Changes in the medium of biological cell nucleus under ion beam action is considered as a possible cause of cell functioning disruption in the living body. As the most long-lived molecular product appeared in the cell after the passage of high energy
ions, the hydrogen peroxide molecule is picked out. The possibility of the formation of stable complexes of hydrogen peroxide molecules with active sites of DNA nonspecific recognition (phosphate groups of the double helix backbone) is studied, and the formation of stable DNA-peroxide complexes is considered. Due to the negative charge on the oxygen atoms of DNA phosphate group in solution the counterions that under natural conditions neutralize the double helix have been also taken into consideration. The complexes consisting of oxygen atoms of DNA phosphate group, H$_2$O$_2$ and H$_2$O molecules, and Na$^{+}$ counterion have been considered. Energy of the complexes have been determined based on the electrostatic and van der Waals interactions within the approach of atom-atom potential functions. The stability of various configurations of molecular complexes has been estimated. It has been found that hydrogen peroxide molecules can form the stable complexes with phosphate groups of DNA and counterions which are no less stable than the complexes with water molecules. It is shown that the formation of stable complexes of H$_2$O$_2$--Na$^{+}$--PO$_{4}^{-}$ can be detected experimentally by the observation of specific DNA vibrations in the low-frequency Raman spectra. The interaction of H$_2 $O$_2$ molecule with phosphate group of the double helix backbone can block the processes of DNA biological functioning and induce the deactivation of the genetic apparatus of the cell. Thus, the new channel of high-energy ions action on living cell has been proposed.
