Chemistry Commons^™

Development Of Inlet And Vacuum Ionization Methods For Characterization Of Biological Materials By Mass Spectrometry, Beixi Wang

Wayne State University Dissertations

Inlet ionization and vacuum ionization are novel ionization methods to produce electrospray ionization (ESI)-like ions from the solid or liquid states, operating from atmospheric pressure (AP) or vacuum, without the use of voltage or the necessity of high energy input such as a laser or particle beam. The fundamental aspects were probed for better understanding of the novel ionization processes. Initial applications were attempted to utilize the novel ionization methods for fast, robust, and quantitative analyses.

For inlet ionizations (laserspray ionization inlet, LSII; matrix assisted ionization inlet, MAII; and solvent assisted ionization inlet, SAII), small (e.g. drugs) to large (e.g. …

(I)Chromatographic Methods For Solute Descriptor Determinations (Ii)Ruthenium Substrate-Catalyzed Growth Of Nickel Nitride Thin Films By Atomic Layer Deposition, Thiloka Chandima Ariyasena

Wayne State University Dissertations

Determination of distribution levels of environmentally important compounds in various environmental compartments is a major procedure in many fields including environmental risk assessment, food and drug safety, and the perfumery industry. Models for direct estimation of environmental properties were developed using gas chromatography and liquid-liquid partitioning. The developed models were used to derive descriptor values for environmentally important organic compounds. The accuracy of the developed models and descriptor values were demonstrated by the application to the estimation of standard environmental properties and by comparison with experimental solute property values.

Quantitative structure property relationships were constructed for totally organic biphasic partition …

Developing A Toolbox To Probe Reaction Dynamics With Strong Field Ionization And Non-Linear Attosecond Spectroscopy, Thushani Nikeshala Herath

Wayne State University Dissertations

Electronic motions which happen in 10 to 100 of attoseconds are the heart of all processes in nature. Therefore monitoring and extracting details in this fundamental level will provide new prospect to the areas as information technology, basic energy science, medicine and life sciences. The challenge being, develop a tool to reach such a fast time scale for real time observation in atomic level. In this thesis work we have address this matter using two interesting approaches related to the laser matter interaction: strong field ionization and nonlinear attosecond spectroscopy. The first part is based on the studies related to …

Biochemical And Structural Characterization Of The Core Subunits Of Gpi Transamidase, Dilani G. Gamage

Wayne State University Dissertations

BIOCHEMICAL AND STRUCTURAL CHARACTERIZATION OF THE CORE SUBUNITS OF GPI TRANSAMIDASE

by

DILANI G GAMAGE

May 2015

Advisor: Prof. Tamara L. Hendrickson

Major: Chemistry (Biochemistry)

Degree: Doctor of Philosophy

Glycosylphosphatidylinositol transamidase (GPI-T) is a complicated, membrane-bound, multi-subunit enzyme that catalyzes an essential post-translational modification. This enzyme attaches GPI anchors to the C-termini of various proteins that contain a proper GPI-T signal sequence. Gpi8, Gaa1, Gpi16, Gpi17 and Gab1 are the five known subunits that may encompass the fungal GPI-T; Gpi8 is the catalytic subunit, but the functions of the other subunits remain essentially unknown. In humans, different GPI-T subunits are …

The Loss Of Genomic Uracil Homeostasis And Aid-Dependent Accumulation Of Dna Damage In B Cell Lymphomas, Sophia Shalhout

Wayne State University Dissertations

Activation-induced deaminase (AID) is a sequence-selective DNA cytosine deaminase that introduces uracils in immunoglobulin genes. This DNA mutator is required for somatic hypermutation and class switch recombination- processes involved in the affinity maturation and diversification of antibodies. AID, however, can also lead to deleterious mutations and translocations promoting lymphomagenesis. The introduction of uracils throughout the genome of activated B cells and the ability of UNG2 glycosylase to excise these uracils is examined here. This interplay was also studied in cancerous B cells, with different results emerging in transformed cells versus healthy cells. Genomic uracil levels are found to remain at …

