Diploma thesis is focused on specifications in pharmaceutical business. It is based on knowledge of pharmacy and economy and their synthesis is describing the most significant differences in pharmacy business and other markets. Overall goal of diploma thesis was to create overview about pharmaceutical industry, its progress, trends and behavior of companies to this high risk and volatile market with keeping the rules and norms of Czech and European authorities. Target was also to form group of recommendations for companies participated in this market. To keep this target I described in the first part of diploma thesis basic terminology and theoretical knowledge about pharmaceutical market including research and development, marketing and sales and pharmakovigilance. Practical part was based on case studies specifying the most common and difficult problems and steps leading to their solutions. My personal contribution in diploma thesis is based on detailed and professional handling of the topic and in the choice of parametres which influence the most timing and capital demands of R&D projects in pharmacy and mitigation of their negative aspects.

We report a rapid additive-free synthesis of nanocrystals (NCs) of RHO-type ZIF-71 (1) of composition [Zn(dcim)₂] (dcim = 4,5-dichloroimidazolate) in 1-propanol as solvent at room temperature. NC-1 has a size of 30–60 nm and exhibits permanent microporosity with a surface area (SBET = 970 m² g−¹) comparable to that of microcrystalline material. When kept under the mother solution NC-1 undergoes transformation into a novel SOD-type polymorph (2), which in turn converts into known ZIF-72 (3) with lcs topology. It is shown that microcrystals (MCs) of 2 can be favourably synthesised using 1-methylimidazole as a coordination modulator. NC-2 with size <200 nm was prepared using NC-ZIF-8 as a template with SOD topology in a solvent assisted ligand exchange-related process. DFT-assisted Rietveld analysis of powder XRD data revealed that novel polymorph 2 possesses an unusual SOD framework conformation. 2 was further characterised with regard to microporosity (SBET = 597 m² g−¹) and thermal as well as chemical stability. DFT calculations were performed to search for further potentially existing but not-yet synthesised polymorphs in the [Zn(dcim)₂] system.

The process of milling drugs to obtain samples with a desirable particle size range has been widely used in the pharmaceutical industry, especially for the production of drugs for inhalation. However by subjecting materials to milling techniques surfaces may become thermodynamically activated which may in turn lead to formation of amorphous material. Polymorphic conversions have also been noted after milling of certain materials. Salt and cocrystal formation is a good way of enhancing the properties of an API but little or no work has been published which investigates the stability of these entities when subjected to milling. Different milling techniques (ball and jet) and temperatures (ambient and cryogenic) were used to investigate the milling behaviour of polymorphs, salts and cocrystals. All materials were analysed by XRPD and DSC to investigate any physical changes, i.e. changes in melting point and by inverse gas chromatography (IGC) to investigate whether any changes in the surface energetics occurred as a result of milling. Another aim of this thesis was to see if it was possible to predict the milling behaviour of polymorphs by calculating the attachment energies of the different crystal facets using Materials Studio 4.0. These results were compared to the IGC data to see if the predicted surface changes had occurred. The data collected in this study showed that different milling techniques can have a different effect on the same material. For example ball milling at ambient temperature and jet micronisation of the SFZ tosylate salt caused a notable increase in the melting point of the material whereas ball milling at cryogenic temperatures did not cause this to happen. The IGC data collected for this form also showed a contrast between cryomilling and the other two techniques. The study also showed that the formation of salts and cocrystals does not necessarily offer any increased stability in terms of physical properties or surface energetics. Changes in melting point were observed for the SFZ tosylate salt and the IMC:Benzamide cocrystal. Changes in the specific surface energies were also observed indicating that the nature of the surfaces was also changing. The materials which appeared to be affected the least were the two stable polymorphs, gamma IMC and SFZ III. The computational approach used has many limitations. The software does not allow for conversion to the amorphous form or polymorphic conversions. Such conversions were seen to occur, particularly for the metastable polymorphs used, meaning that this computational approach may only be suitable for stable polymorphs.

