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Wyszukujesz frazę "Car-Parrinello molecular dynamics" wg kryterium: Temat

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    Tytuł:
    Właściwości czasowo-rozdzielcze słabych międzycząsteczkowych wiązań wodorowych C-H···F
    Time-resolved properties of intermolecular C-H···F hydrogen bonds
    Autorzy:
    Polańska, Marta
    Rodziewicz, Paweł
    Powiązania:
    https://bibliotekanauki.pl/articles/27310029.pdf
    Data publikacji:
    2023
    Wydawca:
    Polskie Towarzystwo Chemiczne
    Tematy:
    wiązanie wodorowe
    teoria funkcjonału gęstości
    dynamika molekularna Cara i Parrinello
    hydrogen bond
    density functional theory
    Car-Parrinello molecular dynamics
    Opis:
    The hydrogen bond is one of the most important and interesting phenomena in nature. In this publication we will shed light on the discovery of hydrogen bond and a time evolution of its definition in the last 100 years. Both structural and spectroscopic parameters of the hydrogen bond will be discussed. A special focus will be given to the latest IUPAC definition of the hydrogen bond and its consequences to scientific research. The main aim of this study is to highlight theoretical studies based on first principles calculations and molecular dynamics simulations which not only support experimental results but also provide parameters which are crucial to understand the nature of hydrogen bonds. Particular attention will be given to methods and theoretical ideas used in the computational studies of hydrogen bonds. Utilizing static DFT/ab initio calculations and molecular dynamics simulations enables comparison of different binding energies and studying time evolution of the hydrogen-bonded molecular system on the atomistic level. We will discuss time-resolved properties of weak intermolecular hydrogen bonds, using as an example C-H···F containing model systems, namely F3CH*(HF)n molecular complexes and (F3CH)2-4 aggregates.
    Źródło:
    Wiadomości Chemiczne; 2023, 77, 9-10; 899--919
    0043-5104
    2300-0295
    Pojawia się w:
    Wiadomości Chemiczne
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    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 1-3 z 3

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