chromatography with sulfate as an indicator for air pollution and …

Geologic Controls On 137cs Cycling By Terrestrial Vegetation In The Eastern U.S., Kathleen Chellman

Undergraduate Honors Theses

¹³⁷Cs is a radioactive trace metal (T_1/2 = 30 y) that was dispersed globally by nuclear weapons testing in the 1950s-1960s. Prevailing winds and precipitation systems caused some areas far from the test sites to receive significant fallout, which is still easily measured in soils, sediments and even some vegetation in the Eastern United States. Recent work near Chernobyl and Fukushima indicates that trace levels of ¹³⁷Cs can harm insects, pollination services, and other ecological functions. In areas with low soil potassium, ¹³⁷Cs is cycled in vegetation; however, soil potassium alone doesn't consistently predict the ^{137 …}

Exploring The Photophysics Of Brown Carbon Chromophores Using Laser-Based Spectroscopy And Computational Methods, Megan Elizabeth Alfieri

Dissertations, Theses, and Masters Projects

Atmospheric aerosols are made up of suspended liquids and solids in the atmosphere. These aerosols play a very important role in the solar energy exchange in Earth’s atmosphere as well have dramatic impact on human health. Different aerosols have different effects on the atmosphere depending on the physical properties of the aerosols.

The purpose of this research project is to understand how the structure of molecular chromophores impacts the solar absorption properties of aerosols. We propose a series of laboratory studies to investigate the outcomes from solar absorption of brown carbon chromophores: 1-phenylpyrrole, 2-phenyl-1-H-pyrrole, 2-phenylimadazole, as well as water complexes. …

Developing Iron Complexes For Electrocatalytic Hydrogen Generation, Benjamin Travis

Undergraduate Honors Theses

Artificial photosynthesis systems convert solar energy into chemical fuels such as hydrogen gas. Photocatalytic hydrogen generation systems have previously been developed, but reliance on expensive metal catalysts limits the viability of these systems. In order for artificial photosynthesis to be used as a large-scale clean energy solution, it is crucial to discover more active and cost-efficient catalysts.

To this end, several novel iron polypyridyl complexes were synthesized using relatively inexpensive reactants. Electrochemical testing revealed that these complexes are active electrocatalysts for the reduction of protons to generate hydrogen gas. Furthermore, a naphthalene-terminated iron polypyridyl complex was found to be an …

Polyaromatic-Terminated Iron Polypyridyl Complexes For The Functionalization Of Carbon Surfaces And Electrocatalytic Hydrogen Generation, Caroline Marie Margonis

Dissertations, Theses, and Masters Projects

Artificial Photosynthesis (AP) focuses on developing methods for the conversion of solar energy into chemical fuel in the form of H2 and O2. Heterogeneous photocatalytic systems incorporating carbon nanotubes (CNTs) have shown much promise but are currently limited and expensive due to their reliance on noble metals. To that end, this work focuses on the development and synthesis of cheaper naphthalene- and pyrene-terminated iron polypyridyl complexes for use in the simultaneous functionalization of carbon surfaces, electrocatalytic proton reduction, and eventual incorporation in photocatalytic systems. Cyclic voltammetry was used to characterize the adsorption behavior of each complex on the surface of …

Evaluating Epoxy Cure And Adhesion Strength Through Single-Sided Nmr Measurements Of Molecular Mobility, Kayla Copeman

Dissertations, Theses, and Masters Projects

Commonly used in aerospace, automotive, marine, defense, electronic, and manufacturing industries, epoxy adhesives offer advantages over mechanical joints by providing stronger and/or more flexible bonds, more uniform stress distribution, low shrinkage, and lightweight connections between materials. Determination of curing kinetics and properties of interfaces between epoxy and inorganic substrates provides insight that is useful for quality control and defect detection for such applications. Single-sided NMR provides a nondestructive and inexpensive method for probing epoxy materials and spatially resolving the decay of spin-lattice and spin-spin relaxation times (T1 and T2) during and after curing of epoxy resins onto substrates. In this …

Investigating Charge Transfer Complexes In Brown Carbon Aerosols, Brianna Peterson

Undergraduate Honors Theses

Aerosols are suspensions of particles in the air, commonly seen as dust or fog in the atmosphere. Brown carbon is a particular classification of carbonaceous atmospheric aerosol that increases in absorption from the visible to ultraviolet region, making it important for radiative forcing models. Elucidating the structures of brown carbon chromophores has been difficult as brown carbon is a broad category and the chromophore type can change depending on emission source, temperature, humidity, and season. Twisted intramolecular charge transfer (TICT) molecules have been identified as potential brown carbon chromophores. TICT molecules are those that allow charge transfer to occur between …

