Atmospheric aerosols encapsulate a wide variety of particles with different compositions, sizes and sources of origin. They also directly and indirectly affect climate by their interactions with sunlight, clouds, atmospheric chemical species, and even other suspended particles. To understand the atmospheric aerosol processes and the effects they have in global and regional climate is of utmost importance for the future establishment of environmental regulations and emission policies that affect aerosol precursor compounds in an effective and beneficial manner. In particular, aerosols are known to be formed from emissions from human activities, such as fossil fuel burning, agriculture, or concentrated animal feeding operations (CAFOs). Secondary organic aerosols (SOA) constitute a type of atmospheric aerosols that are formed from the atmospheric oxidation of organic compounds that are released from various sources into the atmosphere. Due to the complexity of the atmosphere and variability of its conditions, the direct study of SOA formation is a challenging task, but the implementation of atmospheric chamber facilities to study aerosol formation and growth under controlled conditions has provided a way to study the formation and growth of SOA. However, chamber experiments cannot study specific reactions or individual compounds from the aerosol formation mechanisms in isolation, they can only provide insight on what is produced and what it is produced from, and under what conditions. Thus, kinetic modeling of the mechanisms of gas-phase atmospheric oxidation of the compounds of interest is used to develop reliable and accurate chemical models that will help have precise estimations and determine the mechanisms by which volatile organic compounds interact to produce aerosol particles. Dimethyl sulfide (DMS), dimethyl disulfide (DMDS) and trimethylamine (TMA) are three relevant atmospheric compounds, due to their emissions from many natural and anthropogenic sources and recent studies on emissions of these compounds from animal waste from CAFOs has triggered the interests on the study of SOA formation from these and other similar compounds. In this study, kinetic modeling of the atmospheric oxidation mechanisms of DMDS, DMS and TMA is used to simulate atmospheric chamber studies of aerosol formation to develop accurate models and help determine the mechanisms of aerosol formation.

Water has long been assumed to be essential for biological function. To understand the molecular basis of the role of water in protein function, several studies have established a correlation between enzyme activity and hydration level. While a threshold of hydration of 0.2 h (grams of water per gram of dried protein) is usually accepted for the onset of enzyme activity, recent works show that enzyme activity is possible at water contents as low as 0.03 h (Lind et al., 2004). Diffusion limitation in these experiments was avoided by monitoring enzyme-catalyzed hydrolysis of gas-phase esters. However, since water is also a substrate for the enzyme used in these experiments, they cannot be used to probe the possibility of activity at zero hydration. However, the pig liver esterase and C. rugosa lipase B are able to catalyse alcoholysis reactions in which an acyl group is transferred between an ester and an alcohol. Therefore, by following this reaction and using a gas phase catalytic system, we have been able to show that activity can occur at 0 g/g. These results led to the question of the accuracy of determinations of very low water concentrations; i.e., how dry is 0 g/g? Although gravimetric measurements of the hydration level do not allow us to define the anhydrous state of the protein with sufficient sensitivity, using 18O-labeled water, we have been able to quantify the small number of water molecules bound to the protein after drying, using a modification of the method of Dolman et al. (1997). Testing different drying methods, we have been able to determine a level of hydration as low as 2 moles of water per mole of protein (equivalent to 0.0006 h in the case of pig liver esterase) and have shown that in the case of the pig liver esterase, activity can occur at this hydration level. At the molecular level, if the hydration level affects activity, we can expect an effect on the protein dynamics. Neutron scattering spectra of hydrated powders, for instance, show that diffusive motions of the protein increase with the hydration (Kurkal et al., 2005) To address the question of the protein motions involved in the onset of enzyme activity at low hydration, we performed neutron scattering experiments on a pico-second time scale on dried powders. Preliminary results show a dynamical transition at hydration levels as low as 3 h. Molecular dynamic simulations have also been used in this study to access the dynamics of the active site. Overall, the results here show that pig liver esterase can function at zero hydration, or as close to zero hydration as current methods allow us to determine. Since the experimental methodology restricts this work to a small number of enzymes, it is unlikely that it will ever be possible to determine if all enzymes can function in the anhydrous state: however, the results here indicate that water is not an obligatory requirement for enzyme function.

