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Vývoj a aplikace molekulové dynamiky pro chirální systémy
Kessler, Jiří ; Bouř, Petr (vedoucí práce) ; Fanfrlík, Jindřich (oponent)
Souhrn Tato diplomová práce pojednává o molekulárně dynamických simulacích roztoků chirálních látek v chirálních rozpouštědlech. Roztoky se skládaly z 2,2,2-trifluoro-1-fenyletanolu,1- fenyletanolu a 1-fenyletanaminu. Byly zkoumány rozdílnosti v NMR vlastnostech různých kombinací absolutních konfigurací rozpuštěné látky a rozpouštědla. Tyto systémy skutečně vykázaly pro různé kombinace absolutních konfiguraci rozdíly v radiálních distribučních funkcích a zastoupeni konformerů zjištěných pomoci metody WHAM. Tyto zjištěné výsledky zhruba korelovaly s velikostí experimentálních rozdílů NMR posunů. Dále byla v rámci práce vyvinuta metoda selektivního výběru klastrů, která významně snižuje počet klastrů nutných k dosažení konvergované průměrné hodnoty. kličová slova: chiralita, molekulární dynamika, nukleární magnetická rezonance
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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 (vedoucí práce) ; Bludský, Ota (oponent) ; Setnička, Vladimír (oponent)
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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Vývoj a aplikace molekulové dynamiky pro chirální systémy
Kessler, Jiří ; Bouř, Petr (vedoucí práce) ; Fanfrlík, Jindřich (oponent)
Souhrn Tato diplomová práce pojednává o molekulárně dynamických simulacích roztoků chirálních látek v chirálních rozpouštědlech. Roztoky se skládaly z 2,2,2-trifluoro-1-fenyletanolu,1- fenyletanolu a 1-fenyletanaminu. Byly zkoumány rozdílnosti v NMR vlastnostech různých kombinací absolutních konfigurací rozpuštěné látky a rozpouštědla. Tyto systémy skutečně vykázaly pro různé kombinace absolutních konfiguraci rozdíly v radiálních distribučních funkcích a zastoupeni konformerů zjištěných pomoci metody WHAM. Tyto zjištěné výsledky zhruba korelovaly s velikostí experimentálních rozdílů NMR posunů. Dále byla v rámci práce vyvinuta metoda selektivního výběru klastrů, která významně snižuje počet klastrů nutných k dosažení konvergované průměrné hodnoty. kličová slova: chiralita, molekulární dynamika, nukleární magnetická rezonance
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