Molecular Cluster Fragment Machine Learning Training Techniques To Predict Energetics Of Brown Carbon Aerosol Clusters, Emily E. Chappie

Undergraduate Honors Theses

Density functional theory (DFT) has become a popular method for computational work involving larger molecular systems as it provides accuracy that rivals ab initio methods while lowering computational cost. Nevertheless, computational cost is still high for systems greater than ten atoms in size, preventing their application in modeling realistic atmospheric systems at the molecular level. Machine learning techniques, however, show promise as cost-effective tools in predicting chemical properties when properly trained. In the interest of furthering chemical machine learning in the field of atmospheric science, I have developed a training method for predicting cluster energetics of newly characterized nitrogen-based brown …

Proteomic Analysis Of Mycobacteriophage Crimd, William Moeller

Undergraduate Honors Theses

Bacteriophages represent a large portion of the biomatter on our planet, and many of them have yet to be fully characterized. Here we discuss the proteomic analysis of a particular Bacteriophage, Mycobacteriophage CrimD. This phage was discovered on the Campus of William & Mary and has had its genome characterized. We took the next logical step of proteomic analysis.

In our analyses we made use high pressure liquid chromatography paired with linear ion trap mass spectrometry to analyze the proteome of CrimD at specific time points after the infection of its host, Mycobacterium smegmatis. Additionally, we used nanospray ionization with …

Electronic Effects In A Cyclization Cascade To Diversified, Polycyclic, Helical Molecules, Caleb Lee Burns

Dissertations, Theses, and Masters Projects

Heterocyclic aromatic compounds and their derivatives are ubiquitous in the pharmaceutical and photochemical industries. Naphthochromene derivatives in particular have garnered great interest for their photochemical properties and biological activity. Herein, the effects of electronics on a three-step cascade reaction between aryl substituted 2-(4-aryl-3-((triethylsilyl)oxy)but-1-yn-1-yl)phenols and structurally diverse aldehydes is explored. The cascade is initiated by alkynyl substrate addition to BF3-activated aldehydes. The aldehyde undergoes condensation with the substrate phenol moiety forming an oxocarbenium ion, this initiates the alkynyl-Prins cyclization forming a new six-membered heterocyclic ring with an internal alkenyl cation. The cation is subsequently trapped by a Friedel-Crafts (FC) reaction by …

Investigating The Electron Transfer Dynamics Of Eosin Y Photosensitizers Using Single Molecule Spectroscopy, Kelly Margaret Kopera

Dissertations, Theses, and Masters Projects

Growing global energy demands have necessitated the search for alternative sources of renewable fuels. Dye-sensitized photocatalysis (DSP) is a promising low cost, sustainable method that directly converts solar energy to readily usable forms of energy such as hydrogen fuel. While DSP is a promising technology, its efficiency is limited by back electron transfer and kinetic redundancy. In order to fully understand these processes, single-molecule spectroscopy (SMS) is used to probe the electron transfer (ET) dynamics of photosensitizers. In particular, eosin Y (EY), a brominated fluorescein derivative that undergoes intersystem crossing prior to injection, is investigated using SMS. In this approach, …

Indoor Chemistry: Development Of An Indoor Surface Extractor, Hannah Rose Przelomski

Dissertations, Theses, and Masters Projects

People spend around 90% of their time indoors. This means that indoor air can have an impact on human health. One of the main factors that makes indoor air differ from outdoor air is indoor areas have a higher surface area to volume ratio than outdoor areas. Surfaces give aerosol particles a place to deposit where they can stick or react. Some of this material can leave the surface and reenter the air. Being able to analyze the material on different indoor surfaces will help further the understanding of indoor surfaces’ impact on indoor air. A surface extractor was developed …

Mass Spectrometry-Based Proteomics: An Experimental Study Of Differential Bacteriophage Protein Expression And A Computational Investigation Of The Effects Of Proton Affinity On The Fragmentation Of Proline-Containing Dipeptides, Hao Qian

Dissertations, Theses, and Masters Projects

After decades with the development of genetics study, the next step of molecular biology had already been moved onto proteomics. The proteomics study provides an innovative aspect to deduct the relationship between genes and proteins. Meanwhile, research that focuses on the mechanism of protein interactions and intrinsic properties of proteins never cease. The mass spectrometry-based proteomics approaches have already shown their versatile and superior in studying the whole proteome of complicated organisms. This study focuses on practicing bottom-up method in determining and characterizing the expressed proteome of two mycobacteriophages, CrimD and Larva. The expressed proteins of CrimD and Larva in …

