Probing pi-conjugated polymers with circularly polarized light

In this thesis, we use circular polarized light to study aggregation in p-conjugated polymers at various structural levels. The importance of this study stems from the necessity to understand polymer packing and aggregation in thin films, used as active layer in optoelectronic devices like solar cells and light-emitting diodes. A systematic study on understanding polymer aggregation would provide freedom to tune the opto-electronic properties of the polymer in desired fashion. p-conjugated polymer have a backbone consisting of alternating single and double bonds, which gives these polymers semiconducting properties and creates optical transitions in visible wavelength region. These opto-electronic properties depend strongly on the conformation of the polymer backbone and on interchain contacts arising from aggregation of polymer chains. Here we use circularly polarized light to probe the optical, conformational and electronic properties of p-conjugated polymers. This thesis focuses on chiral p-conjugated polymers. Chirality serves here as a spectroscopic ‘label’ allowing us to investigate aggregation and chiroptical properties of the polymer chains using circular dichroism (CD) spectroscopy. CD spectroscopy allows us to study differential absorption between left and right handed circularly polarized light. The dissymmetry ratio in absorbance is often termed as gabs. The gabs can be independent of the amount of the material, in which case the gabs can be regarded as intensive property of the material. On the other hand, if it is dependent on the amount of the material, gabs can be associated as the extensive property. Chapters 2 and 3 utilize these definitions to study the intensive and extensive properties of chiral polythiophene and chiral polyfluorene respectively. Chapter 3 divulges further into the origins of the intensive and extensive nature of gabs, hence outlining the polymer aggregation at different structural levels. On investigating poly[3-((3S)-3,7-dimethyloctyl)thiophene] (PT811), gabs was found to be independent of the film thickness (Chapter 2). Thus the gabs in this case can be regarded as intensive, originating from a chiral molecular organization on a length scale <50 nm. Having understood the intensive nature of gabs, a detailed study on aggregation of poly[9,9-bis((3S)- 3,7-dimethyloctyl)-2,7-fluorene] (PF811) was carried out (Chapter 3). It was found that pristine films of PF811 also show gabs that is independent of the film thickness and hence can be regarded as intensive in nature. AFM reveals that the polymer chains collapse into fibrillous aggregates upon spin coating the solutions of PF811. Similar CD effects were also observed in solution by inducing aggregation in polymer chains by adding a non-solvent (MeOH) to molecularly dissolved solutions of PF811 in chloroform. These aggregates can be transferred from solution to film. These films also show similar fibrillous aggregates. This suggests that the intensive gabs is probably related to chiral arrangement of a few polymer chains within a fibril. Interestingly, it was found that thermally annealed films of PF811 show gabs dependent of the thickness of the film, indicating that here the CD effects arise on a larger length scale (>50 nm). The AFM shows retention of fibrils, suggesting long range ordering of fibrils, probably cholesteric in nature. Chapters 2 and 3 dealt with the differential absorbance of circularly polarized light in transmission mode. However, information about polymer aggregation can also be extracted from reflection and scattering of circularly polarized light, which is emphasized in Chapter 4. It was observed that the annealed films of PF811 show a CD effect for > 450nm, even though polymer does not absorb in this wavelength range. This anomalous behavior was investigated via a tailor-made setup and it was found that this apparent CD is a result of selectivity in scattering of left and right circular polarized light by the polymer film. Interestingly CD effects are also observed in triplet-triplet photoinduced absorbance of the PF811 polymer (Chapter 5). The large CD observed here most likely arises from interaction of the linearly polarized photoinduced transition T1-Tn with the surrounding birefringent matrix of thermally annealed polymer. Besides being an important blue light-emitting polymer, polyfluorenes (PFs) are also interesting because they can occur in a and ß aggregates, each having its own optoelectronic properties. Processing conditions are of paramount importance in promoting the aggregation/phase. Through temperature dependent CD studies of PF811 in 1-octanol, these aggregates could be identified by their different CD spectra for the first time (Chapter 6). It was discovered that dilute solutions often yielded ¿-aggregates, whereas slow controlled cooling of concentrated solutions led to formation of ¿-aggregates. Remarkably though, pi- aggregates were found to appear only via formation of a precursor involving cooperative folding of two or more chains. Rod-like behavior of PFs is well known and anisotropy in achiral PF films has already been established by their different in-plane and out-of-plane optical constants obtained by spectroscopic ellipsometry (SE). Here one essential measures the change of linearly polarized light into elliptically polarized light upon reflection from the polymer film. The anisotropic dielectric tensor of chiral polyfluorene is determined via variable angle spectroscopic ellipsometry and circular dichroism spectroscopy (Chapter 7). The anisotropy was found to be influenced by high in-plane alignment of polymer chains in the thin film. Chirality of the polymer results in small but non-zero off diagonal matrix elements in the dielectric tensor. Subsequently, optical rotation and ellipticity in reflection are predicted for pristine film of chiral polyfluorene. In all previous chapters circular polarized light has been mostly employed to investigate optical and conformational aspects of ¿-conjugated polymers. Chapter 8 utilizes polarized light to study electronic properties of ¿-conjugated polymer in p-n junction device involving poly(ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS) and ZnO. The Moss- Burstein shift, i.e. an apparent increase of the optical band gap, is observed upon UV illumination of a layer of 5 nm ZnO nanoparticles in O2-free atmosphere using spectroscopic ellipsometry. This shift is caused by populating the conduction band with excess free charge carriers and depleting the valence band. The free charge carrier density was determined to be 2 ¿ 10-19 /cm3, about one carrier per particle. The shift can be reversed by introduction of O2. For junctions of ZnO nanoparticle layers with a pH neutral PEDOT:PSS conducting polymer layer a depletion width of 5 nm in ZnO is observed under UV illumination in O2-free atmosphere. At the junction free charge carriers in ZnO are transferred to neutral-PEDOT:PSS causing a slight reduction of the latter

