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2013

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Articles 241 - 270 of 1354

Full-Text Articles in Chemistry

Photocycloaddition Of Silyl-Tethered Alkenes For Cyclobutanes, David Feller, Dr. Steven A. Fleming Sep 2013

Photocycloaddition Of Silyl-Tethered Alkenes For Cyclobutanes, David Feller, Dr. Steven A. Fleming

Journal of Undergraduate Research

Cyclobutane rings occur in many natural products that show important medicinal properties (including sedatives, antiviral, and anti-tumor agents). The intrinsic physiological activities that cyclobutane rings display, draw the attention of synthetic chemists to elucidate total syntheses.1 Many natural products that incorporate chiral cyclobutane systems fascinate synthetic chemists as target molecules.

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Catalytic Reactions For The Production Of Biomarkers From The Biological Warfare Agent Anthrax (Dr.), Jason E. Hawkes, Dr. Milton L. Lee Sep 2013

Catalytic Reactions For The Production Of Biomarkers From The Biological Warfare Agent Anthrax (Dr.), Jason E. Hawkes, Dr. Milton L. Lee

Journal of Undergraduate Research

Bacillus anthracis, more commonly known as anthrax, poses a serious threat to the national security of the United States of America. In its weaponized form, anthrax spores are easily aerosolized, demonstrate long residence times in the atmosphere (typically variable for several days), and can be fatal if ingested or inhaled into the lungs. Following ingestion or inhalation, rapid growth and reproductive activity is triggered, releasing large amounts of deadly toxin. The lethal dose of anthrax spores is very small, approximately 10 nanograms of spores.1 As a result of its easy dispersal, long residence times, and high toxicity, anthrax is becoming …

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Observed Physiological Changes In Na+,K+-Atpase In Bovine Lens Epithelial Cells Upon Ouabain Exposure, Steven Jason Crellin, Dr. Steven Graves Sep 2013

Observed Physiological Changes In Na+,K+-Atpase In Bovine Lens Epithelial Cells Upon Ouabain Exposure, Steven Jason Crellin, Dr. Steven Graves

Journal of Undergraduate Research

Age-related cataractogenesis is a worldwide leading cause of blindness. The fact that the causes as well as the apparent symptoms of cataract are diverse has contributed to increased difficulty in the study of the ailment. However, a ubiquitous symptom in animal cataract is the presence of elevated sodium concentrations within the lens. Therefore, studies have emphasized the importance of the sodium pump, or Na+,K+-ATPase in the lens, particularly in the lens epithelial cells.1 The sodium pump is primarily responsible for extruding three Na+ ions from within the cell and taking in two K+ ions, thus establishing a net negative charge …

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Using The Byu Supercomputer To Simulate Analogs Of The Anti-Cancer Drug Geldanamycin, Joshua Proulx, Dr. Merritt Andrus Sep 2013

Using The Byu Supercomputer To Simulate Analogs Of The Anti-Cancer Drug Geldanamycin, Joshua Proulx, Dr. Merritt Andrus

Journal of Undergraduate Research

For my project I simulated the binding of geldanamycin in the ATP binding site of Heat shock protein-90 to assist Merritt Andrus’s research in designing a better anti-cancer drug. Hsp-90 is a protein found in the cells of many organisms including humans. It functions as a chaperone protein, helping other proteins assume their proper folded shape. When a ligand like geldanamycin binds to the active site on Hsp-90, the protein’s function is inhibited. In many cancer cells Hsp-90 is folded into a 3D shape that allows for easy binding with geldanamycin. A cancerous cell with inhibited Hsp-90 is far more …

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Optimization Of Kidney Cancer Cell Assay Conditions, Bryce Harbertson, Dr. Heidi Vollmer-Snarr Sep 2013

Optimization Of Kidney Cancer Cell Assay Conditions, Bryce Harbertson, Dr. Heidi Vollmer-Snarr

Journal of Undergraduate Research

Photodynamic therapy involves the use of light-sensitive compounds that, upon irradiation, become lethal to cells. These light-sensitive compounds are referred to as photosensitizers. A class of compounds known as pyridinium bis-retinoids are being investigated as potential photosensitizers, and therefore, chemotherapeutic drugs (Figure 1). One of the primary concerns in these investigations is determining the optimal conditions under which to evaluate these drugs. The optimization of these parameters will allow us to compare the effectiveness of our drugs with others already in existence, and will also serve as a basis for further investigations in animal trials and later on in clinical …

