Chemistry Commons^™

An Ab-Initio Study Of Pyrrole And Imidazole Arylamides, Abramyan Ara, Zhiwei Liu, Vojislava Pophristic

College of Science & Mathematics Departmental Research

Arylamide foldamers have been shown to have a number of biological and medicinal applications. For example, a class of pyrrole-imidazole polyamide foldamers is capable of binding specific DNA sequences and preventing development of various gene disorders, most importantly cancer. Molecular dynamics (MD) simulations can provide crucial details in understanding the atomic level events related to foldamer/DNA binding. An important first step in the accurate simulation of these foldamer/DNA systems is the reparametrization of force field parameters for torsion around the aryl-amide bonds. Here we highlight our Density Functional Theory (DFT) potential energy profiles and derived force field parameters for four …

Isolation Of A 55 Kd Protein That Specifically Binds The 3′ Au-Rich Element Of Interleukin-1b Messenger Rna, David Emergy Skarda, Dr. Roger L. Kaspar

Journal of Undergraduate Research

The polypeptide Interleukin- 1(IL-1) is one of the key mediators of the body’s response to microbial invasion, inflammation, immunological reactions, and tissue injury.1 IL- 1gene expression regulation occurs at many steps. One of the steps currently being researched is translation. Recent research indicates that the translational regulation mechanisms of IL- 1include an AU-rich element in the 3′ untranslated region (Fig. 1).2 In this mechanism, an induced protein binds to the AU-rich element (ARE) causing a decrease in translation efficiency. Isolation and subsequent identification of the ARE binding protein may lead to effective new drugs that induce the ARE binding protein …

Function And Distribution Of Apolipoprotein A1 In The Artery Wall Are Markedly Distinct From Those In Plasma, Joseph A. Didonato, Ying Huang, Kulwant S. Aulak, Orli Even-Or, Gary Gerstenecker, Valentin Gogonea, Yuping Wu, Paul L. Fox, W.H. Wilson Tang, Edward F. Plow, Jonathan D. Smith, Edward A. Fisher, Stanley L. Hazen

Chemistry Faculty Publications

Background—Prior studies show that apolipoprotein A1 (apoA1) recovered from human atherosclerotic lesions is highly oxidized. Ex vivo oxidation of apoA1 or high-density lipoprotein (HDL) cross-links apoA1 and impairs lipid binding, cholesterol efflux, and lecithin-cholesterol acyltransferase activities of the lipoprotein. Remarkably, no studies to date directly quantify either the function or HDL particle distribution of apoA1 recovered from the human artery wall. Methods and Results—A monoclonal antibody (10G1.5) was developed that equally recognizes lipid-free and HDL-associated apoA1 in both native and oxidized forms. Examination of homogenates of atherosclerotic plaque–laden aorta showed >100-fold enrichment of apoA1 compared with normal aorta (P<0.001). Surprisingly, buoyant density fractionation revealed that only a minority (<3% of total) of apoA1 recovered from either lesions or normal aorta resides within an HDL-like particle (1.063≤d≤1.21). In contrast, the majority (>90%) …

Gram Scale Synthesis Of The C(1)-C(9) Fragment Of Amphidinolide C, Nicholas A Morra, Brian L Pagenkopf

Chemistry Publications

An allylic cis-epoxide prepared by Sharpless asymmetric epoxidation was transformed in 9 steps and 41% overall yield to the cyclization precursor 4 via a key one carbon homologation. Cobalt catalyzed aerobic oxidative cyclization of 4 gave the trans-THF in 94% yield at gram scale. Subsequent manipulations, including a Still-Gennari olefination, Sharpless asymmetric dihydroxylation, Corey-Fuchs alkynylation and Kazmaier hydrostannylation provided the fully functionalized C(1)-C(9) fragment 2 suitable for cross coupling. The sequence is readily scalable and provides gram quantities of 2

A Green Chemoselective And Practical Approach Toward N-(2-Azetidinonyl) 25-Disubstituted Pyrroles, Debasish Bandyopadhyay, Elvira Rhodes, Bimal K. Banik

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

Pyrrole and 2-azetidinone are two essential heterocyclic scaffolds, which are being broadly used in medicinal chemistry and drug discovery field. A green and practical method to synthesize novel N-(2-azetidinonyl) 2,5-disubstituted pyrroles, which are comprised of both pyrrole and 2-azetidinone moieties, has been developed. The classical Paal–Knorr reaction is one of the simplest and most economical methods for the synthesis of biologically important and pharmacologically useful pyrrole derivatives. The present procedure for the synthesis of N-(2-azetidinonyl) 2,5-disubstituted pyrroles (1,2,5-trisubstituted pyrroles) has been accomplished by reacting 3-amino β-lactams and 2,5-hexanedione in the presence of bismuth nitrate pentahydrate as an ecofriendly …

