Zastosowanie metod dynamiki molekularnej w badaniach nad układami z wiązaniami wodorowymi An application of molecular dynamics methods in investigations of systems with hydrogen bonds
Modern computational chemistry offers a wide variety of methods allowing us
to investigate very complex systems. In the current study, we would like to focus on
ab initio and classical molecular dynamics to show their applications in our research.
Car-Parrinello molecular dynamics (CPMD) was carried out to study compounds
possessing intra- and intermolecular hydrogen bonds. Our simulations
were performed in vacuum, in solvent and in crystalline phase. It is well known that
intramolecular hydrogen bonding stabilizes 3D structure of molecules. The strength
of the bonding and its features are influenced by inductive and steric effects. Our
short overview on CPMD application to systems with intramolecular HB we start
from Schiff and Mannich bases -model compounds to investigate intramolecular
hydrogen bonding. Other examples reported here derive from the class of N-oxide
type compounds. Special attention was devoted to another representative structure
in such investigations – picolinic acid N-oxide. In some examples listed above proton
transfer phenomena occurred making these compounds interesting objects for
future excited state studies. Aliphatic boronic acid was used as a model example
to study intermolecular hydrogen bonds based on CPMD method. Further, classical
molecular dynamics was applied to investigate proteins. Here, we would like to
report our results for two biomolecules. The first one is proteinase K for which the
impact of mercury(II) on its catalytic center was studied. The second one is streptavidin.
For the latter one its complexes with biotinylated ligands were investigated.
We close our review with a paragraph describing further development and perspectives
related to CPMD method.
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