Digital Commons Network^™

Structure Of Polc Reveals Unique Dna Binding And Fidelity Determinants, Ronald J. Evans, Douglas R. Davies, James M. Bullard, Jeffrey Christensen, Louis S. Green, Joseph W. Guiles, Janice D. Pata, Wendy K. Ribble, Nebojsa Janjic, Thale C. Jarvis

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Chemistry)

PolC is the polymerase responsible for genome duplication in many Gram-positive bacteria and represents an attractive target for antibacterial development. We have determined the 2.4-Å resolution crystal structure of Geobacillus kaustophilus PolC in a ternary complex with DNA and dGTP. The structure reveals nascent base pair interactions that lead to highly accurate nucleotide incorporation. A unique β-strand motif in the PolC thumb domain contacts the minor groove, allowing replication errors to be sensed up to 8 nt upstream of the active site. PolC exhibits the potential for large-scale conformational flexibility, which could encompass the catalytic residues. The structure suggests a …

Structure And Dynamics Of Metalloproteins In Live Cells, Jeremy D. Cook, James E. Penner-Hahn, Timothy L. Stemmler

Biochemistry and Molecular Biology Faculty Publications

X-ray absorption spectroscopy (XAS) has emerged as one of the premier tools for investigating the structure and dynamic properties of metals in cells and in metal containing biomolecules. Utilizing the high flux and broad energy range of X-rays supplied by synchrotron light sources, one can selectively excite core electronic transitions in each metal. Spectroscopic signals from these electronic transitions can be used to dissect the chemical architecture of metals in cells, in cellular components and in biomolecules at varying degrees of structural resolution. With the development of ever-brighter X-ray sources, X-ray methods have grown into applications that can be utilized …

Towards The Total Synthesis Of Thioviridamide: Thiyl Radical Approach To The Beta-Thioenamide Linkage Formation, Jung-Hoon Kang

Theses and Dissertations

We developed an approach to the β-thioenamide linkage contained in the S-(2-aminovinyl)cysteine (avCys) residue of thioviridamide.1,2 Kinetic and thermodynamic control of radical additions of thiols to ynamides were studied for the formation of β-thioenamide linkage. Thiyl radicals are electrophilic and ynamides are electron-rich alkynes. This complementary polarity of the radical and acceptor increases the likelihood of a successful radical addition reaction. Because little is known about these types of compounds (β-thioenamides), we were unsure what kinds of yields and stereoselectivities (cis vs. trans) to expect. The adduct stability is another issue to consider. Fortunately, under typical radical addition conditions, the …

Resonance Raman Characterization Of The Peroxo And Hydroperoxo Intermediates In Cytochrome P450, Ilia G. Denisov, Piotr J. Mak, Thomas M. Makris, Stephen G. Sligar, James R. Kincaid

Chemistry Faculty Research and Publications

Resonance Raman (RR) studies of intermediates generated by cryoreduction of the oxyferrous complex of the D251N mutant of cytochrome P450_cam (CYP101) are reported. Owing to the fact that proton delivery to the active site is hindered in this mutant, the unprotonated peroxo-ferric intermediate is observed as the primary species after radiolytic reduction of the oxy-complex in frozen solutions at 77 K. In as much as previous EPR and ENDOR studies have shown that annealing of this species to ∼180 K results in protonation of the distal oxygen atom to form the hydroperoxo intermediate, this system has been exploited to …

Studies Of Surfactants Effect On Riboflavin Fluorescence And Its Determination In Commercial Food Products And Vitamin Tablets., William Emmanuel Ghann

Electronic Theses and Dissertations

A simple and economical fluorometer using blue LEDs excitation sources and simple PMT detection had been built, assembled, optimized, and employed for measurement of fluorescence from riboflavin (vitamin B₂). Surfactants have been known to enhance the intensity of fluorescence of fluorescent compounds. Fluorescence analysis of riboflavin in the presence of various anionic, cationic, and nonionic surfactants was also conducted to determine if they could improve analysis. However, the surfactants employed did not seem to have any meaningful enhancement; in fact, some actually diminished the fluorescence intensity of riboflavin. The procedure was linear for riboflavin from 0.01 to 2.5 …

