This thesis discusses the formation of metal-organic and organic structures grown on surfaces using bottom-up self-assembly techniques. Three systems are investigated primarily using scanning probe microscopy techniques. The growth of metal-organic frameworks (MOFs) on functionalised surfaces is investigated using high resolution atomic force microscopy (AFM). The earliest stages of MOF crystal nucleation are imaged using a layer-by-layer (LBL) growth technique and the ability to track the growth of individual nanocrystallites throughout the LBL process is demonstrated. This LBL method has been suggested as a route to fabricating epitaxially grown, oriented thin-films of MOFs. However, results from these studies indicate that, rather than a uniform crystalline layer, the morphology is that of a preferentially oriented but laterally polycrystalline film and the growth rates of the individual nanocrystallites exceed those expected for a LBL growth mode. This has significant implications for the fabrication of novel devices that incorporate MOFs due to the presence of domain boundaries and defects. Self-assembled monolayers of light-harvesting porphyrin nanorings are investigated with scanning tunnelling microscopy (STM) and AFM. The nanorings are found to form large supramolecular networks in ambient conditions on graphite and boron nitride surfaces. The size and order of these networks is found to be dependent on the number of porphyrin macrocycles that make up each ring. In addition, simulations of isolated nanorings are also performed using Monte Carlo methods to model the distortion previously been observed for isolated nanorings on gold surfaces. These are discussed in the context of spectroscopic measurements which suggest that both size dependent and thermally induced distortion affects the lifetime and delocalisation of excited states in these molecules. Graphene is grown on hexagonal boron nitride surfaces using high-temperature molecular beam epitaxy. Large domains of monolayer graphene are successfully grown and are investigated using AFM and Raman spectroscopy. These domains are found to exhibit hexagonal moiré patterns on the graphene surface which is suggestive of orientational alignment with the underlying boron nitride substrate. Regions with high period and distorted moiré patterns are also observed which suggest that the graphene is under tensile strain which is attributed to the high growth temperatures used. The strain is found to significantly affect the Raman spectrum of graphene and a relationship between the strain and the shifting of Raman spectral peaks is determined. Successful attempts are also made to modify the strain in the graphene monolayer using an AFM tip which is observed to relax when defects are introduced in a controlled manner to the graphene monolayer. These results represent new approaches to the introduction and control of strain in graphene which may be useful for the fabrication of high-performance graphene devices.

1) species show a preference for the MJ = ±1 sub-levels. For these bands the electronic alignment is very similar to that observed in the dissociation of OCS, indicating a similar mechanism, at least in the exit channel, is responsible for the polarisation in both systems.

Monolayer organic thin films and heterostructures are of great interest for their optical and electronic properties and as systems which allow the interplay between the structural and functional properties of organic molecules to be investigated. In the first experimental section of this thesis, sub-monolayer coverages of perylene tetracarboxylic diimide (PTCDI) were grown on hBN substrates and found to form needle-like monolayer islands at room temperature, while higher growth temperatures gave larger monolayer islands. The molecular packing of monolayer PTCDI was confirmed, using AFM, to correspond to the canted phase. The 0-0 fluorescence peak of this structure was found to occur at 2.208 ± 0.002 eV. The fluorescence of multi-layer PTCDI samples was mapped, with additional peaks measured at 2.135 ± 0.002 eV (580.7 ± 0.5 nm) and 2.118 ± 0.002 eV (585.4 ± 0.5 nm). Relating the morphology and fluorescence of such films using AFM and fluorescence microscopy is a promising way to investigate structural effects on the optical properties of multi-layer organic systems. Using solution deposition techniques, the PTCDI-melamine supramolecular network and the canted phase of PTCDI were deposited on hBN. The molecular packing of both structures was confirmed using AFM and the 0-0 fluorescence peaks were measured to be 2.245 ± 0.002 eV and 2.214 ± 0.002 eV for the PTCDI-melamine network and PTCDI respectively. The fluorescence of sublimed PTCDI, solution deposited PTCDI, PTCDI-melamine and measurements of Me-PTCDI doped helium nano droplets (HND) were compared. A 0.031 ± 0.002 eV red shift was measured from PTCDI-melamine to PTCDI while a 0.346 ± 0.002 eV red shift was measured from doped HND to PTCDI on hBN. A second perylene derivative, perylene tetracarboxylic dianhidride (PTCDA), was also deposited on hBN. Comparing the fluorescence of PTCDA monolayers on various dielectric substrates suggested a large shift due to the coupling of transition dipole moments and image dipoles