Electronic spectroscopy of thiones

The phosphorescence excitation spectra of two thiones, 4-H-1-xanthione (XT) and 4-H-1-pyrane-4-thione (PT), cooled in a supersonic jet were investigated. The vibronic lineshape of the T1z origin of PT measured by cavity ring-down spectroscopy is considered and the excited state rotational constants are calculated. For XT the 3A2(nπ* ) → X1A1 phosphorescence excitation spectrum was investigated in the region 14900-17600 cm-1. The structure observed is shown to be due to the T1← S0 absorption and an assignment in terms of the vibronic structure of the band is proposed. A previous assignment of the S1 ← S0 origin is considered and the transition involved is shown to be most probably due to the absorption of a vibronic tiplet state T1z,v7. An alternative but tentative assignment of the S1,0 ←S0,0 transition is suggested. In the case of PT the phosphorescence excitation spectrum was investigated in the region of the 1A2(ππ*) ← X1A1 absorption band between 27300 and 28800 cm-1. The spectrum exhibits complex features which are typical for the strong vibronic coupling case of two adjacent electronic states. The observed intermediate level structure was attributed to the coupling with a lower lying dark electronic state 1B1(nπ*2), whose origin was estimated to be ~ 825 - 1025 cm-1 below the origin of 1A2(ππ*)0. Consequences of the vibronic coupling on the decay dynamics of 1A2(ππ*) as well as tentative assignments of vibronic transitions 1A2(ππ*)v ← X1A1 are also discussed. In the T1z ← S0 cavity ring-down absorption spectrum of PT, the vibronic lineshape of the T1z origin is analysed. As the T1z line is separated from the T1x,1y lines by a large zero-field splitting it is possible to use an Asyrot-like program to calculate the vibrational-rotational parameters determining the lineshape. It is shown that PT is non-planar in the first excited triplet state and the lineshape is composed of a mixture of A-type and C-type bandshapes. The non-planarity of PT is discussed.

Visualising ribosome profiling and using it for reading frame detection and exploration of eukaryotic translation initiation

Ribosome profiling (ribo-seq) is a recently developed technique that provides genomewide information on protein synthesis (GWIPS) in vivo. The high resolution of ribo-seq is one of the exciting properties of this technique. In Chapter 2, I present a computational method that utilises the sub-codon precision and triplet periodicity of ribosome profiling data to detect transitions in the translated reading frame. Application of this method to ribosome profiling data generated for human HeLa cells allowed us to detect several human genes where the same genomic segment is translated in more than one reading frame. Since the initial publication of the ribosome profiling technique in 2009, there has been a proliferation of studies that have used the technique to explore various questions with respect to translation. A review of the many uses and adaptations of the technique is provided in Chapter 1. Indeed, owing to the increasing popularity of the technique and the growing number of published ribosome profiling datasets, we have developed GWIPS-viz (http://gwips.ucc.ie), a ribo-seq dedicated genome browser. Details on the development of the browser and its usage are provided in Chapter 3. One of the surprising findings of ribosome profiling of initiating ribosomes carried out in 3 independent studies, was the widespread use of non-AUG codons as translation initiation start sites in mammals. Although initiation at non-AUG codons in mammals has been documented for some time, the extent of non-AUG initiation reported by these ribo-seq studies was unexpected. In Chapter 4, I present an approach for estimating the strength of initiating codons based on the leaky scanning model of translation initiation. Application of this approach to ribo-seq data illustrates that initiation at non-AUG codons is inefficient compared to initiation at AUG codons. In addition, our approach provides a probability of initiation score for each start site that allows its strength of initiation to be evaluated.

Atomic layer structure of vanadium oxide nanotubes grown on nanourchin structures

We report the detailed characterization of high quality vanadium oxide (VOx) nanotubes (NTs) and highlight the zipping of adjacent vanadate layers in such NTs formed on remarkable nanourchin structures. These nanostructures consist of high-density spherical radial arrays of NTs. The results evidence vanadate NTs with unprecedented uniformity and evidences the first report of vanadate atomic layer zipping. The NTs are ∼2 μm in length with inner diameters of 20-30 nm. The tube walls comprise scrolled triplet-layers of vanadate intercalated with organic surfactant. Such high-volume structures might be useful as open-access electrolyte scaffolds for lithium insertion-based charge storage devices.

Synthesis and characterization of oxide materials

Nanostructured materials are central to the evolution of future electronics and biomedical applications amongst other applications. This thesis is focused on developing novel methods to prepare a number of nanostructured metal oxide particles and films by a number of different routes. Part of the aim was to see how techniques used in nanoparticle science could be applied to thin film methods to develop functional surfaces. Wet-chemical methods were employed to synthesize and modify the metal oxide nanostructures (CeO2 and SiO2) and their structural properties were characterized through advanced X-ray diffraction, electron microscopy, photoelectron spectroscopy and other techniques. Whilst particulates have uses in many applications, their attachment to surfaces is of importance and this is frequently challenging. We examined the use of block copolymer methods to form very well defined metal oxide particulate-like structures on the surface of a number of substrates. Chapter 2 describes a robust method to synthesize various sized silica nanoparticles. As-synthesized silica nanoparticles were further functionalized with IR-820 and FITC dyes. The ability to create size controlled nanoparticles with associated (optical) functionality may have significant importance in bio-medical imaging. Thesis further describes how non-organic modified fluorescent particles might be prepared using inorganic oxides. A study of the concentrations and distributions of europium dopants within the CeO2 nanoparticles was undertaken and investigated by different microscopic and spectroscopic techniques. The luminescent properties were enhanced by doping and detailed explanations are reported. Additionally, the morphological and structural evolution and optical properties were correlated as a function of concentrations of europium doping as well as with further annealing. Further work using positron annihilation spectroscopy allowed the study of vacancy type defects formed due to europium doping in CeO2 crystallites and this was supported by complimentary UV-Vis spectra and XRD work. During the last few years the interest in mesoporous silica materials has increased due to their typical characteristics such as potential ultra-low dielectric constant materials, large surface area and pore volume, well-ordered and uniform pores with adjustable pores between 2 and 50 nm. A simple, generic and cost-effective route was used to demonstrate the synthesis of 2D mesoporous silica thin films over wafer scale dimensions in chapter 5. Lithographic resist and in situ hard mask block copolymer followed by ICP dry etching were used to fabricate mesoporous silica nanostructures. The width of mesoporous silica channels can be varied by using a variety of commercially available lithographic resists whereas depth of the mesoporous silica channels can be varied by altering the etch time. The crystal structure, morphology, pore arrangement, pore diameters, thickness of films and channels were determined by XRD, SEM, ellipsometry and the results reported. This project also extended work towards the study of the antimicrobial study of nanopatterned silver nanodot arrays formed using the block copolymer approach defined above. Silver nanodot arrays were successfully tested for antimicrobial activity over S. aureus and P. aeruginosa biofilms and results shows silver nanodots has good antimicrobial activity for both S. aureus and P. aeruginosa biofilms. Thus, these silver nanodot arrays shows a potential to be used as a substitute for the resolution of infection complications in many areas.