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Chemistry Matters Fall 2018, Otterbein University Chemistry Department

Chemistry Matters Department Newsletter

In this issue:

Fall 2017 Sabbatical in Cambridge, UK/New Study Abroad Course in Chemistry/Students and Faculty Present at the 255th ACS National Meeting in New Orleans, March 2018/Exploring Biodiesel Chemistry in Multiple Lab Courses

Synthesis And Evaluation Of Protein-Phenylboronic Acid Conjugates As Lectin Mimetics, Joshua Whited, Czharena Kay Rama, Xue-Long Sun

Chemistry Faculty Publications

Glycan-binding molecules, such as lectins, are very important tools for characterizing, imaging, or targeting glycans and are often involved in either physiological or pathological processes. However, their availability is far less compared to the diversity of native glycans. Therefore, development of lectin mimetics with desired specificity and affinity is in high demand. Boronic acid reacts with 1,2- and 1,3-diols of saccharides in aqueous media through reversible boronate ester formation and are regarded as synthetic lectin mimetics. In this study, bovine serum albumin (BSA)-phenylboronic acid (PBA) conjugates were synthesized in a density-controlled manner by targeting both aspartic and glutamic acids to …

Regulation Of Kv11.1 Potassium Channel C-Terminal Isoform Expression By The Rna-Binding Proteins Hur And Hud, Qiuming Gong, Matthew R. Stump, Zhengfeng Zhou

Faculty Publications - Department of Biological & Molecular Science

The potassium voltage-gated channel subfamily H member 2 (KCNH2) gene encodes the Kv11.1 potassium channel, which conducts the rapidly activating delayed rectifier current in the heart. KCNH2 pre-mRNA undergoes alternative polyadenylation and forms a functional, full-length Kv11.1a isoform if exon 15 is polyadenylated or a nonfunctional, C-terminally truncated Kv11.1a-USO isoform if intron 9 is polyadenylated. The molecular mechanisms that regulate Kv11.1 isoform expression are poorly understood. In this study, using HEK293 cells and reporter gene expression, pulldown assays, and RNase protection assays, we identified the RNA-binding proteins Hu antigen R (HuR) and Hu antigen D (HuD) as regulators of Kv11.1 …

Polymer Coated Gold-Ferric Oxide Superparamagnetic Nanoparticles For Theranostic Applications, Muhammad Raisul Abedin, Siddesh Umapathi, Harika Mahendrakar, Tunyaboon Laemthong, Holly Coleman, Denise Muchangi, Santimukul Santra, Manashi Nath, Sutapa Barua

Chemistry Faculty Research & Creative Works

Background: Engineered inorganic nanoparticles (NPs) are essential components in the development of nanotechnologies. For applications in nanomedicine, particles need to be functionalized to ensure a good dispersibility in biological fluids. In many cases however, functionalization is not sufficient: the particles become either coated by a corona of serum proteins or precipitate out of the solvent. We show that by changing the coating of magnetic iron oxide NPs using poly-l-lysine (PLL) polymer the colloidal stability of the dispersion is improved in aqueous solutions including water, phosphate buffered saline (PBS), PBS with 10% fetal bovine serum (FBS) and cell culture medium, and …

Thermochemistry: Heat Of Neutralization And Hess’S Law [Chemistry], Kevin Mark, Phil Mercier, Janet Gonzalez, Burl Yearwood

Open Educational Resources

The General Chemistry 1 (SCC 201) course has been designated for the core competency of Inquiry and Problem Solving along with the Written Communication Ability. These abilities are best observed in the laboratory section of the course where SCC 201 students are asked to submit weekly written lab reports that range in chemistry topics from chemical structures to the chemical analysis of polluted environments. SCC 201 will be implementing a new experiment in the laboratory portion of the course entitled, “Thermochemistry: Heat of Neutralization and Hess’s Law.” The design of the experiment incorporates many elements of LaGCC’s Core Competencies and …

