published_or_final_version / Biological Sciences / Doctoral / Doctor of Philosophy

Philosophiae Doctor - PhD / South Africa is undergoing a serious consideration of hydrogen economy in an effort to develop safe clean and reliable alternative energy sources for fossil fuels. Ammonia is one of the promising candidates due to its low production cost, ease in liquefaction at ambient temperatures, and high energy density as compared to methanol. Ammonia has a high content of hydrogen atoms per unit volume and can easily be cracked down into hydrogen and nitrogen. In the last four years carbon intensive coal dependent South Africa has become one of the leading global destinations for renewable energy investment. Another driving force behind the technology is the prevalence of platinum reserves found in South Africa. Platinum group metals are the key catalytic materials used in most fuel cells, and with more than 75 % of the world’s known platinum reserves found within South Africa. In this thesis, I have developed novel electrocatalysts that are highly specific and selective for production of hydrogen using ammonia as a fuel source. The electro-oxidation of ammonia on platinum electrode drop coated platinum nanoparticles (PtNP), platinum iridium nanoparticles (PtIrNP), platinum ruthenium nanoparticles (PtRuNP), platinum telluride nanoparticles (PtTeNP) and ternary nanoparticles (PtIrTeNP) finally (PtRuTeNP) was systematically studied in alkaline solution of potassium hydroxide (KOH) by cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS). The electrocatalysts were synthesised using sodium borohydride as a reducing agent and polyvinylpyrrolidone (PVP) as a stabilising agent from aqueous solutions of H2PtCl6/IrCl3/RuCl3/NaHTe mixtures. XRD confirmed that the binary and ternary electro-catalyst displayed characteristic patterns which indicated that all catalysts have shown the Pt face-centred-cubic (fcc) crystal structure and that the nanoparticles were poly-orientated. The structural characterization was further confirmed with FTIR and UV-vis, FTIR showed the most striking evidence that the PVP stabilized Pt presented a broad peak between 1288 cm-1 and 1638 cm‐1 which corresponded to C‐N stretching motion and C=O stretching motion of monomer for PVP, respectively. The narrow absorption peak centered at 1420 cm‐1 and 2880 cm‐1 occurred in which was ascribed to the C–H bonding due to the presence of PVP. This was due to the formation of coordinate bond between the nitrogen atom of the PVP and the Pt2+, Ir3+, Ru3+ and Te2+ ions. UV-vis was able to show the oxidation state of the nanoparticles and obtained an exponential graph shape which indicated complete reduction because there was no peak observed. Morphological characterization in the form of high resolution scanning electron microscope (HRSEM) revealed the formation of poly-orientated nanoparticles with average particle size of 23- 46 nm with slightly aggregated crystalline materials. The elemental composition of the alloy nanoparticles measured using energy dispersive spectroscopy (EDS) showed the presence of the four elements; Pt, Ir, Ru and Te. High resolution transmission electron microscopy (HRTEM) revealed the formation of crystalline non-aggregated 0.6-5 nm sized nanoparticles. The elemental composition of the alloy nanoparticles measured using energy dispersive X-ray (EDX) showed the presence of the four elements; Pt, Ir, Ru and Te. Selected area electron diffraction pattern (SAED) nanoparticles showed characteristic electron diffraction rings of Pt, PtIr, PtRu, PtTe, PtIrTe and PtRuTe, confirmed the phase and crystallinity of the materials. The electrocatalytic behaviour of the PtIrTe and PtRuTe nanoparticles for ammonia oxidation in KOH solution showed reduced overpotential properties and an increased current density compared to the bare Pt nanoparticles electrode thus providing a promising alternative for development of low-cost and high-performance electrocatalyst for electro-oxidation of ammonia. In terms of minimising the ammonia oxidation overpotential, catalyst selection were ranked as follows PtTe > PtRuTe > PtIr > PtRu > PtIrTe > Pt, with regards to maximising the exchange current density, the ranking was PtTe > PtIrTe > Pt > PtRu > PtIr > PtRuTe. The results were further interrogated with EIS which revealed in terms of minimising charge transfer resistance (Rct) the nano catalysts selection were ranked as follows PtRuTe ˃ PtIrTe ˃ PtRu ˃ PtIr ˃ Pt ˃ Bare Pt electrode ˃ PtTe. That meant that the conductivity of the catalysts facilitated the flow of charge through the nanoalloys onto the surface of the electrode. The difference in charge transfer resistance revealed that PtRuTe and PtIrTe nanoalloys had an obvious advantage in reaction activity. The application of ternary metal nanoparticles had significantly enhanced the catalytic activity toward ammonia oxidation. The role of the third component (Te) had improved the catalysts in reducing Nads adsorption on Pt. The enhanced catalytic activity has been attributed by a number of factors including the change in Pt–Pt inter atomic distance, number of Pt nearest neighbours, Pt 5d band vacancy, and Pt metal content on particle surface.

