Molecular biology and genetics are currently very fast developing disciplines. One of the possibilities how to increase the pupils' interest in studying of molecular biology and genetics, and to support their own curiosity is to use research-based teaching strategies. Although Czech Education tries to correspond with this progress, teaching of molecular biology and genetics is limited not only by financial and material limits but also by a lack of vocational education. The diploma thesis is divided into theoretical and practical part. The theoretical part deals with the position of molecular biology in teaching and model systems in the study and teaching of molecular biology and genetics. The practical part is divided into three chapters. The goal of the first chapter was to present available teaching materials suitable for a teaching at grammar schools, especially with regard to the availability of manuals for practical seminars. The second chapter summarized the results of a questionnaire survey among grammar school teachers, which concerns the position of molecular biology and genetics in teaching. Both of the above-mentioned goals have shown that more needs to be done about the molecular biology of genetics. According to the teachers, students who would like to continue to pursue this...

This study contributes to the literature on national long-distance travel demand modeling by providing an analysis of households' annual destination choices and time allocation patterns for long-distance leisure travel purposes. An annual vacation destination choice and time allocation model is formulated to simultaneously predict the different destinations that a household visits and the time it spends on each of these visited destinations, in a year. The model takes the form of a Multiple Discrete-Continuous Extreme Value (MDCEV) structure (Bhat, 2005; Bhat, 2008). The model assumes that households allocate their annual vacation time to visit one or more destinations in a year to maximize the utility derived from their choices. The model framework accommodates variety-seeking in households' vacation destination choices in that households can potentially visit a variety of destinations rather than spending all of their annual vacation time for visiting a single destination. At the same time, the model accommodates corner solutions to recognize that households may not necessarily visit all available destinations. An annual vacation time budget is also considered to recognize that households may operate under time budget constraints. Further, the paper proposes a variant of the MDCEV model that avoids the prediction of unrealistically small amounts of time allocation to the chosen alternatives. To do so, the continuously non-linear utility functional form in the MDCEV framework is replaced with a combination of a linear and non-linear form. The empirical data for this analysis comes from the 1995 American Travel Survey Data, with the U.S. divided into 210 alternative destinations. The empirical analysis provides important insights into the determinants of households' leisure destination choice and time allocation patterns. An appealing feature of the proposed model is its applicability in a national, long-distance leisure travel demand model system. The annual destination choices and time allocations predicted by this model can be used for subsequent analysis of the number of trips made (in a year) to each destination and the travel choices for each trip. The outputs from such a national travel modeling framework can be used to obtain national-level Origin-Destination demand tables for long-distance leisure travel.

Manufacturing equipments in semiconductor factories (fabs) provide abundant data and opportunities for data-driven process monitoring and modeling. In particular, virtual metrology (VM) is an active area of research. Traditional monitoring techniques using univariate statistical process control charts do not provide immediate feedback to quality excursions, hindering the implementation of fab-wide advanced process control initiatives. VM models or inferential sensors aim to bridge this gap by predicting of quality measurements instantaneously using tool fault detection and classification (FDC) sensor measurements. The existing research in the field of inferential sensor and VM has focused on comparing regressions algorithms to demonstrate their feasibility in various applications. However, two important areas, data pretreatment and post-deployment model maintenance, are usually neglected in these discussions. Since it is well known that the industrial data collected is of poor quality, and that the semiconductor processes undergo drifts and periodic disturbances, these two issues are the roadblocks in furthering the adoption of inferential sensors and VM models. In data pretreatment, batch data collected from FDC systems usually contain inconsistent trajectories of various durations. Most analysis techniques requires the data from all batches to be of same duration with similar trajectory patterns. These inconsistencies, if unresolved, will propagate into the developed model and cause challenges in interpreting the modeling results and degrade model performance. To address this issue, a Constrained selective Derivative Dynamic Time Warping (CsDTW) method was developed to perform automatic alignment of trajectories. CsDTW is designed to preserve the key features that characterizes each batch and can be solved efficiently in polynomial time. Variable selection after trajectory alignment is another topic that requires improvement. To this end, the proposed Moving Window Variable Importance in Projection (MW-VIP) method yields a more robust set of variables with demonstrably more long-term correlation with the predicted output. In model maintenance, model adaptation has been the standard solution for dealing with drifting processes. However, most case studies have already preprocessed the model update data offline. This is an implicit assumption that the adaptation data is free of faults and outliers, which is often not true for practical implementations. To this end, a moving window scheme using Total Projection to Latent Structure (T-PLS) decomposition screens incoming updates to separate the harmless process noise from the outliers that negatively affects the model. The integrated approach was demonstrated to be more robust. In addition, model adaptation is very inefficient when there are multiplicities in the process, multiplicities could occur due to process nonlinearity, switches in product grade, or different operating conditions. A growing structure multiple model system using local PLS and PCA models have been proposed to improve model performance around process conditions with multiplicity. The use of local PLS and PCA models allows the method to handle a much larger set of inputs and overcome several challenges in mixture model systems. In addition, fault detection sensitivities are also improved by using the multivariate monitoring statistics of these local PLS/PCA models. These proposed methods are tested on two plasma etch data sets provided by Texas Instruments. In addition, a proof of concept using virtual metrology in a controller performance assessment application was also tested.

