Chemistry Commons^™

Experimental And Theoretical Studies Of Binding Interactions In Divalent Transition Metal Cation-N-Donor Ligand Complexes: Structures, Sequential Bond Dissociation Energies, Mechanisms And Energetics Of Collision-Induced Dissociation, Holliness Nose

Wayne State University Dissertations

The thesis research described here involves a series of experiments that have been designed to probe the influence of the electronic structure of the metal cation, the nature and number of ligands, as well as the effects of chelation and steric interactions on the geometry and binding strength of transition metal cation-ligand complexes. The experimental studies make use of energy-resolved collision-induced dissociation (CID) techniques that are carried out in a custom-built guided ion beam tandem mass spectrometer (GIBMS) to probe the structures, energetics, and fragmentation behavior of the complexes of interest. Electronic structure theory calculations including several density functional theory …

Computational Studies Of Enzymatic Reactions And Inorganic Compounds, Dong Fang

Wayne State University Dissertations

Quantum mechanics (QM) calculations have been demonstrated to give very accurate results in studying a variety of chemical reactions. However, the current computing resources limits its use in large-size systems such as enzymes. Compared to QM, Molecular Mechanics (MM) have an advantage in computing time but disadvantage in accuracy, and MM cannot be used in reactions involving bonding forming and breaking. To combine the advantages of these two types of methods, QM/MM has been introduced to study reactions and processes in large-size systems, and it has been proven to give accurate results with moderate computational expense. When studying enzymatic reactions, …

Theoretical And Experimental Studies Of Noncovalent Metal Cation Binding And Base Pairing Interactions Of Cytosine And Modified Cytosines, Bo Yang

Wayne State University Dissertations

ABSTRACT

THEORETICAL AND EXPERIMENTAL STUDIES OF NONCOVALENT METAL CATION BINDING AND BASE PARING INTERACTIONS OF CYTOSINE AND MODIFIED CYTOSINES

by

BO YANG

December 2014

Advisor: Professor Mary T. Rodgers

Major: Analytical Chemistry

Degree: Doctor of Philosophy

Binding of metal cations to the nucleobases can lead to formation of rare tautomers of the nucleobases. The infrared multiple photon dissociation (IRMPD) action spectroscopy of five alkali metal cation-cytosine complexes, M⁺(cytosine), where M⁺ = Li⁺, Na⁺, K⁺, Rb⁺, and Cs⁺, are examined using a Fourier transform ion cyclotron resonance mass …

Structural And Functional Characterization Of Proteins Of Unknown Function (Hp0495, Hp0100 And Hp1259) In Helicobacter Pylori, Shirin Fatma

Wayne State University Dissertations

H. pylori is missing the glutaminyl- and asparaginyl-tRNA synthetases (GlnRS and AsnRS, respectively). Consequently, H. pylori uses an indirect aminoacylation pathway to generate Gln-tRNAGln and Asn-tRNAAsn. Within this process, Asn-tRNAAsn is produced by misacylation of tRNAAsn with aspartate by a non-discriminating aspartyl-tRNA synthetase (ND-AspRS). Next, the heterotrimeric, glutamine-dependent amidotransferase (called AdT or GatCAB) converts the misacylated Asp-tRNAAsn into Asn-tRNAAsn. A parallel pathway exists for the synthesis of Gln-tRNAGln, wherein misacylation of tRNAGln with glutamate is catalyzed by a tRNAGln-specific glutamyl-tRNA synthetase (GluRS2) to generate Glu-tRNAGln; this misacylated intermediate is converted to Gln-tRNAGln by the same AdT. This dependence on misacylated …

Evolution Of Selected Isoprene Oxidation Products In Dark Aqueous Ammonium Sulfate, D.M. Ashraf Ul Habib

Dissertations, Master's Theses and Master's Reports - Open

The aqueous phase processing of glyoxylic acid, pyruvic acid, oxalic acid and methylglyoxal was studied simulating dark and radical free atmospheric aqueous aerosol. A novel observation of the cleavage of a carbon-carbon bond in pyruvic acid and glyoxylic acid leading to their decarboxylation was made in the presence of ammonium salts but no decarboxylation was observed from oxalic acid. The empirical rate constants for decarboxylation were determined. The structure of the acid, ionic environment of solution and concentration of species found to affect the decarboxylation process. A tentative set of reaction mechanisms was proposed involving nucleophilic attack by ammonia on …

