Magnetic fields influence the rate and/or yield of chemical reactions that proceed via spin correlated radical pair intermediates. The field of spin chemistry centres around the study of such magnetic field effects (MFEs). This thesis is particularly concerned with the effects of the weak magnetic fields B₀ ~ 1mT relevant in the ongoing debates on the mechanism by which animals sense the geomagnetic field and on the putative health effects of environmental electromagnetic fields. Relatively few previous studies have dealt with such weak magnetic fields. This thesis presents several new theoretical tools and applies them to interpret experimental measurements. Chapter 1 surveys the development and theory of spin chemistry. Chapter 2 introduces the use of Tikhonov and Maximum Entropy Regularisation methods as a new means of analysing MARY field effect data. These are applied to recover details of the diffusive motion of reacting pyrene and N,N-dimethylaniline radicals. Chapter 3 gives a fresh derivation and appraisal of an approximate, semiclassical approach to MFEs. Monte Carlo calculations allow the elucidation of several "rules of thumb" for interpreting MFE data. Chapter 4 discusses recent optically-detected zero-field EPR measurements, adapting the gamma-COMPUTE algorithm from solid state NMR for their interpretation. Chapter 5 explores the role of RF polarisation in producing MFEs. The breakdown in weak fields of the familiar rotating frame approximation is analysed. Chapter 6 reviews current knowledge and landmark experiments in the area of animal magnetoreception. The origins of the sensitivity of European robins Erithacus rubecula to the Earth’s magnetic field are given particular attention. In Chapter 7, Schulten and Ritz’s hypothesis that avian magnetoreception is founded on a radical pair mechanism (RPM) reaction is appraised through calculations in model systems. Chapter 8 introduces quantitative methods of analysing anisotropic magnetic field effects using spherical harmonics. Chapter 9 considers recent observations that European robins may sometimes be disoriented by minuscule RF fields. These are shown to be consistent with magnetoreception via a radical pair with no (effective) magnetic nuclei in one of the radicals.

Time resolved spectroscopy is one of the crucial methods used to study processes on molecular level in biological systems. It is useful especially for monitoring fast processes that take a place in photosynthetic apparatus of photosynthetic organisms, such as electron and energy transfer. The integral parts of photosynthetic apparatus are carotenoids, whose role in the photosynthetic apparatus is not as well explored as it is for chlorophylls. It was proved that carotenoids actively participate in energy transfer processes in photosynthetic antennas. They have a crucial role in protection against excess energy damage. They are also electron donors in both antennas and reaction centers. The fact that photo-physical properties of carotenoids are much different from properties of others organic pigments, complicates studies of their functions in photosynthesis as well as in other biological systems. This thesis employs advanced methods of femtosecond spectroscopy to obtain more information about carotenoid functions in some biological systems and in solution with special focus on carotenoids containing carbonyl group.

Neste trabalho foram sintetizados a poli-2-etinilpiridina (P2EP), poli-4etinilpiridina (P4EP), o iodeto de poli(2-N-t-butilpiridiniumilacetileno) (P2EPtBu) e a poli-β-etinilnaftaleno (P&#946:EN), os quais são poliacetilenos substituídos. Estes polímeros, juntamente com o cloreto de poli(2-piridínio-2-piridilacetileno) (P2EPH), foram caracterizados por espectroscopia vibracional no infravermelho e Raman. Estes polímeros apresentaram variação na posição das bandas Raman com a energia da radiação excitante - chamada dispersão Raman ou fotosseletividade - da ordem de 10 cm-1, bem inferior ao apresentado pelo poliacetileno (cerca de 60 cm-1). Este deslocamento foi interpretado utilizando-se dois dos modelos existentes para descrever este fenômeno: o Modelo de Modo de Amplitude (AMM) e o Modelo de Coordenada de Conjugação