Site-specific measurement of adatom binding energy differences by atom extraction with the STM

Supramolecular Chemistry: Host-Guest Molecular Complexes

In recent times, researchers have emphasized practical approaches for capturing coordinated and selective guest entrap. The physisorbed nanoporous supramolecular complexes have been widely used to restrain various guest species on compact supporting surfaces. The host-guest (HG) interactions in two-dimensional (2D) permeable porous linkages are growing expeditiously due to their future applications in biocatalysis, separation technology, or nanoscale patterning. The different crystal-like nanoporous network has been acquired to enclose and trap guest molecules of various dimensions and contours. The host centers have been lumped together via noncovalent interactions (such as hydrogen bonds, van der Waals (vdW) interactions, or coordinate bonds). In this review article, we enlighten and elucidate recent progress in HG chemistry, explored via scanning tunneling microscopy (STM). We summarize the synthesis, design, and characterization of typical HG structural design examined on various substrates, under ambient surroundings at the liquid-solid (LS) interface, or during ultrahigh vacuum (UHV). We emphasize isoreticular complexes, vibrant HG coordination, or hosts functional cavities responsive to the applied stimulus. Finally, we critically discuss the significant challenges in advancing this developing electrochemical field.

Peptide Self-Assembly and Its Modulation: Imaging on the Nanoscale

This chapter intends to review the progress in obtaining site-specific structural information for peptide assemblies using scanning tunneling microscopy. The effects on assembly propensity due to mutations and modifications in peptide sequences, small organic molecules and conformational transitions of peptides are identified. The obtained structural insights into the sequence-dependent assembly propensity could inspire rational design of peptide architectures at the molecular level.

Force-Driven Single-Atom Manipulation on a Low-Reactive Si Surface for Tip Sharpening

A single atomic manipulation on the delta-doped B:Si(111)-(√3x√3)R30° surface using a low temperature dynamic atomic force microscopy based on the Kolibri sensor is investigated. Through a controlled vertical displacement of the probe, a single Si adatom in order to open a vacancy is removed. It is shown that this process is completely reversible, by accurately placing a Si atom back into the vacancy site. In addition, density functional theory simulations are carried out to understand the underlying mechanism of the atomic manipulation in detail. This process also rearranges the atoms at the tip apex, which can be effectively sharpened in this way. Such sharper tips allow for a deeper look into the Si adatom vacancy site. Namely, high-resolution images of the vacancy showing subsurface Si dangling bond triplets, which surround the substitutional B dopant atom in the first bilayer, are achieved.

High-resolution scanning tunneling microscopy imaging of Si(1 1 1)-7 × 7 structure and intrinsic molecular states

We review our achievements in exploring the high resolution imaging of scanning tunneling microscopy (STM) on the surface and adsorbates in a ultra-high vacuum system, by modifying the STM tip or introducing a decoupled layer onto the substrate. With an ultra-sharp tip, the highest resolution of Si(1 1 1)-7 × 7 reconstruction can be achieved, in which all the rest atoms and adatoms are observed simultaneously with high contrast. Further functionalization of STM tips can realize selective imaging of inherent molecular states. The electronic states of perylene and metal-phthalocyanine molecules are resolved with special decorated tips on metal substrates at low temperature. Moreover, we present two kinds of buffer layer: an organic molecular layer and epitaxially grown graphene to decouple the molecular electronic structure from the influence of the underlying metallic substrate and allow the direct imaging of the intrinsic orbitals of the adsorbed molecules. Theoretical calculations and STM simulations, based on first-principle density function theory, are performed in order to understand and verify the mechanism of high-resolution images. We propose that our results provide impactful routes to pursue the goal of higher resolution, more detailed information and extensive properties for future STM applications.

Vertical manipulation of native adatoms on the InAs(111)A surface

We achieved the repositioning of native In adatoms on the polar III-V semiconductor surface InAs(111)A-(2 × 2) with atomic precision in a scanning tunnelling microscope (STM) operated at 5 K. The repositioning is performed by vertical manipulation, i.e., a reversible transfer of an individual adatom between the surface and the STM tip. Surface-to-tip transfer is achieved by a stepwise vibrational excitation of the adsorbate-surface bond via inelastic electron tunnelling assisted by the tip-induced electric field. In contrast, tip-to-surface back-transfer occurs upon tip-surface point contact formation governed by short-range adhesive forces between the surface and the In atom located at the tip apex. In addition, we found that carrier transport through the point contact is not of ballistic nature but is due to electron tunnelling. The vertical manipulation scheme used here enables us to assemble nanostructures of diverse sizes and shapes with the In adatoms residing on vacancy sites of the (2 × 2)-reconstructed surface (nearest-neighbour vacancy spacing: 8.57 Å).

Localized deposition of coronene molecules on Si(001)-2x1 using a scanning tunneling microscope tip source

The deposition of coronene molecules from scanning tunneling microscope (STM) tips onto a clean Si(001)-2x1 surface at 25 degrees C was investigated. The STM tips, contaminated with coronene, were found to deposit coronene molecules on the clean Si(001) surface, allowing patterns to be generated. Covalent Si-C chemical bonds, formed between the coronene molecules and the Si substrate, froze the flip-flop motion of the adjacent Si-Si dimers on the substrate. In most cases, the mode of coronene bonding to Si(001) is independent of whether deposition occurs from the gas phase or from the STM tip. Despite the covalent chemical bonds formed between the coronene molecule and the Si substrate, the STM tip can drag the coronene laterally on the Si substrate without inducing a chemical change in the molecule. Sharp spikes observed in the tunneling current during the coronene deposition reflect the abrupt decrease of the tip-substrate distance at the instant of transport of the molecule from tip to surface.

Selective internal manipulation of a single molecule by scanning tunneling microscopy

We have studied the adsorption of the polyaromatic molecule 1,4"-paratriphenyldimethylacetone, which we have nicknamed Trima. The originality of this linear molecule is that it was designed and synthesized to have two functionalities. First, chemisorb itself to the surface by its two ends rather like a bridge. Second, the central part of the molecule could then be rotated by injecting electrons with the tip of the scanning tunneling microscope (STM). The length of the molecule corresponds exactly to the spacing between five dimers in a row on the Si(100)-2 x 1 surface. We found that the molecule adsorbs as expected on the clean silicon surface by using complementary STM and synchrotron radiation studies. Manipulation of individual molecules with the STM tip showed selective internal modifications that were highly voltage dependent. These manipulations were found to be compatible with an electronic excitation of the pi-pi* transition of the molecule.

Mechanical vertical manipulation of selected single atoms by soft nanoindentation using near contact atomic force microscopy

A near contact atomic force microscope operated at low-temperature is used for vertical manipulation of selected single atoms from the Si(111)-(7 x 7) surface. The strong repulsive short-range chemical force interaction between the closest atoms of both tip apex and surface during a soft nanoindentation leads to the removal of a selected silicon atom from its equilibrium position at the surface without additional perturbation of the (7 x 7) unit cell. Deposition of a single atom on a created vacancy at the surface is achieved as well. These manipulation processes are purely mechanical, since neither bias voltage nor voltage pulse is applied between probe and sample. Differences in the mechanical response of the two nonequivalent adatoms of the Si(111)-(7 x 7) with the load applied is also detected.