Nanoscale
PAPER

Cite this: Nanoscale, 2019, 11, 5951

Evolution of local conductance pathways ina single-molecule junction studied using thethree-dimensional dynamic probe method†
Atsushi Taninaka, Shoji Yoshida, Yoshihiro Sugita, Osamu Takeuchi and
Hidemi Shigekawa *Understanding of the dynamics of the bonding states of molecules with electrodes while the molecularconformation is changed is particularly important for elucidating the details of electrochemical devices aswell as molecular devices in which the reaction dynamics of the electrodes and molecules plays animportant role, such as in fuel cells, catalysis and bioelectrochemical devices. However, it has beendiﬃcult to make measurements when the distance between counter electrodes is short, namely, themolecule is raised from a lying form, almost parallel and close to the electrodes, toward a standing form
and vice versa. We previously have developed a method called the three-dimensional (3D) dynamic probe
method, which enables conductance measurement while the conformation of a single-molecule junction
is precisely controlled by scanning tunneling microscopy (STM) techniques. Here, by combining thismethod with density functional theory (DFT) calculations, it has become possible to simultaneously con-

Received 23rd January 2019,
Accepted 1st March 2019
DOI: 10.1039/c9nr00717b
rsc.li/nanoscale

sider the eﬀects of the dynamics of molecular structures and the bonding states at the electrodes on thelocal transmission pathways, local-bond contributions to conductance. Here, by performing an analysis
on 1,4-benzenediamine (BDA) and 1,4-benzenedithiol (BDT) single molecule junctions, we have observed,
for the ﬁrst time, the eﬀect of a change in the molecular conformations and bonding states on the local
transmission pathways for a short Au electrode distance condition.

Introduction
In the design of nanoscale electronic devices making full useof single molecule characteristics, it is essential to elucidate
the relationship between the conformations of single molecules and the conduction properties. Furthermore, understanding of the dynamics of the bonding states of moleculeswith electrodes while the molecular conformation is changed
is particularly important for elucidating the details of electrochemical devices as well as molecular devices in which thereaction dynamics of the electrodes and molecules plays animportant role, such as in fuel cells, catalysis and bioelectrochemical devices.1–4
Such conduction properties of single molecules have beenstudied for various molecules by the break junction (BJ)
method, and valuable results have been obtained.5–17
However, in the BJ method, since the electrodes are connected
and ruptured in each measurement, the junction structure is

Faculty of Pure and Applied Sciences, University of Tsukuba, Tsukuba 305-8571,
Japan. E-mail: hidemi@ims.tsukuba.ac.jp† Electronic supplementary information (ESI) available. See DOI: 10.1039/
c9nr00717b

This journal is © The Royal Society of Chemistry 2019

unknown and it is diﬃcult to analyze whether the change inthe measured conductance corresponds to the change in the
conduction path due to the change in the contact structure orto the change in the transmittance due to the change in themolecular conformation.
Recently, a method that enables conductance measurement
while changing the angle of the molecule to the substrate
without destroying the junction has been developed as a typeof BJ method;6,11,17 however, it is still diﬃcult to analyze thestructure of the bonding states. Since the dynamics of thecontact point between the molecule and substrate aﬀects thescattering of electrons when electrons are injected, it is necessary to simultaneously elucidate the conduction characteristics
and the structures of the bonding states.
We previously developed a method called the three-dimensional (3D) dynamic probe method, which enables conductance measurement while the conformation of a single-molecule junction is precisely controlled by scanning tunnelingmicroscopy (STM) techniques.18–21 By combining this methodwith density functional theory (DFT) calculations, it has
become possible to simultaneously consider the eﬀects of the
dynamics of molecular structures and the bonding states atthe electrodes on the local transmission pathways andconductance.18–20,22–24

