Le potentiel des nanoparticules d'or (AuNPs) pour améliorer l’efficacité de la radiothérapie est démontré par de nombreuses études expérimentales in vivo et in vitro. Ces particules métalliques augmentent significativement l’effet de la radiosensibilisation. La réaction en jeu est la radiolyse de l’eau: une fois excitées par un rayon X, elles génèrent des espèces réactives oxygénées qui amplifient les dégâts d’ADN et mènent à une plus grande destruction des cellules cancéreuses. Cependant, pour une efficacité thérapeutique plus optimale, plusieurs propriétés des AuNPs doivent être prises en compte lors de la synthèse comme leur taille, leur forme et leur surface qui sont suspectibles d’influencer ses effets catalytiques dans l’environnement biologique (majoritairement de liquide d’eau). Ces aspects structuraux ne sont pas encore examinés dans l’état de l’art, ni expérimentalement ni théoriquement. Ce travail de thèse a pour but de rationaliser la stabilité de AuNPs dans un environnement chimique ou biologique avant l’irradiation par des outils de modélisation théorique. Dans un premier temps, nous nous sommes intéressés à la stabilité des AuNPs dans la gamme de 1- 3.4 nm. Nous étudions ensuite le comportement de ces nanoparticules dans un environnement biologique (hydratation) et chimique modèle (PEGylation), et la combinaison des deux environnements. Quand les nanoclusters de 0.9-1.8 nm sont en interaction avec une couche de molécules d’eau à saturation, nous avons montré qu’il y a une transformation de NPs métastables (dans le vide) telles que l'ino-décaèdre en NPs métastables plus favorables telles que l'icosaèdre. Alors qu’en présence d’une couche de ligands PEG, la liaison forte Au-S et les liaisons hydrogène entre les ligands entraînent une déformation significative de la morphologie de la nanoparticule, à savoir une stellation du décaèdre Au54. Par ailleurs, nous avons montré que les ligands PEG promeuvent le confinement de quelques molécules d’eau à proximité des AuNPs. Nos conclusions ouvrent des perspectives intéressantes pour la modélisation théorique de la radiolyse de l’eau. Parallèlement à ces études, nous nous sommes intéressés à la caractérisation de différents types de lésions d’ADN. Deux projets ont été menés: premièrement, nous démontrons l’interaction d’un peptide trilysine avec un oligonucléotide qui pourrait conduire à la formation de pontage d’ADN-polyamine. Ensuite, le deuxième projet porte sur la rationalisation de différents taux de réparation de dimères de cyclobutanemathide iochella pyrimidine en présence de l’enzyme de reconnaissance DDB2 à l’échelle atomique. / The potential of gold nanoparticles (AuNPs) to improve the performance of radiotherapy is demonstrated by numerous in vivo and in vitro experimental studies. These metallic particles increase significantly the radiosensitization effect. Upon water radiolysis, AuNPs generate reactive oxygen species that amplify DNA damage and lead to a greater destruction of cancerous cells. Nevertheless, for a more optimal therapeutic efficacy, several properties of AuNPs must be taken into account during the synthesis, such as their size, shape and surface which can tune their catalytic effects in the biological environment (mainly liquid water). These structural aspects are not yet examined in the state-of-the-art, either experimentally or theoretically. This thesis aims to rationalize the stability of AuNPs in the presence of chemical or biological environment before irradiation by using theoretical approaches. Firstly, we have modeled the stability of AuNPs in the range 1- 3.4 nm. We have then studied the behavior of these nanoparticles in a biological (hydration) and chemical (PEGylation) model environment, and the combination of the two environments. When 0.9-1.8 nm nanoclusters interact with a complete shell of water molecules, we have shown that metastable ino-decahedrons (in vacuum) are transformed into more favourable metastable icosahedrons. While in the presence of monoshell of PEG ligands, the strong Au-S bond and the hydrogen bonds between the ligands induce a significant deformation on the nanoparticle morphology, i.e. stellation of the Au54 decahedron. In addition, we have shown that PEG ligands promote the confinement of a few water molecules in the vicinity of AuNPs. Our conclusions open interesting perspectives for the theoretical modeling of water radiolysis. In parallel with these studies, we have focused on the characterization of different types of DNA lesions. Two projects have been performed: firstly, we have studied the interaction of a trilysine peptide with an oligonucleotide which could lead to the formation of DNA-polyamine cross link. Then, the second project focuses on rationalizing different repair rates of cyclobutane pyrimidine dimers in the presence of the DDB2 recognition enzyme at the atomic scale.

