Chemistry Commons^™

Structural Dynamics Of A Single-Stranded Rna–Helix Junction Using Nmr, Catherine D. Eichhorn, Hashim M. Al-Hashimi

Department of Chemistry: Faculty Publications

Many regulatory RNAs contain long single strands (ssRNA) that adjoin secondary structural elements. Here, we use NMR spectroscopy to study the dynamic properties of a 12-nucleotide (nt) ssRNA tail derived from the prequeuosine riboswitch linked to the 3′ end of a 48-nt hairpin. Analysis of chemical shifts, NOE connectivity, ¹³C spin relaxation, and residual dipolar coupling data suggests that the first two residues (A25 and U26) in the ssRNA tail stack onto the adjacent helix and assume an ordered conformation. The following U26-A27 step marks the beginning of an A₆-tract and forms an acute pivot point for …

Evolution Of Selected Isoprene Oxidation Products In Dark Aqueous Ammonium Sulfate, D.M. Ashraf Ul Habib

Dissertations, Master's Theses and Master's Reports - Open

The aqueous phase processing of glyoxylic acid, pyruvic acid, oxalic acid and methylglyoxal was studied simulating dark and radical free atmospheric aqueous aerosol. A novel observation of the cleavage of a carbon-carbon bond in pyruvic acid and glyoxylic acid leading to their decarboxylation was made in the presence of ammonium salts but no decarboxylation was observed from oxalic acid. The empirical rate constants for decarboxylation were determined. The structure of the acid, ionic environment of solution and concentration of species found to affect the decarboxylation process. A tentative set of reaction mechanisms was proposed involving nucleophilic attack by ammonia on …

Jupiter's Great Red Spot Is Composed Of Ammonia And Phosphine, Erika Rosenberger

Natural Sciences Student Research Presentations

In Jupiter's Great Red Spot, ammonia, phosphine, and para-Hydrogen were found. The Great Red Spot is the local maximum of ammonia, the most abundant compound of the atmosphere. The abundance of ammonia in the Spot is regulated by a complex interaction between photochemistry, condensation, precipitation, and atmospheric dynamics. Ammonia is found most abundant in the regions at around 400-500 mbar when phosphine is the most abundant at 600 mbar. The photo-dissociation reaction of phosphine that occurs in the Spot helps explain why the planet Jupiter and the Great Red Spot is red. The reaction sequence proposed by scientists Prinn and …

Spatial And Seasonal Variability Of Cloud Condensation Nuclei Number Concentrations Over The Extended North African Continent And The Mediterranean, Hesham Abdel-Monem Afify Hassan

Legacy Theses & Dissertations (2009 - 2024)

The spatiotemporal variability of cloud condensation nuclei (CCN) number concentration is investigated over the extended domain of the North African continent and Mediterranean which is an essential step for better understanding of aerosol-cloud interactions and associated climate impacts over the region. The study is performed by analyzing the output for the period from 2004 to 2011 from the well-validated global chemistry and aerosol transport model GEOS-Chem-APM. The analysis shows that the dominant aerosol type for CCN number concentration is secondary particles all over the domain. Spatial analysis reveals the existence of four characteristic subdomains of variability: over the Mediterranean and …

Thin Layer Chromatography For Forensic Science, Kseniya Chumachenko

A with Honors Projects

For this Parkland A with Honors project, the author works to identify a good or better recipe for the solution for chromatography projects in a forensic science lab class.

Science Classics, Mark Masthay

Chemistry Faculty Publications

An essay on the impact of the works in the Imprints and Impressions: Milestones in Human Progress, an exhibition of rare books from the collection of Stuart Rose. Exhibition was held Sept. 29-Nov. 9, 2014, at the University of Dayton.

Stop Rotating! One Substitution Halts The B19- Motor, Francisco Cervantes-Navarro, Gerarso Martínez-Guajardo, Edison Osorio, Diego Moreno, William Tiznado, Rafael Islas, Kelling J. Donald, Gabriel Merino

Chemistry Faculty Publications

The B₁₉^- anion and other boron species have been dubbed ‘Wankel motors’ for the almost barrierless rotation of inner and outer concentric rings relative to each other in these compounds. A single substitution in B₁₉^- is shown to shut down the well-established fluxionality in the anion. A carbon atom substituted in the structure to give a neutral CB₁₈ species is shown computationally to enforce bond localization.

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.

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 …

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.

