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Modelowanie właściwosci wiązań wodorowych na przykładzie kompleksów układ amidowy - woda

Rzepiela Kacper, Buczek Aneta, Kupka Teobald, Kar Tapas, Broda Małgorzta A.

Wiadomości Chemiczne

2023

[Z] 77, 7-8

629--645

The energy and structure of intermolecular hydrogen bonds between water molecule and N-methylamide (NMA) or uracil (U) are discussed on the basis of DFT calculations. Theoretical methods are applied to calculate properties of cis- and trans- NMA complexes with one water molecule. Subsequently, H-bonds in six uracil – water complexes are analyzed. The influence of dispersion interactions and the polar environment on the hydrogen bond energy was analyzed. Results obtained by B3LYP functional with and without Grimme D3 dispersion correction indicate that dispersion interaction plays a significant role in an association process. In addition, the polar solvent reduces the hydrogen bond energy and this reduction is directly proportional to the hydrogen bond energy.

Benzen i metan jako wzorce przesunięcia chemicznego 1 H I 13 C NMR w obliczeniach teoretycznych

Rzepiela Kacper, Gajda Tomasz, Buczek Aneta, Broda Małgorzta A., Kupka Teobalt

Wiadomości Chemiczne

2020

[Z] 74, 9-10

609--627

NMR spectroscopy belongs to the most versatile techniques used in chemical laboratory for testing the presence of various compounds and elucidation of their structure. In case of more complex natural products chemical intuition and experience applied to analysis of experimental spectra is often supported by theoretical modeling of NMR spectra. However, theoretical predictions should be reliable and the errors associated with the approximations inherent to the existing methods minimized. In this respect, systematic errors, present in calculation of isotropic nuclear magnetic shieldings of the studied molecule need to be minimized. Conversion of nuclear shieldings of the studied molecule to the corresponding chemical shifts is performed by using a calculated reference molecule. This way systematic errors partly cancel and the remaining inaccuracies are efficiently decreased by using a properly selected theoretical reference molecule. In this work we demonstrate the impact of calculation method (selected density functional) and basis set on the predicted isotropic nuclear magnetic shieldings of free benzene and methane in vacuum and in popular solvents using a simple PCM approach. We propose the use of B3LYP, OPBE density functionals and recently designed xOPBE one in combination with Pople’s and Dunning’s basis sets, as well as with the modified STO-3G one. The new, STO(1M)-3G basis set was designed by Leszczyński and co-workers for efficient prediction of 13C NMR parameters in large organic molecules. Two molecules were selected to demonstrate the performance of GIAO B3LYP, OPBE and xOPBE for prediction of 1H and 13C NMR chemical shifts in vacuum and solution in comparison with available experimental data.