Chemistry Commons^™

Characterizing The Antioxidant Capacity Of Gevalia Traditional Roast Coffee Based On Brew Method, Erica Mendoza

Summer Community of Scholars Posters (RCEU and HCR Combined Programs)

No abstract provided.

Critical Phenoneme In A Ternary System Of Water, Isobutyric Acid, And Octanol, Kerry Rice

Summer Community of Scholars Posters (RCEU and HCR Combined Programs)

No abstract provided.

Antileishmanial Agents From Sassafras Albidum Bark Extract, Kelly Marie Steinberg

Summer Community of Scholars Posters (RCEU and HCR Combined Programs)

No abstract provided.

Identification And Characterization Of Functionally Critical, Conserved Motifs In The Internal Repeats And N-Terminal Domain Of Yeast Translation Initiation Factor 4b (Yeif4b), Sarah F. Mitchell

Chemistry and Biochemistry Faculty Works

EIF4B has been implicated in attachment of the 43 S preinitiation complex (PIC) to mRNAs and scanning to the start codon. We recently determined that the internal seven repeats (of ∼26 amino acids each) of Saccharomyces cerevisiae eIF4B (yeIF4B) compose the region most critically required to enhance mRNA recruitment by 43 S PICs in vitro and stimulate general translation initiation in yeast. Moreover, although the N-terminal domain (NTD) of yeIF4B contributes to these activities, the RNA recognition motif is dispensable. We have now determined that only two of the seven internal repeats are sufficient for wildtype (WT) yeIF4B function in …

Structure And Dynamics Of The Hiv-1 Frameshift Element Rna, Kathryn Mouzakis

Chemistry and Biochemistry Faculty Works

The HIV-1 ribosomal frameshift element is highly structured, regulates translation of all virally encoded enzymes, and is a promising therapeutic target. The prior model for this motif contains two helices separated by a three-nucleotide bulge. Modifications to this model were suggested by SHAPE chemical probing of an entire HIV-1 RNA genome. Novel features of the SHAPE-directed model include alternate helical conformations and a larger, more complex structure. These structural elements also support the presence of a secondary frameshift site within the frameshift domain. Here, we use oligonucleotide-directed structure perturbation, probing in the presence of formamide, and in-virion experiments to examine …

Principles And Properties Of Eukaryotic Mrnps, Sarah F. Mitchell

Chemistry and Biochemistry Faculty Works

The proper processing, export, localization, translation, and degradation of mRNAs are necessary for regulation of gene expression. These processes are controlled by mRNA-specific regulatory proteins, noncoding RNAs, and core machineries common to most mRNAs. These factors bind the mRNA in large complexes known as messenger ribonucleoprotein particles (mRNPs). Herein, we review the components of mRNPs, how they assemble and rearrange, and how mRNP composition differentially affects mRNA biogenesis, function, and degradation. We also describe how properties of the mRNP "interactome" lead to emergent principles affecting the control of gene expression.

Synthesis And Characterization Of A New Bimetallic Catalyst, Gjl-46, And Its Use In The Catalytic Hydrosilylation Of Phenylacetylene, Gabriel J. Labonia

Honors Theses

A new bimetallic catalyst was synthesized from the metalation of 1,1'-(1,3-phenylene) bis(4-butyl-1 H-1,2,4-triazol-4-ium) iodide with silver oxide and the transmetalation of that complex with Rh(COD)2OTf. The structure of the compound, GJL-46, with molecular formula C34H46I2N6Rh2, was confirmed with mass spectra analysis, 1H NMR and 13C NMR. The catalytic activity of the produced molecule, GJL-46, with molecular formula C34H46I2N6Rh2, in the hydrosilylation of phenylacetylene is reported.