Dans cette thèse, nous étudions deux aspects de la dynamique d'impuretés atomiques interagissant avec des nanogouttes d'hélium superfluide (He) : la photo-excitation d'alcalins sur une nanogoutte et le dopage de nanogouttes contenant des tourbillons (vortex) quantiques avec des atomes de gaz rares. Nous utilisons la théorie de la fonctionnelle de la densité d'hélium ainsi que sa version dépendante du temps pour en faire la description théorique. Le premier aspect a été effectué dans le cadre d'une collaboration avec des expérimentateurs sur la photo-excitation du rubidium (Rb). Les alcalins sont une sonde très intéressante des gouttelettes d'hélium car ils résident dans leur zone de surface, où il a été prédit qu'un taux de condensation de Bose-Einstein de 100% était possible en raison d'une densité inférieure à celle de l'hélium superfluide. Nos simulations montrent que les états excités 5p et 6p désorbent à des échelles de temps très différentes, séparées par 2 ordres de grandeur (~100 ps et ~1 ps pour 5p et 6p respectivement). Ces résultats sont en accord avec ceux de l'expérience pompe-sonde à l'échelle femtoseconde qui a étudié la photodesorption d'atomes de Rb. Cependant, dans nos simulations, l'excitation vers 5pPi_{3/2} aboutit à un exciplexe RbHe lié à la surface, contrairement à l'expérience où RbHe est éjecté. L'introduction de la relaxation de spin de Pi_{3/2} à Pi_{1/2} nous a permis de résoudre ce désaccord, l'exciplexe RbHe ayant alors assez d'énergie pour désorber. Le deuxième aspect concerne une investigation purement théorique inspirée par les travaux récents de Gomez et Vilesov et al., où les tourbillons quantiques étaient visualisés en dopant les nanogouttes d'hélium avec des atomes d'argent, puis en les faisant atterrir en douceur (soft landing) sur un écran de carbone. Les images au microscope électronique montrent de longs filaments d'agrégats d'atomes d'argent qui s'étaient accumulés le long des coeurs des vortex. La formation de réseaux de tourbillons quantiques à l'intérieur de nanogoutelettes dopées par du xénon est également mise en évidence par diffraction de rayons X qui montrent des pics de Bragg caractéristiques d'agrégats de xénon piégés dans les coeurs des vortex. Nous avons d'abord étudié des collisions frontales entre un atome de xénon, héliophile, et une nanogoutte de 1000 héliums, et comparé les résultats à ceux d'une étude précédente sur le même processus avec le césium (Cs), qui est héliophobe. Dans le cas de Xe une «boule de neige» se forme autour de lui quand il entre dans la nanogoutte, et il lui faut beaucoup plus d'énergie qu'au Cs pour qu'il puisse en ressortir. Quand il le fait, il emporte des héliums avec lui, contrairement au Cs. Nous avons ensuite simulé des collisions entre Ar/Xe et des nanogouttes d'hélium superfluides pour différentes vitesses initiales et paramètres d'impact afin de déterminer leur section efficace de capture. Ces simulations ont ensuite été répétées pour des gouttelettes hébergeant un vortex quantique. On observe que l'impact des impuretés induit de grandes déformations de flexion et de torsion de la ligne de vortex, allant jusqu'à la génération d'ondes de Kelvin hélicoïdales qui se propagent le long du coeur du vortex. Ar/Xe est bien finalement capturé par le vortex, mais pas dans son coeur. Nous avons également découvert que l'existence d'un réseau de 6 lignes de vortex dont les noyaux sont remplis d'atomes d'Ar donne une rigidité accrue à la nanogoutte qui permet de stabiliser le système nano-goutte + vortex même à de faibles vitesses angulaires. Nos simulations impliquant des nanogouttes d'hélium comportant des tourbillons