Chemical and steric effects in simulating noncontact atomic force microscopy images of organic molecules on a Cu (111) substrate

摘要: Noncontact mode of atomic force microscopy (nc-AFM) employing a CO-functionalized tip is very powerful tool for studying molecular structures. However, interpreting nc-AFM images nonplanar molecules can sometimes be problematic. To illustrate and resolve the nature such problematic systems, we employ real-space pseudopotentials constructed within density functional theory to simulate images. We focus on several representative organic (pentacene, naphthanthrone, olympicene, 6-phenylhexa-1,3,5-triynybenzene (PHTB)) typical substrate: Cu (111) surface. This substrate results in significant distortions geometries pentacene naphthanthrone. Including these simulated imaging notably improves agreement between measured In relatively large interaction O atom offers straightforward explanation absence $\mathrm{C}=\mathrm{O}$ bond image. Nonplanar features as tilting or twisting are also apparent olympicene PHTB. A ``triangular'' bright feature associated with $\ensuremath{-}\mathrm{C}{\mathrm{H}}_{2}$ group appears directly related angle molecule respect substrate. The ``defective'' benzene ring faint ellipsoidal $\mathrm{C}\ensuremath{\equiv}\mathrm{C}$ PHTB ascribed its twisted nature. ability subatomic reflects accuracy efficiency calculating quantum forces real space.