Chemistry Commons^™

Variable Van Der Waals Radii Derived From A Hybrid Gaussian Charge Distribution Model For Continuum-Solvent Electrostatic Calculations, Renlong Ye, Xuemei Nie, Chung Wong, Xuedong Gong, Yan Wang, Thomas Heine, Baojing Zhou

Chemistry & Biochemistry Faculty Works

We introduce a hybrid Gaussian charge distribution model (HGM) that partitions the molecular electron density into overlapping spherical atomic domains. The semi-empirical HGM consists of atom-centered spherical Gaussian functions and discrete point charges, which are optimized to reproduce the electrostatic potential on the molecular surface as well as the number of electrons in atom-centered and certain off-atom-centered spherical regions as closely as possible. In contrast, our previous Gaussian charge distribution model [J. Chem. Phys. 129, 014509 (2008)] contained only spherical Gaussian functions and was not required to reproduce the number of electrons in off-atom-centered regions. Variable van der Waals (vdW) …

Microwave Measurements Of The Tropolone-Formic Acid Doubly Hydrogen Bonded Dimer, Aaron M. Pejlovas, Agapito Serrato, Wei Lin, Stephen G. Kukolich

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

The microwave spectrum was measured for the doubly hydrogen bonded dimer formed between tropolone and formic acid. The predicted symmetry of this dimer was C2v(M), and it was expected that the concerted proton tunneling motion would be observed. After measuring 25 a- and b-type rotational transitions, no splittings which could be associated with a concerted double proton tunneling motion were observed. The calculated barrier to the proton tunneling motion is near 15 000 cm-1, which would likely make the tunneling frequencies too small to observe in the microwave spectra. The rotational and centrifugal distortion constants determined from the measured transitions …

Recent Advances In Development And Applications Of The Mixed Quantum/Classical Theory For Inelastic Scattering, Dmitri Babikov, Alexander Semenov

Chemistry Faculty Research and Publications

A mixed quantum/classical approach to inelastic scattering (MQCT) is developed in which the relative motion of two collision partners is treated classically, and the rotational and vibrational motion of each molecule is treated quantum mechanically. The cases of molecule + atom and molecule + molecule are considered including diatomics, symmetric-top rotors, and asymmetric-top rotor molecules. Phase information is taken into consideration, permitting calculations of elastic and inelastic, total and differential cross sections for excitation and quenching. The method is numerically efficient and intrinsically parallel. The scaling law of MQCT is favorable, which enables calculations at high collision energies and for …

Rapid Access To Conformationally-Constrained Oxatricycles Via Ugi-Smiles Couplings, Bree Richey, Katelynn M. Mason, Michael S. Meyers, Sarah Luesse

SIUE Faculty Research, Scholarship, and Creative Activity

Use of allylamine and substituted 2-furaldehydes as components in Ugi-Smiles couplings of 2-nitrophenol provide ready access to N-aryl epoxyisoindolines. These adducts form via a dual event involving the Ugi-Smiles multicomponent reaction and an intramolecular Diels-Alder cycloaddition with the furan ring.

Chem & Biochem Again Shows Program Excellence: American Chemical Society Approves Department For 40th Year, Alixandria Reiner

Andrews Agenda: Campus News

No abstract provided.

Potential Regulation Of Deadly Water-Borne Shigella Bacteria Pathogenesis Through The Shigella Infection Protein Spa47, Jamie Kingsford

Research on Capitol Hill

• Shigella is a gram-negative, bacterial pathogen typically found in contaminated water sources.
• Each year, Shigella is responsible for over 90 million infections and 100,000 deaths stemming from symptoms of severe dysentery, fever, nausea and vomiting.
• A needle-like apparatus found on the surface of Shigella allows the bacterium to infect host cells.
• Each needle-apparatus has an associated ATPase, a protein that can hydrolyze ATP into ADP and P_i.
• The Shigella needle-apparatus ATPase Spa47 is predicted to provide the energy for infection.
• Spa47 has been shown to be essential for infection – without Spa47, no infection will occur.
• We were …

Purification Of Synthetic Oligonucleotides, Shiyue Fang

Michigan Tech Patents

This invention provides a method for purifying synthetic oligonucleotides comprising capping, polymerizing and separating any failure sequences produced during oligonucleotide synthesis. The invention also provides a method for purifying synthetic oligonucleotides comprising reacting a full length oligonucleotide with a compound to attach a polymerizable functional group to an end of the full length oligonucleotide, polymerizing the full length oligonucleotides and removing the failure sequences, and recovering the full length oligonucleotides. The invention also provides novel capping agents having a polymerizable functional group, and kits comprising at least one composition of the present invention.