Le cancer épithélial de l’ovaire (EOC) est le plus mortel des cancers gynécologiques. Cette maladie complexe progresse rapidement de façon difficilement décelable aux stades précoces. De plus, malgré une chirurgie cytoréductive et des traitements de chimiothérapie le taux de survie des patientes diagnostiquées aux stades avancées demeurt faible. Dans le but d’étudier l’EOC dans un contexte ex vivo, l’utilisation de modèles cellulaires est indispensable. Les lignées cellulaires d’EOC sont un outil pratique pour la recherche cependant, la façon dont l'expression des gènes est affectée en culture par comparaison à la tumeur d'origine n'est pas encore bien élucidée. Notre objectif était donc de développer et de caractériser de nouveaux modèles de culture in vitro qui réflèteront plus fidèlement la maladie in vivo. Nous avons tout d’abord utiliser des lignées cellulaires disponibles au laboratoire afin de mettre au point un modèle 3D de culture in vitro d’EOC. Des sphéroïdes ont été générés à l’aide de la méthode des gouttelettes inversées, une méthode pionnière pour la culture des cellules tumorales. Nous avons ensuite procédé à une analyse des profils d’expression afin de comparer le modèle sphéroïde au modèle de culture en monocouche et le modèle xénogreffe in vivo. Ainsi, nous avons identifié des gènes stratifiant les modèles tridimensionnels, tant in vivo qu’in vitro, du modèle 2D monocouche. Parmi les meilleurs candidats, nous avons sélectionné S100A6 pour une caractérisation ultérieure. L’expression de ce gène fût modulée afin d’étudier l’impact de son inhibition sur les paramètres de croissance des sphéroïdes. L’inhibition de ce gène a comme effet de réduire la motilité cellulaire mais seulement au niveau du modèle sphéroïde. Finalement, toujours dans l’optique de développer des modèles d’EOC les plus représentatifs de la maladie in vivo, nous avons réussi à développer des lignées cellulaires uniques dérivées de patientes atteintes d’EOC du type séreux, soit le plus commun des EOC. Jusque là, très peu de lignées cellulaires provenant de ce type de cancer et de patientes n’ayant pas reçu de chimiothérapie ont été produites. De plus, nous avons pour la première fois caractérise des lignées d’EOC de type séreux provenant à la fois de l’ascite et de la tumeur solide de la même patiente. / The epithelial ovarian cancer (EOC) is the most lethal of gynecological cancers. This complexe and heterogenous disease progresses rapidly and is almost asymptomatic in early stages. The survival rate of patients with late stage diagnosis remains low albeit cytoreductive surgery and chemotherapy. In order to study the EOC disease in an ex vivo context, the use of different cellular models is necessary. EOC cell lines derived from long-term passages of malignant ovarian cancers are useful tools for molecular and cellular research but it is not clear how culture conditions affect overall gene expression and oncogenic potential as compared to the original tumor. The main goal of this research was to develo and characterize new in vitro model systems that will recapitulate more closely some of the growth conditions encountered by tumor cells in vivo. In order to develop an in vitro tridimensional EOC spheroid model, we have used cell lines previously established in our laboratory. Spheroids were generated using the hanging droplet method, which was innovative for the culture of cancer cells. Comparative gene expression profile analysis of monolayer cultures, 3D spheroids and in vivo xenografts were performed and we have shown that the spheroid transcriptome more closely reflects expression patterns of the in vivo model compared to that of monolayer cultures. Among the best candidates, S100A6 gene over-expressed in the 3D models versus monolayer cultures was chosen for further analysis. To begin to address how S100A6 might affect EOC growth parameters, we have inhibited its expression in our in vitro models. The loss of S100A6 in the spheroid model results in an reduction of cellular migration, which seems to be in line with previous in vivo results published by other researchers. Always with the objective of developing the most relevant to the in vivo disease model systems, we have also succeeded in developing a unique EOC cell lines derived from patients with the most frequently diagnosed serous type of cancer. Very few cell lines derived from this type of cancers and from chemotherapy naïve patients are available. Moreover, we characterize for the first time EOC serous type cell lines derived from the ascites and the solid tumor of the same patient.

