The Phthalocyanines (Pc’s) are a group of macro-cyclic molecules, widely investigated due to the possibility to use them in a variety of applications. Electronic and geometrical structure investigations of molecular model systems of Pc’s adsorbed on surfaces are important for a deeper understanding of the functionality of different Pc-based devices. Here, Pc’s monolayers and films, deposited on different surfaces, were investigated by X-ray Photoelectron Spectroscopy (XPS), X-ray Absorption Spectroscopy (XAS) and Scanning Tunneling Microscopy (STM). In addition Density Functional Theory (DFT) simulations were performed. For molecular films of Metal-free (H2Pc) and Iron (FePc) Pc’s, on surfaces, it is found that the intermolecular interaction is weak and the molecules arrange with their molecular plane mainly perpendicular to the surface. Several monolayer systems were characterized, namely H2Pc and FePc adsorbed on Graphite, ZnPc on InSb(001)-c(8x2), H2Pc on Al(110) and on Au(111). For all the studied monolayers it was found that the molecules are oriented with their molecular plane parallel to the surface. The electronic structure of the molecules is differently influenced by interaction with the surfaces. For H2Pc adsorbed on Graphite the nearly negligible effect of the surface on the molecular electronic structure allowed STM characterization of different molecular orbitals. A strong interaction is instead found in the case of H2Pc on Al(110) resulting in molecules strongly adsorbed, and partly dissociated. Modifications of the electronic and geometrical structure induced by alkali doping of H2Pc films and monolayers were characterized. It is found both for the H2Pc film on Al(110) and monolayer adsorbed on Au(111), that the molecular arrangement is changed upon doping by Potassium and Rubidium, respectively. Potassium doping of the H2Pc films results in a filling of previously empty molecular orbitals by a charge transfer from the alkali to the molecule, with significant modification of the molecular electronic structure.

A Emodina (EMH) é uma das antraquinonas mais abundantes na natureza. Essa molécula vem sendo largamente usada como material de estudo científico por apresentar diversas atividades farmacológicas, tais como antiviral, antitumoral, antifungal, digestiva e outras. É conhecido que a Emodina em solução aquosa alcalina pode sofrer mais de um processo de desprotonação, apresentando-se na forma desprotonada, EM-, após a primeira desprotonação. Nesta tese de doutorado estudamos as propriedades estruturais e eletrônicas da molécula Emodina em meio solvente e em bicamadas lipídicas a fim de caracterizar as propriedades relacionadas à espectroscopia UV-Vis, à reatividade e à termodinâmica dessa molécula nesses ambientes. Realizamos cálculos quânticos com a Emodina em vácuo e em meio solvente, onde consideramos todos os possíveis sítios de desprotonação. Como resultados desses cálculos, identificamos os sítios da primeira, segunda e terceira desprotonação. Calculamos o pKa1 da Emodina em água e o pK*a1 em metanol através de simulações computacionais com o método Monte Carlo e cálculos quânticos, com o solvente descrito com o modelo contínuo polarizável. Nossos melhores valores para o pKa1 da Emodina determinados nesses solventes foram 8.4±0.5 e 10.3±1.5, que estão em boa concordância com os valores experimentais, (pKa1=8.0±0.2 e pK*a1=11.1±0.1) obtidos nesta tese para Emodina em água e metanol, respectivamente. Adicionalmente realizamos simulações com Dinâmica Molecular com as espécies EMH e EM- em bicamada lipídica de DMPC, para investigar a nível atômico as interações dessas espécies com a bicamada e determinar as posições preferenciais dessas espécies nesse ambiente anfifílico. Os resultados dessas simulações mostraram que as espécies EMH e EM- ficam inseridas na bicamada, na região polar dos lipídios, próximos aos gliceróis. Esses resultados corroboram as nossas medidas do espectro de absorção dessas espécies em bicamada lipídica, onde mostramos de forma qualitativa, que ambas as espécies ficam inseridas na bicamada, na região das cabeças polares dos lipídios. A análise das propriedades estruturais da bicamada na vizinhança das espécies da Emodina como área por lipídio e densidade eletrônica dos lipídios, mostrou que o efeito da EM- na estrutura da bicamada lipídica é maior do que o da EMH. Esses resultados corroboram as nossas medidas de DSC(Differential Scanning Calorimetry) das espécies da Emodina na bicamada. / Emodin (EMH) is one of the most abundant anthraquinone derivatives found in nature. This molecule has been used widely as research material, due to its biological and pharmacological activities such as antiviral, anticancer, antifungal, digestive and antibacterial activities. It is known that Emodin in alkaline aqueous solution can undergo more than one deprotonation, leading to the specie EM- in the first deprotonation process. In this PhD thesis, we studied the structural and electronic properties of this molecule in several solvents and lipid bilayers, in order to characterize the properties related to UV-Vis absorption spectroscopy, reactivity and thermodynamics of this molecule in these environments. Performing quantum mechanics (QM) calculations for all possible deprotonation sites and tautomeric isomers of Emodin in vacuum and in water, we identified the sites of the first, second and third deprotonations. We calculated the pKa1 of Emodin in water and pK*a1 in methanol with free energy perturbation method, implemented in the Monte Carlo simulation, and with QM calculations, where the solvent was treated as a polarizable continuum medium. Our best values for pKa1 of Emodin in these solvents were 8.4±0.5 and 10.3±1.5, which are in very good agreement with the experimental values obtained in this thesis pKa1=8.0±0.2 and pK*a1=11.1±0.1, for water and methanol, respectively. Additionally, we performed molecular dynamics simulations of both species in fully hydrated lipid bilayers of DMPC to investigate at atomic detail the molecular mechanism of the interaction of these species with lipid membrane and its preferred positions in this amphiphilic environment. As results of these simulations, we obtained that both species of Emodin have a strong tendency to insert into the lipid bilayer, remaining near the glycerol group of DMPC. These results corroborate our measured absorption spectra of these species in the bilayer, which qualitatively showed that both species are within the bilayer, inserted in the lipid headgroup region. Our results also show that the effect of EM- specie in the lipid bilayer structure is stronger than the EMH, which corroborate our DSC(Differential Scanning Calorimetry) measurements.