Dna Damage Repair Genes Controlling Human Papillomavirus (Hpv) Episome Levels Under Conditions Of Stability And Extreme Instability, Terri G. Edwards, Thomas J. Vidmar, Kevin Koeller, James K. Bashkin, Chris Fisher

Educator Preparation & Leadership Faculty Works

DNA damage response (DDR) genes and pathways controlling the stability of HPV episomal DNA are reported here. We set out to understand the mechanism by which a DNA-binding, N-methylpyrrole-imidazole hairpin polyamide (PA25) acts to cause the dramatic loss of HPV DNA from cells. Southern blots revealed that PA25 alters HPV episomes within 5 hours of treatment. Gene expression arrays identified numerous DDR genes that were specifically altered in HPV16 episome-containing cells (W12E) by PA25, but not in HPV-negative (C33A) cells or in cells with integrated HPV16 (SiHa). A siRNA screen of 240 DDR genes was then conducted to identify enhancers …

Improving The Sweeping Efficiency Of Permanganate Into Low Permeable Zones To Treat Tce: Experimental Results And Model Development, Chanat Chokejaroenrat, Negin Kananizadeh, Chainarong Sakulthaew, Steve D. Comfort, Yusong Li

Nebraska Water Center: Faculty Publications

The residual buildup and treatment of dissolved contaminants in low permeable zones (LPZs) is a particularly challenging issue for injection-based remedial treatments. Our objective was to improve the sweeping efficiency of permanganate into LPZs to treat dissolved-phase TCE. This was accomplished by conducting transport experiments that quantified the ability of xanthan-MnO₄⁻ solutions to penetrate and cover (i.e., sweep) an LPZ that was surrounded by transmissive sands. By incorporating the non-Newtonian fluid xanthan with MnO₄⁻, penetration of MnO₄⁻ into the LPZ improved dramatically and sweeping efficiency reached 100% in fewer pore volumes. To quantify …

Raman Spectroscopy As A Teaching Tool In The Forensic Science And Chemistry Courses, Zhaohua Dai, Elmer-Rico E. Mojico

Cornerstone 3 Reports : Interdisciplinary Informatics

No abstract provided.

Synthesis Of Orthogonally Protected 1,2-Diaminopropanoic Acids By Ring-Opening Of 3-Unsubstituted N-Activated Aziridine 2-Carboxylates With Para-Methoxybenzylamine: A Study Of The Regioselectivity Of The Reaction, Fintan Kelleher, Keith O'Brien

Articles

Orthogonally protected 1,2-diaminopropanoic acids (DAPs) have been synthesised in good yields by the ring-opening of 3-unsubstituted N-activated aziridine 2-carboxylates with para-methoxybenzylamine. The choice of both the N-activating group and ester alkyl group had a significant influence on the ratio of attack at the a or b positions of the aziridine. However, the regiochemical outcome is not predictable.

Influence Of Cholesterol And Bilayer Asymmetry On Membrane Protein Distribution In Polymer-Tethered Raft-Mimicking Lipid Membranes, Noor Fueza Hussain

Open Access Dissertations

It is now widely recognized that lipid rafts, which are membrane domains enriched in cholesterol (CHOL) and sphingolipids (SL), play a significant functional role in the plasma membrane. Raft domains particularly affect membrane functionality by causing sequestering of membrane proteins. Underlying mechanisms of raft-associated membrane protein sequestration remain elusive, due to the complexity, transient nature, and small size of raft domains in cellular membranes. To address these challenges, this dissertation unveils the relationship between lipid raft composition and membrane protein sequestration and function using raft-mimicking model membrane mixtures comprised of coexisting liquid-ordered (lo) and liquid-disordered (ld) domains with reconstituted membrane …

Development Of A Field-Portable Miniature Mass Spectrometer Designed For In-Situ Analysis And Ion Trap Miniaturization, Paul Isaac Hendricks

Open Access Dissertations

Chemical analysis by mass spectrometry has become the gold standard due to the sensitivity, selectivity, and short analysis times that are afforded by the method. Advances in miniaturized vacuum systems, mass analyzers, electronics, and ionization sources have allowed for the development of field-portable mass spectrometers. The performance of portable instruments has received much attention for their utility in the detection of illicit drugs, explosives, environmental contaminants, therapeutic drugs, and more recently, biological tissues. Furthermore, detection of the aforementioned compounds can be completed at atmospheric pressures and in the presence of complex matrices and sample surfaces when used in conjunction with …

