Chemistry Commons^™

Coherent Vibrational And Dissociation Dynamics Of Polyatomic Radical Cations, Katharine M. Tibbetts

Chemistry Publications

The ultrafast dynamics of polyatomic radical cat- ions contribute to important processes including energy transfer in photovoltaics, electron transfer in photocataly- sis, radiation-induced DNA damage, and chemical reac- tions in the upper atmosphere and space. Probing these dynamics in the gas phase is challenging due to the rapid dissociation of polyatomic radical cations following elec- tron removal, which arises from excess electronic excita- tion of the molecule during the ionization process. This Concept article introduces the reader to how the pump- probe technique of femtosecond time-resolved mass spectrometry (FTRMS) can overcome this challenge to capture coherent vibrational dynamics on the …

Probing Coherent Vibrations Of Organic Phosphonate Radical Cations With Femtosecond Time-Resolved Mass Spectrometry, Derrick Ampadu Boateng, Mi'kayla D. Word, Katharine M. Tibbetts

Chemistry Publications

Organic phosphates and phosphonates are present in a number of cellular components that can be damaged by exposure to ionizing radiation. This work reports femtosecond time-resolved mass spectrometry (FTRMS) studies of three organic phosphonate radical cations that model the DNA sugar-phosphate backbone: dimethyl methylphosphonate (DMMP), diethyl methylphosphonate (DEMP), and diisopropyl methylphosphonate (DIMP). Upon ionization, each molecular radical cation exhibits unique oscillatory dynamics in its ion yields resulting from coherent vibrational excitation. DMMP has particularly well-resolved 45 fs (732 ± 28 cm−1) oscillations with a weak feature at 610–650 cm−1, while DIMP exhibits bimodal oscillations with a period of ∼55 fs …

Multifaceted Water Dynamics In Spherical Nanocages, M. Von Domaros, D. Bratko, B. Kirchner, G. Hummer, A. Luzar

Chemistry Publications

We present a new method to study position- dependent, anisotropic diffusion tensors inside spherically confined systems—a geometry that is common to many chemical nanoreactors. We use this method to elucidate the surprisingly rich solvent dynamics of confined water. The spatial variation of the strongly anisotropic diffusion predicted by the model agrees with the results of explicit molecular dynamics simulations. The same approach can be directly transferred to the transport of solutes to and from reaction sites located at nanoreactor interfaces. We com- plement our study by a detailed analysis of wa- ter hydrogen bond kinetics, which is intimately coupled to …

Molecular Polarizability In Open Ensemble Simulations Of Aqueous Nanoconfinements Under Electric Field, F. Moucka, S. Zamfir, D. Bratko, A. Luzar

Chemistry Publications

Molecular polarization at aqueous interfaces involves fast degrees of freedom that are often averaged-out in atomistic-modeling approaches. The resulting effective interactions depend on a specific environment, making explicit account of molecular polarizability particularly important in solutions with pronounced anisotropic perturbations, including solid/liquid interfaces and external fields. Our work concerns polarizability effects in nanoscale confinements under electric field, open to an unperturbed bulk environment. We model aqueous molecules and ions in hydrophobic pores using the Gaussian-charge-on-spring BK3-AH representation. This involves nontrivial methodology devel- opments in expanded ensemble Monte Carlo simulations for open systems with long-ranged multibody interactions and necessitates further improvements …

Applications Of Chemically Modified Nitrogen Doped Carbon, Zirconium Phosphate, Metal Organic Frameworks, And Functionalized Graphene Oxide Nanostructured Adsorbents In Water Treatment, Ayyob Mohammed A Bakry

Theses and Dissertations

Water contaminations by many pollutants, especially heavy metals such as Pb(II), Hg(II), Cu(II), Cd(II), and Cr(VI) pose many public health and environmental concerns as reported in the list of hazardous substances compiled by the US Environmental Protection Agency due to their high toxicity, refractory degradation, and ease of entering food chain. Adsorption by chelating resins is proven to be the most effective method for the extraction of metal ions from polluted and wastewater. However, traditional absorbents such as activated carbon, activated alumina, clay, zeolite, etc., show limited adsorption abilities for these heavy metal ions. The major goal of this thesis …

