Physical Chemistry Commons^™

Free Energy Approaches To Understanding The Mechanism Of Membrane-Active Peptides, Hannah R. Scott

Graduate Theses, Dissertations, and Problem Reports (ETD)

Cancer is a leading cause of death in the world today. Current methods of treatment fail to distinguish the difference between cancer cells and cells of healthy tissue, leading to off-target effects, often with terminal outcomes. A potential solution to this challenge is to target the cancer cells’ microenvironment. One universal characteristic across all cancer cells is the acidic extracellular environment. The pH-Low Insertion Peptide (pHLIP) is a membrane-active peptide with acid-sensitive function, undergoing folding and insertion into a transmembrane alpha-helix. pHLIP is a promising candidate to be used to deliver anti-cancer agents exclusively to cancer cells. Although the mechanism …

Rational Design Of Small Molecules Targeting Mitochondrial Redox Proteins, Matheus Barbosa Belchior

Graduate Theses, Dissertations, and Problem Reports (ETD)

Reactive oxygen species play a crucial role in many cellular processes. Despite being a natural byproduct of cellular metabolism, overexpression of these species causes damage to the cell, leading to cell dysfunction. Central to the regulation of these highly reactive molecule is the mitochondria. Impairment in its function has been associated with oxidative stress within the cell. Herein, a ligand-based and structure-based approach to design new small molecules to inhibit mitochondrial redox proteins associated with oxidative stress and reactive oxygen species. In the first project two molecules were synthesized and characterized as potential monoamine oxidase B inhibitors. Results showed two …

Individual And Collective Properties Of Tunable Photochemical Belousov-Zhabotinsky Micro-Reactors, Kudakwashe Benedict Shumba

Graduate Theses, Dissertations, and Problem Reports (ETD)

Cell-like model chemical systems are powerful tools that can be used to explore the role of intercellular coupling on population level behaviors in communities of biological cells. Firstly, we present a new method for fabricating such micro-reactors using the photosensitive Belousov–Zhabotinsky (BZ) reaction system employed in silica microparticles. These BZ micro-reactors have a tunable response to photochemical coupling, varying from a fully excitatory response to a fully inhibitory response. Their response can be tuned through variations in either the reactive mixture or, on an individual micro-reactor level, by changes in the synthesis temperature used during the fabrication of the silica …

Experimental And Chemical Modeling Of Applied Dc Electric Field Induced H2 – Air Axisymmetric Laminar Co-Flow Diffusion Flames With Low Carbon Impurities, Susith Dilshan Pathmasiri Gunamuni Halowitage

Graduate Theses, Dissertations, and Problem Reports (ETD)

The effect of externally applied DC electric fields on flame structure was investigated in a stationary atmospheric axisymmetric laminar H₂–Air flame with less than 100 ppm carbon equivalent impurities. Flame OH chemiluminescence signals were recorded using a UV-sensitive CCD array as a function of voltage (+10 to -10 kV) applied to a stainless-steel ring electrode placed around the burner nozzle. Changes in chemiluminescence signal are reported as a function of electrode height above the burner, airflow, and fuel composition. Significant changes in OH* distributions were observed for voltages below -5 kV. Under optimum conditions, the height of the …

Use Of Interlaboratory Studies For The Development Of Consensus-Based Criteria For The Elemental Analysis Of Electrical Tapes, Lacey M. Leatherland

Graduate Theses, Dissertations, and Problem Reports (ETD)

Tape evidence is often used in criminal cases involving violent crimes, kidnappings, improvised explosive devices (IEDs), and drug trafficking. This evidence can reveal potential links between suspects, items, or scenes. The forensic examination of electrical tape can provide investigative leads or offer support to alternative hypotheses evaluated in the courtroom. A conventional analytical scheme includes microscopic examination, Fourier Transform Infrared Spectroscopy (FTIR), Scanning Electron Microscopy Energy Dispersive Spectrometry (SEM-EDS), and Pyrolysis Gas Chromatography Mass Spectrometry (Py-GC/MS). Elemental analysis of electrical tapes is commonly achieved using SEM-EDS; however, recent scientific literature suggests that this analysis can evolve from using SEM-EDS to …

