Pomocí molekulového modelování je možné předpovídat chování nových látek a napomáhá při jinak obtížné interpretaci experimentálních dat. Cílem práce byla predikce vybraných vlastností polymeračních katalyzátorů na bázi karbenů, predikce jejich struktur a spektrálních charakteristik a studie mechanismu polymerace za otevření kruhu laktidu. K ověření chování karbenů a jejich prekurzorů ve formě chloridů byly studovány vybrané charakteristiky molekuly. Byl proveden výpočet vybraných molekulových orbitalů a elektrostatických map. Následně pomocí počítačových programů byly získány teoretické vazebné délky a úhly vybraných imidazolových a imidazolinových sloučenin, karbenů a jejich možných produktů hydrolýzy. Data strukturně podobných, již charakterizovaných sloučenin, byla získána z CCDC (Cambridge Crystallographic Data Centre) a následně byla konfrontována s vypočítanými daty. Byla změřena infračervená a Ramanova spektra imidazolové soli a infračervené spektrum příslušného karbenu. Tato spektra byla konfrontována s napredikovanými. Pro lepší interpretaci spekter byla spočítána spektra možných produktů hydrolýzy. Následně byl studován mechanismus polymerace za otevření kruhu laktidu. Na základě spočítaných energií stacionárních bodů byl navržen nový mechanismus polymerace.

Oleogenic yeasts under appropriate conditions produce and accumulate lipids and lipid-soluble metabolites in high amounts. This attribute is characteristic also for red yeasts that except lipids accumulate also carotenoids – natural pigments used in food industry and dietary supplements. The aim of this diploma thesis was designed as a comparative screening study of production properties of strains Cystofilobasidium capitatum, Rhodotorula glutinis, Sporobolomyces roseus and Sporobolomyces shibatanus. Choosen carbon sources were glucose and glycerol as waste by-product in biofuel industry. The best production properties were found in Cystofilobasidium capitatum and Rhodotorula glutinis. These two strains produced increased amounts of lipids as well as higher amounts of carotenoids. Strains were tested by FTIR spectroscopy that enables high-throughput, uncomplicated and accurate analysis.

When microalgae are exposed to changing environmental conditions, e.g., light-dark cycles or oscillations in nutrient availability (CO2, nitrogen, phosphate or silicate) they respond with metabolic changes in the carbon allocation pattern. Short time regulations in the time range of few seconds to minutes can be mirrored best by mass spectroscopy based metabolomics. However, these snap shots do not reflect the alterations in the carbon flow to the cellular macromolecules like protein, carbohydrate or lipid. In this review it is shown how the combination of FTIR spectroscopy and Chla-in-vivo-fluorescence based electron transport rates can reveal changes in the metabolic flux rates of carbon during a shift of the environmental conditions. The review will demonstrate in which time range FTIR spectroscopy can deliver significant information and how FTIR spectroscopy data can synergistically support metabolome analysis by mass-spectroscopy.

The dissertation work focuses on the whole route of material development starting from the investigations of properties of the initial (raw) HBPs to their applications. Each research step is given in a separate chapter to enhance attention to various aspects of the aim of the work. Thus, every chapter is started with an introduction. After that, the methods applied and experimental procedure are described. Next part tries to give the comprehensive description of the results obtained. At the end of the chapter, the main points are summarized. The Chapter 1 gives the theoretical description of the main experimental techniques used in this work. In Chapter 2 the chemical (chemical composition, purity, typical structure elements) and physical (glass transition temperature, the temperature of the maximum decomposition, the thermal stability at the high temperatures, molar mass, polydispersity and possible aggregation in solution) properties examined by different techniques of polymer analysis are described. The Chapter 3 is divided into three separate parts: In Chapter 3.1 the description of the formation and modification of inter- and intramolecular hydrogen bonds of hydroxyl terminated HBP is presented to reveal the information of hydroxyl groups re- and/or association due to the high temperatures applied. In Chapter 3.2 the nature of the solid-liquid interface of HBP thin films have been studied by different surface sensitive techniques with respect to further protein adsorption investigations. In Chapter 3.3 the strategy for the fabrication of surface attached carboxyl terminated HBP using "grafting to" technique is developed. The Chapter 4 consists of two parts: The first (theoretic) part outlines the basic principles of protein chemistry, factors influencing on the protein molecule stability in aqueous medium, the mechanism of protein adsorption and forces involved in the adsorption process. In the second part the combination of different in situ techniques was applied to obtain a comprehensive description of complex adsorption processes of protein molecules on different polymer surfaces.