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Synthesizing Racemic And Optical Active 6-Methylsulfinylhexyl Isothiocyanate, Bo Duan, Dr. Merritt Andrus Sep 2013

Synthesizing Racemic And Optical Active 6-Methylsulfinylhexyl Isothiocyanate, Bo Duan, Dr. Merritt Andrus

Journal of Undergraduate Research

6–methylsulfinylhexyl isothiocyanate (MS-ITC) is the active component of wasabi, Japanese horseradish. Wasabi plant (Wasabia Japonica), a member of the Cruciferae family, is native to Japan and is traditionally found growing in or by cold mountain streams. The root and stem of this plant has a fiery hot flavor that quickly dissipates in the mouth, leaving a lingering sweet taste.

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Chemical Isolation From Plant Endophytes, David Dahl, Dr. Steven Wood Sep 2013

Chemical Isolation From Plant Endophytes, David Dahl, Dr. Steven Wood

Journal of Undergraduate Research

The major research that I have worked with is on the extraction of biologically active compounds from plant endophytes native to the west desert of Utah and high altitude Paramo of Ecuador. For a year I have been working the Department of Chemistry and Biochemistry’s Natural Product Research Group under Dr. Noel Owen and Dr. Steven Wood. I planned and am executing a project that combines several different disciplines; anthropology, botany, and chemistry.

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A Study Of Collisional Energy Transfer As A Function Of Vibrational Frequency Using Isotopically Substituted Benzene Molecules, Andrew Duffin, Dr. Eric Sevy Sep 2013

A Study Of Collisional Energy Transfer As A Function Of Vibrational Frequency Using Isotopically Substituted Benzene Molecules, Andrew Duffin, Dr. Eric Sevy

Journal of Undergraduate Research

Gas phase atoms and molecules constantly exchange energy in collisions. These energy transfer events are the rate limiting processes in reactions that are important for understanding atmospheric and combustion chemistry. While a great deal is known about collisional energy transfer, there is no good theory for predicting the outcome of energy transfer collisions. A study of energy transfer as a function of vibrational frequency would aid in formulating a model that would accurately describe energy transfer events.

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Total Synthesis Of The Natural Product Hasubanonine, Spencer Jones, Dr. Steven Castle Sep 2013

Total Synthesis Of The Natural Product Hasubanonine, Spencer Jones, Dr. Steven Castle

Journal of Undergraduate Research

Hasubanonine is a tetracyclic alkaloid with potential analgesic activity. The total synthesis of this alkaloid has been undertaken in order to demonstrate the applicability of the methodology developed for the synthesis of acutumine and to assay the potential medicinal activity of the compound. The key steps in the synthesis include the ruthenium catalyzed ring closing metathesis, anionic oxy-Cope rearrangement, and intramolecular Michael addition. Future work includes the completion of the racemic synthesis of hasubanonine as well as the investigation into the asymmetric allylation required for the enantioselective synthesis of hasubanonine.

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Engineering Small Molecule-Dependent Tools For The Study Of Protein Function In Vivo, Jonathan Dewey, Dr. Allen R. Buskirk Sep 2013

Engineering Small Molecule-Dependent Tools For The Study Of Protein Function In Vivo, Jonathan Dewey, Dr. Allen R. Buskirk

Journal of Undergraduate Research

Analyzing the function of newly discovered genes and the proteins that they encode is crucial to the advancement of genetics, cell and molecular biology, and medicine. Scientists have implemented various methods to study individual proteins within a cell, including genetic and small-molecule dependent approaches. Our goal is to combine the generality of genetic manipulation with the time-sensitivity of small-molecule dependence to create tools to study the function of Hedgehog pathway proteins and validate them as drug targets.

