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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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Development and applications of molecular dynamics for molecular spectroscopy
Kessler, Jiří
This Thesis deals with simulations of chiroptical spectra using a combination of molecular dynamics and quantum chemistry. Molecular dynamics was used to explore conformational behaviour of studied systems (proteins), quantum chemistry for calculation of spectral prop- erties. The Quantum chemical methods are limited to relatively small systems. We overcome this problem mostly by a fragmentation of studied systems, when smaller, computationally feasible, fragments are created and used for the quantum chemical calculations. Calculated properties were then transferred to the big molecule. Vibrational Optical Activity (VOA) spectra of poly-L-glutamic acid fibrils (PLGA), insulin prefibrillar form and native globular proteins were studied. The simulated spectra provided satisfactory agreement with the experiment and were used for its interpretation. Experimental Vibrational Circular Dichroism (VCD) spectra of poly-L-glutamic acid fibrils were only qualitatively reproduced by the simulation. We could reproduce the major amide I band and a smaller negative band associated with the side chain carboxyl group. Our simulation procedure was then extended to a set of globular proteins and their Raman Optical Activity (ROA) spectra. Here we achieved an exceptional precision. For example, we were able to reproduce...
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Development and applications of molecular dynamics for molecular spectroscopy
Kessler, Jiří
This Thesis deals with simulations of chiroptical spectra using a combination of molecular dynamics and quantum chemistry. Molecular dynamics was used to explore conformational behaviour of studied systems (proteins), quantum chemistry for calculation of spectral prop- erties. The Quantum chemical methods are limited to relatively small systems. We overcome this problem mostly by a fragmentation of studied systems, when smaller, computationally feasible, fragments are created and used for the quantum chemical calculations. Calculated properties were then transferred to the big molecule. Vibrational Optical Activity (VOA) spectra of poly-L-glutamic acid fibrils (PLGA), insulin prefibrillar form and native globular proteins were studied. The simulated spectra provided satisfactory agreement with the experiment and were used for its interpretation. Experimental Vibrational Circular Dichroism (VCD) spectra of poly-L-glutamic acid fibrils were only qualitatively reproduced by the simulation. We could reproduce the major amide I band and a smaller negative band associated with the side chain carboxyl group. Our simulation procedure was then extended to a set of globular proteins and their Raman Optical Activity (ROA) spectra. Here we achieved an exceptional precision. For example, we were able to reproduce...
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Development and applications of molecular dynamics for molecular spectroscopy
Kessler, Jiří ; Bouř, Petr (advisor) ; Bludský, Ota (referee) ; Setnička, Vladimír (referee)
This Thesis deals with simulations of chiroptical spectra using a combination of molecular dynamics and quantum chemistry. Molecular dynamics was used to explore conformational behaviour of studied systems (proteins), quantum chemistry for calculation of spectral prop- erties. The Quantum chemical methods are limited to relatively small systems. We overcome this problem mostly by a fragmentation of studied systems, when smaller, computationally feasible, fragments are created and used for the quantum chemical calculations. Calculated properties were then transferred to the big molecule. Vibrational Optical Activity (VOA) spectra of poly-L-glutamic acid fibrils (PLGA), insulin prefibrillar form and native globular proteins were studied. The simulated spectra provided satisfactory agreement with the experiment and were used for its interpretation. Experimental Vibrational Circular Dichroism (VCD) spectra of poly-L-glutamic acid fibrils were only qualitatively reproduced by the simulation. We could reproduce the major amide I band and a smaller negative band associated with the side chain carboxyl group. Our simulation procedure was then extended to a set of globular proteins and their Raman Optical Activity (ROA) spectra. Here we achieved an exceptional precision. For example, we were able to reproduce...
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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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