Modified Seed Growth Of Iron Oxide Nanoparticles In Benzyl Alcohol: Magnetic Nanoparticles For Radio Frequency Hyperthermia Treatment Of Cancer, Stanley E. Gilliland Iii

Theses and Dissertations

Iron oxide nanoparticles have received sustained interest for biomedical applications as synthetic approaches are continually developed for precise control of nanoparticle properties. This thesis presents an investigation of parameters in the benzyl alcohol synthesis of iron oxide nanoparticles. A modified seed growth method was designed for obtaining optimal nanoparticle properties for magnetic fluid hyperthermia. With a one or two addition process, iron oxide nanoparticles were produced with crystallite sizes ranging from 5-20 nm using only benzyl alcohol and iron precursor. The effects of reaction environment, temperature, concentration, and modified seed growth parameters were investigated to obtain precise control over properties …

Fabrication And Characterization Of High Surface Area Gold Electrodes, Madhura S. Damle

Theses and Dissertations

High surface area gold electrodes are very good substrates for biosensors, catalysis and drug delivery. Their performance is characterized by good sensitivity, low detection limit and high signal. As a result, extensive research is being carried out in this field using different approaches of fabrication to generate high surface area porous electrodes of different morphology, pore size and structure. The morphology of the electrodes can be changed based on whether the approach involves a template or not, types of metal deposition, method and time of dealloying etc. The deposition of metal can be carried out using various approaches such as …

Structure Assignment And H/D-Exchange Behavior Of Several Glycosylated Polyphenols, Andreas H. Franz, Ilona Serebnitskaya, Gurbir Gudial, Christopher Wallis

College of the Pacific Faculty Articles

The NMR-structures of six polyphenols, resveratrol (1), (-)-epicatechin (2), pelargonidin chloride (3), cyanidin chloride (4), cyanin chloride (5), and keracyanin chloride (6), were fully assigned. For the glycosylated polyphenols 5 and 6, the three-dimensional solution structure and long-range 1 H- 13C-coupling constants across the glycosidic bond were measured. Satisfactory fit to standard Karplus-equations was achieved for glycosides directly attached to the aromatic core in cyanin chloride. Molecular dynamics simulation data in vacuum at the AM1-level of theory were shown to approximate the NMR-solution data reasonably well. Selective HCl-catalyzed H/D-exchange was observed for aromatic protons H6 and H8 in flavonoid structures …

Investigating Dna Barcoding Potentials And Genetic Structure In Ozobranchus Spp. From Atlantic And Pacific Ocean Sea Turtles, Triet Minh Truong

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The Ozobranchidae family is the smallest and least studied hirudinean taxon. Our research includes the largest molecular dataset yet reported for marine ozobranchids (Ozobranchus margoi and Ozobranchus branchiatus) with the most number of documented turtle hosts (57) from the Atlantic and Pacific Oceans to date of any marine turtle epibiont study. Turtle species sampled in this study include loggerheads (Caretta caretta), hawksbill (Eretmochelys imbricata), olive ridley (Lepidochelys olivacea), and green turtles (Chelonia mydas). Phylogenetic analyses of mitochondrial (COI) and nuclear ribosomal (18S and 28S) genes all support the monophyly of marine Ozobranchidae leeches with speciation occurring over an extensive period …

A Chemical Free Approach For Increasing The Biochemical Surface-Enhanced Raman Spectroscopy (Sers)-Based Sensing Capabilities Of Colloidal Silver Nanoparticles, Kevin Michael Dorney

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The unique optoelectronic properties of silver nanoparticles (AgNPs) have led to their explosive use in a multitude of both research and industrial settings in recent years. Localized surface plasmon resonance (LSPR) exhibited by AgNPs has been exploited extensively as a nano-scale probe in a variety of spectroscopic detection modalities, particularly in surface-enhanced Raman spectroscopy (SERS). The SERS effect is highly dependent upon the LSPR interaction with optical laser frequencies, thus optimization of LSPR via specific control of AgNP dimensionality and composition of the surrounding medium is vital for increasing the efficacy of SERS-based nano-sensing. This work aimed to augment LSPR …