The goal of my dissertation research was to investigate the structure and function of ammonia-oxidizing microbial communities in temperate forest soils. Accomplishing this goal required a hybrid approach: I used modern molecular biology techniques alongside soil biogeochemical measurements and framed my research using ecological theory largely developed in plant systems. All of my field work was done at Coweeta Hydrologic Laboratory, a Forest Service Station and Long Term Ecological Research Site near Otto, NC. Watershed-level land use manipulations have been performed at Coweeta since the 1930s, including clear-cutting, fertilizing, liming, burning, grazing by cattle, and replanting entire watersheds in white pine. While these treatments were originally imposed to assess the effects of land use on water yield, they have resulted in changes in soil characteristics as well. Working at Coweeta has therefore allowed me to sample ammonia-oxidizer communities across a gradient of soil variables, such as pH and nitrogen (N) availability, within the geographically-constrained area of the Coweeta Basin. First, I used amplicon-based pyrosequencing to independently assess the diversity of ammonia-oxidizing archaea (AOA) and bacteria (AOB) at several sites within Coweeta. I found that AOA and AOB diversity were a function of both resource availability (i.e. N availability) and environmental harshness (i.e. soil pH) in line with general ecological theory developed for plant systems by Tilman and Grime, respectively. Next, I tested whether AOA and AOB were substrate or nutrient limited in this system by adding either N or a nutrient solution containing both potassium and phosphorus to soil incubations and assessing the growth response of AOA and AOB using quantitative polymerase chain reaction (qPCR). I found strong evidence for substrate limitation by AOB and a marginally-significant positive effect of nutrient addition on growth of AOA. Another intriguing finding from this study was that both AOA and AOB grew during unamended soil incubations. Unamended (buried-bag) incubations have been used to estimate in situ rates of nitrification for over 50 years. By measuring the growth of AOA and AOB alongside nitrification during buried-bag incubations, I discovered that AOA are the dominant ammonia-oxidizers in temperate forest soils. However, I found that AOA are much less efficient at using the energy from ammonia oxidation to create biomass than AOB in the forest soils I sampled. Overall, I found that temperate forest soils contain low abundances of AOA and AOB, with relatively low diversity in both groups. This is especially true for the diversity of AOA, where a single taxon dominated the community at every site. Soil pH and N availability seem to be major selective forces for forest soil ammonia oxidizers, though other nutrients such as potassium and phosphorus may regulate the activity of AOA as well. AOA are most-likely the dominant ammonia oxidizers in temperate forest systems, though this may change with increased disturbance. In a broader sense, I found that ecological theory developed for plant communities was applicable to chemoautotrophic microbes despite the large differences in life history between these groups of organisms. / Ph. D.

Abstract Ammonia (NH3) is one of valuable chemicals which is commonly used in manufacturing the fertilizer, synthetic fiber, synthetic plastics, and dynamites, and is used in the factories such as papermaking, textile mill, camera and electrical. NH3 is also a typical pollutant which is found to be emitted from industrial processes, agriculture areas and livestock farm. It causes burn damage due to the corrosion and has a long-term impact on human bronchus. This study was to investigate the performance and kinetics in oxidation of ammonia by using a method of selective catalytic oxidation (denoted by SCO) over a series catalysts of Cu/Ce . The major parameters were performed at the following conditions: initial concentration NH3 of influent in ranging from 500 ppm to 1000 ppm, temperatures ranging from 150¢J to 500¢J, oxygen content in inlet stream in ranging from 4¢Hto 20¢Hand humidity in ranging from 1¢Hto 20¢H(or an absolute humidity of 607 ppm-12136 ppm). In the first stage experiments, the purpose was to select a best catalyst, which had the great activity and highest selectivity on nitrogen. The catalysts used in this work were prepared into three types in the following: Cu/La/Ce (molar ratio: 8/1/1, 7/1/2, 7/2/1, 6/1/3, 6/2/2 and 6/3/1), Cu/La (molar ratio: 6/4, 7/3, 8/2 and 9/1) and Cu/Ce (molar ratio: 6/4, 7/3, 8/2 and 9/1); total numbers of catalysts were 14. Test results showed the molar ratio 6:4 of Cu/Ce catalyst was found to have the best activity and selectivity to convert NH3 in this work. The second stage experiments were carried to investigate the effect of parameters on conversion of NH3 over a Cu/Ce catalyst of molar ratio 6:4. The conversion of NH3 in process of SCO increased with operation conditions such as the going up of temperature, and the increasing both of oxygen content and of residence time. The lower conversion of NH3 was achieved by an increasing on initial concentration of NH3, space velocity and humidity. The third stage experiments were conducted to investigate the effect of operation period on deactivation of NH3 over the above catalyst. At constant initial concentration of NH3, oxygen content and space velocity for 30 hr continuously, we found Cu/Ce catalyst had an excellent stability in conversion of NH3. Further tests by XRD, SEM and EA were determined. The kinetics of SCO over a Cu/Ce catalyst of molar ratio 6:4 in oxidation of NH3, using differential method, was found that a pseudo-first order reaction could be described by Mars-Van Krevelend model. An equation of destruction efficiency in terms of NH3 was obtained, and a good fitting was got between the predicted and the experimental values.

