Repozytorium
Wyszukaj
Kolekcje
Inne
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
Rok wydania
2017
Czasopismo
Numer woluminu
71
Strony
473-495
Kolekcja
Język
Polski
Typ publikacji
Artykuł
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 rese-arch. Car-Parrinello molecular dynamics (CPMD) was carried out to study com-pounds 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 pro-ton 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, classi-cal 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 strep-tavidin. For the latter one its complexes with biotinylated ligands were investigated. We close our review with a paragraph describing further development and perspec-tives related to CPMD method.
Słowa kluczowe
cPMD, classical MD, intramolecular hydrogen bond, intermolecular HB, schiff base, mannich base, n -oxides, proteins
cPMD, klasyczna dynamika molekularna, wewnątrzczasteczkowe wiązanie wodorowe,, międzycząsteczkowe wiązanie wodorowe,, zasada Schiffa, zasada Mannicha, n -tlenki, białka
Licencja otwartego dostępu
Adres publiczny
http://yadda.icm.edu.pl/baztech/element/bwmeta1.element.baztech-a7a6c59a-607e-41ed-aaf4-c40d0df9b92a
Podobne publikacje
Some brief notes on theoretical and experimental investigations of intramolecular hydrogen bonding.
Sobczyk Lucjan, Chudoba Dorota, Tolstoy Peter M., Filarowski Aleksander
Inside Out Approach to Rotator State in Hydrogen-Bonded System — Experimental and Theoretical Cross-Examination in n-Octanol.
Pocheć Michał, Krupka Katarzyna M., Panek Jarosław J., Orzechowski Kazimierz, Jezierska Aneta