Proteins play an important role in the function of biological systems. Developing a thorough understanding of the dynamics, structure and function is a goal of many biological spectroscopists. One commonly used tool for probing different features and properties of proteins and polypeptides is infrared (IR) spectroscopy. The spectra obtained however lacks resolution due to broad, featureless peaks that are hard to interpret. Overlapping of the bands is also an issue, especially from the amide I region; an important region that is sensitive to secondary structure elements of proteins. Isotope labelling of residues of interest is a solution to disentangle the band profiles, however the technique lacks any meaningful insight regarding coupling between different local sites. For the past few decades, 2D IR (an analogue of its NMR counterpart) has been used in various experiments to improve the quality of 1D IR by spreading the signal to a second frequency domain, thus revealing coupling interactions. The technique has helped reveal different relationships between the secondary structural elements of proteins or between protein-ligand complexes. The main challenge so far has been the computational requirement needed to compute the 2D IR signals of large proteins. This is due to the nonlinear response function scaling with the fourth power of the number of residues involved in the calculations. Moreover, convolution of the bands is still an issue as the number of residues grows, albeit not so much compared with 1D IR. In this thesis, we utilize the exciton approach and molecular dynamics (MD) simulations to compute the 1D and 2D IR signals of small peptides, globular proteins and [Leu]-Enkephalin in the presence of three opioid receptors of interest. The work presented in this thesis complements previous experiments on globular proteins and the behaviour of [Leu]-enkephalin and aims to provide more insight into the behaviour of such systems under the conditions outlined.

In the first chapter of this thesis the aluminium promoted zinc Schlenk equilibrium of FG-ArZnX/AlMe3 is shown to provide good access for the synthesis of chiral secondary alcohols. This practical asymmetric 1,2-addition to aliphatic and aromatic aldehydes uses only commercially available reagents and ligands. Enantioselectivity is provided by the use of (1R,2S)-dibutylnorephedrine (1,2-amino alcohol ligand) giving selectivity, in most cases, between 80-96% ee. Yields are moderate to good, typically alcohols are prepared in 50-97% yield. Uniquely the FG-ArZnBr species can be prepared in situ directly from Ar-Br or Ar-I, via the cobalt catalysed zinc insertion. Optimisation of the zinc insertion allowed for rate acceleration and a subsequent slight reduction in enantiocontrol. Furthermore, enantioselectivity of the reaction can be enhanced via the simple addition of LiBr to the FG-ArZnBr species. A LiBr promoter can dramatically enhance the enantioselectivity of such ‘home made’ reagents (from 30 to ca. 90% ee in one case), however studies to explain this effect have not been investigated. Further investigation into zinc source optimisation via electron microscopy and energy dispersive X-ray (EDX) spectroscopy, has highlighted the necessity to use small particulate zinc in the range of 2-10 muM and having little surface oxide. Stereo correlations of the secondary alcohol products highlight a reverse in stereochemistry compared to the ‘classic Noyori’ transition state for the addition of ZnEt2 to PhCHO using chiral 1,2-aminoalcohol ligands. Analysis and investigation of our system showed there was no non-linear effect associated with the process, suggesting the catalyst to be monomeric in solution. A second thesis chapter describes facile DABAL-Me3 mediated preparation of aromatic and aliphatic amides. This procedure allows the coupling of a wide range of functionalised primary and secondary amines and esters, secondary amines and allows formation of versatile Weinreb amides. Microwave irradiation provides an improved rate of reaction allowing excellent yields (51-99%) in short reaction times (8-16 min). Wide applicability is shown in the variation and tolerance of a wide range of functional groups in both coupling partners. Functional groups tolerated include: acetal, alcohol, alkene, alkyne, Ar-X, cyano and ethers. Furthermore the stereochemical integrity of the coupling partners is retained in two representative examples with an epimerisable carbon centre. This procedure enables the coupling of less nucleophillic amines such as anilines. However, the reaction yields are diminished when highly electron poor anilines are used, or when highly sterically hindered esters or amines are used.