The interaction of a shock wave with a boundary layer is a classic viscous/inviscid interaction problem that occurs over a wide range of high speed aerodynamic flows. For example, on transonic wings, in supersonic air intakes, in propelling nozzles at offdesign conditions and on deflected controls at supersonic/transonic speeds, to name a few. The transonic interaction takes place at Mach numbers typically between 1.1 and 1.5. On an aerofoil, its existence can cause problems that range from a mild increase in section drag to flow separation and buffeting. In the absence of separation the drag increase is predominantly due to wave drag, caused by a rise in entropy through the interaction. The control of the turbulent interaction as applied to a transonic aerofoil is addressed in this thesis. However, the work can equally be applied to the control of interaction for numerous other occurrences where a shock meets a turbulent boundary layer. It is assumed that, for both swept normal shock and unswept normal shock interactions, as long as the Mach number normal to the shock is the same, then the interaction, and therefore its control, should be the same. Numerous schemes have been suggested to control such interaction. However, they have generally been marred by the drag reduction obtained being negated by the additional drag due to the power requirements, for example the pumping power in the case of mass transfer and the drag of the devices in the case of vortex generators. A system of piezoelectrically controlled flaps is presented for the control of the interaction. The flaps would aeroelastically deflect due to the pressure difference created by the pressure rise across the shock and by piezoelectrically induced strains. The amount of deflection, and hence the mass flow through the plenum chamber, would control the interaction. It is proposed that the flaps will delay separation of the boundary layer whilst reducing wave drag and overcome the disadvantages of previous control methods. Active control can be utilised to optimise the effects of the boundary layer shock wave interaction as it would allow the ability to control the position of the control region around the original shock position, mass transfer rate and distribution. A number of design options were considered for the integration of the piezoelectric ceramic into the flap structure. These included the use of unimorphs, bimorphs and polymorphs, with the latter capable of being directly employed as the flap. Unimorphs, with an aluminium substrate, produce less deflection than bimorphs and multimorphs. However, they can withstand and overcome the pressure loads associated with SBLI control. For the current experiments, it was found that near optimal control of the swept and unswept shock wave boundary layer interactions was attained with flap deflections between 1mm and 3mm. However, to obtain the deflection required for optimal performance in a full scale situation, a more powerful piezoelectric actuator material is required than currently available. A theoretical model is developed to predict the effect of unimorph flap deflection on the displacement thickness growth angles, the leading shock angle and the triple point height. It is shown that optimal deflection for SBLI control is a trade-off between reducing the total pressure losses, which is implied with increasing the triple point height, and minimising the frictional losses.

<p>The main aim of the thesis was to explore the potential of supercritical fluid (SF) techniques in the field of drug delivery. In particular, the relatively recently developed solution-enhanced dispersion by supercritical fluids (SEDS) technology has been employed in the preparation of particles/powders. </p><p>The manufacturing, stability and bioavailability of a dosage form strongly depend on the physicochemical properties of the formulation particles. For example, dry powder inhalation (DPI) for administering drugs to the respiratory tract require particles in a narrow size range (1-5 μm) to be effective. The identification of polymorphs and control of purity are also important issues since the physicochemical properties and therapeutic effects of the alternative forms of a drug may differ substantially. Solvent-based traditional crystallisation processes provide the product that may require further down-stream processing to obtain particles for advanced drug delivery applications. This can result in unwanted changes in the physicochemical properties of the particles and thus affect the performance of the dosage form. SF processing has addressed many of the challenges in particle formation research. Among several SF technologies developed for particle processing over the last decade, the SEDS process with its specially designed co-axial nozzle with mixing chamber has resulted in improved control over the particle formation process. Carbon dioxide (CO₂) was used as the SF, because it has low critical points and is non-toxic, non-flammable and relatively inexpensive. </p><p>The initial part of the thesis concerns the formation of particles of model drugs such as hydrocortisone, budesonide and flunisolide using SEDS technology and the determination of the influence of processing conditions and solvents on particle characteristics such as size, shape and crystal structure. Particles of model drugs of differing shapes in a size range suitable for inhalation delivery were prepared. In the process, two new polymorphic forms of flunisolide were identified. This was the first report of SEDS technology being shown as a polymorph-screening tool. The remainder of the thesis deals with the development of SEDS technology for precipitating therapeutic proteins such as recombinant human growth hormone (hGH) from aqueous solutions. Powders of hGH were precipitated using SEDS without significant changes in the chemical or physical stability of the protein. The addition of sucrose to hGH in the feed solution promoted precipitation and minimised the detrimental effects of the solvent and/or the process on the physical aggregation of the protein. </p><p>In conclusion, this thesis highlights the applicability of the SEDS process in drug delivery research and advances general understanding of the particle formation phenomenon. The SEDS process may also prove to be a potential alternative technology for the precipitation of stable powders of therapeutic proteins.</p>

