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

• Authors: Pablo López-Tarifa , Marie-Anne Hervé du Penhoat , Rodophe Vuilleumier , Marie-Pierre Gaigeot , Ursula Rothlisberger , Ivano Tavernelli , Arnaud Le Padellec , Jean-Philippe Champeaux , Manuel Alcamí , Patrick Moretto-Capelle , Fernando Martín , Marie-Françoise Politis
• Languages of publication: EN

Abstracts

EN

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.

Keywords

EN

uracil; proton collision; nonadiabatic dynamics; biological damage

• Publisher: De Gruyter Open
• Journal: Open Physics
• Year: 2014
• Volume: 12
• Issue: 2
• Pages: 97-102

Dates

published

1 - 2 - 2014

online

15 - 2 - 2014

Contributors

author

Pablo López-Tarifa

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

author

Marie-Anne Hervé du Penhoat

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

author

Rodophe Vuilleumier

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

author

Marie-Pierre Gaigeot

author

Ursula Rothlisberger

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

author

Ivano Tavernelli

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

author

Arnaud Le Padellec

author

Jean-Philippe Champeaux

author

Manuel Alcamí

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

author

Patrick Moretto-Capelle

author

Fernando Martín

author

Marie-Françoise Politis

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

References

• [1] S. Braccini, Nucl. Phys. B 172, 8 (2007) http://dx.doi.org/10.1016/j.nuclphysbps.2007.07.003[Crossref]
• [2] H. Tsujii et al., J. Radiat. Res. 48, A1–A13 (2007) http://dx.doi.org/10.1269/jrr.48.A1[Crossref]
• [3] J. Ward, Prog. Nucleic Acid Res. Mol. Biol. 35, 95 (1988) http://dx.doi.org/10.1016/S0079-6603(08)60611-X[Crossref]
• [4] J. de Vries et al., Phys. Rev. Lett. 91, 053401 (2003) http://dx.doi.org/10.1103/PhysRevLett.91.053401[Crossref]
• [5] B. Liu et al., Phys. Rev. Lett. 97, 133401 (2006) http://dx.doi.org/10.1103/PhysRevLett.97.133401[Crossref]
• [6] J. Tabet et al., Phys. Rev. A 81, 012711 (2010) http://dx.doi.org/10.1103/PhysRevA.81.012711[Crossref]
• [7] J.-P. Champeaux et al., J. Phys. B: At. Mol. Opt. Phys. (2011)
• [8] F. Ban, K. Rankin, J. Gauld, R. Boyd, Theor. Chem. Acc. 108, 11 (2002) http://dx.doi.org/10.1007/s00214-002-0344-z[Crossref]
• [9] S. Naumov, C. von Sonntag, Radiat. Res. 169, 355 (2008) http://dx.doi.org/10.1667/RR1081.1[Crossref]
• [10] N. Jena, P. C. Mishra, J. Phys. Chem. B. 109, 14205 (2005) http://dx.doi.org/10.1021/jp050646j[Crossref]
• [11] A. Kumar, M. Sevilla, Radiation effects on DNA: theoretical investigations of electron hole and excitation pathways to DNA damage (Springer-Verlag, Berlin, 2008)
• [12] X. Li, M. Sevilla, Adv. Quant. Chem. 52, 59 (2007) http://dx.doi.org/10.1016/S0065-3276(06)52004-0[Crossref]
• [13] R. H. D. Lyngdoh et al., Acc. Chem. Res. 42, 563 (2009) http://dx.doi.org/10.1021/ar800077q[Crossref]
• [14] C. J. Mundy, M. E. Colvin, A. A. Quong, J. Phys. Chem. A 106, 10063 (2002) http://dx.doi.org/10.1021/jp0212904[Crossref]
• [15] Y. Wu, C. Mundy, M. Colvin, R. Car, J. Phys. Chem. A 108, 2922 (2004) http://dx.doi.org/10.1021/jp0363592[Crossref]
