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Quantum-chemical and Molecular-dynamical Study of Noncovalent interactions

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Quantum-chemical and Molecular-dynamical Study of Noncovalent interactions
Název v češtině:
Kvantově-chemické a molekulárnědynamické studium nekovalentních interakcí
Disertační práce
RNDr. Jan Řezáč, Ph.D.
prof. Ing. Pavel Hobza, DrSc.
RNDr. Zdeněk Havlas, DrSc.
doc. RNDr. Michal Otyepka, Ph.D.
Id práce:
Přírodovědecká fakulta (PřF)
Katedra fyzikální a makromol. chemie (31-260)
Program studia:
Modelování chemických vlastností nano- a biostruktur (P1415)
Obor studia:
Přidělovaný titul:
Datum obhajoby:
26. 8. 2008
Výsledek obhajoby:
Jazyk práce:
Abstract v angličtině:
Introduction First part of thc thcsis summarizcs rcsults of our studics of noncovalcnt intcractions, invcstigatcd bl cfficicnt computational mcthods. Noncovalcnt interactions are rveaker than covalent bonds, but it does not mean they are iess important. It is cspccialh' ttuc in biornolcculcs - their primary structurc is simple, they are composed from limited number of building blocks. \X/hat detetmines theit strucrure and birllogical functirrn are noncovalent interacťions. Ma)or part of this lr'ork is <]cr-otcd to DN,.\. Structure and funcúon of thc DNÁ molecule is determined by interaction oí nucleic acid bases, which can bc studicd using <luanturn-rncchanical mcthods. Iinorvlcdgc of stabiliry of thc DN:\ doublc hclix, mcasurcd as frcc cncrgy of its unwinding (dissociation, denaturation). is irnporrant not only for understanding of the function of DN,\, but also for ri'orking rvith DN''\ in laboratory. Stabiliry of DNA oligomers is knos'n do be dependent on sequence of nucleotides and can be cstimatcd using cmpincal statistical modcls. In ru'o papcrs prcsented herc, wc investigated the relationship bets'een interaction betrveen DN;\ bases, which can be readilv calculated, and experimental\' evaluated stabiliry of DNA oligomcrs. Long DN;\ molecule is structure large enough to be mechanically manipulatcd, tbr cxamplc strctchcd, using recent cxperimental tcchniqucs. Wc simulatcd this cxpcrimcnt in molccular dynamics simulations and studied resulting stfucrufes rvith QM methods. f)ifíerent behavior was obsen'ed in poly-AT and poly-CG, which can bc cxplaincd by differcnt pÍopcÍtics of the bases and ůcir rnteraction. Anothcr paÍt of this work focuses on small pcptidcs. Thcsc peptidcs can be studicd bv accuratc cxpcrimcnts in gas phasc, which, in conjunction with theory, help to understand their properties and properties of peptides in gcneral. In onc papcr, wc thoroughly invcstigatcd frcc cncrgy surfacc of glycyl- phen1'Ialan1'I-alanine tripeptide (GFÁ) to assig.rr stfllctuÍe to measured infrared spectra of dif|crcnt conformcrs. In sccond papcÍ' wc cr'aluatecl thc performancc oí *-idc array o[ computational mcthods applied to scl-cral small peptides. r\lthough a tripepride is relatively small molecule, its structure is dctermincd by intramolccular noncovalcnt intcractions. Development of efficient densitl' functional theory methods rvith dispersion cortection PFT-D) in our laboratorl, allowed us to move from stacic dcscription of sclcctcd points to on-thc-Íly mo]ccular dynamics (tr,ÍD) simulations rvith accurate potential calculated using QM in each step. We have dcvclopcd ncw paÍamctrizadon of DF*I.-D for bcnzcnc dimer, a prototypc systcm fot studying n...n intcractions in aromatic systclns. 'l'his accuratc potcntial vas then used in MD simulations invcstigating structurc and ůennodynamics of benzcne dimcr. Another part of my work rvas impiementation of the DFÍ-D method within combincd quaÍrfum-mcchanical / molecular mcchanical (QM/MN! calculations. Rcsulting codc is uscd to study carborane ínhibitors of HI\l protease. Specialized implementation of DFT-D w'as also used in study of adsolption of atomatic molccules on water surfacc. Second patt of the thesis is documentacion for Cuby (Chemistry in Ruby), an cnvitonmcnt for chcmical calculations. It relies on extcrnal soft"varc for QM and N{I\{ calcularions and can manipulate and combine the results using various mcthods and simulation protocols. 'fhc most important rcason for dcvelopment of out orv'n software was the need to implement adr'anced simuiatitln pttltocols, such as QM/NÍN{ based on DI'-T-D mcthod or on-thc-fly NID simulations. 'l'he code is based on reusable libraries. and once these foundations wete set up, it was possible to coveť all the most common computational tasks easily. And advantagc of using Cuby is that it providcs unificd and user-fricndly access to se.r,etal computational software packages. It is now widely used in our laboratory.
Stáhnout Dokument Autor Typ Velikost
Stáhnout Text práce RNDr. Jan Řezáč, Ph.D. 3.02 MB
Stáhnout Abstrakt v českém jazyce RNDr. Jan Řezáč, Ph.D. 615 kB
Stáhnout Abstrakt anglicky RNDr. Jan Řezáč, Ph.D. 691 kB
Stáhnout Posudek oponenta RNDr. Zdeněk Havlas, DrSc. 134 kB
Stáhnout Posudek oponenta doc. RNDr. Michal Otyepka, Ph.D. 132 kB
Stáhnout Záznam o průběhu obhajoby 147 kB