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Nanotechnology is the manipulation of matter at the supramolecular, molecular and atomic scale. As a result, nanotechnology is included in various fields of science including surface science, organic chemistry, molecular biology, semiconductor physics, microfabrication and molecular engineering. One of the ambitions for nanotechnology is to develop electrical devices where the active component is a single molecule or nanomoiety. In order to fabricate such devices, it is of paramount importance to develop strategies beyond the current top-down lithographic approaches typically employed in the semiconductor industry. In this regard, the ability to control the assembly of single-molecules and individual nanomoieties directly in solution can allow for the development of solution-processable approaches in nanotechnology, towards the fabrication of single-molecule devices. In this thesis, it will be discussed how molecular junctions with functional single molecules are fabricated in aqueous solutions employing single-walled carbon nanotubes as potential nanoelectrodes. Furthermore, it will be demonstrated how the assembly of molecular junctions can facilitate other functions and the construction of both nanostructures and microstructures. To begin, relevant work will be discussed that has been done in this field to date and outline clear ambitions of the study presented here. Subsequently, the key characterisation techniques that underpin all the results in this study will be described. In this work, it will be reported how metallic carbon nanotubes can act as nanoelectrodes in molecular junction assemblies and how conductive measurements of individual molecules are performed. Therefore, for the first time, the molecular junction conductance of a series of oligophenyls were successfully measured, which were formed via a solution-based assembly method. Measured molecular conductance values of the series of oligophenyls resulted in a β value of 0.5 Å−1. Furthermore, it will be described how the approach outlined previously can be extended to the synthesis of tri-amine molecular linkers as well as the formation of three-terminal junctions as the foundation of carbon nanotube-based single-molecule electronic devices. This research resulted in an increase in the formation of Y-shape molecular junctions by ~25%. Next, this report will outline the formation of molecular junctions in two-dimensional structures, which can allow for the development of electrical devices into networks. Utilising modified DNA sequences, "click" chemistry can lead to nanotube network with dimensions ranging into the micrometre scale. Building on this work, it will be further report on the change in physical properties when these two-dimensional superstructures are embedded into polymeric thin films. Finally, conclusions of the research will be drawn and it will be discussed how the findings obtained in this work can contribute to the development of novel single-molecule electronic devices.

The sense of smell is a primal sense for humans as well as animals.In everyday life the smells encountered are composed of dozens, even hundreds of odors; few arise from a single odorant. Enormous numbers of odors occur due to the vast variation in the concentration, size and structure of odorant molecules that makes olfaction differ from simpler visual or auditory dimensions. Accordingly, little is known about the ways in which changes in molecular structure and concentration of individual odorants change odor quality. Also, currently not much is understood about synergism/antagonism, how one odorant masks or suppresses another in mixtures and there is no method for predicting which odor will be suppressed. The two main objectives of this thesis were to determine whether a part of a molecular structure rather than the whole structure plays a key role in odor quality and whether a key part of a molecule can be used to choose antagonists for that odorant. For this study three classes of musks and two potential antagonists were used. The results of the study are discussed in some detail. It is concluded that future studies of the importance of molecular structure in mixture interactions require substantially more information on the relation between structure and odor quality to allow systematic studies to be developed. In summary the two hypotheses investigated were not supported by the results. Importantly, however, they do support the view that it is likely that odor quality is dependent on the whole structure of an odorant not a single feature. / Master of Science (Hons)

