We investigate systems comprising chains and rings of quantum dots, coupled to two metallic leads. Such systems allow to study the competition between orbital and spin degrees of freedom in a nanodevice, and the effect this subtle interplay has on two-channel Kondo (2CK) physics. We demonstrate that a rich range of strongly correlated electron behaviour results, with non-Fermi liquid 2CK phases and non-trivial phase transitions accessible. We employ physical arguments and the numerical renormalization group (NRG) technique to analyse these systems in detail, examining in particular both thermodynamic and dynamical properties. When leads are coupled to either end of a chain of dots, we show that the resulting behaviour on low temperature/energy scales can be understood in terms of simpler paradigmatic quantum `impurity' models. An effective low-energy single-spin 2CK model is derived for all odd-length chains, while the behaviour of even-length chains is related fundamentally to that of the classic `two-impurity Kondo' model. In particular, for small interdot coupling, we show that an effective coupling mediated though incipient single-channel Kondo states drives all odd chains to the 2CK fixed point (FP) on the lowest temperature/energy scales. A theory is also developed to describe a phase transition in even chains. We derive an effective channel-anisotropic 2CK model, which indicates that the critical FP of such models must be the 2CK FP. This physical picture is confirmed using NRG for various chain systems. We also examine the effect of local frustration on 2CK physics in mirror-symmetric ring systems. The importance of geometry and symmetry is demonstrated clearly in the markedly different physical behaviour that arises in systems where two leads are either connected to the same dot, or to neighbouring dots. In the latter case, we show for all odd-membered rings that two distinct 2CK phases, with different ground state parities, arise on tuning the interdot couplings. A frustration-induced phase transition thus occurs, the 2CK phases being separated by a novel critical point for which an effective low-energy model is derived. Precisely at the transition, parity mixing of the quasidegenerate local trimer states acts to destabilise the 2CK FPs, and the critical FP is shown to consist of a free pseudospin together with effective single-channel spin quenching. While connecting both leads to the same dot again results in two parity-distinct phases, a simple level-crossing transition now results due to the symmetry of the setup. The proposed geometry also allows access to a novel ferromagnetically-coupled two-channel local moment phase. Driven by varying the interdot couplings and occurring at the point of inherent magnetic frustration, such transitions in ring structures provide a striking example of the subtle interplay between internal spin and orbital degrees of freedom in coupled quantum dot systems, and the resulting effect on Kondo physics.

Enolate formation by proton abstraction from an sp3-hybridized carbon atom situated next to a carbonyl or carboxylate group is an abundant process in nature. Since the corresponding nonenzymatic process in water is slow and unfavorable due to high intrinsic free energy barriers and high substrate pKa s, enzymes catalyzing such reaction steps must overcome both kinetic and thermodynamic obstacles. Computer simulations were used to study enolate formation catalyzed by glyoxalase I (GlxI) and 3-oxo-Δ5-steroid isomerase (KSI). The results, which reproduce experimental kinetic data, indicate that for both enzymes the free energy barrier reduction originates mainly from the balancing of substrate and catalytic base pKas. This was found to be accomplished primarily by electrostatic interactions. The results also suggest that the remaining barrier reduction can be explained by the lower reorganization energy in the preorganized enzyme compared to the solution reaction. Moreover, it seems that quantum effects, arising from zero-point vibrations and proton tunnelling, do not contribute significantly to the barrier reduction in GlxI. For KSI, the formation of a low-barrier hydrogen bond between the enzyme and the enolate, which is suggested to stabilize the enolate, was investigated and found unlikely. The low pKa of the catalytic base in the nonpolar active site of KSI may possibly be explained by the presence of a water molecule not detected by experiments. The hemoglobin-degrading aspartic proteases plasmepsinI and plasmepsin II from Plasmodium falciparum have emerged as putative drug targets against malaria. A series of C2- symmetric compounds with a 1,2-dihydroxyethylene scaffold were investigated for plasmepsin affinity, using computer simulations and enzyme inhibition assays. The calculations correctly predicted the stereochemical preferences of the scaffold and the effect of chemical modifications. Calculated absolute binding free energies reproduced experimental data well. As these inhibitors have down to subnanomolar inhibition constants of the plasmepsins and no measurable affinity to human cathepsin D, they constitute promising lead compounds for further drug development.

