ARTICLE
Received 15 Jul 2015 | Accepted 24 Aug 2015 | Published 6 Oct 2015

DOI: 10.1038/ncomms9465

Mechanically activated switching of Si-based
single-molecule junction as imaged withthree-dimensional dynamic probe
Miki Nakamura1, Shoji Yoshida1, Tomoki Katayama1, Atsushi Taninaka1, Yutaka Mera2, Susumu Okada1,
Osamu Takeuchi1 & Hidemi Shigekawa1

Understanding and extracting the full functions of single-molecule characteristics are key
factors in the development of future device technologies, as well as in basic research on
molecular electronics. Here we report a new methodology for realizing a three-dimensional(3D) dynamic probe of single-molecule conductance, which enables the elaborate 3D
analysis of the conformational effect on molecular electronics, by the formation of a Si/single
molecule/Si structure using scanning tunnelling microscopy (STM). The formation of robust
covalent bonds between a molecule and Si electrodes, together with STM-related techniques,enables the stable and repeated control of the conformational modulation of the molecule.
By 3D imaging of the conformational effect on a 1,4-diethynylbenzene molecule, a binarychange in conductance with hysteresis is observed for the ﬁrst time, which is considered tooriginate from a mechanically activated conformational change.

1 Faculty of Pure and Applied Sciences, University of Tsukuba, Tsukuba 305-8571, Japan. 2 Shiga University of Medical Science, Shiga 520-2122, Japan.
Correspondence and requests for materials should be addressed to H.S. (email: hidemi@ims.tsukuba.ac.jp).

NATURE COMMUNICATIONS | 6:8465 | DOI: 10.1038/ncomms9465 | www.nature.com/naturecommunications& 2015 Macmillan Publishers Limited. All rights reserved.

1

ARTICLE

NATURE COMMUNICATIONS | DOI: 10.1038/ncomms9465

T

he understanding of a variety of single-molecule characteristics, such as rectiﬁcation, negative resistance, switching, spin properties and ﬂexibility, has been a major
concept in developing future device technologies, as well as inbasic research on molecular electronics1–23. As pioneering works,
measurements, such as by the break junction method, of metal/
single molecule/metal structures have revealed various intriguing
molecular characteristics9–23. In this decade, the importanceof mechanically activated processes has been recognized
and the study of their effects has been attracting considerable
attention13–18. A new type of mechanism has been proposed
theoretically to explain molecular conductance switching, inwhich mechanically activated dynamic bistability in molecularconformations and its effect on molecular electronic structures
play an essential role17. Towards the understanding andextraction of the full functions of molecules, dynamic analysisof the conformational effect is a key factor.
Here we report a new methodology for realizing a threedimensional (3D) dynamic probe of single-molecule conductance,
which enables elaborate 3D analysis, by the formation of a Si/
single molecule/Si structure using scanning tunnelling microscopy (STM). The formation of robust covalent bonds between amolecule and Si electrodes24,25, together with STM-related
techniques, enables the stable and repeated control of theconformational modulation of the molecule. A binary change in
conductance with hysteresis, which is considered to originate
from a mechanically activated conformational change, is observed
for the ﬁrst time.
Results
3D dynamic probe STM. The 3D measurement system is schematically shown in Fig. 1a. The current I ﬂowing through asingle-molecule junction with a Si STM tip/single molecule/Si
substrate structure was measured with a ﬁxed bias voltage Vs
applied between the STM tip and the substrate, while the STM
tip, which was moved back and forth in the z direction inaccordance with a sinusoidal function, was scanned two-dimensionally (x and y directions) (see Methods section). Figure 1b–d
show an example of data that were acquired over a bare Si(001)surface at 77 K without a molecule between the STM tip and thesubstrate to examine our newly developed system. The blue,
yellow, green and red lines in Fig. 1b indicate the x and y scans,z modulation and current, respectively. Figure 1c shows a magniﬁcation of Fig. 1b. The data in the light blue region in Fig. 1b(21  21  200 measurement points in the x, y and z directions)were analysed and are shown in Fig. 1d. Here the equicurrent
surfaces of It ¼ 1.5, 2.5 and 3.5 nA are shown in the central cube.