Single-molecule (SM) fluorescence spectroscopy has become a useful and important experimental approach for investigating the optical properties of chemical systems. In this thesis, four subprojects in the field of SM fluorescence spectroscopy are presented in which SM spectroscopy has provided invaluable experimental insight into the systems of interest.<p> In the first project, the photophysical properties of Calcium-Green 1 (CG-1), a calcium-ion indicator, were studied at both the ensemble and SM levels. CG-1 is non-fluorescent in the absence of Ca2+ and becomes strongly fluorescent when bound to Ca2+. In the ensemble measurements, the absorption and fluorescence spectra were collected under various Ca2+ concentrations. In addition, the fluorescence lifetime of CG-2 was also studied as a function of [Ca2+]. From SM measurements, the photobleaching time and fluorescence intensity distributions of CG-1 were studied both in the presence and in absence of Ca2+. The results were compared with those obtained for the dual-fluorophoric variant, Calcium-Green 2 (CG-2), whose photophysical properties have been investigated by previous researchers. The experimental results reveal that CG-1 can exist in two different forms: a highly-quenched form due to the occurrence of photoinduced electron transfer (PET) in the absence of Ca2+, and a strongly fluorescent form when bound to Ca2+.<p> The second project is a continuation of a previous study on CG-2. In the dual-chromophore CG-2 system, energy transfer between chromophores is controlled by the orientation and spatial separation between chromophores. Dual polarization fluorescence microscopy was used to determine the relative conformation of the two fluorophores in the emissive form of CG-2. Distributions of fluorescence polarization of individual CG-2 molecules were collected for both Ca2+-free and Ca2+-saturated conditions. The experimental polarization results were compared to those calculated from a simple geometric model based on randomly-orientated fluorescent dimers. The results show good agreement with previous calculations of the molecular conformation of CG-2. This indicates that the dual polarization imaging approach has significant potential as a general tool for characterizing chromophore orientation in coupled-fluorophore systems.<p> In the third project, Nile Red (NR), a solvatochromic lipid stain, was incorporated into phase separated Langmuir-Blodgett (LB) films composed of arachidic acid (AA) and perfluorotetradecanoic acid (PA). According to previous studies by atomic force microscopy (AFM), two types of separated domains are formed in the LB films: micron-sized hexagonal discontinuous domains that are exclusively comprised of AA, and the surrounding continuous domains which are enriched in PA. The photophysical properties of NR were characterized in the two physically and chemically distinct domains via bulk and SM fluorescence measurements. In addition to fluorescence microscopy, fluorescence confocal spectromicroscopy was also applied in the ensemble measurements to determine the spectral properties of NR in different sub-environments. Experimental results indicated that a small sub-population of dye molecules localize on the perfluorinated regions of the sample, but this sub-population is spectroscopically indistinguishable from that associated with the hydrogenated domains. Contrast in images was primarily due to preferential accumulation of the hydrophobic dye on the hydrophobic regions of the LB films.<p> In the final project, the fluorescence quenching behavior of a strongly fluorescent probe Alexa Fluor 514 (AF514) was investigated when it was covalently bound to gold metal protected clusters (AuMPC) with negligible plasmon bands. The fluorescence emission of the dye-AuMPCs system was characterized at different dye/Au MPC loading ratios with a combination of steady state and time-resolved ensemble spectroscopic measurements. It was found that the extent of fluorescence quenching in the system was small. After correction of inner filter effects, the results from bulk measurement demonstrate that the weak quenching is due to static quenching of the dye by the AuMPCs. SM measurements provided further support for the bulk measurements, with the fluorescence intensity of coupled AF514 molecules being comparable with that of unconjugated molecules. The photobleaching of the dye-AuMPC conjugates took place as a series of consecutive photobleaching events, without additional blinking dynamics within the time resolution of the experiment. These results suggest that the fluorophores on the AuMPCs are either entirely quenched, or remaining unquenched, as is consistent with the ensemble measurements.

