Using real-space simulations of non-contact atomic force microscopy to distinguish functional groups, atomic species and molecular geometries in organic molecules*

Imaging the internal chemical structure of molecules remains an ongoing challenge. Noncontact atomic force microscopy (nc-AFM) with a CO functionalized probe tip is a powerful tool for molecular structure characterizations. For many organic molecules, the visualization of individual atoms is a real possibility using nc-AFM, save for the complexity of interpreting the measured images. In order to gain a better understanding of such images, we employ real-space pseudopotentials constructed within density functional theory code, PARSEC, to simulate nc-AFM images. We are able to discriminate functional groups (such as -C≡C-, -CH₂ and -C=O groups) and heteroatoms (such as O, N and S atoms) in organic molecules by mapping our simulated images to experimental images. Also, we find that nc-AFM is capable of directly visualizing the orientation of organic molecules at varies adsorption sites on metal substrates.