Chemistry Commons^™

Temporal Variation In Optical Properties Of Chromophoric Dissolved Organic Matter (Cdom) In Southern California Coastal Waters With Nearshore Kelp And Seagrass, Catherine D. Clark, Warren J. De Bruyn, Paige Aiona

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Optical properties of chromophoric dissolved organic matter (CDOM) were measured in surf zone waters in diurnal field studies at a Southern California beach with nearshore kelp and seagrass beds and intertidal plant wrack. Absorption coefficients (aCDOM(300 nm)) ranged from 0.35 m21 to 3.7 m21 with short-term variability<1 h, increases at ebb and flood tides and higher values (6 m21) during an offshore storm event. Spectral slopes (S) ranged from 0.0028 nm21 to 0.017 nm21, with higher values after the storm; S was generally inversely correlated with aCDOM(300 nm). 3-D excitation–emission matrix spectra (EEMs) for samples with lower S values had humic-type peaks associated with terrestrial material (A, C), marine microbial material (M) and protein peaks, characteristic of freshly produced organic material. Samples with high S values had no or reduced protein peaks, consistent with aged material. Fluorescent indexes (f450/f500 >2.5, BIX>1.1) were consistent with microbial aquatic sources. Leachates of senescent kelp and seagrass had protein and humic-type EEM peaks. After solar simulator irradiation (4 h), protein peaks rapidly photochemically degraded, humic-type peak C increased in intensity and peak M disappeared. Optical characteristics of kelp leachates were most similar to field samples, …

Stress Granules Modulate Syk To Cause Microglial Cell Dysfunction In Alzheimer's Disease, Soumira Ghosh, Robert Geahlen

Borch Department of Medicinal Chemistry and Molecular Pharmacology Faculty Publications

Microglial cells in the brains of Alzheimer's patients are known to be recruited to amyloid-beta (Aβ) plaques where they exhibit an activated phenotype, but are defective for plaque removal by phagocytosis. In this study, we show that microglia stressed by exposure to sodium arsenite or Aβ(1–42) peptides or fibrils form ex- tensive stress granules (SGs) to which the tyrosine kinase, SYK, is recruited. SYK enhances the formation of SGs, is active within the resulting SGs and stimulates the production of reactive oxygen and nitrogen species that are toxic to neuronal cells. This sequestration of SYK inhibits the ability of microglial …

The Nicotine Metabolite, Cotinine, Alters The Assembly And Trafficking Of A Subset Of Nicotinic Acetylcholine Receptors, Ashley M. Fox, Faruk H. Moonschi, Christopher I. Richards

Chemistry Faculty Publications

Exposure to nicotine alters the trafficking and assembly of nicotinic receptors (nAChRs), leading to their up-regulation on the plasma membrane. Although the mechanism is not fully understood, nicotine-induced up-regulation is believed to contribute to nicotine addiction. The effect of cotinine, the primary metabolite of nicotine, on nAChR trafficking and assembly has not been extensively investigated. We utilize a pH-sensitive variant of GFP, super ecliptic pHluorin, to differentiate between intracellular nAChRs and those expressed on the plasma membrane to quantify changes resulting from cotinine and nicotine exposure. Similar to nicotine, exposure to cotinine increases the number of α4β2 receptors on the …

Small Molecule Inhibitor Design For Anaplastic Lymphoma Kinase Inhibition, Theodore D. Hansel, David J. Grabovsky

Interface Compendium of Student Work

The Anaplastic Lymphoma Kinase (ALK) gene has been linked to tumorigenesis in a number of human cancers, including anaplastic large cell lymphoma (ALCL) and neuroblastoma. While ALK mutations in ALCL and many other cancers occur as a result of gene fusions with wild type kinase domains, those in neuroblastoma stem from single nucleotide polymorphisms (SNPs) in the kinase domain. These lead to autophosphorylation and constitutive signaling by ALK for cell growth and division, ultimately causing cancer. Crizotinib, an ATP-competitive ALK inhibitor, has proven to be an effective inhibitor of both ALKWT and ALKMutant kinase domains, and is in the middle …

Chemistry Department Newsletter 2015, Ken Overway

Chemistry Department Newsletters

This document contains a summary of news and events from the chemistry department from the 2014-2015 academic year.