Stepwise Solvation Of Organic Radical Cations By Ionic Hydrogen And Halogen Bonding In The Gas Phase, Kyle Mason

Theses and Dissertations

The ability to characterize the interactions between ions and solvent molecules plays a critical role in understanding fundamental aspects of thermodynamics in solution chemistry. These interactions are often difficult if not impossible to observe in solution due to the number of solvent molecules far exceeding that of the ions. However, this challenge can be circumvented in the gas phase which enables the isolation and study of reactions between a single ion and single solvent molecule.

Within the field of ion-molecule chemistry are two sub-categories of interactions known as ionic hydrogen bonds (IHBs) and ionic halogen bonds (IXBs). In these interactions, …

Engineering High Reaction Economy Or, An Intensification/Scoring Program For The Preparation Of Simple And Complex Molecules, Caleb J. Kong

Theses and Dissertations

Success of newly discovered chemistry in academia is often scored in terms of its novelty and level of scholarship. In industrial settings, cost, safety and quality are often times the ruler by which new processes are measured. Our group has identified that there is a gap between these two measures of success and has sought to develop principles in order formalize an approach to synthetic strategy and developing ready-to-implement manufacturing processes for molecules, simple and complex.

Some of these principles include (1) the development and application of new chemical methods and reactor technologies (2) recognition of globally amenable chemical environments …

An Enzymology And Inhibition Study Of A Camp-Dependent Protein Kinase Linked To Acth-Independent Cushing's Syndrome, Nicole Luzi

Theses and Dissertations

Cyclic-AMP dependent protein kinase (PKA) is a key intracellular signal transduction kinase that is modulated by G_s- and G_i-coupled GPCRs. Under normal physiological conditions, PKA exists as an inactive holoenzyme made up of two catalytic subunits and two regulatory subunits. Upon cAMP binding to the regulatory subunits, the catalytic subunits (PKACa) are released to perform various downstream phosphorylation events. However, aberrant PKA activation can cause various diseases including Cushing’s Syndrome, which is an endocrine disorder caused by the overproduction of cortisol by the hypothalamus-pituitary-adrenal hormone system. This disorder can be caused by pituitary adenomas that release …

Expansion Of The Genetic Code To Include Acylated Lysine Derivatives And Photocaged Histidine, William D. Kinney

Theses and Dissertations

The genetic code of all known organisms is comprised of the 20 proteinogenic amino acids that serve as building blocks on a peptide chain to form a vast array of proteins. Proteins are responsible for virtually every biological process in all organisms; however, the 20 amino acids contain a limited number of functional groups that often leaves much to be desired. The lack of diversity addresses the need to increase the genetic repertoire of living cells to include a variety of amino acids with novel structural, chemical, and physical properties not found in the common 20 amino acids. In order …

Biometal-Induced Structural Consequences Of Α-Synuclein – The Parkinson’S Disease Protein, Dinendra L. Abeyawardhane

Theses and Dissertations

The pre-synaptic protein α-Synuclein (αS) is often linked to the pathology of Parkinson’s disease (PD), an age-related neurodegenerative disorder. Lewy bodies, the cytopathological hallmarks of PD, are found to be rich in aggregates of misfolded αS protein. Metal dyshomeostasis has also been linked to PD due to the accumulation of iron in the substantia nigra pars compacta, and diminished copper levels reported in this same region. Metal dyshomeostasis in the brain coupled with oxidative stress can enhance the aggregation of αS. Recently, it was confirmed that mammalian αS is universally acetylated at the N-terminus, a common post-translational modification in …

The Development Of Intrinsically Cell-Permeable Peptide Libraries Using Mrna Display, Nicolas A. Abrigo

Theses and Dissertations

Peptides are emerging as promising therapeutics due to their inhibitory affinity towards protein-protein interactions (PPI). However, peptides have been limited mainly by their poor bio-stability and lack of cell permeability. Efforts to generate drug-like peptides have led to the development of macrocyclic peptides, which exhibit improved stability. Yet, most macrocyclic peptides still require the assistance of a cell penetrating peptide (CPP) for cellular entry.

