Chemistry Commons^™

Ion Beam Mapping Inside An Inductively Coupled Plasma Mass Spectrometer Using Laser Induced Fluorescence, Brett S. Duersch, Dr. Paul B. Farnsworth

Journal of Undergraduate Research

Inductively coupled plasma mass spectrometry (ICP-MS) is one of the fastest growing fields in analytical chemistry. This discipline combines the powerful detection of mass spectrometry (MS) with the almost universal ionization capabilities of the inductively coupled plasma (ICP) . Combing these two techniques is not a trivial matter, since ions must be extracted from a plasma operating at atmospheric pressures and at temperatures ranging from 6,000­ to 10,000­ C into a mass spectrometer which operates at vacuum pressures(10 -10 torr). At present the ICP and -3 -6 the MS are typically interfaced with a series of two cones. The first …

Membrane Depolarization Due To Cationic Steroid Antibiotics, Jonathan O. Wright, Dr. Paul Savage

Journal of Undergraduate Research

The project that I have worked on this past year has been focused on a novel group of antibiotics developed in the lab of Dr. Savage. The antibiotics, called ceragenins or cationic steroid antibiotics (CSA’s), are molecules synthesized from cholic acid, a common bile acid, and they mimic the structure and functionality of antimicrobial peptides found in nature. Although the CSA’s are much smaller than the peptides, they have similar structural aspects, a hydrophobic side as well as a cationic side, and are believed to have a similar mechanism of action. They, like the antimicrobial peptides, have been found to …

Composite Teflon And Polymer Inclusion Membranes For Use In Ion Chromatography Suppressors, Tyler L. Crawford, Dr. John D. Lamb

Journal of Undergraduate Research

Ion chromatography (IC) has a need for a suppressor which would allow the simultaneous conductitnetric detection of both cations and anions. Such a suppressor’s membrane would need to exhibit a large flux and a high level of selectivity. Polymer inclusion membranes (PIMS) containing macrocycles have been shown to exhibit high selectivity over a long period of time. The structure of the macrocycle 1 determines the affinity these Ugands exhibit toward cations. By completing metal salts, the macrocycles are able to extract ionic species into solvents that these metal salts would not be soluble in alone. The macrocycle can then transport …

Fractionation And Isolation Of The Anti-Tumoral Activity Of An Indigenous Tongan Medicinal Extract, Steven D. Christenson, Dr. Gary M. Booth, Dr. Steven G. Wood

Journal of Undergraduate Research

Vai Haka is the Tongan name given to a medicinal extract prepared and prescribed by indigenous healers on the island kingdom of Tonga. Used as a treatment for morning sickness (hyper-emesis), the mixture is prepared by boiling the barks of four different rainforest tree species. These species are Tarrena sambucina, Syzigium malaccense, Alphitonia zizyphoides, and Macaranga harveyana. Studies by Cox (et al) demonstrated biological activity in each of these species from a Guinea Pig Ileum assay.1 Further work by Cox documented that each species is used individually by Samoan healers to treat internal distress.2 Thus bioactivity is well documented through …

Pixe Analysis Of Human Hair From An Egyptian Cemetery, Rafael Casellas, Dr. Nolan F. Mangelson, Dr. Lawrence B. Rees

Journal of Undergraduate Research

Human hair is considered to be a minor excretory organ for trace elements. The literature suggests that in some cases trace elemental concentration varies in different races of people. In addition, hair analysis has been used to assess nutritional status in humans. These characteristics attracted archeologists because of the potential of using hair analysis to understand past cultures.1

Researching Molecular Mechanics, Kent Bower

Journal of Undergraduate Research

The use of Molecular Mechanics has taken a strong foothold in the world of computational chemistry today. Molecular Mechanics methods offer quick solutions to complex molecular conformation calculations that could take up to days or even months to perform on supercomputers using more exact methods, such as ab initio calculations. For this speed the price of accuracy is often paid when using Molecular Mechanics methods, particularly when the system under inspection is very specialized. For example, much current research centers on the conformations of crown-ether systems with metal-cation ligands. The C-C-O-C-C pattern in these ethers exhibits specific properties which make …

Development Of New Lipid A-Binding Agents, Mark Benson, Dr. Paul B. Savage

Journal of Undergraduate Research

The aim of this project is to synthesize a non-peptide lipid A-binding agent which is less toxic and simpler than polymyxin B. Such a binding agent could be used to fight sepsis, a toxic condition where the body overreacts to the lipid A portion of bacterial endotoxin released by Gram-negative bacteria.

