DSpace Collection: Middlebury College Chemistry Theses

Ruthenium-Promoted Radical Addition Reactions to Arenes

Sun, 06 May 2007 22:58:59 GMT

Title: Ruthenium-Promoted Radical Addition Reactions to Arenes

Authors: O’Mara, Daniel

Abstract: Arenes have been shown to be activated by transition metals toward nucleophilic attack by radicals. The goal of this research was to determine whether or not the organometallic group cyclopentadienylruthenium would alter the reactivity of the complexed arene 1,2-dihydronapthalene to the extent that it could undergo nucleophilic radical addition reactions. This project also focused on creating addition products with high diastereoselectivity. It was predicted that cyclopentadienylruthenium would effectively activate 1,2-dihydronapthalene and create products with high diastereoselectivity. Radical additions of a cyclohexyl group, an isopropyl group and an octyl group were attempted in order to determine the ability of (1,2-dihydronapthalene)cyclopentadienylruthenium to undergo nucleophilic attack. Additions of the cyclohexyl and isopropyl groups were successful using tris(trimethylsilyl)silane in the presence of azobisisobutyronitrile in refluxing 1,2-dichloroethane. The cyclohexyl group addition provided evidence that the reaction resulted in high diastereoselectivity. Only a trace amount of the octyl addition product was formed. Purification of the addition products was complicated by the similar polarities of the products and the starting material. Analysis of the addition products was performed using LC/MS, HRMS and NMR.

Description: Submitted in partial fulfillment of Honors in the Department of Chemistry and Biochemistry Middlebury College

The influence of surface roughness on air-water interfacial areas in porous media

Sat, 28 Apr 2007 22:58:59 GMT

Title: The influence of surface roughness on air-water interfacial areas in porous media

Authors: Lieb-Lappen, Ross

Abstract: The air-water interface (AWI) is a critical parameter that influences the retention and transport of volatile contaminants through porous media, including soils. The areal extent of the AWI, Aia, has been shown to vary with media texture and water saturation (Sw), with larger Aia values generally corresponding to increased adsorption capacity and retention of contaminants. The objective of this work is to characterize the Aia–Sw relationship using gas-phase interfacial tracer tests for two media: Vinton (fine sand with small amounts of silt and clay) and Granusil 7030 (fine sand). The media were chosen to represent two sands with similar particle sizes, but different surface roughness as represented by N2/BET surface areas of 3.33 and 0.56 m2/g, respectively. Media with greater surface roughness are hypothesized to yield larger interfacial areas, leading to increased retardation of contaminant transport. Aia was measured using decane vapor as the interfacial tracer for porous media at water saturations ranging from approximately 2.5% to 20%. Once Aia was measured for a particular system, its value was used to predict the gas-phase retardation of a contaminant, trichloroethylene (TCE) vapor, an industrial organic solvent and carcinogen, traveling through the same soil system. The predicted retardation for TCE was then compared to its observed retardation through the soil column. Results show that overall, Aia generally decreased with increasing Sw, in agreement with the literature. For all Sw studied, measured Aia values were greater for Vinton than for Granusil 7030 as a result of the greater surface roughness for Vinton. Predicted retardation factors for TCE matched the general Sw trend of the observed data, however, predictions were consistently greater than observed values. This difference is attributed to uncertainty in the interfacial adsorption coefficient for decane.

Description: Submitted in partial fulfillment of High Honors in the Department of Chemistry and Biochemistry and the Program of Environmental Studies Middlebury College.

Investigation of the DNA Base-Flipping Mechanism by NMR and Fluorescence Spectroscopy

Sat, 28 Apr 2007 22:58:59 GMT

Title: Investigation of the DNA Base-Flipping Mechanism by NMR and Fluorescence Spectroscopy

Authors: Eisenstein, Anna

Abstract: The DNA base flipping mechanism is a method employed by some enzymes in order to access the nucleotides that normally reside within the DNA helix. Base flipping involves the 180° rotation around the sugar phosphate backbone of a nucleoside residing within the helix to the extrahelical position. The lifetime of a 2-aminopurine to uracil base pair was calculated through the inversion recovery method using 1H NMR spectroscopy. The calculated lifetime for the (2AP)U base pair was 50 ± 20 ms. The procedures and parameter sets were optimized for the determination of the base pair lifetime. The kinetics of the reaction catalyzed by uracil DNA glycosylase, which cleaves uracil from DNA, was measured using fluorescence spectroscopy. The calculated Vmax and Km values were 0.7 ± 0.6 uM/sec and 40 ± 10 uM, respectively. Given this research, further studies can be done to determine the base pair lifetime between 2AP and a uracil with a methyl group attached to the 5’ carbon of the sugar. We hypothesize that the base pair lifetime will be longer in the modified dodecamer as compared to the unmodified dodecamer because the methyl group will provide steric hinderance as the nucleoside rotates around specific bonds in the sugar phosphate backbone. Comparing the Vmax values between the two dodecamers may provide information about the rate determining step of the UDG catalyzed reaction and any differences in Km may elucidate the binding affinity of the enzyme for the ribose moiety. In conclusion, this research has provided a good starting point for future studies on the base flipping mechanism.

Description: Submitted in partial fulfillment of High Honors in the Department of Chemistry and Biochemistry Middlebury College.

Radical Reactions of Acyclic Butadienyliron and Cyclohexadienyliron Tricarbonyl Complexes

Sun, 06 May 2007 22:58:59 GMT

Title: Radical Reactions of Acyclic Butadienyliron and Cyclohexadienyliron Tricarbonyl Complexes

Authors: Chen, Ming Z.

Abstract: Density functional calculations in combination with isodesmic reactions indicated that acyclic butadienyliron and cyclohexadienyliron tricarbonyl radicals were 13.7 and 16.3 kcal/mole more stable than benzylic radical, respectively. This exceptional stability was a result of substantial spin delocalization onto the iron atom. The thiocarbonyl diimidazole (TCDI) derivatives of the two complexes were used as the radical precursors. These two radicals were found to be too stable to propagate radical chain reactions with Bu3SnH. Their nucleophilicity was demonstrated by trapping them with electron-deficient alkene, namely 2-carboethoxyallyltributylstannane. The alkylated product of acyclic butadienyliron tricarbonyl radical could not be fully characterized since complete removal of the chromatographically “streaky” tin byproducts was not successful. Cyclohexadienyliron tricarbonyl radical was found to be unreactive with the alkene. Addition of tert-butyl radical to tricarbonyl(1-methylpentadienyl)iron (I) cation gave rise to a minor alkylated product as evidenced by GC/MS, while addition to tricarbonyl(cyclohexadienyl)iron (I) cation gave rise to the desired product in greater than 50% yield. One-electron reduction of tricarbonyl(1-methylpentadienyl)iron (I) cation by zinc followed by nucleophilic addition to 2-carboethoxyallyltributylstannane gave rise to a dimerization product rather than the expected alkylated product.