Supplementary information

Revealing the Conformational Dynamics in a Single-molecule Junction
by Site- and Angle-Resolved Dynamic Probe Method

Shoji Yoshida, Atsushi Taninaka, Yoshihiro Sugita, Tomoki Katayama, Osamu Takeuchi,and Hidemi Shigekawa
Faculty of Pure and Applied Sciences, University of Tsukuba, Tsukuba 305-8571, Japan1

Fig. S1 Measurement scheme and example of data for BDT/Au(111). a Schematic
illustration of the 3D dynamic probe. b, c Measurement scheme and an example of asignal. A high-conductance signal was obtained above the molecule. d G-z curvesshowing an exponential characteristic. e Volume plot of the 3D dynamic probe dataobtained for a BDT/Au(111) surface before forming a junction (data for STM tipretraction). The cross sections correspond to the frames indicated by the red lines in thevolume plot.

2Fig. S2 Stability of the bond structure at the STM tip apex. The z-dependences of theHC patterns in the xy cross sections obtained for three different scan angles (x- and ydirections) are shown with the angle of the left patterns set to 0°. The dotted lines indicatethe z-dependent positional change. As shown by the images and ∆1 and ∆2, HC patterns
were stably observed for different scan angles, indicating the stability of the bondstructure at the STM tip apex. The high reproducibility of the 3D patterns in xy-planes
reflecting the periodicity of the Au(111) atomic structure indicates that the substrate-side
Auad atom reproducibly changed its position on the Au surface while the STM tip position
was three-dimensionally controlled. In other words, if the bonds at the apex were notstably fixed, the HC pattern would have changed during the measurement, or no stable
patterns would have been obtained. In fact, several scans were necessary to obtain a clear
pattern after a junction was formed. See Fig. S4 regarding the instability of the bondstructure at the STM tip apex.

3Fig. S3 Variations in a volume plot and fitting. a Volume plot shown in Fig. 1h, thecolor scale of which is changed to increase the contrast. When arcs were drawn on the HC
patterns in the xy-plane with the hollow and bridge sites as centers, which were brightly
imaged in experiments, the HC patterns were almost completely reproduced as shown inb to d. The cross sections indicated in red and blue and labeled I to III (experimental) andIS to IIIS (simulated) correspond to the frames indicated by the same letters in the volume
plots shown in d. Three movies have been prepared to show the 3D reproducibility. θ andφ were obtained from the 3D fitting.
movie 1: Movie to show the y-dependence of G in the xz cross section.
movie 2: Movie to show the x-dependence of G in the yz cross section.
movie 3: Movie to show the z-dependence of G in the xy cross section.

4Fig. S4 Transmission pathway (TP) between S and Au atoms. The TP between S andAu atoms, which is formed by the overlap of S-p and Au-d orbitals, is shown by the solid
red lines. Its appearance and disappearance were caused by the change in the distance
between S and Au atoms corresponding to the change in the molecular structure shownin Fig. 4e. The blue dashed lines show other TPs without direct bonds. The angle of theview point here was adjusted to make it easier to see the TPs.

5Fig. S5 Examination of effect of bond structure at STM tip apex in the case of low
G. a Example of a volume plot and G-d curves with one order lower (~0.005) values of
G/G0 despite having G-z curves similar to those shown in Figs. 1 and 2 (G/G0 ~ 0.01 forφ from ~50° to ~80°). For the examples shown in b and c, the direction of bright imageof arc indicated by dashed lines changed alternately with the x-direction of the STM scan,
as schematically shown in d, suggesting a weaker bond structure at the STM tip apex inthis case, allowing the rotation of the molecule around the Auad-Auad axis.

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