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Accurate Quantum Mechanical Calculations on Noncovalent Interactions: Rationalization of X-ray Crystal Geometries by Quantum Chemistry Tools
Hostaš, Jiří ; Hobza, Pavel (advisor) ; Burda, Jaroslav (referee) ; Jurečka, Petr (referee)
There is a need for reliable rules of thumb for various applications in the area of biochemistry, supramolecular chemistry and material sciences. Simultaneously, the amount of information, which we can gather from X-ray crystal geometries about the nature of recognition processes, is limited. Deeper insight into the noncovalent interactions playing the most important role is needed in order to revise these universal rules governing any recognition process. In this thesis, systematic development and study of the accuracy of the computational chemistry methods followed by their applications in protein DNA and host guest systems, are presented. The non-empirical quantum mechanical tools (DFT-D, MP2.5, CCSD(T) etc. methods) were utilized in several projects. We found and confirmed unique low lying interaction energies distinct from the rest of the distributions in several amino acid−base pairs opening a way toward universal rules governing the selective binding of any DNA sequence. Further, the predictions and examination of changes of Gibbs energies (ΔG) and its subcomponents have been made in several cases and carefully compared with experiments. We determined that the choline (Ch+) guest is bound 2.8 kcal/mol stronger (calculated ΔG) than acetylcholine (ACh+) to self-assembled triple helicate rigid...
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Accurate Quantum Mechanical Calculations on Noncovalent Interactions: Rationalization of X-ray Crystal Geometries by Quantum Chemistry Tools
Hostaš, Jiří
There is a need for reliable rules of thumb for various applications in the area of biochemistry, supramolecular chemistry and material sciences. Simultaneously, the amount of information, which we can gather from X-ray crystal geometries about the nature of recognition processes, is limited. Deeper insight into the noncovalent interactions playing the most important role is needed in order to revise these universal rules governing any recognition process. In this thesis, systematic development and study of the accuracy of the computational chemistry methods followed by their applications in protein DNA and host guest systems, are presented. The non-empirical quantum mechanical tools (DFT-D, MP2.5, CCSD(T) etc. methods) were utilized in several projects. We found and confirmed unique low lying interaction energies distinct from the rest of the distributions in several amino acid−base pairs opening a way toward universal rules governing the selective binding of any DNA sequence. Further, the predictions and examination of changes of Gibbs energies (ΔG) and its subcomponents have been made in several cases and carefully compared with experiments. We determined that the choline guest is bound 2.8 kcal/mol stronger (calculated ΔG) than acetylcholine to self-assembled triple helicate rigid cage,...
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Accurate Quantum Mechanical Calculations on Noncovalent Interactions: Rationalization of X-ray Crystal Geometries by Quantum Chemistry Tools
Hostaš, Jiří
There is a need for reliable rules of thumb for various applications in the area of biochemistry, supramolecular chemistry and material sciences. Simultaneously, the amount of information, which we can gather from X-ray crystal geometries about the nature of recognition processes, is limited. Deeper insight into the noncovalent interactions playing the most important role is needed in order to revise these universal rules governing any recognition process. In this thesis, systematic development and study of the accuracy of the computational chemistry methods followed by their applications in protein DNA and host guest systems, are presented. The non-empirical quantum mechanical tools (DFT-D, MP2.5, CCSD(T) etc. methods) were utilized in several projects. We found and confirmed unique low lying interaction energies distinct from the rest of the distributions in several amino acid−base pairs opening a way toward universal rules governing the selective binding of any DNA sequence. Further, the predictions and examination of changes of Gibbs energies (ΔG) and its subcomponents have been made in several cases and carefully compared with experiments. We determined that the choline guest is bound 2.8 kcal/mol stronger (calculated ΔG) than acetylcholine to self-assembled triple helicate rigid cage,...
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Accurate Quantum Mechanical Calculations on Noncovalent Interactions: Rationalization of X-ray Crystal Geometries by Quantum Chemistry Tools
Hostaš, Jiří ; Hobza, Pavel (advisor) ; Burda, Jaroslav (referee) ; Jurečka, Petr (referee)
There is a need for reliable rules of thumb for various applications in the area of biochemistry, supramolecular chemistry and material sciences. Simultaneously, the amount of information, which we can gather from X-ray crystal geometries about the nature of recognition processes, is limited. Deeper insight into the noncovalent interactions playing the most important role is needed in order to revise these universal rules governing any recognition process. In this thesis, systematic development and study of the accuracy of the computational chemistry methods followed by their applications in protein DNA and host guest systems, are presented. The non-empirical quantum mechanical tools (DFT-D, MP2.5, CCSD(T) etc. methods) were utilized in several projects. We found and confirmed unique low lying interaction energies distinct from the rest of the distributions in several amino acid−base pairs opening a way toward universal rules governing the selective binding of any DNA sequence. Further, the predictions and examination of changes of Gibbs energies (ΔG) and its subcomponents have been made in several cases and carefully compared with experiments. We determined that the choline (Ch+) guest is bound 2.8 kcal/mol stronger (calculated ΔG) than acetylcholine (ACh+) to self-assembled triple helicate rigid...
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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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