Chemistry & Biochemistry Theses and Dissertations

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THE REACTION OF THE MONO ETHYL ENOL ETHER OF DIHYDRORESORCINOL WITH o-, m- AND p-TOLYLMAGNESIUM BROMIDES
(1949) Van Artsdale, Anna Lee; Chemistry; University of Maryland (College Park); Digital Repository at the University of Maryland
Heats of Combustion and Formation of Some Simple Aliphatic Amines
(1958) Jaffe, Irving; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, MD)
The Effect of Changes in Structure of the Reactants on the Rate of Enamine Formation
(1964) Marchese, James Salvatore; Pratt, Ernest F.; Chemistry & Biochemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md)
It has been found that the rate of formation of a wide variety of enamines can be accurately determined by observing the rate at which the by-product water collects in a Dean-Stark trap. On the basis of the results observed upon varing the reactant ratio, the catalyst concentration and the temperature, 0.125 mole of carbonyl compound, 0.375 mole of amine and .001 mole of p-toluenesulfonic acid dissolved in sufficient benzene to give a total volume of 500 ml. were employed in the standard procedure. The solution of reactants was heated under reflux in an apparatus fitted with a water trap and frequent readings of time and water volume were taken until the reaction was complete. Nearly quantitative (98 to 100%) yields of water were ordinarily obtained and 85 to 100% yields of enamine were usually isolated. As the structure of the carbonyl component was varied an extremely wide range of reaction rates was encountered. The relative reactivity of many of these compounds had not been determined preciously. It was found that the rate decreased markedly among cyclic ketones as the ring was expanded from five to six to seven members and also when the methyl group of methylcylohexanones were shifted from the four to the three to the two position, Steric effects appear to be responsible for these rate differences. Somewhat unexpectedly ∝-tetralone did not react while β-tetralone reacted smoothly. Although the literature contains very little information on the formation of enamines of diketones a number of these were converted to the mono-enamines very smoothly. The rate decreased in the sequence, 1, 3-cyclohexanedione, dimedone, acetylacetone, benzoylacetone and 2-acetylcyclopentanone. Some evidence that ketones having planar structures reacted faster than those with non-planar structures was found, but no obvious correlation between degree of enolization and rate of reaction was observed. The reaction of acetophenones was much improved when the reaction temperature was changed from 82° to 112° by using toluene as a solvent. As the electron attracting ability of the para substitute was inreased in the order, CH3, H, Cl and N02 the rate consistently increased. Phenylacetone reacted smoothly under the standard conditions, but heptanone-2 gave only a 27% yield of water in five days . The importance of steric factors is emphasized by the fact that cyclohexanone gave a 98% yield of water in two hours. Typical aliphatic aldehydes reacted so rapidly that in order to increase the accuracy of t;he rate measurements 0.000125 mole of catalyst was used in place of the standard 0.001 mole. The order of decreasing rate was phenylacetaldehyde, It is apparent that the rate decreasing effect of chain branching at the alpha position diminishes when the branches are joined into a ring. The results for phenylacetaldehyde and phenylacetone indicated that aldehydes react over one thousand times as fast as ketones. The rate of formation of enamines from cyclohexanone and a variety of amines was also determined under the standard conditions. Shifting a methyl group on the piperidine ring from the four to the three to the two position greatly decreased the rate and pyrrolidine reacted faster than both piperidine the and hexamethylene imine. Morpholine and especially N methylpiperazine reacted much faster than piperidine while n-butylmethylamine reacted most slowly of all the amines mentioned. In only a few special cases was integral order kinetics obtained. The results can, however, be quite well correlated with a straightforward mechanism if it is assumed that both the step in which the amine adds to the carbonyl group and the step in which this addition product is dehydrated ordinarily affect the overall rate.
