Physical Sciences and Mathematics Commons^™

Quantum Computations And Molecular Dynamics Simulations: From The Fundamentals Of Antimicrobial Resistance To Neurological Diseases, Angel Tamez

Electronic Theses and Dissertations

Biophysical phenomena are modeled using a combination of quantum and classical methods to interpret and supplement three distinct and diverse problems in this dissertation. In the first project, decarboxylation reactions are ubiquitous across chemical and biological disciplines, yet the origin of non-catalytic solvent effects remains elusive. Specific solvent structure and energetics have not been well described for the monoanion of malonate, nor corrected from the gas-phase charge-assisted intramolecular hydrogen bond model known as “pseudochair”. In the aqueous phase, a low-lying energy conformer known as the “orthogonal conformation” is computed to be preferred by a three-water cluster of hydrogen bonding over …

Acetylacetone Oxidation At Room Temperature: A Multiplexed Photoionization Mass Spectrometric Investigation, Study Of The Russell Intermediates In Gas Phase Reactions, And The Investigation Of Oxidation Reaction Products Of Ethanol At Room Temperature, Sara Gallarati

Master's Theses

This thesis presents the combustion study of acetyl acetone using synchrotron radiation coupled with multiplexed photoionization mass spectrometry at 298 K. The experiments were performed at the Chemical Dynamics Beamline 9.0.2 at the Advanced Light Source of the Lawrence Berkeley National Laboratory. The reaction of acetyl acetone with chlorine (Cl) radicals was analyzed based on their photoionization spectra and reaction kinetic profiles.

Additionally, a study of the Russell intermediate has been performed. Previous to experimentation at the Advanced Light Source, computational analysis has been investigated to evaluate compounds that could possibly lead to the formation of a stable species. The …

The Effect Of Ionization Density In Applications Of Radiation Detection, Dosimetry, And Therapy, Daniel Mulrow

Arts & Sciences Electronic Theses and Dissertations

This dissertation covers a wide range of topics but is linked by the common theme of radiation interacting with materials and studying the result of those interactions. The introduction describes the fundamentals of how radiation interacts with material and how we are able to detect that radiation and the application of how we use those interactions in radiation oncology. The thesis starts with a chapter detailing the temperature dependence of the photophysics in two organic scintillators. This chapter is the foundation for a future study that will look the degree to which these scintillators can distinguish between gammas and neutrons …

Molecular Insights Into The Redox Of Atmospheric Mercury Through Laser Spectroscopy, Rongrong Wu Cohen

Theses and Dissertations

The widespread pollution of mercury motivates research into its atmospheric chemistry and transport. Gaseous elemental mercury (Hg(0)) dominates mercury emission to the atmosphere, but the rate of its oxidation to mercury compound (Hg(II)) plays a significant role in controlling where and when mercury deposits to ecosystems. Atomic bromine is regarded as the main oxidant for Hg(0) oxidation, known to initiate the oxidation via a two-step process in the atmosphere – formation of BrHg (R1) and subsequent reactions of BrHg with abundant free radicals Y, i.e., NO2, HOO, etc. (R2), where the reaction of BrHg +Y could also lead to the …

Light Matter Interactions: A Study Of Soft Materials Using Linear And Nonlinear Spectroscopy, Muhammad Redwan Hassan

Doctoral Dissertations

The adoption of complex fluids for various industrial applications is becoming normal. Complex fluids offer tunability, wide range solubility, and chemical and thermal stability which are the factors that conventional polar and non-polar solvents often lack. However, fundamental studies of these fluid systems are still lacking which is limiting the appropriate use of these complex fluids in many applications. The goal of this dissertation was to study and characterize complex fluids for application in electrolytes for redox flow batteries. Chapter 3 and chapter 4 feature the study of microemulsions and deep eutectic solvents (DES) by fluorescence techniques. Fluorescence studies of …

Turning Ligands On Their Side: Computational Investigation Into The Binding Of N2o And N2 In Transition Metal Complexes, Cole Donald

Electronic Theses and Dissertations

Common greenhouse gas nitrous oxide (N₂O) is a thermodynamically potent and environmentally benign oxidant, making it a desirable target for metal center activation. Unfortunately, N₂O is a poor ligand for transition metals due to its weak sigma-donating and pi-accepting properties; as a result, few transition metal complexes capable of interacting with N₂O have been found. As the primary source of all nitrogen in organisms, abundant gas dinitrogen (N₂) is a crucially important tiny molecule and an essential part of daily existence. However, due to its inertness, it has limited practical uses in …