Effect Of Base-Pairing Partner On The Thermodynamic Stability Of The Diastereomeric Spiroiminodihydantoin Lesion, Brian Gruessner, Megana Dwarakanath, Elizabeth Stewart, Yoon Bae, Elizabeth R. Jamieson

Chemistry: Faculty Publications

Oxidation of guanine by reactive oxygen species and high valent metals produces damaging DNA base lesions like 8-oxo-7,8-dihydroguanine (8-oxoG). 8-oxoG can be further oxidized to form the spiroiminodihydantoin (Sp) lesion, which is even more mutagenic. DNA polymerases preferentially incorporate purines opposite the Sp lesion, and DNA glycosylases excise the Sp lesion from the duplex, although the rate of repair is different for the two Sp diastereomers. To further understand the biological processing of the Sp lesion, differential scanning calorimetry (DSC) studies were performed on a series of 15-mer DNA duplexes. The thermal and thermodynamic stability of each of the Sp …

The Dual Regulatory Role Of Amino Acids Leu480 And Gln481 Of Prothrombin, Joesph R. Wiencek, Jamila Hirbawi, Vivien C. Yee, Michael Kalafatis

Chemistry Faculty Publications

Prothrombin (FII) is activated to α-thrombin (IIa) by prothrombinase. Prothrombinase is composed of a catalytic subunit, factor Xa (fXa), and a regulatory subunit, factor Va (fVa), assembled on a membrane surface in the presence of divalent metal ions. We constructed, expressed, and purified several mutated recombinant FII (rFII) molecules within the previously determined fVa-dependent binding site for fXa (amino acid region 473–487 of FII). rFII molecules bearing overlapping deletions within this significant region first established the minimal stretch of amino acids required for the fVa-dependent recognition exosite for fXa in prothrombinase within the amino acid sequence Ser⁴⁷⁸–Val^{479 …}

Identification Of Critical Paraoxonase 1 Residues Involved In High Density Lipoprotein Interaction, Xiaodong Gu, Ying Huang, Bruce S. Levison, Gary Gerstenecker, Anthony J. Didonato, Leah B. Hazen, Joonsue Lee, Valentin Gogonea, Joseph A. Didonato, Stanley L. Hazen

Chemistry Faculty Publications

Paraoxonase 1 (PON1) is a high density lipoprotein (HDL)-associated protein with atherosclerosis-protective and systemic anti-oxidant functions. We recently showed that PON1, myeloperoxidase, and HDL bind to one another in vivo forming a functional ternary complex (Huang, Y., Wu, Z., Riwanto, M., Gao, S., Levison, B. S., Gu, X., Fu, X., Wagner, M. A., Besler, C., Gerstenecker, G., Zhang, R., Li, X. M., Didonato, A. J., Gogonea, V., Tang, W. H., et al. (2013) J. Clin. Invest. 123, 3815–3828). However, specific residues on PON1 involved in the HDL-PON1 interaction remain unclear. Unambiguous identification of protein residues involved in docking interactions to …

Hyperfine Rather Than Spin Splittings Dominate The Fine Structure Of The B 4Σ-–X 4Σ- Bands Of Aic, Dennis J. Clouthier, Aimable Kalume

Chemistry Faculty Publications

Laser-induced fluorescence and wavelength resolved emission spectra of the B ⁴Σ⁻–X ⁴Σ⁻ band system of the gas phase cold aluminum carbide free radical have been obtained using the pulsed discharge jet technique. The radical was produced by electron bombardment of a precursor mixture of trimethylaluminum in high pressure argon. High resolution spectra show that each rotational line of the 0-0 and 1-1 bands of AlC is split into at least three components, with very similar splittings and intensities in both the P- and R-branches. The observed structure was reproduced by assuming b …

