Properties of molecules in tunnel junctions

Molecular tunnel junctions involve studying the behaviour of a single molecule sandwiched between metal leads. When a molecule makes contact with electrodes, it becomes open to the environment which can heavily influence its properties, such as electronegativity and electron transport. While the most common computational approaches remain to be single particle approximations, in this thesis it is shown that a more explicit treatment of electron interactions can be required. By studying an open atomic chain junction, it is found that including electron correlations corrects the strong lead-molecule interaction seen by the ΔSCF approximation, and has an impact on junction I − V properties. The need for an accurate description of electronegativity is highlighted by studying a correlated model of hexatriene-di-thiol with a systematically varied correlation parameter and comparing the results to various electronic structure treatments. The results indicating an overestimation of the band gap and underestimation of charge transfer in the Hartree-Fock regime is equivalent to not treating electron-electron correlations. While in the opposite limit, over-compensating for electron-electron interaction leads to underestimated band gap and too high an electron current as seen in DFT/LDA treatment. It is emphasised in this thesis that correcting electronegativity is equivalent to maximising the overlap of the approximate density matrix to the exact reduced density matrix found at the exact many-body solution. In this work, the complex absorbing potential (CAP) formalism which allows for the inclusion metal electrodes into explicit wavefunction many-body formalisms is further developed. The CAP methodology is applied to study the electron state lifetimes and shifts as the junction is made open.

The role of the IL-1 type 1 receptor in the life, death and differentiation of adult hippocampal neural precursor cells

Neurogenesis occurs in two distinct regions of the adult brain; the subgranular zone (SGZ) of the dentate gyrus (DG) in the hippocampus, and the subventricular zone (SVZ) lining the lateral ventricles. It is now well-known that adult hippocampal neurogenesis can be modulated by a number of intrinsic and extrinsic factors e.g. local signalling molecules, exercise, environmental enrichment and learning. Moreover, levels of adult hippocampal neurogenesis decrease with age, at least in rodents, and alterations in hippocampal neurogenesis have been reported in animal models and human studies of neuropsychiatric and neurodegenerative conditions. Neuroinflammation is a common pathological feature of these conditions and is also a potent modulator of adult hippocampal neurogenesis. Recently, the orphan nuclear receptor TLX has been identified as an important regulator of adult hippocampal neurogenesis as its expression is necessary to maintain the neural precursor cell (NPC) pool in the adult DG. Likewise, exposure of animals to voluntary exercise has been consistently demonstrated to promote adult hippocampal neurogenesis. Lentivirus (LV)- mediated gene transfer is a useful tool to elucidate gene function and to explore potential therapeutic candidates across an array of conditions as it facilitates sustained gene expression in both dividing and post-mitotic cell populations. Both intrinsic and extrinsic factors are important regulators of adult hippocampal neurogenesis. Examining how these factors are affected by an inflammatory stimulus, and the subsequent effects on adult hippocampal neurogenesis provides important information for the development of novel treatment strategies for neuropsychiatric and neurodegenerative conditions in which adult hippocampal neurogenesis is impaired. The aims of the series of experiments presented in this thesis were to examine the effect of the pro-inflammatory cytokine interleukin-1β (IL-1β) on adult hippocampal NPCs both in vitro and in vivo. In vitro, we have shown that IL-1β reduces proliferation of adult hippocampal NPCs in a dose and time-dependent manner. In addition, we have demonstrated that TLX expression is reduced by IL-1β. Blockade of IL-1β signalling prevented both the IL-1β-induced reduction in cell proliferation and TLX expression. In vivo, we examined the effect of short term and long term exposure to LV-IL-1β in sedentary mice and in mice exposed to voluntary running. We demonstrated that impaired hippocampal neurogenesis is only evident after long term exposure to IL-1β. In mice exposed to voluntary running, hippocampal neurogenesis is significantly increased following short-term but not long-term exposure to running. Moreover, short-term running effectively prevents any IL-1β-induced effects on hippocampal neurogenesis; however, no such effects are seen following long-term exposure to running.

Synthesis and characterisation of novel superficially porous silica based stationary phases for use in liquid chromatography