Copper(I) Iodide-Based Chemical Sensor Materials In Gaseous And Aqueous Media, Matthew D. Kessler

Dissertations, Theses, and Masters Projects

Chemical detection is an area of great importance in the shift to more green approaches to industry. Some of the chemical species produced by assorted industries can be harmful, long lived, and challenging to differentiate. Copper(I) iodide (CuI) is a material that readily forms complexes of multiple colors, both under visible and ultraviolet (UV) light. The process of CuI reacting with dimethyl sulfide vapor to produce a color change (vapochromism) has been analyzed to propose mechanistic information about the process. Using the information obtained, a series of potential sensor materials were developed with CuI as the base. The complexes were …

Unravelling The Aggregation Of Eosin Y Photosensitisers For Solar Energy Conversion, Huw Richards

Dissertations, Theses, and Masters Projects

The impact of molecular aggregation on the photophysics of eosin y adsorbed to TiO₂ was investigated using diffuse reflectance spectroscopy, steady-state fluorescence and time correlated single photon counting (TCSPC) measurements. Deconvolution of the diffuse reflectance spectra of eosin y on TiO₂ revealed the formation of H-aggregates, with the extent of H-aggregation increasing with increasing dye-loading concentration. The resultant bathochromic shift from the monomer diffuse reflectance maximum is due to Charge-transfermediated H-aggregates The fluorescent maximum also shifts with increasing dye loading concentration starting at 537.5 nm at a dye loading concentration of 7.5x10^-7 M and shifting to 585 …

Structural And Dosage Dependence Of Electron Transfer From Conjugated Polymer Nanoparticles, Jaclyn Rebstock

Dissertations, Theses, and Masters Projects

Conjugated polymer nanoparticles (CPNs or Pdots) have become popular fluorophores for a variety of fluorescence imaging applications due to their brightness, photostability, and aqueous compatibility. Recently, their ability to generate charged species has begun to be exploited in applications ranging from photocatalysis to photovoltaic cells. Upon excitation, CPNs can eject an electron via photoinduced electron transfer (PET) to oxygen or other acceptors. The competition between fluorescence and PET is undesirable in redox-based applications. However, CPNs are capable of the simultaneous generation and detection of reactive oxygen species, expanding their use in photodynamic therapy (PDT). We seek to determine the dependence …

Investigating The Molecular Choreography Of Atmospherically Relevant Molecules: A Dynamics Study, Kenneth Jacob Blackshaw

Dissertations, Theses, and Masters Projects

Investigating and understanding the chemistry of the atmosphere has historically been an important research topic. This importance has only strengthened in the recent decades as technological advancements have drastically increased anthropogenic emissions of hydrocarbons and nitroaromatic compounds. Indeed, we are in an era of unprecedented change of the chemical composition of the troposphere and never before has an in-depth understanding of atmospheric chemical properties been more sought-after. This study seeks to fill that need by probing the molecular dynamics of atmospherically relevant molecules through the use of velocity map imaging (VMI). In particular, we utilize VMI to study the photolysis …

Complex Mixtures: Identifying And Characterizing Secondary Organic Aerosols, Emma Quinn Walhout

Dissertations, Theses, and Masters Projects

Complex organic mixtures in the environment can contain hundreds to thousands of different organic molecules, and their composition and reactivity can have important environmental implications. In addition to gases, the atmosphere is made of a variety of small liquids and solids called aerosols. These aerosols have large impacts on human health, climate, and atmospheric chemical reactions. Here, secondary organic aerosol (SOA) from the ozonolysis of α-pinene is characterized. The atmospheric lifetime of SOA is very uncertain, but recent laboratory and modeling studies have demonstrated that photolysis is potentially an important process for organic mass loss from aerosol particles.1-5 Photolysis modifies …

Computational Investigations Of The Structure And Spectroscopy Of Small Biomolecules In The Gas Phase, Zachary Michael Smith

Dissertations, Theses, and Masters Projects

Small biomolecule systems were interrogated using infrared multiple photon dissociation (IRMPD) action spectroscopy and corresponding quantum chemical calculations with a particular focus on peptide fragmentation and protonation site preference. b2+ and b3+ fragment ions with a terminal lysine homolog residue were investigated using IRMPD in the fingerprint region (1000 cm-1 – 2000 cm-1) and a variety of computational methods. We present the first spectroscopic confirmation of b-ion formation with a lactam structure. Infrared spectra for b2+ fragment system indicate the presence of a mixture of structures, though final determination will require further investigation. The b3+ fragment ion infrared spectra show …