Ligand Discovery For The Alanine-Serine-Cysteine Transporter (Asct2, Slc1a5) From Homology Modeling And Virtual Screening, Colas Claire, Christof Grewer, Nicholas J. Otte, Armanda Gameiro, Thomas Albers, Kurnvir Singh, Helen Shere, Massimiliano Bonomi, Jeff Holst, Avner Schlessinger

Chemistry Faculty Scholarship

The Alanine-Serine-Cysteine transporter ASCT2 (SLC1A5) is a membrane protein that transports neutral amino acids into cells in exchange for outward movement of intracellular amino acids. ASCT2 is highly expressed in peripheral tissues such as the lung and intestines where it contributes to the homeostasis of intracellular concentrations of neutral amino acids. ASCT2 also plays an important role in the development of a variety of cancers such as melanoma by transporting amino acid nutrients such as glutamine into the proliferating tumors. Therefore, ASCT2 is a key drug target with potentially great pharmacological importance. Here, we identify seven ASCT2 ligands by computational …

Ua66 Ogden College Of Science & Engineering Newsletter, Cheryl Stevens, Dean

Ogden College of Science & Engineering Publications

No abstract provided.

Chemistry & Biochemistry Newsletter, Department Of Chemistry & Biochemistry, South Dakota State University

Chemistry & Biochemistry Newsletter: 2002-2015

Inside:

Page 2 Avera Health and Science’s 5th Year Celebration
Page 3 Harvest Table Food Drive — Round Two
Page 4 New Graduates Students
Page 5 Department to Host CHEM Ed 2017
Page 6 ACS Student Affiliate Chapter Activities
Page 7 Faculty and Staff News
Page 8 Publications & Grants

Distributed Approach For Peptide Identification, Naga V K Abhinav Vedanbhatla

Masters Theses & Specialist Projects

A crucial step in protein identification is peptide identification. The Peptide Spectrum Match (PSM) information set is enormous. Hence, it is a time-consuming procedure to work on a single machine. PSMs are situated by a cross connection, a factual score, or a probability that the match between the trial and speculative is right and original. This procedure takes quite a while to execute. So, there is demand for enhancement of the performance to handle extensive peptide information sets. Development of appropriate distributed frameworks are expected to lessen the processing time.

The designed framework uses a peptide handling algorithm named C-Ranker, …

Expression And Purification Of Unlabelled And Isotopically Labelled Human Fibroblast Growth Factor-1 And Its Receptor Relevance In Cancer Research, Oluwadamilola Filani

Masters Theses & Specialist Projects

Studies show that fibroblast growth factors (FGFs) control variety of cellular activities such as mitosis, cell differentiation, survival and angiogenesis. The FGF family consists of 23 different heparin-binding proteins. One of the most intensively studied members is human FGF-1 (hFGF-1) because of its critical role in the formation of blood vessels and cell proliferation in some types of cancer. The biological activities of FGFs are primarily mediated via interactions with fibroblast growth factor receptors (FGFR) and are a potent target in cancer. In this study, we report an efficient affinity column purification of hFGF-1 and the D2 domain of FGFR-2 …

A Sem Study Of Copper Corrosion In Bowling Green Supply Lines, Reema M. Alghamdi

Masters Theses & Specialist Projects

Recently, the rate of corrosion of copper water pipes in Bowling Green, Kentucky has unexpectedly accelerated. The specific reasons for this are unknown. Our aim is to elucidate the factors enhancing the corrosion and help understand the primary mechanisms of action. This will help in combating and reducing future corrosion incidents leading to pipe failure, thus reducing losses experienced when these pipes are replaced. This study seeks to explore the characteristics and factors involved. The scanning electron microscopy was used to obtain elemental composition, and images of both inside and outside of the corroded pipes. Strikingly, corrosion primarily occurred on …

The Periodical Fall 2015, Southern Adventist University

the Periodical – Chemistry Department Newsletter

Volume 2, issue 2 of the Periodical includes articles about the Chemistry Department's partnership with Georgia-Cumberland Academy, a pictorial listing of December 2015 graduates, new service-learning tutoring classes, and an alumni spotlight.