Characterization Of 1, 4, 7-Trithiacyclononane, [9]Anes3 As A Potential Toxic Heavy Metal Chelator, Nahid Bakhtari

Student Theses and Dissertations

Toxic heavy metal poisoning with metals including lead, mercury, and cadmium, whether in the environment or through ingestion, remains a persistent problem. Remediation of metal contamination and poisoning has generally been treated with chelating agents that bind metals, rendering them inert, and allow for easier removal. Chelation involves the formation of two or more separate coordinate covalent bonds between a polydentate ligand and a single central atom. However, chelators are not without side effects. Due to the similar size of metal ions and lack of specificity of ligands, chelators can also remove beneficial metals like iron and zinc from the …

Synthesis, Characterization, And Thin-Film Properties Of 6-Oxoverdazyl Polymers Prepared By Ring-Opening Metathesis Polymerization, Joseph A. Paquette, Sabastine Ezugwu, Vishal Yadav, Giovanni Fanchini, Joe Gilroy

Chemistry Publications

Redox-active 6-oxoverdazyl polymers were synthesized via ring-opening metathesis polymerization (ROMP) and their solution, bulk, and thin-film properties investigated. Detailed studies of the ROMP method employed confirmed that stable radical polymers with controlled molecular weights and narrow molecular weight distributions (Ð < 1.2) were produced. Thermal gravimetric analysis of a representative example of the title polymers demonstrated stability up to 190 °C, while differential scanning calorimetry studies revealed a glass transition temperature of 152 °C. Comparison of the spectra of 6-oxoverdazyl monomer 12 and polymer 13, including FT-IR, UV-vis absorption, and electron paramagnetic resonance spectroscopy, was used to confirm the tolerance of the ROMP mechanism for the 6-oxoverdazyl radical both qualitatively and quantitatively. Cyclic voltammetry studies demonstrated the ambipolar redox properties of polymer 13 (E_1/2,ox = 0.25 and E_1/2,red = −1.35 V relative to ferrocene/ferrocenium), which were …

Orally Active And Selective Tubulin Inhibitors As Anti-Trypanosome Agents, Vishal Nanavaty, Rati Lama, Ranjodh Sandhu, Bo Zhong, Daniel Kulman, Viharika Bobba, Anran Zhao, Bibo Li, Bin Su

Chemistry Faculty Publications

Objectives: There is an urgent need to develop a safe, effective, orally active, and inexpensive therapy for African trypanosomiasis due to the drawbacks of current drugs. Selective tubulin inhibitors have the potential to be promising drug candidates for the treatment of this disease, which is based on the tubulin protein structural difference between mammalian and trypanosome cells. We propose to identify novel tubulin inhibitors from a compound library developed based on the lead compounds that selectively target trypanosomiasis. Methods: We used Trypanosoma brucei brucei as the parasite model, and human normal kidney cells and mouse microphage cells as the host …

Efficient Bimolecular Mechanism Of Photochemical Hydrogen Production Using Halogenated Boron-Dipyrromethene (Bodipy) Dyes And A Bis(Dimethylglyoxime) Cobalt(Iii) Complex, Randy Pat Sabatini, Brian M. Lindley, Theresa M. Mccormick, Theodore Lazarides, William Brennessel, David W. Mccamant, Richard Eisenberg

Chemistry Faculty Publications and Presentations

A series of Boron-­dipyrromethene (Bodipy) dyes were used as photosensitizers for photochemical hydrogen production in conjunction with [Co^III(dmgH)2pyCl] (where dmgH = dimethylglyoximate, py = pyridine) as the catalyst and triethanolamine (TEOA) as the sacrificial electron donor. The Bodipy dyes are fully characterized by electrochemistry, x-­‐ray crystallography, quantum chemistry calculations, femtosecond transient absorption and time-­‐resolved fluorescence, as well as in long-­‐term hydrogen production assays. Consistent with other recent reports, only systems containing halogenated chromophores were active for hydrogen production, as the long-­‐lived triplet state is necessary for efficient bimolecular electron transfer. Here, it is shown that the photostability of …