5-aminolevulinic acid (5-ALA) and derivatives thereof are widely usedprodrugs in treatment of pre-malignant skin diseases of the cancer treatmentmethod photodynamic therapy (PDT). The target molecule in 5-ALAPDTis protoporphyrin IX (PpIX), which is synthesized endogenously from5-ALA via the heme pathway in the cell. This thesis is focused on 5-ALA,which is studied in different perspectives and with a variety of computationalmethods. The structural and energetic properties of 5-ALA, itsmethyl-, ethyl- and hexyl esters, four different 5-ALA enols, and hydrated5-ALA have been investigated using Quantum Mechanical (QM) first principlesdensity functional theory (DFT) calculations. 5-ALA is found to bemore stable than its isomers and the hydrolysations of the esters are morespontaneous for longer 5-ALA ester chains than shorter. The keto-enoltautomerization mechanism of 5-ALA has been studied, and a self-catalysismechanism has been proposed to be the most probable. Molecular Dynamics(MD) simulations of a lipid bilayer have been performed to study themembrane permeability of 5-ALA and its esters. The methyl ester of 5-ALAwas found to have the highest permeability constant (PMe-5-ALA = 52.8 cm/s).The mechanism of the two heme pathway enzymes; Porphobilinogen synthase(PBGS) and Uroporphyrinogen III decarboxylase (UROD), have beenstudied by DFT calculations and QM/MM methodology. The rate-limitingstep is found to have a barrier of 19.4 kcal/mol for PBGS and 13.7kcal/mol for the first decarboxylation step in UROD. Generally, the resultsare in good agreement with experimental results available to date.

<p>This thesis presents and uses the techniques of computational chemistry to explore two different processes induced in human skin by ultraviolet light. The first is the transformation of urocanic acid into a immunosuppressing agent, and the other is the enzymatic action of the 8-oxoguanine glycosylase enzyme. </p><p>The photochemistry of urocanic acid is investigated by time-dependent density functional theory. Vertical absorption spectra of the molecule in different forms and environments is assigned and candidate states for the photochemistry at different wavelengths are identified. </p><p>Molecular dynamics simulations of urocanic acid in gas phase and aqueous solution reveals considerable flexibility under experimental conditions, particularly for for the <i>cis</i> isomer where competition between intra- and inter-molecular interactions increases flexibility. </p><p>A model to explain the observed gas phase photochemistry of urocanic acid is developed and it is shown that a reinterpretation in terms of a mixture between isomers significantly enhances the agreement between theory and experiment , and resolves several peculiarities in the spectrum. </p><p>A model for the photochemistry in the aqueous phase of urocanic acid is then developed, in which two excited states governs the efficiency of photoisomerization. The point of entrance into a conical intersection seam is shown to explain the wavelength dependence of photoisomerization quantum yield. </p><p>Finally some mechanistic aspects of the DNA repair enzyme 8-oxoguanine glycosylase is investigated with density functional theory. It is found that the critical amino acid of the active site can provide catalytic power in several different manners, and that a recent proposal involving a S<i>N</i>1 type of mechanism seems the most efficient one.</p>

This thesis presents a theoretical and experimental investigation of the interaction of electronically excited Rydberg hydrogen atoms with metal surfaces and the associated charge-transfer process. As a Rydberg atom approaches a metal surface, the energies of the Rydberg states are perturbed by the surface potential generated by the image charges of the Rydberg electron and core. At small atom-surface separations, the Rydberg atom may be ionised by resonant charge transfer of the Rydberg electron to the continuum of delocalised unoccupied metal states, with which the Rydberg electron is degenerate in energy. Typically, this ‘surface ionisation’ can be measured by extracting the remaining positively charged ion-cores with externally applied electric fields. By applying various levels of theory, from classical to fully time-dependent quantum calculations, this thesis explores various experimentally relevant effects on the charge-transfer process, such as the magnitude and direction of the externally applied electric field, the atom collisional velocity, the presence of local surface stray fields and electronically