This Thesis explores the role of structural defects and disorder and their relationship to experimental data, with a particular emphasis on molecular framework materials. The question of how we can build atomistic models of amorphous materials from experimental data without needing to make system-specific assumptions is addressed. The role of 'structural invariance', <i>i.e.</i> the limited range of distinct local atomic environments within a material, as a restraint within reverse Monte Carlo refinement (RMC) is investigated. The operation of these invariance restraints operate is shown to be system-dependent and the challenges associated with effective refinement, <i>e.g.</i> configurational 'jamming', are also investigated. A generalisation to the 'structural simplicity', <i>i.e.</i> the simplest model, holding all else constant, is most likely to be correct. Three new metrics of structural simplicity are proposed: two intrinsically three-dimensional measures of local geometric invariance and one measure of local symmetry. These metrics are shown to robustly quantify the configurational quality. The ability of these metrics to act as effective restraints for the RMC refinement of amorphous materials is demonstrated by the construction of the first data-driven tetrahedral models of amorphous silicon. The role of defects and disorder within metal–organic frameworks (MOFs) is investigated through the canonical MOF UiO-66(Hf). Through a combination of techniques, including X-ray diffuse scattering, anomalous diffraction, total scattering and electron diffraction measurements, the existence of correlated metal-cluster absences in UiO-66(Hf) is demonstrated. Furthermore the ability to synthetically tune both the interactions and concentration of defects is shown. The thermomechanical properties of defective UiO-66(Hf) are also examined. UiO-66(Hf) is shown to rapidly densify by up to 5% (ΔV/V ) on ligand elimination. The resultant densified phase exhibits colossal (≥100MK^-1) volumetric negative thermal expansion (NTE); the largest reported value for any MOF. Finally, the capability to tune the physical properties of MOFs through defect incorporation is demonstrated through the defect-dependence of both the densification and the NTE.

A percepção gestual de três licenciandos em situações de uso de representações estruturais químicas (REQ) foi caracterizada em uma disciplina do curso de licenciatura de Metodologia de Ensino de uma universidade pública. Esta percepção foi construída a partir da análise em entrevistas de Lembrança Estimulada por Vídeo (LEV), de uma enquete e da análise de situações de sala de aula de episódios de ensino. A LEV é uma técnica de origem cognitiva que foi adaptada para o estudo em uma abordagem sociocultural. A comparação de dados nesta pesquisa empregou a multimodalidade como modelo teórico e metodológico para caracterizar as interações multimodais em sala de aula. Na categorização de episódios de ensino, adaptamos algumas categorias de Silva (2008) como as operações epistêmicas, a proxêmica e os suportes. Na análise gestual, utilizamos a categorização de Kendon (2004). A percepção gestual foi construída com categorias inspiradas no funcionalismo de Lemke (2009). Contrastamos a análise de aula com a entrevista e a enquete para validar as respostas da entrevista. Os resultados da comparação entre a percepção dos licenciandos contribuíram para diferenciar como cada sujeito identifica sua performance gestual. / The gestural perception of three pre-service teachers has been characterized when using of chemical structural representations (CSR) from public university in a course of Chemistry Teaching. This perception has been constructed with analysis of Stimulated Recall Interviews (SRI), polls and classroom analysis of teaching episodes. SRI is a technique based on cognitive approach which has adapted to sociocultural perspective. We compared data using multimodality as a theoretical methodological model to characterize multimodal interactions at classroom. In categorization of teaching episodes, we adapted some categories from Silva (2008) like epistemic operations, proxemic and media. In gestural analysis, we used Kendon (2004) categories. The gestural perception has been constructed motivate by functionalist of Lemke (2009). We contrast classroom analysis with interviews and polls to increase the reliability of answers in interviews. Results of comparative between pre-service teacher perceptions is some differences how each subject index their gestural performance.