Spiral Wave Teleportation And Multiplex Network Synchronization In Light Sensitive Belousov-Zhabotinsky Systems, Shannyn Alicia Tyler

Graduate Theses, Dissertations, and Problem Reports (ETD)

We experimentally and computationally investigate dynamical behaviors in excitable and oscillatory media using light sensitive Belousov-Zhabotinsky (BZ) systems. These systems are not in a state of thermodynamic equilibrium, and have been proven to show various interesting phenomena including spatiotemporal patterns, self-organization, and chaos. We utilize the BZ reaction, a nonlinear chemical reaction, known for its relaxation-type oscillations, to explore the dynamics of these systems.

We examine spiral wave teleportation in an excitable media as an effective alternate defibrillation method. Spiral waves have emerged as a key phenomenon associated with the initiation and persistence of cardiac arrhythmias. Using a light sensitive …

Exogenous Factors That Impact Huntingtin Aggregation, Adam Skeens

Graduate Theses, Dissertations, and Problem Reports (ETD)

While expansion of a polyglutamine (polyQ) domain is the immediate cause of huntingtin (htt) aggregation associated with Huntington’s Disease (HD), other cellular factors modify aggregation. These include interactions with cellular membranes, protein biding partners, molecular crowding, and proteinaceous seeds. Here, two important factors are biophysically characterized: 1) the interaction of htt with endomembranes and 2) proteinaceous seeds obtained from a variety of htt-derived peptides. In the first project, the aggregation of htt at bilayer interfaces and in the presence of divalent cations was investigated. A major cellular factor implicated in altered htt aggregation is the binding of lipids. Furthermore, the …

Application Of Computational Biophysics Techniques To Characterize Cell Membrane-Associated Events, Kyle Billings

Graduate Theses, Dissertations, and Problem Reports (ETD)

Cell membranes are crowded environments which can modulate protein structure-function relationships through interaction with lipids, other proteins, carbohydrate structures and so on. This work focuses the impact of the membrane environment on two varieties of peptides: Microbial rhodopsin proteins, and cyclic peptides.

Life on Earth is dependent on the ability of plants and microbes to harness sunlight for energy production. Their ability to transform light into carbohydrates requires tailor-made machinery, and for a wealth of microorganisms, microbial rhodopsin proteins (MR) are critical for maintaining the concentration gradients used to produce the energy molecule Adenosine triphosphate (ATP). The central retinal molecule …

Investigation Of Early Complex Formation Of Huntingtin Protein With And Without Lipids, Alyssa R. Stonebraker

Graduate Theses, Dissertations, and Problem Reports (ETD)

Huntington’s disease (HD) is a fatal neurodegenerative disease caused by the expansion of the polyglutamine (polyQ) domain of the huntingtin protein (htt). The expansion of the polyQ domain beyond a threshold of approximately 35 repeats triggers complex toxic aggregation mechanisms and results in altered interactions between htt and lipid membranes. Many factors modulate these processes. One such modulator includes sequences flanking the polyQ domain, most notably the first 17 amino acids at the N-terminus of the protein (Nt17), and environmental factors including the presence of membranous structures. Nt17 has the propensity to form an amphipathic a-helix in the presence of …

Solid State Nmr Analysis Of Insect Wing Membranes, Samuel Eddy

Graduate Theses, Dissertations, and Problem Reports (ETD)

Solid State NMR is a powerful tool for analyzing the chemical composition of insects. Previous studies have used Solid State NMR to investigate the chemical composition and investigate the sclerotization (tanning) process of insect exoskeletons. Acquiring sufficient exoskeleton sample for analysis has been relatively simple. This is however not the case for other components of an insect’s physiology, particularly the wing membrane material. The wings of an insect only compose a small percentage of their overall body mass, and many hundreds to thousands of insects must be processed in order to achieve a few milligrams of wing membrane sample. The …

Novel Modes Of Synchronization And Extreme Events In Coupled Chemical Oscillators, David Allen Mersing

Graduate Theses, Dissertations, and Problem Reports (ETD)

