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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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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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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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Raman optical activity of biomolecules: From simple models to complex systems
Pazderková, Markéta ; Baumruk, Vladimír (advisor) ; Kapitán, Josef (referee) ; Matějka, Pavel (referee)
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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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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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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