structured surfaces. The theoretical results give insight into the previous experimental work carried out for the xenon atom and hydrogen molecule, and point out some of the fundamental differences from the hydrogen atom system. Experiments involving Rydberg hydrogen atoms incident on an atomically flat gold surface, a rough machined aluminium surface and a single crystal copper (100) surface are presented, providing for the first time the opportunity to make a quantitative comparison of theory and experiments. The ability to control the critical distance at which charge-transfer occurs is demonstrated by using Rydberg states of varying dimensions and collisional velocities. By changing the collisional angle of the incident Rydberg beam, the effect of Rydberg trajectory is also investigated. By manipulating the polarisation of the Rydberg electron with electric fields, genuine control over the orientation of the electron density distribution in the charge-transfer process is demonstrated. This property was predicted by the theory and should be unique to the hydrogen atom due to its intrinsic symmetry. By reversing the direction of the electric field with respect to the metal surface, electrons rather than positive ions are detected, with ionisation dynamics that appear to be very different, as predicted by quantum calculations. Experiments involving the single crystal Cu(100) surface also suggests possible resonance effects from image states embedded in the projected bandgap which are shown from quantum calculations to play an important role in the surface charge transfer of electronically structured metal substrates. The experimental technique developed in this work provides some exciting future applications to study quantum confinement effects with thin films, nanoparticles and other bandgap surfaces. The ability to control the Rydberg orbital size, electronic energy, collisional velocity and orientation in the charge-transfer process will provide novel ways of probing the surface’s electronic and physical structure, as well as being a valuable feature in offering new opportunities for controlling reactive processes at metallic surfaces.

The measurement of radical species in the atmosphere has far reaching implications. For example, it is necessary to both understand and improve our knowledge of radicals in the atmosphere to better inform the models which in many cases are the best way of predicting future air quality and climate change. Although many of these models are often not fully representative of all the processes occurring, they are the current best estimate based on the knowledge available, and can be useful in informing and directing future policy. The numerous, varied and interlinked cycles in the atmosphere are complex and only by obtaining data on specific species can accurate concentrations be retrieved and fed back into the models to improve their accuracy. This work is concerned with the development and application of an ultrasensitive absorption spectroscopy technique to the problem of detection of the peroxy radical, HO₂. Noise Immune Cavity Enhanced Optical Heterodyne Molecular Spectroscopy (NICE-OHMS) combines cavity enhancement techniques (in order to increase the path length) with frequency and wavelength modulation techniques (in order to reduce the noise). Following a discussion of the current detection methods used by atmospheric scientists to accurately measure and quantitative concentrations, some preliminary work on the detection of ammonia by a simple cavity enhanced absorption setup is presented. Pressure broadening and shift results were obtained for a number of ammonia transitions in the near infrared region, broadened by He, Ne, Ar, Xe, O₂ and N₂. The bulk of the work concentrates on the implementation of the NICE-OHMS technique, presenting the first results with the use of an external cavity diode laser and a ring shaped cavity. A sensitivity of 4 x 10⁻¹¹ cm⁻¹ Hz⁻^1/2 is obtained on an individual rovibrational transition of methane at 6610.063 cm⁻¹, along with a selection of other data from the atmospherically important molecules methane, nitrogen dioxide and carbon dioxide, highlighting the broad wavelength range over which the instrument can operate. Finally, the NICE-OHMS technique is used to probe HO₂ radicals formed through the photolysis of a Cl₂/CH₃OH/O₂ mixture. Following the creation and detection of HO₂ radicals in the cavity, and based on the optimum sensitivity outlined above, a minimum concentration of 1 x 10⁹ molecules cm⁻³ has been demonstrated.