The Photochemistry of Amides and Phthalimides
(1977) Bowen, Michael William; Mazzocchi, Paul H.; Organic Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md); ILLiad # 1481769
N-Alkyl amides undergo photodecomposition much slower than their ketone, ester, and aldehyde analogs . The Norrish Type II process in amides is also less important than in these other classes of compounds due to electronic and geometric effects. Type II products account for less than 10% of the decomposed amides in all cases and usually less than 5%. A 2% solution of amide in dioxane, when irradiated through quartz with light >200 nm, did not decompose in the Type II fashion to yield N-alkyl acetamides, alkenes, and unsubstituted amides. The preferred reaction mode was the Norrish Type I process where the O=C+N bond or the O=C+C bond was cleaved to yield either an acyl radical and amine radical or an acyl radical and alkyl radical. These photochemically unstable radicals, once produced, rapidly underwent secondary reactions to yield smaller molecules. These molecules were detected, underwent further reactions (polymerization; photoreduction), or interacted with the solvent . The dimers of dioxane and cyclohexane, created via hydrogen abstraction, were the main products of amide photodecomposition in these solvents. Small aldehydes and alkenes produced as intermediates, underwent inefficient photoreductions with solvent to afford alkyl dioxanes and cyclohexanes and the two diastereomers of ( 2-p-dioxyl ) ethanol as other major products. The alcohols were also produced by photoreduction of acetaldehyde and hexanal as well as by direct photodecomposition of dioxane . Tertiary amides reacted faster than secondary amides. The Type I reaction was accelerated by electronic (inductive) factors. The Type II reaction was also more efficient due to geometric and electronic factors. The Type I amine product, dihexylamine, was observed as an intermediate in the photodecomposition of N, N-dihexylhexanoamide . Unsymmetrical anilide imides photodecomposed in dioxane to yield a wide variety of products. The Photo-Fries decomposition mode was most favored where acyl groups migrated to positions ortho and para to the amine substituent. For example, N-acetyl-butyranilide decomposed to yield o- and p-acetoaniline, o - and p-butyraniline , o- and p-acetobutyranilide, and o- and p-butyracetanilide. Very little Type II decomposition was observed, that is, N-acetyl-butyranilide yielding N, N -diacetylaniline or o- and p-acetoacetanilide. N-Alkylphthalimides were the sole group of amides or imides reported in the literature to undergo efficient Y-hydrogen abstraction. These compounds underwent initial Y-hydrogen abstraction to yield a 1,4-biradical followed by ring closure to form an azacyclobutanol intermediate. The intermediate then underwent retrotransannular ring opening to yield various 3,4-benzo-6,7-dihydro(1H)azepine-2,5-diones. Dihydrophthalimide alkenes were minor products in acetonitrile which arose after the initial y-hydrogen abstraction via subsequent δ-hydrogen transfer. Quantum yield determination as well as mechanistic investigation was conducted . The quantum yields varied from 0.023 to 0.003. Photolysis of an optically active phthalimide with an asymmetric Y-position to yield starting material of the same activity proved that the initial hydrogen abstraction was irreversible. A Type I cleavage to yield phthalic anhydride on treatment with silica gel and heat was important when they Y-position was tertiary. A quenching study of these N-alkylphthalimides with piperylene showed acceleration of starting material disappearance but decrease in product formation. An additional reaction process was interfering with the azepinedione formation. Liquid chromatography showed formation of several highly alkylated products which could not be isolated in pure form. N-Methylphthalimide, which could not ring expand, was irradiated with various alkenes to produce analogous N-methylazepinediones. The mechanism involved a 2 + 2 cyclo-addition of the double bond to the C-N bond to yield a dipolar azacyclobutanc intermediate. The intermediate with a retrotransannular ring opening yielded the observed 3, 4- benzo-6,7-dihydro-1-methylazepine-2,5-diones. These reactions prove that the C-N bond in phthalimide is of a substantial double bond character.
Micro-scale Chemical Effects of Low Temperature Weathering of DSDP Basaltic Glasses
(1979) Ailin-Pyzik, Iris Blanche; Sommer, Sheldon E.; Chemistry & Biochemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md)
Unaltered deep-sea basaltic g lasses are believed to be the best record of initial magma composition , and as such are important in the study of petrogenesis. However , these glasses are altered by their long contact with seawater, becoming hydrated and undergoing chemical exchange. This chemical exchange affects the composition of seawater and plays a role in the chemical equilibrium of t he oceans. A study of the trace metal and major element alteration of glasses from Deep Sea Drilling Project Site 396B has been conducted, using a selected area x - ray fluorescence technique (developed for this study) for the trace metal analyses, and the electron rnicroprobe for the major elements. The samples included sections of pillow basalt rinds, hyaloclastite s, and a few crystalline sections. The glasses were found to release a bout o ne- half the original Si and Al, two- thirds of the Mg and Na , and over 90% of the Ca originally present, during alteration to palagonite. Fe and Ti were found to be immobile, and K was increased 40-fold by concentration from seawater. For the trace metals, over one-quarter of the Zn, Cu and Ni were released, 40% of the Mn, and over 10% of the Cr. These changes apply only to the conversion of fresh glass (sideromelane ) to palagonite (smectite), and do not include the effects of authigenic phillipsite and calcite reprecipitated locally. Differences between the effects of low temperature weathering on the crystalline basalts and the glasses appear to be primarily a function of the susceptibility of the primary mineral phases to attack, with the glass, being the least stable phase, being the most altered.