Design, Synthesis And Applications Of Fluorescent And Electrochemical Probes, Giri K. Vegesna

Dissertations, Master's Theses and Master's Reports - Open

“Seeing is believing” the proverb well suits for fluorescent imaging probes. Since we can selectively and sensitively visualize small biomolecules, organelles such as lysosomes, neutral molecules, metal ions, anions through cellular imaging, fluorescent probes can help shed light on the physiological and pathophysiological path ways. Since these biomolecules are produced in low concentrations in the biochemical pathways, general analytical techniques either fail to detect or are not sensitive enough to differentiate the relative concentrations. During my Ph.D. study, I exploited synthetic organic techniques to design and synthesize fluorescent probes with desirable properties such as high water solubility, high sensitivity and …

Using Spe And Hplc-Ms To Quantify And Identify Pharmaceutical Compounds In St. John's University Wastewater, Melissa E. Stuckey

Honors Theses, 1963-2015

Pharmaceuticals in wastewater have become a concern of environmental toxicologists. An efficient method of discovering the concentrations of these pharmaceuticals in wastewater has not yet been produced. The method we developed includes an automated Solid Phase Extraction (SPE) procedure prior to injecting a sample of wastewater into the High Performance Liquid Chromatograph (HPLC) and Mass Spectrometer – Electrospray Ionization (MS-ESI). Three unknown peaks were identified on the HPLC and MS from wastewater obtained from the St. John’s Wastewater Treatment Plant in June 2013. Methods of analysis including NMR, GC-MS and IR have been used to determine the composition of these …

Enhanced Lifetime Of Excitons In Nonepitaxial Au/Cds Core/Shell Nanocrystals, Scott Lambright, Evgeniia Butaeva, Natalia Razgoniaeva, Thomas Hopkins, Bryan Smith, Dimuthu Perera, Jonathan Corbin, Elena Khon, Rebekah Thomas, Pavel Moroz, Andrey Mereshchenko, Alexander N. Tarnovsky, Mikhail Zamkov

Chemistry Faculty Publications

The ability of metal nanoparticles to capture light through plasmon excitations offers an opportunity for enhancing the optical absorption of plasmon-coupled semiconductor materials via energy transfer. This process, however, requires that the semiconductor component is electrically insulated to prevent a "backward" charge flow into metal and interfacial states, which causes a premature dissociation of excitons. Here we demonstrate that such an energy exchange can be achieved on the nanoscale by using nonepitaxial Au/CdS core/shell nanocomposites. These materials are fabricated via a multistep cation exchange reaction, which decouples metal and semiconductor phases leading to fewer interfacial defects. Ultrafast transient absorption measurements …

Probing Proteasome Inhibition By Metal Copmplexes As A New Route For Anticancer Therapy, Dajena Tomco

Wayne State University Dissertations

The scope of this thesis is focused towards the development of metal-containing coordination compounds as potential therapeutic agents. Efforts of this research involve the design, synthesis, and purification of these complexes, as well as their evaluation by spectroscopic, spectrometric, and electrochemical characterization. The antineoplastic properties of these metal-containing pro-drugs are tested against the inhibition activity of the 26S proteasome. Selected metal ions ranging from transition to main group elements have been incorporated in various ligand systems containing phenolate and pyridyl donor sets. The mechanistic behavior of these complexes in solution has been thoroughly investigated along with their in vitro anticancer …

Control Of Emission Color With N-Heterocyclic Carbene (Nhc) Ligands In Phosphorescent Three-Coordinate Cu(I) Complexes, Valentina A. Krylova, Peter I. Djurovich, Brian L. Conley, Ralf Haiges, Matthew T. Whited, Travis J.. Williams, Mark E. Thompson

Chemistry Faculty Work

A series of three phosphorescent mononuclear (NHC)–Cu(I) complexes were prepared and characterized. Photophysical properties were found to be largely controlled by the NHC ligand chromophore. Variation of the NHC ligand leads to emission colour tuning over 200 nm range from blue to red, and emission efficiencies of 0.16–0.80 in the solid state.

