Nanopatterning by molecular polygons

Article abstract of DOI:10.1021/ja203536t

Molecular polygons with three to six sides and binary mixtures thereof form long-range ordered patterns at the TCB/HOPG interface. This includes also the 2D crystallization of pentagons. The results provide an insight into how the symmetry of molecules is

Full text of DOI:10.1021/ja203536t

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pubs.acs.org/JACS
Nanopatterning by Molecular Polygons
Stefan-S. Jester,* Eva Sigmund, and Sigurd H€oger*
Kekulꢀe-Institut f€ur Organische Chemie und Biochemie, Rheinische Friedrich-Wilhelms-Universit€at Bonn, Gerhard-Domagk-Strasse 1,
53121 Bonn, Germany
S Supporting Information
b
ABSTRACT: Molecular polygons with three to six sides
and binary mixtures thereof form long-range ordered pat-
terns at the TCB/HOPG interface. This includes also the
2D crystallization of pentagons. The results provide an
insight into how the symmetry of molecules is translated
into periodic structures.
Figure 1. Molecular models of the cyclooligomers [1]n, n = 3À6.
Maximum diameters of circles fitted into the cores: [1]3, 1.5 nm; [1]4,
2.4 nm; [1]5, 3.0 nm; [1]6, 3.8 nm.
he adsorption of rigid (conjugated) oligomers on solid
surfaces is an effective way to produce long-range ordered
T
two-dimensional nanoscale functional arrays.1 To ensure suffi-
cient compound solubility—necessary to isolate, purify and
characterize the final target structures and their precursors—
alkyl chains are attached to the molecular backbones. Moreover,
linear alkyl chains drive the molecule physisorption onto the
substrate, and link the adsorbates by side chain interdigitation.2,3
A powerful tool for the investigation of monolayers on solid
surfaces is scanning tunneling microscopy (STM), often performed
in situ at the liquid/solid interface using 1,2,4-trichlorobenzene
(TCB) as solvent and highly ordered pyrolytic graphite (HOPG)
as substrate. Surface regions covered with backbones and crystal-
lized alkoxy substituents appear in bright and dark color, re-
presenting high and low tunneling efficiencies, respectively.4,5
Within the past decade, considerable effort has been given to ex-
plore the design rules for the creation of superstructures that are based
not only on linear but also on kinked and cyclic oligomers.7 Never-
theless, research on molecular multicomponent architectures8,9 and
on patterns by pentagonal10 or heptagonal molecules is still in its
infancy. However, it is of fundamental relevance how the symmetry of
molecules is translated into periodic patterns.11
Here we report the synthesis and patterns of shape-persistent
macrocycles [1]n (n = 3À6) based on condensed oligothiophene
corner pieces linked via phenylene-ethynylene-butadiynylene
(PEB) units (molecular models and chemical structures are
shown in Figures 1 and 2, respectively).12
The macrocycles were prepared by Pd-catalyzed oxidative cyclo-
oligomerization of the appropriate bisacetylenes.13 Separation
of the crude product by recycling gel permeation chromato-
graphy (recGPC) yielded the monodisperse compounds [1]n
(n = 3À6) (see Supporting Information). All macrocycles carry
extraannular butyloxy chains at the heteropolycyclic corners and
hexadecyloxy chains at the adaptable positions of the polygon
sides, ensuring sufficient solubility of the target structures and the
respective precursors. The molecules can be viewed as building
blocks with symmetries Dnh (n = 3À6); however, the ring sizes
and the alkoxy substituents guarantee a slight elastic deform-
ability of the compounds (“soft polygons”).
Figure 2. Molecular structures of the cyclooligomers [1]n, n = 3À6.
We investigated the molecular surface patterns of the pure
compounds [1]n and binary mixtures thereof by means of STM.
The experiments were performed under ambient conditions at
the interface of 10À4À10À7 M solutions of the respective com-
pound in TCB and HOPG. All macrocyclic oligomers assemble
to highly ordered 2D patterns.