beneath the dielectric surface. The shift between PTCDI and PTCDI-melamine was attributed to the coupling of transition dipole moments, for which the exciton bandstructure of both phases has been calculated with and without screening. The growth of sublimed C60 was also investigated, with monolayer islands observed for growth at room temperature and faceted bi-layer islands observed at 212 °C. The growth of PTCDI/C60 ¬heterostructures was also investigated, with C60 found to form monolayer islands on monolayer PTCDI at room temperature. At higher growth temperatures, C60 was found to form multilayers, with a reduced island density at PTCDI island edges, suggesting upward and downward hopping from the PTCDI surface to the second C60 layer and hBN respectively. C60 was found to quench the fluorescence of PTCDI and led to a 0.032 ± 0.02 eV blue shift. Finally, the growth of cyanuric acid-melamine (CA.M) on CVD graphene and CA.M/PTCDI heterostructures on hBN was investigated. Cyanuric acid-melamine was found to form monolayers with a honeycomb packing structure on CVD graphene. On monolayers of CA.M, PTCDI was found to form needle-like monolayer islands, the row direction of PTCDI is thought to have an on-axis registry with the substrate. Finally, the fluorescence of CA.M/PTCDI heterostructures on hBN was measured, with a 0.045 ± 0.002 eV blue shift from PTCDI on hBN.

Clostridium autoethanogenum is an important organism for biofuel production. Other 'omics' approaches have been used to understand the mode of operation of the organism but metabolomics gives information on the cellular activities in the cell. Metabolomics combined with other 'omics' data can provide a deeper understanding for pathway interpretation. This project sets out to develop an analytical method that is suitable for analysis of highly charged polar compounds found in C. autoethanogenum metabolic pathways. Also investigate suitable isotope labelled internal standards to improve matrix effects to the metabolites as a result of the biological matrix. A high-throughput hydrophilic interaction liquid chromatography isotope dilution mass spectrometry (HILIC-IDMS) was developed and validated using high resolution hybrid orbital trap MS for both targeted and untargeted metabolomics analysis of intracellular metabolic pathways of Clostridium autoethanogenum. Extraction of intracellular metabolites from C. autoethanogenum was achieved using a specifically developed sample preparation protocol using freeze thaw cycles (freeze in liquid nitrogen and thaw on ice repeated 3x). A total of 133 metabolites were monitored and validated. Limits of detection (LODs) ranged from 0.001 µM to 5 µM reported for compounds such as NADPH and NADH. Limits of quantification (LOQs) for all metabolites ranged from 0.001 µM to 10 µM for metabolites such as glucose-6-phosphate and glyceraldehyde-3 phosphate. Precision and accuracy were evaluated for all metabolites and found to be within the acceptable limits of ±15 % with few exceptions for some nucleotides and organic acids. Stable isotopically labelled internal standards were generated from C. pasteurianum cells that provided coverage for about 100 metabolites. This enabled absolute intracellular concentrations to be obtained in combination with the estimated cell volume of C. autoethanogenum that was obtained from microscopy and flow cytometry measurements. The developed HILIC-IDMS method was applied to various solvent production optimisation experiments conducted using C. autoethanogenum and the main findings are reported below. In chapter 4, the HILIC-IDMS method was applied to C. autoethanogenum in an experiment where the pH of the media was reduced to improve ethanol and solvent production. The metabolomics studies of this experiment gave intracellular concentrations that differentiated the acidogenic phase from the solventogenic phase. A total of 86 metabolites were quantified in this experiment. Intermediates in the tricarboxylic acid (TCA) cycle were the most affected during the acidogenic/solventogenic transition. Metabolites concentrations were used for metabolic pathways analysis to understand the pathways affected during the pH shift. The pathway analysis also confirmed the TCA cycle was the most affected pathway during the acidogenic/solventogenic transition. In chapter 5, The HILIC-IDMS method was applied to a gas shift experiment to optimise ethanol and solvent production. Gas shift is another approach that can be used to optimise solvent production in similar as the pH shift experiment. The use of gas shift to induce solventogenic phase can be difficult as C. autoethanogenum has little tolerance for high levels of CO hence the increase in gas (CO) flow rate has to be done in a gradual fashion. Equally, TCA intermediates were observed to be the most affected as observed in the pH shift experiment. In chapter 6, the method was applied to a study where pantothenate and phosphate concentrations in the growth media of C. autoethanogenum were reduced to increase ethanol production. Pantothenate is the precursor for coenzyme A (CoA) production and metabolomics study confirmed a decrease in CoA concentration when pantothenate concentration was reduced. Metabolomics also showed decrease in