Self-assembly of fivefold-symmetric molecules on a threefold-symmetric surface

Article abstract of DOI:10.1002/anie.200805689

Buckybowls: The adsorption of penta-tert-butylcorannulene, a molecule with fivefold symmetry, on Cu(111), a surface with threefold symmetry, is investigated by scanning tunneling microscopy complemented by structure calculations. The symmetry mismatch is

Full text of DOI:10.1002/anie.200805689

Communications
DOI: 10.1002/anie.200805689
Corannulene Derivatives
Self-Assembly of Fivefold-Symmetric Molecules on a Threefold-
Symmetric Surface**
Olivier Guillermet, Eeva Niemi, Samuthira Nagarajan, Xavier Bouju, David Martrou,
Andrꢀ Gourdon, and Sꢀbastien Gauthier*
Fivefold rotational point-group symmetry plays a special role
because of its incompatibility with translational symmetry.
This symmetry mismatch has attracted interest for a long
time, going back to Dꢀrer[1] and Kepler,[2] who demonstrated
that a wealth of unusual structures could be produced by tiling
the plane with regular pentagons. These ideas have been used
with great success in biology to understand the structure of
virus capsids made from pentamers[3,4] and in material science
to clarify the nature of quasi-crystals.[5,6] Transposed into the
domain of surface science, they suggest that new and
interesting patterns could be formed by depositing fivefold-
symmetric molecules onto a substrate.[7] An example of this
approach was reported recently. The adsorption on Cu(110)
of corannulene, which is a C60 fragment bowl with a fivefold
Figure 1. Ball-and-stick representations and van der Waals surfaces of
symmetry axis (Figure 1a), was studied by scanning tunneling
microscopy (STM) and other techniques.[7] The molecules
form a quasi-hexagonal superlattice whose structure is
dominated by the vertical molecule–substrate interaction.
The molecules occupy identical adsorption sites in one
domain. But the large distance between these sites leads to
a rather small contribution of the fivefold molecular symme-
try to the intermolecular interaction, which appears not to be
strong enough for the symmetry mismatch to significantly
influence the resulting structure. To observe more pro-
nounced effects, the strength of the intermolecular interac-
tions must be increased to reach the onset of short-range
repulsive interactions, at which point the fivefold shape of the
molecule is expected to contribute in a much stronger way. On
crystalline surfaces, where the molecules tend to stay at or
near their preferred adsorption site, this requirement can be
met if the size of the molecule fits adequately with the
substrate (i.e. if it is “commensurate”) for neighboring
molecules to approach closely or even to come in “contact”.
a) corannulene and b) PTBC (top and side views). The van der Waals
surfaces were produced with Jmol.[10]
We report herein on the adsorption of a corannulene
derivative, penta-tert-butylcorannulene[8] (PTBC; Figure 1b),
on the high-symmetry Cu(111) surface studied by low-
temperature STM (5 K) and structure calculations. Note
that the synthesis of corannulene has been improved to
achieve an overall yield of 32% from 2,7-dimethylnaphtha-
lene, compared to 13% with standard methods (see the
Supporting Information). The addition of five tert-butyl
groups enhances the fivefold shape of the molecule relative
to that of corannulene, as indicated qualitatively by the van
À
der Waals surfaces displayed in Figure 1. Furthermore, the C
C s bonds connecting these lateral groups to the central part
of the corannulene molecule are rather flexible, giving the
molecule the possibility to adapt itself to the substrate surface
structure and rendering the commensurability condition
mentioned above less stringent.
Note that the bowl-to-bowl inversion, which is known to
happen easily at room temperature in corannulene,[9] is also
likely to affect PTBC, but this process should be frozen at low
temperature and for the adsorbed molecule. The PTBC
molecule thus adopts two chiralities, as two equivalent sets of
sites are available for the tert-butyl groups on the corannulene
core.
