Optical second harmonic generation (SHG) is a nonlinear process that converts two photons of frequency w to a single photon of frequency 2w. In the electricdipole approximation, this process requires a noncentrosymmetric medium. For thin films present at the interface between two centrosymmetric media¡Ðsuch as the interface between two liquids, the interface between a liquid and air, or for the surface of a variety of insulators and semiconductors¡Ðonly the molecules which participate in the asymmetry of the interface contribute to the SHG. Surface SGH from molecules which exhibit a large nonlinear optical response at a specific wavelength can be used to measure the relative surface coverage of molecules at the interface as a function of the external electrochemical parameters. The polarization dependence of the surface SHG can be used to estimate the average molecular orientation of chromophores at the liquid/liquid electrochemical interface. The potential dependence of the SHG from the interface provides important information on the position of the adsorbed chromophores with respect to the interface.

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No / Raman spectra of an extremophile cyanobacterial colony in hydromagnesite from Lake Salda in Turkey have revealed a biogeological modification which is manifest as aragonite in the stratum associated with the colony. The presence of key spectral biomarkers of organic protectant molecules such as (8-carotene and scytonemin indicate that the survival strategy of the cyanobacteria is significantly one of UV-radiation protection. The terrestrial location of this extremophile is worthy of consideration further because of its possible putative link with the White Rock formations in Sabaea Terra and Juventae Chasma on Mars.

This licentiate thesis is devoted to the investigation of how bonding in simple organic molecules are affected by X-ray beam irradiation. The investigation targets molecules with three carbons as their main-chain structure. The stability of the bonds under ionization are simulated using the SIESTA package. SIESTA is a simulation package that provides molecular dynamics simulations based on density functional theory within the Born-Oppenheimer approximation. The aim of this study is to understand statistically the damaging process and selectivity among different types of bond. As the first targets, 4 hydrocarbons are investigated. They are propane, propene, propyne and propadiene, which have different combinations of single, double and triple bonds as their main-chain structures. Depending on the combinations, the structures can be either symmetric around the central atom or not. The structure of the symmetric molecules propane and propadiene are  stable until charge +3. In contrast, the asymmetric molecules propene and propyne, the  main-chain bonds show a tendency towards a more similar bond-distance as the level of ionization increases. In addition, hydrogens relocation occurs in propene, leading to a symmetric structure. Secondly, the bond fluctuations are investigated among 4 types of three-carbon molecules which have functional parts. Alcohol and carboxyl groups molecules show the stable bond integrities at charging 0 to +2. On the other hand, the carbon-carbon bonds in molecules with  acetyl and ketone groups are broken by ionization. Comparing the 8 kinds of bond breaking processes in these molecules, this statistical study gives an insight to organic molecules bonding systems.

This dissertation reports on the investigation of the relationships between molecular structure and two-photon absorption (2PA) properties for a series of polymethine and squaraine molecules. Current and emerging applications exploiting the quadratic dependence upon laser intensity, such as two-photon fluorescence imaging, three-dimensional microfabrication, optical data storage and optical limiting, have motivated researchers to find novel materials exhibiting strong 2PA. Organic materials are promising candidates because their linear and nonlinear optical properties can be optimized for applications by changing their structures through molecular engineering. Polymethine and squaraine dyes are particularly interesting because they are fluorescent and showing large 2PA. We used three independent nonlinear spectroscopic techniques (Z-scan, two-photon fluorescence and white-light continuum pump-probe spectroscopy) to obtain the 2PA spectra revealing 2PA bands, and we confirm the experimental data by comparing the results from the different methods mentioned. By systematically altering the structure of polyemthines and squaraines, we studied the effects of molecular symmetry, strength of donor terminal groups, conjugation length of the chromophore chain, polarity of solvents, and the effects of placing bridge molecules inside the chromophore chain on the 2PA properties. We also compared polymethine, squaraine, croconium and tetraon dyes with the same terminal groups to study the effects of the different additions inserted within the chromophore chain on their optical properties. Near IR absorbing squaraine dyes were experimentally observed to show extremely large 2PA cross sections ([approximately equal to] 30000GM). A simplified three-level model was used to fit the measured 2PA spectra and detailed quantum chemical calculations revealed the reasons for the squaraine to exhibit strong 2PA. In addition, two-photon excitation fluorescence anisotropy spectra were measured through multiple 2PA transitions. A theoretical model based on four-levels with two intermediate states was derived and used for analysis of the experimental data.

