Rozprawy doktorskie na temat „Atmospheric chemistry”

The focus of this work is the development and improvement of chemistry schemes in both 1D and 3D atmosphere models, applied to exoplanets. With an ever increasing number of known exoplanets, planets orbiting stars other than the Sun, the diversity in the physical and chemical nature of planets and their atmospheres is becoming more apparent. One of the prime targets, and the focus of many observational and theoretical studies, are the subclass of exoplanets termed hot Jupiters, Jovian sized planets on very short period orbits around their host star. Due to their close orbit, with orbital periods of just a few days, the atmospheres of such planets are heated to very high temperatures (~1000-2000 K) by the intense irradiation from the star. In addition, it is expected that these planets should have synchronised their rotation with their orbital period, a phenomenon called tidal-locking, that leads to a permanently illuminated dayside and a perpetually dark nightside. This combination of intense heating and tidal-locking leads to an exotic type of atmosphere that is without analogue in our own Solar system. Observational constraints suggest that some of these atmospheres may be clear whilst others may be cloudy or contain haze. Some hot Jupiters appear to be inflated with radii larger than is expected for their mass. For the warmest hot Jupiters optical absorbing species TiO and VO are expected to be present, due to the thermodynamical conditions, where they can strongly influence the thermal structure of the atmosphere, yet so far these species have remained elusive in observations. Theoretical simulations of these planets appear to provide poor matches to the observed emission flux from the nightside of the planet whilst providing a much better agreement with the observed dayside flux. These outstanding questions can be tackled in two complimentary ways. Firstly, the number of exoplanets subject to intense observational scrutiny must be increased to improve the statistical significance of observed trends. Secondly, and in tandem, the suite of available theoretical models applied to such atmospheres must be improved to allow for a more comprehensive understanding of the potential physical and chemical processes that occur in these atmospheres, as well as for better comparison of model predictions with observations. In this thesis we present the development and application of one-dimensional (1D) and three-dimensional (3D) models to the atmospheres of hot exoplanets, with a focus on improving the representation of chemistry. One of the concerns of this work is to couple the radiative transfer and chemistry calculations in a one-dimensional model to allow for a self-consistent model that includes feedback between the chemical composition and the thermal structure. We apply this model to the atmospheres of two typical hot Jupiters to quantify this effect. Implications for previous models that do not include this consistency are discussed. Another major focus is to improve the representation of chemistry in the Met Office Unified Model (UM) for exoplanet applications, a three-dimensional model with its heritage in modelling the Earth atmosphere that has recently been applied to exoplanets. We discuss the coupling of two new chemistry schemes that improve both the flexibility and capabilities of the UM applied to exoplanets. Ultimately these developments will allow for a consistent approach to calculate the 3D chemical composition of the atmosphere taking into account the effect of large scale advection, one of the processes currently hypothesised to cause the discrepancy between model predictions and observations of the nightside emission flux of many hot Jupiters.

Saccharides and furfural are derived from biomass burning and contribute to aerosol composition. This study examined the potential of saccharides and furfural to be tracers of biomass combustion. Furfural is likely to be oxidized quickly so comparison with saccharides may give a sense of the age of the aerosols in biomass smoke. However, few furfural emissions are available for biomass combustion. Saccharides and furfural were determined in coarse aerosols (diameter> 2.4/lm ) and fine aerosols (diameter < 2.4/lm ) collected in 24 hour periods during different seasons in the United Kingdom and PMIO collected from Thailand and Malaysia including biomass burning areas such as haze episodes and forest fires. Also total suspended particulate matter (TSP) was collected from Taiwan. Saccharides and furfural dominated in fine fractions, especially in the UK autumn. The Principle component analysis showed that the fine mode UK aerosols probably originate from long-range transport emissions from Europe. This was also an important contribution for the crustal group and the biomass burning emission. Sea salt and combustion emission may contribute to coarse mode aerosols. Fraction of saccharides and furfural in aerosols were higher during Southeast Asian haze episodes and forest fires. They were also correlated to potassium and total carbon. Collection of aerosol particles led to blackening on filter papers. The oxidation processes in the atmosphere may lead to more yellowness of aerosols. The yellowness of aerosols collected from forest fires correlated with saccharides and furfural. This may indicate that the organic carbons from forest fires are related to the oxidation process. Although the emission rates of saccharides and furfural from biomass burning were found to have similar levels, furfural was detected at low concentration suggesting loss from atmospheric aerosols. Laboratory experimental simulation suggested furfural is more rapid destroyed by UV, sunlight and ozone than saccharides.

Volcanoes are the principal way by which volatiles are transferred from the solid Earth to the atmosphere-hydrosphere system. Once released into the atmosphere, volcanic emissions rapidly undergo a complex series of chemical reactions. This thesis seeks to further the understanding of such processes by both observation and numerical modelling. I have adapted WRF-Chem to model passive degassing from Mount Etna, the chemistry of its plume, and its influence on the wider atmosphere. This investigation considers model plumes from the point of emission up to a day’s travel from the vent and is able to reproduce observed phenomena of BrO formation and O3 depletion within volcanic plumes. The model plume influences several atmospheric chemistry systems, including reactive nitrogen and organic chemistry. Plume chemistry is driven by sunlight, and I examine how the modelled phenomena identified in this investigation vary with the diurnal cycle. In the modelled plume all of the bromine is involved in O3-destructive cycling. When HBr is exhausted, volcanic HCl sustains the cycling. The rate-limiting factor of this cycling, and therefore the rate of O3 destruction, is sunlight. I find qualitative differences between the chemistry of low and high intensity plumes, with the bromine chemistry in the latter case being limited by O3 depletion. This modelling investigation is complemented by an observational study of O3 in a young Etnean plume from which I estimate the rate of in-plume O3 destruction within seconds to minutes after emission. These investigations demonstrate that volcanic plumes can be included in complex, 3D atmospheric chemistry models, and that the output from these can be used to observe and quantify influences of volcanic plumes on the wider atmosphere.

