Using real space pseudopotentials to simulate non-contact atomic force microscopy images of organic molecules*

Non-contact atomic force microscopy (nc-AFM) is a popular instrument to visualize the nano world with unprecedented resolution. nc-AFM, with a CO functionalized probe tip, can be used to distinguish different organic molecules, and serves as a very powerful analytical tool in organic chemistry research to identify the molecular structures of reactants, intermediates and products. However, a one-to-one mapping between the functional groups and nc-AFM images is often lacking. We employ a real-space pseudopotential method to simulate nc-AFM images and to provide a “database” for various functional groups, such as -C≡C-, -C=C-, and -C=O. We will also assess new functionalized tips by performing calculations to simulate nc-AFM images.