No / Crystal structure prediction simulations are reported on 5-hydroxymethyl-2-oxazolidinone and 4-hydroxymethyl-2-oxazolidinone to establish the feasibility of predicting the spontaneous resolution of racemates of small organic molecules. It is assumed that spontaneous resolution occurs when the enantiomorph is more stable than the racemic solid. The starting point is a gas phase conformational search to locate all low-energy conformations. These conformations are used to predict the possible crystal structures of 5- and 4-hydroxymethyl-2-oxazolidinone. In both cases, the racemic crystal structure is predicted to have the lowest energy. The energy differences between the lowest-energy racemic solids and the lowest-energy enantiomorphs are 0.2 kcal mol-1 for 5-hydroxymethyl-2-oxazolidinone and 0.9 kcal mol-1 for 4-hydroxymethyl-2-oxazolidinone. In the case of 4-hydroxymethyl-2-oxazolidinone, where the racemic crystal is known to be more stable and the experimental crystal structures of both the racemate and the enantiomorph are available, the simulation results match the observed data. For 5-hydroxymethyl-2-oxazolidinone, where only enantiopure crystals are observed experimentally, the known experimental structure is found 1.6 kcal mol-1 above the lowest-energy predicted structure. This work shows that it is possible to predict whether the racemate of a small chiral molecule can be resolved spontaneously, although further advances in the accuracy of lattice energy calculations are required.

Les premières étapes de la formation stellaire sont accompagnées d'une évolution de la chimie, à partir de molécules simples dans les nuages froids et sombres vers la détection de molécules organiques complexes autour des étoiles de Classe 0. Bien que principalement composés de gaz, ces nuages contiennent également une petite quantité de poussière microscopique. La contribution de cette poussière est toutefois importante car elle agit comme un catalyseur pour la formation de molécules clés observées dans les glaces froides interstellaires, telles que l'eau ou le méthanol. Ces glaces seraient la première étape d'une chimie riche observée dans les enveloppes tièdes des protoétoiles. Durant cette thèse, je me suis concentré sur la première étape en utilisant une double approche. i) Modélisation. J'ai développé un modèle astrochimique couplant la chimie en phase gazeuse et à la surface des grains. Ce modèle suit la formation multicouche des glaces interstellaires et, grace à une approche multiparamètre, nous permet également d'étudier l'influence de paramètres physiques, chimiques, et de surface, tels que la porosité des grains, sur la composition chimique des glaces. Le modèle a ensuite été utilisé pour prédire la différenciation chimique et la deutéra- tion des glaces interstellaires. Ainsi, j'ai construit un réseau chimique en prenant en compte les travaux expérimentaux et théoriques les plus récents. J'ai ensuite appliqué ce modèle à différents cas. J'ai par exemple montré que les glaces sont très hétérogènes et que leurs compositions sont très sensibles aux conditions physiques ainsi qu'à différents paramètres de surface. La deutéra- tion élevée du formaldehyde et du méthanol a été prédite pour une phase dense (nH ∼ 5 × 10^6 cm−3) et rapide (∼ 5000 ans) tandis que la deutération plus faible de l'eau est prédite pour des conditions typiques de nuages moléculaires. La deutération est très sensible et peut donc etre utilisée comme un traceur des conditions physiques. ii) Observations. J'ai été impliqué dans différents projets observationnels dont les buts étaient reliés aux problèmes de la chimie à la surface des grains. J'ai obtenu les trois résultats suivants. Nous avons montré une évolution de la deutération sélective du méthanol avec le type de la protoétoile, le rapport d'abondance [CH2DOH]/[CH3OD] diminuant avec la masse de la protoé- toile. Une cartographie interféromètrique de l'eau deutérée vers deux protoétoiles de faible masse nous a permis de contraindre un fort degré de deutération de l'eau dans de nouvelles sources. Finalement, nous avons détecté pour la première fois plusieurs molécules organiques complexes dans un coeur prestellaire, remettant en question le scénario actuel de formation des molécules organiques complexes dans des conditions tièdes. / The first stages of star formation are accompanied by an evolution of the chemistry, starting from simple molecules in cold dark clouds to the detection of complex organic molecules around Class 0 protostars. Although mostly composed of gas, these clouds also contain small amounts of microscopic dust. The contribution of this dust is nevertheless important because it acts as a catalyst for the formation of key molecules seen in cold interstellar ices, such as water or methanol. These ices are believed to be the first step towards the rich chemistry seen in the warm envelope of protostars. During my thesis, I focused on this first step and I did so by taking a twofold approach. i) Modelling. I have developed an astrochemical model coupling the chemistry in the gas phase and on the grain surfaces. This model follows the multilayer formation of interstellar ices and allows us to investigate the influence of key physical, chemical, and surface parameters, such as grain porosity, on the chemical composition of ices via a multiparameter approach. The model has been applied to predict the chemical differentiation and the deuteration of interstellar ices. To this end, I have built up a chemical network taking into account the most recent experimental and theoretical works. I applied then the model to various cases. For example, I showed that ices are heterogeneous and their composition are sensitive to the physical conditions as well as several grain surface parameters. The high deuteration of formaldehyde, and methanol observed around low-mass protostars has been predicted by a dense (nH ∼ 5 × 106 cm−3) and fast (∼ 5000 years) phase while the lower deuteration of water is predicted for typical molecular cloud conditions. The deuterium fractionation is very sensitive and can be used as a tracer of the physical conditions. ii) Observations. I have been involved in observational projects whose goals are related to the grain surface chemical problems. I obtained the following three results. We showed an evolution of the selective deuteration with the protostar type, the [CH2DOH]/[CH3OD] abundance ratio decreasing with the protostar mass. Interferometric mapping of deuterated water towards low- mass protostars has allowed us to constrain a high deuteration level of water in new sources. Finally, we detected several complex organic molecules in a cold prestellar core for the first time, challenging the current scenario of complex organic molecules in warm conditions.

