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Time-dependent density functional theory molecular dynamics simulation of doubly charged uracil in gas phase

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Central European Journal of Physics

Abstract

We use time-dependent density functional theory and Born-Oppenheimer molecular dynamics methods to investigate the fragmentation of doubly ionized uracil in gas phase. Different initial electronic excited states of the dication are obtained by removing electrons from different inner-shell orbitals of the neutral species. We show that shape-equivalent orbitals lead to very different fragmentation patterns revealing the importance of the intramolecular chemical environment. The results are in good agreement with ionion coincidence measurements of uracil collision with 100 keV protons.

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References

  1. S. Braccini, Nucl. Phys. B 172, 8 (2007)

    Article  Google Scholar 

  2. H. Tsujii et al., J. Radiat. Res. 48, A1–A13 (2007)

    Article  Google Scholar 

  3. J. Ward, Prog. Nucleic Acid Res. Mol. Biol. 35, 95 (1988)

    Article  Google Scholar 

  4. J. de Vries et al., Phys. Rev. Lett. 91, 053401 (2003)

    Article  ADS  Google Scholar 

  5. B. Liu et al., Phys. Rev. Lett. 97, 133401 (2006)

    Article  ADS  Google Scholar 

  6. J. Tabet et al., Phys. Rev. A 81, 012711 (2010)

    Article  ADS  Google Scholar 

  7. J.-P. Champeaux et al., J. Phys. B: At. Mol. Opt. Phys. (2011)

    Google Scholar 

  8. F. Ban, K. Rankin, J. Gauld, R. Boyd, Theor. Chem. Acc. 108, 11 (2002)

    Article  Google Scholar 

  9. S. Naumov, C. von Sonntag, Radiat. Res. 169, 355 (2008)

    Article  Google Scholar 

  10. N. Jena, P. C. Mishra, J. Phys. Chem. B. 109, 14205 (2005)

    Article  Google Scholar 

  11. A. Kumar, M. Sevilla, Radiation effects on DNA: theoretical investigations of electron hole and excitation pathways to DNA damage (Springer-Verlag, Berlin, 2008)