Structural Insights Into High Density Lipoprotein: Old Models And New Facts, Valentin Gogonea

Chemistry Faculty Publications

The physiological link between circulating high density lipoprotein (HDL) levels and cardiovascular disease is well-documented, albeit its intricacies are not well-understood. An improved appreciation of HDL function and overall role in vascular health and disease requires at its foundation a better understanding of the lipoprotein's molecular structure, its formation, and its process of maturation through interactions with various plasma enzymes and cell receptors that intervene along the pathway of reverse cholesterol transport. This review focuses on summarizing recent developments in the field of lipid free apoA-I and HDL structure, with emphasis on new insights revealed by newly published nascent and …

Building A Better Halide Receptor: Optimum Choice Of Spacer, Binding Unit, And Halosubstitution, Binod Nepal, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Quantum calculations are used to measure the binding of halides to a number of bipodal dicationic receptors, constructed as a pair of binding units separated by a spacer group. A number of variations are studied. A H atom on each binding unit (imidazolium or triazolium) is replaced by Br or I. Benzene, thiophene, carbazole, and dimethylnaphthalene are considered as spacer groups. Each receptor is paired with halides F-, Cl-, Br-, and I-. I-substitution on the binding unit yields a large enhancement of binding, as much as 13 orders of magnitude; a much smaller increase occurs for bromosubstitution. Imidazolium is a …

Adsorption And Unfolding Of A Single Protein Triggers Nanoparticle Aggregation, Lydia Kisley

Faculty Scholarship

The response of living systems to nanoparticles is thought to depend on the protein corona, which forms shortly after exposure to physiological fluids and which is linked to a wide array of pathophysiologies. A mechanistic understanding of the dynamic interaction between proteins and nanoparticles and thus the biological fate of nanoparticles and associated proteins is, however, often missing mainly due to the inadequacies in current ensemble experimental approaches. Through the application of a variety of single molecule and single particle spectroscopic techniques in combination with ensemble level characterization tools, we identified different interaction pathways between gold nanorods and bovine serum …

A Computational And Experimental Study Of Thieno[3,4-B]Thiophene As A Proaromatic Π-Bridge In Dye-Sensitized Solar Cells, Phillip Brogdon, Fabrizio Giordano, George A. Puneky, Amala Dass, Shaik M. Zakeeruddin, Mohammad Khaja Nazeeruddin, Michael Grätzel, Gregory S. Tschumper, Jared H. Delcamp

Chemistry Faculty Research & Creative Works

Four D-π-A dyes (D=donor, A=acceptor) based on a 3,4-thienothiophene π-bridge were synthesized for use in dye-sensitized solar cells (DSCs). The proaromatic building block 3,4-thienothiophene is incorporated to stabilize dye excited-state oxidation potentials. This lowering of the excited-state energy levels allows for deeper absorption into the NIR region with relatively low molecular weight dyes. The influence of proaromatic functionality is probed through a computational analysis of optimized bond lengths and nucleus independent chemical shifts (NICS) for both the ground- and excited- states. To avoid a necessary lowering of the TiO₂ semiconductor conduction band (CB) to promote efficient dye-TiO₂ electron …

Phase Transition Enthalpy Measurements Of Organic And Organometallic Compounds. Sublimation, Vaporization And Fusion Enthalpies From 1880 To 2015. Part 1. C1 − C10, William Acree, James Chickos

Chemistry & Biochemistry Faculty Works

A compendium of phase change enthalpies published in 2010 is updated to include the period 1880–2015. Phase change enthalpies including fusion, vaporization, and sublimation enthalpies are included for organic, organometallic, and a few inorganic compounds. Part 1 of this compendium includes organic compounds from C1 to C10. Part 2 of this compendium, to be published separately, will include organic and organometallic compounds from C11 to C192. Sufficient data are presently available to permit thermodynamic cycles to be constructed as an independent means of evaluating the reliability of the data. Temperature adjustments of phase change enthalpies from the temperature of measurement …

