Unique determination of "subatomic" contrast by imaging covalent backbonding

Reducing molecular simulation time for AFM images based on super-resolution methods

Atomic force microscopy (AFM) has been an important tool for nanoscale imaging and characterization with atomic and subatomic resolution. Theoretical investigations are getting highly important for the interpretation of AFM images. Researchers have used molecular simulation to examine the AFM imaging mechanism. With a recent flurry of researches applying machine learning to AFM, AFM images obtained from molecular simulation have also been used as training data. However, the simulation is incredibly time consuming. In this paper, we apply super-resolution methods, including compressed sensing and deep learning methods, to reconstruct simulated images and to reduce simulation time. Several molecular simulation energy maps under different conditions are presented to demonstrate the performance of reconstruction algorithms. Through the analysis of reconstructed results, we find that both presented algorithms could complete the reconstruction with good quality and greatly reduce simulation time. Moreover, the super-resolution methods can be used to speed up the generation of training data and vary simulation resolution for AFM machine learning.

Indications of chemical bond contrast in AFM images of a hydrogen-terminated silicon surface

The origin of bond-resolved atomic force microscope images remains controversial. Moreover, most work to date has involved planar, conjugated hydrocarbon molecules on a metal substrate thereby limiting knowledge of the generality of findings made about the imaging mechanism. Here we report the study of a very different sample; a hydrogen-terminated silicon surface. A procedure to obtain a passivated hydrogen-functionalized tip is defined and evolution of atomic force microscopy images at different tip elevations are shown. At relatively large tip-sample distances, the topmost atoms appear as distinct protrusions. However, on decreasing the tip-sample distance, features consistent with the silicon covalent bonds of the surface emerge. Using a density functional tight-binding-based method to simulate atomic force microscopy images, we reproduce the experimental results. The role of the tip flexibility and the nature of bonds and false bond-like features are discussed.

Whether and under what circumstances chemical bonds could be imaged via force microscopy is a controversial topic. Here authors develop a particular combination of model surface, imaging procedures and simulation approach and discuss possible indications of chemical contrast in imaging data they obtain.

Modelling of 'sub-atomic' contrast resulting from back-bonding on Si(111)-7×7

It has recently been shown that 'sub-atomic' contrast can be observed during NC-AFM imaging of the Si(111)-7×7 substrate with a passivated tip, resulting in triangular shaped atoms [Sweetman et al. Nano Lett. 2014, 14, 2265]. The symmetry of the features, and the well-established nature of the dangling bond structure of the silicon adatom means that in this instance the contrast cannot arise from the orbital structure of the atoms, and it was suggested by simple symmetry arguments that the contrast could only arise from the backbonding symmetry of the surface adatoms. However, no modelling of the system has been performed in order to understand the precise origin of the contrast. In this paper we provide a detailed explanation for 'sub-atomic' contrast observed on Si(111)-7×7 using a simple model based on Lennard-Jones potentials, coupled with a flexible tip, as proposed by Hapala et al. [Phys. Rev. B 2014, 90, 085421] in the context of interpreting sub-molecular contrast. Our results show a striking similarity to experimental results, and demonstrate how 'sub-atomic' contrast can arise from a flexible tip exploring an asymmetric potential created due to the positioning of the surrounding surface atoms.

Simulated structure and imaging of NTCDI on Si(1 1 1)-7 × 7 : a combined STM, NC-AFM and DFT study

The adsorption of naphthalene tetracarboxylic diimide (NTCDI) on Si(1 1 1)-7 × 7 is investigated through a combination of scanning tunnelling microscopy (STM), noncontact atomic force microscopy (NC-AFM) and density functional theory (DFT) calculations. We show that NTCDI adopts multiple planar adsorption geometries on the Si(1 1 1)-7 × 7 surface which can be imaged with intramolecular bond resolution using NC-AFM. DFT calculations reveal adsorption is dominated by covalent bond formation between the molecular oxygen atoms and the surface silicon adatoms. The chemisorption of the molecule is found to induce subtle distortions to the molecular structure, which are observed in NC-AFM images.

Identifying tips for intramolecular NC-AFM imaging via in situ fingerprinting

A practical experimental strategy is proposed that could potentially enable greater control of the tip apex in non-contact atomic force microscopy experiments. It is based on a preparation of a structure of interest alongside a reference surface reconstruction on the same sample. Our proposed strategy is as follows. Spectroscopy measurements are first performed on the reference surface to identify the tip apex structure using a previously collected database of responses of different tips to this surface. Next, immediately following the tip identification protocol, the surface of interest is studied (imaging, manipulation and/or spectroscopy). The prototype system we choose is the mixed Si(111)-7×7 and Ag:Si(111)-(√3 × √3) R30° surface which can be prepared on the same sample with a controlled ratio of reactive and passivated regions. Using an "in silico" approach based on ab initio density functional calculations and a set of tips with varying chemical reactivities, we show how one can perform tip fingerprinting using the Si(111)-7×7 reference surface. Then it is found by examining the imaging of a naphthalene tetracarboxylic diimide (NTCDI) molecule adsorbed on Ag:Si(111)-(√3 × √3) R30° surface that negatively charged tips produce the best intramolecular contrast attributed to the enhancement of repulsive interactions.