Thesis advisor: Jianmin Gao / A common method of studying proteins is to introduce mutations into the amino acid sequence of the system. Incorporating phenylalanine analogs of varying degrees and sites of fluorination on the aromatic system gave substantial insight into the structure—function relationship of model peptide systems. By strategically placing tetrafluorinated phenylalanine mutants into the villin headpiece, HP35, increased thermodynamic and thermal stability was achieved. Using these highly but not fully fluorinated novel amino acid analogs allowed for the retention of the important ArH•••π interactions of the system. Furthermore, fluorinated amino acid residues were introduced into peptide systems known to form pores in lipid membrane systems. Certain fluorinated mutants of the membrane pore-forming peptides (MPP) showed increased membrane activity. Thus, fluorinated amino acids have tremendous potential to create hyperstable protein conformations, as well as increase the activity of proteins in membranes. / Thesis (BS) — Boston College, 2009. / Submitted to: Boston College. College of Arts and Sciences. / Discipline: College Honors Program. / Discipline: Chemistry.

Thesis advisor: Jianmin Gao / Thesis advisor: James P. Morken / This thesis includes two projects: "Novel perfluorinated aromatic amino acids: synthesis and applications" and "Thioflavin T dimers as novel amyloid ligands". I) Novel perfluorinated aromatic amino acids: synthesis and applications. Fluorinated amino acids serve as powerful tools in protein chemistry. Using the commercially available Boc-protected pentafluorophenylalanine, we synthesized a series of para-substituted tetrafluorophenylalanines via the regioselective SNAr reaction. These novel unnatural amino acids display useful and unique properties that can be applied to biological systems, including distinct 19F NMR signatures, pH-dependent amphiphilicity, lipid-binding selectivities, and halogen bonding capabilities. II) Thioflavin T dimers as novel amyloid ligands. Fluorescent molecules that specifically target amyloid structures are highly desirable for Alzheimer's disease research. We have designed a dimeric Thioflavin T that, through a reduced entropic penalty, has an improved binding affinity to Aβ amyloid by up to 70 fold. More importantly, the specificity and the "light-up" feature upon amyloid binding have not been sacrificed. Encouraged by the successful dimer design, we are further investigating the potential of amyloid-templated reactions to tailor-make ligands for amyloids. / Thesis (PhD) — Boston College, 2012. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Chemistry.

Thesis (Ph. D.)--University of Washington, 2005. / Vita. Includes bibliographical references (leaves 167-186).

Diss. (sammanfattning) Stockholm : Karolinska institutet, 2007. / Härtill 4 uppsatser.

In this thesis work, the results of microwave investigation and structural determination for benzonitrile and some of its fluorinated derivatives are presented. The pure rotational spectra of the studied compounds including benzonitrile, 2-fluorobenzonitrile, 3-fluorobenzonitrile, 2,3-difluorobenzonitrile, 2,4-difluorobenzonitrile and pentafluorobenzonitrile were investigated. Measuring the rotational spectra of the parent molecules and the minor 13C and 15N isotopic species allowed the derivation of the substitution and effective structures for these molecules. Using the effective and the calculated ab initio structures, the geometries of the fluorinated derivatives were compared to that of the reference compound (benzonitrile) and the effect of single, double and full fluorination on the geometry of benzonitrile was examined. The observed distortions in the BN geometry caused by single, double and full fluorination were interpreted by hybridization theory and intramolecular non-bonded interactions. / February 2015

In this thesis investigations into chemically modified graphene structures are presented. Chemical functionalization of graphene is the chemical attachment of molecules or atoms to the graphene surface via covalent or Van der Waals bonds, this process offers a unique way to tailor the properties of graphene to make it useful for a wide range of device applications. One type of chemical functionalization presented in this thesis is fluorination of graphene which is the covalent attachment of fluorine to the carbon atoms of graphene and the resultant material is fluorographene which is a wide band-gap semiconductor. For low fluorine coverage the low temperature electron transport is through localized states due to the presence of disorder induced sub-gap states. For high fluorine coverage the electron transport can be explained by a lightly doped semiconductor model where transport is through thermal activation across an energy gap between an impurity and conduction bands. On the other hand, at low temperatures the disorder induced sub-gap density of states dominates the electrical properties, and the conduction takes place via hopping through these localized states. In this thesis it is also shown that electron beam irradiation can be used to tune the coverage of fluorine adatoms and therefore control energy gap between the impurity and conduction bands. Futhermore, electron beam irradiation also offers a valuable way to pattern conductive structures in fluorinated graphene \textit{via} the irradiation-induced dissociation of fluorine from the fluorinated graphene. This technique can be extended to the patterning of semiconducting nano-ribbons in fluorinated graphene where the spatial localization of electrons is just a few nm. The second type of chemical functionalization presented in this thesis is the intercalation of few layer graphene with ferric chloride which greatly enhances the electrical conductivity of few layer graphene materials making them the best known transparent conductors.

