The current climate in research has focused on the rational design of new materials with desirable characteristics. The demand for their full characterisation has in turn placed a new importance on structural chemistry, and important developments have taken place as a consequence. For instance an important probe to understand the interactions between molecules is to use variable pressure, and this has been exploited experimentally through the design and implementation of the diamond anvil compression cell (DAC). Using a DAC to study molecular materials at high pressure can result in problems, however: in X-ray diffraction the physical presence of the cell restricts access to reciprocal space, resulting in experimental structures of lower precision and often missing hydrogen atom location data. Traditionally the solution has been sought in neutron diffraction where hydrogen (deuterium) atoms scatter more intensely and so contribute more to the scattering pattern. This introduces another set of problems, however, in that the assumption is made that the isotope substitution does not alter the overall structure. In addition expense and time delays are incurred through this protracted experimental route. This thesis reports the development of a computational technique which can be used to reliably locate hydrogen atoms without the need for neutron diffraction data. The project reports rigorous testing on cases of varying difficulty, from the simple to the more complex. The test cases selected were also of industrial and environmental importance, so determining their complete structures under high pressure conditions was in itself a desirable outcome. Computationally completed structures were then compared to neutron diffraction results or used as the model to be refined against the neutron diffraction pattern.

This thesis describes the effects of the application of high pressure to single crystals of small organic compounds. A range of different structural analysis techniques have been used with the emphasis on whole molecule interactions rather than atom-atom contacts. A study of the effect of pressure on the crystal structure of salicylaldoxime showed that the size of a pseudo-macrocyclic cavity within the structure is tuneable by compression. This cavity determines the reactivity of salicylaldoxime as a ligand, when deprotonated it is known to preferentially bind Cu 2+ ions over other cations in a bis(salicylaldoximato) complex due to the compatibility between the cavity size and the ionic radius of Cu 2+. Further compression studies on a range of substituted salicylaldoximes with different ambient cavity sizes showed that the application of pressure consistently decreases the cavity size across the whole series. Variation of substituent and the pressure yields cavities which span the covalent radii of many of the 1st transition series metal dications. This should allow the selectivity of metal extraction to be tuned using pressure. Computational studies of lattice energies and conformational energies in the compression studies of L-serine and 3-aza-bicyclo(3.3.1)nonane-2,4-dione have shown that significant molecular distortions can occur during compression of a crystal structure below 10 GPa. L-serine shows different conformations between phases with an energy difference of 40 kJ mol-1, whereas the conformation of 3-aza-bicyclo(3.3.1)nonane-2,4-dione is seen to distort within the same phase. Analysis of a database of compression studies using Hirshfeld surfaces has highlighted the fact that all different types of intermolecular interaction have a lower limit for compression, at least in the pressure regime below 10 GPa. These studies, along with theoretical calculations, have suggested a lower distance limit for H…H contacts of 1.7 A. This is potentially very useful for prediction of the effects of compression as H…H contacts are almost universal across small organic crystal structures.

The effect of temperature on the crystal structure of deuterated piperidine has been studied using neutron powder diffraction. Differential scanning calorimetry indicates that there are multiple phases accessible via changes in temperature however there is no evidence of this in the neutron powder diffraction study with only one phase observed in the range 2 – 250 K and under various crystallisation conditions. The effect of pressure up to 2.79 GPa has also been determined. The compression of the structure is facilitated through the closing up of voids in the structure and no phase transition is observed. Differential scanning calorimetry has shown N-methyl and N,N-dimethylformamide both exhibit a thermal event prior to melting. Low temperature neutron powder diffraction has shown these transitions are associated with the onset of methyl group rotation. Neutron powder diffraction studies show formamide exhibits remarkable polymorphism at ambient temperature and pressures between 0.1 GPa and 3.6 GPa, forming four new polymorphs. All the structures consist of N-H…O hydrogen bonded chains. The formation of the various polymorphs can be rationalised in terms of the orientation of the molecules within the hydrogen bonded chains and the resultant structures formed by further hydrogen bonds between the chains. This is in stark contrast to the effect of varying conditions of temperature where only one structure exists from 2 K right up to the melting point. The effect of temperature on the crystal structure of pyrazine in the range 8 – 315 K is described. At temperatures below 90 K the structure undergoes a phase transition to a previously uncharacterised phase, designated phase IV, which is closely related to the previously known phase I. The crystal structure of phase III has been determined at 315 K. The crystal structure of pyrazine has been determined at room temperature at pressures between 0.11 GPa and 9.36 GPa. At 0.94 GPa a transition from phase I to phase IV is observed. This is the same phase as observed at low temperatures. Crystal growth at 215 K results in the formation of two different phases of mesitylene; phase II and a new previously unknown phase designated phase IV. The structure of phase IV has been determined and found to be stable in the range 90 – 221 K. On cooling a crystal of deuterated mesitylene in phase II to 90 K a transition to phase III was observed and the resultant crystal structure is closely related to that of phase II.