Deposition of PTBC on Cu(111) at room temperature and
subsequent annealing at 1008C for one hour leads to the
formation of molecular islands, (STM image in Figure 2a),
which coalesce to form a monolayer at higher coverage (see
Supporting Information Figure S2). In this structure, individ-
ual molecules appear as five lobes surrounding a central
depression in a fivefold-symmetric pattern (Figure 2b). As
shown below, each of the five lobes marks the position of a
[*] Dr. O. Guillermet, Dr. E. Niemi, Dr. S. Nagarajan, Dr. X. Bouju,
Dr. D. Martrou, Dr. A. Gourdon, Dr. S. Gauthier
CEMES-CNRS
29 rue J. Marvig, P.O. Box 94347, 31055 Toulouse (France)
Fax: (+33)5-6225-7999
E-mail: gauthier@cemes.fr
[**] Partial support by the European Commission within the project
PicoInside (Contract No. IST-015847) is gratefully acknowledged.
E.N. thanks CNRS for a postdoctoral fellowship, Academy of
Finland and Tekniikan edistꢀmissꢀꢀtiꢁ. S.N. acknowledges the
award of a BOYSCAST fellowship from the Department of Science
and Technology of the Indian Government. Computational resour-
ces at the Centre de Calcul Midi-Pyrꢂnꢂes are gratefully acknowl-
edged.
Supporting information for this article is available on the WWW
under http://dx.doi.org/10.1002/anie.200805689.
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Figure 2. a) STM image of an island of PTBC on Cu(111). M indicates
a single PTBC molecule (monomer), and T indicates an assembly of
three molecules (trimer). The rhombus and the hexagon delineate a
unit cell and its seven-molecule basis. T=5 K, V=À1.1 V, I=174 pA.
Image size 18.1ꢃ21.4 nm. b) Enlargement of a single PTBC molecule
(off-center monomer in a cavity). Image size 1.94ꢃ2.1 nm. c) Com-
puted STM image of a single PTBC molecule.
Figure 3. Calculated adsorption configuration of a,b) the PTBC mono-
mer on Cu(111), c) the homochiral dimer and d) the heterochiral
dimer. The white lines in (c) and (d) correspond to the van der Waals
surfaces of the molecules, and the arrows show the symmetry
operations in the dimers.
tert-butyl group, as previously observed with Lander mole-
cules.[11,12]
As can be inferred from Figure 3b, the tert-butyl groups
do not play a major role in the adsorption of a single PTBC
molecule. They are too far from the surface to contribute
except by their van der Waals interaction with the substrate.
The adsorption configuration of a single PTBC molecule
should then be comparable to that of corannulene. Indeed,
the adsorption configuration of PTBC is close to that
determined for corannulene in a monolayer domain on
Cu(110),[7] except that the molecular axis is tilted by 68
relative to the surface normal on Cu(110).
The STM image of a PTBC monomer on a bridge site was
computationally reproduced with the elastic quantum chemis-
try scattering technique (ESQC;[14] Figure 2c), which takes
into account the complete atomic structure of the tip and the
surface (see the Supporting Information). A good qualitative
correspondence with the experimental STM images is found
(Figure 2b), with the five lobes corresponding to the five tert-
butyl groups.
This supramolecular structure can be described as a tiling
of the plane involving two types of units: single PTBC
molecules (monomers) and assemblies of three molecules
(trimers). The trimers appear as compact, apparently three-
fold-symmetric objects, with a shape similar to a tip-truncated
triangle. Because they are not perfect triangles, they cannot
fill the plane, and some space is necessarily not covered. This
“lost” space is used to generate hexagonal cavities, which can
accommodate one monomer (Figure 2a). This particular
arrangement results in a nearly perfect filling of the plane.
A careful examination of Figure 2a (see Supporting
Information Figure S3) shows that the monomer can be
imaged in two different ways in the cavities: In the first one,
the molecule is off-center in the cavities, with two tert-butyl
groups closer to adjacent trimers. In the second, the monomer
appears with six lobes. The reasons for this latter phenom-
enon are unclear, and a definitive interpretation cannot be
provided at this stage.