Towards The Design And Syntheses Of Novel Triads Comprising Single Robson-Type Macrocyclic Dicopper(Ii) Cores Flanked By Two Terminal Polypyridyl Ruthenium(Ii) Complexes., Leslie Shane Moody

Electronic Theses and Dissertations

Progress toward the syntheses of new tetranuclear bimetallic complexes of copper(II) and ruthenium(II) was realized. The designed triads comprise a central binuclear copper(II) complex with a tetraiminodiphenolate macrocyclic Robson-type compartmental ligand. In the envisioned complexes, the macrocyclic core is further functionalized by attachment of two polypyridyl ruthenium(II) complexes. A novel dibrominated dicopper(II) Robson complex was formed by the 2:2:2 condensation reaction of 4-bromo-2,6-diformylphenol and 1,3- diaminopropane with cupric chloride. Similarly, a new dibrominated dizinc(II) was synthesized from zinc tetrafluoroborate and the same diamine and dialdehyde. The new dicopper(II) complex did not heterocouple with borylated substrates under explored Suzuki reaction conditions. …

Nondestructive Evaluation Of Aircraft Composites Using Terahertz Time Domain Spectroscopy, Christopher D. Stoik

Theses and Dissertations

Terahertz (THz) time domain spectroscopy (TDS) was assessed as a nondestructive evaluation technique for aircraft composites. Material properties of glass fiber composite were measured using both transmission and reflection configuration. The interaction of THz with a glass fiber composite was then analyzed, including the effects of scattering, absorption, and the index of refraction, as well as effective medium approximations. THz TDS, in both transmission and reflection configuration, was used to study composite damage, including voids, delaminations, mechanical damage, and heat damage. Measurement of the material properties on samples with localized heat damage showed that burning did not change the refractive …

Synthesis And Evaluation Of Structural Analogs Of Escherichia Coli Lipid A For Application Towards Cd14-Targeting Glycotherapeutics, Aileen Fay Galos Bongat

Dissertations

Lipid A is a glucosamine-based phospholipid that anchors carbohydrate molecules to the outer membrane of most Gram-negative bacteria. During severe infection, this amphiphilic macromolecule invoke a strong and acute pro-inflammatory response that leads to sepsis and ultimately to septic shock, organ failure and death. Thus, following the convention that the best antidote is often a derivative of the parent agonistic molecule, researchers have actively pursued the idea of creating an analog of Lipid A that can block the cellular receptor for this molecule and thereby arrest the cascade of events that lead to sepsis. Consequently, we became interested in creating …

Dynamic Ordering Transitions Of Liquid Crystals Driven By Interfacial Complexes Formed Between Polyanions And Amphiphilic Polyamines, Michael I. Kinsinger, Maren E. Buck, Fernando Campos, David M. Lynn, Nicholas L. Abbott

Chemistry: Faculty Publications

We report the design of an amphiphilic polyamine (polymer 1) based on poly(2-alkenyl azlactone) that strongly couples the formation of polyelectrolyte complexes at aqueous/liquid crystal (LC) interfaces to ordering transitions in the LC. We demonstrate that the addition of a strong anionic polyelectrolyte to aqueous solutions in contact with polymer 1-laden LC interfaces (prepared by Langmuir-Schaefer transfer of monolayers of polymer 1 onto micrometerthick films of nematic LC) triggers ordering transitions in the LCs. We further demonstrate that changes in the ordering of the LCs (i) are driven by electrostatic interactions between the polyelectrolytes, (ii) involve multivalent interactions between the …

Resonance Raman Interrogation Of The Consequences Of Heme Rotational Disorder In Myoglobin And Its Ligated Derivatives, Freeborn Rwere, Piotr J. Mak, James R. Kincaid

