Origin of the Contrast Interpreted as Intermolecular and Intramolecular Bonds in Atomic Force Microscopy Images

The origin of the contrast in noncontact atomic force microscopy (NC-AFM) images, which is interpreted as intramolecular and intermolecular bonds, is still under debate. On the basis of the ab initio approach and explicitly including the tilt effect of the flexible CO tip, we reveal that the outermost electron density of the sample dominates the AFM contrast by corrugating of the repulsive force that determines the frequency shift and the lateral behavior of the flexible tip. Consequently, we find that various aspects of bond images in AFM are governed by features of the electron density residing between nuclei; for example, in a π-conjugated system, the brightness of bonds is similar to that of atoms in AFM images due to the gently undulating π electron density; bright lines can arise between two bonded atoms (e.g., in a hydrogen bond) and also between “nonbonded” atoms (e.g., between two Xe atoms) due to the spatial overlapping of the outermost electrons.