X-ray diffraction techniques have been used to examine the structural chemistry of three compounds of Group II metals. The crystal structures of all three compounds were solved by the heavy atom method and refined, with three dimensional data, by the method of least squares.

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This thesis focuses on materials whose properties are directly linked with the dimensionality of their structures. We utilise diffraction techniques to characterise three systems. The first of these is an organic crystal, 2,3,6,7,10,11-hexahydroxytriphenylene tetrahydrate that contains one-dimensional water channels. These channels are polar and net polarity is achieved at low temperatures. The structure undergoes a phase transition to a non-polar state at higher temperatures. Mapping this finding onto an Ising model is undertaken in this thesis. We also investigate the possibility of transforming the same crystals to an organic metal with oxidation. Furthermore, this work characterises two-dimensional layered structures silver(I) tricyanomethanide and nickel(II) cyanide. We show that the former possesses the unprecedented property of negative area compressibility and the latter shows ordinary compressibility behaviour. Both these structures exhibit area negative thermal expansion. Finally, we investigate copper(II) and cobalt(II) doping into the structure of nickel(II) cyanide and demonstrate that the latter leads to a 10-fold increase in area negative thermal expansion.

O estudo termoquímico de adutos de quelatos de acetilacetonatos com bases heterocíclicas, realizado pelo Prof. Dr. P. O. Dunstan do IQ da Unicamp, mostrou as seguinte ordem de basicidade: morfolina > piperidina> γ-picolina > piridina> quinolina> β-picolina> 4-cianopiridina> 3-cianopiridina. No caso da 3-cianopiridina e da 4-cianopiridina a ordem esperada era a inversa da obtida, entretanto no caso da piridina, quinolina, morfolina e γ-picolina a ordem obtida foi a esperada. A inversão no caso da 3 e 4-cianopiridina foi atribuída a existência de ligações de hidrogênio, que não deveriam estar presentes nas outras estruturas. Para comprovar isto foi tentada a cristalização de todos os compostos, mas somente foram obtidos cristais adequados de seis compostos e sua estrutura tridimensional determinada por difração de raios-X. Em todas as estruturas foi encontrado que o átomo de níquel está situado num centro de simetria, exceto no caso da γ-picolina no qual está numa posição de simetria m2m. O Ni(II) se encontra em todas as estruturas octaedricamente ligado a dois ânions acetilacetonato (AcAc) equatoriais e a dois ligantes em uma configuração trans. As distâncias Ni-OAcAc mostram que o poliedro de coordenação apresenta diferentes graus da chamada distorção tetragonal. Os estudos cristalográficos mostram a existência de ligações de hidrogênio em todos os compostos. Os tipos de ligações de hidrogênio encontradas são do tipo C-H...N, C-H...O e C-H...π. Mais ainda, no caso da 3 e 4-cianopiridina elas apresentam um conjunto de ligações de hidrogênio muito similares. / The thermochemical studies of adducts of Ni(II) acetylacetonate chelate with heterocyclic bases, accomplished by Prof. Dr. P. O. Dunstan of IQ-UNICAMP, showed the following basicity order: morpholine> piperidine> γ-picoline> pyridine> quinoline> &#946-picoline> 4-cyanopyridine> 3-cyanopyridine. In the case of 3-cianopyridine and 4-cianopyridine the expected order was the inverse of the one obtained, and in the case of the pyridine, quinoline, morpholine and γ-picoline the order was the expected one. The inversion in the case of 3 and 4-cyanopyridine was postulated to be due to the existence of hydrogen bonds, that should not be present in the other structures. To check this hypothesis it was tried the recrystalization of all the compounds, but only suitable crystals of six of them, namely 3 and 4-cyanopyridine, pyridine, quinoline, morpholine and γ-picoline, were obtained and their three-dimensional structure determined by X-ray diffraction. In the structures the nickel atom is sited on a center of symmetry, except in the case of the γ-picoline in which it is in a position of symmetry m2m. In all the structures the Ni(II) is octahedrically bonded to two equatorial acetylacetonate (AcAc) groups and two ligands that are in a trans configuration. The Ni-OAcAc distances show that the coordination polyhedra present different degrees of the so called tetragonal distortion. The cristallographics studies show the existence of hydrogen bonds in all the compounds. The types of hydrogen bonds found are: C-H...N, C-H...O and C-H...π. Moreover, in the case of 3 and 4-cyanopyridine these compounds present a similar pattern of hydrogen bonds.