Chemistry Faculty Research and Publications

Resonance Raman spectroscopy is employed to characterize heme site structural changes arising from conformational heterogeneity in deoxyMb and ligated derivatives, i.e., the ferrous CO (MbCO) and ferric cyanide (MbCN) complexes. The spectra for the reversed forms of these derivatives have been extracted from the spectra of reconstituted samples. Dramatic changes in the low-frequency spectra are observed, where newly observed RR modes of the reversed forms are assigned using protohemes that are selectively deuterated at the four methyl groups or at the four methine carbons. Interestingly, while substantial changes in the disposition of the peripheral vinyl and propionate groups can be …

Examination Of An Aloe Vera Galacturonate Polysaccharide Capable Of In Situ Gelation For The Controlled Release Of Protein Therapeutics, Shawn David Mcconaughy

Dissertations

A therapeutic delivery platform has been investigated with the ultimate goal of designing a sustained protein release matrix utilizing an in-situ gelling, acidic polysaccharide derived from the Aloe vera plant. The Aloe vera polysaccharide (AvP) has been examined in order to determine how chemical composition, structure, molecular weight and solution behavior affect gelation and protein/peptide delivery. Correlations are drawn between structural characteristics and solution behavior in order to determine the impact of polymer conformation and solvation on gel formation under conditions designed to simulate nasal applications. Steady state and dynamic rheology, classic and dynamic light scattering, zeta potential, pulse field …

Three-Dimensional Microfluidic Devices Fabricated In Layered Paper And Tape, Andres W. Martinez, Scott T. Phillips, George M. Whitesides

Chemistry and Biochemistry

This article describes a method for fabricating 3D microfluidic devices by stacking layers of patterned paper and double-sided adhesive tape. Paper-based 3D microfluidic devices have capabilities in microfluidics that are difficult to achieve using conventional open-channel microsystems made from glass or polymers. In particular, 3D paper-based devices wick fluids and distribute microliter volumes of samples from single inlet points into arrays of detection zones (with numbers up to thousands). This capability makes it possible to carry out a range of new analytical protocols simply and inexpensively (all on a piece of paper) without external pumps. We demonstrate a prototype 3D …

Synthesis And Characterization Of Biodegradable Polyurethanes For Biomedical Application, Changhong Zhang

All Dissertations

This dissertation constitutes the studies about the biomedical materials research of novel polyurethanes. These elastic and degradable polyurethanes exhibited the potential for drug delivery, scaffold fabrication by novel ink-jet printing technology or other biomedical applications. This dissertation includes two parts about two different types of polyurethanes.
In the first part of this dissertation, we studied a polyurethane that was synthesized from methylene di-p-phenyl-diisocyanate (MDI), polycaprolactone diol (PCL-diol) and N, N-bis (2-hydorxyethyl)-2-aminoethane-sulfonic acid (BES). MDI, PCL-diol and BES were polymerized into polyurethane and served as the hard segment, soft segment and chain extender respectively. The effects of the chain extender BES …

Department Of Chemistry News For Alumni And Friends, Decemember 2008, Illinois State University, Department Of Chemistry

Chem Letter

Newsletter of the Illinois State University Department of Chemistry

Preparation Of Carboxylic Acid Functionalized Glycopolymers Through Raft And Post-Polymerization Modification For Biomedical Application, Husnu Alp Alidedeoglu

Dissertations

The primary theme of this dissertation involves the synthesis of well-defined primary amine functionalized polymers, subsequent modification of the polymers to produce novel carboxylic acid functionalized glycopolymers and surface polymerization of these systems utilizing controlled polymerization techniques. Additionally, the synthesis of new water-based allylic copolymer latexes is described. Carbohydrates are natural polymers which possess unlimited structural variations. They carry a huge density of information, and play major roles in recognition events and complex biological operations. For example, hyaluronic acid (HA), an anionic glycosaminoglycan, provides lubricating and cushioning properties in the extracellular matrix and has been found to be involved in …

