Room temperature covalent bonds between bonded silicon oxide layers can be realized by forming surface and subsurface absorption layers followed by terminating outmost bonding surfaces with desired bonding groups prior to bonding. For example, by introducing fluorine into bonding oxide layers and NH2 groups onto surfaces of bonding oxide layers before bonding, bonding energy equivalent to silicon fracture energy (2500mJ∕m2) has been realized at room temperature after storage in air. Fluorine incorporation causes Si–O–Si ring breaking leading to fluorinated oxide formation with lower density, thus facilitating a higher diffusion rate of polymerization by-products and enhanced moisture absorptivity. Results indicate that by-products of the polymerization reaction between NH2 groups on mating surfaces appear to be more easily diffused and dispersed away from the bonding interface by the low density fluorinated oxide than are polymerization by-products of OH groups. This enhanced by-product removal results in covalent bonding at room temperature.