Digital Commons Network^™

Three Unique Coordination Geometries Involving 1,2-Dimethoxy-4,5-Bis(2-Pyridylethynyl)Benzene, Jeffrey E. Fiscus, Sandra Shotwell, Ralph C. Layland, Mark D. Smith, Hans Conrad Zur Loye, Uwe H. F. Bunz

Faculty Publications

Reaction of the new ligand 1,2-dimethoxy-4,5-bis(2-pyridylethynyl) benzene with different metal centers under similar reaction conditions led to three distinct structure formation processes: molecular ring closure, dimerization, and polymer formation.

The Study Of Biological Membranes Using The Atomic Force Microscope, Brandy L. Perkins

Electronic Dissertations and Theses

In the past research, when a carbon nanotube enhanced cantilever was probed along a living cell membrane, carboxylic acid groups located at the tips of the nanotubes would interact with various groups on the surface of the membrane causing it to rupture. A method to re-derivatize the tips of the nanotubes through covalent bonding by allowing the amine groups to attach to the carboxylic acid groups was developed. This chemical change perhaps will allow one to probe a cell surface without rupturing it. Successful nanotube derivatization will eventually lead to a map of the surface of living cell membranes and …

Phytoremediation Of Lead By Chinese Tallow (Sapium Sebiferum) Plant, Oluwaseumi A. Odebunmi

Electronic Dissertations and Theses

Over the past several decades, health and environmental risks of pollution have become apparent. As a result, environmental regulations have been created to remediate areas where environmental contamination is tremendous, therefore, a low-cost alternative to the already existing technology is needed. Using plants to eliminate hazardous organic compounds from contaminated soils has been proposed as an efficient means of remediation. Phytoremediation is the direct use of living green plants to remediate soil, sludge, sediments and ground water contaminated with toxic compounds. The four processes of phytoremediation are rhizofiltration, phytoextraction, phytostabilization and phytodegradation. As they 'grow and develop, plants will use …

The Biosynthetic Gene Cluster For The Anticancer Drug Bleomycin From Streptomyces Verticillus Atcc15003 As A Model For Hybrid Peptide–Polyketide Natural Product Biosynthesis, B. Shen, Liangcheng Du, C. Sanchez, D. J. Edwards, M. Chen, J. M. Murrell

Liangcheng Du Publications

The hybrid peptide–polyketide backbone of bleomycin (BLM) is assembled by the BLM megasynthetase that consists of both nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) modules. BlmIX/BlmVIII/BlmVII constitute a natural hybrid NRPS/PKS/NRPS system, serving as a model for both hybrid NRPS/PKS and PKS/NRPS systems. Sequence analysis and functional comparison of domains and modules of BlmIX/BlmVIII/BlmVII with those of nonhybrid NRPS and PKS systems suggest that (1) the same catalytic sites appear to be conserved in both hybrid NRPS–PKS and nonhybrid NRPS or PKS systems, with the exception of the KS domains in the hybrid NRPS/PKS systems that are unique; (2) …

Fluorescence And Light Scattering Studies Of Aromatic Polymers Near The Critical Concentration C*, M.Sean Healy

Seton Hall University Dissertations and Theses (ETDs)

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Direct Imaging Of Human Swi/Snf-Remodeled Mono- And Polynucleosomes By Atomic Force Microscopy Employing Carbon Nanotube Tips, Gavin R. Schnitzler, Chin Li Cheung, Jason H. Hafner, Andrew J. Saurin, Robert E. Kingston, Charles M. Lieber

Barry Chin Li Cheung Publications

Chromatin-remodeling complexes alter chromatin structure to facilitate, or in some cases repress, gene expression. Recent studies have suggested two potential pathways by which such regulation might occur. In the first, the remodeling complex repositions nucleosomes along DNA to open or occlude regulatory sites. In the second, the remodeling complex creates an altered dimeric form of the nucleosome that has altered accessibility to transcription factors. The extent of translational repositioning, the structure of the remodeled dimer, and the presence of dimers on remodeled polynucleosomes have been difficult to gauge by biochemical assays. To address these questions, ultrahigh-resolution carbon nanotube tip atomic …

Simultaneous Determination Of Enantiomers Of Structurally Related Anticholinergic Analogs In Human Serum By Liquid Chromatography–Electrospray Ionization Mass Spectrometry With On-Line Sample Cleanup, Vladimı́R Čápka, Yan Xu

