Chemistry Commons^™

Stability And Kinetics Of Dna Pseudoknots: Formation Of T∗A•T Base-Triplets And Their Targeting Reactions, Calliste Steffensmeier

Theses & Dissertations

Pseudoknots have been found to play important roles in the biology of RNA. These stem-loop motifs are considered to be very compact and the targeting of their loops with complementary strands is accompanied with lower favorable free energy terms. We used a combination of spectroscopic (UV, CD and fluorescence), calorimetric (DSC, PPC and ITC) and kinetic (SPR) techniques to investigate: 1) Local base-triplet formation in pseudoknots; 2) energetic contributions for the association of pseudoknots with their complementary strands; and 3) the kinetic rates as a function of targeting strand length.

We investigated a set of DNA pseudoknots with sequence: d(TCTCT …

Evidence That Cytochrome B5 Acts As A Redox Donor In Cyp17a1 Mediated Androgen Synthesis, Ruchia Duggal, Yilin Liu, Michael C. Gregory, Ilia G. Denisov, James R. Kincaid, Stephen G. Sligar

Chemistry Faculty Research and Publications

Cytochrome P450 17A1 (CYP17A1) is an important drug target for castration resistant prostate cancer. It is a bi-functional enzyme, catalyzing production of glucocorticoid precursors by hydroxylation of pregnene-nucleus, and androgen biosynthesis by a second C--C lyase step, at the expense of glucocorticoid production. Cytochrome b₅(cyt b₅) is known to be a key regulator of the androgen synthesis reaction in vivo, by a mechanism that is not well understood. Two hypotheses have been proposed for the mechanism by which cyt b₅ increases androgen biosynthesis. Cyt b₅ could act as an allosteric effector, binding to …

Ionophoric Polyphenols Selectively Bind Cu2+, Display Potent Antioxidant And Anti-Amyloidogenic Properties, And Are Non-Toxic Toward Tetrahymena Thermophila, Alberto Martinez, Ralph Alcendor, Tanzeen Rahman, Magdalena Podgorny, Ismaila Sanogo, Rebecca Mccurdy

Publications and Research

Alzheimer’s disease (AD) is the most common form of dementia affecting more than 28 million people in the world. Only symptomatic treatments are currently available. Anticipated tri-fold increase of AD incidence in the next 50 years has established the need to explore new possible treatments. Accumulation of extracellular amyloid-b (Ab) plaques, intracellular tangles in the brain, and formation of reactive oxygen species (ROS) are the major hallmarks of the disease. The active role of some metal ions, especially Cu²⁺, in promoting both Ab aggregation and reactive oxygen species formation has rendered ionophoric drugs as a promising treatment strategy. …

Shining Light On Beta-Lactam Synthesis: The Photochemical Synthesis Of 3-Oh-Beta-Lactams, Tyler L. Morse

Arts & Sciences Graduate Student Theses and Dissertations

No abstract provided.

Continuum Nuclear Structure Of Light Nuclei, Kyle Wayne Brown

Arts & Sciences Graduate Student Theses and Dissertations

In this work, the continuum decay of proton-rich nuclei with mass number A ≤ 17 was studied. The nuclear structure of these nuclei was assessed by measuring the decay energy, width, and momentum correlations between the decay fragments. In particular the Isobaric Analog State in 8B, the ground-state and excited states of 16Ne, the T = 3/2 states in the A = 7 isobaric chain, and the excited states of 9C and 17Ne were all studied. In addition a first measurement of 17Na was made. These states decay by emission of 1 or more protons and were populated through knockout …

Synthesis Of Two-Dimensional Copper Indium Disulfide Nanocrystals And Study Of Exciton Splitting In Thin Nanosheets, Linjia Mu

Arts & Sciences Graduate Student Theses and Dissertations

This dissertation presents the preparation of two-dimensional (2D) CuInS2 nanocrystals by the ion-exchange method and the exciton splitting observed in thin CuInS2 nanosheets. After monitoring the one-pot synthesis of CuInS2 by energy-dispersive X-ray spectroscopy (EDS), an ion-exchange method is developed as an improvement for the synthesis of CuInS2 nanocrystals, to control the morphology and size. CuInS2 nanocrystals are prepared by ion exchange with template Cu2-xS nanoplatelets and InX3 [X = chloride, iodide, acetate (OAc), or acetylacetonate (acac)]. The morphologies of the resultant nanocrystals depend on the InX3 precursor and the reaction temperature. Exchange with InCl3 at 150 °C produces CuInS2 …

Anodic Electrochemistry: Controlling The Reactivity Of Radical Cation Intermediates, Robert John Perkins