Air Pollution [Liberal Arts: Math And Science/Natural Science], Ian Alberts

Open Educational Resources

This assignment was designed for students in the pathways introductory chemistry class and the first year seminar and aligns with the Inquiry and Problem Solving core competency. In this context, there is a focus on “framing the issues” (identifies and/or addresses questions and problems), “evidence gathering” (assembles, reviews and synthesizes evidence from several diverse sources), “evidence” (analyze the data to address the questions posed) and “conclusions” (critical thinking, reflect on the outcomes, draw conclusions and generate new knowledge). There is also a Global Learning component based on comparing data collected locally with corresponding data from other locations or countries. The …

Electro- And Photocatalytic Carbon Dioxide Reduction With Mononuclear And Dinuclear Rhenium Polypyridyl Complexes, Eva Amatya

Honors Theses

The main challenge of reducing carbon dioxide (CO2) to value-added products lies in designing more efficient catalysts that are long-lived, selective, and operate near the thermodynamic potential for the reaction. In this work, mononuclear and dinuclear Re complexes containing diamine ligands linked to a pendant anthracene moiety have been synthesized and studied for both electrocatalytic and photocatalytic CO2 reduction. Electrocatalytically, the performances of both catalysts were studied in N,N-dimethylformamide (DMF) and acetonitrile (MeCN) solutions to determine their turnover frequencies (TOFs) for CO2 reduction. Catalyst performance was compared to previously reported rhenium systems, and both systems studied here were shown to …

Folding Of Gα Subunits: Implications For Disease States, Matthew Najor, Brian D. Leverson, Jesse L. Goossens, Saad Kothawala, Kenneth W. Olsen, Duarte Mota De Freitas

Chemistry: Faculty Publications and Other Works

G-proteins play a central role in signal transduction by fluctuating between “on” and “off” phases that are determined by a conformational change. cAMP is a secondary messenger whose formation is inhibited or stimulated by activated Giα1 or Gsα subunit. We used tryptophan fluorescence, UV/vis spectrophotometry, and circular dichroism to probe distinct structural features within active and inactive conformations from wild-type and tryptophan mutants of Giα1 and Gsα. For all proteins studied, we found that the active conformations were more stable than the inactive conformations, and upon refolding from higher temperatures, activated wild-type subunits recovered significantly more native structure. We also …

Superresolution Mapping Of Energy Landscape For Single Charge Carriers In Plastic Semiconductors, Yifei Jiang, Jason Mcneill

Publications

The performance of conjugated polymer devices is largely dictated by charge transport processes. However, it is difficult to obtain a clear relationship between conjugated polymer structures and charge transport properties, due to the complexity of the structure and the dispersive nature of charge transport in conjugated polymers. Here, we develop a method to map the energy landscape for charge transport in conjugated polymers based on simultaneous, correlated charge carrier tracking and single-particle fluorescence spectroscopy. In nanoparticles of the conjugated polymer poly[9,9-dioctylfluorenyl-2,7-diyl)-co-1,4-benzo-{2,1′-3}-thiadiazole)], two dominant chain conformations were observed, a blue-emitting phase (λmax = 550 nm) and a …

Vitamin D: Controversy Cancer And Beyond, Cristian J. Rosales, Debasish Bandyopadhyay

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

Vitamins are an essential part to wellbeing. This was not something always known however, as the Germ theory was the accepted thesis of the 18th century. It was found that certain accessory factors helped mitigate and even cure these diseases such as beriberi, scurvy, and rickets. Accessory factors, later coined vitamins by Casimir Funk, are an essential constituent of the human diet. Vitamin D is technically not a vitamin but functions as a steroid hormone whose most well-known purpose is calcification of the human skeleton. This helps prevent osteomalacia in adults and rickets, a serious problem in children due to …

Advanced Cotton Fibers Exhibit Efficient Photocatalytic Self-Cleaning And Antimicrobial Activity, Jared Jaksik, Phong Tran, Veronica Galvez, Isaac Martinez, Darian Ortiz, Andy Ly, Monica Mcentee, Erin M. Durke, Sayeeda Tj Aishee, Margaret Cua, Ahmed Touhami, H. Justin Moore, M. Jasim Uddin

