No description available.

No description available.

Ces dernières années, la mise au point de matériaux hybrides organique-inorganiques a fait l’objet d’un intérêt grandissant dans le domaine de la chimie verte. Les matériaux hybrides a base de silice fonctionnalisée par des molécules organiques possèdent des propriétés modulables, permettant leur application dans plusieurs domaines (photochimie, médecine, dépollution . . .). D’un point de vue théorique, le challenge d’une telle étude résulte dans la détermination des propriétés d’optiques. En effet, la taille de ces systèmes ne permet pas un traitement de ces derniers d’un point de vue strictement quantique. L’enjeu de ce travail de recherche est le développement d’un programme qm/mm/tddft (Quantum Mechanic/Molecular Mechanic/ Time Dependant Density Functional Theory), pour le calcul des états électroniques excités localisés dans les solides, avec une applicationparticulière au domaine UV-visible dans les matériaux hybrides organique-inorganiques.Dans la pratique, l’intégration des équations classiques du mouvement de tous les noyaux est effectuée par le programme de dynamique moléculaire dl poly, tandis que les contributions aux forces issues des atomes dans la partie de la simulation quantique sont évaluées par le code siesta en utilisant la méthode dft (Density Functional Theory). Les spectres électroniques seront calculés avec un nouveau code de tddft (Time Dependant Density Fuctional Theory) développé pour ce projet, dans lequel l’utilisation d’une base de produits dominants accélère le calcul de façon notable. / Last years, the development of organic-inorganic hybrid materials has been a growing interest in the field of green chemistry. Hybrid materials based on silica functionalized with organic molecules have flexible properties, allowing their application in several fields (photochemistry, medicine, ...). From a theoretical point of view, the challenge of such a study results in determination of the optical properties. Indeed, the size of the system does not allow treatment with a purely quantum theory. The aim of this research is to develop a qm/mm/tddft (Quantum Mechanic / Molecular Mechanic / Time Dependent Density Functional Theory) code to calculate the excited electronic states localized in solids, with a particular application for the UV-visible region in organic-inorganic hybrid materials. In practice, the integration of classical equations of motion of all the nuclei are made by the molecular dynamics program dl poly, while contributions from the forces in the quantum simulation are evaluated by using the code siesta with the dft (Density Functional Theory) method . The electronic spectra are calculated with a new tddft code developed for this project, in which the use of dominants products accelerates the calculation significantly.

Actuellement, les photochromes photoréversibles présentent un intérêt important en vue de leurs applications éventuelles comme interrupteurs optiques ou pour le traitement et le stockage de données. L’objectif principal de ce travail de thèse a été d’évaluer les 3-­-(2-­-benzylbenzoyl)-­-4-­-quinolones en tant que système photochromique photoréversible. Afin d’étudier la relation entre la structure chimique et le comportement photochromique de ce système, une série de nouvelles 3-­-(2-­-benzylbenzoyl)-­-4-­-quinolones à substitution variée a été préparée à l’aide de procédures connues ainsi qu’élaborées lors de ce travail. La photoréaction de ces nouveaux molecules étant très complexe, une méthode d’étude a été établie avec des 2-­-benzyl-­-3-­-benzoyl-­-4-­-quinolones photoénolisables au comportement plus simple. Leurs spectres d’absorption modélisés à l’aide de fonctions pekariennes ont été comparés avec les résultats des calculs quantiques. Le mécanisme selon lequel la réaction de décoloration se fait par l’ionisation des photoénols fortement acides via protonation des molécules du solvant a été établi. Enfin, la troisième partie est consacrée à l’étude des nouveaux dérivés de quinolones. D’après l’analyse de leurs spectres d’absorption, ainsi que les résultats des calculs quantiques, nous proposons un mécanisme où le transfert d’hydrogène photo-­-induit conduirait à la formation d’un intermédiaire biradicalaire, capable de se cycliser en dibenzo[b]acrydinones hydroxysubstituées. Un tel mécanisme expliquerait la forte influence qu’ont la nature des substituants en positions 1 et 2, ainsi que la température et la présence d’oxygène sur la régio-­- et stéréo-­-sélectivité de cette photoréaction. / Photoreversible photochromic compounds are currently of considerable interest from the point of view of their potential applications as molecular switches and for data storage and processing. The main target of the present investigation is to evaluate the scope and limitations of 3-­-(2-­-benzylbenzoyl)-­-4-­-quinolones as a photoreversible photochromic system. In order to investigate the relationship between quinolone chemical structures and photochemical behavior, a large series of new 3-­-(2-­-benzylbenzoyl)-­-4-­-quinolones