Chemistry Commons^™

Purine-Based Triazoles, Prakash Reddy, Nanditha G. Nair, Mark A. Smith, Wataru Kudo

Chemistry Faculty Research & Creative Works

A pharmaceutical composition for inhibiting at least protein kinase in a cell of a subject includes a purine based triazole.

Mechanism Of N -Hydroxylation Catalyzed By Flavin-Dependent Monooxygenases, Somayesadat Badieyan, Robert D. Bach, Pablo Sobrado

Chemistry Faculty Research & Creative Works

Aspergillus fumigatus siderophore (SidA), a member of class B flavin-dependent monooxygenases, was selected as a model system to investigate the hydroxylation mechanism of heteroatom-containing molecules by this group of enzymes. SidA selectively hydroxylates ornithine to produce N5-hydroxyornithine. However, SidA is also able to hydroxylate lysine with lower efficiency. In this study, the hydroxylation mechanism and substrate selectivity of SidA were systematically studied using DFT calculations. The data show that the hydroxylation reaction is initiated by homolytic cleavage of the O-O bond in the C4a-hydroperoxyflavin intermediate, resulting in the formation of an internal hydrogen-bonded hydroxyl radical (HO•). As the HO• moves …

State-To-State Reaction Dynamics Of ¹⁸O+³²O₂ Studied By A Time-Dependent Quantum Wavepacket Method, Wenbo Xie, Lan Liu, Zhigang Sun, Hua Guo, Richard Dawes

Chemistry Faculty Research & Creative Works

The title isotope exchange reaction was studied by converged time-dependent wave packet calculations, where an efficient 4th order split operator was applied to propagate the initial wave packet. State-to-state differential and integral cross sections up to the collision energy of 0.35 eV were obtained with ³²O₂ in the hypothetical j₀ = 0 state. It is discovered that the differential cross sections are largely forward biased in the studied collision energy range, due to the fact that there is a considerable part of the reaction occurring with large impact parameter and short lifetime relative to the rotational period …

Cappack Devices For Enhanced Qnmr Measurements In 1H Nmr Spectroscopy, Lingyu Chi

Masters Theses

"Quantitative NMR analyses can be improved by adding well-defined external references for measuring sample properties on absolute scales. Special Capillary-tube Package (CapPack) devices were invented that provide in situ information (e.g., temperature, pH, pressure, integration, chemical shift, lock, etc.) about a sample with spectral imprimaturs. A new microscale glass-sealing technique produced CapPack devices that can survive high temperatures and pressures in harsh environments. Two CapPack devices are discussed: (1) Gradient CapPack-- a device for examining the irradiation bandwidth of solvent-suppression pulse sequences; (2) T₁ CapPack - a device for examining the T₁ robustness of solvent-suppression pulse sequences. A …

Nmr T₁ Studies Of Colloidal Unimolecular Polymer (Cup) Surface Water, Yousef Abobaker Dawib

Doctoral Dissertations

"This dissertation is subdivided into three topics: Experimental study of colloidal unimolecular polymer (CUP) hydration; probing of polymer chain dynamics by ¹³C solid state NMR technique; and the anticorrosive effect of 5-mercapto-1, 3, 4-thiadiazole-2(3H)-thione (MTT) derivatives.

The states of water in colloidal unimolecular polymer system were investigated by low field proton NMR. Bound and free water fractions were determined using spin-lattice relaxation measurements. A model equation was used to analyze the inversion recovery data.

The proton cross polarization and the pulse sequence for total spinning sideband suppression CP-TOSS NMR method were developed to determine the chain mobility of polymers …

Synthesis And Electrochemical Studies Of Novel Ionic Liquid Based Electrolytes, Avinash Raju Vadapalli

Doctoral Dissertations

"Room temperature ionic liquids (RTILs) have received substantial interest as nonaqueous electrolytes in lithium ion- and metal-air batteries in recent years due to their low volatility, non-flammability, wide liquid range, and thermal stability characteristics. Towards developing a new generation of high specific energy lithium ion batteries, a series of imidazolium and pyrrolidinium based ionic liquids were synthesized and explored as nonaqueous electrolytes in lithium-, lithium ion-, and lithium-air batteries. Pyrrolidinium-TFSI based ionic liquids have wide electrochemical stability (5.7 - 6.2 V vs Li/Li⁺); however, they show limited thermal stabilities and lithium cell discharge characteristics. TFSI-based ionic liquids are …