Advances In Chemical And Structural Characterization Of Concretion With Implications For Modeling Marine Corrosion, Donald L. Johnson, Robert J. Deangelis, Dana J. Medlin, James D. Carr, David L. Conlin

Department of Chemistry: Faculty Publications

The Weinsnumber model and concretion equivalent corrosion rate methodology were developed as potential minimum-impact, cost-effective techniques to determine corrosion damage on submerged steel structures. To apply the full potential of these technologies, a detailed chemical and structural characterization of the concretion (hard biofouling) that transforms into iron bearing minerals is required. The fractions of existing compounds and the quantitative chemistries are difficult to determine from x-ray diffraction. Environmental scanning electron microscopy was used to present chemical compositions by means of energy-dispersive spectroscopy (EDS). EDS demonstrates the chemical data in mapping format or in point or selected area chemistries. Selectedarea EDS …

Analogues Of (-)-Picropodophyllin, Synthesis And Uses Thereof, David B. Berkowitz, Sylvain Broussy

Department of Chemistry: Faculty Publications

Analogs of (-)-Picropodophyllin, synthesis thereof, and uses in pharmaceuticals as inhibitors of IGF1RK.

Electron And Ion Spectroscopy Of Metal Hydrocarbon Complexes, Sudesh Kumari

Theses and Dissertations--Chemistry

Metal-hydrocarbon complexes were prepared in a laser-vaporization molecular beam source and studied by single-photon zero electron kinetic energy (ZEKE) and mass-analyzed threshold ionization (MATI) spectroscopy. The ionization energies and vibrational frequencies of the metal complexes were measured from the ZEKE and MATI spectra. Metal-ligand bonding and low-lying electronic states of the neutral and ionized complexes were analyzed by combining the spectroscopic measurements with quantum chemical calculations and spectral simulations.

In this dissertation, the metal complexes of mesitylene, aniline, cyclooctatetraene, benzene, ethene, and propene were studied. For each complex, different effects from metal coordination have been identified. Although metal-bis(mesitylene) sandwich complexes …

Structure Vs. Properties Using Chemical Graph Theory, Tabitha N. Williford

College of Graduate Studies: Theses & Dissertations

Chemical graph theory began as a way for mathematicians to bring together the areas of the Physical Sciences and Mathematics. Through its use, mathematicians are able to model chemical systems, predict their properties as well as structure-property relationships. In this dissertation, we consider two questions involving chemical graph theory and its applications. We first look at tree-like polyphenyl systems, which form an important family of compounds in Chemistry, particularly in Material Science. The importance can be seen in LEDs, transmitters, and electronics. In recent years, many extremal results regarding such systems under specific constraints have been reported. More specifically are …

Investigations Into The Fluorescent Covalent Labeling Of Biomolecules Utilizing Rhodamine Dyes, Electrophilic Leaving Groups And Mrna Display., Susan D. Selaya

Theses and Dissertations

The discovery of a method by which proteins of interest can selectively be labeled with a probe of choice intracellularly is a longstanding goal in chemical biology research. Conventional labeling techniques have utilized large domain tags but despite the development of small labeling molecules there have been no short peptide sequences known to covalently label a small molecule without the aid of an enzymatic process or metal chelation. We aimed to find a sequence of nucleophilic peptides that reacted covalently and specifically with electrophilic small labeling molecules using mRNA display. Our goal was to show that an electrophilic small labeling …

Light Mediated Drug Delivery Using Photocaged Molecules And Photoswitchable Peptides, Deboleena Mitra

Theses and Dissertations

There are many different types of targeted therapy for cancer treatment. The method of light mediated targeted therapy that we have developed uses photocaged molecules and photoswitchable peptides.

In photocaging, a biologically active molecule is made inactive by the attachment of a photocleavable blocking group. On exposure to UV radiation the photocleavable entity is removed and the biologically active molecule is released. Using this concept we have designed a prodrug that consists of a cell impermeable hydrophilic molecule attached to a photocaged doxorubicin. Upon irradiation with UV light the photosensitive group is removed and cytotoxic doxorubicin is released at the …

Fluorination Of Aromatic Ring Systems, Stephen G. Dimagno

Department of Chemistry: Faculty Publications

This disclosure relates to reagents and methods useful in the synthesis of aryl fluorides, for example, in the preparation of ¹⁸F labeled radiotracers. The reagents and methods provided herein may be used to access a broad range of compounds, including aromatic compounds, heteroaromatic compounds, amino acids, nucleotides, and synthetic compounds.

Phosphate Esters, Thiophosphate Esters And Metal Thiophosphates As Lubricant Additives, David W. Johnson, John E. Hils

Chemistry Faculty Publications

Phosphate esters, thiophosphate esters and metal thiophosphates have been used as lubricant additives for over 50 years. While their use has been extensive, a detailed knowledge of how they work has been a much more recent development. In this paper, the use of phosphate esters and thiophosphate esters as anti-wear or extreme pressure additives is reviewed with an emphasis on their mechanism of action. The review includes the use of alkyl phosphates, triaryl phosphates and metal containing thiophosphate esters. The mechanisms of these materials interacting with a range of iron and steel based bearing material are examined.

