Arrhenius activation parameters for the loss of neutral nucleobases from deprotonated oligonucleotide anions in the gas phase

  • Rambod Daneshfar
  • John S. KlassenEmail author


Arrhenius activation parameters (E a and A) for the loss of neutral nucleobase from a series of doubly deprotonated oligodexoynucleotide 10-mers of the type XT9, T9X, and T5XT4, where X=A, C, and G, have been determined using the blackbody infrared radiative dissociation technique. At temperatures of 120 to 190 °C, the anions dissociate exclusively by the loss of a neutral nucleobase (XH), followed by cleavage of the sugar 3′ C-O bond leading to (a-XH) and w type ions or, in the case of the T9X2− ions, the loss of H2O. The dissociation kinetics and energetics are sensitive to the nature and position of X. Over the temperature range investigated, the kinetics for the loss of AH and GH were similar, but ∼100 times faster than for the loss of CH. For the loss of AH and GH, the values of E a are sensitive to the position of the base. The order of the E as for the loss of XH from the 5′ and 3′ termini is: C>G>A; while for T5XT4 the order is: C>A>G. The trends in the values of E a do not parallel the trend in deprotonation enthalpies or proton affinities of the nucleobases in the gas phase, indicating that the energetic differences do not simply reflect differences in their gas phase acidity or basicity. The pre-exponential factors (A) vary from 1010 to 1015 s−1, depending on the nature and position of X. These results suggest that the reactivity of individual nucleobases is influenced by stabilizing intramolecular interactions.