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PaperHowever, the measurements in the previous studies werecarried out with a gold STM tip suﬃciently retracted fromthe substrate surface, namely molecules were in a standing
form and thus formed junctions with the electrodes only attheir two ends. When a molecule is in a lying form, almost
parallel and close to the electrodes, the interaction between
the molecule and the substrate is considered to be stronger,
and conduction pathways are considered to exist between
the electrodes via various parts of the molecule instead of asingle flow through the molecule. As the molecule is raised,such direct conduction pathways between the electrodes
begin to break and the bonding state changes into structures
where junctions are formed only at the two ends of themolecule and an influence of the structure peculiar to eachmolecule appears. Although it is very important to understand the conductance properties appearing in such a
dynamic change, as described above, they have not yet been
investigated.
To clarify the change in the bonding states while the molecular conformation is varied from a lying to standing conformation and vice versa, we carried out 3D dynamic probe experiments and DFT simulations on 1,4-benzenediamine (BDA) and1,4-benzenedithiol (BDT) molecules for comparison. BDA andBDT are compounds having one benzene ring. BDA is not connected to Au adatoms on the substrate but its lone pair forms
a bond, which is expected to attract the molecule to the substrate and prevent the rotation of the molecule.19 In contrast,
BDT, one of the simplest molecules which has often been used
for BJ analysis,5,6,8–10,20 forms bonds with the Au adatoms on
both electrodes, which allows rotational motion during a conformational change.20 Understanding of such diﬀerences isimportant for elucidating the details of electrochemical
devices as well as molecular devices in which the reaction
dynamics of the electrodes and molecules plays an importantrole, such as in fuel cells, catalytic actions and bioelectrochemical devices.1–4

Experimental
Sample and tip preparation
A clean flat Au(111) surface was prepared by evaporating Au of
100 nm thickness on a mica substrate that had been subjected
to Ar sputtering (5 min, 1 μA cm−2) and annealing (30 min,
700 K) for 3–5 cycles. Then the Au(111) surface was exposed to
BDA or BDT molecules introduced through a variable leak valve(10 s, partial pressure: 1.0 × 10−6 Pa). The STM tip was formedby cutting a Au wire (0.3 mm diameter). All measurements werecarried out under vacuum (<5.0 × 10−8 Pa) using an Omicron LT
STM system. By cooling the STM unit with liquid nitrogen forover one week, the temperature in the STM chamber was maintained at 83 K and the thermal drift was reduced.
Experimental scheme and measurements
Fig. 1a and b show the schematics of the molecular structuresof BDA and BDT deposited on a Au(111) surface, respec-

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NanoscaleFig. 1 Measurement setup. (a, b) Schematics of the molecular structures of BDA and BDT deposited on a Au(111) surface, respectively.
(c, d) STM images of BDA and BDT molecules on a Au (111) surface, respectively. (e) Schematic of the 3D dynamic probe method. (f ) Schematicof the measurement scheme.

tively.25,26 In BDA, the N atoms connected to the surface sideand the probe (STM tip) side are denoted by NS and Nt,
respectively. On the other hand, BDT adsorbs with a Au
adatom bound to thiol groups at both ends.20 For convenience,
we denote the Au atoms on the substrate side and probe (tip)side as Auads and Auadt, respectively, and the S atoms bonded
to Auads and Auadt atoms are indicated by the slightly smaller
red circles and named SS and St, respectively. Fig. 1c and dshow STM images obtained after the deposition of BDA andBDT molecules on a Au (111) surface, respectively. Similar tothat in previous papers,19,20 it was confirmed that single BDT
and BDA molecules were adsorbed at the elbow sites of theherringbone structure of the Au (111) surface, as shown byyellow arrows.
After observing a target BDA or BDT molecule (VS = 0.2 V,
I = +0.2 nA), the STM tip was moved above it. When the molecule was picked up, a rapid increase in conductance wasobserved. Since the molecular junction was unstable above theherringbone structure, we moved the junction away from thestructure for measurement. Then the feedback was turned oﬀ
and the sample bias voltage VS was decreased to 10 mV
because the bond was unstable at high bias voltages. Then, theSTM tip was moved back and forth in the Z-direction inaccordance with a sinusoidal function (zp–p = 0.224 nm,
50 Hz), and was made to slowly approach the target molecule.
The formation of a junction was confirmed by a rapid increasein current. After the formation was confirmed, the STM tip
was moved back slightly (0.14 nm) to ensure a stable measure-This journal is © The Royal Society of Chemistry 2019