The Synthesis Of 1,4-Bis(2-(4-(4-Fluorobenzoyl)Phenoxyethoxy)Benzene And Poly(Aralkyl Ether)S Derived From 1,4-Bis(2-Tosyloxyethoxy)Benzene, Juraj Drzic

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The reaction of 1,4-bis(2-tosyloxyethoxy)benzene or 1,4-bis(bromoethoxy)-benzene with 4-fluoro-4'-hydroxybenzophenone was carried out under a variety of conditions. Changes were made in solvent, reaction time, work-up and base. All attempts to generate a bis(fluorobenzophenone) monomer were unsuccessful. In some cases the presence of the half-product could be determined. In other cases, an elimination product was indicated. The ditosylate, 1,4-bis(2-tosyloxyethoxy)benzene was reacted with bisphenol-A, bisphenol-AF, bis(4-hydroxyphenyl)diphenylmethane and 9,9-bis(4-hydroxyphenyl)fluorene in a dioxane - water solution in the presence of sodium hydroxide to produce four polymers. The polymers were characterized by thermal analysis (TGA) to reveal 5% weight loss temperatures of 338°, 350°, 365° and …

The Synthesis Of Polyimides Containing Oxyalkylene Units, Kristy Wickman

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A series of oxyalkylene containing diamines, 1,4-bis(2-(4-aminophenoxy)-ethoxy)benzene, 2,2-bis[4-(2-(4-nitrophenoxy)ethoxy)phenyl]hexafluoropropane, 9,9-bis(4-(2-(4-nitrophenoxy)ethoxy)phenyl)fluorene, and bis(4-(2-(4-nitrophenoxy)ethoxy)-phenyl)diphenylmethane, has been synthesized from the reduction of 1,4-bis(2-(4-nitrophenoxy)ethoxy)benzene, 2,2-bis[4-(2-(4-nitrophenoxy)ethoxy)phenyl]-hexafluoropropane, 9,9-bis(4-(2-(4-nitrophenoxy)ethoxy)phenyl)fluorene, bis(4-(2-(4-nitrophenoxy)ethoxy)phenyl)diphenylmethane, respectively. The diamine compounds were reacted reacted with 6FDA to obtain the corresponding polyimide. The polymerization was done in a one-pot reaction with m-cresol and isoquinoline. The polyimides displayed glass transition temperatures ranging from 186-231°C and thermal stability <400°C.

Stop Cheating!: An Evaluation Of A Scientific Integrity Writing Strategy In General Chemistry I, Michelle L. Edwards

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Cheating in America has become an epidemic, which has unfortunately spread to academia. Researchers have long been interested in the trends in cheating behavior and the factors that influence these trends among undergraduate college students. Though cheating can take on many forms, in science, there is a deep concern about scientific misconduct related to research. Because training for future scientists begins in undergraduate courses, this study investigated the use of scientific integrity writing strategy in General Chemistry I at Wright State University. The goal of the study was to determine if providing scientific integrity and ethics training, while teaching students …

Routes To N-Heterocycle Functionalized Poly(Arylene Ether Sulfone)S, Jesse L. Picker

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The synthesis of poly(arylene ether sulfone)s, with a pendant aryl iodide, was achieved via nucleophilic aromatic substitution (NAS) polycondensation of 3-iodo-3',5'-difluoro-diphenylsulfone. The polymer series was subjected to amino acid promoted, copper catalyzed coupling reactions with various N-heterocycles. The resulting polymers became crosslinked and insoluble in any organic solvents. The iodo monomer was then subjected to an amino acid promoted, copper catalyzed coupling reaction with carbazole. The successful synthesis of 3'-(9-carbazole) 3,5-difluorodiphenylsulfone is reported. A series of PAES containing a carbazole substituent were synthesized and characterized. The polymers were characterized by a combination of NMR spectroscopy, SEC, TGA, DSC, UV-Vis spectroscopy. …

