Constructing covalent organic nanoarchitectures molecule by molecule via scanning probe manipulation

Constructing low-dimensional covalent assemblies with tailored size and connectivity is challenging yet often key for applications in molecular electronics where optical and electronic properties of the quantum materials are highly structure dependent. We present a versatile approach for building such structures block by block on bilayer sodium chloride (NaCl) films on Cu(111) with the tip of an atomic force microscope, while tracking the structural changes with single-bond resolution. Covalent homo-dimers in cis and trans configurations and homo-/hetero-trimers were selectively synthesized by a sequence of dehalogenation, translational manipulation and intermolecular coupling of halogenated precursors. Further demonstrations of structural build-up include complex bonding motifs, like carbon–iodine–carbon bonds and fused carbon pentagons. This work paves the way for synthesizing elusive covalent nanoarchitectures, studying structural modifications and revealing pathways of intermolecular reactions.

A similar method was used to measure the voltage thresholds for voltage pulse-induced dehalogenation on Cu(111). A CO tip was positioned over the center of an IT molecule with an STM set point of 100 mV and 10 pA. Then, we switched off the STM feedback and lifted up the tip by 200 pm. Finally, the sample voltage was ramped up from 1.5 V until a sudden change in the current channel occurred. A voltage of about 1.9 V led to the deiodination of the IT molecule ( Supplementary Fig. 5). However, the voltage threshold of the first debromination of DBP is difficult to measure with this method because a voltage ramp often induced the lateral motion of DBP molecules before debromination. Instead, we triggered the first debromination by directly applying voltage pulses (2.9 V, 100 ms) above the C-Br bonds at a tip-height determined by the tunneling set point (100 mV, 10 pA). To cleave the second C-Br bond, the same method for deiodination was used and a voltage threshold of about 3.1 V was measured ( Supplementary Fig. 5).

Charge states of free and bound radicals.
As reported in the literature the charge states of molecules can be distinguished by using Kelvin probe force spectroscopy (KPFS), which measures the local contact potential difference (LCPD) between the tip and the sample 1 . Differently charged states of the molecules change the LCPD, which shifts the Δf(V) parabolas vertically and laterally with respect to that of the neutral state. To perform a KPFS measurement, the tip was first positioned above the radical site of a molecule with an STM set point (e.g., 500 mV, 2pA); Then the STM feedback was deactivated and the tip was lifted up by 200 pm; Finally, a Δf(V) spectrum was recorded.
The lateral and vertical shift of the Δf(V) parabolas suggests that the bound states of the T  radical ( Supplementary Fig. 7) and the BP  monoradical ( Supplementary Fig. 19) should be both negatively charged 1 , while the free states should be neutral. Due to their high mobility the molecules tend to shift/rotate away from the tip at high negative and positive sample bias voltages (< −0.5 V and > 1.5 V), which prevents from the record of a wide-range (−1.0 V to 2.0 V) Δf(V) or I(V) spectrum.
Please note that molecules are dominantly found in their bound state (presumably negatively charged). In case a molecule in the bound state was repositioned for a voltage > 1.5 V it was found either in the same state or in the free state (presumably neutral). We rationalize that the electron can tunnel from the molecule into the Cu(111) substrate during the lateral movement of the molecule since we use an NaCl film of only 2ML thickness. In case a molecule in the bound state was repositioned by a voltage of < −0.5 V it usually changed to the free state, which would imply a discharging process, i.e., an electron transfer from the molecule into the tip.
In case a free (presumably neutral) molecule was repositioned for a voltage > 1.5 V it was afterwards often found in the bound state (presumably negative). This would imply a charging process i.e., an electron transfer from the tip into the molecule.

Bond length measurements.
Bond-resolved AFM images often encounter distortions due to the flexibility of the CO molecule at the tip apex, making it difficult to determine reliable bond lengths [2][3][4] . To measure the length of the newly formed C-C bonds between molecules, we first fitted the chemical structures of the monomers onto the AFM images, and then took the distance between two connected carbon atoms as the measured bond length (see red lines in Supplementary Figs. 15 and 26). The measured bond lengths are between 1.21-1.62 Å which are close to the length of sp 2 -sp 2 C-C bonds (about 1.47 Å).
Supplementary Figure 1 | Pristine IT molecules on NaCl(2ML)/Cu(111). a, STM overview after in-situ deposition of IT molecules onto a cold (about 6 K) NaCl(2ML)/Cu(111) surface. b, Zoom-in STM image of the area marked with a red rectangle in a. c, Constant-current AFM frequency shift image recorded simultaneously with b. Imaging parameters: (a-c) 500mV, 1.5 pA. Scale bars, 5 nm (a) and 2 nm (b,c).

