Chemistry Commons^™

Organization, Structure, And Assembly Of Alpha-Carboxysomes Determined By Electron Cryotomography Of Intact Cells, Cristina V. Iancu, Dylan M. Morris, Zhicheng Dou, Sabine Heinhorst, Gordon C. Cannon, Grant J. Jensen

Faculty Publications

Carboxysomes are polyhedral inclusion bodies that play a key role in autotrophic metabolism in many bacteria. Using electron cryotomography, we examined carboxysomes in their native states within intact cells of three chemolithoautotrophic bacteria. We found that carboxysomes generally cluster into distinct groups within the cytoplasm, often in the immediate vicinity of polyphosphate granules, and a regular lattice of density frequently connects granules to nearby carboxysomes. Small granular bodies were also seen within carboxysomes. These observations suggest a functional relationship between carboxysomes and polyphosphate granules. Carboxysomes exhibited greater size, shape, and compositional variability in cells than in purified preparations. Finally, we …

Open Notebook Science Challenge Solubilities Of Organic Compounds In Organic Solvents, Andrew Lang, Jean-Claude Bradley, Cameron Neylon, Rajarshi Guha, Antony J. Williams, Bill Hooker, Brent Friesen

College of Science and Engineering Faculty Research and Scholarship

The Open Notebook Science Solubility Challenge Solubility is an important consideration for many chemistry applications. Synthetic chemists usually use a solvent to perform reactions and knowledge of the solubility of the starting materials or products can be very useful to pick an appropriate solvent. Analytical chemists can use solubility to design separation techniques and factor in dynamic range considerations. Physical chemists can create and evaluate their models of how molecules interact in the solubilization and precipitation processes. Solubility data can be obtained from a variety of online and offline sources. As with all chemical data, it can be a challenge …

Dual-Action Hygienic Coatings: Benefits Of Hydrophobicity And Silver Ion Release And Surface Analysis, Niall Stobie, Brendan Duffy, John Colreavy, Patrick Mchale, Steven Hinder, Declan Mccormack

Articles

Coatings that demonstrate reduced attachment of crystalline precipitates and the medical device colonising Staphylococcus epidermidis were prepared by the immobilisation of silver doped perfluoropolyether–urethane siloxane thin films on glass substrates. The presence of stratified hydrophobic perfluoropolyether groups protects the coating surface from the attachment of crystalline hydrophilic species such as chlorides and phosphates, whilst silver ion release inhibited attachment of S. epidermidis and subsequent biofilm formation in vitro. The release of silver ions protects the perfluoro groups from the hydrophobic interactions of S. epidermidis cells, which can reduce the hydrophobicity of the protective coating. These coatings also exhibited significant antibacterial …

Methods And Kit For Determination Of Prostacyclin In Plasma, Sylvia Daunert, Michael Poon, Urvee Desai, Sapna K. Deo

Chemistry Faculty Patents

A solid-phase immunoassay for 6-keto-Prostaglandin F_1α, the stable hydrolysis product of prostacyclin (Prostaglandin I₂) is disclosed. Prostacyclin, a potent vasodilator with anti-platelet and anti-proliferative properties is an effective treatment for primary pulmonary hypertension and pulmonary arterial hypertension associated with scleroderma and scleroderma-like syndrome. Levels of 6-keto-Prostaglandin F_1α can be directly correlated with levels of prostacyclin. Therefore, 6-keto-Prostaglandin F_1α has become the indicator of choice to measure prostacyclin levels. The single step immunoassay for 6-keto-Prostaglandin F_1α uses the bioluminescent protein, aequorin as a label. Analyte-label conjugates were constructed by linking the carboxyl group of …

Development Of Novel Synthetic Methodologies And Their Use In Approaches For The Preparation Of Lactacystin, Lepadiformine And A Giardia Lamblia Fructose-1,6-Bisphosphate Aldolase Inhibitor, Jiwen Zou