Reactivity Ratio Controlled Polycondensation As A Route To Synthesize Functional Poly(Arylene Ether)S, Godfred Boakye

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Two monomers, 4',3,5-trifluorodiphenylsulfone, 1, and 4',3,5-trifluorobenzophenone, 2, have been investigated for their potential use as special BB'B''type monomers to synthesize functionalized, linear PAEs via a process called reactivity ratio controlled polycondensation (RRCP). A model study with monomer 1 resulted in a mixture of unreacted starting material, two mono-substitution products (para-and meta-F substitution) and a significant amount of di-substitution products as evidenced by the GC/MS and 13C DEPT-90 NMR spectroscopy. Conversely, subjecting monomer 2 to similar conditions, using 3-aminophenol (3f) as the nucleophile, afforded mono-substitution exclusively. A series of functionalized, linear PAEs polymers were prepared by reaction of compound 2 with …

Ferroelectric Hexagonal And Rhombic Monolayer Ice Phases, Wen-Hui Zhao, Jaeil Bai, Lan-Feng Yuan, Jinlong Yang, Xiao Cheng Zeng

Xiao Cheng Zeng Publications

Two new phases of water, the mid-density hexagonal monolayer ice and the high-density flat rhombic monolayer ice, are observed in our molecular dynamics simulations of monolayer water confined between two smooth hydrophobic walls. These are in addition to the two monolayer ices reported previously, namely, the low-density 4∙8² monolayer ice and the high-density puckered rhombic monolayer ice (HD-pRMI). Stabilities of the structures are confirmed by ab initio computation. Importantly, both new phases and the HD-pRMI are predicted to be ferroelectric. An in-plane external electric field can further stabilize these ferroelectric monolayer ices.

Mos2/Mx2 Heterobilayers: Bandgap Engineering Via Tensile Strain Or External Electrical Field, Ning Lu, Hongyan Guo, Lei Li, Jun Dai, Lu Wang, Wai-Ning Mei, Xiaojun Wu, Xiao Cheng Zeng

Xiao Cheng Zeng Publications

We have performed a comprehensive first-principles study of the electronic and magnetic properties of two-dimensional (2D) transition-metal dichalcogenide (TMD) heterobilayers MX₂/MoS₂ (M = Mo, Cr, W, Fe, V; X = S, Se). For M = Mo, Cr, W; X = S, Se, all heterobilayers show semiconducting characteristics with an indirect bandgap with the exception of the WSe2/MoS2 heterobilayer which retains the directbandgap character of the constituent monolayer. For M = Fe, V; X = S, Se, the MX₂/MoS₂ heterobilayers exhibit metallic characters. Particular attention of this study has been focused on engineering the bandgap …

Van Der Waals Trilayers And Superlattices: Modification Of Electronic Structures Of Mos2 By Intercalation, Ning Lu, Hongyan Guo, Lu Wang, Xiaojun Wu, Xiao Cheng Zeng

Xiao Cheng Zeng Publications

We perform a comprehensive first-principles study of the electronic properties of van der Waals (vdW) trilayers via intercalating a twodimensional (2D) monolayer (ML = BN, MoSe₂, WS₂, orWSe₂) between a MoS₂ bilayer to form various MoS₂/ML/MoS₂ sandwich trilayers. We find that the BN monolayer is themost effective sheet to decouple the interlayer vdW coupling of the MoS₂ bilayer, and the resulting sandwich trilayer can recover the electronic structures of the MoS₂ monolayer, particularly the direct-gap character. Further study of the MoS₂/BN superlattices confirms the effectiveness of …

Unraveling Crystalline Structure Of High-Pressure Phase Of Silicon Carbonate, Rulong Zhou, Bingyan Qu, Jun Dai, Xiao Cheng Zeng

