Chemistry Commons^™

Modeling Chemical Reactions In Aqueous Solutions, Osman Uner

Graduate Theses and Dissertations

The energy barriers for SN2 ligand exchange reactions between the chloride anion and para-substituted benzyl chlorides were investigated both in water solution and in the gas phase by using quantum chemical simulations at the DFT and Hartree-Fock levels. The question addressed was the effect of the solvent (water) and of the substituent on the barrier height. The para substitutient groups included NH2, OH, OCH3, CH3, C(CH3)3, H, F, Cl, Br, I, CF3, CN, NO2, and SO3- . The calculations in aqueous solution were carried out with the recently developed Ultrafast Monte Carlo method using the TIP3P explicit water model. The …

Synthesis Of Platinum And Platinum-Copper Branched Nanoparticles For Electrooxidation Of Methanol, Eric Courtland Taylor

Graduate Theses and Dissertations

Platinum and Pt alloys are among the most important heterogeneous catalysts for many organic reactions and electrochemical reactions associated with the fuel cell technologies. How to reduce Pt usage while maintaining the performance of the catalysts becomes a subject for intensive research in materials chemistry. For heterogeneous catalysis, the catalytic reactivity and selectivity are strongly correlated with different crystallographic facets exposed on the surface. The facets with high-index planes whose Miller indices with at one is larger than unity are generally more active than those with low-index planes (e.g., {100}, {111}, and {110}). Tuning the morphology of the nanoparticles to …

Optimization Of Sample Preparation In Matrix-Assisted Laser Desorption/Ionization (Maldi) Mass Spectrometry Of Macromolecules, Evgenia Akhmetova

Graduate Theses and Dissertations

New method for the matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) and Fourier transform mass spectrometry (MALDI-FTMS) analysis of low molecular weight polyvinyl acetate (PVAc) was developed and then applied to the characterization of commercially available chewing gum. The optimization of MALDI analysis of PVAc was achieved by investigating the influence of sample preparation variables such as the choice of solvent and choice of matrix-analyte ratio. It was demonstrated that the use of ethyl acetate as a solvent and 2,5-Dihydroxybenzoic acid as a matrix yielded the highest signal intensity for the pure polymer sample. The application of TOF technique did not …

Polysaccharide-Based Nanocarriers For Improved Drug Delivery, Nan Zhang

Dissertations - ALL

The field of drug delivery has provided a solution to the limited efficacy and high toxicity of many drugs. Nano-sized drug carriers are popular because their size allows for selective accumulation in the diseased area. Polysaccharides are non-toxic and biodegradable natural polymers that can serve as the basis for these nano-sized carriers. Polysialic acid (PSA) is such a polysaccharide with strong hydrophilicity that may reduce uptake by the reticuloendothelial system and prolong drug circulation. In this study, we developed PSA-based nanocarriers, specifically micelles and nanoparticles, for improved drug delivery with improved efficacy and minimized toxicity. PSA-based micelle systems were developed …

Recyclable Synthesis, Characterization, And Antimicrobial Activity Of Chitosan-Based Polysaccharide Composite Materials, Chieu D. Tran, Simon Duri, April L. Harkins

Chemistry Faculty Research and Publications

We have successfully developed a simple and totally recyclable method to synthesize novel, biocompatible, and biodegradable composite materials from cellulose (CEL) and chitosan (CS). In this method, [BMIm⁺Cl⁻], an ionic liquid (IL), was used as a green solvent to dissolve and synthesize the [CEL+CS] composites. Since, the IL can be removed from the composites by washing them with water, and recovered by distilling the washed solution, the method is totally recyclable. Spectroscopic and imaging techniques including XRD, FTIR, NIR, and SEM were used to monitor the dissolution, to characterize and to confirm that CEL and CS …

Visible-Light Activatable Organic Co-Releasing Molecules (Photocorms) That Simultaneously Generate Fluorophores, Ping Peng, Chaoming Wang, Zheng Shi, Valentine K. Johns, Liyuan Ma, Jeremiah Oyer, Alicja Copik, Robert Igarashi, Yi Liao

Chemistry and Chemical Engineering Faculty Publications

Novel organic photoCORMs based on micelle-encapsulated unsaturated cyclic α-diketones were designed and synthesized. These photoCORMs can be activated by visible light, have potentially low toxicity, allow the delivery of carbon monoxide to be monitored by fluorescence imaging techniques, and thus are useful tools for the study of the biological function of CO.

