This study is primarily concerned with the application of energy landscape theory to problems in molecular science. Due to the diverse nature of the research undertaken, the thesis is divided into two parts. In the first part, the energy landscapes of the BLN-69 and G\={o}-69 model proteins are investigated using metric disconnectivity graph analysis, which incorporates both the kinetic and geometric structure of an energy landscape. Results are presented which demonstrate the effectiveness with which metric disconnectivity graphs can elucidate the connection between structures in the energy landscape, such as funnels and barriers, with certain structural motifs of the protein, including chain slips and twists in the turn regions. The second part of the thesis focuses on the energy landscape exploration of micro-hydrated ions. A combination of global optimisation and discrete path sampling is used to study the energy landscapes of five anionic species; sulfate, thiocyanate, perchlorate, ferricyanide and ferrocyanide. For the hydrated sulfate and ferricyanide ions, rigid-body modelling of the clusters is capable of replicating the physical chemistry of these systems, with both exhibiting a size-dependent suppression of dangling OH bonds, provisionally consistent with infrared photodissociation spectroscopy of size selected hydrated ions. For all the systems studied, it is demonstrated that ions and water molecules modelled as rigid-bodies interacting via pair-wise empirical potentials are capable of exhibiting a wide range of water structure morphologies.

Matrix-assisted laser desorption/ionisation (MALDI) has rapidly been established as a suitable technique for lipid analysis. In MALDI lipids form a range of adducts (protonated ([M+H] \(^+\)) and cationic ([M+Na] \(^+\), [M+K] \(^+\))), leading to spectral complexity. Promotion of a single adduct type is therefore desirable. This thesis describes optimised sample preparation strategies for MALDI-MS and imaging of lipids in biological samples. Inclusion of salt additives in MALDI matrix solutions for analysis of biological samples is considered. Nitrate salt additives are found to increase sensitivity of a given adduct type in extract samples. Similar preparations deposited via airspray for imaging are shown to have limited use owing to blockage of the spray nozzle. Incorporation of lithium into tissue samples via formal fixation is demonstrated, enabling in situ structural characterisation of highly abundant lithium-lipid adducts in MALDI-MS and imaging. Analysis of formal fixed tissues is also shown to be compatible with a relatively new surface sampling technique: liquid-extraction surface-an) complexes, was used to allow electron-transfer dissocation (ETD) of [Mg+L\(_2\)]\(^2\)\(^+\) and [Ca+L\(_2\)]\(^2\)\(^+\)), giving rise to highly abundant fatty acid side-chain informative product ions.

Ultrafast photodissociation is a fundamental process in nature. In this thesis we present a study of three very different systems which undergo photodissociation on the femtosecond timescale. A major feature of these processes is the often complex topology of the potential energy surfaces due to coupling between the nuclear and electron motion: termed vibronic coupling. A known feature in potential energy surfaces due to vibronic coupling is the conical intersection and these play a role in all three systems studied. In the first study we investigate NH\(_3\), which exhibits an intersection between the ground and first excited state. As a consequence the dissociation occurs on both states. We use two models to study this system, a 2D and a 6D, contrasting greatly in their complexity and ability to describe the whole molecule. Wavepacket dynamics are used to probe the reaction mechanism and to calculate the branching ratio. A detailed investigation of electronic structure theory methods forms a large part of this research. We apply it to the FNO molecule, a system in which there is coupling amongst the states giving rise to certain topological features on the first excited state. These features are both subtle and difficult to reproduce with ab initio methods. We also present a potential fit of this data and implement wavepacket dynamics simulations on the surfaces. A study of Cr(CO)\(_6\) using electronic structure theory is the final system investigated in this work. In contrast to the other systems, Cr(CO)\(_6\) has many low lying excited electronic states and we investigate this system using Complete Active Space Self- Consistent Field (CASSCF) methods. Using a large active space allows us to include all of the states of interest within one calculation.