Linear polyamides, commonly known as Nylons, are widely used for their high melting temperatures, heat stability, toughness and abrasion resistance, allowing diverse commercial applications such as carpets, nylon stockings and automotive parts. The work here has possible ramifications for membrane production and drug delivery systems and makes a scientific contribution to the area of binary polymer/diluent systems where the polymer is semicrystalline and the diluent crystallises at a quite different temperature to the polymer. Melt blended crystalline/crystalline systems have, so far, not received the attention that amorphous/amorphous or crystalline/amorphous systems have, perhaps due to the complexity of the morphology that often results within such systems.

For the past 75 years gas-phase electron diffraction (GED) has remained the most valuable technique for determining structures of small molecules, free from intermolecular interactions. Throughout this period many improvements have been made to both the experimental and theoretical aspects of this technique, leading to the determination of more accurate structures. As the uncertainties associated with many stages of the process have been greatly reduced, errors introduced by assumptions, which were previously neglected, now play an important role in the overall accuracy of the determined structure. This work is focused on two such areas, namely the treatment of vibrational corrections and the vibrational effects on the scattering of individual electrons by multiple atoms. A novel method has been developed which allows the extraction of equilibrium structures (re) from distances obtained directly from GED experiments (ra). In unfavourable cases (such as small molecules with large-amplitude and / or highly anharmonic modes of vibration) traditional methods can introduce errors of comparable size to those obtained from the experiment. The newly developed method, EXPRESS (EXPeriments Resulting in Equilibrium StructureS), overcomes the problems which have plagued previous attempts through exploring a more extensive region of the potential-energy surface (PES), specifically regions relating to the normal modes of vibration. The method has been applied, initially, to sodium chloride in the gas phase as this contains dimer molecules with very low-frequency large-amplitude modes of vibration. The experimentally determined re structure gives good agreement with high-level ab initio calculations. Following this success, the EXPRESS method was then applied to sodium fluoride, sodium bromide and sodium iodide, giving similarly good agreement with theoretical calculations. The regular mixed alkali halide dimers (D2h symmetry) cannot be studied by microwave spectroscopy as they do not have a permanent dipole moment. However, vi mixed dimers (C2v) and asymmetric dimers (Cs) do not suffer from this constraint. Using insights learned from the ab initio studies of the sodium halides, geometries and dipole moments have been calculated for a range of mixed and asymmetric alkali halide dimers to enable their study by microwave spectroscopy. A multi-dimensional version of the EXPRESS method has been applied to the lowfrequency modes of chlorofluoroacetylene and chlorodifluoronitrosomethane to assess the effects of coupling between these modes of vibration in these structurally challenging systems. To obtain re structures of larger molecules a second method, using molecular dynamics (MD), has been developed and has been implemented on two test cases: the sodium chloride dimer and octasilsesquioxane. Traditional scattering theory used in GED employs the first-order Born approximation (FBO). However, this ignores any multiple scattering events, which are important for heavier atoms. Using a method similar in nature to EXPRESS a full vibrational analysis of three-atom scattering has been conducted on tellurium dibromide and tellurium tetrabromide.

