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The European Physical Journal D

, Volume 60, Issue 1, pp 77–83 | Cite as

Theoretical investigation of the ultrafast dissociation of core-ionized water and uracil molecules immersed in liquid water

  • C. R. Stia
  • M.-P. Gaigeot
  • R. Vuilleumier
  • O. A. Fojón
  • M.-A. Hervé du PenhoatEmail author
  • M.-F. Politis
Topical issue on Molecular level assessments of radiation biodamage

Abstract

We present a series of ab initio density functional based calculations of the fragmentation dynamics of core-ionized biomolecules. The computations are performed for pure liquid water, aqueous and isolated Uracil. Core ionization is described by replacing the 1s 2 pseudopotential of one atom of the target molecule (C, N or O) with a pseudopotential for a 1s 1 core-hole state. Our results predict that the dissociation of core-ionized water molecules may be reached during the lifetime of inner-shell vacancy (less than 10 fs), leading to OH bond breakage as a primary outcome. We also observe a second fragmentation channel in which total Coulomb explosion of the ionized water molecule occurs. Fragmentation pathways are found similar for pure water or when the water molecule is in the primary hydration shell of the uracil molecule. In the latter case, the proton may be transferred towards the uracil oxygen atoms. When the core hole is located on the uracil molecule, ultrafast dissociation is only observed in the aqueous environment and for nitrogen-K vacancies, resulting in proton transfers towards the hydrogen-bonded water molecule.

Keywords

Water Molecule Uracil Proton Transfer Liquid Water Hydration Shell 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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References