Synthesis And Physico-Chemical Studies Of Azo Dyes From Anacardic Acid, An Inexpensive Renewable Resource, John Mkungu, Quintino Mgani, Stephen Mdachi

Tanzania Journal of Science

(3AP) and 4-aminophenol (4AP) with both unsaturated (UA) and saturated (SA) anacardic acidsand the calcium salt (CA) of the unsaturated acid. The six prepared dyes are, thus, given theacronyms 3APSA, 3APUA, 3APCA, 4APSA, 4APUA, and 4APCA depending on the source of thediazonium salt and the form of anacardic acid used. The dyes were characterized using UV-Visand FT-IR spectroscopic techniques. The UV-Vis absorption spectra of the dyes were found tohave maximum peaks at 520 nm for the dyes of 3AP origin and at 295 nm for the dyes of 4APorigin. The FT-IR spectra for the dyes indicated presence of the azo …

55th Annual Rocky Mountain Conference On Magnetic Resonance

Rocky Mountain Conference on Magnetic Resonance

Final program, abstracts, and information about the 55th annual meeting of the Rocky Mountain Conference on Magnetic Resonance, co-endorsed by the Colorado Section of the American Chemical Society and the Society for Applied Spectroscopy. Held in Denver, Colorado, July 28 - August 1, 2013.

Electron-Phonon And Magnetoelastic Interactions In Ferromagnetic Co[N(Cn)(2)](2), T V. Brinzari, J T. Haraldsen, P Chen, Q C. Sun, Y Kim, L C. Tung, A P. Litvinchuk, J A. Schlueter, D Smirnov, Jamie L. Manson, J Singleton, J L. Musfeldt

Chemistry and Biochemistry Faculty Publications

We combined Raman and infrared vibrational spectroscopies with complementary lattice dynamics calculations and magnetization measurements to reveal the dynamic aspects of charge-lattice-spin coupling in Co[N(CN)(2)](2). Our work uncovers electron-phonon coupling as a magnetic field-driven avoided crossing of the low-lying Co2+ electronic excitation with two ligand phonons and a magnetoelastic effect that signals a flexible local CoN6 environment. Their simultaneous presence indicates the ease with which energy is transferred over multiple length and time scales in this system.

Fabrication Of Surface Amine Gradients By Controlled-Rate Infusion For Chromatographic Applications, Balamurali Kannan

Theses and Dissertations

Surface gradients are materials that exhibit a variation in properties such as chemical composition, topography etc., in a continuous and/or discrete fashion. They are broadly classified as chemical and physical gradients depending upon the properties that gradient exhibits. Among those, chemical gradients on various surfaces have been a great interest in materials research for the last two decades. This is due to the applications of gradients in various fields such as biological sciences, separation science, etc. There have been several different approaches developed for the preparation of chemical gradients. Silane-based approaches are among those that are widely used because of …

Cyclic Versus Polymeric Supramolecular Architectures In Metal Complexes Of Dinucleating Ligands: Silver(I) Trifluoromethanesulfonate Complexes Of The Isomers Of Bis(Di(1h-Pyrazolyl)Methyl)-1,1′-Biphenyl, James R. Gardinier, Heidi M. Tatlock, Jeewantha S. Hewage, Sergey V. Lindeman