Oxidative Cyclization Of Tertiary Pentenol Derivatives Forming 2,5,5-Trisubstituted Thf Rings And The Total Synthesis Of Cyclocapitelline, Geoffrey A. Phillips, Cory Palmer, Andrew C. Stevens, Mattew L. Piotrowski, Daryyl Sr Dekruyf, Brian Pagenkopf

Chemistry Publications

The synthesis of 2,5,5-trisubstituted tetrahydrofuran rings was accomplished via the Mukaiyama aerobic oxidative cyclization of tertiary 5-pentenols employing the Co(nmp)₂catalyst. A variety of THFs were formed in moderate to good yield and diastereoselectivity. The method developed herein was successfully applied to an enantioselective total synthesis of cyclocapitelline.

Fused-Molecular Systems For Organic Light Emitting Diodes, Avinash Jami

Masters Theses & Specialist Projects

Organic light emitting diodes (OLEDs) are electronic devices made by sandwitching organic light emissive materials between two electrodes. When voltage is applied across the two conductors, a bright light is generated. The color of the emitting light depends on the band gap of the semiconducting material. The work described here focuses on designing and synthesizing narrow band gap molecular systems derived from fused-arene derivatives for producing organic blue light emitting diodes. Three molecular systems derived from anthracene, pyrene, and carbazole, were designed and synthesized. Two molecular systems of anthracen-9-ylmethyl anthracene-9- carboxylate and pyren-1-ylmethyl 4-bromobenzoate were synthesized through Steglich esterification reaction …

Multi-Dimensional Glycan Microarrays With Glyco-Macroligands, Satya Nandana Narla, Huan Nie, Yu Li, Xue-Long Sun

Chemistry Faculty Publications

Glycan microarray has become a powerful high-throughput tool for examining binding interactions of carbohydrates with the carbohydrate binding biomolecules like proteins, enzymes, antibodies etc. It has shown great potential for biomedical research and applications, such as antibody detection and profiling, vaccine development, biomarker discovery, and drug screening. Most glycan microarrays were made with monovalent glycans immobilized directly onto the array surface via either covalent or non-covalent bond, which afford a multivalent glycans in two dimensional (2D) displaying. A variety of glyco-macroligands have been developed to mimic multivalent carbohydrate-protein interactions for studying carbohydrate-protein interactions and biomedical research and applications. Recently, a …

Synthesis, Characterisation, Electrochemical, And Spectroscopic Studies Of Cobaloximes: Unique Clues Of Cobalt(I) Species In Various Solvents, Michael John Celestine

Chemistry & Biochemistry Theses & Dissertations

With the dwindling amount of fossil fuels in the world’s reserve is said to run out in the future. The use of alternative fuels such as hydrogen can be produced from renewable sources. One source is the use of first row transition metal complexes that can harness the power of the sun to reduce protons to hydrogen. In this thesis we investigated a well-known hydrogen evolution catalyst in a quest to understand the behavior of different oxidation states that occur during the catalytic cycle.

In an attempt to synthesize a binuclear ruthenium(II) complex, [{Ru(phen)2}2{µmes(1,4-phO-Izphen)3}](PF6)4, as a possible photosensitizer for the …

Electron Transfer During Metal-Assisted And Stain Etching Of Silicon, Kurt W. Kolasinski

Chemistry Faculty Publications

The etching of silicon in fluoride solutions is limited by the kinetics of charge transfer not thermodynamics. This characteristic is what gives fluoride etching its great versatility in making different types of nanostructures as the result of self-limiting chemistry. This review approaches the kinetics of electron transfer from silicon and metal coated silicon to a solution phase species from a fundamental point of view in order to establish a better understanding of the mechanisms of nanostructure formation during metal assisted and stain etching of silicon. Band bending calculations demonstrate that diffusion of holes away from low work function metals such …

Asymmetric Transfer Hydrogenation Of Secondary Allylic Alcohols, Christopher Olugbenga Olusegun Shoola

Seton Hall University Dissertations and Theses (ETDs)

This dissertation highlights the developments and optimization of a new reaction method that transforms racemic secondary allylic alcohols into optically active secondary alcohols. The key step in this methodology occurs through a ruthenium catalyzed tandem isomerization and asymmetric transfer hydrogenation reaction. This reaction is a one pot, two-step process, which utilizes the unique ability of a transition metal catalyst to effect a combined reduction of the C-C double bond and the carbonyl group in a selected class of secondary allylic alcohols.