Lattice Boltzmann Method simulations of high Reynolds number flows past porous obstacles

Lattice Boltzmann Method (LBM) simulations for turbulent flows over fractal and non-fractal obstacles are presented. The wake hydrodynamics are compared and discussed in terms of flow relaxation, Strouhal numbers and wake length for different Reynolds numbers. Three obstacle topologies are studied, Solid (SS), Porous Regular (PR) and Porous Fractal (FR). In particular, we observe that the oscillation present in the case of the solid square can be annihilated or only pushed downstream depending on the topology of the porous obstacle. The LBM is implemented over a range of four Reynolds numbers from 12,352 to 49,410. The suitability of LBM for these high Reynolds number cases is studied. Its results are compared to available experimental data and published literature. Compelling agreements between all three tested obstacles show a significant validation of LBM as a tool to investigate high Reynolds number flows in complex geometries. This is particularly important as the LBM method is much less time consuming than a classical Navier–Stokes equation-based computing method and high Reynolds numbers need to be achieved with enough details (i.e., resolution) to predict for example canopy flows

A Fibreoptic Endoscopic Study of Upper Gastrointestinal Bleeding at Bugando Medical Centre in Northwestern Tanzania: a Retrospective Review of 240 Cases.

Upper gastrointestinal (GI) bleeding is recognized as a common and potentially life-threatening abdominal emergency that needs a prompt assessment and aggressive emergency treatment. A retrospective study was undertaken at Bugando Medical Centre in northwestern Tanzania between March 2010 and September 2011 to describe our own experiences with fibreoptic upper GI endoscopy in the management of patients with upper gastrointestinal bleeding in our setting and compare our results with those from other centers in the world. A total of 240 patients representing 18.7% of all patients (i.e. 1292) who had fibreoptic upper GI endoscopy during the study period were studied. Males outnumbered female by a ratio of 2.1:1. Their median age was 37 years and most of patients (60.0%) were aged 40 years and below. The vast majority of the patients (80.4%) presented with haematemesis alone followed by malaena alone in 9.2% of cases. The use of non-steroidal anti-inflammatory drugs, alcohol and smoking prior to the onset of bleeding was recorded in 7.9%, 51.7% and 38.3% of cases respectively. Previous history of peptic ulcer disease was reported in 22(9.2%) patients. Nine (3.8%) patients were HIV positive. The source of bleeding was accurately identified in 97.7% of patients. Diagnostic accuracy was greater within the first 24 h of the bleeding onset, and in the presence of haematemesis. Oesophageal varices were the most frequent cause of upper GI bleeding (51.3%) followed by peptic ulcers in 25.0% of cases. The majority of patients (60.8%) were treated conservatively. Endoscopic and surgical treatments were performed in 30.8% and 5.8% of cases respectively. 140 (58.3%) patients received blood transfusion. The median length of hospitalization was 8 days and it was significantly longer in patients who underwent surgical treatment and those with higher Rockall scores (P < 0.001). Rebleeding was reported in 3.3% of the patients. The overall mortality rate of 11.7% was significantly higher in patients with variceal bleeding, shock, hepatic decompensation, HIV infection, comorbidities, malignancy, age > 60 years and in patients with higher Rockall scores and those who underwent surgery (P < 0.001). Oesophageal varices are the commonest cause of upper gastrointestinal bleeding in our environment and it is associated with high morbidity and mortality. The diagnostic accuracy of fibreoptic endoscopy was related to the time interval between the onset of bleeding and endoscopy. Therefore, it is recommended that early endoscopy should be performed within 24 h of the onset of bleeding