Arts & Sciences Graduate Student Theses and Dissertations

Radical cations are highly reactive intermediates which when formed can lead to a variety of interesting and efficient synthetic transformation. Electrochemical oxidations may be used to generate radical cations from electron rich, nucleophilic functional groups, triggering intramolecular cyclization reactions. These intramolecular anodic olefin coupling reactions are a powerful synthetic tool for coupling electron-rich olefins with a second nucleophile to form complex ring systems. However, they do not all work well. The main focus of this dissertation research is to diagnose the main causes of failed anodic olefin coupling reactions, devise new methods to overcome or circumvent these causes, and then …

Synthesis Of Simplified Ym-254890 Analogs, Derek Thomas Rensing

Arts & Sciences Graduate Student Theses and Dissertations

G Protein Coupled Receptors (GPCR’s) are responsible for a multitude of physiological, cellular, and disease processes. GPCR’s signal through non-receptor based heterotrimeric G proteins and since G proteins effectively mediate GPCR signal transduction they are attractive therapeutic targets. However, little is known about the signaling pathways associated with individual G proteins. For this reason, there is intense interest in the development of chemical probes that can help identify the downstream biochemistry of individual G proteins.One small molecule natural product that shows promise along these lines is YM-254890 (YM). YM has been shown to specifically and potently inhibit the α subunit …

Synthesis And Characterization Of Amphiphiles For Mammalian Cell Transfection And Antimicrobial Activity, Joseph William Meisel

Dissertations

Amphiphiles are molecules that contain both water-soluble and water-insoluble components. The dual nature of these molecules engenders remarkable properties including the ability to self-assemble into ordered structures. Cell membranes are composed of amphiphilic phospholipids that organize into a bilayer motif. Synthetic amphiphiles can interact with natural membranes and influence the transport of molecules across the cell membrane. The work elaborated in this report employs amphiphiles to co-assemble with DNA and transport the genetic material across cell membranes. First, a simplified method for interacting DNA with amphiphiles was developed. Second, a series of known ion-transporting compounds were assayed for their interaction …

Interactions Of Nucleic Acid Bases With Temozolomide. Stacked, Perpendicular, And Coplanar Heterodimers, Okuma Emile Kasende, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Temozolomide (TMZ) was paired with each of the five nucleic acid bases, and the potential energy surface searched for all minima, in the context of dispersion-corrected density functional theory and MP2 methods. Three types of arrangements were observed, with competitive stabilities. Coplanar H-bonding structures, reminiscent of Watson–Crick base pairs were typically the lowest in energy, albeit by a small amount. Also very stable were perpendicular arrangements that included one or more H-bonds. The two monomers were stacked approximately parallel to one another in the third category, some of which contained weak and distorted H-bonds. Dispersion was found to be a …

Study Of Vaporization Enthalpies And Vapor Pressures Of Potential Environmental Pollutants By Correlation-Gas Chromatography, Chase Patrick Gobble

Dissertations

The focus of this dissertation is on the measurement and analysis of thermodynamic data, including vaporization, fusion, and sublimation enthalpies and vapor pressures of dialkyl phthalates, as well as aliphatic and aromatic primary and tertiary amines by correlation gas chromatography (CGC). These compounds are important industrial and pharmaceutical substances whose prolonged use and sometimes misuse with regards to their disposal has created an environmental concern. Thermodynamic properties, such as vaporization enthalpy and vapor pressure provide crucial information to numerous industries and fields of study that include the chemical and petrochemical industry, chemical engineering and environmental science. Dialkyl phthalates are essential …

App Regulates Microglial Phenotype In A Mouse Model Of Alzheimer's Disease, Gunjan Manocha, Angela Floden, Keiko Rausch, Joshua Kulas, Brett Mcgregor, Lalida Rojanathammanee, Kelley Puig, Kendra Puig, Sanjib Karki, Michael Nichols, Diane Darland, James Porter, Colin Combs

Chemistry & Biochemistry Faculty Works

Prior work suggests that amyloid precursor protein (APP) can function as a proinflammatory receptor on immune cells, such as monocytes and microglia. Therefore, we hypothesized that APP serves this function in microglia during Alzheimer's disease. Although fibrillar amyloid β (Aβ)-stimulated cytokine secretion from both wild-type and APP knock-out (mAPP−/−) microglial cultures, oligomeric Aβ was unable to stimulate increased secretion from mAPP−/− cells. This was consistent with an ability of oligomeric Aβ to bind APP. Similarly, intracerebroventricular infusions of oligomeric Aβ produced less microgliosis in mAPP−/− mice compared with wild-type mice. The mAPP−/− mice crossed to an APP/PS1 transgenic mouse line …

