Chemistry Commons^™

Mentoring Undergraduates Via Organic Synthesis, Steven L. Castle

Journal of Undergraduate Research

This report summarizes the results of the mentoring environment in my laboratory that were generated from January 2012 to present. During this period, a total of seven undergraduates performed research in my laboratory. Their names and accomplishments are listed below.

Gene And Protein Sequence Optimization For High-Level Production Of Fully Active And Aglycosylated Lysostaphin In Pichia Pastoris, Hongliang Zhao, Kristina Blazanovic, Yoonjoo Choi, Chris Bailey-Kellogg, Karl E. Griswold

Dartmouth Scholarship

Lysostaphin represents a promising therapeutic agent for the treatment of staphylococcal infections, in particular those of methicillin-resistant Staphylococcus aureus (MRSA). However, conventional expression systems for the enzyme suffer from various limitations, and there remains a need for an efficient and cost-effective production process to facilitate clinical translation and the development of nonmedical applications. While Pichia pastoris is widely used for high-level production of recombinant proteins, there are two major barriers to the production of lysostaphin in this industrially relevant host: lack of expression from the wild-type lysostaphin gene and aberrant glycosylation of the wild-type protein sequence. The first barrier can …

Mimics Of Antimicrobial Peptides And Glycolipid Immunology, Paul Savage

Journal of Undergraduate Research

The primary objective of this project was to provide a research experience for as many undergraduate students as possible in a laboratory involved in research in fields spanning chemical, immunological and microbiological disciplines. By working closely with senior graduate students and postdoctoral researchers, undergraduate researchers learned how research is conducted in academic laboratories and were able to contribute to this research.

Thermodynamic Studies Of Technologically Significant Silicides, Rebecca Stevens, Dr. Juliana Boerio-Goates

Journal of Undergraduate Research

Vanadium, molybdenum, and tungsten silicides are inorganic materials that have many practical applications at high temperatures and high pressures1. Eight compounds which are of particular interest are found in Table 1. Accurate thermodynamic data aids in the synthesis of high purity, single phase materials. For example, knowledge of the Gibbs free energies as a function of temperature and pressure allows one to predict relative stabilities of the binary compounds. Calculation of this thermodynamic property requires the enthalpy of formation of these materials as well as their entropies and heat capacities. The enthalpies have been reported for many of these compounds …

Isolation And Structural Elucidation Of Cancer Therapeutic Agents In Rhamnaecae Ziziphus Obtusifolia, Matthew Woll, Dr. Noel Owen

Journal of Undergraduate Research

Many important and useful biological compounds are found in plants. Extensive work has been done on evaluating anti-cancer 1, 2, anti-malarial 3, and anti-viral 4 properties of plants. The Yaqui Indians of northern Mexico have traditionally used many natural products to cure various diseases. Gloria Moroyoqui, the daughter of a Yaqui Indian shaman (medicine man) explained to us some of the plants and their uses as medicine. The Yaqui Indians have used Rhamnacae ziziphus obtusifolia, commonly known as graythorn, as a cancer chemotherapeutic agent.

The [4+2] Cycloaddition Of Donor-Acceptor Cyclobutanes And Nitrosoarenes., Naresh Vemula, Andrew C Stevens, Tyler B Schon, Brian L Pagenkopf

Chemistry Publications

The Yb(OTf)3 catalyzed [4+2] cycloaddition between donor-acceptor cyclobutanes and nitrosoarenes is disclosed. This method facilitates the synthesis of tetrahydro-1,2-oxazines in good to excellent yields as single diastereomers. Except for a few electron-deficient nitrosoarenes, excellent regioselectivity was observed throughout these studies.

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). NSAIDS inhibit COX from producing arachdonic acid, a precursor to prostaglandins (2). Prostaglandins have been indicated in platelet aggregation, cancer, the processing of pain information in the spinal cord, septic shock, smooth muscle contraction during ovulation, cell proliferation, rheumatoid arthritis and inflammation.

