Towards thiol functionalization of vanadium pentoxide nanotubes using gold nanoparticles

Template-directed synthesis is a promising route to realize vanadate-based 1-D nanostructures, an example of which is the formation of vanadium pentoxide nanotubes and associated nanostructures. In this work, we report the interchange of long-chained alkyl amines with alkyl thiols. This reaction was followed using gold nanoparticles prepared by the Chemical Liquid Deposition (CLD) method with an average diameter of ∼0.9 nm and a stability of ∼85 days. V2 O5 nanotubes (VOx-NTs) with lengths of ∼2 μm and internal hollow diameters of 20-100 nm were synthesized and functionalized in a Au-acetone colloid with a nominal concentration of ∼ 4 × 1 0- 3 mol dm-3. The interchange reaction with dodecylamine is found only to occur in polar solvents and incorporation of the gold nanoparticles is not observed in the presence of n-decane.

Advancing atomic nanolithography: cold atomic Cs beam exposure of alkanethiol self-assembled monolayers

We report the results of a study into the quality of functionalized surfaces for nanolithographic imaging. Self-assembled monolayer (SAM) coverage, subsequent post-etch pattern definition and minimum feature size all depend on the quality of the Au substrate used in atomic nanolithographic experiments. We find sputtered Au substrates yield much smoother surfaces and a higher density of {111} oriented grains than evaporated Au surfaces. A detailed study of the self-assembly mechanism using molecular resolution AFM and STM has shown that the monolayer is composed of domains with sizes typically of 5-25 nm, and multiple molecular domains can exist within one Au grain. Exposure of the SAM to an optically-cooled atomic Cs beam traversing a two-dimensional array of submicron material masks ans also standing wave optical masks allowed determination of the minimum average Cs dose (2 Cs atoms per SAM molecule) and the realization of < 50 nm structures. The SAM monolayer contains many non-uniformities such as pin-holes, domain boundaries and monoatomic depressions which are present in the Au surface prior to SAM adsorption. These imperfections limit the use of alkanethiols as a resist in atomic nanolithography experiments. These studies have allowed us to realize an Atom Pencil suitable for deposition of precision quantities of material at the microand nanoscale to an active surface.

Writing self-assembled monolayers with Cs: Optimization of atomic nanolithography imaging using self-assembled monolayers on gold substrates

We report the results of a study into the factors controlling the quality of nanolithographic imaging. Self-assembled monolayer (SAM) coverage, subsequent postetch pattern definition, and minimum feature size all depend on the quality of the Au substrate used in material mask atomic nanolithographic experiments. We find that sputtered Au substrates yield much smoother surfaces and a higher density of {111}-oriented grains than evaporated Au surfaces. Phase imaging with an atomic force microscope shows that the quality and percentage coverage of SAM adsorption are much greater for sputtered Au surfaces. Exposure of the self-assembled monolayer to an optically cooled atomic Cs beam traversing a two-dimensional array of submicron material masks mounted a few microns above the self-assembled monolayer surface allowed determination of the minimum average Cs dose (2 Cs atoms per self-assembled monolayer molecule) to write the monolayer. Suitable wet etching, with etch rates of 2.2 nm min-1, results in optimized pattern definition. Utilizing these optimizations, material mask features as small as 230 nm in diameter with a fractional depth gradient of 0.820 nm were realized.

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.

Electrochemical biosensor based on microfabricated electrode arrays for life sciences applications

In developing a biosensor, the utmost important aspects that need to be emphasized are the specificity and selectivity of the transducer. These two vital prerequisites are of paramount in ensuring a robust and reliable biosensor. Improvements in electrochemical sensors can be achieved by using microelectrodes and to modify the electrode surface (using chemical or biological recognition layers to improve the sensitivity and selectivity). The fabrication and characterisations of silicon-based and glass-based gold microelectrode arrays with various geometries (band and disc) and dimension (ranging from 10 μm-100 nm) were reported. It was found that silicon-based transducers of 10 μm gold microelectrode array exhibited the most stable and reproducible electrochemical measurements hence this dimension was selected for further study. Chemical electrodeposition on both 10 μm microband and microdisc were found viable by electro-assisted self-assembled sol-gel silica film and nanoporous-gold electrodeposition respectively. The fabrication and characterisations of on-chip electrochemical cell was also reported with a fixed diameter/width dimension and interspacing variation. With this regard, the 10 μm microelectrode array with interspacing distance of 100 μm exhibited the best electrochemical response. Surface functionalisations on single chip of planar gold macroelectrodes were also studied for the immobilisation of histidine-tagged protein and antibody. Imaging techniques such as atomic force microscopy, fluorescent microscopy or scanning electron microscope were employed to complement the electrochemical characterisations. The long-chain thiol of self-assembled monolayer with NTA-metal ligand coordination was selected for the histidine-tagged protein while silanisation technique was selected for the antibody immobilisation. The final part of the thesis described the development of a T-2 labelless immunosensor using impedimetric approach. Good antibody calibration curve was obtained for both 10 μm microband and 10 μm microdisc array. For the establishment of the T-2/HT-2 toxin calibration curve, it was found that larger microdisc array dimension was required to produce better calibration curve. The calibration curves established in buffer solution show that the microelectrode arrays were sensitive and able to detect levels of T-2/HT-2 toxin as low as 25 ppb (25 μg kg-1) with a limit of quantitation of 4.89 ppb for a 10 μm microband array and 1.53 ppb for the 40 μm microdisc array.