  1. 1.
    A. Chetioui, I. Despiney, L. Guiraud, L. Adoui, L. Sabatier, B. Dutrillaux, Int. J. Radiat. Biol. 65, 511 (1994) CrossRefGoogle Scholar
  2. 2.
    M. Watanabe, M. Susuki, K. Watanabe, K. Suzuki, N. Usami, A. Yokoya, K. Kobayashi, Int. J. Radiat. Biol. 61, 161 (1992) CrossRefGoogle Scholar
  3. 3.
    M.-A. Hervé du Penhoat, B. Fayard, F. Abel, A. Touati, F. Gobert, I. Despiney-Bailly, M. Ricoul, L. Sabatier, D.L. Stevens, M.A. Hill, D.T. Goodhead, A. Chetioui, Radiat. Res. 151, 649 (1999) CrossRefGoogle Scholar
  4. 4.
    B. Fayard, A. Touati, F. Abel, M.-A. Hervé du Penhoat, I. Despiney-Bailly, F. Gobert, M. Ricoul, A. L’Hoir, M.-F. Politis, M.A. Hill, D.L. Stevens, L. Sabatier, E. Sage, D.T. Goodhead, A. Chetioui, Radiat. Res. 157, 128 (2002) CrossRefGoogle Scholar
  5. 5.
    S. Saigusa, Y. Ejima, K. Kobayashi, M.S. Sasaki, Int. J. Radiat. Biol. 61, 785 (1992) CrossRefGoogle Scholar
  6. 6.
    F.-N. Gobert, M. Lamoureux, M.-A. Hervé du Penhoat, M. Ricoul, A. Boissière, A. Touati, F. Abel, M.-F. Politis, B. Fayard, J.M. Guigner, L. Martins, I. Testard, L. Sabatier, A. Chetioui, Int. J. Radiat. Biol. 80, 135 (2004) CrossRefGoogle Scholar
  7. 7.
    A. Eschenbrenner, M.-A. Hervé du Penhoat, A. Boissière, G. Eot-Houllier, F. Abel, M.-F. Politis, A. Touati, E. Sage, A. Chetioui, Int. J. Radiat. Biol. 83, 687 (2007) CrossRefGoogle Scholar
  8. 8.
    M.-A. Hervé du Penhoat, A. Eschenbrenner, F. Abel, A. Boissire, J.-M. Guigner, A. Chetioui, M.-F. Politis, A. Touati, E. Sage, T.J. Jenner, D.L. Stevens, M.A. Hill, Int. J. Radiat. Biol. (2010) DOI:  10.3109/09553000903419296
  9. 9.
    P.K. Agrawala, A. Eschenbrenner, M.-A. Hervé du Penhoat, A. Boissière, M.F. Politis, A. Touati, E. Sage, A. Chetioui, Int. J. Radiat. Biol. 84, 1093 (2008) CrossRefGoogle Scholar
  10. 10.
    K. Fujii, N. Shikazono, A. Yokoya, J. Phys. Chem. B 113, 16007 (2009) CrossRefGoogle Scholar
  11. 11.
    K. Fujii, A. Yokoya, Radiat. Phys. Chem. 78, 1188 (2009) ADSCrossRefGoogle Scholar
  12. 12.
    K. Akamatsu, K. Fujii, A. Yokoya, Radiat. Res. 161, 442 (2004) CrossRefGoogle Scholar
  13. 13.
    K. Akamatsu, K. Fujii, A. Yokoya, Int. J. Radiat. Biol. 80, 849 (2004) CrossRefGoogle Scholar
  14. 14.
    K. Fujii, K. Akamatsu, A. Yokoya, Radiat. Res. 161, 435 (2004) CrossRefGoogle Scholar
  15. 15.
    K. Fujii, K. Akamatsu, A. Yokoya, Int. J. Radiat. Biol. 80, 909 (2004) CrossRefGoogle Scholar
  16. 16.
    A. Yokoya, K. Akamatsu, K. Fujii, M. Ukai, Int. J. Radiat. Biol. 80, 833 (2004) CrossRefGoogle Scholar
  17. 17.
    M. Falk, M.A.G. Poole, C.G. Goymour, Can. J. Chem. 48, 1536 (1970) CrossRefGoogle Scholar
  18. 18.
    N.J. Tao, S.M. Lindsay, Biopolymers 28, 1019 (1989) CrossRefGoogle Scholar
  19. 19.
    E. Westhof, Ann. Rev. Biophys. Biophys. Chem. 17, 125 (1988) CrossRefGoogle Scholar
  20. 20.
    S. Gregoli, S.M. Olast, A. Bertinchamps, Radiat. Res. 89, 238 (1982) CrossRefGoogle Scholar
  21. 21.
    D. Becker, M.D. Sevilla, Adv. Radiat. Biol. 17, 121 (1993) Google Scholar
  22. 22.
    T. La Vere, D. Becker, M.D. Sevilla, Radiat. Res. 145, 673 (1996) CrossRefGoogle Scholar
  23. 23.
    M.G. Debije, M.D. Strickler, A. Bernhard, Radiat. Res. 154, 163 (2000) CrossRefGoogle Scholar
  24. 24.
    A. Naves de Brito, R. Feifel, A. Mocellin, A.B. Machado, S. Sundin, I. Hjelte, S.L. Sorensen, O. Björneholm, Chem. Phys. Lett. 309, 377 (1999) ADSCrossRefGoogle Scholar
  25. 25.
    I. Hjelte, M.N. Piancastelli, R.F. Fink, O. Björneholm, M. Bässler, R. Feifel, A. Giertz, H. Wang, K. Wiesner, A. Ausmees, C. Miron, S.L. Sorensen, S. Svensson, Chem. Phys. Lett. 334, 151 (2001) ADSCrossRefGoogle Scholar
  26. 26.
    B. Brena, D. Nordlund, M. Odelius, H. Ogasawara, A. Nilsson, L.G.M. Petterson, Phys. Rev. Lett. 93, 148302 (2004). ADSCrossRefGoogle Scholar