The Effect Of The Amide Substituent On The Biodistribution And Tolerance Of Lanthanide(Iii) Dota-Tetraamide Derivatives, Mark Woods, Peter Caravan, Carlos F.G.C. Geraldes, Matthew T. Greenfield, Garry Kiefer, Mai Lin, Kenneth Mcmillan, M. Isabel M. Prata, Ana C. Santos, Xiankai Sun, Jufeng Wang, Shanrong Zhang, Piyu Zhao, A. Dean Sherry

Chemistry Faculty Publications and Presentations

Objectives—Recent advances in the design of MRI contrast agents have rendered the lanthanide complexes of DOTA-tetraamide ligands of considerable interest, both as responsive MR agents and paramagnetic chemical exchange saturation transfer agents. The potential utility of these complexes for in vivo applications is contingent upon them being well tolerated by the body. The purpose of this study was to examine how the nature of the amide substituent, and in particular its charge, affected the fate of these chelates postinjection.

Materials and Methods—Complexes of 6 DOTA-tetraamide ligands were prepared in which the nature of the amide substituent was systematically …

Fluorescent Conjugated Polymer Dots For Single Molecule Imaging And Sensing Applications, Changfeng Wu

All Dissertations

While single molecule imaging and sensing hold the promise of providing unprecedented detail about cellular processes, many advanced applications are limited by the lack of appropriate fluorescence probes. In many cases, currently available fluorescent labels are not sufficiently bright and photostable to overcome the background associated with various autofluorescence and scattering processes. This dissertation describes research efforts focused on the development of a novel class of fluorescent nanoparticles called conjugated polymers dots (CPdots) for single molecule fluorescence detection. The CPdots contain highly fluorescent π-conjugated polymers that have been refined over the last decades as the active material in polymer light-emitting …

Synthesis, Characterization, And Application Of Ag Nanostructures, Stephen Hudson

All Dissertations

Noble metal nanoparticles (NPs) have been used for many centuries; however their properties were not truly scrutinized until Michael Farady's investigations in the 1850's. Advances in the field of nanotechnology over the last three decades have enabled insights into the properties of materials as their dimensions are reduced to the nanoscale. The repercussions of these insights are seen in many modern applications.
In this dissertation, properties of novel nanostructures based on Ag NPs are presented and discussed. The exceptional optical properties of Ag NPs stem from the collective oscillations of the conduction electrons known as plasmon resonances. The excitation of …

Synthetic Complexes Of Relevance To Ni(Ii)-Containing Enzymes, Katarzyna Rudzka

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The work outlined herein presents an investigation of synthetic model complexes of relevance to the active sites of Ni(II)-containing enzymes, particularly urease, glyoxalase I, and acireductone dioxygenase. The research focuses on studying the structural and reactivity features of nickel complexes with biologically relevant substrates. The anion of acetohydroxamic acid is a well-known inhibitor of urease enzymes, including those isolated from Klebsiella aerogenes and Bacillus pasteurii. A precursor to the acetohydroxamate coordination in ureases is proposed to be an interaction between Ni(II) and acetohydroxamic acid. By using a novel supporting chelate ligand capable of secondary hydrogen bonding interactions a novel …

Evaluation Of Electron Donor Materials Used To Create Subsurface Permeable Reactive Barriers For Enhanced Reductive Dechlorination Of Chlorinated Ethenes, Elizabeth S. Semkiw

Dissertations

Chlorinated ethenes (CEs) are widespread ground water contaminants, apparently due to their extensive migration from numerous contamination source points. In this study, a long-term field investigation and aquifer microcosm experiments were combined to evaluate the effectiveness of electron donor materials used to create and maintain subsurface permeable reactive barriers (PRBs) for the enhanced in-situ biodegradation of CEs. The laboratory component includes the first side-by-side comparison of electron donor materials dairy whey, lactate syrup, and Hydrogen Release Compound® (HRC), in which dechlorination rates, fermentation product distributions, and H₂ production were monitored as measures of substrate efficiency. Field study allowed the …

Pulse-Laser Infrared Photothermal Spectrometry Of Condensed-Phase Aerosols Based On Photothermal Deflection Spectroscopy, Oluwatosin Olubunmi Dada

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The research reported in this dissertation is aimed at development of photothermal deflection detector that is consistent with constraints imposed by aerosols sampling and analysis. The main objectives of this project are: 1) the design and evaluation of initial apparatus prototypes and 2) a test of the prototype apparatus with surrogate substances using conventional mid-infrared gas lasers.