Chemistry Faculty Publications

Trihexyphenidyl, biperiden and procyclidine are anticholinergic drugs produced as racemates for the treatment of Parkinson’s disease. This paper describes a simple and sensitive LC–MS method for the simultaneous determination of these compounds in human serum. An on-line sample clean-up procedure was used, where serum samples were directly injected into a “restricted-access media” pre-column. After the exclusion of the serum proteins, the drug molecules were eluted to a β-cyclodextrin analytical column for chiral separation. The quantitation was done by electrospray ionization MS using diphenidol as an internal standard. The method developed has limits of detection of 1 ng/ml, at least two-orders-of-magnitude …

Effect Of Surface Charges On The Rates Of Intermolecular Electron-Transfer Between De Novo Designed Metalloproteins, Anna Y. Kornilova, James F. Wishart, Michael Y. Ogawa

Chemistry Faculty Publications

A de novo designed coiled-coil metalloprotein was prepared that uses electrostatic interactions to control both its conformational and bimolecular electron-transfer properties. The title protein exists as a coiled-coil heterodimer of the [Ru(trpy)(bpy)-KK(37-mer)] and [Ru(NH3)(5)-EE(37-mer)] polypeptides which is formed by interhelix electrostatic attractions. Circular dichroism studies show that the electrostatic heterodimer has Kd 0.19 +/- 0.03 muM and is 96% helical at high concentrations. Intercomplex electron-transfer reactions were studied that involve the [Ru(NH3)(5)-H21](2+) electron-donor and the [Ru(trpy)(bpy)H21](3+) electron-acceptor belonging to different electrostatic dimers. An important feature of the designed metalloprotein is its two cationic redox centers embedded within protein surfaces having …

Energetics And Cooperativity In Three-Center Hydrogen Bonding Interactions. I. Diacetamide-X Dimers .X=Hcn, Ch3Oh., Ruben D. Parra, Makoto Furukawa, Bing Gong, Xiao Cheng Zeng

Xiao Cheng Zeng Publications

High level ab initio calculations are carried out on diacetamide–X (DA–X) dimers, X=HCN, CH₃OH. The dimers are used as model systems to investigate the energetics and cooperative phenomomena in intermolecular three-center hydrogen-bond (H-bond) interactions relative to two-center H-bond interactions. The trans–trans conformer of diacetamide is chosen as a suitable model for intermolecular three-center H bonding where one H atom is interacting with two acceptor atoms. The proton–acceptor atoms are rigidly held in the same molecule. For both model systems, it is found that the calculated interaction energy per H bond is appreciably smaller in the three-center than in …

Crystal Structure Of Mtan, A Global Multidrug Transporter Gene Activator, Michael H. Godsey, Natalya N. Baranova, Alexander A. Neyfakh, Richard G. Brennan

CUP Faculty Research

MtaN (Multidrug Transporter Activation, N terminus) is a constitutive, transcriptionally active 109-residue truncation mutant, which contains only the N-terminal DNA-binding and dimerization domains of MerR family member Mta. The 2.75 Å resolution crystal structure of apo-MtaN reveals a winged helix-turn-helix protein with a protruding 8-turn helix (α5) that is involved in dimerization by the formation of an antiparallel coiled-coil. The hydrophobic core and helices α1 through α4 are structurally homologous to MerR family member BmrR bound to DNA, whereas one wing (Wing 1) is shifted. Differences between the orientation of α5 with respect to the core and the revolution of …

Energetics And Cooperativity In Three-Center Hydrogen Bonding Interactions. Ii. Intramolecular Hydrogen Bonding Systems, Ruben D. Parra, Bing Gong, Xiao Cheng Zeng

Xiao Cheng Zeng Publications

High level ab initio calculations have been carried out on a number of intramolecular two- and three-center H-bonding structures containing the amide motif, NHC=O. These structures serve as model systems for probing the stability of intramolecular three-center H bonds of the type A₁HA₂. Particular attention is given to cooperative effects in the three-center H-bonding structures. A systematic assessment of cooperativity for intramolecular H-bonding systems is presented.

Synthesis Of Cyclopropane Containing Natural Products, William A. Donaldson

Chemistry Faculty Research and Publications

The synthesis of select cyclopropane containing natural products is presented.

Studies On The Electrochemical Properties Of Phosphate Derivatives Of C60, Ying Liu, Li Ding, Lou-Zhen Fan, Fu-Yong Cheng, Zhong-Da Wu

Journal of Electrochemistry

The phosphorus chemistry of fullerene was investigated for the first time. We have synthesised three novel phosphate derivatives of C₆₀. Their electrochemical properties were detected by cyclic voltammetry (CV). The influence of different substituents on the electron-accepting ability of methanofullerenes was also observed by the comparative study on the electrochemical properties of different C₆₀ derivertives.