Les fibres amyloïdes sont des biomatériaux prometteurs pour la bioélectronique, en particulier pour l’interfaçage avec les systèmes biologiques. Ces fibres, formées par l’auto-assemblage de protéines, sont aisément synthétisables et modifiables/fonctionnalisables. Elles possèdent de surcroît des propriétés physiques remarquables notamment en termes de stabilité et de résistance mécanique. Nous avons étudié les mécanismes de conductions de charges dans les fibres formées par la protéine HET-s(218-289), seules fibres amyloïdes dont la structure atomique soit connue. Les échantillons ont été caractérisés électriquement et électrochimiquement sous la forme de films « secs ». L’influence de plusieurs paramètres sur la conductivité, entre autres la température, l’humidité ou encore la lumière, a été investiguée. Nous avons montré que l’organisation de la protéine en fibres permet la mise en place de processus de transport de charges intrinsèques. De plus, l’eau joue un rôle essentiel dans ces mécanismes et les principaux porteurs de charges sont certainement des protons. En parallèle, une simulation de dynamique moléculaire appuyée notamment par des expériences de diffusions des neutrons, a mis en évidence une forte interaction entre l’eau et les fibres. Deux canaux d’eau stabilisés par liaisons hydrogènes se formeraient le long des fibres. Ces derniers peuvent permettre le transport de protons par un mécanisme de type Grotthuss. Des réactions électrochimiques, en particulier l’électrolyse de l’eau, seraient la source des protons transportés grâce aux fibres. Cela conduit à l’instauration d’un courant catalytique à partir d’un seuil de tension de polarisation. Enfin, deux effets photo-électriques ont été observés lorsque les fibres sont irradiées entre 200 et 400 nm. Le premier est un photo-courant qui serait dû à la photolyse de l’eau adsorbée dans les échantillons. Le second, qualifié de « photo-courant inverse », se produit plus spécifiquement à la longueur d’onde de 280nm et seulement en présence de dioxygène. Il engendre une diminution de la conductivité. Cela serait dû à une réaction entre l’état triplet des tryptophanes des fibres et le dioxygène, captant in fine des protons. / Amyloid fibers are very promising biomaterials for bioelectronics, especially for interfacing with biological systems. These self-assembled proteins fibers are easy to synthetize, to tune and to functionalize. Their physical properties such as stability and mechanical strength are noticeable. We studied charge transport processes in HET-s(218-289), the only amyloid fibers we know the atomic structure. The samples were characterized as “dried” films by electrical measurement and electrochemistry. The influence of several parameters such as temperature, humidity or light was investigated. We demonstrated that the fiber organization allows intrinsic charge transport mechanisms in which water plays a crucial role. Furthermore, the dominant charge carriers would be protons. Molecular dynamic simulation and neutron diffusion experiments run in parallel show strong water-fibers interactions. In particular, H-bonded water wires can be formed along the fibers and support proton transport according to a Grotthuss-like mechanism. Proton production would result from electrochemical reactions, especially from water electrolysis. Therefore a catalytic current is detected when the bias exceeds a certain threshold. In addition, two photoelectric phenomena were observed when the fibers are irradiated with near UV light (200-400nm). The first one is a photocurrent probably due to water photo-splitting. The other occurs specifically at 280nm wavelength and in the presence of molecular oxygen. It leads to a decrease of the sample conductivity. This likely results from chemical reaction(s) between triplet-state tryptophan and oxygen that consumes protons.

