The aim of the thesis is to utilize Raman optical activity (ROA) to get unique information on peptide/protein conformation, which is otherwise difficult or even impossible to obtain. We have focused on investigation of amide and disulfide groups. Utilizing tailor-made model structures (rigid tricyclic spirodilactams with two interacting nonplanar amide groups), special model peptides and even biologically active molecules (neurohypophyseal hormones and their agonistic and antagonistic analogs, antimicrobial peptide lasiocepsin and its analogs having different disulfide pattern) we have traced specific spectral manifestation of nonplanar amides and disulfides. ROA results were supplemented by data obtained by complementary chiroptical methods - electronic (including vacuum UV - SRCD) and vibrational circular dichroism. When used in a concerted fashion, these techniques provide complex information on peptide/protein secondary structure. Where possible, experimental chiroptical data were compared to ab initio calculations. In chiroptical spectra we have found and interpreted signals reflecting nonplanarity of the amide group. Moreover, in ROA spectra we have identified signals due to S-S stretching vibrations which seem to reflect sense of the disulfide group torsion.

Our investigation was focused on a secondary protein structure called polyproline I. This helical structure has been known for a long time, but its occurrence and significance in nature is not yet fully known. In this thesis, we use Raman spectroscopy and chiral sensitive Raman optical activity. These methods are sensitive to the structure of proteins but are more informative and sensitive to the local arrangement than the commonly used ECD and UV absorption. We were able to obtain polyproline I Raman and ROA spectra that have not yet been published. We have described important differences between the spectra of polyproline I and II and observed the process of mutarotation. The experimental part of the work is supplemented by quantum chemistry calculations of spectra using the transfer of molecular property tensor. The calculated spectra corresponded very well with the experimental spectra.

This Thesis deals with simulations of chiroptical spectra using a combination of molecular dynamics and quantum chemistry. Molecular dynamics was used to explore conformational behaviour of studied systems (proteins), quantum chemistry for calculation of spectral prop- erties. The Quantum chemical methods are limited to relatively small systems. We overcome this problem mostly by a fragmentation of studied systems, when smaller, computationally feasible, fragments are created and used for the quantum chemical calculations. Calculated properties were then transferred to the big molecule. Vibrational Optical Activity (VOA) spectra of poly-L-glutamic acid fibrils (PLGA), insulin prefibrillar form and native globular proteins were studied. The simulated spectra provided satisfactory agreement with the experiment and were used for its interpretation. Experimental Vibrational Circular Dichroism (VCD) spectra of poly-L-glutamic acid fibrils were only qualitatively reproduced by the simulation. We could reproduce the major amide I band and a smaller negative band associated with the side chain carboxyl group. Our simulation procedure was then extended to a set of globular proteins and their Raman Optical Activity (ROA) spectra. Here we achieved an exceptional precision. For example, we were able to reproduce...

Study of plasma in the mixtures with molecular gas at wide pressure range Matěj Jan Morávek Abstract: The positive column of DC glow discharge sustained in oxygen and oxygen-nitrogen mixtures has been studied in two discharge tubes of the same shape made from different materials (Silica and Pyrex glass) for total pressures 650 - 2000 Pa and discharge currents up to 40 mA. Various parameters of the discharge - axial electric field strength, concentration of electrons and emission spectra - were studied with emphasis placed on transition region between low- and high-gradient form of the positive column. We have focused on the qualitative and quantitative analysis of the differences in emission spectra for both particular forms and the transitional region between them. The impact of 1 % admixture of nitrogen was also studied.

