The electrocatalytic and stoichiometric oxidation chemistry of binuclear ruthenium complexes incorporating the anionic tripod ligand {(η5-C5H5)Co[P(OCH3)2(=O)]3}-

The anionic tripod ligand NaLoMe (L_(oMe) - = [(η^5-C_5H_5)Co{P(O)(OCH_3)_2}_3]^-) reacts with RuO_4 in a biphasic reaction mixture of 1% H_2SO_4 and CCI_4 to afford [(L_(oMe) (HO)Ru^(IV) (µ-O)_2Ru ^(IV)(OH)(L_(oMe)] (1), which is treated with aqueous CF_3S0_3H to generate [(L_(oMe)(H_2O)Ru^(IV) (µ-O)_2R^(IV) (OH_2)(L_(oMe)][CF_3SO_3]_2 ([H_21][CF_3SO_3]_2). Addition of iodosobenzene to an acetonitrile solution of this salt yields [(L_(oMe)(O)Ru^v(µ-0)2Ru^v-(O)(_(LoMe)] (2). The dimer 1 can be reduced chemically or electrochemically to the Ru^(III)- Ru^(III) dimers [(L_(oMe)(H_20)Ru^(III) (µ-OH)_2Ru^(III) (OH_2)(L_(oMe)) ]^2+ and [(L_(oMe)) ^(III) (µ-0Hh(µ-0H2)Ru^(III) (L_(oMe)]^2+ which interconvert in aqueous media. Two electron processes dominate both the bulk chemistry and the electrochemistry of 1. Among these processes are the quasi-reversible Ru^(IV) - Ru^(IV)/Ru^(III)- Ru^(III) and Ru^(III)- Ru^(III)/ Ru^(II)- Ru^(II) reductions and a largely irreversible Ru^(V) - Ru^(V)/ Ru^(IV) - Ru^(IV)/oxidation. The dioxo dimer 2 oxidizes alcohols and aldehydes in organic media to afford 1 and the corresponding aldehydes and acids. Analogously, the Ru^(V) - Ru^(V)/ Ru^(IV)- Ru^(IV) redox wave mediates the electrooxidation of alcohols and aldehydes in aqueous buffer. In this system, substrates can be oxidized completely to CO_2. The kinetic behavior of these oxidations was examined by UV-vis and chronoamperometry, respectively, and the chemistry is typical of metal-oxo complexes, indicating that electronic coupling between two metal centers does not dramatically affect the metal-oxo chemistry. Dimer [H_21]^(2+) also reacts with alcohols, aldehydes, and triphenylphosphine in CH_3CN to afford Ru^(III)- Ru^(III) products including [(L_(oMe))CH_3CN) Ru^(III) (µ-OH)_2 Ru^(III) (NCCH_3)( L_(oMe))][CF_3SO_3]2 (characterized by X-ray crystallography) and the corresponding organic products. Reaction of 1 with formaldehyde in aqueous buffer quantitatively affords the triply bridged dimer [(L_(oMe)Ru^(III) (µ-OH)2- (µ-HCOO) Ru^(III) (L_(oMe)][CF_3SO_3] (characterized by X-ray crystallography). This reaction evidently proceeds by two parallel inner-sphere pathways, one of which is autocatalytic. Neither pathway exhibits a primary isotope effect suggesting the rate determining process could be the formation of an intermediate, perhaps a Ru^(IV) - Ru^(IV) formate adduct. The Ru^(III)- Ru^(III)formate adduct is easily oxidized to the Ru^(IV) - Ru^(IV) analog [(L_(oMe)Ru^(IV)(µ-OH)_2-(µ-HCOO) Ru^(IV) (L_(oMe)][CF_3SO_3], which, after isolation, reacts slowly with aqueous formaldehyde to generate free formate and the Ru^(III)- Ru^(III) formate adduct. These dimers function as catalysts for the electrooxidation of formaldehyde at low anodic potentials (+0.0 V versus SCE in aqueous buffer, pH 8.5) and enhance the activity of Nafion treated palladium/carbon heterogeneous fuel cell catalysts.

Novel roles of the SRP RNA in co-translational protein targeting

The signal recognition particle (SRP) and its receptor (SR) are universally conserved protein machineries that deliver nascent peptides to their proper destination. The SRP RNA is a universally conserved and essential component of SRP, which serves as the “catalyst” of the protein targeting cycle. The SRP RNA accelerates SRP-SR complex formation at the beginning of the protein targeting reaction, and triggers GTP hydrolysis and SRP-SR complex disassembly at the end. Here we combined biochemical and biophysical approaches to investigate the molecular mechanism of the functions of the SRP RNA. We found that two functional ends in the SRP RNA mediate distinct functions. The tetraloop end facilitates initial assembly of SRP and SR by mediating an electrostatic interaction with the Lys399 receptor, which ensures efficient and accurate substrate targeting. At the later stage of the SRP cycle, the SRP-SR complex relocalizes ~ 100 Angstrom to the 5’,3’-distal end of the RNA, a conformation crucial for GTPase activation and cargo handover. These results, combined with recent structural work, elucidate the functions of the SRP RNA during the protein targeting reaction.

