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Letter
Transport through a Single Octanethiol Molecule
Daan Kockmann, Bene Poelsema, and Harold J. W. Zandvliet
Nano Lett., 2009, 9 (3), 1147-1151• DOI: 10.1021/nl803767c • Publication Date (Web): 30 January 2009
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Transport through a Single Octanethiol
Molecule
Daan Kockmann,*,† Bene Poelsema,‡ and Harold J. W. Zandvliet†
Physical Aspects of Nanoelectronics and Solid State Physics,
MESA+ Institute for Nanotechnology, UniVersity of Twente, P.O. Box 217,
7500 AE Enschede, The Netherlands
Received December 13, 2008; Revised Manuscript Received January 17, 2009
ABSTRACT
Octanethiol molecules adsorbed on Pt chains are studied with scanning tunneling microscopy and spectroscopy at 77 K. The head of the
octanethiol binds to a Pt atom and the tail is lying flat down on the chain. Open-loop current time traces reveal that the molecule wags its
tail and attaches to the scanning tunneling microscopy-tip resulting in a dramatic increase of the current. We measured a single molecule
resistance of 100-150 MΩ.
The adsorption of molecules on surfaces has been of interest
for more than a century. In the mid seventies, this interest
was heavily enhanced by the first molecular electronics
publication by Aviram and Ratner.1 In this landmark article
they put forward the idea to use a single organic molecule
as a molecular rectifier. A single molecule that has a donor-
spacer-acceptor like structure could behave as a p-n-junction
and thus exhibit rectifying IV behavior. At that time, the
so-called top-down approach was the only way of creating
electronic components. However, Aviram and Ratner pro-
posed a novel method: the so-called bottom-up approach.
With this method devices/components are assembled, taking
the individual molecules or atoms as a starting point.
Nonetheless, it took more than two decades before the
physical and chemical properties of an individual molecule
could be measured successfully. In particular the introduction
of scanning probe techniques2-5 in the 1980s has given an
enormous boost to this field. Meanwhile, numerous papers
are published on molecular electronics, demonstrating many
intriguing and exotic phenomena. Single molecules, or small
bundles of molecules, have been trapped between elec-
trodes6-13 and researches have measured Coulomb gaps and
Coulomb staircases,6 bistable switching,7 current rectifica-
tion,8 negative differential resistance characteristics,9 Kondo
resonances,10 and conductance switching.11
The use of alkanethiols in molecular electronics is now
well established14 since these molecules form densely packed
and well-ordered self-assembled monolayers on metal sur-
faces. An alkanethiol molecule basically consists of three
* To whom correspondence should be addressed. E-mail: d.kockmann@
utwente.nl.
†
Physical Aspects of Nanoelectronics.
‡
Solid State Physics.
10.1021/nl803767c CCC: $40.75  2009 American Chemical Society
Published on Web 01/30/2009
NANO
LETTERS
2009
Vol. 9, No. 3
1147-1151
parts: a sulfur-hydrogen head, a hydrocarbon chain of
variable length, and an end group. The basic picture used to
explain the adsorption of an alkanethiol on a metal substrate,
ending in self-assembly, entails physisorption followed by
chemisorption.15 After physisorption, the molecule binds via
the sulfur atom to the surface. The H-atom is released and
the alkanethiol transforms to an alkanethiolate. At low
coverage, the alkanethiolate molecules are flat-lying on the
surface in ordered domains, referred to as the striped or lying
down phase. Upon increasing the coverage to one monolayer,
the thiolate molecules will eventually convert to a standing-
up phase. By using nanostructured surfaces instead of normal
metal surfaces as a template, one could construct or assemble
more sophisticated nanostructures.
Here we report on the adsorption of octanethiol molecules
on atomic Pt chains. These Pt chains were grown on Ge(001)
via a self-organization process. The Pt/Ge(001) surface is a
particularly attractive candidate to be used as a template in
molecular electronics since it predominantly consists of
arrays of dimerized, perfectly straight, and virtually defect-
free monatomic Pt chains.16-18 The Pt/Ge(001) substrate is
exposed to octanethiol at room temperature and subsequently
cooled down to 77 K. After adsorption and cooling down to
77 K, the structural and electronic properties of the adsorbed
thiolate molecules were studied. We found that the head of
the thiolate, that is, the sulfur atom, binds to an on-top Pt
site. Next we measured the I(V) properties of the head and
tail of the octanethiolate molecules separately. There ap-
peared to be a distinct difference in the I(V) responses of
both parts. Additionally, we measured open-loop I(t) tran-
sients above the adsorbed thiolate molecules. While measur-
ing the tunneling current in the open-loop configuration, we
frequently noticed that the current jumps back and forth
between the current set point value (typically 1 nA) and a
much higher current value of 10-15 nA. In order to
understand this dramatic increase in the tunnel current, we
suggest that the octane-tail of the adsorbed molecule (initially
lying flat on the Pt chain) flips upward and makes contact
with the scanning tunneling microscopy (STM) tip. Hence,
we can now simply extract the resistance of a single
octanethiolate molecule.