High throughput technologies have been exceptional tools for the discovery of peptides to interrupt PPIs. This work details the recent advancements we have made to improve our high throughput technique, mRNA display, to yield more therapeutically …

Nanostructured Materials For Photocatalysis, Water Treatment And Solar Desalination, Hiran D. Kiriarachchi

Theses and Dissertations

Maintaining a constant supply of clean drinking water is among the most pressing global challenges in our time. About one-third of the population is affected by the water scarcity and it can only get worse with climate change, rapid industrialization, and the population growth. Even though nearly 70 percent of the planet is covered by water, the consumable freshwater content is only 2.5 percent of it. Unfortunately, the accessible portion of it is only 1 percent. Even so, most of the freshwater bodies are choked with pollution. Considering the vast availability of saline water on the planet and the increasing …

Explosive Residue Transfer From Various Explosive Ordinance Disposal (Eod) Render Safe Procedures (Rsp), Joseph A. Stein

Master of Science in Forensic Science Directed Research Projects

Before an IED is sent to a laboratory for analysis, it needs to be rendered safe if it did not already initiate. Render safe procedures (RSPs) include utilizing a percussion-actuated non-electric (PAN) disrupter or a mineral water bottle disrupter. Each disrupter utilizes explosives to render the device safe by breaking open the container or disrupting the fuzing system. However, the same explosives used in the RSP are also used by criminals in IED construction. As such, the explosives used in the RSP can cause problems with the interpretation of the results from forensic analysis of the IED fragments. Compounds of …

Metallic Systems At The Nano And Micro Scale: Bimetallic Nanoparticles As Catalysts And Mcraly Bond Coats In Thermal Barrier Coatings, Kenneth Kane

Theses and Dissertations

The dissertation is split into two parts. The first part will be focused on changes in material properties found at the nanoscale, as miscibility and electronic structure can change significantly with size. The formation of classically-immiscible bimetallic nanoparticles (BNPs) becomes favorable at the nanoscale and novel catalytic properties can emerge from the bimetallic alloying. The formation of alloyed and non-alloyed BNPs is achieved through pulse laser ablation (PLA) and a significant increase in catalytic activity is observed for both. Recently discovered, the increased activity in the non-alloyed BNPs, deemed multicomponent photocatalysis, is examined and the proposed mechanism discussed. The second …

Development And Characterization Of Stationary Phase Gradients For High Performance Liquid Chromatography, Anna Forzano

Theses and Dissertations

Choosing a stationary phase is the first step in developing a liquid chromatography (LC) separation method, where the selectivity is governed by the differential interactions of the analytes with the stationary and mobile phases. Introducing a gradient in stationary phase functionality allows for tuning of analyte retention, translating to a possible improvement in selectivity and an increase in resolution versus that offered by uniform stationary phases.

In this work, C₁₈-silica, phenylbutyl-silica, and phenylbutyl-ammonium opposed continuous stationary phase gradients were fabricated using controlled rate infusion (CRI) on particle packed LC columns. Characterization of the stationary phase was carried out …

Non-Covalent And Covalent Interactions Between Phenylacetylene And Quinoline Radical Cations With Polar And Non-Polar Molecules In The Gas Phase, Adam C. Pearcy

Theses and Dissertations

Gas phase molecular clusters present an ideal medium for observing factors that drive chemical reactions without outside interferences from excessive solvent molecules. Introducing an ion into the cluster promotes ion-molecule interactions that may manifest in a variety of non-covalent or even covalent binding motifs and are of significant importance in many fields including atmospheric and astronomical sciences. For instance, in outer space, molecules are subject to ionizing radiation where ion-molecule reactions become increasingly competitive to molecule-molecule interactions. To elucidate individual ion-molecule interaction information, mass spectrometry was used in conjunction with appropriate theoretical calculations.

