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Wyświetlanie 1-2 z 2
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
Tytuł:
Właściwości wewnątrzcząsteczkowych wiązań wodorowych w wybranych N-tlenkach pochodnych chinoliny
Intramolecular hydrogen bonds properties in selected N-oxides of quinoline derivatives
Autorzy:
Jezierska, Aneta
Panek, Jarosław J.
Błaziak, Kacper
Powiązania:
https://bibliotekanauki.pl/articles/171511.pdf
Data publikacji:
2019
Wydawca:
Polskie Towarzystwo Chemiczne
Tematy:
DFT
teoria funkcjonału gęstości
MP2
metoda rachunku zaburzeń drugiego rzędu Møllera-Plesseta
CPMD
dynamika molekularna Cara-Parrinello
wewnątrzcząsteczkowe wiązanie wodorowe
N-tlenki pochodnych chinoliny
density functional theory
Møller-Plesset second order perturbation method
Car-Parrinello molecular dynamics
intramolecular HB
N-oxides of quinoline derivatives
Opis:
In the current article we would like to summarize our research shedding light onto properties of intramolecular hydrogen bonds present in N-oxide quinoline derivatives. The compounds for the current study were chosen to contain diverse types of hydrogen bonds. Therefore, in the current study we analyze three kinds of hydrogen bonding and their properties. It is well known, that the presence of intramolecular hydrogen bonds stabilizes conformations of molecules. Substituent effects (inductive and steric) influence the strength of the H-bonding as well as its features. Moreover, the intramolecular hydrogen bond in the studied N-oxides belongs to the family of resonance assisted hydrogen bonds (RAHB). Our short overview presents the summary of results obtained for twelve N-oxides of quinoline derivatives. Quantum-chemical simulations were performed on the basis of static models (classical DFT and MP2 approaches) as well as ab initio molecular dynamics (Car-Parrinello MD). The metadynamics method was applied to reproduce the maps of free energy for the motion of the bridged proton. The computations were performed in the gas and in the crystalline phases. Electronic ground state is a natural framework in which chemical compounds exist most of the time. However, in many chemical species we observe a spontaneous internal reorganization of their chemical bonds and atoms e.g. proton transfer phenomenon and the appearance of tautomeric forms already in the ground state. Therefore, it was interesting to investigate some N-oxides in the excited electron state knowing that they exhibit excited- state-induced proton transfer (ESIPT effect). At the end of the article we draw some conclusions related to the intramolecular H-bond properties present in the discussed N-oxides of quinoline derivatives.
Źródło:
Wiadomości Chemiczne; 2019, 73, 1-2; 75-95
0043-5104
2300-0295
Pojawia się w:
Wiadomości Chemiczne
Dostawca treści:
Biblioteka Nauki
Artykuł
    Wyświetlanie 1-2 z 2

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