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Development and applications of molecular dynamics for chiral systems
Kessler, Jiří ; Bouř, Petr (advisor) ; Fanfrlík, Jindřich (referee)
The Thesis deals with MD simulations of solutions of chiral solutes in chiral solvents. These solutions consist of 2,2,2-trifluoro-1-phenylethanol, 1-phenylethanol and 1-phenyl- ethanamine.The differences in NMR properties between different combnations of solvent and solute absolute configuration were modeled. Indeed, differences in radial distribution functions and conformer abundances of solute calculated by the WHAM method were found. These results correlated with experimental differences in NMR shifts. Additionally, a method of cluster preselection was developed. It significantly decreased the amount of clusters needed for computations of NMR shieldings and hence the computer time. Keywords: chirality, molecular dynamic, nuclear magnetic resonance
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Variational and perturbational calculations of interaction energies of noncovalent clusters
Hostaš, Jiří ; Hobza, Pavel (advisor) ; Fanfrlík, Jindřich (referee)
Calculation of noncovalent interactions in set of complexes containing halogen atom (called Halogensx10) is the main subject of this thesis. Wide variety of semiempirical quantum mechanical (SQM) methods (AM1, RM1, PM3, PM6 and SCC-DFTB augmented with empirical correction for dispersion interaction and hydrogen bonding (D3H4)) have been tested and their accuracy was discussed. The SCC-DFTB-D3H4 method showed the advantage of no artificial behaviour for other types of interactions with exception of halogen bonding which is underestimated. Specific correction for halogen bonding was designed as a purely empirical fix of serious underestimation of interaction energy in halogen bonded complexes that yields results for validation set very close to benchmark interaction energies with average error is 0.3 kcal/mol ~ 6% of the interaction energy. As a benchmark method the CCSD(T) extrapolated to the CBS limit, according to Helgaker's scheme with rather large correlation consistent basis sets has been used. The results presented herein can be used in the rational design of halogenated ligands as well as in research of another halogen enriched compounds.
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Development and applications of molecular dynamics for chiral systems
Kessler, Jiří ; Bouř, Petr (advisor) ; Fanfrlík, Jindřich (referee)
The Thesis deals with MD simulations of solutions of chiral solutes in chiral solvents. These solutions consist of 2,2,2-trifluoro-1-phenylethanol, 1-phenylethanol and 1-phenyl- ethanamine.The differences in NMR properties between different combnations of solvent and solute absolute configuration were modeled. Indeed, differences in radial distribution functions and conformer abundances of solute calculated by the WHAM method were found. These results correlated with experimental differences in NMR shifts. Additionally, a method of cluster preselection was developed. It significantly decreased the amount of clusters needed for computations of NMR shieldings and hence the computer time. Keywords: chirality, molecular dynamic, nuclear magnetic resonance
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Interaction of heteroboranes with biomolecules: Accurate quantum chemical study
Fanfrlík, Jindřich ; Hobza, Pavel (advisor) ; Fišer, Jiří (referee) ; Otyepka, Michal (referee) ; Vondrášek, Jiří (referee)
Charles University in Prague Faculty of Science Department of Physical and Macromolecular Chemistry Interaction of heteroboranes with biomolecules: Accurate quantum chemical study Doctoral Thesis Abstract RNDr. Jindřich Fanfrlík Advisor: Prof. Ing. Pavel Hobza, DrSc. Institute of Organic Chemistry and Biochemistry, AS CR Center for Biomolecules and Complex Molecular Systems Prague 2008 Univerzita Karlova v Praze Přírodovĕdecká Fakulta Katedra fyzikální a makromolekulární chemie Interakce heteroboranů s biomolekulami: kvantovĕ chemická studie Autoreferát disertační práce RNDr. Jindřich Fanfrlík Školitel: Prof. Ing. Pavel Hobza, DrSc. Ústav organické chemie and biochemie, AV ČR Centrum biomolekul a komplexních molekulových systémů Praha 2008 Introduction The world wide epidemic of AIDS is caused by two species of the human immunodeficiency virus (HIV-1 and HIV-2). Its 9200-bases-long RNA genome contains three main genes: gag, pol and env. The enzymes located within the pol gene (protease PR and reverse transcriptase RT) have become major targets for drug discovery, e.g. RT inhibitor Tenofovir disoproxil fumarate (DF) discovered by A. Holy at UOCHB in Prague and manufactured by Gilead Sciences and also already ten HIV-1 PR inhibitors (PIs) have been approved for use in the clinics: The evolution of drug...
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