A Supramolecular Strategy To Assemble Multifunctional Viral Nanoparticles, Limin Chen, Xia Zhao, Yuan Lin, Yubin Huang, Qian Wang

Faculty Publications

Using a one-pot approach driven by the supramolecular interaction between β-cyclodextrin and adamantyl moieties, multifunctional viral nanoparticles can be facilely formulated for biomedical applications.

Photoisomerization And Photoinduced Reactions In Liquid Ccl4 And Chcl3, Scott A. Reid, Fawzi Abou-Chahine, Thomas J. Preston, Greg T. Dunning, Andrew J. Orr-Ewing, Gregory M. Greetham, Ian P. Clark, Mike Towrie

Chemistry Faculty Research and Publications

Transient absorption spectroscopy is used to follow the reactive intermediates involved in the first steps in the photochemistry initiated by ultraviolet (266-nm wavelength) excitation of solutions of 1,5-hexadiene, isoprene, and 2,3-dimethylbut-2-ene in carbon tetrachloride or chloroform. Ultraviolet and visible bands centered close to 330 and 500 nm in both solvents are assigned respectively to a charge transfer band of Cl-solvent complexes and the strong absorption band of a higher energy isomeric form of the solvent molecules (iso-CCl₃–Cl or iso-CHCl₂–Cl). These assignments are supported by calculations of electronic excitation energies. The isomeric forms have …

Synthesis Of Lipid A Analogues And The Study Of Their Interactions With Antibiotics, Glade E. Roper, Dr. Paul B. Savage

Journal of Undergraduate Research

Septic shock is a disease that kills over 100,000 hospitalized patients in the United States every year. The mortality rate for those who fall into septic shock is between fifty and eighty percent, and despite advances in medicine this rate has remained constant over the years.1 Septic shock is caused by an inflammatory response to Gram–negative endotoxin, also known as lipopolysaccharide (LPS).

Annotated Chromatographic Isotope Features From A Highly Complex Mass Spectrometry Proteomic Dataset (Mouse) For Feature Detection Algorithm Evaluation, John T. Prince, Christoper Conley

ScholarsArchive Data

This data set and accompanying annotations, referred to as the MOUSE data set, were used for feature detection algorithm evaluation (FDAE) as described in "Massifquant: open-source Kalman filter based XC-MS feature detection". Bioinformatics. 2013. (additional citation details available after publication). Existing and future feature detection and quantitation methods designed for LC-MS are welcome to make use of the data. Since the annotation has isotopic information, users are encouraged to develop other meaningful algorithm evaluations at the isotopic-level. Finally, it serves as an example to be improved upon for future manual-annotation efforts undertaken by the XC-MS community.

Transition Metals As Tools To Probe The Electronic Properties Of Porphyrinoids, Jillian Worlinsky

Chemistry Education Materials

This thesis describes in a number of separate chapters a range of studies that measure the variation of specific physical properties with structural modification of the macrocycles, with a particular focus also on using their coordinated metals as probes. Specifically, the transition metal ions are used as tools for interrogation of the electronic properties of porphyrins and pyrrole-modified porphyrins. With the aim of better understanding the electronic and structural factors that govern the optical responses, axial binding strengths, fragmentation patterns and carbonyl stretching frequencies of meso-tetraarylporphyrins, a rational design of pyrrole-modified metalloporphyrins with designed optical properties is derived.

Synthesis And Evaluation Of Thermally-Responsive Coatings Based Upon Diels–Alder Chemistry And Renewable Materials, Dahlia N. Amato, Gregory A. Strange, John P. Swanson, Anton D. Chavez, Suzanne E. Roy, Kim L. Varney, Craig A. Machado, Douglas V. Amato, Philip Costanzo

Chemistry and Biochemistry

A soybean based coating with thermally responsive Diels–Alder linkages has been prepared following an automotive 2-component formulation. The resulting coatings displayed the capability to be healed following physical deformation by a thermal stimulus, and such a material has significant potential for end users. Various curing agents were employed, and resulted in variation of scratch resistance and re-healablity. Different thermally responsive soybean resins were synthesized to have varying amounts reversible and nonreversible linkages when incorporated into the coating. Additionally, different isocyanates were added at differing ratios of NCO:OH in search of the optimum coating. It was found through the analysis of …

