Physical Sciences and Mathematics Commons^™

Mechanisms And Applications Of Improved Protein Analysis By Desorption Electrospray Ionization Mass Spectrometry (Desi-Ms), Roshan Javanshad

Dissertations

Electrospray ionization mass spectrometry (ESI-MS) is a soft ionization technique that allows detection of macromolecules, such as intact proteins, by the formation of multiply charged ions from solutions. Desorption electrospray ionization mass spectrometry (DESI-MS) is an ambient ionization technique that directly samples analyte from a surface during ESI-MS analysis. Although DESI-MS is highly accomplished at the analyses of metabolites, lipids, and other small molecules, it is far more limited when it comes to protein analysis. While most of the field in ambient ionization MS has moved towards primarily applications, our approach has been to explore the use of DESI-MS and …

Exploration Of Fluorinated Α,Β-Dehydroamino Acids And Their Structure, Austin Lesueur

Undergraduate Honors Theses

This thesis explores the synthesis of fluorinated α,β-dehydroamino acids, specifically a fluorinated dehydrovaline derivative. Previous work has been done on the equivalent dehydrovaline derivative without fluorine present and this work builds toward the fluorinated version with the goal of comparing the two structurally. The synthesis presented here pulls from previous synthetic strategies employed for dehydrovaline while also exploring the synthetic impact of the electronegative fluorine atoms.

Synthetic Methods And Biological Applications Of Nitrogen Heterocycles To Compounds Of Biological Interest., Jarrid Ronnebaum

Electronic Theses and Dissertations

Thalidomide analogues were synthesized utilizing optimized click conditions from 3-azidoglutarimide and an array of arylacetylenes or N-ethynyl/N-propargyl phthalimide derivatives. The intermediate, 3-azidoglutarimde, was pivotal and yielded a new and scalable synthesis. The reaction conditions utilized a copper sulfate/sodium ascorbate system in aqueous tetrahydrofuran to propagate the dipolar cycloaddition reactions between the azidoglutarimide and the alkynyl coupling partners. The first explored substrates were substituted arylalkynes to optimize the click reaction. Arylalkynes selected were to exhibit similar electron deficient rings to mimic phthalimide. Along with the synthesis of click thalidomide analogues, click analogue of the antiangiogenic and more potent …

Advances In Amino Acid Analysis For Marine Related Matrices And Its Application To Coastal Shelf Settings In The Canadian Arctic, Rachel M. Mcmahon

OES Theses and Dissertations

Amino acids comprise up to 50% of organic matter in cellular material and are a major fraction of oceanic organic carbon. Amino acids are also considered highly labile during organic matter recycling, making them useful proxies for organic carbon cycling. Nevertheless, analysis of individual amino acids has been burdened by lengthy derivatization and complex analysis since the 1950s. In this thesis, I describe the modification of advanced analytical techniques, developed in the biomedical field, for analysis of marine matrices which allow the determination of at least 40 amino acids without the need for lengthy sample preparation and derivatization, twice the …

Organocatalyzed Synthesis Of Epoxides From Chalcones Utilizing Amino Acids, Sabrina N. Kegeler

Masters Theses

The epoxide functional group is important throughout the chemical and pharmaceutical industries, as well as in nature. In the chemical industry, epoxides are present in resins and fragrances. In the pharmaceutical industry, epoxide-containing compounds are used as intermediates in the manufacturing of drugs. In nature, many natural products contain epoxide groups and are used for medicinal purposes, and for models to create synthetic molecules.

One approach to epoxide synthesis involves the use of an alkene precursor, a base, and an oxidizing agent. This is where my investigations began. The first step was to optimize the epoxidation reaction, examining substrate scope, …

A Comprehensive Analysis Of Aromatic-Proton Mediated Hydrogen Bonds, Mona S. Alshamrani