In recent years there has been much progress in the field of cold and ultracold molecular physics and a variety of experimental techniques for producing cold matter now exist. In particular, the generation of trapped molecular ions at mK temperatures has been achieved by sympathetic-cooling with laser-cooled atomic ions. By implementing schemes to selectively prepare and control the internal quantum state of molecular ions, and developing detection techniques, it will be increasingly possible to study cold state-selected chemical collisions in an ion-trap. Most molecular species produced in a selected rovibrational state have a lifetime of a few seconds, before the population is redistributed across numerous rovibrational states by interaction with the ambient blackbody radiation (BBR). Consequently, the investigation of state-selected reaction dynamics at low temperatures in experiments where long time scales (minutes to hours) are required, is hindered. This thesis looks into developing strategies that maintain state selection in molecular ions, allowing one to observe state-selected reactions in cold environments, in particular the state-selected reaction between C₂H⁺₂ and ND₃. Examining reactive ion molecule collisions under cold conditions provides insight into fundamental reaction dynamics, which are thermally averaged out at higher temperatures. A theoretical model is used to investigate laser-driven, blackbody-mediated, rotational cooling schemes for several ¹&Sigma; and ²Π diatomic species. The rotational cooling is particularly effective for DCl⁺ and HCl⁺, for which 92&percnt; and >99&percnt; (respectively) of the population can be driven into the rovibrational ground state. For the other systems a broadband optical pumping source is found to enhance the population that can be accumulated in the rovibrational ground state by up to 29&percnt; more than that achieved when exciting a single transition. The influence of the rotational constant, dipole moments and electronic state of the diatomics on the achievable rotational cooling is also studied. This approach is extended to consider the BBR interaction and rotational cooling of a linear polyatomic ion, C₂H⁺₂, which has a ²&Pi; electronic ground state. The (1-0) band of the &nu;₅ cis-bending mode is infrared active and strongly overlaps the 300 K blackbody spectrum. Hence the lifetimes of state-selected rotational levels are found to be short compared to the typical timescale of ion trapping experiments. Laser cooling schemes are proposed that could be experimentally viable, which involves simultaneous pumping of a set of closely spaced Q-branch transitions on the ²&Delta;_5/2-²&Pi;_3/2 band together with two ²&Sigma;⁺– ²&Pi;_1/2 lines. It is shown that this should lead to >70&percnt; of total population in the lowest rotational level at 300 K and over 99&percnt; at 77 K. In order to identify states of the acetylene ion that could be trapped sufficiently long enough for state-selected reactions in the ion trap with decelerated ND3, the theoretical work has been complemented by experimental investigations into the production of C₂H⁺₂ in selected states, and ion trapping of the same using sinusoidal and digital trapping voltages. Appropriate (2+1) REMPI (Resonance Enhanced Multiphoton Ionization) schemes are used to produce C₂H⁺₂ in different quantum states, with (1+1) Resonance Enhanced Multiphoton Dissociation (REMPD) employed to detect the ion thus produced. The concept of digital ion trapping for ejection onto MCPs is introduced. A comprehensive comparison between sinusoidal and digital trapping fields has been performed with respect to trap depth and stability regions. Programs have been developed to calculate the stability regions for different ions under varying experimental conditions. The trap depth has been derived for both digital and sinusoidal trapping fields. It is observed that as &tau; increases, the trap depth of a digital trap increases. For &tau; = 0.293, the trap depth and stability diagram for both sinusoidal and