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Constructing An Ideal Metal Ion Chemosensor For Cadmium, David Michaelis, Dr. Paul B. Savage Sep 2013

Constructing An Ideal Metal Ion Chemosensor For Cadmium, David Michaelis, Dr. Paul B. Savage

Journal of Undergraduate Research

As society today continues to evolve technologically at a rapid rate, problems dealing with contamination of our natural resources become increasingly complex. Not only are new toxins introduced into the environment, but selective detection and removal of these contaminants proves ever more difficult. Heavy metals such as cadmium, lead, mercury, and radioactive nucleotides pose special problems to human health because of their tendency to accumulate in the body. Metal ions are specifically difficult to detect because of the large amount of benign ions (calcium, zinc, copper, sodium, etc.) that are naturally present in any water source. Fluorescence spectroscopy has made …

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Toward Electrical Characterization Of Dna-Templated Copper Nanowires Subtitle (If Applicable), Randall Stoltenberg, Dr. Adam T. Woolley Sep 2013

Toward Electrical Characterization Of Dna-Templated Copper Nanowires Subtitle (If Applicable), Randall Stoltenberg, Dr. Adam T. Woolley

Journal of Undergraduate Research

DNA-templated nanofabrication is a promising route toward miniaturization of electronic devices below the 100 nm range. We have developed methods for fabricating micrometer-length copper nanostructures with nanometer heights from DNA templates on silicon surfaces. These structures have been integrated into simple circuits for electrical characterization. Atomic force microscopy and transmission electron microscopy suggest that these constructs are composed of copper metal. However, copper metal was not detected by scanning electron microscopy analysis. The present structures have resistances in the TΩ range or higher, and approaches for achieving improved conductivity are presented.

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Three-Dimensional Modeling Of Poliovirus Structure And Activity, Roane Noel, Dr. David Belnap Sep 2013

Three-Dimensional Modeling Of Poliovirus Structure And Activity, Roane Noel, Dr. David Belnap

Journal of Undergraduate Research

The Poliovirus image to the left is from a collection of three-dimensionally reconstructed images of virus particles found at the website: http://www.cgl.ucsf.edu/Research/virus/capsids/viruses.html October 10, 2005. This image is identical to the type of Poliovirus image I reconstructed with the help of mentor Dr. David Belnap.

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Metallic Nanostructures Of Substituted Cavitands, Martin Conda-Sheridan, Dr. John D. Lamb Sep 2013

Metallic Nanostructures Of Substituted Cavitands, Martin Conda-Sheridan, Dr. John D. Lamb

Journal of Undergraduate Research

The aim of the project was to prepare monomers, dimmers and trimmers of pyridine substituted resorcinarenes. This work was the continuation of a previous project in which we studied the interactions of a dipicolilamine cavitand with anions. We decided to go a step further by investigating the reactions of our compound with metals. In addition to that we intend to see how the mentioned metal will bind or coordinate with organic and inorganic anions. Furthermore we tried to achieve host guest interactions between the mentioned anions and our compounds. The knowledge of such interactions has potential applications in medicine, the …

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A Study Of Collisional Energy Transfer As A Function Of Donor Molecule Energy, Jeremy Johnson, Dr. Eric Sevy Sep 2013

A Study Of Collisional Energy Transfer As A Function Of Donor Molecule Energy, Jeremy Johnson, Dr. Eric Sevy

Journal of Undergraduate Research

When chemical reactions take place, energy is transferred between the different atoms and molecules as they collide. The energy transfer in these collisions is the rate-limiting step of reactions. Therefore, to be able to accurately model reactions we need a good understanding of how energy is transferred. The probability distribution function, P(E,E’), is fundamental to predicting the efficiency of specific energy transfer events. It has not been possible, until recently, to measure this function experimentally because energy transfer studies only obtained measurements of the average energy transfer. Using an ultra high-resolution IR diode (~0.0003 cm-1), we can measure energy transfer …

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Effects Of Follicular Dentritic Cells On Recombination Rates Of Human Immunodeficiency Virus Type 1, Ericf Burgon, Dr. Greg Burton Sep 2013

Effects Of Follicular Dentritic Cells On Recombination Rates Of Human Immunodeficiency Virus Type 1, Ericf Burgon, Dr. Greg Burton

Journal of Undergraduate Research

Recombination is a major mechanism that generates variation in populations of human immunodeficiency type 1 (HIV-1). Mutations often confer replication advantages, such as drug resistance, which can lead to increased pathogenicity. This project is the first phase of a larger projected intended to study the effects of follicular dentritic cells (FDCs) on recombination rates.