Framework materials that contain molecular bridging ligands between metal nodes—as seen in coordination polymers—not only give rise to enhanced structural diversity, but also to a range of useful and unusual mechanical properties. This thesis demonstrates the general structure–property relationships that are developed for coordination polymers in order to enable prediction and design of their mechanical properties, and hence structural flexibility. Variable-temperature and -pressure diffraction experiments are employed for the determination of their mechanical properties, namely by calculating thermal expansion and compressibility coefficients. The anomalous and varied mechanical responses observed are rationalised by the important structural features, or the so-called mechanical building units (XBUs), of the coordination polymers. The XBUs are considered within the setting of framework topology, geometry, and composition in order to establish general design principles for targeting different degrees of flexibility within coordination polymers. The XBUs are identified first in silver(I) 2-methylimidazolate, Ag(mim), a framework which is comprised of structural motifs of varying strength, namely argentophilic interactions, hinge points and metal–ligand bonding. The anomalous mechanical responses in Ag(mim) are shown to be rationalised entirely by the XBUs present in the structure. The XBU abstraction is then applied to a range of other coordination polymers and shown to correspond directly with the anomalous responses known in these materials. The metal–ligand–metal linker XBU is investigated further in both cadmium imidazolate, Cd(im)₂, and zinc cyanide, Zn(CN)₂. Here, the linker chemistries are completely different between the two frameworks, but the diamondoid arrangement of the linkers, and thus the topology, is the same. The structural responses of the two frameworks are examined to unravel the extent of topology- and chemistry-driven mechanics. It is found that the topology dominates the atomic displacements of both frameworks, indicating the existence of common soft-mode dynamics which are likely to extend to other coordination polymers with the same topology. The three-dimensional framework-hinging XBUs in zinc isonicotinate, Zn(ISN)₂, and indium deuterium terephthalate, InD(BDC)₂, are considered next. These frameworks have the same topology but contrasting framework geometries, evident from the differing c/a-lattice parameter ratios. In this case, a geometric formalism is derived which can predict the direction of framework mechanical anisotropy in Zn(ISN)₂ and InD(BDC)₂ and other uniaxial coordination polymers. Finally, a family of ABX₃-type transition metal(II) formates are investigated, where both the B-site and A-site cations are varied. The chemical modifications give rise to variations in B- or A-site cation sizes, which are found to correlate with the magnitude of mechanical responses. These structure–mechanical property relationships—based upon framework topology, geometry and composition—are presented in separate chapters, and in each case generalised so that they can be applied to a range of coordination polymers. Hence the design principles determined here can provide the materials science community with an intuition on the type and magnitude of responses possible in these materials under different external stimuli.

It is increasingly being realised that localised deviations from the average structure can play an important role in a material's properties, and hence an understanding of these deviations is essential when constructing a coherent picture of a system. In this thesis, both neutron and X-ray total scattering data have been collected and used to reveal information on three canonical systems: the high-temperature superconductor YBa₂Cu₃O_7-x; the parent compound of the colossal magnetoresistive manganites, LaMnO₃; and the oldest known magnetic material, Fe₃O₄. Reverse Monte Carlo refinements-using the RMCProfile implementation of the algorithm-have been used as the principal analysis technique, and the functionality of the RMCProfile program has been extended to allow the refinement of magnetic systems involving substitutional disorder. For YBa₂Cu₃O_7-x, the focus of this thesis is on the apical Cu{O bond length. This is shown to have a bimodal distribution, but correlations in the displacements of both atoms disguise this fact in the average structure, thus resolving the apparent controversy that had existed between local- and average-structure probes. LaMnO₃ displays (what was thought to be) a simple order{disorder transition that results in the Jahn-Teller distortion becoming invisible in the average structure above ~ 750 K. Here it is shown that in fact the transition is more complicated, and involves a change in the symmetry of the Jahn-Teller distortion, whereby the long Mn-O bonds move from being opposite one another in the octahedra to being adjacent to one another. This new distortion still breaks the degeneracy of the system, and is consistent with a wide range of existing observations. Finally the low temperature structure of Fe₃O₄ is examined using the updated RMCProfile code. The refinements show sensitivity to local structure variations, producing a bimodal Fe atom bond valence distribution. In addition, the refined magnetic spin configuration is presented, providing the first detailed description of the low-temperature magnetic structure. It is found to be a canted ferrimagnet, and appears to be consistent with Cc symmetry.

