Chemistry Commons^™

Nmr And Computational Studies Of Nad(P)(H) Cofactor Binding, Junghwa Kim

Master's Theses (2009 -)

Tuberculosis (TB) is one of the most dangerous diseases in a sense of spread method. According W.H.O., one third of world population has this disease and annual one of these infected people spreads 10 -15 people unintentionally. To protect human from this bacterial, the unique feature of mycrobacterial [sic] TB was studied previously. The unique cell wall, peptidoglycan, has high content of DAP (diaminopimelic acid). The disruption of synthesis DAP results in cell death due to instability of cell wall. One way to inhibiting synthesis of DAP is to modify cofactor which acts with dehydrogenase. To do that the study …

Flame Retardancy Of Polymer Nanocomposites Based On Layered Aluminum Phosphate And Computational Study Of Intercalation Of Amines Into Α-Zirconium Phosphate And Adsorption Of A Model Organic Pollutant, Ning Wang 1982-

Master's Theses (2009 -)

Layered metal materials, such as layered metal hydroxides, hydroxy double salts, and layered metal phosphates can be used for applications such as fire retardancy, ion exchangers, or removal of pollutants. Optimization of materials for these applications requires an understanding of their physical and chemical properties.

Part A: Flame retardancy of polymer nanocomposites based on taranakite

Taranakite with tunable interlayer spacing has been prepared and modified by sodium dodecyl sulfate (AL-SDS). The layered materials are used as the additive to study the fire retardancy of polymers, including polystyrene (PS), polypropylene (PP), and polyvinyl alcohol (PVA). The dispersion of taranakite was characterized …

Analytic Energy Gradients In Combined Second Order Møller-Plesset Perturbation Theory And Conductorlike Polarizable Continuum Model Calculation, Dejun Si, Hui Li

Hui Li Publications

The analytic energy gradients in combined second order Møller-Plesset perturbation theory and conductor-like polarizable continuum model calculations are derived and implemented for spin-restricted closed shell (RMP2), Z-averaged spin-restricted open shell (ZAPT2), and spin-unrestricted open shell (UMP2) cases. Using these methods, the geometries of the S0 ground state and the T₁ state of three nucleobase pairs (guanine-cytosine, adenine-thymine, and adenine-uracil) in the gas phase and aqueous solution phase are optimized. It is found that in both the gas phase and the aqueous solution phase the hydrogen bonds in the T₁ state pairs are weakened by ∼1 kcal/mol as compared …

A Truly Green Synthesis Of A-Aminonitriles Via Strecker Reaction, Debasish Bandyopadhyay, Juliana M. Velazquez, Bimal K. Banik

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

Background: The classical Strecker reaction is one of the simplest and most economical methods for the synthesis of racemic a-aminonitriles (precursor of a-amino acids) and pharmacologically useful compounds.

Results: Indium powder in water is shown to act as a very efficient catalyst for one-pot, three-component synthesis of a-aminonitriles from diverse amines, aldehydes and TMSCN. This general rapid method is applicable to a wide range of amines and aldehydes and produces products in excellent yield.

Conclusions: The present one-pot, three-component environmentally benign procedure for the synthesis of aaminonitriles will find application in the synthesis of complex biologically active molecules.

Optical And Electrochemical Properties Of Multi-Layer Polyelectrolyte Thin Films Incorporating Spherical, Gold Colloid Nanomaterials, Tran T. Doan, Robert W. Day, Michael C. Leopold

Chemistry Faculty Publications

Polyelectrolyte multilayer (PEM) films incorporating various types of spherical, gold nanomaterials (NMs) were investigated to assess the existence of electrochemical and/or optical signal enhancement effects directly attributable to embedded NMs and the relationship of these effects to film structure and composition. Specifically, electrostatically assembled films of cationic poly-L-lysine (PLL) and anionic poly(4-styrene sulfonate) (PSS) incorporating one of four types of spherical, gold colloid NMs were constructed on 3-(aminopropyl)trimethoxysilane (3-APTMS)-modified glass substrates for optical studies or 11-mercaptoundecanoic (MUA)-modified gold electrodes for electrochemical studies. The NMs inserted into the PEM films include citrate-stabilized gold nanoparticles, thioctic acid-stabilized gold nanoparticles (TAS-NPs), MUA-modified monolayer …

