Revealing the Conformational Dynamics in aSingle-Molecule Junction by Site- and AngleResolved 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, JapanS Supporting Information*

ABSTRACT: Single-molecule junctions have been extensively studied because of their high potential for futurenanoscale device applications as well as their importance inbasic studies for molecular science and technology.
However, since the bonding sites at an electrode and themolecular tilt angles, for example, cannot be determined
experimentally, analyses have been performed assuming thestructures of such interactive key factors, with uncertainties
and inconsistencies remaining in the proposed mechanisms.
We have developed a methodology that enables the probingof conformational dynamics in single-molecule junctions simultaneously with the direct characterization of molecularbonding sites and tilt angles. This technique has revealed the elemental processes in single-molecule junctions, which havenot been clariﬁed using conventional methods. The mechanisms of the molecular dynamics in 1,4-benzenedithiol and 4,4′bipyridine single-molecule junctions, which, for example, produce binary conductance switching of diﬀerent types, wereclearly discriminated and comprehensively explained.
KEYWORDS: molecular electronics, molecular junction, single molecule, scanning tunneling microscopy

I

RESULTS AND DISCUSSION
Three-Dimensional (3D) Dynamic Probe Measurement. Figure 1a schematically shows the 3D dynamic probe
system.10 The current I ﬂowing through a Au scanning tunnelingmicroscopy (STM) tip/1,4-benzenedithiol (BDT)/Au substrate
single-molecule junction was measured, while the STM tip,which was moved back and forth in the z-direction in accordancewith a sinusoidal function (green line), was scanned twodimensionally (x- and y-directions) (see Methods). Figure 1b
shows an STM image of a Au(111) surface with six BDT
molecules deposited on the elbow sites of a herringbone
structure, as indicated by blue arrows, similarly to in a previous
report,11,12 and its schematic conformation is shown in Figure 1c.
The S atoms at both ends of the BDT molecule are terminatedwith a Au atom (adatom) labeled Auad.13,14 A Au/BDT/Au
junction was formed by picking up one of the two Auad atoms
with the STM tip after observing a target molecule (see Methods
and Figure S1).10,15 Figures 1d and 1e show an example of theobtained data, in which the green, blue, and orange lines indicate
the z modulation and x- and y-scans, respectively, and the red line

deas involving the use of individual molecules as active
electronic components to create new functional materials
based on new concepts and/or combining them with, forexample, semiconductor technologies to produce multifunctional devices have been among the central targets of researchers
in recent decades. Single-molecule junctions have been a basic
platform for experimental and theoretical studies.1−3 Mechanically controlled break junctions (MCBJs) and scanningtunneling microscopy break junctions (STM-BJs) have generally
been used to analyze the characteristics of single-moleculejunctions.4,5 However, analyses have been performed assuming
the interactive parameters of conformations such as bonding sites
and molecular tilt angles, resulting in uncertainties andinconsistencies in the proposed mechanisms.6−9 Therefore,
direct approach to experimentally visualize the conformationalparameters is strongly required. Here, we present a methodologythat enables the analysis of conformational dynamics in singlemolecule junctions simultaneously with the direct and systematiccharacterization of molecular bonding sites, tilt angles, anddeformation. The variations of the molecular dynamics in 1,4benzenedithiol and 4,4′-bipyridine single-molecule junctions
were clearly discriminated, and the mechanisms to produce
binary conductance switching of diﬀerent types were comprehensively explained.
© 2016 American Chemical Society

Received: September 16, 2016
Accepted: November 23, 2016
Published: December 2, 2016
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Figure 1. Measurement scheme and data display. (a) Schematic illustration of the 3D dynamic probe. (b) BDT molecules deposited on a Au(111)
surface with the herringbone structure. (c) Schematic of the conformation of a BDT molecule on a Au(111) surface. (d, e) Measurement scheme
and an example of a 3D dynamic probe signal. (f) Typical G−z curves obtained in regions I and II in (e). (g, h) 3D volume plots obtained while theSTM tip was retracted and approached, respectively. The xy, yz, and xz cross sections, corresponding to the frames indicated by the red lines inthe volume plots, are shown together. The Au(111) surface atomic structure is shown at the bottom.