A percepção gestual de três licenciandos em situações de uso de representações estruturais químicas (REQ) foi caracterizada em uma disciplina do curso de licenciatura de Metodologia de Ensino de uma universidade pública. Esta percepção foi construída a partir da análise em entrevistas de Lembrança Estimulada por Vídeo (LEV), de uma enquete e da análise de situações de sala de aula de episódios de ensino. A LEV é uma técnica de origem cognitiva que foi adaptada para o estudo em uma abordagem sociocultural. A comparação de dados nesta pesquisa empregou a multimodalidade como modelo teórico e metodológico para caracterizar as interações multimodais em sala de aula. Na categorização de episódios de ensino, adaptamos algumas categorias de Silva (2008) como as operações epistêmicas, a proxêmica e os suportes. Na análise gestual, utilizamos a categorização de Kendon (2004). A percepção gestual foi construída com categorias inspiradas no funcionalismo de Lemke (2009). Contrastamos a análise de aula com a entrevista e a enquete para validar as respostas da entrevista. Os resultados da comparação entre a percepção dos licenciandos contribuíram para diferenciar como cada sujeito identifica sua performance gestual. / The gestural perception of three pre-service teachers has been characterized when using of chemical structural representations (CSR) from public university in a course of Chemistry Teaching. This perception has been constructed with analysis of Stimulated Recall Interviews (SRI), polls and classroom analysis of teaching episodes. SRI is a technique based on cognitive approach which has adapted to sociocultural perspective. We compared data using multimodality as a theoretical methodological model to characterize multimodal interactions at classroom. In categorization of teaching episodes, we adapted some categories from Silva (2008) like epistemic operations, proxemic and media. In gestural analysis, we used Kendon (2004) categories. The gestural perception has been constructed motivate by functionalist of Lemke (2009). We contrast classroom analysis with interviews and polls to increase the reliability of answers in interviews. Results of comparative between pre-service teacher perceptions is some differences how each subject index their gestural performance.

Crystal engineering offers a rational way of analyzing crystal structures and designing new structures with properties. The supramolecular synthon concept was introduced in 1995 and has shown versatility and utility in the design of molecular solids. Chapter 1 gives a general introduction about the development of the concept of supramolecular synthons over the years which has seen a transition from synthesis to structures and dynamics. This thesis focuses on the later phase of the development of the concept of supramolecular synthons. Chapter 2 introduces the idea of structural landscape and describes a structural landscape of a conformationally flexible molecule, orcinol, and explores the synthon preferences of this particular molecule towards cocrystal formation. Chapter 3 explores a combinatorial matrix to show both global and local features of a structural landscape. Chapter 4 takes a component of this landscape namely 4,4'-bipyridine and 4-hydroxybenzoic acid and shows the occurrence of synthon polymorphism in cocrystals which originates from the interplay of geometrical and chemical factors. Chapter 5 introduces a four step method for the identification of multiple synthons by FTIR spectroscopy. Along with, it shows that the rarity of synthon polymorphism is not a case of overlooking of crystals in the process of selecting good looking crystals. Chapter 6 takes a series of dihalogenated phenols and indicates that the Br prefers type II. This chapter also explains elastic bending on the basis of halogen bonds. Chapter 7 attempts to explore the Cl/Br isostructurality in the light of type I and type II contacts and concludes that Cl/Br isostructurality arises from a geometrical model and therefore it is quite similar to Cl/Me isostructurality. Chapter 8 attempts to analyze the class of trichlorophenols and reveals structural modularity in this class of compounds. The modularity of 3,4,5-trichlorophenol is explored in crystal design in chapter 9 in terms of LSAM (Long Range Synthon Aufbau Module) A subsequent study in solution by NMR reveals the presence of LSAM in solution and establishes a hierarchy of the dissociation of its components. The concept of supramolecular synthon has come a long way from being a tool in a crystal engineer’s toolbox to a structural unit responsible for crystallization and therefore offer multiple possibilities both in terms of structures and dynamics. This thesis attempts to explore some of these possibilities based mainly on the concepts of structural landscape and halogen bonds which are blended with the concept of supramolecular synthons.

