Probing the relationships between molecular conformation and intermolecular contacts in N,N-dibenzyl-N '-(furan-2-carbonyl)thiourea

In the crystal structure of the title compound, C20H18N2O2S, molecules are linked by bifurcated C-H center dot center dot center dot O hydrogen-bond interactions, giving rise to chains whose links are composed of alternating centrosymmetrically disposed pairs of molecules and characterized by R-2(2)(10) and R-2(2)(20) hydrogen-bonding motifs. Also, N-H center dot center dot center dot S hydrogen bonds form infinite zigzag chains along the [010] direction, which exhibit the C(4) motif. Hirshfeld surface and fingerprint plots were used to explore the intermolecular interactions in the crystal structure. This analysis confirms the important role of C-H center dot center dot center dot O hydrogen bonds in the molecular conformation and in the crystal structure, providing a potentially useful tool for a full understanding of the intermolecular interactions in acylthiourea derivatives.

Size-dependent phase transitions in nanostructured zirconia-scandia solid solutions.

Size effects on phase stability and phase transitions in technologically relevant materials have received growing attention. Several works reported that metastable phases can be retained at room temperature in nanomaterials, these phases generally corresponding to the high-temperature polymorph of the same material in bulk state. Additionally, size-dependent shifts in solubility limits and/or in the transition temperatures for on heating or on cooling cycles have been observed. ZrO2-Sc2O3 (zirconia-scandia) solid solutions are known to exhibit very high oxygen ion conductivity provided their structure is composed of cubic and/or pseudocubic tetragonal phases. Unfortunately, for solid zirconia-scandia polycrystalline samples with typical micrometrical average crystal sizes, the high-conductivity cubic phase is only stable above 600°C. Depending on composition, three low-conductivity rhombo-hedral phases (β, γ and δ) are stable below 600°C down to room temperature, within the compositional range of interest for SOFCs. In previous investigations, we showed that the rhombohedral phases can be avoided in nanopowders with average crystallite size lower than 35 nm.

Synthesis, structure and conformation of oligo- and polysaccharides

Carbohydrates are a complex group of biomolecules with a high structural diversity. Their almost omnipresent occurrence has generated a broad field of research in both biology and chemistry. This thesis focuses on three different aspects of carbohydrate chemistry, synthesis, structure elucidation and the conformational analysis of carbohydrates. The first paper describes the synthesis of a penta- and a tetrasaccharide related to the highly branched capsular polysaccharide from Streptococcus pneumoniae type 37. In the second paper, the structure of the O-antigenic repeating unit from the lipopolysaccharide of E. coli 396/C1 was determined along with indications of the structure of the biological repeating unit. In addition, its structural and immunological relationship with E. coli O126 is discussed. In the third paper, partially protected galactopyranosides were examined to clarify the origin of an intriguing 4JHO,H coupling, where a W-mediated coupling pathway was found to operate. In the fourth paper, the conformation of methyl a-cellobioside is studied with a combination of molecular dynamics simulations and NMR spectroscopy. In addition to the expected syn-conformation, detection and quantification of anti-ø and anti-ψ conformers was also possible.

Human Abuses of Coral Reefs- Adaptive Responses and Regime Transitions

During the last few decades, coral reefs have become a disappearing feature of tropical marine environments, and those reefs that do remain are severely threatened. It is understood that humans have greately altered the environment under which these ecosystems previously have thrived and evoloved. Overharvesting of fish stocks, global warming and pollution are some of the most prominent threats, acting on coral reefs at several spatial and temporal scales. Presently, it is common that coral reefs have been degraded into alternative ecosystem regimes, such as macroalgae-dominated or sea urchin-barren. Although these ecosystems could potentially return to coral dominance in a long-term perspective, when considdering current conditions, it seems likely that they will persist in their degraded states. Thus, recovery of coral reefs cannot be taken for granted on a human timescale. Multiple stressors and disturbances, which are increasingly characteristic of coral reef environments today, are believed to act synergistically and produce ecological surprises. However, current knowledge of effects of compounded disturbances and stress is limited. Based on five papers, this thesis investigates the sublethal response of multiple stressors on coral physiology, as well as the effects of compounded stress and disturbance on coral reef structure and function. Adaptive responses to stress and disturbance in relation to prior experience are highlighted. The thesis further explores how inherent characteristics (traits) of corals and macroalgae may influence regime expression when faced with altered disturbance regimes, in particular overfishing, eutrophication, elevated temperature, and enhanced substrate availability. Finally, possibilities of affecting the resilience of macroalgae-dominaed reefs and shifting the community composition towards a coral-dominated regime are explored.

