Honors Projects for Chemistry

Permanent URI for this collectionhttps://hdl.handle.net/10125/31085

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Extended Reality Case Presentation for Online Case-Based Learning with emphasis on Biochemical and Molecular Biology Concepts of Disease Pathogenesis.
(University of Hawaii at Manoa, 2024) Slane, Kylah; Lozanoff, Scott; Chemistry
Transcriptomic Changes in Broiler Chicken Hypothalamus Following Chronic Heat Stress
(University of Hawaii at Manoa, 2020) Zhou, Angeline; Mishra, Birendra; Chemistry
Chronic heat stress induces severely detrimental effects on bird health by interfering with numerous aspects of a bird’s health. One of the primary homeostasis-defending organs of the body is surprisingly small given its integrative capacity and ability to effect multi-system, dramatic downstream changes: the hypothalamus. RNA-Seq was used to identify the differentially expressed genes (DEG) in the Chronic Heat Stress (CHS) group compared to the Control. Ingenuity Pathway Analysis was performed on the DEG and used the identifiable DEG to generate the most likely ontological pathways affected during CHS. The top up and downregulated genes were then validated using quantitative Real-Time PCR (qPCR). RNA-Seq identified “Nervous System Development and Function” as a top affected pathway, and three significantly downregulated proteins (p ≤ 0.05, Fold Change ≤ -1.5) stood out: DCX, GAN, and SPECC1L, all of which have been implicated in some aspect of cytoskeletal development or organization within the CNS. qPCR found that separate treatment groups of DP and LA antioxidants under CHS resulted in significantly elevated levels of SEMA and DAPK (p-values: 0.008 and 0.033, respectively). SEMA is associated with aiding proper growth in POMC neurons, thus contributing to normal energy-related neuronal functioning. DAPK is associated with programmed cell death and tumor suppression. While the downregulation of DCX, GAN, and SPECC1L may compromise the hypothalamus, SEMA and DAPK seem to functionally be protective measures against the molecular impacts of CHS. Thus, using RNA-Seq we identified previously unstudied genes that appear to be implicated in the mediation of chronic heat stress in the hypothalamus tissue.
Selenoprotein K Modulates Diverse Calcium Signaling Pathways in the Human Melanoma Cells
(University of Hawaii at Manoa, 2018) Lee, Katie; Hoffman, Peter R.; Chemistry
Store-operated calcium (Ca2+) entry (SOCE) is vital to melanoma cells for proliferation, migration, and invasion into secondary tissues. Previous work in immune cells showed that Sele-noprotein K (SELENOK) is required for efficient SOCE by palmitoylating
Progress in Selective Hydrogenation: Reactivity Trends in PdAu Heterogeneous Catalysts & Developing Chiral Building Blocks for New Homogeneous Catalysts
(University of Hawaii at Manoa, 2017-05) Chinen, Amy; Cain, Matthew; Chemistry
Selective hydrogenation is an essential method for converting cheap starting materials into more valuable chemical building blocks. Whether regioselectivity or diastereoselectivity is desired, catalysts are often employed to aid in this transformation. This work explores possibilities for finetuning both homogeneous and heterogeneous catalysts. Previously, bimetallic PdAu catalysts were used to enable the conversion of biologically produced 4-hydroxycoumarin (4HC) to pharmaceutically relevant coumarin and dihydroxycoumarin (DHC), but the subtleties of catalyst preparation and the effect of Pd loading were not known. Part I focuses on identifying reactivity trends resulting from variations in PdAu catalysts. Several PdAu catalysts with varying Pd:Au ratios were prepared by controlled surface reactions (CSR) or incipient wetness impregnation (IWI). Using high performance liquid chromatography (HPLC) and gas chromatography-mass spectrometry (GCMS), we determined the effects of the preparation method and Pd loading on reactivity, selectivity, and resistance to deactivation for the selective hydrogenation of 4HC to DHC. Part II aims to develop chiral building blocks for C1-symmetric, P-stereogenic ligands that will be used in the asymmetric hydrogenation of heavily functionalized substrates. To date, a new diastereoselective method of adding RO-H across a P=P double bond was identified and a new sterically dominating R group was generated. The results were analyzed by nuclear magnetic resonance (NMR) spectroscopy.
The Preparation and X-Ray Crystallographic Study of Several Ion-Exchanged, Complexed Synthetic Zeolites
(1973) Kunz, Kevin Benedict; Seff, Karl
Zeolithic ion-exchange experiments were carried out; five ion-exchanged samples of synthetic zeolite were exchanged stoichiometrically. A successful structure determination was achieved for the hydrated zinc-exchanged zeolite, and was refined to R1 and R2 error indices of 0.097 and 0,092, respectively. The methods used for ion-exchange, zeolite complexation, and crystallographic investigation are discussed. The molecular geometries for the hydrated zinc-exchange zeolite re presented.