apex (Auad atom) position (x, y, z) relative to its initial position(0, 0, 0) after the junction was formed (see Methods), which
consist of the G/G0 data obtained while the STM tip was
retracted from and made to approach the Au surface,respectively. The cross sections of the xz-, yz-, and xy-planes,
corresponding to the frames indicated by the red lines in thevolume plots, are shown together. Two xy-planes at two diﬀerentz(zH and zL) were found to show z-dependence. For z = zH, thecharacteristic patterns in the brightness (map of G) in the xyplanes showed the periodicity of the Au(111) atomic structure
for the cases of both retraction and approach, as indicated by theunit cell. Although the patterns obtained for STM tip retraction

shows the corresponding change in the normalized conductance
G/G0 (G0 = 2e2/h, where h is the Planck constant). Figure 1f
shows typical G−z curves obtained in regions I and II in Figure
1e. The red and blue G−z curves were obtained, while the STM
tip was retracted from and subsequently made to approach theAu surface, respectively. The G−z curves show nonexponential
characteristics, indicating the formation of a single-moleculejunction (see Figure S1). As shown in Figure 1f, the red and blue
G−z curves have a similar form in region I but exhibit hysteresis
in region II, showing the existence of binary switching of the
conductance for the latter case. Figure 1g,h shows volume plotsin the form of conductance maps as a function of the STM tip
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and approach were similar for a large z(z = zH), a diﬀerence
between them appeared when z decreased. The conductance G
decreased for the case of retraction, as indicated by a change inthe color of the xy-plane into blue for a short z(zL) with site
dependence and as shown in Figure 1g. This produced thehysteresis observed in the G−z curves in case II (Figure 1f),
conﬁrming the existence of site-dependent binary switching of
the conductance with z-dependence. From the high reproducibility of the 3D patterns, the bond structure at the STM tip apex
is considered to have been stable during the measurement (seeFigure S2).
Determining Conformational Parameters from 3D
Volume Plot. The complex variations in G shown in thevolume plot in Figure 1g,h are considered to originate from themultiple factors determining the conformation in the junction,such as the molecular tilt angle,16−18 the site dependence19,20(site hopping), and the deformation of the molecule;21 detailed
information on these parameters is included in the volume plot.
We analyzed the 3D volume plot to determine such parametersexperimentally. Figure 2a,b, respectively, shows the z-dependences of the conductance patterns in Figure 1g,h in more detail.
Three xy-planes at three diﬀerent z(zH, zM, and zL, corresponding
to those marked in the xz cross sections) are shown. In Figure 2b,
the pattern in the xy-plane is schematically drawn in the ﬁgure
below the xy cross sections, which is superimposed on theAu(111) surface structure. When the bright positions, i.e., highconductance (HC) regions, were superimposed on the hollow
sites and on some of the bridge sites on the Au surface, excellent
agreement was obtained. The pattern of the HC regions shifted in
the xy-plane with decreasing z, as indicated by the unit cells andarrows in Figure 2a,b, which produced the z-dependent
trajectories of the bright arcs shown in the xz cross sections.
As shown in the schematic illustrations of the junction in Figure
2c,d, the arcs drawn with the radius equal to the Auad−Auadlength (0.92 nm) with the hollow sites as the centers well
reproduced the (HC) pattern. Namely, when the Auad atom on
the STM tip is at (x, y, z) in the HC regions of the patterns while
the STM tip is moved back and forth, the Auad atom on the otherside is considered to be located on a hollow or a bridge site. The
high reproducibility of the 3D patterns in the xy-planes thatreﬂected 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. From the analysis of the 3Dvolume plot, we can obtain the conformational parameters. H1and H2 and T in Figure 2c,d indicate the hollow and top sites of
the Au surface, respectively. The purple and green curves labeled
H1 and H2 were obtained by drawing arcs with radius equal to theAuad−Auad length with the H1 and H2 sites as the centers,
respectively. When the Auad at the STM tip was on arc H2, theAuad on the surface side was located at the H2 site. While theSTM tip was made to approach to arc H1, the Auad on the surface
side is considered to have moved to the H1 site. Figure 2e shows
the parameters used to represent the molecular conformation ina junction. θ is the angle between the Auad−Auad axis and the⟨121⟩ axis in the xy-plane and φ is the tilt angle of the Auad−Auadaxis from the xy-plane. Here, the schematic was drawn with θ = 0°
for simplicity, and the actual positional relationships between thesubstrate and the STM tip (H1 and H2 positions), θ and φ were
determined by 3D ﬁtting of the arcs to the experimentallyobtained HC regions (see Figure S3 for more detail). Figure 2f
shows the G−z curves shown in Figure 1f with the obtained
values of φ (the best ﬁt for θ was 6° in this case). Conformational