quantiques ouvrent la voie à d'autres investigations sur des nanogouttes hébergeant un ensemble de vortex, en collision avec de multiples impuretés. / In this thesis we investigate two aspects of the dynamics of atomic impurities interacting with superfluid helium (He) nanodroplets, namely the photo-excitation of alkalis on a nanodroplet and the doping process of nanodroplets hosting quantised vortices with noble gas atoms. For the theoretical investigations we use He density functional theory and its time-dependent version. The first aspect involves a joint experimental and theoretical collaboration that focusses on the photo-excitation of the alkali rubidium (Rb). Alkalis are a very interesting probe of He droplets since they reside in their surface region, where it has been argued that almost 100% Bose-Einstein condensation could be achieved due to a density that is lower than in bulk superfluid He. In our simulations we find that states excited to the 5p and 6p manifold desorb at very different timescales, separated by 2 orders of magnitude (~100 ps and ~1 ps for 5p and 6p respectively). This is in good agreement with experimental results where the desorption behaviour of photo-excited Rb atoms is determined using a femtosecond pump-probe scheme. However, in our simulations excitation to the 5pPi_{3/2}-state results in a surface-bound RbHe exciplex, contrary to the experimental case where the RbHe exciplex desorbs from the droplets surface. Introducing spin-relaxation from Pi_{3/2} to Pi_{1/2} into the simulations, the RbHe exciplex is able to desorb from the droplet's surface, which resolves this contradiction. The second aspect concerns a purely theoretical investigation that is inspired by recent work of Gomez and Vilesov et al., where quantised vortices were visualised by doping He nanodroplets with silver atoms, subsequently "soft landing" them on a carbon screen. Electron-microscope images show long filaments of silver atom clusters that accumulated along the vortex cores. Also the formation of quantum-vortex lattices inside nanodroplets is evidenced by using X-ray diffractive imaging to visualise the characteristic Bragg patterns from xenon (Xe) clusters trapped inside the vortex cores. First, head-on collisions between heliophilic Xe and a He nanodroplet made of 1000 He atoms are studied. The results are then compared with the results of a previous study of an equivalent kinematic case with cesium (Cs), which is heliophobic. Xe acquires a "snowball" of He around itself when it traverses the droplet and much more kinetic energy is required before Xe is able to pierce the droplet completely. When it does, it takes away some He with it, contrary to the Cs case. Next, collisions between argon (Ar)/Xe and pristine superfluid He nanodroplets are performed for various initial velocities and impact parameters to determine the effective cross-section for capture. Finally, the simulations are then repeated for droplets hosting a single quantised vortex line. It is observed that the impact of the impurities induces large bending and twisting excitations of the vortex line, including the generation of helical Kelvin waves propagating along the vortex core. We conclude that Ar/Xe is captured by the quantised vortex line, although not in its core. Also we find that a He droplet, hosting a 6-vortex line array whose cores are filled with Ar atoms, results in added rigidity to the system which stabilises the droplets at low angular velocities. Our simulations involving droplets hosting quantum vortices open the way to further investigations on droplets hosting an array of vortices, involving multiple impurities.