Scale Up Isolation Of Aaptamine For In Vivo Evaluation Indicates Its Neurobiological Activity Is Linked To The Delta Opioid Receptor, Nicole L. Mcintosh, Eptisam Lambu, Laura Millan-Lobo, Fei Li, Li He, Phillip Crews, Jennifer L. Whistler, Tyler Johnson

Student Research Posters

Opioid receptors belong to the large superfamily of seven transmembrane-spanning (7TM) G protein-coupled receptors (GPCRs). As a class, GPCRs are of fundamental physiological importance mediating the actions of the majority of known neurotransmitters and hormones. The Mu, Delta, and Kappa (MOP, DOP, KOP) opioid receptors are particularly intriguing members of this receptor family as they are the targets involved in many neurobiological diseases such as addiction, pain, stress, anxiety, and depression. Recently we discovered that the aaptamine class of marine sponge derived natural products exhibit selective agonist activity in vitro for the DOP versus MOP receptor. Our findings may explain …

Determination Of Inhibitor Specificity For Low Molecular Weight Protein Tyrosine Phosphatase Isoforms A And B, Erica K. Sinner

Honors Theses, 1963-2015

The two active isoforms of Low Molecular Weight Protein Tyrosine Phosphatase (LMW-PTP) have inverse cellular effects on cancer. Isoform A has been found to be anti-oncogenic, while overexpression of Isoform B is oncogenic. Inhibitors of Isoform B could have anti-cancer effects, however, it is of utmost importance that these inhibitors exhibit specificity for Isoform B and do not affect the function of Isoform A. Isoform A was recombinantly expressed, purified and characterized in order to compare its structure and function to Isoform B. It is hoped that this characterization, along with the synthesis and screening of potential inhibitors for both …

Efficient Utilization Of Solar Energy In Dye-Sensitized Solar Cells And In The Photocatalytic Reduction Of Carbon Dioxide, Aron Joel Huckaba

Electronic Theses and Dissertations

One of the most important questions humanity will face in the next 100 years is going to be "What will happen when oil runs out?" This dissertation describes efforts to utilize solar energy to improve renewable energy technology in two ways: First, through the improvement of dye sensitized solar cells by theimprovement of D-π-A dye subunits, the development of practical sensitizers, and progress towards stable, tunable redox shuttles. A novel indolizine donor subunit was synthesized that was shown to be the strongest reported donor. Dyes made from this novel donor and devices using the Γ-/I 3- reached up to 5.4% …

Cappack Devices For Enhanced Qnmr Measurements In 1H Nmr Spectroscopy, Lingyu Chi

Masters Theses

"Quantitative NMR analyses can be improved by adding well-defined external references for measuring sample properties on absolute scales. Special Capillary-tube Package (CapPack) devices were invented that provide in situ information (e.g., temperature, pH, pressure, integration, chemical shift, lock, etc.) about a sample with spectral imprimaturs. A new microscale glass-sealing technique produced CapPack devices that can survive high temperatures and pressures in harsh environments. Two CapPack devices are discussed: (1) Gradient CapPack-- a device for examining the irradiation bandwidth of solvent-suppression pulse sequences; (2) T₁ CapPack - a device for examining the T₁ robustness of solvent-suppression pulse sequences. A …

Dna Aptamers Selected Against Wild-Type Helix 69 Ribosomal Rna And Their Implications In Combating Antibiotic Resistance, Sakina Miriam Hill

Wayne State University Dissertations

Outbreaks of advanced antibiotic-resistant strains of microbes have hastened the need to identify new viable molecular targets for the development of novel anti-infectives. For this purpose, helix 69 (H69, or m3a 19-nucleotide (nt) hairpin motif that is highly conserved throughout phylogeny and rich in modified nucleotides, including pseudouridine () and 3-methylpseudouridine (m3) was chosen as a potential target. Helix 69, which is located in domain IV of Escherichia coli 23S ribosomal RNA (rRNA), undergoes conformational changes when in close proximity to the decoding region of 16S rRNA and transfer RNAs (tRNAs) in the peptidyl-transferase center (PTC). Functionally, the exact biological …

Unraveling The Mechanism Of Selective Ion Transport In Hydrophobic Subnanometer Channels, Hui Li, Joseph S. Francisco, Xiao Cheng Zeng

