Simulation chamber studies of the atmospheric degradation of naphthalene, 1-nitronaphthalene and phthaldialdehyde

A detailed series of simulation chamber experiments has been performed on the atmospheric degradation pathways of the primary air pollutant naphthalene and two of its photooxidation products, phthaldialdehyde and 1-nitronaphthalene. The measured yields of secondary organic aerosol (SOA) arising from the photooxidation of naphthalene varied from 6-20%, depending on the concentrations of naphthalene and nitrogen oxides as well as relative humidity. A range of carbonyls, nitro-compounds, phenols and carboxylic acids were identified among the gas- and particle-phase products. On-line analysis of the chemical composition of naphthalene SOA was performed using aerosol time-of-flight mass spectrometry (ATOFMS) for the first time. The results indicate that enhanced formation of carboxylic acids may contribute to the observed increase in SOA yields at higher relative humidity. The photolysis of phthaldialdehyde and 1-nitronaphthalene was investigated using natural light at the European Photoreactor (EUPHORE) in Valencia, Spain. The photolysis rate coefficients were measured directly and used to confirm that photolysis is the major atmospheric loss process for these compounds. For phthaldialdehyde, the main gas-phase products were phthalide and phthalic anhydride. SOA yields in the range 2-11% were observed, with phthalic acid and dihydroxyphthalic acid identified among the particle phase products. The photolysis of 1-nitronaphthalene yielded nitric oxide and a naphthoxy radical which reacted to form several products. SOA yields in the range 57-71% were observed, with 1,4-naphthoquinone, 1-naphthol and 1,4-naphthalenediol identified in the particle phase. On-line analysis of the SOA generated in an indoor chamber using ATOFMS provided evidence for the formation of high-molecular-weight products. Further investigations revealed that these products are oxygenated polycyclic compounds most likely produced from the dimerization of naphthoxy radicals. These results of this work indicate that naphthalene is a potentially large source of SOA in urban areas and should be included in atmospheric models. The kinetic and mechanistic information could be combined with existing literature data to produce an overall degradation mechanism for naphthalene suitable for inclusion in photochemical models that are used to predict the effect of emissions on air quality.

Synthetic and mechanistic aspects of the reactions of α-diazosulfoxides

The research described in this thesis focuses, principally, on synthesis of stable α-diazosulfoxides and investigation of their reactivity under various reaction conditions (transition-metal catalysed, photochemical, thermal and microwave) with a particular emphasis on the reactive intermediates and mechanistic aspects of the reaction pathways involved. In agreement with previous studies carried out on these compounds, the key reaction pathway of α-diazosulfoxides was found to be hetero-Wolff rearrangement to give α-oxosulfine intermediates. However, a competing reaction pathway involving oxygen migration from sulfur to oxygen was also observed. Critically, isomerisation of α-oxosulfine stereoisomers was observed directly by 1H NMR spectroscopy in this work and this observation accounts for the stereochemical outcomes of the various cycloaddition reactions, whether carried out with in situ trapping or with preformed solutions of sulfines. Furthermore, matrix isolation experiments have shown that electrocyclisation of α-oxosulfines to oxathiiranes takes place and this verifies the proposed mechanisms for enol and disulfide formation. The introductory chapter includes a brief literature review of the synthesis and reactivity of α-diazosulfoxides prior to the commencement of research in this field by the Maguire group. The Wolff rearrangement is also discussed and the characteristic reactions of a number of reactive intermediates (sulfines, sulfenes and oxathiiranes) are outlined. The use of microwave-assisted organic synthesis is also examined, specifically, in the context of α-diazocarbonyl compounds as substrates. The second chapter describes the synthesis of stable monocyclic and bicyclic lactone derivatives of α-diazosulfoxides from sulfide precursors according to established experimental procedures. Approaches to precursors of ketone and sulfimide derivatives of α-diazosulfoxides are also described. The third chapter examines the reactivity of α-diazosulfoxides under thermal, microwave, rhodium(II)-catalysed and photochemical conditions. Comparison of the results obtained under thermal and microwave conditions indicates that there was no evidence for any effect, other than thermal, induced by microwave irradiation. The results of catalyst studies involving several rhodium(II) carboxylate and rhodium(II) carboxamidate catalysts are outlined. Under photochemical conditions, sulfur extrusion is a significant reaction pathway while under thermal or transition metal catalysed conditions, oxygen extrusion is observed. One of the most important observations in this work was the direct spectroscopic observation (by 1H NMR) of interconversion of the E and Z-oxosulfines. Trapping of the α-oxosulfine intermediates as cycloadducts by reaction with 2,3-dimethyl-1,3-butadiene proved useful both synthetically and mechanistically. As the stereochemistry of the α-oxosulfine is retained in the cycloadducts, this provided an ideal method for characterisation of this key feature. In the case of one α-oxosulfine, a novel [2+2] cycloaddition was observed. Preliminary experiments to investigate the reactivity of an α-diazosulfone under rhodium(II) catalysis and microwave irradiation are also described. The fourth chapter describes matrix isolation experiments which were carried out in Rühr Universität, Bochum in collaboration with Prof. Wolfram Sander. These experiments provide direct spectroscopic evidence of an α-oxosulfine intermediate formed by hetero-Wolff rearrangement of an α-diazosulfoxide and subsequent cyclisation of the sulfine to an oxathiirane was also observed. Furthermore, it was possible to identify which stereoisomer of the α-oxosulfine was present in the matrix. A preliminary laser flash photolysis experiment is also discussed. The experimental details, including all spectral and analytical data, are reported at the end of each chapter. The structural interpretation of 1H NMR spectra of the cycloadducts, described in Chapter 3, is discussed in Appendix I.