Alterations In The Mouse Striatum Following Acute And Repeated Ethanol Exposure, Brooke D. Newman

Wayne State University Dissertations

Brain-derived neurotrophic factor (BDNF) is an important neuromodulator that has implicated in regard to several neurological disorders, including alcohol addiction. BDNF is also an important modulator of dopamine (DA), a neurotransmitter that is heavily implicated in addiction with one of the DA rich brain regions being referred to as the reward center of the brain. One of the focuses in alcohol dependence research includes determining risk factors that make an individual more susceptible to becoming dependent. BDNF has been of interest as a risk factor due to its involvement in ethanol consumption and addiction evidenced in a vast number of …

Investigation Into The Binding Interactions Of Klenow Fragment To Dna Modified With Carcinogens Af And Aaf Using Surface Plasmon Resonance, Ashley M. Floyd

Wayne State University Dissertations

The two major forms of DNA adducts from the carcinogen N-acetoxyacetyl-2-aminofluorene, N-(deoxygunanonsin-8-yl)-2-acetylaminofluorene (dG-C8-AAF) and N-(deoxyguanosin-8-yl)-2-aminofluorene (dG-C8-AF), are both known to impede replication, though in different ways. AAF is a strong block to replication leading to frameshift mutations, while the AF adduct is more easily bypassed, causing base substitutions. Surface plasmon resonance (SPR) was used to study the binding of exonuclease deficient E. coli polymerase I, Klenow fragment (KF), to DNA modified with AF or AAF at two locations: as a templating base or in the last formed base pair. KF binding to the modified DNA bases was also monitored to …

New Carbohydrate-Based Anti-Cancer And Anti-Bacterial Vaccines, Zhifang Zhou

Wayne State University Dissertations

The unique carbohydrates expressed on the surface of cancer, bacterial, viral and fungal cells are excellent target antigens for the design of therapeutic or preventive vaccines. However, as antigens carbohydrates have problems. First, carbohydrates usually have low immunogenicity. Second, even if immunogenic, carbohydrates typically elicit T cell-independent immune responses. To overcome these problems and design useful vaccines based on carbohydrate antigens, they are usually coupled with carrier proteins to form conjugates to enhance the immunogenicity of the antigens. However, there are still some issues existing in glycoprotein vaccines, such as poor reproducibility of the conjugates, difficulties in quality control and …

Lanthanide-Based Precatalysts For Carbon-Carbon Bond-Forming Reactions In Aqueous Media, Derek James Averill

Wayne State University Dissertations

The formation of carbon-carbon bonds is of great interest to synthetic chemists because these bonds make up the majority of biologically active compounds. The Mukaiyama aldol reaction is a Lewis-acid-catalyzed carbon-carbon bond-forming reaction that has the ability to produce optically active β-hydroxy carbonyls which can be found in many pharmaceuticals and natural products. Because of precatalyst instability towards hydrolysis, anhydrous solvents are commonly used. Recent efforts have focused on water-tolerant versions of enantioselective Mukaiyama aldol reactions because of the financial and environmental benefits of using aqueous media. Consequently, the Lewis-acidic and water-tolerant features of Ln³⁺ ions have aroused great …

Synthesis And Characterization Of Discrete Fexni2-Xp Nanoparticles; Assembly Of Phosphide Nanoparticles Into Porous Networks, Asha Hitihami Mudiyanselage

Wayne State University Dissertations

This dissertation research is focused on synthesis, characterization and assembly of metal phosphide nanoparticles of relevance to catalysis, magnetism, and optoelectronic applications. These include (1) synthesis of discrete FexNi2-xP ternary nanocrystals of relevance to hydrodesulfurization (HDS) catalysis and magnetism, and (2) 3-dimensional nanostructures (gels and aerogels) of InP and Ni2P.