Site-selective photocatalytic functionalization of peptides and proteins at selenocysteine

The importance of modified peptides and proteins for applications in drug discovery, and for illuminating biological processes at the molecular level, is fueling a demand for efficient methods that facilitate the precise modification of these biomolecules. Herein, we describe the development of a photocatalytic method for the rapid and efficient dimerization and site-specific functionalization of peptide and protein diselenides. This methodology, dubbed the photocatalytic diselenide contraction, involves irradiation at 450 nm in the presence of an iridium photocatalyst and a phosphine and results in rapid and clean conversion of diselenides to reductively stable selenoethers. A mechanism for this photocatalytic transformation is proposed, which is supported by photoluminescence spectroscopy and density functional theory calculations. The utility of the photocatalytic diselenide contraction transformation is highlighted through the dimerization of selenopeptides, and by the generation of two families of protein conjugates via the site-selective modification of calmodulin containing the 21st amino acid selenocysteine, and the C-terminal modification of a ubiquitin diselenide.Luke J. Dowman, Sameer S. Kulkarni, Juan V. Alegre-Requena, Andrew M. Giltrap, Alexander R. Norman, Ashish Sharma, Liliana C. Gallegos, Angus S.Mackay, Adarshi P. Welegedara, Emma E. Watson, Damian van Raad, Gerhard Niederacher, Susanne Huhmann, Nicholas Proschogo, Karishma Patel, Mark Larance, Christian F. W. Becker, Joel P. Mackay, Girish Lakhwani, Thomas Huber, Robert S. Paton, Richard J. Payn

A New Mechanistic Scenario for the Origin and Evolution of Vertebrate Cartilage

The appearance of cellular cartilage was a defining event in vertebrate evolution because it made possible the physical expansion of the vertebrate “new head”. Despite its central role in vertebrate evolution, the origin of cellular cartilage has been difficult to understand. This is largely due to a lack of informative evolutionary intermediates linking vertebrate cellular cartilage to the acellular cartilage of invertebrate chordates. The basal jawless vertebrate, lamprey, has long been considered key to understanding the evolution of vertebrate cartilage. However, histological analyses of the lamprey head skeleton suggest it is composed of modern cellular cartilage and a putatively unrelated connective tissue called mucocartilage, with no obvious transitional tissue. Here we take a molecular approach to better understand the evolutionary relationships between lamprey cellular cartilage, gnathostome cellular cartilage, and lamprey mucocartilage. We find that despite overt histological similarity, lamprey and gnathostome cellular cartilage utilize divergent gene regulatory networks (GRNs). While the gnathostome cellular cartilage GRN broadly incorporates Runx, Barx, and Alx transcription factors, lamprey cellular cartilage does not express Runx or Barx, and only deploys Alx genes in certain regions. Furthermore, we find that lamprey mucocartilage, despite its distinctive mesenchymal morphology, deploys every component of the gnathostome cartilage GRN, albeit in different domains. Based on these findings, and previous work, we propose a stepwise model for the evolution of vertebrate cellular cartilage in which the appearance of a generic neural crest-derived skeletal tissue was followed by a phase of skeletal tissue diversification in early agnathans. In the gnathostome lineage, a single type of rigid cellular cartilage became dominant, replacing other skeletal tissues and evolving via gene cooption to become the definitive cellular cartilage of modern jawed vertebrates