Efetiva (ECCM), os quais fornecem informações sobre a estrutura polimérica e sobre seus níveis eletrônicos. Utilizando-se o AMM foi possível obter informações sobre os níveis eletrônicos excitados de mesma simetria que o estado eletrônico fundamental. Por outro lado, o ECCM, com a ajuda de cálculos DFT, mostrou diferenças na extensão da conjugação e no grau de dimerização entre o P2EP na forma cis e trans e indicou que este polímero apresentava, predominantemente, a estrutura cis, fato este confirmado pelos espectros no infravermelho. A dopagem com I2 provocou efeitos diferentes na estrutura dos polímeros. Os espectros no infravermelho dos polímeros dopados indicaram que o P2EP e o P2EPH apresentaram aumento na quantidade de segmentos cis enquanto o P2EPtBu apresentou diminuição na quantidade desses segmentos. Os espectros Raman dos polímeros dopados confirmaram os dados dos espectros no infravermelho. Esta diferença foi interpretada como sendo devida à diferença no volume do substituinte, pois grupos volumosos favorecem o isômero trans-cisóide onde a distância entre os substituintes é maior. A dopagem também levou a um aumento na condutividade dos polímeros, porém os valores de condutividade obtidos foram bem inferiores que os apresentados pelo poliacetileno dopado (10-5 a 10-7 contra 102 S cm-1, tipicamente). / In this work poly-2-ethynylpyridine (P2EP), poly-4-ethynylpyridine (P2EP), poly(2-N-t-butylpyridiniumylacetylene) iodide (P2EPtBu) and poly-β-pethynylnaphthalene (PβEN) were synthesized. These polymers, which are polyacetylenes derivatives, and poly(2-pyridinium-2-pyridylacetylene) chloride (P2EPH) were analyzed by vibrational techniques. It was observed that some Raman band positions shifted when excitation energy was changed, however this shift (ca. 10 cm-1) was substantially smaller than the presented by polyacetylene (ca. 60 cm-1). This phenomenon called Raman dispersion or photoselectivity - was examinated using Amplitude Mode Model (AMM) and Effective Conjugation Coordinate Model (ECCM) and gave us important information about polymer structure and its electronic energies levels. Using AMM it was possible to infere information about electronic excited states with the same symmetry of the electronic ground state. ECCM gave us evidences about differences in conjugation extension and dimerization degree between cis and trans structures. Besides this, ECCM was successful in indicating cis structure to P2EP. Infrared spectrum confirmed that this polymer is mainly cis. I2 doping of P2EP, P2EPH and P2EPtBu provoked differents perturbations in these systems. P2EP and P2EPH increased their cis segments amount, as showed by infrared spectra. On the other hand, this doping induced the decrease of cis segments in P2EPtBu. Raman spectroscopy supported these conclusions too. This difference was interpretated as due to the side group volume, which could favour one or another isomerization. Electronic conductivity increased by doping for all these three polymers, however the conductivity is considerably lower than the presented by polyacetylene (from 10-5 to 10-7 S cm-1 for these substituted polyacetylenes against typically 10-2 S cm-1 for polyacetylene).

Greater understanding of how we can use protein simulations and statistical characteristics of biomolecular interfaces as proxies for biological function will make manifest major advances in protein engineering. Here we show how to use calculated change in binding affinity and coevolutionary scores to predict the functional effect of mutations in the interface between a Histidine Kinase and a Response Regulator. These proteins participate in the Two-Component Regulatory system, a system for intracellular signalling found in bacteria. We find that both scores work as proxies for functional mutants and demonstrate a ~30 fold improvement in initial positive predictive value compared with choosing randomly from a sequence space of 160 000 variants in the top 20 mutants. We also demonstrate qualitative differences in the predictions of the two scores, primarily a tendency for the coevolutionary score to miss out on one class of functional mutants with enriched frequency of the amino acid threonine in one position.