Nanoscale

Paper

Fig. 2 3D plot and the analysis method. (a, b) 3D plots obtained for BDA and BDT molecules, respectively. (c) Schematic diagram to determine theadsorption angle. φ represents the angle between the molecule and the substrate considering the direction of the molecule (see Fig. S1† for details).
(d, e) YZ cross sections for the cases of BDA and BDT, respectively.

ment, and a two-dimensional scan was carried out step by stepafter each cycle of Z-modulation (X, Y, Z: 56 × 36 × 200 and
40 × 40 × 200 points in the case of Fig. 2a and b, respectively) overthe molecule, as shown in Fig. 1e. Fig. 1f shows the measurement scheme and an example of the obtained data and theirmagnifications. The blue, orange, green, and red lines indicate
X- and Y-scans, the Z-modulation, and the normalized conductance G/G0, respectively (G0 = 2e2/h, h is Planck’s constant). By
plotting the value of G/G0 obtained at the STM tip position(X, Y, Z), a 3D volume plot can be obtained, as shown in
Fig. 2a and b. This shows the change in conductance with theconformational change of the single molecule junction. The
eﬀect of the sample gradient was removed by linear correction.

Results and discussion
Experimental results
Fig. 2a and b show 3D plots obtained for BDA and BDT molecules, respectively. The high-conductance regions in the XY
cross sections have the same periodicity as the Au(111) atomic
structure. Therefore, it is considered that the Auads and the NS
moved reproducibly on the Au(111) surface during measurement, which reflects the change in conductance with the position of the Auads and the NS on the Au(111) surface, as wasobserved in our previous studies.19,20 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, showing the single-molecule level analysis reliable.

This journal is © The Royal Society of Chemistry 2019

This measurement method allows the adsorption angle of amolecule (φ in Fig. 2c) to be obtained from the XZ and YZ
cross sections of the conductance map, and the location of thejunction point can be obtained from the XY cross section.19,20
Fig. 2c shows a schematic diagram showing the relationshipbetween the YZ cross section of the conductance map and theadsorption angle of the molecule in the case of BDT. During
the conformational change of BDT induced by Z-modulation,
the location of Auads moves. When Auads is on hollow and ontop sites, the conductance is large and small, respectively. The
motion of the molecule induced by Z-modulation is schematically shown in Fig. 2c for the movement of Auads (i) from ahollow site to an on-top site, (ii) from a bridge site to anotherbridge site via a hollow site, and (iii) from an on-top site to ahollow site.
The conduction depends on the adsorption position of
Auads as shown in the color bars in the upper part of eachfigure in Fig. 2c. When the probe moves in the X- or
Y-direction, the relationship between the height of the probe
and the adsorption position of Auads changes. For example, if
the pulling of the molecule starts from a (ii) bridge site and(iii) an on-top site, the probe height when Auads reaches thehollow site changes, resulting in a change in the red squares
in the color bars. That is, the Z position at which the conductance becomes large follows that of the upper end of a BDT
molecule whose lower end is on a hollow site. Namely, the redline drawn over the color bars corresponds to the trajectory of
the upper Auadt when an arc of the molecular length is drawn
with the lower-end Auads placed on a hollow site, as shown in