Chemistry Faculty Research and Publications

In the search for new examples of systems that self-assemble into cyclic metal–organic architectures, the six isomers of X,Y′-bis(di(1H-pyrazolyl)methane)-1,1′-biphenyl, L_XY, and their silver(I) trifluoromethanesulfonate complexes were prepared. Five of the six silver complexes gave crystals suitable for single crystal X-ray diffraction, with only the microcrystalline derivative of 2,3′-bis(di(1H-pyrazolyl)methane)-1,1′-biphenyl, L₂₃, proving to be unsuitable for this analysis. Of the structurally characterized silver(I) complexes, that with L₂₂ showed an unusual trans-spanning chelating coordination mode to silver. At the same time the ligand was also bound to a second silver center …

Electron Transfer By Excited Benzoquinone Anions: Slow Rates For Two-Electron Transitions, Matibur Zamadar, Andrew R. Cook, Anna Lewandowska-Andralojc, Richard Holroyd, Yan Jiang, Jin Bikalis, John R. Miller

Faculty Publications

Electron transfer (ET) rate constants from the lowest excited state of the radical anion of benzoquinone, BQ−•*, were measured in THF solution. Rate constants for bimolecular electron transfer reactions typically reach the diffusion-controlled limit when the free-energy change, ΔG°, reaches −0.3 eV. The rate constants for ET from BQ−•* are one-to-two decades smaller at this energy and do not reach the diffusion-controlled limit until −ΔG° is 1.5−2.0 eV. The rates are so slow probably because a second electron must also undergo a transition to make use of the energy of the excited state. Similarly, ET, from solvated electrons to neutral …

Developing Thyronamine Analog Pharmaceuticals Targeting Taar1 To Treat Methamphetamine Addiction, Troy Andrew Wahl

Dissertations and Theses

As a part of the overall program in the Grandy laboratory at Oregon Health & Science University (OHSU), studying the underlying chemical biology of methamphetamine (Meth) addiction, this dissertation reports on the development of six new thyronamine analogs which were synthesized and assayed against trace amine associated receptor 1 (TAAR1), giving preliminary results consistent with the analogs being inverse agonists. Due to highly variable TAAR1 expression levels in the assays, based on inter-assay response to control Meth stimulation as well as other possible factors, kinetic models were developed to qualitatively explain the assay results. The models set approximate limits on …

Studies Toward The Synthesis Of Lyconadin A And Cranomycin, Brad M. Loertscher

Theses and Dissertations

Lyconadin A is a pentacyclic Lycopodium alkaloid isolated from the club moss Lycopodium companatum with anticancer activity. Our approach sought to incorporate a 7-exo–6-exo acyl radical cyclization cascade to access the bicyclo[5.4.0]undecane framework of lyconadin A. Our studies created methodology for the synthesis of 5-alkyl and 3,5-dialkyl-6-carbomethoxy-2-pyridones and sterically demanding epoxide substrates. These epoxide substrates underwent an unanticipated Payne rearrangement.Cranomycin is a potent antibiotic with antiprotozoal activity. Structurally it is a cyclopentane ring system with substitution at each carbon in the ring. Another interesting structural aspect is the existence of three contiguous quaternary stereocenters including two tertiary alcohols and a …

Vpt2+K Spectroscopic Constants And Matrix Elements Of The Transformed Vibrational Hamiltonian Of A Polyatomic Molecule With Resonances Using Van Vleck Perturbation Theory, Andreana M. Rosnik, William F. Polik

Faculty Publications

Vibrational levels of polyatomic molecules are analysed with Van Vleck perturbation theory to connect experimental energy levels to computed molecular potential energy surfaces. Vibrational matrix elements are calculated from a quartic potential function via second-order Van Vleck perturbation theory, a procedure that treats both weak and strong interactions among vibrational states by approximately block-diagonalising the vibrational Hamiltonian. A clear and complete derivation of anharmonic and resonance constants as well as general expressions for both on- and off-diagonal matrix elements of the transformed Hamiltonian is presented. The equations are written in partial fraction form and as a constant multiplied by a …

Synthetic, Spectroscopic And Dft Studies Of Iron Complexes With Iminobenzo(Semi)Quinone Ligands: Implications For O-Aminophenol Dioxygenases, Michael M. Bittner, David S. Krause, Sergey V. Lindeman, Cordina V. Popescu, Adam T. Fiedler