Synthesizing A Solution Phase Combinatorial Library To Discover Potent Mdr Reversal Agents, John T. Prince, Dr. Merritt B. Andrus

Journal of Undergraduate Research

The failure of chemotherapy in treating cancer is largely due to a phenomenon known as Multidrug Resistance (MDR). In MDR, cancer cells that have been exposed to a particular chemotherapeutic drug build up resistance not only to the drug originally administered, but to a host of other chemodrugs that may or may not be structurally related.1 P-glycoprotein (Pgp), a large, membrane bound transporter, is primarily responsible for MDR. Pgp acts as a pump to efflux cytotoxic drugs, keeping internal concentrations at less than cytotoxic levels. Although other factors contribute to MDR, it is generally thought that the most promising approach …

Investigation Of The Pyrularia Thionin-Egf Mitotoxin On Cell Signal Transduction, Andrew B. Adams, Dr. Steven G. Wood

Journal of Undergraduate Research

Recently more emphasis has been placed on developing anti-cancer agents with greater specificity and fewer side effects. Immunotoxins and their relatives, mitotoxins, have arisen as possible answers. Mitotoxins are composed of mitogens coupled to plant or bacterial toxins. The mitotoxin under investigation is the EGF-Pyrularia Thionin combination.

Bcl-2 Promoter Sequence G-Quadruplex Interactions With Three Planar And Non-Planar Cationic Porphyrins: Tmpyp4, Tmpyp3, And Tmpyp2., Vu H. Le, Narayana Nagesh, Edwin A. Lewis

CAS Publications

The interactions of three related cationic porphyrins, TMPyP4, TMPyP3 and TMPyP2, with a WT 39-mer Bcl-2 promoter sequence G-quadruplex were studied using Circular Dichroism, ESI mass spectrometry, Isothermal Titration Calorimetry, and Fluorescence spectroscopy. The planar cationic porphyrin TMPyP4 (5, 10, 15, 20-meso-tetra (N-methyl-4-pyridyl) porphine) is shown to bind to a WT Bcl-2 G-quadruplex via two different binding modes, an end binding mode and a weaker mode attributed to intercalation. The related non-planar ligands, TMPyP3 and TMPyP2, are shown to bind to the Bcl-2 G-quadruplex by a single mode. ESI mass spectrometry experiments confirmed that the saturation stoichiometry is 4:1 for …

Thimerosal Exposure And The Role Of Sulfation Chemistry And Thiol Availability In Autism, Janet K. Kern, Boyd E. Haley, David A. Geier, Lisa K. Sykes, Paul G. King, Mark R. Geier

Chemistry Faculty Publications

Autism spectrum disorder (ASD) is a neurological disorder in which a significant number of the children experience a developmental regression characterized by a loss of previously acquired skills and abilities. Typically reported are losses of verbal, nonverbal, and social abilities. Several recent studies suggest that children diagnosed with an ASD have abnormal sulfation chemistry, limited thiol availability, and decreased glutathione (GSH) reserve capacity, resulting in a compromised oxidation/reduction (redox) and detoxification capacity. Research indicates that the availability of thiols, particularly GSH, can influence the effects of thimerosal (TM) and other mercury (Hg) compounds. TM is an organomercurial compound (49.55% Hg …

Synthesis And Characterization Of Polypyrrole-Metal Complexes As Electrocatalysts, Nandan K. Peddi

Theses and Dissertations

Modern fuel cells convert chemical energy to electrical energy due to the reaction between hydrogen and oxygen to produce water using a platinum electrocatalyst. The scarcity and high cost of platinum have led to the development of various less expensive and efficient electrocatalysts. Polypyrrole-cobalt (CoPPy) complex has been developed as a nonplatinum electrocatalyst for oxygen reduction reaction (ORR) and potential application as a cathode in fuel cells. The complex was synthesized by refluxing pyrrole monomer and cobalt acetate tetrahydrate in dimethylformamide (DMF) for two hours followed by vacuum distillation to collect the solid electrocatalyst. Cyclic voltammetry, rotating disk electrode voltammetry …

Distribution And Regulation Of Na,K-Atpase In Ocular Lens, Adam L. Lunceford, Dr. Steven W. Graves

