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.