This thesis explores the capacity of sterically and electronically unsaturated boranes to bind substrates of biological and environmental interest, and transduce such binding events into a photo-physical and/or electrochemical response, hence reporting the presence of these substrates. Chapter three details the synthesis of a range of novel ferrocenyl boranes featuring either a proximal hydrogen-bond donor or a second Lewis acidic centre. These novel boranes were shown to be competent at binding both cyanide and fluoride anions, with the role played by a proximal hydrogen-bond donor or a second Lewis acidic centre in anion binding investigated by both NMR and crystallographic studies. Chapter four reports the synthesis of novel pyridinyl and related boronic esters, as well as unexpected mixed alkenyl/aryl boranes. The capacity of both types of system to bind fluoride or cyanide anions in solution was investigated by UV-Vis and NMR studies. The photo-physical responses to these anions were also probed, leading to the establishment of both switch-on and switch-off fluorescent responses. Chapter five extends the knowledge derived from selective anion receptor design and combines this with recent developments in the field of frustrated Lewis pairs (FLPs) to activate, bind and report the presence of nitrous oxide (N₂O) molecule. Thus, the syntheses of novel, highly Lewis acidic ferrocenyl boranes that incorporate a high degree of steric loading around the boron centre are reported. The electrochemical and photo-physical response of an FLP system to the presence of N₂O was investigated leading to the development of a novel N₂O reporting system.

Confocal single-molecule fluorescence is a powerful tool for monitoring conformational dynamics, and has provided new insight into the enzymatic activities of complex biological molecules such as DNA and RNA polymerases. Though useful, such studies are typically qualitative in nature, and performed almost exclusively in highly purified, in vitro settings. In this work, I focus on improving the methodology of confocal single-molecule fluorescence in two broad ways: (i) by enabling the quantitative identification of molecular dynamics in proteins and nucleic acids in vitro, and (ii) developing the tools needed to perform these analyses in vivo. Toward the first goal, and together with several colleagues, I have developed three novel methods for the quantitative identification of dynamics in biomolecules: (i) Burst Variance Analysis (BVA), which unambiguously identifies dynamics in single-molecule FRET experiments; (ii) Dynamic Probability Density Analysis (PDA), which hypothesis-tests specific kinetic models against smFRET data and extracts rate information; and (iii) a novel molecular counting method useful for studying single-molecule thermodynamics. We validated these methods against Monte Carlo simulations and experimental DNA controls, and demonstrated their practical application in vitro by analyzing the “fingers-closing” conformational change in E.coli DNA Polymerase I; these studies identified unexpected conformational flexibility which may be important to the fidelity of DNA synthesis. To enable similar studies in the context of a living cell, we generated a nuclease-resistant DNA analogue of the Green Fluorescent Protein, or “Green Fluorescent DNA,” and developed an electroporation method to efficiently transfer it into the cytoplasm of E.coli. We demonstrate in vivo confocal detection of smFRET from this construct, which is both bright and photostable in the cellular milieu. In combination with PDA, BVA and our novel molecular counting method, this Green Fluorescent DNA should enable the characterization of DNA and protein-DNA dynamics in living cells, at the single-molecule level. I conclude by discussing the ways in which these methods may be useful in investigating the dynamics of processes such as transcription, translation and recombination, both in vitro and in vivo.