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This thesis is based on the study of ammonia oxidation on platinum group metals. The objectives of this thesis are accept or discard the diverse mechanisms proposed. Even suggest the most appropriate according to the data obtained. To carry out this work is necessary to know the geometry of each species that may exist on the surface of the catalyst and the transition states of the reactions that lead from one species (or combination of species) to another. This is know the key points of a reaction (activation energy and reaction enthalpy). With all data obtained was proposed a microkinetic model of the process and analysis this to obtain a reduced model, equivalent to a mechanism. With this model it is possible to obtain a simulation of the temporal evolution of each species, both in gas phase on the surface, depending on initial conditions. All this information is useful to know how the mechanism works and the evolution of products depending on the temperature or the oxygen-ammonia ratio. To carry out this thesis has used the density functional theory (DFT) implemented in VASP code on a model of a periodic cell of 2 ¡Á 2 with four layers of metal where the two more superficial are entirely free, being able to deform and adapt the molecule adsorbed. The Encut and k-points used are 400 eV and 5 ¡Á 5 ¡Á 1, respectively.This thesis is divided in three chapters. The first examines and compares the dehydrogenation of ammonia on platinum in the faces 100 and 111. The second chapter examines and compares the dehydrogenation on platinum, palladium and rhodium on both sides, 100 and 111. And the third chapter examines the process of ammonia oxidation on Pt(100).The first part has been carried out a systematic study of adsorption and the relative stability of the ammonia and the species of dehydrogenation on the surfaces of Pt (111) and Pt (100). Different adsorption geometries and positions have been studied. The vibrational spectra of various fragments of ammonia have been calculated and were compared with the experimental data available. The adsorption of NH3 is on top position and for the NH2 is on bridge and it is the most stable on Pt (100) than on Pt (111). For the NH and N are adsorbed on the hollow site. There is a considerable difference in the energy of adsorption of NH2 on both sides. This difference is mainly explained by the geometry that takes the kind on both sides. Being much more stable on the 100 side than on the face 111. Accordingly, the platinum surface determines the most stable species NHx: On Pt(100) has more affinity NH2 species, whereas species prefer NH Pt(111).The second part extends the study of the dehydrogenation to other metals such as Palladium and Rhodium. The different adsorption geometries and positions have been studied for the intermediate of ammonia dehydrogenation (NHx, x=0-2). The six surfaces studied, the NH3 adsorbs preferably on the top position, the NH2 on bridge, NH and N on hollow. However, the adsorption energies of the fragments NHx fluctuate considerably from one surface to another. All species absorbs more strongly on the face 100 than on face 111. The Rh(100) is the surface that provides maximum stability for the different NHx species. The reaction energy, the activation energy and the geometry of the transition state for the successive of ammonia dehydrogenation (NHx ¡ú NHx-1) have been determined, which allows calculating the rate coefficients. Our results prove that the reaction is structure sensitive. As a general trend, the first step of dehydrogenation is the limiting step, especially for palladium. According to the experimental data Rhodium is a good catalyst for the decomposition of NH3 compared to Pt and Pd. It has also been observed a linear relationship between the potential energy of the transition state and the adsorption energy of the products. The third part studies the ammonia oxidation on Pt(100). The conversion of NH3 leading to NHx intermediate species that reacts with adsorbed oxygen species and ultimately the formation of the products (NO, N2O, N2 and H2O) that it has been systematically calculated. The reaction comes through an imine mechanism, while the classical mechanisms postulated by Bodenstein and Andrussow (nytroxyl and hydroxilamine, respectively) as reaction intermediates can be discarded. The activation energy for the oxidative ammonia dehydrogenation on Pt(100) has been drastically reduced compared to the non-oxidative ammonia dehydrogenation. The barriers of ammonia dehydrogenation are greatly favored by the O-assisted way than the