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Optimization of high-pressure experiments for measurement of optical activity
Plamitzer, Luboš ; Valenta, Jan (advisor) ; Baumruk, Vladimír (referee)
The presented bachelor thesis focuses on the effects of high hydrostatic pressure on Raman spectra of selected monoterpenes: (−)-fenchone, (−)-carvone, (−)-limonene and (−)-α-pinene. The spectra under pressures up to 13 GPa were obtained using a diamond anvil cell. All compounds show a significant shift of vibration peak maxima and a change of their intensity. In the case of (−)-fenchone and (−)-α-pinene an "anomalous" decrease of vibrational frequency with increasing pressure was observed, which for (−)-fenchone corresponds to available results of high pressure experiments on structurally similar cam- phor. Pressure-induced spectral and structural changes were also modelled using both classical and quantum-mechanical simulation methods. 1
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PFM and Raman spectroscopy of selected dielectric materials
Borodavka, Fedir ; Gregora, Ivan (advisor) ; Baumruk, Vladimír (referee) ; Hehlen, Bernard (referee)
Title: PFM and Raman spectroscopy of selected dielectric materials Author: Fedir Borodavka Institute: Department of Dielectrics, Institute of Physics of the Academy of Sciences, Na Slovance 2, 182 21, Prague 8, Czech Republic Supervisor: Ing. Ivan Gregora, CSc. Training institute: Department of Dielectrics, Institute of Physics of the Academy of Sciences, Na Slovance 2, 182 21, Prague 8, Czech Republic Consultants: RNDr. Stanislav Kamba, CSc. and RNDr. Vladimír Vorlíček, CSc. Abstract: The thesis is devoted to a detailed investigation of dielectric materials using Raman spectroscopy and PFM microscopy techniques. Phonon properties of a newly synthesized guanylurea(1+) hydrogen phosphite single crystals have been studied. A tentative assignment of the observed Raman peaks has been done and the sets of A′ MIX, A′ TO and A′′ TO mode frequencies have been determined. Phonon behaviour of BiMnO3 ceramics, obtained from Raman spectra, has been char- acterized. After comparing the factor group analysis with the Raman spectra it has been concluded that the material has a centrosymmetric C2/c structure and is not ferroelectric. Lattice modes of the complex La1/2Na1/2TiO3 single crystal have been investigated. We have numerically analysed the intensity behaviour of the sharp peak at 455 cm−1 on heating and...
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Raman optical activity and conformational flexibility of peptides in solution
Hrudíková, Jana ; Baumruk, Vladimír (advisor) ; Kapitán, Josef (referee)
Title: Raman optical activity and conformational flexibility of peptides in solution Author: Jana Hrudíková Department: Institute of Physics of Charles University Supervisor: Doc. RNDr. Vladimír Baumruk, DrSc. Supervisor's e-mail address: baumruk@karlov.mff.cuni.cz Abstract: Molecular flexibility can significantly modify Raman and ROA spectral intensities, band positions and the ROA signs. Taking into account dynamic aspects of behavior of studied molecules in solution via conformational averaging therefore seems to be crucial for spectral interpretation. The first of studied models, histidine, plays an important role in metallo-enzymatic reactions and peptide folding, due to its imidazole ring. ROA spectra of His at different pH, His complexed with Cu2+ and dipeptides His- Gly and Gly-His were recorded on the spectrometer built at the Institute of Physics of the Charles University as a first step of the subsequent study. The second studied system, a cyclic hexapeptide c-(Phe-D-Pro-Gly-Arg-Gly-Asp), serves as a convenient model for β- hairpin and anti-parallel β-sheet. It was previously studied by means of VCD and IR. From molecular dynamics simulations 10 peptide geometries were selected for spectral modeling. The Raman and ROA spectra were calculated ab initio. For a model fragment Phe-D-Pro, which...
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Theory and applications of optical activity of biomolecules
Krupová, Monika ; Bouř, Petr (advisor) ; Baumruk, Vladimír (referee) ; Záruba, Kamil (referee)
Title: Theory and Applications of Optical Activity of Biomolecules Author: Monika Krupová Supervisor: prof. RNDr. Petr Bouř, DSc. Institutions: Faculty of Mathematics and Physics, Charles University, and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic Abstract: This thesis describes how we used several chiroptical spectroscopic methods to study chiral molecules: vibrational circular dichroism (VCD), circularly polarized luminescence (CPL) and magnetic circular dichroism (MCD). VCD and induced lanthanide CPL were used to study the structure of amyloid protein fibrils. We found out that VCD is very sensitive to their structure and supramolecular chirality. It could be used to distinguish between various polymorphic fibrils. On the other hand, induced lanthanide CPL provided information on the local structure. VCD was also used to study the hydration polymorphism of nucleoside crystals. Due to the crystal packing, the VCD signal was strong and specific for different types of crystals. Finally, electronic structure of hydrated Ln3+ ions was studied by MCD. Molecular dynamics simulations together with crystal field theory (CFT) and multistate complete active space calculations with second order perturbation correction (MS-CASPT2) were used to interpret the spectra. CFT...
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Raman optical activity of biomolecules: From simple models to complex systems
Pazderková, Markéta ; Baumruk, Vladimír (advisor)
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.
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Raman optical activity and conformational flexibility of peptides in solution
Hudecová, Jana ; Baumruk, Vladimír (advisor)
Title: Raman optical activity and conformational flexibility of peptides in solution Author: Jana Hrudíková Department: Institute of Physics of Charles University Supervisor: Doc. RNDr. Vladimír Baumruk, DrSc. Supervisor's e-mail address: baumruk@karlov.mff.cuni.cz Abstract: Molecular flexibility can significantly modify Raman and ROA spectral intensities, band positions and the ROA signs. Taking into account dynamic aspects of behavior of studied molecules in solution via conformational averaging therefore seems to be crucial for spectral interpretation. The first of studied models, histidine, plays an important role in metallo-enzymatic reactions and peptide folding, due to its imidazole ring. ROA spectra of His at different pH, His complexed with Cu2+ and dipeptides His- Gly and Gly-His were recorded on the spectrometer built at the Institute of Physics of the Charles University as a first step of the subsequent study. The second studied system, a cyclic hexapeptide c-(Phe-D-Pro-Gly-Arg-Gly-Asp), serves as a convenient model for β- hairpin and anti-parallel β-sheet. It was previously studied by means of VCD and IR. From molecular dynamics simulations 10 peptide geometries were selected for spectral modeling. The Raman and ROA spectra were calculated ab initio. For a model fragment Phe-D-Pro, which...
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Structure and dynamics of peptides and proteins in solution: application of Raman optical activity
Profant, Václav ; Baumruk, Vladimír (advisor) ; Kapitán, Josef (referee) ; Setnička, Vladimír (referee)
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...
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Vibrational optical activity of biomolecules
Ješko, Eduard ; Baumruk, Vladimír (advisor) ; Kaminský, Jakub (referee)
The thesis aims at the study of conformation of a dimethyl tartrate molecule using the methods of vibrational optical activity (VOA), namely vibrational circular dichroism (VCD) and Raman optical activity (ROA). Based on the theoretical background of both VOA methods and current state of research of the studied molecule there was a sample of dimethyl tartrate dissolved in different solvents and its properties were measured using VCD and ROA spectrometers. In addition to the experiment, ab initio calculations were carried out in order to compare calculated and experimental spectra. Based on the comparison, the possible conformations present in water solution of the studied molecule are described in detail.
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