Redox remodelling in diaphragm muscle adaptation to chronic sustained hypoxia

Chronic sustained hypoxia (CH) induces functional weakness, atrophy, and mitochondrial remodelling in the diaphragm muscle. Animal models of CH present with changes similar to patients with respiratory-related disease, thus, elucidating the molecular mechanisms driving these adaptations is clinically important. We hypothesize that ROS are pivotal in diaphragm muscle adaptation to CH. C57BL6/J mice were exposed to CH (FiO2=0.1) for one, three, and six weeks. Sternohyoid (upper airway dilator), extensor digitorum longus (EDL), and soleus were studied as reference muscles as well as the diaphragm. The diaphragm was profiled using a redox proteomics approach followed by mass spectrometry. Following this, redox-modified metabolic enzyme activities and atrophy signalling were assessed using spectrophotometric assays and ELISA. Diaphragm isotonic performance was assessed after six weeks of CH ± chronic antioxidant supplementation. Protein carbonyl and free thiol content in the diaphragm were increased and decreased respectively after six weeks of CH – indicative of protein oxidation. These changes were temporally modulated and muscle specific. Extensive remodelling of metabolic proteins occurred and the stress reached the cross-bridge. Metabolic enzyme activities in the diaphragm were, for the most part, decreased by CH and differential muscle responses were observed. Redox sensitive chymotrypsin-like proteasome activity of the diaphragm was increased and atrophy signalling was observed through decreased phospho-FOXO3a and phospho-mTOR. Phospho-p38 MAPK content was increased and this was attenuated by antioxidant treatment. Hypoxia decreased power generating capacity of the diaphragm and this was restored by N-acetyl-cysteine (NAC) but not by tempol. Redox remodelling is pivotal for diaphragm adaptation to chronic sustained hypoxia. Muscle changes are dependent on duration of the hypoxia stimulus, activity profile of the muscle, and molecular composition of the muscle. The working respiratory muscles and slow oxidative fibres are particularly susceptible. NAC (antioxidant) may be useful as an adjunct therapy in respiratory-related diseases characterised by hypoxic stress.

Synthesis, characterisation and applications of group IV nanocrystals

Group IV materials such as silicon nanocrystals (Si NCs) and carbon quantum dots (CQDs) have received great attention as new functional materials with unique physical/chemical properties that are not found in the bulk material. This thesis reports the synthesis and characterisation of both types of nanocrystal and their application as fluorescence probes for the detection of metal ions. In chapter 2, a simple method is described for the size controlled synthesis of Si NCs within inverse micelles having well defined core diameters ranging from 2 to 6 nm using inert atmospheric synthetic methods. In addition, ligands with different molecular structures were utilised to reduce inter-nanocrystal attraction forces and improve the stability of the NC dispersions in water and a variety of organic solvents. Regulation of the Si NCs size is achieved by variation of the surfactants and addition rates, resulting high quality NCs with standard deviations (σ = Δd/d) of less than 10 %. Large scale production of highly mondisperse Si NC was also successfully demonstrated. In chapter 3, a simple solution phase synthesis of size monodisperse carbon quantum dots (CQDs) using a room temperature microemulsion strategy is demonstrated. The CQDs are synthesized in reverse micelles via the reduction of carbon tetrachloride using a hydride reducing agent. CQDs may be functionalised with covalently attached alkyl or amine monolayers, rendering the CQDs dispersible in wide range of polar or non-polar solvents. Regulation of the CQDs size was achieved by utilizing hydride reducing agents of different strengths. The CQDs possess a high photoluminescence quantum yield in the visible region and exhibit excellent photostability. In chapter 4, a simple and rapid assay for detection of Fe3+ ions was developed, based on quenching of the strong blue-green Si NC photoluminescence. The detection method showed a high selectivity, with only Fe3+ resulting in strong quenching of the fluorescence signal. No quenching of the fluorescence signal was induced by Fe2+ ions, allowing for solution phase discrimination between the same ion in different charge states. The optimised sensor system showed a sensitive detection range from 25- 900 μM and a limit of detection of 20.8 μM

