Studies of the equation of state and elasticity of mantle minerals

Because the Earth’s upper mantle is inaccessible to us, in order to understand the chemical and physical processes that occur in the Earth’s interior we must rely on both experimental work and computational modeling. This thesis addresses both of these geochemical methods. In the first chapter, I develop an internally consistent comprehensive molar volume model for spinels in the oxide system FeO-MgO-Fe₂O₃-Cr₂O₃-Al₂O₃-TiO₂. The model is compared to the current MELTS spinel model with a demonstration of the impact of the model difference on the estimated spinel-garnet lherzolite transition pressure. In the second chapter, I calibrate a molar volume model for cubic garnets in the system SiO₂-Al₂O₃-TiO₂-Fe₂O₃-Cr₂O₃-FeO-MnO-MgO-CaO-Na₂O. I use the method of singular value analysis to calibrate excess volume of mixing parameters for the garnet model. The implications the model has for the density of the lithospheric mantle are explored. In the third chapter, I discuss the nuclear inelastic X-ray scattering (NRIXS) method, and present analysis of three orthopyroxene samples with different Fe contents. Longitudinal and shear wave velocities, elastic parameters, and other thermodynamic information are extracted from the raw NRIXS data.

Revealing, illuminating, and modifying proteins in human diseases using noncanonical amino acids

To better understand human diseases, much recent work has focused on proteins to either identify disease targets through proteomics or produce therapeutics via protein engineering. Noncanonical amino acids (ncAAs) are tools for altering the chemical and physical properties of proteins, providing a facile strategy not only to label proteins but also to engineer proteins with novel properties. My thesis research has focused on the development and applications of noncanonical amino acids in identifying, imaging, and engineering proteins for studying human diseases. Chapter 1 introduces the concept of ncAAs and reveals insights to how I chose my thesis projects.

ncAAs have been incorporated to tag and enrich newly synthesized proteins for mass spectrometry through a method termed BONCAT, or bioorthogonal noncanonical amino acid tagging. Chapter 2 describes the investigation of the proteomic response of human breast cancer cells to induced expression of tumor suppressor microRNA miR-126 by combining BONCAT with another proteomic method, SILAC or stable isotope labeling by amino acids in cell culture. This proteomic analysis led to the discovery of a direct target of miR-126, shedding new light on its role in suppressing cancer metastasis.

In addition to mass spectrometry, ncAAs can also be utilized to fluorescently label proteins. Chapter 3 details the synthesis of a set of cell-permeant cyclooctyne probes and demonstration of selective labeling of newly synthesized proteins in live mammalian cells using azidohomoalanine. Similar to live cell imaging, the ability to selectively label a particular cell type within a mixed cell population is important to interrogating many biological systems, such as tumor microenvironments. By taking advantage of the metabolic differences between cancer and normal cells, Chapter 5 discusses efforts to develop selective labeling of cancer cells using a glutamine analogue.

Furthermore, Chapter 4 describes the first demonstration of global replacement at polar amino acid positions and its application in developing an alternative PEGylation strategy for therapeutic proteins. Polar amino acids typically occupy solvent-exposed positions on the protein surface, and incorporation of noncanonical amino acids at these positions should allow easier modification and cause less perturbation compared to replacements at the interior positions of proteins.

Chemical and mineralogical characterization of micro-inclusions in diamonds

Secondary-ion mass spectrometry (SIMS), electron probe analysis (EPMA), analytical scanning electron microscopy (SEM) and infrared (IR) spectroscopy were used to determine the chemical composition and the mineralogy of sub-micrometer inclusions in cubic diamonds and in overgrowths (coats) on octahedral diamonds from Zaire, Botswana, and some unknown localities.

The inclusions are sub-micrometer in size. The typical diameter encountered during transmission electron microscope (TEM) examination was 0.1-0.5 µm. The micro-inclusions are sub-rounded and their shape is crystallographically controlled by the diamond. Normally they are not associated with cracks or dislocations and appear to be well isolated within the diamond matrix. The number density of inclusions is highly variable on any scale and may reach 10^(11) inclusions/cm^3 in the most densely populated zones. The total concentration of metal oxides in the diamonds varies between 20 and 1270 ppm (by weight).