Printed circuit board manufacturing involves subtractive copper (Cu) etching where fine features are developed with a specific spatial resolution and etch profile of the Cu interconnects. A UV-Vis ATR metrology, to characterize the chemical transitions, has been developed to monitor the state of the bath by an in-situ measurement. This method provides a direct correlation of the Cu etch bath and was able to predict a 35% lower etch rate that was not predicted by the three current monitoring methods (ORP, specific gravity, and conductivity). Application of this UV-Vis ATR probe confirmed that two industrial etch baths, in identical working conditions, confirmed a difference in Cu2+ concentration by the difference of the near IR 860nm peak. The scope of this probe allowed chemically specific monitoring of the Cu etch bath to achieve a successful regeneration for repeated use. Interlayer dielectrics (ILDs) provide mechanical and electrical stability to the 3D electrical interconnects found in IC devices. It is particularly important that the structural support is created properly in the multilayered architecture to prevent the electrical cross signaling in short range distances. A combined multiple internal reflection and transmission FTIR has been employed for the characterization of silicon oxycarbonitride (SiOCN) films. These dielectric low-k films incorporate various functional groups bonded to silicon and require chemical bonding insight in the transformation and curing process. Distinct SiOx bonding patterns were differentiated, and the structure of the films can be predicted based on the amount of Si network and caged species. Further optimization of the FTIR analysis must minimize interference from moisture that can impact the judgement of peak heights. To accommodate this, a high-quality glove box was designed for dry air feedthrough to achieve a 95% moisture reduction during analysis, where less than 0.1 mAbs of moisture is detected in the spectra (without additional correction). The glove box allows for the rapid analysis of multiple sample throughput to outpace alternative characterization methods while retaining low spectral noise and a dry environment for 24/7 analysis. There is a great need to identify new catalysts that are suitable for tackling current economic demands, one of which is the nitrogen reduction reaction (NRR). The development of the surface enhanced infrared absorption spectroscopy (SEIRAS) has been applied to characterize the NRR mechanisms on the vanadium oxynitride electrocatalyst. Electrochemical measurements demonstrate NRR activity that is up to three times greater in the presence of N2 than the control Ar. FTIR operando suggests that a considerable number of intermediates were formed and continued to increase in absorbing value under an applied potential of -0.8 V vs Ag/AgCl. XPS results of the post-NRR film suggest a restricting of the film where vanadium oxynitride films are prone to instabilities under the possible MvK mechanism. After 90 minutes of NRR, the NH3 generated was approximately 0.01 ppm was calculated for through the salicylate colorimetric method. On-going efforts are focusing on optimizing the vanadium oxynitride film by the tuning of the oxynitride ratios and crystalline properties to promote the formation of V≡N: during the nitrogen reduction reaction.