Xiao Cheng Zeng Publications

Recently reported synthetic organic nanopore (SONP) can mimic a key feature of natural ion channels, i.e., selective ion transport. However, the physical mechanism underlying the K⁺/Na⁺ selectivity for the SONPs is dramatically different from that of natural ion channels. To achieve a better understanding of the selective ion transport in hydrophobic subnanometer channels in general and SONPs in particular, we perform a series of ab initio molecular dynamics simulations to investigate the diffusivity of aqua Na⁺ and K⁺ ions in two prototype hydrophobic nanochannels: (i) an SONP with radius of 3.2 Å, and (ii) single-walled …

Medium-Sized Au40(Sr)24 And Au52(Sr)32 Nanoclusters With Distinct Gold-Kernel Structures And Spectroscopic Features, Wen Wu Xu, Yadong Li, Yi Gao, Xiao Cheng Zeng

Xiao Cheng Zeng Publications

We have analyzed the structures of two medium-sized thiolateprotected gold nanoparticles (RS-AuNPs) Au₄₀(SR)₂₄ and Au₅₂(SR)₃₂ and identified the distinct structural features in their Au kernels [Sci. Adv., 2015, 1, e1500425]. We find that both Au kernels of the Au₄₀(SR)₂₄ and Au₅₂(SR)₃₂ nanoclusters can be classified as interpenetrating cuboctahedra. Simulated X-ray diffraction patterns of the RS-AuNPs with the cuboctahedral kernel are collected and then compared with the X-ray diffraction patterns of the RS-AuNPs of two other prevailing Au-kernels identified from previous experiments, namely the Ino-decahedral kernel and icosahedral kernel. …

Sustainable Activity Of Hydrothermally Synthesized Mesoporous Silicates In Acetic Acid Esterification, Veli̇ Şi̇mşek, Levent Deği̇rmenci̇, Kirali̇ Mürtezaoğlu

Turkish Journal of Chemistry

A hydrothermal method was applied in the synthesis of mesoporous silicates containing silicotungstic acid (STA). The synthesis procedures were developed by modification of procedures previously applied in the synthesis of MCM-41 and SBA-15. The synthesized catalysts were named MCM-41-S and SBA-15-S based on MCM-41 and SBA-15. Their activities were investigated in ethyl acetate production, which was selected as the model reaction. The results indicated that the activity of SBA-15-S catalysts increased with increasing STA in the catalyst. Reaction experiments were also conducted in identical conditions in the presence of catalysts recovered after the reaction. The results indicated that sustainable activity …

Solution Combustion Synthesis Of Oxide Semiconductors, Abegayl Lorenda Shara-Lynn Thomas

Chemistry & Biochemistry Dissertations - Archive

The quest for stable and efficient photocatalytic materials beyond TiO2 and WO3 has over the years led to the development of new materials that possess varied interfacial energetics. This dissertation study focused on using for the first time a novel method, solution combustion synthesis (SCS), to prepare two distinct families of binary metal-based oxide semiconductor materials. Detailed studies on material characteristics and applications were carried out on tungsten- and niobium-based oxide semiconductors with varying principal metals. Initial emphasis was placed on the SCS of tungsten-based oxide semiconductors (ZnWO4, CuWO4, and Ag2WO4). The influence of different tungsten precursor’s on the resultant …

Nickel (Ii) Pincer Complexes Supported By 2,6-Bis(3,5-Ditolyl-2-Pyrrolyl)Pyridine, Abhijit Pramanik

Chemistry & Biochemistry Theses - Archive

Ni(II) pincer complexes are among the most important and useful compounds in homogeneous catalysis. Significant advancement has been made in this field in recent years. Many Ni(II) pincer complexes have been prepared and utilized in various catalytic reactions e.g. cross coupling reactions, C-H activation, carbon dioxide activation etc. Still, nickel(II) complexes supported by the pincer ligand with three nitrogen donors are relatively less explored and catalytic applications with those complexes are scarce in literature. This thesis describes the synthesis of a new pyrrolyl pyridine based pincer ligand and its Ni(II) complexes. The pyrrolyl pyridine pincer ligand, a relatively new class …