Photoprotection by Plant-derived Compounds
(University of Hawaii at Manoa, 2014-09-26) Shelton, Hannah; Williams, Philip; Chemistry
Current topical sunscreens, although effective, may not be the safest way to prevent UVradiation based skin damage. Active petroleum-derived ingredients may be toxic, and may not be the most cost-effective solution for sunscreen production. The compounds responsible for protecting plants' cellular structures from UV radiation have the potential to be an effective alternative. This project sought to determine the worth of three plant-derived compounds – lycopene, genistein, and astaxanthin – as potential sunscreen ingredients. First, SPF and Boots Star System data from in vitro UV absorption spectra were collected. Second, each compound was exposed over UV-sensitive cyantoype emulsion, in lieu of human skin, in order to determine comparative in vivo properties. While not as effective as petroleum based ingredients, these compounds showed the potential to be safe sunscreen additives, or the primary active ingredients in low SPF lotions. Additionally, the use of cyanotype emulsion was effective at determining the level of UV light permitted through a solution. Although not perfect, it has proved to be a versatile and inexpensive replacement for human skin in this experiment.
Misincorporation of Beta-Methylamino-L-Alanine Into Protein: A Potential Mechanism for Motor Neuron Disease
(University of Hawaii at Manoa, 2014-09-26) Liu, Jenny; Hemscheidt, Thomas; Chemistry
Imagine living in an immobilized body, while being fully aware of your surroundings. This is the experience of many motor neuron disease afflicted patients, especially those with amyotrophic lateral sclerosis (ALS). ALS-Parkinsonism Dementia complex (ALS-PDC) is a form of ALS with an abnormally high incidence in members of certain ethnicities. An ethnobotanical connection to nutrition involving the cyanobacterial neurotoxin beta- methylamino-L-alanine (BMAA) has long been postulated. Specifically, incorporation of BMAA into human protein has been suggested to contribute significantly to the etiology of ALS-PDC. Using an in-vivo approach, this research project focused on determining whether BMAA is transformed into high molecular weight substances such as proteins. The uptake and metabolic fate of BMAA was followed within a prokaryotic model system, a cyanobacterium, during the logarithmic growth phase. Prokaryotes generally have higher error rates for the misincorporation of non-proteinogenic amino acids into protein than eukaryotes. Observation of BMAA in the protein fraction would therefore provide a first estimate of the potential significance of the misincorporation of BMAA in a eukaryotic system. Chemical analysis showed that about 1% of the initial amount of BMAA added to the cell culture was present within intracellular, hydrolyzable, low molecular weight compounds below 10 kilodaltons, and only 6 × 10-4 %, if any, was present in the high molecular mass, i.e. protein, form. This suggests that intracellular protein is not a primary reservoir of BMAA in this model system and, by extension, in eukaryotes, and that an unexpectedly large percentage of BMAA, 98%, is metabolized. Imagine living in an immobilized body, while being fully aware of your surroundings.
Minimal nucleotide sequence divergence detected in the sea urchin Strongylocentrotus, droebachiensis by direct sequencing of enzymatically amplified DNA
(University of Hawaii at Manoa, 2014-01-15) Stice, Ligaya; Chemistry
The assumptions that have been made concerning mitochondrial DNA (mtDNA) variability have been based on studies on Drosophila and vertebrates. Recent studies on marine species show marked differences in comparison to terrestrial populations. Terrestrial populations tend to show considerable amounts of mtDNA variability accompanied by distinct population structure. My study is concerned with the variation present in the mitochondrial genome of Strongylocentrotus droebachiensis populations. This sea urchin has a distribution throughout the Arctic Ocean and in both the North Pacific and the North Atlantic Oceans. Based on the previous assumptions about mtDNA variation, we should expect large degrees of sequence difference due to the mere magnitude of geographic distances involved. Using the polymerase chain reaction we have been able to determine the sequence of the ATPase 6 gene in the mitochondrial genome of six S. droebachiensis sea urchins from the North Atlantic. These sequences were compared both among themselves and to a S. droebachiensis urchin from Puget Sound, Washington. Of the approximately 1500 base pairs that were sequenced, only one base substitution was found. This indicates dramatic differences between the amounts of variation present in the sea urchin genome versus the greater diversity found in genomes previously studied.