Single-molecule (SM) fluorescence spectroscopy has become a useful and important experimental approach for investigating the optical properties of chemical systems. In this thesis, four subprojects in the field of SM fluorescence spectroscopy are presented in which SM spectroscopy has provided invaluable experimental insight into the systems of interest.<p> In the first project, the photophysical properties of Calcium-Green 1 (CG-1), a calcium-ion indicator, were studied at both the ensemble and SM levels. CG-1 is non-fluorescent in the absence of Ca2+ and becomes strongly fluorescent when bound to Ca2+. In the ensemble measurements, the absorption and fluorescence spectra were collected under various Ca2+ concentrations. In addition, the fluorescence lifetime of CG-2 was also studied as a function of [Ca2+]. From SM measurements, the photobleaching time and fluorescence intensity distributions of CG-1 were studied both in the presence and in absence of Ca2+. The results were compared with those obtained for the dual-fluorophoric variant, Calcium-Green 2 (CG-2), whose photophysical properties have been investigated by previous researchers. The experimental results reveal that CG-1 can exist in two different forms: a highly-quenched form due to the occurrence of photoinduced electron transfer (PET) in the absence of Ca2+, and a strongly fluorescent form when bound to Ca2+.<p> The second project is a continuation of a previous study on CG-2. In the dual-chromophore CG-2 system, energy transfer between chromophores is controlled by the orientation and spatial separation between chromophores. Dual polarization fluorescence microscopy was used to determine the relative conformation of the two fluorophores in the emissive form of CG-2. Distributions of fluorescence polarization of individual CG-2 molecules were collected for both Ca2+-free and Ca2+-saturated conditions. The experimental polarization results were compared to those calculated from a simple geometric model based on randomly-orientated fluorescent dimers. The results show good agreement with previous calculations of the molecular conformation of CG-2. This indicates that the dual polarization imaging approach has significant potential as a general tool for characterizing chromophore orientation in coupled-fluorophore systems.<p> In the third project, Nile Red (NR), a solvatochromic lipid stain, was incorporated into phase separated Langmuir-Blodgett (LB) films composed of arachidic acid (AA) and perfluorotetradecanoic acid (PA). According to previous studies by atomic force microscopy (AFM), two types of separated domains are formed in the LB films: micron-sized hexagonal discontinuous domains that are exclusively comprised of AA, and the surrounding continuous domains which are enriched in PA. The photophysical properties of NR were characterized in the two physically and chemically distinct domains via bulk and SM fluorescence measurements. In addition to fluorescence microscopy, fluorescence confocal spectromicroscopy was also applied in the ensemble measurements to determine the spectral properties of NR in different sub-environments. Experimental results indicated that a small sub-population of dye molecules localize on the perfluorinated regions of the sample, but this sub-population is spectroscopically indistinguishable from that associated with the hydrogenated domains. Contrast in images was primarily due to preferential accumulation of the hydrophobic dye on the hydrophobic regions of the LB films.<p> In the final project, the fluorescence quenching behavior of a strongly fluorescent probe Alexa Fluor 514 (AF514) was investigated when it was covalently bound to gold metal protected clusters (AuMPC) with negligible plasmon bands. The fluorescence emission of the dye-AuMPCs system was characterized at different dye/Au MPC loading ratios with a combination of steady state and time-resolved ensemble spectroscopic measurements. It was found that the extent of fluorescence quenching in the system was small. After correction of inner filter effects, the results from bulk measurement demonstrate that the weak quenching is due to static quenching of the dye by the AuMPCs. SM measurements provided further support for the bulk measurements, with the fluorescence intensity of coupled AF514 molecules being comparable with that of unconjugated molecules. The photobleaching of the dye-AuMPC conjugates took place as a series of consecutive photobleaching events, without additional blinking dynamics within the time resolution of the experiment. These results suggest that the fluorophores on the AuMPCs are either entirely quenched, or remaining unquenched, as is consistent with the ensemble measurements.

The solid phase combinatorial method is an excellent tool for the modulation of protein-protein interactions through focused library generations. Nucleophilic aromatic substitution reactions with an iodinated template on solid phase has opened a door for easy and pure libraries of 13-22 membered medium and macrocyclic peptidomimetics. These peptide mimics showed promising activities for tyrosine kinase receptors. Iodine functionality can then be used to modify the products, on the resin, via Sonogashira and Suzuki couplings and presumably through other organometallic catalysis. The coupled products can have conformational biases that differ from the iodinated macrocycles. These coupling reactions also provide a means to introduce additional pharmacophores and to adjust the solubilities of the products. The fluorinated template also gave libraries of cyclic peptidomimetics on solid phase in good yields and purities. These libraries have improved water solubility over the iodinated libraries. The 3-fluorinated template yielded better results than the 5- fluorinated template. Some compounds showed biological activities in cell survival assays providing strong support of our approach to mimic external β-turn sequences in target proteins. Intrasite dimerization with 1,5-hexadiyne gave a homodimer as a byproduct. Solidphase synthesis of bivalent turn mimics with fluorescent tags has been demonstrated. The key feature of this synthetic route is that homo- and hetero-dimers can be formed chemoselectively from unprotected monomeric precursors. The dimerization reaction is very mild and versatile, as only potassium carbonate is required to affect the coupling. Solution phase library synthesis of small molecule mimics is presented. Some monomers of full sequence mimics have been prepared to afford dimer generations. Theses monomers were combined with linker handles to afford diverse length of dimers. Final combination of monomers to make bivalent compounds is in progress.