Molecular Biology has allowed the characterization and manipulation of the molecules of life in the wet lab. Also the structures of those macromolecules are being continuously elucidated. During the last decades of the past century, there was an increasing interest to study how the different genes are organized into different organisms (‘genomes’) and how those genes are expressed into proteins to achieve their functions. Currently the sequences for many genes over several genomes have been determined. In parallel, the efforts to have the structure of the proteins coded by those genes go on. However it is experimentally much harder to obtain the structure of a protein, rather than just its sequence. For this reason, the number of protein structures available in databases is an order of magnitude or so lower than protein sequences. Furthermore, in order to understand how living organisms work at molecular level we need the information about the interaction of those proteins. Elucidating the structure of protein macromolecular assemblies is still more difficult. To that end, the use of computers to predict the structure of these complexes has gained interest over the last decades.<p>The main subject of this thesis is the evaluation of current available computational methods to predict protein – protein interactions and build an atomic model of the complex. The core of the thesis is the evaluation protocol I have developed at Service de Conformation des Macromolécules Biologiques et de Bioinformatique, Université Libre de Bruxelles, and its computer implementation. This method has been massively used to evaluate the results on blind protein – protein interaction prediction in the context of the world-wide experiment CAPRI, which have been thoroughly reviewed in several publications [1-3]. In this experiment the structure of a protein complex (‘the target’) had to be modeled starting from the coordinates of the isolated molecules, prior to the release of the structure of the complex (this is commonly referred as ‘docking’).<p>The assessment protocol let us compute some parameters to rank docking models according to their quality, into 3 main categories: ‘Highly Accurate’, ‘Medium Accurate’, ‘Acceptable’ and ‘Incorrect’. The efficiency of our evaluation and ranking is clearly shown, even for borderline cases between categories. The correlation of the ranking parameters is analyzed further. In the same section where the evaluation protocol is presented, the ranking participants give to their predictions is also studied, since often, good solutions are not easily recognized among the pool of computer generated decoys.<p>An overview of the CAPRI results made per target structure and per participant regarding the computational method they used and the difficulty of the complex. Also in CAPRI there is a new ongoing experiment about scoring previously and anonymously generated models by other participants (the ‘Scoring’ experiment). Its promising results are also analyzed, in respect of the original CAPRI experiment. The Scoring experiment was a step towards the use of combine methods to predict the structure of protein – protein complexes. We discuss here its possible application to predict the structure of protein complexes, from a clustering study on the different results.<p>In the last chapter of the thesis, I present the preliminary results of an ongoing study on the conformational changes in protein structures upon complexation, as those rearrangements pose serious limitations to current computational methods predicting the structure protein complexes. Protein structures are classified according to the magnitude of its conformational re-arrangement and the involvement of interfaces and particular secondary structure elements is discussed. At the end of the chapter, some guidelines and future work is proposed to complete the survey. / Doctorat en Sciences / info:eu-repo/semantics/nonPublished

Open–framework inorganic materials are an important class of compounds because of their many applications in the areas of ion–exchange, separation and catalysis. Ever since the discovery of microporous aluminophosphates by Flanigen and co–workers in the early 80’s, the field of open–framework compounds has witnessed explosive growth. It is now established that the open–framework compounds comprise of almost all the elements of the periodic table. In addition, it has been shown that the inorganic anions in the open–framework compounds can be partially substituted by rigid organic linkers such as the oxalate. The resulting inorganic–organic hybrid structures are interesting due to the variable nature of the binding properties of the