Experimental and Theoretical Characterization of Effective Interactions Near 132Sn
(1987) Stone, Craig A.; Walters, William B.; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, MD)
Experimental investigations have been undertaken to study the multiplet structure in six nuclei near 132Sn: 132,130Sb, 131,129,127Sb, and 132Te. Experiments were performed using ion beams of mass-separated fission products produced by the TRISTAN mass separator at Brookhaven National Laboratory. Extensive four-detector gamma-gamma coincidences, gamma-multiscaling and conversion-electron data have been collected. Ultralarge shell model calculations were performed using the VLADIMIR shell model code on the Cray/CDC 7600 supercomputer system at Lawrence Livermore National Laboratory. These calculations were designed to look at the performance of the Kallio-Kolltveit and Siemen's g-matiix potentials on the 1-3 quasiparticle nuclides in the gddsh model space. Results show that realistic potentials work well on nuclei near 132Sn but show problems with 129,130Sn and 131Sb which can not be accounted for by core-polarization corrections. Problems are shown to be due to the use of a potential derived with the Scott-Moszkowski separation metl1od. The separation distance was demonstrated to have a weak dependence on the principal quantum number but a strong dependence on the orbital angular momentum. This suggests the Kallio-Kolltveit potential is underestimating the strength of the h11/2 interactions in 129,130Sn and 131Sb.
The Role of Hydrogen Cyanide in Chemical Evolution
(1989) Navarro-González, Rafael; Ponnamperuma, Cyril; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md)
Two major research areas are investigated: The electrosynthesis of hydrogen cyanide; and the role of cyanocomplexes in the free - radical oligomerization of hydrogen cyanide. The electric discharge production of hydrogen cyanide from a simulated primitive atmosphere composed of methane, nitrogen and water vapor was investigated. The radiation chemical yield (G) of formation of HCN was determined to be 0.26. A free radical mechanism was proposed to account for the observed chemical changes. Computer simulations of the reaction mechanism could effectively model the early stages of electrolysis of the gas mixture, and permitted the estimation of the rate of electrosynthesis of hydrogen cyanide under various atmospheric conditions . The possible role of cyanocomplexes of transition elements on the free- radical oligomerization of hydrogen cyanide was investigated. Aqueous, oxygenfree, dilute solutions of hydrogen cyanide and hexacyanoferrate(II) or (III) were submitted to various doses of gamma irradiation. The presence of either cyanocomplex led to a significant decrease in the rate of decomposition of hydrogen cyanide. The major products were ammonia and carbon dioxide . Computer simulations of these systems permitted the elucidation of the reaction mechanism and the derivation of rates of reactions of free- radicals with the cyanocomplexes. The results obtained provide an insight into the possible role of cyanocomplexes of transition elements in chemical evolution.
Investigation of the Tetrahymena Pyriformis 2-Aminoethylphosphonic Acid Biosynthetic Pathway and the P-C Bond Forming Enzyme Phosphoenolpyruvate Mutase
(1991) McQueney, Michael Scott; Dunaway-Mariano, Debra; Chemistry and Biochemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md)
The biosynthetic pathway leading to 2-aminoethylphosphonate in Tetrahymena pyriformis was determined. A cell-free homogenate of T. pyriformis converted phosphoenolpyruvate to AEP in 37% yield, phosphonopyruvate to AEP in a 11 % yield and phophonoacetaldehyde to AEP in an 83% yield. The Tetrahymena pyriformis enzyme, PEP mutase was purified. The PEP Mutase catalyzes the rearrangement of phosphoenolpyruvate to phosphonopyruvate and the equilibrium constant is >500:1 in favor of phosphoenolpyruvate. To distinguish between an intra-and intermolecular reaction pathway for this process an equimolar mixture of [P= ^18O, C(2)- ^18 O]thiophosphonopyruvate and (all - ^16Q)thiophosphonopyruvate was reacted with the PEP mutase and the resulting products were analyzed by ^31P-NMR. The absence of the cross over product [C(2)-18O]thiophosphonoenolpyruvate in the product mixture was interpreted as evidence for an intramolecular reaction pathway. To distinguish between a concerted and stepwise intramolecular reaction pathway the pure enantiomers of the chiral substrate [P= ^18Q]thiophosphonopyruvate were prepared and the stereochemical course of their conversion to chiral [P= ^18O]thiophosphoenolpyruvate was determined. Based on the observed conversion of (Sp) - [P= ^18O]thiophosphonopyruvate to (Sp)-[P= ^18O]thiophosphoenolpyruvate and (Rp) - [P = ^18O]thiophosphonopyruvate to (Rp)[P= ^18O]thiophosphoenolpyruvate it was concluded that the PEP phosphomutase reaction proceeds with retention of the phosphorus configuration and therefore by a stepwise mechanism. The similar reactivity of the oxo and thio substituted phosphonopyruvate substrates (i.e., nearly equal Vmax) was interpreted to suggest that addition to the phosphorus atom is not rate limiting among the reaction steps. Lastly, single turnover experiments failed to trap a pyruvate in the PEP mutase reaction.