The arrival of the Cassini-Huygens mission to the Saturn system ushered in a new era in the study of Titan. Armed with a variety of instruments capable of remote sensing and in situ investigations of Titan's atmosphere and surface, Cassini and Huygens have provided a wealth of new information about Titan and have finally allowed humankind to see its surface. This work focuses on two discoveries made by the Cassini Plasma Spectrometer (CAPS): the detection of oxygen ions (O+) precipitating into Titan's atmosphere (Hartle et al., 2006) and the discovery of very large positive (Waite et al., 2007; Crary et al., 2009) and negative ions (Coates et al., 2007, 2009) present in Titan's thermosphere.Through the use of a photochemical model, I demonstrate that the observed densities of CO, CO₂ and H₂O can be explained by a combination of O and OH or H₂O input to the upper atmosphere. Given the detection of O+ precipitation into Titan's upper atmosphere, it is no longer necessary to invoke outgassing from Titan's interior as a source for atmospheric CO or to assume that the observed CO is the remnant of a larger primordial abundance in Titan's atmosphere. Instead, it is most likely that the oxygen bearing species in Titan's atmosphere are the result of external input, most likely from Enceladus.I have also used very high resolution mass spectrometry to investigate the com- position of Titan aerosol analogues, or "tholins". Although there are an enormous number of molecules present in tholin samples, they exhibit numerous patterns, in- cluding very regular spectral spacing. These patterns may help constrain the com- position of the very large ions observed in the CAPS spectra, since the resolution of the instrument makes identification of the molecules impossible. Additionally, tholins produced with CO possess molecules of prebiotic interest, including all 5 nucleotide bases and the 2 smallest amino acids (glycine and alanine). This indicates that chemistry occurring in Titan's upper atmosphere may be capable of forming incredibly complex organic molecules, which may have implications for the origin of life on Earth and elsewhere in the universe.

A new model for the simulation of street canyon atmospheric chemical processing has been developed, by integrating an existing Large-Eddy Simulation (LES) dynamical model of canyon atmospheric motion with a detailed chemical reaction mechanism, the Reduced Chemical Scheme (RCS), comprising 51 chemical species and 136 reactions, based upon a subset of the Master Chemical Mechanism (MCM). The combined LES-RCS model is used to investigate both the effects of mixing and chemical processing upon air quality within an idealised street canyon. The effect of the combination of dynamical (segregation) and chemical effects is determined by comparing the outputs of the full LES-RCS canyon model with those obtained when representing the canyon as a zero-dimensional box model (i.e. assuming mixing is complete and instantaneous). The LES-RCS approach predicts lower (canyon-averaged) levels of NOX, OH and HO2, but higher levels of O3, compared with the box model run under identical chemical and emission conditions. Chemical processing of emissions within the canyon leads to a significant increase in the Ox flux from the canyon into the overlying boundary layer, relative to primary emissions, for the idealised case and a number of pollution scenarios considered. These results demonstrate that within-canyon atmospheric chemical processing can substantially alter the concentrations of pollutants injected into the urban canopy layer, compared with the raw emission rates within the street canyon and that such variations have a considerable effect on average within canyon concentrations and the flux of pollutants out of the canyon into the urban background environment.