Photodynamic Therapy As A Cure For Ick, Spencer C. Davis, Dr. James Thorne

Journal of Undergraduate Research

Photodynamic Therapy (PDT) is a new technique currently used to treat malignant cancer tumors in humans. This treatment uses the principles of light in a manner similar to types of radiation therapy. In PDT a photosensitizing dye is injected intraveneously diffusing to all cells. Tumor cell absorption of the dye is targeted by tailoring chemical properties of the photosensitizer, concentrating it in the tumor. The sensitizers absorb light energy, producing an excited singlet oxygen that readily reacts with double bonds and oxidizes adjacent molecules. PDT is very effective because the extremely reactive singlet oxygen travels only a short distance before …

Synthesis Of Bioconjugate Dimers Used To Probe The Structure Of Pglycoprotein, Emily Parker, Dr. Merritt B. Andrus

Journal of Undergraduate Research

Chemotherapy is one of the primary treatments for cancer today. A patient’s life may depend on its efficacy, so when he or she develops multi-drug resistance (MDR) the results can be devastating. MDR, a clinical condition manifested by the failure of chemotherapy, is primarily due to the expression of P-glycoprotein (Pgp), a membrane-bound small molecule transport protein which is found normally in some cells but is greatly over expressed in drug resistant cancer cells1. It is believed that after chemotherapy drugs diffuse into the cell, Pgp effluxes them out using energy from ATP hydrolysis, thus imparting drug resistance.

The Process Of Creating Microsolvated Ions Using Electrospray Ionization And Fourier-Transform Ion Cycoltron Resonance Mass Spectrometry, Laura Cunningham, Dr. David V. Dearden

Journal of Undergraduate Research

Microsolvation is the process of attaching solvent molecules to a host molecule in the gas phase, creating a system which exhibits characteristics between that of gas-phase and solution-phase systems. Study of these microsolvated systems can help us to understand the difference between gas-phase and solution-phase behavior, and uncover the conditions under which an ion may be considered solvated. Using electrospray ionization and Fourier-transform ion cyclotron resonance mass spectrometry, our team studied the best methods for creating microsolvated systems between alkali metals and various solvents.

Multi-Technique Quantitative Analysis And Socioeconomic Considerations Of Lead, Cadmium, And Arsenic In Children's Toys And Toy Jewelry, Margot M. Hillyer, Lauren E. Finch, Alisha S. Cerel, Jonathan D. Dattelbaum, Michael C. Leopold

Chemistry Faculty Publications

A wide spectrum and large number of children’s toys and toy jewelry items were purchased from both bargain and retail vendors and analyzed for arsenic, cadmium, and lead metal content using multiple analytical techniques, including flame and furnace atomic absorption spectroscopy as well as X-ray fluorescence spectroscopy. Particularly dangerous for young children, metal concentrations in toys/toy jewelry were assessed for compliance with current Consumer Safety Product Commission (CPSC) regulations (F963-11). A conservative metric involving multiple analytical techniques was used to categorize compliance: one technique confirmation of metal in excess of CPSC limits indicated a “suspect” item while confirmation on two …

Electrocatalytic Co2 Reduction By M(Bpy-R)(Co)4 (M = Mo, W; R = H, Tbu) Complexes. Electrochemical, Spectroscopic, And Computational Studies And Comparison With Group 7 Catalysts, Melissa L. Clark, Kyle A. Grice, Curtis E. Moore, Arnold L. Rheingold, Clifford P. Kubiak

College of Science and Health Faculty and Staff Works

The tetracarbonyl molybdenum and tungsten complexes of 2,2′-bipyridine and 4,4′-di-tert-butyl-2,2′-bipyridine (M(bpy-R)(CO)4; R = H, M = Mo (1), W (2); R = tBu, M = Mo (3), W (4)) are found to be active electrocatalysts for the reduction of CO2. The crystal structures of M(bpy-tBu)(CO)4 (M = Mo (3), W (4)), the singly reduced complex [W(bpy)(CO)4][K(18-crown-6] (5) and the doubly reduced complex [W(bpy-tBu)(CO)3][K(18-crown-6)]2 (6) are reported. DFT calculations have been used to characterize the reduced species from the reduction of W(bpy-tBu)(CO)4 (4). These compounds represent rare examples of group 6 electrocatalysts …

Less Cookbook And More Research! Synthetic Efforts Toward Jbir-94 And Jbir-125: A Student-Designed Research Project In A Sophomore Organic Chemistry Lab, Mike A. Christiansen, C. L. Crawford, C. D. Mangum