with different substituents has been prepared using known as well as newly elaborated synthetic procedures. In the second part of the work a series of simpler photoenolizable 2-­-benzyl-­-3-­-benzoyl quinolones is studied by the means of fitting their UV-­-Vis absorption spectra and comparison with the results of quantum mechanical calculations at the TD DFT level. It was concluded that the mechanism of the reverse reaction involves ionization of the strongly acidic photoenols via protonation of the solvent molecules. The third part of the work includes investigation of the new quinolone derivatives. From the analyses of their absorption spectra and the results of quantum mechanical calculations, we propose a tentative mechanism, according to which the photoinduced hydrogen transfer yields a biradical, capable of cyclization into the hydroxy substituted dibenzo[b]acrydinones. This mechanism accounts for the observation that the nature of substituents in positions 1 and 2, the temperature and the presence of oxygen strongly affect regio-­- and stereoselectivity of the cyclization.

In order to understand the behaviour and function of proteins, their three dimensional structure needs to be known. Determination of macro-molecules’ structures is done using X-ray diffraction or electron microscopy, where the resulting diffraction pattern is used for molecular reconstruction. These methods are however limited by radiation damage.The aim of this work is to study radiation damage of peptides in proteins using computer simulations. Increased understanding of the atomic and molecular dynamics can contribute to an improvement of the method ofimaging biological molecules. To be able to describe the processes that take place as accurately as possible, the problem must treated quantum mechanically.Thus, the simulations are performed with molecular dynamics based on first principles. In order to capture the dynamics of the excited states of the molecule when exposed to X-rays, time-dependent density functional theory with delta self-consistent field is used. These simulations are compared to ground state simulations. The results of the thesis conclude that the excited and ground state simulations result in differences in the dynamics, which are most pronounced for lager molecules.

For every phenomenon found in inorganic materials, organic counterparts have been found in the last 50 years. The discovery of metallic conductivity in the inorganic conjugated polymer (SN)x was a forerunner to the discovery of metallic conductivity in Polyacetylene [1]. It was soon followed by the development of Polypyrrole and Polythiophene, and by the rediscovery of Polyaniline as a conducting polymer [2]. In polymers like Polyacetylene and Polythiophene, doping is by a redox reaction where the incorporation of electron withdrawing groups creates charge carriers in the polymer backbone. In contrast to these polymers, the main doping mechanism in Polyaniline is protonation, that is the attachment of a proton (donated by an acid) to specific sites (imine and amine groups) in the polymer. The protonated groups are also the sites where water and oxygen interact with the charge carriers on the polymer chain. A wide variety of quasi-particle states (excitons, bipolarons, separated polarons and polaron lattice forms) exist in Polyaniline, in its different states of oxidation and protonation. All of them have different transport and optical signatures. Out of these, only the polaron lattice gives rise to a half-filled conduction band, and therefore a metallic state [3]. This fascinating interplay of protonation and metallic features in Polyaniline, combined with its easy processibility, has made Polyaniline an attractive conducting polymer. Therefore the main focus of this thesis is on the role of the dopant on the electronic and optical properties of doped Polyaniline. The first chapter describes the main features of Polyaniline and its doping by protonation. The second chapter describes the experimental and simulation methods used in this thesis. Steady improvements in processing have led to reduced disorder in the samples, and have given rise to stronger metallic features like metallic (Drude-like) reflectivity in the infrared frequencies, and a positive temperature coefficient of the logarithmic derivative of the conductivity. High molecular weight Polyaniline doped with sulfonic acid dopants by surfactant-counterion processing, like Polyaniline doped with AMPSA (2-acrylamido-2-methyl-1-propanesulfonic acid) [4] and cast from dichloroacetic acid (DCA), shows all the metallic features indicative of an intrinsic metallic state [5]. In this thesis, the third chapter describes the spin-charge dynamics of Polyaniline doped with AMPSA (PANIAMPSA) through X-band Electron Spin Resonance studies [6]. Electron Spin Resonance (ESR) is an important technique to probe the spin-charge dynamics of conducting polymers [7, 8]. The X-band ESR spectra of PANI doped with AMPSA showed the presence of two lines (one broad and one narrow) at all temperatures and