A three-step solution-phase arrested precipitation method was employed for bimetallic nanocrystal synthesis. The synthesis of nanocrystals involves preparation of amorphous NixPy amorphous particles, introduction of the Fe precursor to form amorphous Fe-Ni-P particles, and high temperature conversion of Fe-Ni-P particles into crystalline ternary phosphide nanocrystals. Ternary FexNi2-xP nanocrystals crystalize in …

Electrodeposited Nickel-Sulfide Films As Competent Hydrogen Evolution Catalysts In Neutral Water, N. Jiang, L. Bogoev, M. Popova, S. Gul, J. Yano, Y. Sun

Chemistry and Biochemistry Faculty Publications

The development of low-cost, efficient, and robust electrocatalysts of the hydrogen evolution reaction (HER) is a crucial step toward the conversion and storage of sustainable and carbon-neutral energy resources, such as solar energy. Not only the HER catalysts need to be composed of inexpensive elements, they are also desirable to be prepared at low energy cost. In this work, we report that nickel-sulfide (Ni-S) films prepared by facile potentiodynamic deposition are active HER catalysts in aqueous media. Notably, the Ni-S films showed catalytic activity in water with a wide range of pH values (0 to 14), as well as in …

Synthesis And Evaluation Of Some New Aza-B-Homocholestane Derivatives As Anticancer Agents, Yanmin Huang, Jianguo Cui, Sijing Chen, Qifu Lin, Huacan Song, Chunfang Gan, Bin Su, Aimin Zhou

Chemistry Faculty Publications

Using analogues of some marine steroidal oximes as precursors, a series of aza-B-homocholestane derivatives possessing different substituted groups at the 3-position of the steroidal nucleus were synthesized. Their biological activity against cancer cell proliferation was determined with multiple cancer cell lines. Aza-B-homocholestane derivatives possessing 3-hydroxyl, 3-hydroximino and 3-thiosemicarbazone groups displayed remarkable cytotoxicity to cancer cells via apoptosis inducing mechanism. Compounds 5, 10, 12, 15 and 18 exhibited better potency to inhibit cancer cell proliferation. In addition, compound 15 was further evaluated with three dimensional (3D) multicellular spheroids assay to determine its potency against spheroid growth. The structure-activity relationship (SAR) generated …

Spontaneous Formation Of One-Dimensional Hydrogen Gas Hydrate In Carbon Nanotubes, Wenhui Zhao, Lu Wang, Jaeil Bai, Joseph S. Francisco, Xiao Cheng Zeng

Xiao Cheng Zeng Publications

We present molecular dynamics simulation evidence of spontaneous formation of quasi-one-dimensional (Q1D) hydrogen gas hydrates within single-walled carbon nanotubes (SW-CNTs) of nanometer-sized diameter (1−1.3 nm) near ambient temperature. Contrary to conventional 3D gas hydrates in which the guest molecules are typically contained in individual and isolated cages in the host lattice, the guest H₂ molecules in the Q1D gas hydrates are contained within a 1D nanochannel in which the H₂ molecules form a molecule wire. In particular, we show that in the (15,0) zigzag SW-CNT, the hexagonal H₂ hydrate tends to form, with one H₂ molecule …

Strongly Bound Noncovalent (So3)N:H2co Complexes (N = 1, 2), L. M. Azofra, I. Alkorta, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

The potential energy surfaces (PES) for the SO3:H2CO and (SO3)2:H2CO complexes were thoroughly examined at the MP2/aug-cc-pVDZ computational level. Heterodimers and trimers are held together primarily by SO chalcogen bonds, supplemented by weaker CHO and/or OC bonds. The nature of the interactions is probed by a variety of means, including electrostatic potentials, AIM, NBO, energy decomposition, and electron density redistribution maps. The most stable dimer is strongly bound, with an interaction energy exceeding 10 kcal mol(-1). Trimers adopt the geometry of the most stable dimer, with an added SO3 molecule situated so as to interact with both of the original …

The Mtr4 Ratchet Helix And Arch Domain Both Function To Promote Rna Unwinding, Lacy L. Taylor, Ryan N. Jackson, Megi Rexhepaj, Alejandra Klauer King, Lindsey K. Lott, Ambro Van Hoof, Sean J. Johnson

Chemistry and Biochemistry Faculty Publications

Mtr4 is a conserved Ski2-like RNA helicase and a subunit of the TRAMP complex that activates exosomemiated 3-5 turnover in nuclear RNA surveillance and processing pathways. Prominent features of the Mtr4 structure include a four-domain ring-like helicase core and a large arch domain that spans the core. The ‘ratchet helix’ is positioned to interact with RNA substrates as they move through the helicase. However, the contribution of the ratchet helix in Mtr4 activity is poorly understood. Here we show that strict conservation along the ratchet helix is particularly extensive for Ski2-like RNA helicases compared to related helicases. Mutation of residues …

