- Tytuł:
-
Zastosowanie metod dynamiki molekularnej w badaniach nad układami z wiązaniami wodorowymi
An application of molecular dynamics methods in investigations of systems with hydrogen bonds - Autorzy:
-
Jezierska, A.
Panek, J. J. - Powiązania:
- https://bibliotekanauki.pl/articles/172356.pdf
- Data publikacji:
- 2017
- Wydawca:
- Polskie Towarzystwo Chemiczne
- Tematy:
-
CPMD
dynamika molekularna Cara-Parrinello
klasyczna dynamika molekularna
wewnątrzcząsteczkowe wiązanie wodorowe
międzycząsteczkowe wiązanie wodorowe
zasada Schiffa
zasada Mannicha
N-tlenki
białka
Car-Parrinello molecular dynamics
classical MD
intramolecular HB
intermolecular HB
Schiff base
Mannich base
N-oxides
proteins - Opis:
- 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.
- Źródło:
-
Wiadomości Chemiczne; 2017, 71, 7-8; 473-495
0043-5104
2300-0295 - Pojawia się w:
- Wiadomości Chemiczne
- Dostawca treści:
- Biblioteka Nauki
Artykuł