Exploring The Roles Of Nucleobase Desolvation And Shape Complementarity During The Misreplication Of O6-Methylguanine, Delia Chavarria, Andrea Ramos Serrano, Ichiro Hirao, Anthony J. Berdis

Chemistry Faculty Publications

O6-methylguanine is a miscoding DNA lesion arising from the alkylation of guanine. This report uses the bacteriophage T4 DNA polymerase as a model to probe the roles hydrogen-bonding interactions, shape/size, and nucleobase desolvation during the replication of this miscoding lesion. This was accomplished by using transient kinetic techniques to monitor the kinetic parameters for incorporating and extending natural and non-natural nucleotides. In general, the efficiency of nucleotide incorporation does not depend on the hydrogen-bonding potential of the incoming nucleotide. Instead, nucleobase hydrophobicity and shape complementarity appear to be the preeminent factors controlling nucleotide incorporation. In addition, shape complementarity plays a …

Wetting Properties Induced In Nano-Composite Poss-Ma Polymer Films By Atomic Layer Deposited Oxides, Kyle A. Vasquez, Anita J. Vincent-Johnson, W. Chris Hughes, Brian H. Augustine, Kyoungmi Lee, Gregory N. Parsons, Giovanna Scarel

Department of Physics and Astronomy - Faculty Scholarship

Due to their unique properties, nano-composite polyhedral oligomeric silsequioxane (POSS) copolymer films are attractive for various applications. Here we show that their natural hydrophobic character can become hydrophilic when the films are modified by a thin oxide layer, up to 8 nm thick, prepared using atomic layer deposition. A proper choice of the deposition temperature and thickness of the oxide layer are required to achieve this goal. Unlike other polymeric systems, a marked transition to a hydrophilic state is observed with oxide layers deposited at increasing temperatures up to the glass transition temperature (∼110 °C) of the POSS copolymer film. …

Rna Oxidation Adducts 8-Ohg And 8-Oha Change With Aβ42 Levels In Late-Stage Alzheimer's Disease, Adam M. Weidner, Melissa A. Bradley, Tina L. Beckett, Dana M. Niedowicz, Amy L.S. Dowling, Sergey V. Matveev, Harry Levine, Mark A. Lovell, M. Paul Murphy

Sanders-Brown Center on Aging Faculty Publications

While research supports amyloid-β (Aβ) as the etiologic agent of Alzheimer's disease (AD), the mechanism of action remains unclear. Evidence indicates that adducts of RNA caused by oxidation also represent an early phenomenon in AD. It is currently unknown what type of influence these two observations have on each other, if any. We quantified five RNA adducts by gas chromatography/mass spectroscopy across five brain regions from AD cases and age-matched controls. We then used a reductive directed analysis to compare the RNA adducts to common indices of AD neuropathology and various pools of Aβ. Using data from four disease-affected brain …

The Regulation Of Skeletal Muscle Protein Turnover During The Progression Of Cancer Cachexia In The ApcMin/+ Mouse, James P. White, John W. Baynes, Stephen L. Welle, Matthew C. Kostek, Lydia E. Matesic, Shuichi Sato, James A. Carson

Faculty Publications

Muscle wasting that occurs with cancer cachexia is caused by an imbalance in the rates of muscle protein synthesis and degradation. The Apc(Min/+) mouse is a model of colorectal cancer that develops cachexia that is dependent on circulating IL-6. However, the IL-6 regulation of muscle protein turnover during the initiation and progression of cachexia in the Apc(Min/+) mouse is not known. Cachexia progression was studied in Apc(Min/+) mice that were either weight stable (WS) or had initial (≤5%), intermediate (6-19%), or extreme (≥20%) body weight loss. The initiation of cachexia reduced %MPS 19% and a further ∼50% with additional weight …

Cucurbit[8]Uril Rotaxanes, Vijayakumar Ramalingam, Adam R. Urbach

Chemistry Faculty Research

The synthesis of [2]rotaxanes, each comprising a viologen core threaded through a cucurbit[8]uril (Q8, Figure 1) macrocycle and stoppered by tetraphenylmethane groups, and their binding to second guests as inclusion complexes in organic and aqueous media are described. Stoppering was observed to have little effect on binding. Chemical modification of the threaded guest was used to control solubility and binding characteristics, thus demonstrating a novel approach to making artificial receptors with readily modifiable properties.

