Real-space pseudopotential calculations for simulating noncontact atomic force microscopy images

Abstract

Noncontact atomic force microscopy (nc-AFM) with a CO-functionalized tip yields high resolution images under many situations. However, nc-AFM images are sometimes difficult to interpret when visualizing polycyclic aromatic hydrocarbons. The authors employ real-space pseudopotentials constructed using density functional theory to simulate nc-AFM images of benzene and dibenzo(cd,n)naphtho(3,2,1,8-pqra)perylene molecules with selected probe tips (such as CO, H2, N2, Br, and CH2O). The selected tips provide accurate simulations, save for the tip functionalized with a Br atom. The authors find contrast inversion with CO and N2 tips at small tip heights and image distortion with the CH2O tip.

Discrimination of Bond Order in Organic Molecules Using Noncontact Atomic Force Microscopy

“…FDET calculations for the tip were performed following a full DFT run of the sample system and using the Hartree potential, nuclear potential, and the charge density of the sample system as input. Our previous studies have shown the assumption that the tip does not have a significant effect on the structural and electronic properties of the sample is valid for the systems examined here. ,, …”

“…We generate 2D uniform grids over the sample molecule at three different tip heights and compute the total energy of the tip–sample system ( E ts ) at each grid point. In previous work, we verified that the tip–sample force gradient can be taken to be constant within an oscillation cycle. − The relative frequency shift (Δ f ) can be computed from total energy calculations using a three-point central finite difference method , where E –1 , E 0 , and E 1 correspond to the total energy of the tip–sample system at three different heights for each grid point, and h is the separation distance between the planes.…”

“…The noncontact mode keeps the probe tip active for a long time and prevents the sample from degradation. ,, Operating constant height noncontact AFM (nc-AFM) mode in vacuum and at extremely low temperature allows one to reach ultrahigh resolution . Numerous experimental and theoretical studies have shown that submolecular resolution nc-AFM images can be obtained by employing a carbon monoxide (CO)-functionalized tip. − Specifically, nc-AFM experiments with a CO tip are able to distinguish bond orders. − Direct imaging of chemical bonds at submolecular resolution provides a new perspective for characterization of molecular systems.…”

“…We employ a simulation method based on the ab initio real-space pseudopotentials to simulate nc-AFM images. Our previous work has successively simulated some features of nc-AFM images, including contrast inversion, , image distortion, and possibly hydrogen bonding . We simulate nc-AFM images generated with a CO tip for dibenzo­(cd,n)­naphtho­(3,2,1,8-pqra)­perylene (DBNP), hexabenzo­(bc,ef,hi,kl,no,qr)­coronene (HBC), 1,2-bis­[2-(2-ethynylphenyl)­ethynyl]-benzene (BEEB), and 6-phenylhexa-1,3,5-triynylbenzene (PHTB).…”

Atomic Fingerprinting of Heteroatoms Using Noncontact Atomic Force Microscopy

“…The challenge now is to distinguish the N atom. We observe contrast inversion [28][29][30] between C sites and hollow or heteroatom sites. Inversion usually hampers image interpretation; however, here it can be used to identify N from C. We employ a metallic tip composed of a Cu dimer.…”