Trimers [1]3 form at low concentration (10À6 M, Figure 3a) a
honeycomb network (p6mm symmetry)14 where the macrocycle
backbones (macrocyclic triangles) and interdigitating hexade-
cyloxy substituents define the corners and sides of the hexagonal
Received: April 18, 2011
Published: June 16, 2011
r
2011 American Chemical Society
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Figure 3. STM images and molecular models of the cyclooligomer patterns at the TCB/HOPG interface. (a), (b) [1]3 (a: c = 10À6 M, 40.0 Â 40.0 nm2,
VS = À1.0 V, It = 4 pA, thermally annealed for 30 s at 60 °C; p6mm, a = 8.2 ( 0.2 nm, b = 8.1 ( 0.2 nm, γ(a,b) = 60 ( 2°; b: c = 10À5 M, 35.5 Â 35.5 nm2,
VS = À1.0 V, It = 4 pA, thermally annealed for 1 min at 60 °C; p2mg, a = 7.8 ( 0.2 nm, b = 3.7 ( 0.1 nm, γ(a,b) = 90 ( 2°), and (c), (d) [1]4 (c: c = 10À6 M,
29.5 Â 29.5 nm2, VS = À0.8 V, It = 30 pA, thermally annealed for 1 min at 80 °C; p2, a = 5.6 ( 0.2 nm, b = 5.4 ( 0.2 nm, γ(a,b) = 73 ( 2°; d: c = 10À5 M,
34.9 Â 34.9 nm2, VS = À1.2 V, It = 10 pA, thermally annealedfor1 min at60 °C; p2, a = 5.6( 0.2 nm, b = 3.8 ( 0.1 nm, γ(a,b) = 76 ( 2°). The unit cells are
shown in red; the white lines indicate the HOPG main axis directions.5
intermolecular cavities with 6 nm diameter, respectively. In
addition, the triangles provide interior pores with diameters of
about 2 nm. The packing is supported by the 3-fold backbone
symmetry, in accordance with the directions of the hexadecyloxy
substituents, located at the adaptable positions of the triangle
sides. They point outward to maximize the intermolecular
linkages by an interdigitated alignment (along the HOPG main
axis directions). At increased concentration (10À5 M, Figure 3b),
a more dense packing results as an effect of higher adsorption
degree.6c The macrocycles are assembled toward a crystal with
mirror lines in one direction and glide mirror lines in the
perpendicular direction to yield a p2mg plane group. Four
hexadecyloxy substituents of two sides adsorb at the interface—
intermolecularly interdigitated along two main axes of the
substrate—while the other two chains point toward the solution
phase or fill the inner ring cavity in a disordered fashion.
Tetramers [1]4 (c = 10À6 M) assemble into an oblique pattern
(Figure 3c) with p2 symmetry. All eight hexadecyloxy chains are
extraannularly oriented and adsorbed along the substrate main
axes with 60° alignment between the substituents of adjacent
backbone sides. This leads to a distortion of the (predicted)
quadratic backbone conformation (R] = 90°) toward a rhombic
shape (R] = 102 ( 3°). At increased concentration (10À5 M,
Figure 3d), only four alkoxy substituents of two opposing sides of
[1]4 adsorb onto the substrate, while the other four substituents
are not imaged. The alkoxy chain commensurability with the
underlying graphite allows in this case a (nearly) quadratic struc-
ture of the backbones. p2 symmetry is observed.15
Figure 4. STM images and molecular models of the patterns of (a) [1]6
(c = 2 Â 10À6 M, 62.8 Â 62.8 nm2, VS = À1.0 V, It = 6 pA, thermally
annealed for 1 min at 60 °C; p6mm, a = 7.5 ( 0.1 nm, b = 7.5 ( 0.1 nm,
γ(a,b) = 60 ( 2°) and (b) a binary mixture of [1]3 and [1]6 (c([1]3) =
10À5 M; c([1]6) = 10À7 M; c([1]3)/c([1]6) = 100:1; 79.9 Â 79.9 nm2,
VS = À0.8 V, It = 9 pA; p6mm, a = 9.8 ( 0.2 nm, b = 10.1 ( 0.2 nm,
γ(a,b) = 60 ( 2°) at the TCB/HOPG interface. The unit cells and sub-
strate main axis directions are indicated in red and white color, respectively.16
Hexamers [1]6 at 2 Â 10À6 M adsorb in an oblique nearly
hexagonal packing (Figure 4a; p6mm plane group). The back-
bone geometries match the substrate symmetry, and all hexade-
cyloxy substituents point outward, interdigitate, are aligned along
the HOPG main axes and stabilize a dense network. Trigonal and
hexagonal pores are here defined as intermolecular and intramo-
lecular cavities, respectively, inversely to [1]3, although of
comparable size. At increased concentration, the backbones of
[1]6 collapse toward a rectangular shape and assemble to a more
dense packing, where the alkoxy substituents of two opposing
sides interdigitate intermolecularly, and the remaining alkoxy
substituents interdigitate within the cavity (see Supporting
Information).
