Solvent effects on the NMR shieldings of stacked DNA base pairs

MARTINEZ, F.A.; ADLER, NATALIA S; CAVASOTTO, CLAUDIO N.; AUCAR, GUSTAVO A.

PHYSICAL CHEMISTRY CHEMICAL PHYSICS

ROYAL SOC CHEMISTRY

Lugar: CAMBRIDGE; Año: 2022 vol. 24 p. 18150 - 18160

1463-9076

Stacking effects are among the most important ones in DNA. We have recently studied its influence in fragments of DNA through the analysis of NMR magnetic shieldings, firstly in vacuo. As a continuation of this line of research we show here the influence of solvent effects on those shieldings through the application of both, explicit and implicit models. We found that the explict solvent model is the most appropiate to consider due to results match in general better with experiments and also one get a clear knowledge of the electronic origin of the value of the shieldings. Our study is grounded on a recently developed theoretical model of our own, by which we are able to learn about magnetic effects of given fragments of DNA molecules on selected base pairs. We use the shieldings of the atoms of a central base pair (guanine-cytosine) of a selected fragment of DNA molecules as descriptors of physical effects, like pi-stacking and solvent. They can be taken separately and altogether. The former is introduced through the addition of some pairs above and below of the central one, and now, the latter is considered including a network of water molecules that consist of two solvation layers which were fixed in the calculations performed in all fragments. We show that solvent effects enhance the stacking effects on magnetic shieldings of atoms that belongs to the external N--H bonds. The net effect is of deshielding on both atoms. There is also a deshielding effect on Carbon atoms that belongs to C=O bonds for which the Oxygen atom has an explicit HB with a solvent water molecule. Solvent effects are found to be not higher than few percent of the total value of shieldings (between 1% to 5%) for most atoms, but there are few for which such effect can be higher. There is one nitrogen atom, the acceptor of the HB between guanine and cytosine, that is highly more shielded (around 15 ppm or 10%) when the explicit solvent is considered. In a similar manner the most external nitrogen atom of cytosine and the Hydrogen atom that is bonded to it, are highly deshielded (around 10 ppm for nitrogen and around 3 ppm for Hydrogen).