Crystal engineering underlies the essence of natural affiliation between the molecule on the one side and the crystal as a supramolecular assembly on the other. Molecular recognition is the fundamental cause for this efficient transformation and if we consider the crystal as a supramolecular entity then it is not at all difficult to conceive crystallization as an outstanding example of molecular recognition. In general, organic compounds often facilitate closed packed crystal structures as described by A. I. Kitaigorodskii in the form of the close packing principle but based on chemical features, there is still a small window to understand, to rationalize and to fashion new crystal structures. Extending the chemical viewpoint as first proposed by J. M. Robertson, the supramolecular synthon model as a descriptor of collective crystal structures has been invoked that enables one to trail the molecular behaviour from an entropy dominated situation in solution to an enthalpy driven progression in the solid state. After 20 years, the concept of the supramolecular synthon has stood the test of time because of its simplicity and effectiveness towards the implementation in complex crystal structures and has led the scientific community to further handle complex and interesting ideas in structural chemistry and supramolecular synthesis. The complexity of dynamic and progressive behavior of molecules during crystallization may be understood by the analogous argument of protein folding; both these complex phenomena decode the emergence of multiple metastable forms before the final structures are attained. These intermediate kinetically driven species may be high energy polymorphs and pseudopolymorphs of the compound in question or semicompact random globules for proteins. Understanding the role of these species in their respective processes is of critical importance in elucidating mechanisms. As an alternative approach, crystal structure prediction (CSP) is also of fundamental importance in the context of understanding the crystallization process. All energy based computational methods of CSP address this problem by scanning the multi-dimensional energy hypersurface. This is performed by computing lattice energy changes with respect to parameters like unit cell dimensions, space group symmetry and the positional coordinates of atoms in the asymmetric unit. Further, the computational prediction of the crystal structure of an organic compound results in several choices, and it is possible that a collection of some of these when taken together forms a pattern that mimics the course of the crystallization process very much in the manner that structure correlation mimics covalent bond breaking and making. With all these developments, one is truly at the stage today when any experimental or computed crystal structure is just that, a crystal structure of the molecule in question and it is part of a complex and dynamic structural space which may include a part of the supramolecular reaction trajectory for crystallization itself. Accordingly, this thesis emphasizes the importance of kinetic events during crystallization and proposes some strategies to access the inaccessible domains of this structural space of a given compound. I have exploited the supramolecular synthon model to understand the kinetics of the crystallization process and have further extended this understanding towards the isolation of stoichiometric ternary solids. The synthon model also helps one to provide a logical step to explore these remote domains of the complex hyperenergy surface that have collectively been termed as the crystal structure landscape of the compound in question. The precise descriptions of the chapters are mentioned below. Chapter 2 describes fluorosubstitution as a unique chemical probe to explore the high energy crystal structures of benzoic acid in ambient conditions. This landscape exploration of benzoic acid is based on the robust (kinetically favoured) supramolecular homosynthon as well as consistent fluorosubstitution in native compound. This analysis is also supported by synthon based crystal structure prediction which is one of the best ways of monitoring high energy virtual crystal structures. Chapter 3 extends the idea of landscape exploration towards multicomponent systems. The incorporation of an additional compound during crystallization facilitates even complex kinetic environments but using fluorosubstitution as a chemical probe, it again helps to analyse the high energy virtual domains of the given multicomponent system. Similar to chapter 2, the landscape exploration of multicomponent system is also based on the robust (kinetically favoured) supramolecular heterosynthon as well as consistent fluorosubstitution in the native multicomponent system. Chapter 4 emphasizes the importance of synthon modularity as a chemical probe to traverse in the crystal structure landscape of the given multicomponent system. Here, I have quantified the role of the definitive synthon, by using the supramolecular synthon based fragment approach (SBFA), in the emergence of polymorphism in cocrystals. In latter part of this chapter, I utilized this collective kinetic information in order to realize the combinatorial nature of the crystallization process and showed the complex combinatorial synthesis of ternary solids which itself is considered to be an arduous exercise. Chapter 5 discusses the importance of kinetic information which were fetched from the corresponding multicomponent landscapes and were further utilized for combinatorial synthesis of ternary solids. Although the combinatorial idea is well established in solution, this chapter highlights the first experimental evidence of this idea in the solid state and shows preferred amplification of certain supramolecular synthons from corresponding libraries in the supersaturated crystallizing medium. Chapter 6 extends the combinatorial idea of crystallization even further by using highly flexible organic compounds that collectively provide larger structural space during crystallization. Using the delicate kinetic information about the molecular and supramolecular features, this chapter describes the preferential selection of molecular conformation and supramolecular synthons from the supersaturated solution during the molecule→crystal pathway. In summary, the idea of the crystal structure landscape provides an extended interpretation about some of the complex ideas namely, crystal energy landscape and polymorphism in modern crystal engineering. The crystallization of an organic compound often depends upon intrinsic chemical features and accordingly one selects optimized crystallization routes in the corresponding landscape through decisive experimental conditions. As a final note, the idea of the crystal structure landscape enables one to (at least qualitatively) understand the importance of crystallization kinetics which is understandably a difficult task.