Investigation of polyhydroxyalkanoate production by an activated sludge microbial consortium treating artificial dairy wastewater

Petrochemical plastics/polymers are a common feature of day to day living as they occur in packaging, furniture, mobile phones, computers, construction equipment etc. However, these materials are produced from non-renewable materials and are resistant to microbial degradation in the environment. Considerable research has therefore been carried out into the production of sustainable, biodegradable polymers, amenable to microbial catabolism to CO2 and H2O. A key group of microbial polyesters, widely considered as optimal replacement polymers, are the Polyhydroxyalkaonates (PHAs). Primary research in this area has focused on using recombinant pure cultures to optimise PHA yields, however, despite considerable success, the high costs of pure culture fermentation have thus far hindered the commercial viability of PHAs thus produced. In more recent years work has begun to focus on mixed cultures for the optimisation of PHA production, with waste incorporations offering optimal production cost reductions. The scale of dairy processing in Ireland, and the high organic load wastewaters generated, represent an excellent potential substrate for bioconversion to PHAs in a mixed culture system. The current study sought to investigate the potential for such bioconversion in a laboratory scale biological system and to establish key operational and microbial characteristics of same. Two sequencing batch reactors were set up and operated along the lines of an enhanced biological phosphate removal (EBPR) system, which has PHA accumulation as a key step within repeated rounds of anaerobic/aerobic cycling. Influents to the reactors varied only in the carbon sources provided. Reactor 1 received artificial wastewater with acetate alone, which is known to be readily converted to PHA in the anaerobic step of EBPR. Reactor 2 wastewater influent contained acetate and skim milk to imitate a dairy processing effluent. Chemical monitoring of nutrient remediation within the reactors as continuously applied and EBPR consistent performances observed. Qualitative analysis of the sludge was carried out using fluorescence microscopy with Nile Blue A lipophillic stain and PHA production was confirmed in both reactors. Quantitative analysis via HPLC detection of crotonic acid derivatives revealed the fluorescence to be short chain length Polyhydroxybutyrate, with biomass dry weight accumulations of 11% and 13% being observed in reactors 1 and 2, respectively. Gas Chromatography-Mass Spectrometry for medium chain length methyl ester derivatives revealed the presence of hydroxyoctanoic, -decanoic and -dodecanoic acids in reactor 1. Similar analyses in reactor 2 revealed monomers of 3-hydroxydodecenoic and 3-hydroxytetradecanoic acids. Investigation of the microbial ecology of both reactors as conducted in an attempt to identify key species potentially contributing to reactor performance. Culture dependent investigations indicated that quite different communities were present in both reactors. Reactor 1 isolates demonstrated the following species distributions Pseudomonas (82%), Delftia acidovorans (3%), Acinetobacter sp. (5%) Aminobacter sp., (3%) Bacillus sp. (3%), Thauera sp., (3%) and Cytophaga sp. (3%). Relative species distributions among reactor 2 profiled isolates were more evenly distributed between Pseudoxanthomonas (32%), Thauera sp (24%), Acinetobacter (24%), Citrobacter sp (8%), Lactococcus lactis (5%), Lysinibacillus (5%) and Elizabethkingia (2%). In both reactors Gammaproteobacteria dominated the cultured isolates. Culture independent 16S rRNA gene analyses revealed differing profiles for both reactors. Reactor 1 clone distribution was as follows; Zooglea resiniphila (83%), Zooglea oryzae (2%), Pedobacter composti (5%), Neissericeae sp. (2%) Rhodobacter sp. (2%), Runella defluvii (3%) and Streptococcus sp. (3%). RFLP based species distribution among the reactor 2 clones was as follows; Runella defluvii (50%), Zoogloea oryzae (20%), Flavobacterium sp. (9%), Simplicispira sp. (6%), Uncultured Sphingobacteria sp. (6%), Arcicella (6%) and Leadbetterella bysophila (3%). Betaproteobacteria dominated the 16S rRNA gene clones identified in both reactors. FISH analysis with Nile Blue dual staining resolved these divergent findings, identifying the Betaproteobacteria as dominant PHA accumulators within the reactor sludges, although species/strain specific allocations could not be made. GC analysis of the sludge had indicated the presence of both medium chain length as well short chain length PHAs accumulating in both reactors. In addition the cultured isolates from the reactors had been identified previously as mcl and scl PHA producers, respectively. Characterisations of the PHA monomer profiles of the individual isolates were therefore performed to screen for potential novel scl-mcl PHAs. Nitrogen limitation driven PHA accumulation in E2 minimal media revealed a greater propensity among isoates for mcl-pHA production. HPLC analysis indicated that PHB production was not a major feature of the reactor isolates and this was supported by the low presence of scl phaC1 genes among PCR screened isolates. A high percentage distribution of phaC2 mcl-PHA synthase genes was recorded, with the majority sharing high percentage homology with class II synthases from Pseudomonas sp. The common presence of a phaC2 homologue was not reflected in the production of a common polymer. Considerable variation was noted in both the monomer composition and ratios following GC analysis. While co-polymer production could not be demonstrated, potentially novel synthase substrate specificities were noted which could be exploited further in the future.