digital trapping fields would be equivalent. The trap depth at which the sinusoidal trap operates experimentally in our research group is ~1.36 eV. In contrast, the experimental parameters at which the digital trap operates generates a trap depth of 1.21 eV. Ca⁺ Coulomb crystals have been formed, stably trapped and stored for extended periods of time in both sinusoidally and digitally time-varying trapping fields. The sympathetic cooling of a diverse range of ions into Ca⁺ Coulomb crystals is demonstrated, again using both sinusoidal and digital trapping fields. Mass spectrometric detection of ionic reaction products using a novel ejection scheme has been developed, where ejection is achieved by switching off the trapping voltage and converting the quadrupole trap into an extractor-repeller pair by providing the ion trap electrodes with appropriate ejection pulses. This technique is developed using a digital trapping voltage rather than the sinusoidal trapping voltage, as ejection with sinusoidal trapping voltages is not clean (resonance circuitry used in the electronics induces ringing after switching off the trapping voltage). Coulomb crystals, both pure Ca⁺ and multi-component crystals, are ejected from the ion trap and the TOF trace obtained is recorded on an oscilloscope. When the integrated, base-line subtracted TOF peak is plotted against the number of ions in a Ca+ crystal and sympathetically-cooled Ca⁺ – CaF⁺ crystal, a linear relationship is obtained. This technique is found to be well mass-resolved, with the signal arising from CaOH⁺ (57 amu) and CaOD⁺ (58 amu) resolvable on the TOF trace. This technique would enable one to monitor a reaction in a Coulomb crystal where the reactant and product species are both either lighter or heavier than calcium, such as the reaction between C₂H⁺₂ and ND₃, something which has not been previously possible. It is, also, potentially a very important technique for reactions with many product channels.

SPM, optical microscopy, and electrochemical techniques are used to study a range of electrochemical deposition processes on carbon electrodes, particularly those associated with diffusion-controlled multiple nucleation. Anodic stripping voltammetry for analytical measurements using solid electrodes is addressed in the light of limitations arising from electrode heterogeneity, electrode morphology, inhibited electrodeposition, and incomplete stripping of deposited metal. It is shown, using direct imaging of electrode surfaces, that each of the preceding factors may produce significant deviations from ideal electrode behaviour. The electrochemical nucleation of silver on BDD is examined. Data are obtained for the nucleation rate by interpretation of the deposition voltammetry, and by inspection of in-situ optical microscopic images. The particle distributions are analyzed and a stochastic model of nucleation developed. A model for the potentiostatic nucleation and three dimensional growth of deposits on an electrode surface under hydrodynamic conditions is examined. A wall-tube and stirred cell are used to generate conditions in which the diffusion layer thickness is in the range 10 – 40 μm. It is shown that the model provides excellent fits to the experimental data. A previously unrecognised correlation between the morphology of the PbO2 deposits and their electrocatalytic activity is established. The morphology of the films are observed as a function of time and potential using in-situ AFM. Nanotrench arrays are fabricated on HOPG surfaces. Cyclic voltammetry in simple redox couples is used to provide experimental evidence that the voltammetric response of a graphite electrode is solely due to the edge plane sites, with the basal plane sites having no measurable contribution. Nanotrenches are used as templates in a simple method for generating random assemblies of metal nanobands. This method is shown to be effective for generating gold, silver and copper nanowires. The electrochemical properties of the array are investigated via cyclic voltammetry.