Figure 2. Models used to analyze the variation of G in the volume
plots. (a, b) xz cross sections obtained from the volume plots shownin Figure 1g,h, respectively, and three HC patterns in the xy crosssections obtained at three values of zH, zM, and zL. (c, d) Schematic
illustrations of the models used to analyze the variation of G in thevolume plots. θ and φ are the angles of the Auad−Auad axis from the⟨121⟩ axis in the xy-plane and that from the xy-plane, respectively.
Here, Auad atoms are schematically drawn as small circles, which may
appear to shorten the distance between the STM tip and the Au
substrate in the ﬁgures but does not aﬀect the discussion in the text.
T, H1, and H2 indicate the top site and two hollow sites, respectively.
The purple and green arcs labeled H1 and H2 have radii equal to thelength of the Auad−Auad axis with the H1 and H2 sites as the centers,
respectively. (e) Schematic illustrations showing parameters θ and φ.
(f) The xz cross sections corresponding to those in (a) and (b), andG−z curves obtained for cases I and II shown in (c) and (d).

eﬀects have generally been analyzed by comparing experimental
results with simulations performed assuming the above
parameters in various forms, 6−9 with uncertainties andinconsistencies remaining in previously proposed models;these key factors can now be determined experimentally in thepresent method, which enables the discussion of conformational
dynamics in single-molecule junctions simultaneously with thedirect characterization of molecular bonding sites and tilt angles.
For case I, when the STM tip is retracted, the Auad atom is
considered to move from H1 (φ1 = 54°) to H2 (φ2 = 66°), as
indicated by the blue arrows, which decreases G on the bridge site
because the number of bonds is reduced. After the subsequent
increase in G at the H2 site, it decreases again with increasing z.
For case II (Figures 2e and 3b), the Auad atom is considered tomove from H1 (φ1 = 58°) to H2 (the other hollow site with φ2 =77°) by passing through the T-site between them. A rapid
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Figure 3. Fluctuation in the binary conformations. (a) G−z curves obtained along line III in Figure 2a. (b) Mapping of zapp and zret determined in(a). (c) G−z curves obtained along line IV in (a). Fluctuations were observed between the blue and red lines in case IV. (d) Conductance map
obtained by xy-scan of the STM tip with the value of z kept at z0 in (c). (e) Magniﬁcation of the rectangular area in (d) and cross sections along
AB. The bottom graph shows the step-by-step changes in x. (f−i) The z dependence of HC patterns obtained by xy-scan of the STM tip withrespect to z0 in (c) and (d) (see Figure S2 for z0 < z). ΔH, L indicates the shift of the two unit cells. (j) Schematic illustration of a possible modelfor the binary switching between the high- (coplanar) and low-conductance (out of plane) states.

