Angewandte
Chemie
linear dimers) the observed molecular arrangements (Fig-
ure 3b). The array of trimers results in a honeycomb arrange-
ment of molecules which is aligned with the graphene
monolayer superstructure and encloses the areas of bright
contrast arising from the moirꢀ pattern.
0.1 nm) than their expected separation in an extended array,
pffiffiffi
am= 3 (1.70 ꢁ 0.06 nm). Thus, we expect these junctions to be
strained in an extended honeycomb array, leading to a
reduced binding energy, and propose that this accounts for
the stability of rows for the two molecules PTCDI and DP-
PTCDI, whereas only the molecule with the strongest
predicted trimer junction, DB-CTCDI forms a honeycomb
array.
The presence of alkyl side-chains is known from previous
studies of DP-PTCDI to enhance the stability of a chiral
molecular trimer vertex (illustrated in Figure 3d) as com-
pared with the linear hydrogen-bonded PTCDI-PTCDI
junctions.[22] A comparison of Figures 2a and 3a,b indicates
a progressively enhanced stabilization of a trimer vertex as
the alkyl chain length increases from zero length (PTCDI)
through to the longest chain (DB-CTCDI). This leads to a
change in morphology from the rows, for PTCDI, through to
the honeycomb DB-CTCDI, with the DP-PTCDI being
considered as an intermediate case where linear segments
co-exist with junctions of three molecules. The enhanced
stability of the trimer vertex for molecules with longer alkane
chains is supported by density functional theory (DFT)
calculations (performed in the gas-phase in the absence of
the substrate; see Supporting Information) as summarized in
Table 1 which shows the greatest difference between trimer
The images in Figures 2 and 3 show clearly that the
adsorbed molecules experience a local potential due to the
graphene superstructure which is sufficiently strong to inhibit
the formation of two-dimensional islands. The origin of this
potential has recently been discussed by Brugger et al.[13] who
showed that for both graphene and boron nitride monolayers
on Ru(0001) (closely related to Rh(111)) variations in local
work function lead to a periodic potential. However, the
topography of the resulting potentials which arise for
graphene and BN show significant differences. In particular,
for graphene on Ru(0001) the high symmetry points (equiv-
alent to the centers of the light blue hexagon in Figure 1b)
were shown to be energy maxima, while the energy minima
were shown to form a honeycomb network corresponding to a
connected region following, approximately, the edges of the
light blue hexagon in Figure 1b). In contrast, molecular
adsorption on BN occurs preferentially approximately mid-
way between the center and edge of the unit cell of the moirꢀ
superstructure as previously discussed by Dil et al.[26] The
placement of molecules which we observe is in excellent
agreement with the different potential landscapes arising
from the homoatomic character of graphene and the heter-
oatomic character of BN, respectively, as discussed by
Brugger et al.[13]
There are parallels with other systems where molecules or
clusters are adsorbed at sites on an ordered array of local
potential wells arising from self-organization due to, for
example, surface reconstruction or dislocation arrays,[27–29]
including those adsorbed on boron nitride[15] and graphene
monolayers.[6] However a distinguishing feature of our work is
the observation that the trapping potential is sufficiently
compliant to allow the molecules to relax and adopt a local
configuration which is controlled by interactions with mole-
cules trapped in neighboring energy minima so that extended,
connected structures may be formed. This represents an
example of a system which exhibits hierarchies of order,[30]
since the formation of the molecular rows is determined by
intermolecular interactions but the placement and separation
of the rows is guided by the underlying level of organization
due to the moirꢀ pattern. The control of row separation is
shown in Figure 2a and more clearly for a higher molecular
coverage in Figure 2g.
Table 1: Calculated binding energies, intermolecular separations d and
vertex separations 2r.[a]
EdHB [eV] d [nm] EtHB [eV] 2r [nm] EtHBꢀEdHB [eV]
(DFT)
PTCDI
DP-PTCDI 0.46
DB-CTCDI 0.45
0.46
1.44
1.45
1.44
0.52
0.57
0.57
1.61
1.63
1.60
0.06
0.11
0.12
[a] EdHB: energy per molecule in a row of dimers; EtHB: energy per
molecule in an extended honeycomb array of trimers. The values are
calculated as described in the Supporting Information. The relative
stability of the trimers over the dimers shows a trend of increasing
stability from PTCDI to DB-CTCDI, which is consistent with our
experimental observations. Also tabulated are the calculated intermo-
lecular separations for the dimer, d, and the vertex separation, 2r, for the
trimer (see Figures 2 and 3 for definition of distances).
and dimer binding energies is predicted for DB-CTCDI.
These data also indicate that, in the gas phase, the trimer is
more stable for DP-PTCDI and even for PTCDI. An
additional contribution to the stabilization energy arises due
to the van der Waals interactions of the alkyl chains, but is not
captured in the DFT calculations. This is estimated, using
classical force fields (see Supporting Information) applied to
the optimized geometries calculated using DFT. We find that,
for DP-PTCDI and DB-CTCDI, the difference in energies
between trimers and dimers is increased by ca. 0.2 eV due to
the presence of the alkyl chains.
Also tabulated in Table 1 are the calculated separations of
the intermolecular junctions. For dimers formed from all of
the molecules investigated, the calculated equilibrium sepa-
ration is very close (within 0.03 nm) to am/2 (the observed
spacing of molecules in the commensurate rows is 1.47 ꢁ
0.05 nm). However, the predicted separation for intermolec-
ular trimer junctions (Table 1) is significantly lower (by up to
The attachment of alkane chains to DP-PTCDI and DB-
CTCDI leads to a surface-induced chirality[31] for these
molecules. Furthermore, the trimer junction is intrinsically
chiral. Images of the DB-CTCDI network shown in Fig-
ures 3g and h confirm that the molecules are in a chiral
arrangement (both chiralities have been observed with
domain sizes of up to 30 nm). Specifically in Figure 3h the
bright intramolecular features form a hexagon with an axis of
symmetry rotated with respect to the principal axes of the
Angew. Chem. Int. Ed. 2010, 49, 1794 –1799
ꢀ 2010 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
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