Fragmentation of Biomolecular Ions (P 18052)

funded by FWF

Principal Investigator: Paul Scheier
Duration: 01.06.2005 - 31.05.2008 (Approval date: 02.05.2005)
Scientific fields: 1242 Mass Spectrometry (40%)
1207 Bio Physics (1403,3203) (30%)
1235 Ion Physics (20%)
1249 Radiation Physics (3218) (10%)
Keywords: Cold neutral biomolecules; Kinetic energy release; Unimolecular dissociation; Radiation damage


The studies of biomolecules (DNA components such as bases, phosphate, deoxyribose, or hydration water) in isolated conditions are of fundamental interest for modeling their behavior in real biosystems, e.g., during exposure to ionizing radiation. The yield of several anions, formed by dissociative electron attachment to gas phase biomolecules, exhibits the same electron energy dependence as the yield of single and double strand breaks of plasmid DNA attached to a surface. This indicates that the formation of transient negative ions plays an important role in radiation damage of cells and living organisms. Scientists all over the world have probed the inelastic interaction of electrons with gas phase biomolecules, utilizing electron transmission spectroscopy and mass spectrometry. In all of these studies the target molecules were vaporized in an oven at temperatures up to 500 K. So far, all mass spectrometric investigations were probing ions that are formed in the ion source and do not decay on their way to the detector.
By means of sector field mass spectrometry it is planned to study unimolecular and collision induced dissociation reactions of positively and negatively charged product ions generated upon electron collisions with gas phase biomolecules. The correlation between fragmentation patterns and the arrangement of the atoms of the precursor ion can be used to probe temperature induced modifications of neutral biomolecules such as isomerization, tautomerization or thermal decomposition. In addition, the careful analysis of the shape of the parent and fragment ion yield gives access to the kinetic energy release distribution of a decay reaction. The kinetic energy that is released in a fragmentation process determines how far from the point of formation reactive fragments can migrate and induce further damage to the biological system.
Seeded beams and pickup of gas phase biomolecules with cold rare gas clusters (including helium clusters) will be used to cool the gas phase biomolecules prior to the interaction with the electron beam.
Furthermore, it is planned to develop a source to bring large and complex biomolecules such as short sequences of DNA into the gas phase. Spray sources seem to be the appropriate technique, however, in contrast to electrospray the source will be optimized for NEUTRAL molecules. The group of Prof. Hvelplund in Aarhus will support us with know-how in the construction and operation of spray sources.


Final Report (PDF)