The main aim of the thesis was to explore the potential of supercritical fluid (SF) techniques in the field of drug delivery. In particular, the relatively recently developed solution-enhanced dispersion by supercritical fluids (SEDS) technology has been employed in the preparation of particles/powders. The manufacturing, stability and bioavailability of a dosage form strongly depend on the physicochemical properties of the formulation particles. For example, dry powder inhalation (DPI) for administering drugs to the respiratory tract require particles in a narrow size range (1-5 μm) to be effective. The identification of polymorphs and control of purity are also important issues since the physicochemical properties and therapeutic effects of the alternative forms of a drug may differ substantially. Solvent-based traditional crystallisation processes provide the product that may require further down-stream processing to obtain particles for advanced drug delivery applications. This can result in unwanted changes in the physicochemical properties of the particles and thus affect the performance of the dosage form. SF processing has addressed many of the challenges in particle formation research. Among several SF technologies developed for particle processing over the last decade, the SEDS process with its specially designed co-axial nozzle with mixing chamber has resulted in improved control over the particle formation process. Carbon dioxide (CO2) was used as the SF, because it has low critical points and is non-toxic, non-flammable and relatively inexpensive. The initial part of the thesis concerns the formation of particles of model drugs such as hydrocortisone, budesonide and flunisolide using SEDS technology and the determination of the influence of processing conditions and solvents on particle characteristics such as size, shape and crystal structure. Particles of model drugs of differing shapes in a size range suitable for inhalation delivery were prepared. In the process, two new polymorphic forms of flunisolide were identified. This was the first report of SEDS technology being shown as a polymorph-screening tool. The remainder of the thesis deals with the development of SEDS technology for precipitating therapeutic proteins such as recombinant human growth hormone (hGH) from aqueous solutions. Powders of hGH were precipitated using SEDS without significant changes in the chemical or physical stability of the protein. The addition of sucrose to hGH in the feed solution promoted precipitation and minimised the detrimental effects of the solvent and/or the process on the physical aggregation of the protein. In conclusion, this thesis highlights the applicability of the SEDS process in drug delivery research and advances general understanding of the particle formation phenomenon. The SEDS process may also prove to be a potential alternative technology for the precipitation of stable powders of therapeutic proteins.

The interaction of a shock wave with a boundary layer is a classic viscous/inviscid interaction problem that occurs over a wide range of high speed aerodynamic flows. For example, on transonic wings, in supersonic air intakes, in propelling nozzles at offdesign conditions and on deflected controls at supersonic/transonic speeds, to name a few. The transonic interaction takes place at Mach numbers typically between 1.1 and 1.5. On an aerofoil, its existence can cause problems that range from a mild increase in section drag to flow separation and buffeting. In the absence of separation the drag increase is predominantly due to wave drag, caused by a rise in entropy through the interaction. The control of the turbulent interaction as applied to a transonic aerofoil is addressed in this thesis. However, the work can equally be applied to the control of interaction for numerous other occurrences where a shock meets a turbulent boundary layer. It is assumed that, for both swept normal shock and unswept normal shock interactions, as long as the Mach number normal to the shock is the same, then the interaction, and therefore its control, should be the same. Numerous schemes have been suggested to control such interaction. However, they have generally been marred by the drag reduction obtained being negated by the additional drag due to the power requirements, for example the pumping power in the case of mass transfer and the drag of the devices in the case of vortex generators. A system of piezoelectrically controlled flaps is presented for the control of the interaction. The flaps would aeroelastically deflect due to the pressure difference created by the pressure rise across the shock and by piezoelectrically induced strains. The amount of deflection, and hence the mass flow through the plenum chamber, would control the interaction. It is proposed that the flaps will delay separation of the boundary layer whilst reducing wave drag and overcome the disadvantages of previous control methods. Active control can be utilised to optimise the effects of the boundary layer shock wave interaction as it would allow the ability to control the position of the control region around the original shock position, mass transfer rate and distribution. A number of design options were considered for the integration of the piezoelectric ceramic into the flap structure. These included the use of unimorphs, bimorphs and polymorphs, with the latter capable of being directly employed as the flap. Unimorphs, with an aluminium substrate, produce less deflection than bimorphs and multimorphs. However, they can withstand and overcome the pressure loads associated with SBLI control. For the current experiments, it was found that near optimal control of the swept and unswept shock wave boundary layer interactions was attained with flap deflections between 1mm and 3mm. However, to obtain the deflection required for optimal performance in a full scale situation, a more powerful piezoelectric actuator material is required than currently available. A theoretical model is developed to predict the effect of unimorph flap deflection on the displacement thickness growth angles, the leading shock angle and the triple point height. It is shown that optimal deflection for SBLI control is a trade-off between reducing the total pressure losses, which is implied with increasing the triple point height, and minimising the frictional losses.