organic and inorganic moieties. The present thesis consists of systematic studies on the formation of amine–templated inorganic open–framework structures and inorganic–organic hybrid compounds based on the main group, transition metal and actinide elements. In Chapter 1 of the thesis an overview of inorganic open-framework materials is presented, with an emphasis on the elements that have been employed in the present study. Chapter 2 has two parts (Parts A and B) describing the synthesis and structure of open-framework tin(II) containing compounds. In Part A, the syntheses and structures of amine–templated tin(II) phosphates are presented, and in Part B, the syntheses and structures of a family of tin(II) oxalate compounds are discussed. Weak intermolecular forces such as hydrogen-bond interactions, π•••π interactions, and lone-pair–π interactions have been observed in these compounds, and appear to lend structural stability. As part of this study, efforts have been made to evaluate the energies associated with the π•••π interactions and the lone-pair–π interactions using suitable theoretical models. In Chapter 3, a new family of organically templated hybrid materials based on indium, synthesized by partially substituting the inorganic anion (phosphite/phosphate/suphate) by the oxalate group, is presented. These compounds exhibit a wide range of structures in which the oxalates play a variety of roles. The observation of the first zero-dimensional molecular hybrid structure and the isolation of concomitant polymorphic compounds is noteworthy. The molecular hybrid structure is reactive and undergoes transformation reactions under both acidic and basic conditions. In Chapter 4, the synthesis and structural studies of five new open–framework phosphate and phosphite compounds of gallium are presented. All the compounds have three-dimensional structures, and the formation of a gallium phosphate based on only one type of building unit (spiro–5) is noteworthy. While a large number of organically templated transition metal phosphates have been synthesized, studies on transition metal phosphites are not many. In Chapter 5, the synthesis, structure and magnetic properties of a family of transition metal (cobalt, vanadium, manganese) phosphite structures templated by the organic amines are presented. A previously known vanadyl phosphite has also been isolated and investigated by temperature dependent ESR and magnetic susceptibility studies. All the transition metal compounds exhibit antiferromagnetic behavior. In Chapter 6, the synthesis, structure, and transformation reactions in amine-templated actinide phosphonoacetates are presented. The compounds, which are based on uranium and thorium, are built up from the connectivity between the metal polyhedra and the phosphonoacetate/oxalate units, forming two– and three–dimensional structures. It has been shown that the two–dimensional uranyl phosphonoacetate–oxalate compound can be prepared by two different synthetic approaches: (i) solvent–free solid state reaction at 150˚C and (ii) room temperature mechanochemical (grinding) route. The formation of oxalate hybrids using the phosphonocarboxylate ligand is a new approach in the synthesis of multi-component hybrid compounds.

This thesis deals with several aspects of the structure and dynamics of water molecules confined in nanoscopic pores. Water molecules confined in hydrophobic nanocavities exhibit unusual structural and dynamic properties. Confining walls of single-wall carbon nanotubes (SWCNTs) promote strong inter-water hydrogen bonding which in turn leads to several novel structural, dynamic and thermodynamic features not found in bulk water. Confined water molecules form ordered hydrogen-bonded networks, exhibit exceptionally high flow rates as compared to conventional flow in pipes, allow fast proton conduction and exhibit various other anomalous properties. Proteins are known to exploit some of the properties of confined water to perform certain physiological functions. Various properties of confined water can also be exploited in the design of nanofludic devices such as those for desalination and flow sensors. In addition, water molecules confined in SWCNTs and near graphene sheets serve as model systems to study various effects of confinement on the properties of liquids. In this thesis, we present the results of detailed molecular dynamics simulation studies of confined water molecules. In chapter 1, we summarize the findings of existing simulations and experimental studies of bulk and confined water molecules. We also highlight the significance of studying the structure and dynamics of confined water molecules in