Title: Role of surface defects in ceria-based catalysis Author: Andrii Tovt Department: Department of Surface and Plasma Science Supervisor of the doctoral thesis: doc. Mgr. Josef Mysliveček Ph.D., Department of Surface and Plasma Science Abstract: This work concentrates on the analysis of fundamental physicochemical properties of Pt-CeOx, single-atom Pt1 /CeOx, and inverse CeOx/Cu(111) catalysts. Preparation method for stabilized atomically-dispersed Pt2+ ions on ceria was developed and adsorption sites for Pt ions were thoroughly studied using advanced surface science techniques supported by theoretical methods. The mechanism of Pt2+ stabilization on ceria steps was revealed and the step capacity towards Pt2+ ions was estimated. Also, the preparation method for well-ordered cerium oxide ultrathin films with different stoichiometry and ordering of surface oxygen vacancies was developed, and the Ceria/Cu(111) interaction was investigated. Key words: heterogeneous catalysis, model systems, single-atom catalysis, platinum ions, cerium oxide.

Poor skeletal health results from aging and metabolic diseases such as obesity and diabetes and involves impaired homeostatic balance between marrow osteogenesis and adipogenesis. Tissue engineering provides researchers with the ability to generate improved, highly controlled and tailorable in vitro model systems to better understand mechanisms of homeostasis, disease, and healing and regeneration. Model systems that allow assembly of modules of MSCs, osteoblasts, and adipocytes in a number of configurations to engage in signaling crosstalk offer the potential to study integrative physiological aspects and complex interactions in the face of changes in local and systemic microenvironments. Thus, the overall goal of this dissertation was to examine integrative physiological aspects between MSCs, osteoblasts, and adipocytes that exist within the marrow microenvironment. To investigate the effects of intercellular signaling in different microenvironmental contexts, methods were developed to photolithographically pattern and assemble cell-laden PEG-based hydrogels with high spatial fidelity and tissue-scale thickness for long-term 3D co-culture of multiple cell types. This platform was applied to study effects of crosstalk between MSCs, osteoblasts and adipocytes on markers of differentiation in each cell type. Additionally, responses of MSCs to systemic perturbations in glucose concentration were modulated by mono-, co-, and tri-culture with these cell types in a model of diabetes-induced skeletal disease. Together, these studies provided valuable insight into unique and differential effects of intercellular signaling within the niche environment of MSCs and their terminally differentiated progeny during homeostatic and pathological states, and offer opportunities further study of integrative physiological interactions between mesenchymal lineage cells.

This thesis entitled “Investigating the Intercarbonyl X···C′ (X = O/S/N) Interactions in Short Peptides and Peptidomimetics. Evidence of Charge→π* Interactions. Synthesis and Characterization of Thioimidate Isostere Containing Peptidomimetics” is divided into two chapters. First chapter is further subdivided into four sections where investigation of the nature of intercarbonyl X···C′ (X = O/S/N) interactions in short peptides and peptidomimetics has been described. The second chapter also has been subdivided into three parts where the syntheses and characterization of thioimidate (1,3-thiazine) and imidate (1,3-oxazine) isostere containing peptidomimetics have been discussed. Chapter 1: Section A: Revisiting the earlier models for the intercarbonyl O···C′ interactions The proximity between carbonyls is ubiquitous in crystals. Here we review the key reports that have assigned an n→π* nature to interactions between carbonyl oxygen (O) atoms and adjacent carbonyl carbon (C′) atoms (O···C′). Based on earlier hypotheses (by Burgi-Dunitz) that suggest that “the minimum energy trajectory of a nitrogen nucleophile adding to the C′ of carbonyl is at N···C′ distances of ≤ 3.2 Å and along N···C′=O angles of 109±10o”, the optimum trajectory for addition of an O to an adjacent C′ has also been assigned to be the same (O···C′ distance ≤ 3.2 Å and O···C′=O angle is 109±10o). Additionally, all O and C′ atoms within these boundary conditions in crystal structures were assigned a status of interacting and those outside of the same as non-interacting. Based on quantum mechanical models for electronic orbitals that contain the valence electrons of such proximal O and C′ atoms – derived through NBO (Natural Bond Order) calculations (on crystal structures) – it has been proposed that the filled non-bonding lone pair orbital of the O (donor) overlaps with the empty π* orbital of the carbonyl C′ (acceptor), in these O···C′ interactions. Hence, these have been termed as n→π* interactions. Using