OH-assisted way. The final products are formed by recombination of adsorbed Nitrogen with N (N2), O (NO) and NO (N2O). The water is formed through the recombination of two adsorbed OH, regenerating adsorbed oxygen. The limiting step in the oxidative ammonia dehydrogenation is the first step, abstraction of the first proton of ammonia (NH3¡úNH2+H). While the nitric oxide desorption is the rate determining step (rds) of the process. We calculated the reaction rate coefficients of elementary steps involved in the reaction mechanism allows doing a microkinetic analysis. The simulations carried out with the microkinetic model describe well the experimental distribution of products obtained at different temperatures, depending on the time and the ratio of initial NH3/O2. Getting a temporal distribution of each species in gas phase and on the surface. / Esta tesis se basa en el estudio de la oxidación de amoniaco sobre el grupo del platino. El objetivo de esta tesis es descartar o aceptar los diversos mecanismos propuestos. Incluso proponer el más correcto según los datos obtenidos. Para llevar a cabo esta acometida es necesario conocer cada geometría de las diferentes especies que pueden existir sobre la superficie del catalizador, así como los estados de transición entre las reacciones que lleven de una especie (o combinación de especies) a otras. Es decir conocer los puntos claves de una reacción (energía de activación y entalpía de reacción). Con los datos obtenidos se ha realizado la microcin¨¦tica del proceso completo y se ha realizado un análisis microcinético, llegando a obtener un modelo reducido, el equivalente a un mecanismo de reacción. Con este modelo es posible obtener una simulación de la evolución temporal de cada especie, tanto en fase gas como sobre la superficie, en función de unas condiciones iniciales. Toda esta información es de gran utilidad para conocer el funcionamiento del mecanismo y conocer la evolución de los productos en función de la temperatura, o de la relación de amoniaco-oxigeno. Para realizar esta tesis se ha usado la Teoría del funcional de la Densidad (DFT), el programa VASP usa esta teoría con ondas planas para realizar los cílculos sobre un modelo periódico de una celda de 2¡Á2 con cuatro capas de metal donde las dos más superficiales están totalmente libres, pudiéndose deformar y adaptar al adsorbato. El Encut y los k-points usados son de 400 eV y 5¡Á5¡Á1, respectivamente. La tesis se ha dividido en tres capítulos. En el primero se estudia y compara la deshidrogenación del amoniaco sobre Platino en las caras 100 y 111. En el segundo capitulo se estudia y compara la deshidrogenación sobre Platino, Paladio y Rodio en las dos caras, 100 y 111. Y en el tercer capítulo se estudia el proceso de la oxidación de amoniaco sobre Platino en la cara 100.En la primera parte se han llevado a cabo una estudio sistemático de la adsorción y la estabilidad relativa del amoniaco y de las especies de la deshidrogenación sobre las superficies de Pt (111) y Pt (100). Diferentes geometrías y posiciones de adsorción han sido estudiadas. Los espectros vibracionales de los diversos fragmentos de amoníaco se han calculado y se han comparado con los datos experimentales disponibles. La adsorción de NH3 se realiza sobre la posici¨®n top el NH2 sobre la posición bridge y es la más estable sobre Pt (100) que sobre Pt (111). Para el NH y el N se adsorben sobre el hollow. Existe una diferencia considerable en la energía de adsorción del NH2 sobre las dos caras. Esta diferencia se explica principalmente por la geometría que adopta la especie sobre las dos caras. Siendo mucho más estable sobre la cara 100 que sobre la cara 111. En consecuencia, la superficie de platino determina la especie NHx más estable: Sobre Pt(100) tiene más afinidad la especie NH2, mientras que la especie NH prefiere el Pt (111). En la segunda parte el estudio de la deshidrogenación se ha ampliado a otros metales como el Paladio y el Rodio. Diferentes geometrías de adsorción y posiciones han sido estudiados para NH3 y los intermedios de la deshidrogenación del amoniaco (NHx, x = 0 - 2). En las seis superficies investigadas, el NH3 adsorbe preferentemente sobre la posición top, el NH2 en bridge, el NH y el N lo hacen sobre el hollow. Sin embargo, las energías de adsorción los fragmentos NHx difieren considerablemente de una superficie a otra. Todas las especies de absorber con más fuerza en la cara 100 que en el la cara 111. El Rh(100) es la superficie que proporciona la máxima estabilidad para las diferentes especies. La energía de reacción, la geometría del estado de transición y la barrera de