biological and biotechnological applications. Chapter 2 provides a brief ac-count of the methods and techniques used to perform the simulations described in subsequent chapters of the thesis. We also present a brief overview of the methods used to extract physical properties of water molecules from simulation data, with emphasis on the Two Phase Thermodynamics (2PT) method which we have used to compute the entropy of confined and bulk water molecules. In chapter 3, we discuss the thermodynamics of water entry in SWCNTs of various diameters. Experiments and computer simulations demonstrate that water spontaneously fills the interior of a carbon nanotube. Given the hydrophobic nature of the interior of carbon nanotubes and the strong confinement produced by narrow nanotubes, the spontaneous entry of water molecules in the pores of such nanotubes is surprising. To gain a quantitative thermodynamic understanding of this phenomenon, we use the recently developed Two Phase Thermodynamics (2PT) method to compute translational and rotational entropies of water molecules confined in SWCNTs and show that the increase in energy of a water molecule inside the nanotube is compensated by the gain in its rotational entropy. The confined water is in equilibrium with the bulk water and the Helmholtz free energy per water molecule of confined water is the same as that in the bulk within the accuracy of the simulation results. A comparison of translational and rotational spectra of water molecules confined in carbon nanotubes with those of bulk water shows significant shifts in the positions of spectral peaks that are directly related to the tube radius. These peaks are experimentally accessible and can be used to characterize water dynamics from spectroscopy experiments. We have also computed the free-energy transfer when a bulk water molecule enters a SWCNT for various temperatures and carbon-water interactions. We show that for reduced carbon-oxygen interaction, the free energy transfer is unfavourable and the SWCNT remains unoccupied for significant periods of time. As the temperature is increased, the free energy of confined water becomes unfavourable and reduced occupancy of water is observed. Bulk water exhibits many anomalous properties. No single water model is able to reproduce all properties of bulk water. Different empirical water models have been developed to reproduce different properties of water. In chapter 4, a comparative study of the structure, dynamics and thermodynamic proper-ties of water molecules confined in narrow SWCNTs, obtained from simulations using several water models including polarizable ones, is presented. We show that the inclusion of polarizability quantitatively affects the nature of hydro-gen bonding which governs different properties of water molecules. The SPC/E water model is shown to reproduce results in close agreement with those from polarizable water models with much less computational cost. In chapter 5, we report results obtained from simulations of the properties of water confined in the space between two planar surfaces. We consider three cases: two graphene surfaces, two Boron Nitride (BN) surfaces and one graphene and one BN surface. This is the first detailed study of the behaviour of water near extended BN surfaces. We show that the hydrophilic nature of the BN surface leads to several interesting effects on the dynamics of water molecules near it. We have observed a change in the activation energy, extracted from the temperature dependence of the translational and rotational dynamics, near 280K. This change in activation energy coincides with a change in the structure of the confined sheet of water, indicated by a sudden change in energy. We have also found signatures of glassy dynamics at low temperatures for all three cases, the glassy effects being the strongest for water molecules confined between two BN sheets. These results are similar to those of earlier studies in which novel phases of water have been found for water molecules confined between other surfaces at high pressure. In chapter 6, we have described our observation of a novel phenomenon exhibited by water molecules flowing through a SWCNT under a pressure gradient. We have shown that the flow induces changes in the orientation of the water molecules flowing through the nanotube. In particular, the dipole moments of the water molecules inside the nanotube get aligned along the axis of the nanotube under the effect of the flow. With increasing flow velocities, the net dipole moment first increases and eventually saturates to a constant value. This behaviour is similar to the Langevin theory of paramagnetism with the flow velocity acting as an effective aligning field. Preferential entry of water molecules with dipole moments pointing inward is shown to be the main cause of this effect. This observation provides a way to control the dipolar alignment of water molecules inside nano-channels, with possible applications in nanofluidic devices. Chapter 7 contains a summary of our main results and a few concluding re-marks.