Upregulation Of Functional Kv11.1 Isoform Expression By Inhibition Of Intronic Polyadenylation With Antisense Morpholino Oligonucleotides, Qiuming Gong, Matthew R. Stump, Zhengfeng Zhou

Faculty Publications - Department of Biological & Molecular Science

The KCNH2 gene encodes the Kv11.1 potassium channel that conducts the rapidly activating delayed rectifier current in the heart. KCNH2 pre-mRNA undergoes alternative processing; intron 9 splicing leads to the formation of a functional, full-length Kv11.1a isoform, while polyadenylationwithin intron 9 generates a non-functional, Cterminally truncated Kv11.1a-USO isoform. The relative expression of Kv11.1 isoforms plays an important role in the regulation of Kv11.1 channel function and the pathogenesis of long QT syndrome. In this study,we identified cis-acting elements that are required for KCNH2 intron 9 poly(A) signal activity. Mutation of these elements decreased Kv11.1a-USO expression and increased the expression of …

Fundamental And Applied Studies Of An Ambient Ionization Technique: Continuous Flow-Extractive Desorption Electrospray Ionization - Mass Spectrometry, Li Li

Chemistry & Biochemistry Dissertations - Archive

Continuous flow extractive desorption electrospray ionization (CF-EDESI) is a novel ambient ionization technique that was developed to help analyze samples from non-ESI-friendly solvents, manipulate protein charge states, and couple to a flowing sample solution stream. CF-EDESI is performed by introducing a sample solution through a hypodermic needle set orthogonal to an on-axis electrospray ionization source. Samples dissolved in non-ESI-friendly solvents such as hexanes, ethyl acetate etc. can be successfully detected in CF-EDESI which then makes it an attractive detection technique for normal phase separation. Additionally, introducing samples separated from electrospray has provided freedom to optimize both the sample solvents and …

Supporting Traditional Instructional Methods With A Constructivist Approach To Learning: Promoting Conceptual Change And Understanding Of Stoichiometry Using E-Learning Tools, Kenneth Munoz Abayan

Chemistry & Biochemistry Dissertations - Archive

Stoichiometry is a fundamental topic in chemistry that measures a quantifiable relationship between atoms, molecules, etc. Stoichiometry is usually taught using expository teaching methods. Students are passively given information, in the hopes they will retain the transmission of information to be able to solve stoichiometry problems masterfully. Cognitive science research has shown that this kind of instructional teaching method is not very effecting in meaningful learning practice. Instead, students must take ownership of their learning. The students need to actively construct their own knowledge by receiving, interpreting, integrating and reorganizing that information into their own mental schemas. In the absence …

Development Of Paired Ion Electrospray Ionization Mass Spectrometry For Ultrasensitive Detection Of Anions, Chengdong Xu

Chemistry & Biochemistry Dissertations - Archive

Mass spectrometry (MS) has emerged as an essential analytical technique over the last several decades. It is a widely applicable and powerful tool for determination and identification of different types of molecules. Electrospray ionization (ESI) is one of the most commonly used ionization sources for mass spectrometry. ESI-MS has advantages for the analysis of both small molecules and macromolecules due to its outstanding sensitivity, specificity, speed, and the capability for analyte structure elucidation. Currently, one challenging aspect in ESI-MS is the qualitative and quantitative determination of anionic species. This is due to the inherently poor detection sensitivity in the negative …

Mechanistic Study Of Cysteine Dioxygenase, A Non-Heme Mononuclear Iron Enzyme, Wei Li

Chemistry & Biochemistry Dissertations - Archive

Cysteine dioxygenase (CDO) is an non-heme mononuclear iron enzymes that catalyzes the O2-dependent oxidation of L-cysteine (Cys) to produce cysteine sulfinic acid (CSA). CDO controls cysteine levels in cells and is a potential drug target for some diseases such as Parkinson's and Alzhermer's. Several crystal structures of CDO have been determined and they reveal a ferrous iron active site coordinated by three histidine residues. This feature is divergent from the monoanionic 2-histidine-1-carboxylate coordination typically observed within the non-heme mononuclear iron super family of oxidase/oxygenase enzymes. Furthermore, within 3.3 Å of the CDO active site iron is an unusual covalently crosslinked …