Concomitant Studies Of Two F420 Cofactor Dependent Enzymes: Binding Isotherms Of F420 Cofactor Dependent Glucose-6-Phosphate Dehydrogenase And Kinetic Analysis Of F420h2: Nadp+ Oxidoreductase Utilizing Isotope Effects Methods, Siqi Du

Chemistry & Biochemistry Theses - Archive

F420 cofactor, a flavin analogue, is a unique two electron carrier that has been found in a number of microorganisms. This thesis focuses on two F420-dependent enzymes (F420-dependent glucose-6-phosphate dehydrogenase and F420H2: NADP+ Oxidoreductase). First, F420-dependent glucose-6-phosphate dehydrogenase (FGD) from Mycobacterium tuberculosis has been shown to be essential for activation of the anti-TB prodrug PA-824. It has been suggested the Trp44 residue in the active side aids in the stabilization of possible intermediates during catalysis. Here, we examined the role of Trp44 during catalysis by creating the FGD W44A variant, which was catalytically inactive. However, we were able to isolate …

Studies On Reductive Horner-Wadsworth-Emmons Olefination Using Mixed Silyl Acetals, Udaya Sree Dakarapu

Chemistry & Biochemistry Theses - Archive

Homologation of esters to α,β-unsaturated esters is a useful transformation in organic synthesis. We have developed a new approach for the Ir-catalyzed reductive Horner-Wadsworth-Emmons olefination of esters; a one-pot method for the transformation of esters to α,β-unsaturated esters utilizing silyl acetals as aldehyde equivalents followed by Horner-Wadsworth-Emmons olefination. Lewis based activation of silyl acetals formed by Ir-catalyzed hydrosilylation of esters initially generates putative penta-coordinate silicate acetals which fragment into aldehydes, silanes and alkoxides in situ. The alkoxides deprotonate phosphonate esters which subsequently react with the aldehydes to furnish α,β-unsaturated esters. This method is operationally simple compared with aluminium hydride-based reductive …

Pyrolysis-Gc-Ms For The Rapid Environmental Forensic Screening Of Contaminated Brownfield Soil, Azucena Lara-Gonzalo, Michael A. Kruge, I Lores, B Gutiérrez, José Luis Gallego

Department of Earth and Environmental Studies Faculty Scholarship and Creative Works

An abandoned chemical plant in Asturias (Spain) was studied using a multi-faceted molecular fingerprinting approach, demonstrating that it is possible to: (1) carefully unravel tangled evidence resulting from multiple pollution sources, and (2) recognize major contaminants largely ignored by conventional analyses. This methodology employed a battery of GC-MS analyses of liquid chromatographic fractions of soil extracts, plus the pyrolysis products of the soil extract's asphaltene fraction and the whole soil itself. In this example, coal tar distillation and the subsequent production of naphthalene, phenols and polymer resins are responsible for most of the soil contamination. Styrene, naphthalene, indene, and their …

Analytical Pyrolysis Principles And Applications To Environmental Science, Michael A. Kruge

Department of Earth and Environmental Studies Faculty Scholarship and Creative Works

Over the past half century, analytical pyrolysis has proven itself to be an effective means for the semiquantitative characterization of complex macromolecular organic substances. It has been demonstrated that instruments such as Py-FID, Py-MS, and in particular, Py-GC/MS can provide valuable geochemical insights when applied to a wide variety of problems in environmental science. The more widespread use of analytical pyrolysis methods in the evaluation of environmental pollution is recommended, because of their relatively low cost and information-rich results.

Pyrolysis is the heating of organic substances in an inert, oxygen-free atmosphere, thereby avoiding combustion. When performed on a large scale, …

Magnetic Mineral Diagenesis In The River‐Dominated Inner Shelf Of The East China Sea, China, Can Ge, Weiguo Zhang, Chenyin Dong, Yan Dong, Jinyan Liu, Nguyen Thi Thu Hien, Huan Feng, Lizhong Yu

Department of Earth and Environmental Studies Faculty Scholarship and Creative Works