Palladium-Catalyzed Annulation Of 9-Halophenanthrenes With Alkynes: Synthesis, Structural Analysis, And Properties Of Acephenanthrylene-Based Derivatives, En Chih Liu, Min-Kuan Chen, Jen-Yi Li, Yao-Ting Wu

Chemistry Faculty Research & Creative Works

The palladium-catalyzed annulation of 9-bromoand 9-chlorophenanthrenes with alkynes gave 4,5-disubstituted acephenanthrylenes in yields of 58–95% (9 examples). Asymmetric alkynes, such as 1-phenyl-1-propyne, 1-phenyl- 1-hexyne, and 1-cyclopropyl-2-phenylethyne, regioselectively form (cyclo)alkyl-substituted products, following the regular rule that governs the carbopalladation of alkynes. This synthetic protocol can also be utilized in annulations with several p-extended bromoarenes, such as 7-5] helicene, 5- 4] helicene, 9-bromoanthracene, 3-bromoperylene, and 3-bromofluoranthene, to give the corresponding annulated products in moderate to good yields (51–86 %; 6 examples). Similarly, bromocorannulene produced highly curved 1,2-disubstituted cyclopentacorannulenes. Reactions of 6,12-dibromochrysene and 4,7-4] helicene with di(4-tolyl) ethyne provided the twofold annulated products …

Palladium-Catalyzed Reaction Of Haloarenes With Diarylethynes: Synthesis, Structural Analysis, And Properties Of Methylene-Bridged Arenes, Che-Wei Lee, En Chih Liu, Yao-Ting Wu

Chemistry Faculty Research & Creative Works

Fluorenes and methylene-bridged polyarenes were easily and efficiently synthesized from haloarenes (or aryl triflates) and diarylethynes by a one-pot, two-step procedure. This protocol involves the palladium-catalyzed cycloisomerization and a subsequent base-mediated retro-aldol condensation. A major advantage is that the starting materials need not have ortho functional groups to complete the annulation. The backbone of the designed products was enlarged using dihaloarenes, highly π-conjugated haloarenes, or diarylalkynes. The mechanism of the formation of benzo[a]fluorene was investigated. The bowl-shaped structure of methylene-bridged indenocorannulene was verified by X-ray crystallography. The photophysical and electrochemical properties of the products thus prepared were investigated.

Mitochondria- Targeted Antioxidant Skq1 Reverses Glaucomatous Lesions In Rabbits, Elena N. Iomdina, Inna P. Khoroshilova-Maslova, Olga V. Robustova, Olga A. Averina, Nadezhda A. Kovaleva, Gjumrakch Aliev, V. Prakash Reddy, Andrey A. Zamyatnin, Maxim V. Skulachev, Ivan I. Senin, Vladimir P. Skulachev

Chemistry Faculty Research & Creative Works

Glaucoma is the main cause of irreversible blindness worldwide. This disease is characterized by apoptosis of retinal ganglion cells (RGC) and visual field loss that seems to be related to elevated intraocular pressure (IOP). Several lines of evidences have implicated the crucial role of mitochondrial dysfunction in the pathogenesis of glaucoma. Increased mitochondrial oxidative stress in RGC may underlie or contribute to susceptibility of RGC to apoptosis. In our work we (i) designed a rabbit model of chronic, moderately elevated IOP for studying glaucoma and (ii) demonstrated efficacy of mitochondria- Targeted antioxidant SkQ1 as a tool to reverse several traits …

In Planta Variation Of Volatile Biosynthesis: An Alternative Biosynthetic Route To The Formation Of The Pathogen-Induced Volatile Homoterpene Dmnt Via Triterpene Degradation In Arabidopsis Roots, Reza Sohrabi, Jung Hyun Huh, Somayesadat Badieyan, Liva Harinantenaina Rakotondraibe, Daniel J. Kliebenstein, Pablo Sobrado, Dorothea Tholl