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

Functional cotton fibers have a wide range of applications in domestic, commercial, and military settings, and so enhancing the properties of these materials can yield substantial benefits. Herein, we report the creation of functional fibers that are self-cleaning, anti-microbial, and protective against UV radiation. A uniform, and high surface area films of TiO2 were deposited on cotton fibers and gold/silver nanoparticles were directly incorporated on the nanostructured TiO2 surface. The synthetic method is simple and the produced TiO2 film is homogenous and the nanoparticles were shown to be effectively distributed on the surface using a simple photocatalytic reduction method. …

Development Of A Fluorescence Imaging Photometer-Based Method For Characterization Of Phytoplankton Communities, Cameron Maxwell Rekully

Theses and Dissertations

The development of methods for real-time characterization of phytoplankton community structure has important implications for environmental monitoring and the prediction of harmful algal blooms. Our research group has developed an instrument, the Fluorescence Imaging Photometer (FIP), which is capable of rapid classification of phytoplankton via imaging single-cell chlorophyll a fluorescence under different excitation conditions. Discrimination of cells from different taxonomic groups is achieved using optical bandpass filters that have been chosen to selectively excite pigments which occur in characteristic ratios that vary from one group to the next. The relative fluorescence intensity emitted by cells under these different excitation conditions …

Hierarchical Corannulene-Based Materials, Allison M. Rice

Theses and Dissertations

Merging the intrinsic properties of fullerene (buckyball) and corannulene (buckybowl) derivatives with the inherent properties of crystalline metal- and covalent- organic frameworks (MOFs and COFs), including their modularity, porosity, versatility, high surface area, and structural tunability, opens a pathway to unlock a novel class of fulleretic materials. Despite the great interest in MOFs and COFs, as well as fullerene derivatives, this dissertation is focused on crystalline fullerene- and corannulene- containing frameworks, highlighting their potential contributions in the fields of optoelectronic devices, electrodes, and photosensitizers. We have revealed a dual role of fullerene- and corannulene-containing building blocks showing their versatility to …

Π-Π Stacking Vs. C–H/Π Interaction: Excimer Formation And Charge Resonance Stabilization In Van Der Waals Clusters Of 9,9′-Dimethylfluorene, Damian Kokkin, Maxim Vadimovich Ivanov, John Loman, Sheng Cai, Brandon Uhler, Neil Reilly, Rajendra Rathore, Scott A. Reid

Chemistry Faculty Research and Publications

Studies of exciton and hole stabilization in multichromophoric systems underpin our understanding of electron transfer and transport in materials and biomolecules. The simplest model systems are dimeric, and recently we compared the gas-phase spectroscopy and dynamics of van der Waals dimers of fluorene, 9-methylfluorene (MF), and 9,9′-dimethylfluorene (F1) to assess how sterically controlled facial encumbrance modulates the dynamics of excimer formation and charge resonance stabilization (CRS). Dimers of fluorene and MF show only excimer emission upon electronic excitation, and significant CRS as evidenced in a reduced ionization potential for the dimer relative the monomer. By contrast, the dimer of F1 …

The Rotational Spectrum And Potential Energy Surface Of The Ar-Sio Complex, Michael C. Mccarthy, Steve Alexandre Ndengue, Richard Dawes

Chemistry Faculty Research & Creative Works

The rotational spectra of five isotopic species of the Ar-SiO complex have been observed at high-spectral resolution between 8 and 18 GHz using chirped Fourier transform microwave spectroscopy and a discharge nozzle source; follow-up cavity measurements have extended these measurements to as high as 35 GHz. The spectrum of the normal species is dominated by an intense progression of a-type rotational transitions arising from increasing quanta in the Si-O stretch, in which lines up to v = 12 (~14 500 cm^-1) were identified. A structural determination by isotopic substitution and a hyperfine analysis of the Ar-Si¹⁷O …