My Ph.D. activity developed along four lines of research dealing with non-thermal plasma (NTP) induced chemical processes for water remediation and biomedical applications. Specifically, I studied the effectiveness of atmospheric air plasma treatment in decomposing emerging organic contaminants (EOCs). The experimental setup used was a dielectric barrier discharge (DBD) reactor, a prototype developed in collaboration with the Department of Industrial Engineering of the University of Padova. Among EOCs, I chose six different contaminants, notably sulfamethoxazole, a veterinary antibiotic, triclosan, an antibacterial agent, perfluorooctanoic acid (PFOA), a perfluorinated organic contaminant, and the herbicides irgarol, metolachlor and mesotrione. Kinetics of their removal by plasma, intermediates of oxidation, possible degradation pathways and conversion to CO2 were evaluated. The achievement of more than 93% of conversion was observed for all the contaminants used at the initial concentration of 5 μM, except for PFOA (42%). An important advancement in my research involved the assessment of residual toxicity of plasma treated water samples. For this purpose, in collaboration with Prof. Giovanni Libralato (University of Naples), we tested the efficiency of plasma treatment in producing water free from ecotoxicological effects due to potentially toxic by-product residues. We tested one of the pollutants mentioned above, sulfamethoxazole (SMZ), an antibiotic listed among the most important emerging organic contaminants. A battery of acute and chronic toxicological test were employed: Daphnia magna, Raphidocaeilis Subcapitata and Vibrio Fischeri. It was found that toxicity of SMZ 5×10-4 M is minimized (V.fischeri) or reduced to zero (D. magna, R. Subcapitata) after 4 h of plasma treatment. To improve the efficiency of our DBD reactor, we tested the effect of addition of a photocatalyst, TiO2. We compared the kinetics of degradation of Irgarol in photocatalytic plasma process with those obtained when TiO2 was not included. The results obtained suggest that the effect of photoactivation by titanium dioxide in our reactor was negligible under the conditions employed. Possible reciprocal effects of different organic pollutants dissolved in water subjected to plasma induced advanced oxidation in our dielectric barrier discharge (DBD) reactor were then evaluated. As case study for this investigation, I chose the herbicides S-metolachlor and mesotrione, which are commonly applied in mixture. Results revealed that metolachlor does not affect mesotrione kinetics and viceversa when they are in solution, in 1:1 ratio. A new reactor was developed in our lab, in collaboration with Dr. Bosi from the Department of Industrial Engineering (University of Padova) with improved design and features with respect to the existing DBD reactor. The new reactor, operating in streamer discharge regime, was exhaustively characterized in collaboration with Dr. Gabriele Neretti (University of Bologna) and Dr. Barbara Zaniol (Consorzio RFX), and tested on phenol and metolachlor. Finally, during a four-month stage at the University of Bochum (Germany) I had the opportunity to work on a project dealing with plasma applications in the biomedical field under the supervision of Profs. Julia Bandow and Jan Benedikt. In particular, the effects of two plasma sources were tested in vitro on glyceraldehyde 3-phosphate dehydrogenase and E. coli. The results obtained for the enzyme suggest the importance of oxidation of the thiol group of the active site in plasma mode of action. The same approach was applied to assess the effect of ionic components of plasma by a new source developed by Prof. Benedikt (University of Bochum). The study of inactivation of the enzyme via plasma, with and without ions, showed a synergic effect between radicals and ions.
La Tesi riporta e discute i risultati ottenuti nell’applicazione di plasmi non termici per il trattamento ossidativo di inquinanti modello e ulteriori risultati relativi all’utilizzo del plasma in campo biomedico. L’apparato sperimentale impiegato è stato progettato e realizzato in collaborazione con il Dipartimento di Ingegneria Elettrica e produce una scarica a barriera di dielettrico (reattore DBD). Il sistema era già in uso nel periodo antecedente l’inizio della mia attività di dottorato. Le specie reattive che si generano a causa della scarica elettrica nell’aria umida sovrastante la fase liquida entrano in contatto con essa e possono reagire con l’inquinante organico in soluzione. Le specie reattive possono essere distinte in primarie, cioè generate direttamente dalla scarica per reazione del gas con gli elettroni energetici formando radicali, ioni e specie eccitate altamente reattive ed instabili, e secondarie prodotte per reazione delle stesse specie con le molecole del gas oppure con l’umidità presente. Il primo passo è stato quello di applicare tali scariche elettriche per il trattamento di diverse categorie di inquinanti emergenti allo scopo di valutare le potenziali applicazioni di questa tecnologia in relazione alle proprietà chimico fisiche degli inquinanti trattati. Sono stati selezionati i seguenti contaminanti organici persistenti: il sulfametossazolo, un antibiotico veterinario, il triclosan, un antibatterico, l’acido perfluoroacetico e tre erbicidi, l’irgarol, il metolachlor ed il mesotrione. Per tutti i composti in esame ho ottenuto profili esponenziali di degradazione in funzione del tempo di trattamento, da cui sono state ricavate le costanti cinetiche di pseudo-primo ordine. L’analisi HPLC-MS ha consentito l’identificazione degli intermedi e prodotti di degradazione, compatibili con possibili reazioni dovute all’azione dell’ozono e dei radicali ∙OH. Sono stati proposti inoltre i meccanismi di degradazione dei composti organici trattati. Lo scopo finale nell’uso di processi di degradazione avanzata è la completa conversione della componente organica a CO2. In seguito al trattamento al plasma, sono state riscontrate percentuali di mineralizzazione pari o maggiori al 93% per tutti gli inquinanti considerati, usati in concentrazione pari a 5 μM, fatta eccezione per l’acido perfluoroottanoico per cui la percentuale di mineralizzazione è stata considerevolmente più bassa (42%). Lo studio dei processi di degradazione al plasma è inoltre servito in alcuni casi da punto di partenza per ulteriori approfondimenti. È questo il caso dell’irgarol, in cui si è cercato di implementare l’effetto del plasma aggiungendo un fotocatalizzatore ampiamente utilizzato, TiO2. Non sono stati riscontrati tuttavia miglioramenti nell’effetto della scarica su tale inquinante indicando un trascurabile effetto fotocatalitico nelle condizioni sperimentali adottate. Un ulteriore avanzamento nelle ricerche in questo ambito è consistito nell’applicazione della scarica DBD su una miscela di inquinanti, il metolachlor e il mesotrione, solitamente utilizzati in combinazione in diverse formulazioni agricole. Gli studi cinetici effettuati hanno evidenziato che i due composti non si influenzano reciprocamente quando subiscono il trattamento al plasma in soluzioni miste in cui sono presenti in rapporto molare 1:1. Un importante parametro nella valutazione di una tecnica di depurazione consiste nell’analisi ecotossicologica del campione acquoso dopo il trattamento. A tale scopo, in collaborazione con il Prof. Giovanni Libralato del Dipartimento di Biologia dell’Università di Napoli, sono stati effettuati test tossicologici su campioni contenenti sulfametossazolo (SMZ), prima e dopo il trattamento nel reattore DBD. Allo scopo è stata utilizzata una batteria di test acuti e cronici per Vibrio Fischeri, Daphnia magna e Raphidocaelis subcapitata. I dati ottenuti a partire da una soluzione di SMZ 5·10-4 M hanno mostrato un elevato livello di tossicità della soluzione iniziale e la riduzione (V.fischeri) o l’azzeramento di tali effetti (D.magna e R.subcapitata) a seguito del trattamento nel reattore al plasma. Un nuovo reattore è stato inoltre ideato e realizzato in collaborazione con il Dr. Franco Bosi, del Dipartimento di Ingegneria Industriale dell’Università di Padova. La sorgente di plasma utilizza una scarica di tipo streamer ed è stata realizzata allo scopo di favorire un migliore trasporto delle specie reattive prodotte dalla scarica e ottimizzare la loro interazione con la soluzione da trattare. Il reattore è stato quindi caratterizzato in collaborazione con il Dr. Gabriele Neretti (Università di Bologna) e la Dr.ssa Barbara Zaniol (Consorzio RFX, Padova) e collaudato nel trattamento di due inquinanti organici, il fenolo ed il metolachlor. Infine nel corso di un periodo di quattro mesi di attività di ricerca presso il laboratorio della Prof.ssa Bandow dell’Università di Bochum (Germania) ho avuto modo di approfondire alcuni aspetti legati alle applicazioni del plasma atmosferico in campo biomedico. In particolare ho partecipato a studi sugli effetti di due diverse sorgenti al plasma su un enzima, gliceraldeide-3-fosfato deidrogenasi, in vitro e sul batterio E. coli. Il sito di attacco principale è risultato essere il sito attivo cisteina con conseguente ossidazione del gruppo -SH. Lo stesso approccio è stato applicato, in collaborazione con il Prof. Benedikt per lo studio degli effetti del plasma, in assenza e in presenza delle specie ioniche. I risultati ottenuti hanno evidenziato un effetto sinergico dovuto alla copresenza di specie neutre e ioniche.

