Photodissociation and reaction dynamics of chlorine-containing species important in stratospheric ozone chemistry

Chlorine oxide species have received considerable attention in recent years due to their central role in the balance of stratospheric ozone. Many questions pertaining to the behavior of such species still remain unanswered and plague the ability of researchers to develop accurate chemical models of the stratosphere. Presented in this thesis are three experiments that study various properties of some specific chlorine oxide species.

In the first chapter, the reaction between ClONO_2 and protonated water clusters is investigated to elucidate a possible reaction mechanism for the heterogeneous reaction of chlorine nitrate on ice. The ionic products were various forms of protonated nitric acid, NO_2 +(H_20)_m, m = 0, 1, 2. These products are analogous to products previously reported in the literature for the neutral reaction occurring on ice surfaces. Our results support the hypothesis that the heterogeneous reaction is acid-catalyzed.

In the second chapter, the photochemistry of ClONO_2 was investigated at two wavelengths, 193 and 248 nm, using the technique of photofragmentation translational spectroscopy. At both wavelengths, the predominant dissociation pathways were Cl + NO_3 and ClO + NO_2. Channel assignments were confirmed by momentum matching the counterfragments from each channel. A one-dimensional stratospheric model using the new 248 nm branching ratio determined how our results would affect the predicted Cl_x and NO_x partitioning in the stratosphere.

Chapter three explores the photodissociation dynamics of Cl_2O at 193, 248 and 308 nm. At 193 nm, we found evidence for the concerted reaction channel, Cl_2 + O. The ClO + Cl channel was also accessed, however, the majority of the ClO fragments were formed with sufficient internal energies for spontaneous secondary dissociation to occur. At 248 and 308 nm, we only observed only the ClO + Cl channel. . Some of the ClO formed at 248 nm was formed internally hot and spontaneously dissociated. Bimodal translational energy distributions of the ClO and Cl products indicate two pathways leading to the same product exist.

Appendix A, B and C discuss the details of data analysis techniques used in Chapters 1 and 2. The development of a molecular beam source of ClO dimer is presented in Appendix D.

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.

Expression of eph-family receptor tyrosine kinases and ephrins in the tadpole of the frog Xenopus laevis, and possible roles in the development of retinotectal topography

Assembling a nervous system requires exquisite specificity in the construction of neuronal connectivity. One method by which such specificity is implemented is the presence of chemical cues within the tissues, differentiating one region from another, and the presence of receptors for those cues on the surface of neurons and their axons that are navigating within this cellular environment.

Connections from one part of the nervous system to another often take the form of a topographic mapping. One widely studied model system that involves such a mapping is the vertebrate retinotectal projection-the set of connections between the eye and the optic tectum of the midbrain, which is the primary visual center in non-mammals and is homologous to the superior colliculus in mammals. In this projection the two-dimensional surface of the retina is mapped smoothly onto the two-dimensional surface of the tectum, such that light from neighboring points in visual space excites neighboring cells in the brain. This mapping is implemented at least in part via differential chemical cues in different regions of the tectum.

The Eph family of receptor tyrosine kinases and their cell-surface ligands, the ephrins, have been implicated in a wide variety of processes, generally involving cellular movement in response to extracellular cues. In particular, they possess expression patterns-i.e., complementary gradients of receptor in retina and ligand in tectum- and in vitro and in vivo activities and phenotypes-i.e., repulsive guidance of axons and defective mapping in mutants, respectively-consistent with the long-sought retinotectal chemical mapping cues.

The tadpole of Xenopus laevis, the South African clawed frog, is advantageous for in vivo retinotectal studies because of its transparency and manipulability. However, neither the expression patterns nor the retinotectal roles of these proteins have been well characterized in this system. We report here comprehensive descriptions in swimming stage tadpoles of the messenger RNA expression patterns of eleven known Xenopus Eph and ephrin genes, including xephrin-A3, which is novel, and xEphB2, whose expression pattern has not previously been published in detail. We also report the results of in vivo protein injection perturbation studies on Xenopus retinotectal topography, which were negative, and of in vitro axonal guidance assays, which suggest a previously unrecognized attractive activity of ephrins at low concentrations on retinal ganglion cell axons. This raises the possibility that these axons find their correct targets in part by seeking out a preferred concentration of ligands appropriate to their individual receptor expression levels, rather than by being repelled to greater or lesser degrees by the ephrins but attracted by some as-yet-unknown cue(s).