concentration of metabolites directly linked to CoA synthesis such as L- Aspartate. Metabolic pathway analysis also confirmed the pantothenate and CoA biosynthesis and its associated pathways were the most affected pathways during the pantothenate-limiting phase. Both targeted and untargeted metabolomics analysis were performed on these nutrient-limiting experiments and there were clear differences between the two different conditions before and after nutrient limitation. Supervised multivariate data analysis using OPLS-DA was used to compare higher pantothenate and low pantothenate concentration and there were clear separation and clustering between the two conditions. Cross validation obtained for R2Y and Q2 were 0.993 and 0.941 respectively. OPLS-DA plots for phosphate limitation also showed clustering and separation between the high phosphate concentration and reduced phosphate concentration with R2Y and Q2 0.981and 0.837 respectively. In conclusion, a novel high-throughput HILIC-IDMS method was developed and validated for analysis of different classes of polar compounds in bacteria. The method has the potential to be applied in other biological matrices for coverage of diverse range of polar compounds.

This Thesis describes the application of niobium oxide and niobium phosphate as solid acids for conducting continuous flow reactions, such as the Friedel-Crafts Reaction and the Skraup Reaction, and also as supports for photosensitiser immobilisation. Chapter 1 introduces the concepts of green and sustainable chemistry, and give a review of niobium and niobium compounds, especially niobium oxide and niobium phosphate as well as their applications. A summary of flow chemistry is also presented. The continuous flow systems used to conduct the work of this Thesis are described in Chapter 2. Chapter 3 introduces continuous alkylation of aniline with dimethyl carbonate or methanol over niobium solid acids. The synthesis process is automated by a self-optimisation system to search the best conditions for different products, including the NH2 group methylation product monomethyl aniline and dimethyl aniline, and the Friedel-Crafts alkylation product N,N-dimethyl-p-toluidine. Chapter 4 describes the first exploration of the continuous Skraup synthesis of quinolones with heterogeneous catalyst niobium phosphate. A dissymmetrics substituted quinoline compound, 4-(quinolin-6-yl methyl)aniline, was synthesized, and its crystal was grown and the structure was determined by crystallographic analysis for the first time. Chapter 5 discussed the immobilisation of a photosensitiser meso-tetraphenylporphyrin on niobium solid acids, and the activity of these supported photocatalysts in continuous photo-oxidation, including the photo-oxidation of α-terpinene to ascaridole and the semi-synthesis of an antimalarial drug, artemisinin ART. Finally, Chapter 6 summarises the work described in this Thesis and examines the success of the techniques and approaches discussed. A summary of potential routes for further study is also presented.

This thesis addresses the concept of atomically precise manufacturing and aims to examine some likely aspects of the necessary infrastructure and knowledge that will be required from a theoretical standpoint. By way of introduction, I trace the history of Science Fiction's influence on scientific research and examine some examples that have specifically inspired the thinking behind nanoscience and nanotechnology. More serious speculation, both in favour of and arguing against the possibility of bottom-up manufacturing is also discussed. I look at two schools of thought; directed assembly, typified by the ambition to assemble molecular structures piece by piece and self assembly, where networks of molecules form into arrays on substrates, imparting novel properties. Various methodologies and tools available to the nanotechnologist are examined. Density functional theory, as employed in the AIMpro code, and Molecular Mechanics are discussed, particularly in respect of their strengths and weaknesses for use in simulating the kind of nanoscale processes appropriate to nanomanufacturing. The theoretical basis behind scanning tunneling microscopes is also examined, with particular attention paid to their potential for upscaling in the future. Some components found within scanning tunneling microscopes are simulated using Density Functional Theory. Models of pure tungsten tips are studied at various levels of complexity in order to decide upon a reasonable compromise between accuracy and ease of computation. The nature of the interlayer interaction in few layer graphenes is examined and pristine and defected graphitic surfaces, are studied with a view towards their use as nano-workbenches. Their images as produced in scanning tunneling microscopes are simulated. Density Functional Theory is applied to organic molecules self-assembling on metallic substrates. Specifically, tetracene on a clean copper surface and on an oxygen-terminated copper surface is studied. Finally, I discuss the significance of the results of each section, taken individually and as a whole, and try to put it into perspective regarding the practicality of actually employing this paradigm realistically in the near future.