Design Of Control Release Drug Delivery System (Dds) For Imaging And Therapeutic Applications, Sweta Naik

Theses and Dissertations

The main challenge in disease treatment is no more the discovery of new therapeutic drugs, but to provide targeted delivery of therapeutic drugs to specific sites without incurring systemic toxicity effects. An efficient way of reducing the toxicity is by encapsulating the drug with a biodegradable matrix that can provide controlled release of the drug along with local heating of the drug. Local heating can be obtained by incorporating magnetic iron oxide particles that heat upon exposure to AC electromagnetic fields. The magnetic iron oxide nanoparticles are also gaining much attention as MRI contrast agents. Thus it would be of …

Design And Synthesis Of A Biotinylated Probe Of Cox-2 Inhibitor Nimesulide Analog Jcc76, Bo Zhong, Rati Lama, Kerri M. Smith, Yan Xu, Bin Su

Chemistry Faculty Publications

JCC76 is a derivative of cyclooxygenase-2(COX-2) selective inhibitor nimesulide and exhibits potent anti-breast cancer activity. It selectively induces apoptosis of Her2 positive breast cancer cells. However, the specific molecular targets of JCC76 still remain unclear, which significantly withdraw the further drug development of JCC76. To identify the molecular targets of JCC76, a six carbon linker and biotin conjugated JCC76 probe was designed and synthesized. The anti-proliferation activity of the probe and its analogs was evaluated.

A Modified Surface On Titanium Deposited By A Blasting Process, Caroline O' Sullivan, Peter O'Hare, Greg Byrne, Liam O'Neill, Katie B. Ryan, Abina M. Crean

Publications

Abstract

: Hydroxyapatite (HA) coating of hard tissue implants is widely employed for its biocompatible and osteoconductive properties as well as its improved mechanical properties. Plasma technology is the principal deposition process for coating HA on bioactive metals for this application. However, thermal decomposition of HA can occur during the plasma deposition process, resulting in coating variability in terms of purity, uniformity and crystallinity, which can lead to implant failure caused by aseptic loosening. In this study, CoBlast™, a novel blasting process has been used to successfully modify a titanium (V) substrate with a HA treatment using a dopant/abrasive regime. …

Efficient And Accurate Methods For The Geometry Optimization Of Water Clusters: Application Of Analytic Gradients For The Two-Body:Many-Body Qm:Qm Fragmentation Method To (H2o)N, N = 3-10, Desiree M. Bates, Joshua R. Smith, Gregory S. Tschumper

Chemistry Faculty Research & Creative Works

The structures of more than 70 low-lying water clusters ranging in size from (H₂O)₃ to (H₂O)₁₀ have been fully optimized with several different quantum mechanical electronic structure methods, including second-order Møller-Plesset perturbation theory (MP2) in conjunction with correlation consistent triple-ζ basis sets (aug-cc-pVTZ for O and cc-pVTZ for H, abbreviated haTZ). Optimized structures obtained with less demanding computational procedures were compared to the MP2/haTZ ones using both MP2/haTZ single point energies and the root-mean-square (RMS) deviations of unweighted Cartesian coordinates. Based on these criteria, B3LYP/6-31+G(d,2p) substantially outperforms both HF/haTZ and MP2/6-31Gz.ast. B3LYP/6-31+G(d,2p) structures never …

Accurate Interaction Energies For Problematic Dispersion-Bound Complexes: Homogeneous Dimers Of Nccn, P2, And Pccp, Edward G. Hohenstein, Heather M. Jaeger, Emily J. Carrell, Gregory S. Tschumper, C. David Sherrill

Chemistry Faculty Research & Creative Works

All intermolecular interactions involve London dispersion forces. The accurate treatment of dispersion is essential for the computation of realistic interaction potentials. In general, the most reliable method for computing intermolecular interactions is coupled-cluster singles and doubles with perturbative triples [CCSD(T)] in conjunction with a sufficiently flexible Gaussian atomic orbital basis set, a combination which is not routinely applicable due to its excessive computational demands (CPU time, memory, storage). Recently, many theoretical methods have been developed that attempt to account for dispersion in a more efficient manner. It is well-known that dispersion interactions are more difficult to compute in some systems …

