Supplementary Information

Different observations of CO molecules by using the W-tip and the CO-tip

Figure S1. Different STM observations by using a clean W tip and a CO-terminated W tip. (a, b) STM
images (10×10 nm2) of single CO molecules on Cu(111) observed with a W tip at a sample bias of (a) Vs=–
0.5 V and (b) Vs=+0.5 V (I=500 pA). Single CO molecules were observed as dark spots with halo protrusion.
(c) Line profile along the CO molecule in (b) (green line): 2.4±0.5 nm in width and 1.3±0.5 nm in peak-topeak width. The height of the depression from the Cu substrate surface is 24.0±2.2 pm. Z=0 pm is set to theCu substrate surface. X=0 pm is set to the center of the molecule. (d, e) STM images (10×10 nm2) of single
CO molecules on Cu(111) observed with a CO-tip, fabricated by vertical manipulation, at a sample bias of(d) Vs=–0.5 V and (e) Vs=+0.5 V (I=500 pA). Inversely, CO molecules were observed as bright protrusions
with halo depression. (f) Line profile of the CO molecule in (e) (green line): 1.0±0.2 nm in width. Thedepression height is 12±2 pm from the Cu surface. Z=0 pm is set to the Cu substrate surface. X=0 pm is set
to the center of the molecule. (g, h) STM images of a metal-free phthalocyanine H2Pc molecule obtainedwith a clean W-tip and a CO-tip, respectively. The CO-tip shows a C2 symmetry of the molecule, while theW tip does not.

Tip-sample distance by varying sample voltage
The influence of the molecular vibration excited via the electron injection from the STM tip may also beconsidered. From previous studies that used electron energy loss spectroscopy, the vibration of the entire
CO molecule against the surface is known to be approximately 50 meV.1-3
To rule this factor out, we verified this argument by changing the tip-sample distance by varying the samplevoltage. We scanned the adsorbed CO with the CO tip at biases ranging from 50 mV to 10 mV (I=1 nA).
Notably, we did not observe CO hopping in the STM scanning at 50 mV and above. Instead, we observed
the hopping after decreasing the bias gradually in steps of 10 mV (see solid line in Fig. S2a). At 50 mV (seeFig. S2b), the hopping probability below 1% was observed. After decreasing the sample bias, the hopping
probability increased, e.g. at 30 mV, almost 90% of the adsorbed CO molecules on the surface were pushed

by the CO tip (see Fig. S2c), i.e., the observed CO manipulation was not due to the voltage-induced electronexcitation. Upon further lowering the bias voltage to 10 mV, almost all the CO molecules were moved byscanning and therefore, no stationary images of a single CO molecule were captured.
The above behavior is consistent with the hopping induced by dipole–dipole interaction. With STM, owing
to the constant current feedback, bias variation also changed the tip–sample separation as I∝exp[-κ(S0+z)]=
exp[-2(2m(ϕ-eV))1/2/h (S0+z)], where h is the Planck’s constant, m is the electron mass, and ϕ is the barrierheight. The dashed line in Fig. S2a shows the tip–sample separation as a function of the bias voltage
estimated from the above formula. As it can be observed, lowering the bias voltage renders the tip–sample
gap smaller. The higher hopping probability at low-bias voltage can be explained by the enhanced repulsive
interaction owing to a smaller tip–sample gap.

Figure S2. (a) Hopping probability as a function of sample bias (solid line) and tip apex displacement (dashedline) at a constant tunneling current of 1.0 nA. STM images (10×10 nm2) of CO single molecules on Cu(111) scanned with the CO-tip in sequence of the bias voltage of (b) 50 mV to (c) 30 mV, and (d) 50 mV to(e) 10 mV, where the tunneling current was fixed: I=1 nA. The white arrows show the CO-tip scanning
directions, i.e. from bottom to top or vice versa. CO molecules are observed like multiple chains because
together with the scanned CO-tip the CO molecules on the substrate moved. At low biases, the opposing
COs from the tip and the sample repel each other making the chain-like contrast as in (c). At 10 mV, nostationary CO could be observed as the tip-sample are very close together as seen in (e).

DFT calculation model for CO-monomer and CO-pairFigure S3. Sphere models for calculation of electrostatic potential in Fig. 3c. Blue spheres denote Cu atomsof the substrate, forming a (7×7) unit cell (Cu five monolayer stacking). Red spheres denote adsorbed CO
single molecules.

