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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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The Study of the Molecular Structure of Various Forms of Conducting Polymers using FTIR and Raman Spectroscopies
Morávková, Zuzana ; Trchová, Miroslava (advisor) ; Baumruk, Vladimír (referee) ; Matějka, Pavel (referee)
In this Thesis, the structure of thin films formed by a conducting polymer, polyaniline, was studied using mainly infrared and Raman spectroscopies. That led to the study of aniline oligomers. The oligomers play a key role in the formation of thin films and nanostructures of polyaniline. Furthermore, the Thesis deals with the carbonization of various forms of polyaniline (granular polyaniline base, thin films of polyaniline salt, multi-wall carbon nanotubes coated with polyaniline salt or base, polyaniline nanotubes/nanorods prepared in the presence of ethanol). The two topics, aniline oligomers and carbonization of polyaniline, are connected by a paper concerning the carbonization of microspheres formed during oxidation of aniline in alkaline medium. Optical microscopy, transmission and scanning electron microscopy, UV-Vis spectroscopy, spectroscopic ellipsometry, wide angle X-ray scattering and thermogravimetric analysis were used.
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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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Modern computational techniques for simulations of molecular spectra
Ivani, Ivan ; Baumruk, Vladimír (advisor) ; Kapitán, Josef (referee)
Accurate computations of vibrational energies and vibrational spectra of molecules require an inclusion of the anharmonic forces. In standard computational protocols, a large vibrational Hamiltonian matrix is diagonalized, and spectral intensities are calculated for individual transitions separately. In this work we propose an alternate direct generation of the spectral curves based on a temporal propagation of a trial vibrational wavefunction followed by a Fourier transformation. The lack of the lengthy and computer-memory demanding diagonalization makes the method suitable for larger molecules. It is especially convenient for sparse Hamiltonians that are commonly obtained within the harmonic oscillator basis set, and the algorithm is amendable to parallelization. On a model water dimer basic convergence properties are discussed. The method is then applied to vibrational Raman intensities of the fenchone compound, were it provides spectral shapes comparable with those obtained by the classical approaches.
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Raman optical activity and conformation of structurally important groups in peptides and proteins
Kubáňová, Markéta ; Baumruk, Vladimír (advisor) ; Kapitán, Josef (referee)
Raman optical activity (ROA) represents a modern spectroscopic technique that can be applied to a wide range of chiral molecules starting from small organic molecules up to complex biomolecular systems. Among other things ROA provides information about solution structure of peptides and proteins. The aim of the thesis was to determine the relationship between three-dimensional structure and Raman optical activity of disulphide and amide groups in peptides. Characteristic band patterns of the polyproline II conformation (left-handed 31-helix) were found in the ROA spectra of poly(Pro-Gly-Pro), oxytocin and hinge peptide linked to the antigen sequence. ROA signal in the S-S and C-S stretching region was observed in ROA spectra of model cyclodextrin compounds connected with disulphide bonds. Positive ROA band in the S-S stretching region was found in the ROA spectrum of oxytocin (the peptide with one S-S bridge). According to the theoretical studies of model disulphides, positive ROA signal in this region indicates positive dihedral angle C- S-S-C. This result is in agreement with the crystal structure. We have also worked on extension of ROA measurements to the hydrogen stretching region (2500-3200 cm-1).
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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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