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Accurate simulations of the global radiative impact of anthropogenic emissions must employ a tropospheric chemistry model that predicts realistic distributions of aerosols of all types. The need for a such a comprehensive yet computationally efficient tropospheric chemistry model is addressed in this research via systematic development of the various sub-models/mechanisms representing the gas-, aerosol-, and cloud-phase chemistries. The gas-phase model encompasses three tropospheric chemical regimes - background and urban, continental rural, and remote marine. The background and urban gas-phase mechanism is based on the paradigm of the Carbon Bond approach, modified for global-scale applications. The rural gas-phase chemistry includes highly condensed isoprene and a-pinene reactions. The isoprene photooxidation scheme is adapted for the present model from an available mechanism in the literature, while an a-pinene photooxidation mechanism, capable of predicting secondary organic aerosol formation, is developed for the first time from the available kinetic and product formation data. The remote marine gas- phase chemistry includes a highly condensed dimethylsulfide (DMS) photooxidation mechanism, based on a comprehensive scheme available in the literature. The proposed DMS mechanism can successfully explain the observed latitudinal variation in the ratios of methanesulfonic acid to non-sea-salt sulfate concentrations. A highly efficient dynamic aerosol growth model is developed for condensing inorganic gases. Algorithms are presented for calculating equilibrium surface concentrations over dry and wet multicomponent aerosols containing sulfate, nitrate, chloride, ammonium, and sodium. This alternative model is capable of predictions as accurate for completely dissolved aerosols, and more accurate for completely dry aerosols than some of the similar models available in the literature. For cloud processes, gas to liquid mass-transfer limitations to aqueous-phase reactions within cloud droplets are examined for all absorbing species by using the two-film model coupled with a comprehensive gas and aqueous-phase reaction mechanisms. Results indicate appreciable limitations only for the OH, HO₂, and NO₃ radicals. Subsequently, an accurate highly condensed aqueous-phase mechanism is derived for global-scale applications. / Ph. D.

Chemical weathering reactions are important for the physical, chemical, and biological development of the critical zone. We present findings from aqueous phase chemical analyses of surface and soil pore waters during a 15 month study in a small semi-arid mountain catchment of the Santa Catalina Mountain Critical Zone Observatory. Stream water geochemical solutes are sourced to two distinct locations - fractured bedrock baseflow stores and soil quickflow stores. Solid phase observations of albite, anorthite, and K-feldspar transformation to Ca-montmorillonite and kaolinite are supported by stream water saturation states calculated via a PHREEQC geochemical model. While differences in mineral assemblages, soil depths, and horizonation suggest greater weathering in schist versus granite lithologies and in hillslope divergent versus convergent zones, soil pore water solute ratio analysis does not readily distinguish these differences. However, preliminary investigation of aqueous rare earth elements suggests detectable lithologic and landscape positional differences warranting focus for future research efforts.

I present detailed mechanistic analysis on the chemistry of glyoxylate as it pertains to forming biologically relevant molecules on the Hadean Earth. Chemistry covered includes: 1) the dimerization of glyoxylate to form dihydroxyfumarate(DHF), a heretofore unknown reaction, important to substantiating Eschenmoser's glyoxylate scenario. 2) Formation of sugars from polymerization of glyoxylate. 3) Formation of tartrate and sugar acids from high pH reactions of DHF. 4) Formation of glycine polypeptides from glyoxylate by transamination and coupling promoted by hexamethylenetetramine. 5) Formation of glyoxylate under conditions which could be plausibly found on the early earth.

Chemical modification of proteins is critical for many areas of biochemistry and medicine. Several methods for site-selective protein modification are reported in this Thesis that are useful in accessing both natural and artificial protein architectures. Multiple, complementary methods for the conversion of cysteine to dehydroalanine are described. Dehydroalanine is used as a general precursor to several post-translational modifications and glycosylation, polyprenylation, phosphorylation, and lysine methylation and acetylation are all accessible. These modifications and their mimics were explored on multiple proteins, including histone proteins. Unnatural modifications were also explored. The first examples of olefin metathesis and Suzuki-Miyaura cross-coupling on protein substrates are reported. Allyl sulfides were discovered to be remarkably reactive substrates in olefin metathesis, allowing use of this reaction in water and on proteins. For Suzuki-Miyaura cross-coupling, a new catalyst is described that is fully compatible with proteins. Both olefin metathesis and cross-coupling allow the formation of carbon-carbon bonds on proteins. The prospects of these transformations in chemical biology are discussed. Finally, a novel strategy is reported for the installation of natural, unnatural, and post-translationally modified amino acid residues on proteins. This technology relies on addition of carbon radicals to dehydroalanine. This method of "chemical mutagenesis" is anticipated to complement standard genetic manipulation of protein structure.