Electronic Theses and Dissertations

Hydrogen bonds play critical role in folding, structure and recognition of biological macromolecules (e.g., proteins, RNA, DNA). In addition to classical hydrogen bonds (e.g., ─OH---O=, ─OH---O─, ─NH---O─ etc.), structural analysis of protein and nucleic acids, almost a decade ago, showed that hydrogen bonds (e.g., CH---O) with hydrogen atoms on aliphatic carbon atoms (hereafter, aliphatic-protons) also play very important role in the structure and function of biomolecules. Even though, protons of aromatic ring systems (hereafter, aromatic-protons) are more polar than the aliphatic-protons, systematic analysis of hydrogen bonds of aromatic-protons have not been carried out. Therefore, I carried out a systematic analysis …

Synthesis And Catalytic Evaluation Of Novel C-Alpha-Methyl-Beta-Proline Analogues, And Concise Synthetic Approach To Nh-Fmoc-S-Trityl-C-Alpha-Methyl Cysteine, Hari Kiran Kotapati

Dissertations

In the field of chemistry there is a growing demand for small molecule organocatalysts such as amino acids, more specifically proline and its analogues, which could catalyze various key chemical reactions in the synthesis of several biologically important molecules. Even though natural proline is reported to catalyze various chemical reactions, its use as organocatalyst is limited mainly due to the solubility issues in the reaction media and high catalyst loadings, which is not very ideal for bulk scale manufacturing. To address these limitations we planned to develop unnatural analogues of proline that could catalyze the reactions with lower catalyst loadings …

Effects Of Anions And Amino Acids On Surface Tension Of Water, Diana Al Husseini

Senior Honors Projects, 2010-2019

Hofmeister series is a set of ions in order of their abilities to affect physical properties in aqueous solutions. Franz Hofmeister was the first to discover the specific ion effects on protein solubility in aqueous solutions. Although the Hofmeister phenomena are general, their mechanisms are still not fully understood. Herein, we use optical tensiometry by a pendant drop method to study the Hofmeister anion effects on the surface tension of water. It has been observed that the surface tension of water increases linearly as the salt concentrations increase. The effects of salts follow a specific trend with respect to the …

Determination Of Thiamine In Solution By Uv-Visible Spectrophotometry: The Effect Of Interactions With Gold Nanoparticles, Michael Vincent Zielinski

Master's Theses and Doctoral Dissertations

The method presented here provides the foundation for a simple and selective qualitative determination of thiamine in solution. Gold nanoparticles in the presence of thiamine results in the formation of a secondary peak in the absorbance spectrum of the mixture. This peak can be used as an indicator of thiamine, which is useful for the qualitative analysis of solutions, and may provide an alternative to other methods for evaluating thiamine in blood and other biological systems. This method uses gold nanoparticles of a size around 20 to 30 nm and involves their selective interaction with thiamine, compared to selected amino …

(S)-Trifluoroselenomethionine : A New Non-Natural Amino Acid With Enhanced Methioninase-Induced Cytotoxicity Toward Human Colon Cancer Cells, Stephene Nathele Lodge

Legacy Theses & Dissertations (2009 - 2024)

Abstract

Identification Of Persistent Long Range Interactions In GA95 And GB95 Through Thermal Unfolding Simulations, Milen Redai Tesfamariam

Chemistry & Biochemistry Theses & Dissertations

For over five decades, different experiments have been performed to research how proteins attain their native three dimensional structures. However, the folding problem continues to be a puzzle in modern science. The design of two proteins that have maximal sequence identity but different folds and functions is one method that is being used to study the relationship between protein structure and amino acid sequence. In particular, mutant proteins of Streptococcus protein G, G_A and G_B, have 95% sequence identity and a 3a helix fold and β4/a fold, respectively. Molecular dynamics simulations of G_A95 …

Chiral Recognition Study Of A Bimolecular Process In Amino Acid Chiral Ionic Liquids, Laurel Millikan Heckman

Undergraduate Honors Thesis Collection

In this study, chiral ionic liquid (CIL) solvents were prepared and tested for their chiral discrimination ability by probing with luminescence quenching. The CIL's were also tested for their impurities, viscosity and density. These experiments will help to determine the ability of CIL's to act as solvents in asymmetric catalysis. The chiral ionic liquids in this study were composed of amino acid methyl ester cations and bis(trifluoromethane) sulfonimide or bistri flimide anions (i.e. I-alanine methyl ester bistriflimid e, d-alanine methyl ester bistr iflim ide and I-leuci ne methyl ester bistriflimde). Circularly polarized luminescence (CPL) and its quenching in the chiral …