Current lxyz modulation

xz

yz

Tip
yz

Tip positional contol

y

xz

x
x

y
z

xy

Substrate

5
4

Current I (nA)

Current I (nA)

10

5

0.1
0
–0.1

10

5
y

0

20

40
Time (s)60

5Approach4

Retract

3
2
1

0

0

2
xy

Current I (nA)

–0.1x,y (nm)x,y (nm)

0

1.0
0.5
0.0
–0.5
–1.0

z (nm)

0.1

z (nm)

1.0
0.5
0.0
–0.5
–1.0

3

xz

yz

Current I (nA)

Time

39.6

39.7

39.8

x

Time (s)

1 nm

–0.10

0.00
z (nm)

0.10

Figure 1 | 3D measurement system and results for Si(001) surface. (a) Schematics of measurement setup (left) and tip control scheme. The STM tip,which was moved back and forth in the z direction in accordance with a sinusoidal function (green), was scanned two-dimensionally in the x (blue) andy (yellow) directions, as shown in the scheme. (b,c) Change in current (red) obtained for a Si(001)-c(4  2) surface and its magniﬁcation. Measurement
was carried out over a scanning range with Dx, Dy and Dz ¼ 2, 2 and 0.2 nm, respectively, at 21  21  200 mesh points. (d) 3D map of acquired current.
The equicurrent surfaces of It ¼ 1.5, 2.5 and 3.5 nA are shown in the central cube. The cross-sectional xy, yz and zx planes show 2D maps of the current
obtained at the 21  21 (xy plane) and 21  200 (yz and zx planes) mesh points on the plane indicated by the arrows and the green frames drawn on thecube, where, for example, xym and xykindicate that the data in cross sections were obtained while the STM tip was retracted from and made to approach
the Si surface, respectively. (e) STM image and schematic of a surface with a c(4  2) phase, whose structural model is also drawn in the xym plane in d.
(f) Tunnelling current as a function of the STM tip-substrate distance. The cross sections of xzm and yzm are similar to those of xzk and yzk, respectively.
2

NATURE COMMUNICATIONS | 6:8465 | DOI: 10.1038/ncomms9465 | www.nature.com/naturecommunications& 2015 Macmillan Publishers Limited. All rights reserved.

ARTICLE

NATURE COMMUNICATIONS | DOI: 10.1038/ncomms9465

Sample preparations. After the system was examined using abare Si surface, we carried out similar 3D measurements to study
the effect of different molecular conformations on single-molecule conductance. We realized a robust single-molecule junction
by forming rigid Si–C bonds between a molecule and electrodesconsisting of a Si STM tip and a Si substrate (see Methods section)27–29. 1,4-divinylbenzene (DVB) and 1,4-diethynylbenzene(DEB) schematically shown in Fig. 2a,b, respectively, were chosen
as the single molecules to examine the conformational effect on
the electronic structures. The double and triple bonds at bothends of the DVB and DEB molecules, respectively, make themsuitable for the study of Si/single molecule/Si junctions and forthe comparison of results. Isolated DVB or DEB molecules wereprepared on a H-terminated Si(001) surface. On the basis of thereaction reported in previous papers for styrene andphenylacetylene molecules on H–Si(001)30,31, an adsorbed DVB

a

b

DVB
CH2

3D imaging of molecular dynamics. Figure 3a,c show 3D mapsof the data shown in Fig. 3b,d, respectively. Here the equicurrent
surfaces of It ¼ 2.5 and 40 nA are drawn in the cubes corresponding to the DVB (Fig. 3a) and DEB (Fig. 3c) molecules,
respectively. The equicurrent surfaces are almost smooth andhave a roughly hemispherical contour, which is different from the
3D map obtained for the bare Si surface without a moleculeshown in Fig. 1d. As can be seen in the cross sections, the change
in current owing to z modulation is smooth for both molecules
over the scanning range, indicating a reasonably smooth change
in the conductance caused by the structural change in this range.
The smooth change in current obtained at neighbouring measurement points over the surface indicates the high reproducibility of this process.

e

DEB
HC

H2C

(DEB) molecule is considered to be tilted from the direction
normal to the Si(001) substrate surface, as shown in Fig. 2c,d. The
difference in the molecular height in the STM image observed
when using DVB and DEB shown in Fig. 2e indicates a differencein the conductance of these molecules depending on the existenceor nonexistence of double bonds in the junction31. A Si STM tip/
single molecule/Si substrate junction was formed by the point
contact method11 (Methods section). Stable contact between the
STM tip and the DVB or DEB molecule was conﬁrmed by theabrupt change in current (Fig. 2f) and the repeatability of I–V
curve measurement (Fig. 2g). Although these measurements werecarried out at room temperature, similar I–V curves were stably
reproduced in measurements, showing the reliability of thefollowing analysis. Hereafter, measurements were carried out at
78 K (see Methods section).