Nazarov Synthesis of Cyclopentenones and Some of their Reactions
(University of Hawaii at Manoa, 2014-01-15) Solick, Michael; Chemistry
During the creation of a molecular library of cyclopentenones, we discovered a new variant of the allenyl Nazarov cyclization process. The compounds that were being created for the library were β-aminoketones and epoxides that were synthesized using cyclopentenones as the precursor molecule. The precursory cyclopentenones were synthesized using the allenyl Nazarov cyclization variant developed by Dr. Tius. We wished to investigate the reactions that could be performed on these Nazarov adducts to further expand the number of compounds that may be created using the allenyl Nazarov. During the project, a new variant of the allenyl Nazarov process was discovered. The new reaction utilizes a Lewis acid, specifically ytterbium (Ill) triflate to catalyze the electrocyclic ring closure of an allenyl aryl ketone. Literature experiments similar to our reaction have shown re-aromatization of the aryl group that participates in the ring closure. Our new method yields a cyclized product in which aromaticity has been disrupted. Further experimentation and optimization of the methodology is needed, as preliminary reactions have shown poor yields (30%); however this methodology presents exciting new synthesis possibilities.
The Effect of the Adsorption of Substituted Phenols on the Dark and Photoconductivity of Zinc Oxide
(University of Hawaii at Manoa, 2014-01-15) Shiigi, Stanley; Chemistry
One of the most active areas of present day research is in the area of heterogeneous catalysis. These studies are usually directed toward characterizing the changes which take place in the absorbate (that which is absorbed), or characterizing the changes which take place in the catalysis. The study of an absorbate on the surface of a catalysis is usually carried out using spectroscopic methods (1-3). Eischens (1) has studied the infrared spectrum of hydrogen chemisorbed on zinc oxide and has found evidence of new bands at 2.86u and 5.85u, which were proposed to be due to the oxygen-hydrogen stretching vibration of the OH group and the zinc-hydrogen stretching vibration of the ZnH or (ZnH)+ group, respectively. Zeitlin (2) has done work with o-nitrophenol adsorbed on alkaline earth oxides. A bathochromic shift in the UV maxima of o-nitrophenol was found. Terenin (3) reviews the work being done in the area of spectral studies of adsorbed molecules. The study of the changes that occur in the catalysis are being carried out by many investigators. One of the catalysis under study by these investigators is zinc oxide (4-22). Pure zinc oxide is a non-conductor; however, through various heating procedures zinc oxide may be transformed into a semiconductor that also shows varying degrees of photoconductivity. It has been shown that the electrical conductivity properties of zinc oxide is a function of the type and amount of gas molecules adsorbed on the zinc oxide surface (4,6,8,10,13,15,17). This present study attempts to characterize the effects the adsorption of substituted phenols have on the dark- and photoconductivity of pressed powder samples of zinc oxide.
Phosphorus-Nitrogen Dative Pi Bond Character in O, N-Dimethylhydroxylaminohalophosphines and Related Compounds
(University of Hawaii at Manoa, 2014-01-15) Rosario, Marshal; Chemistry
The chloro and fluorohalophosphines of O,N-dimethylhydroxylamine were prepared and characterized by NMR and mass spectral analyses. Some conclusions as to the dative π-character of the P-N bond are drawn from the 19F NMR temperature studies and from the localization of charge in the parent ions of the mass spectra.
Electrochemical and Theorectical Studies of Oxidation-Reduction Reactions of Platinum (II) and (IV) Complexes
(University of Hawaii at Manoa, 2014-01-15) Lai, Chiu-Nan; Hubbard, Arthur; Chemistry
Electrochemical interconversion of complexes of Pt(II) and Pt(IV) is accelerated by the presence of halideions and halogen ligands. Semi-empirical MO Calculation and spectra data suggest that oxidation of PT(II) involves the transfer of electron density from filled orbitals of the complex, such as a1g( σ*) [5dz2] through unfilled orbitals of the compact layer or the electrode surface. Similarly, reduction of Pt(IV) complexes, for instance those of D4h symmetry such as PtIVL4X4, may proceed through interaction of a low-energy unfilled orbital if Pt(IV), such as a1g( σ*), with filled orbitals of the compact layer or the electrode surface by way of the unfilled ndz2 orbital of a bridging halide ligand. Pt(II) complexes containing unsaturated ligands such as CN of SCN- are less rapidly oxidized than their saturated analogs. Evidence is presented that unsaturated ligands having suitable π* orbitals stabilize the particular orbitals from which electron density is removed in the rate-limiting step. Pt(IV) complexes having a CN- ligand situated trans to a lone halide ligand are reduced with difficulty, whereas complexes having a trans-pair of halide ligands react readily; this trend is consistent with stabilization of the leaving trans-axis and de-stabilization of the interaction between the bridging ligand and the electrode surface due to d-π* back-bonding between Pt( IV) and the unsaturated ligand. A Molecular Orbital approach to the study of electrochemical reactions is presented. The calculated electrochemical rate constants are compared to experimental values obtained at thin-layer electrode. The qualitative trends agree in general. Suggestion for improvement of the calculation also included.