Les oxydes doubles lamellaires de cobalt et les oxydes de vanadium ont récemment suscité un vifintérêt suite à la découverte de leurs propriétés thermoélectriques prometteuses. Nos efforts visentà synthétiser de nouveaux composés dérivés de ces systèmes en utilisant la synthèse à l'étatsolide, l'échange d'ions et/ou les techniques hydrothermales. Afin de moduler et d'optimiser leurscaractéristiques thermoélectriques, nous avons ajusté la composition des oxydes de cobalt grâce àdes substitutions appropriées. Au sein du dioxyde de vanadium quasi-1D, nous avons considérétrois différentes structures polymorphes : M1, A et B. Nous avons exploré les différents systèmesen construisant l’ensemble des diagrammes de phases. Nous avons également étudié l'effet de lasubstitution du vanadium par le molybdène et le chrome sur la stabilité de ces structurespolymorphes et caractérisé leurs propriétés électroniques en relation avec les mécanismes detransition de phase. / Lamellar cobalt double oxides and vanadium oxides have recently attracted tremendous interestafter the discovery of their interesting thermoelectric properties. Our efforts aimed at synthesizingnovel related compounds using standard solid state, ion exchange and/or hydrothermaltechniques. In order to modulate and optimize their thermoelectric characteristics, we have tunedthe composition of cobalt double oxides by appropriate substitutions. In quasi 1D vanadiumoxides, the interplay between spin, charge and orbital degrees of freedom often leads toremarkable properties. Here we dealt with three different polymorphs of vanadium dioxide,namely M1, A and B. We explored the several novel systems by constructing systematic phasediagrams. We also studied the effect of Mo and Cr:V substitution on the stability of thesepolymorphs and characterized their electronic properties in relation with the structural phasetransition mechanisms. Finally, we explored their potentiality for thermoelectric applications.