Wastewater Electrolysis Cell for Environmental Pollutants Degradation and Molecular Hydrogen Generation

This study proposes a wastewater electrolysis cell (WEC) for on-site treatment of human waste coupled with decentralized molecular H₂ production. The core of the WEC includes mixed metal oxides anodes functionalized with bismuth doped TiO₂ (BiO_x/TiO₂). The BiO_x/TiO₂ anode shows reliable electro-catalytic activity to oxidize Cl- to reactive chlorine species (RCS), which degrades environmental pollutants including chemical oxygen demand (COD), protein, NH4⁺, urea, and total coliforms. The WEC experiments for treatment of various kinds of synthetic and real wastewater demonstrate sufficient water quality of effluent for reuse for toilet flushing and environmental purposes. Cathodic reduction of water and proton on stainless steel cathodes produced molecular H2 with moderate levels of current and energy efficiency. This thesis presents a comprehensive environmental analysis together with kinetic models to provide an in-depth understanding of reaction pathways mediated by the RCS and the effects of key operating parameters. The latter part of this thesis is dedicated to bilayer hetero-junction anodes which show enhanced generation efficiency of RCS and long-term stability.

Chapter 2 describes the reaction pathway and kinetics of urea degradation mediated by electrochemically generated RCS. The urea oxidation involves chloramines and chlorinated urea as reaction intermediates, for which the mass/charge balance analysis reveals that N₂ and CO₂ are the primary products. Chapter 3 investigates direct-current and photovoltaic powered WEC for domestic wastewater treatment, while Chapter 4 demonstrates the feasibility of the WEC to treat model septic tank effluents. The results in Chapter 2 and 3 corroborate the active roles of chlorine radicals (Cl•/Cl₂^-•) based on iR-compensated anodic potential (thermodynamic basis) and enhanced pseudo-first-order rate constants (kinetic basis). The effects of operating parameters (anodic potential and [Cl^-] in Chapter 3; influent dilution and anaerobic pretreatment in Chapter 4) on the rate and current/energy efficiency of pollutants degradation and H₂ production are thoroughly discussed based on robust kinetic models. Chapter 5 reports the generation of RCS on Ir_0.7Ta_0.3O_y/Bi_xTi_1-xO_z hetero-junction anodes with enhanced rate, current efficiency, and long-term stability compared to the Ir_0.7Ta_0.3O_y anode. The effects of surficial Bi concentration are interrogated, focusing on relative distributions between surface-bound hydroxyl radical and higher oxide.

Cavity-enhanced spectroscopies for applications of remote sensing, chemical kinetics and detection of radical species

This thesis describes applications of cavity enhanced spectroscopy towards applications of remote sensing, chemical kinetics and detection of transient radical molecular species. Both direct absorption spectroscopy and cavity ring-down spectroscopy are used in this work. Frequency-stabilized cavity ring-down spectroscopy (FS-CRDS) was utilized for measurements of spectral lineshapes of O₂ and CO₂ for obtaining laboratory reference data in support of NASA’s OCO-2 mission. FS-CRDS is highly sensitive (> 10 km absorption path length) and precise (> 10000:1 SNR), making it ideal to study subtle non-Voigt lineshape effects. In addition, these advantages of FS-CRDS were further extended for measuring kinetic isotope effects: A dual-wavelength variation of FS-CRDS was used for measuring precise D/H and ¹³C/¹²C methane isotope ratios (sigma>0.026%) for the purpose of measuring the temperature dependent kinetic isotope effects of methane oxidation with O(¹D) and OH radicals. Finally, direct absorption spectroscopic detection of the trans-DOCO radical via a frequency combs spectrometer was conducted in collaboration with professor Jun Ye at JILA/University of Colorado.