In vitro protein selection has had major impacts in the field of protein engineering. Traditional screens assay individual proteins for specific function. Selection, however, analyzes a pool of mutants and yields the best variants. Phage display, a successful selection technique, also provides a reliable link between variant phenotype and genotype. It can also be coupled with high throughput sequencing to map protein mutations; potentially highlighting vital mutations in variants. We propose to apply this technique to cancer therapy. RAF, a serine/threonine kinase, is critical for cell regulation in mammals. RAF can be activated by oncogenic RAS, found in over 30% of cancers, to drive cancer proliferation. Rigosertib, a benzyl styryl sulfone in phase III clinical trials for myelodysplastic syndrome (MDS), is an inhibitor of the RAS binding domain (RBD) in RAF. Phage display can be used to select RAF mutants for RAS binding affinity, in the presence of Rigosertib. High-throughput sequencing of these variants can provide a means of anticipating, and mapping resistance to this anti-cancer drug.

Hemimicelles and admicelles are well-investigated wonders in modern science; they are surfactant monolayers and surface adsorbed micelles, respectively. Capacitance measurements for monitoring the formation of dodecyl sulfate (DS) surfactant monolayer on positively charged gold substrates (planar gold) and the adsorbance of 2-naphthol onto DS surfactant monolayer were performed. The investigation of the electrical control of DS at various concentrations (4, 6, 16, and 32 mM) below and above the critical micelle concentration (CMC= 8 mM) on gold surfaces for analyte preconcentration, prior to chromatographic analysis, is presented. Charged ionic surfactants, such as DS, drawn to a surface of opposite charge (porous nickel substrates coated with gold) serve as a stationary phase to trap organic analytes. It is believed that these DS assemblies gain stability through surfactant chain–chain interactions. The attachment and the removal of the surfactant are controlled using an electric field. Due to the fact that the surfactantanalyte association is released by electrical control, organic solvents, which are used in conventional solid phase extraction, are not required, making this procedure environmentally friendly. Electrical Impedance Spectroscopy was used to investigate the formation of the DS layer and the preconcentration of 2-naphthol in the presence of an applied electric field. High performance liquid chromatography was used to determine 2- naphthol concentrations. Anthracene and 9-anthracenecarboxylic acid were substituted as additional test molecules as well. Presented are the results of the preconcentration of 2-naphthol, anthracene and 9-anthracenecarboxylic acid using the DS layer with various concentrations of sodium dodecyl sulfate on a gold electrode surface.

The discovery of a method by which proteins of interest can selectively be labeled with a probe of choice intracellularly is a longstanding goal in chemical biology research. Conventional labeling techniques have utilized large domain tags but despite the development of small labeling molecules there have been no short peptide sequences known to covalently label a small molecule without the aid of an enzymatic process or metal chelation. We aimed to find a sequence of nucleophilic peptides that reacted covalently and specifically with electrophilic small labeling molecules using mRNA display. Our goal was to show that an electrophilic small labeling molecule that is brought in proximal distance to a protein of interest via affinity can result in nucleophilic attack by a neighboring nucleophilic amino acid to covalently label the protein of interest. Utilizing affinity between a small labeling molecule and a protein of interest to bring them spatially close to one another maximizes the chance that a covalent reaction can take place and provides selectivity between two components in a complex mixture. Towards this goal, we developed several electrophilic fluorescent small molecules. Covalent labeling was achieved using electrophilic bait in the form of sulfonate esters, a polyethylene oxide linker provided structural flexibility, and a fluorescent affinity tag containing a rhodamine backbone served as the potential binding site to a key peptide sequence encoded within a protein of interest. The synthetic routes to access our electrophilic rhodamine B and sulforhodamine 101 fluorophores were optimized. Key intermediates were produced and served as flexible points of modification to make various analogs of our desired electrophilic fluorophores. The affinity between proteins containing the peptide sequence and the fluorescent electrophiles were determined by fluorescence polarization. Covalent labeling was determined to be both time and concentration dependent. The expected published affinity between the peptides and fluorophore was not high enough to produce selective labeling. However, our small labeling molecules were found to be effective at labeling various proteins in vitro. In addition, our electrophilic fluorophores have been found superior to sulforhodamine 101 in live cell imaging of astrocytes.