Chemistry and Chemical Biology ETDs

The investigations carried out in my doctoral studies focus on (1) applications of pyridinium salt photochemical and tandem ene-yne-ene metathesis reactions to the synthesis of the natural products (+)-lactacystin and lepadiformine C, and (2) the preparation of a novel inhibitor for the class II Giardia lamblia fructose-1,6-bisphosphate aldolase. New developments in the area of pyridinium salt photochemistry were explored in the context of approaches to the natural product (+)-lactacystin. The results of this effort show that irradiation of a substituted 1,2-cyclopenta-fused pyridinium salt in aqueous solution followed by treatment with sodium bicarbonate leads to selective production of an unusual, structural …

Investigation Of Co2 Insertion Into Lanthanide Amides, Alkoxides, And Mixed Amide/Alkoxides, Leigh Anna M. Ottley

Chemistry and Chemical Biology ETDs

A novel set of lanthanide (Ln) alkoxycarbonates, [Ln(μ-CO₂-DBP)(DBP)₂]₂ where Ln = lanthanide; and DBP = OC₆H₃-2,6-C(CH₃)₃, were isolated from a systematic study of the insertion of CO_2(g) (referred to as CO₂) into the Ln-O bonds of a series of new lanthanide alkoxides, Ln(OR)₃. This study was undertaken to determine if the deleterious metal carbonate [M(CO₃)_y] formation that promotes higher thermal budgets during processing could be avoided. While processing controls can reduce the formation of the M(CO₃) …

Development Of Novel Fluorescent Sensors For The Detection Of Functional And Bio-Interesting Small Molecules And Metal Ions, Wei Jiang

Chemistry and Chemical Biology ETDs

As one important kind of sensitive analytical technology, fluorescence method is widely applied in environmental science, materials, medicine pharmacy and nowadays much popularly in cellular biological science, which requires the development of diverse fluorescent sensors to meet various analytical and researching demands. During my Ph.D. study, my work focuses on the development of novel fluorescent sensors for the detection and specific recognition of functional and bio-interesting small molecules and metal ions, and the contents are described in this dissertation using three sections. In the first part, novel fluorescent sensors for the specific recognition of bio-toxic thiophenols have been developed based …

Mesoporous Silica Microparticles Enhance The Cytotoxicity Of Anticancer Platinum Drugs, Zhimin Tao, Bonnie Toms, Jerry Goodisman, Tewodros Asefa

Chemistry - All Scholarship

We report on the endocytosis and the time-dependent enhanced cytotoxicity of anticancer platinum drugs when the drugs are combined with (or loaded into) one of the two most common types of mesoporous silica materials, MCM-41 or SBA-15. The anticancer drug cisplatin and its isomer transplatin, when loaded on MCM-41 and SBA-15 microparticles, were less cytotoxic to leukemia cells than the drugs alone after 12 h exposure. However, the drug-loaded microparticles exhibited unprecedented enhanced cytotoxicity to the cancerous cells after 24 h of exposure. This cytotoxicity of the drug-loaded microparticles was even higher than of the pure drugs in solutions, suggesting …

The Heat Capacity And Thermodynamic Properties Of The Iron Oxides And Their Relation To The Mineral Core Of The Iron Storage Protein Ferritin, Claine Lindsey Morton Snow

Theses and Dissertations

The iron oxides are a group of materials with geological, biological, and technological importance. A thermodynamic understanding of these materials is important because it provides information about their relative stabilities, chemical reactivity, and transformations. This study provides the heat capacity of a nanocrystalline magnetite (Fe3O4) sample, bulk hematite (α-Fe2O3), nanocrystalline hematite, akaganéite (β-FeOOH), and lepidocrocite (γ-FeOOH) at temperatures as low as 0.5 K. These measurements were fit to theoretical functions at temperatures lower than 15 K, and the respective thermophysical properties of these materials are discussed. Also the molar entropies of bulk hematite and hydrous nanocrystalline hematite as well as …

Tetraaquabis(3-Fluoropyridine-4-Carboxylato-Κn)Zinc(Ii) Dihydrate, Jonetha Fleming, Jennifer Kelley, Leroy Peterson Jr., Mark D. Smith, Hans-Conrad Zur Loye

Faculty Publications

In the title compound, [Zn(C₆H₃FNO₂)₂(H₂O)₄]·2H₂O, the Zn^II atom is octahedrally coordinated in a ZnO₄N₂ environment by two 3-fluoropyridine-4-carboxylate (3-fpy4-cbx) ligands and four water molecules. The [Zn(3-fpy4-cbx)₂(H₂O)₄] molecules form a three-dimensional network through strong O-HO and weak O-HF hydrogen bonds between 3-fpy4-cbx and water molecules. The crystal used for data collection was a twin, with the twin law corresponding to a 180° rotation about the real-space [001] axis. The major twin fraction refined to 0.795 (1).