The inner shelf of the East China Sea is a river-dominated margin characterized by fine-grained mud deposits and a rapid sedimentation rate. Three short sediment cores (similar to 2.7m in length) were examined to characterize spatial variations in magnetic mineral diagenesis. The sediment cores were analyzed for sedimentation rates, magnetic properties, particle size distribution, organic carbon, and total sulfur content. The two more proximal cores with higher sedimentation rates (similar to 2.2cm/yr and similar to 0.96cm/yr) do not exhibit obvious effects of reductive dissolution of magnetite with increasing depth, which is consistent with their lower total sulfur content. The offshore …

Classical And Ab Initio Qm/Mm Simulations Of Bacterial Enzymes, Sajeewa Walimuni Dewage

Wayne State University Dissertations

This thesis describes analyses performed on three enzyme systems. Chapter 2, 3, and 4 involve studies carried out on the GatCAB enzyme of H. pylori and S. aureus. Since information at the electronic level was not required for these studies, sampling of the configuration space carried out at the molecular mechanics level was adequate. In Chapter 2, the snapshots sampled using MD were used as input for average correlation difference calculations and average RMSD difference calculations to ascertain the existence of a communication pathway between two subunits of GatCAB. Experimental and computational results obtained, suggest the existence of a communication …

Novel Sustainable Polymers Derived From Renewable Rosin And Fatty Acids, Perry Wilbon

Theses and Dissertations

In the work of this dissertation, polymers derived from renewable bio-based resources prepared by various polymerization techniques were investigated. The properties of these polymeric materials were characterized and discussed. Rosin was first converted into acrylate or methacrylate monomers for atom transfer radical polymerization (ATRP). Second, rosin was combined with vegetable oil to produce completely renewable novel polyesters by acyclic diene metathesis (ADMET) polymerization. Third, degradable block copolymers were synthesized composed of polycaprolactone and rosin grafted polycaprolactone with the aid of ring-opening polymerization (ROP). Finally, degradable polyesters were produced using vegetable oil derivatives as starting materials. These new rosin and fatty …

Design, Synthesis, And Biological Evaluation Of Folate Targeted Photosensitizers For Photodynamic Therapy, Laura Jean Donahue

Dissertations

Photodynamic therapy (PDT) is used to treat cancer, and involves a highly conjugated molecule, called a photosensitizer (PS), which is excited by wavelengths of light from visible to infrared. Photosensitizers that are highly conjugated will absorb longer wavelengths (600 – 900 nm), and have the potential to destroy cells of deeper tissue cancers. In PDT, a PS is administered to the patient, and after an appropriate time delay, the tissue is then exposed to light of a specific wavelength necessary for excitation of the PS. A transfer of energy can take place between the excited PS and oxygen that is …

Methods Of Analysis For Fermentation Science Products Using Various Analytical Techniques, Casey Jay Howdieshell

Online Theses and Dissertations

Fermentation science, the study of microorganisms as they digest food sources to produce usable products for consumption, has been around since the dawn of modern civilization. Historically, the fermentation process has been utilized for the production of alcoholic beverages. More recently, however, the production of bioethanol and biodiesel as a fuel source alternative to classical fossil fuels has gained increased popularity. As with any synthetic process, derivations and optimizations for ideal production are needed. As such, analytical techniques must be implemented to ensure quality control and pinnacle efficiency. This body of work describes analytical techniques providing key qualitative and quantitative …

Preparation And Characterization Of Self-Assembled Monolayers And Mesoscale Protein Patterning, Panae Noomuna

Online Theses and Dissertations

Bottom-up approach was used to develop self-assembled monolayers of octadecyltrichlorosilane (OTS) and undecenyltrichlorosilane(UTS) on Si(100) wafer. Undecenyltrichlorosilane monolayer was oxidized at the vinyl terminal to generate a carboxylic acid group. Lysozyme protein was immobilized on the polar carboxylic acid group. The developed protein patterns were investigated using fluorescence microscopy. Lysozyme has an isoelectronic point of 11.35. At a pH below this value the protein is positively charged making it a good candidate for electrostatic adsorption on the negatively charge -COO- group. Fluorescence images confirm formation of lysozyme across the silicon wafer. The patterned Si(100) wafer can be used as a …

