Chemistry Commons^™

Dnmt1 Stability Is Regulated By Proteins Coordinating Deubiquitination And Acetylation-Driven Ubiquitination, Zhanwen Du, Jing Song, Yong Wang, Yiqing Zhao, Kishore Guda, Shuming Yang, Hung Ying Kao, Yan Xu, Joseph Willis, Sanford D. Markowitz, David Sedwick, Robert M. Ewing, Zhenghe Wang

Chemistry Faculty Publications

DNA methyltransferase 1 (DNMT1) is the primary enzyme that maintains DNA methylation. We describe a previously unknown mode of regulation of DNMT1 protein stability through the coordinated action of an array of DNMT1-associated proteins. DNMT1 was destabilized by acetylation by the acetyltransferase Tip60, which triggered ubiquitination by the E3 ligase UHRF1, thereby targeting DNMT1 for proteasomal degradation. In contrast, DNMT1 was stabilized by histone deacetylase 1 (HDAC1) and the deubiquitinase HAUSP (herpes virus–associated ubiquitin-specific protease). Analysis of the abundance of DNMT1 and Tip60, as well as the association between HAUSP and DNMT1, suggested that during the cell cycle the initiation …

Halo Ion Trap Mass Spectrometry: Design, Instrumentation, And Performance, Miao Wang

Theses and Dissertations

New ion trap mass spectrometry (ITMS) instrumentation, the toroidal IT and halo IT, were developed to meet the significant growth in on-site analysis applications. The miniature toroidal IT mass analyzer was operated with radio frequency (RF) trapping voltages of 3 kVp-p or less. Despite its reduced dimensions, it has roughly the same ion trapping capacity as conventional 3D quadrupole ITs. Unit-mass resolved spectra for n-butylbenzene, xenon, and naphthalene were obtained. The desired linear mass scale was obtained using conventional mass-selective instability scan combined with resonance ejection. The halo IT was also based on toroidal trapping geometry and microfabrication technology, consisting …

Electronic Properties Of N(5)-Ethyl Flavinium Ion, Vincent Sichula, Pavel Kucheryavy, Renat Khatmullin, Ying Hu, Ekaterina Mirzakulova, Shubham Vyas, Samuel F. Manzer, Christopher M. Hadad, Ksenija D. Glusac

Chemistry Faculty Publications

We investigated the electronic properties of N(5)-ethyl flavinium perchlorate (Et-Fl(+)) and compared them to those of its parent compound, 3-methyllumiflavin (Fl). Absorption and fluorescence spectra of Fl and Et-Fl(+) exhibit similar spectral features, but the absorption energy of Et-Fl(+) is substantially lower than that of Fl. We calculated the absorption signatures of Fl and Et-Fl(+) using time-dependent density functional theory (TD-DFT) methods and found that the main absorption bands of Fl and Et-Fl(+) are (pi,pi*) transitions for the S(1) and S(3) excited states. Furthermore, calculations predict that the S(2) state has (n,pi*) character. Using cyclic voltammetry and a simplistic consideration …

Photoinduced Charge Separation In Platinum Acetylide Oligomers, Chen Liao, James E. Yarnell, Ksenija D. Glusac, Kirk S. Schanze

Chemistry Faculty Publications

The series of three donor-spacer-acceptor complexes, DPAF-Ptn-NDI, has been synthesized and characterized using time-resolved absorption spectroscopy In these complexes, the donor is a (diphenylamino)-2,7-fluorenylene (DPAF) unit, the acceptor is a naphthalene diimide (NDI), and the spacers are a series of platinum acetylides of varying lengths, [-Pt(PBu(3))(2)C C-Ph-C C-](n) (where Bu = n-butyl Ph = 1,4-phenylene and n = 1 2, and 3) Electrochemistry indicates that the DPAF-Ptn-NDI system has a charge transfer state at ca 1 5 eV above the ground state that is based on one electron transfer from the DPAF donor to the NDI acceptor Transient absorption spectroscopy …