1 Nucleotides are organic molecules that have a wide range of functions in living organisms. They participate in cell signaling, serve as cofactors of enzymatic reactions, play a central role in cellular metabolism, and are the basic monomeric units of nucleic acid polymers. Nucleotides consist of three subunit molecules - nitrogen nucleobase, a five-carbon sugar (ribose or 2'-deoxyribose), and a phosphate group containing one to three phosphates. The subject of this master thesis is the study of various nucleotides and their self-assemblies in water by means of vibrational spectroscopy - Raman scattering and its chirally sensitive variant Raman optical activity (ROA). ROA has the potential to provide new information about the structural arrangement, dynamics, and interactions of nucleotides, as it supposes to be much more sensitive to vibrations of its sugar part containing three to four chiral carbons, compared to Raman scattering. We study spectral manifestations associated with chemical modifications (difference between ribo- and deoxyribonucleotides, the influence of different phosphate positions) and the change of physical conditions (various charge states according to the set pH, effect of concentration, influence of ions). A substantial amount of work is devoted to studying the self-association of...

The aim of this thesis is a study of processes during organosilicone thin film deposition via plasma polymerization. Recently, thin films are the most expanding way of surface modification of materials. They are used as protective coatings, functional layers, they can increase or decrease adhesion to different compounds (e.g. water), or just improve mechanical properties of bulk materials. Plasma polymers, which are not known so long, are a modern trend in evolution of thin film deposition. They have perfect adhesion to the substrate and they are highly resistant against most of chemical compounds. Their structure is quite different from the structure of classical polymers. Recently, organosilicon compounds are used as precursors for plasma polymers because silicon built in the structure of plasma polymer allows thin film deposition on glass substrate and the organic part of monomer gives us infinite possibilities of modification. In our case dimethylphenylsilane (DMPS) was used as a monomer. Various RF low pressure discharges were used during this study. Plasma diagnostic was performed by optical emission spectroscopy of inductive coupled plasma. This method allows us to determine plasma composition during the deposition process. Thus we can predict the composition of deposited thin film according to input parameters. From relative populations of fragments we are able to find out optimal conditions for deposition process. We can also calculate temperature of particles in plasma which gives us some information about particle energies. The first part of the study deals with the identification of particles (fragments) created by fragmentation of monomer in plasma environment. We successfully identified hydrogen atomic lines of Balmer’s series in the spectra. Many rotational lines of hydrogen molecule were also detected. Atomic carbon occurred only in small amount. Much more carbon was detected in the form of CH radical. We also found some weak lines connected to atomic silicon. When we used a mixture of DMPS and oxygen, OH radical and O2+ were present in spectra. Next, optimal settings of deposition were determined for particular fragments from relative intensities of these fragments in optical emission spectra. Using this information we are able to set up the process to deposit thin films of desired composition and properties. We calculated electron temperature from intensities of hydrogen lines in Balmer’s series. Rotational temperature was obtained from CH radical intensity. Unfortunately, there was no convenient radical from which intensity we would be able to calculate vibrational temperature. All results and information obtained during the research can be used in industrial plasma polymerization processes and development of new coatings and functional thin films. Other studies on DMPS or similar monomer may also be realized to get more knowledge about processes in plasma and this thesis could serve as a basis for further research. Moreover, this study is a part of an international project. The aim of this project is to study processes during plasma polymerization both theoretically and practically. Once finished, the project and its results will be presented in scientific literature and at international conferences.

The main goal of this diploma thesis was to implement the proposal of optical access networks in the selected location. Introduce is focused on the physical layer of network. This includes optical fibers, optical cables, connectors, optical splitters, and more. According to the place of termination of optical fiber will be studied best FTTx connections. According to network topology distinguished point to point and point to multipoint network. Networks points to point are also known as an active optical network and for each user are restricted to a separate fiber. Point to multipoint networks known as passive optical network. In terms of the PON is defined by many standards. For a selected location will be choice the most appropriate solution. Finally, the measurement will be made and will be considered for monitoring the route. Before the design of optical access networks, I made an illustrative simulation in program OptSim. Performed simulations helps to study the transmission characters of optical networks, depending on the physical architecture. In general, for the design of high-capabilities networks for large companies will be more appropriate active topology that provides due wavelength multiplexes high transmission capacity. To join in the urban areas with a large number of separate houses, it is more appropriate use of passive topology. For the design of optical networks has been selected location with multiple housing buildings. The end customer is not given the requirement for high data transfer rates as large companies. For the proposal was selected FTTB networks which is suitable because of lower costs. The second variant of the proposal was a passive optical network according to standard GPON. This standard was chosen because of the high splitting ratio. For both solutions was developed the entire proposal by ITU-T with a detailed drawing documentation. In the selected area was conducted measuring the optical networks in order to verify the possibility of extension actual solutions. For a sample issue of measurements, I made several measurements using optical reflectometer over an optical splitter in order to prove the need for measurements during construction. FTTH networks gaining in popularity more and more, but price is the limiting factor.