doping levels, indicative of two types of spin carriers. Three interesting features were observed in our study: a large linewidth ( ~100 Gauss), a maximum of ESR linewidth at ~ 25 K, and a surprising independence of linewidth on water/O2 . The temperature dependence of both linewidths suggests that the broad line is due to the delocalised charge carriers in well-ordered regions, and that the narrow line is due to localised spins in the disordered regions in the sample. Although the XRD spectra showed minimal crystallinity, the ESR and SQUID susceptibility had a strong Pauli contribution, indicative of an intrinsic metallic state. A similarity of the temperature dependence of linewidths of PANI-AMPSA with MWNT-s and HOPG graphite suggested that some quasi-2-D (Q2D) ordering is present in PANI-AMPSA. From Semi-empirical molecular modelling studies, a plausible hydrogen bonding pattern is suggested that can give rise to the Q2D graphene-like arrangement of the PANI polymer chains. This ordering is due to hydrogen bonding between the acrylamido group of the dopant and the amine fragment of the Polyaniline backbone. Hydrogen bonds are not just structural linkers between adjacent chains; they can have subtle effects on electronic states of the polymer backbone due to charge transfer/withdrawal by the hydrogen bond from the delocalised β-electron system of the backbone. The same Q2D model is used to explain the water/oxygen independence of linewidth in PANI-AMPSA. The temperature dependence of linewidth of both lines has been explained in terms of the QTDG (Quasi Two Dimensional Graphite) model, where a strong exchange interaction is presumed to arise between the 2D delocalised charge carriers and the localised spins, leading to a low-temperature peak in the the linewidth. Water is known to significantly enhance the conductive properties of doped Polyaniline [9]. A detailed DFT (Density Functional Theory) modelling study of the influence of water in doped Polyanilines is presented, which clearly indicated that water enhances the charge transfer between the counterion and the polymer backbone. The torsion angles between the adjacent phenyl rings of the emeraldine base decrease when the imine nitrogens are protonated by inorganic acids like HCl and HBr, and hydration of the acid counterions further decrease the torsion angles. In contrast, the torsion angles of the AMPSA protonated Polyaniline are already low (comparable to the hydrated cases), and the charge transferred by AMPSA is also enhanced. Visualisation of the molecular structure of the PANI-AMPSA complex suggested that water molecules may play a minimal role in the electronic properties of AMPSA doped Polyaniline. We suggest the Q2D ordering as the reason for the temperature dependence of the linewidth, the lack of oxygen and water dependence of the linewidth, as well as the enhanced metallic properties in PANI-AMPSA, as compared to other doped Polyanilines. The electronic states of Polyaniline are modified by both redox processes and protonation. This gives rise to a wide variety of optical states, which can be easily accessed by both applied potential and pH [10]. Therefore Polyaniline displays strong electrochromism across the visible, near-IR (NIR), IR and even microwave spectral regions. This feature has wide applications in electrochromic devices. However, a fundamental understanding of the phenomena behind this electrochromism, the charge carrier(s) responsible, and the relation of nanoscopic morphology and electrochemical properties to the electrochromism, is still not clear. In the fourth chapter, we have analysed extensive data from electrochromic devices [11]. Clear assignments are that certain population states contribute predominantly to certain spectral regions (e.g. bipolaron states to the IR, the valence band to the visible and other mid-gap states to the microwave). Among more specific findings, a prominent 7µm (0.16 eV) peak in MIR devices is ascribed to bipolarons, while a low-energy transition at 0.054 eV is ascribed to inter/intra-chain transitions. Each of these transitions is tracked with respect to changes in applied potential, as well as correlated with device morphology and construction. Our analysis of UV-Vis-MIR-FIR-microwave results along with detailed SEM data clearly relates performance in different wavelength regions to morphology. Preliminary kinetics analysis show that the diffusion rates in these devices could be improved further. These findings point to the potential design of very broad-band electrochromic systems encompassing the visible through microwave regions. Polyaniline in its insulating states can be considered as a series of linked oligoanilines. These oligoaniline states can either be considered as a model for describing the properties of the polymer, or can be interesting systems themselves in the light of single-molecular electronic devices [12]. Both applied potential and pH can change the electronic states of these systems. The ability of pH to modify the oxidation states in these systems (and induce electronic