Synthesis and evaluation of novel azaindolocarbazole derivatives as cancer chemotherapeutics

This thesis details the design and implementation of novel chemical routes towards a series of highly propitious 7-azaindolyl derivatives of the indolocarbazole (ICZ) and bisindolylmaleimide (BIM) families, with subsequent evaluation for use as cancer chemotherapeutic agents. A robust synthetic strategy was devised to allow the introduction of a 7-azaindolyl moiety into our molecular template. This approach allowed access to a wide range of β-keto ester and β-keto nitrile intermediates. Critical analysis identified F-ring modulation as a major theme towards the advancement of ICZ and BIM derivatives in drug therapy. Thus, the employment of cyclocondensation methodology furnished a number of novel aminopyrazole, isoxazolone, pyrazolone and pyrimidinone analogues, considerably widening the scope of the prevalent maleimide functionality. Photochemical cyclisation provided for the first reported aza ICZ containing a six-membered F-ring. Another method towards achieving the aza ICZ core involved use of a Perkin-type condensation approach, with chemical elaboration of the headgroup instigated post-aromatisation. Subsequent use of a modified Lossen rearrangement allowed access to further analogues containing a six-membered F-ring. Extensive screening of the novel aza ICZ and BIM derivatives was carried out against the NCI-60 cancer cell array, with nine prospective candidates selected for continued biological evaluation. From these assays, a number of compounds were shown to inhibit cancer cell growth at concentrations of below 10 nM. Indeed, the most active aza ICZ tested is currently under assessment by the Biological Evaluation Committee of the NCI due to excellent antiproliferative activity demonstrated across the panel of cell lines, with a mean GI50 of 34 nM, a mean total growth inhibition (TGI) of 4.6 μM and a mean cytotoxicity (LC50) of 63.1 μM. Correlation to known topoisomerase I (topo I) inhibitors was revealed by COMPARE analysis, and subsequent topo I-mediated DNA cleavage assays showed inhibitory activity below 1 μM for several derivatives.

