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Manipulation of a single molecule ground state by means of gold atom
contacts
C. Manzano
a,
⇑
, W.H. Soe
a
, M. Hliwa
c
, M. Grisolia
b
, H.S. Wong
a
, C. Joachim
a,b
a
IMRE, A
⁄
STAR (Agency for Science, Technology and Research), 3-Research Link, 117602 Singapore, Singapore
b
GNS-CEMES & MANA Satellite, CNRS, 29 rue J. Marvig, 31055 Toulouse Cedex, France
c
Faculté des Science Ben M’Sik, Université Hassan II-Mohammedia-Casablanca, Morocco
article info
Article history:
Received 24 April 2013
In final form 13 September 2013
Available online 20 September 2013
abstract
Single gold adatoms were manipulated on a Au(1 11) surface with the tip of a scanning tunnelling
microscope to contact selected peripheral
p
bonds of a single Coronene molecule. Tunnelling electron
spectroscopy and differential conductance mapping of the Au–Coronene complexes show how Coron-
ene’s electronic ground state is shifted down in energy as the function of the number of interacting Au
atoms, demonstrating that a Coronene molecule can function like a single molecule counter. The number
of interacting atoms can be counted by simply following the linear energy downshift of Coronene’s
ground state.
Ó2013 Elsevier B.V. All rights reserved.
1. Introduction
Single organic molecules are often considered as the building
blocks for the future generations of electronic circuits miniaturized
down to the atomic scale. They can be chemically designed to
mimic standard electronic circuits by using chemical groups sup-
posed to function like the basic elements of a digital electronic cir-
cuit [1–6]. It has also been proposed to abandon classical electronic
circuit design and to operate Boolean logic operations by only
manipulating the electronic quantum states of a single custom de-
signed molecule [7,8]. For example, by using single Au adatoms on
a Au(111) surface as classical logical inputs, a trinaphthylene mol-
ecule functions as a NOR logic gate [9,10]. It converts classical On/
Off information per input in quantum information leading to a con-
trolled shift of the trinaphthylene electronic quantum states con-
forming with a NOR Boolean truth table. The rationale here is
that it is better to embed higher level functionalities within one
single molecule rather than to try to implement a switching func-
tion within a single molecule or to pursue the chemical synthesis
of large molecules having the shape of a complete electronic
circuit.
Intramolecular quantum behaviours are rich enough to imple-
ment simple analogue functions inside a single molecule without
forcing the molecule to have the shape of an analogue electrical
circuit. To demonstrate this, we have selected the Coronene mole-
cule and manipulated its ground electronic state by contacting its
p
electronic system with single Au atoms. We demonstrate herein
that when Au atoms are interacting at very specific positions
around its external crown, a Coronene molecule is able to count
the number of Au atoms interacting with its
p
system. Since a Cor-
onene molecule has six-equivalent external peripheral phenyl
rings (see Coronene’s model in Figure 1), six equivalent sites are
accessible for contacting a first Au atom. To contact two Au atoms,
three different possible types of configurations are possible: the 2
Au can be bound to two nearest neighbouring phenyl rings like
(1,2) or (2,3), they could be also bind to non-adjacent phenyl rings
like (1,3) or (1,5) or be in diametrical opposite positions like (1,4)
(The numbers in parenthesis indicate the external Coronene phe-
nyl ring where each single Au is contacted to (see Figure 1)). For
2 atom inputs and starting from the first selected input on a phenyl
1, only the (1,3) or (1,5) can be used for counting to avoid any di-
rect through space electronic interactions between the two Au
atoms. For 3 Au contacted atoms, three fully equivalent interacting
configurations like (1,3,5) are possible, configurations like (1,2,4)
although experimentally feasible should be avoided, as it will be
shown further in the article, so that the inputs are symmetric
and the counting response linear. Once a given phenyl is selected
for the first Au input, the other Au atoms must be contacted
respecting those specific input positions for the Coronene to Letter
as a counter even if other configurations are accessible. The output
reading is performed by recording the tunnel current intensity I
passing from the STM tip apex to the Au(1 11) surface through very
specific positions on the Coronene
p
system without the need for
this current to pass through the entire conjugated board of the
molecule.
