Trimodular engineering of linear supramolecular miniatures on Ag(111) surfaces controlled by complementary triple hydrogen bonds

Article abstract of DOI:10.1002/anie.200802325

Simultaneous three-component assembly on surfaces mediated by triple H-bonding interactions leading to the formation of linear supramolecular miniatures has been studied on Ag(111) surfaces by STM. In particular, the complementary assembly of two linear m

Full text of DOI:10.1002/anie.200802325

Communications
DOI: 10.1002/anie.200802325
Supramolecular Surface Chemistry
Trimodular Engineering of Linear Supramolecular Miniatures on
Ag(111) Surfaces Controlled by Complementary Triple Hydrogen
Bonds**
Anna Llanes-Pallas, Manfred Matena, Thomas Jung, Maurizio Prato, Meike Stöhr,* and
Davide Bonifazi*
The basic concept of supramolecular chemistry is rooted in
the exploitation of molecular recognition events that take
advantage of spontaneous and reversible noncovalent inter-
actions for the assembly of two or more molecules into
organized architectures.[1] Selective noncovalent interactions
have been widely exploited both in solution and in the solid
state to prepare extended one- (1D), two- (2D), and three-
dimensional (3D) assemblies.[2] In this context, linear ordered
assemblies, such as supramolecular polymer-like wires,[3] are
appealing nanostructured systems because of their potential
applications as 1D electron-transfer mediators in futuristic
molecular-based devices.[4] To probe the local properties and
functions of the supramolecular assemblies, immobilization
on surfaces is a promising approach, as a direct insight into the
self-assembly mechanism, the ordering, and the functional
properties at the molecular level[5] can be obtained by
scanning probe microscopy (SPM) techniques (for example,
scanning tunneling microscopy (STM)).[6]
A classical approach towards the formation of supra-
molecular species by the spontaneous self-assembly of
precursor building blocks is the use of H bonds.[7] The
specificity, directionality, dynamics, and complementarity of
such interactions can allow for the design of a large library of
organic modules bearing H-bond donor (D) and/or acceptor
(A) moieties with specific programmed functions and struc-
tures that could ultimately lead to the construction of many
desired functional assemblies. So far, this method has been
successfully employed on solid surfaces for the preparation of
extended one-[8] and two-component[9] assemblies. To the best
of our knowledge, no examples of three-component mini-
aturized H-bonded architectures have yet been described.
Herein we report on the supramolecular engineering of
miniaturized assemblies in which three conjugated molecular
modules, 1–3 (Figure 1), are linearly assembled through
complementary triple H bonds. Specifically, by using low-
temperature (LT) STM under ultrahigh vacuum (UHV)
conditions we show that modules 1 and 2 form periodic
wire-like assemblies [(1·2)n] on Ag(111)surfaces. The struc-
ture and the length of the assembly can be changed by the co-
deposition of a molecular stopper (3), which terminates the
wires governing the formation of linear oligomeric minia-
tures.
[*] M. Matena, Dr. M. Stöhr
NCCR Nanoscale Science and Department of Physics
University of Basel
Klingelbergstrasse 82, 4056 Basel (Switzerland)
Fax: (+41)61-267-3784
E-mail: meike.stoehr@unibas.ch
A. Llanes-Pallas, Prof. Dr. M. Prato, Dr. D. Bonifazi
Dip. Scienze Farmaceutiche and INSTM UdR di Trieste
Università degli studi di Trieste
Piazzale Europa 1, 34127 Trieste (Italy)
Fax: (+39)040-52527
E-mail: dbonifazi@units.it
Dr. D. Bonifazi
Department of Chemistry, University of Namur
5000 Namur (Belgium)
Fax: (+32)81-725-433
E-mail: davide.bonifazi@fundp.ac.be
Dr. T. Jung
Laboratory for Micro- and Nanotechnology
Paul Scherrer Institute
5232 Villigen PSI (Switzerland)
[**] This work was financially supported by the EU RTN PRAIRIES,
contract MRTN-CT-2006-035810, MIUR (Firb RBIN04HC3S), the
SNSF, the NCCR “Nanoscale Science” in Basel, the Belgian
National Research Foundation (FRS-FNRS, through the contract
No. 2.4.625.08 F), and the University of Namur. A.L.P. thanks the
University of Trieste for the doctoral fellowship. We also thank the
Swiss Federal Commission for Technology and Innovation, KTI, and
Nanonis Inc. for the fruitful collaboration on the data acquisition
system.
Supporting Information for this article is available on the WWW
under http://dx.doi.org/10.1002/anie.200802325.
Figure 1. Chemical structures of the molecular modules bearing com-
plementary H-bonding recognition sites.
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The concept of obtaining linear
assemblies by association of mon-
omeric units through noncovalent
interactions was first reported by
Lehn and co-workers, who pre-
pared helical H-bonded polymers
with liquid-crystalline proper-
ties.[10] Inspired by the wealth of
this approach, we prepared mod-
ules 1–3. Molecules 1 and 2 feature
two complementary terminal H-
bonding sites, namely the 2,6-
di(acylamino)pyridyl (DAD, in 1)
and uracil (ADA, in 2) moieties,
which, in both cases, are connected
to a central phenyl ring through an
ethynyl spacer. Molecule 3, which
is terminated with an anthracyl
