Zastosowanie metod dynamiki molekularnej w badaniach nad układami z wiązaniami wodorowymi

Jezierska, A.; Panek, J. J.

Artykuł - szczegóły

Tytuł artykułu

Zastosowanie metod dynamiki molekularnej w badaniach nad układami z wiązaniami wodorowymi

Autorzy

Jezierska A. , Panek J. J.

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Warianty tytułu

An application of molecular dynamics methods in investigations of systems with hydrogen bonds

Języki publikacji

Abstrakty

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.

Słowa kluczowe

CPMD dynamika molekularna Cara-Parrinello klasyczna dynamika molekularna wewnątrzcząsteczkowe wiązanie wodorowe międzycząsteczkowe wiązanie wodorowe zasada Schiffa zasada Mannicha N-tlenki białka

CPMD Car-Parrinello molecular dynamics classical MD intramolecular HB intermolecular HB Schiff base Mannich base N-oxides proteins

Wydawca

Polskie Towarzystwo Chemiczne

Czasopismo

Wiadomości Chemiczne

Rocznik

2017

Tom

[Z] 71, 7-8

Strony

473--495

Opis fizyczny

Bibliogr. 41 poz., schem., wykr.

Twórcy

autor

Jezierska A.

aneta.jezierska@chem.uni.wroc.pl

Wydział Chemii, Uniwersytet Wrocławski, ul. F. Joliot-Curie 14, 50-383 Wrocław

autor

Panek J. J.

Wydział Chemii, Uniwersytet Wrocławski, ul. F. Joliot-Curie 14, 50-383 Wrocław

Bibliografia

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Uwagi

Praca dedykowana Profesorowi Lucjanowi Sobczykowi z okazji 90. rocznicy urodzin

Opracowanie ze środków MNiSW w ramach umowy 812/P-DUN/2016 na działalność upowszechniającą naukę (zadania 2017).

Typ dokumentu

Bibliografia

Identyfikator YADDA

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