Synthesis, Characterization And Application Of Two-Dimensional Layered Metal Hydroxides For Environmental Remediation Purposes, Cleopas Machingauta

Dissertations (1934 -)

Two-dimensional layered nano composites, which include layered double hydroxides (LDHs), hydroxy double salts (HDSs) and layered hydroxide salts (LHSs) are able to intercalate different molecular species within their gallery space. These materials have a tunable structural composition which has made them applicable as fire retardants, adsorbents, catalysts, catalyst support materials, and ion exchangers. Thermal treatment of these materials results in destruction of the layers and formation of mixed metal oxides (MMOs) and spinels. MMOs have the ability to adsorb anions from solution and may also regenerate layered structures through a phenomenon known as “memory effect”. Zinc-nickel hydroxy nitrate was used …

Nmr And Computational Characterization Of Protein Structure And Ligand Binding, Terrence Neumann

Dissertations (1934 -)

Nuclear magnetic resonance (NMR) techniques combined with computational methods such as docking and cheminformatics were used to characterize protein structure and ligand binding. The thioredoxin system of Mycobacterium tuberculosis consists of a thioredoxin reductase and at least three thioredoxins. This system is responsible for maintaining the cellular protein thiol redox state in normal state. This maintenance is important as the bacterium is engulfed by the human macrophage. Here it is bombarded by reactive oxygen and nitrogen species in an attempt to disrupt normal cellular function in part by perturbing the protein thiols. To this end, the solution structures of the …

Acquisition Of An Electrochemical System Instrument For The Development Of Sensors, Elmer-Rico E. Mojico

Cornerstone 1 Reports : Expansion and Enhancements of the Thinkfinity Platform

No abstract provided.

Interactive Whiteboards And Computerized Assistance In Chemistry, Rita K. Upmacis, Elmer-Rico E. Mojico, Canan Karaalioglu

Cornerstone 3 Reports : Interdisciplinary Informatics

No abstract provided.

Suspended Lipid Bilayer For Optical And Electrical Measurements Of Single Ion Channel Proteins, Suneth P. Rajapaksha, Xuefei Wang, H. Peter Lu

Chemistry Faculty Publications

Making and holding an artificial lipid bilayer horizontally in an aqueous solution within the microscopic working distance of similar to 100 mu m are essential for simultaneous single molecule imaging and single ion-channel electrical current recording. However, preparation of such a lipid bilayer without a solid support is technically challenging. In a typical supported lipid bilayer, the asymmetric local environments and the strong perturbation of the underneath solid or dense surface can diverge the normal behavior of membrane proteins and lipids. On the other hand, the suspended lipid bilayers can provide a native local environment for the membrane proteins and …

Multianalyte Sensing Of Addictive Over-The-Counter (Otc) Drugs, Tsuyoshi Minami, Nina A. Esipenko, Ali Akdeniz, Ben Zhang, Lyle Isaacs, Pavel Anzenbacher Jr.

Chemistry Faculty Publications

A supramolecular sensor array composed of two fluorescent cucurbit[n]uril-type receptors (probe 1 and probe 2) displaying complementary selectivities was tested for its ability to detect and quantify drug-related amines. The fluorimetric titration of the individual probes showed highly variable and cross-reactive analyte-dependent changes in fluorescence. An excellent ability to recognize a variety of analytes was demonstrated in qualitative as well as quantitative assays. Importantly, a successful quantitative analysis of several analytes of interest was achieved in mixtures and in human urine. The throughput and sensitivity surpass those of the current state-of-the-art methods that usually require analyte solid-phase extraction …

Mapping The Excited State Potential Energy Surface Of A Retinal Chromophore Model With Multireference And Equation-Of-Motion Coupled-Cluster Methods, Samer Gozem, Federico Melaccio, Roland Lindh, Anna I. Krylov, Alexander A. Granovsky, Celestino Angeli, Massimo Olivucci

Chemistry Faculty Publications

The photoisomerization of the retinal chromophore of visual pigments proceeds along a complex reaction coordinate on a multidimensional surface that comprises a hydrogen-out-of-plane (HOOP) coordinate, a bond length alternation (BLA) coordinate, a single bond torsion and, finally, the reactive double bond torsion. These degrees of freedom are coupled with changes in the electronic structure of the chromophore and, therefore, the computational investigation of the photochemistry of such systems requires the use of a methodology capable of describing electronic structure changes along all those coordinates. Here, we employ the penta-2,4-dieniminium (PSB3) cation as a minimal model of the retinal chromophore of …

Acquisition Of A Polarimeter For Teaching And Research In The Forensic Science And Chemistry Laboratories, Zhaohua Dai

Cornerstone 3 Reports : Interdisciplinary Informatics

No abstract provided.