Collision Cross Section Arrhenius Parameter Deprotonated Form Dissociation Kinetic Base Loss 
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  1. 1.
    Zhu, L.; Parr, G. R.; Fitzgerald, M. C.; Nelson, C. M.; Smith, L. M. J. Am. Chem. Soc. 1995, 117, 6048–6056.CrossRefGoogle Scholar
  2. 2.
    McLuckey, S. A.; Vaidyanathan, G.; Habibi-Goudarzi, S. J. Mass Spectrom. 1995, 30, 1222–1229.CrossRefGoogle Scholar
  3. 3.
    Phillips, D. R.; McCloskey, J. A. Int. J. Mass Spectrom. Ion Processes 1993, 128, 61–82.CrossRefGoogle Scholar
  4. 4.
    Barry, J. P.; Vouros, P.; Schepdael, A. V.; Law, S.-J. J. Mass Spectrom. 1995, 30, 993–1006.CrossRefGoogle Scholar
  5. 5.
    Bartlett, M. G.; McCloskey, J. A.; Manalili, S.; Griffey, R. H. J. Mass Spectrom. 1996, 31, 1277–1283.CrossRefGoogle Scholar
  6. 6.
    McLuckey, S. A.; Vaidyanathan, G. Int. J. Mass Spectrom. Ion Processes 1997, 162, 1–16.CrossRefGoogle Scholar
  7. 7.
    McLuckey, S. A.; Van Berkel, G. J.; Glish, G. L. J. Am. Soc. Mass Spectrom. 1992, 3, 60–70.CrossRefGoogle Scholar
  8. 8.
    McLuckey, S. A.; Habibi-Goudarzi, S. J. Am. Chem. Soc. 1993, 115, 12085–12095.CrossRefGoogle Scholar
  9. 9.
    Little, D. P.; Aaserud, D. J.; Valaskovic, G. A.; McLafferty, F. W. J. Am. Chem. Soc. 1996, 118, 9352–9359.CrossRefGoogle Scholar
  10. 10.
    Rodgers, M. T.; Campell, S.; Marzluff, E. M.; Beauchamp, J. L. Int. J. Mass Spectrom. Ion Processes 1994, 137, 121–149.CrossRefGoogle Scholar
  11. 11.
    Wan, K. X.; Gross, M. L. J. Am. Soc. Mass Spectrom. 2001, 12, 580–589.CrossRefGoogle Scholar
  12. 12.
    Luo, H.; Lipton, M. S.; Smith, R. D. J. Am. Soc. Mass Spectrom. 2002, 13, 195–199.CrossRefGoogle Scholar
  13. 13.
    Wan, K. X.; Gross, J.; Hillenkamp, F.; Gross, M. L. J. Am. Soc. Mass Spectrom. 2001, 12, 193–205.CrossRefGoogle Scholar
  14. 14.
    Wang, Z.; Wan, K. X.; Ramanathan, R.; Taylor, J. S.; Gross, M. L. J. Am. Soc. Mass Spectrom. 1998, 9, 683–691.CrossRefGoogle Scholar
  15. 15.
    Gross, J.; Hillenkamp, F.; Wan, K. X.; Gross, M. L. J. Am. Soc. Mass Spectrom. 2001, 12, 180–192.CrossRefGoogle Scholar
  16. 16.
    Klassen, J. S.; Schnier, P. D.; Williams, E. R. J. Am. Soc. Mass Spectrom. 1998, 9, 1117–1124.CrossRefGoogle Scholar
  17. 17.
    Ho, Y.; Kebarle, P. Int. J. Mass Spectrom. Ion Processes 1997, 165, 433–455.CrossRefGoogle Scholar
  18. 18.
    Hannis, J. C.; Muddiman, D. C. Int. J. Mass Spectrom. 2002, 219, 139–150.CrossRefGoogle Scholar
  19. 19.
    Felitsyn, N.; Kitova, E. N.; Klassen, J. S. Anal. Chem. 2001, 73, 4647–4661.CrossRefGoogle Scholar
  20. 20.
    Price, W. D.; Williams, E. R. J. Phys. Chem. A 1997, 101, 8844–8852.CrossRefGoogle Scholar
  21. 21.
    Greco, F.; Liguori, A.; Sindona, G.; Uccella, N. J. Am. Chem. Soc. 1990, 112, 9092–9096.CrossRefGoogle Scholar
  22. 22.
    Russo, N.; Toscano, M.; Grand, A.; Jolibois, F. J. Comp. Chem. 1998, 19, 989–1000.CrossRefGoogle Scholar
  23. 23.
    Cerny, R. L.; Gross, M. L.; Grotjahn, L. Anal. Biochem. 1986, 156, 424–435.CrossRefGoogle Scholar
  24. 24.
    Chen, E. S. D.; Chen, E. C. M.; Sane, N. Biochem. Biophys. Res. Commun. 1998, 246, 228–230.CrossRefGoogle Scholar
  25. 25.
    Freitas, M. A.; Shi, S. D.-H.; Hendrickson, C. L.; Marshall, A. G. J. Am. Chem. Soc. 1998, 120, 10187–10193.CrossRefGoogle Scholar
  26. 26.
    Gidden, J.; Bowers, M. T. Eur. Phys. J. D 2002, 20, 409–419.CrossRefGoogle Scholar
  27. 27.
    Hoaglund, C. S.; Liu, Y.; Ellington, A. D.; Pagel, M.; Clemmer, D. E. J. Am. Chem. Soc. 1997, 119, 9051–9052.CrossRefGoogle Scholar
  28. 28.
    Moradian, A.; Scalf, M.; Westphall, M. S.; Smith, L. M.; Douglas, D. J. Int. J. Mass Spectrom. 2002, 219, 161–170.CrossRefGoogle Scholar
  29. 29.
    Kitova, E. N.; Bundle, D. R.; Klassen, J. S. J. Am. Chem. Soc. 2002, 124, 5902–5913.CrossRefGoogle Scholar
  30. 30.
    Nir, E.; Imhof, P.; Kleinermanns, K.; de Vries, M. S. J. Am. Chem. Soc. 2000, 122, 8091–8092.CrossRefGoogle Scholar
  31. 31.
    Marshall, A. G.; Grosshans, P. B. Anal. Chem. 1991, 63, 215A-229A.CrossRefGoogle Scholar

Copyright information

© American Society for Mass Spectrometry 2004

Authors and Affiliations

  1. 1.Department of ChemistryUniversity of AlbertaEdmontonCanada

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