A Novel Choline Cotransporter Sequestration Compartment In Cholinergic Neurons Revealed By Selective Endosomal Ablation, Michael T. Ivy, Robert F. Newkirk, Yilun Wang, James G. Townsel

Biology Faculty Research

The sodium-dependent, high affinity choline transporter – choline cotransporter – (ChCoT, aka: cho-1, CHT1, CHT) undergoes constitutive and regulated trafficking between the plasma membrane and cytoplasmic compartments. The pathways and regulatory mechanisms of this trafficking are not well understood. We report herein studies involving selective endosomal ablation to further our understanding of the trafficking of the ChCoT. Selective ablation of early sorting and recycling endosomes resulted in a decrease of ∼75% of [3H]choline uptake and ∼70% of [3H]hemicholinium-3 binding. Western blot analysis showed that ablation produced a similar decrease in ChCoTs in the plasma membrane subcellular fraction. The time frame …

A Natural Missing Link Between Activated And Downhill Protein Folding Scenarios, Feng Liu, Caroline Maynard, Gregory E. Scott, Artem Melnykov, Kathleen B. Hall, Martin Gruebele

Chemistry and Biochemistry

We propose protein PTB1:4W as a good candidate for engineering into a downhill folder. PTB1:4W has a probe-dependent thermal unfolding curve and sub-millisecond T-jump relaxation kinetics on more than one time scale. Its refolding rate in denaturant is a non-linear function of denaturant concentration (curved chevron plot). Yet at high denaturant concentration its unfolding is probe-independent, and the folding kinetics can be fitted to a single exponential decay. The domain appears to fold via a mechanism between downhill folding and activated folding over several small barriers, and when denaturant is added, one of these barriers greatly increases and simplifies the …

Combined Single-Molecule Photon-Stamping Spectroscopy And Femtosecond Transient Absorption Spectroscopy Studies Of Interfacial Electron Transfer Dynamics, Lijun Guo, Yuanmin Wang, H. Peter Lu

Chemistry Faculty Publications

The inhomogeneous interfacial electron transfer (IET) dynamics of 9-phenyl-2,3,7-trihydroxy-6-fluorone (PF)-sensitized TiO2 nanoparticles (NPs) has been probed by a single-molecule photon-stamping technique as well as ensemble-averaged femtosecond transient absorption spectroscopy. The forward electron transfer (FET) time shows a broad distribution at the single-molecule level, indicating the inhomogeneous interactions and ET reactivity of the PF/TiO2 NP system. The broad distribution of the FET time is measured to be 0.4 ± 0.1 ps in the transient absorption and picoseconds to nanoseconds in the photon-stamping measurements. The charge recombination time, having a broad distribution at the single-molecule level, clearly shows a biexponential dynamic behavior …

Carboxysomal Carbonic Anhydrases: Structure And Role In Microbial Co2 Fixation, Gordon C. Cannon, Sabine Heinhorst, Cheryl A. Kerfeld

Faculty Publications

Cyanobacteria and some chemoautotrophic bacteria are able to grow in environments with limiting CO₂ concentrations by employing a CO₂-concentrating mechanism (CCM) that allows them to accumulate inorganic carbon in their cytoplasm to concentrations several orders of magnitude higher than that on the outside. The final step of this process takes place in polyhedral protein microcompartments known as carboxysomes, which contain the majority of the CO₂-fixing enzyme, RubisCO. The efficiency of CO₂ fixation by the sequestered RubisCO is enhanced by co-localization with a specialized carbonic anhydrase that catalyzes dehydration of the …

Magnetic Properties Of The Quasi-Two-Dimensional S=1/2 Heisenberg Antiferromagnet [Cu(Pyz)(2)(Hf2)]Pf6, E Cizmar, S A. Zvyagin, R Beyer, M Uhlarz, M Ozerov, Y Skourski, Jamie L. Manson, J A. Schlueter, J Wosnitza