Ein limitierender Faktor der Leitfähigkeit ist die Wechselwirkung der Ladungsträger mit polaren Phononenmoden; das resultierende Quasiteilchen wird als Polaron bezeichnet. Die Stärke der Elektron-Phonon (el-ph)-Wechselwirkung bestimmt die Stärke der Lokalisierung des Polarons, die z.B. die Charakteristik der Temperaturabhängigkeit der Mobliltät definiert. Wir fokussieren uns auf Metalloxide mit starker (el-ph)-Kopplung, bei der sich kleine Polaronen bilden. Die Dichtefunktionaltheorie wird häufig für zur Simulation von Polaronen verwendet. Jedoch treten hierbei zwei Schwierigkeiten auf: Die Sensitivität der berechneten Eigenschaften in Abhängigkeit der Fehler im Austausch-Korrelations (XC)-Funktional und der Effekt der endlichen Superzellgröße. Beide Probleme werden in dieser Arbeit untersucht. Die Polaroneneigenschaften werden auf einer modifizierten Potentialoberfläche (PES) berechnet. Durch Variierung des Anteils der exakten Austauschenergie im hybriden HSE-Funktional zeigen wir, dass das modifizierte PES-Modell deutlich die Abhängigkeit der Polaroneneigenschaften vom XC-Funktional reduziert. Basierend auf dem Potential der el-ph-Kopplung von Pekar leiten wir das korrekte elastische langreichweitige Verhalten des Polarons und darauf aufbauend eine Korrektur für den Fehler durch die endliche Superzellgröße her. Diese Erkenntnisse werden durch ausgiebige Tests an MgO und Rutil TiO2 überprüft. Die oben beschriebene Methode wird zur Untersuchung des Einflusses der Kristallstruktur auf die Bildung von Polaronen in Rutil und Anatas TiO2 und in der β- und κ-Phase von Ga2O3 angewendet. Während in Rutil nur kleine Elektronpolaronen stabil sind, finden wir in Anatas nur stabile Lochpolaronen. Hingegen existieren in beiden Phasen von Ga2O3 nur stabile Lochpolaronen, jedoch mit deutlich unterschiedlichen Bindungsenergien. Dadurch kann durch Verwendung unterschiedlicher Kristallstrukturen Eigenschaften wie Leitfähigkeit und Mobilität der Ladungsträger beeinflusst werden. / An important factor limiting the conductivity is the interaction of the charge carrier with polar phonon modes. Such a phonon-dressed charge carrier is called polaron. The strength of the electron-phonon (el-ph) interaction determines the localization of the polaron, which in turn e.g. defines its characteristic temperature dependence for the charge-carrier mobility. We focus on metal oxides with strong el-ph coupling, where small polarons are formed. Density-functional theory is often used for calculating properties of polarons. However, there are two challenges: sensitivity of the calculated properties to the errors in exchange-correlation (XC) treatment and finite-size effects in supercell calculations. In this work, we develop an approach that addresses both challenges. The polaron properties are obtained using a modified neutral potential-energy surface (PES). By changing the fraction of exact exchange in the hybrid HSE functional we show that the modified PES model significantly reduces the dependence of the polaron properties on the XC functional. Based on Pekar's potential for the long-range el-ph coupling, we derive the proper elastic long-range behavior of the polaron and a finite-size correction for the polaron properties. These findings are proofed by an extensively test for rock salt MgO and rutile TiO2. Finally, the approach is used to investigate the influence of the crystal structure on the polaron properties for rutile and anatase TiO2, as well as for the monoclinic β- and orthorhombic κ-phase of Ga2O3. While in rutile TiO2 only small electron polarons are stable, only small hole polarons are found in anatase. Further, small hole polarons exist in both Ga2O3 polymorphs but have significantly different binding energies. Thus, we conclude that growing crystals of the same material but with different structure can be used to manipulate conductivity and charge-carrier mobility.