Shapes and sizes of the oligomers discussed above encouraged
us to investigate binary mixed adlayers formed by macrocycles
(polygons) which differ in the degree of oligomerization (corner
or side numbers). In some cases only short-range adsorbate
ordering (e.g., [1]3 and [1]4) is observed, or island structures of
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Figure 5. STM image and molecular model of a self-assembled mono-
layer of a mixture of [1]4 and [1]6 at the TCB/HOPG interface (c([1]4) =
c([1]6) = 7 Â 10À7 M, 37.2 Â 37.2 nm2, VS = À0.8 V, It = 5 pA,
thermally annealed for 30 s to 80 °C). The white lines indicate the
HOPG main axis directions. Arrows indicate molecules [1]6 of a
structure allowing intraannular alkoxy chain interdigitation (dark intra-
annular regions in the STM image).5
one compound are fenced by another macrocycle (e.g., [1]6 and
[1]5) (see Supporting Information). However, [1]3 and [1]6
form spontaneously a mixed phase after applying a solution of
10À5 M [1]3 and 10À7 M [1]6 (100:1) to the HOPG substrate
(Figure 4b). The interdigitation of the hexadecyloxy substituents
and the shape complementarity of the trigonal backbone of [1]3
and the hexagonal backbone of [1]6 lead to a 2:1 mixed pattern of
triangles and hexagons with a p6mm plane group, similar to the
isolated compounds (cf. Figures 3a and 4a).17 No triangle is (by
the binding motif of interdigitating hexadecyloxy chains) con-
nected to other triangles and no hexagon is connected
to other hexagons À only heterogeneous neighboring occurs.
Occasionally, also another phase of the mixed compounds [1]3
and [1]6 is observed, where the hexagonal porous structure of
pure [1]3 is maintained (as seen in Figure 3a), and hexagons [1]6
intercalate randomly into some of the cavities (and no alkoxy
substituents of [1]6 contribute to the packing, see Supporting
Information).
The importance of the match of the components’ symmetry
for the formation of ordered coadsorbates becomes clear when a
mixture of [1]4 and [1]6 is investigated. No long-range ordered
pattern could be observed. Occasionally, [1]4 induces a lattice
distortion in [1]6, leading in some cases even to a conformational
flip (Figure 5). One corner of a hexagon turns inward, reduces
the distances between sides aligned in parallel, and leads to an
intraannular interdigitation of the alkoxy substituents.
Figure 6. (a), (b) STM images and models of patterns of [1]5 at the
TCB/HOPG interface (a: c = 4 Â 10À7 M, 73.2 Â 73.2 nm2, VS = À1.0 V,
It = 5 pA, thermally annealed for 1 min at 80 °C; p6, a = 19.6 ( 0.5 nm,
b = 19.3 ( 0.5 nm, γ(a,b) = 61 ( 2°; b: c = 10À6 M, 73.2 Â 73.2 nm2,
VS = À0.6 V, It = 5 pA, thermally annealed for 1 min at 80 °C; p2, a = 12.7
( 0.2 nm, b = 12.6 ( 0.2 nm, γ(a,b) = 89 ( 2°). In the molecular model
shown in (a), only commensurably adsorbed hexadecyloxy substituents
interdigitating with chains of adjacent molecules are shown. The unit
cells are displayed in red, the repeating units are marked by the blue
polygons, and the white lines indicate the HOPG main axis directions. In
the schematic representations in the lower part, colors indicate different
orientations of the pentagons. In (a), six different orientations occur
to form a hexagonal repeating unit, while in (b) only four different
orientations are observed and form the rhombic repeating unit. In (a)
and (b), the linear rows (indicated by blue rectangular boxes) can be
divided into hexuples and quadruples/dimers, respectively. Note: The
idealistic molecular model in (b) involves equilateral pentagons, while
the pentagons observed in the STM image are significantly distorted.
With regard to the importance of the symmetry the pattern
formation of the pentagons [1]5 is of special interest. 5-fold-symmetric
molecules can not form crystalline tilings (i.e., densely packed
patterns) on the Euclidean plane. However, recent work, for
example, on corannulenes,10 has displayed how nature generates
structures with appropriate symmetry to resolve this problem. In
the present case, it is neither clear if the pentagons form an
ordered pattern at all, nor how the molecules achieve that.17,18
Figures 6a and b show that we are indeed able to observe two
distinguishable long-range ordered patterns when solutions of
pentamers [1]5 are brought into contact with the HOPG surface.