The ever increasing demand for more efficient and environmentally benign routes for synthesizing target compounds, has led to the use of organometallic catalysts. This demand has created the need to understand the mechanistic details that are at work in these organometallic catalytic cycles. Along with this, there is a demand for new organometallic catalysts that are tailored for specific transformations. This presents a myriad of challenges for organometallic chemists. Unfortunately, it is often difficult to gain an understanding of the reaction mechanisms at work when the intermediates are too short lived to be observed in the condensed phase. It is also very time consuming to synthesize, purify, and characterize organometallic catalysts following standard condensed phase methods. Therefore, it would be beneficial to probe organometallic reactions in a way that the inherent reactivity of the organometallic complex can be uncovered and where purity is not a prerequisite. Using an ion-trap mass spectrometer that has been modified to allow introduction of neutral reagents to the buffer gas, organometallic ion-molecule reactions can be probed in an environment free from solvation effects. This enables the study of the inherent reactivity of the complexes and also provides insight into reaction mechanisms by allowing reactive intermediates to be probed. In addition, organometallic complexes probed in this manner do not need to be pure due to ability of the ion trap to function as a mass filter. This results in a quick and efficient method. This dissertation presents results found during the investigation of the reactions and mechanistic details of gold, silver, and iridium complexes using a modified ion-trap mass spectrometer.

This work presents heuristics for searching large sets of molecular structures for low-energy, stable systems. The goal is to find the globally optimal structures in less time or by consuming less computational resources. The strategies intermittently evaluate and rank structures during molecular dynamics optimizations, culling possible weaker solutions from evaluations earlier, leaving better solutions to receive more simulation time. Although some imprecision was introduced from not allowing all structures to fully optimize before ranking, the strategies identify metrics that can be used to make these searches more efficient when computational resources are limited.

The objective of this study was to evaluate the chemical resistance of common shoe materials regularly worn in undergraduate chemistry laboratories by subjecting the materials to hydrochloric acid and sodium hydroxide. The materials tested were leather, canvas cotton, and polyester. Due to the lack of restriction on undergraduate laboratory footwear, the research discussed in this thesis is important to undergraduate universities. Currently, many universities across the nation only require undergraduate students to wear close-toed, close-heeled shoes in chemistry laboratories, and often the resistance of the shoe material to acids and bases may not be taken into careful consideration. Overall, the results of this experiment revealed that exposure to the different chemical concentrations of NaOH and HCl did not appear to negatively affect the structural integrity of the fabrics, but according to the mass spectrometry results gathered in this experiment, the three fabrics differed in individual complexities as well as in the compounds extracted following acid and base treatments.

Bromoarenes are important aromatic building blocks that are commonly used to synthesize various functional compounds in pharmaceutical, agrochemical and related industries.1,2 This great demand for bromoarenes makes their preparation a widely studied area of synthetic organic chemistry. However, further understanding of the reactivity and regiochemistry of aromatic functionalization reactions is still necessary, as much about the secondary substitution and solvent effects remain unknown. Resonance Theory is a widely used theoretical model to predict the regiospecifity and reactivity of the bromination of various aromatic compounds.3 The reactivity and regiospecificity of many substituted aromatic compounds is well explained using resonance theory.4 However, kinetic understanding of the p-bromination of halosubstituted aromatic compounds has not been investigated to the best of our knowledge.5,6In this thesis, the reactivity and regiospecifity of the p-bromination of activated secondary substituted aromatic compounds as well as media effects on the process will be discussed. Synthesizing bromoarenes has been accomplished using many different experimental setups.7-11 N-bromosuccinimide is the most highly utilized electrophilic aromatic brominating agent. Many of the NBS- based aromatic bromination reactions have been reported using strong acids, strong bases, halogenated solvents, nonpolar solvents and polar solvents alike.12 The bromination reactions reported herein were performed using two different solvents, acetonitrile and acetone, to investigate the effects of solvent polarity on p-bromination. Although acetonitrile is one of the most commonly used solvents in the p-bromination of aromatic compounds, acetone has not been investigated.