Engineering Nanoarchitectures From Nanosheets, Nanoscrolls, And Nanoparticles, Taha Rostamzadeh

LSU New Orleans Theses and Dissertations

The ability to encapsulate/insert different kinds of nanoparticles (NPs) in scrolled nanosheets (NSs) may lead to the formation of new nanocomposite materials that yield novel properties. These nanostructures resemble “peapods” that consist of NPs chains (“peas”) located in a hollow space of desired nanoscrolls (“pods”). Depending on different combinations of “peas” and “pods” diverse families of nanopeapods (NPPs) can be synthesized which may exhibit interesting properties not accessible from the individual components. Though there exist various synthetic methods for the formation of NPPs, more development in terms of simplicity, flexibility, and productivity of synthetic approaches are needed so that different …

Quef And Quef-Like: Diverse Chemistries In A Common Fold, Adriana Bon Ramos

Dissertations and Theses

The tunneling fold (T-Fold) superfamily is a small superfamily of enzymes found in organisms encompassing all kingdoms of life. Seven members have been identified thus far. Despite sharing a common three-dimensional structure these enzymes perform very diverse chemistries.

QueF is a bacterial NADPH-dependent oxidoreductase that catalyzes the reduction of the nitrile group of 7-cyano-7-deazaguanine (preQ₀) to a primary amine (preQ₁) in the queuosine biosynthetic pathway. Previous work on this enzyme has revealed the mechanism of reaction but the cofactor binding residues remain unknown. The experiments discussed herein aim to elucidate the role of residues lysine 80, …

Fluorescent Conjugated Polymers With A Bodipy-Based Backbone And Uses Thereof, Haiying Liu

Michigan Tech Patents

The present invention provides various fluorescent conjugated polymers with a BODIPY-based backbone. The invention also provides methods of using the polymers of the invention, such as for imaging and detection of cells, tumors, bacteria and viruses.

0+ States In 130,132Xe: A Search For E(5) Behavior, Erin E. Peters, T. J. Ross, S. F. Ashley, Anagha Chakraborty, Benjamin P. Crider, M. D. Hennek, Sinong Liu, Marcus T. Mcellistrem, Sharmistha Mukhopadhyay, Francisco M. Prados-Estévez, Anthony Paul Ramirez, J. S. Thrasher, Steven W. Yates

Chemistry Faculty Publications

The level structures of ^130,132Xe were studied with the inelastic neutron scattering reaction followed by γ-ray detection. Level lifetimes were measured using the Doppler-shift attenuation method and low-lying excited states in these nuclei were characterized. With a focus on the decay properties of the 0⁺ states, these nuclei were examined as representations of the E(5) critical-point symmetry.

Verwiebe's "3-D" Ice Phase Diagram Reworked, Carl W. David

Chemistry Education Materials

The two dimensional phase diagrams of the various forms of ice are difficult to read and understand. A ``3D'' versions appearing ~80 years ago helps understanding of the phases and their inter-conversion into other phases.

Monitoring The Charge Distribution During Proton And Sodium Ion Conduction Along Chains Of Water Molecules And Protein Residues, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Quantum calculations are used to determine the level of delocalization of the charge of a cation as it translates along a chain of water molecules or glycine residues. Charge dispersal is monitored via the molecular electrostatic potential and the dipole moment of the entire system. The positive charge is largely localized on the water molecule on which the proton is situated, but becomes more intense and extended as the proton moves along the chain. The positive charge is more delocalized in protonated polyglycine, where it extends over at least an entire residue. Displacement of the proton along the chain intensifies …

Inhibiting Androgen Receptor Nuclear Entry In Castration-Resistant Prostate Cancer, Julie A. Pollock, Suzanne E. Wardell, Alexander A. Parent, David B. Stagg, Stephanie J. Ellison, Holly M. Alley, Christina A. Chao, Scott A. Lawrence, James P. Stice, Ivan Spasojevic, Jennifer G. Baker, Sung Hoon Kim, Donald P. Mcdonnell, John A. Katzenellenbogen, John D. Norris

Chemistry Faculty Publications

Clinical resistance to the second-generation antiandrogen enzalutamide in castration resistant prostate cancer (CRPC), despite persistent androgen receptor (AR) activity in tumors, highlights the unmet medical need for next generation antagonists. We have identified and characterized tetra-aryl cyclobutanes (CBs) as a new class of competitive AR antagonists that exhibit a unique mechanism of action. These CBs are structurally distinct from current antiandrogens (hydroxyflutamide, bicalutamide, and enzalutamide), and inhibit AR-mediated gene expression, cell proliferation, and tumor growth in several models of CRPC. Conformational profiling revealed that CBs stabilize an AR conformation resembling an unliganded receptor. Using a variety of techniques, it was …