Thyroid hormones, which are secreted by the thyroid gland, are one of the most important halogenated compounds in the body. Thyroid hormones control almost every processes in the body including growth, body temperature, protein synthesis, carbohydrate and fat metabolism, heart rate, and cardiovascular, renal and brain function. Thyroid gland secretes L-thyroxine or 3,3',5,5'-tetraiodothyronine (T4) as a prohormone. While the biologically active hormone 3,3',5-triiodothyronine (T3) is produced by selective phenolic ring deiodination of T4, selective tyrosyl ring deiodination of T4 produces a biologically less active metabolite 3,3',5'-triiodothyronine (rT3). Tyrosyl and phenolic ring deiodination of T3 and rT3, respectively, also produces a biologically inactive metabolite 3,3'-diiodothyronine (3,3'-T2). Regioselective deiodinations of thyroid hormones are catalysed by three isoforms of a selenoenzyme iodothyronine deiodinase (DIO1, DIO2, DIO3). DIO1 can remove iodine from both the tyrosyl and phenolic rings of thyroid hormones, whereas DIO2 and DIO3 are selective towards phenolic and tyrosyl ring, respectively. Although the Figure 1. (A) Deiodination of thyroid hormones by iodothyronine deiodinases (DIOs) (A) and naphthyl-based selenium and/or sulphur compounds (B). mystery behind the origin of regioselectivity of deiodination by DIOs remains unsolved, formation of halogen bonding between selenium in the active site of DIOs and iodine of thyroid hormones has been widely accepted as the mechanism of deiodination. Halogen bonding, a noncovalent interaction between halogen and an electron donor such as nitrogen, oxygen, sulphur, selenium etc., elongates the C-I bond and impart a carbanionic character on the carbon atom that gets protonated after the removal of iodide. Apart from the deiodination, thyroid hormones also undergo decarboxylation, oxidative deamination, sulphate-conjugation to form iodothyronamines, iodothyroaetic acids and sulphated thyroid hormones, respectively. Figure 2. (A) Proposed mechanism of deiodination of thyroid hormones by deiodinase mimics. (B) Halogenation of uracil- and cytosine-containing nucleosides by hypohalous acid (HOX). Recently, naphthyl-based selenium/sulphur-containing compounds, such as compound 1 (Figure 1B), have been reported to mediate the selective tyrosyl ring deiodination of T4 and T3 to form rT3 and 3,3'-T2, respectively. Interestingly, replacement of the selenol moiety in compound 1 with a thiol decreases the activity, whereas replacement of the thiol moiety with another selenol dramatically increases the deiodination activity. Based on the detailed experimental and theoretical investigations, a mechanism involving the Se···I halogen bonding was proposed (Figure 2A). In addition to the halogen bonding between selenium and iodine atom, chalcogen bonding between two nearby chalcogen atoms was also shown to be important for the deiodination activity. Another important class of halogenated compounds in the body are the halogenated nucleosides. Myeloperoxidase and eosinophil peroxidase are heme-containing enzymes, which can convert halide ions (X¯) into a toxic reactive halogen species hypohalous acid (HOX) in presence of hydrogen peroxide (H2O2). Uracil- and cytosine-containing nucleosides are known to undergo halogenation at the 5-position of the nucleobase to form the halogenated nucleosides (Figure 2B). Interestingly, halogenated nucleosides such as 5-halo-2'-deoxyuridine are known to be incorporated in the DNA of dividing cells essentially substituting for thymidine. Incorporation of halogenated nucleosides into the DNA leads to mutagenesis, carcinogenesis and loss of genome integrity. Thymidylate synthase (TSase), the key enzyme involved in the biosynthesis of 2'-deoxythmidine-5'-monophosphate (dTMP) from 2'-deoxyuridine-5'-monophosphate (dUMP), can catalyse the dehalogenation of halogenated nucleotides in presence of external thiols. This thesis consists of five chapters. The first chapter provides a general introduction to halogen bonding, thyroid hormones and halogenated nucleosides. This chapter also briefly describes the halogen bond-mediated biochemical and biomimetic deiodinations of thyroid hormones by iodothyronine deiodinases and naphthyl-based organoselenium compounds. Dehalogenation of halogenated nucleotides by thymidylate synthase and thiol-based small molecules has also been discussed in this chapter. The second chapter of this thesis contains the regioselective deiodination of iodothyronamines (TAMs) by deiodinases mimics. TAMs are the endogenous metabolites produced by the decarboxylation of β-alanine side chain of thyroid hormones (THs). 