In this thesis a variety of topics concerning 2D materials that have been separated from bulk layered crystals are discussed. Throughout the thesis, single and few layers of graphene, fluorinated graphene, MoS2 and WS2 are used. Two new methods of freely suspending 2D materials are presented as well as a method of removing the background from optical images. This aids contrast measurements for the determination of the number of layers. Fluorinated graphene is found to be sensitive to beta radiation; the resistance of fluorinated graphene transistors is shown to decrease upon exposure to the radiation. This happens due to the carbon-fluorine bond breaking. The sp3 hybridised structure of the fluorinated graphene is reduced back into the sp2 hybridised structure of pristine graphene. The superconducting properties of molybdenum-rhenium are characterised. It is shown to have a transition temperature of 7.5 K. It is also discovered that the material has a resistance to hydrofluoric acid; the acid etches nearly all other superconducting materials. This makes MoRe a possible candidate to explore superconductivity in conjunction with high mobility suspended graphene. To see if the material is compatible with graphene, a supported Josephson junction is fabricated. A proximity induced super current is sustained through the junction up to biases of ∼ 200 nA. The temperature dependence of the conductivity is measured for both suspended MoS2 and WS2 on a hexagonal boron nitride substrate. The dominant hopping mechanism that contributes to the conductivity at low temperatures is found to be Mott variable range hopping, with the characteristic T−1/3 dependence. The hopping transport is due to impurities that are intrinsic to the crystals, this is confirmed by comparing the results with those of supported devices on SiO2.

In this study, SiO2-xFx films were deposited on Si and amorphous silicon, their physical and chemical properties were measured. An Al/ SiO2-xFx /Si and Al/ SiO2-xFx/a-Si/Si MOS structures were used for the electrical measurements. To improve the electrical properties, we investigated the characteristics of SiO2-xFx films after annealing in nitrogen and oxygen ambient. We can find the leakage current density can be reduced to about 1.09¡Ñ 10-6 A/cm2 and 1.03¡Ñ 10-7 at -1 MV/cm and at 1 MV/cm after annealing in oxygen ambient. Although the leakage current is improved one order but the dielectric constant is increase.

Many producing volatile oil reservoirs experience a significant decrease in well deliverability when the bottom-hole pressure of the well falls below the bubble point pressure. This is due to the liberation of a gas phase which resides in the pore space and blocks the flow of the oil phase. This situation is known as "gas blocking". This occurs because the presence of two or three immiscible phases (gas, oil and water) results in a reduction of the oil saturation and a decrease in the oil relative permeability. The main objective of this research was to develop an effective and durable chemical treatment method to improve and/or restore the productivity of volatile oil wells undergoing "gas blocking". The treatment method is based on the use of fluorinated surfactants in tailored solvents to increase the oil relative permeability by changing the wettability of the rock’s surface. High-temperature high-pressure (HTHP) core flood experiments were used to evaluate the uses of fluorinated surfactants under reservoir conditions. Analytical tools such as X-ray photoelectron spectroscopy (XPS), high-performance liquid chromatography (HPLC) and computerized axial tomography (CT Scan) were also used to interpret the experimental results. High-pressure high-temperature (HPHT) coreflood tests showed that the treatments improved the oil and gas relative permeability in both sandstone and limestone cores. This was observed for synthetic volatile oil mixtures with gas-oil ratios (GOR) in the range of 4000 to 13,000 scf/STB at low capillary numbers (Nc) on the order of 1x10-5 to 1x10-6 and for PVT ratios greater than 0.5. The fluorinated chemical treatments were effective in the presence of connate water over the temperature range of 155°F to 275°F. Wettability alteration was measured using contact angle and imbibition rate tests. Results from analytical tools showed that fluorinated surfactants were uniformly adsorbed along the core and the surfactant desorption after treatment was low (10 ppm or less). The gas saturation decreased following treatment and both the oil and gas relative permeability increased. Numerical simulations using the measured relative permeability data were used to estimate the gain in productivity for treated wells. The proposed fluorinated chemical treatments could be used as a preventive treatment or for a damaged well that has already been producing below the bubble point to increase oil production rates and recoverable reserves. / text

This dissertation addresses three research areas in the sol-gel synthesis of functionalmaterials. The first is the kinetics of hydrolysis and condensation of variousorganoalkoxysilanes. Two mathematical models are developed for the sol-gel reaction inbasic conditions with and without nearest-neighbor effects. Effects on reactivity aremeasured with systematic changes in the organic group structure. Replacing onemethoxy group on the precursor with a methyl group decelerates hydrolysis under basicconditions, but accelerates condensation under acidic conditions. Replacing two methylfunctionalprecursors with one ethylene-bridged precursor accelerates hydrolysis in base,but decelerates condensation in acid. Replacing an ethylene bridge with a hexylenebridge always decelerates the sol-gel reactions. Adding an amine into the hexylenebridge always accelerates the sol-gel reactions. These trends show inductive effectsplaying a role only under basic conditions, while steric effects play a role at all pHvalues. The second topic of this thesis is the synthesis of organic-inorganic materialswith bridging or non-bridging organics. The structure of the organic-inorganic hybrids ispartially correlated with the kinetics of the precursors, but the trends indicate anadditional structural role of siloxane cyclization. The third topic of this thesis is thesynthesis of surfactant-templated nanoporous particles. The key to preparing orderedhybrid materials is found to be encouraging aggregation with a surfactant whilediscouraging random condensation of silanes independent of the surfactants. Ahomologous series of cationic pyridinium chloride fluorinated surfactants with varyingchain length are used as pore templates. Typical pore structures such as hexagonal closepackedcylinders are synthesized, as well as new pore structures including random meshphase pores and vesicular silica particles with bilayer or multilayer shells.Fluorosurfactants enable the formation of unusually small pores (1.6 nm) and poresformed from discs or bilayers. In the presence of ethanol, spherical particles with radiallyoriented pores are shown by TEM to form by precipitation of disordered silica-surfactantparticles followed by assembly into organized structures. High-capacity hollow particleswith ordered mesoporous shells are prepared by dual latex / surfactant templating.Finally, we load amine-functionalized mesoporous silica with highly dispersedsuperparamagnetic iron oxide nanoparticles.