Three main categories of experiment were conducted …

Metal Nanoparticle Synthesis By Photochemical Reduction With A High-Intensity Focused Laser Beam, Victoria K. Meader

Theses and Dissertations

Colloidal, metallic nanoparticles have myriad applications, but they are most ideal when they are monodisperse, and demonstrate maximum catalytic utility when they are small (< 5 nm) and uncoated; because their surface area is accessible and maximized. Laser- assisted metal nanoparticle synthesis is a ‘green’ method that has become a topic of active research because it is able to produce uncoated or ‘naked’ products. The nanoparticles synthesized in this work were formed through the reduction of metal salts in aqueous solutions; but the reducing agent is an electron-dense microplasma generated by the laser pulse interacting with the media. Because no chemical reducing agents or stabilizers are needed, the products have no surfactants.

The underlying reaction mechanisms that drive this type of synthesis are generally understood, however, there is insufficient detail that would allow control over the formation of ultimate product morphologies and size distributions. The metals examined in this thesis are: gold, whose formation follows an autocatalytic rate law; and silver, whose formation follows a first-order rate law. Through my research, I was able to …

2nd Tier Assay For The Detection Of Congenital Adrenal Hyperplasia By Virginia’S Newborn Screening Laboratory: Steroid Profile By Hplc-Ms/Ms, Christopher E. Nixon

Theses and Dissertations

Congenital Adrenal Hyperplasia (CAH) encompasses several disorders related to disruptions in the adrenal steroid production pathway. These disruptions may cause virilization of the external female sex organs, incorrect gender assignment, precocious puberty, and in the most severe form, may cause life-threatening salt wasting and adrenal crisis if not detected and treated early in the newborn period.

17α-Hydroxyprogesterone (17-OHP) is the primary target for immunofluorescence detection of CAH from dried blood spots in newborn screening (NBS). Unfortunately, current immunoassay techniques for the detection of CAH suffer from high false positive rates. The primary factors contributing to false positive determinations can include …

Adhesion At Solid/Liquid Interfaces, Neda Ojaghlou

Theses and Dissertations

The adhesion at solid/liquid interface plays a fundamental role in diverse fields and helps explain the structure and physical properties of interfaces, at the atomic scale, for example in catalysis, crystal growth, lubrication, electrochemistry, colloidal system, and in many biological reactions. Unraveling the atomic structure at the solid/liquid interface is, therefore, one of the major challenges facing the surface science today to understand the physical processes in the phenomena such as surface coating, self-cleaning, and oil recovery applications. In this thesis, a variety of theory/computational methods in statistical physics and statistical mechanics are used to improve understanding of water adhesion …

Electrokinetic Flow Of Aqueous Electrolyte In Amorphous Silica Nanotubes, Chris D. Daub, Natalie Cann, D. Bratko, Alenka Luzar

Chemistry Publications

We study the pressure-driven flow of aqueous NaCl in amorphous silica nanotubes using nonequilibrium molecular dynamics simulations featuring both polarizable and non-polarizable molecular models. Different pressures, electrolyte concentrations and pore sizes are examined. Our results indicate a flow that deviates considerably from the predictions of Poiseuille fluid mechanics. Due to preferential adsorption of the different ionic species by surface SiO! or SiOH groups, we find that a significant electric current is generated, but with opposite polarities using polarizable vs. fixed charge models for water and ions, emphasizing the need for careful parameterization in such complex systems. We also examine the …

Curvature Dependence Of The Effect Of Ionic Functionalization On The Attraction Among Nanoparticles In Dispersion, B. Shadrack Jabes, D. Bratko, Alenka Luzar