We experimentally and computationally investigate dynamical behaviors in coupled chemical oscillators. These networks of chemical oscillators are created using catalytic Ru(bpy)₃²⁺ loaded cation exchange beads submerged in catalyst-free Belousov-Zhabotinsky (BZ) solutions. Various network structures are created by utilizing the photosensitive nature of the Ru(bpy) ₃²⁺ catalyst. The response of the oscillators due to light stimuli can be characterized by constructing a phase response curve (PRC). The PRC quantifies the excitatory and inhibitory responses of BZ oscillators due to applied light perturbations as a function of the oscillators' phase. Different initial concentrations of reactants in the BZ reaction …

Study Of Resonantly Stabilized Radicals In Combustion Environments, James H. Lee

Graduate Theses, Dissertations, and Problem Reports (ETD)

Resonantly stabilized radicals (RSRs) play an important role in combustion environments due to their high stability resulting from resonance. Many RSRs such as the propargyl, allyl, or benzyl radicals are precursors to the formation of polycyclic aromatic hydrocarbons (PAHs), which can aggregate to form soot. Due to their stability, these RSRs can accumulate in combustion environments in significant quantities. The primary way these radical species are consumed in flames or by reactions with other abundant radicals, by self-recombination of propargyl to form benzene, or in the form of other abundant radicals such as the hydroxyl radical. Experimentally determining the pathways …

From Evaluating The Performance Of Approximations In Density Functional Theory To A Machine Learning Design, Pedram Tavazohi

Graduate Theses, Dissertations, and Problem Reports (ETD)

Density-functional theory (DFT) has gained popularity because of its ability to predict the properties of a large group of materials a priori. Even though DFT is exact, there are inaccuracies introduced into the theory due to the approximations in the exchange-correlation (XC) functionals. Over the 50 years of its existence, scientists have tried to improve the design of the XC functionals. The errors introduced by these functionals are not consistent across all types of solid-state materials. In this project, a high throughput framework was utilized to compare the theoretical DFT predictions with the experimental results available in the Inorganic Crystal …

Heterogeneous Oxidation Of Multi-Component Aqueous Organic Aerosols: The Effect Of Transport Phenomena And Reaction Compartment On Reaction Kinetics., Tadini Wenyika Masaya

Graduate Theses, Dissertations, and Problem Reports (ETD)

The surface-bulk partitioning of small organic molecules in aqueous droplets was investigated using molecular dynamics. The air-particle interface was modeled using a 80-Å cubic water box containing series of organic molecules and surrounded by gaseous OH radicals. The properties of the organic solutes within the interface and the water-bulk were examined at a molecular-level using density profiles and radial pair distribution functions. Molecules containing only polar functional groups such as urea and glucose are found predominantly in the water bulk, forming an exclusion layer near the water surface. Substitution of a single polar group by an alkyl group in sugars …

Electronic Structure Of Early Transition Metal Complexes Supported By Pyridine Polypyrrolide Ligands, Dylan Connor Leary

Graduate Theses, Dissertations, and Problem Reports (ETD)

A thorough study of photoluminescent molecules involving the pyridine polypyrrole(ide) ligand platform has been conducted. A detailed analysis on speciation of the proligand H₂(^MesPDP^Ph) (H₂^MesPDP^Ph = 2,6-bis(5-mesityl-3-phenyl-1H-pyrrol-2-yl)-pyridine) and its dilithium salt Li₂(^MesPDP^Ph) revealed temperature- and solvent-dependent effects. These molecules, along with the hydrochloric acid adduct [H₃(^MesPDP^Ph)]Cl were found to exhibit short-lived photoluminescence in both tetrahydrofuran and benzene solution. These findings confirm the hypothesis that heavy-atom involvement is crucial for the favorable photophysical properties observed for the Zr(PDP)_{2 …}

Gas Phase Reactions Of Cyclopentadiene With Ch And Oh Radicals, Kacee Lynn Caster

Graduate Theses, Dissertations, and Problem Reports (ETD)

The formation of polycyclic aromatic hydrocarbons (PAHs) and carbon-based nanoparticles in combustion environments is driven by the pyrolysis and oxidation of abundant fuel molecules. The subsequent growth of these pyrolytic byproducts is then propagated by reactions with small free radical species like OH, CH, O atoms, and C₂H. Cyclopentadiene (C₅H₆) is a significant five-member combustion intermediate that has been detected in many high temperature reactions, such as in the pyrolysis of jet fuels like JP-10. Experimental and theoretical investigations in the reactions of cyclopentadiene with these small free radical species are necessary towards understanding …

