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Quantum-chemical study of noncovalent interactions
Sedlák, Róbert ; Hobza, Pavel (advisor) ; Havlas, Zdeněk (referee) ; Černušák, Ivan (referee)
The aim of this thesis is to investigate strength and origin of the stabilization for various types of noncovalent interactions. As this knowledge could lead to a deeper understand- ing and rationalization of the binding phenomena. Further, to participate on the de- velopment of new noncovalent data sets, which are nowadays inevitable in the process of parametrization and validation of new computational methods. In all the studies, different binding motifs of model complexes, which represent usually crystal structures, structures from unrelaxed scans or the local minima, were investi- gated. The calculations of the reference stabilization energies were carried out at ab initio level (e.g. CCSD(T)/CBS, QCISD(T)/CBS). Further, the accuracy of more ap- proximate methods (e.g. MP2.5, DFT-D or SQM methods) toward reference method, was tested. In order to obtain the nature of the stabilization the DFT-SAPT decompo- sition was frequently utilized. In the first part of the thesis, the importance and basic characteristics of different types of noncovalent interactions (e.g. halogen bond, hydrogen bond, π· · · π interaction etc.), are discussed. The second part provides the description of computational methods which were essential for our investigation. The third part of the thesis provides an overview for part...
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Použitelnost výpočetních metod kvantové chemie pro studium interakcí v biologických systémech
PLAČKOVÁ, Lydie
The theoretical part of the Master´s thesis describes ab initio methods in quantum chemistry and semiempirical methods, which represents a way in overcoming of main disadvantages in ab initio methods (costs, speed). The experimental part was focused on comparison highly accurate CCSD(T) method with used semiempirical methods (AM1, PM3, PM6, and PM7). The data were mostly compared on small model systems with ions, which are an essential part of many biological systems. Furthermore, the applicability of semiempirical methods was examined for the description of intra- and intermolecular hydrogen bonds and van der Waals interactions.
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