Journal of Undergraduate Research

The Na,K-ATPase is a membrane-bound enzyme found in all cells. This enzyme is composed of an a subunit, which is responsible for the enzyme’s catalytic activity, and a b subunit, which assists in the binding of ions. The three main isoforms of the a subunit are designated a1, a2, and a3. The Na,K-ATPase is responsible for maintaining the proper balance of sodium and potassium ions in the intracellular and extracellular fluids Inhibition or decreased activity of the Na,K-ATPase enzyme has been implicated in the development of cataracts. Without the proper ionic balance, lens cells may be damaged and experience protein …

A Hybrid Approach To Calculating Coulombic Interactions: An Effective And Efficient Method For Optimization Of Simulations Of Many Ions In Quadrupole Ion Trap Device With Simion, Kenichiro Saito

Student Theses and Dissertations

An efficient algorithm is needed to handle space charge driven processes in the large number of ions limit. We have developed a "hybrid" algorithm that lightens the computational load required for these simulations by calculating total dynamical forces by efficiently and effectively approximating two-body Coulomb interactions. We took one step further and applied the algorithm in massively parallel general-purpose computing with GPU (GPGPU) to test its performance. In this study, we tested the parallel hybrid algorithm with a couple of basic models and analyzed the performances by comparing it to that of the original, fully-explicit method written in serial code. …

Synthesis Of Fullerene-Amine Adducts Under Various Reaction Conditions, Amy Alexander

Theses and Dissertations

The discovery of fullerenes was a significant scientific event for which the Nobel Prize was awarded in 1996. Since that time, research involving fullerene C60 has gained significant momentum due to the unique chemical, optical, and electronic properties of the molecule. The attachment of a polymer chain to C60 results in increased solubility and decreased aggregation, characteristics which can then be exploited for use in organic photovoltaic devices (OPVs), catalysts, fuel cells, and photonics. This research focuses on the synthesis of polymer-tethered fullerenes (PTFs) by reaction with amine-terminated polystyrene. Solvent polarity, light exposure, and the presence of molecular oxygen were …

Rapid Capillary Electrophoresis Assay For The Isoenzyme, Tk1, As An Indicator For Breast Cancer, Mari Evans, Dr. Milton L. Lee

Journal of Undergraduate Research

The isoenzyme thymidine kinase (TK1), found in human serum, has been shown to be a cancer tumor marker. It has demonstrated both diagnostic and prognostic value in the treatment of breast cancer.1 Currently TK1 levels are measured by radioimmunoassay and enzyme-linked immunosorbant assay (ELISA). Radioimmunoassay is not specific for TK1, is relatively expensive, uses radioactive materials and is labor intensive. Immunoassays of TK1 have been developed which are selective and sensitive but they are still labor intensive. A new assay is needed to make the information TK1 can provide accessible to physicians who treat and diagnose cancer. Capillary electrophoresis (CE) …

Can Achiral Hosts Perform Chiral Induction?, Eric S. Handberg, Dr. David V. Dearden

Journal of Undergraduate Research

Host exchange experiments (see Figure 1) compare the fit of left-handed molecules (L-) and right-handed molecules (D-) in a host. Molecules that possess this “handedness” property are said to be chiral. In chiral crown ether host exchange experiments, chiral crown ethers distinguish the fit of D-phenylalanine (Phe), D-tyrosine (Tyr), D-tryptophan (Trp), D-histadine (His), and D-aspartic acid (Asp) apart from L-Phe, L-Tyr, L-Trp , L-His, and L-Asp by forming chemically distinct complexes between the chiral host and the left- and right-handed amino acids1-3. Because the L- and D-handed molecules have different physical properties, the rate constants for exchange reactions differ. The …

Cytotoxic Activity Of Euphorbia Polycarpa, Larry C. Ford, Dr.Noel L. Owen, Dr. Steven G. Wood

Journal of Undergraduate Research

With antimicrobial resistance on the rise, research is turning more and more to natural sources for medicinal products (the original source, ironically, for most known antimicrobials). Under the aegis of the Natural Product Center here on campus, I had contact with the daughter of a shaman from the Yaqui Indian Tribe. The Yaqui people use Euphorbia polycarpa, commonly known as sandspurge, to treat snakebites, scorpion stings, and yeast infections. The latter ethnobotanical usage being the most testable, I chose to pursue the bioactive compounds in sandspurge.

