Real-Space Investigation of the Multiple Halogen Bonds by Ultrahigh-Resolution Scanning Probe Microscopy

Result of the Month

The chemical bond is of central interest in chemistry, and it is of significance to study the nature of intermolecular bonds in real-space. Herein, non-contact atomic force microscopy (nc-AFM) and low-temperature scanning tunneling microscopy (LT-STM) are employed to acquire real-space atomic information of molecular clusters, i.e., monomer, dimer, trimer, tetramer, formed on Au(111). The formation of the various molecular clusters is due to the diversity of halogen bonds, and AFM images clearly show bright line features at the specific sites where halogen bond forms. DFT calculation also suggest the formation of three distinct halogen bonds among the molecular clusters, which originate from the noncovalent interactions of Br-atoms with the positive potential H-atoms, neutral potential Br-atoms and negative potential N-atoms, respectively. This work shows that nc-AFM and BR-STM can directly investigate halogen bonds in real-space and can be used to unambiguously discriminate their bonding features. This work demonstrates the potential use of this technique to study other non-covalent intermolecular bonds and to understand complex supramolecular assemblies at the sub-molecular level.

Figure 1. Atomic structure of a single 2-TBQP molecule. (a) Atomic structure of 2-TBQP molecule. (b) Atomic resolution nc-AFM image of a single 2-TBQP molecule on Au(111) acquired with a CO-modified tip, set-point: V = 50 mV, I = 20 pA, tip height Z = -0.1 Å and oscillation amplitude A = 40 pm.

Figure 1 displays atomic structure of a 2-TBQP molecule. The 2-TBQP molecule is a planar polycyclic hydrocarbon with four doping nitrogen atoms (red atoms) and four bromine atom terminals (blue atoms). An atomic resolution nc-AFM image of a single 2-TBQP molecule is acquired with a CO-modified tip. Nine benzene rings are clearly imaged with four bright spots at the terminals, corresponding to the four Br-atoms.


LT-STM/nc-AFM measurements were carried out an integrated scanning probe system consists of Scienta Omicron low-temperature scanning tunneling microscopy (LT-STM) combined with non-contact atomic force microscopy (nc-AFM). The LT-STM images were recorded in both constant current/height mode using AFM tip with functional CO molecule, and bias voltages were applied to the sample. For nc-AFM images, the constant-height mode with AFM CO-tip was used to record the frequency shift (Δf) of the qPlus resonator (sensor frequency f0 ≈ 27000 Hz, Q ≈ 25000). All the measurements were performed at 4.2 K under a base pressure better than 10-11 mbar.

Figure 2. Two types of Br-N halogen bonds. (a) Atomic resolution nc-AFM image of type-1 dimer, set-point: V = 60 mV, I = 20 pA, tip height Z = 0.3 Å and oscillation amplitude A = 40 pm. (b) An enlarged nc-AFM image of type-1 dimer, set-point: V = 60 mV, I = 20 pA, tip height Z = -0.2 Å and oscillation amplitude A = 40 pm.

Figure 2 displays a 2-TBQP dimer. Two Br-atoms are observed to be adjacent to two N-atoms, respectively. An enlarged nc-AFM image in Figure 2b shows that a bright line (labeled by a red arrow) between the adjacent Br-N atoms appears. Three bright lines (labeled by blue arrows) are also observed at the vicinity of the Br-N bright line, which connects three series of Br-H atoms, respectively.

Figure 3. A 2-TBQP trimer stablized by the combination of Br-Br and Br-N halogen bonds. (a) LT-STM image and (b) high-resolution nc-AFM image (c) molecular packing structure of a 2-TBQP trimer on Au(111), set point: a) V = 100 mV and I = 20 pA; b) V= 60 mV, I= 20 pA, tip height Z = -0.1 Å and oscillation amplitude A = 40 pm. The blue arrow indicates a Br atom absorption that is adjacent to one nitrogen atom site, and the black arrows indicate the Br-Br/Br-H and Br-N/Br-H halogen bonds.

Figure 3 displays a 2-TBQP trimer. The trimer forms by the combination of a dimer (stabilized by Br-N/Br-H halogen bonds, as previously discussed) and a third molecule joined via Br-Br/Br-H bonds. The Br-N/Br-H and Br-Br/Br-H halogen bonds are labeled by black arrows. An individual Br-atom (labeled by a blue arrow) adsorbs on the N-atom site of the dimer. We propose that due to steric hindrance arising from individual Br-atom adsorption, a third molecule joins to the dimer via Br-Br/Br-H bonds rather than Br-N/Br-H bonds.

Figure 4. Formation of 2-TBQP tetramer stablized by tetragonal halogen bonds. (a) STM and (b) nc-AFM images of 2-TBQP tetramer on Au(111), set point: a) V = 50 mV and I = 20 pA; b) V=50 mV, I=20 pA, Z=0 Å and oscillation amplitude A = 60 pm; the blue arrows indicate the two kinds of Br-atoms.

Figure 4 displays another self-assembled structure of 2-TBQP tetramer. Figure 4a gives a STM image of the 2-TBQP tetramer. Individual Br-atoms (labeled by blue arrows) adsorb on the periphery of 2-TBQP molecules. Four Br-atoms (labeled by a blue quadrate in Figure 4a) are adjacent, suggesting that the formation of tetragonal Br-Br halogen bonds governs the self-assembled 2-TBQP tetramer. To verify our hypothesis, nc-AFM measurements were carried out. Figure 4b shows a nc-AFM image of the 2-TBQP tetramer, which shows their molecular atomic structure and the real-sapce atom array.

Corresponding author: 

Prof. A. T. S. Wee