Towards Establishing The Mechanism Of Dna Cleavage By Redox-Active Ruthenium(Ii) Polypyridyl Complexes, Cynthia Ann Griffith

Chemistry & Biochemistry Theses - Archive

In earlier reports, it was established that ruthenium (II) polypyridyl complexes RPCs, [Ru(tatpp)]²⁺ (3²⁺) and [Ru(tatpp)Ru]⁴⁺ (4⁴⁺) show potent antitumor properties in vivo in nude mouse lung cancer models.² These RPC's undergo in vitro reduction by glutathione (GSH) to form a species that induces DNA cleavage. It was also demonstrated that the mechanism of DNA cleavage follows an unusual dependence on dioxygen (O₂) concentration: the increase in cleavage activity of these RPC complexes are inversely proportional to O₂ concentration. In fact, cleavage is quenched in the complete absence of O₂. In this work we currently postulate when 3²⁺ and 4⁴⁺ …

Light Driven Reduction Of Carbon Dioxide Via Ruthenium Polypyridyl Complexes In The Presence Of A Pyridinium Cocatalyst, Matthew West

Chemistry & Biochemistry Theses - Archive

The rapid increase in atmospheric carbon dioxide since the industrial revolution is now beginning to cause global climate changes which could adversely affect our planets ecosystem. Nonetheless, our ability to sustain the current world population and standard of living relies on cheap and abundant energy which is only currently obtainable from the continued use of fossil fuels, which further add CO2 to the atmosphere. Given these circumstances, there is considerable interest and urgency in the development of new technology which would help us replace fossil fuels with fuels derived from sustainable energy sources, and in particular, the sun. In particular, …

Cytotoxicty, Cellular Localization And Fluorescent Microscopy Of Malignant Cells Treated With Ruthenium (Ii) Complexes Of The Tetraazatetrapyridopentacene Ligand, Adam S. Dayoub

Chemistry & Biochemistry Theses - Archive

The ruthenium (II) polypyridyl complexes [(phen)2Ru(tatpp)Ru(phen)2]4+, (P) and [(phen)2Ru(tatpp)]2+, (MP) are promising anticancer activity candidates due to their observed cytotoxic effect against multiple cancer cell lines. These complexes contain a redox-active (tatpp) bridge and a cytotoxic selectivity against cancer lines that are of interest in cellular biological systems. They also exhibit the ability to regress tumor growth in mouse models and have been shown to cleave DNA with an inverse dependence with (O2). Significantly, these complexes may show a higher cytotoxic action in a hypoxic environment similar to that of tumors in vivo. This thesis is a direct test of …

Mechanistic And Kinetic Studies On F420h2: Nadp+ Oxidoreductase From Archeoglobus Fulgidus, Cuong Quang Le

Chemistry & Biochemistry Dissertations - Archive

F420H2: NADP+ Oxidoreductase (Fno) is an F420 cofactor dependent enzyme that catalyzes the reversible reduction of NADP+ to NADPH by transferring a hydride from the reduced F420 cofactor. F420 cofactor is an essential electron transfer carrier in methanogens. Methanogens play a critical role in carbon cycling because the methanogenic pathway reduces carbon dioxide to produce methane and is therefore linked to energy (1). The focus of this thesis is to study the hydride transfer mechanism of Fno from the extreme thermophile, Archeoglobus fulgidus using site directed mutagenesis, steady-state and pre-steady state kinetic methods. F420 is essential for catalysis within enzymes …

Nmr Kinetics Of The Diels-Alder Reactions Of 9-Substituted Anthracenes: Development Of An Organic Chemistry Lab Experience, Kira Oyama, Andrew Johnson

CUP Undergraduate Research

NMR spectroscopy plays an integral role in the teaching of organic chemistry. With the integration of conceptual understanding and problem solving, deciphering spectrums of an unknown chemical structure can provide many necessary challenges. The Diels-Alder reaction ([4π + 2π] cycloaddition reaction) is one of the most important reactions in synthetic organic chemistry as it allows for the formation of two C-C bonds and displays good regioand stereoselectivity. The kinetics of the reaction between maleic anhydride and anthracene and two of its derivatives (9-methylanthracene & 9-anthracenecarboxaldehyde) were the main focus of this experiment.