3,3',5-triiodothyronamine (T3AM) and 3,5-diiodothyronamine (3,5-T2AM) undergoes selective tyrosyl ring deiodination by deiodinase mimics to form 3,3'-diiodothyronamine (3,3'-T2AM) and 3-iodothyronamine (3-T1AM), respectively. Interestingly, when the initial rates of deiodinations of T3 and T3AM were compared, deiodination of T3 was found to be several fold faster than that of T3AM under identical reaction conditions. To understand the ability of the iodine atoms to form Figure 3. (A) HPLC chromatogram of deiodination of T3. (B) Proposed mode of interaction of dimeric T3 and monomeric T3AM with organoselenium compounds. halogen bonding, a model selenolate (MeSe¯) was optimized with the T3 and T3AM. Although both T3 and T3AM forms the expected Se···I halogen bonding with MeSe¯, the strength of halogen bonding was found to be less for T3AM than T3. Furthermore, detailed kinetic and spectroscopic studies indicate that T3 and T3AM exist as dimeric and monomeric species in solution. The dimerization of T3 in solution was shown to have remarkable impact on the activation energy and pre-exponential factor of the deiodination reactions. Single crystal X-Ray crystallography and theoretical calculations indicated that in addition to Se···I halogen bonding, I···I halogen bonding may play an important role in the deodination of thyroid hormones by deiodinase mimics. Furthermore, the presence of heteroatoms such as nitrogen, oxygen and sulphur in the close proximity of one of the selenium atoms of deiodinase mimics was shown to have significant effect on the rate of deiodination reactions. The third chapter of the thesis focusses on the conformational polymorphism and conformation-dependent halogen bonding of L-thyroxine. Synthetic version of L-thyroxine (T4) is a life-saver for millions of people who are suffering from hypothyroidism, a thyroidal disorder recognised by low levels of T4 and elevated levels of TSH in blood plasma. Synthetic version of L-thyroxine is available in the Figure 4. Ball and stick model of the single crystal X-Ray structure of the conformational polymorphs of L-thyroxine. Form I and Form II was exclusively crystallized from methanol and acetonitrile, respectively. Water molecules are omitted for clarity. market with various brand names. However, adverse effects have been observed in the patients when they switch their brand of thyroxine. Based on these observations, the American Thyroid Association (ATA), the Endocrine Society (TES), and the American Association of Clinical Endocrinologists (AACE) declared that the different brands of T4 are not bioequivalent, thus leading to differences in the bioavailability of the drug. We have shown that the commercially available thyroxine exists in at least two stable forms (Form I and Form II) with different three-dimensional structures (Figure 4). These two forms exhibit different intermolecular interactions in crystal packing, spectral behaviours, thermal stabilities, optical activity and very interestingly, different solubility in acidic and basic pH. At pH 4, solubility of Form I is about 42% and 45% greater than that of Form II and bulk T4, respectively, whereas at pH 9, the solubility of Form II is about 38% and 42% higher than that of Form I and bulk T4, respectively. As T4 is a narrow therapeutic index drug, these differences in solubility may have remarkable impact on the bioavailability of the drug. In addition to this, we have shown that the ability of the iodine atoms in the C-I bonds to form halogen bond with donor atoms can be altered by changing the relative orientation of tyrosyl and phenolic rings in T4. In the fourth chapter, the three-dimensional structures and conformations of thyroid hormones (THs) and iodothyronamines (TAMs) are discussed. TAMs, the endogenous decarboxylated metabolites of THs, exhibit different binding affinities to the transport proteins and iodothyronine deiodinases (DIOs) compared to the THs. Figure 5. Change in the structure and conformations of thyroid hormones and iodothyronamines with the decarboxylation of amino acid side chain and deiodination of phenolic and tyrosyl ring. Furthermore, the substrate specificities of DIOs have been found to be dependent on the position of iodine atoms on the phenolic and tyrosyl ring of TAMs and THs. Single crystal X-ray structures of TAMs indicate that decarboxylation of amino acid side chain of THs induces significant changes in the structure and conformation. Furthermore, the positional isomers of THs and TAMs exhibit remarkably different conformations, which may have significant effect on the binding of these metabolites to the active site of DIOs. In addition to the structure and conformations, different categories of the intermolecular halogen···halogen (X···X) interactions in the crystal packing of THs and TAMs have also been discussed. Natural bond