Materials chemistry basically deals with rational design and synthesis of new solids exhibiting various functional properties. A sound knowledge of crystal structures and chemical bonding is needed to understand the properties of materials. Space group, cell parameters and atomic positions provide a basic crystallographic description of the structure. Crystal structure could be described in a detailed way in terms of close packing of anions and occupancy of cations in different coordination sites. The coordination polyhedra and their interconnectivity bring out the interrelationships between different structures and the properties exhibited. Transition metals (TMs) are d-block elements which occupy groups 3-12 in Periodic Table. IUPAC defines a TM as ‘an element whose atoms have partially filled d-shell, or which can give rise to cations with an incomplete d-shell’. The partially filled d-shell in TMs plays an important role in various chemical and physical properties of TMs. Although TM cations can form compounds with different anions, most of the TM containing compounds are metal oxides due to the large free energies for formation of oxides. Binary TM oxides adopt different kinds of structures among which rock salt (e.g. NiO), rutile (e.g. TiO2), and corundum (e.g. Cr2O3) are most common. Ternary TM oxides are also known to form in variety of structures with the perovskite (e.g. BaTiO3), and the spinel (e.g. MgFe2O4) structures being well known. TM oxides exhibit a broad range of electronic and magnetic properties. TM oxides, at one end, display metallic behavior (e.g. ReO3, RuO2, LaNiO3) due to the delocalized electrons and at other end, show insulating behavior (e.g. NiO) due to the localized electrons. In between, TM oxides have semiconducting properties involving either the hopping of carriers (e.g. partially reduced TiO2, Nb2O5, WO3 and so on) or the electron excitation from the valence band to the conduction band (e.g. SnO2). TM oxides are known to have diverse magnetic properties: diamagnetic (e.g. TiO2, ZrO2), paramagnetic (e.g. VO2, NbO2), ferromagnetic (e.g. CrO2, La0.67Ca0.33MnO3), ferrimagnetic (e.g. Fe3O4, MnFe2O4) and antiferromagnetic (e.g. NiO, LaCrO3). TM oxides with partially filled 3d-shell are expected to be ‘metallic’ according to Bloch-Wilson theory, but in practice they are Mott insulators (localized 3d electrons) because of correlation energy (U) involved in the transfer of d-electrons between adjacent sites. Certain TM oxides also show insulator-metal (I-M) transitions induced by change of temperature, pressure or composition. For example, VO2 and Ba2IrO4 are known for their temperature and pressure induced I-M transitions, respectively. La1-xSrxCoO3 becomes metal at a particular Sr concentration being one of the examples for composition-dependent I-M transition. TM oxides are usually synthesized by conventional ceramic method in which stoichiometric mixture of starting materials is reacted at elevated temperatures. Multiple prolonged heating with intermittent grindings in ceramic method generally results in thermodynamically controlled products. The metastable phases which are of interest may not be obtained by ceramic method. Chimie douce/soft chemistry methods are generally adopted to stabilize the metastable phases. The guiding principle behind the chimie douce is to have kinetic control (rather than thermodynamic control) to realize metastable phases. Accordingly, metastable derivatives are obtained by choosing appropriate precursors, or adopting sol-gel and molten flux or ion exchange/intercalation methods. The present thesis is devoted to an investigation of transition metal oxides towards development of functional materials exhibiting visible light absorption/emission and lithium insertion/extraction for cathode materials in lithium ion battery. TM oxides find application as photovoltaic materials, luminescent emission materials, photocatalysts, light absorption/pigment materials and so on, based on their optical properties. Ferroelectric TM oxides with perovskite structure [Green coloured (KNbO3)1-x (BaNi1/2Nb1/2O3-δ)x] are studied currently as photovoltaic materials which show high open circuit voltage (Voc = 3.5 V) despite very low short circuit current (Vsc = 40 nA cm-2). TM oxides are also known to exhibit photoluminescent emission which could be due to the doping activator ions (e.g. MnII doped Zn2GeO4) or TM oxide (e.g. CaWO4) itself being self-activator. While