In this Letter, the atom by atom counting effect is demonstrated
experimentally using a low temperature STM, single atom and
molecule STM manipulations, differential conductance (dI/dV)
constant current imaging and dI/dV spectroscopy. The STM images
0009-2614/$ - see front matter Ó2013 Elsevier B.V. All rights reserved.
http://dx.doi.org/10.1016/j.cplett.2013.09.039
⇑
Corresponding author.
E-mail address: garciac@imre.a-star.edu.sg (C. Manzano).
Chemical Physics Letters 587 (2013) 35–39
Contents lists available at ScienceDirect
Chemical Physics Letters
journal homepage: www.elsevier.com/locate/cplett
were also calculated using the Elastic Scattering Quantum Chemis-
try technique in the framework of the Extended Hückel Molecular
Orbitals approximation (EHMO–ESQC) [11].
2. Low temperature STM characterisation of a single Coronene
with Au atom classical inputs
To experimentally demonstrate the Coronene counting func-
tion, a sub-monolayer of Coronene molecules (C
24
H
12
, Sigma–Al-
drich 99.99% purity) was first deposited on the Au(111) surface
of a gold mono-crystal using free evaporation. The Au(1 11) crystal
was prepared following standard cleaning methods by undergoing
several ion sputtering and annealing cycles. The crucible contain-
ing Coronene molecules was heated at 192 °C, during the mole-
cules deposition the substrate temperature was kept below 80 °C.
Thereafter, the sample was cooled down using liquid helium and
transferred to the STM chamber. All STM imaging, atom manipula-
tion and spectroscopy measurements were done at 7K.
After sublimation, constant current STM images show that Cor-
onene molecules adsorbed both on Au(1 11) terraces and at step
edges. Besides the molecules, the characteristic herringbone recon-
struction of Au(111) can also be observed. In the topographic STM
images, single Coronene molecules are imaged like a 6 branched
star as presented in Figure 1. dI/dV spectra of an isolated Coronene
molecule were obtained by positioning the STM tip over its center
and over one of its 6 outer lobes. Recorded on a given outer lobe,
the main features of a characteristic dI/dV spectrum are a reso-
nance peak at 1.4 V corresponding to Coronene’s electronic
ground state, and a broad tail at positive bias showing no distinc-
tive resonance. Furthermore dI/dV spectra taken at the molecule
center appear featureless. On a constant current dI/dV image re-
corded at 1.4 V, Coronene’s six external lobes are clearly imaged
while its center appears featureless (see Figure 1). ESQC calculated
STM images allow to identify and to extract Coronene’s structure
from the experimental STM images. Constant current images cal-
culated at the Highest Occupied Molecular Orbital (HOMO) reso-
nance are perfectly matching the experimental images, shown in
Figure 1. This confirms the position of the 6 outer phenyls of the
Coronene crown exactly at the location of the 6 lobes observed
on the experimental dI/dV images.
In order to form the Au
n
–Coronene complexes, Au atoms were
extracted from the Au(111) surface after a soft indentation of
the STM tip apex. Prior to any experiment an oxide free electro-
chemically etched Tungsten tip is gold coated by indenting it in
the Au(111) substrate following the method described by Hla
et al. [12]. After series of indentations, spectra are taken to test
whether the tip is ready for obtaining spectroscopic data. Only tips
whose dI/dV spectra recorded on a clean Au terrace showed the
Au(111) surface state resonance were used in our experiments.
STM tips showing any other spectral features are again treated un-
til their spectra show only the characteristic Au(1 11) surface state
resonance. Thereafter the tip approaching parameters like tip-
indentation depth and bias voltage were adjusted as required to
crash the tip in the substrate until adatoms are clearly observed
around the indentation sites [12].
Au adatoms and a Coronene molecule were brought together in
electronic interaction by manipulating the atoms using the STM tip
[9,10]. The single Au atom manipulations were performed keeping
the STM current feedback loop on. After each manipulation, param-
eters like the tunnelling resistance and tip lateral motion speed
were adjusted until a new successful manipulation is produced
again. A tunnelling resistance of <0.5 MOwas used to manipulate
the Au atoms, tip height variations recorded during the manipula-
tion sequences prove that the atoms were typically manipulated in
a ‘pulling’ mode. In those conditions, manipulated single Au atoms
arrange selectively in a surface configuration where a given Au is
always underneath an outer Coronene phenyl ring. Attempts to ob-
tain single atom contacts at other positions of the Coronene exter-
nal crown resulted in configurations that were not stable enough
to enable the formation of other Au–Coronene conformations. By
moving the molecule away using the STM tip, all the Au atoms of
a given Au
n
–Coronene complex can be detached from this Coron-
ene, hence resetting the counter to zero, since the gold adatoms
are weakly bonded to the Coronene as compared to their stronger
interaction with the Au(111) surface.