Cocristais fármaco-fármaco envolvem a junção de dois ou mais insumos farmacêuticos ativos (IFAs), preservando seu caráter neutro e sem a necessidade de quebra ou formação de ligação covalente, mantendo desta maneira sua eficácia. Propriedades dos IFAs em estado sólido, como as interações entre grupos farmacofóricos e receptores, são determinadas pela polaridade dos grupos funcionais e potencial eletrostático assim como pelas interações intermoleculares, que por sua vez dependem das características eletrônicas e moleculares do arranjo tridimensional. Propriedades eletrônicas moleculares e sua relação com a topologia da densidade de carga eletrônica é parte dos estudos teóricos apresentados neste trabalho. Estes estudos envolvem cálculos da distribuição da densidade de carga eletrônica e sua topologia por meio da Teoria Quântica de Átomos em Moléculas AIM (do inglês, atoms in molecules) de Bader. Neste contexto, o presente trabalho apresentou cálculos teóricos da densidade de carga em um sistema periódico tridimensional, utilizando como modelo de partida os dados cristalográficos do cocristal fármaco-fármaco constituído da 5-Fluorocitosina (antimetabólito) e da Isoniazida (tuberculostático), nomeado por 5FC-INH. A função de onda deste sistema foi calculada por meio da teoria do funcional da densidade DFT (do inglês, density functional theory), com alguns níveis de teoria em conjunto com funções de base, utilizando o pacote de programas CRYSTAL14. A distribuição da densidade de carga, resultante destes cálculos, foi analisada por meio da AIM utilizando alguns descritores topológicos, como densidade de carga, Laplaciano da densidade de carga e a elipticidade nos pontos críticos das ligações de enlace covalentes e as interações intermoleculares da unidade assimétrica. Uma análise preliminar dos valores da densidade de carga eletrônica, calculada nos pontos críticos de ligação da 5FC-INH, permitiu selecionar o nível de teoria e conjunto de funções base que melhor reproduziu os dados experimentais, como sendo o B3LYP/6-311++G**. Os valores dos descritores, obtidos dos cálculos com este nível de teoria, foram comparados com os provenientes dos experimentos de difração de raios X de alta resolução e resultaram em boa concordância na descrição da topologia da densidade de carga eletrônica. Os descritores apresentaram valores muito próximos dos reportados na literatura para os grupos funcionais da 5-FC e da INH. Imagens dos mapas das trajetórias do gradiente e do Laplaciano da densidade de carga, dos caminhos de ligação e dos contornos das bacias atômicas, permitiram visualizar as regiões de depleção e acúmulo da densidade de carga. Por meio destas representações foi possível descrever as ligações de hidrogênio responsáveis pela estabilização do cocristal, as ligações químicas covalentes, as deformações das bacias atômicas que caracterizam as polarizações e os mapas do Laplaciano que permitem observar os pares solitários de elétrons, como dos átomos de flúor, oxigênio e nitrogênio. / Drug-drug cocrystals involve the formation of crystals of two or more active pharmaceutical ingredients (APIs) preserving their original chemical characteristics since no breakage or formation of covalent bonds is observed, thus maintaining their effectiveness. APIs solid state properties, such as pharmacophoric and receptor group interactions are determined by the polarity of functional groups, electrostatic potential and potential intermolecular interactions, which in turn depend on the electronic and molecular characteristics of the three-dimensional arrangement. Molecular electron properties and their relationship with charge density topology is part of the theoretical studies presented in this dissertation. These studies involve electron charge density distribution calculations and their topology through the Bader’s quantum theory of atoms in molecules (AIM). To that aim, the present work presents theoretical calculations of the charge density in a three-dimensional periodic system, using crystallographic data of the drug-drug cocrystal involving the antimetabolite prodrug 5-Fluorocytosine (5-FC) and the tuberculostatic drug Isoniazid (INH), namely, 5FC-INH, as a starting model. The wave function of this system was calculated through density functional theory (DFT), with some levels of theory together with an adequate basis set, using the CRYSTAL14 program package. The charge density distribution resulting from these calculations was analyzed for the asymmetric unit using the AIM model where topological descriptors such as charge density, charge density Laplacian and ellipticity at bond critical points (for covalent bonds and intermolecular interactions). A preliminary analysis of the electronic charge density values, calculated at the bond critical points of 5FC-INH, allowed us to select the level of theory and basis set that best reproduced the experimental data, in this case B3LYP/6-311++G**. The values of the descriptors obtained from the calculations with this level of theory were compared with those obtained from the high resolution X-ray diffraction experiments and resulted in good agreement in the description of the topology of the electronic charge density. The descriptors presented values are very close to those reported in the literature for the functional groups in the 5-FC and INH molecules. Images of the maps of the gradient trajectory and Laplacian of charge density, bond paths and atomic basins contours, allowed visualizing the regions of depletion and accumulation of charge density. Through these representations it was possible to describe the hydrogen bonds responsible for the stabilization of the cocrystal, the covalent chemical bonds and the deformations of the atomic basins that characterize the polarizations and the maps of the Laplacian that allow to observe the pairs of isolated electrons, such as those in fluorine, oxygen and nitrogen atoms.