the green and red emissions are common for TM oxides, blue emission is rare (e.g. Ar+ irradiated SrTiO3 is a blue emitter). Coloured TM oxides with band gap in visible region are employed as photocatalysts for solar water splitting (e.g. yellow BiVO4, yellow Ag3PO4, yellow TaON, red Fe2O3) and photo-oxidation of organic pollutants (e.g. TiO2-xNx and CaCu3Ti4O12). The coloured TM oxides also find application as pigments from early times, for example, Egyptian blue (CaCuSi4O10), Han blue (BaCuSi4O10), Han purple (BaCuSi2O6), Malachite green (Cu2CO3(OH)2), Ochre red (Fe2O3) and many others. A list of pigments based on TM oxides is given in Table 1. Pigment materials are applied as colouring materials in inks, dyes, paints, plastics, ceramics glazers, enamels and textiles. Table 1. List of TM oxide based pigments and their colours Pigment colour Compound White Titanium dioxide (TiO2) Black Iron oxide black (Fe3O4) Red Iron oxide red (Fe2O3), Ca1-xLaxTaO2-xN1+x (yellow-red) Orange Iron oxide orange (Fe2O3) Yellow Yellow ochre [FeO(OH)·H2O] Green Malachite green [Cu2CO3(OH)2], Viridian (Cr2O3. 2H2O), Y2BaCuO5 Blue Egyptian blue (CaCuSi4O10),Cobalt aluminate (CoAl2O4), YIn1-xMnxO3 Purple Han purple (BaCuSi2O6) Violet Cobalt phosphate [Co3(PO4)2] Colours of the TM oxides arise from visible light absorption due to the ligand field d-d electronic transitions. Though d-d transitions are parity forbidden, the selection rules get relaxed due to different reasons such as symmetry reduction (due to distortion) and vibronic couplings. The colour of the TM oxides is influenced mainly by two factors (i) oxidation state of TM ion present and (ii) ligand field around the TM ion produced by anion geometry. In order to develop new pigment oxides, our strategy was to choose colourless metal oxides having unusual (five coordinated geometry) or irregular/distorted (distorted octahedral/tetrahedral) coordination geometries around metal ion and produce coloured oxides by substituting 3d-TM ions at the metal ion site. We made a detailed study on the origin of the colour and pigment quality of the resulting coloured oxides. In the present thesis, which has two parts, the first part (Part 1) discusses the development of 3d-TM ion substituted coloured oxides with potential for pigment applications. Chapter 1.1 describes the purple inorganic pigment, YGa1-xMnxO3 (0 < x ≤ 0.10), based on the hexagonal YGaO3. The metastable series of oxides were prepared by a sol-gel technique where the dried gels, obtained from aqueous solutions of metal nitrates-citric acid mixtures, were calcined for a short duration in preheated furnace around 850°C/10 mins. The purple colour of the oxides arises from the specific trigonal bipyramidal ligand field around MnIII that obtains in the YGaO3 host. Other hexagonal RGaO3 hosts for R = Lu, Tm and Ho substituted with MnIII also produce similar purple coloured materials. In Chapter 1.2, we present a study on substitution of 3d-TM ions in LiMgBO3 host [where Mg(II) has a trigonal bipyramidal (TBP) oxygen coordination)]. We find that single-phase materials are formed for LiMg1-xCo(II)xBO3 (0 < x ≤ 1.0), LiMg1-xNi(II)xBO3 (0 < x ≤ 0.1), LiMg1-xCu(II)xBO3 (0 < x ≤ 0.1) and also Li1-xMg1-xFe(III)xBO3 (0 < x ≤ 0.1) of which the Co(II) and Ni(II) derivatives are strongly coloured, purple-blue and beige-red respectively, thus identifying TBP CoO5 and NiO5 as the new chromophores for these colours. Chapter 1.3 describes the synthesis, crystal structures and optical absorption spectra/colours of 3d-TM substituted α-LiZnBO3 derivatives: α-LiZn1-xMIIxBO3 [MII = CoII (0 < x < 0.50), NiII (0 < x ≤ 0.05) and CuII (0 < x 0.10)] and α-Li1+xZn1-2xMIIIxBO3 [MIII = MnIII (0 < x ≤ 0.10) and FeIII (0 < x 0.25)]. The crystal structure of the host α-LiZnBO3, which is both disordered and distorted with respect to Li and Zn occupancies and coordination geometries, is largely retained in the derivatives, giving rise to unique colours [blue for CoII, magenta for NiII and violet for CuII], that could be of significance for the development of new, inexpensive and environmentally-benevolent pigment materials, especially for the blue colour. Accordingly, the work indentifies distorted tetrahedral MO4 (M = Co, Ni, Cu) (together with a long M-O bond that gives a trigonal bipyramidal geometry) structural units as the new chromophores for the blue, magenta and violet colours respectively, in the α-LiZnBO3 host. In Chapter 1.4, we