Chemistry Faculty Research & Creative Works

Plant-derived volatile compounds such as terpenes exhibit substantial structural variation and serve multiple ecological functions. Despite their structural diversity, volatile terpenes are generally produced from a small number of core 5- to 20-carbon intermediates. Here, we present unexpected plasticity in volatile terpene biosynthesis by showing that irregular homo/norterpenes can arise from different biosynthetic routes in a tissue specific manner. While Arabidopsis thaliana and other angiosperms are known to produce the homoterpene (E)-4,8-dimethyl-1,3,7-nonatriene (DMNT) or its C16-analog (E,E)-4,8,12-trimethyl-1,3,7,11-tridecatetraene by the breakdown of sesquiterpene and diterpene tertiary alcohols in aboveground tissues, we demonstrate that Arabidopsis roots biosynthesize DMNT by the degradation of …

Boron Nitride Colloidal Solutions, Ultralight Aerogels And Freestanding Membranes Through One-Step Exfoliation And Functionalization, Weiwei Lei, Vadym Mochalin, Dan Liu, Si Qin, Yury G. Gogotsi, Ying Chen

Chemistry Faculty Research & Creative Works

Manufacturing of aerogels and membranes from hexagonal boron nitride (h-BN) is much more difficult than from graphene or graphene oxides because of the poor dispersibility of h-BN in water, which limits its exfoliation and preparation of colloidal solutions. Here, a simple, one-step mechano-chemical process to exfoliate and functionalize h-BN into highly water-dispersible, few-layer h-BN containing amino groups is presented. The colloidal solutions of few-layer h-BN can have unprecedentedly high concentrations, up to 30 mg ml^-1, and are stable for up to several months. They can be used to produce ultralight aerogels with a density of 1.4 mg cm …

Detection And Removal Of Emerging Environmental Contaminants, Ruipu Mu

Doctoral Dissertations

"Water is a very crucial natural resource for human. The increasing number of contaminants detected in water bodies has drawn considerable increasing attention over the last decade. There are numerous emerging environmental contaminants which may cause serious health issues. The recent occurrence studies of these contaminants show both industrial and household activity introduction of chemicals into water resources. These various sources result in a large variety of chemicals such as explosives, pharmaceutical and personal care products (PPCPs) and disinfection byproducts detected in water worldwide. Due to the relatively low contaminant concentrations, development of new and improved detection methods along with …

Synthesis Of Different Sizes & Functions Nanoparticles, Jiaming Geng

Masters Theses

"Nanogels, whose size range from 1 to 100nm, have been interested in many research areas: cosmetics, pharmaceuticals, catalysts, photochemistry, and in optical switches or sensors. In Petroleum Engineering area, nanogels can be used as conformance control agent and emulsion stabilizer. And after grafting functional groups or hybrid, nanogels can be used as tracer for the visual modeling.

Though nanoparticles have been studied for more than 20 years, few of them are about nanogels. In the thesis, stirring rate, surfactant type and concentration were found have a large impact on the synthesis of nanogels. And cationic nanogels have salt and acid …

In Vitro Study Of Wound-Healing Capabilities Of Bioactive Glass Fibers Under Various Culture Conditions, Sisi Chen

Masters Theses

"Bioactive borate glass has been recognized to have both hard and soft tissue repair and regeneration capabilities through stimulating both osteogenesis and angiogenesis. However, the underlying physiological and cellular mechanism behind this function remains unclear. In this study, in vitro dynamic flow modules were designed to mimic the micro-environment near the vascular depletion and hyperplasia area in wound-healing regions, and were used to investigate the biocompatibility and functionality of borate glass nano-/micro-fibers. Glass-cell interactions were investigated either by dosing fibers to the upstream of or co-cultured with cells, and two types of borate glasses (with or without CuO/ZnO doped were …

A Rapid And High Content Assay That Measures Cyto-Id-Stained Autophagic Compartments And Estimates Autophagy Flux With Potential Clinical Applications, Sujuan Guo, Yanping Liang, Susan F. Murphy, Angela Huang, Haihong Shen, Deborah F. Kelly, Pablo Sobrado, Zhi Sheng

Chemistry Faculty Research & Creative Works

The lack of a rapid and quantitative autophagy assay has substantially hindered the development and implementation of autophagy-targeting therapies for a variety of human diseases. To address this critical issue, we developed a novel autophagy assay using the newly developed Cyto-ID fluorescence dye. We first verified that the Cyto-ID dye specifically labels autophagic compartments with minimal staining of lysosomes and endosomes. We then developed a new Cyto-ID fluorescence spectrophotometric assay that makes it possible to estimate autophagy flux based on measurements of the Cyto-ID-stained autophagic compartments. By comparing to traditional autophagy approaches, we found that this assay yielded a more …