This thesis describes the application of mass spectrometry (MS) to glycoprotein and oligosaccharide analysis. Glycosylated proteins are involved in cell-cell and cell-matrix recognition. Applications of trypsin and proteinase K to hydrolyze glycoproteins into glycopeptides that are compatible with MS and MS/MS analysis are investigated. For successful site-specific analysis of glycans, glycopeptides with short peptide (3-8 residues) are needed. Although trypsin is an important enzyme for protein identification, proteinase K is superior for site-specific glycan analysis due to its potential to hydrolyze every glycoprotein to short glycopeptides. The gas-phase dissociation pathways, kinetics and energetics of protonated oligosaccharides are described. The oligosaccharides dissociate via cleavage at the glycosidic linkages during thermal activation. Using double resonance experiments, it was established that oligosaccharides undergo sequential and parallel fragmentation reactions. Furthermore, dissociation of product ions to secondary ions was confirmed. Arrhenius activation parameters, Ea and A for protonated alpha- and beta-linked D-glucopyranose oligosaccharides are reported.

No description available.

No description available.

Biogeochemical reactions and vadose zone transport, in particular gas phase transport, are inherently coupled processes. To explore feedback mechanisms between these processes in a quantitative manner, multicomponent gas diffusion and advection are implemented into an existing reactive transport model that includes a full suite of geochemical reactions. Multicomponent gas diffusion is described based on the Dusty Gas Model, which provides the most generally applicable description for gas diffusion. Gas advection is described by Darcy's Law, which in the current formulation, is directly substituted into the transport equations. The model is used to investigate the interactions between geochemical reactions and transport processes with an emphasis to quantify reaction-induced gas migration in the vadose zone. Simulations of pyrite oxidation in mine tailings, gas attenuation in partially saturated landfill soil covers, and methane production and oxidation in aquifers contaminated by organic compounds demonstrate how biogeochemical reactions drive diffusive and advective transport of reactive and non-reactive gases. Pyrite oxidation in mine tailings causes a pressure reduction in the reaction zone and drives advective gas flow into the sediment column, enhancing the oxidation process. Release of carbon dioxide by carbonate mineral dissolution partly offsets pressure reduction, and illustrates the role of water-rock interaction on gas transport. Microbially mediated methane oxidation in landfill covers reduces the existing upward pressure gradient, thereby decreasing the contribution of advective methane emissions to the atmosphere and enhancing the net flux of atmospheric oxygen into the soil column. At an oil spill site, both generation of CH4 in the methanogenic zone and oxidation of CH4 in the methanotrophic zone contribute to drive advective and diffusive fluxes. The model confirmed that non-reactive gases tend to accumulate in zones of gas consumption and become depleted in zones of gas production. In most cases, the model was able to quantify existing conceptual models, but also proved useful to identify data gaps, sensitivity, and inconsistencies in conceptual models. The formulation of the model is general and can be applied to other vadose zone systems in which reaction-induced gas transport is of importance.

A growing interest in the strengths of several interactions that play important structural roles in biochemical systems has been building over the past couple decades. The binding energies and entropies of formation of the clusters of several protonated amino acids and nucleic acid bases with methanol have been measured using High Pressure Mass Spectrometry. The results generally show that binding energy decreases when the proton affinity difference between the alcohol and amino acid is increased. The structures and energies of various alcohol stabilized conformers of these protonated biomolecules were computed using ab initio calculations at the MP2(Full)/6‐311++g(2d,2p) level of theory. The enthalpies of formation of the lowest energy conformers of the proton‐bound clusters between the alcohols and amino acids or peptides match very closely with the experimental values, indicating that protonation and subsequent methanol attachment occurs primarily at the terminal amine functionality. The methanol stabilized protonated nucleic acid bases have energies that match closely with a more entropically favourable conformation of the cluster, hence yielding less negative enthalpy changes experimentally. The effect of alcohol size on binding energy was also monitored through measurements of enthalpies and entropies of formation for the clusters of protonated diglycine with several alcohols. The binding energy between protonated diglycine and benzene was also measured, yielding a measurable cation‐π interaction of over 20 kcal mol‐1, a comparable value to typical strong hydrogen bonds.

A growing interest in the strengths of several interactions that play important structural roles in biochemical systems has been building over the past couple decades. The binding energies and entropies of formation of the clusters of several protonated amino acids and nucleic acid bases with methanol have been measured using High Pressure Mass Spectrometry. The results generally show that binding energy decreases when the proton affinity difference between the alcohol and amino acid is increased. The structures and energies of various alcohol stabilized conformers of these protonated biomolecules were computed using ab initio calculations at the MP2(Full)/6‐311++g(2d,2p) level of theory. The enthalpies of formation of the lowest energy conformers of the proton‐bound clusters between the alcohols and amino acids or peptides match very closely with the experimental values, indicating that protonation and subsequent methanol attachment occurs primarily at the terminal amine functionality. The methanol stabilized protonated nucleic acid bases have energies that match closely with a more entropically favourable conformation of the cluster, hence yielding less negative enthalpy changes experimentally. The effect of alcohol size on binding energy was also monitored through measurements of enthalpies and entropies of formation for the clusters of protonated diglycine with several alcohols. The binding energy between protonated diglycine and benzene was also measured, yielding a measurable cation‐π interaction of over 20 kcal mol‐1, a comparable value to typical strong hydrogen bonds.