describe the synthesis, crystal structures and optical absorption spectra of 3d-TM substituted spiroffite derivatives, Zn2-xMxTe3O8 (MII = Co, Ni, Cu; 0 < x ≤ 1.0). The oxides are readily synthesized by solid state reaction of stoichiometric mixtures of the constituent binaries at 620°C/12h. Rietveld refinement of the crystal structures from powder XRD data shows that the Zn/MO6 octahedra are strongly distorted, as in the parent Zn2Te3O8 structure, consisting of five relatively short Zn/MII – O bonds (1.898 – 2.236 Å) and one longer Zn/MII– O bond (2.356 – 2.519 Å). We have interpreted the unique colors and the optical absorption/diffuse reflectance spectra of Zn2-xMxTe3O8 in the visible, in terms of the observed/irregular coordination geometry of the Zn/MII – O chromophores. We could not however prepare the fully-substituted M2Te3O8 (MII = Co, Ni, Cu) by the direct solid state reaction method. Density Functional Theory (DFT) modeling of the electronic structure of both the parent and the transition metal substituted derivatives provides new insights into the bonding and the role of transition metals toward the origin of color in these materials. We believe that transition metal substituted spiroffites Zn2-xMxTe3O8 reported here suggest new directions for the development of colored inorganic materials/pigments featuring irregular/distorted oxygen coordination polyhedra around transition metal ions. Red coloured materials are rare in nature. Li2MnO3 is a unique oxide with an unusual red colour imparted by MnIV ions. Chapter 1.5 describes a detailed experimental investigation of Li2MnO3 together with other related MnIV oxides that probes the red colour of Li2MnO3 as well as its photoluminescence. Optical absorption spectra reveal a strong band gap absorption with a sharp edge at ~ 610 nm and a transparent region between ~ 610 and ~ 650 nm that causes the red colour of Li2MnO3 samples. Octahedral MnIV ligand field transitions, corresponding to both MnIV at ideal sites and MnIV displaced to Li sites in the rock salt based layered structure of Li2MnO3, are observed in the excitation spectra of Li2MnO3 samples. Optical excitation at the ligand field transition energies produces tunable emission in the red-yellow-green region, rendering Li2MnO3 a unique MnIV oxide. The honeycomb ordered [LiMn6] units in the structure likely causes both the absorption and photoluminescence properties of Li2MnO3. Lithium containing TM oxides with rock salt related structure are being investigated extensively for application as next generation cathode materials for Lithium ion batteries (LIBs). Recent research is focused on lithium-rich layered oxides (LLOs) which are solid solutions between Li2MO3 (where M = Ti, Mn and Ru) and LiMO2 (where M = Cr, Mn, Fe, Co, Ni). LLOs have excess lithium in the TM layer in addition to lithium in lithium layer of rock salt derived structure. LLOs have gained attention because of their higher discharge capacity in the range of ~ 250 mAhg-1. While most of the LLOs investigated so far contain 3d-TM ions (Mn, Fe, Co, Ni), recently there has been an interest in the study of the role of ruthenium in addition to 3d-TM ions. We have investigated ruthenium containing LLOs with a view to probe (i) the role of ruthenium and (ii) the concentration of excess lithium in the TM layers in producing higher discharge capacities. The results are discussed in the Part 2 of the thesis.Li5NiMnRuO8(Li[Li0.25Ni0.25Mn0.25Ru0.25]O2) form in the Li2RuO3 crystal structure. Electrochemical studies indicate that the Co-containing oxides exhibit a higher initial discharge capacity (for e.g. ~ 180 mAhg-1 for Li4CoRuO6) as well as a higher reversible discharge capacity (~130 mAhg-1 for Li4CoRuO6) compared to the corresponding Ni-analogs. Participation of oxide ions (higher oxidation state of Ru) in the redox process could explain the higher discharge capacity during the first cycle. Reduced capacity (capacity fade) during the subsequent cycles could arise from the oxygen evolution due to the redox process (2O2- → 2O- → O2), which is not reversible. The present work shows that ruthenium incorporation in rock salt layered oxides along with Co/Ni appears to give a beneficial effect in producing a higher discharge capacity. In addition, the compounds crystallizing with the R-3m structure (related to LiCoO2) appear to give a better reversible capacity than the compounds crystallizing in the C2/c structures (Li2TiO3 and Li2RuO3).