Interfacial instabilities and wetting phenomena of phase separated colloid-polymer mixtures are addressed in this study. Colloidal particles offer certain advantages over molecular systems, due to their larger lengthscales and slower timescales. Moreover, the phenomena can be directly visualised using laser scanning confocal microscopy, and a perfect match with soft-lithography fabrication techniques can be exploited. In particular, we study the viscous fingering instability in three dimensions, focusing on the role of wetting conditions and of thermal fluctuations. Combined with results obtained by lattice Boltzmann simulations, we reveal that the cross-over of the meniscus in the direction across the channel thickness is controlled by the capillary and Peclet numbers, and viscosity contrast of the system. The curvature of the meniscus has a pronounced effect on the onset of the Saffman-Taylor instability, in which the formation of the viscous fingers is suppressed up to a certain threshold. Furthermore, we investigate a related contact line instability, which leads to entrainment and subsequent droplet pinch-off. A theoretical prediction for the onset of the instability is developed, which shows a good agreement with the experimental observations and yields a method to directly measure the slip length of the interface. The large thermal fluctuations of our interface play an important role in pinch-off events, leading to periodic emission of droplets of similar sizes. Finally, we study wetting phenomena at geometrically sculpted walls. We focus on the shape, the thickness and the radius of curvature of the adsorbed liquid film, and find good agreement with theory. Changing the curvature of the wedge from a flat surface to a capil- lary slit furthermore smoothly connects wetting behaviour and capillary condensation, again in qualitative agreement with theory. Non-equilibrium effects may interfere with the data and are difficult to rule out. We end with recommendations for future work.

CVD diamond possesses certain attractive electrochemical properties inter alia low background current, broad potential window, chemical inertness and resistance to electrocorrosion and fouling. As a consequence its use in various areas of electrochemistry, such as electrochemical sensing, wastewater treatment and electrocatalysis is being explored. Unfortunately, alongside these attractive features, bare CVD diamond electrodes, in common with all other electrode materials, cannot be effectively applied in all electrochemical systems of interest, since for example it may not display useful electrochemical activity for the redox process of interest. In these circumstances it may be possible to modify the electrode by addition of other chemical species to the surface, to introduce the relevant activity. One of the main aims of this thesis was therefore to investigate the properties of certain chemical modifications to the diamond electrode surface. A second aim was also to explore for the first time the use of a practically useful form of single crystal diamond, so-called heteroepitaxial diamond, in electrochemistry. The diamond electrodes used were boron-doped material grown by chemical vapour deposition. A range of electrochemical methods, including especially cyclic voltammetry, square-wave voltammetry, impedance spectroscopy and scanning electrochemical microscopy, were used to characterise electrode properties. Other physical methods employed included scanning electron and atomic force microscopy, X-ray photoelectron spectroscopy and dynamic light scattering techniques. The electrochemical properties of heteroepitaxial single crystal diamond were explored and compared to polycrystalline counterparts. The single crystal diamond electrode was found to show superior properties in terms of wide potential window, low background current and homogeneous activity across the electrode surface, coupled with resistance to fouling. Heterogenous electron transfer rate constants were found to be lower than normally found on polycrystalline diamond; this was attributed to reduced density of states and absence of functional groups. An electrochemical route to the preparation of diamond electrodes, modified by PrOx@Pt core-shell particles was demonstrated. It was observed that these electrode modifiers were far less susceptible to poisoning than bare Pt nanoparticles when used in the electrochemical oxidation of methanol. It was also shown that diamond electrodes with these core-shell particles deposited on them, displayed useful activity for the electrochemical oxidation of nitric oxide. The presence of the PrOx layer was shown to impart useful selectivity against the oxidation of interfering compounds such as nitrite and ascorbic acid, without the loss of sensitivity which normally occurs if nafion coatings are used instead. Basic electrochemical characterisation of the PrOx coating showed that the layer was chemically active and did not serve as a simple blocking layer when deposited on the electrode. The activity of Pt modified diamond electrodes for the oxidation of nitrite species was also studied. It was also shown that the addition of carbon black to a diamond electrode resulted in much enhanced electrochemical properties in the detection of riboflavin.