Induction Of A Novel Form Of Cyclooxygenase By Non-Steroidal Anti-Inflammatory Drugs, Nathan K. Evanson, Dr. Daniel L. Simmons

Journal of Undergraduate Research

For many years, non-steroidal anti-inflammatory drugs (NSAIDs) have been used to treat pain, fever, and inflammation. The analgesic, antipyretic, and anti-inflammatory effects of these drugs have been attributed to the ability of these drugs to inhibit the activity of cyclooxygenase (COX) enzymes1. COX enzymes catalyze the rate-limiting step in the conversion of arachidonic acid (an unsaturated fatty acid) to potent signaling molecules called prostaglandins, which in turn mediate the inflammatory process. However, NSAIDs, such as diclofenac, have been reported to induce COX activity in certain cell lines2. These studies were done to determine whether a similar induction of COX in …

Regulation Of G-Protein Signaling By Phosducin-Like Protein, Steven M. Bray, Steven M. Bray

Journal of Undergraduate Research

G-protein signaling is one of the major pathways which cells utilize to transmit messages. The signaling pathway consists of a receptor coupled to a G-protein, which activates secondary messengers. Signaling molecules, such as hormones and neurotransmitters, bind receptors on the cell surface, which in-turn activates G-proteins by dissociating them into a and bg subunits. These subunits bind to other molecules, secondary messengers, which further propagate the signal.

Amyloid Β-Peptide (1–42)-Induced Oxidative Stress In Alzheimer Disease: Importance In Disease Pathogenesis And Progression, D. Allan Butterfield, Aaron M. Swomley, Rukhsana Sultana

Chemistry Faculty Publications

Significance: Alzheimer disease (AD) is an age-related neurodegenerative disease. AD is characterized by progressive cognitive impairment. One of the main histopathological hallmarks of AD brain is the presence of senile plaques (SPs) and another is elevated oxidative stress. The main component of SPs is amyloid beta-peptide (Aβ) that is derived from the proteolytic cleavage of amyloid precursor protein.

Recent Advances: Recent studies are consistent with the notion that methionine present at 35 position of Aβ is critical to Aβ-induced oxidative stress and neurotoxicity. Further, we also discuss the signatures of oxidatively modified brain proteins, identified using redox proteomics approaches, during …

Cyclooxygenase 1 And 2: Development Of Canine Invitro And Whole Blood Assays For Non-Steroidal Anti-Inflammatory Drugs, Nicole L. Hatch, Dr. Daniel L. Simmons

Journal of Undergraduate Research

Non-steroidal anti-inflammatory drugs (NSAIDS) are the basis for a multi-billion dollar pharmaceutical market. Their target, Cyclooxygenase (COX), might from an economic standpoint be considered the most important enzyme known to man.1 COX is the key enzyme in the transformation of arachidonic acid into prostaglandins, is the target of non-steroidal antiinflammatory drugs (NSAIDs). Prostaglandins are very important signaling molecules that are involved in many body functions. From physiological and pathological standpoints the most interesting functions are in arthritis, inflammatory pain, ovulation, and cancer. Two isoforms of COX are known to exist in mammals: COX-1 and COX-2. Although very similar in structure, …

Phosphate And Ferritin Iron Deposition Kinetics, David D. Brosnahan, Dr. Gerald D. Watt

Journal of Undergraduate Research

I performed a ferritin iron reconstitution experiment, making 10 sequential additions of 10 ferrous ions per ferritin molecule at 10- minute intervals (see Figure 1). Monitoring the reaction at 375 nm, I observed a fast initial absorbance change representing iron oxidation. After the initial oxidation, I observed a gradual increase in absorbance that was complete in 10 minutes. I fit the plot of the change in absorbance versus time for each addition of iron to a double exponential equation (dA/dt = -A1ekt + -A2e-kt + c). The double exponential consisted of two negative terms. k1 has a relatively large value …

Calorimitry Data Tracking The Encapsulation Of Small Organic Water Contaminants By Cavitand [Co412]-8, Julie K. Cope, Dr. Roger G. Harrison

Journal of Undergraduate Research

Cavitand [Co412]-8 is a cage-like molecule having an inner cavity with a volume of approximately 1375 Å that traps small organic molecules. The “1” in the chemical formula represents resorc[4]arene, a bowl-shaped molecule1. Two resorc[4]arenes are connected with four cobalt molecules to form the cavitand [Co412]-8. Experiments were conducted in which resorc[4]arene was mixed with a small organic guest, then cobalt was added to connect the cage and trap the organic guests. These experiments were conducted in a calorimeter and the heat of the reaction was measured. From this data one is able to calculate the heat released during encapsulation …