transport), and the influence of water on these properties can be a model for biological systems too. While a wealth of information on oligoanilines has been generated from experiments, computational modelling of these systems is less reported. Among many computational methods that have been developed for calculation of optical absorption spectra of molecules, Time Dependent Density Functional Theory (TDDFT) is the method with the widest use. TDDFT obtains the excitation energies of a molecule from the linear response of the electronic density to a external perturbing field [13]. Solvent effects, which are known to affect the excitation energies, are included through the SCRF/PCM (Self-consistent Reaction Field/ Polarizable Continuum Model). PCM is a method that treats the solvent molecules as a continuum, and self-consistently evaluates their electronic distribution around the solute. In the fifth chapter, a systematic study of the optical properties of neutral oligoaniline, in three oxidation states, is performed by varying the chain length and linearity of the backbone. The intrinsic accuracy in the excitation energies obtainable by the combined TDDFT/PCM formalism has enabled us to suggest effective oligomer lengths for the optical transitions in Polyaniline; these are 4 rings for emeraldine base, 4–8 rings for leucoemeraldine base and 4 rings for pernigraniline. The sensitivity of the 2.0 eV exciton peak in emeraldine base to the chemical environment is also apparent from this work. The Valence Density of States (VDOS) and vibrational frequencies, that have been obtained in course of these simulations, have been quantitatively analysed and are a useful addition to understanding the optical properties of neutral Polyanilines. A summary of the results of the dopant and water dependence on the electronic and structural properties of protonated oligoanilines was presented in the third chapter; the appendix describes the methodology in detail. It is worthwhile to emphasize that doped Polyaniline is a system where protonation, hydration and extended β-conjugation all occur together synergistically, and a good overall description of this system is necessary. Modelling the doped state of Polyaniline is a bit more difficult, due to spin polarisation. Ideally, conducting Polyaniline should be modelled in the solid state, with neighbouring chains, counterions and water molecules. Water is known to reversibly increase the macroscopic conductivity and ESR linewidth of doped Polyaniline. In the sixth chapter of this thesis, optical spectra of the bipolaron, separated polaron, and the polaron lattice forms of doped Polyaniline, explicitly including the counterions (Cl, Br, AMPSA) are obtained by the TDDFT method. All the polaronic lattice forms show a dominant absorption at 1.0–1.2 eV, with no absorptions in the range 1.4–2.0 eV. The inclusion of water molecules to solvate the counterions is shown to only weakly modify the optical properties in the polaron lattice form. In the case of polarons on a twisted chain, the 1.0 eV peak is shifted to 1.5 eV. For bipolarons, there is an absorption at 1.3–1.5 eV, along with another peak at 1.8 eV. Comparing with experimental spectra we suggest that the 1.5, 2.8 eV set belongs to a polaron lattice form wherein the chains are twisted. However, individually the 1.5 eV peak may equally come from bipolarons or separated polarons. The peak at 1.8 eV may either be ascribed to a bipolaron form (in which case there should be a 1.5 eV peak too), or to an isolated polaron. The isolated polaron may also show a peak at 2 eV and 3.5 eV that is clearly from a residual emeraldine base electronic state. The steady evolution of the (a) 2 eV exciton peak in emeraldine base to a (b) 1.6– 1.8 eV peak (isolated polarons) to a (c) 1.5 eV peak in the bipolaron form to (d) 1.3 eV peak in the separated polaron form to (e) a 1.0–1.2 eV peak in the fully doped metallic polaron lattice form is clear. This steady evolution observed from TDDFT simulations may help in clarifying the experimental assignments, especially in electrochemical studies on Polyaniline. Simulations including the water molecules were performed to study the experimentally observed dramatic changes on hydration in Polyaniline. However hydration of ions is a dynamic process and static geometries may not provide a fully realistic description. Combined ab initio Molecular Dynamics (AIMD) and TDDFT calculations may be necessary to realistically model the transport properties of doped Polyaniline. This chapter tries to lay a foundation for such work. The main results obtained in this thesis are summarized in the conclusion. To conclude, this thesis is on the electronic and optical properties of Polyaniline. An ESR study on AMPSA doped Polyaniline indicated a unique 2D nanoscopic morphology, and this structure was validated by molecular modelling. The detailed analyses on electrochromic devices led us to perform TDDFT simulations of neutral and doped Polyanilines. These simulations have resulted in clear UV-VIS-IR assignments in all forms of Polyaniline.