Enhanced Electrochemistry Of Nanoparticle-Embedded Polyelectrolyte Films: Interfacial Electronic Coupling And Distance Dependence, Callie E. Dowdy, Michael C. Leopold

Chemistry Faculty Publications

Factors affecting the electronic communication believed to be responsible for the enhanced solution electrochemistry observed at electrodes modified with hybrid polyelectrolyte–nanoparticle (PE–NP) film assemblies were systematically investigated. Specifically, the faradaic current and voltammetric peak splitting recorded for cyclic voltammetry of ferricyanide redox species (Fe(CN)63−/4−) at films constructed with various architectures of citrate-stabilized gold NPs embedded in polyelectrolyte films composed of poly-l-lysine and poly-S-styrene were used to establish the relative importance of both distance and electronic coupling. Layer-by-layer construction of PE–NP films allowed for the position and density of NPs to be varied within the film to assess electronic coupling between …

Isotherms And Kinetics Studies Of Lead Adsorption On Jatropha Seed Husk., Faheem Ahmed Qaid Mohammed

Student Works (2010-2019)

Presence of lead, a heavy metal in the environment has been a serious concern especially with rapid industrialization which has created new uses for lead. The acute toxicity of lead to aquatic Life and humans and the stringent effluent standard to be met by industries as specified by regulatory organizations has necessitated the development of innovative, effective and economical methods for treating lead-bearing wastewater. An adsorption process using an inexpensive adsorbent such as Jatropha seed husk is an attractive option for the removal of lead from wastewater. In this study batch isotherm and kinetic studies were carried out on a …

Fluoride-Promoted Ligand Exchange In Diaryliodonium Salts, Bijia Wang, Ronald Cerny, Shriharsha Uppaluri, Jayson J. Kempinger, Stephen G. Dimagno

Stephen DiMagno Papers

Diaryliodonium salts are shown to undergo rapid, fluoride-promoted aryl exchange reactions at room temperature in acetonitrile. Aryl exchange is shown to be exquisitely sensitive to the concentration of fluoride ion in solution; fast exchange is observed as the fluoride concentration approaches a stoichiometric amount at 50 mM substrate concentration. The reaction is slowed, but not halted if benzene is the solvent, indicating that free fluoride ion or a four-coordinate anionic I(III) species may be responsible for the exchange. The fluoride-promoted aryl exchange reaction is general and allows direct measurement of the relative stabilities of diaryliodonium salts featuring different aryl substituents. …

Bandwidth Tuning Triggers Interplay Of Charge Order And Superconductivity In Two-Dimensional Organic Materials, S. Kaiser, M. Dressel, Y. Sun, A. Greco, J. A. Schlueter, Gary L. Gard, N. Drichko

Chemistry Faculty Publications and Presentations

We observe charge-order fluctuations in the quasi-two-dimensional organic superconductor β″-(BEDT-TTF)₂SF₅CH₂CF₂SO₃, both by means of vibrational spectroscopy, locally probing the fluctuating charge order, and by investigating the in-plane dynamical response by infrared reflectance spectroscopy. The decrease of the effective electronic interaction in an isostructural metal suppresses both charge-order fluctuations and superconductivity, pointing to their interplay. We compare the results of our experiments with calculations on the extended Hubbard model.

