Real-space Imaging of the Multiple Halogen Bonds by Ultrahigh-resolution Scanning Probe Microscopy

Abstract

Understanding the physical origin of STM/AFM image contrast is of significance for not only promoting surface characterization techniques, but also probing surface nanostructures with the atomic/sub-molecular resolution. Herein, we demonstrate the real-space imaging of halogen bonds acquired by non-contact atomic force microscopy (nc-AFM)/bond-resolution scanning tunneling microscopy (BR-STM) with functional CO-tip, and study the image contrast origin of halogen bonds. The presence of bright line features is associated to the specific site where halogen bond forms, which is experimentally evidenced to be contributed by both CO-tip bending and electron density exchange. Three distinct types of halogen bonds are observed, which origin from the noncovalent interactions of Br-atoms with positive potential H-atom, neutral potential Br-atom and negative potential N-atom, respectively. Our work shows that nc-AFM and BR-STM can directly image halogen bonds and can be used to unambiguously discriminate their bonding features. This work demonstrates the potential use of this technique to image other non-covalent intermolecular bonds and to understand complex supramolecular assemblies at the sub-molecular level.

Coverage Modulated Transformation of the Supramolecular Assembly Structure of Brominated N-Heterocyclic Molecules on Au(111) Surfaces

“…Obvious electron density accumulation (yellow regions in Figure 4c,f) along the direction of both Br•••Br and Br•••H is observed, suggesting the charge transfer between Br atoms and Br atoms/H atoms. Similar results were also reported by Lawrence et al 12 and Wang et al 16 4c is consistent with the typical structure mentioned by Teyssandier et al 10 However, the differential charge density results in Figure 4f show that there are only two Br•••Br halogen bonds and Br•••H hydrogen bonds among every four molecules, which can be attributed to the strong steric hindrance between the benzene ring added in the molecular center and the terminal benzene ring of adjacent molecules, making it difficult to form halogen bonds and hydrogen bonds between molecules at a relatively long distance (4.39 ± 0.2 and 6.02 ± 0.2 Å). In addition, significant electron density accumulation was observed along the H•••N direction, proving that the two H•••N hydrogen bonds (marked by blue dashed lines in Figure 4e) also contribute to stabilizing the supramolecular assembly structure.…”

“…Furthermore, the BR-STM images reveal the formation of the H•••Br hydrogen bonds (marked by green arrows in Figure 2b,d Based on the previous study by Wang et al, 16 we infer that the formation of the Br•••N bond results from the interaction of electron pairs in the N atom with the electron-depleted σ hole at the terminal of the C−Br.…”

“…Halogen bonds and hydrogen bonds possess these properties to different extents, providing different potential nanostructure fabrication pathways. Halogen bonds mainly form by interactions with halogen atoms (e.g., F, Cl, Br, and I) 16 and non-halogen elements (e.g., O and N elements) that act as acceptor sites in heteromolecular combinations. 12,16−18 Imidazole moieties are in many biologically relevant compounds, 19 and their oligomer chains and derivatives are often used to improve effective charge transport due to the strong donor and acceptor functions, which make it easy for imidazole to form hydrogen bonding networks.…”

On-Surface Molecular Recognition Driven by Chalcogen Bonding

“…23 The second aspect that drives flourishing interest for SBIs relies on the orbital mixing, 24 described as n 2 (Y) → σ*(E−X) donation involving nonbonding electrons of the electron-rich Y atom, and the antibonding σ E−X * on the E atom (with X being its covalent substituent). Within the category of SBIs, halogen bonding interactions 25−29 have demonstrated their efficacy in creating regular supramolecular networks on surfaces, 30,31 as revealed by scanning tunneling microscopy (STM) studies highlighting intermolecular Br•••O, 32,33 Br•••Br, 34,35 and Br•••S 36 halogen bonds (Figure 1d) governing the self-assembly. However, chalcogen bonding interactions (ChBIs) 37 have not yet demonstrated comparable effectiveness on surfaces as they have in crystal engineering 38−42 for developing functional materials, 43 such as supramolecular semiconductors.…”

Low-Dimensional Porous Carbon Networks Using Single-/Triple-Coupling Polycyclic Hydrocarbon Precursors

“…37−41 The atomiclevel electronic structure can also be precisely adjusted via heteroatom doping which was demonstrated to tune the conduction and valence bands of 2D porous PHs. 42 These fascinating electronic properties can be achieved by engineering the atomic structure of targeted PHs via a bottom-up synthetic strategy. This strategy bonds small organic building blocks into large PHs using various kinds of covalent bonds.…”