Chemistry and Biochemistry Faculty Publications

In light of the meaningful learning gains that can be obtained through a genuine research experience, chemistry educators have had a longstanding interest in making teaching labs less “cookbook-like” and more research-driven [1]. With this mindset, we recently restructured our two-semester sophomore organic chemistry lab course to include a synthesis project that was chosen, designed, and carried out by students. This led to progress toward the syntheses of JBIR-94 and JBIR-125, two antioxidative/anticancer natural products that have yet to be assembled through organic chemistry. The major drawback of our course redesign is that it requires close supervision by an instructor …

Simulations Of Chemical Catalysis, Gregory K. Smith

Chemistry and Chemical Biology ETDs

This dissertation contains simulations of chemical catalysis in both biological and heterogeneous contexts. A mixture of classical, quantum, and hybrid techniques are applied to explore the energy profiles and compare possible chemical mechanisms both within the context of human and bacterial enzymes, as well as exploring surface reactions on a metal catalyst. A brief summary of each project follows.

Project 1 — Bacterial Enzyme SpvC

The newly discovered SpvC effector protein from Salmonella typhimurium interferes with the host immune response by dephosphorylating mitogen-activated protein kinases (MAPKs) with a β-elimination mechanism. The dynamics of the enzyme substrate complex of the SpvC …

Synthesis, Characterization, And Electrochemical Evaluation Of Novel, Highly Active Catalysts For The Oxygen Reduction Reaction In Alkaline Media, Danae Jacquelyne Davis

Chemistry and Chemical Biology ETDs

Efficient electrocatalysts for the oxygen reduction reaction (ORR) are needed for fuel cells and next generation metal-air batteries, as the overall efficiency of these systems is currently limited by cathode kinetics. While Pt and Pt-based alloys demonstrate excellent electrocatalytic activities, their prohibitive cost and rarity ultimately prevents their widespread utilization. Catalyst materials that are highly active, stable, and cost effective are needed. Manganese oxide (α-MnO₂) catalysts doped with varying amounts of Cu or Ni were synthesized, characterized, and evaluated for their performance as catalysts for the oxygen reduction reaction in alkaline electrolyte. Cu-α-MnO₂ nanowire catalysts consistently attained …

Functional Relevance Of Acrb Trimerization In Pump Assembly And Substrate Binding, Wei Lu, Meng Zhong, Qian Chai, Zhaoshuai Wang, Linliang Yu, Yinan Wei

Chemistry Faculty Publications

AcrB is a multidrug transporter in the inner membrane of Escherichia coli. It is an obligate homotrimer and forms a tripartite efflux complex with AcrA and TolC. AcrB is the engine of the efflux machinery and determines substrate specificity. Active efflux depends on several functional features including proton translocation across the inner membrane through a proton relay pathway in the transmembrane domain of AcrB; substrate binding and migration through the substrate translocation pathway; the interaction of AcrB with AcrA and TolC; and the formation of AcrB homotrimer. Here we investigated two aspects of the inter-correlation between these functional features, …

Spectroscopic Studies Of Conformation And Packing In Polythiophenes, Edwards T. Niles

Chemistry and Chemical Biology ETDs

This thesis employs variants of spectroscopic techniques to evaluate intermolecular interactions between P3HT chains in solution and in the solid state. Emphasis was put on understanding not only how intermolecular interactions within P3HT chains affect electronic properties, but also to assess changes due to the addition of weak and strong electron acceptors. To this end, optical and magnetic spectroscopies were focused on to correlate observed changes in electronic properties to physical changes in the polymer structure. To assess changes in intermolecular interactions, self-assembly was used to form P3HT nanofibers and were studied using resonance Raman, and transient absorption, and temperature- …

Determining The Function Of Hotdog-Fold Thioesterases, Yajun Wu

Chemistry and Chemical Biology ETDs

The enzymes that hydrolyze thioesters to the free acids and free thiols are called thioesterases. Based on the different folding strategy, most thioesterases are classified into two superfamiles: the hotdog-fold enzyme superfamily or alpha/beta-fold hydrolase enzyme superfamily. Hotdog-fold thioesterases share high degree similarity in structure which resembles a hotdog'. YigI is one of the last two uncharacterized hotdog-fold thioesterases from E.coli. To study the function of YigI, substrate specificity profile was determined by thioesterase activity assay. YigI possesses a preference for long chain acyl-CoA over shorter chain acyl-CoA. The highest activity was found in catalysis of myristoyl-CoA. By alignment with …

An Efficient Reductive Amination Protocol Using Benzylamine-Borane As Reducing Agent, Adam M. Bowman, Dr. Matt A. Peterson

Journal of Undergraduate Research

Reductive amination is an important method used to generate amines from aldehydes or ketones. This process occurs in a two-step in situ reaction. First, an iminium intermediate is formed when the carbonyl compound condenses with ammonia or a primary or secondary amine. This intermediate is then reduced by a reducing agent already present in the reaction mixture (Scheme 1).

