We analyse the 6.4 keV iron line component produced in the Galactic Center (GC) region by cosmic rays in dense molecular clouds (MCs) and in the diffuse molecular gas. We showed that this component, in principle, can be seen in several years in the direction of the cloud Srg B2. If this emission is produced by low energy CRs which ionize the interstellar molecular gas the intensity of the line is quite small, < 1%. However, we cannot exclude that local sources of CRs or X-ray photons nearby the cloud may provide much higher intensity of the line from there. Production of the line emission from molecular clouds depends strongly on processes of CR penetration into them. We show that turbulent motions of neutral gas may generate strong magnetic fluctuations in the clouds which prevent free penetration of CRs into the clouds from outside. We provide a special analysis of the line production by high energy electrons. We concluded that these electrons hardly provide the diffuse 6.4 keV line emission from the GC because their density is depleted by ionization losses. We do not exclude that local sources of electrons may provide an excesses of the 6.4 keV line emission in some molecular clouds and even reproduce a relatively short time variations of the iron line emission. However, we doubt whether a single electron source provides the simultaneous short time variability of the iron line emission from clouds which are distant from each other on hundred pc as observed for the GC clouds. An alternative speculation is that local electron sources could also provide the necessary effect of the line variations in different clouds that are seen simultaneously by chance that seems, however, very unlikely.
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