Chemistry and Biochemistry Faculty Publications

We report on high-field magnetization, specific heat, and electron-spin-resonance (ESR) studies of the quasi-two-dimensional spin-1/2 Heisenberg antiferromagnet [Cu(pyz)(2)(HF2)]PF6. The frequency-field diagram of ESR modes below T-N=4.38 K is described in the frame of the mean-field theory, confirming a collinear magnetic structure with an easy-plane anisotropy. The obtained results allowed us to determine the anisotropy/exchange interaction ratio, A/J=0.003, and the upper limit for the interplane/intraplane exchange interaction ratio, J'/J=1/16. It is argued that despite the onset of three-dimensional long-range magnetic ordering the magnetic properties of this material (including high-magnetic-field magnetization and nonmonotonic field dependence of the Neel temperature) are strongly affected …

Spectrophotometric And Colorimetic Methodology To Detect And Quantify Hydrazide Based Chemotherapeutic Drugs, Ronald Bartzatt

Chemistry Faculty Publications

Pharmaceuticals having the hydrazide functional group are an important division within anti-tuberculosis, anti-parasitic, anti-cancer, and anti-radiation chemotherapeutics. This work presents a colorimetric methodology to detect and quantify hydrazide based pharmaceuticals. Processes for rapid spot test, qualitative colorimetric assay, and spectrophotometric quantitative assay are presented. The reagent 2,6-dichloroquinon-4-chloroimine (Gibb's reagent) is utilized to accomplish the various analytical objectives. The rapid spot test and qualitative colorimetric assay enables a detection of hydrazide drugs to a level of 0.0037 grams per milliliter. Quantitative spectrophotometric detection of hydrazide drugs is sensitive to a level of 128.2 micrograms permilliliter. The molar absorptivity () is calculated …

Effects Of Metal Compounds With Distinct Physicochemical Properties On Iron Homeostasis And Antibacterial Activity In The Lungs: Chromium And Vanadium, Mitchell D. Cohen, Maureen Sisco, Colleen Prophete, Kotaro Yoshida, Lung-Chi Chen, Judith T. Zelikoff, Jason Smee, Alvin A. Holder, Jacqueline Stormhuerner, Debbie C. Crans, Andrew J. Ghio

Faculty Publications

In situ reactions of metal ions or their compounds are important mechanisms by which particles alter lung immune responses. The authors hypothesized that major determinants of the immunomodulatory effect of any metal include its redox behavior/properties, oxidation state, and/or solubility, and that the toxicities arising from differences in physicochemical parameters are manifest, in part, via differential shifts in lung iron (Fe) homeostasis. To test the hypotheses, immunomodulatory potentials for both pentavalent vanadium (V(V); as soluble metavanadate or insoluble vanadium pentoxide) and hexavalent chromium (Cr(VI); as soluble sodium chromate or insoluble calcium chromate) were quantified in rats after inhalation (5 h/day …

Proton Disorder And The Dielectric Constant Of Type Ii Clathrate Hydrates, Steven W. Rick

Chemistry Faculty Publications

Computational studies are presented examining the degree of proton disorder in argon and molecular hydrogen sII clathrate hydrates. Results are presented using a variety of model potentials for the dielectric constant, the proton order parameter, and the molecular volume for the clathrate systems. The dielectric constant for the clathrate systems is found to be lower than the dielectric constant of ice in all models. The ratio of the clathrate to ice dielectric constant correlates well with the ratio of the densities, which is not the case for comparisons to the liquid, so that differences in the dielectric constants between ice …

[Diphenyldi(Pyrazol-1-Yl)Methane]Dinitratocobalt(Ii), Janet L. Shaw, Bruce C. Noll

Faculty Articles

In the title compound, [Co(NO₃)₂(C₁₉H₁₆N₄)], the diphenyldipyrazolylmethane ligand coordinates to Co^II in a bidentate fashion forming a six-membered ring with an approximate boat configuration. The mean planes of the two pyrazolyl rings are separated by an angle of 39.6 (2)°. The coordination at the Co^II center is best described as distorted octahedral with two NO₃^- anions serving as bidentate ligands for charge balance. The dihedral angle between the mean planes of the two nitrate rings is 85.0 (1)° and that between the mean planes of the …

