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Zastosowanie metod dynamiki molekularnej w badaniach nad układami z wiązaniami wodorowymi

Jezierska A., Panek J. J.

Wiadomości Chemiczne

2017

[Z] 71, 7-8

473--495

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.

The Nature of Hydrogen Bonding in Selected Hydrazide Derivatives Investigated via Static Models and Car-Parrinello Molecular Dynamics

Jezierska A., Novič M., Panek J. J.

Polish Journal of Chemistry

2009

Vol. 83, nr 5

799-819

The geometric and spectrocopic properties of 2-hydroxy-thiobenzhydrazide and 2-hydroxy-benzhydrazide were investigated within the frame work of Density Functional Theory (DFT). Special attention was devoted to the description and analysis of intra- and intermolecular hydrogen bonds. The choice of the compounds was dictated by their structural similarity and the presence of two types of hydrogen bridges: O–H...S (in 2-hydroxy-thiobenzhydrazide, less common) and O–H...O (in 2-hydroxy-benzhydrazide). The latter could be classified as a low-barrier hydrogen bond (LBHB). First the DFT method was used to obtain the geometric parameters for the monomeric and dimeric forms of the compounds at various levels of theory. Then the binding energy was calculated for the dimeric forms to estimate the strength of the intermolecular hydrogen bonds. Atoms in Molecules (AIM) theory was applied to show quantitatively how the formation of the intermolecular hydrogen bonds affects the strength of the intramolecular hydrogen bonds. The electron density and its Laplacian were calculated for the bond critical points defining the H-bridges. Car-Parrinello molecular dynamics (CPMD) was then used to investigate the changes in the geometric parameters as a function of simulation time. This part of the computational study was performed in vacuo and in the solid state. The vibrational properties of the investigated hydrazides were obtained via Fourier transform of the autocorrelation functions of the dipole moment and atomic velocity. It was found that the formation of the intermolecular H-bonds does not significantly affect the strength of the intramolecular H-bonds. There fore inductive and steric effects out side the immediate vicinity of the intramolecular bridge have minor influence on its investigated properties. The application of CPMD gave a more detailed picture of the bridged protons’ dynamics. The computational results agree with available experimental data. The influence of the intermolecular hydrogen bonding net work and non-bonded crystal field interactions on the vibrational features of the investigated molecules is demonstrated and discussed.