Die Vorverarbeitung und Analyse von spektrometrischen und spektroskopischen Daten von Pflanzengewebe sind in den unterschiedlichsten Forschungsbereichen wie der Pflanzenbiologie, Agrarwissenschaften und Klimaforschung von großer Bedeutung. Der Schwerpunkt dieser Arbeit liegt auf der optimierten Nutzung von Daten von Pflanzengeweben, insbesondere der Daten gewonnen durch Matrix–Assistierte Laser–Desorption–Ionisierung Massenspektrometrie, Raman-Spektroskopie und Fourier-Transform-Infrarotspektroskopie. Die Klassifizierungsfähigkeit mit diesen Methoden wird insbesondere nach Kombination der Daten untereinander und mit zusätzlichen chemischen und biologischen Informationen verglichen. Die diskutierten Beispiele befassen sich mit der Untersuchung und Einordnung innerhalb einer bestimmten Pflanzenart, beispielsweise der Unterscheidung von Proben aus unterschiedlichen Populationen, Wachstumsbedingungen oder Gewebeunterstrukturen. Die Daten wurden mit sowohl mit explorativen Werkzeugen wie der Hauptkomponentenanalyse und der hierarchischen Clusteranalyse, als auch mit Methoden des maschinellen Lernens wie die Diskriminanzanalyse oder künstliche neuronale Netzwerke umfassten. Konkret zeigen die Ergebnisse, dass die Kombination der Methoden mit zusätzlichen pflanzenbezogenen Informationen in einer Konsensus-Hauptkomponentenanalyse zu einer umfassenden Charakterisierung der Proben führt. Es werden verschiedene Strategien zur Datenvorbehandlung diskutiert, um nicht relevante spektrale Information zu reduzieren, z.B. aus Karten von Pflanzengeweben oder eingebetteten Pollenkörnern. Die Ergebnisse dieser Arbeit weisen auf die Relevanz der gezielten Nutzung spektrometrischer und spektroskopischer Daten hin und lassen sich nicht nur auf pflanzenbezogene Themen, sondern auch auf andere analytische Klassifizierungsprobleme übertragen. / The pre-processing and analysis of spectrometric and spectroscopic data of plant tissue are important in a wide variety of research areas, such as plant biology, agricultural science, and climate research. The focus of the thesis is the optimized utilization of data from plant tissues, which includes data from Matrix-Assisted-Laser Desorption/Ionization time of flight mass spectrometry, Raman spectroscopy, and Fourier transform infrared spectroscopy. The ability to attain a classification using these methods is compared, in particular after combination of the data with each other and with additional chemical and biological information. The discussed examples are concerned with the investigation and classification within a particular plant species, such as the distinction of samples from different populations, growth conditions, or tissue substructures. The data were analyzed by exploratory tools such as principal component analysis and hierarchical cluster analysis, as well as by predictive tools that included partial least square-discriminant analysis and machine learning approaches. Specifically, the results show that combination of the methods with additional plant-related information in a consensus principal component analysis leads to a comprehensive characterization of the samples. Different data pre-treatment strategies are discussed to reduce non-relevant spectral information, e.g., from maps of plant tissues or embedded pollen grains. The results in this work indicate the relevance of the targeted utilization of spectrometric and spectroscopic data and could be applied not only to plant-related topics but also to other analytical classification problems.

The group 2 late embryogenesis abundant (LEA) proteins, also known as the dehydrins, are intrinsically disordered proteins that are expressed in plants experiencing extreme environmental conditions such as drought or low temperature. In this work, we study the potential roles that dehydrins may have in stabilizing membranes and actin microfilaments during cold stress. We have cloned and expressed in E. coli two dehydrins from Thellungiella salsuginea, denoted TsDHN-1 (acidic) and TsDHN-2 (basic). These proteins were expressed as SUMO-fusion proteins for in vitro phosphorylation by casein kinase II (CKII), and for structural analysis by CD and Fourier transform infrared (FTIR) spectroscopy. We show using transmission-FTIR spectroscopy that ordered secondary structure is induced and stabilized in these proteins by association with large unilamellar vesicles emulating the lipid compositions of plant plasma and organellar membranes. The increase in secondary structure by membrane association is further facilitated by the presence of Zn2+. Lipid composition and temperature have synergistic effects on the secondary structure. Our single molecule force spectroscopy studies also suggest tertiary folding of both TsDHN-1 and TsDHN-2 induced by association with lipids. From Langmuir-Blodgett monolayer compression studies, and from topographic studies using atomic force microscopy at variable temperature, we conclude that TsDHN-1 stabilizes the membrane at lower temperatures. Finally, we show that the conformations of TsDHN-1 and TsDHN-2 are affected by pH, interactions with cations and membranes, and phosphorylation. Actin assembly by these dehydrins was assessed by sedimentation assays, and viewed by transmission electron and atomic force microscopy. Phosphorylation enabled both dehydrins to polymerize actin filaments, a phenomenon that may occur in the cytosols of plant cells undergoing environmental stress. These results support the hypothesis that dehydrins stabilize plant organellar membranes and/or the cytoskeleton in conditions of stress, and further that phosphorylation may be an important feature of this stabilization. / NSERC