Near-Ir Laser Ablation Of Simulated Radiologically Contaminated Oxides On Carbon Steel Feeder Pipes, Thao Viet Do

Electronic Thesis and Dissertation Repository

As nuclear power plants age and retire from service, many countries face significant challenges concerning the safe long-term storage and disposal of large volumes of low and intermediate level radioactive wastes (L&ILW). The volumes of metallic waste are of particular concern, as when metal corrodes it produces hydrogen that could lead to pressure build-up in interim storage and disposal. In Canada, a significant fraction of the metallic wastes for Canada Deuterium Uranium (CANDU) nuclear reactors are out-of-core reactor components, such as carbon steel (CS) feeder pipes. The radioactive contamination is expected to be largely confined to the surface oxide layers …

Expanding The Scope Of Clickable Azide-Functionalized Nanoclusters To Include Au144, Johanna A. De Jong

Electronic Thesis and Dissertation Repository

Thiolate-protected Au₁₄₄ nanoclusters (NCs) are an intriguing member of the gold NC family. Their geometric structure, distinct electrochemical features, and susceptibility to structural rearrangement under the duress of ligand exchange have been studied. However, there are currently no established protocols for surface modification or tuning of their ligand shells post synthesis. Here, the direct synthesis of three regioisomers of azide-modified Au₁₄₄ NCs with 60 azide moieties, i.e., Au₁₄₄(SC₂H₄C₆H₄-N₃)₆₀, is reported, in which the azide functionality is located at the ortho-, meta-, or …

Theoretical Studies Of Molecule-Surface Interactions And Dynamics, Yingqi Wang

Chemistry and Chemical Biology ETDs

Gas-surface scattering involves the conversion of energy in different forms in the impinging molecule, possible bond breaking and forming, and the energy transfer across gas-solid interface. Possible energy dissipation channels include adiabatic energy transfer to the motion of surface phonons and non-adiabatic interactions with surface electron-hole pairs. A complete understanding of the interplay of energy dissipation and physical/chemical changes in the molecule is vital for many important applications such as materials fabrication and heterogenous catalysis.

Gas-surface encounters may occur where non-adiabatic effects are negligible. Two such systems were investigated, both with ample experimental data. One is concerned with the scattering …

Frontiers In The Self-Assembly Of Charged Macromolecules, Khatcher O. Margossian

Doctoral Dissertations

The self-assembly of charged macromolecules forms the basis of all life on earth. From the synthesis and replication of nucleic acids, to the association of DNA to chromatin, to the targeting of RNA to various cellular compartments, to the astonishingly consistent folding of proteins, all life depends on the physics of the organization and dynamics of charged polymers. In this dissertation, I address several of the newest challenges in the assembly of these types of materials. First, I describe the exciting new physics of the complexation between polyzwitterions and polyelectrolytes. These materials open new questions and possibilities within the context …

Characterization Of 1d And 2d Materials With Tip-Enhanced Raman Spectroscopy, María Olivia Avilés

Electronic Thesis and Dissertation Repository

Carbon-based materials, such as 1D single-walled carbon nanotubes (SWCNT) or 2D graphene, are promising materials for a variety of applications in energy storage, biosensors, and medical imaging applications. Similarly, beyond graphene, 2D transition metal dichalcogenides (TDM) that can have either a metallic or semiconducting character have gained interest for potential applications in electronics and photonics. Specifically, metallic TMDs such as vanadium disulfide (VS₂) show potential applications in optoelectronics and lithium-ion batteries. On the other hand, semiconducting TDMs like tungsten disulfide (WS₂) show a direct band gap, making them interesting for photovoltaic applications, transistors, or photodetectors. The …

Investigating The Mechanism Of Protein And Peptide Electrospray Ionization, Elnaz Aliyari

Electronic Thesis and Dissertation Repository

Electrospray ionization (ESI) mass spectrometry (MS) is widely used for the detection and characterization of various analytes. However, many fundamental aspects of the ESI process remain poorly understood. Using molecular dynamics (MD) simulations, MS, and ion mobility spectrometry (IMS), this thesis sheds light on the mechanisms whereby gaseous analyte ions are formed from highly charged ESI nanodroplets. After a general introduction (Chapter 1), Chapter 2 focuses on the ion evaporation mechanism (IEM), i.e., the ejection of analyte ions from the droplet surface. The IEM is well established for low MW compounds, but it has remained contentious whether this pathway is …