Activation Of The Innate Immune Response By The Alzheimer's Amyloid Beta Protein Via Toll-Like Receptors, Udan Lourdes Maria

Dissertations

Alzheimer’s Disease (AD) is the most common form of neurodegenerative disease characterized by the generation and deposition of amyloid beta plaques and the formation of neurofibrillary tangles. A wealth of data now demonstrate that inflammation is a prominent feature in AD pathology and a potential therapeutic target for the treatment and prevention of the disease. The emergence of evidence linking amyloid beta protein (Aβ), the primary component of senile plaques, to inflammation has led to new insights into understanding AD pathology. Aβ, a protein fragment resulting from cleavage of human amyloid precursor protein (APP), primarily exists in two forms: a …

Synthesis Of An Ortho-Triazacyclophane: N,N',N''-Trimethyltribenzo-1,4,7-Triazacyclononatriene, Andria M. Panagopoulos, Matthias Zeller, Daniel P. Becker

Chemistry: Faculty Publications and Other Works

N,N',N''-Trimethyltribenzo-1,4,7-triazacyclononatriene has been synthesized via sequential palladium-catalyzed Buchwald-Hartwig N-arylation reactions affording the 9-membered triaza o-cyclophane in 35% overall yield. An X-ray crystal structure shows the new cyclophane to have a C(2)-symmetric saddle conformation, as compared to the crown conformation exhibited by the related carbocyclic cyclotriveratrylene (CTV).

Chelate-Assisted Oxidative Coupling Reaction Of Arylamides And Unactivated Alkenes: Mechanistic Evidence For Vinyl C–H Bond Activation Promoted By An Electrophilic Ruthenium-Hydride Catalyst, Ki Hyeok Kwon, Do W. Lee, Chae S. Yi

Chemistry Faculty Research and Publications

The cationic ruthenium hydride complex [(η⁶-C₆H₆)(PCy₃)(CO)RuH]⁺BF₄⁻ was found to be a highly regioselective catalyst for the oxidative C−H coupling reaction of aryl-substituted amides and unactivated alkenes to give o-alkenylamide products. The kinetic and spectroscopic analyses support a mechanism involving a rapid vinyl C−H activation followed by a rate-limiting C−C bond formation step.

The Design And Synthesis Of Functionalized Porphyrins And Their Applications In Group Transfer Reactions, Medicine, And Materials, Kimberly Bliss Fields

USF Tampa Graduate Theses and Dissertations

Porphyrins and their analogs are a class of chemically and biologically important compounds that have found a variety of applications in different fields such as catalysis, medicine, and materials. The physical, chemical, and biological dependence of the peripheral substituents of porphyrins on their properties has prompted great effort towards the synthesis of new porphyrins with different electronic, steric, and conformational environments. To this end, porphyrins have been prepared using a modular approach from bromo- and triflate synthons. These synthons underwent palladium-catalyzed cross-coupling with chiral amines, amides, alcohols, and boronic esters to create products that were tested for biological activity.

Metalloporphyrins …

Synthesis Of Functionalized Resorcin[4]Arene Via Click Chemistry, Ali Husain

USF Tampa Graduate Theses and Dissertations

Click chemistry is a very powerful chemical strategy that overcome carbon-carbon bond with carbon-heteroatom bond by joining small units with heteroatom links (C-X-C) using spring-loaded reactants. The Cu(I)-catalyzed Huisgen 1,3-dipolar cycloaddition is a major example based on the click chemistry philosophy. This method was used for the last 10 years to join different functional groups, carbohydrates, aminoacids, polymers to calix[4]arene and resorcin[4]arene cavitands by a stable 1,2,3-triazole linkages.

Herein I describe our interest in this type of click chemistry reaction in the synthesis of dimeric capsules resorcin[4]arene via four 1,2,3-triazole linkages. Two different resorcin[4]arene derivatives were synthesized in which four …

(1e,3e)-1,4-Bis(4-Methoxyphenyl)Buta1,3-Diene, Gopinathan Narayan, Nigam Rath, Suresh Das

Chemistry & Biochemistry Faculty Works

The title compound, C18H18O2, which exhibits blue emission in the solid state, is an inter­mediate in the preparation of liquid crystals and polymers. The mol­ecule is located on an inversion centre. In the crystal, mol­ecules are arranged in a herringbone motif.