This thesis is a summary of five papers with focus on adsorption processes of various monocarboxylates and aminocarboxylates at the water/goethite interface. Interaction of organic acids at the water/mineral interfaces are of importance in biogeochemical processes, since such processes have potential to alter mobility and bioavailability of the acids and metal ions. In order to determine the coordination chemistry of acetate, benzoate, cyclohexanecarboxylate, sarcosine, MIDA (methyliminediacetic acid), EDDA (ethylenediamine-N,N’-diacetic acid) and EDTA (ethylenediamine-N,N’-tetraacetic acid) upon adsorption to the goethite (alpha-FeOOH) surface, a combination of quantitative measurements with attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR) was utilized. Over the pH range studied here (pH 3- 9) all ligands, except for sarcosine, have been found to form surface complexes with goethite. In general, theses were characterized as outer sphere surface complexes i.e. with no direct interaction with surface Fe(III) metal ions. Furthermore, two types of different outer-sphere complexes were identified, the solvent-surface hydration-separated ion pair, and hydration-shared ion pair. For the monocarboxylate surface complexes distinction between these two could be made. At high pH values the solvent-surface hydration-separated ion pair was the predominating complex, while at low pH the surface complex is stabilized through the formation of strong hydrogen bonds with the goethite surface. However, it was not possible to clearly separate between the two outer-sphere complexes for coordination of the aminocarboxylates with the surface of goethite. Additionally, EDDA also formed an inner-sphere surface complex at high pH values. The EDDA molecule was suggested to coordinate to the surface by forming a five membered ring with an iron at the goethite surface, through the amine and carboxylate groups. Contrary to the other ligands studied, EDTA significantly induced dissolution of goethite. Some of the dissolved iron, in the form of the highly stable FeEDTA- solution complex, was indicated to re-adsorb to the mineral surface as a ternary complex. Similar ternary surface complexes were also found in the Ga(III)EDTA/goethite system, and quantitative and spectroscopic studies on adsorption of Ga(III) in presence and absence of EDTA showed that EDTA considerably effects speciation of gallium at goethite surface. The collective results in this thesis show that the affinity of these ligands for the surface of goethite is primarily governed by their chemical composition and structure, and especially important are the types, numbers and relative position of functional groups within the molecular structure.

Ziel der vorliegenden Promotionsarbeit war die Entwicklung einer Methode zur Quantifizierung saurer Zentren auf Festkörperoberflächen mittels 15N-Festkörper-NMR-Spektroskopie von adsorbierten Pyridinmolekülen. Die 15N-Festkörper-NMR von adsorbiertem Pyridin ermöglicht die Unterscheidung verschiedener Arten von sauren Zentren, wie Lewis- und Brønsted-Zentren. Die Bestimmung der Art und der Konzentration auftretender saurer Zentren ist entscheidend, um die katalytische Aktivität fester Katalysatoren in einer Reaktion zu verstehen. Da 15N-NMR-Messungen zumeist zeitaufwendig sind, wurde in dieser Arbeit eine zeitoptimierte Messroutine entwickelt, die auf der Messung von 15N-Einzelpuls-Spektren mit kurzen Pulswiederholzeiten beruht. Um diese Spektren quantitativ auswerten zu können, müssen die detektierten NMR-Signale bezüglich ihrer T1-Relaxation korrigiert werden. Zudem treten in 15N-Einzelpuls-NMR-Spektren oft starke Störungen der Basislinie auf. Zur Unterdrückung dieser Störsignale wurde die EASY-Methode entwickelt, die auf der Messung von zwei schnell aufeinander folgenden Spektren basiert. Mittels dieser Methode können auftretende Störsignale in quantitativen 15N-NMR-Spektren unterdrückt werden. Die entwickelte zeitoptimierte Quantifizierungsmethode wurde an zwei Probenserien von festen Säuren getestet; zum einen an Aluminiumhydroxidfluoriden, als Vertreter von Verbindungen mit stark sauren Zentren, und zum anderen an hydroxylierten Magnesiumfluoriden, als Vertreter schwach saurer Verbindungen. Der Vergleich mit anderen quantitativen Methoden zeigte, dass die 15N-Festkörper-NMR-Spektroskopie von adsorbiertem Pyridin hervorragend für die Quantifizierung saurer Zentren geeignet ist und Einblicke in die katalytische Aktivität fester Katalysatoren ermöglicht. / The aim of the present dissertation was to develop a method for the quantification of acidic sites on solid surfaces by 15N solid-state NMR with pyridine as probe molecule. 15N NMR of adsorbed pyridine allows to distinguish different types of acidic sites like Lewis and Brønsted sites. The determination of the kind and concentrations of occurring acidic sites is crucial to understand the catalytic activity of a solid catalyst in a reaction.15N NMR measurements are often time-consuming. Hence, a time-optimized NMR quantification procedure was developed which uses 15N single pulse spectra with short pulse repetition delays. For quantitative analysis of these spectra, occurring signals were corrected according to their T1 relaxation. Furthermore, often strong baseline disturbances are observed in single pulse spectra. For the suppression of these disturbances, the EASY method was developed. The EASY method uses two successive scans to obtain quantitative NMR spectra, in which baseline disturbances are suppressed. The developed time-optimized method for the quantification of acidic sites was applied on two series of samples. One series of aluminum hydroxide fluorides as representatives of catalysts with strong acid sites and one series of hydroxylated magnesium fluorides as representatives of weak acidic catalysts. The comparison with other quantitative methods shows that 15N solid-state NMR of adsorbed pyridine is an excellent method for the quantification of acidic sites, because insights in the catalytic activity of a catalyst can be gained.