Templated Oligosaccharide Synthesis, Jia Guang Xiao

Dissertations

Glycosyl transfer within the active site of an enzyme involves the arrangement of the gly-cosyl donor and glycosyl acceptor in close proximity to each other. To mimic this pro-cess, intramolecular glycosylations are carried out where the donor and acceptor are linked together via a spacer. Correct orientation, rigidity and position of the spacer play a vital role in the selectivity and yield of reactions in this “molecular clamp method”. Though current methodologies show promising results in terms of yield and selectivity, the need to synthesize different complexes to ensure selectivities in all types of glycosidic linkages is a large deterrent …

Synthesis Of Cyclic Enolphosphonates And Enolphosphates As Inhibitors Of Serine Hydrolases, Benjamin Patrick Martin

Dissertations

Cyclophostin is a potent naturally occurring inhibitor of acetylcholinesterase with a novel bicyclic enolphosphate structure. The cyclipostins are a family of potent hormone-sensitive lipase inhibitors which share the same bicyclic enolphosphate core structure with cyclophostin which but differ primarily in that they are long-chain alkyl phosphate esters whereas cyclophostin is a methyl phosphate ester. Due to the novelty of the inhibitor structure, potency, and ability to select between two serine hydrolase enzymes with a simple change in the ester substituent, the ongoing structure activity relationship investigation of this family of inhibitors was continued. Methods of transesterification were investigated in order …

Persistence Of Trace Organic Contaminants From A Commercial Biosolids-Based Fertilizer In Aerobic Soils, Travis A. Banet, Jihyun R. Kim, Michael L. Mashtare

The Summer Undergraduate Research Fellowship (SURF) Symposium

Municipal biosolids are recycled as agricultural fertilizers. Recent studies have raised concerns due to the presence of emerging contaminants in municipal biosolids. Previous research suggests that these contaminants have the potential to reside in biosolids-based fertilizers that are commercially distributed. Use of these products in urban/suburban areas may provide a pathway for these contaminants to enter ecosystems and impact human and environmental health. Soils from Purdue University’s community garden and MiracleGro Potting Mix were chosen to represent commonly used urban/suburban growth media. Triclosan, triclocarban, and methyl parabens were selected as compounds of interest for this study. A heat treated commercial …

Assembly Of Nucleic Acid-Based Nanoparticles By Gas-Liquid Segmented Flow Microfluidics, Matthew L. Capek, Ross Verheul, David H. Thompson

The Summer Undergraduate Research Fellowship (SURF) Symposium

The development of novel and efficient mixing methods is important for optimizing the efficiency of many biological and chemical processes. Tuning the physical and performance properties of nucleic acid-based nanoparticles is one such example known to be strongly affected by mixing efficiency. The characteristics of DNA nanoparticles (such as size, polydispersity, ζ-potential, and gel shift) are important to ensure their therapeutic potency, and new methods to optimize these characteristics are of significant importance to achieve the highest efficacy. In the present study, a simple segmented flow microfluidics system has been developed to augment mixing of pDNA/bPEI nanoparticles. This DNA and …

Thermal Decomposition Of Electronic Cigarette Liquids, Robert Paul Jensen

Dissertations and Theses

Electronic cigarette liquid (e-liquid) is a solution of propylene glycol and/or glycerol with varying concentrations of nicotine and flavorants. Inhalation of vaporized e-liquid is a method of nicotine delivery that is growing in popularity and is commonly regarded as safe relative to smoking traditional tobacco products. The thermal decomposition of glycerol and propylene glycol is typical of alcohols and has been investigated, although not exhaustively. In this work, samples of propylene glycol and glycerol were vaporized using an electronic cigarette (e-cigarette) and were analyzed for evidence of decomposition using nuclear magnetic resonance (NMR) spectroscopy. E-cigarettes are shown to degrade glycerol …

First Experimental Evidence For The Diverse Requirements Of Excimer Vs Hole Stabilization In Π-Stacked Assemblies, Neil Reilly, Maxim Vadimovich Ivanov, Brandon Uhler, Marat R. Talipov, Rajendra Rathore, Scott A. Reid

Chemistry Faculty Research and Publications

Exciton formation and charge separation and transport are key dynamical events in a variety of functional polymeric materials and biological systems, including DNA. Beyond the necessary cofacial approach of a pair of aromatic molecules at van der Waals contact, the extent of overlap and necessary geometrical reorganization for optimal stabilization of an excimer vs dimer cation radical remain unresolved. Here, we compare experimentally the dynamics of excimer formation (via emission) and charge stabilization (via threshold ionization) of a novel covalently linked, cofacially stacked fluorene dimer (F2) with the unlinked van der Waals dimer of fluorene, that is, (F)₂. …