Chemistry Faculty Research and Publications

The oxidative CC bond cleavage of o-aminophenols by nonheme Fe dioxygenases is a critical step in both human metabolism (the kynurenine pathway) and the microbial degradation of nitroaromatic pollutants. The catalytic cycle of o-aminophenol dioxygenases (APDOs) has been proposed to involve formation of an Fe^II/O₂/iminobenzosemiquinone complex, although the presence of a substrate radical has been called into question by studies of related ring-cleaving dioxygenases. Recently, we reported the first synthesis of an iron(II) complex coordinated to an iminobenzosemiquinone (ISQ) ligand, namely, [Fe(Tp)(^tBuISQ)] (2 a; where Tp=hydrotris(3,5-diphenylpyrazol-1-yl)borate and ^{tBu …}

Case Of The Missing Isomer: Pathways For Molecular Elimination In The Photo-Induced Decomposition Of 1,1-Dibromoethane, Aimable Kalume, Lisa George, Nicole Cunningham, Scott A. Reid

Chemistry Faculty Research and Publications

We report an experimental and computational study of the photodecomposition pathways of a prototypical gem-dihalide, 1,1-dibromoethane (1,1-EDB), in the condensed phase. Following photolysis of the matrix isolated parent compound in Ar at 5 K, photoproducts are observed corresponding to Br₂ elimination (+ C₂H₄ or C₂H₂) and HBr elimination (+ vinyl bromide). The elimination products are observed in the matrix as complexes. In contrast to our recent studies of the photolysis of matrix isolated polyhalomethanes, no evidence for the iso-1,1-EDB species is found, although studies of the matrix isolated 1,1-dibromo-2,2,2-trifluoroethane analogue show that …

Spectroscopic And Computational Electronic Structure Studies Of Donor-Acceptor Systems, Diana Habel-Rodriguez

Chemistry and Chemical Biology ETDs

Three molecular systems have been studied, which exhibit strong intramolecular electronic communication between constituent moieties. Experimental results for electronic absorption, resonance Raman, electron paramagnetic resonance (EPR), and magnetic circular dichroism (MCD) spectroscopies are presented. Density functional theory (DFT) electronic structure calculations were employed to augment the interpretation of experimental results. Using a valence bond configuration interaction (VBCI) model we show that the ground state properties of the molecules are influenced by excited state configurations. Donor ( = semiquinone)-bridge-acceptor ( = nitronylnitroxide) biradicals show strong ferromagnetic donor-acceptor coupling, and contributions to the ferromagnetic coupling from spin delocalization and spin polarization mechanisms …

Catalytic Mechanism And Function Evolvement Studies Of Phosphatases Within Haloacid Dehalogenase Superfamily (Hadsf), Li Zheng

Chemistry and Chemical Biology ETDs

The haloacid dehalogenase superfamily (HADSF) is one of the largest known enzyme superfamilies, having more than 32,000 nonredundant members. Enzymes in this superfamily catalyze a number of different chemical reactions including dehalogenation, phosphoryl transfer, and hydrolysis of phosphate esters and phosphates. The vast majority of HADSF members are phosphatases, which contain a highly conserved core domain that is constructed to catalyze hydrolysis reactions of phosphorylated sugars or nucleotides by using an active site Asp nucleophile and a Mg²⁺ cofactor. Most phosphatases possess a cap domain, which in association with the core domain assists active site desolvation and binds the …

Developmental Signaling Requires Inwardly Rectifying K+ Channels In Drosophila Melanogaster, Giri Raj Dahal

Theses and Dissertations

Inwardly rectifying potassium (IRK/Kir) channels regulate intracellular K+ concentrations and membrane potential. Disruption of Kir2.1 causes dominantly inherited Andersen Tawil Syndrome (ATS). ATS patients suffer from cardiac arrhythmias, periodic paralysis, and cognitive impairment. These symptoms are consistent with current understanding of the role of ion channels in muscle cells and neurons. However, ATS symptoms also include craniofacial and digital deformities such as cleft palate, dental defects, wide set eyes, low set ears, and crooked or fused digits. These developmental defects were not consistent with current understanding of developmental signaling or previously described roles for ion channels. We found that phenotypes …

