The European Physical Journal D

, Volume 60, Issue 1, pp 71–76 | Cite as

Comparison of the directional characteristics of swift ion excitation for two small biomolecules: glycine and alanine

  • S. Bruun-Ghalbia
  • S. P.A. Sauer
  • J. Oddershede
  • J. R. Sabin
Topical issue on Molecular level assessments of radiation biodamage

Abstract

The dependence of the damage caused to biomolecules by a swift ion beam on the target molecule’s orientation with respect to the beam has implications for radiation protection and therapy. At the most basic level, it is first necessary to understand energy deposition in these systems. As the material constants describing energy deposition are the target mean excitation energies (\(I_{0})\) we report here the directional components of the mean excitation energies of the two simplest amino acids, glycine and alanine. It is found that the directional components of the mean excitation energies are similar in the two amino acids, and that both have a preferred direction for energy absorption.

Keywords

Excitation Energy Oscillator Strength Energy Deposition Random Phase Approximation Directional Component 

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References

  1. 1.
    S.P.A. Sauer, J.R. Sabin, J. Oddershede, Phys. Rev. A 47, 1123 (1993) ADSCrossRefGoogle Scholar
  2. 2.
    H.H. Mikkelsen, J. Oddershede, J.R. Sabin, E. Bonderup, Nucl. Instrum. Meth. B 100, 451 (1995) ADSCrossRefGoogle Scholar
  3. 3.
    S.P.A. Sauer, J.R. Sabin, J. Oddershede, Nucl. Instrum. Meth. B 100, 458 (1995) ADSCrossRefGoogle Scholar
  4. 4.
    S.P. Appell, S.B. Trickey, J.R. Sabin, Phys. Rev. A 58, 4616 (1998) ADSCrossRefGoogle Scholar
  5. 5.
    S.P.A. Sauer, J. Oddershede, J.R. Sabin, J. Phys. Chem. A 110, 8811 (2006) CrossRefGoogle Scholar
  6. 6.
    J. Sisterson, Nucl. Instrum. Meth. B 241, 713 (2005) ADSCrossRefGoogle Scholar
  7. 7.
    U. Amaldi, G. Kraft, Rep. Prog. Phys. 68, 1861 (2005) ADSCrossRefGoogle Scholar
  8. 8.
    H. Bethe, Ann. Phys. (Leipzig) 5, 325 (1930) ADSGoogle Scholar
  9. 9.
    M. Inokuti, Phys. Rev. A 12, 102 (1975) ADSCrossRefGoogle Scholar
  10. 10.
    C. von Sonntag, The Chemical Basis for Radiation Biology (Taylor and Francis, London, 1987) Google Scholar
  11. 11.
    C. von Sonntag, Free Radical DNA Damage and its Repair – A Chemical Perspective (Springer Verlag, Heidelberg, 2005) Google Scholar
  12. 12.
    J.O. Hirschfelder, W.B. Brown, S.T. Epstein, Adv. Quantum Chem. 1, 255 (1964) ADSCrossRefGoogle Scholar
  13. 13.
    Cf. e.g. W.J. Meath, B.L. Jahnwar, A. Kumar, Coll. Czech. Chem. Comm. 70, 1196 (2005), and references therein CrossRefGoogle Scholar
  14. 14.
    R.A. Harris, J. Chem. Phys. 50, 3947 (1969) ADSCrossRefGoogle Scholar
  15. 15.
    J. Lindhard, Nucl. Instrum. Meth. 132, 1 (1976) ADSCrossRefGoogle Scholar
  16. 16.
    R.D. Suenram, F.J. Lovas, J. Am. Chem. Soc. 102, 7180 (1980) CrossRefGoogle Scholar
  17. 17.