3a,c. A positional shift of the two states, ΔH,L, is shown in Figure
3g. These results support the existence of conformationdependent binary conductance states, which produce thehysteresis in the G−z curve, in addition to a monotonic increasein G with decreasing z(φ)16 and a site-dependent change in G.
Figure 3j shows a possible mechanism for the binary states,
conformational change between coplanar (high) and out-ofplane (low) structures. The change is considered to be caused byz-dependent strain. The site dependence may be produced by thediﬀerence in the distance between the STM tip and Au surface,depending on the hollow site and top site. For the case of the G−z curve without hysteresis (Figure 2f, case I), the molecularconformation remained in the high-conductance (coplanar) state
independently of z in this region.
Theoretical Simulations of the Conformational
Change. To understand the dynamics in more detail, we carriedout simple simulations of cases I and II, while the STM tip was
retracted as respectively shown in Figure 2c,d (see Methods).
Figure 4a,b and Figure 4c,d show the G−z curves and paths of thecenter of the Auad atom moved in accordance with the simulation
for cases I and II, respectively. The obtained G−z curves closely
reproduced the experimental results. For case II, the conformational change is shown in Figure 4e, with the number of Auad−Au
bonds (Figure 4f) and the rotation angle of the benzene ring
(Figure 4g) shown in Figure 4h. The following were observed:(1) H1 to B: one of the three Auad−Au bonds is broken and G
decreases. (2) B to T: one of the two bonds is broken, and G

site. After the rapid increase in G at H2, it subsequently decreased
again. When the STM tip was made to approach the Au surface
after its retraction, the Auad atom moved along the same path asduring the retraction in case I, while hysteresis was observed incase II, as shown in Figure 2f.
Analysis of the Binary Switching Producing the
Hysteresis in the G−z Curve. A G−z curve with characteristics
between those for cases I and II, i.e., partial hysteresis, appeared atsome STM tip positions, for example, along line III in Figure 2f,
as shown in Figure 3a. Figure 3b shows the maps of zapp and zretdeﬁned in Figure 3a, indicating a change on the T-site andsuggesting the existence of z- and/or site-dependent switching
between binary conductance states with some activation barrier.
In some cases (along line IV in Figure 2f), a ﬂuctuation between
the blue (approach) and red (retraction) lines was observed
during the approach of the STM tip, as shown in Figure 3c. To
observe this instability in more detail, we carried out an xy-scan of
the STM tip with the value of z ﬁxed at z0 in Figure 3c (Figure3d). As shown in the magniﬁed image and the cross section(Figure 3e), the ﬂuctuation occurred between binary states on
the top site. Figure 3f−i shows the z- and scan angle dependencesof the HC patterns with respect to z0 (see Figure S2 for z0 < z).
The area of preferentially staying at the low-G state increased
with decreasing z independently of the scan angle and covered
the entire surface in Figure 3h. Then G increased again in Figure
3i, in which ﬂuctuation occurred at hollow sites. This change in G
corresponds to the changes in the G−z curves shown in Figure
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Figure 4. Conformational change and conductance characteristics in Au/BDT/Au junction obtained by simulation. (a, b) and (c, d) G−z curves
obtained by simulation and schematic illustrations showing the paths of the Auad atom (red open triangles), while the STM tip was retracted asshown in Figure 2c (for case I) and 2d (for case II), respectively. (e) Molecular conformations corresponding to the points shown in (c). (f, g)
Number of Auad−Au bonds, the distance between the S and Au atoms, and the rotation angle α. (h) Coplanar and out-of-plane molecularconformations with the deﬁnition of α.

decreasing φ (region I in Figure 5d), while it decreased to
0.0005 with increasing z (Figure 5f, region III), which, forexample, is caused by the change in the transmission pathway
between the S atom and the surface Au atoms, as explained forthe conformational change in Figure 4e. A possible model that
explains the change in conductance in regions I, II, and III isillustrated in Figure 5g. (1) In region I (φ < ∼ 50°), the benzene
ring is nearly parallel to the Au surface and the interaction
between the π orbital and the surface Au increases, resulting in
the formation of a channel between them with a highconductance exceeding 0.1G0.22 G decreases with increasing z
owing to the reduction of the interaction. (2) In region II (∼50°< φ < 90°), the transmission between the S atom and the surface
Au atoms changes, as explained for the conformational change in
Figure 4e. (3) In region III (φ ∼ 90°), the distance between AuAd
and Au on the electrodes changes. The change in the low-G
region shows a similar characteristic to that reported in a previous
simulation.6 Despite a number of experimental and theoreticalstudies on this prototype single-molecule junction, a wide rangeof conductance of 0.001−0.1G0 order has been reported, and its
relationship with conformational eﬀects is not yet comprehensively understood.6−9,21−24 Here, we presented results obtainedby a methodology of using a three-dimensional dynamic probe,10and such eﬀects were clearly visualized.
3D Dynamic Probe Analysis of 4,4′-Bipyridine SingleMolecule Junction. Finally, for comparison, we carried out
site- and angle-resolved experiments on 4,4′-bipyridine (BPY),
which has been considered to have angle-dependent binary
conductance states for φ < 90°,25 and the results are shown in
Figure 6. Figure 6a−d depicts a volume plot showing the value of
G/G0 and yz cross sections showing the values of G/G0 and Gn,