Functionalization Of Diamond And Its Application In High Performance Liquid Chromatography And Solid Phase Extraction, Gaurav Saini

Theses and Dissertations

The primary focus of my work was to chemically functionalize diamond as normal and reversed phases for solid phase extraction (SPE) and high performance liquid chromatography (HPLC). Diamond was functionalized with -NH2 groups via self-limiting adsorption of an amine-containing polymer, polyallylamine (PAAm), onto oxidized diamond particles. The chemical stability of these particles was improved by thermal curing or chemical crosslinking with 1,2,5,6-diepoxycyclooctane. The reversed phase material for SPE was synthesized by reacting amine-functionalized diamond particles with long chain alkyl and a perfluorinated isocyanate. Unlike commercially available silica, functionalized diamond particles were stable under extreme pH conditions (pH 0-14). Functionalized diamond …

Scoring Function To Predict Solubility Mutagenesis, Ye Tian, Christopher Deutsch, Bala Krishnamoorthy

Chemistry Faculty Publications and Presentations

Background: Mutagenesis is commonly used to engineer proteins with desirable properties not present in the wild type (WT) protein, such as increased or decreased stability, reactivity, or solubility. Experimentalists often have to choose a small subset of mutations from a large number of candidates to obtain the desired change, and computational techniques are invaluable to make the choices. While several such methods have been proposed to predict stability and reactivity mutagenesis, solubility has not received much attention. Results: We use concepts from computational geometry to define a three body scoring function that predicts the change in protein solubility due to …

Ytterbium Triflate Catalyzed Synthesis Of Alkoxy-Substituted Donor-Acceptor Cyclobutanes And Their Formal [4 + 2] Cycloaddition With Imines: Stereoselective Synthesis Of Piperidines., Mahmoud M Abd Rabo Moustafa, Brian L Pagenkopf

Chemistry Publications

A new synthesis of 2-alkoxy-1,1-cyclobutane diesters and their first use in dipolar cycloadditions is reported. Both the formation of the donor-acceptor cyclobutanes and their subsequent annulation with in situ formed imines are catalyzed by Yb(OTf)(3). Cyclobutanes with carbon donor groups give piperidines with high trans stereoselectivity.

Formal [4 + 2] Cycloaddition Of Alkoxy-Substituted Donor-Acceptor Cyclobutanes And Aldehydes Catalyzed By Yb(Otf)3., Mahmoud M Abd Rabo Moustafa, Andrew C Stevens, Ben P Machin, Brian L Pagenkopf

Chemistry Publications

The cycloaddition between 2-alkoxy-1,1-cyclobutane diesters and aromatic, heteroaromatic, or aliphatic aldehydes under Yb(OTf)(3) catalysis generates tetrahydropyrans in high yields with exclusive cis-stereochemistry.

Polymeric Monolithic Stationary Phases For Capillary Hydrophobic Interaction Chromatography, Yuanyuan Li

Theses and Dissertations

Rigid poly[hydroxyethyl acrylate-co-poly(ethylene glycol) diacrylate] (Poly(HEA-co-PEGDA) monoliths were synthesized inside 75-µm i.d. capillaries by one-step UV-initiated copolymerization using methanol and ethyl ether as porogens. The optimized monolithic column was evaluated for hydrophobic interaction chromatography (HIC) of standard proteins. Six proteins were separated within 20 min with high resolution using a 20 min elution gradient, resulting in a peak capacity of 54. The performance of this monolithic column for HIC was comparable or superior to the performance of columns packed with small particles. Monoliths synthesized solely from PEGDA were also found to show excellent performance in HIC …

Electronic Structure Based Classification Of Neurotransmitters And Related Drugs, Amrita Jha