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Size-Based Separation Of Bioparticles Using Planar Nanofluidic Devices, Jie Xuan Sep 2013

Size-Based Separation Of Bioparticles Using Planar Nanofluidic Devices, Jie Xuan

Theses and Dissertations

Nanofluidic devices are structures having at least one dimension in the submicron range, which is of the same order of magnitude as the sizes of biomolecules and bioparticles such as proteins and viruses. As a result, size-selective separations are important applications for nanofluidics. Well-defined micro or nano device structures fabricated via micromachining have greatly reduced sample consumption and enabled separations in a parallel fashion, promising significant speed and resolution advantages over conventional size separation techniques, such as gel electrophoresis and size exclusion chromatography. In collaboration with others, I have developed a size separation method using nanofluidic devices consisting of an …

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A Novel Asymmetric Phase-Transfer Catalyzed Approach To The Compounds Ragaglitazar And Kuarsoin A, D. Karl Bedke Sep 2013

A Novel Asymmetric Phase-Transfer Catalyzed Approach To The Compounds Ragaglitazar And Kuarsoin A, D. Karl Bedke

Journal of Undergraduate Research

Asymmetric glycolate alkylation plays a key role in the synthesis of complex biologically active compounds. Such asymmetric transformations have largely to date been accomplished by employing chiral auxiliaries which have shown remarkable success in asymmetric synthesis. However, auxiliaries must also be used in stoichiometric amounts and can become quite expensive. A catalytic approach to asymmetric glycolate alkylations presents an attractive option to the use of auxiliaries. Andrus2,3 et al. have recently developed a methodology utilizing phase-transfer catalyst 1 for alkylation of a novel alkoxyacetophenone substrate 2 that can be readily oxidized to its glycolic ester derivative to provide access to …

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Derivative Couplings And Analytic Gradients For Diabatic States, With An Implementation For Boys-Localized Configuration-Interaction Singles, Shervin Fatehi, Ethan Alguire, Joseph Subotnik Sep 2013

Derivative Couplings And Analytic Gradients For Diabatic States, With An Implementation For Boys-Localized Configuration-Interaction Singles, Shervin Fatehi, Ethan Alguire, Joseph Subotnik

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

We demonstrate that Boys-localized diabatic states do indeed exhibit small derivative couplings, as is required of quasidiabatic states. In doing so, we present a general formalism for calculating derivative couplings and analytic gradients for diabatic states. We then develop additional equations specific to the case of Boys-localized configuration-interaction singles (CIS)—in particular, the analytic gradient of the CIS dipole matrix—and we validate our implementation against finite-difference results. In a forthcoming paper, we will publish additional algorithmic and computational details and apply our method to the Closs energy-transfer systems as a further test of the validity of Boys-localized diabatic states.

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Evaluation Of Fluorescent Folate Bis-Retinoid Bioconjugates As Chemotherapeutic Agents, Britta Bergstrom, Dr. Heidi Vollmer-Snarr Sep 2013

Evaluation Of Fluorescent Folate Bis-Retinoid Bioconjugates As Chemotherapeutic Agents, Britta Bergstrom, Dr. Heidi Vollmer-Snarr

Journal of Undergraduate Research

The purpose of my project was to evaluate how effective a certain class of organic chemical compounds, known as fluorescent folate bis-retinoid bioconjugates, is for use as chemotherapy agents. An important part of my research involved developing techniques for the growth and maintenance of healthy cancer-cell cultures. I focused especially on the use of a new kidney cancer cell culture, because kidney cancers are hypothesized to be especially susceptible to chemotherapy with folate bioconjugates. The purpose of the folate part of the bioconjugate is to direct the drug to the cancer cells, because cancer cells tend to take in more …

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The Essence Of Nature, Bradley M. Bricker, Dr. Steven Wood Sep 2013

The Essence Of Nature, Bradley M. Bricker, Dr. Steven Wood

Journal of Undergraduate Research

It is the volatile aromatic compounds found in flowers that give them their distinctive aroma. These volatile compounds in their extracted form are often referred to as “essential oils.” And for thousands of years civilizations have been extracting these essential oils from flowers. There are many methods for obtaining these volatile compounds from flowers. Likewise, there are many intended purposes for the resulting extracts, ranging from aesthetic to medicinal.