Much important work has been done to understand reaction pathways and identify products, yields, and reaction rates for atmospheric oxidation processes. Non-methane hydrocarbons (NMHCs) are the most significant of the organic compounds present in the atmosphere from a chemical perspective and are released into the atmosphere from both natural and anthropogenic sources. The oxidation of these hydrocarbons by hydroxyl radical HO generates products that may themselves be toxic, that play a major role in the formation of photochemical smog, and that to a lesser extent contribute to the formation of acid precipitation. NMHCs have chemical reactivities many times that of methane, the most abundant HC in the atmosphere. However, the atmospheric oxidation processes of less than 50% of atmospheric NMHCs are known. A new experimental technique is needed that can provide insight into atmospheric oxidation products, reaction intermediates, and the relative importance of secondary reaction pathways that follow the initial attack of HO upon a hydrocarbon. The technique should operate at atmospheric pressure to better represent natural reaction processes and conditions, and provide a rapid and direct measure of product identities and yields. In this study we will describe the development and application of a technique that we believe meets these requirements, a technique we call High Resolution Kinetic Atmospheric Pressure Ionization Mass Spectrometry (HRKAPIMS). We begin with the use of atmospheric pressure ionization mass spectrometry in studies of atmospheric oxidation processes. We first describe a potential pitfall in the use of APIMS for the analysis of smog chamber experiments, a common APIMS application, discussing methods to eliminate interference reactions that would otherwise make interpretation difficult. A new experimental approach to the use of APIMS for the analysis of oxidation processes is next described and its use demonstrated. The oxidation of toluene by API source-generated HO produces oxidation products that are protonated and detected by the mass spectrometer. With this approach, we observe all the products found in a variety of previous studies employing a large array of experimental setups and analytical instrumentation. This is significant because our experiments are carried out in a far simpler experimental environment. Toluene is chosen for these experiments because it is an important constituent in polluted urban atmospheres with a complex oxidation mechanism that remains poorly understood. We describe the development of HRKAPIMS, a powerful new approach that allows the simultaneous detection of stable products along with free radical intermediates. The use of nitric oxide to affect product yields is demonstrated, giving valuable insights into reaction kinetics and mechanisms. We also address the theoretical aspects of HRKAPIMS, describing semiempirical calculations to estimate gas-phase basicities for a wide variety of compounds and discuss the errors implicit in this approach. The use of gas-phase basicities is discussed in terms of mass spectrometric analysis and analyte response. Kinetic and thermodynamic modeling is used to address the issues of APIMS and HRKAPIMS sensitivity and response and gain insights into the conditions necessary for linear response and quantitative detection of analytes.

Atmospherically-relevant surface reactions were studied. These reactions were investigated to provide insight into the products formed on sea salt atmospheric particle surfaces, the quantitative distribution of species on the surface of model sea salt particles, and the molecular environment of the interfacial region of HNO₃/H₂O ices. The reactions of model sea salt particles (NaCl) exposed to mineral acids (HNO₃ and H₂SO₄) were studied using Raman spectroscopy and atomic force microscopy (AFM). The reaction of powdered NaCl with HNO₃ was studied using Raman spectroscopy. NaNO₃ growth was monitored as a function of HNO₃ exposure in a flow cell. Mode-specific changes in the NO₃- vibrational mode intensities with HNO₃ exposure suggest a rearrangement of the NaNO₃ film with coverage. In the absence of H₂O, intensities of NaNO₃ bands increase with HNO₃ exposure until a capping layer of NaNO₃ forms. The capping layer prevents subsequent HNO₃ from reacting with the underlying. The reaction of NaCl with H₂SO₄ is investigated using Raman spectroscopy and atomic force microscopy (AFM). Raman spectra are consistent with the formation of NaHSO4 with no evidence for Na₂SO₄. The spectra indicate that the phase of NaHSO₄ varies with the amount of H₂O in the H₂SO₄. The reaction produces anhydrous β-NaHSO₄ which undergoes a phase change to anhydrous α-NaHSO₄. AFM measurements on NaCl (100) show the formation of two distinct types of NaHSO4 structures consistent in shape with α-NaHSO₄ and β-NaHSO₄ . Model sea salt particles were gown from solution to determine the surface Br/Cl of crystals grown from solution. These studies show surface Br concentration is 35 times that of the bulk concentration. This data is useful in the understanding of enhanced volatile Br compounds in the Arctic troposphere. Thin films of model polar stratospheric cloud (PSC) surfaces were studied in ultrahigh vacuum. Low temperature data show the preferential orientation of HNO₃ on crystalline H₂O ice. Thermodynamically-stable HNO₃ · 3H₂O is formed at ∼170 K, and subsequently desorbs from the surface. These studies show the chemical specificity of Raman spectroscopy in this chemical system. Studies of ClONO₂ adsorption onto crystalline H₂O ice suggest that ClONO₂ is weakly adsorbed.

This treatise studied two correlated important issues in atmospheric chemistry: real-time monitoring of ambient air and removal mechanisms of atmospheric hydrocarbons. An analytical system was designed for the purpose of identification and measurement of sub-ppb level hydrocarbons of different reactivities in air samples. This analytical system was then applied to a series of smog-chamber studies which simulated the removal of reactive hydrocarbons from the atmosphere by reaction with hydroxyl radicals. Six representative atmospheric hydrocarbons ( hexane, octane, toluene, m-xylene, a-xylene and mesitylene) were selected for these experiments. The experimental data indicated that the decay of atmospheric hydrocarbons under laboratory conditions is entirely due to reaction with hydroxyl radicals. The conclusion drawn from a time-resolved plume study that aromatic molecules decay much faster than could be accounted for solely by reaction with hydroxyl radicals was not verified; this indicates a difference between laboratory study and the study in the real atmosphere, and some physical factors besides chemical mechanism might take a more significant role in removing aromatics faster from the atmosphere.