Kdac8 With High Basal Velocity Is Not Activated By N-Acetylthioureas, Tasha B. Toro, Subramanya Pingali, Thao P. Nguyen, Destane S. Garrett, Kyra A. Dodson, Kyara A. Nichols, Rashad A. Haynes, Florastina Payton-Stewart, Terry J. Watt

Faculty and Staff Publications

Lysine deacetylases (KDACs) are enzymes that reverse the post-translational modification of lysine acetylation. Recently, a series of N-acetylthioureas were synthesized and reported to enhance the activity of KDAC8 with a fluorogenic substrate. To determine if the activation was general, we synthesized three of the most potent N-acetylthioureas and measured their effect with peptide substrates and the fluorogenic substrate under multiple reaction conditions and utilizing two enzyme purification approaches. No activation was observed for any of the three N-acetylthioureas under any assayed conditions. Further characteriza- tion of KDAC8 kinetics with the fluorogenic substrate yielded a k cat /K M of 164 …

Random Number Simulations Reveal How Random Noise Affects The Measurements And Graphical Portrayals Of Self-Assessed Competency, Edward Nuhfer, Christopher Cogan, Steven Fleisher, Eric Gaze, Karl Wirth

Numeracy

Self-assessment measures of competency are blends of an authentic self-assessment signal that researchers seek to measure and random disorder or "noise" that accompanies that signal. In this study, we use random number simulations to explore how random noise affects critical aspects of self-assessment investigations: reliability, correlation, critical sample size, and the graphical representations of self-assessment data. We show that graphical conventions common in the self-assessment literature introduce artifacts that invite misinterpretation. Troublesome conventions include: (y minus x) vs. (x) scatterplots; (y minus x) vs. (x) column graphs aggregated as quantiles; line …

Pore Structure And Synergy In Antimicrobial Peptides Of The Magainin Family, Almudena Pino-Angeles, John M. Leveritt Iii, Themis Lazaridis

Publications and Research

Magainin 2 and PGLa are among the best-studied cationic antimicrobial peptides. They bind preferentially to negatively charged membranes and apparently cause their disruption by the formation of transmembrane pores, whose detailed structure is still unclear. Here we report the results of 5–9 μs all-atom molecular dynamics simulations starting from tetrameric transmembrane helical bundles of these two peptides, as well as their stoichiometric mixture, and the analog MG-H2 in DMPC or 3:1 DMPC/DMPG membranes. The simulations produce pore structures that appear converged, although some effect of the starting peptide arrangement (parallel vs. antiparallel) is still observed on this timescale. The peptides …

Fortilin Potentiates The Peroxidase Activity Of Peroxiredoxin-1 And Protects Against Alcohol-Induced Liver Damage In Mice, Owen M. Mcdougal

Chemistry and Biochemistry Faculty Publications and Presentations

Fortilin, a pro-survival molecule, inhibits p53-induced apoptosis by binding to the sequence-specific DNA-binding domain of the tumor suppressor protein and preventing it from transcriptionally activating Bax. Intriguingly, fortilin protects cells against ROS-induced cell death, independent of p53. The signaling pathway through which fortilin protects cells against ROS-induced cell death, however, is unknown. Here we report that fortilin physically interacts with the antioxidant enzyme peroxiredoxin-1 (PRX1), protects it from proteasome-mediated degradation, and keeps it enzymatically active by blocking its deactivating phosphorylation by Mst1, a serine/threonine kinase. At the whole animal level, the liver-specific overexpression of fortilin reduced PRX1 phosphorylation in the …

Reactivity Measurement In Estimation Of Benzoquinone And Benzoquinone Derivatives’ Allergenicity, Wilbes Mbiya, Ita Chipinda, Reuben H. Simoyi, Paul D. Siegel