This thesis is concerned with the influence of nanoscale boundaries and interfaces upon the electronic processes that occur within the inorganic semiconductors. Inorganic semiconductor nanowires and their blends with semiconducting polymers have been investigated using state-of-the-art ultrafast optical techniques to provide information on the sub-picosecond to nanosecond photoexcitation dynamics in these systems. Chapters 1 and 2 introduce the theory and background behind the work and present a literature review of previous work utilising nanowires in hybrid organic photovoltaic devices, revealing the performances to date. The experimental methods used during the thesis are detailed in Chapter 3. Chapter 4 describes the crucial roles of surface passivation on the ultrafast dynamics of exciton formation in gallium arsenide (GaAs) nanowires. By passivating the surface states of nanowires, exciton formation via the bimolecular conversion of electron-hole plasma can observed over few hundred picoseconds, in-contrast to the fast carrier trapping in 10 ps observed in the uncoated nanowires. Chapter 5 presents a novel method to passivate the surface-states of GaAs nanowires using semiconducting polymer. The carrier lifetime in the nanowires can be strongly enhanced when the ionization potential of the overcoated semiconducting polymer is smaller than the work function of the nanowires and the surface native oxide layers of nanowires are removed. Finally, Chapter 6 shows that the carrier cooling in the type-II wurtzite-zincblend InP nanowires is reduced by order-of magnitude during the spatial charge-transfer across the type-II heterojunction. The works decribed in this thesis reveals the crucial role of surface-states and bulk defects on the carrier dynamics of semiconductor nanowires. In-addition, a novel approach to passivate the surface defect states of nanowires using semiconducting polymers was developed.

Metal oxides are of immense technological importance. Their wide variety of structural and electronic characteristics leads to a flexibility unrivalled by other groups of materials. However, there is still much debate about the fundamental properties of some of the most widely used oxides, including TiO₂ and In₂O₃. This work presents high quality, in-depth characterisation of these two oxides in pure and doped form, including soft and hard X-ray photoelectron spectroscopy and X-ray diffraction. Bulk samples as well as thin film samples were prepared analysed. For the preparation of thin films a high quality sol-gel dip-coating method was developed, which resulted in epitaxial films. In more detail the organisation of the thesis is as follows: Chapter 1 provides an introduction to key ideas related to metal oxides and presents the metal oxides investigated in this thesis, In₂O₃, Ga₂O₃, Tl₂O₃, TiO₂, and SnO₂. Chapter 2 presents background information and Chapter 3 gives the practical details of the experimental techniques employed. Chapters 4 presents reciprocal space maps of MBE-grown In₂O₃ thin films and nanorods on YSZ substrates. Chapters 5 and 6 investigate the doping of In₂O₃ bulk samples with gallium and thallium and introduce a range of solid state characterisation techniques. Chapter 7 describes the development of a dip-coating sol-gel method for the growth of thin films of TiO₂ and shows 3D reciprocal space maps of the resulting films. Chapter 8 concerns hard x-ray photoelectron spectroscopy of undoped and Sn-doped TiO₂. Chapter 9 interconnects previous chapters by presenting 2D reciprocal space maps of nano structured epitaxial samples of In₂O₃ grown by the newly developed sol-gel based method. Chapter 10 concludes this thesis with a summary of the results.

Monolayers of the cationic surfactant hexadecyltrimethylammonium halide (CTAX, where X = F¯, Cl¯, Br¯, and I¯) have been studied at the air-water and oilwater interfaces. At the air-water interface, the effects of the halide counterion and the addition of counterion were investigated. Sum-frequency spectroscopy (SFS), ellipsometry, and surface tensiometry indicated that the counterion changed the efficiency and effectiveness of the surfactant, both decreasing in the order of Br¯> Cl¯>F¯. The addition of salt in the form of 0.1 M KX was found to reduce the cmc but had little effect on the limiting area per molecule attained at the cmc, which increased from 44 Ų for CTAB to 65 Ų for CTAC and ca. 94 Ų for CTAF. Neither SFS nor ellipsometry provided any firm evidence for specific effects of the halide ions on the structure of the surfactant monolayers. For CTAB monolayers in the absence of excess electrolyte, the effect of area per molecule on the sum-frequency (SF) spectra was studied. Mixed monolayers of CTAB and tetradecane at the air-water interface exhibit a first-order phase transition from a conformationally disordered to a conformationally ordered state as the temperature is lowered. The phase transition occurs ca. 11 °C above the bulk melting point of tetradecane. A new experimental arrangement is described for acquiring SF spectra from surfactants at the oil-water interface. The key features of this approach are the stabilisation of a thin oil film between a sapphire prism and an aqueous phase, and the use of total internal reflection to enhance the total signal and discriminate against signals from other interfaces in the system. With this new methodology, the first SF vibrational spectra of surfactant monolayers at an alkane-water interface were obtained. Surface tensiometry was used to characterise the monolayers further. The structure of CTAB monolayers at the hexadecane-water interface was determined by SFS and compared with monolayers of CTAB at the air-water interface. At low concentrations, CTAB/hexadecane showed the expected features in the C-H stretching region, characteristic of a conformationally disordered monolayer. As the bulk concentration approached the critical micelle concentration, the spectra changed to one characteristic of a more ordered, upright conformation. Ellipsometric measurements supported this conclusion. This qualitative structural change is not observed in analogous monolayers at the air-water interface or CCl₄-water interface, or in surfactant solutions in contact with a hydrophobic solid surface.