Rotational polarisation effects have been investigated in the rotationally inelastic collisions of NO(X) and Ar by means of theoretical and experimental methods. Rotational polarisation describes the correlation between the <strong>k</strong>–<strong>k'</strong>–<strong>j'</strong> vectors, that is the initial and final relative velocities of the colliding partners and the final rotational angular momentum of the diatom, respectively. The simplest types of polarisation are the rotational orientation, or preferred sense of rotation, and the rotational alignment, or preferred plane of rotation. They are quantised by the renormalised polarisation dependent differential cross sections (PDDCSs) In this thesis the theoretical methods included exact quantum mechanical, quasi- classical trajectory and Monte Carlo classical hard shell calculations. Various features of the interaction potential influence differently the polarisation dynamics. The effects of attraction and soft repulsion were elucidated employing a number of differently modified potentials. The rotational alignment is primarily determined by a classical impulsive, or hard shell mechanism at a collision energy of 66 meV. The attractive and soft repulsive forces only perturb this underlying mechanism. On the other hand, the parity dependent oscillations of the open shell alignment moments are due to differences between the quantum mechanical differential cross sections. It has been shown the bigger the well depth compared to the collision energy, the less applicable becomes the classical hard shell model to describe rotational alignment. The quantum mechanical rotational alignment in the collisions of hard shells was also calculated. The classical and quantum mechanical hard shell models predict different rotational alignment. Nevertheless, the classical alignment is a good approximation to the exact quantum mechanical results. The rotational orientation is much more sensitive to the details of the interaction potential. It does not exist in the classical description of hard shell collisions, if the system exhibits certain symmetry properties. The attraction and finite range repulsion break this symmetry and leads to the molecule having a preferred sense of rotation. In general there is non-vanishing rotational orientation in the collisions of a hard shell in the framework of quantum mechanics. This is due to the finite spatial and temporal interaction of the colliding partners. Quantum mechanical interference effects also play an important role in this phenomenon. The rotational alignment was experimentally determined in the collisions of NO(X) and Ar at collision energy of 66meV with a hexapole state selective ion-imaging apparatus. An algorithm was developed based on the Fourier moment analysis to extract rotational polarisation information from the experimental ion images. It is fast and robust and can also be of used to simulate experimental images. This algorithm was used to retrieve the experimental renormalised PDDCSs ion images. The measurements confirmed that a classical, impulsive dynamics is mainly responsible for the rotational alignment in these collisions.

This thesis explores the structures and dynamics of optically confined matter, ranging from single particle traps to complex optically bound colloidal arrays, investigating and quantifying the behaviour of each system. It begins with an introduction to optical manipulation techniques and a discussion of the development of the single beam gradient force trap, more commonly referred to as optical tweezers. Following this, the building of a single beam optical trap will be presented alongside a discussion of some of the key components in such a setup, before it is calibrated, allowing a demonstration of some of the techniques which are utilised later in the thesis. The optical trapping of aerosol droplets is an area of key importance in atmospheric chemistry, as optical tweezers provide a valuable and versatile tool for droplet manipulation and characterisation. Trapping single aerosol droplets is facilitated by using annular rather than conventional Gaussian beams, as will be demonstrated, with significant advantages in increasing the size range of trappable droplets, and improving their axial localisation. These improvements will be demonstrated experimentally with an in-depth comparison of Gaussian and annular beam trapping. These enhancements are also verified theoretically using a model developed by Burnham and McGloin, showing excellent agreement with experimental results. Ionic liquids, defined as organic salts with melting points below room temperature, are another area of great contemporary interest. They are highly tunable and so have been referred to as "designer solvents", and also have important applications as "green" solvents in organic chemistry. Trapping particles within these novel liquids allows a micro-rheological investigation of their properties to be conducted. This is demonstrated by determining the temperature dependent viscosity changes of these media, showing excellent agreement with previous macro-rheological studies. In addition, hydrodynamic effects such as Faxen's correction to viscous drag in proximity to a surface, and hydrodynamic coupling between pairs of colloids trapped in ionic liquids are demonstrated. Following these single and dual particle studies, this thesis continues with an investigation of the structures and dynamics of optically bound matter formed of larger numbers of particles. The behaviour of these optically bound structures is particularly sensitive to the number of particles involved, and so a counter-propagating evanescent field trap in conjunction with an inverted optical tweezers setup is utilised in order to controllably assemble these structures and study the factors affecting their behaviour. Initially one-dimensional chains of optically bound 3.5 um diameter silica particles are studied, allowing an implementation of Generalized Lorentz-Mie Theory (GLMT) to be developed through collaboration with Dr. Jonathan Taylor of The University of Glasgow. Experimental and theoretical insights allow further understanding of the processes involved in the formation of these structures. Having studied the behaviour of 3.5 um diameter silica particles in a counter-propagating evanescent wave trap, the effects of changing particle size and refractive index are presented by using smaller silica and melamine particles. These results are explained in terms of the increased importance of interference fringes in determining the arrangement of the optically bound structures of smaller particles, and due to the increased interaction of the melamine particles with the evanescent field as a result of the larger refractive index contrast between them and the trapping medium. The thesis then concludes with a study of the dynamics of the previously presented optically bound chains. Initially the diffusion of single particles in the evanescent field is compared to their freely-diffusing behaviour, quantifying the confining effect of the field. The addition of particles to the field then allows the diffusive behaviour to be studied as a function of particle number, and understood in terms of on-axis confinement by adjacent particles. The tilting of these optically bound chains relative to the inter-beam axis is also explored as a function of particle number, as is the rigidity of these chains. Finally a more complex, dynamic effect is presented, dubbed "Newton's Cradle", in which particles are ejected from the ends of the chains before returning and repeating this process. This behaviour is understood by utilising the previously developed GLMT simulations.