A Qualitative Investigation Of The Polymerization Process In The Ihss Humic Substances Extraction Procedure Using Model Phenolic Compounds, Roger J. Germay

Masters Theses

Achard (1786) extracted peat with alkali and reported obtaining dark compounds now called humic substances. These are complex, high molecular weight, polyphenolic compounds naturally occurring in soil, in fresh-water and in marine environments. They are biodegradation products of plant materials.

The International Humic Substances Society (IHSS) adapted Achard's method to separate humic substances into three fractions: (1) humic acids (HA), soluble only at high pH; (2) fulvic acids (FA), water-soluble at any pH; and (3) humin, insoluble at any pH. The IHSS method involves contact of soil with 0.1N.NaOH solution, followed by acidification with HCl.

In this study, 0.01 N. …

Physicochemical Characteristics Of Some Locally Manufactured Edible Vegetable Oils Marketed In Dar Es Salaam, F N Ngassapa, O C Othman

Tanzania Journal of Science

The physicochemical properties (refractive index, saponification value, Free Fatty Acid (FFA) value, iodine value, acid value, peroxide value and tocopherol content) of seven edible vegetable oils manufactured in Tanzania, were assessed using standard procedures of the Association of Official Analytical Chemists (AOAC). Also determined were the levels of these properties with respect to shelf storage of the products. When compared with standard values recommended by the Codex Alimentarius Commission of FAO/WHO and with other published results, the locally produced vegetable oils were found to be of fair quality but of poor storage stability.

43rd Rocky Mountain Conference On Analytical Chemistry

Rocky Mountain Conference on Magnetic Resonance

Final program, abstracts, and information about the 43rd annual meeting of the Rocky Mountain Conference on Analytical Chemistry, co-sponsored by the Colorado Section of the American Chemical Society and the Rocky Mountain Section of the Society for Applied Spectroscopy. Held in Denver, Colorado, July 29 - August 2, 2001.

Structural And Functional Imaging With Carbon Nanotube Afm Probes, J. H. Hafner, Chin Li Cheung, A. T. Woolley, C. M. Lieber

Barry Chin Li Cheung Publications

Atomic force microscopy (AFM) has great potential as a tool for structural biology, a field in which there is increasing demand to characterize larger and more complex biomolecular systems. However, the poorly characterized silicon and silicon nitride probe tips currently employed in AFM limit its biological applications. Carbon nanotubes represent ideal AFM tip materials due to their small diameter, high aspect ratio, large Young’s modulus, mechanical robustness, well-defined structure, and unique chemical properties. Nanotube probes were first fabricated by manual assembly, but more recent methods based on chemical vapor deposition provide higher resolution probes and are geared towards mass production, …

Cyp83b1 Is The Oxime-Metabolizing Enzyme In The Glucosinolate Pathway In Arabidopsis, Carsten Horslev Hansen, Liangcheng Du, Peter Naur, Carl Erik Olsen, Kristian B. Axelsen, Alastair J. Hick, John A. Pickett, Barbara Ann Halkier

Liangcheng Du Publications

CYP83B1 from Arabidopsis thaliana has been identified as the oxime-metabolizing enzyme in the biosynthetic pathway of glucosinolates. Biosynthetically active microsomes isolated from Sinapis alba converted p-hydroxyphenylacetaldoxime and cysteine into S-alkylated p-hydroxyphenylacetothiohydroximate, S-(p-hydroxyphenylacetohydroximoyl)-L-cysteine, the next proposed intermediate in the glucosinolate pathway. The production was shown to be dependent on a cytochrome P450 monooxygenase. We searched the genome of A. thaliana for homologues of CYP71E1 (P450ox), the only known oxime-metabolizing enzyme in the biosynthetic pathway of the evolutionarily related cyanogenic glucosides. By a combined use of bioinformatics, published expression data, and knock-out phenotypes, we identified the …

Intrasteric Inhibition Of Atp Binding Is Not Required To Prevent Unregulated Autophosphorylation Or Signaling By The Insulin Receptor, Mark Frankel, Ararat J. Ablooglu, Joseph W. Leone, Elena Rusinova, J. B. A. Ross, Robert L. Heinrikson, Ronald A. Kohanski