This thesis describes the synthesis and characterisation of metal complexes that contain chemically reduced bipyridyl ligands. The crystal structures of twenty-six novel complexes are reported alongside detailed discussions on the electronic and spectroscopic effects and trends associated with the different oxidation states within these species. Chapter One introduces the isomers of bipyridine and their redox chemistry, the concept of non-innocent ligands and the spectroscopic techniques that are currently used in determining ligand oxidation states. Subsequently, examples of main group, transition metal, lanthanide and actinide species that contain or may contain reduced forms of the ligand are discussed. Chapter Two details the synthesis and structural characterisation of alkali metal salts of singly and doubly reduced forms of the three commercially available bipyridine isomers. The effects of this reduction are investigated with the aim of developing diagnostic fingerprints for each of the ligand oxidation states. Chapter Three discusses the synthesis of an homologous series of compounds of the form [M(2,2'-bipy)(mes)₂]^n– where M = Cr, Mn, Fe, Co, Ni and n = 0, 1. Trends in magnetism, bonding and electronic structure are investigated with reference to theoretical calculations and the diagnostic fingerprints identified in the previous chapter. Chapter Four describes the synthesis and characterisation of three compounds containing the isostructural motif [Zn₂(4,4'-bipy)(mes)₄]^n– where n = 0, 1, 2. Structural and spectroscopic changes are discussed and com- pared to theoretical calculations. Chapter Five contains descriptions of the spectroscopic techniques employed in the above research and synthesis routes to all compounds featured in this thesis.

Few experimental techniques have found such a diverse range of applications as has ion imaging. The field of chemical dynamics is constantly advancing, and new applications of ion imaging are being realised with increasing frequency. This thesis is concerned with the application of a fast pixelated imaging sensor, the Pixel Imaging Mass Spectrometry (PImMS) camera, to ion imaging applications. The experimental possibilities of such a marriage are exceptionally broad in scope, and this thesis is concerned with the development of a selection of velocity-map imaging applications within the field of photoinduced molecular dynamics. The capabilities of the PImMS camera in three-dimensional and slice imaging applications are investigated, in which the product fragment Newton-sphere is temporally stretched along the time-of-flight axis, and time-resolved slices through the product fragment distribution are acquired. Through experimental results following the photodissociation of ethyl iodide (CH₃CH₂I) at around 230 nm, the PImMS camera is demonstrated to be capable of recording well-resolved time slices through the product fragment Newton-sphere in a single experiment, without the requirement to time-gate the acquisition. The various multi-hit capabilities of the device represent a unique and significant advantage over alternative technologies. The details of a new experiment that allows the simultaneous imaging of both photoelectrons and photoions on a single detector for each experimental acquisition cycle using pulsed ion extraction are presented. It is demonstrated that it is possible to maintain a high velocity resolution using this approach through the simultaneous imaging of the photoelectrons and photoions that result from the (3 + 2) resonantly enhanced multi-photon ionisation of Br atoms produced following the photodissociation of Br₂ at 446.41 nm. Pulsed ion extraction represents a substantial simplification in experimental design over conventional photoelectron-photoion coincidence (PEPICO) imaging spectrometers and is an important step towards performing coincidence experiments using a conventional ion imaging apparatus coupled with a fast imaging detector. The performance of the PImMS camera in this application is investigated, and a new method for the determination of the photofragment detection efficiencies based on a statistical fitting of the coincident photoelectron and photoion data is presented. The PImMS camera is applied to laser-induced Coulomb explosion imaging (CEI) of an axially chiral substituted biphenyl molecule. The multi-hit capabilities of the device allow the concurrent detection of individual 2D momentum images of all ionic fragments resulting from the Coulomb explosion of multiple molecules in each acquisition cycle. Correlations between the recoil directions of the fragment ions are determined through a covariance analysis. In combination with the ability to align the molecules in space prior to the Coulomb explosion event, the experimental results demonstrate that it is possible to extract extensive information pertaining to the parent molecular structure and fragmentation dynamics following strong field ionisation. Preliminary simulations of the Coulomb explosion dynamics suggest that such an approach may hold promise for determining elements of molecular structure on a femtosecond timescale, bringing the concept of the `molecular movie' closer to realisation. Finally, the PImMS camera is applied to the imaging of laser-induced torsional motion of axially chiral biphenyl molecules through femtosecond Coulomb explosion imaging. The target molecules are initially aligned in space using a nanosecond laser pulse, and torsional motion induced using a femtosecond 'kick' pulse. Instantaneous measurements of the dihedral angle of the molecules are inferred from the correlated F+ and Br+ ion trajectories following photoinitiated Coulomb explosion at various time delays after the initial kick pulse. The technique is extended to include a second kick pulse, in order to achieve either an increase in the amplitude of the oscillations or to damp the motion, representing a substantial degree of control of the system. Measurements out to long kick-probe delays (200 ps) reveal that the initially prepared torsional wave packet periodically dephases and rephases, in accordance with the predictions of recent theoretical work.