In addition to a central circadian clock in the suprachiasmatic nucleus (SCN), zebrafish (Danio rerio) have local clock systems in their peripheral tissues. These peripheral tissues express a complement of clock genes that can be synchronized with the 24 h light/dark cycle and thus may be entrained by light. To date, teleost multiple tissue (tmt) opsin identified from Fugu rubripes and Danio rerio is the only opsin that has been proposed as a candidate to mediate this cellular photoentrainment (Moutsaki et al., 2003). Here we report the discovery of a multigene family of tmt opsins found not only in the teleost fishes, but in vertebrates,including amphibians, birds, reptiles, and some mammals. Phylogenetic analysis demonstrated that this gene family consists of three main classes, tmtI, tmtII and tmtIII, with each duplicating further to give two paralogues in the zebrafish genome. Their predicted amino acid sequences contain most of the characteristic features for the function of a photopigment opsin, as well as seven transmembrane segments indicative of a G protein coupled receptor (GPCR) superfamily. Significantly, reverse transcription polymerase chain reaction (RT-PCR) reveals that the tmt opsin genes in zebrafish are both temporally and spatially regulated. To investigate if these tmt photopigments mediate light-activated currents in cells, each opsin was expressed in vitro and the responses characterised by calcium imaging, whole-cell patch clamp electrophysiology, UV-Vis spectrophotometric analysis, and bioluminescence reporter assay. Collectively, these data suggest that some of the opsin photoproteins signal via Gi-type G protein pathway. Interestingly, the spectral analysis obtained shows that most tmt opsins tested are UV-sensitive when reconstituted in vitro with 11-cis and all-trans retinal, indicating an intrinsic bistable dynamics. Using site directed mutagenesis on one of the tmt opsins, tmt10, the potential spectral tuning sites involved in UV detection were tested. As part of this study, tmt opsin cDNAs were isolated from three populations of Mexican tetra (Astyanax mexicanus): surface, Pachon and Steinhardt. This allowed for a direct comparison between the tmt opsins present in the dark adapted species (cavefish) versus those of the light adapted species (zebrafish). It is hoped that the findings from this project will contribute to our understanding of non-visual light detection in fish and the evolution of their non-image forming photoreception.

Molecular biophysics is a rapidly evolving field aimed at the physics-based investigation of the biomolecular processes that enable life. In this thesis, we explore two such processes: the thermodynamics of DNA bending, and the mechanism of the RecQ DNA helicase. A computational approach using a coarse-grained model of DNA is employed for the former; an experimental approach relying heavily on single-molecule fluorescence for the latter. There is much interest in understanding the physics of DNA bending, due to both its biological role in genome regulation and its relevance to nanotechnology. Small DNA bending fluctuations are well described by existing models; however, there is less consensus on what happens at larger bending fluctuations. A coarse-grained simulation is used to fully characterize the thermodynamics and mechanics of duplex DNA bending. We then use this newfound insight to harmonize experimental results between four distinct experimental systems: a 'molecular vise', DNA cyclization, DNA minicircles and a 'strained duplex'. We find that a specific structural defect present at large bending fluctuations, a 'kink', is responsible for the deviation from existing theory at lengths below about 80 base pairs. The RecQ DNA helicase is also of much biological and clinical interest, owing to its essential role in genome integrity via replication, recombination and repair. In humans, heritable defects in the RecQ helicases manifest clinically as premature aging and a greatly elevated cancer risk, in disorders such as Werner and Bloom syndromes. Unfortunately, the mechanism by which the RecQ helicase processes DNA remains poorly understood. Although several models have been proposed to describe the mechanics of helicases based on biochemical and structural data, ensemble experiments have been unable to address some of the more nuanced questions of helicase function. We prepare novel substrates to probe the mechanism of the RecQ helicase via single-molecule fluorescence, exploring DNA binding, translocation and unwinding. Using this insight, we propose a model for RecQ helicase activity.