DFT (Density Functional Theory) calculations energies for these interactions have been predicted to range from 0.5 to 5.0 kcal mol-1, which are similar to those for other strong non-covalent interactions such as H-bonding, weak cation-π, etc. This n→π* interaction model is assumed to prevail between adjacent carbonyls (Oi-1···C′i) at Xaa-Pro dipeptide motifs and to be exclusively responsible for the changes in equilibrium constant values (Kc/t) for the trans to cis isomerisation reaction at Xaa-Pro peptide bond in chosen analogue molecules. Based on this assumption, these Kc/t values have been used as direct experimental equivalents for the energies of these n→π* interactions. Simultaneous to such review of literature, this chapter highlights several anomalies in this n→π* model for the intercarbonyl O···C′ interactions. We discuss the alternate models that also exist for the O···C′ proximities and show that several features – such as improved pyramidalization at the acceptor carbonyl; decrease in Kc/t values at Xaa-Pro peptide bonds; and small changes in 13C NMR chemical shift values for the acceptor carbonyls; etc. – that accompany the shortening of O···C′ distance, can be explained without invoking the n→π* interaction model. Moreover, we discuss key observations such as the presence of near-symmetric antiparallel short contacts between carbonyl groups (C=O) in crystal structures, which cannot be explained by the quantum mechanical n→π* model for the O···C′ interactions. Chapter 1: Section B: Spectroscopic and kinetic investigations into the nature of X···C′ (X = O/S) interactions in N-acyl homoserine lactones (AHLs) In this section the key interactions involving the adjacent carbonyls in model N-acyl homoserine lactones (AHLs) (which are signalling molecules in quorum sensing) in solution, their electronic nature and their influence on solvolysis of the lactone ring have been investigated. Earlier, in the crystal structures of two sterically encumbered synthetic AHL analogues N-trimethyl acetyl homoserine lactone and N-tribromoacetyl homosrine lactone the presence of an n→π* orbital overlap type interaction between Oacyl and C′lact had been suggested. Based primarily on this, the operation of similar OacylC′lact interaction was proposed in all AHLs in their solution conformations as well. More intriguingly, the interaction was hypothesized to decrease the rates of lactone hydrolysis, rendering AHLs with longer biological half-life. This is contrary to physical organic understanding of nucleophilic catalysis of addition to carbonyls. Here we synthesize a variety of AHLs and analyze their NMR and FT-IR data in solution. The spectral data reveal that the role of the N-acyl group in AHLs is to withdraw eˉs from lactone C=O inductively and to improve electronic shielding at C′lact. Lack of appreciable changes in C=O stretching frequencies of lactone and 13C NMR chemical shift values of C′lact indicate the absence of electronic perturbation of the π* of the lactone. Similar non-variance of spectral bands with improvement in nucleophilicity of the N-acyl group indicates the absence of any evidence for n→π* nature for the O···C′ interactions (between the lone pair of eˉs from Oacyl to π* at C′lact). Further the spectroscopic data indicate that any change in charge at the acyl O is felt by C′lact and this weak interaction releases energy in the order of ≤ 0.05 kcal mol-1. The combined influence of the electron withdrawing N-acyl group and the weak Oacyl···C′lact interaction in AHLs is that, increasing the charge at Oacyl increases the rate of solvolysis of lactone. Analysis of the conformation of the lactone ring in the LuxR receptor-bound and unbound crystal structure forms reveals the flattening of the puckered ring in the LuxR bound state – facilitated by several interactions with the receptor. Conserved interactions between LuxR and AHLs lock the N-acyl carbonyl motif such that they are orthogonal to the lactone carbonyl and intramolecular interaction between Oacyl and C′lact is precluded. We propose the design of flat cyclic analogues of γ-butyrolactone bearing electron withdrawing side chains as potential molecules for taking advantage of bacterial quorum sensing in environmental applications and biotechnology. Chapter 1: Section C: Spectroscopic investigation into the nature of intercarbonyl X•••C′ (X = O/S/N) interactions: Carbamyl-cisPro model systems In this section we investigate the nature of intercarbonyl X···C′ interactions in carbamyl-Pro model systems using spectroscopic methods like FT-IR and 1D NMR. Further we derive the enthalpic and entropic contributions towards the free energy for trans to cis isomerization (Kc/t) at these model carbamyl-Pro systems. Our results reveal that changes in Kc/t values cannot always be used as proof for the presence or absence of electronic interactions, and hence to unambiguously suggest the nature of these