This thesis focuses on the applications of molecular dynamics simulation techniques in the fields of solution chemistry and atmospheric chemistry. The work behind the thesis takes account of the fast development of computer hardware, which has made computationally intensive simulations become more and more popular in disciplines like pharmacy, biology and materials science. In molecular dynamics simulations using classical force fields, the atoms are represented by mass points with partial charges and the inter-atomic interactions are modeled by approximate potential functions that produce satisfactory results at an economical computational cost. The three-dimensional trajectory of a many-body system is generated by integrating Newton’s equations of motion, and subsequent statistical analysis on the trajectories provides microscopic insight into the physical properties of the system. The applications in this thesis of molecular dynamics simulations in solution chemistry comprise four aspects: the 113Cd nuclear magnetic resonance shielding constant of aqua Cd(II) ions, paramagnetic 19F nuclear magnetic resonance shift in fluorinated cysteine, solvation free energies and structures of metal ions, and protein adsorption onto TiO2. In the studies of nuclear magnetic resonance parameters, the relativistic effect of the 113Cd nucleus and the paramagnetic shift of 19F induced by triplet O2 are well reproduced by a combined molecular dynamics and density functional theory approach. The simulation of the aqua Cd(II) ion is also extended to several other monovalent, divalent and trivalent metal ions, where careful parameterization of the metal ions ensures the reproduction of experimental solvation structures and free energies. Molecular dynamics simulations also provided insight into the mechanism of protein adsorption onto the TiO2 surface by suggesting that the interfacial water molecules play an important role of mediating the adsorption and that the hydroxylated TiO2 surface has a large affinity to the proteins. The applications of molecular dynamics simulations in atmospheric chemistry are mainly focused on two types of organic components in aerosol droplets: humic-like compounds and amino acids. The humic-like substances, including cis-pinonic acid, pinic acid and pinonaldehyde, are surface-active organic compounds that are able to depress the surface tension of water droplets, as revealed by both experimental measurements and theoretical computations. These compounds either concentrate on the droplet surface or aggregate inside the droplet. Their effects on the surface tension can be modeled by the Langmuir-Szyszkowski equation. The amino acids are not strong surfactants and their influence on the surface tension is much smaller. Simulations show that the zwitterionic forms of serine, glycine and alanine have hydrophilic characteristics, while those of valine, methionine and phenylalanine are hydrophobic. The curvature dependence of the surface tension is also analyzed, and a slight improvement in the Köhler equation is obtained by introducing surface tension corrections for droplets containing glycine and serine. Through several examples it is shown that molecular dynamics simulations serve as a promising tool in the study of aqueous systems. Both solute-solvent interactions and interfaces can be treated properly by choosing suitable potential functions and parameters. Specifically, molecular dynamics simulations provide a microscopic picture that evolves with time, making it possible to follow the dynamic processes such as protein adsorption or atmospheric droplet formation. Moreover, molecular dynamics simulations treat a large number of molecules and give a statistical description of the system; therefore it is convenient to compare the simulated results with experimentally measured data. The simulations can provide hints for better design of experiments, while experimental data can be fed into the refinement of the simulation model. As an important complementary to experiments, molecular dynamics simulations will continue to play significant roles in the research fields of physics, chemistry, materials science, biology and medicine.
QC 20110511

In this thesis, the broad topic of atmosphere chemistry over the Northern Atlantic is considered, especially using trace gas climatologies as indicators of the influence of continental outflow of anthropogenic pollutants on the composition and chemistry of this region. The data described were obtained during recent aircraft measurements campaigns conducted aboard the UK MRF C-130 Hercules platform, under the auspices of the UK-NERC ACSOE (Atmospheric Chemistry Studies in Oceanic Environment) and the EU MAXOX (MAXimum OXidation rates in the free troposphere) campaigns. Instruments mounted on this aircraft platform provided in situ measurements of the concentrations of O3, NOx, NOy, H2O2, CH3OOH, CO and HCHO in the free troposphere over the North Atlantic. This thesis describes, in part, the validation of measured modelled trace gas distributions via trace gas climatologies over the broad latitude range 20°N to 60°N by way of data bins ranging from 0-8 km. This climatological analysis provides an insight into the distribution of trace gas in this region, especially on a seasonal basis. Results suggest a number of photochemical tracers show pronounced seasonal variation over altitudes less than 8km. The exact nature of this seasonal variation is discussed, along with possible evidence of a wide spread photochemical source for a pronounced springtime ozone maximum in these environments. The validation of aircraft measurements has been investigated via model analysis. Climatology data has been compared to the outputs of a chemistry transport model. This work shows that for some tracers the model is able to reproduce measured values with a high degree of accuracy.

Two approaches have been used in this investigation. The first involved the employment of the technique of molecular modulation kinetic (MMK) spectroscopy in the study of reaction kinetics of transient species. Previous research at Aberdeen had established a systematic error in both the kinetic (k_obs) and spectroscopic (σ_λ) parameters determined. Therefore it was intended to investigate the source of this error through the study of the kinetics of the association of the trichloromethyl radical with oxygen, producing the trichloromethyl peroxy (CCl₃O₂) radical. However, over a period of thirty-three months, no sensible results were obtained, as a result of severe instrumental component problems and the lack of in-house technical expertise. The project ultimately had to be abandoned. Since the kinetic investigation and the attempted rectification of the many problems encountered with the MMK spectrometer constituted a major portion of the allocated research time, they are reported in the final chapter of this thesis. In the second approach, two computational procedures, applying the Rice-Ramsperger-Kassel-Marcus (RRKM) theory of unimolecular reactions, have been used to evaluate kinetic parameters for the decomposition of two distinct chemical systems, namely tert-butoxy radical and peracetic acid. The programmes used are the Rabinovitch-RRKM programme and the programme UNIMOL (Gilbert et al), the latter of which is the more sophisticated. Fall-off data for the decomposition of tert-butoxy radical have been modelled over the temperature range 402-443 K relative to the experimental Arrhenius parameters, evaluated from both thermal and photolysis rate data obtained in previous investigations. The reaction was found to be pressure dependent over the range 1-1500 Torr. The refined high-pressure limit rate parameters obtained in this work are found to be in reasonable agreement with related rate constants reported from different laboratories. A value of the decomposition rate constant is extrapolated for atmospheric conditions. The efficiencies of energy transfer for three inert bath-gases, namely sulphur hexafluoride, carbon tetrafluoride and nitrogen, at 402 K, are examined using the weak collision model. RRKM modelling predicts very little difference in the efficiencies of these bath-gases - an unexpected result.