A coupling-limited approach for the Ullmann reaction-like on-surface synthesis of a two-dimensional covalent organic network starting from a halogenated metallo-porphyrin is demonstrated. Copper-octabromo-tetraphenylporphyrin molecules can diffuse and self-assemble when adsorbed on the inert Au(111) surface. Splitting-off of bromine atoms bonded at the macrocyclic core of the porphyrin starts at room temperature after the deposition and is monitored by X-ray photoelectron spectroscopy for different annealing steps. Direct coupling between the reactive carbon sites of the molecules is, however, hindered by the molecular shape. This leads initially to an ordered non-covalently interconnected supramolecular structure. Further heating to 300 °C and an additional hydrogen dissociation step is required to link the molecular macrocycles via a phenyl group and form large ordered polymeric networks. This approach leads to a close-packed covalently bonded network of overall good quality. The structures are characterized using scanning tunneling microscopy. Different kinds of lattice defects and, furthermore, the impact of polymerization on the HOMO–LUMO gap are discussed. Density functional theory calculations corroborate the interpretations and give further insight into the adsorption of the debrominated molecule on the surface and the geometry and coupling reaction of the polymeric structure. / Dieser Beitrag ist aufgrund einer (DFG-geförderten) Allianz- bzw. Nationallizenz frei zugänglich.

In this licentiate thesis, organic molecules, namely Cobalt Phthalocyanine (CoPc) and Biphenylene, have been studied by means of synchrotron radiation-based spectroscopic methods (Photoemission Spectroscopy (PES) and X-ray Absorption Spectroscopy (XAS) in combination with Density Functional Theory (DFT) calculations. Paper I is a combined experimental and theoretical investigation of electronic structure of CoPc. addressing the atomic character of the Highest Occupied Molecular Orbital (HOMO) and the electronic configuration of the molecular ground state. Both these aspects are still under discussion since different experimental and theoretical studies have given controversial results. Previous works have indicated the CoPc ground state to either be described by the 2A1g or 2Eg, or by a mix of the two electronic configurations. Regrading the debated the atomic character of the HOMO of CoPc, it has been suggested to be either metal 3d-like and localized on the central Co atom or originating in the organic ligand of the molecule. In this thesis the valence photoemission results for CoPc in gas phase and as adsorbed films on Au(111) together with the DFT simulations, consistently indicate that the HOMO is derived only by the organic ligand, with mainly contribution from the carbon atoms with no metal character. Moreover, the good agreement between the experimental and theoretical results, confirms that the ground state of CoPc is correctly described by the 2A1g configuration. In Paper II, PES and XAS have been used to investigate the occupied and empty density of states of biphenylene films of different thicknesses, deposited onto a Cu(111) crystal. The results have been compared to previous gas phase spectra and single molecule Density Functional Theory (DFT) calculations to get insights into the possible modification of the molecular electronic structure in the film induced by the adsorption on a surface. Furthermore, XAS measurements allowed the characterizion of the variation of the molecular arrangement with the film thickness and helped to clarify the substrate-molecule interaction.