Master of Science / Department of Chemistry / Mark Hollingsworth / The crystal structures of the inclusion compounds 1,6-diisocyanohexane/urea and 1,6-dicyanohexane/urea were refined at several temperatures from X-ray data. These urea inclusion compounds are commensurate structures with host:guest ratios of 6:1. In contrast with the ordinary helical topology of the urea host, these structures have stacked loop topologies of the host hydrogen bonds and crystallize in space group P21/n. At room temperature, both structures are distorted along [001] from hexagonal metric symmetry. As in earlier studies of 1-chloro-6-cyanohexane/urea, cooling 1,6-diisocyanohexane/urea gives rise to an exothermic phase transition (Hº = -856 cal mol 1, Sº = -5 cal mol-1 K-1) at 175 K that results in the cooperative translation of guest molecules by 5.5 Å along the channel axis. In the low temperature form, 1,6-diisocyanohexane/urea is distorted along [100], much like X(CH2)6Y, where X, Y = Br, Cl. Although the crystal structure of 1,6-dicyanohexane/urea is essentially isomorphous with that of the high temperature form of 1,6-diisocyanohexane/urea, it does not undergo an equivalent phase transition at low temperatures. Both of these systems exhibit dynamic disorder between two gauche conformers of the guest, which have mean planes of the alkyl chains lying within 1º of [100] (major conformer) and approximately 14º from [001] (minor conformer). The temperature dependence of site occupancy factors for the disordered sites yielded enthalpy differences between major and minor sites in 1,6-diisocyanohexane/urea and 1,6-dicyanohexane/urea of 216 and 127 cal mol 1, respectively. Since the low temperature form of 1,6-diisocyanohexane/urea is distorted along [100], this is favored at low temperatures by an increased concentration of the major conformer, which predominates in 1,6-dibromohexane/urea and congeners. In 1,6-diisocyanohexane/urea, the phase transition to the low temperature form occurs at a threshold concentration for the major conformer of 67%. With its shallower temperature dependence, 1,6-dicyanohexane/urea should not reach this threshold population until approximately 92 K, at which temperature the system cannot overcome the barrier for cooperative translation of guests along the channel axis.

This work examines various light metal borohydrides, particularly those formed from group II metals, with the aim of understanding their fundamental physical properties and improving their hydrogen storage ability. The structure of a new phase (γ) of Mg(BH₄)₂ is reported and the decomposition is fully characterized in a combination of diffraction and thermogravimetric studies. The bulk properties of γ-Mg(BH₄)₂ are compared to those of an SiO₂ isostructure and probed by various neutron scattering techniques. Negative thermal expansion is observed at low temperatures and the material absorbs up to 1.5 moles of hydrogen gas to form one of the most gravimetrically hydrogen-dense materials ever reported. The structural evolution of Ca(BH₄)₂ under different synthetic conditions and external influences (e.g. temperature) is studied up until the material decomposes. The effects of various additives on group II metal borohydrides are also examined and the influence of each is justified by observing subtle structural changes in the mixed system via in situ synchrotron X-ray powder diffraction and ¹¹B NMR measurements.

Branched chain sugars display a varied and valuable range of biological activities. This thesis concerns the synthesis of 3,5-di-C-methyl-D-glucose, a potential inhibitor of glycogen phosphorylase (GP), and therefore a proposed therapeutic agent for type 2 diabetes. Chapter 1 looks at the occurrence of branched sugars in the natural world and current therapies for type 2 diabetes. Inhibition of GP is explored, and the molecular modelling studies which led to the design of the project target. Chapter 1 also looks into the development of new foodstuffs, the chemistry and biochemistry of imino sugars and branched hydroxy proline analogues. In Chapter 2, a range of different approaches to 3,5-di-C-methyl-D-glucose are investigated. Most of the initial investigations were carried out on the L-enantiomer, a readily available test system deriving from 2-C-methyl-D-ribono lactone. 2-C-Methyl-D-ribono lactone is synthesised rapidly from D-glucose in a one-pot reaction; as the key starting material for this work, the scalability of this process was investigated. One of the attempted syntheses of di-C-methyl glucose lead to the development of a route towards 3,5-di-C-methyl fructose, a novel dibranched ketose sugar. It was envisaged that through an enzymatic transformation, it might be possible to produce 3,5-di-C-methyl glucose stereoselectively. Synthesis of both enantiomers of 3,5-di-C-methyl glucose and mannose are reported, alongside results of GPb inhibition studies. Analysis of the preferred ring size of a range of di-C-methyl branched sugars and sugar lactones generated in this work is also presented. Chapter 3 explores the chemistry of 2,4-di-C-methyl-L-arabinono lactone, a key intermediate in the synthesis of 3,5-di-C-methyl-L-glucose. From this lactone a novel deoxy sugar, 2-deoxy-2,4-di-C-methyl-L-arabinono lactone, was generated. Routes towards a selection of imino sugars were explored, resulting in the synthesis of a methyl branched isofagomine analogue. A substituted aziridine was synthesised, from which a route to a di-C-methyl branched piperidine was proposed, and a pyrrolidine. Also presented is a synthesis of a dihydroxy di-C-methyl branched proline analogue. Detailed NMR analysis of several of the sugars generated in this work was carried out by Dr M. Wormald, of the University of Oxford Biochemistry department. The results of these investigations are presented in the Appendix. Throughout this work, the presence of quaternary centres has posed a problem with the assignment of relative configuration. As a result, this work has been greatly supported by X-ray crystallography, and the structures shown herein were wholly generated by me. Several other crystals were run during the course of this work, not all pertaining to these projects, and are provided in the CD appendix.

