dc.contributor.advisor | Bouř, Petr | |
dc.creator | Kessler, Jiří | |
dc.date.accessioned | 2020-07-07T21:44:03Z | |
dc.date.available | 2020-07-07T21:44:03Z | |
dc.date.issued | 2017 | |
dc.identifier.uri | http://hdl.handle.net/20.500.11956/86694 | |
dc.description.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... | en_US |
dc.language | English | cs_CZ |
dc.language.iso | en_US | |
dc.publisher | Univerzita Karlova, Přírodovědecká fakulta | cs_CZ |
dc.subject | molekulární dynamika | cs_CZ |
dc.subject | simulace spekter | cs_CZ |
dc.subject | kvantová chemie | cs_CZ |
dc.subject | chiralita | cs_CZ |
dc.subject | optická aktivita | cs_CZ |
dc.subject | molecular dynamics | en_US |
dc.subject | spectra simulations | en_US |
dc.subject | quantum chemistry | en_US |
dc.subject | chirality | en_US |
dc.subject | optical activity | en_US |
dc.title | Development and applications of molecular dynamics for molecular spectroscopy | en_US |
dc.type | dizertační práce | cs_CZ |
dcterms.created | 2017 | |
dcterms.dateAccepted | 2017-06-27 | |
dc.description.department | Katedra fyzikální a makromol. chemie | cs_CZ |
dc.description.department | Department of Physical and Macromolecular Chemistry | en_US |
dc.description.faculty | Přírodovědecká fakulta | cs_CZ |
dc.description.faculty | Faculty of Science | en_US |
dc.identifier.repId | 128928 | |
dc.title.translated | Vývoj a aplikace molekulové dynamiky pro molekulovou spektroskopii | cs_CZ |
dc.contributor.referee | Bludský, Ota | |
dc.contributor.referee | Setnička, Vladimír | |
dc.identifier.aleph | 002145367 | |
thesis.degree.name | Ph.D. | |
thesis.degree.level | doktorské | cs_CZ |
thesis.degree.discipline | - | en_US |
thesis.degree.discipline | - | cs_CZ |
thesis.degree.program | Modeling of Chemical Properties of Nano- and Biostructures | en_US |
thesis.degree.program | Modelování chemických vlastností nano- a biostruktur | cs_CZ |
uk.thesis.type | dizertační práce | cs_CZ |
uk.taxonomy.organization-cs | Přírodovědecká fakulta::Katedra fyzikální a makromol. chemie | cs_CZ |
uk.taxonomy.organization-en | Faculty of Science::Department of Physical and Macromolecular Chemistry | en_US |
uk.faculty-name.cs | Přírodovědecká fakulta | cs_CZ |
uk.faculty-name.en | Faculty of Science | en_US |
uk.faculty-abbr.cs | PřF | cs_CZ |
uk.degree-discipline.cs | - | cs_CZ |
uk.degree-discipline.en | - | en_US |
uk.degree-program.cs | Modelování chemických vlastností nano- a biostruktur | cs_CZ |
uk.degree-program.en | Modeling of Chemical Properties of Nano- and Biostructures | en_US |
thesis.grade.cs | Prospěl/a | cs_CZ |
thesis.grade.en | Pass | en_US |
uk.abstract.en | 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... | en_US |
uk.file-availability | V | |
uk.grantor | Univerzita Karlova, Přírodovědecká fakulta, Katedra fyzikální a makromol. chemie | cs_CZ |
thesis.grade.code | P | |
uk.publication-place | Praha | cs_CZ |
dc.identifier.lisID | 990021453670106986 | |