A New Photochemical Method For The Preparation Of Amino Acid-α-Phenylthioesters And Peptide-α-Phenylthioesters, Tyrone Hogenauer

Open Access Theses & Dissertations

We describe the development of a novel resin with a photoreactive N-acylnitroindoline linker that allows for the synthesis of amino acid- (in solution) or peptide-α-thioesters using standard Fmoc/t-Bu standard solid phase peptide synthesis (SPPS). Recent advances have shown that the yields of this thioesterification reaction have dramatically increased due to a simple change in the order of addition of reagents. Upon illumination with UV-light, in the presence of N-hydroxybenzotriazole (HOBt), the amino acid- or peptide-α-OBt ester is generated by direct photo-release from the nitroindoline linker with minimal epimerization, followed by reaction with thiophenol in the dark to produce amino acid-α-phenylthioesters …

The Use Of Fourier Transform (Ft) Surface-Enhanced Raman Scattering For Biochemical Analysis, Robert Butler Jeffers

Chemistry & Biochemistry Theses & Dissertations

Surface-enhanced Raman scattering (SERS) is a powerful spectroscopic technique that has created exciting opportunities in the field of bioanalytical chemistry, where it combines ultrasensitive detection of biologically relevant molecules with vibrational spectroscopy. Due to the difficulties in preparing reproducible SERS active substrates, SERS has been mainly used as a qualitative tool. In order for SERS to be utilized as a viable tool for quantitative analysis, simple, facile SERS substrates which generate clean, highly reproducible signals must be developed. This dissertation deals with the evaluation of three different methods of SERS that led to the development of a novel substrate for …

Polymer Microchips For Capillary Electrophoresis And Electric Field Gradient Focusing Of Biomolecules, Ryan Thomas Kelly

Theses and Dissertations

Polymeric materials have seen increasing use as microfluidic device substrates due to their low cost and the simplicity of templated fabrication procedures. I showed that poly(methyl methacrylate) (PMMA) microdevices could be enclosed in a boiling water bath, which allowed the seal to form more quickly than in conventional approaches, and enabled microchannels to remain hydrated throughout the bonding process. Microchip capillary electrophoresis (µ-CE) devices were fabricated using water-based enclosure, and a mixture of fluorescently labeled amino acids was separated in 30 s in these microchips. To create more robust capillary electrophoresis (CE) microdevices with improved separation performance, phase-changing sacrificial materials …

Guest-Host Chemistry Of P-Sulfonatocalix[6]Arene And Nizatidine, Galia Debelouchina

Honors Theses

This work investigates the guest-host chemistry in water of p-sulfonatocalix[6]arene and a number of guests related to the amino acids arginine and lysine. Two questions are particularly important: what are the interactions that drive guest-host binding and what is the role of the solvent. The answers to these questions are investigated with isothermal titration calorimetry (lTC), which gives K, ?H, and ?S, and pressure perturbation calorimetry (PPC), which allows the calculation of the thermal coefficient of expansion ? and relating it to a molecule's structure-breaking or structure-making properties. The ITC data suggests that hydrogen bonding and charge-charge interactions are the …

Synthesis, Characterization And Study Of Novel Reagents For The Detection Of Saccharides And Amino Acids, Nadia Nadette St. Luce

LSU Doctoral Dissertations

The design of synthetic receptors for the recognition and sensing of saccharides and amino acids is currently a major challenge. This is due to inherent structural similarity and a lack of chromophoric or fluorophoric properties of these compounds. The synthesis and study of novel detection agents for bioactive molecules as well as mechanistic studies are presented herein. The elucidation of the mechanism by which tetraarylboronic acid resorcinarene interact with sugar molecules and promote a solution color change is explored. This vast collaborative study, reveals that DMSO solutions of boronic acid functionalized resorcinarene macrocycles afford visual color changes upon heating or …

Design, Synthesis, And Applications Of Bio-Derived Crosslinking Monomers For Molecular Imprinting, Martha Sibrian-Vazquez