orbital (NBO) analysis have been done on the halogen-bonded geometries to understand the electronic nature of these interactions. In the fifth chapter, the dehalogenation of halogenated nucleosides and nucleobases by naphthyl-based sulphur/selenium compounds is discussed. Purine and pyrimidine nucleosides are halogenated at various positions of the aromatic ring by different peroxidases such as myeloperoxidase and eosinophil peroxidase present in the white blood cells. Incorporation of the halogenated nucleosides into the DNA of replicating cells leads to DNA-strand breaks, mutagenesis, carcinogenesis and loss of Figure 6. (A) Dehalogenation of halogenated nucleosides. Effect of base-pairing wih adenine and guanine on the deiodination of IU (B) and debromination of BrU (C) by compound 2. genome integrity. We have shown that the naphthalene-based organoselenium compounds such as compound 2 can mediate the dehalogenation of 5-iodo-2'-deoxyuridine (5-IdUd) and 5-bromo-2'-deoxyuridine (5-BrdUd) to produce 2'-deoxyuridine (dUd) (Figure 6A). The deiodination of 5-IdUd was found to be faster than the debromination of 5-BrdUd by compound 2. The mechanism of dehalogenation of halogenated nucleosides by compound 2 was found to be dependent on the nature of halogen. While the deiodination of 5-IdUd by compound 2 follow halogen bond-mediated pathway like thyroid hormones, debromination of 5-BrdUd follow a Michael addition-elimination pathway. Similar results were obtained when 5-iodo-2'-deoxycytidine (5-IdCd) or 5-bromo-2'-deoxycytidine (5-BrdCd) was used as substrate for dehalogenation reaction. Base-pairing of 5-iodouracil (IU) and 5-bromouracil (5-BrU) with adenine and guanine has a significant effect on the rate of dehalogenations of IU and BrU by compound 2 (Figure 6B and 6C).

L’objectif de ce travail consiste à développer un nouveau potentiel SMTB-Q, puis à l’incorporer dans un code de dynamique moléculaire (DM) afin d’étudier les premiers stades de l’oxydation de l’aluminium. Le potentiel peut modéliser les différents polymorphes de l’alumine ainsi qu’une transition de la phase amorphe vers une phase cristalline. Notre approche couple un terme covalent avec la charge. Il utilise le schéma de Rappé et Goddard pour la partie électrostatique et le modèle du réseau alterné de C. Noguera pour la partie covalente. Le potentiel SMTB-Q obtenu est validé par une approche Monte Carlo. Nous y présentons les outils utilisés pour l’optimisation du potentiel ou analyser les résultats obtenus pour les situations hétérogènes. Cette étude permet de montrer que le potentiel SMTB-Q donne une description satisfaisante de la liaison Al-O dans différentes configurations atomiques. Cette liaison résulte de la compétition entre trois contributions énergétiques : électrostatique, covalente et répulsion de Pauli entre les oxygènes. Après son incorporation dans le logiciel LAMMPS, le potentiel SMTB-Q est utilisé en DM pour l'étude d'oxydes à stœchiométrie constante. Les transitions de phases de l’alumine sont étudiées sous haute pression et en température. Le problème du changement de stœchiométrie de l’oxyde est traité à partir de l'étude de diverses structures de différentes stœchiométries. Nous introduirons la liaison métallique dans le potentiel. La superposition des liaisons iono-covalentes et métalliques sera étudiée pour des systèmes métal/oxyde. Enfin, nous discuterons du formalisme du potentiel SMTB-Q face au changement de stœchiométrie dans l’oxyde. / The goal of this work is to develop a new SMTB-Q potential in order to study the early stages of the oxidation of aluminium by molecular dynamics (MD).Our potential is able to model different alumina polymorphs as well as transitions from the amorphous state to a crystalline phase. Our approach couples a covalent term with the charge. It uses Rapp_ and Goddard scheme for the electrostatic part and the model of alternating network developed by C. Noguera for the covalent part.The SMTB-Q potential was validated with a Monte Carlo approach. This study shows that the potential SMTB-Q gives satisfactory results for the Al-O bonding in different atomic configurations. The bonding results from the competition between three energy contributions: electrostatic, covalent and Pauli repulsion between the oxygens.After implementation in the LAMMPS software, the potential SMTB-Q is used to study by DM constant stoichiometry oxides. Alumina phase transitions are observed under high pressure and temperature. We also introduce the metallic bonding in the potential. The superposition of the iono-covalent and metallic bonds was investigated for metal / oxide systems. Finally, we discuss the formalism of the SMTB-Q potential to take into account the change of stoichiometry in the oxide.