decreases to its lowest value. (3) T to B: G increases because the
Auad atom forms a second bond (Figure 4f). In addition, theinteraction between the S and Au atoms increases withdecreasing distance between them owing to the rotation of themolecular plane (Figure 4g) from out-of-plane to coplanar
conﬁgurations (Figure 4h) to reduce the conformation energy,
which increases G. (4) B to H2: The formation of a third bondincreases G, but the reduction in the interaction between the S
and Au atoms decreases the conductance. The change in theinteraction between the S and Au atoms, owing to the rotation of
the molecular plane (benzene ring) between the coplanar andout-of-plane conformations, was found to play an important rolein the change in conductance (see Figure S4 for more detail).
Analysis of G−z Curve Over a Wide Range. We can now
discuss the site and angle dependences separately. Figure 5ashows a volume plot obtained by measurement over a wide range(zp−p ∼ 0.58 nm). Figure 5b,c shows xz cross sections obtained
from the volume plot in Figure 5a. We used the normalized Gn(=
(G(x, y, z) − Gavg(z))/Gsd(z) to obtain the G maps without theeﬀect of the strong z-dependence, where Gavg(z) and Gsd(z) are
the conductance averaged over each xy-plane and the standard
deviation of G obtained for each of the xy-planes, respectively.
Figure 5d shows G−z curves obtained for motion over a wide
range of z(zp−p ∼ 0.58 nm). Figure 5e,f shows magniﬁcations ofrectangular areas A and B in Figure 5d, respectively. The
magniﬁcation of the rectangular area A in Figure 5e (region II)
showing the change in G with z (i.e., φ) is similar to those in
Figures 1 and 3. The high reproducibility was obtained whenstable 3D patterns were observed (see Figure S5) for the othercase). As has been pointed out in a previous paper,16,22 the valueof G/G0 markedly increased to the orders of ∼0.1 with
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ACS Nanoregion IV. In contrast to the case of BDT, the change between thebinary states occurs without activation barrier, that is, hysteresis
does not appear. The positional shift in the HC pattern is
considered to be related to the change in the bonding
conformation.