Das wesentliche Ziel dieser Doktorarbeit ist es, die Zusammenhänge zwischen der Struktur von kleinen organischen Molekülen, deren Anordnung in der Dünnschicht und der Effizienz organischer Solarzellen zu beleuchten. Die Kombination der komplementären Methoden spektroskopischer Ellipsometrie (VASE) und Röntgenstreuung, vor allem der unter streifendem Einfall (GIXRD), hat sich als sehr effiient für die Strukturuntersuchungen organischer Dünnschichten erwiesen. Zusammen geben sie einen detailreichen Einblick in die intermolekulare Anordnung, die Kristallinität, die molekulare Orientierung, die optischen Konstanten n und k und die Phasenseparation von organischen Schichten. Zusätzlich wird die Topografie der organischen Dünnschicht mit Rasterkraftmikroskopie untersucht. Der erste Fokus liegt auf der Analyse des Dünnschichtwachstums von Zink-Phthalocyanin (ZnPc) Einzelschichten. Für alle untersuchten Schichtdicken (5, 10, 25, 50 nm) und Substrattemperaturen (Tsub=30°C, 60°C, 90°C) zeigt ZnPc ein kristallines Schichtwachstum mit aufrecht stehenden ZnPc Molekülen. Um effiziente organische Solarzellen herzustellen, werden Donor- und Akzeptormoleküle üblicherweise koverdampft. Bei der Mischung von Donor- und Akzeptormolekülen bildet sich eine gewisse Phasenseparation aus, deren Form wesentlich für die Ladungsträgerextraktion entlang der Perkolationpfade ist. Der Ursprung dieser Phasenseparation wird innerhalb dieser Arbeit experimentell für ZnPc:C60 Absorber-Mischschichten untersucht. Um die Ausprägung der Phasenseparation zu variieren, werden verschiedene Tsub (30°C, 100°C, 140°C) und Mischverhältnisse (6:1, 3:1, 2:1, 1:1, 1:2, 1:3, 1:6) bei der Koverdampfung von ZnPc und C60 angewendet. GIXRD Messungen zeigen, dass hier der bevorzugte Kristallisationsprozess von C60 Molekülen die treibende Kraft für eine effiziente Phasenseparation ist. Solarzellen, die ZnPc:C60 Mischschichten mit verbesserter Phasenseparation enthalten (Tsub=140°C, 1:1), zeigen eine verbesserte Ladungsträgerextraktion und somit eine höhere Effizienz von 3,0% im Vergleich zu 2,5% für die entsprechende Referenzsolarzelle (Tsub=30°C, 1:1). Im zweiten Teil der Arbeit wird der Einfluss der Molekülorientierung auf die Dünnschichtabsorption beispielhaft an ZnPc und Diindenoperylen (DIP) untersucht. DIP und ZnPc Moleküle, die auf schwach wechselwirkenden Substraten wie Glas, SiO2, amorphen organischen Transportschichten oder C60 aufgedampft sind, zeigen eine eher stehende Orientierung innerhalb der Dünnschicht in Bezug zur Substratoberfläche. Im Gegensatz dazu führt die Abscheidung auf stark wechselwirkenden Substraten, wie z.B. einer Gold- oder Silberschicht oder 0.5 nm bis 2 nm dünnen PTCDA (3,4,9,10-Perylentetracarbonsäuredianhydrid) Templatschichten laut GIXRD und VASE Messungen dazu, dass sich die ZnPc und DIP Moleküle eher flach liegend orientieren. Dies führt zu einer wesentlich besseren Dünnschichtabsorption da das molekulare Übergangsdipolmoment jeweils innerhalb der Ebene des ZnPc und des DIP Moleküls liegt. Ein Einbetten von Gold- oder Silberzwischenschichten in organischen Solarzellen führt leider zu keinen klaren Abhängigkeiten, da die verbesserte Absorption durch die flach liegenden Moleküle von Mikrokavitäts- und plasmonischen Effekten überlagert wird. Ebenso wenig führte das Einfügen einer PTCDA-Zwischenschicht in organischen Solarzellen zum Erfolg, da hier Transportbarrieren den Effekt der verbesserten Absorption überlagern. Das letzte Kapitel konzentriert sich auf den Einfluss der Molekülstruktur auf das Dünnschichtwachstum am Beispiel von DIP und dessen Derivaten Ph4-DIP und P4-Ph4-DIP, Isoviolanthron und Bis-nFl-NTCDI (N,N-Bis(fluorene-2-yl)-naphthalenetetra-carboxylic Diimid) Derivaten. GIXRD Messungen belegen deutlich, dass die sterischen Behinderungen, hervorgerufen durch die Phenylringe (für Ph4-DIP und P4-Ph4-DIP) und Seitenketten (für Bis-nFl-NTCDI), ein amorphes Schichtwachstum induzieren. Im Vergleich sind die Dünnschichten von DIP und Bis-HFl-NTCDI kristallin. Bezüglich der Molekülorientierung und folglich der Absorption von DIP und dessen Derivaten kann ein starker Einfluss des Schichtwachstums beobachtet werden. In Solarzellen verhindert die Präsenz der Phenylringe eine effiziente Phasenseparation der Mischschichten aus (P4-)Ph4-DIP:C60, was zu einer verschlechterten Ladungsträgerextraktion und damit zu einem reduzierten Füllfaktor (FF) von 52% im Vergleich zu dem entsprechender DIP:C60 Solarzellen mit FF=62% führt Die Untersuchungen an der Bis-nFl-NTICDI Serie zeigen ein ähnliches Ergebnis: Auch hier zeichnen sich die amorphen Schichten aus Bis-nFl-NTCDI Molekülen mit Seitenketten durch schlechtere Transporteigenschaften aus als nanokristalline Bis-HFl-NTCDI Schichten. / The aim of this thesis is to demonstrate correlations between the molecular structure of small organic molecules, their arrangement in thin films, and the solar cell performance. For structure analysis of the organic thin films, the combination of variable angle spectroscopic ellipsometry (VASE) and grazing incidence X-ray diffraction (GIXRD) as complementary methods turned out to be a powerful combination. Using both methods, it is possible to obtain information about the crystallinity, crystallite size, intermolecular arrangement, mean molecular orientation, optical constants n and k, and phase separation within thin films. In addition, the topography of thin films is analyzed by atomic force microscopy. First, the thin film morphology of pristine zinc-phthalocyanine (ZnPc) films deposited at different substrate temperatures (Tsub=30°C, 60°C, 90°C) and for varying film thicknesses (5, 10, 25, 50 nm) is investigated. The ZnPc films grow highly crystalline with an upright standing molecular orientation with respect to the substrate surface for all investigated Tsub and all film thicknesses. In effcient organic solar cells, donor and acceptor molecules are commonly co-deposited to form a blend absorber film. This is usually accompanied by a certain phase separation between donor and acceptor molecules leads to a formation of percolation paths necessary to extract electrons and holes towards the electrodes. For ZnPc:C60 blends the origin of this phase separation process is analyzed by investigating different degrees of phase separation induced by film deposition at different Tsub (30°C, 100°C, 140°C) and for different blend ratios (6:1, ... , 1:6 (vol%)). GIXRD measurements indicate that the preferred crystallization of C60 is the driving force for good phase separation. Solar cells with improved phase separation of ZnPc:C60 blends (Tsub=140°C, 1:1) reveal a better charge carrier extraction and thus enhanced effciencies of 3.0% in comparison to 2.5% for the reference device (Tsub=30°C, 1:1). In the second part, the impact of molecular orientation within the absorber thin films on light harvesting is examined for pristine ZnPc and diindenoperylene (DIP) films. For film deposition on weakly interacting substrates like glass, SiO2, amorphous organic transport films, or C60, the orientation of DIP and ZnPc molecules is found to be upright standing. In contrast, GIXRD and VASE measurements show that films deposited onto strongly interacting substrates like Au and Ag, as well as on thin PTCDA templating layers lead to nearly flat-lying ZnPc and DIP molecules. Since the molecular transition dipole moment is oriented in the plane of the DIP and ZnPc molecules, the light absorption in films with flat-lying molecules is strongly improved. Unfortunately, an implementation of Au or Ag sublayers in organic solar cells does not result in reliable dependencies since the enhanced absorption by an improved molecular orientation is superimposed by different effects like microcavity and plasmonic effects. The implementation of PTCDA interlayers leads to transport barriers making the solar cell data interpretation difficult. In the last part, the influence of molecular structure on thin film growth is studied for DIP and its derivatives Ph4-DIP and P4-Ph4-DIP, isoviolanthrone, and Bis-nFl-NTCDI derivatives. GIXRD measurements reveal that steric hindrance is induced by the addition of side chains (for Bis-nFl-NTCDI) and phenyl rings (for Ph4-DIP and P4-Ph4-DIP) (N,N-Bis(fluorene-2-yl)-naphthalenetetra-carboxylic diimide) leading to an amorphous thin film growth. In contrast, DIP films and Bis-HFl-NTCDI films are found to be crystalline. The mean molecular orientation and hence the absorption is strongly affected by the different growth modes of DIP and its derivatives. In OSC, the presence of the phenyl rings prevents an effcient phase separation for (P4-)Ph4-DIP:C60 blends which causes diminished charge extraction in comparison to the crystalline DIP:C60 blends. For the Bis-nFl-NTCDI series, the transport properties are significantly worse in the amorphous films composed of Bis-nFl-NTCDI derivatives with alkyl chains in comparison to the nanocrystalline films made of the bare Bis-HFl-NTCDI.