Ge(001) substrates (5.0 mm × 10.0 mm) were cut from
nominally flat, single-side polished n-type wafers. After ex situ
rinsing with isopropanol, the samples were placed into the
ultrahigh vacuum low-temperature (UHV LT)-STM (Omicron).
Here, they were slowly degassed. Subsequently, the samples
were cleaned in situ by sputtering with 800 eV argon ions and
thermal annealing to 1100 K (using a dc current) during 2 min.
This in situ procedure was repeated several times before
atomically clean Ge(001) surfaces were obtained. Imaging with
STM at 77 K revealed that the surface predominantly consists
of two different, well-ordered domain patterns: p(2 × 2) and
c(4 × 2).19 Subsequently, we deposited a submonolayer amount
of Pt onto the atomically clean Ge(001) surface at room
temperature. Pt was evaporated onto the surface using a
straightforward home-built Pt evaporator; a high-purity Pt-wire
was wrapped around a W filament. Evaporation occurs simply
by heating the W filament via dc current. After evaporation
the Pt/Ge(001) substrate was annealed up to 1100 K for 2 min Figure 1. STM image (25 nm × 25 nm; VS ) -0.90 V; I ) 0.5
and subsequently cooled down to room temperature by radiative nA) of a Pt-modified Ge(001) surface after exposure to 60 L of
octanethiol, recorded at 77 K (A). The octanethiol molecules
quenching. Following this procedure, we found large patches (circular white spots) almost exclusively adsorb on the Pt atomic
of Pt chains that are spaced 1.6 nm apart. A more detailed chains. In panel B, we show a model of the region enclosed by the
explanation on the procedure and formation of the Pt chains is square in panel A. Grey dumbbells are substrate dimers, dark
given in refs 16-18. dumbbells are Pt dimers, and the adsorbed molecule is shown in
orange.
After formation of the Pt chains, the surface was exposed
to octanethiol (Sigma-Aldrich). A small amount of oc- molecules adsorbed on the atomic Pt chains. The density of
tanethiol was introduced in the preparation chamber of our these white spots increases with increasing exposure to
UHV system via a leak valve. This valve allows us to octanethiol up to about 2000 Langmuir. Between 2000-3000
controllably adjust the pressure of the octanethiol in our Langmuir the density of white blobs on the Pt chains
preparation chamber. We exposed the samples to 10-16000 becomes so high that we cannot recognize the separate
L. However, results shown in this paper were all acquired molecules anymore. In addition, the STM image reveals that
on samples exposed to less than 60 L. After reaching the the octanethiolate molecules almost exclusively adsorb on
normal background pressure again, the sample is transferred the Pt chains and only very rarely on the underlying troughs
to the STM chamber for cooling down and imaging. in between the chains.
In Figure 1 an overview STM image (25nm × 25nm) of The adsorbed octanethiolate molecules were scanned at
a Pt modified Ge(001) surface after being exposed to 60 L biases from -1.5 to +1.5 V. At both positive and negative
of octanethiol is shown (A), together with a model of the sample bias, the Pt chains are easy recognizable. Regarding
surface structure (B). The surface was scanned at 77 K with the adsorbed octanethiolate molecules a clear distinction can
a sample bias VS ) -0.90 V and a tunnel current of I ) be made between negative sample bias (filled state) and
0.50 nA. The chains of Pt appear as “dashed bars”. The positive sample bias (empty state).