SIMS analysis yields the average composition of about 100 inclusions contained in the sputtered volume. Comparison of analyses of different volumes of an individual diamond show roughly uniform composition (typically ±10% relative). The variation among the average compositions of different diamonds is somewhat greater (typically ±30%). Nevertheless, all diamonds exhibit similar characteristics, being rich in water, carbonate, SiO_2, and K_2O, and depleted in MgO. The composition of micro-inclusions in most diamonds vary within the following ranges: SiO_2, 30-53%; K_2O, 12-30%; CaO, 8-19%; FeO, 6-11%; Al_2O_3, 3-6%; MgO, 2-6%; TiO_2, 2-4%; Na_2O, 1-5%; P_2O_5, 1-4%; and Cl, 1-3%. In addition, BaO, 1-4%; SrO, 0.7-1.5%; La_2O_3, 0.1-0.3%; Ce_2O_3, 0.3-0.5%; smaller amounts of other rare-earth elements (REE), as well as Mn, Th, and U were also detected by instrumental neutron activation analysis (INAA). Mg/(Fe+Mg), 0.40-0.62 is low compared with other mantle derived phases; K/ AI ratios of 2-7 are very high, and the chondrite-normalized Ce/Eu ratios of 10-21 are also high, indicating extremely fractionated REE patterns.

SEM analyses indicate that individual inclusions within a single diamond are roughly of similar composition. The average composition of individual inclusions as measured with the SEM is similar to that measured by SIMS. Compositional variations revealed by the SEM are larger than those detected by SIMS and indicate a small variability in the composition of individual inclusions. No compositions of individual inclusions were determined that might correspond to mono-mineralic inclusions.

IR spectra of inclusion- bearing zones exhibit characteristic absorption due to: (1) pure diamonds, (2) nitrogen and hydrogen in the diamond matrix; and (3) mineral phases in the micro-inclusions. Nitrogen concentrations of 500-1100 ppm, typical of the micro-inclusion-bearing zones, are higher than the average nitrogen content of diamonds. Only type IaA centers were detected by IR. A yellow coloration may indicate small concentration of type IB centers.

The absorption due to the micro-inclusions in all diamonds produces similar spectra and indicates the presence of hydrated sheet silicates (most likely, Fe-rich clay minerals), carbonates (most likely calcite), and apatite. Small quantities of molecular CO_2 are also present in most diamonds. Water is probably associated with the silicates but the possibility of its presence as a fluid phase cannot be excluded. Characteristic lines of olivine, pyroxene and garnet were not detected and these phases cannot be significant components of the inclusions. Preliminary quantification of the IR data suggests that water and carbonate account for, on average, 20-40 wt% of the micro-inclusions.

The composition and mineralogy of the micro-inclusions are completely different from those of the more common, larger inclusions of the peridotitic or eclogitic assemblages. Their bulk composition resembles that of potassic magmas, such as kimberlites and lamproites, but is enriched in H_2O, CO_3, K_2O, and incompatible elements, and depleted in MgO.

It is suggested that the composition of the micro-inclusions represents a volatile-rich fluid or a melt trapped by the diamond during its growth. The high content of K, Na, P, and incompatible elements suggests that the trapped material found in the micro-inclusions may represent an effective metasomatizing agent. It may also be possible that fluids of similar composition are responsible for the extreme enrichment of incompatible elements documented in garnet and pyroxene inclusions in diamonds.

The origin of the fluid trapped in the micro-inclusions is still uncertain. It may have been formed by incipient melting of a highly metasomatized mantle rocks. More likely, it is the result of fractional crystallization of a potassic parental magma at depth. In either case, the micro-inclusions document the presence of highly potassic fluids or melts at depths corresponding to the diamond stability field in the upper mantle. The phases presently identified in the inclusions are believed to be the result of closed system reactions at lower pressures.

Time-Domain TeraHertz Spectroscopy and Observational Probes of Prebiotic Interstellar Gas and Ice Chemistry

Understanding the origin of life on Earth has long fascinated the minds of the global community, and has been a driving factor in interdisciplinary research for centuries. Beyond the pioneering work of Darwin, perhaps the most widely known study in the last century is that of Miller and Urey, who examined the possibility of the formation of prebiotic chemical precursors on the primordial Earth [1]. More recent studies have shown that amino acids, the chemical building blocks of the biopolymers that comprise life as we know it on Earth, are present in meteoritic samples, and that the molecules extracted from the meteorites display isotopic signatures indicative of an extraterrestrial origin [2]. The most recent major discovery in this area has been the detection of glycine (NH₂CH₂COOH), the simplest amino acid, in pristine cometary samples returned by the NASA STARDUST mission [3]. Indeed, the open questions left by these discoveries, both in the public and scientific communities, hold such fascination that NASA has designated the understanding of our "Cosmic Origins" as a key mission priority.