Experimental evaluation of reduced size photothermal apparatus is first performed with gaseous samples. Analysis of trichlorofluoromethane (CFC-11) and ethanol vapors is performed with both conventional large apparatus and the prototype small apparatus. Comparison studies in terms of photothermal signal from both apparatuses are …

The Performance Of Maize Crop During Acid Amelioration With Organic Residues In Soils Of Mtwara, Tanzania, Ae Majule, Jo Omollo

Tanzania Journal of Science

This study evaluated acid ameliorative potential and their effects on maize growth of four organic residues namely wild spikenard, cordia, cowpea and pigeon peas through incubations with or without sulphur. This was done in order to recommend potential organic residue source that could ameliorate soil acidity associated with sulphur dusting. Increased levels of sulphur in the soils reduced the growth and dry matter yields of maize due to intense acidification while maize growth and dry matter yields in soils which organic residues were incorporated was enhanced. Enhancement in maize performance may be a result of reduced soil acidity due to …

Direct Electrochemistry Of Chloroperoxidase At Gc Electrode Modified With Swnts, Hong-Xia Zhang, Xia-Qin Wu, Wen-Jing Hou, Wen Xie, Zhong-Qing Lu, Rong Wang, He-Xing Li

Journal of Electrochemistry

The chloroperoxidase(CPO) was immobilized onto the surface of SWNTs modified electrodes.The electrochemical behaviors of modified electrode have been investigated by cyclic voltammetry.The appearance of a pair of well-defined redox peaks in the CV curve indicated that SWNTs can promote the electron transfer reaction of CPO.The results of cyclic voltammetry in PBS of different pH,from 3~9,showed that the reaction of CPO on the modified electrode was with equal numbers of electron and protein.This readily prepared SWNTs modified electrode showed excellent stability and good catalysis to O₂.

Alkoxyamine Polymers: Versatile Materials For Surface Ligation Applications, Lindsey Hines, Jessica Moore, David Dahl, Belinda Lady, Johnathan Brantley, Hasan Palandoken

Chemistry and Biochemistry

Immobilization of biomolecules (i.e., proteins, carbohydrates), on polymeric surfaces has been an area of intense research. The resultant bioconjugates often display increased stability, bioavailability and activity. Our research program seeks to explore the utility of the alkoxyamine (RONH2) functional group in new materials as versatile ligating sites for the immobilization of various compounds.

The ease with which alkoxyamines (RONH2) condense with aldehydes or ketones has prompted their widespread use in labelling liposome, bacterial and mammalian cell surfaces as well as chemoselectively ligating small molecule ‘recognition elements' onto polyfunctional substrates. These condensation reactions proceed in aqueous media to afford the robust …

Cariporide Prodrugs: Targeting Brain Cancer Cells Through Sodium-Proton Exchange Inhibition, Jacob Vervynckt, Johnathan Brantley, Jessica Moore, Mark Graves Ii, William Harley, Fredric A. Gorin, Hasan Palandoken

Chemistry and Biochemistry

More than 200,000 people in the United States are diagnosed with a primary or metastatic brain tumor annually. The life expectancy for these individuals is approximately 9-12 months from the time of diagnosis. This poor prognosis is due to the ineffectiveness of existing therapies (i.e., chemotherapy and radiotherapy) against brain cancer, where the primary problem is the inability to differentiate cancer cells from healthy brain cells.