• [16] E. Runge, E. K. U. Gross, Phys. Rev. Lett. 52, 997 (1984) http://dx.doi.org/10.1103/PhysRevLett.52.997[Crossref]
• [17] A. Castro, M. A. L. Marques, J. A. Alonso, G. F. Bertsch, A. Rubio, Eur. Phys. J. D 28, 211 (2004) http://dx.doi.org/10.1140/epjd/e2003-00306-3[Crossref]
• [18] I. Tavernelli, U. F. Rohrig, U. Rothlisberger, Mol. Phys. 103, 963 (2005) http://dx.doi.org/10.1080/00268970512331339378[Crossref]
• [19] G. Avendaño-Franco, B. Piraux, M. Grüning, X. Gonze, Theor. Chem. Acc. 131, 1289 (2012) http://dx.doi.org/10.1007/s00214-012-1289-5[Crossref]
• [20] I. Tavernelli et al., Chem. Phys. Chem. 9, 2099 (2008) http://dx.doi.org/10.1002/cphc.200800177[Crossref]
• [21] L. Adoui et al. J. Phys. B: At. Mol. Opt. Phys. (2009)
• [22] P. López-Tarifa et al., Phys. Rev. Lett. 107, 023202 (2011) http://dx.doi.org/10.1103/PhysRevLett.107.023202[Crossref]
• [23] B. Coupier et al., Eur. Phys. J. D 20, 459 (2002) http://dx.doi.org/10.1140/epjd/e2002-00166-3[Crossref]
• [24] J. de Vries et al., J. Phys. B 35, 4373 (2002) http://dx.doi.org/10.1088/0953-4075/35/21/304[Crossref]
• [25] J. de Vries, R. Hoekstra, R. Morgenstern, T. Schlathoelter, Phys. Scr. T 110, 336 (2004) http://dx.doi.org/10.1238/Physica.Topical.110a00336[Crossref]
• [26] T. Schlatholter, R. Hoekstra, R. Morgenstern, Int. J. Mass Spectrom. 233, 173 (2004) http://dx.doi.org/10.1016/j.ijms.2003.12.029[Crossref]
• [27] P. Moretto-Capelle, A. Le Padellec, Phys. Rev. A 74, 062705 (2006) http://dx.doi.org/10.1103/PhysRevA.74.062705[Crossref]
• [28] N. Troullier, J. L. Martins, Phys. Rev. B 43, 1993 (1991) http://dx.doi.org/10.1103/PhysRevB.43.1993[Crossref]
• [29] A. D. Becke, Phys. Rev. A 38, 3098 (1988) http://dx.doi.org/10.1103/PhysRevA.38.3098[Crossref]
• [30] C. Lee, W. Yang, R. G. Parr, Phys. Rev. B 37, 785 (1988) http://dx.doi.org/10.1103/PhysRevB.37.785[Crossref]
• [31] R. Car, M. Parrinello, Phys. Rev. Lett. 22, 2471 (1985) http://dx.doi.org/10.1103/PhysRevLett.55.2471[Crossref]
• [32] M. P. Gaigeot et al., J. Phys. B: At. Mol. Opt. Phys. 40, 1 (2007) http://dx.doi.org/10.1088/0953-4075/40/1/001[Crossref]
• [33] I. Tavernelli, M. P. Gaigeot, R. Vuilleumier, C. Stia, M. A. Hervé du Penhoat, M. F. Politis, Chem. Phys. Chem. 9, 2099 (2008) http://dx.doi.org/10.1002/cphc.200800177[Crossref]
• [34] W. Tang, E. Sanville, G. Henkelman, J. Phys.: Comput. Mater. 21, 084204 (2009)
• [35] P. Cafarelli et al., AIP Conf. Proc. 1080, 71 (2008) http://dx.doi.org/10.1063/1.3058990[Crossref]
• [36] D. M. P. Holland, A. W. Potts, L. Karlsson, I. L. Zaytseva, A. B. Trofimov, J. Schirmer, Chem. Phys. 353, 47 (2008) http://dx.doi.org/10.1016/j.chemphys.2008.07.022[Crossref]
• [37] N. L. Doltsinis, D. Marx, J. Theor. Comp. Chem. 1, 319 (2002) http://dx.doi.org/10.1142/S0219633602000257[Crossref]
• [38] A. J. Cohen, P. Mori-Sánchez, W. Yang, Science 321, 792 (2008) http://dx.doi.org/10.1126/science.1158722[Crossref]
• [39] P. López-Tarifa et al., Angew. Chem. 52, 3160 (2013) http://dx.doi.org/10.1002/anie.201208038[Crossref]

Identifiers

DOI

10.2478/s11534-014-0428-0