CH

0.5 nmThe cross-sectional xy, yz and zx planes obtained at the positions
indicated by the red arrows and green frames drawn on the cube areshown together, in which arrows such as xym and xykindicate thatthe data in the cross sections were obtained while the tip was
retracted from and made to approach the Si surface, respectively.
For the cross sections, all the data in each plane were used to
produce each map with the color scale. Figure 1e shows an STM
image obtained for a Si surface with a c (4  2) phase; its structuralmodel is also drawn in the xym plane in Fig. 1d (ref. 26). As
expected, the three equicurrent surfaces in the cube in Fig. 1d areparallel to the Si surface except for the c(4  2) atomic structure, andsimple exponential decay of the tunnelling current was observedwith increasing tip-sample distance along the z direction (Fig. 1f).

DB
DVB
DEB

DB

0

DB
B

DV

10 nm

c

10 nm

2
4
6
Cross section (nm)

8

0.2
0.1
z (nm)

0–1
01
Bias voltage (V)2fCurrent I (nA)

B
DE

100

50

0
0.3

d
g

DB

DB

Current I (nA)

300
200
100
0
–2

Figure 2 | Si/single molecule/Si junction. (a,b) STM images of H-terminated Si(100) (H-Si(100)) surface after dosing small amount of DVB and DEB
molecules at room temperature, respectively. (c,d) A Si/DVB (DEB) molecule/Si junction was formed via the approach of a Si STM tip toward an isolated
DVB/DEB molecule after conﬁrming the sufﬁcient isolation by STM. The double (triple) bond at the free end of the DVB (DEB) molecule covalently reacts
with Si-dangling bond (Si-DB) on the STM tip. (e). Cross sections obtained for DB, and for DVB and DEB molecules. (f). Current as a function of the STM
tip-substrate distance, where the jump in current indicates the formation of a bond. (g) Twenty I–V curves repeatedly measured for a DEB molecule. Here allmeasurements were carried out at room temperature.
NATURE COMMUNICATIONS | 6:8465 | DOI: 10.1038/ncomms9465 | www.nature.com/naturecommunications& 2015 Macmillan Publishers Limited. All rights reserved.

3

ARTICLE

NATURE COMMUNICATIONS | DOI: 10.1038/ncomms9465

a

c

xy

xz

yz

xy

yz

xz

xz

yz

yz

0

0.08
0.04

xz

0

xy
3
2

xzz

1

0.05
0.05
0
0
)
y ( –0.05 –0.05
nm
(nm
x
)

yz

xy

d

6
4
2
2

4
6
Time (s)x,y (nm)

0.10
0

0.0

–0.10

–0.1

–0.10
Current I (nA)

Current I (nA)

0.1

100
50
0
0

8

z (nm)

0.10
0.05
0
–0.05

0.2
0.1
0.0
–0.1
–0.2

z (nm)

x,y (nm)

b

0

40
20

xy

0

60
xz

Current / (nA)

yz

80

xy

–0.1
0
0.1 (nm)x

Current I (nA)

–0.1
y( 0
nm 0.1)z (nm)

0.02

z (nm)

0.04

4

8Time (s)12Figure 3 | 3D dynamic measurement using Si/DVB(DEB)/Si single-molecule junctions. (a,b) and (c,d) are 3D maps and their raw data obtained for DVB
and DEB molecules, respectively. Here the equicurrent surfaces of It ¼ 2.5 and 40 nA are drawn in the cubes corresponding to DVB and DEB molecules,
respectively.

The intensity of the current observed for the DEB molecule
was one order larger than that for the DVB molecule, as
shown in Fig. 3b,d, which is consistent with the above
mentioned fact that a double bond remained at both ends ofthe junction in the case of the DEB molecule, producing a higher
conductance. Experiments carried out for 220 DVB molecules
showed the smooth change in the current shown in Fig. 3b,din this scan range. In contrast, another type of change in
conductance was observed in 20% of the measurements using 103
DEB molecules.
Binary change in conductance with hysteresis. Figure 4 shows
an example of the other type of change observed for the DEB
molecules. Figure 4a shows a 3D image of the data in Fig. 4e.
Figure 4b–d show magniﬁcations of the three regions of Fig. 4e.
As shown in Fig. 4c,d, there are two different states producing
two different currents. In addition to the smooth change incurrent while remaining in the two states, an abrupt change incurrent between the two states was observed during z modulation,
as shown in Fig. 4b, which can be clearly seen as the abruptchange between the blue and yellow colours in the xz and yz crosssections in Fig. 4a.
Furthermore, the difference in the positions where the abruptchange occurs, for example, between the yzm and yzk crosssections, indicates the existence of hysteresis in this process.
Namely, the abrupt change occurs at different z positions when
the STM tip is being retracted from and made to approach thesubstrate. Figure 4f shows an example obtained at the position
4