Microscopic Formulation Of The Zimm-Bragg Model For The Helix-Coil Transition, A. V. Badasyan, A. Giacometti, Y. S. Mamasakhlisov, V. F. Morozov, Albert S. Benight

Chemistry Faculty Publications and Presentations

A microscopic spin model is proposed for the phenomenological Zimm-Bragg model for the helix-coil transition in biopolymers. This model is shown to provide the same thermophysical properties of the original Zimm-Bragg model and it allows a very convenient framework to compute statistical quantities. Physical origins of this spin model are made transparent by an exact mapping into a one-dimensional Ising model with an external field. However, the dependence on temperature of the reduced external field turns out to differ from the standard one-dimensional Ising model and hence it gives rise to different thermophysical properties, despite the exact mapping connecting them. …

An In Vitro Spectroscopic Analysis To Determine Whether Para-Chloroaniline Is Produced From Mixing Sodium Hypochlorite And Chlorhexidine, John Thomas, Daniel S. Sem

Chemistry Faculty Research and Publications

Introduction: The purpose of this in vitro study was to determine whether para-chloroaniline (PCA) is formed through the reaction of mixing sodium hypochlorite (NaOCl) and chlorhexidine (CHX).

Methods: Initially, commercially available samples of chlorhexidine acetate (CHXa) and PCA were analyzed with ¹H nuclear magnetic resonance (NMR) spectroscopy. Two solutions, NaOCl and CHXa, were warmed to 37ºC, and when mixed they produced a brown precipitate. This precipitate was separated in half, and pure PCA was added to 1 of the samples for comparison before they were each analyzed with ¹H NMR spectroscopy.

Results: The peaks in …

Development Of Pharmacophore And Comfa Study Of Rigid And Flexible Sigma 2 Receptor Ligands, Hemantbhai Patel

Theses

In the present study a pharmacophore and CoMFA model was derived for sigma 2 (62) receptors by using Sybyl 7.2 Software Package. The CoMFA studies used 22 bioactive molecules as a training set and 4 molecules as a test set for the o2 receptor ligands. The geometries and electrostatic charges of all molecules were calculated using various levels of calculations. The geometry optimization and electrostatic charges of all 26 molecules were performed by using semiemprical AM1, ab initio HF/6-31G* and density functional B3LYP/6-31G* in Gaussian 98. The pharmacophore model was derived by using Distance Comparisions (DISCOtech) from 4 partially to …

Poly[[(Μ-2,2'-Bipyrimidine-Κ4N1,N1':N3,N3')(Μ-Sulfato-Κ2O:O')Zinc(Ii)] Monohydrate], Aaron Oxendine, Jennifer Kelley, Leroy Peterson Jr., Mark D. Smith, Hans-Conrad Zur Loye

Faculty Publications

In the title compound, {[Zn(SO₄)(C₈H₆N₄)]·H₂O}_n, the Zn^II atom is in a distorted octahedral environment. The Zn^II atoms are bridged by both 2,2'-bipyrimidine and sulfate ligands, thus forming a three-dimensional polymeric metal-organic solid that contains uncoordinated water molecules in the interstitial space. O-HO hydrogen bonding consolidates the crystal structure.

Identification And Quantitation Of 3,4-Methylenedioxy-N-Methylamphetamine (Mdma, Ecstasy) In Human Urine By 1h Nmr Spectroscopy. Application To Five Cases Of Intoxication, Jonathan Liu, John Decatur, Gloria Proni, Elise Champeil

Publications and Research

Identification of 3,4-methylenedioxy-N-methylamphetamine (MDMA, ecstasy) in five cases of intoxication using nuclear magnetic resonance (NMR) spectroscopy of human urine is reported. A new water suppression technique PURGE (Presaturation Utilizing Relaxation Gradients and Echoes) was used. A calibration curve was obtained using spiked samples. The method gave a linear response (correlation coefficient of 0.992) over the range 0.01–1 mg/mL. Subsequently, quantitation of the amount of MDMA present in the samples was performed. The benefit and reliability of NMR investigations of human urine for cases of intoxication with MDMA are discussed.