Development Of Bioactive Peptidomimetics, Fengyu She

USF Tampa Graduate Theses and Dissertations

Peptidomimetics are synthetic foldamers that expected more resistant to proteolytic degradation and enormous chemodiversity when compared with peptides. To date, the functional peptidomimetics such as β-peptides, peptoids, oligoureas, etc have been developed in many science fields. In order to explore the unnatural foldameric architectures, it’s necessary to discover the novel frameworks and molecular scaffolds. γ-AApeptides were reported to be a new class of peptidomimetics that showed its potential applications in drug discovery and chemical biology. However, a wide function and property of γ-AApeptides need to be further explored. To expand the potential application of γ-AApeptides in biochemistry, I have been …

Quinolines From The Cyclocondensation Of Isatoic Anhydride With Ethyl Acetoacetate: Preparation Of Ethyl 4-Hydroxy-2-Methylquinoline-3-Carboxylate And Derivatives, Nicholas Jentsch, Jared D. Hume, Emily B. Crull, Samer M. Beauti, Amy H. Pham, Julie A. Pigza, Jacques Kessl, Matthew G. Donahue

Faculty Publications

A convenient two-step synthesis of ethyl 4-hydroxy-2-methylquinoline-3-carboxylate derivatives has been developed starting from commercially available 2-aminobenzoic acids. In step 1, the anthranilic acids are smoothly converted to isatoic anhydrides using solid triphosgene in THF. In step 2, the anhydride electrophiles are reacted with the sodium enolate of ethyl acetoacetate, generated from sodium hydroxide, in warm N,N-dimethylacetamide resulting in the formation of substituted quinolines. A degradation–build-up strategy of the ethyl ester at the 3-position allowed for the construction of the α-hydroxyacetic acid residue required for the synthesis of key arylquinolines involved in an HIV integrase project.

Ultrafine Mineral Associations In Superhigh-Organic-Sulfur Kentucky Coals, James C. Hower, Debora Berti, Michael F. Hochella Jr.

Center for Applied Energy Research Faculty and Staff Publications

Two high-organic-sulfur Kentucky coals, the eastern Kentucky River Gem coal and the western Kentucky Davis coal, are examined by scanning electron microscopy (SEM) and transmission electron microscopy (TEM), both including elemental analysis by energy-dispersive spectroscopy (EDS). From the SEM–EDS analysis, it is observed that the western Kentucky coal had areas with Pb and Cd in addition to the expected Fe and S and the eastern Kentucky coal had individual Fe–S-rich areas with La and Ni and with Si, Al, Cr, Ni, and Ti. TEM and selected area electron diffraction (SAED) analyses demonstrate that anglesite with a rim of Pb-bearing amorphous …

Novel Porous Polymer Compositions For The Synthesis Of Monolithic Bimodal Microporous/Macroporous Carbon Compositions Useful For Selective Co₂ Sequestration, Nicholas Leventis, Chariklia Sotiriou-Leventis, Malik Adnan Saeed

Chemistry Faculty Research & Creative Works

The present invention discloses novel porous polymeric compositions comprising random copolymers of amides, imides, ureas, and carbamic-anhydrides, useful for the synthesis of monolithic bimodal microporous/macroporous carbon aerogels. It also discloses methods for producing said microporous/macroporous carbon aerogels by the reaction of a polyisocyanate compound and a polycarboxylic acid compound, followed by pyrolytic carbonization, and by reactive etching with CO₂ at elevated temperatures. Also disclosed are methods for using the microporous/macroporous carbon aerogels in the selective capture and sequestration of carbon dioxide.

Solution And Solid-State Emission Toggling Of A Photochromic Hydrazone, Baihao Shao, Massimo Baroncini, Laura Bussotti, Mariangela Di Donato, Alberto Credi, Ivan Aprahamian

Dartmouth Scholarship

The proliferation of light-activated switches in recent years has enabled their use in a broad range of applications encompassing an array of research fields and disciplines. All current systems, however, have limitations (e.g., from complicated synthesis to incompatibility in biologically relevant media and lack of switching in the solid-state) that can stifle their real-life application. Here we report on a system that packs most, if not all, the desired, targeted and sought-after traits from photochromic compounds (bistability, switching in various media ranging from serum to solid-state, while exhibiting ON/OFF fluorescence emission switching, and two-photon assisted near-infrared light toggling) in an …