Formation and characterisation of ordered porous vanadium oxide inverse opal materials for Li-ion batteries

This thesis presents several routes towards achieving artificial opal templates by colloidal self-assembly of polystyrene (PS) or poly(methyl methacrylate) (PMMA) spheres and the use of these template for the fabrication of V2O5 inverse opals as cathode materials for lithium ion battery applications. First, through the manipulation of different experimental factors, several methods of affecting or directing opal growth towards realizing different structures, improving order and/or achieving faster formation on a variety of substrates are presented. The addition of the surfactant sodium dodecyl sulphate (SDS) at a concentration above the critical micelle concentration for SDS to a 5 wt% solution of PMMA spheres before dip-coating is presented as a method of achieving ordered 2D PhC monolayers on hydrophobic Au-coated silicon substrates at fast and slow rates of withdrawal. The effect that the degree of hydrophilicity of glass substrates has on the ordering of PMMA spheres is next investigated for a slow rate of withdrawal under noise agitation. Heating of the colloidal solution is also presented as a means of affecting order and thickness of opal deposits formed using fast rate dip coating. E-beam patterned substrates are shown as a means of altering the thermodynamically favoured FCC ordering of polystyrene spheres (PS) when dip coated at slow rate. Facile routes toward the synthesis of ordered V2O5 inverse opals are presented with direct infiltration of polymer sphere templates using liquid precursor. The use of different opal templates, both 2D and 3D partially ordered templates, is compared and the composition and arrangement of the subsequent IO structures post infiltration and calcination for various procedures is characterised. V2O5 IOs are also synthesised by electrodeposition from an aqueous VOSO4 solution at constant voltage. Electrochemical characterisation of these structures as cathode material for Li-ion batteries is assessed in a half cell arrangement for samples deposited on stainless steel foil substrates. Improved rate capabilities are demonstrated for these materials over bulk V2O5, with the improvement attributed to the shorter Li ion diffusion distances and increased electrolyte infiltration provided by the IO structure.

A microscopic study of structural and electronic properties of functionalized silicon surfaces based on first-principles

Surface modification of silicon with organic monolayers tethered to the surface by different linkers is an important process in realizing future (opto-)electronic devices. Understanding the role played by the nature of the linking group and the chain length on the adsorption structures and electronic properties of these assemblies is vital to advance this technology. This Thesis is a study of such properties and contributes in particular to a microscopic understanding of induced changes in the work function of experimentally studied functionalized silicon surfaces. Using first-principles density functional theory (DFT), at the first step, we provide predictions for chemical trends in the work function of hydrogenated silicon (111) surfaces modified with various terminations. For nonpolar terminating atomic species such as F, Cl, Br, and I, the change in the work function is directly proportional to the amount of charge transferred from the surface, thus relating to the difference in electronegativity of the adsorbate and silicon atoms. The change is a monotonic function of coverage in this case, and the work function increases with increasing electronegativity. Polar species such as −TeH, −SeH, −SH, −OH, −NH2, −CH3, and −BH2 do not follow this trend due to the interaction of their dipole with the induced electric field at the surface. In this case, the magnitude and sign of the surface dipole moment need to be considered in addition to the bond dipole to generally describe the change in work function. Compared to hydrogenated surfaces, there is slight increase in the work function of H:Si(111)-XH, where X = Te, Se, and S, whereas reduction is observed for surfaces covered with −OH, −CH3, and −NH2. Next, we study the hydrogen passivated Si(111) surface modified with alkyl chains of the general formula H:Si–(CH2)n–CH2 and H:Si–X–(CH2)n–CH3, where X = NH, O, S and n = (0, 1, 3, 5, 7, 9, 11), at half coverage. For (X)–Hexyl and (X)–Dodecyl functionalization, we also examined various coverages up to full monolayer grafting in order to validate the result of half covered surface and the linker effect on the coverage. We find that it is necessary to take into account the van der Waals interaction between the alkyl chains. The strongest binding is for the oxygen linker, followed by S, N, and C, irrespective of chain length. The result revealed that the sequence of the stability is independent of coverage; however, linkers other than carbon can shift the optimum coverage considerably and allow further packing density. For all linkers apart from sulfur, structural properties, in particular, surface-linker-chain angles, saturate to a single value once n > 3. For sulfur, we identify three regimes, namely, n = 0–3, n = 5–7, and n = 9–11, each with its own characteristic adsorption structures. Where possible, our computational results are shown to be consistent with the available experimental data and show how the fundamental structural properties of modified Si surfaces can be controlled by the choice of linking group and chain length. Later we continue by examining the work function tuning of H:Si(111) over a range of 1.73 eV through adsorption of alkyl monolayers with general formula -[Xhead-group]-(CnH2n)-[Xtail-group], X = O(H), S(H), NH(2). The work function is practically converged at 4 carbons (8 for oxygen), for head-group functionalization. For tail-group functionalization and with both head- and tail-groups, there is an odd-even effect in the behavior of the work function, with peak-to-peak amplitudes of up to 1.7 eV in the oscillations. This behavior is explained through the orientation of the terminal-group's dipole. The shift in the work function is largest for NH2-linked and smallest for SH-linked chains and is rationalized in terms of interface dipoles. Our study reveals that the choice of the head- and/or tail-groups effectively changes the impact of the alkyl chain length on the work function tuning using self-assembled monolayers and this is an important advance in utilizing hybrid functionalized Si surfaces. Bringing together the understanding gained from studying single type functionalization of H:Si(111) with different alkyl chains and bearing in mind how to utilize head-group, tail-group or both as well as monolayer coverage, in the final part of this Thesis we study functionalized H:Si(111) with binary SAMs. Aiming at enhancing work function adjustment together with SAM stability and coverage we choose a range of terminations and linker-chains denoted as –X–(Alkyl) with X = CH3, O(H), S(H), NH(2) and investigate the stability and work function of various binary components grafted onto H:Si(111) surface. Using binary functionalization with -[NH(2)/O(H)/S(H)]-[Hexyl/Dodecyl] we show that work function can be tuned within the interval of 3.65-4.94 eV and furthermore, enhance the SAM’s stability. Although direct Si-C grafted SAMs are less favourable compared to their counterparts with O, N or S linkage, regardless of the ratio, binary functionalized alkyl monolayers with X-alkyl (X = NH, O) is always more stable than single type alkyl functionalization with the same coverage. Our results indicate that it is possible to go beyond the optimum coverage of pure alkyl functionalized SAMs (50%) by adding a linker with the correct choice of the linker. This is very important since dense packed monolayers have fewer defects and deliver higher efficiency. Our results indicate that binary anchoring can modify the charge injection and therefore bond stability while preserving the interface electronic structure.