Coronene’s ground state as a function of the number Nof Au
interacting atoms was determined by systematically recording its
dI/dV spectra on a lobe away from the outer phenyls where the
Au atoms are interacting. After contacting one Au atom at any of
the six outer phenyl rings, the dI/dV spectrum is presenting a shift
of the ground state resonance by nearly 200 mV as compared to a
bare Coronene (see Figure 1). ASED+ [13] and ESQC image calcula-
tions were done to determine precisely where the contacted Au
atoms coordinate on the Coronene. At this stage image calculations
are utmost necessary since it is not possible to know where Au
atoms coordinate to Coronene solely based on experimental imag-
ing. Experimental STM images taken after Au atoms are manipu-
lated and contacted to Coronene show that each Au atom
contacts an outer Coronene lobe. ASED+ calculations were used
to determine how an Au atom binds to an outer phenyl ring. These
calculations show that a gold atom binds to the two outermost car-
bon atoms of a phenyl ring deforming locally the Coronene board.
An ESQC calculated image done using this deformed atom-Coron-
ene conformation reproduces very well the experimental dI/dV
map of the Au
1
–Coronene complex showed in Figure 1 indicating
that the interaction of a single Au atom with the Coronene has bro-
ken the HOMO symmetry due to the deformation of Coronene’s
skeleton at the Au interaction location. This deformation was
Figure 1. Characteristic dI/dV tunnelling electronic spectra recorded on a single
Coronene molecule and on a Au
1
–Coronene complex. In these spectra, the energy
shift of Coronene’s ground state resonance (HOMO) peak occurring after the
Coronene molecule is coordinated with one gold adatom is clearly observed. Two
columns of images show the corresponding structure model, STM topography
image, dI/dV map and ESQC calculated conductance image for Au
1
–Coronene (left)
and Coronene (right) respectively (image size: 2 nm 2 nm). The ESQC dI/dV maps
were both calculated at the energy corresponding to the respective HOMO
resonances of Coronene and Au
1
–Coronene. Tunnelling set point parameters used
for topographic images and dI/dV maps: Coronene (1.4 V, 0.7 nA), Au
1
–Coronene
(1.6 V, 0.8 nA).
36 C. Manzano et al. / Chemical Physics Letters 587 (2013) 35–39
already observed to occur for a trinaphthylene molecule interact-
ing with a single Au atom [9,10]. The two carbon atoms at the
end of the phenyl ring interacting directly with the Au atom are
moved up together with their corresponding hydrogen atoms. This
breaks the delocalization of the Coronene
p
system explaining how
both the experimental and the calculated images are showing only
4 lobes instead of the 6 lobes imaged for a bare non deformed
physisorbed Coronene.
A large down shift in energy of the native Coronene ground
state resonance (HOMO) is observed for each subsequent addition
of single Au atoms. As presented in Figure 2, the dI/dV spectra re-
corded for the different Au
2
–Coronene complexes (1,2), (1,3), (1,4)
show its negative resonance peak shifted by 400 mV relative to the
HOMO of a bare Coronene. The (1,3,5) Au
3
–Coronene complex
shows a resonance peak shifted also by nearly 200 mV as com-
pared to the Au
2
–Coronene complexes that is a 600 mV spectral
shift from the HOMO of the bare Coronene (See Figure 2).