The work presented in this thesis describes the development and applications of hollow carbon nanostructures both as the catalytically active, magnetically separable carbon nanoreactors, and electrodes for electrocatalytic reactions. The work is separated into three distinct parts, the formation of carbon nanoreactors of different diameters and shapes in which the effect of confinement imposed by the nanotube is probed in exploratory hydrogenation reactions, the functionalisation of carbon nanoreactors with magnetic nanoparticles for magnetically separable catalyst supports, and the development of new hybrid metal-carbon nanoreactors as efficient electrocatalysts for hydrogen fuel cell applications. In the first part of the thesis, a Ru3(CO)12 precursor was successfully inserted into carbon nanoreactors of different diameters – very narrow single walled carbon nanotubes (SWNTs, DSWNT ~1.5 nm) and much wider hollow graphitised carbon nanofibers (GNFs, internal dGNF ~50 nm) using sublimation followed by the formation of uncoated metallic Ru nanoparticles via thermal decomposition. The resultant RuNPs@SWNT and RuNPs@GNF nanoreactors were then tested in hydrogenation reactions using a high pressure scCO2 batch reactor, where the excellent diffusivity and mass transfer properties of scCO2 as solvent enabled the efficient delivery of the reagents to the catalyst surface within the narrow nanoreactors. RuNPs confined in the narrowest channels of SWNT was observed to be highly active and selective in competitive hydrogenation reaction of alkenes, but concurrently reduce the accessible volume of the SWNTs by 30-40 % resulting in lower overall turnover numbers (TONs). In contrast, RuNPs confined in wider GNFs were entirely accessible and indicated outstanding activity in comparison to unconfined RuNPs on the outer surface of SWNTs or carbon black. In the second part of the work, GNFs sidewalls were functionalised by non-covalent attachment of commercial graphene-like carbon coated magnetic Co nanomagnets (Co@Cn) exploiting van der Waals forces via dispersion in an organic solvent using ultrasonic treatment, and by the in situ formation of carbon coated iron nanomagnets (Fe@Cn). A number of experiments were carried out to find the minimum amount of nanomagnets required to enable complete separation of the nanotubes from the solution with an external magnetic field. Characterisation of this composite material by high resolution transmission electron microscopy (HRTEM) showed that Co@Cn and Fe@Cn successfully attached to the GNFs. Magnetic functionalisation steps were then combined with uncoated, palladium and platinum nanoparticle catalyst formation and the resultant catalytically active and magnetically separable hybrid materials were investigated in the reduction of nitrobenzene. The recyclability and stability of these magnetic and catalytic nanoreactors were studied in the reduction of nitrobenzene using magnetic recovery, and only negligible catalyst loss (< 0.5% by wt.) was observed over 5 cycles in comparison to that of filtration based catalyst recovery (>10% catalyst loss by wt.). In the third part, GNFs were shortened by ball milling and combined with palladium catalyst to form (PdNPs/-PdNPs@)s-GNF using a novel procedure and the resultant activity and stability towards hydrogen evolution and hydrogen oxidation reactions (HER/HOR) in acid media was studied. (PdNPs/-PdNPs@)s-GNF exhibited enhanced activity and excellent durability during 30000 electro-catalytic cycles in HER compared to that of state-art commercial Pt/C which exhibited decreasing activity and poor durability during the cycling in acid. Moreover, s-GNF demonstrated an enhanced HER activity and stability during 5000 cycles. HRTEM revealed some chemical transformations at the step edges within GNF during the electrochemical cycling contributing to durability of the electrocatalyst. Overall, the superior HER/HOR activity and durability was attributed to the corrugated morphology of s-GNF, and therefore the ability to stabilise the Pd nanoparticles at the graphitic step-edges effectively through strong bonding and synergetic effects between the Pd and s-GNF support. These results clearly indicate that carbon nanoreactors as catalyst supports and electrocatalystd show significant promise for a variety of chemical reactions.