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PaperFig. 2c(iv). Thus, the adsorption angle of the molecule can bederived from the analysis of the arc pattern shown in the YZ
and XZ cross sections, as was carried out in previous
studies.19,20
Fig. 2d and e show the YZ cross sections for the cases of
BDA and BDT, respectively. In previous experiments, theresults were obtained for a region where the probe–substratedistance was larger than 0.58 nm for BDA and larger than
0.74 nm for BDT. Thus, the initial Z distance is shorter in eachcase in this experiment than in the previous experiments. In
the case of BDA, there was no arc-like change in the conductance map (Fig. 2d). This is considered to be due to the BDA
molecule not being bound to Auads and Auadt and it being
almost parallel and closer to the surface in the lying conformation. This allowed conduction pathways to form between
the functional groups other than the amino groups, such as
benzene rings, and the substrate surface; thus, no site-dependent change in the conductance was observed.
In contrast, in the case of BDT, a bright region was observedin the Z-range of 0.08–0.26 nm, which is considered to be dueto the Auads and Auadt bound to the end of the BDT, meaningthat the number of conductive pathways was limited comparedwith that in the case of BDA, and a change in the conductance
map was observed. However, the Z-region with high conductance is wide, which indicates that Auads does not move from ahollow site during the Z-modulation of ∼ 0.15 nm (Fig. 2e).
Taking into account the angle of the molecule in the XY plane
and assuming that BDT is parallel to the substrate at Z = 0, theangle becomes 20° and 26° at Z = 0.1 and 0.2 nm, respectively(see Fig. S1† and its caption for details).
Fig. 3a and b show two typical conductance curves, namely,
the normalized conductance G/G0 as a function of the probe–
substrate distance for retract and approach motion, obtained
for a BDA molecule at positions A and B in Fig. 3c(i). Unlike
the results in the previous paper,19 where the distance between
the probe and the substrate was suﬃciently large, no hysteresis
appeared and the conductance curves obtained for the retract
and approach motion were almost the same. According to theprevious results, the hysteresis of the conductance in BDA wasfound to be due to the diﬀerence in the timing of the formation of the bond between the lone pair and the on-top site
in the retract and approach motion. Therefore, when theprobe–substrate distance was short, as in this case, such achange in the timing did not occur while Z was changed inthis range.
The diﬀerence between the conductance curve in Fig. 3aand b is the change observed from (IV) to (V); the conductancebecame large and then gradually decreased as shown in
Fig. 3a, while it continued to gradually increase as shown in
Fig. 3b. This diﬀerence is considered to be because of thechange in the bonding state between the lone pair of NS and
the Auads atom while the BDA molecule being pulled up anddown is not large. Namely, instead of the binding site moving
between two adjacent on-top sites, it is considered to movefrom an on-top site to a bridge site, which does not produce
hysteresis.

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NanoscaleFig. 3 Data obtained for BDA. (a, b) Two typical conductance curves ofa BDA molecule obtained by the retract and approach motion at positions A and B in (c) (i). (c) XY conductance maps corresponding to theZ-positions (I) to (V) in (a).

Fig. 3c shows the XY conductance maps corresponding to
the Z-positions (I) to (V) shown in Fig. 3a. The structure of theAu(111) surface was not observed in Fig. 3c(I), but it started toappear in (III), where the details are shown in the images in
the lower row ((III)-1 to (III)-3). This is considered to be due tothe fact that BDA stood from the surface and the functionalgroup forming the transmission pathway with the on-top site
became only the amino group on the surface side. The atomic
pattern of Au was shifted upward by about 0.1 nm in the
Y direction, as indicated by the broken line in Fig. 3c(III)and (IV). Since this is less than the distance between two
on-top sites, the shift is considered to be due to the movementof the Auad from an on-top site to a bridge site, as describedabove.
Fig. 4a and b show the conductance curves of BDT and the
XY conductance maps obtained at diﬀerent probe–substratedistances ((I) to (VIII) in Fig. 4a), respectively. The location
where the conductance became large in Fig. 4b was determined in a previous work to be the hollow site on the Au(111)
surface.20 As shown in Fig. 4a, similar to the case of BDA, theconductance curves in the retract and approach motion did
not show any hysteresis and were almost identical, unlike theThis journal is © The Royal Society of Chemistry 2019

NanoscaleFig. 4 Data obtained for BDT. (a) Typical conductance curves of a BDT
molecule obtained by the retract and approach motion. (b) XY conductance map corresponding to the Z-positions (I) to (VIII) in (a).