A Study Of Random Amplified Polymorphic Dna (Rapd) As Markers In A Linkage Map Of Peromvscus Using Two Inbred Strains, Dan Ririe

Journal of Undergraduate Research

Within the mouse genus Peromyscus there exists many pericentric inversions containing linkage groups, genes which do not recombine. It has been hypothesized that genes inherited together provide the selective pressure which has caused speciation within the genus. The purpose of this project was to aid ongoing research in the lab of Dr. Duke Rogers in finding genetic markers in the mouse genus Peromyscus. From these markers a linkage map will eventually be developed, It is this linkage map which can help answer several evolutionary questions concerning this genus.

Creation Of Mutations Of The Human Cdc34 Gene: A Regulator Of The Cell Division Cycle, Craig Rogers

Journal of Undergraduate Research

In the yeast strain Saccharomyces cerevlslae, the gene CDC34 encodes for a ubiquitln ligase necessary for the transition from GI to the S phase of the cell division cycle.

Thick Target Applications Of Particle Induced X-Ray Emission (Pixe), Renee Williams

Journal of Undergraduate Research

Particle induced X-ray emission (PIXE) accomplishes simultaneous multiple- trace element analysis with samples weighing less than one milligram. Having such rare capabilities, PIXE has applications in many disciplines. Environmental, industrial and medical fields span only a few of the areas where PIXE has been used. Brigham Young University has conducted PIXE research in these disciplines and others for over 25 years. One of the current research projects involves the elemental analysis of lichens from Federal lands in the Intermountain west. During this project, weaknesses in the existing PIXE system became more apparent which sacrificed the precision of the method. Research …

Na+/K+ Atpase Concentrations In Pregnancy-Related Tissues, Sarah M. Buck, Dr. Steven Graves

Journal of Undergraduate Research

Na+/K+ ATPase, or sodium pump, is an integral protein that is essential in maintaining proper intracellular concentrations of Na+ and K+. The sodium pump exists in three isoforms which are present in varying numbers and relative distribution in different tissues. As the pump moves the ions in and out of the cell, it creates a cell membrane potential. When this potential decreases, muscle contracts. It is proposed that this may be a factor in the initiation or the sustaining of labor status. This study is concerned mainly with determining a possible correlation between sodium pump concentrations in pregnancy-related tissues and …

Transfected Rna Used In Determining The Location Of Splicing In The Cell And As A Treatment For Disease, Weston E. Spencer, Dr. Daniel L. Simmons

Journal of Undergraduate Research

Among the fastest moving areas of research today is that of RNA splicing and protein synthesis. Recently, a new gene (Cyclooxygenase-2) was discovered that encodes a protein in chicken embryo fibroblasts (CEF-147) believed to be involved in the synthesis of prostaglandins. Prostaglandins are naturally occurring fatty acids that can lower blood pressure, regulate acid secretion of the stomach, regulate body temperature, control inflammation, and can affect the action of certain hormones. This novel gene is found in tumor cells in the colon. When the tumor cells become malignant the gene becomes extremely active, thus producing more of its corresponding protein …

A Review Of Air–Ice Chemical And Physical Interactions (Aici): Liquids, Quasi-Liquids, And Solids In Snow, T. Bartels-Rausch, H-W Jacobi, T. F. Kahan, J. L. Thomas, E. S. Thomson, J. P. D. Abbatt, M. Ammann, J. R. Blackford, H. Bluhm, Chris Boxe, F. Domine, M. M. Frey, I. Gladich, M. I. Guzmán, D. Heger, Th. Huthwelker, P. Klán, W. F. Kuhs, M. H. Kuo, S. Maus, S. G. Moussa, V. F. Mcneill, J. T. Newberg, J. B. C. Pettersson, M. Roeselová, J. R. Sodeau