Release of Aluminum, Arsenic, Cadmium, Chromium, Copper, Iron, Lead, and Zinc in a Coal Leachate, and their Removal from Solution Undergoing Neutralization
(1992) Tatum, Thomas Lee; Helz, George R.; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md)
Whole coal contains significant amounts of iron pyrite which is oxidized ultimately to ferric acid sulfate. As a result, trace elements are released from the coal and other minerals in potentially hazardous concentrations. The purpose of this research was to: 1) study the release and mobility of selected trace elements during the weathering of coal; 2) seek to understand factors controlling solubility of trace elements in a synthetic, acidic leachate undergoing gradual neutralization; and 3) develop a chemical thermodynamic computer model to predict the effects of dilution and neutralization of leachate on trace element mobility and speciation. Samples collected periodically from a slurry of whole ground coal in water were filtered and analyzed for dissolved sulfate (by ion chromatrography), iron (by flame atomic absorption spectrophotometry), and Al, Zn, Cd, Cu, Cr, Pb, As, and Se (by graphite furnace AAS). Iron, copper, and probably arsenic tracked the production of sulfate, while aluminum, zinc, chromium, and cadmium concentrations were stable or rose slightly. A synthetic leachate of ferric sulfate and sulfuric acid was doped with trace levels of Al, Zn, Cu, Cd, Cr, Pb, As, and Se. Slow injection of sodium bicarbonate solution neutralized the stirred system, though hydrolysis of iron buffered the pH near 2.5. Computer modeling of the sample analyses indicated that sulfate complexes dominated the speciation of iron and the trace elements. The other findings were used to develop a thermodynamic equilibrium model based on the aqueous geochemistry computer model PHREEQE. Iron and sulfate removal were best modeled by the precipitation of Fe16O16 (OH) 12 (SO4 ) 2. Aluminum solubility was modeled by precipitation of jurbanite below pH 4, of bayerite and basaluminite for pH 4 - 5, and of gibbsite at pH above 5. Chromium, copper, and lead removal was modeled by solid solution formation with the ferric oxyhydroxysulfate precipitates. Program convergence failures above pH 5 precluded the modeling of zinc and cadmium, but it is hypothesized that their ions are adsorbed onto suspended particles of hydrous ferric oxyhydroxides. The model was tested with our laboratory data, and field data from a creek system contaminated with acid sulfate mine drainage.
Spacial and Temporal Variations in 36CI Deposition in the Northern United States
(1994) Hainsworth, Laura J.; Mignerey, Alice C.; Chemistry and Biochemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md)
Chlorine-36, a cosmogenic radioisotope, has been developed for use as a tracer in hydrological systems. The deposition of atmospheric 36Cl, although of primary importance to hydrological applications, has not been well studied. To begin to address this problem, 36Cl has been measured in monthly, wet-only, precipitation samples collected from February, 1991, to January, 1993, at the Elms Environmental Education Center in St. Mary's County, Maryland. In addition, bulk deposition samples were collected over a 1 y period at seven sites across the Northern United States and analyzed for 36CI. The mean, wet-only 36Cl/Cl ratio for the 2 y sampling period is 68±19 (x10 -15), and the mean 36 CI concentration is 1.2±0. 1 (x10 6) atoms/L. The 36Cl wet deposition flux data reveal a distinct seasonal deposition pattern, with peaks occurring in March and April. This pattern is attributed to stratospheric/ tropospheric exchange. The mean 36Cl wet deposition flux is 38.2±5 atoms/m2s. Comparison between wet-only and bulk deposition samples indicates that the difference accounts for approximately 25% of the total 36Cl deposition flux at the Elms site. A new model, using 90Sr to predict the 36CI deposition pattern, is developed to predict 36Cl/Cl ratios across the United States. Chlorine-36/Cl ratios in bulk deposition samples collected across the northern United States agree well with the model predictions. A mean global 36Cl production rate of approximately 28 to 38 atoms/m2s is indicated by these samples. A comparison between 36Cl concentrations in the Aquia and Magothy aquifers is southern Maryland and bulk deposition samples collected at the Elms, MD, site indicated that modern precipitation can account for the 36Cl content in the youngest water in these aquifers. Surface water samples from the Susquehanna River basin reveal 36 Cl and stable chloride concentrations an order of magnitude higher than in bulk deposition samples collected at State College, PA. The source of excess 36Cl in the Susquehanna is not known. Possible explanations include 'bomb-pulse' 36Cl and in-situ 36CI production in surface rocks.