Chemistry Publications

Solubilization of nanoparticles facilitates nanomaterial processing and enables new applications. An effective method to improve dispersibility in water is provided by ionic functionalization.We explore how the necessary extent of functionalization depends on the particle geometry. Using molecular dynamics/umbrella sampling simulations, we determine the effect of the solute curvature on solventaveraged interactions among ionizing graphitic nanoparticles in aqueous dispersion. We tune the hydrophilicity of molecular-brush coated fullerenes, carbon nanotubes, and graphane platelets by gradually replacing a fraction of the methyl end groups of the alkyl coating by the ionizing –COOK or –NH3Cl groups. To assess the change in nanoparticles’ dispersibility in …

Radical Chemistry In A Femtosecond Laser Plasma: Photochemical Reduction Of Ag+ In Liquid Ammonia Solution, Victoria K. Meader, Mallory G. John, Laysa M. Frias Batista, Syeda Ahsan, Katharine M. Tibbetts

Chemistry Publications

Plasmas with dense concentrations of reactive species such as hydrated electrons and hydroxyl radicals are generated from focusing intense femtosecond laser pulses into aqueous media. These radical species can reduce metal ions such as Au3+ to form metal nanoparticles (NPs). However, the formation of H2O2 by the recombination of hydroxyl radicals inhibits the reduction of Ag+ through back-oxidation. This work has explored the control of hydroxyl radical chemistry in a femtosecond laser-generated plasma through the addition of liquid ammonia. The irradiation of liquid ammonia solutions resulted in a reaction between NH3 and OH·, forming peroxynitrite and ONOO−, and significantly reducing …

Nucleation And Growth Of Gold Nanoparticles Initiated By Nanosecond And Femtosecond Laser Irradiation Of Aqueous [Aucl4]-, Collin Rodrigues, Julian A. Bobb, Mallory G. John, Sergey Fisenko, M. S. El-Shall, Katharine M. Tibbetts

Chemistry Publications

Irradiation of aqueous [AuCl4]with 532 nm nanosecond (ns) laser pulses produces monodisperse (PDI = 0.04) 5 nm Au nanoparticles (AuNPs) without any additives or capping agents via a plasmon- enhanced photothermal autocatalytic mechanism. Compared with 800 nm femtosecond (fs) laser pulses, the AuNP growth kinetics under ns laser irradiation follow the same autocatalytic rate law, but with a significantly lower sensitivity to laser pulse energy. The results are explained using a simple model for simulating heat transfer in liquid water and at the interface with AuNPs. While the extent of water superheating with the ns laser is smaller compared to …

Biosensing And Catalysis Applications Of Nanoporous Gold (Npg) And Platinum-Speckled Nanoporous Gold (Npg-Pt) Electrodes, Christopher J. Freeman

Theses and Dissertations

The importance of porous materials has risen substantially in the last few decades due to their ability to reduce the size and cost of bioanalytical devices and fuel cells. First, this work aims to describe the fabrication of nanoporous gold (NPG) electrodes that are resistant to electrode passivation due to fibrinogen biofouling in redox solutions. The effect on potentiometric and voltammetric experiments was seen as a deviation from ideal behavior on planar gold electrodes, whereas NPG electrodes were consistently behaving in a Nernstian fashion at low concentrations of ferri-ferrocyanide (£100 mM). An improvement in electrode behavior on NPG electrodes versus …

Synthesis And Characterization Of Magnetic Cabides And Oxides Nanomaterials, Hei Man Tsui

Theses and Dissertations

The design and development of nanoparticles is of great interest in the current energy and electronic industry. However, based on the current materials available the production cost can be high with insignificant magnetic and mechanical properties. Specifically, rare-earth magnetic materials composed of neodymium and samarium are known for their high magnetic performance, however, due to the cost of development there is a need to develop a versatile and cost effective material. Alternatively, cobalt carbide nanomaterials have shown to be a promising alternative for rare-earth free magnets as they exhibit comparable properties as hexaferrite magnetic materials. The primary goal of this …

