THE INFLUENCE OF BACKBONE AND SOLVENT DYNAMICS ON ³¹P CHEMICAL SHIFT TENSORS IN DICKERSON DODECAMER: A COMBINED MD/DFT STUDY

J. Přecechtělová¹, P. Novák¹, Martin Kaupp², M.L. Munzarová¹, and Vladimír Sklenář¹

¹National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2,

CZ-611 37, Brno, Czech Republic

²Institut für Anorganische Chemie, Universität Würzburg, Am Hubland D-97074, Germany

janap@ncbr.chemi.muni.cz

³¹P chemical shift tensors (δ_ii) can aid nucleic acid structure determination [1]. Due to the lack of experimental data, theoretical calculations are a valuable method of choice to obtain δ_ii. Previous results of such calculations on static models of phosphate groups proved to provide useful, yet rather limited information, as they do not account for dynamical effects [2,3]. Internal conformational motion as well as the continuous breaking and forming of hydrogen bonds between solvent molecules and phosphate oxygens influence ³¹P chemical shift tensors considerably. Therefore, we have performed classical molecular dynamics (MD) simulation of [d(CGCGAATTCGCG)]₂ and used the snapshots from the MD trajectory for chemical shift tensor calculations. Small cluster models consisting of dimethyl phosphate and water molecules within the first solvation shell have been employed. Calculations were carried out at the density functional level (DFT) of theory, applying gradient-corrected BP86 functional and IGLO-III basis set. Changes in chemical shift tensors introduced 1) by extending the explicit solvent beyond the first solvation shell and 2) by adding implicit solvent or partial point charges to the small cluster models have been analysed. In order to assess the direct effect of hydrogen-bonding, the results obtained are also compared to chemical shift tensors calculated for dimethyl phosphate without any coordinated water molecules.

1. Z. Wu, N. Tjandra, A. Bax, J. Am. Chem. Soc., 123, (2001), 3617.

2. J. Přecechtělová, Markéta L. Munzarová, P. Novák, V. Sklenář, J. Phys. Chem. B, 111, (2007), 2658.

3. J. Přecechtělová, P. Padrta, Markéta L. Munzarová, V. Sklenář, J. Phys. Chem. B, 112, (2008), 3470.

Acknowledgements

This work was supported by the Grants MSM0021622413 and LC06030 of the Ministry of Education, Youth, and Sports of the Czech Republic. Deutscher Akademischer Austausch Dienst (DAAD) is acknowledged for providing a scholarship to Jana Přecechtělová for her research stay at Universtät Würzburg, Germany.