interactions. Cis/trans isomerism exists at Xaa-Pro amide and carbamate motifs, and it was proposed that in acyl-Pro systems the O···C′ interactions are responsible for the stability of either cis or trans depending upon their direction of operation (Forward direction: O of Xaa is the donor of electrons to π* at C′ of Pro; Reverse direction: O of Pro is the donor of electrons to π* at C′ of Xaa). Investigation of the carbamyl-Pro systems can shed further light on this hypothesis. Hence we undertook the first spectroscopic and Van’t Hoff analysis of homologous carbamyl-Pro model systems. The Kc/t of the homologous series surprisingly increased with increase in the bulk at R (R varies from Me to tBu). The spectroscopic data revealed the presence of charge→σ* interactions at carbamyl groups. This interaction locks the carbamyl motif in the s-transoid conformation, along the C′-O σ-bond. Such conformational lock is observed to be greater in carbamyl groups where R has at least one Cα-H bond. Interestingly, we observe the absence of X···C′ electronic interactions that may selectively stabilize the cisPro conformer in these molecules. Van’t Hoff analyses on the other hand showed that as the number of Me substituents in R increases (R = Me to iPr), there is a favorable increase in entropy ( So) associated with the transPro to cisPro conformational isomerism. As a result, the population of the cisPro conformer improves significantly as the steric bulk at R increases. We note that the enthalpy of cisPro is however relatively small and remains unfavourable as R-bulk increases (Me to iPr). These data reveal the influence of electrostatic interactions between charged groups, on the change in entropy associated with cis/trans isomerism at carbamayl-Pro motifs. This not only opposes the n→π* model, but also provides an example for the important point that changes in Kc/t can/should not be taken as direct evidences of any single electronic interaction. Importantly, this study provides another example where electronic interactions between charged, polarized carbonyl motif rather than nonbonding lone pair eˉs of carbonyl motifs influence cis/trans isomerism at Xaa-Pro systems. Chapter 1: Section D: Investigation of the stereoelectronic nature of the X···C′ (X = O/S) contacts In this section we provide experimental evidence for the existence of inverse correlation between the charge on the O nucleophile and the O···C′ distances. We show that O and C′ atoms (of adjacent carbonyls), which are separated at distances > 3.20 Å in carefully chosen analogues, come together to σ-bonding distances when the charge on O is increased to -1. Additionally, the influence of backbone steric factors on these charge→π* interactions is investigated. A partial covalent nature was proposed for the O···C′ interactions. Our study showed that the shortest intercarbonyl O···C′ distances between the O of 1°, 2° and 3° amide carbonyls and proximal C′ in molecules found in the Cambridge Structural Database (CSD) (v5.36, November 2014) show an inverse linear correlation with the partial negative charge (δ‾) on the amide carbonyl O rendered by natural amide carbonyl polarization. These data suggest the interaction of charge on the nucleophilic O with π* of the acceptor carbonyl. Further on increasing the charge on nucleophilic carbonyl O to -1 in the model compound, we achieved the formation of σ-bond through non-native (natively disallowed) Oi‾¹→C′i-1 interaction. Here we provide the first experimental evidences that suggest the interaction between charge of O and π* at adjacent C′ (the charge→π* interaction) and the latent covalent nature of the O···C′ interactions. This charge→π* model explains the origins of variations in O···C′ distances (3.20 Å–1.43 Å) in proteins and complexes that occur to suit biological functions; and the mutual interactions between antiparallel carbonyls. Further the effect of 3 key steric factors – namely the allowed τ (N-Cα-C′) angle, entropy and allowed (ϕ,ψ) angles – on the non-native Oi→C′i-1 interactions were investigated in the model compounds. Our kinetic data revealed that, the allowed τ angles have the greatest influence on charge→π* interaction, followed by entropy. Importantly the allowed (ϕ,ψ) torsional angles for residues, that govern protein folding pathways, have little influence on the O···C′ electronic interactions. Chapter 2: Section A: Design and synthesis of novel 1,3-Thiazine containing peptidomimetics This section describes the first synthesis of peptidomimetics containing the 1,3-thiazine isostere (thioimidate isostere for the peptide bond), at the C-terminus and also at the middle of the peptide. The synthesis of the 6-membered heterocycles – 1,3-oxazine (Oxa) – have earlier been reported. Oxa motifs constrain preceding amino acid backbones into natively disallowed conformations. Here we present the first synthesis of peptidomimetics containing the 