Despite these exciting discoveries, our understanding of the chemical and physical pathways to the formation of prebiotic molecules is woefully incomplete. This is largely because we do not yet fully understand how the interplay between grain-surface and sub-surface ice reactions and the gas-phase affects astrophysical chemical evolution, and our knowledge of chemical inventories in these regions is incomplete. The research presented here aims to directly address both these issues, so that future work to understand the formation of prebiotic molecules has a solid foundation from which to work.

From an observational standpoint, a dedicated campaign to identify hydroxylamine (NH₂OH), potentially a direct precursor to glycine, in the gas-phase was undertaken. No trace of NH₂OH was found. These observations motivated a refinement of the chemical models of glycine formation, and have largely ruled out a gas-phase route to the synthesis of the simplest amino acid in the ISM. A molecular mystery in the case of the carrier of a series of transitions was resolved using observational data toward a large number of sources, confirming the identity of this important carbon-chemistry intermediate B11244 as l-C₃H⁺ and identifying it in at least two new environments. Finally, the doubly-nitrogenated molecule carbodiimide HNCNH was identified in the ISM for the first time through maser emission features in the centimeter-wavelength regime.

In the laboratory, a TeraHertz Time-Domain Spectrometer was constructed to obtain the experimental spectra necessary to search for solid-phase species in the ISM in the THz region of the spectrum. These investigations have shown a striking dependence on large-scale, long-range (i.e. lattice) structure of the ices on the spectra they present in the THz. A database of molecular spectra has been started, and both the simplest and most abundant ice species, which have already been identified, as well as a number of more complex species, have been studied. The exquisite sensitivity of the THz spectra to both the structure and thermal history of these ices may lead to better probes of complex chemical and dynamical evolution in interstellar environments.

Field and Laboratory Studies of Atmospheric Organic Aerosol

This thesis is the culmination of field and laboratory studies aimed at assessing processes that affect the composition and distribution of atmospheric organic aerosol. An emphasis is placed on measurements conducted using compact and high-resolution Aerodyne Aerosol Mass Spectrometers (AMS). The first three chapters summarize results from aircraft campaigns designed to evaluate anthropogenic and biogenic impacts on marine aerosol and clouds off the coast of California. Subsequent chapters describe laboratory studies intended to evaluate gas and particle-phase mechanisms of organic aerosol oxidation.

The 2013 Nucleation in California Experiment (NiCE) was a campaign designed to study environments impacted by nucleated and/or freshly formed aerosol particles. Terrestrial biogenic aerosol with > 85% organic mass was observed to reside in the free troposphere above marine stratocumulus. This biogenic organic aerosol (BOA) originated from the Northwestern United States and was transported to the marine atmosphere during periodic cloud-clearing events. Spectra recorded by a cloud condensation nuclei counter demonstrated that BOA is CCN active. BOA enhancements at latitudes north of San Francisco, CA coincided with enhanced cloud water concentrations of organic species such as acetate and formate.

Airborne measurements conducted during the 2011 Eastern Pacific Emitted Aerosol Cloud Experiment (E-PEACE) were aimed at evaluating the contribution of ship emissions to the properties of marine aerosol and clouds off the coast of central California. In one study, analysis of organic aerosol mass spectra during periods of enhanced shipping activity yielded unique tracers indicative of cloud-processed ship emissions (m/z 42 and 99). The variation of their organic fraction (f₄₂ and f₉₉) was found to coincide with periods of heavy (f₄₂ > 0.15; f₉₉ > 0.04), moderate (0.05 < f₄₂ < 0.15; 0.01 < f₉₉ < 0.04), and negligible (f₄₂ < 0.05; f₉₉ < 0.01) ship influence. Application of these conditions to all measurements conducted during E-PEACE demonstrated that a large fraction of cloud droplet (72%) and dry aerosol mass (12%) sampled in the California coastal study region was heavily or moderately influenced by ship emissions. Another study investigated the chemical and physical evolution of a controlled organic plume emitted from the R/V Point Sur. Under sunny conditions, nucleated particles composed of oxidized organic compounds contributed nearly an order of magnitude more cloud condensation nuclei (CCN) than less oxidized particles formed under cloudy conditions. The processing time necessary for particles to become CCN active was short ( < 1 hr) compared to the time needed for particles to become hygroscopic at sub-saturated humidity ( > 4 hr).

