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Theoretical Study of Non-covalent Interaction from small molecules to Biomolecules
Haldar, Susanta ; Hobza, Pavel (advisor) ; Havlas, Zdeněk (referee) ; Jurečka, Petr (referee)
xv Abstract The aim of this thesis is to investigate the accurate stabilization energy and binding free energy in various non-covalent complexes spanned from small organic molecules to biomolecules. Non-covalent interactions such as H-bonds, π...π stacking and halogen bonds are mainly responsible for understanding of most biological processes, such as small molecule interactions with surface, protein-ligand binding in the cell machinery, etc. In the thesis, different non-covalent complexes such as graphene…electron donor- acceptor complexes, DNA base pair interaction with silica surface, etc, were investigated. The reference stabilization energies were calculated at ab initio level, e.g., CCSD(T)/CBS method wherever possible. On the other hand, more approximated scaled MP2 method (MP2.5/CBS/6-31G*(0.25)) is taken as reference instead of CCSD(T)/CBS due to the size of the complexes. Further, the DFT and MM energies were also tested towards the reference one. The knowledge of non- covalent interaction is required for rationalizing of any association processes in nature which requires accurate description of the free energy change. The state-of- the-art molecular dynamics simulation in full atomic scale and biased metadynamics free energy method is used for binding free energy calculations. The well tempered...
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