Statistical distribution analysis

Figure S4: Statistical distribution analysis of CO-monomer and CO-pair. (a) Success/fail manipulation
probability. (b) Adsorption site preference after the hopping.

Cu(111) substrate and CO lateral manipulation
After cleaning the Cu (111), an STM topographic image obtained on Cu(111) shows atomic terraces larger
than 100 nm (see Fig. S5a). An enlarged image of the surface shows a hexagonal symmetry of fcc-Cu(111)atomic array (see Fig. S5b). A dI/dV spectroscopy curve averaged more than 100 single curves lowering
signal-to-noise ratio shows a peak at –0.35 eV below the Fermi energy, which energy position corresponds
to the Cu(111) surface state (see Fig. S5c). A chemical-identified tip found three kinds of impurities on thesurface (Fig. S5d), where after further deposition of CO gas at 0.1 L (Langmuir), one of the three started toincrease to about 15 single molecules per 15×15 nm2, thus we confirmed the dark depression to be the COsingle molecule. From line profiles across the dark spots at +0.5 V, depicting electron tunneling from the tip
to the CO molecule’s LUMO orbital, where a bright halo-shaped protrusion with a diameter of ~2.4 nm(height ~5 pm) was observed. The single dark-spot has a depth of ~24 pm, which observation is in good
agreement with previously done experiments.4,5
Further, we succeeded to manipulate these dark spots by using a W tip. Series of STM images are shown inFig. S5e, from (1) to (8), where between each image the W tip was approached (Vs=–50 mV, I=30-35 nA)
and moved lateral direction that we wanted to move the CO molecule, and then the tip was retracted as theoriginal position (Vs=–50 mV, I=1 nA). At the step (8) we made a “smiley” face on the Cu(111) with 11
single CO molecules. Such manipulation process also confirmed that the dark spots are indeed CO.

Figure S5. Cu(111) substrate and CO lateral manipulations. (a) An STM image obtained on the Cu (111)substrate after the cleaning process. (b) Atomically-resolved STM image obtained on the Cu(111). Brightspots correspond to single Cu atoms. (c) dI/dV curve obtained on the Cu(111). (d) Three kinds of dark spots
were found on the cleaned Cu(111) surface. One of these increase by introducing CO gas. (e) STM images
at the same area, where dark spots are adsorbed CO single molecules. Here, we performed lateralmanipulation of the molecule. From (1) to (8), one by one single CO molecules were manipulated and finallyin (8) ‘smiley’ face was fabricated. STM images were obtained at (a) Vs=+0.8 V, I=0.35 nA, (b) Vs=–0.17
V, I=0.73 nA, (d) Vs=–0.5 V, I=1.0 nA, (e) Vs=–0.05 V, I=1.0 nA.

Home-built low-temperature UHV-STM setups

Figure S6. CAD image of our home-built UHV low-temperature STM setup, which consists of introduction,preparation, and STM chambers. Normal STM measurements were performed at 4.6 K with liquid He. Allchambers are in UHV condition (<5×10-8 Pa). Bottom right inset shows STM body and zoomed in CAD
image of sample stage and piezo tube holding the tip. Right inset is the image of Cu(111) single crystal
pinned to a molybdenum sample plate. Bottom left inset shows the CO gas exposure process. CO gas wasleaked inside the STM chamber and the cooling shield was opened to expose Cu(111) for deposition. The
temperature of substrate recorded was around 10 K.

References in Supplementary Information(1) Uvdal, P.; Karlsson, P.-A.; Nyberg, C.; Andersson, S.; Richardson, N. V. On the structure of dense COoverlayers. Surface Science 1988, 202, 1-2, 167-182.
(2) Froitzheim, H.; Ibach, H.; Lehwald, S. Surface vibrations of CO on W(100). Surface Science 1977, 63,56-66.

(3) Held, G.; Schuler, J.; Sklarek, W.; Steinrück, H. -P. Determination of adsorption sites of pure andcoadsorbed CO on Ni(111) by high resolution X-ray photoelectron spectroscopy. Surface Science 1998, 398,1, 154-171.
(4) Gross, L.; Mohn, F.; Moll, N.; Liljeroth, P.; Meyer, G. The chemical structure of a molecule resolved byatomic force microscopy. Science 2009, 325, 1110-1114.
(5) Bartels, L.; Meyer, G.; Rieder, K. –H. The evolution of CO adsorption on Cu(111) as studied with bare andCO-functionalized scanning tunneling tips. Surface Science 1999, 432, 621-626.