marked by the red small triangles on the yzm and yzk crosssections. In Fig. 4a, the equicurrent surfaces of I ¼ 20 nA for the
STM tip being retracted (red) and approached (grey) are shownin the cube. The distance between the two equicurrent surfaces
shows the characteristic of hysteresis over the surface.
To clarify the origin of the observed change in current, we
obtained I–V curves as a function of z modulation (see Methods
section). Figure 4g shows a color scale graph of a seriesof I–V curves, which shows the change in the initial point where
the I–V curves start to rise. A change in the I–V curves that
depended on the electrode-gap distance, that is, the existence ofthe two states, is clearly observed. Figure 4h shows typical I–V
curves obtained at two different electrode-gap distances(A and B in Fig. 4g), where the rising point is different
for the two states, as shown in the logarithmic plot in the inset.
On the basis of the results of the theoretical analysis of thejunction with semiconductor electrodes, in which the existence ofa band gap affects the conductance characteristics differently
from the cases of metal electrodes32,33, the difference in the rising
point of the I–V curve is considered to reﬂect the difference in theposition of lowest unoccupied molecular orbital (LUMO)/highest
occupied molecular orbital energy level29,34 and the dominantcurrent is caused by the LUMO level in the case of the DEB
molecule27. The observed phenomena are consistent with theresults of analysis. The slight asymmetry in the I–V curves is
considered to be produced by the STM tip and the substrate in
the junction.
The observed binary switching of conductance between thetwo current states is based on the robust Si–C covalent bonds

NATURE COMMUNICATIONS | 6:8465 | DOI: 10.1038/ncomms9465 | www.nature.com/naturecommunications& 2015 Macmillan Publishers Limited. All rights reserved.

ARTICLE

NATURE COMMUNICATIONS | DOI: 10.1038/ncomms9465

f

xy

xz

yz
10

Current I (nA)

30

yz

40
Current I (nA)aApproach20

Retract

0.04
0.02

z (nm)

xz

–0.05

0

0.00
z (nm)

g

–0.02

A

xy

B

0.05

0

Current I [nA)2Bias voltage (V)

–0.04
0.1
0
–0.05
y (nm –0.1
)

0

m)

n

x(

xz

yz

1.0
0
–1.0

xy

b

c

Δz (nm)

0.05

d

0

Current I
(nA)
x,y
(nm)

–0.05

40
30
20
10
0.1

0.1

0.0

0

–0.1
5.5

–0.1

0

Current I
(nA)
x,y
(nm)

0.0

0

–0.1

–0.1

–0.1

0

5

10
Time (s)z (nm)

40
30
20
10
0.1

50

Il I(nA)

13.7

e

100
1

Current I (nA)

8.0 13.5z (nm)

5.7 7.8h

16Time (s)
ΔVth

ΔVth

0.1
–1.4 –1.2 –1.0 0.4 0.6
Bias voltage (V)

0.8

0
A
B

–50

15

–1.0
0
1.0
Bias voltage (V)Figure 4 | Hysteresis characteristics observed for Si/DEB/Si single-molecule junction. (a) 3D map, where the equicurrent surfaces of I ¼ 20 nA for the
STM tip being retracted (red) and approached (grey) are shown in the cube. (b–e) Raw data (e) and magniﬁcations of three parts of e (b–d). (c,d) Show thetwo different states with high and low currents, respectively. (b) shows the change between the two states caused by z modulation. (f) I–z curves measured
for the STM tip being retracted and approached, showing hysteresis, which corresponds to the change at the position marked by the red small triangles on
the xym and xyk cross sections. (g) Color scale image of I–V curves (upper), taken at each step in the z direction (green lines in the lower graph) (seeMethods section). (h) I–V curves obtained at A and B in g. The inset is current in a logarithmic form, ln|I|, which shows the rising point of current. DVthindicates the shift of the rising point of I–V curve.

and has a reproducible hysteresis characteristic. Furthermore,
once a change from a low- to high-current state or from ahigh- to low-current state has occurred during a change in theelectrode-gap distance, the reverse change does not occur
without the opposite change in the electrode-gap distance, evenwhen the bias voltage is changed between  2.0 and þ 2.0 V,
which suggests that the change is not simply induced by
the bias voltage or tunnelling current35–38. Namely, themechanism underlying the observed characteristics is not
simply similar to those proposed in previous works, such as thecontinuous modulation of p orbitals and the change in adsorption
sites on electrodes11,14,39. The DEB molecule originallyhas a symmetric structure similarly to the DVB molecule, as
shown in Fig. 2b. However, the DEB molecule becomesasymmetric on bonding with Si electrodes, that is, it can havecis and trans conformations after losing the triple bonds at bothits ends, as shown in Fig. 5a, which may produce the observed
characteristics.