Conformation and Stereodynamic of Hindered Aromatic System

The preparation of conformationally hindered molecules and their study by DNMR and computational methods are my thesis’s core. In the first chapter, the conformations and the stereodynamics of symmetrically ortho-disubstituted aryl carbinols and aryl ethers are described. In the second chapter, the structures of axially chiral atropisomers of hindered biphenyl carbinols are studied. In the third chapter, the steric barriers and the -barrier of 1,8-di-aylbiphenylenes are determined. Interesting atropisomers are found in the cases of arylanthrones, arylanthraquinones and arylanthracenes and are reported in the fourth chapter. By the combined use of dynamic NMR, ECD spectroscopy and DFT computations, the conformations and the absolute configurations of 2-Naphthylalkylsulfoxides are studied in the fifth chapter. In the last chapter, a new synthetic route to ,’-arylated secondary or tertiary alcohols by lithiated O-benzyl-carbamates carrying an N-aryl substituent and DFT calculations to determinate the cyclic intermediate are reported. This work was done in the research group of Prof. Jonathan Clayden, at the University of Manchester.

Noisy Oncology: applications of bounded noise transitions in modelling tumor growth

I tumori macroscopici e microscopici, dopo la loro prima fase di crescita, sono composti da un numero medio elevato di cellule. Così, in assenza di perturbazioni esterne, la loro crescita e i punti di equilibrio possono essere descritti da equazioni differenziali. Tuttavia, il tumore interagisce fortemente col macroambiente che lo circonda e di conseguenza una descrizione del tutto deterministica risulta a volte inappropriata. In questo caso si può considerare l'interazione con fluttuazioni statistiche, causate da disturbi esterni, utilizzando le equazioni differenziali stocastiche (SDE). Questo è vero in modo particolare quando si cerca di modellizzare tumori altamente immunogenici che interagiscono con il sistema immunitario, in quanto la complessità di questa interazione risulta in fenomeni di multistabilità. Così, il rumore può provocare disturbi e indurre transizioni di stato (Noise-Induced-Transitions). E' importante notare che una NIT può avere implicazioni profonde sulla vita di un paziente, dal momento che una transizione da uno stato di equilibrio piccolo, nelle dimensioni del tumore, ad uno stato di equilibrio macroscopico, nella maggior parte dei casi significa il passaggio dalla vita alla morte. Generalmente l'approccio standard è quello di modellizzare le fluttuazioni stocastiche dei parametri per mezzo di rumore gaussiano bianco o colorato. In alcuni casi però questa procedura è altamente inadeguata, a causa della illimitatezza intrinseca dei rumori gaussiani che può portare a gravi incongruenze biologiche: pertanto devono essere utilizzati dei rumori "limitati", che, tuttavia, sono molto meno studiati di quelli gaussiani. Inoltre, l'insorgenza di NIT dipende dal tipo di rumore scelto, che rivela un nuovo livello di complessità in biologia. Lo scopo di questa tesi è quello di studiare le applicazioni di due tipi diversi di "rumori limitati" nelle transizioni indotte in due casi: interazione tra tumore e sistema immunitario e chemioterapia dei tumori. Nel primo caso, abbiamo anche introdotto un nuovo modello matematico di terapia, che estende, in modo nuovo, il noto modello di Norton-Simon.

Morphological transitions in molecular and polymeric materials: patterning, fabrication, devices

This thesis individuates and characterizes irreversible transformations occurring in specific organic and oligomeric/polymeric thin films. These transformations are dewetting in discotic liquid crystals thin films and dewetting and smoothing in oligomeric and polyemeric films. Irreversible transformations are extensively characterized by means of optical and atomic force microscopy. In the case of discotic liquid crystals films the morphological characterization is performed sinchronically with electrical measurements of current during dewetting.

