Development and applications of molecular dynamics for molecular spectroscopy
Vývoj a aplikace molekulové dynamiky pro molekulovou spektroskopii
rigorózní práce (UZNÁNO)
Zobrazit/ otevřít
Trvalý odkaz
http://hdl.handle.net/20.500.11956/87765Identifikátory
SIS: 193071
Kolekce
- Kvalifikační práce [20073]
Autor
Fakulta / součást
Přírodovědecká fakulta
Obor
Modelování chemických vlastností nano- a biostruktur
Katedra / ústav / klinika
Katedra fyzikální a makromol. chemie
Datum obhajoby
31. 8. 2017
Nakladatel
Univerzita Karlova, Přírodovědecká fakultaJazyk
Angličtina
Známka
Uznáno
Klíčová slova (česky)
molekulární dynamika, simulace spekter, kvantová chemie, chiralita, optická aktivitaKlíčová slova (anglicky)
molecular dynamics, spectra simulations, quantum chemistry, chirality, optical activityThis 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...