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Determination of structure and dynamics of biomolecules by theoretical calculations of NMR spectroscopic parameters
Benda, Ladislav ; Sychrovský, Vladimír (advisor) ; Munzarová, Markéta (referee) ; Hrabal, Richard (referee)
iv Abstract Subject: Determination of structure and dynamics of biomolecules by theoretical calcu- lations of NMR spectroscopic parameters Author: Ladislav Benda, ladislav.benda@gmail.com Department/Institute: Institute of Organic Chemistry and Biochemistry, AS CR Supervisor: Dr. Vladim'ır Sychrovsk'y, Institute of Organic Chemistry and Biochemistry, AS CR, vladimir.sychrovsky@uochb.cas.cz Abstract: This doctoral work was focused on theoretical modeling of nuclear magnetic resonance (NMR) parameters in peptides and nucleic acids. Dependences of NMR para- meters on molecular structure and solvation were primarily modeled. Great emphasis was put on the comparison of the calculated data with the NMR experiment. The molecular models studied included the l-alanyl-l-alanine di-peptide (AA) and the phosphate group of nucleic acid backbone. Conformations of all three charged forms of AA in solution were determined and the respective pH-induced changes of experimental NMR chemical shifts and nuclear spin-spin coupling constants were explained. Dependences of NMR cross-correlated relaxation rates on the AA backbone geometry were calibrated. The 31 P NMR parameters in nucleic acid phosphate were systematically calculated in dependence on the backbone conformation and the phosphate solvation pattern. Qualitative rules...
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Theory and application of optical spectroscopic methods for structural molecular studies
Hudecová, Jana ; Bouř, Petr (advisor) ; Setnička, Vladimír (referee) ; Valenta, Jan (referee)
Title: Theory and application of optical spectroscopic methods for structural molecular studies Author: RNDr. Jana Hudecová Department / Institute: Institute of Organic Chemistry and Biochemistry Supervisor of the doctoral thesis: Prof. RNDr. Petr Bouř, DSc. Abstract: In the thesis, methods of the chiroptical spectroscopy (Raman optical activity, electronic and vibrational circular dichroism, circularly polarized luminescence) were utilized to obtain information on structure of chiral molecules. In four main projects, we focused on improving accuracy of quantum-chemical computations used for interpretation of experimental spectra by including anharmonic effects, solvent, molecular flexibility and dynamics. In the first project, the normal mode geometry optimization method was investigated and a suitable frequency limit providing realistic vibrational band broadening was found. Then the ability of harmonic and anharmonic computational approaches to describe the C-H stretching vibrations was explored for three terpene molecules and four spectroscopic methods. In the third project, we estimated the role of dispersion forces and different organic solvents for conformer equilibria and dynamics of cyclic dipeptides containing tryptophan. In the last project, circularly polarized luminiscence spectra, which were...
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Synthesis and study of crystalline materials for NLO
Janatková, Tereza ; Němec, Ivan (advisor) ; Vojtíšek, Pavel (referee)
This thesis is focused on preparation and study of new compounds of chosen organic bases with potential use in nonlinear optics. 2-amino-5-nitropyrimidine, 2-amino-4-methylpyrimidine and their salts with inorganic and organic acids are compounds of the main interest. Diffraction and vibrational-spectroscopic methods of characterization were used in combination with quantum chemical calculation methods. Another aim of this thesis was preparation of new salts of chosen pyrimidine derivates with the use of methylsulphonic acid. Part of this section is devoted to completion of pyridinium methylsulphonate phase transition and nonlinear optical property studies.
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Molecular crystals for NLO applications - compounds of 1H-pyrazole-carboxamidine
Kohúteková, Soňa ; Němec, Ivan (advisor) ; Šloufová, Ivana (referee)
Title: Molecular crystals for NLO applications - compounds of 1H-pyrazole-carboxamidine Author: Bc. Soňa Kohúteková Department: Department of Inorganic Chemistry Supervisor: prof. RNDr. Ivan Němec, Ph.D. Abstract: The aim of this diploma thesis is preparation and characterisation of novel compounds of 1H-pyrazole-carboxamidine in consideration of their potential application in the field of nonlinear optics. This thesis is focused on preparation of crystalline salts or adducts combining 1H-pyrazole-carboxamidine with selected inorganic and organic acids. Prepared materials were characterised mainly by the means of vibrational spectroscopy and X-ray diffraction analysis. Quantum-chemical calculations were used for a prediction of nonlinear optical properties as well as for interpretation of measured vibrational spectra. Four different approaches of calculations were used for an optimisation of computing time together with accuracy of the fit of calculated and measured spectra. Finally, measurements of second harmonic generation efficiency of two powder samples with non-centrosymmetric crystal structures were performed. Key words: NLO, vibrational spectroscopy, crystal structure, quantum-chemical calculations
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Determination of structure and dynamics of biomolecules by theoretical calculations of NMR spectroscopic parameters
Benda, Ladislav ; Sychrovský, Vladimír (advisor) ; Munzarová, Markéta (referee) ; Hrabal, Richard (referee)
iv Abstract Subject: Determination of structure and dynamics of biomolecules by theoretical calcu- lations of NMR spectroscopic parameters Author: Ladislav Benda, ladislav.benda@gmail.com Department/Institute: Institute of Organic Chemistry and Biochemistry, AS CR Supervisor: Dr. Vladim'ır Sychrovsk'y, Institute of Organic Chemistry and Biochemistry, AS CR, vladimir.sychrovsky@uochb.cas.cz Abstract: This doctoral work was focused on theoretical modeling of nuclear magnetic resonance (NMR) parameters in peptides and nucleic acids. Dependences of NMR para- meters on molecular structure and solvation were primarily modeled. Great emphasis was put on the comparison of the calculated data with the NMR experiment. The molecular models studied included the l-alanyl-l-alanine di-peptide (AA) and the phosphate group of nucleic acid backbone. Conformations of all three charged forms of AA in solution were determined and the respective pH-induced changes of experimental NMR chemical shifts and nuclear spin-spin coupling constants were explained. Dependences of NMR cross-correlated relaxation rates on the AA backbone geometry were calibrated. The 31 P NMR parameters in nucleic acid phosphate were systematically calculated in dependence on the backbone conformation and the phosphate solvation pattern. Qualitative rules...
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