Ma thèse porte sur l’étude par simulations numériques à l’échelle atomique de l’adsorption de molécules uniques et d’auto-assemblages moléculaires sur la surface de silicium Si(111) dopée bore notée Si(111) (√(3 ) x√3)R30°-B. Après un premier chapitre de présentation des méthodes de calcul, puis un chapitre consacré à la surface Si(111)-B, la thèse se divise en deux grandes parties : l’une concernant l’adsorption de molécules uniques et l’autre consacrée à l’adsorption de tapis moléculaire.La première partie concerne l’adsorption de molécules uniques sur la surface de Si(111) (√(3 ) x√3)R30°-B. Nous avons plus particulièrement étudié trois molécules présentant des mécanismes d’adsorption différents : la molécule de pyridile-azobenzène, une molécule de la famille des porphyrines (Cu-TBPP) et deux molécules appartenant à la famille des phtalocyanines (H2Pc et CuPc). Dans chaque étude, nous avons effectué une étude énergétique, structurale et électronique. Dans la plupart des cas, nous avons complété l’étude par un calcul d’image STM pour comparer avec les résultats expérimentaux. A partir de cette étude, nous avons montré que les molécules interagissent différemment avec la surface via des interactions électrostatiques, des liaisons datives, des liaisons ioniques et un mécanisme de cycloaddition. La deuxième partie de la thèse est dédiée à l’étude de l’auto-assemblage de molécules organiques sur la surface Si(111) (√(3 ) x√3)R30°-B. L’auto-assemblage moléculaire est une technique permettant la fabrication d’architectures hautement organisées à l’échelle atomique. Nous avons étudié trois molécules différentes formant un auto-assemblage sur la surface de Si(111)-B : 1,3,5-tri(4-bromophényle benzène) notée TBB, 1,3,5-tri(4-iodophényle benzène) notée TIB et 1,3,5-triphenylbenzene notée THB. Comme la formation d’un réseau auto-organisé est la conséquence d’un équilibre entre les interactions molécule-molécule et molécules-substrat, nous avons évalué les énergies d’interaction mises en jeu en utilisant différentes approximations (LDA, GGA et GGA+D). Nous avons étudié, ensuite, les propriétés électroniques de ces assemblages par le calcul des densités d’états projetées, de la différence de la densité de charge, du Laplacien de la charge ou de la fonction ELF. Afin de comparer nos résultats avec les résultats expérimentaux, nous avons effectué un calcul d’image STM en utilisant deux approches : l’approche de Tersoff-Hamann et l’approche multidiffusion proposée par le code bSKAN. Dans une dernière étape, nous avons étudié la recroissance de molécules de fullerène C60 sur le réseau auto-organisé de molécules de TBB déposées sur la surface Si(111) (√(3 ) x√3)R30° -B. Nous avons effectué une étude énergétique des molécules de C60 qui se déposent préférentiellement dans les nanopores de forme hexagonale en accord avec les expériences STM. / My thesis presents the study of the adsorption of single molecules and molecular self-assembly, by numerical simulations at the atomic scale, on a boron doped silicon surface denoted Si(111)(√(3 ) x√3)R30°-B. After presenting the calculation methods and describing the surface model, this thesis is made of two parts: the first one is about the adsorption of single molecules and the second one is devoted to the formation of supramolecular network. In the first part, I studied the adsorption of single molecules on the silicon surface doped boron Si (111)(√(3 ) x√3)R30°-B. I have investigated the adsorption mechanisms of three different molecules: a molecule of pyridyl-azobenzene, a molecule of the family of porphyrin (Cu-TBBP) and two molecules which belong to the family of phtalocyanine (H2Pc and CuPc). For every molecule, I conducted energetic, structural and electronic studies. In most of the cases, I completed this work by calculating STM images in order to compare with experimental results. The second part of this thesis deals with the study of self assembly of organic molecules on the surface of Si(111)(√(3 ) x√3)R30°-B. Molecular self assembly is a technique which allows the formation of highly organized architectures at the atomic scale. I have studied three different molecules forming self assembly on the surface of Si (111)(√(3 ) x√3)R30°-B : 1,3,5-tri(4-bromophenyl benzene) denoted TBB, 1,3,5-tri(4-iodophenyle benzene) denoted TIB et 1,3,5-triphenylbenzene denoted THB. As the formation of a self organized network is a result of equilibrium between molecule-molecule interaction and molecule-substrate one, I have evaluated the interaction energies by using different approximations (LDA, GGA and GGA+D). Then, I have studied the electronic properties of these assemblies by calculating the projected density of states, the charge difference and the Laplacien of the charge or the ELF function (Electronic Localization Function). In order to compare our results with experimental ones, STM images calculations were performed by using two different approaches: the approach of Tersoff-Hamann and the multi-scattering approach proposed by bSKAN code. Finally, I have studied the growth of C60 molecules on the self organized network formed by the TBB molecules deposited on the Si (111)(√(3 ) x√3)R30°-B surface. The energetic study shows that C60 molecules are adsorbed preferentially in the hexagonal nanopores in agreement with the STM observations.