Investigation Of Carbon Dioxide Oxidation Reaction Pathways On Rh(111) Via Reflection Absorption Infrared Spectroscopy (Rairs), Elizabeth A. Jamka

Dissertations

CO oxidation, RAIRS, Rh(111), Surface Science, UHV

Converting Hydrazone-Based Photoswitches Into Functional Materials, Sirun Yang

Dartmouth College Ph.D Dissertations

The development of new classes of molecular switches with enhanced performance and brand-new functionalities enables practitioners to push the frontiers of adaptive materials. In the realm of photoswitches, the bistability of hydrazones (i.e., molecules that incorporate the C=N-NH functional group) allows for the kinetic trapping of polymer and supramolecular assemblies resulting in multistate actuation and emergent phenomena that are not tractable with other photoswitches. This property has transformed hydrazone photoswitches into powerful tools that can be used in understanding fundamental molecular interactions and how to apply them in modulating the physicochemical properties of materials.

Progressing from disordered to …

Pressure-Induced Modifications To The Structural And Optoelectronic Properties Of 2d Hybrid Organic-Inorganic Perovskites, Jesse Ratte

Electronic Thesis and Dissertation Repository

Recently, 2D hybrid organic-inorganic perovskites (HOIP) have garnered lots of research interest for their applications in optoelectronic devices, especially in solar cells. The optoelectronic properties of 2D HOIPs have yet to be optimized for these applications. High external pressure is well known to induce structural modifications to 2D HOIPs, and thus modify their optoelectronic properties. Herein, we report a study of the effects of high pressure (HP) on the structures and optoelectronic properties of cyclohexane methylamine (CMA) lead iodide (CMA2PbI4) and the structures of N,N-dimethylphenylene-p-diammonium (DPDA) lead iodide (DPDAPbI4).

High pressure measurements of CMA2PbI4 were performed using Raman spectroscopy, Fourier-transform …

Sensitized Photooxidation Of Prenylated Compounds: Mechanisms Of Downstream Dark Effects And Phototoxicity Priming, Shakeela Jabeen

Dissertations, Theses, and Capstone Projects

This thesis consists of four chapters as detailed below.

Chapter 1 discusses a singlet oxygen priming mechanism. Airborne singlet oxygen derived from photosensitization of triplet dioxygen is shown to react with an alkene surfactant (8-methylnon-7-ene-1 sulfonate) leading to ‘ene’ hydroperoxides that in the dark inactivate planktonic E. coli. The ‘ene’ hydroperoxide photoproducts are not toxic on their own, but they become toxic after the bacteria are pretreated with singlet oxygen. The total quenching rate constant (k_T) of singlet oxygen of the alkene surfactant was measured to be 1.1 × 10⁶ M⁻¹ s^{− …}

Design And Surface Modification Of Noble Metal-Based Nanocatalysts, Xuchun Wang

Electronic Thesis and Dissertation Repository

This thesis investigates approaches to modifying the surface structure of noble metal-based nanocatalysts. Noble metal-based nanocatalysts, such as Pt and Pd, play a significant role in heterogeneous catalysis due to their capabilities in activating the cleavage or formation of chemical bonds, but still suffer from the high-cost issue and unsatisfied catalytic performance due to too strong or too weak adsorption of intermediates. Considering the surface specificity of heterogeneous catalysis, Bi, a cheap metal, was used to modify the surface of Pt- and Pd-based nanocatalysts. This thesis aims to unveil the role of Bi in improving their catalytic performance from both …

Intersections Of Environmentalism, Chemistry, And Racism: An Experimental Study Of Halobenzene Hydrogenolysis And Critical Communication Studies Of Equitable Learning Practices Rooted In Black Feminism, Lauren O. Babb

Electronic Theses and Dissertations

Increasing concentrations of fluorinated aromatic compounds in surface water, groundwater, and soil pose threats to the environment. Fundamental studies that elucidate mechanisms of dehalogenation for C-X compounds (where X represents a halide) are required to develop effective remediation strategies. For halogenated benzenes, previously published research has suggested that the strength of the C-X bond is not rate-determining in the overall rate of dehalogenation. Instead, the rate-determining step has been hypothesized to be adsorption of the C-X compound onto the surface of a catalyst. Building on this hypothesis, in this work, we examine the reaction kinetics of fluorobenzene conversion to benzene, …

Driving Piezochromism And Metallicity In Van Der Waals Materials Under Compression, Nathan Harms