Transition Metal Polypnictides from Zintl Ions
(1995) Charles, Scott; Eichhorn, Bryan W.; Chemistry & Biochemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md)
The chemistry of the soluble E7 3- ions (E = P, As, Sb) with various transition metal complexes has been investigated. Alloys of K3E7 react with (arene)M(CO)3 (M = Cr, Mo, W) complexes in the presence of three equivalents of 2,2,2-crypt in ethylenediamine to give [K(2,2,2-crypt)]3[E7M(CO)3] complexes. Nine [E7M(CO)3] 3- compounds (E = P, As, Sb; M = Cr, Mo, W) have been prepared. The compounds have norbomadiene-like E7 fragments, with a formal negative charge associated with the unique two-coordinate pnictogen furthest from the transition metal. The bonding is described as E7 π-type interactions with the metal center. 31p NMR studies show that these compounds undergo an intramolecular wagging process in solution. The [E7M(C0)3] 3- ions are modestly basic and highly nucleophilic. The complexes react with weak acids, tetraalkylammonium salts and (arene)M'(CO)3 complexes to form the [K(2,2,2-crypt)]2[HE7M(CO)3], [K(2,2,2- crypt)]2[RE7M(CO)3] and [K(2,2,2-crypt)]3[(L2)(CO)3M'E7M(CO)3] compounds, respectively. Each of the structures contains a norbornadiene-like E7 fragment bound η4 to the M(CO)3 fragment and η1 to the appended moiety [H+, R+, M(CO)3(en)] that is attached to the pnictogen atom furthest from the M(CO)3 center. The [K(2,2,2-crypt)]3 [η4-E7M(CO)3] complexes also react with carbon monoxide at the M(CO)3 center and reversible binds CO to form [K(2,2,2-crypt)]3[η4-E7M(CO)4] complexes. These complexes are more easily protonated and undergo faster alkylations of the E7 cages than the parent [K(2,2,2-crypt)]3[η4-E7M(CO)3] compounds. Each of these structures contains an E7 fragment bound η2 to the M(C0)4 center. Products were characterized by various physical and spectroscopic techniques including UV-vis, IR, 1H, 13C, and 31P NMR spectroscopies, mass spectrometry, elemental analyses, and single crystal X-ray diffraction studies.
CHROMIUM OXIDATION AND REDUCTION BY HYDROGEN PEROXIDE IN DIVERSE SOILS AND SIMPLE AQUEOUS SYSTEMS
(1999) Rock, Melanie Louise; Helz, George R.; James, Bruce R.; Chemistry; Environmental Science & Technology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md)
Hydrogen peroxide is being tested for in situ remediation of buried contaminants - either as a direct chemical oxidant in Fenton-type reactions or as a source of oxidizing equivalents in bioremediation. How it affects a common co-contaminant, Cr, is explored here in four chemically diverse high-Cr soils. Soils contaminated with high levels of soluble Cr(VI) from ore processing and soils containing high levels of recently reduced Cr(III) from electroplating waste showed marked increases in chromate after single applications of J-25 mM peroxide. Cr(VI) in the leachates exceeded the drinking water standard (2μM) by 1-3 orders of magnitude. Soluble Cr(III), in the form of dissolved organic complexes, contributed to the likelihood of Cr(III) oxidation. Anaerobic soil conditions at a tannery site prevented oxidation of Cr(III). Naturally occurring Cr in serpentine soil also resisted oxidation. Ambient soluble Cr(VI) in a contaminated aquifer disappeared from peroxide leachates below pH 5, then reappeared as peroxide levels declined. In solutions prepared under environmentally relevant conditions, aged 280 μM Cr(III) treated with 100 μM H2O2 showed increases in Cr(VI) over weeks with maximum oxidation rates achieved in solutions prepared with 2:1 and 4:1 OH^-:Cr. Although Cr(III) speciation differs in fresh and aged aqueous systems, a similar mechanism involving the pre-equilibrium step: Cr(OH)/ + OH- .,. Cr(OH)/ may account for Cr(III) oxidation in both systems. Under alkaline conditions, H2O2 enhanced the oxidative dissolution of Crn(OH)3n^0. The formation of peroxochromium compounds in the presence of H2O2 and Cr(VI) may account for the disappearance and reappearance of Cr(VI) in H2O2 treated soils; as does the possible formation and subsequent reoxidation of Crm\(OH)3n-2^2+ oligomers. Mobilization of hazardous Cr(VI) must be considered in plans to use H2O2 for remediation of chemically complex wastes. Once Cr(III) is oxidized to Cr(VI) by H2O2 it may persist long after applied H2O2 treatments have disappeared. Further, hexavalent Cr will behave as a catalyst toward H20 2 in soils, enhancing its oxidative capacity while helping to dissipate high levels of applied H2O2.
Multidimensional Protein Separations in a Plastic Microfluidic Network
(2003) Li, Yan; Lee, Cheng S.; Fenselau, Catherine C.; Reutt-Robey, Janice E.; English, Douglas; Chemistry
The field of microfabrication of bioanalytical devices has grown significantly over the last decade from academic research to several commercially available systems. The performances of the microfluidic systems in terms of reproducibility, resolution, sensitivity, and speed can be achieved by applying these technologies to complex biological samples. A commonly used capillary fitting is employed for housing miniaturized membrane chromatography for performing reversed-phase peptide separations. Separation performance of cytochrome C digest in miniaturized membrane chromatography is compared with the results obtained from μ-LC and capillary LC. The use of miniaturized membrane chromatography allows significant reduction in sample consumption together with enhanced detection sensitivity. In order to further reduce sample consumption and dead volume, an isoelectric focusing separation and dynamic sample introduction are demonstrated in a microfluidic microchannel. The dynamic sample introduction in plastic microfluidic devices can be directly controlled by various electrokinetic conditions, including the injection time and the applied electric field strength. It enhances sample loading and therefore the concentrations of focused analytes by approximately 10-100 fold in comparison with conventional isoelectric focusing. An integrated 2-D protein separation system provides significant resolving power for complex protein mixtures. Non-native IEF is chosen for the first separation dimension and gel electrophoresis for the second dimension. Once the focusing is complete, the focusing proteins at IEF microchannel are simultaneously transferred using an electrokinetic method from the first dimensional microchannel into an array of the second dimensional microchannels for achieving parallel size-depended separation on each sampled fraction. Although this simple study involves a limited number of second dimensional microchannels, the ability for a microfluidic platform to perform parallel 2-D separations of complex protein samples has been successfully demonstrated. This study investigates that microfabricated systems have the potential to automate and combine high throughput multidimensional protein separations in a microfluidic network. It is crucial to combine various microfluidic components, which enable all required proteome technologies in an integrated platform for a true lab-on-a-chip.