A model for diffusive and displacive phase transitions in steels

Heat treatment of steels is a process of fundamental importance in tailoring the properties of a material to the desired application; developing a model able to describe such process would allow to predict the microstructure obtained from the treatment and the consequent mechanical properties of the material. A steel, during a heat treatment, can undergo two different kinds of phase transitions [p.t.]: diffusive (second order p.t.) and displacive (first order p.t.); in this thesis, an attempt to describe both in a thermodynamically consistent framework is made; a phase field, diffuse interface model accounting for the coupling between thermal, chemical and mechanical effects is developed, and a way to overcome the difficulties arising from the treatment of the non-local effects (gradient terms) is proposed. The governing equations are the balance of linear momentum equation, the Cahn-Hilliard equation and the balance of internal energy equation. The model is completed with a suitable description of the free energy, from which constitutive relations are drawn. The equations are then cast in a variational form and different numerical techniques are used to deal with the principal features of the model: time-dependency, non-linearity and presence of high order spatial derivatives. Simulations are performed using DOLFIN, a C++ library for the automated solution of partial differential equations by means of the finite element method; results are shown for different test-cases. The analysis is reduced to a two dimensional setting, which is simpler than a three dimensional one, but still meaningful.

Visualization, manipulation and force spectroscopy of cylindrical polymer brushes

The Ph.D. thesis deals with the conformational study of individual cylindrical polymer brush molecules using atomic force microscopy (AFM). Imaging combined with single molecule manipulation has been used to unravel questions concerning conformational changes, desorption behavior and mechanical properties of individual macromolecules and supramolecular structures. In the first part of the thesis (chapter 5) molecular conformations of cylindrical polymer brushes with poly-(N-isopropylacrylamide) (PNIPAM) side chains were studied in various environmental conditions. Also micelle formation of cylindrical brush-coil blockcopolymers with polyacrylic acid side chains and polystyrene coil have been visualized. In chapter 6 the mechanical properties of single cylindrical polymer brushes with (PNIPAM) side chains were investigated. Assuming that the brushes adopt equilibrium conformation on the surface, an average persistence length of lp= (29 ± 3) nm was determined by the end-to-end distance vs. contour length analysis in terms of the wormlike chain (WLC) model. Stretching experiments suggest that an exact determination of the persistence length using force extension curves is impeded by the contribution of the side chains. Modeling the stretching of the bottle brush molecule as extension of a dual spring (side chain and main chain) explains the frequently observed very low persistence length arising from a dominant contribution of the side chain elasticity at small overall contour lengths. It has been shown that it is possible to estimate the “true” persistence length of the bottle brush molecule from the intercept of a linear extrapolation of the inverse square root of the apparent persistence length vs. the inverse contour length plot. By virtue of this procedure a “true” persistence length of 140 nm for the PNIPAM brush molecules is predicted. Chapter 7 and 8 deal with the force-extension behavior of PNIPAM cylindrical brushes studied in poor solvent conditions. The behavior is shown to be qualitatively different from that in a good solvent. Force induced globule-cylinder conformational changes are monitored using “molecule specific force spectroscopy” which is a combined AFM imaging and SMFS technique. An interesting behavior of the unfolding-folding transitions of single collapsed PNIPAM brush molecules has been observed by force spectroscopy using the so called “fly-fishing” mode. A plateau force is observed upon unfolding the collapsed molecule, which is attributed to a phase transition from a collapsed brush to a stretched conformation. Chapter 9 describes the desorption behavior of single cylindrical polyelectrolyte brushes with poly-L-lysine side chains deposited on a mica surface using the “molecule specific force spectroscopy” technique to resolve statistical discrepancies usually observed in SMFS experiments. Imaging of the brushes and inferring the persistence length from a end-to-end distance vs. contour length analysis results in an average persistence length of lp = (25 ± 5) nm assuming that the chains adopt their equilibrium conformation on the surface. Stretching experiments carried out on individual poly-L-lysine brush molecules by force spectroscopy using the “fly-fishing” mode provide a persistence length in the range of 7-23 nm in reasonable accordance with the imaging results. In chapter 10 the conformational behavior of cylindrical poly-L-lysine brush-sodium dodecyl sulfate complexes was studied using AFM imaging. Surfactant induced cylinder to helix like to globule conformational transitions were observed.