No description available.

Depuis la fin des années 80 et l'avènement de la femto-chimie nous pouvons sonder la dynamique nucléaire à l’œuvre au cours de réactions chimiques à l'échelle de la femtoseconde. Plus récemment, la production d'impulsions lasers attosecondes isolées permet d'atteindre une résolution temporelle plus grande encore. Par elle, il devient possible de sonder la dynamique d'origine purement électronique induite par photo-excitation, et notamment photo-ionisation. Dans ce contexte, avec le développement des techniques de spectroscopie résolue en temps, il est important de disposer d'approches théoriques fiables aidant à l'appréhension de résultats toujours plus nombreux dans ce domaine. La tâche et néanmoins rendue difficile par le caractère profondément multi-électronique des processus en jeu. Traiter de tels effets précisément requiert une grande puissance de calcul, ce qui a limité les études disponibles aujourd'hui à de petits systèmes. Au cours de cette thèse, j'ai tenté d'expliquer les résultats d'une expérience de type "pompe-sonde" (UVX-IR) sur molécule de Caféine menée par une équipe de collaborateurs à l'Institut lumière matière. J'ai utilisé pour cela une méthode basée sur la théorie de la fonctionnelle de la densité dépendante du temps, la TD-DFTB dont le coût numérique réduit par rapport à cette dernière permet des calculs sur de gros systèmes en temps raisonnable. J'y présente une étude du paysage énergétique de la Caféine ainsi que le résultat de 2 approches distinctes pour simuler l'ionisation de ce composé. La première, l'approximation de l'ionisation soudaine cosiste à retirer "à la main" un électron à l'une des orbitales Kohn-Sham occupées du système neutre et ne tient pas compte du champ laser. La seconde à recours à un potentiel imaginaire (ou CAP - Complex Absorbing Potential) pour simuler la perte d'electrons, et tiens explicitement compte du champ laser / Since the advent of femtochemistry, at the end of 1980's, we are able to probe the nuclear dynamics underlying chemical reactions down to the scale of a femtosecond. More recently, the production of isolated attosecond pulses allows to reach an even bigger temporal resolution. It is now possible to probe the ultrafast electronic dynamics following a photo-excitation. In this context, with the developpement of time-resolved spectroscopy techniques, it is important to have reliable theorectical approaches in order to apprehend the increasing number of results in this field. This task is made difficult by the intrinsic multi-electronic nature processes at play. The precise treatment of such effects requires a considerable computing power, and have thus limited the availables studies to relatively small systems. In this thesis, I tried to explain the outcome of a "pump-probe" (XUV-IR) experiment on Caffeine molecule realized by our collaborators at the Insitut Lumière Matière. To do so, I used a method based on density functional theory, the TD-DFTB, which lower numerical cost with respect to TD-DFT allows calculation on bigger compounds. I present in the document a study of the energetical landscape of Caffeine, and 2 approaches to simulate ionization. The first one, the so called sudden-ionization approximation consist to retrieve "by hand" an electron from the occupied Kohn-Sham orbitals of the neutral system without taking the laser field into account. The other one is based on the introduction of a complex absorbing potential (CAP) to account for electron loss and take explicitely the laser field into account.