Chemistry Faculty Publications and Presentations

Benzoquinone (BQ) and benzoquinone derivatives (BQD) are used in the production of dyes and cosmetics. While BQ, an extreme skin sensitizer, is an electrophile known to covalently modify proteins via Michael Addition (MA) reaction whilst halogen substituted BQD undergo nucleophilic vinylic substitution (SNV) mechanism onto amine and thiol moieties on proteins, the allergenic effects of adding substituents on BQ have not been reported. The effects of inserting substituents on the BQ ring has not been studied in animal assays. However, mandated reduction/elimination of animals used in cosmetics testing in Europe has led to an increased need for alternatives for the …

The Effects Of Rain On Elemental Transport In Soils, Laura Schoenfeld

STAR Program Research Presentations

Mini Landscape Evolution Observatory (miniLEO) is a model landscape slope composed of granular basalt used to conduct small scale experiments to more clearly understand how elemental transport occurs during simulated rain events. For this experiment, rain events occurred three times a day in two hour increments at a rate of 30 mm/hr for 14 days to determine if exchangeable ions and target elements dissolve over time. An auto sampler collected the waterseepage every half hour at the bottom of the slope of miniLEO. Each seepage sample was tested or the amount of elements present in solution using ion chromatography and …

Probing The Transport Properties Of Chemically-Doped Single-Walled Carbon Nantotube Polymer Composites, Tammy Pheuphong, Tamara El-Hayek, Jeffrey Blackburn, Andrew Ferguson

STAR Program Research Presentations

Thermoelectric (TE) materials are used to convert waste heat into electrical power. Semiconducting single-walled carbon nanotubes (s-SWCNT) have great potential to be used in thermoelectric devices, either on their own or in composites with conducting polymers. Certain polymers can selectively extract s-SWCNT from raw carbon nanotube soot (containing impurities such as metallic SWCNT, amorphous carbon, metal catalysts particles), but most of these polymers (e.g. polyfluorenes) are electrical insulators, rendering them inefficient in TE nanocomposites. On the other hand, conducting polymers, such as poly(3,4-ethylenedioxythiophene) polystyrene sulfonate (PEDOT:PSS), have been used in efficient TE nanocomposites, but have never been rationally designed with …

Synthesis Of Porous Manganese Oxides With Unsaturated Alcohols And Subsequent Characterization And Catalytic Activity, Chrismary De La Cruz

Chemistry Honors Papers

Porous manganese oxides have been synthesized using unsaturated alcohols (allyl alcohol and propargyl alcohol) as reducing agents in a redox reaction with KMnO4 in the presence of butyric acid. Materials have an approximate MnO2 stoichiometry and surface areas of 280 m2/g for materials made with allyl alcohol and 260 m2/g for those made with propargyl alcohol. Materials also showed a good deal of monodispersity, with the materials made from allyl alcohol having an average diameter of 156 nm± 61 nm. The materials made with propargyl alcohol had an average diameter of 143 nm ±49 nm.

Previously, highly monodisperse porous spheres …

Effect Of Spalled Particles Thermal Degradation On A Hypersonic Flow Field Environment, Raghava S. C. Davuluri, Huaibao Zhang, Alexandre Martin

Mechanical Engineering Faculty Publications

Two-way coupling is performed between a spallation code and a hypersonic aerothermodynamics CFD solver to evaluate the effect of spalled particles on the flow field. Time accurate solutions are computed in argon and air flow fields. A single particle simulations and multiple particles simulations are performed and studied. The results show that the carbon vapor released by spalled particles tend to change the composition of the flow field, particularly the upstream region of the shock.

Methane Emissions As Energy Reservoir: Context, Scope, Causes And Mitigation Strategies, Xiaoli Chai, David J. Tonjes, Devinder Mahajan

Technology & Society Faculty Publications

Methane (CH4) is now considered a bridge fuel between present fossil (carbon) economy and desired renewables and this energy molecule is projected to play an important role in the global energy mix well beyond 2035. The atmospheric warming potential of CH4 is 28-36 times, when averaged over a 100-year period, that of carbon dioxide (CO2) and this necessitates a close scrutiny of global CH4 emissions inventory. As the second most abundant greenhouse gas (GHG), the annual global CH4 emissions were 645 million metric tons (MMT), accounting for 14.3% of the global anthropogenic GHG emissions. Of this, five key anthropogenic sources: …