Theoretical analysis of the binary change. To examine theprocess in more detail, theoretical calculations were carried out(see Methods section). Here a one-dimensional change was
examined. The total energy of the DEB molecule as a function ofelectrode-gap distance (d in Fig. 5a) is shown in Fig. 5c. The
minimum energies of the cis and trans conformations are atelectrode-gap distances of B0.96 nm and B1.0 nm, respectively,
and the two curves intersect, indicating the possibility that strain
induces a conformational transformation from cis to trans andvice versa depending on the electrode-gap distance.
Since n-type Si is used for the STM tip and substrate, when the
LUMO level approaches the conduction band edge of Si, ahigher current is expected via the LUMO level27, as shown
schematically in Fig. 5b. Figure 5d shows the shift in the LUMO
levels of the two conformations as a function of electrode-gap
distance. The LUMO level of the trans conformation for longelectrode-gap distances is lower than that of the cis conformation.
Namely, the LUMO level has a low-current state for the

NATURE COMMUNICATIONS | 6:8465 | DOI: 10.1038/ncomms9465 | www.nature.com/naturecommunications& 2015 Macmillan Publishers Limited. All rights reserved.

5

ARTICLE

NATURE COMMUNICATIONS | DOI: 10.1038/ncomms9465cEnergy (eV)

a

0.5

Cis
Trans

0.4
0.3
0.2
0.1
0.0

d

Cis

Energy (eV)d –1.80
Trans

Cis LUMO
Trans LUMO

–1.85
–1.90
–1.95

1

6

5

–2.00

b

4 2

3

e
LUMO
EF
EC

EV

EV
Si

4
5
3
Current

EF
EC

LUMO

Si
Si
DEB

Si

6

1

2

Potential

DEB

Trans
Cis

0.92

Cis
Trans

0.94 0.96 0.98 1.00 1.02 1.04
Electrode-gap distance

Figure 5 | Results of theoretical analysis on the molecular electronic structures associated with the modulation of electrode-gap distance. (a) Cis andtrans conformations of DEB molecule formed in the Si/DEB molecule/Si junction. The electrode-gap distance d in the direction perpendicular to thesubstrate (indicated by arrows) was changed in steps of 0.01 nm. (b) Schematic illustrations of band structures used to explain the change in tunnellingcurrent. (c) Structural energies of cis and trans conformations calculated using Gaussian 03. (d) Change in LUMO levels for cis and trans conformations as afunction of electrode-gap distance. (e) Schematic showing the change in current (the hysteresis in Fig. 4), where the numbers correspond to those in d.
A potential model for the change is also shown.

cis conformation and a high-current state for the transconformation. The difference in the energy level of LUMO in
Fig. 5d at the electrode-gap distance corresponding to the two
minimum energy points in Fig. 5c (  1.962 eV at B0.96 nm and 2.017 eV at B1.0 nm) is B55 meV, which is consistent withthe shift of the rising point of the IV curve (DVth) shown in
Fig. 4h, B78 meV.
Discussion
A possible structural change that may produce the observed
hysteresis loop and the associated change in current is shown in
Fig. 5e. When the electrode-gap distance is increased from arrow
1 to arrow 3, the conformation changes from cis to trans at the
point indicated by arrow 2, and then back from trans to cis at the
point indicated by arrow 5 with decreasing electrode-gap distance(arrow 4 to arrow 6). Accordingly, the current abruptly increases
with the structural change from the cis conformation to the transconformation (arrow 2), and abruptly decreases when the
structure changes from the trans conformation to the cis
conformation (arrow 5). This change in the electronic structure
is consistent with the experimental result, that is, the change in
conductance with hysteresis shown in Fig. 4. The variation in theswitching point is considered to be due to the stochastic processof the conformational change with a potential energy barrier
shown in Fig. 5e.
The observed positional (x and y) and molecular dependencesof the hysteresis characteristics may be due to the initialconformation of the junctions. For example, the molecules
deposited on a Si substrate have a degree of rotational freedom
along the axis of the Si–C bond before the formation of a bondwith the STM tip apex, and although we veriﬁed the atomic
6