chains are comprised of Pt dimers, which are aligned in the Figure 2 shows filled-state (A) and an empty-state (B)
direction of the chains. The width of a single chain is exactly images (5 nm × 5 nm) of an adsorbed octanethiolate
one Pt atom, and the distance to neighboring chains is 1.6 molecule on a Pt chain. In the filled-state image (VS ) -1.5
nm. Clearly present in the image are many white circular V), a large white protrusion covers virtually one and a half
spots located on top of the Pt chains. These spots were not Pt dimer. The topographic center of the molecule is
present before exposure to octanethiol. The apparent size of positioned on one of the Pt atoms of the fully decorated Pt-
the spherical features is consistent with the size of an dimer. More clearly this is shown in the height profile in
octanethiolate molecule, namely 1.0 nm.20 Moreover, an Figure 3A; the profile in this figure is taken across the Pt
increase of the exposure of octanethiol leads to an increase chain as indicated by the red arrow. As a reference profile,
in the number density of these white spots. Therefore, we we also plotted the height profile of a clean Pt chain, as
attribute these white spherical features to octanethiolate indicated by the black arrow in Figure 2A.
1148 Nano Lett., Vol. 9, No. 3, 2009
Figure 2. Two STM images (5 nm × 5 nm; I ) 0.50 nA; 77 K) recorded simultaneously at the same position at different biases, VS )
-1.50 V (A) and VS ) +1.50 V (B). In the center of both images, one can clearly see the adsorbed molecule on the Pt atomic chain. At
negative bias (panel A) the thiolate molecule shows up as a large protuberance on top of the chain; at positive bias (panel B) a small
protuberance is accompanied by a small depression in the chain. Furthermore, when looking at the troughs flanked by the chains, there is
no difference between the region near the adsorbed molecule and the regions further away from the adsorbed molecule.

Figure 3. Height profiles of Pt chains with (red) and without (black) adsorbed thiolate molecule taken from both filled state (A) and empty
state (B) images as indicated in Figure 2. The center of the molecular profile is for both polarities located on top of one of the atoms of a
dimer.

Simultaneously with the filled-state image of Figure 2A,
we recorded an empty-state image of the same area (see
Figure 2B). This image shows that the adsorbed octanethi-
olate now exhibits a completely different shape. The protru-
sion, which is much smaller in size, is located on one side
of the Pt dimer. Additionally, on the other side of this dimer,
the protrusion is accompanied by an even smaller depression.
The height characteristics at positive sample bias of a bare
Pt chain and a Pt chain decorated with an adsorbed molecule
are presented in Figure 3B (black and red arrows as indicated
in Figure 2B).
As mentioned before, alkanethiols are well studied because
of their ideal self-assembly properties on metal surfaces. The
sulfur atom of the thiol headgroup binds to the surface and
for a densely packed monolayer the alkane chains are
standing upward due to the intermolecular Van der Waals
forces. At low thiolate coverage, the alkane chains are lying
flat down on the surface. On the basis of both these
observations and our STM measurements, we assume that
the octanethiolates are also lying flat on the Pt chains at least
in the low coverage regime. In fact, if we take a closer look
Nano Lett., Vol. 9, No. 3, 2009
at the region in the troughs between the Pt chains we see no
difference between before and after adsorption of the
octanethiolate molecules. Moreover, the region in the troughs
between the Pt chains near an adsorbed octanethiolate
molecule is virtually identical to a molecule-free trough
region. Hence, the tail of the octanethiolate molecules must
be located on the Pt chains rather than in troughs between
the chains. Thus, on the basis of our STM data we tentatively
conclude that the sulfur atom binds on-top to one of the
atoms of the Pt dimer and the tail of the octanethiolate
molecule lies flat on the Pt chain.
In order to obtain more insight in the exact adsorption
geometry of the octanethiolate molecule we have recorded
I(V) curves on the head and the tail of the molecule. It must
be noted that at this moment we do not know which part is
the head and which part is the tail. We only know that one
part should be the head, while the other should then be the
tail. In Figure 4A, we show I(V) curves recorded on both
parts of the octanethiolate molecule; the spectra were
acquired as indicated by the blue circle and the red triangle
in the STM image in Figure 4A. Both spectra are averaged
1149
Figure 4. I(V) characteristics taken on two different parts of an octanethiolate molecule adsorbed on a Pt chain, as indicated by the blue
dot and the red triangle in the STM image of panel A. Panel B shows a detailed view of the voltage window from 0 to 0.4 V. We ascribe
the curve with the highest current ratio (red) to the sulfur-side of the molecule and the blue curve to the octane-side of the molecule.

Figure 5. (A) I(t) transient recorded on an octanethiolate molecule that is adsorbed on a Pt chain. The trace is recorded at constant height.