  27. 27.
    M. Odelius, H. Ogasawara, D. Nordlund, O. Fuchs, L. Weinhardt, F. Maier, E. Umbach, C. Heske, Y. Zubavichus, M. Grunze, J.D. Denlinger, L.G.M. Petterson, A. Nilsson, Phys. Rev. Lett. 94, 227401 (2005) ADSCrossRefGoogle Scholar
  28. 28.
    O. Takahashi, M. Odelius, D. Nordlund, A. Nilsson, H. Bluhm, L.G.M. Pettersson, J. Chem. Phys. 124, 064307 (2006) ADSCrossRefGoogle Scholar
  29. 29.
    M. Odelius, Phys. Rev. B 79, 144204 (2009) ADSCrossRefGoogle Scholar
  30. 30.
    R. Car, M. Parrinello, Phys. Rev. Lett. 55, 2471 (1985) ADSCrossRefGoogle Scholar
  31. 31.
    CPMD V3.9 Copyright IBM Corp 1990–2004, Copyright MPI für Festkörperforschung Stuttgart (1997–2001) Google Scholar
  32. 32.
    A. Becke, Phys. Rev. A 38, 3098 (1988) ADSCrossRefGoogle Scholar
  33. 33.
    C. Lee, W. Yang, R.G. Parr, Phys. Rev. B 37, 785 (1988) ADSCrossRefGoogle Scholar
  34. 34.
    N. Troullier, J.L. Martins, Phys. Rev. B 43, 1993 (1991) ADSCrossRefGoogle Scholar
  35. 35.
    E. Schwegler, J.C. Grossman, F. Gygi, G. Galli, J. Chem. Phys. 121, 4500 (2004) CrossRefGoogle Scholar
  36. 36.
    J.C. Grossman, E. Schwegler, E.W. Draeger, G. Galli, J. Chem. Phys. 120, 300 (2004) ADSCrossRefGoogle Scholar
  37. 37.
    D. Prendergast, J.C. Grossman, G. Galli, J. Chem. Phys. 123, 014501 (2005) ADSCrossRefGoogle Scholar
  38. 38.
    M.-P. Gaigeot, M. Sprik, J. Phys. Chem. B 108, 7458 (2004) CrossRefGoogle Scholar
  39. 39.
    M.-P. Gaigeot, R. Vuilleumier, C. Stia, M.E. Galassi, R. Rivarola, B. Gervais, M.F. Politis, Phys. B: At. Mol. Opt. Phys. 40, 1 (2007) ADSCrossRefGoogle Scholar
  40. 40.
    R. Sankari, M. Ehara, H. Nakatsuji, Y. Senba, K. Hosokawa, H. Yoshida, A. De Fanis, Y. Tamenori, S. Aksela, K. Ueda, Chem. Phys. Lett. 380, 647 (2003) ADSCrossRefGoogle Scholar
  41. 41.
    D. Prendergast, G. Galli, Phys. Rev. Lett. 96, 215502 (2006) ADSCrossRefGoogle Scholar
  42. 42.
    H. Lapid, N. Agmon, M.K. Petersen, G.A. Voth, J. Chem. Phys. 122, 014506 (2005) ADSCrossRefGoogle Scholar
  43. 43.
    A. Chandra, M.E. Tuckerman, D. Marx, Phys. Rev. Lett. 99, 145901 (2007) ADSCrossRefGoogle Scholar
  44. 44.
    R. Vuilleumier, D. Borgis, J. Chem. Phys. 111, 4251 (1999) ADSCrossRefGoogle Scholar
  45. 45.
    R.F.W. Bader, Atoms in Molecules – A Quantum Theory (Oxford University Press, Oxford, UK, 1990) Google Scholar
  46. 46.
    B.P. Uberuaga, E.R. Batista, H. Jonsson, J. Chem. Phys. 111, 10664 (1999) ADSCrossRefGoogle Scholar
  47. 47.
    M. Dal Peraro, S. Raugei, P. Carloni, M.L. Klein, Chem. Phys. Chem. 6, 1715 (2005) Google Scholar
  48. 48.
    I. Tavernelli, M.-P. Gaigeot, R. Vuilleumier, C. Stia, M.-A. Hervé du Penhoat, M.-F. Politis, Chem. Phys. Chem. 9, 2099 (2008) Google Scholar
  49. 49.
    M.-P. Gaigeot, P. Lopez-Tarifa, R. Vuilleumier, I. Tavernelli, F. Martin, M. Alcami, M.-A. Hervé du Penhoat, M.-F. Politis, Mutation Research/Reviews in Mutation Research (in press) Google Scholar

Copyright information

© EDP Sciences, SIF, Springer-Verlag Berlin Heidelberg 2010

Authors and Affiliations

  • C. R. Stia
    • 1
  • M.-P. Gaigeot
    • 2
    • 3
  • R. Vuilleumier
    • 4
  • O. A. Fojón
    • 1
  • M.-A. Hervé du Penhoat
    • 5
    Email author
  • M.-F. Politis
    • 5
  1. 1.Instituto de Física Rosario (CONICET-Universidad Nacional de Rosario)RosarioArgentina
  2. 2.Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, LAMBE, UMR-CNRS 8587, Université d’Evry-Val-d’EssonneEvryFrance
  3. 3.Institut Universitaire de FranceParisFrance
  4. 4.Département de chimie, École Normale Supérieure, 24 rue LhomondParisFrance
  5. 5.Institut de Minéralogie et de Physique des Milieux Condensés, IMPMC, UMR-CNRS 7590, Université Pierre et Marie CurieParisFrance

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