resolution before forming the junction, that is, the quality of the
STM tip, the atomic structure of the Si STM tip apex cannot bewell deﬁned at this stage. To enable further analysis, moredetailed calculations for the 3D conformational change arenecessary, which are left as future work.
In conclusion, a new methodology of realizing the 3D dynamic
probe of single-molecule conductance, which enables elaborate
analysis, was demonstrated. A binary change in conductance withhysteresis, which is considered to originate from a mechanically
activated conformational change, was observed for a DEB
molecule. As a possible mechanism, a cis–trans conformationalchange was discussed. The formation of stable covalent bonds
between a molecule and semiconductor electrodes, together withthe use of high-controllability semiconductor technologies, is
expected to enable both basic research and the fabrication of avariety of molecular devices24,25,28–31,40,41. By choosing suitablemolecules, new functions originating from the ﬂexibility ofmolecules, which solid-state devices themselves may not have,
have the potential to be actively used for the formation of
integrated functions.
Methods
Sample and tip preparation. A STM tip and a substrate were prepared fromthe same n-type Si(001) wafer (As-doped, 0.003±0.001 Ocm). The STM tip cut outof the wafer (B1  3  0.3 mm3), one end of which was cut along a diagonalline, was attached to a Mo holder and cleaned by heating with an electron beam at
B1,100 °C. The Si substrate was cleaned by resistive heating and the qualityof the surface was conﬁrmed by taking STM images, as shown in Fig. 1e. After
conﬁrming the quality of the hydrogen-terminated Si surface by STM, DVB or
DEB molecules (Sigma-Aldrich, 86 and 96% purity for DVB and DEB, respectively)
were deposited on the surface at room temperature. For all measurements, a STM
tip that provides a STM image with atomic resolution, as shown in Figs 1e and 2a,b,
was used.

NATURE COMMUNICATIONS | 6:8465 | DOI: 10.1038/ncomms9465 | www.nature.com/naturecommunications& 2015 Macmillan Publishers Limited. All rights reserved.

ARTICLE

NATURE COMMUNICATIONS | DOI: 10.1038/ncomms9465

Measurements. We have improved the point contact method of STM11 to enable
3D dynamic analysis of the effect of different molecular conformations on the
conductance in a single-molecule junction. In each measurement, we moved the
STM tip towards an isolated molecule from just above it after observing the target
molecule at atomic resolution. The observed current abruptly increases when ajunction is formed. The probability for the formation of a junction was as low as
10% in this experiment, probably owing to the relative positional relationshipbetween the bonds of Si and the molecule, which also reduces the probability of theformation of a multimolecule junction. After conﬁrming the chemical contact
between the STM tip and a DVB or DEB molecule, a 3D dynamic measurement ofconductance was carried out using an Omicron LT-STM at 78 K. Samples were
kept at a 78 K for 2–3 days before measurements to reduce thermal drift. Then, thecurrent I (x, y, z, Vs) measured at each (x, y, z) point (21  21  200 mesh points)
with a bias voltage of Vs was three-dimensionally mapped using a color scaledepending on the purpose, to illustrate the relationship between the 3D molecularconformation and its conductance.
To obtain the I–V curves shown in Fig. 4g, the STM tip was reversibly moved±0.05 nm up and down from the contact point using a step-like function(0.011 nm per step) instead of the sinusoidal function, as shown by the green line in
Fig. 4g. I-V measurement was carried out after each step-like change in theelectrode-gap distance, where the bias voltage was changed between  2.0 andþ 2.0 V in each measurement.
Calculation of electronic structures. The electronic structures of the DEB
molecule in the cis and trans conformations were calculated using Gaussian 03 inthe DFT method with the B3LYP hybrid functional, which is most commonly used
for the analysis of molecular systems42–44, in which the HF functional, Slater
functional and Becke functional based on the generalized gradient approximation43
are used as exchange functionals, and the Lee–Yang–Parr functional and Vosko–
Wilk–Nusair functional are used as correlation functionals. Correlation-consistentpolarization plus valence double-zeta basis sets, which are widely used for the
calculation of molecules adsorbed on Si surfaces44, were used for H, C and Si
atoms.
Both ends of the cis and trans conformations of the DEB molecule were
terminated by SiH3. The molecule was placed at an angle that reproduces theconformation shown in Fig. 2, and the electrode-gap distance in the direction
perpendicular to the substrate (indicated by arrows in Fig. 5a) was changed in stepsof 0.01 nm. The bond length between Si and H was ﬁxed at the 0.148 nm observedin SiH4, and the geometry of the molecule was optimized for each step-like change
in the electrode-gap distance. The structural energy and the position of the LUMO
level were calculated for each optimized structure.

