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Studies of Lanthanide Complexes by a Combination of Spectroscopic Methods
Krupová, Monika ; Bouř, Petr (advisor) ; Kapitán, Josef (referee)
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...
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Development and applications of molecular dynamics for chiral systems
Kessler, Jiří ; Bouř, Petr (advisor) ; Fanfrlík, Jindřich (referee)
The Thesis deals with MD simulations of solutions of chiral solutes in chiral solvents. These solutions consist of 2,2,2-trifluoro-1-phenylethanol, 1-phenylethanol and 1-phenyl- ethanamine.The differences in NMR properties between different combnations of solvent and solute absolute configuration were modeled. Indeed, differences in radial distribution functions and conformer abundances of solute calculated by the WHAM method were found. These results correlated with experimental differences in NMR shifts. Additionally, a method of cluster preselection was developed. It significantly decreased the amount of clusters needed for computations of NMR shieldings and hence the computer time. Keywords: chirality, molecular dynamic, nuclear magnetic resonance
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Interaction of Metal Cations in Bioorganic Environment. Computational Study Using Quantum Mechanics and Molecular MechanicsTools.
Futera, Zdeněk ; Burda, Jaroslav (advisor) ; Bouř, Petr (referee) ; Clark, Tim (referee)
Interactions of Metal Cations in Bioorganic Environment Computational Study Using Quantum Mechanics and Molecular Mechanics Tools Zdeněk Futera Biologically relevant interactions of piano-stool ruthenium(II) complexes with ds-DNA are studied by QM/MM computational technique. The whole re- action mechanism is divided into three phases - hydration of [RuII (η6 - benzene)(en)Cl]+ , consequent binding DNA and final intra-strand cross-link formation between two adjacent guanines. Free energy profiles of all reactions are explored by QM/MM MD umbrella sampling approach where the Ru(II) complex is described by DFT. For that purpose, special QM/MM software was developed to couple Gaussian and Amber programs. Calculated free energy barriers of Ru(II) hydration as well as DNA binding process are in good agreement with experimentally determined rate constants. Reaction pathway for cross-link formation was predicted that is feasible from both thermodynamical and kinetical point of view.
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Reaction of prion protein with quinacrine
Zawada, Zbigniew ; Šafařík, Martin ; Šebestík, Jaroslav ; Stibor, Ivan ; Bouř, Petr
Prion protein is supposed to cause Creutzfeld–Jakob disease, which can be treated in cell culture by quinacrine. In this work we study acridinylation reaction of prion protein. We also investigate this reaction theoretically on simple models and calculate activation energies for a large ensemble of acridine derivatives. Found correlation between the reactivity and geometry can enhance the design of the new acridine compounds, particularly for medical purposes.
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Izotopicky značené peptidy poskytující rozlišená strukturní data pomocí infračervených specter. Strukturní limity optické spektroskopie
Keiderling, T. A. ; Huang, R. ; Kubelka, J. ; Bouř, Petr ; Setnička, V. ; Hammer, R. P. ; Etienne, M. A. ; Silva, R. A. G. D. ; Decatur, S. M.
Isotopic labeling, here exemplified by 13C substitution on the amide C=O group, can allow site-specific determination of peptide conformation with IR. Examples of helix and sheet (beta-hairpin) structures are reviewed.
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