The concept of pellicular particles was suggested by Horváth and Lipsky over fifty years ago. The reasoning behind the idea of these particles was to improve column efficiency by shortening the pathways analyte molecules can travel, therefore reducing the effect of the A and C terms. Several types of shell particles were successfully marketed around this time, however with the introduction of high quality fully porous silica under 10 μm, shell particles faded into the background. In recent years a new generation of core shell particles have become popular within the separation science community. These particles allow fast and efficient separations that can be carried out on conventional HPLC systems. Chapter 1 of this thesis introduces the chemistry of chromatographic stationary phases, with an emphasis on silica bonded phases, particularly focusing on the current state of technology in this area. The main focus is on superficially porous silica particles as a support material for liquid chromatography. A summary of the history and development of these particles over the past few decades is explored, along with current methods of synthesis of shell particles. While commercial shell particles have a rough outer surface, Chapter 2 focuses on the novel approach to growth of smooth surface superficially porous particles in a step-by-step manner. From the Stöber methodology to the seeded growth technique, and finally to the layer-bylayer growth of the porous shell. The superficially porous particles generated in this work have an overall diameter of 2.6 μm with a 350 nm porous shell; these silica particles were characterised using SEM, TEM and BET analysis. The uniform spherical nature of the particles along with their surface area, pore size and particle size distribution are examined in this chapter. I discovered that these smooth surface shell particles can be synthesised to give comparable surface area and pore size in comparison to commercial brands. Chapter 3 deals with the bonding of the particles prepared in Chapter 2 with C18 functionality; one with a narrow and one with a wide particle size distribution. This chapter examines the chromatographic and kinetic performance of these silica stationary phases, and compares them to a commercial superficially porous silica phase with a rough outer surface. I found that the particle size distribution does not seem to be the major contributor to the improvement in efficiency. The surface morphology of the particles appears to play an important role in the packing process of these particles and influences the Van Deemter effects. Chapter 4 focuses on the functionalisation of 2.6 μm smooth surface superficially porous particles with a variety of fluorinated and phenyl silanes. The same processes were carried out on 3.0 μm fully porous silica particles to provide a comparison. All phases were accessed using elemental analysis, thermogravimetric analysis, nitrogen sorption analysis and chromatographically evaluated using the Neue test. I observed comparable results for the 2.6 μm shell pentaflurophenyl propyl silica when compared to 3.0 μm fully porous silica. Chapter 5 moves towards nano-particles, with the synthesis of sub-1 μm superficially porous particles, their characterisation and use in chromatography. The particles prepared are 750 nm in total with a 100 nm shell. All reactions and testing carried out on these 750 nm core shell particles are also carried out on 1.5 μm fully porous particles in order to give a comparative result. The 750 nm core shell particles can be synthesised quickly and are very uniform. The main drawback in their use for HPLC is the system itself due to the backpressure experienced using sub – 1 μm particles. The synthesis of modified Stöber particles is also examined in this chapter with a range of non-porous silica and shell silica from 70 nm – 750 nm being tested for use on a Langmuir – Blodgett system. These smooth surface shell particles have only been in existence since 2009. The results displayed in this thesis demonstrate how much potential smooth surface shell particles have provided more in-depth optimisation is carried out. The results on packing studies reported in this thesis aims to be a starting point for a more sophisticated methodology, which in turn can lead to greater chromatographic improvements.

Synthesis and evaluation of novel quinolines and quinazolinediones as potential anti-cancer agents

This thesis outlines the design and effectuation of novel chemical routes towards a nascent class of functionalised quinoline-5,8-diones and the expansion of a series of contemporary quinazolinediones towards an innovative family of pyridinoquinazolinetetrone derivatives. This fragment based approach is envisaged to lead to advancements in the three scaffolds, expanding the SAR pool of both quinolines and quinazolinediones with subsequent evaluation of chemotherapeutic potential as well as furnishing a new class of tricycle for biological investigation. Development of novel quinoline-5,8-diones is provided for by expanding on existing methodology. Using a variety of nucleophiles on a critical intermediate, a broad range of novel compounds was afforded allowing chemotherapeutic potential to be assessed, while also serving as intermediates for accomplishing novel pyridinoquinazolinetetrone congeners. In order to incorporate functionality into our quinazolinedione template, an efficient synthetic strategy was constructed which provided a robust route to effectuate a highly derivatised pyrimidinedione ring. As derivatisation of this template is unreported our chief priority was to synthesise a range of diverse quinazolinediones. The application of annulation methodology using functionalised precursors provided a library of N-3 derivatised quinazolinedione analogues. These, along with their N-1 functionalised derivatives provide a wide scope from which to construct a series of pyridinoquinazolinetetrone derivatives while also serving as a unique class of molecules whose biological potential is uncharted. Although the actualisation of the pyridinoquinazolinetetrone was ultimately unsuccessful, our work has led to the development of novel quinoline-5,8-diones which were found to possess excellent anti-cancer activity when assessed by the NCI screen. Of the quinazolinediones synthesised eight compounds were accepted for screening by the NCI. Results from the single-dose tests however indicated that these compounds possessed little cytotoxic activity at 10 μM. The development of this novel template in conjunction with the highly active quinolinediones serves as an excellent rostrum for future synthetic endeavours.

Study of the kinetics and mechanism of rapid self-assembly in block copolymer thin films during solvo-microwave annealing

Microwave annealing is an emerging technique for achieving ordered patterns of block copolymer films on substrates. Little is understood about the mechanisms of microphase separation during the microwave annealing process and how it promotes the microphase separation of the blocks. Here, we use controlled power microwave irradiation in the presence of tetrahydrofuran (THF) solvent, to achieve lateral microphase separation in high- lamellar-forming poly(styrene-b-lactic acid) PS-b-PLA. A highly ordered line pattern was formed within seconds on silicon, germanium and silicon on insulator (SOI) substrates. In-situ temperature measurement of the silicon substrate coupled to condition changes during "solvo-microwave" annealing allowed understanding of the processes to be attained. Our results suggest that the substrate has little effect on the ordering process and is essentially microwave transparent but rather, it is direct heating of the polar THF molecules that causes microphase separation. It is postulated that the rapid interaction of THF with microwaves and the resultant temperature increase to 55 degrees C within seconds causes an increase of the vapor pressure of the solvent from 19.8 to 70 kPa. This enriched vapor environment increases the plasticity of both PS and PLA chains and leads to the fast self-assembly kinetics. Comparing the patterns formed on silicon, germanium and silicon on insulator (SOI) and also an in situ temperature measurement of silicon in the oven confirms the significance of the solvent over the role of substrate heating during "solvo-microwave" annealing. Besides the short annealing time which has technological importance, the coherence length is on a micron scale and dewetting is not observed after annealing. The etched pattern (PLA was removed by an Ar/O-2 reactive ion etch) was transferred to the underlying silicon substrate fabricating sub-20 nm silicon nanowires over large areas demonstrating that the morphology is consistent both across and through the film.