References
1. Aviram, A. & Ratner, M. A. Molecular rectiﬁers. Chem. Phys. Lett. 29, 277–283(1974).
2. Balzani, V., Credi, A. & Venturi, M. Molecular devices and machines. Nano
Today 2, 18–25 (2007).
3. Browne, W. R. & Feringa, B. L. Making molecular machines work. Nat.
Nanotechnol. 1, 25–35 (2006).
4. Joachim, C., Gimzewski, J. K. & Aviram, A. Electronics using hybrid-molecularand mono-molecular devices. Nature 408, 541–548 (2000).
5. Tsutsui, M. & Taniguchi, M. Single molecule electronics and devices. Sensors
12, 7259–7298 (2012).
6. Troisi, A. & Ratner, M. A. Molecular signatures in the transport properties ofmolecular wire junctions: what makes a junction ‘molecular’? Small 2, 172–181(2006).
7. Song, H., Reed, M. A. & Lee, T. Single molecule electronic devices. Adv. Mater.
23, 1583–1608 (2011).
8. Aradhya, S. V. & Venkataraman, L. Single-molecule junctions beyond
electronic transport. Nat. Nanotechnol. 8, 399–410 (2013).
9. Xu, B. & Tao, N. J. Measurement of single-molecule resistance by repeatedformation of molecular junctions. Science 301, 1221–1223 (2003).
10. Elbing, M. et al. A single-molecule diode. Proc. Natl Acad. Sci. USA 102,
8815–8820 (2005).
11. Yasuda, S. et al. Bond ﬂuctuation of S/Se anchoring observed in single-molecule
conductance measurements using the point contact method with scanningtunneling microscopy. J. Am. Chem. Soc. 128, 7746–7747 (2006).
12. Dı́ez-Pérez, I. et al. Rectiﬁcation and stability of a single molecular diode with
controlled orientation. Nat. Chem. 1, 635–641 (2009).
13. Quek, S. Y. et al. Mechanically controlled binary conductance switching of asingle-molecule junction. Nat. Nanotechnol. 4, 230–234 (2009).
14. Bruot, C., Hihath, J. & Tao, N. Mechanically controlled molecular orbitalalignment in single molecule junctions. Nat. Nanotechnol. 7, 35–40 (2011).
15. Rascón-Ramos, H., Artés, J. M., Li, Y. & Hihath, J. Binding conﬁgurations andintramolecular strain in single-molecule devices. Nat. Mater. 14, 517–522(2015).
16. Diez-Perez, I. et al. Controlling single-molecule conductance through lateralcoupling of p orbitals. Nat. Nanotechnol. 6, 226–231 (2011).

