Both the periodic and non-periodic structures of perchlorocoronene (C(24)Cl(12)) crystals were characterized by high-resolution transmission electron microscopy (HRTEM), electron diffraction (ED), electron energy-loss spectroscopy (EELS), and energy-filtered transmission electron microscopy (EFTEM). The HRTEM images at the boundary of the C(24)Cl(12) crystals exhibit the flexibility of defect structures, where molecules align to compensate for the discontinuity between two different domains. Emphasized by the filtered images, it was found that the non-periodic regions are created everywhere with a small electron beam irradiation (similar to 10(6) electrons nm(-2)) and then spread over the entire regions to completely destroy the periodic structures after a higher electron dose (similar to 2 x 10(6) electrons nm(-2)). The effect of the electron beam irradiation was monitored by ED, EELS, and EFTEM, where periodic structures and content elements are well preserved up to 10(6) electrons nm(-2), but chlorine atoms decreased with a much higher electron dose. This is explained by the breakage of the C-Cl bond to detach chlorine atoms, confirmed by energy-loss near the edge structures (ELNES) of carbon pi* peaks and chlorine loss at the edge of the specimen, as well as by theoretical simulation. The detachment of chlorine is localized at the peripheral edge around a hole confirmed by core-loss EFTEM imaging. (C) 2010 Elsevier B.V. All rights reserved.