Nuclear Magnetic Resonance Studies of Hydrogen-Bonded Complexes of Tri-N-Octylamine Hydrochloride with Chloroform
(University of Hawaii at Manoa, 2014-01-15) Kiyokane, Richard; McDonald, Ray; Chemistry
In this study nuclear magnetic resonance spectroscopic techniques were employed to investigate the hydrogenbonded complex of tri-n-octylamine hydrochloride with chloroform. Concentration studies of tri-n-octylamine hydrochloride in 1,2 dichloroethane, carbon tetrachloride, and cyclohexane with a constant chloroform concentration of 0.09 molar showed a weak but measurable interaction between the chloroform and the anion of the amine salt. The concentration dependence of the chloroform proton shielding was analyzed to reveal shieldings in the complex, and equilibrium constants. The concentration dependence of the chloroform proton shielding was also studied at various temperatures to obtain enthalpy and entropy data for the formation of the hydrogen-bonded complex. The concentration dependence of the N-H proton shielding showed that in the concentration region studied, 0.1-0.5 molar, the anion-cation hydrogen-bond of the tri-n-octylamine hydrochloride is strong and does not dissociate. Also, examination of the N-H proton chemical shifts revealed qualitatively that the tri-n-octylamine hydrochloride in 1,2 dichloroethane exists primarily as a monomer, and in carbon tetrachloride as a trimer, and in cyclohexane probably as some higher n-mer. Analysis of the N-H proton chemical shifts in carbon tetrachloride gave an equilibrium constant for the trimeric self-association of tri-n-octylamine hydrochloride of the order of approximately 25 liter/mole.
Stereoselectivity Studies of the SP2 Carbon on 4-tert-Butylcyclohexylidene Analogues
(University of Hawaii at Manoa, 2014-01-15) Khong, Anthony; Kiefer, Edgar; Chemistry
A study of possible mass effect on the steric course of nucleophilic attack on three analogues of 4-tert-butylcyclohexylidene has been undertaken. 1HNMR analyses have been used to determine the ratios of the trans isomers over the cis ones resulting from axial and equatorial attack of the nucleophile. The preference for axial attack is largest for the heavier brominated indandione substituent and least for the non-halogenated one. Computer simulation studies of our molecular structures were also carried out. Using PCMODEL executed on a Sun Workstation and run on Windows®, the cis and trans structures were optimized by energy minimization procedures in the program. For the minimized structures, it was found that the cis structures have higher energy values than the corresponding trans isomers. The latter is favored by further separation of the tert-butyl groups and the indandione substituent. A pyramidalization experiment was also performed using this program. This was done by displacing the 4-tert-butylcyclohexylidene portion vertically upwards and downwards by 0.1A and then calculating the energies of the structures without minimization. It was found from this study, that the energies of the molecules distorted upwards to 0.4A have lower energies compared to similar molecular structures distorted downwards.
Searching for Anticancer Drugs in Marine Algae
(University of Hawaii at Manoa, 2014-01-15) Janiga, Jessica; Williams, Phillip; Chemistry
Cancer is a global health concern. The need to develop new cancer treatments is vital, as each newborn today has a 41% chance of developing some form of cancer in their lifetime (Howlander, et al. 1975-2009). Since cancer is not one specific disease, but a classification of many evolving types of cell mutations affecting numerous sites in the body, there is no single cure. Instead, a key strategy is to find a treatment that targets one type of cancerous cell while remaining non-toxic to a person’s healthy cells. This characteristic of toxicity at a cellular level while remaining nontoxic to the organism as a whole is known as cytotoxicity.
The Toxin of Pseudomonas Phaseolicola
(University of Hawaii at Manoa, 2014-01-15) Ginoza, Marianne; Moore, Richard; Chemistry
A pathogen is any organism that can cause disease. Pseudomonas phaseolicola is a bacterial pathogen of the kidney bean plant Phaseolus vulgaris L. It enters the plant mainly through the stomata and multiplies primarily in the intercellular spaces. A complex interaction of many factors which include the bacterial strain and the nature of the host plant will then determine whether or not the plant will harbor a disease known as the halo blight. The halo blight is a disease characterized primarily by the appearance of chlorotic or yellow haloes in the leaves-around the infection site. In systemically infected plants, the chlorotic haloes also appear in the developing trifoliate leaves and growth is retarded (11).