Publications and Research

Snow in the environment acts as a host to rich chemistry and provides a matrix for physical exchange of contaminants within the ecosystem. The goal of this review is to summarise the current state of knowledge of physical processes and chemical reactivity in surface snow with relevance to polar regions. It focuses on a description of impurities in distinct compartments present in surface snow, such as snow crystals, grain boundaries, crystal surfaces, and liquid parts. It emphasises the microscopic description of the ice surface and its link with the environment. Distinct differences between the disordered air–ice interface, often termed quasi-liquid …

Report On Redox Centers In Ferritin, Daren Heaton

Journal of Undergraduate Research

As described in my research proposal, I Investigated the redox centers In ferritin. Thanks to the creative activities scholarship, I was able to spend a significant amount of time In this investigation. Some of my work was influential in a grant proposal submitted by Dr. Gary Watt. This proposal received a good rating by NIH and will likely result in future funding for this project.

The Iron Release Mechanism Of Azotobacter Vinelandii: Tracking Heme Mediated Electron Transport, K. R. Pitts, G. D. Watt

Journal of Undergraduate Research

I ron is an essential mineral nutrient required by all living systems. How Iron Is taken up, stored, and utilized by living systems is relevant to the understanding of life In general, and the relationship Iron metabolism has with human health. Azotobacter Vinelandii bacterial ferritin (AVBF) represents the bacterial protein molecule Involved In Iron storage and regulation. The 24 protein subunits and 12 heme groups that comprise A VBF arrange themselves structurally to form a hollow sphere in which AVBF stores Iron. The arrangement of protein subunits create channels roughly 50 nm in diameter that traverse the protein shell. These …

The Synthesis Of Novel Chiral Pyridino Crown Ethers, Steven L. Castle

Journal of Undergraduate Research

0ur research group has been interested in the synthesis of chiral pyridino crown ethers for some time. Many chiral pyridino crown ethers have been shown to exhibit enantiomeric recognition for chiral ammonium salts.1 In other words, the crown compound forms a more stable complex with one enantlomer of the chiral ammonium salt than It does with the other enantiomer. Recent results from de Mendoza, Echegoyen and coworkers’ led us to believe that a new type of chiral pyridino crown ether would exhibit even greater enantiomeric recognition than what was observed with previous compounds. So, my project was to prepare chiral …

A Review Of Air–Ice Chemical And Physical Interactions (Aici): Liquids, Quasi-Liquids, And Solids In Snow, T. Bartels-Rausch, H. -W. Jacobi, T. F. Kahan, J. L. Thomas, E. S. Thomson, J. P. D. Abbatt, M. Ammann, J. R. Blackford, H. Bluhm, C. Boxe, F. Domine, M. M. Frey, I. Gladich, M. I. Guzmán, D. Heger, Th. Huthwelker, P. Klán, W. F. Kuhs, M. H. Kuo, S. Maus, S. G. Moussa, V. F. Mcneill, J. T. Newberg, J. B. C. Pettersson, M. Roeselová, J. R. Sodeau

Chemistry Faculty Publications

Snow in the environment acts as a host to rich chemistry and provides a matrix for physical exchange of contaminants within the ecosystem. The goal of this review is to summarise the current state of knowledge of physical processes and chemical reactivity in surface snow with relevance to polar regions. It focuses on a description of impurities in distinct compartments present in surface snow, such as snow crystals, grain boundaries, crystal surfaces, and liquid parts. It emphasises the microscopic description of the ice surface and its link with the environment. Distinct differences between the disordered air–ice interface, often termed quasi-liquid …

The Location And Role Of Phosphate In Horse Spleen Ferritin (Hosf), Joseph Johnson

Journal of Undergraduate Research

Although iron Is necessary for life, It Is toxic If left free In most organIsms. To control Its toxic effects and still have iron available for biological use, organisms use ferrltins. Ferritins are similar throughout the biological world. Each ferritin is a roughly spherical, hollow protein with a thin, negatively charged shell that can hold up to 4500 Iron atoms. This shell is composed of 24 nearly Identical subunits. Junctions between three or four subunits form channels, 3-fold or 4-fold respectively, that traverse the protein shell. The hydrophilic 3-fold channels are believed to be the key pathway for the uptake …