Constitutive Activity In Orphan G Protein Coupled Receptors, Adam Lee Martin

Doctoral Dissertations

"The goal of this research was to use a distal signaling pathway analysis to evaluate the extent of agonist independent constitutive signaling among orphan class-A G protein coupled receptors (GPCRs). These receptors translate extracellular signals via conformational change into intracellular activation of different G proteins and subsequent second messenger synthesis. These small molecules regulate cellular biochemistry, eventually leading to nuclear signaling that results in changes in gene expression. Some GPCRs are capable of signaling in the absence of an activating ligand, a phenomenon called constitutive activity that is inhibited via an "inverse-agonist". The use of cAMP dependent Luciferase expression is …

Synthesis, Characterization And Application Of Acrylic Colloidal Unimolecular Polymer (Cup), Ameya Manohar Natu

Doctoral Dissertations

"Colloidal Unimolecular Polymer (CUP) particles were prepared by the process of water reduction on amphiphilic acrylic copolymers prepared via free radical polymerization technique. The formation of CUP particles was driven by the polymer-polymer interaction being greater than the polymer-solvent interaction and entropically favored by release of the water. It was demonstrated by Dynamic Light Scattering technique that CUP particles based on copolymers below 13,000 MW were unstable and the particles aggregated to a higher particle size. For the polymers with molecular weight (MW) above 13,000, a good correlation between the theoretical and experimental CUP particle size was observed. The rheology …

Synthesis And Characterization Of Vanadium Oxide Nanomaterials, Tyler M. Fears

Doctoral Dissertations

"This dissertation focuses on the synthesis and characterization of vanadium oxide nanomaterials and neutron-transparent Li-ion battery electrolytes.

Vanadium oxide gels were synthesized via the epoxide-assisted gelation of VOCl₃ using epichlorohydrin in ethanol. This represents the first epoxide-assisted gelation developed for vanadium oxide gels and serves as a potential economical replacement for the fabrication of vanadium oxide gels via the hydrolysis of vanadium alkoxides. Though epoxide-assisted gelation has been demonstrated for a number of transition metal oxides, the gelation mechanism observed here for VOCl₃ appears to be unique.

While investigating the electrochemical and structural properties of lithium vanadates, it …

Mechanical Characteristics Of Organically Modified Fly Ash-Kaolinite Mixtures, Xin Kang

Doctoral Dissertations

"Fly ash is a hazardous waste material to the environment. Beneficial reuse of fly ash, however, brings economic and environmental benefits, i.e., decreases the cost of disposal, reduces greenhouse gas emission, and improves mechanical properties of construction materials. Due to the lack of pozzolanic properties, the reuse rate of Class F fly ash in geotechnical engineering is relatively low (ACAA 2013). In order to promote the effectiveness and sustainability of high volume reuse of class F fly ash in geotechnical engineering, biopolymers (Chitosan, and Xanthan gum) and synthetic polymers (Polyethylene Oxide, PEO) were used instead of the traditional stabilizers to …

Effects Of N-Acetylcysteine Amide In Preventing/Treating Cataracts, Sri Krishna Yasaswi Maddirala

Doctoral Dissertations

"Cataract, the opacification of an eye lens, is a common pathological abnormality of the lens accounting for approximately 50% of all blindness. The only effective treatment currently available for a cataract is the surgical removal of the affected lens and replacement with an artificial lens for the restoration of vision. Although, cataract surgery is considered to be a very successful procedure in terms of visual outcome, the cost of surgery, need for trained personnel and surgeons, and postsurgical complications, limit the worldwide availability and accessibility of this procedure. Hence, alternative preventive and treatment procedures are worthy of investigation. The lens …

The Synthesis And Characterization Of Water-Reducible Nanoscale Colloidal Unimolecular Polymer (Cup) Particles, Cynthia J. Riddles

Doctoral Dissertations

"The coatings industry has adapted to more stringent guidelines in paint formulations. Current VOC (volatile organic compound) limits placed by the federal government have pushed the industry toward the development of paint formulations which have very little to no VOC's. The development of Colloidal Unimolecular Polymer (CUP) particles is a step in the direction of providing a resin system which exists in zero VOC aqueous dispersion.