Beta phase in chiral polyfluorene forms via a precursor

Chiral poly{9,9-bis[(3S)-3,7-dimethyloctyl]-2,7-fluorene) shows temperature-induced aggregation in 1-octanol. For polymer concentrations of > 0.01 mg/mL and cooling rates of = 10 °C/h, aggregates form, showing characteristics of the ß phase of polyfluorene. At higher cooling rates, lower concentration, or both, another type of aggregates forms (a), a and ß phases are distinguished by absorption, fluorescence, and circular dichroism (CD) spectroscopy. Temperature-dependent CD and dynamic light scattering show that the ß phase forms only via a precursor aggregate, whose formation is concentration-, temperature-, and time-dependent. The yield of the ß phase can be optimized by choosing processing conditions that favor the formation of the precursor

Hydrothermal synthesis and stabilization of nanocrystalline cerium (IV) oxide

The effect of key parameters on the hydrothermal synthesis and colloidal stabilization of nanocrystalline CeO2 powders was investigated. In the hydrothermal synthesis, the effects of temperature, time, doping with Y3+ cations and the composition of the starting cerium salt on the characteristics of the powders were studied by X-ray line broadening and transmission electron microscopy. Stabilization of the colloidal suspensions was achieved by electrostatic or steric repulsion in an aqueous solvent. For steric stabilization, the adsorption of polymers was studied as a function of pH. At a given temperature, the coarsening of the particles during hydrothermal synthesis can be described by a parabolic law, indicating that the interfacial reaction (dissolution) step was rate controlling. For powders prepared from Ce(NO3)3, the activation energy for coarsening was 25 ± 1 kJ/mol. The incorporation of Y3+ as a dopant produced a significant reduction in the rate of coarsening, with an activation energy of 27 ± 2 kJ/mol. The coarsening rate for undoped CeO2 prepared from CeCl3 was significantly lower than that for powders prepared from the nitrate. The effect of the particle characteristics on the sintering of powder compacts was also investigated. In aqueous solvents, polyvinylpyrrolidone, PVP, showed significant adsorption which was dependent on the pH of the suspension. At a pH of 3.7 the largest amount of adsorbed PVP, molecular weight 24,000, was 10 wt%, based on the dry weight of the powder. The significance of the adsorption data for controlling the microstructural homogeneity was tested for by the preparation of films via the spin coating of suspensions and their characterization --Abstract, page iii

Insights from chiral polyfluorene on the unification of molecular exciton and cholesteric liquid crystal theories for chiroptical phenomena

The Maugin–Oseen–DeVries theory accounts for chiroptical properties of cholesteric films with long-range order. For molecular systems with short-range structural correlation lengths, molecular exciton theory is used. A consistent description for systems with intermediate correlation lengths is lacking. Films of chiral polyfluorene behave according to Maugin–Oseen–DeVries theory when the film thickness exceeds 300 nm. Properties of thin films are consistent with molecular exciton theory. We describe the crossover in the optical properties of the film in a phenomenological way using a dielectric tensor that contains terms from Maugin–Oseen–DeVries and molecular exciton theory. Guided by the experimental findings, we explore the possibility of a unification of the Maugin–Oseen–DeVries and molecular exciton theory involving a coupled oscillator model

Hydrothermal Coarsening of CeO₂ Particles

The effects of reaction temperature (150-300 °C), chemical composition of the starting cerium salt (cerium nitrate and cerium chloride), and doping with trivalent cations (Sc3+ and Y3+) on the coarsening of CeO2 particles in dilute suspensions under hydrothermal conditions were investigated. The particle size was measured by x-ray line broadening and by transmission electron microscopy. The particle coarsening kinetics followed a parabolic law, indicating that the interfacial reaction (dissolution) was the rate-controlling step. Furthermore, the particle size distribution data can be well-described by the Lifshitz-Slyozov-Wagner theory of Ostwald ripening controlled by the interfacial reaction. Doping with 6 at.% Y3+ produced a significant reduction in the coarsening rate but almost no change in the activation energy. At the same concentration, Sc3+ was more effective than Y3+ in reducing the coarsening rate. Particles synthesized from a starting solution of cerium(III) chloride coarsened at a markedly slower rate than that for particles synthesized from cerium(III) nitrate. The mechanisms controlling the coarsening of the particles are discussed