Supplementary Figure 2 | High-resolution STM and AFM images of single IT molecules and small molecular clusters on NaCl(2ML)/Cu(111)
. a-d, STM images of a "righthanded" Rsurf (a) and a "lefthanded" Ssurf (b) IT molecule, a noncovalent IT dimer (c) and a noncovalent IT trimer (d). e-l, Constant-height AFM images (e-h) and chemical structures (i-l) corresponding to a-d, respectively. Imaging parameters: (a,b) 600 mV, 1.3 pA. (c,d) 500 mV, 1.3 pA. Tip height offset Δz = 80 pm (e,g,h) and 90 pm (f), relative to 500 mV, 1.3 pA. Scale bar, 1 nm.  Cu(111). A copper tip was exploited to trigger the reactions. The tip was lifted up by 300 pm relative to 500 mV, 2 pA at the center of a molecule. An I(V) spectrum was subsequently recorded (parameters: 1.5-2.3 V, ramp speed of 0.016 V/s, Δz = 300 pm relative to 500 mV, 2 pA, metal tip). A sudden change in current often indicates the dissociation of halogens, which was confirmed by STM imaging. In total, ten DBP molecules and seven IT molecules were counted. The average threshold voltages are very similar for the deiodination of IT (2.14 ± 0.11 V) and the debromination of DBP (2.16 ± 0.06 V) on NaCl(2ML)/Cu(111). The error bars represent the standard deviation. ms, Δz = 300 pm, relative to 500 mV, 2 pA, CO tip) over the diradical. e, A partially debrominated pyrene dimer was formed by a voltage pulse (3.0 V, 10 ms, Δz = 300 pm, CO tip). f, The C-Br bond at the bottom end was cleaved and two Br atoms were left in the vicinity after a few pulses (3.0 V, 10 ms, Δz = 300 pm, CO tip). The third Br atom was out of the frame. g, The PP 2 dimer was moved to another pyrene diradical P 2 by voltage pulses (2.0 V, 10 ms, CO tip). h,i, The PP 2 dimer and the pyrene diradical were relocated by a few voltage pulses (3.0-3.5 V, 10 ms, Δz = 300 pm, CO tip). j, STM image of the covalent trimer formed by a few voltage pulses (3.5 V, 10 ms, Δz = 300 pm, CO tip). k,l, Constant-height AFM images and chemical structures corresponding to f and e, respectively. m,n, STM (m) and constant-height AFM (n) images of the defective trimer d-PPP 3 in j. One of the three Br atoms on the left side was removed beforehand by vertical manipulation. Imaging parameters: (b-j and m) 500 mV, 2 pA. (k,l,n) Tip height offset Δz = 100 pm relative to 500 mV, 2 pA. Scale bar, 1 nm.  Cu(111). A few representative AFM images illustrate the essential steps for the manipulation. a, AFM image of an IT and a DBP molecule. b, AFM image after deiodination of the IT molecule and partial debromination of the DBP molecule by voltage pulses (2.0 V, 10 ms, CO tip). c, A TP  -2 dimer resulted from the crosscoupling between a triphenylene radical and a pyrene radical triggered by a voltage pulse (3.0 V, 10 ms, Δz = 300 pm, CO tip). d, A TPP  -2 trimer resulted from the coupling between a TP  -2 dimer and a pyrene radical triggered by voltage pulses (3.0 V, 10 ms, Δz = 300 pm, I tip). The images are collected from different series. Image d is a copy of Fig. 4e. Tip height offset Δz = 100 pm (a,c) and 90 pm (b) relative to 500 mV, 2 pA. Scale bar, 1 nm. Figure 25 | Adsorption position of a TPP  -2 trimer on NaCl(2ML)/Cu(111). a, STM image of a TPP  -2 trimer with atomic resolution of the surrounding surface. b, The same STM image as a on which a NaCl lattice and molecular models are superimposed. Elements are color-coded: Cl (light green), Na (light blue), C (black), H (grey). Imaging parameters: 500 mV, 2 pA. Scale bar, 1 nm. 2 and TPP  trimers. Molecular models of pyrene diradical and triphenylene radical were first fitted onto the constant-height AFM images. The bond length of the new C-C bonds (red) was determined by the distance between the two carbon atoms connected by a red bond. AFM images a-c are copies of Figs. 3e, 4d and 4e, respectively. Scale bar, 1 nm.