Synthesis Of N-Acyl-N,O-Acetals From N-Aryl Amides And Acetals In The Presence Of Tmsotf, C. Wade Downey, Alan S. Fleisher, James T. Rague, Chelsea L. Safran, Megan E. Venable, Robert D. Pike

Chemistry Faculty Publications

Secondary amides undergo in situ silyl imidate formation mediated by TMSOTf and an amine base, followed by addition to acetal acceptors to provide N-acyl-N,O-acetals in good yields. An analogous, high-yielding reaction is observed with 2-mercaptothiazoline as the silyl imidate precursor. Competing reduction of the acetal to the corresponding methyl ether via transfer hydrogenation can be circumvented by the replacement of i-Pr₂NEt with 2,6-lutidine under otherwise identical reaction conditions.

Combinatorial Catalysis Assisted By A Visible Enzymatic Beacon In Real Time: New Synthetically Versatile (Pseudo)Halometalation/Carbocyclizations, Jacob A. Friest, Sylvain Broussy, Woo Jin Chung, David B. Berkowitz

David Berkowitz Publications

Combinatorial approaches to catalysis have made an impact in targeted transformation development, including Ag-mediated carbene insertion,^[1] Sc-pybox-based asymmetric cyclopropanation,^[2] and Rh/Ir-based asymmetric hydrogenation.^[3] Useful design elements have emerged from these studies, e.g. the value of ligand self assembly,^[4] or of the inclusion of peptide-like structural elements^[5],[6],[7] in building ligand arrays. Efficient screening methods are of paramount importance for such efforts. Methods based on fluorescence,^[8] REMPI^,[9] MS,^[10] NMR,^[11] and IR thermography^[12] have appeared. A chromophore may be installed into the substrate^[13] or product^[14] of the reaction under study. Alternatively, …

Wetting Transitions At Nanostructured Surfaces, Yazdi Jamileh Seyed

Theses and Dissertations

Shape of a droplet atop a surface heterogeneity at a nanoscale. Small aqueous droplets on homogeneous surfaces, surrounded by a reservoir of vapor are inherently unstable. In contact with supersaturated vapor, the drops will keep growing until they coalesce and form a contiguous aqueous phase. Alternatively, if vapor pressure is below that of the droplets, the droplets gradually evaporate. Departing from this common picture, when nanoscale droplets sit above hydrophilic patches on a heterogeneous surface, at certain conditions they can maintain a stable volume, determined by the pertinent contact angle and the size of the patches. Only the region under …

Gm-Csf Production Allows The Identification Of Immunoprevalent Antigens Recognized By Human Cd4+ T Cells Following Smallpox Vaccination, Valeria A. Judkowski, Alcinette Bunying, Feng Ge, Jon R. Appel, Kingyee Law, Atima Sharma, Claudia Raja-Gabaglia, Patricia Norori, Radleigh Santos, Marc Giulianotti, Mark K. Slifka, Daniel C. Douek, Barney S. Graham, Clemencia Pinilla

Mathematics Faculty Articles

The threat of bioterrorism with smallpox and the broad use of vaccinia vectors for other vaccines have led to the resurgence in the study of vaccinia immunological memory. The importance of the role of CD4+ T cells in the control of vaccinia infection is well known. However, more CD8+ than CD4+ T cell epitopes recognized by human subjects immunized with vaccinia virus have been reported. This could be, in part, due to the fact that most of the studies that have identified human CD4+ specific protein-derived fragments or peptides have used IFN-γ production to evaluate vaccinia specific T cell responses. …

From Computational Discovery To Experimental Characterization Of A High Hole Mobility Organic Crystal, Anatoliy N. Sokolov, Sule Atahan-Evrenk, Rajib Mondal, Hylke B. Akkerman, Roel S. Sánchez-Carrera, Sergio Granados-Focil, Joshua Schrier, Stefan C.B. Mannsfeld, Arjan P. Zoombelt, Zhenan Bao, Alán Aspuru-Guzik