Two's Company, Three's A Crowd: Exciton Localization In Cofacially Arrayed Polyfluorenes, Marat R. Talipov, Maxim Vadimovich Ivanov, Scott A. Reid, Rajendra Rathore

Chemistry Faculty Research and Publications

Understanding the mechanisms of long-range energy transfer through polychromophoric assemblies is critically important in photovoltaics and biochemical systems. Using a set of cofacially arrayed polyfluorenes (Fn), we investigate the mechanism of (singlet) exciton delocalization in π-stacked polychromophoric assemblies. Calculations reveal that effective stabilization of an excimeric state requires an ideal sandwich-like arrangement; yet surprisingly, emission spectroscopy indicates that exciton delocalization is limited to only two fluorene units for all n. Herein, we show that delocalization is determined by the interplay between the energetic gain from delocalization, which quickly saturates beyond two units in larger Fn, …

Density Functional Theory Based Electrolyte Design Formulation For Lithium-Sulfur Batteries, Cynthia Ly, Carolyn Sturges, Vijay Murugesan

STAR Program Research Presentations

Lithium-ion (Li-ion) batteries are commonly used in portable electronics such as cellphones and laptops. Most Li-ion batteries operate on intercalation principle with typical theoretical specific energy of 400-600 (Wh/Kg). There is great scientific interest in lithium-sulfur (Li-S) batteries as a possible successor of traditional Li-ion batteries because Li-S holds the potential of being a very powerful (1550 Wh/kg theoretical specific energy) yet very cost-efficient battery (due the abundance and inexpensiveness of sulfur). However, one major problem in Li-S battery research is the polysulfide “shuttle phenomenon”, which is the shuttling of polysulfide species due to the dissolution of sulfide from the …

Calculating The Energy Barriers Required To Join Metal-Organic Framework Synthesis Intermediates With Non-Equilibrium Molecular Simulation, Marcus A. Tubbs, David Cantu, Roger Rousseau, Vassiliki-Alexandra Glezakou

STAR Program Research Presentations

Metal organic frameworks are synthetic porous materials with great capacity for adsorption of carbon dioxide and methane. They chemically appear as a chain-link fence with nodes of metal connected by organic linkers. The pores between the nodes define the characteristics of the material, allowing gas particles of specific size to pass through while blocking larger particulates. While there has been success in synthesizing small amounts of metal organic frameworks, the mechanistic details behind their assembly remain unknown. Understanding the synthesis mechanism is necessary to understand the kinetics involved and be able to produce this useful material on an industrial scale. …

Using In Situ Liquid Single Photon Ionization Mass Spectrometry (Spi-Ms) To Probe Lithium Polysulfide Electrolyte In Motion, Aala M. Al Hasan, Jiachao Yu, Juan Yao, Vijayakumar Murugesan, Manjula Nandasiri, Xiao-Ying Yu

STAR Program Research Presentations

The solid-liquid (s-l) interface is the most common interface encountered in electrochemical systems. The s-l interface has wide applications in energy storage, catalysis, and material sciences. In situ studies of chemical reactions taking place on the s-l interfaces can further our understanding of electron transfer and link to real-world device functions under challenging conditions. Direct probing of the solid electrode and liquid electrolyte interface has been realized using a vacuum compatible electrochemical microfluidic reactor, system for analysis at the liquid vacuum interface (SALVI) with time-of-flight secondary ion mass spectrometry (ToF-SIMS). Most recently, the electrochemical version of SALVI was integrated to …

Determination Of Dimethyl Trisulfide In Rabbit Blood Using Stir Bar Sorptive Extraction Gas Chromatography-Mass Spectrometry, Erica Mananadhar, Nujud Maslamani, Ilona Petrikovics, Gary A. Rockwood, Brian A. Logue

Chemistry and Biochemistry Faculty Publications

Cyanide poisoning by accidental or intentional exposure poses a severe health risk. The current Food and Drug Administration approved antidotes for cyanide poisoning can be effective, but each suffers from specific major limitations concerning large effective dosage, delayed onset of action, or dependence on enzymes generally confined to specific organs. Dimethyl trisulfide (DMTS), a sulfur donor that detoxifies cyanide by converting it into thiocyanate (a relatively nontoxic cyanide metabolite), is a promising next generation cyanide antidote. Although a validated analytical method to analyze DMTS from any matrix is not currently available, one will be vital for the approval of DMTS …