results in the previous work in which the probe–substrate distance was suﬃciently large.20 Although there is a Auads in thecase of BDT, when the distance between the probe and thesubstrate is short, it is considered that the BDT molecule andAuads do not move significantly on the surface. Namely, thischange is considered to be due to the fact that Auads moved
between a bridge site and a hollow site via the same pathway
for the retract and approach motion instead of between two
adjacent hollow sites.
As shown in Fig. 4b, the conductance map closely reflects
the atomic structure of the Au(111) surface, in contrast to thecase of BDA. From (I) to (IV), the contrast gradually changed
and, as shown by the broken line in Fig. 4b, the location where
the conductance was large was shifted by about 0.13 nm (halfof the Au atomic radius), which supports the hypothesis that
Auads moved between a bridge site and a hollow site via thesame pathway for the retract and approach motion. From (IV)to (VII), G/G0 gradually decreased, and although the contrast
changed, the location with high conductance did not show any
shifts in Fig. 4b. Then G/G0 rapidly decreased from ∼0.30 to∼0.15 from (VII) to (VII)′. Since the conductance was rapidly
halved, it is considered that the number of transmission pathways was halved.
Simulations
To understand the experimental results in detail, we carriedout simulations for BDA and BDT molecules. We used
Atomistix ToolKit software (version 12.8.2 Quantum Wise A/S),
with DFT within the local density approximation (LDA) using
the Perdew–Zunger (PZ) exchange–correlation function27 toThis journal is © The Royal Society of Chemistry 2019

Paper

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 Brillouinzone integration was performed at 3 × 3 × 400 k-points. The
conductance was calculated by the non-equilibrium Green’s
function (NEGF) method.28,29 A bias voltage of 10 mV wasapplied to the electrodes, and three layers of Au(111) were prepared. Although DFT underestimates the energy gap, which
may result in a larger conductance, the relative change in conductance is reliable.12,30,31
A Au atom (adatom) was added to a hollow site on theAu(111) surface on the upper electrode as the STM tip apex.
Structural optimization was first carried out only with a molecule, where BDA was in the cis conformation. The molecularsurface was made parallel to the substrate and, as shown in
Fig. 1a, it was placed so that both ends were on on-top sites.
This condition was used for the calculation for comparison
with the experimental result shown in Fig. 3a. Next, when theelectrode on the probe side was brought closer, coupling
occurred at a certain distance. The height of the upper-electrode-side N atom from the Au(111) substrate surface (lowerside) was 0.21 nm lower than the initial height in the previous
work (0.58 nm).19 First, optimization was performed in thisstate once. Then the molecule was pulled up step by step
(0.3 nm for each step) and optimization was carried out
again between each step, where the local pathway and G wereobtained. In the calculation for comparison with the experimental result shown in Fig. 3b, the molecule was moved alongthe <110> direction as the NS atom was located on a bridgesite. Then a similar procedure to that described above wascarried out.
For the BDT molecule, similar optimizations were carriedout but with the Au adatoms Auadt and Auads at both ends ofthe molecule, which were placed at hollow sites in accordancewith the structure shown in Fig. 1b. After the first structural
optimization and the calculation of the conductance, the distance between the two electrodes was changed in steps of
0.02 nm up to 0.34 nm. The upper-electrode-side Au adatom(Auadt) was fixed during the whole process to reflect the stablejunction structure at the STM tip apex because highly reproducible conductance patterns were obtained in measurements.
Since more detailed analysis is necessary for the calculations
while the STM tip is made to approach the substrate, simulations were carried out for the case of STM tip retraction here.
First we discuss the case of BDA. Fig. 5a shows a conductance curve obtained for BTA, which is in good agreement withthe experimental result shown in Fig. 3a. Fig. 5b shows theconformations and local transmission contributions obtainedfor (i) to (v) in Fig. 5a, which correspond to the change from(I) to (V) in Fig. 3a. Structural optimization was first carriedout only with a free molecule, where BDA has a cis conformation. The molecular surface was set parallel to the substrate
and it was placed so that both ends were on the on-top sites asshown in Fig. 1a. Then, as the electrode on the probe side wasbrought closer, coupling occurred at a certain distance.

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PaperFig. 5 Simulated conductance curve obtained for BDA. (a) Simulated
conductance curve corresponding to the change from (I) to (V) in
Fig. 3a. (b) Schematics of conformational structures and local transmission contributions for (i) to (v) in (a). Local transmission contributions
are proportional to the thickness of the arrows.