Development Of Isotags For Nmr Based Metabolite Profiling And Applications, Fariba Tayyari

Open Access Dissertations

NMR spectroscopy is a powerful analytical tool for both qualitative and quantitative metabolite profiling analysis. However, accurate quantitative analysis of biological systems especially using one dimensional NMR has been challenging due to signal overlap. In contrast, the enhanced resolution and sensitivity offered by chemoselective isotope tags have enabled new and enhanced methods for detecting hundreds of quantifiable metabolites in biofluids using NMR spectroscopy or mass spectrometry. In this thesis we show improved sensitivity and resolution of NMR experiments imparted by 15N and 13C isotope tagging which enables the accurate analysis of plasma metabolites. To date, isotope tagging has been used …

Construction And Demonstration Of A Tandem Mass Spectrometer Based Instrument For Cold Ion Spectroscopy, James Gerhardt Redwine

Open Access Dissertations

A new instrument incorporating ion trap based tandem mass spectrometry and cold ion UV and UV-IR double resonance spectroscopy has been developed at Purdue University for the study of gas phase, biologically relevant ions. The instrument incorporates multiple quadrupole linear ion trap mass analyzers to prepare and isolate the precursor ions as well as to analyze the resultant photofragments. A 22-pole ion trap cooled to 5 K via a closed cycle helium cryostat is used to cool the ions for spectroscopic interrogation. Results show the vibrational and rotational temperature of a wide assortment of ions to be 12±2 K.

The …

The Carriers Of The Interstellar Unidentified Infrared Emission Features: Constraints From The Interstellar C-H Stretching Features At 3.2-3.5 Μm, Xuejuan Yang, Rainer Glaser, Aigen Li, Jianxin Zhong

Chemistry Faculty Research & Creative Works

The unidentified infrared emission (UIE) features at 3.3, 6.2, 7.7, 8.6, and 11.3 μm, commonly attributed to polycyclic aromatic hydrocarbon (PAH) molecules, have recently been ascribed to mixed aromatic/aliphatic organic nanoparticles. More recently, an upper limit of <9% was placed on the aliphatic fraction (i.e., the fraction of carbon atoms in aliphatic form) of the UIE carriers based on the observed intensities of the 3.4 μm and 3.3 μm emission features by attributing them to aliphatic and aromatic C-H stretching modes, respectively, and assuming A _3.4/A _3.3 ≈ 0.68 derived from a small set of aliphatic and aromatic compounds, where A _3.4 and A _3.3 are, respectively, the band strengths of the 3.4 μm aliphatic and 3.3 μm aromatic C-H bonds. To improve the estimate of the aliphatic fraction of the UIE carriers, here we analyze 35 UIE sources exhibiting both the 3.3 μm and …

Syntheses And Structures Of Iron(Ii) And Cobalt(Ii) Complexes Of Substituted Tetra(Pyrazolyl)Lutidine Derivatives, Heidi Marie Tatlock

Master's Theses (2009 -)

Pentadentate ligands provide stability to metal complexes as well as a binding site for substrates that make them exceptionally useful for studying reactions. They have been used in biomimetic studies, water splitting, and small molecule activation studies. A series of six pentadentate ligands derived from a,a,a',a'-tetra(pyrazolyl)lutidine, pz4lut, with methyl substituents decorating the ligand periphery has been synthesized. These ligands were coordinated to FeIICl, and the electronic and structural properties of the resulting complexes were studied in order to deduce the effects of methyl substitution at the 3-, 4-, and 5-positions of the pyrazolyl groups and at the methine positions. When …

Preparation Of Mesoporous Silica Supported Ruthenium Oxides And The Application And Kinetic Study In The Catalysis Of Water Oxidation, Yang Zhang

Open Access Dissertations

Photo-induced water splitting of water into H2 and O2 has been a major focus in the development of clean and renewable energy. The development of viable and efficient catalysts that facilitates O2 production remains the major challenge in the study of the corresponding half-reaction of water oxidation. There are plenty of metal oxides reported active in the catalysis of water oxidation. However, several important performance bench marks of those materials, such as the non-stoichiometric production of O2, slow reaction rate and/or low quantum efficiency, remain to be improved.