1,3-thiazine (Thi) (the thioimidate analogue of Oxa) motif, by the treatment of N-(3-hydroxypropyl)thioamides with MsCl/Et3N, which leads to intramolecular S-alkylation / cyclization. When placed at the C-terminus of acyl-Pro motifs the Thi group selectively improves the stability of the rare s-cis conformation of the acyl-Pro peptide bond. Further this method has been used to synthesize peptidomimetics in which an endogenous peptide bond is replaced with the Thi isostere. These Thi analogues are shown to be stable to standard conditions of peptide coupling and N- and C- terminus protection, deprotection and can be extended selectively at their N- or C- termini. Chapter 2: Section B: Epimerization in 1,3-Thiazine containing peptidomimetics The epimerization in 1,3-thiazine containing peptidomimetics and its mechanism has been described in this section. Further the aggregation behaviour of these thiazines, in solution and crystal structures, has been studied. It has been well-documented that epimerization (Racemization) occurs at the chiral centers at the C(2) exo methine of 1,3-thiazolines and 1,3-thiazoles. Similar epimerizations in 1,3-thiazines have however not been explored. Here we report our observation of epimerization in chiral aminoacid (non Pro) containing 1,3-thiazine peptidomimetics. Our studies revealed that, the epimerization happens at C2 positions of chiral (non-Pro) amino acids-derived 1,3-thiazine containing peptiomimetics. And NH of chiral (non-Pro) amino acid fused to Thi ring at C2 position is necessary for the epimerization. Further we investigated the Boc-Xaa*-Thi analogues in solution, which showed two resonances for the carbamate N-H (HN) and the H of Xaa*, irrespective of the side chain in Xaa, in CDCl3 a weakly polar solvent. The integral ratios of the major : minor peak increased with increase in concentration for Boc-Val*-Thi, indicating the formation of H-bonded aggregates. Even in the polar aprotic (DMSO-d6) and polar protic (D2O) solvents the two sets of resonances were observed for Boc-Val*-Thi in 1H NMR. But when the thioimidate N is protonated (N of Thi is no longer a H-bond acceptor), showed only a single set of resonances. Formation of intermolecular H-bonds involving N of Thi in solution is thus evident in the aggregates. This is further suggested by the crystal structures obtained for the peptide mimetics Boc-Val*-Thi, Boc-Leu*-Thi and Boc-Phe*-Thi in which the racemic pair, instead of one enantiomer of it, are present in the unit cell and are locked in a pair of intermolecular 10 membered H-bonding interactions between NThi and HLeu* similar to an antiparallel β-sheet. A mechanism for racemization is proposed, where this strong H-bond assists enamination/racemization process. Chapter 2: Section C: Influence of a disallowed conformation of Aib on the structure of a 310-helical fold In this section, the effect of the presence of a disallowed conformation of Aib at the C-terminus of a 310-helical peptide, on the structure and fold of the rest of the peptide body has been studied in solution. We constrain the C-terminal Aib in the Aib-rich octapeptide (N-tert-butoxycarbonyl-Leu1-Aib2-Ala3-Leu4-Aib5-Ala6-Phe7-Aib8-CO2Me (1), which adopts a complete 310-helical conformation throughout the peptide body in the crystal structure and in solution) in one of its disallowed conformations using a method earlier developed in our group. This involves the synthetic modification of the C-terminal ester (Aib8-CO2Me) in 1 to an Oxa (Aib*8-Oxa) in 2 and the study of its effect on the peptide body. Analyses of the solution FT-IR, CD, ¹H, 2D (TOCSY, HSQC, HMBC and ROESY) and solvent polarity dependent NMR data reveal that 2 adopts a 310-helical conformation similar to that of 1. The C-terminal CO2Me → Oxa (E → O) modified Aib*8-Oxa motif is constrained in a unique conformation where the two Cβ atoms of Aib*8 are staggered with respect to the Aib*8 C=O and are both interacting with the two Hβ of Phe7. Here the Aib* backbone is constrained by a 5-membered ring NOxa∙∙∙HAib* H-bond, in a C5i structure. Solvent polarity dependent ¹H NMR data indicate the formation and persistence of C5i H-bond at the Aib*8-Oxa motif in 2. Analyses of the ROESY, solvent polarity dependent ¹H NMR and CD spectra reveal that four crucial changes in ROESY cross peaks occur at the Phe7-Aib*8 motif of 2, compared to that in 1. From these spectroscopic data it has been confirmed that there is no change in the structure of 2 from Leu1 to Ala6. Whatever the crucial changes happened are at Phe7-Aib*8 motif of 2. Hence our study showed that the significant structural consequences of this disallowed conformation of Aib* are primarily observed to occur in the residue in its immediate vicinity, rather than in the whole peptide body. Presence of a disallowed fold at a residue need not result in disruption of the structure, or the overall fold, in the rest of the peptide body.