The sample bias is 1.5 V. The current jumps back and forth between the current set point (1 nA) and a much higher current of 11 nA. We
have measured residence times up to 40 s and currents in the range of 10-15 nA. The current jumps are caused by the octanethiolate
molecule that wags its tail and subsequently contacts the STM tip, as indicated by the schematic drawings in panels B and C.

over 30 different measurements. The tunnel current was
measured between -1.5 V e VS e +1.5 V. Figure 4B shows
a closer look at the region 0.0 to +0.4V.
At negative sample bias, the I(V) curves measured at the
two different sides of the molecule are virtually identical.
However, for positive sample bias the two parts of the
molecule behave differently. The region marked with the red
triangle in the STM image in Figure 4 shows a much higher
current than the region marked with the blue circle. After
superimposing the negative sample bias STM image of
Figure 4 onto its positive bias counterpart, we found that
the blue circle is positioned on the small depression, similar
to the one discussed in Figure 2B. We ascribe the more
metallic curve (red triangle) to the sulfur-head of the
molecule and the other curve (blue circle) to the tail of the
octanethiolate. So while it is hard to discriminate between
the thiolate and the octane part of the adsorbed molecule by
just STM, the combination with scanning tunneling spec-
troscopy (STS) on different parts of a molecule allows one
to discriminate between the two parts.
Additionally, we measured the current as a function of
time on top of adsorbed molecules with the feedback of the
electronics in the open-loop configuration. Therefore the
separation distance between the tip and the surface of the
sample was kept constant during these experiments. So if
there is a change in the geometry of the adsorbed molecule,
which is in between the tip and the surface of the sample,
this should be immediately visible in the measured current.
1150
In Figure 5A, we have plotted an I(t) transient, measured
as described above, with a bias VS ) 1.5 V. Clearly shown
in the graph is the dramatic increase in the current from 1 to
11 nA. After being constant for more than 10 s, the current
drops back abruptly to its original value of 1 nA. During
other experiments, we even measured current jumps from 1
to 15 nA and also high current residence times up to 40 s.
In these experiments, we only observed a current jump
upward and no return to 1 nA.
Although we have measured different maximum currents
and also different residence times at high current, we are
dealing with the same process in all these cases. The simple
fact that the current returns to its starting value (1 nA)
excludes a permanent change in the geometry of the adsorbed
molecule. This is confirmed by comparison of STM images
taken both before and after recording the current traces.
As a most likely explanation of the sudden increase/decrease
in the current signal we propose the following scenario: during
tunneling to the molecule, the tail of the octanethiolate molecule
flips up and jumps into contact with the apex of the STM tip.
Interestingly the length of the tail of the octanethiolate molecule
is about the same as the width of the tunnel gap, that is, about
1 nm. Hence, the tail of the octanethiolate molecule is long
enough to contact the STM tip.
From our experiments, we extract a single-molecule
resistance from 100-150 MΩ, which is in excellent agree-
ment with values reported in literature (ref 14 and references
therein). It should be pointed out here that at the side of
Nano Lett., Vol. 9, No. 3, 2009
STM tip we have not created a chemisorbed contact since
the tail of the octanethiolate detaches typically after 10-40
s. Since the resistance we measured falls in the range of the
reported values for both C6 and C8-thiolates, we cannot
determine whether the current flows through the whole
molecule or just through a major part of the molecule.
Sudden current jumps due to spontaneous flipping of an
adsorbed molecule were reported previously.21,22 However,
in these experiments the current changes were much smaller
and the average residence time of the molecule in contact
with the tip was much shorter.
It should be pointed out here that it does not make sense
to vary the current set point, since an increase (decrease) of
the current by a factor of 10 results in a decrease (increase)
of tip-substrate by only 0.1 nm.
In summary, we have studied the adsorption of octanethiol
molecules on a Pt-modified Ge(001) surface with STM/STS.
The octanethiolate molecules adsorb almost exclusively on
the Pt chains. By measuring the I(V) characteristics on both
the head and tail of the adsorbed molecule, we were able to
discriminate between the two different parts. Finally, during
open-loop I(t) experiments above the adsorbed molecule, the
molecule often wags its tail and thereby contacting the STM-
tip. We were able to keep contact between the tip and the
molecule for tens of seconds. Throughout this contact we
measured the current through the molecule resulting in a
measured single-molecule resistance of 100-150 MΩ.
Acknowledgment. We thank NanoNed for their financial
support.
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