The research described in this thesis employs a variety of Electron Paramagnetic Resonance (EPR) techniques for the study of the electronic and structural properties of artificial supramolecular porphyrin systems and of protein complexes of biological relevance. The electron delocalisation in the cationic radical and photoexcited triplet states of linear and cyclic &Pi;-conjugated multiporphyrin arrays was investigated. In the radical cations, information on the extent of delocalisation can be inferred from the measurement of hyperfine couplings, either indirectly from the continuous wave EPR spectrum or directly using pulsed hyperfine EPR techniques. The results of room temperature EPR experiments showed complete delocalisation of the electron on the timescale of the EPR experiments, but frozen solution EPR measurements revealed localisation onto mainly two to three porphyrin units in the larger porphyrin systems. Information on the delocalisation of the triplet state in the same porphyrin systems is contained both in the hyperfine couplings and in the zero-field splitting (ZFS) interaction. The results outlined in this thesis show that the hyperfine couplings provide a much more accurate estimate of the extent of delocalisation. The trends in proton and nitrogen hyperfine couplings with the size of the porphyrin systems indicate uneven spin density distributions over the linear arrays, but complete delocalisation in the cyclic systems. Time-resolved EPR and magnetophotoselection experiments have shown a reorientation of the zero-field splitting tensor between a single porphyrin unit and longer linear arrays, resulting in alignment of the main optical transition moment and the Z axis of the ZFS tensor. Continuous wave and pulsed dipolar EPR techniques were employed for the determination of the structure of two different protein complexes, the homomultimeric twin-arginine translocase A (TatA) protein channel and the ferredoxin-P450 complex of the electron transport chain in Novosphingobium aromaticivorans. The interaction between nitroxide spin labels introduced at different positions of the TatA monomer was investigated in the complex reconstituted in detergent micelles by analysing the dipolar broadening of the EPR spectra and the results of three- and four-pulse Double Electron-Electron Resonance (DEER) measurements. In combination with results from NMR and molecular dynamics calculations, a structure for the channel complex was proposed. The structure of the ferredoxin-cytochrome P450 complex was investigated by orientation-selective DEER between nitroxide labels introduced on the cytochrome P450 protein and the iron-sulfur cluster of the ferredoxin. The distance and orientation information contained in the experimental DEER data was interpreted in terms of a structural model of the protein complex by orientation-selective DEER simulations combined with a modelling approach based on protein-protein docking.

Interest exists in the development of transparent conducting oxide materials, which have diverse applications in areas such as transparent coatings for display technologies, solar cells, and optoelectronics. Since many of the applications require the use of thin film forms, the need is to establish useful experimental approaches to the fabrication of such structures. One relatively new method in this area is oxygen-plasma assisted atomic beam epitaxy (OPABE) in which oxide layers are grown under normal molecular beam epitaxy (MBE) conditions with the addition of an oxygen atom beam to ensure full oxidation of the depositing metallic species. Work in this area has to date mainly focussed on the growth of relatively stable oxides such as ZnO, MgO and In₂O₃ which are the strongly thermodynamically favoured reaction products, across a broad range of reaction conditions. In contrast, the present work is concerned with the growth of Cu2O and a range of delafossite materials, namely CuInO₂, CuCrO₂ and CuGaO₂, which are expected to require much more sensitive control to achieve the desired reaction product. Studies of the OPABE growth of Cu₂O on MgO (100) and MgO (110) substrates have been carried out, using a broad range of physical techniques to characterise the grown Cu₂O deposits. It is demonstrated that CuO is the favoured reaction product at low growth temperatures, although Cu₂O becomes increasingly favoured as the growth temperature increases. Alternatively, it is also shown that a novel bilayer growth method, whereby some pure Cu is deposited prior to oxide growth, can be used to form the desired Cu (I) phase. Varying crystal orientations are seen, depending on the exact growth conditions; core level and valence band X-ray photoelectron spectroscopy (XPS), optical band gap and atomic force microscopy (AFM) measurements are used to characterise the deposits. Further growth investigations of the delafossite compounds CuInO₂, CuCrO₂ and CuGaO₂ using OPABE are also recorded, and for the case of CuInO₂, comparison is also made with the pulsed laser deposition approach. For all three materials systems, oriented crystal growth on basal planes sapphire substrates is seen, with either the (001) plane or the (015) plane orienting parallel to the substrate depending on the growth temperature, provided approximately correct metal fluxes are used as set by the Knudsen-cell temperatures. The typical valence band electronic structure of delafossite materials is observed in all three cases, and XPS peak shifts suggest that the layers can be electrically doped by adding appropriate metal fluxes during growth. AFM measurements show the grown films are relatively rough and it is suggested that the growth mode follows an island growth mechanism in which oriented three dimensional islands formed at the start of growth gradually enlarge and coalesce as the film thickens. Optical absorption measurements are consistent with the generally accepted optical band gaps of the materials concerned.