Identifying and interpreting stratification in sedimentary rocks on Mars : insight from Rover and orbital observations and terrestrial field analogs

Sedimentary rocks on Mars provide insight into past aqueous and atmospheric processes, climate regimes, and potential habitability. The stratigraphic architecture of sedimentary rocks on Mars is similar to that of Earth, indicating that the processes that govern deposition and erosion on Mars can be reasonably inferred through reference to analogous terrestrial systems. This dissertation aims to understand Martian surface processes through the use of (1) ground-based observations from the Mars Exploration Rovers, (2) orbital data from the High Resolution Imaging Science Experiment onboard the Mars Reconnaissance Orbiter, and (3) the use of terrestrial field analogs to understand bedforms and sediment transport on Mars. Chapters 1 and 2 trace the history of aqueous activity at Meridiani Planum, through the reconstruction of eolian bedforms at Victoria crater, and the identification of a potential mudstone facies at Santa Maria crater. Chapter 3 uses Terrestrial Laser Scanning to study cross-bedding in pyroclastic surge deposits on Earth in order to understand sediment transport in these events and to establish criteria for their identification on Mars. The final chapter analyzes stratal geometries in the Martian North Polar Layered Deposits using tools for sequence stratigraphic analysis, to better constrain past surface processes and past climate conditions on Mars.

Variable-angle electron spectroscopic studies of various polyatomic molecular systems

The complementary techniques of low-energy, variable-angle electron-impact spectroscopy and ultraviolet variable-angle photoelectron spectroscopy have been used to study the electronic spectroscopy and structure of several series of molecules. Electron-impact studies were performed at incident beam energies between 25 eV and 100 eV and at scattering angles ranging from 0° to 90°. The energy-loss regions from 0 eV to greater than 15 eV were studied. Photoelectron spectroscopic studies were conducted using a HeI radiation source and spectra were measured at scattering angles from 45° to 90°. The molecules studied were chosen because of their spectroscopic, chemical, and structural interest. The operation of a new electron-impact spectrometer with multiple-mode target source capability is described. This spectrometer has been used to investigate the spin-forbidden transitions in a number of molecular systems.

The electron-impact spectroscopy of the six chloro-substituted ethylenes has been studied over the energy-loss region from 0-15 eV. Spin-forbidden excitations corresponding to the π → π*, N → T transition have been observed at excitation energies ranging from 4.13 eV in vinyl chloride to 3.54 eV in tetrachloroethylene. Symmetry-forbidden transitions of the type π → np have been oberved in trans-dichloroethyene and tetrachlor oethylene. In addition, transitions to many states lying above the first ionization potential were observed for the first time. Many of these bands have been assigned to Rydberg series converging to higher ionization potentials. The trends observed in the measured transition energies for the π → π*, N → T, and N → V as well as the π → 3s excitation are discussed and compared to those observed in the methyl- and fluoro- substituted ethylenes.

The electron energy-loss spectra of the group VIb transition metal hexacarbonyls have been studied in the 0 eV to 15 eV region. The differential cross sections were obtained for several features in the 3-7 eV energy-loss region. The symmetry-forbidden nature of the ¹A_1g → ¹A_1g, 2t_2g(π) → 3t_2g(π*) transition in these compounds was confirmed by the high-energy, low-angle behavior of their relative intensities. Several low lying transitions have been assigned to ligand field transitions on the basis of the energy and angular behavior of the differential cross sections for these transitions. No transitions which could clearly be assigned to singlet → triplet excitations involving metal orbitals were located. A number of states lying above the first ionization potential have been observed for the first time. A number of features in the 6-14 eV energy-loss region of the spectra of these compounds correspond quite well to those observed in free CO.

A number of exploratory studies have been performed. The π → π*, N → T, singlet → triplet excitation has been located in vinyl bromide at 4.05 eV. We have also observed this transition at approximately 3.8 eV in a cis-/trans- mixture of the 1,2-dibromoethylenes. The low-angle spectrum of iron pentacarbonyl was measured over the energy-loss region extending from 2-12 eV. A number of transitions of 8 eV or greater excitation energy were observed for the first time. Cyclopropane was also studied at both high and low angles but no clear evidence for any spin- forbidden transitions was found. The electron-impact spectrum of the methyl radical resulting from the pyrolysis of tetramethyl tin was obtained at 100 eV incident energy and at 0° scattering angle. Transitions observed at 5.70 eV and 8.30 eV agree well with the previous optical results. In addition, a number of bands were observed in the 8-14 eV region which are most likely due to Rydberg transitions converging to the higher ionization potentials of this molecule. This is the first reported electron-impact spectrum of a polyatomic free radical.