Chemistry

For organic semiconductors to find ubiquitous electronics applications, the development of new materials with high mobility and air stability is critical. Despite the versatility of carbon, exploratory chemical synthesis in the vast chemical space can be hindered by synthetic and characterization difficulties. Here we show that in silico screening of novel derivatives of the dinaphtho[2,3-b:2′2,3′2-f]thieno[3,2-b]thiophene semiconductor with high hole mobility and air stability can lead to the discovery of a new high-performance semiconductor. On the basis of estimates from the Marcus theory of charge transfer rates, we identified a novel compound expected to demonstrate a theoretic twofold improvement in mobility …

Follicular Dendritic Cells, Resting Cd4+ T Cells And Human Immunodeficiency Virus Expression, Changna Wang

Theses and Dissertations

Many events associated with Human Immunodeficiency Virus (HIV) infection/replication occur in and around the germinal centers (GCs) of secondary lymphoid tissues where follicular dendritic cells (FDCs) reside, suggesting that this microenvironment may contribute unique signaling that is important to viral progression. My research focused on characterizing signaling, both positive and negative, contributed by FDCs that affects HIV infection and replication. Specifically, I determined if FDC signals could induce the expression of latent HIV in T cells and if so, to characterize the signaling pathways involved. Moreover, I also examined the ability of FDCs to produce inhibitory signals that might block …

2,5-Dimethyl-1,3-Dinitro­Benzene, Dean Johnston

Chemistry Faculty Scholarship

The title compound, C(8)H(8)N(2)O(4), was prepared via the nitration of p-xylene. The mol-ecules are stacked along the c axis in an antiparallel manner. The two nitro groups are rotated relative to the benzene ring with dihedral angles of 44.50 (7) and 31.67 (8)°. The tilt of the nitro groups allows the formation of C-H⋯O inter-actions between the ring C-H and nitro groups of adjacent mol-ecules creating puckered sheets perpendicular to the c axis. The H atoms of the methyl group in the 5-position are disordered (60° rotation) with an occupancy of 0.616 (19) for the major component. The crystal was …

An Integrated Systems Approach To Deconstructing Glycosylation, L. K. Mahal, John F. Rakus, Kanoelani Pilobello, P. Agrawal

Chemistry Faculty Research

Glycosylation involves the post-translational addition of carbohydrates to protein molecules and is an intricate and indispensable biochemical process. Study of this complicated network of interactions is hindered by the lack of a coding template analogous to the genetic code, and by the vast structural complexity inherent to carbohydrate polymers. We use lectins (non-enzymatic carbohydrate-binding proteins of non-immunological origin) as microarray probes to identify carbohydrate features expressed on cellular surfaces. Specifically, we utilized lectin microarray technology to investigate the differences in carbohydrates expressed by the cell lines of the Nation Cancer Institute’s NCI-60 panel. Our investigation identified tissue-specific expression differences in …

Green Synthesis Of Polycyclic Benzimidazole Derivatives And Organic Semiconductors, Masashi Mamada, Cesar Perez-Bolivar, Pavel Anzenbacher Jr.

Chemistry Faculty Publications

Polycyclic benzimidazole derivatives, an important class of compounds in organic electronics and photovoltaics, were prepared using a solvent-free "green" process based on heating carboxylic acid anhydrides and arylene diamines in the presence of zinc acetate in the solid state. Products were isolated and purified directly by train sublimation of the crude reaction mixtures. The reaction conditions were optimized using various carboxylic acid anhydrides. Optical and electrochemical properties of these materials are also described.

Probing Single-Molecule Enzyme Active-Site Conformational State Intermittent Coherence, Yufan He, Yue Li, Saptarshi Mukherjee, Yan Wu, Honggao Yan, H. Peter Lu

Chemistry Faculty Publications

The relationship between protein conformational dynamics and enzymatic reactions has been a fundamental focus in modern enzymology. Using single-molecule fluorescence resonance energy transfer (FRET) with a combined statistical data analysis approach, we have identified the intermittently appearing coherence of the enzymatic conformational state from the recorded single-molecule intensity-time trajectories of enzyme 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) in catalytic reaction. The coherent conformational state dynamics suggests that the enzymatic catalysis involves a multistep conformational motion along the coordinates of substrate-enzyme complex formation and product releasing, presenting as an extreme dynamic behavior intrinsically related to the time bunching effect that we have reported previously. …