This treatise is a recapitulation of the theoretical and experimental study of hysteresis in atmospheric kinetics. The original problem arose from a theoretical study of a series of reactions for clean air. Upon evaluation a bistable equilibrium was predicted. The steady-state analysis had delineated a metastable region for the set of reactions. This bounded region is the hysteresis that this research project evaluated.

Trace gases and aerosols, or suspended liquid and solid material in the atmosphere, have significant climatological and societal impacts; consequently, accurate representation of their contribution to atmospheric composition is vital to predicting climate change and informing policy actions. Sensitivity analysis allows scientists and environmental decision makers alike to ascertain the role a specific component of the very complex system that is the atmosphere of the Earth. Anthropogenic and natural emissions of gases and aerosol are transported by winds and interact with sunlight, allowing significant transformation before these species reach the end of their atmospheric life on land or in water. The adjoint-based sensitivity method assesses the relative importance of each emissions source to selected results of interest, including aerosol and cloud droplet concentration. In this work, the adjoint of a comprehensive inorganic aerosol thermodynamic equilibrium model was produced to improve the representativeness of regional and global chemical transport modeling. Furthermore, a global chemical transport model adjoint equipped with the adjoint of a cloud droplet activation parameterization was used to explore the footprint of emissions contributing to current and potential future cloud droplet concentrations, which impact the radiative balance of the earth. In future work, these sensitivity relationships can be exploited in optimization frameworks for assimilation of observations of the system, such as satellite-based or in situ measurements of aerosol or precursor trace gas concentrations.

Cirrus clouds are thought to have a significant role in atmospheric processes: specifically; their heating/cooling contribution to the Earth's radiative balance, and the consumption of water substance due to their formation. Their presence in the upper troposphere I lower stratosphere (UTLS) also provides a surface for heterogeneous chemistry. The SLIM CAT-Cirrus model is developed to provide a tool to investigate aspects of these properties. SLIM CAT-Cirrus is based upon the existing SLIM CAT chemistry transport model and a parameterisation of the formation of cirrus ice by homogeneous nucleation. The advantages and drawbacks of the use of legacy models are discussed especially issues regarding the loss of the underlying decision-making regarding design approach, approximations, and assumptions. Techniques adopted and adapted from the software engineering and QA disciplines are used to mitigate these problems and maintain future traceabilty; this takes the form of examples of practical measures that small groups or individuals researchers can use. The difficulty in validating a complex global model in the absence of a definitive reference has been addressed by using diverse measurement data sources, and a suite of statistical merries. Model verification testing is also used to characterise processes that are difficult [0 validate. Validation of the modelled frequency of cirrus occurrence against satellite data showed an initial under-prognosis by the model. To address this a statistical scheme has been devised to reproduce some of the effects of phenomena such as gravity waves that are not resolved by the model grid. The modelled effects of the formation of cirrus on the water budget in the UTLS are comparable with measurements from the HALOE (HALogen Occultation Experiment), and are also in-line with the drying effect cirrus are thought to have on air entering the stratosphere. The radiative effects of cirrus have been represented using specific cirrus radiative parameterisations. The cirrus heating shows positive feedback into vertical transport causing meso-scale uplift of the kind thought to be responsible for part of the BrewerDobson atmospheric circulation.

A mesoscale non-hydrostatic atmospheric model was extended by including both a chemical transport module (CTM) for the chemical triade NO, N02, and 0 3, and an explicit surface-subgrid module (ESSM) for a subscale resolution of the topographical surface. CTEM: The simulated time-dependent concentration fields result from the following processes involved: anthropogenic emission at different heights, biogenic emission, dry deposition on the receptive surface, chemical reactions, turbulent diffusion, and passive transport according to the model dynamics. The calculations in the lowest model layer, usually treated as a constant-flux layer, are now performed on a vertical subgrid that was inserted to better resolve the often observed high concentration gradients within the surface layer. ESSM: Moreover, an equidistant horizontal-subgrid is introduced for finer resolving the topography. The surface fluxes of momentum, sensible and latent heat, long-wave radiation, soil heat flux and wetness as well as the surf ace-energy balance are calculated in the usual approximations, however, employing the individual surface and soil properties of the subgrid cells. The averaged subgrid quantities serve as boundary values required for the model-grid calculations. Within the CTM the ESSM method leads to an intersection of the horizontal ESSM subgrid and the vertical CTM subgrid. Preliminary results representing an interim realization state of the ESSM demonstrate partially strong changes of the dry deposition rates caused by subgrid-resolved surface properties
Ein mesoskaliges nicht-hydrostatisches Atmosphärenmodell ist um ein Chemie-TransportModul (CTM) zur Berücksichtigung der Triaden-Komponenten NO, N02 und 03 sowie um ein Verfahren zur verfeinerten Auflösung der topographischen Unterlage (explicit surface-subgrid modul ESSM) erweitert worden. CTM: Die simulierten zeitabhängigen Konzentrationsfelder sind das Resultat folgender modellierter Prozesse: Anthropogene Emission in verschiedenen Höhenschichten, biogene Emission, trockene Deposition (Rezeption), die speziellen chemischen Umwandlungen, turbulente Diffusion und passiver Transport. Da der Schwerpunkt der Prozesse und die höchsten Konzentrationsgradienten innerhalb der bodennahen ersten Modellschicht vorliegen, werden die Berechnungen in dieser Schicht auf einem verfeinerten vertikalen Untergitter durchgeführt. ESSM: Unabhängig von den Eigenheiten des CTM wird für alle untergrundbezogenen meteorologischen Größen ein regelmäßiges horizontales Untergitter zwecks Berücksichtigung des subskalig aufgelösten topographischen Untergrundes eingeführt. Auf diesem Untergitter werden in den bisherigen Näherungen alle Oberflächenflüsse für Impuls, fühlbare und latente Wärme, langwellige Strahlung, der Bodenwärmefluß, die Bodenfeuchte sowie die Energiebilanz am Boden berechnet. Die über die Untergitterzellen gemittelten Werte dienen den weiteren Berechnungen im normalen Modellgitter als die erforderlichen Randwerte. Innerhalb des CTM führt die ESSM-Methode zu einer Überlagerung des vertikalen CTM-Untergitters mit dem horizontalen Untergitter des ESSM. Erste Simulationsergebnisse, die dem derzeitigen Stand in der Realisierung des ESSM entsprechen, erbringen teilweise stark veränderte Depositionsraten infolge der Berücksichtigung der horizontal feiner aufgelösten Topographie

