Atomic scale mechanisms of the initiation of chemical processes in energetic molecular crystals leading to the decomposition and ultimately to an explosive chain reaction, are far from being completely understood. We investigated the onset of the initiation processes in two energetic crystals - diamino-dinitroethylene (DADNE, C2H4N4O 4) and triamino-trinitrobenzene (TATB, C6H 6N6O6). We suggest that an autocatalytic decomposition mechanism is likely to take place in DADNE crystal that is built out of corrugated, dashboard-shaped molecular layers, and the level of the induced shear-strain perturbation between the layers strongly depends upon the presence of interstitial NO2 groups. Unlike this, in TATB, which consists of flat, graphite-like molecular layers, an interstitial NO2 group positioned between two layers produces a local molecular orientation disorder and barely affects the C-NO2 decomposition barrier. Split off NO2 groups in the interstitial exhibit a series of exothermic reactions. In DADNE, these reactions start at a lower concentration of interstitial nitro-groups which may be correlated to the higher sensitivity of this material to the initiation as compared to TATB.