    P.D. Godfrey, R.D. Brown, J. Amer. Chem. Soc. 117, 2019 (1995) CrossRefGoogle Scholar
  18. 18.
    J.D. Reva, , A.M. Plokhotnichenko, S.G. Stepanian, A.Y. Ivanov, E.D. Radchenko, G.G. Sheina, Y.P. Blagoi, Chem. Phys. Lett. 232, 141 (1995) ADSCrossRefGoogle Scholar
  19. 19.
    S.G. Stepanian, J.D. Reva, E.D. Radchenko, M.L.T.S. Duarte, R. Fausto, L. Adamovicz, J. Phys. Chem. A 102, 1041 (1998) CrossRefGoogle Scholar
  20. 20.
    O. Bludský, J. Chocholoušová, J. Vacek, F. Huisken, P. Hobza, J. Chem. Phys. 113, 4629 (2000) ADSCrossRefGoogle Scholar
  21. 21.
    H.M. Senn, P.M. Margl, R. Schmid, T. Ziegler, P.E. Blöchl, J. Chem. Phys. 118, 1089 (2003) ADSCrossRefGoogle Scholar
  22. 22.
    K. Aidas, J. Kongsted, J.R. Sabin, J. Oddershede, K.V. Mikkelsen, S.P.A. Sauer, J. Phys. Chem. Lett. 1, 242 (2010) CrossRefGoogle Scholar
  23. 23.
    Gaussian 03, Revision B.05, M.J. Frisch et al., Gaussian, Inc., Pittsburgh PA, 2003 Google Scholar
  24. 24.
    C. Lee, W. Yang, R.G. Parr, Phys. Rev. B 37, 785 (1988) ADSCrossRefGoogle Scholar
  25. 25.
    A.D. Becke, J. Chem. Phys. 98, 5648 (1993) ADSCrossRefGoogle Scholar
  26. 26.
    W.J. Hehre, R. Ditchfield, J.A. Pople, J. Chem. Phys. 56, 2257 (1972) ADSCrossRefGoogle Scholar
  27. 27.
    T. Clark, J. Chandrasekhar, P.V.R. Schleyer, J. Comput. Chem. 4, 294 (1983) CrossRefGoogle Scholar
  28. 28.
    K. Iijima, B. Beagley, J. Mol. Struct. 248, 133 (1991) ADSCrossRefGoogle Scholar
  29. 29.
    P.D. Godfrey, S. Firth, L.D. Hatherley, R.D. Brown, A.P. Pierlot, J. Am. Chem. Soc. 115, 9687 (1993) CrossRefGoogle Scholar
  30. 30.
    S.G. Stepanian, I.D. Reva, E.D. Radchenko, L. Adamowicz, J. Phys. Chem. A 102, 4623 (1998) Google Scholar
  31. 31.
    B. Lambie, R. Ramaekers, G. Maes, Spectrochim. Acta A 59, 1387 (2003) ADSCrossRefGoogle Scholar
  32. 32.
    S. Gronert, R.A.J. O’Hair, J. Am. Chem. Soc. 117, 2071 (1995) CrossRefGoogle Scholar
  33. 33.
    A.G. Császár, J. Mol. Struct. 346, 141 (1995) ADSCrossRefGoogle Scholar
  34. 34.
    A.G. Császár, J. Phys. Chem. 100, 3541 (1996) CrossRefGoogle Scholar
  35. 35.
    A.G. Császár, A. Perczel, Prog. Biophys. Mol. Biol. 71, 243 (1999) CrossRefGoogle Scholar
  36. 36.
    D.M. Upadhyay, A.K. Rai, D.K. Rai, A.N. Singh, A. Kumar, Spectrochim. Acta A 66, 909 (2007) ADSCrossRefGoogle Scholar
  37. 37.
    R. Maul, F. Ortmann, M. Preuss, K. Hannewald, F. Bechstedt, J. Comput. Chem. 28, 1817 (2007) CrossRefGoogle Scholar
  38. 38.
    W. Yu, L. Liang, Z. Lin, S. Ling, M. Haranczyk, M, Gutowskij, J. Comput. Chem. 30, 589 (2009) CrossRefGoogle Scholar
  39. 39.
    R. Ahlrichs, M. Bär, M. Häser, H. Horn, C. Kölmel, Chem. Phys. Lett. 162, 165 (1989) ADSCrossRefGoogle Scholar
  40. 40.
    M. Häser, R. Ahlrichs, J. Comput. Chem. 10, 104 (1989) CrossRefGoogle Scholar
  41. 41.
    O. Treutler, R. Ahlrichs, J. Chem. Phys. 102, 346 (1995) ADSCrossRefGoogle Scholar
  42. 42.