Chapter 1: Introduction This Chapter provides an introduction to the study of reactive intermediates and the specialised techniques which have been developed in order to study these extremely short lived species. In particular, it provides an overview of ultrafast Time Resolved Infrared Spectroscopy (TRIR). This key technique underpins a large amount of the work presented in this Thesis as well as a description of the apparatus and methods used across the other Chapters of this Thesis. Chapter 2: Ultrafast TRIR studies of rhenium complexes of thioether substituted hexaazatrinapthylene ligands The excited states and photophysical properties of mono, bi and trinuclear (Re(CO)3Cl) complexes of the 2,3,8,9,1314-hexa (octyl-thioether)-1,6,7,12,13,18-hexaazatrinapthylene ligand (HATN-S(C8H17)6) have been investigated using ultrafast TRIR spectroscopy. These measurements are supported by theoretical calculations and resonance Raman spectroscopic investigations of these compounds. The position and the intensity of the (CO) bands of the photoexcited species directly report on the electron transfer/distribution in the excited state. In all cases the observed product bands were blue shifted compared to the parent, this is consistent with electron transfer away from the metal centre. The observed shift for the thioether substituted HATN complexes studied here was smaller than that reported for the analogous HATN-Me6 complexes, indicating reduced electron transfer upon excitation. Red shifted product bands corresponding to “spectator” metal centres were also observed for the bi and trinuclear species, these bands were shifted by approximately the same amount as for the HATN-Me6 species, indicating a similar reduction of the HATN core upon excitation. These results are consistent with the formation of a dual charge transfer ILCT/MLCT excited state involving electron donation from both a metal centre and the thioether moieties upon excitation. Chapter 3: Ultrafast TRIR studies of rhenium and platinum complexes of Pyridyl-1,2,3-Triazole and related ligands The excited states and photophysics of a series of substituted rhenium and platinum complexes that contain a 2-pyridyl-1,2-3-triazole ligand, an easily modified analogue of the common 2,2’-bipyridine (bpy)ligand, have been studied by TRIR spectroscopy. The compounds are found to be analogous of similar complexes with bpy, exhibiting MLCT or MLLCT exicted states (in the case of the (Re(CO)3X) and (Pt(CCHPh)2) complexes respectively). Changing the substitution of the triazole ring has little effect on the excited state band positions, this is attributed to the insulating effect of the triazole moiety. Complexes substituted with conjugated phenyl groups on the triazole ring exhibit greatly increased excited state lifetimes than those substituted with non-conjugated benzyl groups. This is attributed to the rigid rotor effect. The addition of an electron donating triphenylamine group to the pyridyl moiety results in the observation of ILCT states. Chapter 4: Towards long lived alkane and noble gas complexes from cationic piano stool complexes in the fluorous phase The synthesis and characterisation of a series of cationic transition metal tricarbonyl half sandwich complexes solubilised in perfluoroalkane solvents by means of the weakly coordinating, fluorous solubilising anion tetrakis(3,5-bis(perfluorohexyl)phenyl)borate (BArF64) is described. These complexes were photolysed in perfluoroalkane solutions doped with methane, heptane and xenon and followed by ultrafast TRIR spectroscopy with the aim of generating long-lived organometallic alkane and noble gas complexes suitable for study by NMR at room temperature. While no organometallic alkane or noble gas complexes were observed, several novel transition metal-BArF64 zwitterionic species are generated upon photolysis. These species are the result of -2 binding of one of the aryl moieties of the BArF64 anion to the vacant coordination sites generated following photoejection of a carbonyl ligand. While highly reactive they are long lived and appear to be permanent photoproducts. In the case of the rhenium complex an additional product band assigned as a dimeric species is also observed. Chapter 5: Towards the synthesis of fluorous phase soluble cationic piano stool complexes. The synthesis of fluorous tagged cationic transition metal tricarbonyl complexes is explored with the eventual aim of performing fluorous phase TRIR experiments utilising the more weakly coordinating (but less solubilising) anion tetrakis(perfluoro-tert-butoxy)aluminate in place of the previously studied BArF64 anion. Several routes to perfluoroalkyl arene ligands are explored and evaluated, as is the use of different lengths of alkyl spacer to insulate the ligand binding site from the strong electron withdrawing effects of the perfluoroalkyl moiety. This process lead to the synthesis of the new complexes [(m-(3-(perfluorooctyl)-propyl)n-benzene)manganesetricarbonyl] hexafluorophosphate for n =1-3. These compounds are soluble in the fluorous phase despite their charge. The use of the m-(3-(perfluorooctyl)-propyl)n-benzene ligand to solubilise complexes of rhenium and rhodium was also attempted. The addition of methyl groups to the ring was explored as a route to additional steric bulk and a more electron rich, strongly binding ligand. In addition to arenes, the fluorous tagging of other ligand systems was also investigated, including cyclopentadienyl and tris(1-pyrazolyl)methane.