Studies of Lanthanide Complexes by a Combination of Spectroscopic Methods Monika Krupová (Department of Physical and Macromoecular Chemistry, Faculty of Science, Charles University in Prague) Since conventional structural analysis offers rather limited means for the chirality detection, a series of lanthanide tris-(β-diketonates) are investigated as effective receptors for a better chirality sensing in biomolecular substrates. These lanthanide complexes containing β-diketonate ligands are electrically neutral; they can further coordinate with various small organic molecules such as chiral alcohols, amino alcohols or amino acids in organic solvents and produce a strong chiral signal. Previously, a resonance in Raman scattering was observed in the studied systems due to the correspondence of europium electronic transition energy to the laser excitation wavelength, about a 100-fold signal enhancement if compared to non-resonant vibrational ROA was observed. This enabled shorter detection times as well as lower sample concentrations. In the current work, interaction of the Eu(FOD) complex with (R)- and (S)- enantiomer of 1-phenylethanol in n-hexane was studied using IR spectroscopy, Raman spectroscopy and Raman optical activity (ROA), UV-Vis spectroscopy and ultraviolet circular dichroism (UVCD). Only...

Dizertační práce se zabývá mechanismy mazání v náhradách kyčelního kloubu. Byla provedena systematická studie formování proteinového filmu při zahrnutí různých materiálů a provozních podmínek. Hlavní pozornost je přitom věnována roli jednotlivých proteinů obsažených v synoviální kapalině při současné přítomnosti dalších proteinů. Jelikož metody aplikované v předchozích studiích neumožňovaly separovat jednotlivé složky maziva, byla vyvinuta optická měřící metoda na principu fluorescenční mikroskopie. Z důvodu verifikace metody byly provedeny dvě nezávislé studie zaměřené na měření tloušťky mazacího filmu a dělení maziva na výstupu mazaného kontaktu. Z důvodu určitých limitací fluorescenční mikroskopie byla dále využita i metoda optické interferometrie, jejíž využití je ilustrováno ve studii zabývající se formováním mazacího filmu v náhradách kyčelního klubu při uvažování reálné konformity třecích povrchů. Závěrečná část práce představuje nový metodologický přístup založený na in situ pozorování kontaktní oblasti umožňující popsat roli jednotlivých proteinů ve vztahu k vývoji tloušťky mazacího filmu. Práce obsahuje originální výsledky, které přináší nové poznání v oblasti biotribologie náhrad kyčelního kloubu vedoucí k dalšímu vývoji implantátů při snaze zabránit jejich selhání v důsledku omezené životnosti.

The thesis inquires the specific and advantageous applications of Raman optical activity (ROA) in wide range of diverse structural and conformational studies of biomolecules and other biologically important molecules. Our investigation was focused on several interconnected topics covering the fields of methodology, basic and applied research. The combination of experimental and theoretical approaches facilitated deeper understanding of studied phenomena, and allowed for the effects of solute-solvent interactions. High-quality spectra of model molecules in the C-H stretching region, acquired as a result of successful extension of ROA measurements to the whole region of fundamental molecular vibrations, enabled verification and further development of methods for ROA spectra simulations encompassing anharmonic corrections. Utilizing spirodilactams with highly nonplanar amide groups, we have traced the specific ROA spectral manifestations of amide nonplanarity. In case of antimicrobial peptide lasiocepsine, we have successfully simulated ROA signals of S-S stretching vibrations which contrary to current belief do not seem to reflect sense of the S-S group torsion. In larger molecular systems, we have better understood the process of the formation of stable polyproline II conformation and proved that ROA may...