Chemistry and Biochemistry Faculty Publications

Receptor tyrosine kinases may use intrasteric inhibition to suppress autophosphorylation prior to growth factor stimulation. To test this hypothesis we made an Asp1161Ala mutant in the activation loop that relieved intrasteric inhibition of the unphosphorylated insulin receptor (IR) and its recombinant cytoplasmic kinase domain (IRKD) without affecting the activated state. Solution studies with the unphosphorylated mutant IRKD demonstrated conformational changes and greater catalytic efficiency from a 10-fold increase in kcat and a 15-fold-lower K_{m ATP} although K_{m peptide} was unchanged. Kinetic parameters of the autophosphorylated mutant and wild-type kinase domains were virtually identical. The Asp1161Ala mutation increased the …

Quorum Sensing In The Dimorphic Fungus Candida Albicans Is Mediated By Farnesol, Jacob M. Hornby, Ellen C. Jensen, Amber C. Lisec, Joseph J. Tasto, Brandon Jahnke, Richard Shoemaker, Patrick Dussault, Kenneth W. Nickerson

Patrick Dussault Publications

The inoculum size effect in the dimorphic fungus Candida albicans results from production of an extracellular quorum-sensing molecule (QSM). This molecule prevents mycelial development in both a growth morphology assay and a differentiation assay using three chemically distinct triggers for germ tube formation (GTF): L-proline, N-acetylglucosamine, and serum (either pig or fetal bovine). In all cases, the presence of QSM prevents the yeast-to-mycelium conversion, resulting in actively budding yeasts without influencing cellular growth rates. QSM exhibits general cross-reactivity within C. albicans in that supernatants from strain A72 are active on five other strains of C. albicans and vice versa. …

Complex Effects Arising In Smoke Plume Simulations Due To Inclusion Of Direct Emissions Of Oxygenated Organic Species From Biomass Combustion, Sherri A. Mason, Richard J. Field, Robert J. Yokelson, Michael A. Kochivar, Mark R. Tinsley, Darold E. Ward, Wei Min Hao

Chemistry and Biochemistry Faculty Publications

Oxygenated volatile organic species (oxygenates), including HCOOH, H₂CO, CH₃OH, HOCH₂CHO (hydroxyacetaldehyde), CH₃COOH, and C₆H₅OH, have recently been identified by Fourier transform infrared measurements as a significant component of the direct emissions from biomass combustion. These oxygenates have not generally been included in the hydrocarbon-based initial emission profiles used in previous photochemical simulations of biomass combustion smoke plumes. We explore the effects of oxygenates on this photochemistry by using an established initial emission hydrocarbon profile and comparing simulation results obtained both with and without addition of the above six …

Shape Imprinting Due To Variable Disulfide Bonds In Polyacrylamide Gels, Andrew B. Greytak, Alexander Y. Grosberg, Toyoichi Tanaka

Faculty Publications

Through the use of variable disulfide crosslinkers, we have created polyacrylamide gels whose shape can be altered after polymerization. N,N'-bisacryloylcystamine is incorporated as a crosslinker, along with a smaller amount of a permanent crosslinker. After polymerization, the disulfide bonds are cleaved into thiols through reduction. By reoxidizing the thiols with the gel held in a new macroscopic shape, a new set of disulfide bonds is formed, and the gel is forced to adopt the new shape. Retension of the new shape improves with greater distortion from the original shape, as well as with increased concentration of variable …

Quantification Of Benzo[A]Pyrene-Guanine Adducts In In Vitro And In Vivo Tissue Samples By Lc Tandem Mass Spectrometry, Po-Chang Chiang

Dissertations

No abstract provided.

Efficient New Ribozyme Mimics: Direct Mapping Of Molecular Design Principles From Small Molecules To Macromolecular, Biomimetic Catalysts, William C. Putnam, Andrew T. Daniher, Bobby N. Trawick, James K. Bashkin

Educator Preparation & Leadership Faculty Works

Dramatic improvements in ribozyme mimics have been achieved by employing the principles of small molecule catalysis to the design of macromolecular, biomimetic reagents. Ribozyme mimics derived from the ligand 2,9-dimethylphenanthroline (neocuproine) show at least 30-fold improvements in efficiency at sequence-specific RNA cleavage when compared with analogous o-phenanthroline- and terpyridine-derived reagents. The suppression of hydroxide-bridged dimers and the greater activation of coordinated water by Cu(II) neocuproine (compared with the o-phananthroline and terpyridine complexes) better allow Cu(II) to reach its catalytic potential as a biomimetic RNA cleavage agent. This work demonstrates the direct mapping of molecular design principles from small-molecule …