    Google Scholar 

  12. X. Li, M. Sevilla, Adv. Quant. Chem. 52, 59 (2007)

    Article  Google Scholar 

  13. R. H. D. Lyngdoh et al., Acc. Chem. Res. 42, 563 (2009)

    Article  Google Scholar 

  14. C. J. Mundy, M. E. Colvin, A. A. Quong, J. Phys. Chem. A 106, 10063 (2002)

    Article  Google Scholar 

  15. Y. Wu, C. Mundy, M. Colvin, R. Car, J. Phys. Chem. A 108, 2922 (2004)

    Article  Google Scholar 

  16. E. Runge, E. K. U. Gross, Phys. Rev. Lett. 52, 997 (1984)

    Article  ADS  Google Scholar 

  17. A. Castro, M. A. L. Marques, J. A. Alonso, G. F. Bertsch, A. Rubio, Eur. Phys. J. D 28, 211 (2004)

    Article  ADS  Google Scholar 

  18. I. Tavernelli, U. F. Rohrig, U. Rothlisberger, Mol. Phys. 103, 963 (2005)

    Article  ADS  Google Scholar 

  19. G. Avendaño-Franco, B. Piraux, M. Grüning, X. Gonze, Theor. Chem. Acc. 131, 1289 (2012)

    Article  Google Scholar 

  20. I. Tavernelli et al., Chem. Phys. Chem. 9, 2099 (2008)

    Article  Google Scholar 

  21. L. Adoui et al. J. Phys. B: At. Mol. Opt. Phys. (2009)

    Google Scholar 

  22. P. López-Tarifa et al., Phys. Rev. Lett. 107, 023202 (2011)

    Article  ADS  Google Scholar 

  23. B. Coupier et al., Eur. Phys. J. D 20, 459 (2002)

    Article  ADS  Google Scholar 

  24. J. de Vries et al., J. Phys. B 35, 4373 (2002)

    Article  ADS  Google Scholar 

  25. J. de Vries, R. Hoekstra, R. Morgenstern, T. Schlathoelter, Phys. Scr. T 110, 336 (2004)

    Article  ADS  Google Scholar 

  26. T. Schlatholter, R. Hoekstra, R. Morgenstern, Int. J. Mass Spectrom. 233, 173 (2004)

    Article  ADS  Google Scholar 

  27. P. Moretto-Capelle, A. Le Padellec, Phys. Rev. A 74, 062705 (2006)

    Article  ADS  Google Scholar 

  28. N. Troullier, J. L. Martins, Phys. Rev. B 43, 1993 (1991)

    Article  ADS  Google Scholar 

  29. A. D. Becke, Phys. Rev. A 38, 3098 (1988)

    Article  ADS  Google Scholar 

  30. C. Lee, W. Yang, R. G. Parr, Phys. Rev. B 37, 785 (1988)

    Article  ADS  Google Scholar 

  31. R. Car, M. Parrinello, Phys. Rev. Lett. 22, 2471 (1985)

    Article  ADS  Google Scholar 

  32. M. P. Gaigeot et al., J. Phys. B: At. Mol. Opt. Phys. 40, 1 (2007)

    Article  ADS  Google Scholar 

  33. I. Tavernelli, M. P. Gaigeot, R. Vuilleumier, C. Stia, M. A. Hervé du Penhoat, M. F. Politis, Chem. Phys. Chem. 9, 2099 (2008)

    Article  Google Scholar 

  34. W. Tang, E. Sanville, G. Henkelman, J. Phys.: Comput. Mater. 21, 084204 (2009)

    ADS  Google Scholar 

  35. P. Cafarelli et al., AIP Conf. Proc. 1080, 71 (2008)

    Article  ADS  Google Scholar 

  36. D. M. P. Holland, A. W. Potts, L. Karlsson, I. L. Zaytseva, A. B. Trofimov, J. Schirmer, Chem. Phys. 353, 47 (2008)

    Article  ADS  Google Scholar 

  37. N. L. Doltsinis, D. Marx, J. Theor. Comp. Chem. 1, 319 (2002)

    Article  Google Scholar 

  38. A. J. Cohen, P. Mori-Sánchez, W. Yang, Science 321, 792 (2008)

    Article  ADS  Google Scholar 

  39. P. López-Tarifa et al., Angew. Chem. 52, 3160 (2013)

    Article  Google Scholar 

Download references

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Authors and Affiliations

  1. École Polytechnique Fédérale de Lausanne, EPFL SB-ISIC-LCBC-BCH, 1015, Lausanne, Switzerland

    Pablo López-Tarifa, Ursula Rothlisberger & Ivano Tavernelli

  2. IMPMC UMR-CNRS 7590, Université Pierre et Marie Curie, 4 place Jussieu, 75005, Paris, France

    Marie-Anne Hervé du Penhoat

  3. École Normale Supérieure, Département de Chimie, UMR 8640 CNRS-ENS-UPMC, 75005, Paris, France

    Rodophe Vuilleumier

  4. LAMBE, UMR-CNRS 8587, Université d’Evry val d’Essonne, Blvd F. Mitterrand, 91025, Evry, France

    Marie-Pierre Gaigeot & Marie-Françoise Politis

  5. Institut Universitaire de France, 103 Blvd St Michel, 75005, Paris, France

    Marie-Pierre Gaigeot

  6. CESR, Université de Toulouse, UPS, 31028, Toulouse Cedex 9, France

    Arnaud Le Padellec

  7. CNRS, UMR5187, F-31028, Toulouse, France

    Arnaud Le Padellec

  8. Laboratoire Collisions, Agrégats, Réactivité, Université de Toulouse, UPS, 31062, Toulouse, France

    Jean-Philippe Champeaux & Patrick Moretto-Capelle

  9. CNRS, UMR 5589, F-31062, Toulouse, France

    Jean-Philippe Champeaux & Patrick Moretto-Capelle

  10. Departamento de Qí’mica, Módulo 13, Universidad Autónoma de Madrid, 28049, Madrid, Spain

    Manuel Alcamí & Fernando Martín

  11. Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA-Nanociencia), Cantoblanco, 28049, Madrid, Spain

    Fernando Martín

Authors
  1. Pablo López-Tarifa
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  2. Marie-Anne Hervé du Penhoat
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  3. Rodophe Vuilleumier
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  4. Marie-Pierre Gaigeot
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  5. Ursula Rothlisberger
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  6. Ivano Tavernelli
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  7. Arnaud Le Padellec
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  8. Jean-Philippe Champeaux
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  9. Manuel Alcamí
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  10. Patrick Moretto-Capelle
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  11. Fernando Martín
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  12. Marie-Françoise Politis
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Corresponding author

Correspondence to Pablo López-Tarifa.

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Cite this article

López-Tarifa, P., Hervé du Penhoat, MA., Vuilleumier, R. et al. Time-dependent density functional theory molecular dynamics simulation of doubly charged uracil in gas phase. centr.eur.j.phys. 12, 97–102 (2014). https://doi.org/10.2478/s11534-014-0428-0

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  • DOI: https://doi.org/10.2478/s11534-014-0428-0

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