Le travail théorique présenté dans cette thèse concerne la formation de molécules ultra-froides bialcalines et le contrôle de leurs degrés de liberté externes et internes. Cette étude est motivée par les nombreuses expériences en cours visant à l'obtention d'un gaz quantique dégénéré de molécules dans leur état fondamental absolu. Le schéma de formation étudié repose sur le processus de transfert adiabatique stimulé (STIRAP) réalisé en présence d'un potentiel optique de piégeage (réseau optique) des atomes et des molécules.Nous avons déterminé les paramètres du réseau optique (intensité et fréquence du champ laser) qui permettent de piéger efficacement des dimères d'alcalins en évaluant la polarisabilité dynamique acquise par les molécules soumises à un champ externe. Ces calculs reposent en particulier sur la connaissance détaillée de la structure électronique des molécules. Nous avons identifié des plages de longueur d'ondes dites « magiques » où la polarisabilité est la même pour chaque niveau peuplé au cours du transfert adiabatique, permettant ainsi un transfert optimal. Ce formalisme nous a également permis d'obtenir les coefficients Van der Waals de l'interaction à longue portée nécessaires pour étudier les taux de collisions entre molécules.Nous avons réalisé une étude plus détaillée de la molécule RbCs. En étudiant précisément la probabilité de transition de la molécule vers un niveau excité, nous avons proposé un schéma STIRAP pour transférer des molécules de RbCs, initialement dans un niveau vibrationnel excité, vers leur état rovibrationnel fondamental.Ces travaux ont montré l'importance de la connaissance précise de la structure hyperfine de l'état électronique moléculaire excité pour réaliser un gaz dégénéré de molécules dans un état quantique bien défini. Un modèle asymptotique nous a permis d'obtenir une première estimation de la structure hyperfine des courbes d'énergies potentielles des premiers états moléculaires excités des molécules Cs2 et RbCs. / The theoretical work presented in this thesis is focused on the formation of ultracold bialcaline molecules and on the control of their external and internal degrees of freedom. This study is motivated by the increasing number of experiments aiming at obtaining a quantum degenerate gas of molecules in their absolute ground state. The formation scheme we worked on is based on the Stimulated Raman Adiabatic Passage (STIRAP) technique operated while molecules are trapped inside an optical lattice.We have determined the parameters of the optical lattice (intensity and wavelength of the laser) that allow for an efficient trapping of the alkali dimers by evaluating the dynamic polarizability of molecules in the presence of an external field. Such calculations require the accurate knowledge of the electronic structure of the molecules. We have identified the so-called ``magic'' wavelength for which all levels populated during the STIRAP sequence have the same polarizability, thus ensuring an optimal transfer. The same approach has also been used to compute the strength of the long-range interaction between polar bialkali molecules needed to evaluate collision rates.The particular case of the RbCs molecule has been investigated. We have selected a radiative transition allowing for an efficient STIRAP scheme yielding molecules in their rovibrational ground state. These works have raised the need for the precise knowledge of the hyperfine structure of the excited electronic molecular state involved in the STIRAP scheme. We have developed an asymptotic model to obtain a first estimate of the hyperfine structure for the potential curves of the lowest excited states of Cs2 and RbCs.

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).

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.