Calix[4]arenes in the 1,3-alternate conformation

Calix[4]arenes fixed in the 1,3-alternate conformation offer an interesting platform for the attachment of further functionalities which has been less frequently used than the cone conformer. Several synthetic strategies were developed to attach four amino functions to the narrow rim, to the wide rim and to both rims of the calix[4]arene fixed in the 1,3-alternate conformation. Using different precursor groups (nitrile/phthalimide or nitro/phthalimide) which can be independently converted into amino functions opens the possibility to attach further groups selectively to the amino functions. Here the groups which is newly attached will determine the reaction sequence.

Supramolecular order and dynamics of functional materials studied by solid state NMR

The goal of this thesis was the investigation of the structure, conformation, supramolecular order and molecular dynamics of different classes of functional materials (phthalocyanine, perylene and hexa-peri-hexabenzocoronene derivatives and mixtures of those), all having planar aromatic cores modified with various types of alkyl chains. The planar aromatic systems are known to stack in the solid and the liquid-crystalline state due to p-p interactions forming columnar superstructures with high one-dimensional charge carrier mobility and potential application in photovoltaic devices. The different functionalities attached to the aromatic cores significantly influence the behavior of these systems allowing the experimentalists to modify the structures to fine-tune the desired thermotropic properties or charge carrier mobility. The aim of the presented studies was to understand the interplay between the driving forces causing self-assembly by relating the structural and dynamic information about the investigated systems. The supramolecular organization is investigated by applying 1H solid state NMR recoupling techniques. The results are related with DSC and X-ray scattering data. Detailed information about the site-specific molecular dynamics is gained by recording spinning sideband patterns using 1H-1H and 13C-1H solid state NMR recoupling techniques. The determined dipole-dipole coupling constants are then related with the coupling constants of the respective rigid pairs, thus providing local dynamic order parameters for the respective moieties. The investigations presented reveal that in the crystalline state the preferred arrangement in the columnar stack of discotic molecules modified with alkyl chains is tilted. This leads to characteristic differences in the 1H chemical shifts of otherwise chemically equivalent protons. Introducing branches and increasing the length of the alkyl chains results in lower mesophase transitions and disordered columnar stacks. In the liquid-crystalline state some of the discs lose the tilted orientation, others do not, but all start a rapid rotation about the columnar axis.

Atomic force microscopy of biomimetic systems

This thesis was driven by the ambition to create suitable model systems that mimic complex processes in nature, like intramolecular transitions, such as unfolding and refolding of proteins, or intermolecular interactions between different cell compo-nents. Novel biophysical approaches were adopted by employing atomic force mi-croscopy (AFM) as the main measurement technique due to its broad diversity. Thus, high-resolution imaging, adhesion measurements, and single-molecule force distance experiments were performed on the verge of the instrumental capabilities. As first objective, the interaction between plasma membrane and cytoskeleton, me-diated by the linker protein ezrin, was pursued. Therefore, the adsorption process and the lateral organization of ezrin on PIP2 containing solid-supported membranes were characterized and quantified as a fundament for the establishment of a biomimetic model system. As second component of the model system, actin filaments were coated on functionalized colloidal probes attached on cantilevers, serving as sensor elements. The zealous endeavor of creating this complex biomimetic system was rewarded by successful investigation of the activation process of ezrin. As a result, it can be stated that ezrin is activated by solely binding to PIP2 without any further stimulating agents. Additional cofactors may stabilize and prolong the active conformation but are not essentially required for triggering ezrin’s transformation into an active conformation. In the second project, single-molecule force distance experiments were performed on bis-loop tetra-urea calix[4]arene-catenanes with different loading rates (increase in force per second). These macromolecules were specifically designed to investigate the rupture and rejoining mechanism of hydrogen bonds under external load. The entangled loops of capsule-like molecules locked the unbound state of intramolecular hydrogen bonds mechanically, rendering a rebinding observable on the experimental time scale. In conjunction with Molecular Dynamics simulations, a three-well potential of the bond rupture process was established and all kinetically relevant parameters of the experiments were determined by means of Monte Carlo simulations and stochastic modeling. In summary, it can be stated that atomic force microscopy is an invaluable tool to scrutinize relevant processes in nature, such as investigating activation mechanisms in proteins, as shown by analysis of the interaction between F-actin and ezrin, as well as exploring fundamental properties of single hydrogen bonds that are of paramount interest for the complete understanding of complex supramolecular structures.