Diversos pesquisadores vêm sugerindo o uso de glicerol e outros alcoóis como matéria-prima para produção de bens de maior valor agregado e para geração de energia elétrica, através de células a combustível. Contudo, o sucesso dessas tecnologias de conversão depende do desenvolvimento de catalisadores mais eficientes. Nesse aspecto, abordagens teóricas se apresentam como ferramentas auxiliares, capazes de fornecer informações difíceis de serem acessadas experimentalmente e que são fundamentais para o projeto de materiais mais eficientes. Nesta tese, foram investigados, via teoria do funcional da densidade (DFT), o papel de defeitos de superfície e efeitos de tensão na adsorção de alcoóis como metanol, etanol e glicerol, sobre superfícies Pt(111) contendo defeitos e ligas de Pt3Ni(111). Para melhorar a descrição dos sistemas de adsorção, foi adicionada a correção de dispersão DFT-D3 à abordagem da DFT. Através da dinâmica molecular empregando o potencial ReaxFF, foram estudados os efeitos de temperatura sobre glicerol, em diversos níveis de recobrimento de superfície, interagindo com os substratos Pt3Ni(111). Os resultados mostram que o glicerol se liga através do oxigênio dos grupos hidróxi aos sítios top de metais de transição (TM), orientando sua cadeia carbônica quase que totalmente paralela à superfície. Os cálculos de energia de adsorção indicam que o glicerol interage mais fortemente com sítios de baixa coordenação, presentes em superfícies com defeitos, o que pode ser compreendido por meio do modelo da banda d. Além disso, a presença de múltiplos sítios de baixa coordenação favorece configurações onde o glicerol se liga à superfície por dois grupos hidróxi, um central e um terminal. Entretanto, existe uma clara preferência de alcoóis se ligarem a sítios de adsorção catiônicos, indicando que a influência de interações Coulombianas é um fator preponderante no processo de adsorção de alcoóis sobre TM. Análises de densidade eletrônica dos sistemas adsorvidos sugerem que a adsorção promove perturbações na densidade eletrônica dos alcoóis, como o deslocamento de densidade eletrônica das ligações C-O e O-H para a região de interação entre a molécula e o substrato, que estão associadas ao estiramento/enfraquecimento das ligações C-O e O-H observados através de análises estruturais. Os resultados DFT também demonstraram que a adição da correção de dispersão DFT-D3 melhorou a descrição das energias de adsorção e se mostrou essencial para reproduzir a tendência do crescimento da energia de adsorção com o tamanho molecular dos alcoóis, enquanto sua natureza atrativa promoveu a diminuição das distâncias atômicas entre alcoóis e substratos. O estudo de dinâmica molecular mostrou que a configuração de adsorção DFT se mantém apenas em temperaturas próximas de 0 K e que outras configurações são favorecidas a temperaturas mais altas. A presença de outras moléculas de glicerol promove, mediante o aquecimento do sistema, a formação de aglomerados de moléculas ligadas através de interações de hidrogênio, o que estabiliza as moléculas e, provavelmente, retarda seu processo de dessorção. Nos sistemas com maior densidade de moléculas, observou-se, ao final da simulação, a formação de fragmentos CH3OH-CHOH-CH2O- e átomos de H adsorvidos na superfície, indicando a quebra de ligações O-H do grupo hidróxi terminal. / Several researchers have been suggesting the use of glycerol and other alcohols as a feedstock to produce higher value-added goods and electricity through fuel cells. However, the success of these conversion technologies depends on the development of efficient catalysts. In this context, theoretical approaches are useful tools that are able to yield important insights that could not be easily obtained from experiments and are fundamental for the future design of more efficient materials. Hence, in this thesis, we investigated via density functional theory (DFT) the role of surface defects and strain effects on the adsorption of methanol, ethanol and glycerol on defected Pt(111) and Pt3Ni-based surfaces. To improve the description of the adsorbed systems, we added the van der Waals (vdW) correction DFT-D3 to the DFT approach. We also studied through molecular dynamics, employing the ReaxFF potential, the effects of temperature on the glycerol, considering