activación de los sucesivos pasos de reacción de la deshidrogenación (NHx ¡ú NHx-1) se han determinado, lo que permite calcular los coeficientes de las velocidades de reacción. Nuestros cálculos demuestran que la reacción es sensible a la estructura de la superficie. Como tendencia general, el primer paso de la deshidrogenación es el paso limitante, especialmente para Paladio. De acuerdo con los datos experimentales el Rodio es un buen catalizador para la descomposición de NH3 frente al Pt y el Pd. También se ha observado una relación lineal entre la energía potencial del estado de transición y la energía de adsorción de los productos. En la tercera parte se ha estudiado el proceso de oxidación de amoniaco sobre Pt(100). La conversión de NH3 que lleva a especies intermedias de NHx que reacciona con especies que contienen oxígeno adsorbido y en última instancia la formación de los productos de reacción (NO, N2O, N2 y H2O), han sido calculadas sistemáticamente. La reacción procede a través de un mecanismo de amina, mientras que los mecanismos clásicos postulados por Andrussow y Bodenstein (nitroxilo y hidroxilamina, respectivamente) como productos intermedios de reacción pueden ser descartados. Las barreras de activación para la deshidrogenación oxidativa del amoniaco sobre Pt(100) se han reducido drásticamente con respecto a la deshidrogenación no-oxidativa. La energía de activación de la deshidrogenación de amoniaco y de las subsiguientes deshidrogenaciones (NHx) son en gran medida favorecidas por el oxigeno adsorbido con respecto al hidróxido adsorbido. Los productos finales están formados por recombinación de N adsorbido con N (N2), O (NO) y NO (N2O). El agua se forma a través de la recombinación de OH adsorbido, regenerando un oxígeno.La etapa limitante en la deshidrogenación oxidativa del amoniaco es la primera etapa, la abstracción del primer protón del NH3. Mientras que desorción del NO es la etapa limitante del proceso en general. Se han calculado los coeficientes de velocidad de reacción de los pasos elementales que participan en el mecanismo de reacción, permitiendo obtener un análisis microcinético. Las simulaciones realizadas con el modelo microcinético describen bien la distribución de productos obtenidos experimentalmente a diferentes temperaturas, en función del tiempo y del ratio de NH3/O2 iniciales. Obteniendo una distribución temporal de cada especie, en fase gas y sobre la superficie.

Diss. (sammanfattning) Uppsala : Sveriges lantbruksuniversitet, 2006. / Härtill 5 uppsatser.

abstract: Human activity has increased loading of reactive nitrogen (N) in the environment, with important and often deleterious impacts on biodiversity, climate, and human health. Since the fate of N in the ecosystem is mainly controlled by microorganisms, understanding the factors that shape microbial communities becomes relevant and urgent. In arid land soils, these microbial communities and factors are not well understood. I aimed to study the role of N cycling microbes, such as the ammonia-oxidizing bacteria (AOB), the recently discovered ammonia-oxidizing archaea (AOA), and various fungal groups, in soils of arid lands. I also tested if niche differentiation among microbial populations is a driver of differential biogeochemical outcomes. I found that N cycling microbial communities in arid lands are structured by environmental factors to a stronger degree than what is generally observed in mesic systems. For example, in biological soil crusts, temperature selected for AOA in warmer deserts and for AOB in colder deserts. Land-use change also affects niche differentiation, with fungi being the major agents of N2O production in natural arid lands, whereas emissions could be attributed to bacteria in mesic urban lawns. By contrast, NO3- production in the native desert and managed soils was mainly controlled by autotrophic microbes (i.e., AOB and AOA) rather than by heterotrophic fungi. I could also determine that AOA surprisingly responded positively to inorganic N availability in both short (one month) and long-term (seven years) experimental manipulations in an arid land soil, while environmental N enrichment in other ecosystem types is known to favor AOB over AOA. This work improves our predictions of ecosystem response to anthropogenic N increase and shows that paradigms derived from mesic systems are not always applicable to arid lands. My dissertation also highlights the unique ecology of ammonia oxidizers and draws attention to the importance of N cycling in desert soils. / Dissertation/Thesis / Ph.D. Biology 2013

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