Quantification Of Nanomolar Superoxide In Aqueous Solution : Flow Injection Analysis Using The Chemiluminescent Reagent Mcla., Nathan Boland

Honors Theses

A flow injection system using the chemiluminescent reagent 2-methyl-6-(4methoxyphenyl)- 3,7-dihydroimidazo[1,2-a]pyrazin-3-one (MCLA) was used to quantify aqueous concentrations of superoxide. Stock solutions of superoxide were produced by photolysis of a solution of 2-propanol and benzophenone. The concentration of superoxide was quantified in the stock solutions by direct measurement of the absorbance at 240 nm. Quantified additions of superoxide to the flow injection analysis system reacted with MCLA at pH 5.1 demonstrated a detection limit of 0.074 nM superoxide. Selective superoxide detection was confirmed by pH-dependent decay of superoxide, which was in excellent agreement with published rates.

Metal Ion Stabilization Of G-Tetrads Containing 6-Thioguanosine, Julia Drees

Honors Theses

As alternative structures to the double helix, G-tetrads are thought to occur in DNA with many repeating deoxyguanosines (dG). These tetrads have one dG on each corner of a plane and can stack into tetraplexes that can be aptamers and may be found in telomeres. G-tetrads are destabilized by incorporation of 6-thiodeoxyguanosine (?sdG). Addition of metal ions that bind sulfur may stabilize these ?sdG-tetrads. We have carried out a survey of metal ion titrations into ?sG. Stable ?sG:MD? complexes were found for Hg2? (2:1), Cd2? (4:1), Ag2? (0.7:1) and Pt2? (thought to be 2:1). UV/Visible spectrophotometry indicates that G-tetrads containing …

Effects Of Eluent Ph And Different Types Of Acidic Modifiers On The Retention And Electrospray Ionization Efficiency Of Basic Analytes In Lc-Esi-Ms., Unita L. Peri-Okonny

Seton Hall University Dissertations and Theses (ETDs)

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PkA Determination Of Enzyme Bound Coenzyme M With Epoxyalkane: Com Transferase, Matthew Stephen Mciff

Undergraduate Honors Capstone Projects

Epoxide metabolism in the aerobic bacterium Xanthobacter strain Py2 proceeds by a coenzyme M (2-mercaptoethanesulfonic acid), NADPH, and NAD⁺ dependent carboxylation reaction that form beta keto acids as products. Epoxide carboxylase, the enzyme catalyzing this reaction, was resolved into four protein components that are required for functional reconstitiution of epoxide carboxylase activity. Component I, the first step in epoxide carboxylation, catalyzes the conversion of R and S-epoxypropane into Rand S-hydroxypropyl-coenzyme M respectively. This reaction consists of an epoxide ring opening, nucleophilic addition of coenzyme M, and oxygen reduction. Coenzyme M, a compound previously found only in the methanogenic Archaea, …

New Approaches To Processing Nanoparticles And Nanostructures, Mathew M. Maye

Undergraduate Honors Theses

The study of nanoparticles is an emerging field of nanoscience and nanotechnology. A challenging issue is how deliberate tailoring and processing of the nanoscale materials can lead to well defined and functional nanostructures. In this thesis, we explore new strategies of nanoscale design and processing to address the challenge.

A core-shell chemical processing route towards fabrication of functional composite nanomaterials with defined sizes, shapes, compositions and surface properties is demonstrated. New findings of an investigation of thermally-activated core-shell reactivities of nanoparticles in solutions are described. Gold nanoparticles of ~2-nm core size with thiolate monolayer encapsulation were chosen as a model …

Energy Gaps In “Metallic” Single-Walled Carbon Nanotubes, Min Ouyang, Jin-Lin Huang, Chin Li Cheung, Charles Lieber

Barry Chin Li Cheung Publications

Metallic single-walled carbon nanotubes have been proposed to be good one-dimensional conductors. However, the finite curvature of the graphene sheet that forms the nanotubes and the broken symmetry due to the local environment may modify their electronic properties. We used low-temperature atomically resolved scanning tunneling microscopy to investigate zigzag and armchair nanotubes, both thought to be metallic. “Metallic” zigzag nanotubes were found to have energy gaps with magnitudes that depend inversely on the square of the tube radius, whereas isolated armchair tubes do not have energy gaps. Additionally, armchair nanotubes packed in bundles have pseudogaps, which exhibit an inverse dependence …