With a-vinyl benzyl alcohol as substrate, the optimal catalyst for this reaction was generated in situ from a …

Role Of Annexin A6 In Cancer (Review), Houbao Qi, Shuqing Liu, Chunmei Guo, Jiasheng Wang, Frederick T. Greenaway, Ming Zhong Sun

Chemistry

Annexin A6 (AnxA6) is a member of a conserved superfamily of Ca2+-dependent membrane-binding annexin proteins. It participates in membrane and cytoskeleton organization, cholesterol homeostasis, membrane trafficking, cell adhesion and signal transduction. The expression levels of AnxA6 are closely associated with melanoma, cervical cancer, epithelial carcinoma, breast cancer, gastric cancer, prostate cancer, acute lymphoblastic leukemia, chronic myeloid leukemia, large-cell lymphoma and myeloma. AnxA6 exhibits dual functions in cancer, acting either as a tumor suppressor or promoter, depending on the type of cancer and the degree of malignancy. In several types of cancer, AnxA6 acts via Ras, Ras/MAPK and/or FAK/PI3K signaling pathways …

Image-Charge Detection €“ Novel Instrumentation And Applications, Brandon Lee Barney

Theses and Dissertations

Image-charge detection is an analytical technique in which a highly-charged particle is detected by the magnitude of the image current that it generates in a detecting electrode. This current is represented as a voltage between the charged particle and the sensing electrode. It is a single particle detection method, ideal for the analysis of large, variable mass particles such as biological cells. Some of the physical properties of Bacillus subtilis spores were explored using different applications of image-charge detection. B. subtilis is a gram-negative spore-forming bacteria that has been shown to exhibit extremophile behavior. The particular extremophile behavior that was …

Determination Of The Polymerisation Rate Of A Low-Toxicity Diacetone Acrylamide-Based Holographic Photopolymer Using Raman Spectroscopy, Dervil Cody, Emilia Mihaylova, Luke O'Neill, Izabela Naydenova

Articles

The polymerisation rate of a low-toxicity Diacetone Acrylamide (DA)-based photopolymer has been measured for the first time using Raman spectroscopy. A value for the polymerisation rate of 0.020 s⁻¹ has been obtained for the DA photopolymer by modelling the polymerisation reaction dynamics as a stretched exponential or Kohlrausch decay function. This is significantly lower than the polymerisation rate of 0.100 s⁻¹ measured for the well known Acrylamide (AA)-based photopolymer composition. The effect of the additive glycerol on the polymerisation rate of the DA-based photopolymer has also been investigated. The inclusion of glycerol is observed to increase the rate …

Source-Specific Molecular Signatures For Light-Absorbing Organic Aerosols, Amanda Susan Willoughby

Chemistry & Biochemistry Theses & Dissertations

Organic aerosols (OA) are universally regarded as an important component of the atmosphere based on quantitative significance as well as the far-reaching impact they have on global climate forcing and human health. Despite the acknowledged importance, OA amounts and impacts remain the largest uncertainties regarding radiative forcing estimates. Incomplete chemical characterization of aerosol organic matter (OM) and a lack of concrete source apportionment is a major source of this uncertainty. The primary focus of this study is to provide much needed molecular details regarding ambient OA from key emission sources, and establish links between molecular and optical properties.