Investigating the structures of membrane proteins and their interactions with lipids remains challenging for well-established biophysical techniques. In this thesis the use of mass spectrometry (MS) and ion mobility (IM) spectrometry were explored for the interrogation of membrane proteins, their stoichiometry, stability and interactions with lipids. The techniques used were also applied to the identification of drug metabolites. In the first two chapters reviews of both mass spectrometry methods, and membrane protein biogenesis and membrane protein-lipid interactions are presented. The first challenge for studying membrane proteins by MS was to optimise solution conditions. A detergent screening strategy was developed for this purpose (Chapter 3). The various detergent environments studied revealed dramatic differences in mass spectral quality permitting investigation of membrane protein-lipid interactions. Changes were observed in the electrospray charging of membrane proteins and trends were established from an extensive collection of membrane proteins ejected from a wide variety of detergent environments. The physicochemical principles behind the MS of membrane proteins were deduced and are presented (Chapter 4). The results of these experiments led to a deeper understanding of the ionisation processes and the influence of detergent micelles on both charge state and release mechanisms. Experiments from a range of different micelles also allowed the influence of charge and its effects on the preservation of native-like membrane protein conformations to be monitored by IM-MS. By resolving lipid-protein interactions, and by monitoring the effects of lipid binding on the unfolding of three diverse membrane protein complexes, substantial differences in the selectivity of membrane proteins for different lipids were revealed (Chapter 5). Interestingly lipids that stabilised membrane proteins in the gas-phase were found to induce modifications in structure or function thus providing an approach to assess direct lipid contributions, and to rank order lipids based on their ability to modulate membrane proteins. Using the MS approaches developed here also enabled study of the diversity of oligomeric states of the mechanosensitive channel of large conductance (MscL) (Chapter 6). Results revealed that the oligomeric state of MscL is sensitive to deletions in its C-terminal domain and to its detergent-lipid environment. Additionally, a case study with GlakoSmithKline (GSK) was undertaken using IM-MS technology but in this case applied to the identification of drug metabolites (Chapter 7). The results showed that IM-MS and molecular modelling could inform on the identity of different drug metabolites and highlights the potential of this approach in understanding the structure of various drug metabolites.