17. Franco, I., George, C. B., Solomon, G. C., Schatz, G. C. & Ratner, M. A.
Mechanically activated molecular switch through single-molecule pulling.
J. Am. Chem. Soc. 133, 2242–2249 (2011).
18. Liu, Z. et al. Revealing the molecular structure of single-molecule junctions indifferent conductance states by ﬁshing-mode tip-enhanced Raman
spectroscopy. Nat. Commun. 2, 305 (2011).
19. Schmaus, S. et al. Giant magnetoresistance through a single molecule. Nat.
Nanotechnol. 6, 185–189 (2011).
20. Berg, J. P., Solomon, G. C., Sta, C. A. & Ratner, M. A. Novel quantum interference
effects in transport through molecular radicals. Nano Lett. 11, 2759–2764 (2011).
21. Perrin, M. L. et al. Large tunable image-charge effects in single-moleculejunctions. Nat. Nanotechnol. 8, 282–287 (2013).
22. Perrin, M. L. et al. Large negative differential conductance in single-molecule
break junctions. Nat. Nanotechnol. 9, 830–834 (2014).
23. Vazquez, H. et al. Probing the conductance superposition law in singlemolecule circuits with parallel paths. Nat. Nanotechnol. 7, 663–667 (2012).
24. Vilan, A. et al. Molecules on Si: electronics with chemistry. Adv. Mater. 22,
140–159 (2010).
25. Wolkow, R. A. Controlled molecular adsorption on silicon: laying a foundation
for molecular devices. Annu. Rev. Phys. Chem. 50, 413–441 (1999).
26. Hata, K., Shibata, Y. & Shigekawa, H. Fine electronic structure of the buckled
dimers of Si(100) elucidated by atomically resolved scanning tunnelingspectroscopy and bias-dependent imaging. Phys. Rev. B 64, 235310 (2001).
27. Lu, W., Meunier, V. & Bernholc, J. Nonequilibrium quantum transport
properties of organic molecules on silicon. Phys. Rev. Lett. 95, 206805 (2005).
28. Porphyrin, S., Junctions, S., Ribeiro, F. J., Lu, W. & Bernholc, J. Dopingdependent negative differential resistance in hybrid organic/inorganic Siporphyrin-Si junctions. ACS Nano 2, 1517–1522 (2008).
29. Reuter, M. G., Hansen, T., Seideman, T. & Ratner, M. A. Molecular transportjunctions with semiconductor electrodes: Analytical forms for OneDimensional Self-Energiesf. J. Phys. Chem. A 113, 4665–4676 (2009).
30. Piva, P. G. et al. Field regulation of single-molecule conductivity by a charged
surface atom. Nature 435, 658–661 (2005).
31. Walsh, M. a., Walter, S. R., Bevan, K. H., Geiger, F. M. & Hersam, M. C.
Phenylacetylene one-dimensional nanostructures on the Si(100)-2  1:H
surface. J. Am. Chem. Soc. 132, 3013–3019 (2010).
32. Beebe, J. M., Kim, B., Gadzuk, J. W., Frisbie, C. D. & Kushmerick, J. G.
Transition from direct tunneling to ﬁeld emission in metal-molecule-metaljunctions. Phys. Rev. Lett. 97, 026801 (2006).
33. Araidai, M. & Tsukada, M. Theoretical calculations of electron transport inmolecular junctions: Inﬂection behavior in Fowler-Nordheim plot and its
origin. Phys. Rev. B 81, 1–7 (2010).
34. Choi, J.-K., Pham, H. T. & Jeong, H.-D. A comparative study of electrontransport in benzene molecule covalently bonded to gold and silicon electrodes
for pioneering the electron transport properties of silicon quantum dotmolecule hybrid polymers. Curr. Appl. Phys. 15, 877–884 (2015).
35. Yasuda, S., Nakamura, T., Matsumoto, M. & Shigekawa, H. Phase switching ofa single isomeric molecule and associated characteristic rectiﬁcation. J. Am.
Chem. Soc. 125, 16430–16433 (2003).
36. Donhauser, Z. J. et al. Conductance switching in single molecules throughconformational changes. Science 292, 2303–2307 (2001).
37. Qiu, X. H., Nazin, G. V. & Ho, W. Mechanisms of reversible conformationaltransitions in a single molecule. Phys. Rev. Lett. 93, 1–4 (2004).
38. Dulić, D. et al. One-way optoelectronic switching of photochromic molecules
on gold. Phys. Rev. Lett. 91, 207402 (2003).
39. Ulrich, J. et al. Variability of conductance in molecular junctions. J. Phys. Chem.
B 110, 2462–2466 (2006).
40. Rakshit, T., Liang, G. C., Ghosh, A. W. & Datta, S. Silicon-based molecularelectronics. Nano Lett. 4, 1803–1807 (2004).
41. Guisinger, N. P., Yoder, N. L. & Hersam, M. C. Probing charge transport at thesingle-molecule level on silicon by using cryogenic ultra-high vacuum scanningtunneling microscopy. Proc. Natl Acad. Sci. USA 102, 8838–8843 (2005).
42. Frisch, M. J. et al. Gaussian 03 (Revision B.02) (Gaussian, Inc., Wallingford CT,
2004).
43. Stephens, P., Devlin, F. J., Chabalowski, C. F. & Frisch, M. J. Ab-Initio
calculation of vibrational absorption and circular-dichroism spectra using
density-functional force-ﬁelds. J. Phys. Chem. 98, 11623–11627 (1994).
44. Dunning, T. H. Gaussian basis sets for use in correlated molecular calculations. I.
The atoms boron through neon and hydrogen. J. Chem. Phys. 90, 1007 (1989).

Acknowledgements
H.S. acknowledges the support from Japan Society for the Promotion of Science(Grant-in-Aid for Scientiﬁc Research, 15H05734).

Author contributions
M.N. performed the experiment and data analysis with T.K., in which S.Y. provided
instruction and assistance. S.Y. also worked in developing the three-dimensional control

NATURE COMMUNICATIONS | 6:8465 | DOI: 10.1038/ncomms9465 | www.nature.com/naturecommunications& 2015 Macmillan Publishers Limited. All rights reserved.

7

ARTICLE

NATURE COMMUNICATIONS | DOI: 10.1038/ncomms9465

system. Y.M., A.T. and S.O. examined model simulations. O.T. provided technical advice.
H.S. organized and supervised the project and edited the paper.

Reprints and permission information is available online at http://npg.nature.com/
reprintsandpermissions/

Additional information

How to cite this article: Nakamura, M. et al. Mechanically activated switching of
Si-based single-molecule junction as imaged with three-dimensional dynamic probe.
Nat. Commun. 6:8465 doi: 10.1038/ncomms9465 (2015).

Competing ﬁnancial interests: The authors declare no competing ﬁnancial interests.

8

NATURE COMMUNICATIONS | 6:8465 | DOI: 10.1038/ncomms9465 | www.nature.com/naturecommunications& 2015 Macmillan Publishers Limited. All rights reserved.