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Spectroscopic Evidence Of Work Function Alterations Due To Photoswitchable Monolayers On Gold Surfaces, Matthew Alan Bartucci, Jan Florian, Jacob W. Ciszek Sep 2013

Spectroscopic Evidence Of Work Function Alterations Due To Photoswitchable Monolayers On Gold Surfaces, Matthew Alan Bartucci, Jan Florian, Jacob W. Ciszek

Chemistry: Faculty Publications and Other Works

Taking advantage of surfaces’ response to interfacial dipoles, a class of photochromophores (dihydroindolizine) is demonstrated to alter the work function of the underlying substrate (∼170 meV). This same molecule also provides spectroscopic signatures for correlating the change in molecular structure to the induced change in the surfaces’ electronic properties. Polarization modulation infrared reflection absorption spectroscopy (PM-IRRAS) allows analysis of the characteristic dihydroindolizine C═C (1559 cm–1) and pyridinium (1643 cm–1) stretch as a function of photoexcitation. Structural assignments of this photochromophore are corroborated to density function theory calculations. Conformational changes in the monolayers appear in parallel with …

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Mitochondrial Dna Analysis Of The Inhabitants Of Amantani, Peru, Matthew A. Mcnairy, Dr. David Hart Sep 2013

Mitochondrial Dna Analysis Of The Inhabitants Of Amantani, Peru, Matthew A. Mcnairy, Dr. David Hart

Journal of Undergraduate Research

Mitochondrial DNA (mtDNA) is useful in population genetics studies because it is inherited only from the maternal parent. Because there is no paternal contribution and no recombination, mtDNA represents a clear maternal lineage. Four predominant maternal lineages or mitochondrial haplotypes have been found to exist among natives of North, Central, and South America.1 Each of the four haplotypes, A-D, is associated with a unique set of variations in the mtDNA sequence. Variations associated with types A, C, and D are identified using restriction enzymes that cleave specific DNA sequences. Type B is characterized by the presence of a nine base-pair …

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Number Of Sialic Acid Residues In Ganglioside Headgroup Affects Interactions With Neighboring Lipids, Shelli L. Frey, Ka Yee C. Lee Sep 2013

Number Of Sialic Acid Residues In Ganglioside Headgroup Affects Interactions With Neighboring Lipids, Shelli L. Frey, Ka Yee C. Lee

Chemistry Faculty Publications

Monolayers of binary mixtures of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) and asialo-(GA1), disialo-(GD1b) and trisialo-(GT1b) gangliosides were used to determine the effect of ganglioside headgroup charge and geometry on its interactions with the neighboring zwitterionic lipid. Surface pressure versus molecular area isotherm measurements along with concurrent fluorescence microscopy of the monolayers at the air-water interface were complemented with atomic force microscopy imaging of monolayers deposited on solid substrates. Results were used to further develop a proposed geometric packing model that the complementary geometry of DPPC and monosialoganglioside GM1 headgroups affects their close molecular packing, …

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The Unique Photo-Toxic Properties Of Pyridinium Bis-Retinoid Compounds, Matthew Sparks, Dr. Heidi Vollmer-Snarr Sep 2013

The Unique Photo-Toxic Properties Of Pyridinium Bis-Retinoid Compounds, Matthew Sparks, Dr. Heidi Vollmer-Snarr

Journal of Undergraduate Research

Age-related macular degeneration (AMD) is an ocular disease that currently afflicts approximately 25–30 million people around the globe.1,2 The disease is characterized by the destruction of the macula, the central region of the retina. As the disease progresses, central vision becomes distorted, clouded, and eventually lost entirely.3 Although currently receiving much attention from researchers, the chemical pathway(s) causing the disease have remained elusive. Much research has focused on A2E, the most commonly known photo-toxic compound implicated in AMD pathogenesis.

