Molecular motion and bond dissociation are two of the most fundamental phenomena underpinning properties of molecular materials. We have entrapped HF and H2O molecules within the fullerene C60 cage, encapsulated within a single-walled carbon nanotube (X@C60)@SWNT where X = HF or H2O. (X@C60)@SWNT represents a class of molecular nanomaterial composed of a guest within a molecular host within a nanoscale host, enabling investigations of the interactions of isolated single di-or tri-atomic molecules with the electron beam. The use of the electron beam simultaneously as a stimulus of chemical reactions in molecules and as a sub-Å resolution imaging probe allows investigations of the molecular dynamics and reactivity in real time and at the atomic scale, which are probed directly by chromatic and spherical aberration corrected high resolution transmission electron microscopy (Cc/Cs-corrected HRTEM) imaging, or indirectly by vibrational electron energy loss spectroscopy (EELS) in situ during scanning transmission electron microscopy (STEM) experiments.Experimental measurements indicate that the electron beam triggers homolytic dissociation of the H-F or H-O bonds, respectively, causing the expulsion of the hydrogen atoms from the fullerene cage, leaving fluorine or oxygen behind. Due to a difference in the mechanisms of penetration 2 through the carbon lattice available for F or O atoms, atomic fluorine inside the fullerene cage appears to be more stable than the atomic oxygen under the same conditions. The use of (X@C60)@SWNT, where each molecule X is 'packaged' separately from each other, in combination with the electron microscopy methods and density functional theory (DFT) modelling in this work, enable bond dynamics and reactivity of individual atoms to be probed directly at the singlemolecule level.