The standard preparation of valuable chemical compounds often exploits reactions that are plagued by suboptimal yields and a considerable amount of toxic waste, especially when it comes to asymmetric synthesis and metal catalysts. In the quest to achieve cleaner processes, enzymes are compelling alternatives; these natural devices offer "green" and efficient reactions. Furthermore, they are generally very enantioselective yielding optically pure products. Enzymes however have also many drawbacks: they especially suffer when forced to work under non-physiological conditions. A solution could be to exploit extremophile organisms, which are naturally adapted to work in “extreme” environments, as sources of new biocatalysts. Among the various classes of enzymes, aminotransferases (EC 2.6.1) are particularly interesting, since these biocatalysts are able to catalyze the amino transfer between two molecules, a reaction particularly difficult to perform with traditional synthetic approaches. An aminotransferase from Halomonas elongata (HEWT), a halotolerant organism, was isolated and characterized to verify its ability to work in the presence of organic solvents. Despite a broad substrate scope, HEWT was poorly active against ketones under standard condition. The investigation of the stereoelectronic effects of the reactions through a series of rationally engineered variants, led to a better understanding of the residues in the active pocket but produced only minimal improvement in activity. HEWT was therfore evolved towards the desired substrates applying iterative cycles of mutagenesis and screening to select the ameliorated protein. The development of an efficient high-throughput screening allowed isolation novel mutants with enhanced activity towards substituted acetophenones and small aliphatic ketones, with up to 60-fold improvement in the enzyme reactivity against para-CN-acetophenone. Furthermore, HEWT stability and tolerance were improved through protein immobilization, which showed excellent results especially in the presence of solvents. The methodology adopted was further developed by installing a protein spacer to preserve the integrity of the enzyme and prevent the significant loss of activity upon non-specific covalent linking. Immobilised HEWT was then applied in continuous flow biotransformations for the efficient production and isolation of amines. This cutting-edge approach showed about one order of magnitude higher synthetic efficiency with respect to batch processes and opened new avenues for the efficient application of enzymes in biotechnology.

This thesis primarily concerns the development of new tools and reactions through the activation of chemical moieties to generate either function, as protein labels or the synthetically valuable sulfonyl azides, or unusual chemical reactivity. Chapter 1 contains a brief introduction to the concept of Click Chemistry, with an overview of the nature of Click Chemistry reactions and their corresponding applications. Chapter 2 focusses on the use of diazirines, high energy but remarkably stable functionality as tools to probe protein structure. A protein footprinting technique has been developed employing aromatic based diazirine photoactive labels to decorate the protein surface. Following analysis by mass spectrometry, information could be inferred regarding the binding site of an Ub-IsoT ZnF protein complex. In addition, a range of diazirine probes of varying steric and electronic demands have been synthesised and their labelling properties characterised. The recently developed SuFEx activation has been applied in Chapter 3, with the development of a protocol for formation of sulfonyl azides from the robust sulfonyl fluorides. The methodology was extended to an in situ diazo transfer reaction, which circumvents the requirement to handle the potentially unstable diazo transfer reagent. Additionally, it was the pursuit of a novel mode of activation for the azide-alkyne cycloaddition, which generated a serendipitous result that led to the results in Chapter 4. Radical cation activation led to a selection of reactive intermediates that engaged in unusual chemistry.