Complete chemical …

Comparison Crystal Structure Conformations Of Two Structurally Related Biphenyl Analogues: 4,4'-Bis[3-(Pyrrolidin-1-Yl)Prop-1-Yn-1-Yl]-1,1'-Biphenyl And 4,4'-Bis{3-[(S)-2-Methylpyrrolidin-1-Yl]Prop-1-Yn-1-Yl}-1,1'-Biphenyl, Anqi Wan, Narsimha Reddy Penthala, E. Kim Fifer, Sean Parkin, Peter A. Crooks

Chemistry Faculty Publications

The title compounds, C₂₆H₂₈N₂, (I), and C₂₈H₃₂N₂, (II), were designed based on the structure of the potent 910 nicotinic acetyl­choline receptor antagonist ZZ161C {1,1'-[[1,1'-biphen­yl]-4,4'-diylbis(prop-2-yne-3,1-di­yl)]bis­(3,4-di­methyl­pyridin-1-ium) bromide}. In order to improve the druglikeness properties of ZZ161C for potential oral administration, the title compounds (I) and (II) were prepared by coupling 4,4'-bis­(3-bromo­prop-1-yn-1-yl)-1,1'-biphenyl with pyrrol­idine, (I), and (S)-2-methyl­pyrrolidine, (II), respectively, in aceto­nitrile at room temperature. The asymmetric unit of (I) contains two half mol­ecules that each sit on sites of crystallographic inversion. As a result, the biphenyl ring systems in …

Comparison Of The Crystal Structures Of 4,4′-Bis­­[3-(4-Methyl­Piperidin-1-Yl)Prop-1-Yn-1-Yl]-1,1′-Bi­Phenyl And 4,4′-Bis­­[3-(2,2,6,6-Tetra­Methyl­Piperidin-1-Yl)Prop-1-Yn-1-Yl]-1,1′-Biphen­Yl, Anqi Wan, Narsimha Reddy Penthala, E. Kim Fifer, Sean Parkin, Peter A. Crooks

Chemistry Faculty Publications

As part of a comprehensive program to discover α9α10 nicotinic acetyl­choline receptor antagonists, the title compounds C₃₀H₃₆N₂, (I), and C₃₆H₄₈N₂, (II), were synthesized by coupling 4,4′-bis­(3-bromo­prop-1-yn-1-yl)-1,1′-biphenyl with 4-methyl­piperidine and 2,2,6,6-tetra­methyl­piperidine, respectively, in aceto­nitrile at room temperature. In compound (I), the biphenyl system has a twisted conformation with a dihedral angle of 26.57 (6)° between the two phenyl rings of the biphenyl moiety, while in compound (II), the biphenyl moiety sits on a crystallographic inversion centre so the two phenyl rings are exactly coplanar. The terminal piperidine rings in …

Mixed Valent Metal Pincer Complexes And Reactivity Of Metal Complexes Of Extended Pincer Ligands, Jeewantha Sampath Hewage

Dissertations (1934 -)

Historically, the study of mixed valence complexes has been critical for advancing our understanding of electron transfer processes in biological and abiological systems. The recent use of mixed valence complexes in electrochromic materials, and the promise of their use in future technological or molecular electronic applications, has spurred further interest in this class of compound. Previous studies by our research group have shown that gallium(III) or tricarbonylrhenium(I) complexes of pincer-type ligands with diarylamido anchors and either pyrazol-1-yl (pz) or diarylphosphino (PAr2) flanking donors are electroactive species with quasi reversible ligand-centered oxidations. Moreover, the one-electron oxidized derivative with pz flankers, [Ga(L)(L+)]2+ …

Ligand Frameworks For Transition-Metal Complexes That Model Metalloenzyme Active, Denan Wang

Dissertations (1934 -)

Advances in the field of biomimetic inorganic chemistry require the design of sophisticated ligand frameworks that reflect the amazing complexity of metalloenzyme active sites. For instance, most active sites feature extensive hydrogen-bonding interactions between ligands bound to the metal center (the “first” coordination sphere) and nearby units in the outer (or “second”) sphere. Since these interactions modify the structural and electronic properties of the active sites, a number of inorganic chemists have sought to design ligands that permit outer-sphere functional groups to interact with first-sphere donors. This dissertation describes our contribution to these broader efforts to model the second coordination …