The development of interatomic potentials for magnetic transition metals, and particularly for iron, is difficult, yet it is also necessary for large-scale atomistic simulations of industrially important iron and steel alloys. The magnetism of iron is especially important as it is responsible for many of the element's unique physical properties -- its bcc ground state structure, its high-temperature phase transitions, and the mobility of its self-interstitial atom (SIA) defects. Yet an accurate description of itinerant magnetism within a real-space formalism is particularly challenging and existing interatomic potentials based on the Embedded Atom Method are suited only for studies of near-equilibrium ferritic iron, due to their restricted functional forms. For this work, the magnetic analytic Bond-Order Potential (BOP) method has been implemented in full to test the convergence properties in both collinear and non-collinear magnetic iron. The known problems with negative densities of states (DOS) are addressed by assessing various possible definitions for the bandwidth and by including the damping factors adapted from the Kernel Polynomial Method. A 9-moment approximation is found to be sufficient to reproduce the major structural energy differences observed in Density Functional Theory (DFT) and Tight Binding (TB) reference calculations, as well as the volume dependence of the atomic magnetic moments. The Bain path connecting bcc and fcc structures and the formation energy of mono- and divacancies are also described well at this level of approximation. Other quantities such as the high-spin/low-spin transition in fcc iron, the bcc elastic constants and the SIA formation energies converge more slowly towards the TB reference data. The theory of non-collinear magnetism within analytic BOP is extended as required for a practical implementation. The spin-rotational behaviour of the energy is shown to converge more slowly than the collinear bulk energy differences, and there are specific problems at low angles of rotation where the magnitude of the magnetic moment depends sensitively on the detailed structure of the local DOS. Issues of charge transfer in relation to magnetic defects are discussed, as well as inadequacies in the underlying d-electron TB model.

Careful treatment of water molecules in ligand-protein interactions is required in many cases if the correct binding pose is to be identified for molecular docking. Water can form complex bridging networks and can play a critical role in dictating the binding mode of ligands. A particularly striking example of this can be found in the ionotropic glutamate receptors (iGluRs), a family of ligand gated ion channels that are responsible for a majority of the fast synaptic neurotransmission in the central nervous system that are thought to be essential in memory and learning. Thus, pharmacological intervention at these neuronal receptors is a valuable therapeutic strategy. This thesis relies on various computational studies and X-ray crystallography to investigate the role of ligand-water mediated interactions in iGluRs bound to glutamate and α-amino-3-hydroxy-5-methyl-4- isoxazole-propionic acid (AMPA). Comparative molecular dynamics (MD) simulations of each subtype of iGluRs bound to glutamate revealed that crystal water positions were reproduced and that all but one water molecule, W5, in the binding site can be rearranged or replaced with water molecules from the bulk. Further density functional theory calculations (DFT) have been used to confirm the MD results and characterize the energetics of W5 and another water molecule implicated in influencing the dynamics of a proposed switch in these receptors. Additional comparative studies on the AMPA subtypes of iGluRs show that each step of the calculation must be considered carefully if the results are to be meaningful. Crystal structures of two ligands, glutamate and AMPA revealed two distinct modes of binding when bound to an AMPA subtype of iGluRs, GluA2. The difference is related to the position of water molecules within the binding pocket. DFT calculations investigated the interaction energies and polarisation effects resulting in a prediction of the correct binding mode for glutamate. For AMPA alternative modes of binding have similar interaction energies as a result of a higher internal energy than glutamate. A combined MD and X-ray crystallographic study investigated the binding of the ligand AMPA in the AMPA receptor subtypes. Analysis of the binding pocket show that AMPA is not preserved in the crystal bound mode and can instead adopt an alternative mode of binding. This involves a displacement of a key water molecule followed by AMPA adopting the pose seen by glutamate. Thus, this thesis makes use of various studies to assess the energetics and dynamics of water molecules in iGluRs. The resulting data provides additional information on the importance of water molecules in mediating ligand interactions as well as identifying key water molecules that can be useful in the de novo design of new selective drugs against iGluRs.