5-Ht2b Receptor-Mediated Cardiac Valvulopathy, Pallavi Nistala

Theses and Dissertations

5-HT_2B receptor agonism causes cardiac valvulopathy, a condition characterized by thickening of the heart valves and as a result, regurgitation of blood within the heart. The anti-obesity drug fenfluramine, which was originally prescribed as an anorectic, was withdrawn from the market due to causing cardiac valvulopathy. Fenfluramine, after metabolism by N-dealkylation, produces the metabolite norfenfluramine, which acts as a more potent valvulopathogen. The same was seen with MDMA (ecstasy), a popular drug of abuse, which is metabolized by N-dealkylation to produce MDA, a more potent valvulopathogen. Glennon and co-workers. studied a series of 2,5-dimethoxy-4- substituted phenylisopropylamines (DOX type) hallucinogens …

Mechanistic Studies Of Proton-Coupled Electron Transfer Reactions Involving Antioxidants, Kejie Meng

Theses and Dissertations

The objective of the research was to investigate proton-coupled electron transfer (PCET) reactions involving antioxidants to gain insight into the detailed mechanisms of glutathione (GSH), Trolox, and α-tocopherol (α-TOH). PCET reactions are complex redox reactions that transfer electrons and protons sequentially or in concert. These reactions are ubiquitous in natural or artificial processes that produce electrochemical energy that is extractable as electricity or as chemical fuels of high energy content. Examples of processes based on PCET are photosynthesis, respiration, nitrogen fixation, carbon dioxide reduction, redox fuel cells, and artificial photosynthesis. Antioxidants were selected as a PCET model to understand the …

Gas-Phase Studies Of Nucleophilic Substitution Reactions: Halogenating And Dehalogenating Aromatic Heterocycles, Leah L. Donham

Theses and Dissertations

Halogenated heterocycles are common in pharmaceutical and natural products and there is a need to develop a better understanding of processes used to synthesize them. Although the halogenation of simple aromatic molecules is well understood, the mechanisms behind the halogenation of aromatic heterocycles have been more problematic to elucidate because multiple pathways are possible. Recently, new, radical-based mechanisms have been proposed for heterocycle halogenation. In this study, we examine and test the viability of possible nucleophilic substitution, S_N2@X, mechanisms in the halogenation of anions derived from the deprotonation of aromatic heterocycles. All the experiments were done in a …

Laser Synthesis Of Nanomaterials Incorporated Within High Surface Area Materials: Applications For Heterogeneous Catalysis, Water Treatment, And Photothermal Energy Conversion, Julian A. Bobb

Theses and Dissertations

Chemical methods are generally used for the synthesis of active nanoparticles (metals, semi-metals, metal oxides, and etc) supported on high surface area materials. Chemical methods involve using strong solvents, harmful gases (H₂ & CO), and high temperature techniques such as high boiling solvents, calcination and pyrolysis. The main drawbacks of using this approach, is the prevalence of chemical agents on nanomaterials which tends to negate its applications. Alternatively, photochemical and photothermal methods are widely being considered for the synthesis and design of nanomaterials.

For these studies, the active nanomaterials incorporated within high surface area materials were prepared by the …

Investigation Of Gold(Iii) Complexes With Hiv-Ncp7 And Models, James Beaton

Theses and Dissertations

The medicinal uses of gold date as far back as 2500 B.C. in China. In modern times, gold has been used in the treatment of a number of different human diseases including rheumatoid arthritis, cancer, and viral infections. This dissertation will focus on the development of gold complexes for the purpose of selective inhibition of HIV NCp7, a 55 amino acid zinc finger protein with two Cys₃His zinc binding domains.

NCp7 is involved in a number of viral life cycle processes including activation of reverse transcription, integration, DNA recognition, RNA packaging, and formation of the viral envelope. The …