Optimization was first performed in this state. Then the molecule was pulled up step by step (0.03 nm for each step) and
optimization was carried out between each step, where thelocal pathway and G were obtained. Fig. 5b(i) shows the optimized conformation after one step.
In contrast to the previous work,19 the site of the bond did
not change significantly while the distance between two electrodes was short. In (i), several transmission pathways wereformed around the functional groups other than the amines of
BDA, such as the benzene ring and current flowed from someother sites on the substrate, rather than an electron flow
through the benzene ring of BDA. The existence of several
local transmission pathways is considered to be the reason forthe low contrast of the atomic structures shown in Fig. 3c. In(iii), the contribution of Au/Nt/Au to the local transmission
decreases and the contribution of the local transmission near
the Ns atom becomes large, which is considered to have madethe atomic structure in Fig. 3c clearer.
In Fig. 5b(i)–(iii), the position of the Ns atom slightly moves
from the on-top site, strengthening the transmission pathway
formed by the coordination bond15 between the lone pair of
NS and AuN. However, as the distance between Nt and the substrate increases, its transmission decreases, resulting in theobserved decrease in G/G0 from (i) to (iii). In (iii), NS is above
AuN and forms a transmission pathway via the coordination
bond19 between the lone pair of NS and AuN. At this time,since CN is not above AuC, its contribution is small, and the5956 | Nanoscale, 2019, 11, 5951–5959

Nanoscaleconductance between NS and AuN can be observed in the conductance map. In (iv), since CN moves above AuC, forming two
transmission pathways of NS–AuN and CN–AuC, the conductance becomes large. In (v), CN is pulled away from thesubstrate and the contribution of the conduction between CN
and AuC to the transmission becomes small. These changes
closely reproduce the observed result. From the positions of
the NS atom between Fig. 5b(iii) and (iv), the displacement of
the NS atom was estimated to be 0.11 nm, which is in agreement with the displacement in the conductance map in Fig. 3c(0.1 nm).
To reproduce the conductance curve in Fig. 3b, the initialstructure was changed and calculations were carried out. The
initial position of the molecular end was moved away from theon-top site. Namely, the bond structure between Auad and Nt,
and the position of NS were changed.
Although calculations were carried out for various distances
moved, almost the same results were obtained. Fig. 6a and b
show the calculated conductance curve and the schematic
structures corresponding to (i) to (v) in Fig. 6a, respectively.
The conductance curve was in good agreement with the experimental curve shown in Fig. 3b.
The positional relationship between Auad and Nt was fixedsimilarly to that in a previous work20 so that the relative position between the upper electrode as the probe and Nt did notchange while raising the BDA molecule. The calculated contributions of the local transmission22–24 between Auad and Nt

Fig. 6 Simulated conductance curve obtained for BDA. (a) Simulated
conductance curve corresponding to the change from (I) to (V) in
Fig. 4b. (b) Schematics of conformational structures and local transmission contributions for (i) to (v) in (a). Local transmission contributions
are proportional to the thickness of the arrows.