Laboratory chamber experiments were also conducted to evaluate particle-phase processes influencing aerosol phase and composition. In one study, ammonium sulfate seed was coated with a layer of secondary organic aerosol (SOA) from toluene oxidation followed by a layer of SOA from α-pinene oxidation. The system exhibited different evaporative properties than ammonium sulfate seed initially coated with α-pinene SOA followed by a layer of toluene SOA. This behavior is consistent with a shell-and-core model and suggests limited mixing among different SOA types. Another study investigated the reactive uptake of isoprene epoxy diols (IEPOX) onto non-acidified aerosol. It was demonstrated that particle acidity has limited influence on organic aerosol formation onto ammonium sulfate seed, and that the chemical system is limited by the availability of nucleophiles such as sulfate.

Flow tube experiments were conducted to examine the role of iron in the reactive uptake and chemical oxidation of glycolaldehyde. Aerosol particles doped with iron and hydrogen peroxide were mixed with gas-phase glycolaldehyde and photochemically aged in a custom-built flow reactor. Compared to particles free of iron, iron-doped aerosols significantly enhanced the oxygen to carbon (O/C) ratio of accumulated organic mass. The primary oxidation mechanism is suggested to be a combination of Fenton and photo-Fenton reactions which enhance particle-phase OH radical concentrations.

Chemical and Electrochemical Behavior of Graphene-Covered Silicon Photoanodes

This dissertation describes efforts over the last five years to develop protective layers for semiconductor photoelectrodes based on monolayer or few-layer graphene sheets. Graphene is an attractive candidate for a protective layer because of its known chemical inertness, transparency, ease of deposition, and limited number of electronic states. Monolayer graphene was found to effectively inhibit loss of photocurrent over 1000 seconds at n-Si/aqueous electrolyte interfaces that exhibit total loss over photocurrent over 100 seconds. Further, the presence of graphene was found to effect only partial Fermi level pinning at the Si/graphene interface with respect to a range of nonaqueous electrolytes. Fluorination of graphene was found to extend the stability imparted on n-Si by the monolayer sheet in aqueous Fe(CN)₆^3-/4- electrolyte to over 100,000 seconds. It was demonstrated that the stability of the photocurrent of n-Si/fluorinated graphene/aqueous electrolyte interfaces relative to n-Si/aqueous electrolyte interfaces is likely attributable to the inhibition of oxidation of the silicon surface.

This dissertation also relates efforts to describe and define terminology relevant to the field of photoelectrochemistry and solar fuels production. Terminology describing varying interfaces employed in electrochemical solar fuels devices are defined, and the research challenges associated with each are discussed. Methods for determining the efficiency of varying photoelectrochemical and solar-fuel-producing cells from the current-voltage behavior of the individual components of such a device without requiring the device be constructed are described, and a range of commonly employed performance metrics are explored.

Chemical and electrochemical investigations of cobalt cyanide and ruthenium ammine complexes

Part I.

The stoichiometry and kinetics of the reaction between Co(CN₅H^3- and HgX₂ (X = CN, OH) have been investigated. The products of the reaction are two new complexes, [(NC)₅Co-HgX]^3- and [(NC)₅Co-Hg-Co(CN)₅]^6-, whose spectra are reported. The kinetic measurements produced a value for the forward rate constant of the reaction Co(CN)₅H^3- + OH^- k₁/k_-1 Co(CN)₅^4- +H₂O, k1 = (9.7 ± 0.8) x 10^-2 M^-1 sec^-1 at 24°C, and an equilibrium constant for the reaction K = 10^-6 M^-1.

Part II.

Unusually large and sharp "adsorption waves" appear in cyclic voltammograms of Co(CN)₅^3- and several cobalt(III) pentacyano complexes at stationary mercury electrodes. The nature of the adsorbed species and the reasons for the absence of the adsorption waves in polarograms taken with a d.m.e. have been examined. The data are compatible with the adsorption, in all cases, of a coordinatively unsaturated cobalt(II) complex, Co(CN)₄^2-, by means of a cobalt-mercury bond. When the resulting adsorbed complex is reduced, a series of subsequent chemical and electrode reactions is initiated in which three faradays of charge are consumed for each mole of adsorbed complex. The adsorption of the anionic complex strongly retards the reduction of other negatively charged complexes.

Part III.

A number of formal redox potentials for Ru^III (NH₃)₅L + e = Ru^II (NH₃)₅L and Ru^III(NH₃)₄L₂ + e = Ru^II (NH₃)₄L₂ (where L is various ligands) has been measured by cyclic voltammetry, potentiometry, and polarography and are discussed in terms of the properties of the ligands, such as π-accepting capability. Reduction of coordinated pyrazine in the complexes, Ru(NH₃)₅ Pz²⁺, cis- and trans-Ru(NH₃)₄Pz₂²⁺, on a mercury electrode has been observed. The behavior of this reduction in various acidity of the solution as well as the reoxidation of the reduction products are discussed.