Relative to healthy brain tissue, the heightened metabolism of cancer cells increases their reliance on the ion transport proteins NHE (sodium-proton exchanger) and NCX (sodium-calcium exchanger). Inhibition of these proteins disrupts the intricate pH …

Removal Of Benzaldehyde From Methanol Using Alkoxyamine Functionalized Silica Gel, Dino Sulejmanovic, Carrie Jo Pruitt, Eric Conte, Hasan Palandoken, Shing-Yi Suen

Chemistry and Biochemistry

Alkoxyamines (RONH₂) react readily with aldehydes and ketones to form stable oxime ethers, and, thus are expected to be excellent scavengers of these compounds. We installed alkoxyamines on silica gel surface to remove benzaldehyde from methanol. Silica gel was immersed in H₂O₂/H₂SO₄ solution to activate the surface. Activated silica gel was then reacted with 3-chloropropyltrichlorosilane. Displacement of the chloride with N-hydroxyphthalimide and subsequent treatment with hydrazine provided alkoxyamines on the surface of silica gel. The resulting silica gel surface with alkoxyamine functional groups was immersed in a 100 ppm benzaldehyde solution …

Probing Phenylalanine/Adenine Π-Stacking Interactions In Protein Complexes With Explicitly Correlated And Ccsd(T) Computations, Kari L. Copeland, Julie A. Anderson, Adam R. Farley, James R. Cox, Gregory S. Tschumper

Chemistry Faculty Research & Creative Works

To examine the effects of π-stacking interactions between aromatic amino acid side chains and adenine bearing ligands in crystalline protein structures, 26 toluene/(N9-methyl) adenine model configurations have been constructed from protein/ligand crystal structures. Full geometry optimizations with the MP2 method cause the 26 crystal structures to collapse to six unique structures. The complete basis set (CBS) limit of the CCSD(T) interaction energies has been determined for all 32 structures by combining explicitly correlated MP2-R12 computations with a correction for higher-order correlation effects from CCSD(T) calculations. The CCSD(T) CBS limit interaction energies of the 26 crystal structures range from -3.19 to …

The Effects Of A Networked Data Acquisition System On Student Learning In General Chemistry Laboratories, Stuart C. Burris, Les L. Pesterfield, Darwin Dahl, Hasan Palandoken, Jacqueline Pope-Tarrence

Chemistry and Biochemistry

We have recently incorporated a networked data acquisition and analysis system into in our second semester general chemistry laboratories. Our investigation team has conducted a study to evaluate the effects of the networked data acquisition system on student performance on a Beer's Law laboratory. We focused on two specific phenomena: the effect of the networked data acquisition system on 1) student learning of specific content material and 2) student comfort level with laboratory work and data analysis. The study involved a networked data acquisition group (employing a UV-Vis spectrometer and colorimeters) and a control group (employing traditional, single wavelength spectrometers). …

Photocycloaddition Of Allenes, Crystal Ward

Theses and Dissertations

For the past ten years the Fleming research group has been involved in the research of allene compounds. We have explored the synthesis of allenes as well as several reactions involving allenes, such as oxidation and nitrene addition. Recently, we have explored the synthesis and photochemistry of allenic alcohols tethered to silicon. There are literature examples using allenes in synthesis, but very few examples exist using allenes in photochemical cycloaddition reactions. We have found that a diisopropylallenyloxy(cinnamyloxy)silane derivative undergoes [2+2] photochemical cycloaddition to produce a cyclobutylsilane product when irradiated for 60-75 minutes.

Patent: Cell-Permeable Miniature Proteins, Alanna S. Schepartz, Douglas S. Daniels, Betsy Smith

Chemistry Faculty Publications

Abstract: The present invention generally relates to miniature proteins, including miniature proteins that are permeable to cells. Certain aspects of the invention are generally related to miniature proteins, such as avian pancreatic polypeptide (aPP), modified such that the miniature proteins are permeable to cells. For instance, a portion of the aPP, such as the alpha helix region and/or the type II polyproline helix region, may be modified to render the region substantially cationic. As an example, one or more residues may be substituted with cationic amino acid residues such as arginine. The miniature proteins may also have additional functions, such …