This thesis focuses on our progress towards the total synthesis of N-methylwelwitindolinone C isothiocyanate 7, commonly called welwistatin. This major alkaloid of the welwitindolinone family, which was isolated from Hapalosiphon welwitschii in 1994, represents a particularly attractive target due to its interesting biological activities (MDR reversing agent) and its challenging structure. Welwistatin possesses a complex bicyclo[4.3.1]decane ring system consisting of four stereogenic centres, three quaternary carbons and two unusual reactive functionalities: the isothiocyanate bridgehead and a vinyl chloride group. Inspired by the synthetic challenge of this complex architecture, the Simpkins group reported an expedient four-step synthesis of its core structure in 2005. Three years later, our group had investigated the reactivity at the bridgehead enolate positions. Taking inspiration from this previous work, we successfully synthesised bridgehead alkene 126. The other features present on welwistatin 7 were then investigated and enone 198 was obtained. Facing some difficulties on the model system 88, we turned our attention towards the synthesis of tetracycle 170, possessing the gem-dimethyl at the position C\(_{16}\), and its subsequent functionalisation.

This study concentrates on pair distribution function (PDF) analysis of various related systems under extreme conditions using variable temperatures and pressures. The local structure of BaTiO\(_3\) (BTO) was investigated using x-rays (xPDF) between 0 and 8.78 GPa and x-rays and neutrons (nPDF) between 100 and 500K. Evidence is presented that indicates that the “Comes model” of Ti disorder is too simplistic to describe the local structure of BTO at variable temperature but results from the high pressure xPDF study are inconclusive due to the inability to observe the very weak first Ti-O peak. The ambient structure of related Ba\(_1\)\(_-\)\(_x\)Bi\(_x\)Ti\(_1\)\(_-\)\(_x\)Yb\(_x\)O\(_3\) was also investigated using both nPDF and xPDF between x = 0 and 0.15, with PDFs indicating significant local disorder present on both A and B sites. Cubic ZrMo\(_2\)O\(_7\) undergoes pressure induced amorphisation at ~0.7 GPa and this was investigated up to 11.02 GPa using xPDF which showed an increase in Mo coordination with pressure but no significant change around Zr. Iron undergoes a bcc-hcp phase transition between 10 and 20 GPa and xPDF was used to investigate this phase transition and the local structure of the hcp phase up to 50.07 GPa, but texture in the sample at high pressures hindered analysis.

An understanding of the crystal structure can aid in the rationalisation of physicochemical properties exhibited by a crystalline material. Advances in the area of direct space crystal structure solution means that it is becoming easier to determine crystal structures from powder diffraction data. However, due to the number of structural models generated during structure solution calculations, direct space methods are computationally demanding. Work presented in this thesis reports the optimisation of a differential evolution (DE) algorithm and a cultural differential evolution (CDE) algorithm to reduce the computational demands of direct space methods. Characteristics particular to certain crystal structures are identified as having a significant effect on the efficiency and robustness of structure solution calculations by DE and CDE. The development of a new algorithm that closely mimics the natural evolution of a species is discussed. Results presented in this thesis demonstrate that this new algorithm is significantly more efficient than the DE algorithm. Despite the complexity of powder diffraction patterns recorded for biphasic crystalline materials, in this thesis, the successful development and application of a direct space method to the simultaneous structure solution of two crystals from a biphasic powder pattern is reported.

Bioorganometallic chemistry is a growing field of research in which organometallic chemistry is combined with biology to achieve novel molecules with novel properties at the biological level. In this area, the tagging of DNA with bioorganometallic molecules such as ferrocene has been the object of much attention over the past few decades. In recent years, a novel approach has been developed consisting of replacing parts of nucleic acids with organic groups including metal-binding ligands. Considering this approach, it was decided to investigate the replacement of DNA dinucleotides with a tetra-substituted ferrocenyl monomer containing nucleobases, leading to the formation of a novel nucleic acid analogue called ferrocene nucleic acid (FcNA). The synthesis of several monomers containing adenine and uracil has been the subject of this thesis. Coupling nucleobases to form bis-substituted ferrocenes was first investigated as a model for the subsequent synthesis of tetra-substituted ferrocenyl monomers with high chiral purity. The compounds were characterised using a range of spectroscopic and analytical techniques, including Xray crystallography. The influence of the nucleobases and the nature of the linker to the ferrocenyl group have also been investigated using electrochemistry.