<div>The interactions of femtosecond lasers with gold targets were investigated with a numerical method combining molecular dynamics (MD) and the two-temperature model (TTM). Previous works using MD-TTM method did not consider all the thermodynamic parameters and the interatomic potential dependent of the electron temperature simultaneously. Therefore, we developed a LAMMPS function to achieve this. To accurately capture the physics behind the interactions, we also included the electron blast force from free electron pressure and the modified Fourier law with steep electron temperature gradient in our model. For bulk materials, a stress non-reflecting and heat conducting boundary is added between the atomistic and the continuum parts. The modified boundary force in our study greatly reduces the reflectivity of the atomistic-continuum boundary compared with its original form. Our model is the first to consider all these factors simultaneously and manage to predict four femtosecond laser ablation phenomena observed in the experiments. </div><div><br></div><div>In this dissertation, the thermodynamic parameters in the two-temperature model were extensively explored. We considered three different approaches to calculate these parameters: namely interpolation, <i>ab initio</i> calculation, and analytical expression. We found that simple interpolation between solid state and plasma state could lead to high level of inaccuracy, especially for electron thermal conductivity. Therefore, <i>ab initio</i> calculation and analytical expression were used for the calculation of the thermodynamic parameters in more advanced studies. The effects of electron thermal conductivity and electron-phonon coupling factor on electron and lattice temperatures were analyzed.</div><div><br></div><div>Our studies considered electron temperature dependent (ETD) and electron temperature independent (ETI) interatomic potentials. The ETI interatomic potential is easier to implement and therefore it is used in our phase change study to investigate the effects of target thickness on melting. Homogeneous melting occurred for thin films, while melting can be observed through the movement of the solid-liquid interface in thick or bulk materials. However, the ETI potential overestimated the bond strength at high temperatures. Therefore, ablation process was studied with the ETD potential. Three ablation mechanisms were found in our simulations at different laser fluences. Short nonthermal ablation was only observed at the ablation threshold. With increasing laser fluence, spallation was then seen. In high laser fluence regime, phase explosion occurred on the surface and coexisted with spallation.</div><div><br></div><div>Lastly, we researched on the effects of the delay time between two femtosecond laser pulses. Various delay times did not have much influence on melting depth. In low laser fluence regime, with increasing delay time, the target went through nonthermal ablation, to spallation and to no ablation. In high laser fluence regime, longer delay time encouraged phase explosion while suppressed spallation.</div>

Cette thèse fait l'étude expérimentale de dynamiques de relaxations ultrarapides au sein d'atomes et de molécules (Ar, NO2, C2H2). Les méthodes expérimentales qui sont utilisées sont basées sur l'interaction d'un rayonnement laser avec le système atomique ou moléculaire étudié et font intervenir le processus de génération d'harmoniques d'ordres élevés, ainsi que la spectrométrie d'imagerie de vecteur vitesse. Au cours de cette thèse, deux approchesexpérimentales de type pompe-sonde ont été mises en œuvre. Une première approche exploitela sensibilité du processus de génération d'harmoniques à la structure électronique dumilieu pour la sonder. Cette méthode a été utilisée sur la molécule de dioxyde d'azote pourobserver sa relaxation électronique à travers l'intersection conique des états X2A1-A2B2suite à une excitation autour de 400 nm. Une seconde approche utilise le rayonnementharmonique comme source de photons dans le domaine de l'extrême ultraviolet (EUV)pour exciter ou sonder les espèces d'intérêt. Cette approche a été couplée avec l'utilisationd'un spectromètre d'imagerie de vecteur vitesse (VMIS), qui a été développé durant lathèse. Des expériences menées sur un système modèle comme l'argon ont permis de validerle dispositif expérimental, qui a ensuite été mis en application pour étudier la photodissociationde la molécule d'acétylène, après excitation autour de 9,3 eV du complexe deRydberg 3d-4s. Les deux méthodes mises en œuvre permettent toutes-deux de réaliserdes études dynamiques résolues en temps à l'échelle femtoseconde. / Ultrafast atomic and molecular dynamics (Ar, NO2, C2H2) have been experimentally studied during this PhD. The employed techniques use the laser interaction with the atomic or molecular system produced in gas phase. High harmonic generation (HHG) pump-probe studies allow resolving dynamics on a femtosecond scale. Two applications of high harmonic generation have been implemented here. In the first one, the harmonic generation process is the probe of a vibronic relaxation induced by a pump pulse. This application is currently labeled high harmonic spectroscopy. The sensibility of the high harmonic process to the geometry of the atomic or molecular orbitals is exploited to obtain information about the electronic structure of the generating medium. This method have been used to reveal the electronic relaxation of the nitrogen dioxide molecule (NO2) through the X2A1-A2B2 conical intersection.A second way consists to use the harmonic radiation like a source of XUV photons. The produced XUV radiation permits thus to reach electronically excited energy levels of atoms or molecules, pumping only with a one photon transition. XUV photons can also be used like a probe to ionize products of a molecular reaction. Velocity map imaging spectrometer (VMIS) have been designed and built to complete this fs-VUV source. Above threshold ionization (ATI) experiments and pump-probe XUV-400 nm studies have been performed on reference system like Argon to characterize the built experimental setup. The last excitation scheme has been also applied to study the photodissociation of the Acetylene excited in the 3d-4s Rydberg complex.