When a gold atom is brought into contact with Coronene the
spatial distribution of Coronene’s HOMO electronic state is per-
turbed by the binding atom as it is shown in the dI/dV map of
the Au
1
–Coronene in Figure 1. Likewise for any Au
n
–Coronene
the effects of the contacting Au atoms on the spatial redistribution
of its HOMO electronic cloud would be visible in its corresponding
dI/dV map. Consequently, for tracking the HOMO resonance of
each Au
n
–Coronene investigated tunnelling spectra were taken at
different places of the complex. These spectra are affected by
HOMO’s spatial distribution and the HOMO’s peak intensity shows
accordingly these variations depending on where the spectra were
taken from. For instance, spectra taken on the Au atom contacted
lobe of a Au
1
–Coronene and on the nearest neighbouring phenyl
ring respectively show the same spectral features i.e. the HOMO
resonance is at the same position for both spectra, however the
amplitude of the HOMO resonance of the spectrum from the con-
tacted lobe is smaller than the one in the spectrum taken from
the neighbouring lobe. Accordingly, for each Au
n
–Coronene com-
plex the spectrum with the highest HOMO resonance amplitude
is selected and presented in Figures 1 and 2. The spectra shown
in the Figure 2, which also includes the spectrum for the Au
1
–Cor-
onene, where each taken as indicated in the STM images corre-
sponding to each Au–Coronene complex.
3. Discussion
A simple quantum model of this step by step shifting of Coron-
ene’s ground state electronic tunnelling resonance can be built up
by considering first a non degenerate 2 states quantum system, |g>
being the ground state of the Coronene molecule and |i> the state
corresponding to one Au input. When |i> is electronically coupled
to |g>, there is a shift down in energy of |g> and a shift up in energy
of |i>, with
D
being the initial energy difference between those 2
states. For a small coupling
a
as compared to
D
, |g> still keep its
ground state characteristics and becomes |G> with an energy shift
downwards of
a
2
/
D
, likewise |i> becomes |I> with a
a
2
/
D
upward
energy shift. When now coupling Nidentical |i> states to |g>, the
resulting new |G> ground state will be shifted by (
D
p(
D
2
+4-
N
a
2
))/2. As a function of Nand for
a
<<
D
, |G> will be linearly
shifted down in energy by N
a
2
/
D
. Therefore, the |G> energy posi-
tion can be used to count the number of identically coupled |i>
states. Notice that this counter can saturate when 2p(N)
a
is not
negligible compared to
D
. But this limitation depends on how each
|i> state is spatially coupled to |G>. In Figure 3, we have plotted the
experimental position of Coronene’s ground state tunnel resonance
of selected atom input conformations as a function of the number
Nof contacted Au atoms. Its energy downshift can be very nicely
fitted by a N
a
2
/
D
curve, as derived above, with
D
= 1.442 eV and
a
= 552 meV, where
a
is the electronic interaction between a single
Au adatom and the physisorbed Coronene molecule.
Using the MOPAC2009 semi-empirical quantum chemistry code
in the framework of the Potential Model-parametrization-6 Self
Consistent Field approach (PM6-SCF) [14], the shifts of the
Coronene ground state have also been calculated as a function of
N. As presented in Figure 4, the Single Occupied Molecular Orbital
(SOMO) of a Au
1
–Coronene complex is nearly a pure Au 6s atomic
orbital. The location of this 6s Au orbital in the Coronene HOMO–
LUMO energy gap is responsible for the stabilization of the
Figure 2. Set of spectra recorded on a Coronene molecule and on each of the Au
n
–
Coronene complexes investigated (n: 1, 2, 3) showing how each additionally
coordinated gold atom, resulting in a Au
n
–Coronene, produces a further spectral
shift with respect to Au
(n1)
–Coronene. STM topographic images (2 nm 2 nm) of
each molecule-metal complex the spectra were taken from are also shown, the
exact location each spectrum is taken is also indicated with a solid dot in each
image. Here the numbers in parenthesis indicate the Coronene’s outer phenyl rings
the gold atoms were coordinated to, as it is shown in the hexagon at the bottom left
representing Coronene’s outer phenyl rings symmetry.
Figure 3. Spectral downshift of Coronene’s ground state tunnelling resonance
commensurated to each additional atom coordinated to form Au
n
–Coronene. The
dots correspond to experimentally measured resonances. From the best linear fit,
plotted as a dotted line, the electronic interaction
a
= 552 meV between a single Au
adatom and the physisorbed Coronene molecule is determined. The Coronene
resonances are given in energy scale relative to the Fermi level of the Au(11 1)
surface. Inset: two levels model diagram showing the energy shifts resulting from
the electronic coupling
a
between |g> the ground state of a Coronene molecule and
|i> the state corresponding to one Au atom input. Because this electronic coupling,
|g> shifts down in energy by
a
2
/
D
and |i> shifts up in energy by
a
2
/
D
, with
D
being
the initial energy difference between those 2 states.