Doctoral Dissertations

Complex chalcogenides provide an important platform to explore the interplay between structure, charge, and spin across pressure-induced phase transitions. Where much of the previous research has been focused on tuning these materials towards the single-layer limit, we instead explore the modification of bond lengths and bond angles under compression. In the first project we revealed piezochromism in MnPS₃. We combined high pressure optical spectroscopy and first-principles calculations to analyze the dramatic color change (green → yellow → red → black) that takes place as the charge gap shifts across the visible and into the near infrared region, moving …

Understanding Dynamics Of Polymers Under Confinement: A Molecular Dynamics And Neutron Scattering Study, Supun Samindra Kamkanam Mohottalalage

All Dissertations

The current study probes the structure, dynamics, and rheological behavior of associating polymers including ionomers in melts and solutions as well as conjugated polymers confined into nanoparticles, using molecular dynamics (MD) simulations and neutron scattering techniques. The study focuses on two families of associative polymers, ion containing macromolecules and conjugated polymers.

Polymers that consist of ionizable groups along their backbone found uses in a broad range of applications. Examples include light weight energy storage and generation systems, and biomedical applications, where the polymers act as ion exchange membranes, and actuators. The ionic groups tend to form clusters that are in …

Synthesis And Evaluation Of Water-Dispersed Aryl-Gold Nanoparticles And Applications In Catalysis, Ahmad Al Ahmad

Electronic Theses and Dissertations

Gold nanoparticles have been used in environmental remediation as catalysts through biological and chemical redox reactions of many types of industrial waste including nitroarenes, organic dyes, carbon monoxide, and others. These reactions occur in harsh environmental conditions (e.g. changing temperature, presence of salts, extreme pH solutions) which require robust nanoparticles that can keep their activity and resist aggregation. This thesis describes the synthesis, characterization, and investigation of the catalytic activity of gold-aryl nanoparticles. Gold–aryl nanoparticles (AuNPs-COOH) fabricated using a mild reduction process of a molecular aryldiazonium gold(III) salt [HOOC-4-C6H4N≡N]AuCl4 showed high stability in the presence of high ionic strength salt, …

Designing Dynamic And Degradable Polymeric Materials With Thiol-X Chemistries, Reese Sloan

Dissertations

With plastic production poised to increase in coming years, there arises a need to develop new polymeric materials designed to combat the global pollution crisis. A commonly utilized approach in addressing this challenge is to employ a responsive functional moiety into the polymer architecture. Thiol-X reactions, a commonly utilized class of “click” reactions, have garnered broad implementation in new stimuli-responsive materials. This work specifically focuses on utilizing radical-mediated thiol-ene coupling and base-catalyzed thiol-isocyanate reactions to develop a library of ternary thiol-ene/thiourethane covalent adaptable networks (CANs) and hydrolytically labile poly(thioether ketal) thermoplastics. CANs are a class of network materials capable of …

Computational, Synthetic And Spectroscopic Studies On Donor Acceptor Transition Metal Complexes, Ranjana Dangi

Chemistry and Chemical Biology ETDs

Fundamental advances in our ability to design and construct electronic components at the nanoscale will require new design paradigms. One proposed nanoscale electronic component is the molecular rectifier. Molecular and molecule-based electronic components are advantageous due to their ease of synthetic manipulation, and the fact that the size dimensions of molecules are inherently at the nanoscale (0.5 - 3nm). Our group has shown how the Donor-Bridge-Acceptor biradical approach can be used to derive key structure-property relationships that allow insight into the choice of bridge fragments for molecular rectification by using constitutional isomers of the donor-bridge-acceptor biradical (NN-Th-Py-SQ) (S=1/2 ortho-semiquinonate, …

Evaluation Of The Energetic Factors In Crystalline Pharmaceuticals Using Solid-State Density Functional Theory And Low-Frequency Vibrational Spectroscopy, Margaret P. Davis

Dissertations - ALL

Due to the importance of maintaining stable and effective pharmaceutical solid doses, it is critical to study the variety of solid forms that active pharmaceutical ingredients can adopt including polymorphs, hydrates, and cocrystals. In this work, low-frequency vibrational spectroscopies and rigorous quantum mechanical simulations are combined to provide a new technique for characterizing and investigating pharmaceutically relevant polymorphs, hydrates, and cocrystals as well as a series of model cocrystals. Low-frequency spectra in the sub-200 cm-1 range provide not only unique and characteristic spectra for all of the systems explored here but, along with X-ray structural parameters, they offer a way …

Mechanism Of Sila- And Germafluorenes For Biological Applications, Shelby Jarrett