Theses and Dissertations

A fundamental understanding of the relationship between structure and activity of neurotransmitters in the human brain is of vital importance for the design targeted drugs. Using density functional theory and hybrid exchange correlation energy functionals we have studied the structure-activity-relationships of some important neurotransmitters and selected drugs by calculating their absolute hardness (η) and absolute electronegativity (χ). A plot of the η- χ diagram allowed us to assign them into three distinct groups, namely, (i) Acetylcholine analogs (positively charged structure), (ii) GABA analogs (zwitterionic structures) and (iii) monoamines. The results suggest that brain stem is chemically soft because of distribution …

Oga Inhibition By Glcnac-Selenazoline, E. J. Kim, D. C. Love, E. Darout, M. Abdo, B. Rempel, S. G. Withers, Paul R. Rablen, J. A. Hanover, S. Knapp

Chemistry & Biochemistry Faculty Works

The title compound, which differs from the powerful O-GlcNAcase (OGA) inhibitor GlcNAc-thiazoline only at the chalcogen atom (Se for S), is a much weaker inhibitor in a direct OGA assay. In human cells, however, the selenazoline shows comparable ability to induce hyper-O-GlcNAc-ylation, and the two show similar reduction of insulin-stimulated translocation of glucose transporter 4 in differentiated 3T3 adipocytes. (C) 2010 Elsevier Ltd. All rights reserved.

Chemistry & Biochemistry Newsletter, Department Of Chemistry & Biochemistry, South Dakota State University

Chemistry & Biochemistry Newsletter: 2002-2015

Inside:

Page 2 Career Award Will Help Build High-Tech Microscope

Page 4 Classroom Changes; Krsnak Wins Oz Memorial

Page 5 Chemistry Major John Lee is Academic All-American

Page 6 Program to Address Shortage of Medical Lab Scientists

Page 7 New Graduate Students

Page 8 Publications and Grants

Solving The Low Dimensional Smoluchowski Equation With A Singular Value Basis Set, Gregory E. Scott, Martin Gruebele

Chemistry and Biochemistry

Reaction kinetics on free energy surfaces with small activation barriers can be computed directly with the Smoluchowski equation. The procedure is computationally expensive even in a few dimensions. We present a propagation method that considerably reduces computational time for a particular class of problems: when the free energy surface suddenly switches by a small amount, and the probability distribution relaxes to a new equilibrium value. This case describes relaxation experiments. To achieve efficient solution, we expand the density matrix in a basis set obtained by singular value decomposition of equilibrium density matrices. Grid size during propagation is reduced from (100–1000) …

Nanopod Formation Through Gold Nanoparticle Templated And Catalyzed Cross-Linking Of Polymers Bearing Pendant Propargyl Ethers, Ke Zhang, Joshua I. Cutler, Jian Zhang, Dan Zheng, Evelyn Auyeung, Chad A. Mirkin

Department of Chemistry: Faculty Publications

A novel method for synthesizing polymer nanopods from a linear polymer bearing pendant propargyl ether groups, using gold nanoparticles as both the template and the catalyst for the crosslinking reaction, is reported. The transformations involved in the cross-linking process are unprecedented on the surface of a gold particle. A tentative cross-linking mechanism is proposed.

Includes Supporting Information.

Nanometer To Millimeter Scale Peptide-Porphyrin Materials, Daniil V. Zaytsev, Fei Xie, Madhumita Mukherjee, Alexey Bludin, Borries Demeler, Robert M. Breece, David L. Tierney, Michael Y. Ogawa

Chemistry Faculty Publications

AQ-Pal14 is a 30-residue polypeptide that was designed to form an alpha-helical coiled coil that contains a metal-binding 4-pyridylalanine residue on its solvent-exposed surface. However, characterization of this peptide shows that it exists as a three-stranded coiled coil, not a two-stranded one as predicted from its design. Reaction with cobalt(III) protoporphyrin IX (Co-PPIX) produces a six-coordinate Co-PPIX(AQ-Pal 14)(2) species that creates two coiled-coil oligomerization domains Coordinated to opposite laces of the porphyrin ring. It is found that this species undergoes a buffer-dependent Self-assembly process: nanometer-scale globular materials were formed when these components were reacted in unbuffered H(2)O, while millimeter-scale, rod-like …