This thesis describes the design, construction, operation, and characterisation of an experimental apparatus that produces a source of internally cold, slow molecules that can be used for studying ion-molecule reactions at low temperatures. The apparatus combines buffer-gas cooling with a bent quadrupole velocity selector to cool both the translational and rotational degrees of freedom of the molecules. A cold cell (6 K) is filled with a buffer gas, such as helium, that exhibits sufficiently high vapour pressure for cryogenic applications. Hot molecules (150 to 300 K) enter the cell and thermalise with the buffer gas through collisions. Molecules are subsequently loaded into an electrostatic quadrupole guide, which acts as a velocity filter; only translationally cold polar molecules are guided around the bend. Using a buffer-gas-cooled source of molecules for electrostatic velocity selection, rather than a 300 K effusive source, yields a rotationally cold sample, with J ≤ 3. This rotational selectivity will enable the dependence of reaction cross sections on the reactant rotational state to be examined. Mass spectrometry is used to characterise cold molecular beams of ND3 and CH3F, while (2+1) REMPI spectra are recorded for the ammonia isotopologues. The peak velocity of guided ND3 is 75.86(0.70) ms-1 for standard conditions in a 6 K helium buffer gas cell (1.0 sccm ND3 flow rate, 0.6 mbar helium inlet pressure, ± 5 kV voltage). This corresponds to a peak kinetic energy of 6.92(0.13) K. (2+1) REMPI spectroscopy of the B1E''(v2'=5) ← X(1) transition enabled the rotational state distribution of guided ammonia molecules to be established. PGOPHER simulations of the experimental spectra suggest a rotational temperature of 10 K for ND3 molecules (from a 6 K helium buffer gas cell). The extent of translational and rotational cooling can be controlled by varying the molecular and buffer gas densities within the cell, by changing the temperature of the buffer gas cell (we can operate at 6 K or 17 K), or by changing the buffer gas. The translational temperature of guided ND3 is similar in a 6 K helium and 17 K neon buffer gas cell (peak kinetic energies of 6.92(0.13) K and 5.90(0.01) K, respectively) because the heavier neon gas has a slightly lower thermal velocity at 17 K than helium does at 6 K. Despite similar translational temperatures, the rotational temperature of guided ND3 is lower for molecules exiting the 6 K helium cell compared to the 17 K neon buffer gas cell (10 K and 15 K, respectively). The 6 K helium and 17 K neon buffer gas cells provide an excellent opportunity to investigate the effect of rotational cooling on branching ratios and reaction rates in low temperature ion-molecule reactions. The buffer gas cell and velocity guide described in this work will be combined with a linear Paul ion trap, to facilitate the study of cold ion-molecule reactions.

The dynamics of colloidal particles driven over optical potential energy landscapes is studied. Experiments are conducted using colloids driven by solvent flow or piezo-stage, optical tweezers, magnetic fields, and video-microscopy. Firstly, the properties of optical traps and potential energy landscapes are determined using driven colloidal particles and clusters. The trap stiffness and potential depth of single Gaussian traps are measured directly. It is shown that the nature of optical potential energy landscapes may be fully engineered and predicted using a sum of single Gaussian potentials. Next, the motion of colloidal particles driven by a constant force over a periodic optical potential energy landscape is considered. The average particle velocity is found as a function of the driving velocity, and the wavelength of the optical potential energy landscape, which is found to be sinusoidal at small trap spacings. The critical driving velocity required for a particle to move across the landscape is determined as a function of the wavelength. Brownian motion is found to have a significant effect on the critical driving velocity, but a negligible effect at high driving velocity. Subsequently, the dynamic mode locking caused by adding a modulation to the driving force is studied. This synchronisation manifests as a `Devil's staircase' in the average particle velocity as a function of driving velocity. The amplitude and frequency dependence of the mode locked steps are studied. Furthermore, particle trajectories are examined, and phase portraits show locked (unlocked) states as closed (open) loops in phase space. A state diagram of mode locked steps is constructed. Finally, driven systems of magnetically interacting colloidal particles are examined in potential energy landscapes. The critical driving velocity of a chain of coupled particles driven by a constant force is found to depend strongly on the chain length and the magnetic field. Secondly, a mobile density wave (kink) in an optically pinned chain of coupled particles is exposed to a constant and modulated drive. The kink is found to behave as a quasi-particle, exhibiting analogous dynamic mode locking behaviour to the single particle case. Finally, the mode locking of a finite mobile chain is considered, and found to be affected by the chain flexibility, which is a function of the magnetic field.

