In the new nanotechnology devices design, the stability of the systems is very important, in the present work we report evidences of internal and external changes of nanoparticles passivated by thiol molecules when they are irradiated under a high flux of an electron beam in the transmission electron microscope. High Resolution images were digitized and processed in order to identify the contrast changes produced by the atomic inside the nanoparticles. Fcc and decahedral nanoparticles cases are shown. Molecular dynamics calculations are also included in order to compare the experimental evidences with the cluster conditions of stabilities. Both theoretical and experimental results imply the occurrence of atomic and twining movements, and indicate that the n-alkyl thiol molecules prevent atomic movement and changes on the particle structure are not observed.