X-ray crystallography is a widely used analytical technique for the structure solution of small molecules. Since the determination of the rock salt structure in 1913 by Henry and Lawrence Bragg the technique has developed allowing the solution of larger and more complex structures. The information that can be determined about these structures has increased as X-ray sources, detectors, and computational methods have improved. However, certain properties of molecules cannot always be directly determined from single wavelength X-ray diffraction. These include, inter alia: the site specific oxidation or spin state of an element in compounds where more than one state of the same element exist; discrimination between consecutive heavy elements in the periodic table. As the size of molecules being studied increases, reduced data resolution also becomes a problem. The aim of this research was to determine whether these problems can be addressed by measuring the changing anomalous scattering contribution of heavy atoms within structure through careful selection of the X-ray energy. Firstly, I report an investigation into the problemof discriminating oxidation state, spin state and elements of near identical scattering by exploiting their anomalous signal. I first present DetOx, a program written during the course of the project to deconvolute the fluorescence signal from materials containing more than one state of the same element into their respective spectra. This allows the calculation of anomalous scattering factors for both atomic states of an atom, which can subsequently be used to refine the occupancy of the different states at ambiguous sites within the crystal structure. The approach taken here, to determine differences due to relatively small anomalous signals, is analogous to the refinement of the Flack parameter whereby small changes in many hundreds or thousands of observations can be used to fit a parameter with a high degree of precision and accuracy. I show the application of this technique to the mixed oxidation state compound, GaCl₂, and the two-step spin crossover material, Fe(btr)₃(ClO₄)₂. Refinement of the occupancy of charged ions on multiple sites using data at a single, carefully selected wavelength proved successful for these compounds, although upon extension to materials containing a larger number of anomalous scatterers, the absorption became a major issue in the data along with problems associated with simultaneously refining occupancies at more sites in the structure. We have demonstrated that calculations can be made to select specific experimental data to collect in order to improve the measured signal. However, due to limitation of the current collision model on the diffractometer used we have not yet been able to construct data collection strategies to take advantage of this. I next present a new ratio refinement technique to overcome this absorption problem due to the increased number of scatterers. By using ratios between datasets close in energy, but below the absorption edge, we were able to exploit small changes in f' without encountering absorption problems associated with the increase in f''. These ratio values were then refined against a lab structure using a modified version of CRYSTALS to reveal the site specific occupancies of different atomic species within a given structure. For mixed-valence compounds, e.g. Mn₃ and Mn₆ clusters, the difference in anomalous signal between the different states proved too small for a stable least-squares refinement solution. However, we have shown that using a simulated annealing algorithm (to refine only occupancies), we can consistently obtain the expected structure. For mixed-metal structures e.g. the Mn₅Co₄ cluster, there was enough contrast in the data to refine occupancies with a least-squares approach, and these results were supported using simulated annealing. Lastly, I describe the application of structure solution techniques based on methods used in macromolecular crystallography to 'large' small molecules. Traditionally these have been reserved for non-centrosymmetric protein structures, however with the trend of synthesising larger and larger small molecules, problems encountered in macromolecular crystallography leading to low resolution datasets are becoming increasingly common. I have shown that it is possible to solve the structure of centrosymmetric structures by exploiting the anomalous signal in multiple wavelength diffraction experiments. The technique is applied successfully to two relatively small molecules, however the results are promising for moving to larger structures in the future.