The CUP particles are a part of the polymer field of Single Chain Nano Particles (SCNP) and ranged in diameters of 3-9 nm. The research presented in this dissertation describes the synthesis and design …

Occurrence, Monitoring And Removal Of Drinking Water Contaminants By Advanced Technologies, Danielle Marie West

Doctoral Dissertations

"In order to maintain drinking water primary standards compliance under the USEPA Stage 2 Disinfectant Disinfection Byproducts Rule, drinking water treatment plants (DWTPs) are switching from free chlorine (FC) to chloramines (MCA). Concerns are raised as MCA disinfection has been linked N-nitrosamine formation. N-nitrosamines are a group of nitrogenous DBPs (N-DBPs) which are highly carcinogenic in comparison to regulated DBPs (THMs and HAAs, generated by FC disinfection). Also in the forefront of drinking water concerns are other emerging drinking water contaminants such as perchlorate. Perchlorate is a contaminant which can enter drinking water from natural deposits or through introduction by …

Application Of Colloidal Unimolecular Polymer (Cup) Particles In Coatings, Sagar Vijay Gade

Doctoral Dissertations

"Colloidal unimolecular polymer (CUP) particles were prepared by the process of water reduction on copolymers containing hydrophobic and hydrophilic monomers at definite ratio using free radical polymerization. The CUPs are formed by the effect of hydrophilic /hydrophobic interactions of the polymer with a change in the solvent environment around them. Once formed these colloidal particles are thermodynamically stable with collapsed hydrophobic groups forming a spheroidal core and hydrophilic charges on the surface stabilizing the particle by the charge repulsion. CUPs contain only the charged CUP particles, water and counterions with all the functionality on the surface for further chemistry. CUP …

Photoelectron Spectroscopic And Computational Study Of Hydrated Pyrimidine Anions, John T. Kelly, Shoujun Xu, Jacob Graham, J. Michael Nilles, Dunja Radisic, Angela M. Buonaugurio, Kit H. Bowen, Nathan I. Hammer, Gregory S. Tschumper

Chemistry Faculty Research & Creative Works

The stabilization of the pyrimidine anion by the addition of water molecules is studied experimentally using photoelectron spectroscopy of mass-selected hydrated pyrimidine clusters and computationally using quantum-mechanical electronic structure theory. Although the pyrimidine molecular anion is not observed experimentally, the addition of a single water molecule is sufficient to impart a positive electron affinity. The sequential hydration data have been used to extrapolate to -0.22 eV for the electron affinity of neutral pyrimidine, which agrees very well with previous observations. These results for pyrimidine are consistent with previous studies of the hydrated cluster anions of uridine, cytidine, thymine, adenine, uracil, …

Contributions Of Unique Active Site Residues Of Eukaryotic Udp-Galactopyranose Mutases To Substrate Recognition And Active Site Dynamics, Isabel Da Fonseca, Insaf A. Qureshi, Ritcha Mehra-Chaudhary, Karina Kizjakina, John J. Tanner, Pablo Sobrado

Chemistry Faculty Research & Creative Works

UDP-glucopyranose mutase (UGM) catalyzes the interconversion between UDP-galactopyranose and UDP-galactofuranose. Absent in humans, galactofuranose is found in bacterial and fungal cell walls and is a cell surface virulence factor in protozoan parasites. For these reasons, UGMs are targets for drug discovery. Here, we report a mutagenesis and structural study of the UGMs from Aspergillus fumigatus and Trypanosoma cruzi focused on active site residues that are conserved in eukaryotic UGMs but are absent or different in bacterial UGMs. Kinetic analysis of the variants F66A, Y104A, Q107A, N207A, and Y317A (A. fumigatus numbering) show decreases in kcat/KM values of 200-1000-fold for the …

Getting Down To The Fundamentals Of Hydrogen Bonding: Anharmonic Vibrational Frequencies Of (Hf)2 And (H2o)2 From Ab Initio Electronic Structure Computations, J. Coleman Howard, Jessica L. Gray, Amanda J. Hardwick, Linh T. Nguyen, Gregory S. Tschumper