Ion Binding and Transport by Synthetic Molecular Assemblies
(2003-10-24) Kotch, Frank William; Davis, Jeffery T; Chemistry
Self-assembly of small synthetic molecular building blocks has been applied to generate functional structures capable of binding and transporting cations and anions. Major discoveries from the research include a self-assembled ion pair receptor, ligands capable of K+-selective transport through membranes, a compound that forms Cl--selective ion channels in planar and cellular membranes, and a series of efficient chloride transporters. Calix[4]arene-guanosine conjugates cG 2.26 and cG 2.34 are shown to assemble into Na+-templated tubular architectures by 1H NMR, transmission electron microscopy and isothermal titration calorimetry, and to selectively transport K+ over Na+ and Cs+ across liposome membranes by fluorescent assays. The more lipophilic cG 2.34 forms a water-mediated dimer capable of extracting alkali halide salts from water into organic solution. These conclusions are supported by 1H and 23Na NMR, pulsed-field gradient NMR, ion chromatography and circular dichorism spectroscopy. The (cG 2.34)2(H2O)n dimer is held together by an intermolecular hydrogen-bonded guanosine quartet, based on 1D and 2D NMR experiments, and provides a rare example of a self-assembled ion pair receptor. Calix[4]arene tetrabutylamide 3.1 forms voltage-dependent chloride-selective ion channels in planar bilayers and cell membranes based on voltage and patch clamp experiments. Compound 3.1 selectively transports Cl- over HSO4- across liposome membranes, is capable of binding and transporting HCl, and can alter the pH inside liposomes experiencing a chloride gradient, based on fluorescent assays and 1H NMR experiments. X-ray crystal structures of calix[4]arene tetramethylamide 2.30HCl complexes (2.30 is an analogue of 3.1) provides a rationale for how ions are moved across a membrane by 3.1. From a series of linear analogues of 3.1, oligophenoxyacetamide trimer 3.5 was identified as the most potent chloride transporter. Transport of chloride and H+/Cl- pairs was demonstrated by fluorescent assays and 35Cl NMR. Trimer 3.5 also induces a stable potential into liposomes experiencing a transmembrane anionic gradient, an unprecedented function for a synthetic compound. Compounds capable of transporting chloride or H+/Cl- pairs have potential as drugs for the treatment of cystic fibrosis and cancer.
A TWO-DIMENSIONAL MICROFLUIDIC SEPARATION PLATFORM FOR HIGH-THROUGHPUT GENETIC MUTATIONAL ANALYSIS
(2003-11-21) Buch, Jesse Stephen; Lee, Cheng S; Chemistry
A principal challenge to upgrading genetic-based disease prevention and management is the establishment of new mutation detection strategies that surpass the performance and capabilities of traditional gel-based approaches. The need to screen individuals for the presence of mutations across a large number of genes requires the development of technology that can more rapidly and more cost-effectively identify DNA sequence heterogeneity. In this work, we demonstrate the feasibility of microfluidic separation platforms to transform traditional genetic screening methods by implementing these techniques in miniaturized systems to achieve far superior throughput than what is realized in contemporary clinical laboratories. Furthermore, to maximize the cost-effectiveness of these microfluidic systems, we have explored the use of inexpensive polymer materials as the substrates for these systems. In the initial part of this work, fabrication methods for polymeric microfluidic separation platforms were developed. The initial system consisting of a hybrid polydimthylsiloxane-silicon structure was used to demonstrate the capability of microfluidic platforms to perform field-effect electroosmotic flow control at enhanced efficiencies. Polycarbonate microfluidic devices were developed to demonstrate temperature gradient gel electrophoresis (TGGE) for the first time in a miniaturized platform. TGGE analyses of model mutant DNA fragments, each containing a single base substitution, were achieved using both single and 10-channel parallel measurements in a microfluidic platform. When compared to conventional capillary systems, the polymer microfluidic TGGE system described here demonstrated similar separation efficiency at one tenth of the analysis time, thus displaying the potential of this technology to dramatically increase the throughput of TGGE analyses. Finally the conception and realization of a parallel two-dimensional microfluidic platform for genetic mutation screening is described here. The system provides for online coupling of an initial size-based gel electrophoresis separation with a secondary parallel sequence-based TGGE separation. Such a separation strategy allows for the highthrouput analysis of complex genomic samples such as a mixture of multiplexed polymerase chain reaction (PCR) products. The comprehensive two-dimensional mutation analysis performed using this microfluidic system demonstrated the capability to detect mutations in DNA fragments at speeds approximately one to two orders of magnitude higher than is possible with conventional gel-based gene scanning methods.