Surprising Antibacterial Activity And Selectivity Of Hydrophilic Polyphosphoniums Featuring Sugar And Hydroxy Substituents., Tyler J Cuthbert, Benjamin Hisey, Tristan D Harrison, John F Trant, Elizabeth R Gillies, Paul J Ragogna

Chemistry Publications

There is currently an urgent need for the development of new antibacterial agents to combat the spread of antibiotic-resistant bacteria. We explored the synthesis and antibacterial activities of novel, sugar-functionalized phosphonium polymers. While these compounds exhibited antibacterial activity, we unexpectedly found that the control polymer poly(tris(hydroxypropyl)vinylbenzylphosphonium chloride) showed very high activity against both Gram-negative Escherichia coli and Gram-positive Staphylococcus aureus and very low haemolytic activity against red blood cells. These results challenge the conventional wisdom in the field that lipophilic alkyl substituents are required for high antibacterial activity and opens prospects for new classes of antibacterial polymers.

A Synthetic Model Of The Nonheme Iron–Superoxo Intermediate Of Cysteine Dioxygenase, Anne A. Fischer, Sergey V. Lindeman, Adam T. Fiedler

Chemistry Faculty Research and Publications

A nonheme Fe(II) complex (1) that models substrate-bound cysteine dioxygenase (CDO) reacts with O₂ at −80 °C to yield a purple intermediate (2). Analysis with spectroscopic and computational methods determined that 2 features a thiolate-ligated Fe(III) center bound to a superoxide radical, mimicking the putative structure of a key CDO intermediate.

Efforts Towards The Discovery Of Novel Methods For The Synthesis Of Pharmacologically Relevant Molecular Scaffolds, Graham Joseph Haun

Theses and Dissertations

With the introductions of pharmaceuticals into modern day society many people have been using them to improve their lives. Due to this high increase in demand along with the ever-growing concern of environmental impact pharmaceutical companies have been pressed to synthesis new and existing drugs at a higher rate. This increased rate can cause low yield drugs or have a heavy environmental impact. As the use of pharmaceuticals becomes more widespread the need for greener and simpler organic synthesis methods to make these pharmaceuticals becomes more needed.

Herein is reported the methodological development of different pharmacologically relevant scaffolds. This work …

An Updated Description Of The Hydrogen Bond And Related Noncovalent Bonds, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

The hydrogen bond is typically introduced briefly in General Chemistry as a simple electrostatic phenomenon involving a small and select group of atoms, a definition which is typically unchanged through higher levels in the curriculum. But this definition has undergone dramatic modernization of which students should be made aware. The original formulation in terms of only F, O, and N atoms has broadened very considerably, encompassing C as well as atoms from lower rows in the periodic table. The influence of hybridization, substituents, and overall charge cannot be overlooked. In addition to the Coulombic attraction, there are other “covalent” contributors …

The Role Of Proton Transport In Gating Current In A Voltage Gated Ion Channel, As Shown By Quantum Calculations, Alisher M. Kariev, Michael E. Green

Publications and Research

Over two-thirds of a century ago, Hodgkin and Huxley proposed the existence of voltage gated ion channels (VGIC) to carry Na⁺ and K⁺ ions across the cell membrane to create the nerve impulse, in response to depolarization of the membrane. The channels have multiple physiological roles, and play a central role in a wide variety of diseases when they malfunction. The first channel structure was found by MacKinnon and coworkers in 1998. Subsequently the structure of a number of VGIC was determined in the open (ion conducting) state. This type of channel consists of four voltage sensing domains …

Triel-Bonded Complexes Between Trr3 (Tr = B, Al, Ga; R = H, F, Cl, Br, Ch3) And Pyrazine, Mariusz Michalczyk, Wiktor Zierkiewicz, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Complexes between TrR3 (Tr = B, Al, Ga; R= H, F, Cl, Br, CH3)molecules and pyrazine have been characterized at the MP2 and CCSD(T) levels of theory. The adducts can be grouped according to the type of molecular arrangement. The first situation places the Tr atom in the plane of the pyrazine ring and contains a triel bond to the N lone pair. For the boron complexes the orbital interaction energy is almost equal to the electrostatic component, while the former is only half the latter for Tr= Al and Ga. The two monomers are stacked above one another in …