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Nanoscale

shown in Fig. 6b gradually decreased from (iii) to (v) (3.1 × 10−2,
2.7 × 10−2, and 2.4 × 10−2, respectively), diﬀering from theobserved change shown in Fig. 6a, which is due to the increasein the angle between Nt and the BDA molecular plane. In
addition, although NS moves from an on-top site to a bridge
site from (i) to (v) in Fig. 5b, NS is at a bridge site with low conductivity for (i) to (iii) and moves to an on-top site with highconductivity in Fig. 6b. Actually, the calculated contribution of
the local transmission between NS and AuN increased from (i)to (iii) (7.9 × 10−3, 8.4 × 10−3, and 1.2 × 10−2, respectively),
resulting in an increase in the total conductance, which is ingood agreement with the observed change from (iii) to (v)shown in Fig. 6a.
Although it was diﬃcult to directly evaluate the adsorptionenergy because of the existence of the STM tip which pulled
up the molecule, the interaction between the BDA lone pairand Au atom was dominant even in the lying form in (i) and(ii). The binding between CN and AuC was weaker than that via
the lone pair. As the conformation changed into the standing
form as (iii) to (v), the binding became to be a single interaction. The structure maintained for a further pulling position
as shown in a previous paper,19 which is in good agreementwith the idea that relatively sharp conductance histogram
peaks were observed for the amine–Au system due to the relatively weak gold–amine interaction, namely, amines can only
significantly bind to gold adatoms in a standing form.12
As has been shown, the dynamics of the bond state in the
BDA single-molecule junction for a small probe–substrate distance was well explained by the results obtained by combining
the 3D dynamic probe method and DFT calculations. A similar
simulation was then carried out for the BDT molecule. Fig. 7ashows the conductance curve obtained by the simulation. Thechange in conductance from (i) to (iv) is in good agreementwith the observed change shown in Fig. 4a. However, the calculated conductance rapidly decreases between (iv) and (vi) andgradually decreases from (vi) to (viii), while in the experiments,
it rapidly decreased after a gradual decay.
Fig. 7b shows the conformations used for the calculations
and the obtained contributions to the local transmission.
Similar simulation procedures to those discussed earlier werecarried out (see Experimental for the initial conditions). From(i) to (iv), because the contributions to the local transmission
via the Auadt-St-substrate (upper side) and Auads-SS-substrate(lower side) are larger than that via the phenyl group (benzenering) of the BDT transmission pathway, there is not a single
transmission pathway passing through the BDT molecule, andthese are two dominant pathways at both ends of the moleculeshown by the pink arrows.
In the change from (iv) to (vi), the local transmission contributions of these two pathways become smaller and one ofthem disappears. The calculated values of G/G0 for (iv) and (v)′were 1.11 and 0.53, respectively, in good agreement with thedecrease to the values shown in Fig. 4a (VII) and (VII)′. This
rapid change in conductance is due to the rotation of thebenzene ring of BDT as shown in Fig. 7. Then the local transmission contribution via the phenyl group (benzene ring)This journal is © The Royal Society of Chemistry 2019

Paper

Fig. 7 Simulated conductance curve obtained for BDT. (a) Simulated
conductance curve corresponding to the change in Fig. 4a.
(b) Schematics of conformational structures and local transmission contributions for (i) to (viii) in (a). The direction of the arrows from the upper
substrate to SS shown in (vii) and (viii) indicates the negative contribution. Local transmission contributions are proportional to the thickness of the arrows.

becomes dominant, as shown by the light green arrow in (viii),
which decreases with the increase in Z, producing the gradualdecrease in the conductance shown in Fig. 7a.
In the experiment, a gradual decrease in conductance wasobserved from (IV) to (VII) before the rapid change from (VII)to (VIII) as shown in Fig. 4a. This is considered to be because
the rotation of BDT begins after the two Au/S/Au pathways
become one in the simulation, while the rotation occurred
first in the experiment. This diﬀerence is considered to be
due to the actual tip surface not being flat similarly to thesubstrate used for the calculation, but having a pyramidal
structure, which reduces the eﬀect of steric hindrance in thecalculation.
To see the conformational change in the molecule in moredetail, Fig. 8 shows the conformations shown in Fig. 7b as
seen from the Z-direction. Auads moves from a hollow site to abridge site. The distance moved is 0.15 nm, as shown by thebroken line, which is in good agreement with the value of0.13 nm experimentally obtained for the change from (I) to

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PaperNanoscaleNotes and references

Fig. 8 Schematic structures of BDA on a Au(111) surface.
Conformations of BDA shown in Fig. 7b as seen from the Z-direction.

(IV) as shown in Fig. 4b. Auads does not move from (vi) to (viii)
while the molecule is pulled up, as shown by the broken line,
which is considered to be due to the rotation of the moleculeduring the change in Z.

Conclusions
By performing analysis on 1,4-benzenediamine (BDA) and1,4-benzenedithiol (BDT) single molecule junctions by the 3D
dynamic probe method and DFT calculations, we haveobserved, for the first time, the eﬀect of a change in the molecular conformations and bonding states on the local transmission pathways for a short Au electrode distance. The
obtained results are expected to play an important role inadvancing the development of nanoscale devices making fulluse of the characteristics of single molecules.

Conﬂicts of interest
There are no conflicts to declare.

Acknowledgements
H.S. and S.Y. acknowledge the financial support from theJapan Society for the Promotion of Science, the Grant-in-Aid
for Scientific Research 17H06088, and the Grant-in-Aid forYoung Scientists (A) 16H05982, respectively.

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