A mesoscale non-hydrostatic atmospheric model was extended by including both a chemical transport module (CTM) for the chemical triade NO, N02, and 0 3, and an explicit surface-subgrid module (ESSM) for a subscale resolution of the topographical surface. CTEM: The simulated time-dependent concentration fields result from the following processes involved: anthropogenic emission at different heights, biogenic emission, dry deposition on the receptive surface, chemical reactions, turbulent diffusion, and passive transport according to the model dynamics. The calculations in the lowest model layer, usually treated as a constant-flux layer, are now performed on a vertical subgrid that was inserted to better resolve the often observed high concentration gradients within the surface layer. ESSM: Moreover, an equidistant horizontal-subgrid is introduced for finer resolving the topography. The surface fluxes of momentum, sensible and latent heat, long-wave radiation, soil heat flux and wetness as well as the surf ace-energy balance are calculated in the usual approximations, however, employing the individual surface and soil properties of the subgrid cells. The averaged subgrid quantities serve as boundary values required for the model-grid calculations. Within the CTM the ESSM method leads to an intersection of the horizontal ESSM subgrid and the vertical CTM subgrid. Preliminary results representing an interim realization state of the ESSM demonstrate partially strong changes of the dry deposition rates caused by subgrid-resolved surface properties.
Ein mesoskaliges nicht-hydrostatisches Atmosphärenmodell ist um ein Chemie-TransportModul (CTM) zur Berücksichtigung der Triaden-Komponenten NO, N02 und 03 sowie um ein Verfahren zur verfeinerten Auflösung der topographischen Unterlage (explicit surface-subgrid modul ESSM) erweitert worden. CTM: Die simulierten zeitabhängigen Konzentrationsfelder sind das Resultat folgender modellierter Prozesse: Anthropogene Emission in verschiedenen Höhenschichten, biogene Emission, trockene Deposition (Rezeption), die speziellen chemischen Umwandlungen, turbulente Diffusion und passiver Transport. Da der Schwerpunkt der Prozesse und die höchsten Konzentrationsgradienten innerhalb der bodennahen ersten Modellschicht vorliegen, werden die Berechnungen in dieser Schicht auf einem verfeinerten vertikalen Untergitter durchgeführt. ESSM: Unabhängig von den Eigenheiten des CTM wird für alle untergrundbezogenen meteorologischen Größen ein regelmäßiges horizontales Untergitter zwecks Berücksichtigung des subskalig aufgelösten topographischen Untergrundes eingeführt. Auf diesem Untergitter werden in den bisherigen Näherungen alle Oberflächenflüsse für Impuls, fühlbare und latente Wärme, langwellige Strahlung, der Bodenwärmefluß, die Bodenfeuchte sowie die Energiebilanz am Boden berechnet. Die über die Untergitterzellen gemittelten Werte dienen den weiteren Berechnungen im normalen Modellgitter als die erforderlichen Randwerte. Innerhalb des CTM führt die ESSM-Methode zu einer Überlagerung des vertikalen CTM-Untergitters mit dem horizontalen Untergitter des ESSM. Erste Simulationsergebnisse, die dem derzeitigen Stand in der Realisierung des ESSM entsprechen, erbringen teilweise stark veränderte Depositionsraten infolge der Berücksichtigung der horizontal feiner aufgelösten Topographie.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2005.
Vita.
Includes bibliographical references (p. 129-145).
Trace species play a major role in many physical and chemical processes in the atmosphere. Improving our understanding of the impact of each species requires a combination of laboratory exper- imentation, field measurements, and modeling. The results presented here focus on spectroscopic and kinetic laboratory measurements and photochemical box modeling. Laboratory experiments were conducted using IntraCavity Laser Absorption Spectroscopy (ICLAS), a high-resolution, high sensitivity spectroscopic method that had been used primarily for static cell measurements in the Steinfeld Laboratory at MIT. Several modifications and improvements have been made to expand its versatility. Firstly, a discharge flow tube was coupled with the ICLA Spectrometer, and the formation kinetics of nitrosyl hydride, HNO, were measured as a means to test the system. Secondly, a novel edge-tuner was introduced as a means to expand the spectral range of the ICLA Spectrometer. An experiment for the detection of the hydroperoxyl radical employing the edge-tuner in the ICLA Spectrometer is discussed and proposed. The results from the laboratory measurements are followed by the presentation of a near-explicit kinetic box model designed to improve our understanding of the oxidative capacity of the urban troposphere in the Mexico City Metropolitan Area (MCMA). The box model was constructed using the Master Chemical Mechanism and was constrained using a large dataset of field measurements collected during the 2003 MCMA field campaign.
(cont.) The modeling is focused on the hydroxy and hydroperoxyl radicals (OH and HO₂), with an emphasis on the role of volatile organic compounds (VOCs) in the formation of both species.
by Philip M. Sheehy.
Ph.D.