Proteomic approaches to environmental stress in mussel Mytilus edulis due to emerging classes of anthropogenic pollutants

Anthropogenic pollutant chemicals pose a major threat to aquatic organisms. There is a need for more research on emerging categories of environmental chemicals such as nanomaterials, endocrine disruptors and pharmaceuticals. Proteomics offers options and advantages for early warning of alterations in environmental quality by detecting sub-lethal changes in sentinel species such as the mussel, Mytilus edulis. This thesis aimed to compare the potential of traditional biomarkers (such as enzyme activity measurement) and newer redox proteomic approaches. Environmental proteomics, especially a redox proteomics toolbox, may be a novel way to study pollutant effects on organisms which can also yield information on risks to human health. In particular, it can probe subtle biochemical changes at sub-lethal concentrations and thus offer novel insights to toxicity mechanisms. In the first instance, the present research involved a field-study in three stations in Cork Harbour, Ireland (Haulbowline, Ringaskiddy and Douglas) compared to an outharbour control site in Bantry Bay, Ireland. Then, further research was carried out to detect effects of anthropogenic pollution on selected chemicals. Diclofenac is an example of veterinary and human pharmaceuticals, an emerging category of chemical pollutants, with potential to cause serious toxicity to non-target organisms. A second chemical used for this study was copper which is a key source of contamination in marine ecosystems. Thirdly, bisphenol A is a major anthropogenic chemical mainly used in polycarbonate plastics manufacturing that is widespread in the environment. It is also suspected to be an endocrine disruptor. Effects on the gill, the principal feeding organ of mussels, were investigated in particular. Effects on digestive gland were also investigated to compare different outcomes from each tissue. Across the three anthropogenic chemicals studied (diclofenac, copper and bisphenol A), only diclofenac exposure did not show any significant difference towards glutathione transferase (GST) responses. Meanwhile, copper and bisphenol A significantly increased GST in gill. Glutathione reductase (GR) enzyme analysis revealed that all three chemicals have significant responses in gill. Catalase activity showed significant differences in digestive gland exposed to diclofenac and gills exposed to bisphenol A. This study focused then on application of redox proteomics; the study of the oxidative modification of proteins, to M. edulis. Thiol proteins were labelled with 5-iodoacetamidofluorescein prior to one-dimensional and two-dimensional electrophoresis. This clearly revealed some similarities on a portion of the redox proteome across chemical exposures indicating where toxicity mechanism may be common and where effects are unique to a single treatment. This thesis documents that proteomics is a robust tool to provide valuable insights into possible mechanisms of toxicity of anthropogenic contaminants in M. edulis. It is concluded that future research should focus on gill tissue, on protein thiols and on key individual proteins discovered in this study such as calreticulin and arginine kinase which have not previously been considered as biomarkers in aquatic toxicology prior to this study.