Starting with the structure analysis of ConA in the 70s, the crystal structures of hundreds of different lectins and their carbohydrate complexes have been determined. Lectins, multivalent carbohydrate-binding proteins which specifically bind different sugar structures, have received considerable attention in recent times on account of the realization of the importance of protein−sugar interactions, especially at the cell surface, in biological recognition. They occur in plants, animals, fungi, bacteria and viruses. Plant lectins constitute about 40% of the lectins of known structure. They can be classified into five structural groups, each characterized by a specific fold. Among them, legume lectins constitute the most extensively investigated group. Peanut lectin is a legume lectin which has been studied thoroughly in this laboratory. These studies have provided a wealth of structural and functional information. However, some gaps still exist in our understanding of the structure, interactions and multivalency of peanut lectin. The work presented here addresses these gaps. The hanging drop method was used for crystallizing PNA and its complexes. Intensity data were collected on Mar Research imaging plates mounted on Rigaku RU-200 or ULTRAX-18 X-ray generators. The Oxford cryosystem was used when collecting data at low temperature. The data were processed using DENZO and SCALEPACK of HKL suite of programs. The structure factors from the processed data were calculated using TRUCATE of CCP4 suite of programs. The molecular replacement program AMoRe was used for structure solutions. Structure refinements were carried out using the CNS software package and REFMAC of CCP4. Model building was done using the molecular graphics program FRODO. INSIGHT II, ALIGN, CONTACT and PROCHECK of CCP4 were used for the analysis and validation of the refined structure. Dynamic light scattering experiments were carried out using a Dyanpro Molecular Sizing Instrument, and the collected data were analyzed using Dynamic V6 software. Until recently, it has been possible to grow crystals of peanut lectin only when complexed with sugar ligands. It has now been possible to grow them at acidic pH in the presence of oligopeptides corresponding to a loop in the lectin molecule. Crystals have also been prepared in the presence of the peptides as well as lactose. Low pH crystal forms of the lectin−lactose complex similar to those obtained at neutral pH could also been grown. Thus, crystals of peanut lectin grown in different environmental conditions, at two pHs with and without sugars bound to the lectin, are now available. They have been used to explore the plasticity and hydration of the molecule. A detailed comparison among different structures shows that the lectin molecule is sturdy and the effect of changes in pH, ligand-binding and environment on it is small. The region involving the curved front β-sheet and loops around the second hydrophobic core is comparatively rigid. The back β-sheet involved in quaternary association, which exhibits considerable variability, is substantially flexible. So is the sugar-binding region. The numbers of invariant water molecules in the hydration shell are small and they are mainly involved in metal coordination or in stabilizing rare structural features. Small, consistent movements occur in the combining site on sugar-binding, although the site is essentially preformed. Crystal structures of peanut lectin complexed with Galβ1-3Gal, methyl-T-antigen, Galβ1-6GalNAc, Galα1-3Gal and Galα1-6Glc and that of a crystal grown in the presence of Galα1-3Galβ1-4Gal have been determined using data collected at 100 K. Use of water bridges as a strategy for generating carbohydrate specificity was earlier deduced from the complexes of the lectin with lactose (Galβ1-4Glc) and T-antigen (Galβ1- 3GalNAc). This has been confirmed through the analysis of the complexes with Galβ1-3Gal and methyl-T-antigen (Galβ1-3GalNAc-α-OMe). A detailed analysis of lectin−sugar interactions in the complexes shows that they are more extensive when β-anomer is involved in the linkage. As expected, the second sugar residue is ill defined when the linkage is 1-6. There are more than two-dozen water molecules, which occur in the hydration shells of all structures determined at resolutions better than 2.5 Å. Most of them are involved in stabilizing the structure, particularly loops. Water molecules involved in lectin−sugar interactions are also substantially conserved. The lectin molecule is robust and does not appear to be affected by change in temperature. Multivalency is believed to be important in the activity of lectins, although definitive structural studies on it have been few and far between. A study has been carried out on the complexation of tetravalent peanut lectin with a synthetic compound containing two terminal lactose moieties, using a combination of crystallography, dynamic light scattering and modelling. Light scattering indicates the formation of an apparent dimeric species and also larger aggregates of the tetrameric lectin in the presence of the bivalent ligand. The crystals of presumably crosslinked lectin molecules could be obtained. They diffract very poorly, but the X-ray data from them are good enough to define the positions of the lectin molecules. Extensive modelling on possible crosslinking modes of protein molecules by the ligand indicated that systematic crosslinking could lead to crystalline arrays. The studies also provided a rationale for the crosslinking in the observed crystal structure. The results obtained provide further insights into the general problem of multivalency in lectins. They indicate that crosslinking involving multivalent lectins and multivalent carbohydrates is likely to lead to an ensemble of a finite number of distinct periodic arrays rather than a unique array. PNA is among the most thoroughly studied lectins. Its structure demonstrated that open structures without point group symmetry cannot be ruled out for oligomeric proteins. It also contributed to the identification of legume lectins as a family of proteins in which small alterations in essentially the same tertiary structure lead to large changes in the quaternary association. Among other things, studies on PNA−sugar complexes led to the identification of water bridges as a strategy for generating carbohydrate specificity in addition to providing detailed information on PNA−sugar interactions. The work reported here significantly added to the information on this important lectin provided by earlier studies. On the basis of a detailed examination of structures of crystals grown under different environmental conditions, the relatively rigid and flexible regions of the molecule could be delineated. The picture that emerges is that of a robust protein with a substantially preformed combining site. The work also added to the information on the dependence of protein−sugar interactions on the different glycosidic linkages in disaccharides. The investigations reported here also provided further insights into the multivalency of peanut lectin.

This thesis is concerned with structure-reactivity relationships in metallocene chemistry. In particular new ansa-metallocenes of Groups 5-7 have been prepared. The structure and reactivity of these ansa-metallocenes is compared to the corresponding nonbridged metallocenes.