Chemistry Faculty Research & Creative Works

This work presents a systematic investigation into the basis set convergence of harmonic vibrational frequencies of (H₂O)₂ and (HF)₂ computed with second-order Møller-Plesset perturbation theory (MP2) and the coupled-cluster singles and doubles method with perturbative connected triples, CCSD(T), while employing correlation-consistent basis sets as large as aug-cc-pV6Z. The harmonic vibrational frequencies presented here are expected to lie within a few cm^-1 of the complete basis set (CBS) limit. For these important hydrogen-bonding prototype systems, a basis set of at least quadruple-ζ quality augmented with diffuse functions is required to obtain harmonic vibrational frequencies within 10 …

Manufacturing Of Transparent Composites Using Vacuum Infusion Process, V. G.K. Menta, R. R. Vuppalapati, K. Chandrashekhara, Thomas P. Schuman

Chemistry Faculty Research & Creative Works

A novel optically transparent glass fiber reinforced polymer matrix composite has been developed by infusing a clear epoxy resin system of matching refractive index into a conventional E-glass fabric preform. Transparent composites are manufactured using a low cost, environmentally friendly vacuum infusion process. Physical and mechanical tests have been conducted. Transparent composites manufactured using the modified vacuum infusion process had a fiber volume fraction of 40%. Tensile strength and tensile modulus of these composites were 374.9 MPa and 31.74 GPa respectively. The results indicate that the transparent composites possess good physical and mechanical properties. These transparent composites form a good …

Theoretical/Experimental Comparison Of Deep Tunneling Decay Of Quasi-Bound H(D)Oco To H(D) + Co₂, Albert F. Wagner, Richard Dawes, Robert Continetti, Hua Guo

Chemistry Faculty Research & Creative Works

The measured H(D)OCO survival fractions of the photoelectron-photofragment coincidence experiments by the Continetti group are qualitatively reproduced by tunneling calculations to H(D) + CO₂ on several recent ab initio potential energy surfaces for the HOCO system. the tunneling calculations involve effective one-dimensional barriers based on steepest descent paths computed on each potential energy surface. the resulting tunneling probabilities are converted into H(D)OCO survival fractions using a model developed by the Continetti group in which every oscillation of the H(D)-OCO stretch provides an opportunity to tunnel. Four different potential energy surfaces are examined with the best qualitative agreement with experiment …

Phosphorous Acid Route Synthesis Of Iron Tavorite Phases, Lifepo₄(Oh)ₓf₁₋ₓ [0 ≤ X ≤ 1] And Comparative Study Of Their Electrochemical Activities, Hooman Yaghoobnejad Asl, Amitava Choudhury

Chemistry Faculty Research & Creative Works

New synthesis routes were employed for the synthesis of three derivatives of iron hydroxo-, fluoro-, and mixed hydroxo-fluoro phosphates LiFePO ₄(OH)_xF_1-x where 0 ? x ? 1 with the tavorite structure type, and their detail electrochemical activities have been presented. The hydrothermal synthesis of the pure hydroxo-derivative, LiFePO₄OH, using phosphorous acid as a source of phosphate yielded good quality crystals from which the crystal structure was solved for the first time using SC-XRD (single crystal X-ray diffraction). The fluoro derivative, LiFePO₄F, was prepared as a very fine powder at low temperature in …

Communication: Rigorous Quantum Dynamics Of O + O₂ Exchange Reactions On An Ab Initio Potential Energy Surface Substantiate The Negative Temperature Dependence Of Rate Coefficients, Yaqin Li, Zhigang Sun, Bin Jiang, Daiqian Xie, Richard Dawes, Hua Guo

Chemistry Faculty Research & Creative Works

The kinetics and dynamics of several O + O₂ isotope exchange reactions have been investigated on a recently determined accurate global O₃ potential energy surface using a time-dependent wave packet method. The agreement between calculated and measured rate coefficients is significantly improved over previous work. More importantly, the experimentally observed negative temperature dependence of the rate coefficients is for the first time rigorously reproduced theoretically. This negative temperature dependence can be attributed to the absence in the new potential energy surface of a submerged "reef" structure, which was present in all previous potential energy surfaces. In addition, contributions …