Using Molecular Dynamics To Characterize The Relationship Between Membrane Components And Dynamics And Supramolecular Organization Of Membrane Proteins, Eric Sefah

Graduate Theses, Dissertations, and Problem Reports (ETD)

Molecular dynamics (MD) simulations have gained impetus as a technique for elucidating structural and dynamical information about membrane proteins (MP). In particular, coarse-grained (CG) MD simulations have provided valuable information about the relationship between membrane components and supramolecular organization of MPs. In this work MD simulations are used to characterize the effects of hopanoids on bacterial membrane dynamics and association in a model protein proteorhodopsin (PR), as well as the role of the extended C-terminus of the human adenosine receptor (A_2AR) on its dimerization. PR is found to dimerize in a manner that is dependent on both the …

Huntingtin Aggregation At Interfaces Associated With Membranes And Organelles, Adewale Vincent Adegbuyiro

Graduate Theses, Dissertations, and Problem Reports (ETD)

Huntington’s Disease (HD) is a genetic neurodegenerative disease caused by the expansion of polyglutamine (polyQ) domain within the first exon (exon1) of the huntingtin (htt) protein. Due to this mutation within the polyQ domain, htt aggregates into various toxic species such as oligomers, fibrils, and other amorphous aggregates. While the aggregation of htt strongly correlates with polyQ length, other factors, e.g. interaction with membranes or organelles and posttranslational modifications (PTMs), modulate aggregation. The first 17 N-terminal amino acids (Nt17) that precede the polyQ in htt-exon1 enhances aggregation and facilitated binding of htt to membranous organelles, promoting morphological changes and disfunction. …

Photochemical Motion Control Of Belousov-Zhabotinsky Droplets And Turbulence-Like Patterns In The Aluminum Hydroxide Precipitation System, Syed Jazli Syed Jamaluddin

Graduate Theses, Dissertations, and Problem Reports (ETD)

A Belousov-Zhabotinsky (BZ) droplet that is immersed in an oil-phase can self-propel due to a surface tension gradient that exists on the droplet surface. The surface tension gradient is created as a result of the reactions that occur within and on the surface of the BZ droplet. By affecting the rates of these reactions, the BZ droplet direction can be controlled. In our experiments, we tune the reactions that occur within and on the BZ droplet surface by imposing a light intensity gradient on the droplet. We analyzed the BZ droplet motion and demonstrated that we can control the droplet …

Understanding The Relationship Between Local Environmental Changes And The Function Of The Ph Low Insertion Peptide, Violetta Burns Casamayor

Graduate Theses, Dissertations, and Problem Reports (ETD)

Cancer is the second leading cause of death in the US with over 1.7 million new cases each year. Current cancer treatments tend to also target healthy tissues due to similarities with cancerous ones, resulting in acute side effects. Early detection is the best approach towards defeating cancer, however, modern imaging techniques require sizeable samples, often implying a late stage in the disease. One common attribute of tumors is their acidic microenvironment, which can be taken advantage of.

The pH Low Insertion Peptide (pHLIP) is a membrane-active peptide that can take advantage of the acidic microenvironment surrounding cancer cells. pHLIP …

Modified Firearm Discharge Residue Analysis Utilizing Advanced Analytical Techniques, Complexing Agents, And Quantum Chemical Calculations, William J. Feeney

Graduate Theses, Dissertations, and Problem Reports (ETD)

The use of gunshot residue (GSR) or firearm discharge residue (FDR) evidence faces some challenges because of instrumental and analytical limitations and the difficulties in evaluating and communicating evidentiary value. For instance, the categorization of GSR based only on elemental analysis of single, spherical particles is becoming insufficient because newer ammunition formulations produce residues with varying particle morphology and composition. Also, one common criticism about GSR practitioners is that their reports focus on the presence or absence of GSR in an item without providing an assessment of the weight of the evidence. Such reports leave the end-used with unanswered questions, …