Characterization Of Freshwater Natural Dissolved Organic Matter (Dom): Mechanistic Explanations For Protective Effects Against Metaltoxicity And Direct Effects On Organisms, Hassan A. Al-Reasi, Chris M. Wood, D. Scott Smith

Chemistry Faculty Publications

Dissolved organic matter (DOM) exerts direct and indirect influences on aquatic organisms. In order to better understand how DOM causes these effects, potentiometric titration was carried out for a wide range of autochthonous and terrigenous freshwater DOM isolates. The isolates were previously characterized by absorbance and fluorescence spectroscopy. Proton binding constants (pK_a) were grouped into three classes:acidic (pK_a ≤ 5), intermediate (5 < pK_a ≤ 8.5) and basic (pK_a > 8.5). Generally, the proton site densities (L_T) showed maximum peaks at the acidic and basic ends around pK_a values of 3.5 and 10, respectively. More …

Charge Transfer And Blue Shifting Of Vibrational Frequencies In A Hydrogen Bond Acceptor, Ashley M. Wright, Austin A. Howard, J. Coleman Howard, Gregory S. Tschumper, Nathan I. Hammer

Chemistry Faculty Research & Creative Works

A comprehensive Raman spectroscopic/electronic structure study of hydrogen bonding by pyrimidine with eight different polar solvents is presented. Raman spectra of binary mixtures of pyrimidine with methanol and ethylene glycol are reported, and shifts in ν₁, ν₃, ν_6a, ν_6b, ν_8a, ν_8b, ν_9a, ν₁₅, ν_16a, and ν_16b are compared to earlier results obtained for water. Large shifts to higher vibrational energy, often referred to as blue shifts, are observed for ν₁, ν_6b, and ν_8b (by as much …

The Role Of Smpb In Licensing Tmrna Entry Into Stalled Ribosomes, Mickey R. Miller

Theses and Dissertations

Ribosomes translate the genetic information contained in mRNAs into protein by linking together amino acids with the help of aminoacyl-tRNAs. In bacteria, protein synthesis stalls when the ribosome reaches the 3'-end of truncated mRNA transcripts lacking a stop codon. Trans-translation is a conserved bacterial quality control process that rescues stalled ribosomes. Transfer-messenger RNA (tmRNA) and its protein partner SmpB mimic a tRNA by entering the A site of the ribosome and accepting the growing peptide chain. The ribosome releases the truncated mRNA and resumes translation on the tmRNA template. The open reading frame found on tmRNA encodes a peptide tag …

An Electrolysis Experiment For A Middle School Summer Science Camp, Mike A. Christiansen, Leslie Jessup, Kevin D. Woodward

Chemistry and Biochemistry Faculty Publications

Higher education is often culturally deemphasized in the geographic area served by our rural, regional campus. As a result, faculty members have the opportunity to spearhead teaching efforts designed to educate the community about the importance of obtaining a post-secondary degree. To this end, we recently held a Science Summer Camp for middle school students, designed to infuse young people with an increased excitement for STEM (Science, Technology, Engineering, and Math) education. In this report, we summarize a chemical electrolysis experiment we carried out with middle school students for our annual Science Summer Camp. We also provided procedural guidelines for …

Fe, Co And Ni Adatoms Adsorbed On Silicene: A Dft Study, Kent Gang '14, Siva Gangavarapu '14, Matthew Deng '14, Glenn W. "Max" Mcgee, Ron Hurlbut, Michael Lee Dao Kang, Sean Ng Peng Nam, Harman Johll, Tok Eng Soon