Mechanistic Studies on the Inhibitory Effect of Bamboo Extract on the Proliferation of Breast Cancer Cell Lines
(University of Hawaii at Manoa, 2014-01-15) Gilman, Christy; Berry, Marla; Panee, Jun; Chemistry
Previous research conducted in our laboratory has shown that an extract from bamboo, Phyllostachys edulis, inhibited the development of mammary tumors in female Sprague-Dawley rats treated with 7,12-dimethylbenz[a]anthracene. In addition, the presence of this bamboo extract (BEX) in the cell culture media dramatically inhibited the proliferation of estrogen receptor (ER) positive human breast cancer cell lines T47D and MCF7, but had no inhibitory effect on the ER negative breast cancer cell line MDA-MB-231 and on ER negative non-carcinoma mammary epithelial MCF10A cells. This project employed in vitro cell culture models to investigate the molecular mechanism of the anti-breast cancer function of BEX. T47D, MCF7, MDA-MB-231 and MCF10A cells were incubated with 0.5% (v/v) BEX or the same volume of ethanol as a solvent control for 3 or 7 days, and the total antioxidant capacity of the cells, the cellular contents of total glutathione (GSH, the most abundant thiol antioxidant in mammalian cells), and the mRNA levels of γ-glutamylcysteine synthetase heavy chain and light chain (GCS-HC and GCS-LC, the two subunits of a rate-limiting enzyme in glutathione biosynthesis) were measured. Further studies focusing on T47D cells measured the gene expression and enzymatic activity of galactosidase β1 (GLB1, a biomarker of cellular senescence) as well as the gene expression of estrogen receptor alpha (ERα, involved in breast cancer development and metastasis). Our results showed that the highest increases of total antioxidant capacity and total intracellular GSH were found in MCF7 and T47D cells, and under most conditions, the presence of BEX in the cell culture media increased the gene expression of GCS-HC and GCS-LC. BEX treatment also increased the gene expression and enzymatic activity of GLB1, and decreased the gene expression of ERα in T47D cells. The results indicate that BEX may exert the anti-breast cancer function through multiple and potentially synergistic pathways, including improving antioxidant status in breast cancer cells, regulating cellular senescence, and inhibiting the gene expression of ERα. The biomarkers highlighted in this project will be used for active compound fractionation and identification in future studies. Abbreviations: BEX, Bamboo extract; EtOH, ethanol; DMBA, 7,12-dimethylbenz[a]anthracene; GCS-HC, γ-glutamylcysteine synthetase heavy chain; GCS-LC, γ-glutamylcysteine synthetase light chain; GSH, glutathione; ERα , estrogen receptor alpha; ERβ, estrogen receptor beta; GLBl, galactosidase beta 1.
Secondary Metabolites of Some Marine Invertebrates
(University of Hawaii at Manoa, 2014-01-15) Gerard, Frank; Chemistry
The Pacific ocean is distinguished from other bodies of water by its large number of islands. The Pacific islands have been the objects of praise in literature and art, largely for their surface features and their people. Not until the advent of SCUBA (self-contained-underwater breathing apparatus) have the splendid flora and fauna, that abound just beneath the water's surface, been appreciated. SCUBA has given man the ability to make further use of the sea. It has also enabled man to study the sea in all its glory. No longer must the scientist restrict himself to the confines of knee-deep water or the random catches in a dragnet.
The Separation of Aluminum Phosphate, A Collector of Uranium in Seawater, By Application of Adsorption Colloid Flotation
(University of Hawaii at Manoa, 2014-01-15) Chun, Claire; Zeitlin, Harry; Chemistry
Nine surfactants were screened for their ability to float aluminum phosphate, which has been used to co-precipitate the radio-nuclide uranium, the the surface of seawater by the method of adsorption colloid flotation.
Dynamic NMR Analysis of Hindered Rotation in 7-Cis Retinyl Compounds
(University of Hawaii at Manoa, 2014-01-15) Chu, Dorothy; Chemistry
The crux of visual excitation by light is the photoisomerization of 11-cis retinylidene Schiff base to its all-trans form--a configurational event which leads to the subsequent release of the chromophore from its apoprotein, opsin. The focus of the present study is the kinetic nature of dynamic rate processes involving retinal analogues in solution. Of primary concern are quantitative aspects of intramolecular rotation about the highly hindered C6-C7 sp2–sp2 hybridized single bond in a number of 7 -cis retinyl compounds.

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