a) Peer-reviewed

  • 2008
    1. A. Aleem, A. Mauracher, P. Sulzer, S. Denifl, F. Zappa, A. Bacher, N. Wendt, T. D. Märk, P. Scheier, Relative partial cross sections for anions formed upon electron attachment to nitrotoluene. Int. J. Mass. Spectrom. 1-3/271 (2008) 36-44 doi:10.1016/j.ijms.2007.10.010
    2. S. Denifl, F. Zappa, A. Mauracher, F. Ferreira da Silva, A. Bacher, O. Echt, T. D. Märk, D. K. Böhme, P. Scheier, Dissociative Electron Attachment to DNA Bases Near Absolute Zero Temperature. Freezing Dissociation Intermediates. ChemPhysChem 10/9 (2008) 1387-1389 doi:10.1002/cphc.200800245
    3. S. Denifl, F. Zappa, I. Mähr, A. Mauracher, M. Probst, T. D. Märk, P. Scheier, Inelastic Electron Interaction with Chloroform Clusters embedded in Helium Droplets. J. Am. Chem. Soc. 15/130 (2008) 5065-5071  doi:10.1021/ja075972m
    4. F. Zappa, S. Denifl, I. Mähr, A. Bacher, O. Echt, T. D. Märk, P. Scheier, Ultracold Water Cluster Anions. J. Am. Chem. Soc. 16/130 (2008), 5573-5578  doi:10.1021/ja075421w 
  • 2007
    1. S. Denifl, A. Mauracher, P. Sulzer, A. Bacher, T. D. Märk, P. Scheier, Free electron attachment to the chloromethane CHCl₃. Int. J. Mass. Spectrom. 2-3/265 (2007), 139-145 doi:10.1016/j.ijms.2007.01.021
    2. S. Denifl, P. Sulzer, D. Huber, F. Zappa, M. Probst, T. D. Märk, P. Scheier, N. Injan, J. Limtrakul, R. Abouaf, H. Dunet, Influence of Functional Groups on the Site-Selective Dissociation of Adenine upon Low-Energy Electron Attachment. Angew. Chem. Int. Ed. 27/46 (2007), 5238-5241 doi:10.1002/anie.200700032
    3. H. D. Flosadottir, S. Denifl, F. Zappa, N. Wendt, A. Mauracher, A. Bacher, H. Jonsson, T. D. Märk, P. Scheier, O. Ingolfsson, Combined Experimental and Theoretical Study on the Nature and the Metastable Decay Pathways of the Amino Acid Ion Fragment [M-H]-. Angew. Chem. Int. Ed. 42/46 (2007), 8057-8059  doi:10.1002/anie.200703327;  german reprint in doi:10.1002/ange.200703327
    4. A. Mauracher, S. Denifl, A. Aleem, N. Wendt, F. Zappa, P. Cicman, M. Probst, T. D. Märk, P. Scheier, H. D. Flosadottir, O. Ingolfsson, E. Illenberger, Dissociative electron attachment to gas phase glycine. Exploring the decomposition pathways by mass separation of isobaric fragment anions. Phys. Chem. Chem. Phys. 42/9 (2007), 5680-5685  doi:10.1039/b709140k
    5. P. Sulzer, A. Mauracher, S. Denifl, M. Probst, T. D. Märk, P. Scheier, E. Illenberger, Probing di-nitrobenzene by low energy electrons. Identification of isomers via resonances in dissociative electron attachment. Int. J. Mass. Spectrom. 1-3/266 (2007), 138-148  doi:10.1016/j.ijms.2007.07.018
    6. P. Sulzer, A. Mauracher, S. Denifl, F. Zappa, S. Ptasinska, M. Beikircher, A. Bacher, N. Wendt, A. Aleem, F. Rondino, S. Matejcik, M. Probst, T. D. Märk, P. Scheier, Identification of Isomers of Nitrotoluene via Free Electron Attachment. Anal. Chem. 17/79 (2007), 6585-6591  doi:10.1021/ac070656b 
    7. F. Zappa, S. Denifl, I. Mähr, J. Lecointre, F. Rondino, O. Echt, T. D. Märk, P. Scheier, Electron impact ionization of thymine clusters embedded in superfluid helium droplets. Europ. Phys. J. D 1-3/43 (2007), 117-120 doi:10.1140/epjd/e2007-00093-9
  • 2006
    1. P.D. Burrow, G.A. Gallup, A.M. Scheer, S. Denifl, S. Ptasinska, T. Märk, P. Scheier, Vibrational Feshbach resonances in uracil and thymine. J. Chem. Phys. 124 (2006) 124310-1-7 doi:10.1063/1.2181570; selected for the Virtual Journal of Biological Physics Research 11 (2006) issue 7
    2. S. Denifl, F. Zappa, I. Mähr, J. Lecointre, M. Probst, T. Märk, P. Scheier, Mass Spectrometric Investigation of Anions Formed upon Free Electron Attachment to Nucleobase Molecules and Clusters Embedded in Superfluid Helium Droplets. Phys. Rev. Lett. 4/97 (2006), 043201-4 doi:10.1103/PhysRevLett.97.043201
    3. S. Feil, M. Winkler, P. Sulzer, S. Ptasinska, S. Denifl, F. Zappa, B. Kräutler, T. Märk, P. Scheier, Single, double and triple ionization of tetraphenyl iron(III) porphyrin chloride. Int. J. Mass Spectrom. 255-256 (2006), 232-238 doi:10.1016/j.ijms.2006.01.032
    4. D. Huber, M. Beikircher, S. Denifl, F. Zappa, S. Matejcik, A. Bacher, V. Grill, T. D. Märk, P. Scheier, High resolution dissociative electron attachment to gas phase adenine. J. Chem. Phys. 8/125 (2006), 084304-7 doi:10.1063/1.2336775; selected for the Virtual Journal of Biological Physics Research 12 (2006) issue 5
    5. I. Ipolyi, P. Cicman, S. Denifl, V. Matejcik, P. Mach, J. Urban, P. Scheier, T. Märk, S. Matejcik, Electron impact ionization of alanine. Appearance energies of the ions. Int. J. Mass Spectrom. 3/252 (2006), 228-233 doi:10.1016/j.ijms.2006.03.009
    6. S. Ptasinska, S. Denifl, S. Gohlke, P. Scheier, E. Illenberger, T. Märk, Decomposition of Thymidine by Low-Energy Electrons. Implications for the Molecular Mechanisms of Single-Strand Breaks in DNA. Angew. Chem. Int. Ed. 12/45 (2006), 1893-1896 doi:10.1002/anie.200503930
    7. P. Sulzer, S. Ptasinska, F. Zappa, B. Mielewska, A. R. Milosavljevic, P. Scheier, T. Märk, I. Bald, S. Gohlke, M. Huels, E. Illenberger, Dissociative electron attachment to furan, tetrahydrofuran, and fructose. J. Chem. Phys. 4/125 (2006), 044304-6 doi:10.1063/1.2222370; selected for the Virtual Journal of Biological Physics Research 12 (2006) issue 3
  • 2005
    1. S. Ptasinska, S. Denifl, P. Scheier, E. Illenberger and T.D. Märk, Bond- and Site-Selective Loss of H Atoms from Nucleobases by Very-Low-Energy Electrons (<3 eV). Angew. Chem. Int. Ed. 44 (2005) 6941–6943 doi:10.1002/anie.200502040
    2. S. Ptasinska, S. Denifl, B. Mroz, M. Probst, V. Grill, E. Illenberger, P. Scheier and T.D. Märk, Bond selective dissociative electron attachment to thymine. J. Chem. Phys. 123 (2005) 124302-1-8 doi:10.1063/1.2035592
    3. S. Ptasinska, S. Denifl, V. Grill, T.D. Märk, E. Illenberger and P. Scheier, Bond- and Site-Selective Loss of H- from Pyrimidine Bases. Phys. Rev. Lett. 95 (2005) 093201 doi:10.1103/PhysRevLett.95.093201, also selected for the Virtual Journal of Biological Physics Research 10 (2005) issue 5


b) Media reports (in german)

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