Student Publications & Research

Two-dimensional materials have attracted much research attention given their intriguing properties. The latest member of this class of materials is silicene. In this work, we investigate the adsorption of Fe, Co and Ni adatoms on silicene using plane-wave density functional theory calculations within the Perdew-Burke-Ernzerhof parameterization of the generalized gradient approximation for the exchange-correlation potential. In particular, we calculate the binding energy, magnetization, and projected electronic configurations of these adatoms adsorbed at different sites on the silicene. Our calculations show that the hole site (i.e. in the centre of a hexagonal-like arrangement of Si atoms) is the most stable configuration …

Exploration Of Aqueous Interfaces And Their Effect On Ion Behavior, Oneka T. Cummings

Doctoral Dissertations

An in-depth understanding of a wide range of physical, chemical, atmospheric and biological processes can only be achieved after the structure and dynamics of interfaces and the interfacial behavior of aqueous species, such as ions, are thoroughly studied and understood. This dissertation describes computational studies conducted to gain a more comprehensive understanding of such interfaces and the behavior of ions in the bulk and interfacial regions of the (1) air/water interface, and (2) alkane/water interfaces.

At the air/water interface the effect of counterion (sodium cations) charge and the influence of ion pairing on anion (chloride) propensity for the air/water interface …

Spectroscopic Determination Of Binding Constants Of Modified Β-Cyclodextrins With Brooker’S Merocyanine, Carly Hanson

Symposium on Research and Creative Expression (SORCE)

Host-guest complexation occurs when a guest molecule is held inside a host molecule through weak molecular forces. β-cyclodextrin, a host molecule, has a variety of uses and is often applied in pharmaceuticals. Binding constants of host-guest complexes of Brooker’s merocyanine and various modified β-cyclodextrins (2-hydroxypropyl-β-cyclodextrin, sulfated β-cyclodextrin, and methyl-β-cyclodextrin) were studied using fluorescence and UV-Vis spectrometry to determine the strength of interaction between the host molecule and the guest molecule. By modifying the β-cyclodextrin, the effect of ionic forces, hydrogen bonding, and steric hindrance were compared. It was determined via fluorescence spectrometry that sulfated β-cyclodextrin had a binding constant of …

Posterolateral Neck Texture (Insulin Neck): Early Sign Of Insulin Resistance, Katie S. Payne, Ryan K. Rader, Guido Lastra, William V. Stoecker

Chemistry Faculty Research & Creative Works

No abstract provided.

Structural And Magnetic Properties Of La₀.₇Sr₀.₃Mn₁₋ₓniₓo₃ (X ≤ 0.4), Thomas F. Creel, Jinbo Yang, Mehmet Kahveci, Satish K. Malik, Sylvio Quezado, Oran Allan Pringle, William B. Yelon, William Joseph James

Physics Faculty Research & Creative Works

We have studied the structural and magnetic properties of La_0.7Sr_0.3Mn_1-xNi_xO₃ (x = 0.05, 0.1, 0.20, 0.30, and 0.40) perovskites using x-ray and neutron diffraction and magnetic measurements. Our data consist of neutron (γ = 1.479Å) and x-ray (γ = 1.5481Å; Cu Kα) powder diffraction and magnetization measurements. We previously suggested these systems transition from ferromagnetic to antiferromagnetic ordering with the intermediate concentrations containing coexisting domains of ferromagnetically and antiferromagnetically ordered states. Upon further detailed examination, we find that the samples are homogeneous and that neutron data can be fitted to a …

Improving The Stability Of High And Low Bandgap Polymers Organic Photovoltaic Devices Using A Solution Based Titanium Sub-Oxide Interfacial Layer, Kurniawan Foe

Electrical & Computer Engineering Theses & Dissertations

The improvement in device efficiency has brought organic photovoltaic (OPV) devices closer to commercial viability, highlighting the importance of studying the lifetime and stability of OPV devices. At present, the lifetime and stability of OPV devices is much shorter and poor mainly caused by oxygen, moisture, and light resulting in the oxidation on low work function electrodes and the degradation of the morphology of the photoactive layer. To improve the lifetime and stability of the OPV devices, we used newly developed low bandgap polymer, PCDTBT, as the electron acceptor material and a solution based titanium sub-oxide (TiOx) interfacial layer inserted …