Variable-angle photoelectron spectroscopic studies were performed on a series of three-membered-ring heterocyclic compounds. These compounds are of great interest due to their highly unusual structure. Photoelectron angular distributions using HeI radiation have been measured for the first time for ethylene oxide and ethyleneimine. The measured anisotropy parameters, β, along with those measured for cyclopropane were used to confirm the orbital correlations and photoelectron band assignments. No high values of β similar to those expected for alkene π orbitals were observed for the Walsh or Forster-Coulson-Moffit type orbitals.

A ratiometric-based measure of gene co-expression

Current measures of global gene expression analyses, such as correlation and mutual information-based approaches, largely depend on the degree of association between mRNA levels and to a lesser extent on variability. I develop and implement a new approach, called the Ratiometric method, which is based on the coefficient of variation of the expression ratio of two genes, relying more on variation than previous methods. The advantage of such modus operandi is the ability to detect possible gene pair interactions regardless of the degree of expression dispersion across the sample group. Gene pairs with low expression dispersion, i.e., their absolute expressions remain constant across the sample group, are systematically missed by correlation and mutual information analyses. The superiority of the Ratiometric method in finding these gene pair interactions is demonstrated in a data set of RNA-seq B-cell samples from the 1000 Genomes Project Consortium. The Ratiometric method renders a more comprehensive recovery of KEGG pathways and GO-terms.

Combustion of CS₂/O₂ in a laminar mixing layer and processes in the CO chemical laser

The combustion of CS₂ and O₂ in a free burning laminar mixing layer at low pressure was investigated using emission spectroscopy. The temperature fields, CO vibrational distributions, and CO concentrations were measured. The data indicate that vibration ally excited CO was produced in the mixing layer flames, but that there were no vibrational population inversions. In comparison with the CS₂/O₂ premixed flames, the mixing layer flames favored greater production of COS and CO₂. Computer modeling was used to study the mechanisms responsible for the production of COS and CO₂, and to study how the branching chain mechanism responsible for production of CO affects the behavior of the mixing layer flame. The influences of the gas additives, N₂O, COS, and CNBr, were also investigated.

Influence of composition on the structure, electric and magnetic properties of Pd-Mn-P and Pd-Co-P amorphous alloys

The influence of composition on the structure and on the electric and magnetic properties of amorphous Pd-Mn-P and Pd-Co-P prepared by rapid quenching techniques were investigated in terms of (1) the 3d band filling of the first transition metal group, (2) the phosphorus concentration effect which acts as an electron donor and (3) the transition metal concentration.

The structure is essentially characterized by a set of polyhedra subunits essentially inverse to the packing of hard spheres in real space. Examination of computer generated distribution functions using Monte Carlo random statistical distribution of these polyhedra entities demonstrated tile reproducibility of the experimentally calculated atomic distribution function. As a result, several possible "structural parameters" are proposed such as: the number of nearest neighbors, the metal-to-metal distance, the degree of short-range order and the affinity between metal-metal and metal-metalloid. It is shown that the degree of disorder increases from Ni to Mn. Similar behavior is observed with increase in the phosphorus concentration.

The magnetic properties of Pd-Co-P alloys show that they are ferromagnetic with a Curie temperature between 272 and 399°K as the cobalt concentration increases from 15 to 50 at.%. Below 20 at.% Co the short-range exchange interactions which produce the ferromagnetism are unable to establish a long-range magnetic order and a peak in the magnetization shows up at the lowest temperature range . The electric resistivity measurements were performed from liquid helium temperatures up to the vicinity of the melting point (900°K). The thermomagnetic analysis was carried out under an applied field of 6.0 kOe. The electrical resistivity of Pd-Co-P shows the coexistence of a Kondo-like minimum with ferromagnetism. The minimum becomes less important as the transition metal concentration increases and the coefficients of ℓn T and T^2 become smaller and strongly temperature dependent. The negative magnetoresistivity is a strong indication of the existence of localized moment.

The temperature coefficient of resistivity which is positive for Pd- Fe-P, Pd-Ni-P, and Pd-Co-P becomes negative for Pd-Mn-P. It is possible to account for the negative temperature dependence by the localized spin fluctuation model and the high density of states at the Fermi energy which becomes maximum between Mn and Cr. The magnetization curves for Pd-Mn-P are typical of those resulting from the interplay of different exchange forces. The established relationship between susceptibility and resistivity confirms the localized spin fluctuation model. The magnetoresistivity of Pd-Mn-P could be interpreted in tenns of a short-range magnetic ordering that could arise from the Rudennan-Kittel type interactions.