The effect of Mg++ ion on the solubility of calcium carbonate was determined using P. K. Weyls "carbonate saturometer." The amount of calcium carbonate precipitated or dissolved was measured for five series of waters when equilibrated with solid carbonate. It was found that the effect of Mg++ ion on solubility depend upon the nature of the solid phase: surface area, coprecipitated Mg++, minerology, etc. Pure low area calcite showed an increase in solubility which could be explained by ion-pair formation, while its other carbonates departed from this behavior.

Protein-tyrosine phosphatases (PTPs) catalyze the hydrolysis of phosphorylated tyrosines by a 2-step mechanism involving nucleophilic attack by cysteine and general acid catalysis by aspartic acid. In most PTPs the aspartic acid resides on a flexible protein loop, consisting of about a dozen residues, called the WPD loop. PTP catalysis rates span several orders of magnitude, and differences in WPD loop dynamics have recently been show to correlate with the rate of enzymatic catalysis. The rate of WPD loop motion could possibly be related to a widely conserved tryptophan residue on the WPD loop. Therefore, point mutants were made in PTP1B (a human PTP) to the conserved tryptophan residue and their effects on catalytic rate and chemical reaction were studied. The results of these studies are presented in this thesis.

<p>In order to extend the applications of aluminium, organic coatings may be applied on sheet materials, for instance for corrosion protection or aesthetic surface finish purposes in the automotive and construction industries, or on foil materials in the flexible packaging industry.</p><p>The most common mechanisms for deterioration and structural failure of organically coated aluminium structures are triggered by exposures to the surrounding environment. Despite the great importance to elucidate the influence of exposure parameters on a buried aluminium/polymer interface, there is still a lack of knowledge regarding the mechanisms that destabilise the structure. It is generally believed that a detailed <i>in situ</i> analysis of the transport of corroding species to the buried interface, or of surface processes occurring therein, is most difficult to perform at relevant climatic and real-time conditions.</p><p>In this work, Attenuated Total Reflection Fourier Transform Infrared Spectroscopy (ATR-FTIR) in the Kretschmann-ATR configuration was successfully applied to <i>in situ</i> studies of the transport of water and ionic species through polymer films to the aluminium/polymer interface upon exposure to ultra pure deionised water and to a 1 M sodium thiocyanate (NaSCN) model electrolyte. Other main processes distinguished were the formation of corrosion products on the aluminium surface and swelling of the surface-near polymer network. Hence, <i>in situ</i> ATR-FTIR was capable to separate deterioration-related processes from each other.</p><p>To perform more unambiguous interpretations, a spectro-electrochemical method was also developed for<i> in situ</i> studies of the buried aluminium/polymer interface by integrating the ATR-FTIR technique with a complementary acting technique, Electrical Impedance Spectroscopy (EIS). While transport of water and electrolyte through the polymer film to the aluminium/polymer interface and subsequent oxidation/corrosion of aluminium could be followed by ATR-FTIR, the protective properties of the polymer as well as of processes at the aluminium surface were simultaneously studied by EIS. The integrated set-up provided complementary information of the aluminium/polymer sample investigated, with ATR-FTIR being sensitive to the surface-near region and EIS being sensitive to the whole system. While oxidation/corrosion and delamination are difficult to distinguish by EIS, oxide formation could be confirmed by ATR-FTIR. Additionally, while delamination and polymer swelling may be difficult to separate with ATR-FTIR, EIS distinguished swelling of the polymer network and also identified ultimate failure as a result of delamination.</p><p>The capability of the integrated ATR-FTIR / EIS <i>in situ</i> technique was explored by studying aluminium/polymer systems of varying characteristics. Differences in water and electrolyte ingress could be monitored, as well as metal corrosion, polymer swelling and delamination.</p>