At a concentration of 4 Â 10À7 M, [1]5 forms porous structures
with hexagonal symmetry, where six pentagons assemble around
a central cavity into which the pentagon corners point (see
Figure 6a, bottom). The 5-fold rotational symmetry (C5) is lost
after adsorption to the surface to yield a rotational symmetry C1.
The hexagonal assemblies form an oblique (not ideally
hexagonal) overstructure. The crystal plane group is p6. Six
alkoxy substituents of three sides of each pentagon interdigitate
with substituents of three pentagons of two neighboring hex-
agonal assemblies (and thus contribute to the packing), whereas
the adaptable substituents of the remaining two sides point into
the central cavity or toward the solvent and do not interdigitate.
Not any two neighboring pentagons within such a hexagonal
superstructure are directly linked by side chain interdigitation.
They are always connected via a third (bridging) pentagon,
assembled within a neighboring hexagonal superstructure. Alter-
natively, the packing can be described as parallel linear rows of
macrocycles (following three directions with 60°/120° row-row
angles), interrupted by a void on every seventh lattice site (see
Supporting Information). Every molecule covers 55.2 nm2 (as
derived from the unit cell area divided by the number of
molecules, here 6, per unit cell). If the concentration of penta-
gons [1]5 is increased to 10À6 M, a more dense packing
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(40.0 nm2 per molecule) is observed (Figure 6b). The repeating
unit can be viewed as a rhombic assembly of four pentagons with
corners pointing to the center (blue rhombus in Figure 6b,
middle), and a nearly rectangular unit cell can be indexed. The
molecules pack in a crystal with plane group p2. All five backbone
sides of each pentagon contribute to the intermolecular interac-
tions via interdigitating alkoxy substituents. As for the less dense
packing, the molecules can be viewed as arranged in rows that
are aligned along the three main symmetry axes of the HOPG.
Along two directions, four pentagons [1]5 are connected via interdigi-
tated side chains to form quasi-linear quadruples, discriminated
by interruptsresultingfrom noncomplementaryterminal pentagon
corners of adjacent quadruples, pointing toward each other.
Along the third direction, pentagons connected by interdigitated
side chains assemble to a stepped straight line (* in Figure 6b),
where each dimer of pentagons [1]5 is slightly translated in
parallel. The orientations of the molecules in Figure 6a and b are
not congruent with each other. The intercalation of a seventh
molecule per unit cell in Figure 6a would decrease the required
area to 47.3 nm2 per molecule, still 18% larger than the average
spatial requirement of each molecule in Figure 6b. Thus, the
packing shown in Figure 6a cannot be transferred to the denser
pattern (Figure 6b) without general reorientation of the mol-
ecules and changes of the intermolecular distances.
’ ACKNOWLEDGMENT
Financial support by the DFG, the SFB 624, and the Volks-
wagenStiftung is gratefully acknowledged.
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can cover an HOPG surface.
In summary, we have shown that the oligomeric macrocycles
behave as “molecular polygons” of different symmetries. Cyclo-
oligomerization and separation of the crude product via recGPC
has proven as an efficient method for the preparation of these
molecules, which support the formation of molecular porous and
dense long-range ordered patterns of complementary shapes.
The results allow an efficient and deliberately predictable pattern
design based on equilateral polygons and their mixtures with
periodicities up to 19 nm. In addition, the elasticity of the “soft”
molecule backbones and their flexible alkoxy fringe supports a
crystallization of pentagons. All pattern dimensions are tunable
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distances), but also by the backbone diameters (defined by the
length of the PEB rigid rod units and the corner building
blocks). Current studies will cover that issue and in addition
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and the investigation of their patterns. Ultimately, design rules
for classical (macroscopic) polygon tilings can be adapted to
the supramolecular surface patterning by molecular building
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’ ASSOCIATED CONTENT
(16) The requirement of the concentration ratio c([1]3):c([1]6) =
100:1 originates from different adsorption efficiencies and has been
reported before (cf. ref 9d). In other words, [1]6 adsorbs much more
effectively than [1]3.
S
Supporting Information. Additional STM images, ex-
b
perimental procedures and characterization for all new com-
pounds. This material is available free of charge via the Internet at
http://pubs.acs.org.
(17) Gr€unbaum, B.; Shephard, G. C. Tilings and Patterns; Freeman:
New York, 1987; pp 57À112.
’ AUTHOR INFORMATION
(18) Schilling, T.; Pronk, S.; Mulder, B.; Frenkel, D. Phys. Rev. E
2005, 71, 036138.
Corresponding Author
hoeger@uni-bonn.de; stefan.jester@uni-bonn.de
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