    R. Bauernschmitt, R. Ahlrichs, Chem. Phys. Lett. 256, 454 (1996) ADSCrossRefGoogle Scholar
  43. 43.
    S. Grimme, F. Furche, R. Ahlrichs, Chem. Phys. Lett. 361, 321 (2002) ADSCrossRefGoogle Scholar
  44. 44.
    F. Furche, D. Rappoport, Computational Photochemistry, in Computational and Theoretical Chemistry, edited by M. Olivucci (Elsevier, Amsterdam, 2005), Vol. 16, Chap. III Google Scholar
  45. 45.
    TURBOMOLE V6.0 2009, a development of University of Karlsruhe and Forschungszentrum Karlsruhe GmbH, 1989–2007, TURBOMOLE GmbH, since 2007; available from http://www.turbomole.com
  46. 46.
    For a review of the theory and implementation of the polarization propagator method, see J. Oddershede, P. Jørgensen, D.L. Yaeger, Comput. Phys. Rep. 2, 33 (1984) ADSCrossRefGoogle Scholar
  47. 47.
    J. Oddershede, Adv. Chem. Phys. 69, 201 (1987) CrossRefGoogle Scholar
  48. 48.
    S.P.A. Sauer, M.J. Packer, The ab initio calculation of molecular properties other than the potential energy surface, in Computational Molecular Spectroscopy, edited by P.R. Bunker, P. Jensen (John Wiley and Sons, London, 2000), Chap. 7, pp. 221–252 Google Scholar
  49. 49.
    E. Runge, E.K.U. Gross, Phys. Rev. Lett. 52, 997 (1984) ADSCrossRefGoogle Scholar
  50. 50.
    J. Geertsen, J. Oddershede, J.R. Sabin, Phys. Rev. A 34, 1104 (1986) ADSCrossRefGoogle Scholar
  51. 51.
    P. Jørgensen, J. Oddershede, N.H.F. Beebe, J. Chem. Phys. 68, 2527 (1978) ADSCrossRefGoogle Scholar
  52. 52.
    P. Jørgensen, J. Oddershede, J. Chem. Phys. 78, 1898 (1983) ADSCrossRefGoogle Scholar
  53. 53.
    Aa.E. Hansen, T.D. Bouman, Molec. Phys. 37, 1713 (1979) ADSCrossRefGoogle Scholar
  54. 54.
    The orbital exponents and contraction coefficients for the basis are given in Tables 2–5 of reference [5] Google Scholar
  55. 55.
    M. Ernzerhof, G.E. Scuseria, J. Chem. Phys. 110, 5029 (1999) ADSCrossRefGoogle Scholar
  56. 56.
    C. Adamo, V. Barone, J. Chem. Phys. 110, 6158 (1999) ADSCrossRefGoogle Scholar
  57. 57.
    J.P. Perdew, K. Burke, M. Ernzerhof, Phys. Rev. Lett. 77, 3865 (1996) ADSCrossRefGoogle Scholar
  58. 58.
    W.H. Bragg, R. Kleeman, Philos. Mag. 10, 305 (1918) Google Scholar
  59. 59.
    S. Bruun-Ghalbia, S.P.A. Sauer, J. Oddershede, J.R. Sabin, J. Phys. Chem. B 144, 633 (2010) CrossRefGoogle Scholar
  60. 60.
    J.R. Sabin, J. Oddershede, S.P.A. Sauer, AIP Proceedings CP1080, 138 (2008) ADSCrossRefGoogle Scholar

Copyright information

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

Authors and Affiliations

  • S. Bruun-Ghalbia
    • 1
  • S. P.A. Sauer
    • 1
  • J. Oddershede
    • 2
    • 3
  • J. R. Sabin
    • 2
    • 3
  1. 1.Department of ChemistryUniversity of CopenhagenCopenhagenDenmark
  2. 2.Institute for Physics and Chemistry, University of Southern Denmark, Odense, Denmark, and Quantum Theory ProjectGainesvilleUSA
  3. 3.Department of PhysicsUniversity of FloridaGainesvilleUSA

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