Ruthenium oxide (RuO2) has long been known as one of the most …

Instrumentation, Applications And Fundamentals Of Plasma Ionization Of Organic Molecules From Surfaces, Joshua Scott Wiley

Open Access Dissertations

Various aspects of the interaction of low-temperature plasma (LTP) ambient ionization with organic molecules and surfaces are discussed. As an application, LTP-MS has been used for the analysis of pesticides directly from fruits and vegetables revealing low parts per billion limits of detection (LODs). Due to low power and gas requirements, a battery-operated and handheld LTP probe was developed for the point-and-shoot MS analyses. Handheld LTP was compared with large-scale LTP on a benchtop and miniature MS revealing similar LODs for both. Long-distance ion transport up to one meter was also demonstrated with flexible tubing for non-proximate sample interrogation. Fundamentals …

Utilization Of Biomass Derived Furans In Value-Added Organics And Heterogeneous Oxorhenium Catalysts For Deoxydehydration Of Diols, Benjamin L. Wegenhart

Open Access Dissertations

As fossil fuels are depleted, there is a growing focus on renewable chemicals based on biomass materials, including both fuels and chemical feedstocks. Current methods for biomass utilization include biological conversion to produce ethanol and various thermochemical routes (gasification, pyrolysis, liquefaction, hydrothermal treatment, etc.). Furfural is one particular chemical that can be obtained from lignocellulosic biomass in good yields through the dehydration of sugar residues. It can be used as a feedstock for chemicals such as furan and THF, or as a platform molecule for making liquid fuels. The objective of this research is to investigate new pathways for the …

Development Of Quantitative Ft- Ir Methods For Analyzing The Cure Kinetics Of Epoxy Resins, Sang Ha Son

Open Access Dissertations

Epoxy thermosets are important engineering materials with applications in coating, adhesives, packaging and as structural components in a variety of advanced engineering products. The ultimate performance of polymer critically depends upon the details of the cure chemistry used to produce the thermoset. In order to better understand and monitor the cure chemistry, quantitative analysis of the FT-IR response has been developed for describing the epoxy-amine curing reaction as well as monitoring the hydrogen bonding that occurs in these systems The FT-IR analysis includes (i) quantitative deconvolution of complex peaks into individual spectral contributions, (ii) peak identification via DFT analysis and …

Gas-Phase Covalent And Non-Covalent Ion/Ion Chemistry Of Biological Macromolecules, John Robert Stutzman

Open Access Dissertations

Gas-phase ion/ion chemistry involves the interaction of oppositely charged ions inside of the mass spectrometer. During this gas-phase chemistry, particle transfer (i.e., proton and electron) or synthesis can occur at rapid reaction rates. Particle transfer represents a mature area of ion/ion chemistry, while selective covalent modification represents a fairly new area of gas-phase chemistry. Gas-phase covalent chemistry is based on traditional solution phase organic chemistry.

The work demonstrated in this dissertation greatly involves gas-phase covalent and non-covalent Schiff base chemistry on peptide and protein ions. The reagent dianion, 4-formyl 1,3-benzene disulfonic acid, has been used to covalently modify unprotonated primary …

Elucidation Of Chiral Recognition Mechanisms Of Solutes By Amylose Tris[(S)-Alpha-Methylbenzylcarbamate] Sorbent, Hung-Wei Tsui

Open Access Dissertations

Enantioselective separations of chiral molecules are important in various chemical fields, such as pharmaceuticals and agrochemicals industries. Polysaccharide-based sorbents have been widely used in chiral liquid chromatography. The recognition mechanisms which determine their enantioselectivities are not completely understood.

In this dissertation, the chiral recognition mechanisms of a widely used commercial sorbent, amylose tris[(S)-alpha-methylbenzylcarbamate], for benzoin (B) enantiomers were first studied. The HPLC data for benzoin with pure n-hexane as the mobile phase have been obtained. The behavior of sorbent-solute-hexane systems can be interpreted by considering only sorbent solute two-component interactions. Infrared (IR) spectra showed evidence of substantial hydrogen bonding (H-bonding) …

Design, Synthesis, And Evaluation Of Molecular Inhibitors For Biologically Relevant Enzymes, Sarah Emma St. John

Open Access Dissertations

The work in this thesis details the design, synthesis, and biological evaluation of molecular inhibitors for the inhibition of biologically relevant enzymes. The first three chapters of this thesis concern the polyphenol resveratrol and its inhibition of the quinone reductase 2 (QR2) enzyme. The work on this subject resulted in the complete design, synthesis, biological and structural evaluation of a second generation library of resveratrol analogues. From this work we identified a novel resveratrol analogue that inhibits QR2 in a previously unknown binding orientation. The fourth chapter of this thesis details the de novo design of molecules for the inhibition …