CONCLUSION
In conclusion, the dynamic probe technique that we havedeveloped has revealed the elemental processes in singlemolecule junctions, which have been hidden behind the multiple
factors simultaneously measured in the conventional methods.
The variations of the molecular dynamics in 1,4-benzenedithiol
and 4,4′-bipyridine single-molecule junctions, which, forexample, produce binary conductance switching of diﬀerent
types, were clearly discriminated, showing the high applicabilityof this method for the further development of moleculartechnologies.
METHODS
Sample and Tip Preparation. A clean ﬂat Au(111) surface wasprepared by evaporating Au to a thickness of about 100 nm on a mica
substrate, which was subjected to Ar sputtering (5 min, 1 μA/cm2) andannealing (30 min, 700 K) for 3−5 cycles. Then the Au surface was
exposed to 1,4-benzenethiol (BDT) molecules introduced through avariable leak valve (10 s, partial pressure: 1.0 × 10−6 Pa). The STM tip
was formed by cutting a Au wire (0.3 mm diameter). All measurements
were carried out in vacuum (<5.0 × 10−8 Pa) at 83 K using a lowtemperature STM (Omicron).
Measurement Scheme. After observing a target BDT molecule (VS= 0.2 V, I = +0.2 nA), the feedback was turned oﬀ, and the sample bias
voltage VS was decreased to 10 mV because the bond was unstable athigh bias voltages. Then, the STM tip was moved back and forth in the zdirection in accordance with a sinusoidal function (zp−p = 0.22 nm, 50
Hz), and a two-dimensional scan was carried out for every cycle of zmodulation (x, y, z: 41 × 21 × 200 points in the case of Figure 1) overthe molecule. Without the molecule, an exponential G−z curve wasobserved (Figure S1d), and an STM image of the molecule was obtained
as shown in Figure S1e. To pick up one end of the molecule, the STM tip
was manually made to approach the molecule while observing thechange in G. When the molecule was picked up, a rapid increase in
conductance was observed, and the G−z curve became nonexponential
as shown in Figure 1f. Since the molecular junction was unstable above
the herringbone structure, we moved the junction away from thestructure for measurement. After observing a stable signal, we started
measurement, with the coordinates of the ﬁrst measurement set to (0, 0,0). After cooling the STM unit with liquid nitrogen for over 1 week, thethermal drift over 30 min was reduced, which was suﬃcient time toobtain each 3D volume plot, for which 16 s was required. The eﬀect of
the sample gradient was removed by linear correction.
Simulation. We used Atomistix ToolKit software (version 12. 8.2
Quantum Wise A/S), with density functional theory (DFT) within thelocal density approximation (LDA) using the Perdew−Zunger (PZ)
exchange−correlation function28 to simulate the optimized structures of
the junction and the variation in its conductance while the STM tip was
retracted. A double-ζ basis set was used for all atomic species, and thecutoﬀ energy was set to 100 Ry. The sampling for Brillouin zone
integration was performed at 3 × 3 × 400 k-points. The conductancewas calculated by the nonequilibrium Green’s function (NEGF)
method.29,30 A bias voltage of 10 mV was applied to the electrodes,
assumed to comprise three layers of Au(111). Figure 4d shows
snapshots of the conformational changes while the STM tip was
retracted. In consideration of the adsorption sites of Auad at the STM tip,
the initial values of θ were set to 6° and 20° for cases I and II to simplify
the calculations, respectively. After the structure of the BDT moleculewith the two Auad atoms on both sides was optimized, the distance
between the two Au(111) electrodes was increased by 0.01−0.02 nm ineach step. Structural optimization after each step was carried out for the

Figure 5. Angle-resolved analysis of conformational eﬀect on
conductance for Au/BDT/Au junction. (a) Volume plot. (b, c)
The xz cross sections obtained from the volume plot shown in (a).
We used the normalized Gn(= (G(x, y, z) − Gavg(z))/Gsd(z)) to show
the G maps without the eﬀect of the strong z dependence, where
Gavg(z) and Gsd(z) are the conductance averaged over each xy-plane
and the standard deviation of G obtained for each of the xy-planes.
(d) G−z curves obtained for motion over a wide range of z(zp−p ∼0.58 nm). (e, f) Magniﬁcations of rectangular areas A and B in (d),respectively. (g) Schematic illustrations to show the conformationalchange. A possible model that explains the change in conductance inregions I, II, and III is illustrated.