C. Manzano et al. / Chemical Physics Letters 587 (2013) 35–39 37
Coronene HOMO. When the Coronene is interacting with two Au
atoms, the HOMO and LUMO of the Au
2
–Coronene complex are
essentially the symmetric and anti-symmetric superposition of
the two Au 6s. The native HOMO of the bare Coronene now be-
comes an HOMO-1 and is shifted down again in energy as com-
pared to the Au
1
–Coronene complex. For the Au
3
–Coronene
complex, the three Au 6s give rise to 3 molecular orbitals HOMO,
SOMO, and LUMO. These states are also located within the bare
Coronene HOMO–LUMO energy gap and stabilize even more the
native Coronene HOMO which is again the HOMO-1 of the Au
3
–
Coronene complex. With a good selection of the metal atom input
and of its location relative to the Coronene
p
system, the initial
HOMO of the Coronene can be pushed down in energy following
a linear law as given by the simple model discussed above. For this
reason, we have selected the series (1), (1,3) and (1,3,5) because
this is the only series which ensure a good and symmetric indepen-
dence between the 3 inputs, a linear energy downshift of Coron-
ene’s ground state resulting in a linear counting effect as shown
in Figure 3. Setting another input configuration series like (1),
(1,2) and (1,2,4) will not lead to a linear counting effect since for
(1,2), the direct interaction between the 2 Au atoms is too strong.
This can be observed in Figure 4 where the HOMO–LUMO gap of
the (1,3) and (1,4) complexes is almost the same while the (1,2)
HOMO–LUMO splitting is very large, indicating a large interaction
between the two Au atoms. The only difference between the PM6-
SCF calculations and the Figure 3 curve is that the
a
2
/
D
slope ex-
tracted from the calculated spectra is double the one observed
experimentally since in the Figure 4 calculations, the considered
Au atoms are not adsorbed on a metal surface.
4. Conclusion
In this Letter, we have demonstrated both experimentally and
theoretically that Au adatoms manipulated to interact with a single
Coronene molecule downshift in energy the ground state of the
Au
n
–Coronene complexes. This downshift is linear as a function
of the number of contacted Au atoms. Measured as an output using
the STM tip, these energy shifts can be used to count the number of
atom inputs. This counting effect will not Letter in a hexa-peri-
benzocoronene (HBC) molecule since its six peripheral phenyl
rings are clearly decoupled from the central part of the molecule.
Indeed accordingly to our theoretical model for a target molecule
to function as a counter, the spatial distribution of the molecule
HOMO electron cloud should be fully delocalized over the entire
molecule. In the case of HBC its HOMO is localized on its central
part and consequently is not sensitive to Au atoms interacting with
its peripheral phenyl rings.
Figure 4. Electronic structure diagrams and molecular orbitals of the Coronene molecule and of the Au
n
–Coronene complexes calculated using the PM6-SCF method. These
calculations clearly show the incremental energy shifts of the electronic states corresponding to the HOMO-1 of the Au
n
–Coronene complexes with each subsequent
coordinated gold atom.
38 C. Manzano et al. / Chemical Physics Letters 587 (2013) 35–39
We have also calculated how the counting effect stands using a
larger Au
n
–circumcoronene series where 6 outer phenyls are avail-
able on the circumcoronene external phenyl crown. Indeed the cir-
cumcoronene HOMO is downshifted in energy as a function of the
number of Au atoms interacting with its
p
system. Even if the num-
ber of interacting Au reaches a maximum of 6, the shift is linear
with no apparent saturation because in the HOMO state, the orbital
weight of the outer phenyl decreases due to this ground state
quantum normalization. For even larger circular
p
conjugated sys-
tems corresponding to a nanographene-like macromolecule disk,
the HOMO normalization will stabilize the counting effect since
the number of central phenyl rings will increase faster than the
number of available phenyls on the last outer crown of the disk.
It remains to be determined how fast this effect occurs as a func-
tion of the disk diameter to estimate the maximum number of
Au atoms a nanographene disk can count.
Acknowledgments
We acknowledge financial support from the Agency of Science,
Technology and Research (A⁄STAR) for the Visiting Investigator-
ship Program (Phase III): AtomTech Project and the AtMol (2011–
2014) European Commission integrated project.
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