This work investigates the correlation of structural and photovoltaic properties of dyes used in dye-sensitized solar cells. Experimental methods, including ultraviolet-visible spectroscopy, fluorescence spectroscopy, cyclic voltammetry and electrochemical impedance spectroscopy are employed to study optical and electrochemical properties of dye molecules. Computational methods, including density functional theory and time-dependent density functional theory, are used to validate and predict the optical and electronic properties of dye molecules, in their isolated state and once embedded into a working electrode device environment that comprises a dye...TiO2 interface. The results chapters begin with the presentation of a series of quinodimethene dyes that are experimentally validated for their photovoltaic application, and associated computational studies reveal that an inner structural factor - a phenyl ring rotation occurring during the optical excitation process - leads to the competitive photovoltaic device performance of these dyes. Carbazole-based dyes are then systematically studied by computation, especially considering charge transfer paths and binding modes of these dyes on a titania surface. The theoretical models for the basic building block of this chemical family of dyes, known as MK-44, successfully support and explain structural discoveries from X-ray diffraction and reflectometry that impact of their function. A benzothiadiazole-based dye, RK-1, is then systematically studied by both experimental and computational methods, and the results show that the π-bridge composed of thiophene, benzothiadiazole and benzene rings leads to excellent charge separation; and the rotation of these rings during the optical excitation process may well be consistent with the fluorescence spectrum. Finally, the well-known ruthenium-based dyes are theoretically studied to determine the properties of different ligands connected to the metal core of the complex. Conformations with different NCS ligands are calculated in terms of energy and explain well the corresponding results from X-ray diffraction. Acid-base properties of carboxyl groups connected to pyridine ligands in N3 and N749 are theoretically calculated based on thermodynamics and density functional theory. Implicit and explicit models are both adopted to predict these acid dissociative constant values, which are generally in a good agreement with the reported experimental data. The thesis concludes with conclusions and a future outlook.

Electrochemical systems, which rely on coupled phenomena of the chemical change and electricity, have been utilized for development an interface between biological systems and conventional electronics.  The development and detailed understanding of the operation mechanism of such interfaces have a great importance to many fields within life science and conventional electronics. Conducting polymer materials are extensively used as a building block in various applications due to their ability to transduce chemical signal to electrical one and vice versa. The mechanism of the coupling between the mass and charge transfer in electrochemical systems, and particularly in conductive polymer based system, is highly complex and depends on various physical and chemical properties of the materials composing the system of interest. The aims of this thesis have been to study electrochemical systems including conductive polymer based systems and provide knowledge for future development of the devices, which can operate with both chemical and electrical signals. Within the thesis, we studied the operation mechanism of ion bipolar junction transistor (IBJT), which have been previously utilized to modulate delivery of charged molecules. We analysed the different operation modes of IBJT and transition between them on the basis of detailed concentration and potential profiles provided by the model. We also performed investigation of capacitive charging in conductive PEDOT:PSS polymer electrode. We demonstrated that capacitive charging of PEDOT:PSS electrode at the cyclic voltammetry, can be understood within a modified Nernst-Planck-Poisson formalism for two phase system in terms of the coupled ion-electron diffusion and migration without invoking the assumption of any redox reactions. Further, we studied electronic structure and optical properties of a self-doped p-type conducting polymer, which can polymerize itself along the stem of the plants. We performed ab initio calculations for this system in undoped, polaron and bipolaron electronic states. Comparison with experimental data confirmed the formation of undoped or bipolaron states in polymer film depending on applied biases. Finally, we performed simulation of the reduction-oxidation reaction at microband array electrodes. We showed that faradaic current density at microband array electrodes increases due to non-linear mass transport on the microscale compared to the corresponding macroscale systems.  The studied microband array electrode was used for developing a laccase-based microband biosensor. The biosensor revealed improved analytical performance, and was utilized for in situ phenol detection.