Dissertations

2,7-disubstituted silafluorenes and germafluorenes, originally designed for OLED applications, are a class of fluorescent dyes that have gained recent interest as probes for bioimaging and as biosensors to monitor cellular dynamics and interactions. Desirable biological probes absorb in the visible region, have high extinction coefficients, high quantum yield and excellent photostability. Here, their spectral properties are investigated under aqueous conditions for relevant biological applications. These molecules display intense blue fluorescence in the solid state and in solution, have high extinction coefficients, and exhibit appreciable solubility in aqueous solution. To better understand potential applications, the mechanism of fluorescence was investigated. It …

Molecular Vibrations And Shape-Selectivity: A Computational Model Of Biofuel Precursors In Zeolites, Babgen Manookian

Doctoral Dissertations

We have used Density Functional Theory (DFT) to model acyclic and cyclic olefins in acidic zeolites. We have studied the impact of host-guest interactions between adsorbed molecules and zeolite frameworks through the lens of molecular vibrations and shape-selectivity. This work considered three zeolite frameworks with varying pore structures and environments: large pore zeolite HMOR and medium pore zeolites HZSM-5 and HZSM-22. A key finding is that for acyclic olefins in acidic zeolites there exists two regimes of host-guest interaction: a strong interaction leading to protonation and a weak interaction between charged guest and zeolite framework. We found that these interactions …

Computational Modelling Of Interfacial Properties Of Droplets, Victor Kwan

Electronic Thesis and Dissertation Repository

Aqueous nanodroplets containing reactive species play an important role in atmospheric chemistry and technology. The presence of atmospheric aerosol particles and the chemical reactions that they host plays a critical role in climate, visibility in the atmosphere, quality of air, and health. Man-made aerosols find applications in ink-jet printing, electrospinning, electrospraying, and ionization methods used in mass spectrometry.

Despite their small size, these systems show complex chemical and physical behaviour because a significant portion of the system is occupied by a liquid-vapour interface. Interfaces are distinct regions that are characterized by large mass density gradients, shape fluctuations, the particular orientation …

A New Insight Into Fungal Cell Wall Architecture By Functional Genomics And Solid-State Nmr Along With Recent Advancements In Dynamic Nuclear Polarization For Analyzing Biomolecules, Arnab Chakraborty

LSU Master's Theses

This dissertation summarizes the findings related to the way by which supramolecular architecture of fungal cell wall changes with genetic mutation, dispensing genes responsible for biosynthesis of cell wall polysaccharides. This is necessary because without perfect picture of how supramolecular assembly changes with genetic mutation it is hard to assess new anti-fungal targets. Alongside this we have highlighted how recent advancement into Dynamic Nuclear Polarization (DNP) methods improved characterization of biomolecules both in case of labeled and unlabeled samples.

First study utilized Solid-state NMR (SSNMR) which is a non-destructive technique hence enabled us for the first time to deduce how …

Monitoring Bacteria Cultures Using Near Infrared (Nir) Binary Spectronephelometry (Bsn), Raman Spectra And Principal Component Analysis (Pca), Steven Ortiz

Dissertations - ALL

Current noninvasive methods cannot continuously and simultaneously monitor the concentrations of cells and media components that define the state of native bacterial cultures, because of changing turbidity. A new technique, binary spectronephelometry (BSN) has the same or better sensitivity and precision for population monitoring as optical density at 600nm (OD600), while simultaneously measuring metabolic processes. The BSN algorithm uses laser induced emission to probe mildly turbid media i.e., propagation of light occurs in the single scattering regime. A BSN "training set" associates a grid of elastic emission measurements, comprising Rayleigh and Mie scattering, and inelastic emission measurements, comprising fluorescence and …

A Study Of Cannabigerolic Acid And Its Derivatives Via Raman Spectroscopy And Density Functional Theory, Trevor Wolfe

Honors Theses

The cannabinoids are a class of molecules endogenous to the cannabis plant. Their scientific relevance has increased in recent years due to the mercurial legal status of marijuana across the United States. Some of the most known are cannabidiol (CBD), δ9-tetrahydrocannabinol (δ9-THC), and δ8-THC due in large part to their widespread use, especially in states where marijuana and related products are legal. However, cannabigerolic acid (CBGA) is arguably the most important cannabinoid; it is enzymatically converted into other acidic cannabinoids, which subsequently undergo non-enzymatic processes (isomerization, thermal decarboxylation, oxidation, etc.) to synthesize further cannabinoids. Although there is a wealth of …