cental of the other graphene layer. O atom and the nearest C atom form the C=O bonding with the length of 1.39 ˚ A , smaller than the the length of C-O bonding in the O$_{Bri}$ structure (1.44 ˚ A ). The calculation shows N$_{Hol}$ structure doesn’t exist because of the negative binding energy. Concerning the bilayer distance, with the foreign atom intercalated in the bilayer space, the distance is enlarged for all the investigated systems. Figure 1 displays the ground states for C, N and O configurations, where Fig. 1(b), (c) and (d) are the C$_{Hol}$, N$_{Bri}$, and O$_{Bri}$ structures, respectively. In the C$_{Hol}$ system, the optimized interlayer distance is about 3.39 ˚ A , which is a little larger than the value of 3.34 ˚ A for the pure bilayer graphene. Calculations show that C-C bonding in the upper layer nearly keeps unchanged. The carbon atom which is right below the foreign C is pushed down, forming a “dumbbell” at the saddle point. The foreign C bonds with the adjacent three carbon atoms with bonding length being 1.54 ˚ A , which is a standard length for sp 3 hybridization [20]. In N$_{Bri}$ system, the bilayer distance is enlarged to the value of 3.87 ˚ A , and the length of C-N is 1.43 ˚ A , indicating the chemically adsorption not the physically adsorption. The two carbon atoms bonded with N atom are drawn out of the graphene layer, and the C-C bonding is 1.55 ˚ A , which implies sp 3 hybridization of the two carbon atoms. In O$_{Bri}$ system, bilayer distance is about 3.76 ˚ A , length of C-O bonding is 1.44 ˚ A , and the two carbon atoms bonded with O atom are also drawn out of the graphene layer with the C-C bonding is 1.51 ˚ A . Obviously, N and O atoms have the similar ground state structure. Side-view of the charge distributions for C$_{Bri}$, N$_{Bri}$, and O$_{Bri}$ systems are displayed in Fig. 2. Although C$_{Bri}$ structure is not the ground state for C-intercalated system, we show its charge contour together with those of N$_{Bri}$ and O$_{Bri}$ systems, to provide a clear comparison. We know O atom is lack of two electrons, when it is adsorbed in the bilayer graphene, it strongly interacts with its adjacent carbon atoms and get electrons from them (see the upper panel of Fig. 2). N atom lacks three electrons, it also gets electrons from its adjacent carbon atoms (see the middle panel of Fig.2). C atom lacks four electrons to get saturated, and it tends to share electrons with its adjacent carbon atoms in bilayer graphene (see the lower panel of Fig. 2). All these three atoms show strong interaction with lower graphene layer. Concerning their interactions with the upper graphene layer, judging from Fig. 2, C atom has the strongest interaction with the upper layer, N is the second, and O is the third. We compare the stable positions for C, N and O atoms in monolayer and bilayer graphene, as 4