Poly (N-Isopropylacrylamide) Microgel-Based Etalons And Etalon Arrays For Determining The Molecular Weight Of Polymers In Solution, Molla R. Islam, Michael J. Serpe

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Positively and/or negatively charged poly (N-isopropylacrylamide)-based microgels were deposited on a single substrate and isolated regions of Au overlayers were deposited on top of the microgels. Each spatially isolated Au overlayer region had a different thickness to make an etalon array.We found that areas with a thin Au overlayer (5 nm) responded to a range of polymer molecular weights (MW), while areas with a thick overlayer (35 nm) can only respond to low molecular weight polyelectrolytes. By comparing the optical responses of the device’s individual array elements, a good approximation of the polyelectrolyteMWin solution can be made.

Investigating Intermolecular Interactions In Crystalline Aspirin Using Cdft, Nicholas Turner, Tonglei Li, Mingtao Zhang

The Summer Undergraduate Research Fellowship (SURF) Symposium

Drugs today are widely administered in their crystalline form, namely via tablets and capsules. The crystal structure of a drug molecule affects important drug qualities such as solubility, bioavailability, shelf life, and compaction properties. In order to form a basis for crystal structure prediction, it is necessary to first understand how intermolecular interactions cause molecules to pack in certain ways. Being able to predict and perhaps even control a drug molecule’s crystal structure will lead to the development of higher quality drugs that perform more consistently. Scientists and engineers do not fully understand the reasons for a molecule assuming a …

Surface Modification Of Poly(Dimethylsiloxane) With 254 Nm Irradiation:A Comparison Of Functional Groups, Kenya Wallace

Von Braun Symposium Student Posters

No abstract provided.

Acquisition Of An Electrochemical System Instrument For The Development Of Sensors, Elmer-Rico E. Mojico

Cornerstone 1 Reports : Expansion and Enhancements of the Thinkfinity Platform

No abstract provided.

Structure, Theoretical Studies And Coupling Reactions Of Some New Cyclic Boronic Esters, Andrew Kuttler, Sravanthi Durganala, Albert Fratini, Alexander Morgan, Vladimir Benin

Chemistry Faculty Publications

The present report describes the X-ray structural and theoretical studies of some new pinacolboronate esters, and it also outlines the use of the target structures in Suzuki coupling reactions to produce new aromatic or heteroaromatic esters and amides. X-ray structural analysis of the studied compounds revealed that the pinacolborane ring's position with respect to the benzene ring varies, depending on the particular environment. An ortho-positioned carboxylic ester (methyl ester) causes a nearly perpendicular orientation of the pinacolborane unit with respect to the benzene ring, whereas an ortho-positioned amide (N,N-dimethylamide) causes the pinacolborane unit to orient itself nearly coplanar. A plausible …

Investigation Of Ozone In Urban And Rural Areas Of California, Mia J. Hiles, David Parrish

STAR Program Research Presentations

Ozone is the air pollutant about which we have probably heard the most. Two types of ozone exist: stratospheric and tropospheric. Stratospheric ozone absorbs most of the damaging ultra-violet sunlight and tropospheric ozone comes into direct contact with life-forms and is toxic at high levels. Ozone concentration in California has been studied for over five decades, and there is a long history of control efforts. During 2010, California Air Resources Board (CARB) and National Oceanic and Atmospheric Administration (NOAA) conducted a major climate and air quality study in California called CalNex 2010 (California Research at the Nexus of Air Quality …

Characterization By Nmr Of Reactants And Products Of Hydrofluoroether Isomers, Cf3(Cf2)3och3 And (Cf3)2c(F)Cf2och3, Reacting With Isopropyl Alcohol, Howard Knachel, Vladimir Benin, William E. Moddeman, Janine C. Birkbeck, Thomas A. Kestner, Tayna L. Young

Chemistry Faculty Publications

The 3M Company product Novec™ 71IPA DL, a mixture of methoxyperfluorobutane, methoxyperfluoroisobutane and 4.5 wt.% isopropyl alcohol, has been found to be very stable at ambient temperature, producing fluoride at the rate of ~1 ppm/year. Our earlier kinetic and theoretical studies have identified the reaction mechanism. This paper identifies the ¹H and ¹⁹F NMR chemical shifts, multiplicities, and coupling constants of reactants and the major products that result from aging the mixture in sealed Pyrex NMR tubes for periods up to 1.8 years at temperatures from 26 °C to 102 °C. Chemical shifts and coupling constants of fluorine …

Label-Free Detection Of Low Protein Concentration In Solution Using A Novel Colorimetric Assay, Molla R. Islam, Michael J. Serpe

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Dual pH and temperature sensitive microgel-based etalons were fabricated by sandwiching a “monolithic” microgel layer between two semitransparent, Au layers. The devices exhibit visual color and multipeak reflectance spectra, both of which primarily depend on the distance between the Au surfaces mediated by the microgel diameter. We found that a polycationic polyelectrolyte can penetrate through the Au overlayer to interact with negatively charged microgel confined between Au overlayers. In this submission we report that biotinylated polycationic polymer can penetrate through the Au overlayer of a poly (N-isopropylacrylamide)-co-acrylic acid (pNIPAm-co-AAc) microgel-based etalon and cause the microgel layer to collapse. The collapse …