Molecular Identification, Bond Order Discrimination, and Apparent Intermolecular Features in Atomic Force Microscopy Studied with a Charge Density Based Method

Abstract

We introduce an efficient method to simulate high-resolution atomic force microscopy (HR-AFM) images with CO probes. Our model explicitly takes into account the charge densities of the sample and the probe for the calculation of the short-range (SR) interaction and retains ab initio accuracy with only two parameters, that are essentially universal, independent of the number of chemical species and the complexity of the bonding topology. The application to molecular images shows a strong dependence on the stoichiometry and bonding configuration that precludes the chemical identification of individual atoms based on local force–distance curves. However, we have identified features in the 2D images and 3D force maps that reflect the highly anisotropic spatial decay of the molecular charge density and provide a way toward molecular identification. The model treats SR and electrostatics interactions on an equal footing and correctly pinpoints the Pauli repulsion as the underlying interaction responsible for the bond order discrimination in C60. Finally, we settle the controversy regarding the origin of the intermolecular features, discarding the effect of the charge redistribution associated with the H bonds, and linking them with the overlap of the wave functions of the atoms that constitute the bond. This overlap creates saddle regions in the potential energy landscape that are sensed by the probe.

Polycyclic aromatic chains on metals and insulating layers by repetitive [3+2] cycloadditions

“…2e, f, h, i) between the monomers. In the AFM data, the area around the N1-atom of the imidazole ring appears darker, similar to previously reported nitrogen-doped nanoribbons on Au(111) 36,37 . The simulated AFM image of a dimeric structure ( Fig.…”

Quantifying the evolution of atomic interaction of a complex surface with a functionalized atomic force microscopy tip

“…To understand the rich contrast features observed in the experimental constant-height images, we performed AFM image simulations with a modified version of the probe particle model 17 . The contribution of Pauli repulsion, obtained by calculating the overlap of the electron densities of tip and sample, is added to the attractive van der Waals component 18 . Additionally, Coulomb interaction is added via a convolution between the electrostatic sample potential and the tip's electron density that were obtained independently from density functional theory calculations (see "Methods" for further details).…”

“…Since then, CO-terminated tips (CO tips) have been widely applied in AFM experiments to study molecular adsorbates [3][4][5][6][7][8][9] and various types of surfaces and adsorbates with atomic resolution [10][11][12][13][14][15] . The interaction of a CO tip with a sample surface is composed of different physical mechanisms, including van der Waals attraction and Pauli repulsion, which can be described by a Lennard-Jones potential 12,16,17 , and electrostatic interaction between the complex electric field of the CO tip and the sample electron density 12,13,18 . Recently, an additional transition from a physisorbed to a chemisorbed interaction state has been discovered in the interaction of CO tips with single iron adatoms adsorbed on a copper surface 19 .…”

Guide for Atomic Force Microscopy Image Analysis To Discriminate Heteroatoms in Aromatic Molecules

“…Therefore, elemental types can be mostly identified according to different degrees of faint or bright contrast relative to carbon ( Figure S2 of the Supporting Information), although electrostatic effects introduced by the presence of heteroatoms should also be considered and, sometimes, are responsible for the distortions of bonding structures, as shown in previous work. 24,26 Substrate Interaction. In addition to the bonding geometries of adsorbed molecules, the interactions with the specific substrate with heteroatoms can significantly affect the AFM imaging contrast.…”

“…20 It remains a challenge to understand the contrast mechanism of the bond-like features in AFM images, which is important in interpreting structures, 21 but still under some controversial debates. 22−24 Recent significant progress in computational studies facilitated the understanding of the imaging data, 25,26 including hydrogen bonds 27 and halogen bonds. 28 Another challenge is the identification of heteroatoms only with AFM without the involvement of STM imaging on insulated NaCl layers, which is not always possible for unknown molecular mixtures after surface deposition.…”