Cox-2 Inhibitor Nimesulide Analogs Are Aromatase Suppressors In Breast Cancer Cells, Bin Su, Xiaohan Cai, Yanyan Hong, Shiuan Chen

Chemistry Faculty Publications

Cyclooxygenase-2 (COX-2) inhibitor nimesulide derivatives compounds A and B decreased aromatase activity in breast cancer cells via a novel mechanism different to aromatase inhibitors (AIs), and were defined as “aromatase suppressors”. Breast carcinoma cells (MCF-7aro and T47Daro) transfected with aromatase full gene were used to explore the mechanisms of the two compounds. They dose and time-dependently suppressed aromatase activity in MCF-7aro and T47Daro cells in the nanomole range. However, they neither directly inhibited aromatase, nor improved aromatase degradation even at much higher concentrations. They could also suppress androgen stimulated cell growth, but did not affect estrogen enhanced cell proliferation. These …

Detection Of Quercetin Using Polymer Coated Quartz Crystal Microbalance And The Modification Of Á-Zirconium Phosphate To Develop A Sorbent For Organic Pollutant Removal, Darlington Mlambo

Dissertations (1934 -)

Sorption processes involve physical and chemical interactions of sorbents with analytes. These may involve the physical and/or chemical processes in which a substance is accumulated at an interface between two phases, or the intermixing of a substance with the matrix of a second phase. The two processes are referred to as adsorption and absorption respectively. The sorption capacities of different classes of sorbents have many potential and demonstrated applications such as sensor development, water treatment, environmental remediation and chromatographic separations. The goal of this work is to explore the sorption capacity of polymers as well as nanodimensional layered materials for …

Efficient Synthesis And Conformational Investigations Of Cis-Pentacenediols, Jinyue Jiang, Charles E. Schiaffo, Chris P. Schwartz, Yong Pei, Joseph J. Dumais, Xiao Cheng Zeng, Patrick Dussault, Li Tan

Patrick Dussault Publications

Diisobutylaluminum hydride is utilized to reduce pentacene-6,13-diones to the corresponding diols, useful precursors to functionalized pentacenes. This pathway is mild and efficient, and produces the cis-diols as major products. Further, we found the cis-diols adopt endo conformation, which cannot flip to the exo conformation under ambient conditions. Due to the cis and endo orientation, the cis-diols can be potential bidentates in catalysis, molecular propellers, and optoelectronic devices.

Solvent Effects On Emission Spectra Of Carminic Acid And Determination Of Its Ground And Excited State Dipole Moments, Sarika B. Jaggannagari

All Capstone Projects

Absorption and fluorescence emission spectra of Carminic acid were recorded in solvents with different solvent parameters like polarities, dielectric constant and refractive index. The solvents used in the experiment were water, DMSO, acetonitrile, methanol, propanol and butanol. The atomic radius of the molecule was found out using Hartree-Fock method in molecular modeling using Spartan software and it is applied to find out the dipole moments. The dipole moments of Carminic acid in the ground state and excited states have been determined and Solvatochromic shift method has been used to determine the excited state dipole moments. The linear progressions were made …

Synthesis And Characterization Of An Europium-Porphyrin Complex, Alejandro Blinder

All Capstone Projects

Photodynamic therapy (PDT) is a promising treatment that has continued to improve over the past thirty years when the first commercially approved photosensitizer (PS) was introduced. Although PDT has many successful applications, the terrifying number of new cancer cases reported each year makes scientists focus their efforts towards the development of new efficient PS for PDT. The biggest obstacle that prohibits PDT from becoming a more widely used therapy is the ineffective photosensitizers (PS) that are available on the market today. The purpose of this study was to evaluate the synthesized metal-porphyrin complex as a possible candidate as a PS. …