Synthesis and reactivity of α-diazo-β-keto sulfoxides: scope and synthetic potential

The research described in this thesis focuses on the design and synthesis of stable α-diazosulfoxides and investigation of their reactivity under a variety of conditions (transition-metal catalysis, thermal, photochemical and microwave) with a particular emphasis on the synthesis of novel heterocyclic compounds with potential biological activity. The exclusive reaction pathway for these α-diazosulfoxides was found to be hetero-Wolff rearrangement to give α-oxosulfine intermediates. In the first chapter, a literature review of sulfines is presented, including a discussion of naturally occurring sulfines, and an overview of the synthesis and reactivity of sulfines. The potential of sulfines in organic synthesis and recent developments in particular are highlighted. The second chapter discusses the synthesis and reactivity of α-diazosulfoxides, building on earlier results in this research group. The synthesis of lactone-based α-diazosulfoxides and, for the first time, ketone-based benzofused and monocyclic α-diazosulfoxides is described. The reactivity of these α-diazosulfoxides is then explored under a variety of conditions, such as transition-metal catalysis, photochemical and microwave, generating labile α-oxosulfine intermediates, which are trapped using amines and dienes, in addition to the spontaneous reaction pathways which occur with α-oxosulfines in the absence of a trap. A new reaction pathway was explored with the lactone based α-oxosulfines, involving reaction with amines to generate novel 3-aminofuran-2(5H)-ones via carbophilic attack, in very good yields. The reactivity of ketone-based α-diazosulfoxides was explored for the first time, and once again, pseudo-Wolff rearrangement to the α-oxosulfines was the exclusive reaction pathway observed. The intermediacy of the α-oxosulfines was confirmed by trapping as cycloadducts, with the stereochemical features dependant on the reaction conditions. In the absence of a diene trap, a number of reaction fates from the α-oxosulfines were observed, including complete sulfinyl extrusion to give indanones, sulfur extrusion to give indanediones, and, to a lesser extent, dimerisation. The indanediones were characterised by trapping as quinoxalines, to enable full characterisation. One of the overriding outcomes of this thesis was the provision of new insights into the behaviour of α-oxosulfines with different transition metal catalysts, and under thermal, microwave and photolysis conditions. A series of 3-aminofuran-2(5H)-ones and benzofused dihydro-2H-thiopyran S-oxides were submitted for anticancer screening at the U.S. National Cancer Institute. A number of these derivatives were identified as hit compounds, with excellent cell growth inhibition. One 3-aminofuran-2(5H)-one derivative has been chosen for further screening. The third chapter details the full experimental procedures, including spectroscopic and analytical data for the compounds prepared during this research. The data for the crystal structures are contained in the attached CD.

Biomethane production from food waste and organic residues

Anaerobic digestion (AD) of biodegradable waste is an environmentally and economically sustainable solution which incorporates waste treatment and energy recovery. The organic fraction of municipal solid waste (OFMSW), which comprises mostly of food waste, is highly degradable under anaerobic conditions. Biogas produced from OFMSW, when upgraded to biomethane, is recognised as one of the most sustainable renewable biofuels and can also be one of the cheapest sources of biomethane if a gate fee is associated with the substrate. OFMSW is a complex and heterogeneous material which may have widely different characteristics depending on the source of origin and collection system used. The research presented in this thesis investigates the potential energy resource from a wide range of organic waste streams through field and laboratory research on real world samples. OFMSW samples collected from a range of sources generated methane yields ranging from 75 to 160 m3 per tonne. Higher methane yields are associated with source segregated food waste from commercial catering premises as opposed to domestic sources. The inclusion of garden waste reduces the specific methane yield from household organic waste. In continuous AD trials it was found that a conventional continuously stirred tank reactor (CSTR) gave the highest specific methane yields at a moderate organic loading rate of 2 kg volatile solids (VS) m-3 digester day-1 and a hydraulic retention time of 30 days. The average specific methane yield obtained at this loading rate in continuous digestion was 560 ± 29 L CH4 kg-1 VS which exceeded the biomethane potential test result by 5%. The low carbon to nitrogen ratio (C: N <14:1) associated with canteen food waste lead to increasing concentrations of volatile fatty acids in line with high concentrations of ammonia nitrogen at higher organic loading rates. At an organic loading rate of 4 kg VS m-3day-1 the specific methane yield dropped considerably (381 L CH4 kg-1 VS), the pH rose to 8.1 and free ammonia (NH3 ) concentrations reached toxicity levels towards the end of the trial (ca. 950 mg L-1). A novel two phase AD reactor configuration consisting of a series of sequentially fed leach bed reactors connected to an upflow anaerobic sludge blanket (UASB) demonstrated a high rate of organic matter decay but resulted in lower specific methane yields (384 L CH4 kg-1 VS) than the conventional CSTR system.