Methane (CH₄) is one of the most important greenhouse gases after water vapor and carbon dioxide due to its high concentration and global warming potential 25 times than that of CO₂(based on a 100 year time horizon). Its atmospheric concentration has more than doubled from the preindustrial era due to anthropogenic activities such as rice cultivation, biomass burning, and fossil fuel production. However, the rate of increase of atmospheric CH₄ (or the growth rate) slowed from 1980 until present. The main reason for this trend is a slowdown in the trend of CH ₄sources. Measuring stable isotopes of atmospheric CH₄ can constrain changes of CH₄sources. The main goal of this work is to interpret the CH₄ trend from 1978-2010 in terms of its sources using measurements of CH₄ mixing ratio and its isotopes.

The current work presents the measurements and analysis of CH₄ and its isotopes (δ¹³C and δD) of four air archive sample sets collected by the Oregon Graduate Institute (OGI). CH₄ isotope ratios (δ¹³C and δD) were measured by a continuous flow isotope ratio mass spectrometer technique developed at PSU. The first set is for Cape Meares, Oregon which is the oldest and longest set and spans 1977-1999. The integrity of this sample set was evaluated by comparing between our measured CH₄ mixing ratio values with those measured values by OGI and was found to be stable. Resulting CH₄ seasonal cycle was evaluated from the Cape Meares data. The CH₄ seasonal cycle shows a broad maximum during October-April and a minimum between July and August. The seasonal cycles of δ¹³C and δD have maximum values in May for δ¹³C and in July for δD and minimum values between September-October for δ¹³C and in October for δD. These results indicate a CH₄ source that is more enriched January-May (e.g. biomass burning) and a source that is more depleted August-October (e.g. microbial). In addition to Cape Meares, air archive sets were analyzed from: South Pole (SPO), Samoa (SMO), Mauna Loa (MLO) 1992-1996. The presented δD measurements are unique measured values during these time periods at these stations.

To obtain the long-term in isotopic CH₄ from 1978-2010, other datasets of Northern Hemisphere mid-latitude sites are included with Cape Meares. These sites are Olympic Peninsula, Washington; Montaña de Oro, California; and Niwot Ridge, Colorado. The seasonal cycles of CH₄ and its isotopes from the composite dataset have the same phase and amplitudes as the Cape Meares site. CH₄ growth rate shows a decrease over time 1978-2010 with three main spikes in 1992, 1998, and 2003 consistent with the literature from the global trend. CH₄ lifetime is estimated to 9.7 yrs. The δ¹³C trend in the composite data shows a slow increase from 1978-1987, a more rapid rate of change 1987-2005, and a gradual depletion during 2005-2010. The δD trend in the composite data shows a gradual increase during 1978-2001 and decrease from 2001-2005. From these results, the global CH₄ emissions are estimated and show a leveling off sources 1982-2010 with two large peak anomalies in 1998 and 2003. The global average δ¹³C and δD of CH ₄ sources are estimated from measured values. The results of these calculations indicate that there is more than one source which controls the decrease in the global CH4 trend. From 1982-2001, δ¹³C and δD of CH₄ sources becomes more depleted due to a decrease in fossil and/or biomass burning sources relative to microbial sources. From 2005-2010, δ ¹³C of CH₄ sources returns to its 1981 value. There are two significant peaks in δ¹³C and δD of CH ₄ sources in 1998 and 2003 due to the wildfire emissions in boreal areas and in Europe.

A sectional aerosol model (CARMA) has been developed and coupled with the Community Earth System Model (CESM1). Aerosol microphysics, radiative properties and interactions with clouds are simulated. The model described here uses 20 particle size bins for each aerosol component including freshly nucleated sulfate particles, as well as mixed particles containing sulfate, primary organics, black carbon, dust and sea salt. In this thesis, CESM1/CARMA is firstly constrained by a variety of observations, and then utilized to investigate several scientific topics including aerosol layers in the upper troposphere and lower stratosphere as well as forest fire smoke in the lower troposphere.

Recent studies reveal layers of enhanced aerosol scattering in the upper troposphere and lower stratosphere over Asia (ATAL) and North America (NATAL). The observed aerosol extinction enhancement is reproduced by CESM1/CARMA. Both model and observations indicate a strong gradient of the sulfur-to-carbon ratio from Europe to the Asia on constant pressure surfaces. We found that the ATAL is mostly composed of sulfates, surface-emitted organics and secondary organics; the NATAL is mostly composed of sulfates and secondary organics. The model also suggests emission increases in Asia between 2000 and 2010 led to an increase of aerosol optical depth of the ATAL by 0.002 on average, which is consistent with observations.

The Rim Fire of 2013, the third largest area burned by fire recorded in California history, is simulated by CESM1/CARMA. Modeled aerosol mass, number, effective radius, and extinction coefficient are within variability of data obtained from multiple airborne measurements. Simulations suggest Rim Fire smoke may block 4-6% of sunlight reaching the surface, with a cooling efficiency around 120-150 W m^-2 per unit aerosol optical depth. This study shows that exceptional events like the 2013 Rim Fire can be simulated by a climate model with one-degree resolution, though that resolution is still not sufficient to resolve the smoke peak near the source region.

The chemistry of aerosol particles is critical to the influence said particles have over human health, air quality and the distribution of nutrients across the world. Current models estimate that windborne dust represents the movement of thousands of teragrams of solid material of varying composition and solubility across continents and into the world’s oceans. Understanding the composition and surface reactivity of anthropogenic particles from industry, agriculture and vehicle emissions is vital to understanding their potential impact on the world, and the structure and behaviour of inhalable pharmaceuticals is a strong determinant of their efficacy. The following work examines a broad selection of natural and anthropogenic particulate samples with synchrotron-based techniques, including analysis of ship emissions collected directly from stacks for the first time. The effect of simulated atmospheric acid processing on the solubility of iron on coal fly ash is evaluated, and optical trapping is used in conjunction with analytical techniques to observe the influence of relative humidity on the properties of pharmaceutical aerosols and aqueous droplets containing fluorescent protein solutions.