Atomic force microscopy contrast with CO functionalized tips in hydrogen-bonded molecular layers: Does the real tip charge distribution play a role?

Abstract

The interplay of van der Waals (vdW), electrostatic (ES), and short-range (SR) interactions on both the intraand intermolecular contrast observed in high-resolution atomic force microscopy (HR-AFM) is explored in a hydrogen-bonded monolayer of triazine molecules. Our efficient model to simulate AFM images uses the three-dimensional (3D) charge distribution of both tip and sample to calculate the ES interaction, takes into account the tilting of the CO molecule, and reproduces with high accuracy density functional theory calculations. In spite of triazine's hexagonal structure, the intramolecular contrast has triangular symmetry, reflecting the charge density of the molecule. Stripelike intermolecular features, which join the molecules in the H-bond directions, originate from the overlap of the charge density of the atoms in neighboring molecules and are sharpened by the CO tilt. We demonstrate the existence of different potential energy surface minima for the CO tilt and discuss its influence on imaging. Our results clearly show that the ES interaction maps represent a local 3D average of the ES potential of the sample weighted by the tip's charge density, while the SR interaction resembles a local 3D average of the charge density of the sample. However, the strong cancellation of both contributions results in a net interaction dominated by the ES and vdW far from the molecules, and by the SR at short distance. This cancellation, which essentially removes the dependence on the detailed charge distribution of the tip, explains why AFM images can be reproduced using only sample properties such as the z component of the electric field and the charge density of the molecule, and the success of simple models that only incorporate pairwise, point-charge interactions.

Surface-controlled reversal of the selectivity of halogen bonds

“…S5) 40 . Since the adsorption conformation reflects the molecule-surface interactions, we also validated the image contrast by AFM simulations with a charge density based method [41][42][43] that some of us recently introduced (Figs. 4f, S8, and S9).…”

“…These halobenzene molecules adsorbed on a triangular arrangement with the halogen atoms on bridge positions and the benzene rings on fcchollow positions are suitable models to accurately reproduce the experimental observations. In addition, we use our recently developed method to simulate high resolution AFM images [41][42][43] . This method is able to produce theoretical AFM images at different heights by constructing a potential using some inputs from previous DFT calculations, essentially the total charge densities of the tip and the sample, and the electrostatic potential of the sample.…”

Imaging Titan’s Organic Haze at Atomic Scale

“…These can be resolved with AFM with atomic resolution; the non-planarity only affects the contrast. Moreover, the presence of N atoms within heterocycles leads to distortions in the AFM images as well as subtle contrast variations along the molecular backbone (Ellner et al 2017;Kocic et al 2016). For a detailed description of the Section 4).…”

“…Model compounds containing different linear alkyl chains and cycloaliphatic moieties were studied in detail previously (Schuler et al 2017b). There are also some studies regarding the AFM image contrast of different heteroatoms in polycyclic hydrocarbons (Ellner et al 2017;Gross et al 2010;Kawai et al 2018;Kocic et al 2016;van der Heijden et al 2016;Zahl & Zhang 2019).…”

“…Importantly, the larger electronegativity of nitrogen compared to carbon results in a different electron density above the atomic species and slightly polar C-N bonds, which is relevant for the apparent distortions in AFM imaging (Ellner et al 2017;Hapala et al 2014;Kocic et al 2016). The images for AP, BAA, and BAC in Figure A2 show molecules adsorbed on bilayer NaCl islands.…”