Mesoscopic spin systems can be designed and fabricated using modern nano-fabrication techniques. These systems can contain large numbers of patterned ferromagnetic elements, for which the shape will generally determine their effective mesospin dimensionality. The lateral arrangement of these mesospins can be further used to tune the interactions between them. With an appropriate choice of material, it is possible to define a temperature range where thermal fluctuations of these mesospins are experimentally accessible. To actively define this range, we use δ-doped Palladium, a three-layer system of Palladium—Iron—Palladium, for which the Curie-temperature scales with the Iron layer thickness. The patterned mesoscopic elements used in this work have a stadium-like shape that promotes a single magnetic domain state, thus making these islands behave as one-dimensional Ising-like mesospins that can be observed using magnetic imaging techniques. We investigate the impact on the magnetic order resulting from modifications of the square spin ice geometry. By adding, removing and merging elements in the square artificial spin ice architecture, energy-landscape variations can be realized. Firstly, an added interaction modifier is used to equilibrate the interactions between the mesospins at the vertex level, which can restore the degenerate ground state of the square spin ice model. Secondly, the removal of elements can lead to topologically frustrated spin systems, as not all building blocks can simultaneously be in their lowest energy state. Furthermore, the merging results in multiple element sizes in the mesospin system. As the magnetization reversal barrier is dependent on the element size, these mesospin systems have different energy barriers. The thermal ordering process in such a system differs from a single-size element system with its unique energy barrier. Using reciprocal space analysis tools like the magnetic spin structure factor we show that systems with multiple element sizes achieve a higher short-range order then their single-size element references. The magnetic order in mesoscopic spin systems could successfully be tailored by modifications of the lattice geometry.

Es wurden Untersuchungen zur Synthese von Modellsystemen des heterobicyclischen Grundgerüsts der Saragossasäuren/Squalestatine durch Acetalisierung unterschiedlich konfigurierter acyclischer Diketohexaole durchgeführt. In diesem Zusammenhang gelang die biderektionale Darstellung eines Modellsystems in sieben Stufen mit einer Gesamtausbeute von 34 %. Als Methode zur Etablierung der korrekten Konfiguration der Hydroxygruppen diente die asymmetrische Dihydroxylierung nach Sharples. In einem weiteren Teil der Arbeit wurde die selektive mono-Debenzylierung verschiedener N,N-Dibenzylamine mit Cer(IV)ammoniumnitrat (CAN) und DDQ untersucht. In diesem Kontext konnte eine neue, sehr schonende, Methodik zur chemoselektiven mono-Debenzylierung tertiärer N,N-Dibenzylamine erarbeitet werden. Im letzten Teil der Arbeit wurden zwei neue, verbrückte Heterobimetall-Katalysatoren auf Basis von BINOL-Liganden entwickelt. Diese Katalysatoren wurden für die asymmetrische Ringöffnung verschiedener meso-Epoxide mit 4-Methoxyphenol genutzt und lieferten die Öffnungsprodukte in guten Ausbeuten und Enantiomerenüberschüssen (ee: 80 - 90 %). / The intramolecular acetalisation of several diketohexaols tko the bicyclic skelleton of saragozic acids/squalestatines were investigated. It was possible, by using a bidirectional synthesis sequence, to obtain a model for the core structure of saragozic acids in seven steps with a total yield of 34 %. To establish the correct configuration of up to six hydroxygroups the Sharpless asymmetric dihydroxylation protocoll was used. In the second part of the dissertation a new and mild method for debenzylation of N,N- Dibenzylamines was elaborated. Tertiary amines incorporating two N-benzyl substituents are readily mono-debenzylated with CAN or DDQ. In the last part of the dissertation the synthesis of two bridged heterobimetallic catalysts for the catalytic enantioselective ring opening of meso-epoxides is described. The ring opening reaction was performed using 4-methoxyphenol as a nucleophile an different meso-epoxides to give the ring opened products in good yields and enaniomeric excesses (ee: 80 - 90 %).