Photoinduced electronic transitions and leakage correlation to defects/dislocations in GaN heterostructures

III-nitride materials are very promising for high speed electronics/optical applications but still suffer in performance due to problems during high quality epitaxial growth, evolution of dislocation and defects, less understanding of fundamental physics of materials/processing of devices etc. This thesis mainly focus on GaN based heterostructures to understand the metal-semiconductor interface properties, 2DE(H)G influence on electrical and optical properties, and deep level states in GaN and InAlN, InGaN materials. The detailed electrical characterizations have been employed on Schottky diodes at GaN and InAl(Ga)N/GaN heterostructures in order to understand the metal-semiconductor interface related properties in these materials. I have observed the occurrence of Schottky barrier inhomogenity, role of dislocations in terms of leakage and creating electrically active defect states within energy gap of materials. Deep level transient spectroscopy method is employed on GaN, InAlN and InGaN materials and several defect levels have been observed related to majority and minority carriers. In fact, some defects have been found common in characteristics in ternary layers and GaN layer which indicates that those defect levels are from similar origin, most probably due to Ga/N vacancy in GaN/heterostructures. The role of structural defects, roughness has been extensively understood in terms of enhancing the reverse leakage current, suppressing the mobility in InAlN/AlN/GaN based high electron mobility transistor (HEMT) structures which are identified as key issues for GaN technology. Optical spectroscopy methods have been employed to understand materials quality, sub band and defect related transitions and compared with electrical characterizations. The observation of 2DEG sub band related absorption/emission in optical spectra have been identified and proposed for first time in nitride based polar heterostructures, which is well supported with simulation results. In addition, metal-semiconductor-metal (MSM)-InAl(Ga)N/GaN based photodetector structures have been fabricated and proposed for achieving high efficient optoelectronics devices in future.