Xiao Cheng Zeng Publications

Although CO₂ and SiO₂ both belong to group-IV oxides, they exhibit remarkably different bonding characteristics and phase behavior at ambient conditions. At room temperature, CO₂ is a gas, whereas SiO₂ is a covalent solid with rich polymorphs. A recent successful synthesis of the silicon-carbonate solid from the reaction between CO₂ and SiO₂ under high pressure [M. Santoro et al., Proc. Natl. Acad. Sci. U.S.A. 108, 7689 (2011)] has resolved a long-standing puzzle regarding whether a Si_xC_1−xO₂ compound between CO₂ and SiO₂ exists in nature. Nevertheless, the detailed …

Mvapack: A Complete Data Handling Package For Nmr Metabolomics, Bradley Worley, Robert Powers

Robert Powers Publications

Data handling in the field of NMR metabolomics has historically been reliant on either in-house mathematical routines or long chains of expensive commercial software. Thus, while the relatively simple biochemical protocols of metabolomics maintain a low barrier to entry, new practitioners of metabolomics experiments are forced to either purchase expensive software packages or craft their own data handling solutions from scratch. This inevitably complicates the standardization and communication of data handling protocols in the field. We report a newly developed open-source platform for complete NMR metabolomics data handling, MVAPACK, and describe its application on an example metabolic fingerprinting data set.

Passive Sampling For Quality Monitoring Of Irish Marine Waters, Philip White

Doctoral

This study details the steps involved in fabrication, deployment and retrieval of mainly polydimethyl siloxane (PDMS) passive sampling devices deployed in a number of locations in and around Ireland in an attempt to derive dissolved water concentrations of contaminants in-situ. PDMS samplers were initially deployed in the Burrishoole catchment, Co. Mayo in conjunction with the collection of biological tissues and sediment to investigate the source of elevated dioxins in the catchment. Passive samplers were used to generate dissolved water concentrations of persistent organic pollutants (POPs) and also to successfully screen for the presence of dioxins in the water column. The …

Iterative Assembly Of Two Separate Polyketide Chains By The Same Single-Module Bacterial Polyketide Synthase In The Biosynthesis Of Hsaf, Yaoyao Li, Haotong Chen, Yanjiao Ding, Yunxuan Xie, Haoxin Wang, Ronald Cerny, Yuemao Shen, Liangcheng Du

Ronald Cerny Publications

HSAF (1) was isolated from the biocontrol agent Lysobacter enzymogenes (Figure 1).^[1-4]

This bacterial metabolite belongs to polycyclic tetramate macrolactams (PTM) that are

emerging as a new class of natural products with distinct structural features. ^{[5, 6]} HSAF

exhibits a potent antifungal activity and shows a novel mode of action.^[1-4] The HSAF

biosynthetic gene cluster contains only a single-module hybrid polyketide synthasenonribosomal

peptide synthetase (PKS-NRPS), although the PTM scaffold is apparently

derived from two separate hexaketide chains and an ornithine residue.^[1-4] This suggests that

the same PKS module would act not only iteratively, but also …

Phosphatase-Inert Glucosamine 6‑Phosphate Mimics Serve As Actuators Of The Glms Riboswitch, Xiang Fei, Thomas Holmes, Julianna Diddle, Lauren Hintz, Dan Delaney, Alex Stock, Danielle Renner, Molly Mcdevitt, David B. Berkowitz, Juliane K. Soukup

David Berkowitz Publications

The glmS riboswitch is unique among generegulating riboswitches and catalytic RNAs. This is because its own metabolite, glucosamine-6-phosphate (GlcN6P), binds to the riboswitch and catalytically participates in the RNA selfcleavage reaction, thereby providing a novel negative feedback mechanism. Given that a number of pathogens harbor the glmS riboswitch, artificial actuators of this potential RNA target are of great interest. Structural/kinetic studies point to the 2- amino and 6-phosphate ester functionalities in GlcN6P as being crucial for this actuation. As a first step toward developing artificial actuators, we have synthesized a series of nine GlcN6P analogs bearing phosphatase-inert surrogates in place …