Adsorption simulations were extended to systems of first
two, then three PTBC molecules in close proximity. The
energetically most favored configuration was calculated for
both homochiral (Figure 3c) and heterochiral dimers (Fig-
ure 3d). In both cases, the molecules adopt approximately the
same adsorption site as the isolated molecule. They are
located on the same type of bridge sites with the same
orientation (within Æ 0.2 ꢁ for the position and Æ 28 for the
orientation). In Figure 3c, the two adsorbed molecules are
approximately symmetry related by a 1208 rotation along a C3
axis of the substrate, which does not change the chirality. In
Figure 3d, they are related by a substrate mirror symmetry
The lattice in Figure 2a is hexagonal, with a unit cell given
11
À7 18
7
¯ ¯
in matrix notation by (
) (relative to the ([101], [011]) basis
set), comprising 247 copper atoms and a sixfold-symmetric
basis of seven molecules, as indicated in Figure 2a. On
average, one molecule occupies an area of more than 35
substrate atoms. Two domains of this structure exist, which
are related by a mirror symmetry element of the substrate
(see Supporting Information Figures S4 and S5).
The adsorption calculations for a single molecule were
carried out with an extended semiempirical atom super-
position and electron delocalization approach (ASED + ;[13]
see the Supporting Information). The molecule is found to sit
with the bowl opening pointing outwards from the surface.
The shape of the bowl is close to that in the free molecule, but
its depth has increased by 0.5 ꢁ (see the Supporting
Information). The pentagonal hub is positioned parallel to
the surface on a bridged site with one of the spoke bonds
¯
plane intersecting the surface along the [112] direction, which
changes the chirality of the molecule. The two molecules
constituting the dimer cannot align their edges as in a Dꢀrer–
Kepler pentagon tiling because of the molecular orientation
imposed by the substrate. The center-to-center intermolecular
distance is 14.3 ꢁ. As shown in Figure 3c,d, the van der Waals
surfaces of the two PTBC molecules are in contact for this
distance, suggesting that this structure is the most compact
configuration achievable for a dimer on this substrate.
¯
making an angle of approximately 98 with a [011] row of the
substrate (Figure 3a,b).
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Communications
The optimized structure for the homochiral trimer is
presented in Figure 4a. The molecules occupy approximately
equivalent bridge sites: the positions of two of the molecules
are nearly identical to the dimer positions, while the third
Figure 5. The van der Waals contours of molecular trimers super-
imposed on an STM image (T=5 K, 7.7ꢃ7.7 nm2, V=À0.7 V,
I=124 pA). Surface atoms are indicated by gray circles.
Figure 4. Optimized adsorption configuration of a) a homochiral and
b) a heterochiral PTBC trimer.
contribute in the contact regions between the molecules, and
interaction of the corannulene core with the substrate, which
tries to maintain the molecule in the optimal site of the
isolated molecule. The structure is highly compact: each
PTBC molecule is in contact with at least two neighbors,
except for the PTBC molecule centered in the cavity, as
discussed previously. This arrangement is due to the fulfill-
ment of the commensurability condition discussed above: the
molecules can be very nearly in contact while adsorbed on
their optimal site.
In conclusion, we have found an original structure of self-
assembled molecules in which they form trimers interacting
with each other and giving rise to a cavity hosting a single
molecule. The presence of the trimers can be seen as a way to
generate structures with symmetry compatible with that of
the substrate. The symmetry mismatch between the fivefold
symmetry of the molecules and the threefold symmetry of the
substrate is resolved in this way.
PBTC molecule (in the lower left-hand corner) is shifted by
0.6 ꢁ away from the bridge site and towards a hollow site. The
molecules in the trimer are approximately symmetry related
by 1208 rotations along a C3 axis of the substrate, giving the
trimer an approximate threefold symmetry. Calculations were
also performed for a trimer consisting of two PTBC molecules
of one chirality and a third PTBC molecule of the opposite
enantiomer. The resulting structure (Figure 4b) is not sig-
nificantly different, and the three molecules are even closer to
their optimal adsorption site.
Remarkably, the positions of the tert-butyl groups are
nearly identical for both trimers. These two configurations are
then expected to be indistinguishable in the STM image.