different levels of surface coverage, interacting with the Pt3Ni(111) substrates. Our results show that the glycerol binds through the oxygen from a terminal hidroxi group to top sites of transition-metals (TM) with the carbon chain almost parallel to the surface. The calculations of adsorption energy indicate that glycerol interacts strongly with low-coordinated sites, such as those of surface defects, which can be rationalized through the d-band model. Furthermore, the presence of multiple low-coordinated sites was related with configurations where the glycerol binds to the substrates by two hidroxi groups, the central and a terminal one. However, there is a clear preference of the alcohols to bind on cationic adsorption sites, which indicates that the Coulomb interactions play a major role on the adsorption process of alcohols on TM. Electron density analyzes suggest that the adsorption promotes perturbations in the electronic density of the alcohols, such as a partial displacement of electron density from the C-O and O-H bonds to the region between the molecule and the substrate, which are related with the stretching/weakening of the C-O e O-H, as found in the structural analyzes. The DFT results also show that the addition of the DFT-D3 dispersion correction enhanced the adsorption energies and was essential to reproduce correctly the dependence of the binding energy with the molecule size, while its attractive nature promoted the decrease of the atomic distances between alcohols and substrates. The molecular dynamics showed that the glycerol DFT lowest energy adsorption configuration is maintained for temperatures close to 0 K whereas different configurations are favored in higher temperatures. In the presence of multiple glycerol molecules, the heating of the system promotes the formation of molecular clusters bound through hydrogen interactions, which stabilize the molecules and, probably, delay the desorption process. In the systems with higher molecular density, we found that CH3OH-CHOH-CH2O- fragments and H atoms are formed in the end of the simulation, which indicates that the breaking of O-H bonds from the terminal hidroxi groups is promoted.

<p>Hybrid density functional theory (DFT) B3LYP method is applied to study the four diverse enzyme systems: <i>zinc-containing peptidases</i> (thermolysin and stromelysin),<i> methyl-coenzyme M reductase</i>, <i>ribonucleotide reductases</i> (classes I and III), and <i>superoxide dismutases</i> (Cu,Zn- and Ni-dependent enzymes). Powerfull tools of modern quantum chemistry are used to address the questions of biological pathways at their molecular level, proposing a novel mechanism for methane production by methyl-coenzyme M reductase and providing additional insights into hydrolysis by zinc peptidases, substrate conversion by ribonucleotide reductases, and biological superoxide dismutation. Catalysis by these enzymes, with the exception of zinc peptidases, involves radical chemistry.</p>

<p>The solid oxide fuel cell (SOFC) technology has been under research since thelate 1950s, and most of the research has been on designs utilizing yttria stabilized zirconia (YSZ) as the electrolyte of choice. However, the SOFC technology has the major drawback of requiring high operation temperatures (up to 1000 degrees Celcius), so research of alternative materials have come into interest that would possibly require a lower working temperature without any significant loss of conductivity.One such material of interest for the electrolyte is compounds of ceriumdioxide (ceria). Ceria is well known for its ability to release oxygen by formingoxygen vacancies under oxygen-poor conditions, which increases its oxygen ionconductivity, and works at a lower temperature than the YSZ compounds whenproperly doped. Conversely, ceria is also able to absorb oxygen under oxygen-rich conditions, and those two abilities make it a very good material to use in catalytic converters for reduction of carbon monoxide and nitrogen oxide emission. The ability for the oxygen ions to easily relocate inbetween the different lattice sites is likely the key property of oxygen ion transportation in ceria. Also, in oxygen-rich conditions, the absorbed oxygen atom is assumed to join the structure at either the roomy octrahedral sites, or the vacant tetrahedral sites. Following that, the oxygen atom may relocate to other vacant locations, given it can overcome a possible potential barrier.