LSU Doctoral Dissertations

Most of the research in the field of molecular imprinting has been focused on the development of new functional monomers, in order to improve the molecular recognition properties afforded by these materials. The role of the crosslinking monomer has often been overlooked, since it is considered an inert component that only provides a scaffold to support the binding sites. However, the crosslinking monomer represents a high percent (80-90%) of the composition of molecularly imprinted polymers (MIPs), which can have a large influence on the MIPs properties. This research addresses the design, synthesis, and applications of new crosslinking monomers for molecular …

Artificial Peptides Containing Ca,A- Disubstituted Amino Acids: Synthesis, Conformational Studies, And Application As Β-Strand Mimics, Yanwen Fu

LSU Doctoral Dissertations

Short peptides containing C^α,α-dipropylglycine (Dpg) at alternating sequence positions were synthesized and examined for conformational behavior. Peptide assembly was performed using Fmoc-solid-phase chemistry where the coupling with PyAOP could be significantly enhanced at elevated temperature. Circular dichroism (CD) and NMR conformational studies revealed that incorporation of Dpg residues induced folded structures into peptides. It was observed that Dpg residues adopted helical conformation in a helix-promoting sequence. The resulting helical structure was comprised of consecutive β-turns whose structure was stabilized by salt bridge in aqueous solution. In this study, the preparation of sterically and polyfunctional C^α,α-disubstituted amino …

Polymerization Of Amino Acids On Kaolinite, Z. Badri Adnani-Gleason

Dissertations and Theses

In the origin of life on the primitive earth a major step must have involved the condensation of amino acids to form the first polypeptides. Several suggestions as to how this might have occurred have been made by other workers. One of the more appealing proposals is that the polymerization was catalyzed by clay minerals. It has been reported, for example, that L-apartic acid polymerizes significantly faster than D-aspartic in the presence of kaolinite in aqueous suspension at 90˚. In this work an attempt was made to repeat this report and extend the pH range to include values presumably present …

A Calorimetric Study Of Metal Amino Acid Complexes In Aqueous Solution. I. The Copper (Ii) Glycine System. Ii. The Nickel (Ii) Glycine, Alanine And Phenylalanine Systems, Wilbur Orme Greenhalgh

Theses and Dissertations

Calorimeter values were obtained for the standard enthalpy change for the following reactions at 10,25, and 40 degrees C.: 1. The dissaciation of the amino acid, glycine, in the zwitterion form (HA) to give the basic form (A-) and a proton. 2. The reactions of copper (II) ion with glycine to form the Cu gly+ and Cu (gly)2 complexes. 3. The reactions of nickel (II) ion with glycine and alanine to form Ni gly+, Ni (gly)2, Ni al+, and Ni (al)2 complexes. For calorimetric enthalpy calculations, the initial and final concentrations of all species in the calorimeter must be known; …

Estimation Of Periodate By Oxindolamine, Lester Dale Burgess

University of the Pacific Theses and Dissertations

The carbohydrates play a vital role in the chemistry of the life processes. As man’s study of these processes, both fundamentally and in applied areas such as medicine, becomes ever more intensive, the limitations of our analytical procedures become ever more serious. While there are innumerable quantitative analytic procedures for the monosaccharides, there is a severe dearth of good micro colorimetric procedures. A particularly useful and widely used micro and semimicro procedure, based upon periodic acid oxidation, was originally introduced by Malaprade in France in 1928. In general, the consumption of the periodic acid in estimated by a back titration …

A Thermodynamic Study Of Step-Wise Complex Formation In Several Aqueous Copper (Ii)-Amino Acid Systems, Vipin M. Kothari

Theses and Dissertations

pK_n values for step-wise dissociation of protons from the protonated ligands (glycine, α-amino isobutyric acid, sarcosine and theonine) were determined potentiometrically with a Beckman Model GS pH meter in aqueous solution at 10, 20, 30 and 40° C. Log K values for step-wise interaction of glycine, α-amino isobutyric acid, sarcosine and threonine with copper(II) ion were also determined potentiometrically with a pH meter at 10, 20, 30 and 40° C. The standard free energy of formation for the step-wise interaction of copper(II) with each of the above ligands was calculated from the values of log K. Enthalpy and entropy changes …