Amidverknüpfte Ferrocene - schaltbare molekulare Drähte und Sensoren

In dieser Arbeit werden Synthesen und Eigenschaften von Verbindungen mit einer oder mehreren Ferrocen- bzw. Biferroceneinheiten beschrieben, die über Amid-, Anhydrid- oder Harnstoff-Funktionen verknüpft oder mittels Amidfunktion an α-Aminosäurederivate gebunden sind. Als Zentralbausteine dienen die künstlichen Aminosäuren 1’-Aminoferrocen-1-carbonsäure (Fca) bzw. 1’-Aminobiferrocen-1-carbonsäure (Bfca). Die Ferroceneinheit agiert als redoxschaltbares Gelenk, die Amidfunktion ermöglicht die Ausbildung von Sekundärstrukturen und die Bindung von Anionen. Das redoxschaltbare „Multiwellenlängen“-Sensorpaar [Dansyl-Ala-Fca-Ala-CH2-Naphthyl]0/+ ist in der Lage, insgesamt sieben Anionen aufgrund von sechs einfach zu erhaltenden optischen Messwerten eindeutig zu diskriminieren. Die Vorzugskonformation des neutralen Rezeptors mit intramolekularen Wasserstoffbrücken wird mittels X-Ray, NMR- und DFT-Methoden im Festkörper, in Lösung und in der Gasphase bestimmt. Die oligomeren Fca-Verbindungen SG-Fcan-HN-Fc (SG = Boc, Fmoc; n = 1, 2) und SG-Fca2-OMe (SG = Boc, Fmoc) werden mittels Peptidkupplung in Lösung hergestellt, Fmoc-Fca3-Gly-OMe, Fmoc-Fcan-OMe (n = 3-5) und Fmoc-Fca4-NH2 dagegen durch ein neu entwickeltes Festphasensynthese-Protokoll. Die amidverknüpften Verbindungen bilden eine „Zick-Zack“-Struktur mit 1,2’-Konformation der Fca-Einheiten und achtgliedrigen intramolekularen Wasserstoffbrücken-Ringen, wie durch X-Ray, 2D-NMR-, DFT-Methoden und Dipolmoment-Bestimmung gezeigt wird. Elektrochemische Experimente belegen eine elektronische Wechselwirkung der Eisenzentren. Die gemischt-valenten Verbindungen zeichnen sich durch IVCT-Banden im nahen Infrarot aus. Die elektronische Kopplungskonstante beträgt Hab ≈ 145-215 cm–1 für einen einzelnen FeII/FeIII-Übergang und belegt die Zugehörigkeit der Verbindungen zur Robin-Day-Klasse II. Im Festkörper sind die Valenzen gemäß Mößbauerspektren lokalisiert. Die vollständig oxidierten Verbindungen liegen nach DFT-Rechnungen nicht mehr in einer „Zick-Zack“-Struktur, sondern in einer gestreckten Konformation vor. Als Nebenprodukte bei der Amidkupplung werden die Anhydride SG-(Fca)2O (SG = Ac, Boc, Fmoc) isoliert. Diese zählen aufgrund des Fehlens einer IVCT-Bande zur Klasse I-II. Die ferrocenyloge Bfca wird in Form der N- und C-geschützten Bfca auf zwei Wegen synthetisiert. Schlüsselschritte stellen die Cu(II)-vermittelte Homokupplung bzw. die Pd-katalysierte Stille-Kupplung dar. Bfca und die amid- und harnstoffverknüpften Bis-Bfca-Verbindungen besitzen keine nachweisbare Vorzugskonformation in Lösung. Die gemischt-valenten Bfca-Kationen zeigen eine IVCT-Bande (Hab ≈ 300-600 cm–1) und gehören eher zur Klasse II-III. Die gemischt-valenten Verbindungen des als Nebenprodukt isolierten Tetraferrocenylstannans Sn[Fn(COOMe)4] (Fn = 1,1’-Ferrocenylen) mit einatomiger σ-Brücke zwischen den Ferroceneinheiten, zeigen IVCT-Banden im NIR-Spektrum und gehören somit zur Klasse II. Die elektronischen Kopplungen in Sn[Fn(COOMe)4]+/2+ betragen Hab ≈ 145 und 220 cm–1.

Chiroptical properties of bioactive molecules: sensitivity to conformation and solvation

Chiroptical spectroscopies play a fundamental role in pharmaceutical analysis for the stereochemical characterisation of bioactive molecules, due to the close relationship between chirality and optical activity and the increasing evidence of stereoselectivity in the pharmacological and toxicological profiles of chiral drugs. The correlation between chiroptical properties and absolute stereochemistry, however, requires the development of accurate and reliable theoretical models. The present thesis will report the application of theoretical chiroptical spectroscopies in the field of drug analysis, with particular emphasis on the huge influence of conformational flexibility and solvation on chiroptical properties and on the main computational strategies available to describe their effects by means of electronic circular dichroism (ECD) spectroscopy and time-dependent density functional theory (TD-DFT) calculations. The combination of experimental chiroptical spectroscopies with state-of-the-art computational methods proved to be very efficient at predicting the absolute configuration of a wide range of bioactive molecules (fluorinated 2-arylpropionic acids, β-lactam derivatives, difenoconazole, fenoterol, mycoleptones, austdiol). The results obtained for the investigated systems showed that great care must be taken in describing the molecular system in the most accurate fashion, since chiroptical properties are very sensitive to small electronic and conformational perturbations. In the future, the improvement of theoretical models and methods, such as ab initio molecular dynamics, will benefit pharmaceutical analysis in the investigation of non-trivial effects on the chiroptical properties of solvated systems and in the characterisation of the stereochemistry of complex chiral drugs.