Le procédé de coextrusion permet de combiner à l’état fondu plusieurs couches de polymères dans une même structure. La compatibilisation des différentes couches est généralement réalisée à l’aide de liants qui réagissent in-situ. Bien que la compatibilisation puisse permettre de réduire ou même supprimer les instabilités macroscopiques d’écoulement, un nouveau défaut qualifié de « granité » peut apparaitre. Très peu de travaux de la littérature traitent les mécanismes gouvernant ce type de défaut. Les phénomènes mis en jeu sont particulièrement complexes puisqu’ils impliquent de façon couplée des phénomènes hydrodynamiques via l’écoulement, la rhéologie des différentes couches et des phénomènes physico-chimiques via la diffusion et la réaction chimique aux interfaces polymère/polymère. Ce mémoire s’articule autour d’une étude multi-échelle du rôle des copolymères aux interfaces sur la stabilité des écoulements stratifiés. L’étude a été réalisée à la fois sur des systèmes non-réactifs et réactifs constitués d’une couche barrière, le polyamide 6 (PA6) ou le poly(éthylène-co-alcool vinylique) (EVOH), avec un polypropylène (PP) ou un polypropylène greffé anhydride maléique (PP-g-AM). Le défaut de « granité » a été mis en évidence en coextrusion. Les paramètres procédé et matériaux influençant son apparition ont été identifiés. Il a pu être différencié des défauts et des instabilités interfaciales généralement rencontrées en coextrusion. Le phénomène de compatibilisation a également été étudié via les caractérisations morphologiques (MET, MEB, AFM) et physico-chimiques (XPS) aux interfaces. Le comportement rhéologique en cisaillement et élongation en viscoélasticité linéaire et non linéaire s’est révélé très sensible à l’effet la présence de copolymères aux interfaces et à leur architecture moléculaire. Cette étude a permis de déterminer les propriétés intrinsèques de l’interface/interphase en fonction du copolymère formé entre le liant et le PA6 ou l’EVOH. Elles ont pu être corrélées aux défauts macroscopiques observés dans les films multicouches coextrudés. La stabilité de ces écoulements stratifiés résulte d’un couplage de phénomènes qui se produisent à différentes échelles : nano (réaction de copolymérisation), micro (interphase) et macro (écoulement dans le procédé). / Several polymers can be combined in one multilayer structure by reactive coextrusion. Tie-layers are often used to compatibilize the adjacent layers and may reduce or suppress the interfacial instabilities and the defects in the multilayer coextrusion flow. However, an additional defect defined as the “grainy” defect can be observed. In the best of our knowledge, no study in literature has been devoted to understand its origin. The phenomena are quite complex due to the coupling of the effects of flow and the physico-chemical mechanisms at the interface. The aim of this work is to understand the relations between the instabilities and the defects encountered in multilayer coextruded films and the role of the copolymer formed in-situ between tie and barrier layers. Polyamide 6 (PA6) and ethylene-vinyl alcohol copolymer (EVOH) were used as the barrier layers sandwiched in a polypropylene (PP) with or without a polypropylene grafted maleic anhydride (PP-g-MA) as a tie-layer. The effect of the process parameters and the structure of the polymers on the generation of the “grainy” defect was assessed in correlation with the rheological and the physicochemical properties of the layers. These experiments have shown that this defect appeared mainly in the compatibilized EVOH system and could be distinguished from the usual coextrusion instabilities. The interfacial properties between tie and barrier layers were investigated. The characterization of the interfacial morphology by TEM and AFM highlighted an irregular and rough interface between PP-g-MA and EVOH while a flat interface was observed with PA6 and PP-g-MA. Step shear and startup elongation rheology was shown to be sensitive to the copolymer at the polymer/polymer interface. The study of the interfacial properties highlighted that the copolymer architecture significantly impacts the interfacial roughness and the rheology of the multilayer stuctures. Hence, relations between the relaxation process, the interfacial morphology and the copolymer architecture were established in correlation with the generation of the macroscopic grainy defect in coextrusion.