No description available.

The oxidation of a range of Volatile Organic Compounds (VOCs) has been studied, from small alkenes (e.g. ethene C2) to larger sesquiterpene species (e.g. β-caryophyllene C15). The gas-phase reactions of these VOCs, largely emitted from biogenic sources, can form oxidation products with high mass and low volatility to contribute to aerosol formation, namely for monoterpene and sesquiterpene species. These organic aerosols formed from chemical reactions in the atmosphere are secondary organic aerosols (SOA). Aerosols can have a profound impact on both climate and health issues at regional and global scales. Processes that govern these gas-to-particle phase reactions are still not fully understood. This thesis presents detailed gas-phase composition data from the various VOCs examined, and tries to highlight important gas-phase species involved in the processes for SOA formation in the atmosphere. The gas-phase composition was measured in real-time utilising the University of Leicester Chemical Ionisation Reaction-Time of Flight-Mass Spectrometer (CIR-ToF-MS). Experiments were conducted under two different environments, “dark” ozonolysis experiments were studied at the EUropean PHOtoREactor (EUPHORE) atmospheric simulation chamber (Valencia, Spain) whilst “light” photooxidation experiments were conducted at the Manchester Aerosol Chamber (MAC) facility (Manchester, UK). The ozonolysis experiments focused around small alkene species (ethene, isobutene, and trans-2-butene), isoprene and monoterpenes (myrcene, α-pinene and limonene) in the absence of NOx and investigated with and without radical scavengers in order to suppress side reactions. Under dry conditions the primary oxidation products for smaller alkene ozonolysis averaged yields for formaldehyde (HCHO) as 1.56 ± 0.09, 1.21 ± 0.03 and 0.15 ± 0.01 for ethene, isobutene and trans-2-butene respectively. Other major gas phase product yields were recorded. Under wet conditions HCHO yields increased dramatically for ethene ozonolysis, to 3.09 ± 0.12 and 1.94 ± 0.31 for isobutene, but no substantial difference was observed for trans-2-butene with an average yield of 0.19 ± 0.04. Observations on gas-phase composition varied little based on the latter and model comparisons were made using the Master Chemical Mechanism (MCMv3.1). Photolysis experiments were conducted for isoprene, monoterpenes (limonene, α-pinene and myrcene) and a sesquiterpene, β-caryophyllene. This led to a direct comparison of composition and yields were obtained for certain oxygenated VOCs (oVOCs). The major gas phase products of isoprene ozonolysis, methacrolein (MACR) recorded average yields of 0.24 ± 0.16 and methyl-vinyl ketone (MVK) at 0.15 ± 0.01 for dry conditions, whilst yields of 0.36 ± 0.04 and 0.17 ± 0.02 were observed for wet conditions respectively. Similar yields were observed for photolysis conditions. The highest average yields in the gas phase for all monoterpene species were the primary aldehyde species formed (e.g. pinonaldehyde for α-pinene), ranging averaged yields from 0.115 to 0.583 for ozonolysis reactions and 0.119 to 0.270 under photolysis conditions. Where applicable, SOA yields were determined using a Differential Mobility Particle Sizer (DMPS) and composition of the particle phase made off-line using Liquid chromatography-ion trap mass spectrometry (LC-MSn). A unique method of organic seed formation was also constructed for photolysis experiments for isoprene and limonene using β-caryophyllene as a precursor for the organic seed. Finally mesocosm experiments of direct emissions from tree species Ficus cyathistipula, Ficus benjamina and Caryota millis (to simulate tropical Asian conditions) and Betula Pendula (to encompass European environments). The tropical monoterpene producing species formed SOA, whereas the European isoprene dominant species did not. Implications of this are further discussed along with the difference observed in gas-phase composition and yields of oxidation products produced from all experiments. An Am241 source and a newly developed hollow cathode source was utilised in both campaigns so instrumental sensitivity, in particular for lower mass species is also discussed. Evidence from the experiments shows that SOA formation is only observed from monoterpene and sesquiterpene compounds. Here isoprene did not form any substantial SOA and we argue it can inhibit SOA formation. Important gas phase species for SOA contribution were those of C10 or higher, in particular the primary aldehyde oxidation products of monoterpenes that were observed in both gas and particulate phase.