Energy Transfer From Fluorescent Proteins To Metal Nanoparticles, Suraj Saraswat, Anil Desireddy, Desheng Zheng, Lijun Guo, H. Peter Lu, Terry P. Bigioni, Dragan Isailovic

Chemistry Faculty Publications

Energy transfer plays a significant role in numerous chemical, physical, and biological processes. While the use of fluorescent proteins in Forster resonance energy transfer (FRET) studies of biomolecules is common, energy transfer between fluorescent proteins and inorganic nanoparticles has not been explored in detail. In this study, energy transfer from fluorescent phycobiliproteins to noble metal nanoparticles was analyzed. Solutions of B-phycoerythrin (B-PE) were mixed with colloidal Au and Ag nanoparticles and were characterized by steady-state and time-resolved fluorescence spectroscopy to determine the magnitude and mechanism of the energy transfer. It was found that the protein fluorescence was quenched after the …

Effects Of Weathering On Aromatic Compounds In Beach Tars From The Deepwater Horizon Disaster, Gulf Of Mexico Coast, Usa, Michael A. Kruge

Department of Earth and Environmental Studies Faculty Scholarship and Creative Works

Operators aboard the Deepwater Horizon drilling platform lost control of the Macondo No. 1 well about 90 km southwest of the Louisiana coast on April 20, 2010, leading to a catastrophic release of ca. 550 Gg of crude oil over the next 86 days [1]. Oil from the spill soon found its way to nearby coastal areas, leaving tarry deposits on beaches and marshes. Oil was reported on the beach at Gulf Shores, Alabama (180 km northeast of the well) on June 5 and the relatively fresh sample discussed herein (GSA) was collected that same day. Oil reached the beach …

Eerc Laboratory Capabilities, University Of North Dakota. Energy And Environmental Research Center

EERC Brochures and Fact Sheets

Brochure about the Energy & Environmental Research Center (EERC) laboratory facilities, equipment, and capabilities. Includes information on Analytical Research Laboratory, Natural Materials Analytical Research Laboratory, Applied Geology Laboratory, and Environmental Chemistry Laboratory. [This item is an outdated or superseded version and retained for historical purposes only. It may no longer reflect current information, policies, or practices.]

Towards The Rational Design Of Mri Contrast Agents: Δ-Substitution Of Lanthanide(Iii) Nb-Dota-Tetraamide Chelates Influences But Does Not Control Coordination Geometry, Christiane E. Carney, Anh D. Tran, Jing Wang, Matthias C. Schabel, A. Dean Sherry, Mark Woods

Chemistry Faculty Publications and Presentations

LnDOTA-tetraamide chelates (DOTA=1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid) have received considerable recent attention as a result of their potential to act as PARACEST contrast agents for magnetic resonance imaging (MRI). Although PARACEST agents afford several advantages over conventional contrast agents they suffer from substantially higher detection limits; thus, improving the effectiveness of LnDOTA-tetraamide chelates is an important goal. In this study we investigate the potential to extend conformational control of LnDOTA-type ligands to those applicable to PARACEST. Furthermore, the question of whether δ- rather than α-substitution of the pendant arms could be used to control the chelate coordination geometry is addressed. Although δ-substitution does …

The Vinylguaiacol/Indole Or Vgi ("Veggie") Ratio: Assessing Relative Contributions Of Terrestrial And Aquatic Organic Matter To Sediments, Michael A. Kruge, Kevin K. Olsen, Jaroslaw W. Slusarczyk, Elaine Gomez

Department of Earth and Environmental Studies Faculty Scholarship and Creative Works

In studies of the organic matter (OM) fraction of marine, estuarine, fluvial, or lacustrine sediments, one of the most fundamental distinctions to be made is that between terrestrial and aquatic OM. To supplement the parameters commonly used for this purpose (e.g., C/N and stable isotope ratios), we proposed the Vinylguaiacol/Indole or VGI ("Veggie") ratio, defined as [vinylguaiacol / (indole + vinylguaiacol)] using data produced by analytical pyrolysis-gas chromatography/mass spectrometry of dried, homogenized sediment samples [1]. The ratio employs the peak areas of these two compounds on the mass chromatograms of their molecular ions (m/z 150 and 117, respectively). Major pyrolysis …