</p><p>This thesis studies how those interstitial oxygen vacancies (defects) affect theenergy profile of ceria-based supercells by first principles calculations. The system is modeled within the density functional theory (DFT) with aid of (extended) local density approximation (LDA+U) using the software VASP. Furthermore, it is studied how those vacancies affect neighbouring oxygen atoms, and wether or not it is energetically benificial for the neighbouring atoms to readjust their positions closer or further away from the vacancy. The purpose of this thesis is to analyze wether or not it is theoretically possible that interstitial oxygen vacancies may cause neighbouring oxygen atoms to naturally relocate to the octahedral site in ceria, and how this affects the overall energy profile of the material.</p>

<p>A screened GPM approach in an EMTO-CPA framework was investigated in order to study its ability of describing transition temperatures in phase separating systems, i. e. systems giving either a random or a cluster structure depending on the temperature and the relative concentration of the ingoing atoms of the binary alloy used for the study. A motivation for the study is that the method works well for ordering systems, i. e. systems giving either a random or ordered structure dependent on the temperature and the relative concentration of the components in the binary alloy. Thereby is it of interest to find out the methods capacity in phase separating systems. The so called GPM potentials derived in the approach were applied in statistical Monte Carlo simulations for this purpose. The systems chosen for the investigation were the RhPd and the AlZn binary alloy systems. For both systems the method showed acceptable accuracy when properties as lattice parameter and mixing enthalpy were calculated. The quality of the derived GPM potentials has also been checked by calculating ordering energy for different ordered structures; directly from first principles calculations and from the GPM approach. The results were in acceptable agreement and thereby indicating that the GPM potentials were reliable. The transition temperatures in the RhPd phase diagram, derived by the statistical Monte Carlo simulations showed anyway deviation from experimental results. The error in the predictions might be due to the existing concentration dependencies in the GPM potentials.The conclusion from this study is that the Monte Carlo scheme might be inconvenient in order to handle the concentration dependencies seen in the GPM potentials.</p>

<p>Ab-initio results of the core-level shift and the distribution about the average for the 3<i>d</i>_5/2 electrons of Ag, Pd and 2<i>p</i>_3/2 of Cu are presented for the face-centered-cubic AgPd and CuPd random alloys. The complete screening model, which includes both initial and final states effects in the same scheme, has been used in the investigations. </p><p>The alloys have been modeled with a supercell containing 256 atoms. Density-functional theory calculations are carried out using the locally self consistent Green's function approach. </p><p>Results from the calculations clearly shows that the core-level shift distributions characteristic is Gaussian, but the components reveals a substantial difference in the FWHM (Full-Width at Half-Maximum). Comparison between the experimental and the calculated broadening shows a remarkable agreement.</p>

<p>The vertical electronic excitation energies for the narrow-bandgap polymers LBPF, EP37 and EP62 have been calculated using Density Functional Theory (DFT). Also the vertical excitation energies for the acceptor unit of LBPF have been calculated using the Hartree-Fock (HF), DFT and Coupled Cluster (CC) methods. The calculations cover the visible and infrared wave length region and two strong transitions are obtained, one corresponding to the pi to pi* transition and one corresponding to the pi to Acceptor transition. The excitation energies obtained from DFT are below the corresponding experimental results and attempts have therefore been made to perform bench-marking calculations using a hierarchy of CC methods.</p>