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Effect Of The −1 Triplet In Tmrna, Mickey Miller, Dr. Allen Buskirk Sep 2013

Effect Of The −1 Triplet In Tmrna, Mickey Miller, Dr. Allen Buskirk

Journal of Undergraduate Research

tmRNA (transfer-messenger RNA) is a functional RNA that acts as both tRNA and mRNA to rescue ribosomes stalled on mRNA lacking a stop codon or on nascent peptide sequences in eubacteria (1). When a ribosome stalls, the tRNA-like structure of tmRNA enters the ribosome and adds an alanine to the growing peptide. The ribosome then releases the original mRNA and translation continues with tmRNA as the template. The tmRNA template codes for a 10 amino acid tag sequence followed by a stop codon. With a stop codon, the ribosome is able to dissociate and be recycled. Meanwhile, the tagged peptide …

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Solid Phase Synthesis Of The Peptide Hulhv And Characterization Using Nuclear Magnetic Resonance, Matthew J. Hinton, Dr. Roger G. Harrison Sep 2013

Solid Phase Synthesis Of The Peptide Hulhv And Characterization Using Nuclear Magnetic Resonance, Matthew J. Hinton, Dr. Roger G. Harrison

Journal of Undergraduate Research

An exciting area of research is based on the idea that small molecules can be used to perform the same chemical reactions as enzymes. In living organisms, enzymes play important roles in facilitating the vast majority of biochemical reactions necessary for life. One particular class of these biomolecules, non-heme iron containing enzymes, are of particular interest because they have structural characteristics that may allow their chemistry to be modeled by small molecules. In the active site of these enzymes there is often one or more iron atoms bound by two or three histidine side chains. I was interested in determining …

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Molecular Mechanics Calculations Of The Dissociation Energy Of Alkaline Earth Metal Cations And Various Crown Ether Complexes, Darrell E. Hurt, Dr. Randall B. Shirts Sep 2013

Molecular Mechanics Calculations Of The Dissociation Energy Of Alkaline Earth Metal Cations And Various Crown Ether Complexes, Darrell E. Hurt, Dr. Randall B. Shirts

Journal of Undergraduate Research

Since their discovery in 1967, crown ethers have proved a valuable tool for chemical separations of charged species that are otherwise inseparable.1 Crown ethers are a type of ligand, or a molecule that works by binding to another chemical species without breaking or forming chemical bonds. Crown ethers bind selectively – certain crown ethers bind strongly to certain species and not others. The selectivity of a crown ether is believed to be a function of both the size of its cavity and of the dihedral angle of the binding oxygen atoms.2,3 One can think of a crown ether as a …

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Synthesis Of Lipid A Analogs For Use In Studying The Binding Of Lipid A And Polymyxin B, Bryce A. Harrison, Dr. Paul B. Savage Sep 2013

Synthesis Of Lipid A Analogs For Use In Studying The Binding Of Lipid A And Polymyxin B, Bryce A. Harrison, Dr. Paul B. Savage

Journal of Undergraduate Research

Lipid A (1 in Fig. 1) is a bacterial compound that can cause sepsis, an overreaction of the immune system during bacterial infections.1 Because no good treatment is known, sepsis causes over 100,000 deaths annually in the U.S.1 Treatments for sepsis are difficult to develop partly due to a lack of understanding of how lipid A interacts with other molecules. Consequently, we are synthesizing lipid A analogs (3-6 in Fig. 3) to studying the mechanism of binding of lipid A to polymyxin B (PMB, 2 in Fig. 2), a naturally occurring cyclic peptide. Understanding the mechanism of binding will aid …

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Copper Nanowire Synthesis By Electroless Deposition, Adam Washburn, Dr. Adam Woolley Sep 2013

Copper Nanowire Synthesis By Electroless Deposition, Adam Washburn, Dr. Adam Woolley

Journal of Undergraduate Research

The construction of nanometer-scale electronic devices is an emerging and promising interdisciplinary field. Nanoelectronic devices may reduce size limits in integrated circuits and also function as miniature chemical detectors.1 Nanowire connections are essential components of nanoelectronic devices. A recently developed method for creating nanowires is to deposit metal onto a DNA template. Because DNA can be manipulated into specific shapes and surface patterns, DNA templates are particularly appealing for nanowire formation.2

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