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Impact of DFT functionals on the predicted magnesium–DNA interaction: an ONIOM study

  • José P. Cerón-Carrasco
  • Alberto Requena
  • Denis JacqueminEmail author
Regular Article
Part of the following topical collections:
  1. Barone Festschrift Collection

Abstract

We investigate the descriptions of several density functional theory functionals in modeling the interactions between DNA and magnesium, the divalent cation with the largest intracellular concentration. Precisely, the metal-induced proton transfer (PT) in the guanine-cytosine base pairs is analyzed within an hybrid two-layers QM/QM approach (ONIOM) by combining several functionals: BP86, B3LYP, B97-D, ωB97x-D and M06-2X, as well as the MP2 approach. The aqueous environment is simulated through, on the one hand, explicit solvent molecules present in the first hydration shell and, on the other hand, the well-known polarizable continuum model for the effects of solvation beyond this first shell. Calculations with all methods indicate that the Mg2+ cation coordination to DNA promotes a single PT reaction from the guanine to the cytosine base, characterized by a low back-reaction barrier. M06-2X and ωB97x-D functionals provide consistent results for the simulation of PT reactions. These methods can be combined with B97-D functional in ONIOM partition for the description of the stacking effects.

Keywords

DNA Magnesium Tautomerism Density functional calculations ONIOM 

Notes

Acknowledgments

J.P.C.C. acknowledges the Région des Pays de la Loire and the fellowship provided by the Fundación Séneca, Agencia de Ciencia y Tecnología de la Región de Murcia, within its Postdoctoral Research Staff Training Program. D.J. is indebted to the Région des Pays de la Loire for financial support in the framework of a recrutement sur poste stratégique. The work was partially supported by the Fundación Séneca del Centro de Coordinación de la Investigación de la Región de Murcia under Project 08735/PI/08, and by the Ministerio de Educación y Ciencia of Spain under Projects CTQ2007-66528 and CONSOLIDER CSD2009-00038. This research used resources of (1) the CCIPL (Centre de Calcul Intensif des Pays de Loire) and (2) the GENCI-CINES/IDRIS (Grant C201108547).

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© Springer-Verlag 2012

Authors and Affiliations

  • José P. Cerón-Carrasco
    • 1
  • Alberto Requena
    • 2
  • Denis Jacquemin
    • 1
    Email author
  1. 1.CEISAM UMR CNRS 6230Université de NantesNantes Cedex 3France
  2. 2.Departamento de Química Física, Facultad de QuímicaUniversidad de MurciaCampus de Espinardo, MurciaSpain

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