Determination Of Nicotine And Its Metabolites Accumulated In Fish Tissue Using Quechers And Hydrophilic Interaction Liquid Chromatography And Tandem Mass Spectrometry, Yun-Wei Chang

Chemistry & Biochemistry Theses - Archive

The quantitative determination of nicotine and its major metabolites (cotinine and anabasine) in fish tissue was performed using hydrophilic interaction liquid chromatography (HILIC) coupled with tandem mass spectrometry. Marine and freshwater fish were purchased from local grocery stores and were prepared based on the well-known QuEChERS (quick, easy, cheap, effective, rugged, safe) sample preparation protocol. There were significant suppressions on measured nicotine signals (10%) due to the matrix effects from marine fish, but no obvious effects on freshwater fish signals. Method validation was incorporated with internal standards and carried out with matrix-matched calibration. The detection limits for nicotine, cotinine, and …

A Study On The Elementary School Teachers’ Awareness Of Students’ Alternative Conceptions About Change Of States And Dissolution, Chanho Yang, Taehee Noh, Lawrence C. Scharmann, Sukjin Kang

Department of Teaching, Learning, and Teacher Education: Faculty Publications

Knowledge about students’ conceptions is one of the requisite components of pedagogical content knowledge. A keen awareness of students’ alternative conceptions provides teachers with information about prospective difficulties students may incur as they make attempts to learn more accurate scientific representations of critical concepts. In this study, we investigated elementary school teachers’ understanding of their students’ alternative conceptions about change of states and dissolution. The subjects were 152 elementary school teachers and 529 sixth graders in Korea. A conceptions test and the test of the understanding about students’ conceptions were administered in order to examine students’ alternative conceptions and the …

Exomol Molecular Line Lists V: The Ro-Vibrational Spectra Of Nacl And Kcl, Emma J. Barton, Christopher Chiu, Shirin Golpayegani, Sergei N. Yurchenko, Jonathan Tennyson, Daniel J. Frohman, Peter F. Bernath

Chemistry & Biochemistry Faculty Publications

Accurate rotation-vibration line lists for two molecules, NaCl and KCl, in their ground electronic states are presented. These line lists are suitable for temperatures relevant to exoplanetary atmospheres and cool stars (up to 3000 K). Isotopologues ²³Na³⁵Cl, ²³Na³⁷Cl, ³⁹K³⁵Cl, ³⁹K³⁷Cl, ⁴¹K³⁵Cl and ⁴¹K³⁷Cl are considered. Laboratory data were used to refine ab initio potential energy curves in order to compute accurate ro-vibrational energy levels. Einstein A coefficients are generated using newly determined ab initio dipole moment curves calculated using the CCSD(T) method. …

Advancements In The Design, Synthesis, And Application Of Polybenzimidazoles, Alexander Lanier Gulledge

Theses and Dissertations

The overall goal of the work presented within this thesis is to investigate, understand, and develop structure-property relationships in regards to polymer structure, membrane stability, and device performance. Previous work has shown that material properties such as acid loading, proton conductivity, mechanical integrity, and device performance can be attributed to polymer structure, chemical functionality, and polymer architecture (homo, random, co-polymer etc.). Developing and understanding these relationships is critical to the advancement of fuel cell technology. Within this thesis, several of these relationships are investigated and reported.

Novel polymers and copolymer systems have been developed in this research and have significantly …

Deuterium Tracer Study Of The Mechanism Of Iron Catalyzed Fischer-Tropsch Synthesis, Yunxin Liao

Online Theses and Dissertations

The Fischer-Tropsch Synthesis (FTS) was invented in 1920s, shortly after its invention, it became an important way to produce synthetic fuels. The FTS is also an important way to understand the origin of life. Even though the FTS has been used to produce liquid fuels commercially for a relatively long time, the mechanism of FTS is still unclear, a mechanism can explain all the experimental observations has not been discovered yet.

By conducting H2/D2 switching experiments we found that there was an inverse isotope effect in the Fe catalyzed FTS. The rate of hydrocarbon production was increased when syngas H2/CO …