Three-Dimensional Periodic Graphene Nanostructures, Peter M. Wilson, Gilbert N. Mbah, Thomas G. Smith, Daniel Schmidt, Rebecca Y. Lai, Tino Hofmann, Alexander Sinitskii

Department of Chemistry: Faculty Publications

Graphene is a basic building block for many known and emerging carbon-based materials whose properties largely depend on the way how graphene is structured at the nanoscale. Synthesis of novel threedimensional (3D) nanostructures of graphene would be an important advance for fundamental research and various applications. In this paper, we discuss the possibility of fabricating complex 3D graphene nanostructures by growing graphene on pre-synthesized nanostructured metal templates by chemical vapor deposition (CVD) and then etching away the metal. In the proof-of-concept experiments, we study this idea using two types of metal nanostructures, inverse opals and slanted nanopillar arrays grown by …

Bulk Properties Of Solution-Synthesized Chevron-Like Graphene Nanoribbons, Timothy H. Vo, Mikhail Shekhirev, Alexey Lipatov, Rafal A. Korlacki, Alexander Sinitskii

Department of Chemistry: Faculty Publications

Graphene nanoribbons (GNRs) have received a great deal of attention due to their promise for electronic and optoelectronic applications. Several recent studies have focused on the synthesis of GNRs by the bottom-up approaches that could yield very narrow GNRs with atomically precise edges. One type of GNRs that has received a considerable attention is the chevron-like GNR with a very distinct periodic structure. Surface-assisted and solution-based synthetic approaches for the chevron-like GNRs have been developed, but their electronic properties have not been reported yet. In this work, we synthesized chevron-like GNRs in bulk by a solution-based method, characterized them by …

Highly Selective Gas Sensor Arrays Based On Thermally Reduced Graphene Oxide, Alexey Lipatov, Alexey Varezhnikov, Peter Wilson, Victor Sysoev, Andrei Kolmakov, Alexander Sinitskii

Department of Chemistry: Faculty Publications

The electrical properties of reduced graphene oxide (rGO) have been previously shown to be very sensitive to surface adsorbates, thus making rGO a very promising platform for highly sensitive gas sensors. However, poor selectivity of rGO-based gas sensors remains a major problem for their practical use. In this paper, we address the selectivity problem by employing an array of rGO-based integrated sensors instead of focusing on the performance of a single sensing element. Each rGO-based device in such an array has a unique sensor response due to the irregular structure of rGO films at different levels of organization, ranging from …

Structure And Function Of Preq1 Riboswitches, Catherine D. Eichhorn, Mijeong Kang, Juli Feigon

Department of Chemistry: Faculty Publications

PreQ₁ riboswitches help regulate the biosynthesis and transport of PreQ₁ (7-aminomethyl-7- deazaguanine), a precursor of the hypermodified guanine nucleotide queuosine (Q), in a number of Firmicutes, Proteobacteria, and Fusobacteria. Queuosine is almost universally found at the wobble position of the anticodon in asparaginyl, tyrosyl, histidyl and aspartyl tRNAs, where it contributes to translational fidelity. Two classes of PreQ₁ riboswitches have been identified (PreQ₁-I and PreQ₁-II), and structures of examples from both classes have been determined. Both classes form H-type pseudoknots upon PreQ₁ binding, each of which has distinct unusual features and modes …

Metallurgical And Corrosion Assessment Of Submerged Tanker S.S. Montebello, Dana Medlin, James D. Carr, Donald L. Johnson, David L. Conlin

Department of Chemistry: Faculty Publications

The Union Oil Tanker S.S. Montebello was torpedoed and sunk six miles (9.7 km) off the coast of Cambria, California by a Japanese submarine on December 23, 1941, two weeks after the attack on Pearl Harbor. With close proximity to the National Monterey Bay Marine Sanctuary, concern about possible crude oil contamination led to the most recent expedition to the site in October 2011. Assessment of the shell plate found that the average corrosion rate was very low and the structure will remain stable for many decades.