Original title: Vývoj a aplikace molekulové dynamiky pro molekulovou spektroskopii
Translated title: Development and applications of molecular dynamics for molecular spectroscopy
Authors: Kessler, Jiří ; Bouř, Petr (advisor) ; Bludský, Ota (referee) ; Setnička, Vladimír (referee)
Document type: Doctoral theses
Year: 2017
Language: eng
Abstract: 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...
Keywords: chirality; molecular dynamics; optical activity; quantum chemistry; spectra simulations; chiralita; kvantová chemie; molekulární dynamika; optická aktivita; simulace spekter

Institution: Charles University Faculties (theses) (web)
Document availability information: Available in the Charles University Digital Repository.
Original record: http://hdl.handle.net/20.500.11956/86694

Permalink: http://www.nusl.cz/ntk/nusl-357975


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Universities and colleges > Public universities > Charles University > Charles University Faculties (theses)
Academic theses (ETDs) > Doctoral theses