There are three points of contact between the three PTBC
molecules constituting the trimer, as indicated by the van der
Waals surfaces drawn in Figure 4. This observation suggests
that the compactness of the structure is limited by the short-
range repulsive interactions, which are determined by the
complex details of the conformation of the three tert-butyl
groups involved in the intermolecular contact. Comparison of
the two structures indicates that the interaction of the
corannulene with the surface plays a less important role, as
the adsorption configuration of the individual molecules is
slightly different in the two structures. This observation is
supported by energy calculations, which give a decrease of the
isolated-molecule adsorption energy of 0.04 eV from the
bridge site to the hollow site (0.13 eV to the top site), while
the van der Waals energy of a trimer is 0.15 eV.
The information extracted from the STM data and the
calculations are combined in the model presented in Figure 5.
It was built from trimers with the optimized adsorption
structure in Figure 4a. Note that it could have been done
equally well with the structure in Figure 4b, since the van der
Waals surfaces are nearly identical in both cases. It is seen that
a good agreement with the experimental data can be reached.
There is only one point of contact between adjacent trimers,
as indicated by the van der Waals surfaces drawn in Figure 5.
These observations show that the complex structure
adopted by the PTBC monolayer on Cu(111) results from
the contribution of three distinct interactions: Attractive van
der Waals interactions, which tend to maximize the compact-
ness of the structure, short-range repulsive interactions, which
Received: November 21, 2008
Revised: January 14, 2009
Published online: February 3, 2009
Keywords: corannulenes · scanning probe microscopy ·
.
self-assembly
[1] A. Dꢀrer, Unterweysung der messung mit.., 1st ed. 1525, 2nd ed.
1538, Hieronymus Formschneyder, Nꢀremberg, cited according
to Albrecht Dꢁrerꢂs Unterweisung der Messung (Ed.: A. Peltzer),
Munich, 1908.
[2] J. Kepler, Harmonices Mundi Libri V, Lincii Austriae, Sumptibus
Godofredi Tampachhii, Francof., 1519; German translation:
Johannes Kepler, Gesammelte Werke, Vol. VI, Harmonice
Mundi, (Ed.: Max Caspar), Beck, Munich, 1990.
[3] T. Tarnai, Z. Gaspar, L. Szalai, Biophys. J. 1995, 69, 612.
[4] A. J. Olson, Y. H. E. Hu, E. Keinan, Proc. Natl. Acad. Sci. USA
2007, 104, 20731.
[5] R. Penrose, Bull. Inst. Maths. Appl. 1974, 10, 266.
[6] D. L. D. Caspar, E. Fontano, Proc. Natl. Acad. Sci. USA 1996, 93,
14271.
[7] M. Parschau, R. Fasel, K.-H. Ernst, O. Grꢂning, L. Branden-
berger, R. Schillinger, T. Greber, A. P. Seitsonen, Y.-T. Wu, J. S.
Siegel, Angew. Chem. 2007, 119, 8406; Angew. Chem. Int. Ed.
2007, 46, 8258.
1972
www.angewandte.org
ꢀ 2009 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
Angew. Chem. Int. Ed. 2009, 48, 1970 –1973

Angewandte
Chemie
[8] a) A. Weitz, M. Rabinovitz, P.-C. Cheng, L. T. Scott, Synth. Met.
1997, 86, 2159; b) Y. Sevryugina, A. Y. Rogachev, E. A. Jackson,
L. T. Scott, M. A. Petrukhina, J. Org. Chem. 2006, 71, 6615.
[9] L. T. Scott, M. M. Hashemi, M. S. Bratcher, J. Am. Chem. Soc.
1992, 114, 1920.
[11] M. Alemani, L. Gross, F. Moresco, K.-H. Rieder, C. Wang, X.
Bouju, A. Gourdon, C. Joachim, Chem. Phys. Lett. 2005, 402,
180.
[12] T. Zambelli, S. Goudeau, J. Lagoute, A. Gourdon, X. Bouju, S.
Gauthier, ChemPhysChem 2006, 7, 1917.
[13] F. Ample, C. Joachim, Surf. Sci. 2006, 600, 3243.
[14] P. Sautet, C. Joachim, Phys. Rev. B 1988, 38, 12238.
[10] B. McMahon, R. M. Hanson, J. Appl. Crystallogr. 2008, 41, 811.
Angew. Chem. Int. Ed. 2009, 48, 1970 –1973
ꢀ 2009 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
www.angewandte.org
1973