Molecular Insights On Aging And Aqueous-Phase Processing From Ambient Biomass Burning Emissions-Influenced Po Valley Fog And Aerosol, Matthew Brege, Marco Paglione, Stefania Gilardoni, Maria Cristina Facchini, Lynn Mazzoleni

Department of Chemistry Publications

To study the influence of regional biomass burning emissions and secondary processes, ambient samples of fog and aerosol were collected in the Po Valley (Italy) during the 2013 Supersito field campaign. After the extent of fresh vs. aged biomass burning influence was estimated from proton nuclear magnetic resonance (¹H NMR) and high-resolution time-of-flight aerosol mass spectrometry (HR-ToF-AMS), two samples of fog water and two samples of PM1 aerosol were selected for ultrahigh-resolution Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) analysis. Molecular compositions indicated that the water-soluble organic matter was largely non-polymeric without clearly repeating units. The …

Dft-Assisted Design And Evaluation Of Bifunctional Copper(I) Catalysts For The Direct Intermolecular Addition Of Aldehydes And Ketones To Alkynes, Jacob D. Porter, Eric Greve, Abdulmohsen Alsafran, Adam R. Benoit, Sergey V. Lindeman, Chris Dockendorff

Chemistry Faculty Research and Publications

Bifunctional catalysts containing discrete metal pi-acid and amine sites were designed and investigated for the direct intermolecular addition of aldehydes and ketones to unactivated alkynes. Copper(I)-based catalysts were prioritized based on intramolecular (Conia-ene type) reactions, and complexes were designed with tridentate ligands and potentially hemilabile heterocyclic spacers. The structures of the designed catalysts were computed using density functional theory (DFT), and the relative energies of putative catalytic intermediates were estimated and used to prioritize catalyst designs. Novel bifunctional precatalysts containing a thiazole spacer were synthesized via a 9-step sequence and combined with transition metals before screening for the direct addition …

How To Fold And Protect Mitochondrial Ribosomal Rna With Fewer Guanines, Maryam Hosseini, Poorna Roy, Marie Sissler, Craig L. Zirbel, Eric Westhof, Neocles B. Leontis

Chemistry Faculty Publications

Mammalian mitochondrial ribosomes evolved from bacterial ribosomes by reduction of ribosomal RNAs, increase of ribosomal protein content, and loss of guanine nucleotides. Guanine is the base most sensitive to oxidative damage. By systematically comparing high-quality, small ribosomal subunit RNA sequence alignments and solved 3D ribosome structures from mammalian mitochondria and bacteria, we deduce rules for folding a complex RNA with the remaining guanines shielded from solvent. Almost all conserved guanines in both bacterial and mammalian mitochondrial ribosomal RNA form guaninespecific, local or long-range, RNA–RNA or RNA– protein interactions. Many solvent-exposed guanines conserved in bacteria are replaced in mammalian mitochondria by …

Isolation Of Rna From A Mixture And Its Detection By Utilizing A Microgel-Based Optical Device, Molla R. Islam, Shakiba Azimi, Faranak Teimoory, Glen Loppnow, Michael J. Serpe

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

In this investigation, we show that RNA can be separated from a solution containing DNA and RNA and the isolated RNA can be detected using poly (N-isopropylacrylamide-co-N-(3-aminopropyl) methacrylamide hydrochloride) microgel-based optical devices (etalons). The isolation of RNA was accomplished by using hairpin-functionalized magnetic beads (MMPDNA) and differential melting, based on the fact that the DNA–RNA hybrid duplex is stronger (i.e., high melting temperature) than the DNA–DNA duplex (i.e., low melting temperature). By performing concurrent etalon sensing and fluorescent studies, we found that the MMPDNA combined with differential melting was capable of selectively separating RNA from DNA. This selective separation and …