respectively. As shown in the G−z curve (Figure 6e), binary
conductance states were clearly observed in regions I (High) andIV (Low). However, in contrast to the previous model,25 they
were observed for φ < 90° (region I) and after reaching φ ∼ 90°(region IV) without angle dependence in both cases. Figure 6f−hshows the conductance maps obtained for regions II, III, and IV,
respectively. The HC pattern is similar to that obtained for BDT,
and the conductance is higher at hollow and bridge sites than at
top site.26 As shown in Figure 6g, the image was ﬂuctuated inregion III, and a positional shift occurred, as schematically shownin Figure 6i, as a result of the shift between the two unit cells. A
possible mechanism is shown in Figure 6j. In region I, the change
in the molecular angle does not aﬀect the N−Au angle, and the
conductance is stable. After reaching φ = 90°, a slow change in G
occurs was observed (region II), which is in good agreement withthe result of calculation in ref 27 (Figure 4),26,27 i.e., the gradualdecrease in the transmission caused by the change in the bondstrength weekend by the increase in the N−Au distance. In
region III, ﬂuctuation in the molecular plane occurs because thesteric hindrance between H (3,5- or 3′,5′-) and surface Au atoms
is reduced, resulting in the unstable conductance image shown in
Figure 4f. After the conformational change has been completed, alow-transmission state continues until the bond is broken in
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Figure 6. Angle-resolved analysis of conformational eﬀect on conductance for Au/BPY/Au junction. (a, b) Volume plots obtained, while the STM
tip was retracted and approached, respectively. (c, d) yz-cross sections obtained from the volume plot shown in a showing value of G/G0 and Gn,
respectively. (e) Typical G−z curve. High and Low indicate the two binary conductance states. (f−h) The xy cross sections obtained at three
diﬀerent z points. White and light blue parallelograms indicate unit cells of the bright patterns in regions I and II, respectively. (i) Schematic of
the bright pattern in region I with the two unit cells, showing their shift ΔHC. (j) Schematic illustrations of a possible model for the conformationalchange in the regions I−IV corresponding to those in (e).
BDT molecule with the Auad atom (lower side) while ﬁxing the structureof the upper-side Auad atom (STM tip side) in accordance with theexperimental results (see Figure S2). Although DFT underestimates theenergy gap,1,31 which may result in a larger conductance, the relativechange in conductance is reliable.

eﬀect of bond structure at STM tip apex in the case of low
G (PDF)
Movie 1: The y-dependence of G in the xz cross section(MPG)
Movie 2: The x-dependence of G in the yz cross section(MPG)
Movie 3: The z-dependence of G in the xy cross section(MPG)

ASSOCIATED CONTENT
S Supporting Information*

The following ﬁles are available free of charge. The Supporting
Information is available free of charge via the Internet at . threemovies. The Supporting Information is available free of charge
on the ACS Publications website at DOI: 10.1021/acsnano.6b06278.
Measurement scheme and example of data for BDT/
Au(111), stability of the bond structure at the STM tip
apex, variations in a volume plot and ﬁtting, examination of

AUTHOR INFORMATION
Corresponding Author*E-mail: hidemi@ims.tsukuba.ac.jp.
ORCID

Hidemi Shigekawa: 0000-0001-9550-5148
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Author Contributions(16) Haiss, W.; Wang, C.; Grace, I.; Batsanov, A. S.; Schiffrin, D. J.;
Higgins, S. J.; Bryce, M. R.; Lambert, C. J.; Nichols, R. J. Precisioncontrol of single-molecule electrical junctions. Nat. Mater. 2006, 5, 995−
1002.
(17) Haiss, W.; Wang, C.; Jitchati, R.; Grace, I.; Martín, S.; Batsanov, A.
S.; Higgins, S. J.; Bryce, M. R.; Lambert, C. J.; Jensen, P. S.; et al. Variable
contact gap single-molecule conductance determination for a series ofconjugated molecular bridges. J. Phys.: Condens. Matter 2008, 20,374119.
(18) Diez-Perez, I.; Hihath, J.; Hines, T.; Wang, Z.-S.; Zhou, G.;
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S.Y. worked in developing the 3D control system and data
analysis. Y.S. performed the experiment with T.K., in which S.Y.
instructed and assisted. A.T. considered the model simulations.
O.T. provided technical advice. H.S. organized and supervised
the project and edited the paper with S.Y.
Notes

The authors declare no competing ﬁnancial interest.

ACKNOWLEDGMENTS
S.Y., A.T., O.T., and H.S. acknowledge the ﬁnancial supports
from Japan Society for the Promotion of Science Grant-in-Aid forYoung Scientist (A) (16747650), for Challenging Exploratory
Research (15K13269), and for Scientiﬁc Research (15H02023)
and (15H05734), respectively.
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DOI: 10.1021/acsnano.6b06278
ACS Nano 2016, 10, 11211−11218