Chemistry & Biochemistry Theses and Dissertations
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Item 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.Item 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.Item 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 # 1481769N-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.Item 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.Item 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.Item 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)Item LOCAL MOLECULAR FIELD THEORY FOR NON-EQUILIBRIUM SYSTEMS(2019) Baker III, Edward Bigelow; Weeks, John D; Chemical Physics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Local Molecular Field (LMF) theory is a framework for modeling the long range forces of a statistical system using a mimic system with a modified Hamiltonian that includes a self consistent molecular potential. This theory was formulated in the equilibrium context, being an extension of the Weeks Chandler Andersen (WCA) theory to inhomogeneous systems. This thesis extends the framework further into the nonequilibrium regime. It is first shown that the equilibrium derivation can be generalized readily by using a nonequilibrium ensemble average and its relevant equations of motion. Specifically, the equations of interest are fluid dynamics equations which can be generated as moments of the BBGKY hierarchy. Although this approach works well, for the application to simulations it is desirable to approximate the LMF potential dynamically during a single simulation, instead of a nonequilibrium ensemble. This goal was pursued with a variety of techniques, the most promising of which is a nonequilibrium force balance approach to dynamically approximate the relevant ensemble averages. This method views a quantity such as the particle density as a field, and uses the statistical equations of motion to propagate the field, with the forces in the equations computed from simulation. These results should help LMF theory become more useful in practice, in addition to furthering the theoretical understanding of near equilibrium molecular fluids.Item DEVELOPMENT OF A MICROSCALE ELECTROCHEMICAL PLATFORM FOR THE ANALYSIS OF THERMAL PROFILES OF IMMOBILIZED DNA SECONDARY STRUCTURES(2019) Robinson, Sarah; Lee, Sang Bok; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Understanding the thermal stability of DNA secondary structures is important to the pharmaceutical industry, as drug molecules that strongly bind will increase the stability of the structure, leading to higher measured melting temperatures. Development of an electronic platform that can measure the thermal profiles of small-volume samples with automation and methodology that is scalable for high-throughput screening (HTS) would represent an important asset for the drug discovery process. This thesis endeavored to produce and demonstrate the feasibility of such a technology. A microelectronic device has been fabricated in the configuration of a planar electrochemical platform with an embedded platinum thin film that can function as both a platinum resistance thermometer (PRT) and as a resistive microheater. The device assembly as well as automation of the temperature control and electrochemical methods have been instituted to increase measurement repeatability with the microscale device. The operational program was developed with a variety of features, including a PID controller, and has been demonstrated for a two-device array; functioning is scalable to larger device arrays with the addition of suitable electronics. A proof-of-concept methodology has been shown for monitoring the stabilization effects of ligand binding to duplex DNA. Results are presented for both refrigeration with resistive heating, and thermoelectric cooling and heating. The technology has also been adapted to examine other DNA secondary structures, such as G-quadruplexes, and the stabilization of these structures. The resulting analysis of such immobilized intramolecular secondary structures has demonstrated that the systems are more complicated and further fundamental studies are needed. With the future incorporation of microfluidics and larger-device arrays, a range of effects can be tested based on the demonstrated technology to understand binding events of relevance to drug discovery and the complexities of the surface chemistry effects on the analysis of thermal profiles.Item CHARACTERIZATION OF NON-CODING RNAS VIA NMR SPECTROSCOPY: ANALYSIS OF STRUCTURE, THERMAL STABILITY, AND DYNAMICS(2019) Nam, Hyeyeon; Dayie, Theodore K; Biochemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Non-coding RNAs are involved in various cellular processes and characterization of these RNAs may provide better insights into their functional roles. NMR spectroscopy is a powerful biophysical tool that can provide residue-specific information. Herein we examine an RNA triple helix at the 3' end of the lncRNA MALAT1, which may be a potential therapeutic target for cancer treatment. We investigate the local stability of the MALAT1 triple helix by analyzing the individual base-pair stability via NMR spectroscopy. In addition, we screened small molecules to identify the compounds that can selectively target the MALAT1 triple helix. In the second part, we studied the effect of dipolar couplings on the relaxation measurements of various non-coding RNAs using both computational and experimental measurements. The results suggest an increasing contribution of the dipolar coupling effect with the increasing size of the RNA.Item PROTEIN FOLD SWITCHING: INVESTIGATING THE MECHANISM OF αβ-PLAIT TO 3α FOLD INTERCONVERSION(2019) Solomon, Tsega Lily; Orban, John; Biochemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Naturally occurring metamorphic proteins have the ability to interconvert from one folded state to another through either a limited set of mutations or by way of a change in the local environment. However, the design of these types of proteins has remained challenging. This dissertation shows that it is possible to switch reversibly between two different but common folds employing only temperature changes. The study demonstrates that a latent 3α state can be unmasked from an αβ-plait topology with a single V90T amino acid substitution in a designed system, populating both forms simultaneously. The equilibrium between these two states exhibits temperature dependence, such that the 3α state is predominant (>90%) at 5°C, while the αβ-plait fold is the major species (>90%) at 30°C. The structure and dynamics of these two temperature-dependent topologies, as well as their energetics and kinetics of interconversion, are characterized utilizing NMR spectroscopy. Additional analysis show that the temperature-dependent characteristics of the 3α<->αβ-plait fold switch can be modulated by mutations. Stability studies through H-D exchange approach provide insight on the energetic basis for temperature induced 3α<->αβ-plait fold conversion. Further investigations demonstrated that interconversion between the 3α and αβ-plait states can be triggered by additional environmental factors including pressure, ligand binding, and redox state. This dissertation adds to the growing body of literature on protein fold metamorphism providing the first description of switching between two distinct monomeric protein folds using only temperature or pressure. Additionally, the studies of ligand- and redox-induced 3α<->αβ-plait fold switching emphasize the ability to mimic by design some of the mechanisms of fold interconversion that are found in naturally occurring metamorphic proteins. Given the high occurrence of the 3α and αβ-plait folds in the universe of known protein structures, the results suggest that such fold switching events may have occurred in the evolutionary expansion of function for natural versions of these topologies.