Das aus dem Apoprotein Opsin und dem kovalent gebundenen Liganden bestehende Rhodopsin dient als Modellsystem für den Aktivierungsmechanismus der größten Klasse von G-Protein-gekoppelten Rezeptoren (GPCR). Infolge einer photochemischen Reaktion vollführt Rhodopsin eine Bewegungsabfolge von Sekundärstrukturelementen, wodurch es aktiviert wird, das G-Protein bindet und den Stimulus auf zellinterne Signalwege überträgt. Mithilfe der ortsspezifischen Mutagenese wurden Mutanten des bovinen Rhodopsins erzeugt, in eine künstliche Lipidumgebung eingelagert und hauptsächlich mittels FTIR-Spektroskopie untersucht. Anhand der Y191F- und Y192F-Mutanten konnte die Translokation des transienten Gegenions der Schiffschen Base Glu181 während der Aktivierung bestimmt werden. Die Interaktionen des Tyr206 sind für die gekoppelte Bewegung von EL2 und TM5 mitbestimmend, was mittels Y206F-Mutante gezeigt wurde. Eine Anhäufung von Methioninen auf der cytoplasmatischen Seite des Rezeptors ist u.a. für das Ausklappen der TM6 zuständig. Diese Bewegung ist wichtige Determinante der Rezeptoraktivierung. Hierfür wurden insgesamt fünf Mutanten verwendet. Im zweiten, hauptsächlichen Teil der Arbeit wird das bislang kaum untersuchte humane Rhodopsin mit dem bovinen Rezeptor verglichen. Ausgehend von verschiedenen Dunkelzuständen, konnte gezeigt werden, dass die Aktivierungsmechanismen beider Rezeptoren voneinander divergieren, um letztlich bei der Bildung der aktiven Spezies wieder zu konvergieren. Über die Analyse der Aminosäuresequenzen der Mammalia-Rhodopsine wurden zwei Bereiche hoher Variabilität identifiziert, die u.a. die molekulare Ursache für diese Diskrepanzen liefern. Diese Feststellung wurde mit human-bovinen-Rhodopsinchimären bewiesen. Ergänzend zu dieser Studie wurde Schafsrhodopsin einem Vergleich sowohl mit bovinem als auch mit humanem Rezeptor unterzogen. Es zeigte, als eine weitere natürlich vorkommende Variante des Lichtrezeptors, einen eigenständigen Weg der Aktivierung. / Rhodopsin, which consists of the apoprotein opsin and its covalently bound ligand, is used as a model system to understand the activation mechanism of the large family of G protein coupled receptors (GPCRs). As a result of a photochemical reaction, rhodopsin undergoes activating structural changes, enabling it to bind the G protein and transmitting the stimulus to intracellular signaling pathways. In the first part of this work, site-directed mutants of bovine rhodopsin were produced, incorporated into an artificial lipid environment, and studied mainly by FTIR spectroscopy. The translocation of the transient Schiff base counterion (Glu181) during the activation process was determined using the Y191F- and Y192F-mutants. The interactions of Tyr206 contributed to the coupled movement of EL2 and TM5, which was shown by Y206F-mutant. A striking accumulation of methionines on the cytoplasmic side of the receptor was observed to be a key-player for the activating outward motion of TM6. In the second and primary part of this work, human rhodopsin, which has been rarely studied, was compared with the bovine receptor. Starting from various dark states, it was shown that the activation mechanisms of both receptors diverge from each other and yet ultimately converge in the formation of the active species. By analyzing the amino acid sequences of mammalian rhodopsins, two regions of high variability were identified, which provide the molecular basis for these discrepancies. This finding was verified by the investigation of human/bovine rhodopsin chimeras. In addition to this study, ovine rhodopsin was compared with both the bovine and human forms. It showed, as another naturally occurring variant of the light receptor, an independent pathway of activation.