13 nm and 100 nm citrate-stabilised gold nanoparticles are used as inert scaffolds for the assembly of multiple transition metal lumiphores, and thiol-appended ruthenium(II) and iridium(III) polypyridyl complexes have been synthesised for surface-attachment. The direct attachment of cationic lumiphores to citrate-stabilised gold colloids with negative zeta potentials, affords nanoparticle aggregation, due to loss of electrostatic stabilisation. In order to circumvent this problem, a surfactant pre-coating step has been implemented, and the following commercial surfactants have been evaluated: Triton™ X-100, TWEEN® 20, and Zonyl® 7950. Gold nanoparticles coated with Zonyl® 7950 fluorosurfactant can be functionalised with cationic lumiphores and colloidal stability is maintained even at high nanoparticle concentrations, i.e. 9 nM. The fluorosurfactant not only ensures colloidal stability, but also enhances the emission of the ruthenium(II) and iridium(III) complexes investigated. Importantly, the complexes attached on the resultant luminescent nanoprobes do not exhibit luminescence quenching from the gold nanoparticles. Imaging applications of the resultant luminescent nanoparticles have been demonstrated in in vitro cellular uptake studies and in blood flow particle tracking within the microvasculature. Furthermore, gold nanoparticles have been co-coated with lumiphores and both functional peptides, for targeted delivery in cells, and gadolinium(III) complexes, in order to realise imaging probes for both luminescence and MRI detection.

The trafficking and signalling of cellular receptors are complex, intertwined processes with many feedback mechanisms. Confocal microscopy is a powerful tool to study the trafficking of receptors. The aim of this thesis was to report and develop workflows to quantify the spatio-temporal dynamics of receptor trafficking and colocalization using confocal microscopy. Importantly, the workflows should be reproducible and unbiased, as well as automated and accurate. A 4D level set approach is developed to enable accurate cellular segmentation. Temporal constraints are introduced to further improve segmentation accuracy. This novel approach is thoroughly validated, and statistically significant performance increase over equivalent 2D and 3D approaches is demonstrated. We present a confocal microscopy based RNAi depletion screen. Specifically, quantitative workflows to identify genes which perturb the trafficking of receptor are described. Finally, a critical review of current approaches to the quantification of colocalization between receptors and endosomes is presented. Improvements to existing techniques and complete workflows are provided for 4D data (3D time-lapse). Together the described protocols provide a complete microscopy based platform to identify and investigate regulators of receptor signalling and trafficking.

Precipitated surface films form when metal cations are produced faster than they can move away from the dissolving interface. This build up of cations results in supersaturation conditions, which cause a solid to precipitate. The precipitated solid affects ion transport and thus the dissolution kinetics, which ultimately control the two systems studied here. X-ray diffraction, small angle X-ray scattering and fast radiography were chosen to study the metal/solution interface in-situ, using synchrotron radiation. The AC electrograining system is a widely used industrial process whereby an alternating current is applied to aluminium plates to form a pitted surface. During this process, an Al(OH)3 surface gel (smut) forms within seconds whilst electrograining continues for several minutes in its presence. Although smut formation has been investigated previously, how the smut affects metal dissolution is currently unknown and is the primary goal of this project. The second system is a nickel “artificial pit,” which is commonly used to simulate pit propagation. In this system, a salt film is precipitated by imposing a large overpotential whilst restricting transport through a 1-D pit. Interfacial phenomena that occur during salt film formation are investigated towards an understanding of how the salt film forms.