This thesis examines multiple different molecular networks adsorbed on several different substrates, namely, highly oriented pyrolytic graphite (HOPG), Au(111) and graphene. STM investigations into hydrogen-bonded structures formed by closely related tetracarboxylic acid molecules were performed. The molecule pterphenyl-3,5,3,5-tetracarboxylic acid (TPTC), which is known to form random tiling networks, was observed on a graphene on copper substrate. The network formed from deposition of TPTC from nonanoic acid was examined statistically. Aqueous solutions of TPTC were also examined on HOPG where a new structure, distinct from the random tiling, was observed. Aqueous solutions of related molecules biphenyl-3,3',5,5'-tetracarboxylic acid (BPTC) and quaterphenyl-3,3',5,5'-tetracarboxylic acid (QPTC), were also studied on HOPG. QPTC formed a similar structure to the aqueous solutions of TPTC, but BPTC formed two different phases, one of which was a kagome network. Addition of nonanoic acid to a dried network of TPTC deposited from aqueous solution resulted in solvent induced recrystallisation into a random tiling network comparable to that observed on graphene on copper, which was statistically analysed. Studies investigating the potential for covalent bonded molecular networks identified two distinct phases of the molecule 1,3,5-Tri(4-bromophenyl-benzene (TBPB)) adsorbed on Au(111). Concentration variation indicates an island based growth mechanism for these domains from solution. Dimerisation of TBPB was achieved by deposition onto heated substrates and a discussion of possible reasons for the reaction termination at dimers is provided. Attempts to repeat the TBPB experiments on graphene on copper failed due to excessive corrosion. Variations using larger molecules failed due to lack of solubility. Preliminary experiments on 10,10'-dibromo-9,9'-bianthryl (DBrBA) showed promise but were irreproducible, however micron scale dendritic structures were observed suggesting poor compatibility with the solvent. Finally, a discussion of the development of a nickel catalysis based graphene fabrication method is given and the limits of what is achievable with this method are discussed. The results from this thesis highlight the importance of solvent selection for the future understanding of molecular network fabrication. We also demonstrated the feasibility of covalently bonded networks prepared in ambient conditions.

The quantum motion of guest molecules has been studied in a variety of calixarene host-guest complexes, and in a endohedral fullerene complex. The guest molecules of the calixarene complexes studied each comprise weakly hindered methyl groups, which undergo rotation via quantum tunnelling, even at cryogenic temperatures. The rotational motion of the guest methyl-groups has been studied by making temperature and frequency-dependent measurements of proton T1, using field-cycling NMR, thus revealing the spectral density functions of the magnetic dipole-dipole interaction. Crystallographically inequivalent methyl-group environments have been identified and characterised in p-tert-butylcalix[4]arene(1:1)toluene, p-tert-butylcalix[4]arene(1:1)gamma-picoline and p-isopropylcalix[4]arene(2:1)p-xylene. In many of the calixarene complexes the proton spin-lattice relaxation has been observed to be strongly dependent on the thermal history of the sample. Temperature-dependent measurements of proton T1 in samples of p-tert-butylcalix[4]arene(1:1)toluene with partially deuterated guest molecules reveal a systematic reduction in T1 at low temperatures with increased degree of deuteration. Calixarene and fullerene host-guest complexes have been identified as having a potential application in cryogenic MAS-NMR as cryorelaxor complexes, capable of being attached to a large biomolecule and encouraging proton spin-lattice relaxation. The suitability of the calixarene complexes for use in this capacity has been investigated by measuring the temperature-dependence of proton T1 at low temperatures. The quantised rotational and translational motion of dihydrogen confined within an open-cage fullerene—namely, aza-thio-open-cage-fullerene (ATOCF)—has been revealed by inelastic neutron scattering (INS) measurements. The splitting of excited rotational and translational states, due to the low symmetry of the ellipsoidal fullerene cavity, has been directly measured. Assignment of the peaks observed in the INS spectrum has been aided by analysis of the Q-dependence of excitation bands. The thermodynamics of ortho- and parahydryogen have been investigated via temperature dependence measurements. INS measurements have allowed the anistropic rotational potential experienced by the H2 rotor to be determined.