Superfluidity in a Degenerate Atomic Fermi Gas
(2003-11-25) Nygaard, Nicolai; Alexander, Millard H; Clark, Charles W; Chemical Physics
Dilute atomic gases have become a powerful tool for studying many-body quantum mechanics. The best example of this is the achievement of Bose-Einstein condensation in 1995 in a gas of Bose atoms, a discovery which has invoked a confluence of ideas from condensed matter, atomic and nuclear physics. Now a concerted research effort is focused on creating and studying a BCS superfluid in an atomic Fermi gas. In the work presented here we study in detail pairing superfluidity in a Fermi gas of atoms, by self-consistently solving the Bogoliubov-de Gennes equations, both for bulk systems, and for atoms in a harmonic confining potential. A critical part of this work is the derivation of a regularized theory, which is formulated entirely in terms of physically measurable quantities, such that a quantitative comparison between theory and experiment is possible with no adjustable parameters. The resulting equations form a non-linear problem, and the accurate numerical solution of this poses a formidable challenge. A major component of this thesis is the development of efficient computational approaches to overcome these difficulties. Based on the linear response of the gas to a twisting of the order parameter phase, the superfluid density can be defined as a generalized elasticity of the system. Using finite temperature perturbation theory we calculate the superfluid density in an inhomogeneous system. We investigate the structure and thermodynamic properties of a singly quantized vortex line in a gas of superfluid fermionic atoms, making the first quantitative determination the critical rotation frequency for thermodynamic stability of the vortex state, and study the nature of the bound states in the vortex core. These excitations fill the core, making direct imaging of the vortex unlikely. Instead, we propose an experiment to indirectly probe the vortex density of states with laser fields, in a scheme analogous to Scanning Tunneling Microscopy. Furthermore, it is shown that the vortex state causes a shift of the superfluid transition temperature, which can be understood as a finite size effect.
Allostery in GroEL: Its Role in the Refolding of Protein Substrates
(2003-12-01) Grason, John Peter; Lorimer, George H; Biochemistry
The Escherichia coli chaperonin GroEL assists in the re-folding of misfolded substrate proteins (SPs). In response to the binding of ATP, GroEL undergoes large, allosteric structural transitions, resulting in an expansion of its central cavity and a capping of the cavity by the co-chaperonin GroES. Bound SP is released into the central cavity following the structural transitions. The exact mechanism by which GroEL assists in the re-folding of SPs is unknown, though there is evidence that GroEL has the ability to forcefully unfold bound SPs, giving them another chance to fold to the native state. The studies in this dissertation concentrate on relating the allosteric domain movements of GroEL to the unfolding of SPs: 1) As a means of controlling the domain movements, an intersubunit salt bridge was replaced with a pair of cysteine residues, allowing for the controlled introduction of cross-links that could tether the GroEL rings in their closed conformation. 2) The possible allosteric basis of SP's ability to stimulate the ATPase activity of GroEL was explored using standard kinetic assays. 3) The kinetics of GroES release from the GroEL/GroES complex in response to ATP binding were studied using stopped-flow fluorescence measurements, with an emphasis on determining why SP binding accelerates the rate of release. From these studies, it was concluded that the subunits within a GroEL ring move in a single concerted motion, maximizing the potential unfolding force exerted by GroEL against bound SP. It was also found that SP stimulates ATPase activity by binding to and holding a ring in the more active, closed conformation. To do this, SP must exert a force on the ring, and in order to undergo its structural changes, GroEL must in turn perform work on the SP. GroES release is stimulated for a similar reason. Since unfolded SP increases the number of reaction cycles and decreases the amount of time SP spends encapsulated in the central cavity, it is proposed that a GroEL-assisted refolding mechanism that includes an active unfolding event makes the most sense in physiological terms.