Factors Influencing Huntingtin Aggregation At Surfaces: Implications For Huntington’S Disease, Sharon E. Groover

Graduate Theses, Dissertations, and Problem Reports (ETD)

Huntington’s Disease (HD) is a genetic, neurodegenerative disease characterized by an abnormal polyglutamine (polyQ) expansion in the first exon of the huntingtin protein (htt). The polyQ domain facilitates aggregation and initiates the formation of a diverse collection of aggregate species, including fibrils, oligomers and annular aggregates. The first 17 amino acids of htt (Nt17) directly flank the polyQ domain and is a key factor in htt’s association to membranous structures. In addition to Nt17 being an amphipathic αhelix, it also promotes aggregation through self-association and contains numerous posttranslational modifications (PTMs) that can modulate toxicity and subcellular localization. For in depth …

The Effects Of Membrane Physicochemical Properties On Huntingtin Membrane Association And Downstream Aggregation, Maryssa Beasley

Graduate Theses, Dissertations, and Problem Reports (ETD)

Huntington’s Disease (HD) is a fatal neurodegenerative disorder caused by an expanded glutamine repeat region (polyQ) within the huntingtin protein (htt). As a result of the expanded polyQ domain, htt associates into a variety of toxic aggregate species. The polyQ domain of htt is flanked at the N-terminal end by 17 amino acids (Nt17) that adopt an amphipathic α-helical structure in the presence of binding partners such as lipid membranes. In addition to comprising a lipid binding domain, the Nt17 amphipathic α -helix has been directly implicated in htt aggregation initiation via self-association with other Nt17 α -helices. Due to …

The Impact Of Post Translational Modification On The Aggregation Of The Ss-Amyloid Peptide In The Presence Or Absence Of Lipids, Albert Walton Pilkington Iv

Graduate Theses, Dissertations, and Problem Reports (ETD)

Alzheimer’s disease (AD) is a neurodegenerative condition afflicting 5.7 million Americans with no effective treatments. The pathology of AD is described by the formation of neurotoxic oligomers formed by the self-assembly of amyloid-β (Aβ). The affinity of oligomers for cellular membranes disrupts calcium homeostasis and is believed to be the underlying cause of neurotoxicity; however, due to the metastability of oligomers, it has been difficult to understand their role in membrane interactions and self-assembly. Here we utilize post translational modifications (PTM) to understand the role of specific amino acids on Aβ₄₀-membrane interactions and self-assembly. We employ ThT, AFM, …

Photoluminescent Zirconium Complexes For Visible Light Photoredox Catalysis, Yu Zhang

Graduate Theses, Dissertations, and Problem Reports (ETD)

Early transition metals like zirconium are attractive candidates for the design of luminescent molecules based on earth-abundant elements. Here, a series of zirconium complexes carrying two pyrrolyl-based ligands have been synthesized and characterized. These complexes are photoluminescent upon excitation with visible light and exhibit remarkably long emission lifetimes of hundreds of μs in solution at room temperature. Computational studies using time-dependent density functional theory (TD-DFT) were conducted to identify the nature of the luminescent excited states as mixed intra-ligand/ligand-to-metal charge-transfer (ILCT/LMCT) states. The electrochemistry studies revealed multiple reversible redox events for each zirconium complex. Furthermore, the excited state of the …

Experimental And Modeling Investigation Of The Oh-Initiated Oxidation Of Semi-Solid And Aqueous Saccharide Aerosols, Hanyu Fan

Graduate Theses, Dissertations, and Problem Reports (ETD)

My research focuses on investigating the impact of moisture-induced and oligomer-induced viscosity changes on OH-initiated oxidation of semi-solid aerosols,and the role of gas-liquid interfaces in regulating aqueous aerosol chemistry. Saccharides, which are a major constituent of aqueous atmospheric aerosols, are chosen as model molecules to form highly oxygenated organic aerosols. The experiments are performed using an atmospheric pressure flow-tube reactor with both online VUV-AMS (Vacuum-Ultraviolet Aerosol Mass Spectrometer) and offline GC-MS analysis techniques. The decay rates of saccharide are determined by measuring the loss signal of saccharide in the particle phase as a function of OH exposure (time-integrated total concentration …