Atomic layer deposition of copper for CMOS interconnects

This work concerns the atomic layer deposition (ALD) of copper. ALD is a technique that allows conformal coating of difficult topographies such as narrow trenches and holes or even shadowed regions. However, the deposition of pure metals has so far been less successful than the deposition of oxides except for a few exceptions. Challenges include difficulties associated with the reduction of the metal centre of the precursor at reasonable temperatures and the tendency of metals to agglomerate during the growth process. Cu is a metal of special technical interest as it is widely used for interconnects on CMOS devices. These interconnects are usually fabricated by electroplating, which requires the deposition of thin Cu seed layers onto the trenches and vias. Here, ALD is regarded as potential candidate for replacing the current PVD technique, which is expected to reach its limitations as the critical dimensions continue to shrink. This work is separated into two parts. In the first part, a laboratory-scale ALD reactor was constructed and used for the thermal ALD of Cu. In the second part, the potentials of the application of Cu ALD on industry scale fabrication were examined in a joint project with Applied Materials and Intel. Within this project precursors developed by industrial partners were evaluated on a 300 mm Applied Materials metal-ALD chamber modified with a direct RF-plasma source. A feature that makes ALD a popular technique among researchers is the possibility to produce high- level thin film coatings for micro-electronics and nano-technology with relatively simple laboratory- scale reactors. The advanced materials and surfaces group (AMSG) at Tyndall National Institute operates a range of home-built ALD reactors. In order to carry out Cu ALD experiments, modifications to the normal reactor design had to be made. For example a carrier gas mechanism was necessary to facilitate the transport of the low-volatile Cu precursors. Precursors evaluated included the readily available Cu(II)-diketonates Cu-bis(acetylacetonate), Cu-bis(2,2,6,6-tetramethyl-hepta-3,5-dionate) and Cu-bis(1,1,1,5,5,5-hexafluoacetylacetonate) as well as the Cu-ketoiminate Cu-bis(4N-ethylamino- pent-3-en-2-onate), which is also known under the trade name AbaCus (Air Liquide), and the Cu(I)- silylamide 1,3-diisopropyl-imidazolin-2-ylidene Cu(I) hexamethyldisilazide ([NHC]Cu(hmds)), which was developed at Carleton University Ottawa. Forming gas (10 % H2 in Ar) was used as reducing agent except in early experiments where formalin was used. With all precursors an extreme surface selectivity of the deposition process was observed and significant growth was only achieved on platinum-group metals. Improvements in the Cu deposition process were obtained with [NHC]Cu(hmds) compared with the Cu(II) complexes. A possible reason is the reduced oxidation state of the metal centre. Continuous Cu films were obtained on Pd and indications for saturated growth with a rate of about 0.4 Å/cycle were found for deposition at 220 °C. Deposits obtained on Ru consisted of separated islands. Although no continuous films could be obtained in this work the relatively high density of Cu islands obtained was a clear improvement as compared to the deposits grown with Cu(II) complexes. When ultra-thin Pd films were used as substrates, island growth was also observed. A likely reason for this extreme difference to the Cu films obtained on thicker Pd films is the lack of stress compensation within the thin films. The most likely source of stress compensation in the thicker Pd films is the formation of a graded interlayer between Pd and Cu by inter-diffusion. To obtain continuous Cu films on more materials, reduction of the growth temperature was required. This was achieved in the plasma assisted ALD experiments discussed in the second part of this work. The precursors evaluated included the AbaCus compound and CTA-1, an aliphatic Cu-bis(aminoalkoxide), which was supplied by Adeka Corp.. Depositions could be carried out at very low temperatures (60 °C Abacus, 30 °C CTA-1). Metallic Cu could be obtained on all substrate materials investigated, but the shape of the deposits varied significantly between the substrate materials. On most materials (Si, TaN, Al2O3, CDO) Cu grew in isolated nearly spherical islands even at temperatures as low as 30 °C. It was observed that the reason for the island formation is the coalescence of the initial islands to larger, spherical islands instead of forming a continuous film. On the other hand, the formation of nearly two-dimensional islands was observed on Ru. These islands grew together forming a conductive film after a reasonably small number of cycles. The resulting Cu films were of excellent crystal quality and had good electrical properties; e.g. a resistivity of 2.39 µΩ cm was measured for a 47 nm thick film. Moreover, conformal coating of narrow trenches (1 µm deep 100/1 aspect ratio) was demonstrated showing the feasibility of the ALD process.