Amidinate Based Catalysts for the Stereospecific and Living Ziegler-Natta Polymerization of Alpha-Olefins
(2003-12-04) Keaton, Richard J; Sita, Lawrence R; Chemistry
The living Ziegler-Natta polymerization of alpha-olefins has been accomplished with a series of precatalysts based on cyclopentadienyl and pentamethylcyclopentadienyl zirconium amidinates (Cp and Cp*ZA's, respectively) upon activation by a borate cocatalyst at 10 °C in chlorobenzene. For the latter, the symmetry of the precatalyst determines the polymer microstructure: C(1)-symmetry gives isotactic polymer, while C(s)-symmetry gives nearly atactic material. The living behavior has been proven through kinetic analyses, narrow molecular weight distribution polymers, formation of telechelic polymers, and synthesis of well defined block copolymers. Aside from simple straight chain alpha-olefins, non-conjugated dienes and vinylcyclohexane have also been polymerized in a living fashion with this series of precatalysts. Characterization of several catalytically active derivatives through solution NMR studies and single crystal X-ray analyses were successful. In the solid state, the initiator appears as a Zr-Me cation that is involved in a doubly methyl bridged dimeric structure. The presence of ether is sufficient to break up the dimer affording a monomeric species. Also, substantially increasing the steric hindrance of the amidinate ligand yields a monomeric structure. The Zr-Me cations undergo rapid methyl group exchange as evidenced through a crossover experiment between C(1)- and C(s)-symmetric initiators. Similarly, the methyl cations can engage in methyl-polymer group exchange, thus providing a new method toward stereoblock copolymer production. Insertion of cyclopentene is also successful into the Zr-Me bond, though further propagation steps do not occur. The product of initiation is the previously unobserved cis-1,2-product, which upon warming quantitatively isomerizes to the cis-1,3-product. The former features a beta-hydrogen agostic interaction with a low J value of 87.7 Hz. Upon isomerization, two beta-agostic hydrogens are present, with J values of 97.5 and 107.2 Hz. Oligomeric polymers were prepared from low ratios of monomer to initiator. Extensive NMR studies showed a 9 : 1 selectivity for the enantiofacial selectivity of the initiation step and perfect stereospecificity thereafter. Quenching the polymerization after extremely long times, or performing the polymerization at higher temperatures, afforded evidence that beta-hydride elimination was a rare, yet active, path, and that chain-walking occurs along the alkyl chain of the last inserted monomer unit.
Intercalated MoS2 Nanoparticles for Enhanced Dispersion in Smokes and Obscurants
(2003-12-05) Spence, D'Anne Emmett; Eichhorn, Bryan W; Chemistry
The intercalation of MoS2 with diethyl oxalate (DEO) and Meldrum's Acid (MA) has been achieved via an exfoliation and reflocculation process. Ethyl diazoacetate (EDA) did not intercalate under identical conditions. The resulting compounds, Li0.1MoS2(DEO)0.10 and Li0.1MoS2(MA)0.14, have the metastable 1T-MoS2 crystal structure and have been characterized by XRD, TGA, NMR, and DSC. Based on XRD analysis, the intercalated compounds are trigonal with P3 crystal symmetry where a = b = 3.36 Å and c, which varies with the intercalate, is 10.20 Å and 9.97 Å for Li0.1MoS2(DEO)0.10 and Li0.1MoS2(MA)0.14, respectively. The concentration of the DEO and MA in the intercalated compounds, 0.10 and 0.14, respectively, was calculated using air TGA data and supported by nitrogen TGA data and NMR. The structural models of the new compounds are described within.
Benzoyl-CoA Reductase: A Biological Birch Reduction
(2003-12-08) Poole, Steven Thomas; Jollie, David R; Biochemistry
Benzoyl-CoA reductase, isolated from the anaerobic bacterium Thauera aromatica, catalyzes the ATP-dependent, two-electron reduction of the aromatic ring of benzoyl-CoA. A Birch-like mechanism, which involves two separate one electron and one proton additions to the aromatic ring of benzoyl-CoA, has been previously proposed for benzoyl-CoA reductase. The first electron transfer of this reaction, which produces a radical anion, is thought to be the rate-limiting step. Other mechanisms, such as hydride reduction and catalytic hydrogenation, are possible. In an effort to determine how the enzyme reduces its substrate, several substrate analogues were synthesized and studied using kinetic and/or product analysis. Of the nitrogen-containing, heterocyclic analogues, only picolinoyl-CoA proved to be a substrate for the reductase, having a kcat similar to that of benzoyl-CoA. Nicotinoyl-CoA did not react with the enzyme and isonicotinoyl-CoA was reduced by the electron donor in the absence of the enzyme. Mass spectrometric analysis of the products formed by the fluorinated analogues, m-fluorobenzoyl-CoA and p-fluorobenzoyl-CoA indicated that both substrates were defluorinated by benzoyl-CoA reductase, supporting a Birch-like mechanism with the first electron being added to the carbonyl functionality of the thioester. Also, benzoyl-CoA reductase only exhibited a small kinetic isotope effect (1.8), arguing against simultaneous hydrogen and electron transfer and hydride transfer. It was also found that under aerobic conditions and without ATP, benzoyl-CoA reductase could carry out the oxidation of its native reduction product reforming the substrate of the reaction, benzoyl-CoA. Since the reduction capability of benzoyl-CoA reductase is quickly and irreversibly inactivated by oxygen, it is thought that the enzyme is degraded under aerobic conditions. However, these finding suggest that benzoyl-CoA reductase may only be partially degraded by oxygen exposure and that some of its subunits may still retain some of its functionality and structure.