Orientador: Prof. Dr. Marco Antonio Bueno Filho / Dissertação (mestrado) - Universidade Federal do ABC, Programa De Pós-Graduação em Ensino, História, Filosofia das Ciências e Matemática, 2017. / Este estudo teve como objetivo identificar os conteúdos conceituais e os processos cognitivos gerais mobilizados durante a resolução de tarefas que envolvem a interface entre os campos de conceitos da Cinética Química e da Estrutura e Reatividade por estudantes de graduação sob a luz da Teoria dos Campos Conceituais. Em face disso, buscou-se responder: i. A interação entre estudantes e entre estudantes e professor, enquanto estratégia de ensino para a discussão de transformações enzimáticas, pode mobilizar e entrelaçar conceitualmente o Campo Conceitual Estrutural (CCE) ao do Campo da Cinética Química (CCC)? ii. Em caso afirmativo, quais invariantes operatórios são importantes na interface entre o Campo Conceitual Estrutural (CCE) e o Campo Conceitual da Cinética Química (CCC)? iii. Considerando que as resoluções de tarefas em Bioquímica podem envolver estes campos, qual é a dinâmica ou a contribuição destes campos nos esquemas de ação dos estudantes? Para responder essas questões, um minicurso extracurricular com foi oferecido com tarefas experimentais investigativas onde os estudantes participantes deveriam relacionar conhecimentos conceituais do Campo Estrutural ao Campo da Cinética Química. As explicações sobre estas tarefas foram registradas em vídeo. Estes registros foram analisados com o auxílio do software Transana® com vistas a categorização de acordo com Mullins (2008) e por Justi e Gilbert (1999a; 1999b). Os dados também foram submetidos à análise de correlação entre os conceitos e entre conceitos e as operações do pensamento utilizando-se o coeficiente de Jaccard/Tanimoto (TAN et al., 2006). Os resultados mostraram que os estudantes possuem dificuldade para estabelecer relações conceituais pertinentes e que estas relações quando existentes são caracterizadas pelo estabelecimento de relações de dependência, pela elaboração de hipóteses e pela percepção da simultaneidade de conceitos relativos aos Campos Conceituais da Cinética Química e da Estrutura e Reatividade como principais operações de pensamento. É importante salientar a constatação de esquemas individuais e coletivos, assim como se ressalta, também, a importância da mediação constante do professor no momento do aprendizado e no manejo dos conceitos durante a resolução de tarefas em sala de aula. / This study is devoted to identify the conceptual contents and general cognitive processes mobilized during the resolution of tasks that involve the interface between the fields of concepts of Chemical Kinetics and Structure and Reactivity by undergraduate students under the light of Conceptual Field Theory. In this context, it was sought to answer: i. Can the interplay among students and between students and teachers, as a teaching strategy for discussing enzymatic transformations, conceptually mobilize and interweave the Structural Conceptual Field (CCE) to that of the Field of Chemical Kinetics (CCC)?. ii. If so, which operative invariants are important at the interface between the Structural Conceptual Field (CCE) and the Conceptual Field of Chemical Kinetics (CCC)? iii. Considering that task resolutions in Biochemistry may involve these fields, what are the dynamics or contributions of these fields in the student action schemes? In order to explore these questions, an extracurricular mini-course containing experimental research tasks was offered in which the participating students should relate conceptual knowledge of the Structural Field to the Field of Chemical Kinetics. Explanations of these tasks were recorded on video. These records were analyzed with the help of Transana® software for categorization according to Mullins (2008) and by Justi and Gilbert (1999a; 1999b). The data were also submitted to the correlation analysis throughout concepts and also between concepts and thought operations using the Jaccard / Tanimoto coefficient (TAN et al., 2006). The results showed that students have difficulty in establishing pertinent conceptual relations and that the establishment of dependency relations characterizes these relations when they exist, by the elaboration of hypotheses and by the perception of the simultaneity of concepts related to Conceptual Fields of Chemical Kinetics and Structure and Reactivity as main operations of thought. It is important to emphasize the observation of individual and collective schemes, as well as emphasizing the importance of constant teacher arbitration in the moment of learning and in the concepts¿ handling during the resolution of tasks in the classroom.

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.