Conformations Of A Model Protein Revealed By An Aggregating Cuᴵᴵ Porphyrin: Sensing The Difference, G. De Luca, A. Romeo, L. M. Scolaro, Robert F. Pasternack

Chemistry & Biochemistry Faculty Works

Aggregated t-CuP binds to poly-L-glutamate through supramolecular interactions, revealing itself to be an extremely sensitive probe for the major conformations of the polymeric scaffold.

A Dielectric Affinity Microbiosensor, Xian Huang, Siqi Li, Jerome S. Schultz, Qian Wang, Qiao Lin

Faculty Publications

We present an affinity biosensing approach that exploits changes in dielectric properties of a polymer due to its specific, reversible binding with an analyte. The approach is demonstrated using a microsensor comprising a pair of thin-film capacitive electrodes sandwiching a solution of poly(acrylamide-ran-3-acrylamidophenylboronic acid), a synthetic polymer with specific affinity to glucose. Binding with glucose induces changes in the permittivity of the polymer, which can be measured capacitively for specific glucose detection, as confirmed by experimental results at physiologically relevant concentrations. The dielectric affinity biosensing approach holds the potential for practical applications such as long-term continuous glucose monitoring.

Construction, Figures Of Merit And Testing Of A Single-Cell Fluorescence Excitation Spectroscopy System, Laura S. Hill, Tammi L. Richardson, Louisa T.M. Profeta, Timothy J. Shaw, Christopher J. Hintz, Benjamin S. Twining, Evelyn Lawrenz, Micheal L. Myrick

Faculty Publications

Characterization of phytoplankton community composition is critical to understanding the ecology and biogeochemistry of the oceans. One approach to taxonomic characterization takes advantage of differing pigmentation between algal taxa and thus differences in fluorescence excitation spectra. Analyses of bulk water samples, however, may be confounded by interference from chromophoric dissolved organic matter or suspended particulate matter. Here, we describe an instrument that uses a laser trap based on a Nikon TE2000-U microscope to position individual phytoplankton cells for confocal fluorescence excitation spectroscopy, thus avoiding interference from the surrounding medium. Quantitative measurements of optical power give data in the form of …

Phase Transition Enthalpy Measurements Of Organic And Organometallic Compounds. Sublimation, Vaporization And Fusion Enthalpies From 1880 To 2010, William Acree, James Chickos

Chemistry & Biochemistry Faculty Works

No abstract provided.

Homocystamides Promote Free-Radical And Oxidative Damage To Proteins, Martha Sibrian-Vazquez, Jorge O. Escobedo, Soojin Lim, George K. Samoei, Robert M. Strongin

Chemistry Faculty Publications and Presentations

Elevated levels of homocysteine are associated with several major diseases. However, it is not clear whether homocysteine is a marker or a causative agent. The majority (ca. 80%) of the homocysteine present in humans is protein bound. The study of the posttranslational modification of proteins by homocysteine and its cyclic congener, homocysteine thiolactone, is emerging as an area of great current interest for unraveling the ongoing “mediator/marker controversy” [Jacobsen DW (2009) Clin Chem 55:1–2]. Interestingly, many of the pathologies associated with homocysteine are also linked to oxidative stress. In the current study, chemical evidence for a causal relationship between homocysteine-bound …

Role Of Small Oligomers On The Amyloidogenic Aggregation Free-Energy Landscape, Xianglan He, Jason T. Giurleo, David Talaga

Department of Chemistry and Biochemistry Faculty Scholarship and Creative Works

We combine atomic-force-microscopy particle-size-distribution measurements with earlier measurements on 1-anilino-8-naphthalene sulfonate, thioflavin T, and dynamic light scattering to develop a quantitative kinetic model for the aggregation of β-lactoglobulin into amyloid. We directly compare our simulations to the population distributions provided by dynamic light scattering and atomic force microscopy. We combine species in the simulation according to structural type for comparison with fluorescence fingerprint results. The kinetic model of amyloidogenesis leads to an aggregation free-energy landscape. We define the roles of and propose a classification scheme for different oligomeric species based on their location in the aggregation free-energy landscape. We relate …