S-Nitrosothiols: Electronic Structure And Substituent Effects, Matthew Flister

Dissertations (1934 -)

S-nitrosothiols (RSNOs) are biologically important molecules involved in the storage and transport of nitric oxide (NO) and account for much of its signaling activity in living organisms. RSNOs have significant impact on NO signaling through, S-nitrosation, a major post-translational modification of proteins. These unstable thiol derivatives readily undergo homolytic dissociation of the S–N bond to release NO. RSNOs have potential therapeutic applications as NO donors, although the development of novel RSNOs has been slow due to the complex electronic structure of the –SNO group. A specific focus on the impact of the –R group on RSNO properties via substituent effect …

With Vibrationally Excited Thiophosgene Molecule And Double-Well Ion Traps, Dmytro Shyshlov

Dissertations (1934 -)

For practical realization of quantum information processing we need a quantum system that provides reliable preparation of the initial state, high-fidelity quantum gate operations, error tolerance, readout of the result of quantum computation and scalability of the system to increase the number of qubits. In this dissertation we show how these requirements can be addressed for molecular quantum computer. For computational study of quantum information processing with molecules we employ thiophosgene (SCCl2) molecule that has been used as a test system for quantum control experiments [Mol. Phys. 105, 1999 (2007)]. We investigate the gateway scheme of control in which transitions …

A Deeper Insight Into Strain For The Sila-Bi[6]Prismane (Si18H12) Cluster With Its Endohedrally Trapped Silicon Atom, Si19H12, Vach Holger, Lena V. Ivanova, Qadir K. Timerghazin, Fatme Jardali, Ha-Linh Thi Le

Chemistry Faculty Research and Publications

A new family of over-coordinated hydrogenated silicon nanoclusters with outstanding optical and mechanical properties has recently been proposed. For one member of this family, namely the highly symmetric Si₁₉H₁₂ nanocrystal, strain calculations have been presented with the goal to question its thermal stability and the underlying mechanism of ultrastability and electron-deficiency aromaticity. Here, the invalidity of these strain energy (SE) calculations is demonstrated mainly based on a fundamentally wrong usage of homodesmotic reactions, the miscounting of atomic bonds, and arithmetic errors. Since the article in question is entirely anchored on those erroneous SE values, all of its …

Mass Spectrometry Based Proteomics And Lipidomics Studies, Huan Kang

Theses and Dissertations

Mass spectrometry has emerged as having a vital role in various applications to biochemical fields. In this thesis, we have utilized a variety of mass spectrometry techniques for both bacteriophage proteomics and colostrum and milk lipidomics studies. Our first study was the proteome characterization of Great Salt Lake bacteriophage NS01 with SDS-PAGE GEL to separate the viral proteins and high performance liquid chromatography (HPLC) coupled with an LTQ Orbitrap to identify the proteins after in-gel digestion. In this project, we have successfully identified 11 proteins with high confidence, p-values < 0.01, including coat protein gp88 with a coverage of 91% and tail protein gp86 with a coverage of 40.96%, which facilitated the classification of NS01 as a T7-like phage. Our second study was the discovery of colostrum and milk biomarkers that can be used to predict the likelihood of development of production-related metabolic diseases (PRMDs) in dairy cows through a lipidomics approach. In this study, an electrospray ionization, time-of-flight mass spectrometer was applied to lipid profiling, quantification and significant biomolecule selection. A Q-Star quadrupole, orthogonal time-of-flight mass spectrometer and an Agilent 6530 accurate-mass quadrupole/time-of flight mass spectrometer were both used for lipid biomarker fragmentation and identification. According to linear discriminative statistical modeling, three panels of biomarkers were defined. A combination of 2 milk lipid predictors, including DG18:0/18:0 and TG 18:0/18:0/18:1, provided PRMD predictions with 75.0% sensitivity at 90.0% specificity. A combination of 3 colostrum lipid predictors, including TG16:0/18:1/18:3, DG16:0/16:0 and C₄₀H₆₀NO, provided PRMD prediction with 90.0% sensitivity at …