unit, bears only one uracil moiety
and thus can act as a molecular
stopper. Linear modules 1 and 2
(also called bis-(DAD) and bis-
(ADA) units, respectively) were
synthesized by a Sonogashira-type
cross-coupling reaction of 1,4-diio-
dobenzene with the respective eth-
Scheme 1. a) Ac2O, pyridine, RT, 10 h; b) [Pd(PPh3)4], CuI, TMSA, NEt3, THF, reflux, 12 h; c) KOH,
MeOH, RT, 40 min; d) 1,4-diiodobenzene, [Pd(PPh3)4], CuI, NEt3, THF, reflux, 12 h; e) 1-bromohex-
ane, K2CO3, DMSO, 408C, 20 h; f) LDA, THF, À788C, 1.5 h, then I2, 2 h, then AcOH, RT, 10 h;
g) [PdCl2(PPh3)2], CuI, TMSA, NEt3, toluene, RT, 12 h; h) 1,4-diiodobenzene, [Pd(PPh3)4], CuI, NEt3,
THF, RT, 12 h; i) 9-ethynylanthracene, [Pd(OAc)2], CuI, PPh3, iPr2NH, THF, reflux, 12 h. TMSA=trime-
thylsilylacetylene; LDA=lithium diisopropylamide.
ynyl derivatives 7 and 12, which bear the H-bonding sites
(Scheme 1). 4-Ethynyl-2,6-diamidopyridine 7 was obtained
from 4-bromo-2,6-diaminopyridine.[11] Acetylation of 4, fol-
À
lowed by palladium-catalyzed C C coupling with trimethyl-
silylacetylene and subsequent cleavage of the trimethylsilyl
protecting group with a solution of KOH in MeOH afforded
bis-(DAD) unit 7. Compounds 2 and 3, which bear the uracil
moieties, were prepared in the following way (Scheme 1).
Alkylation of 8 with 1-bromohexane afforded 9, which was
then regioselectively iodinated, affording 1-hexyl-6-iodoura-
cil 10. Sonogashira-type coupling of iododerivative 10 with
TMSA, followed by deprotection of the ethynyl moiety with a
MeOH/KOH mixture gave the uracil–acetylene conjugate 12.
A second Sonogashira coupling of the product 12 with 1,4-
diiodobenzene afforded the bis-ADA unit 2. Stopper 3 was
synthesized by direct Sonogashira-type coupling of 10 with 9-
ethynylanthracene (synthesized by using a slightly modified
procedure than that reported by Dang and Garcia-Gari-
bay[12]).
The homomolecular organization of molecule 2 on Ag-
(111) surfaces was investigated under UHV conditions at
77 K.[13] At submonolayer coverages, di-uracil 2 was found to
assemble in well-ordered patterns as depicted in Figure 2. In
high-resolution STM images, individual molecules within the
ordered pattern can be identified by their characteristic linear
shape, defined by three aligned lobes and two bright
protrusions at each end of 2. Each lobe can be attributed to
an aromatic core: the central lobe corresponds to the 1,4-
disubstituted phenyl moiety, whereas the peripheral lobes
correspond to the uracil groups. The two lateral protrusions
correspond to the hexyl chains attached to the uracil moieties.
Depending on the relative spatial disposition of the hexyl
chains, molecule 2 can display two configurations: cis-2 or
Figure 2. a) STM image of 2 on Ag(111). Scan range: 16”16 nm2,
V
bias =À0.8 V, It =20 pA. b), d) STM images of the two zoomed regions
indicated in a). b) scan range: 4”4 nm2, Vbias =À0.8 V, It =20 pA, and
d) scan range: 4.5”4.5 nm2, Vbias =À0.8 V, It =20 pA. c), e) proposed
corresponding H-bonding patterns.
trans-2, in which the alkyl chains lie on the same or on
opposite sides of the molecular backbone, respectively.
Along the high-symmetry direction (see white arrow in
Figure 2a), the molecules interact with each other through
double H bonds, forming linear assemblies which additionally
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interact between themselves by van der Waals forces. Two
configuration corresponding to the hexyl chains. The large
unit cells (3.7 Æ 0.4 nm ” 2.4 Æ 0.2 nm, a ꢀ 58 Æ 48, see also
Supporting Information) measured for this arrangement
derive from the fact that the distance between the bimolec-
ular wires is alternating (denoted as i, ii, and iii in Figure 3b).
In general, molecules adsorbed on surfaces tend to pack as
densely as possible, to minimize the occupied area, and thus,
to reduce the free surface energy. As a consequence, shorter
interwire distances should be preferred. However, as mole-
cule 2 is functionalized with two lateral hexyl chains, densely
packed arrangements are limited by the space requirements
of such aliphatic chains. Therefore, the observed pattern is a
compromise between both requirements. In most cases, the
linear module 2 adopts a cis-2 configuration (for example, the
hexyl chains of row iii point towards ii), whereas the trans
configuration, trans-2 (white dotted circle, Figure 3b), is
rarely found. Sequential sublimation of molecules 1, 2, and 3
on Ag(111) yielded the linear assemblies shown in the STM
images of Figure 4. In contrast to the seemingly endless wire-
like assemblies [(1·2)n] the length of which is mainly
determined by the size of the terraces of the silver substrate
different organizational motifs (Figure 2b and d) could be
identified within the self-assembled network of 2. In the first
motif (Figure 2b and c), two adjacent rows composed of
molecules cis-2 are laterally interacting by van der Waals
forces through directional interdigitation of the hexyl
chains,[14] resulting in double-row wires. In the second one
(Figure 2d and e), two lateral rows are linked through
sandwiched modules of trans-2, which are noncovalently
À
interacting through the N H groups with the free carbonyl
groups of cis-2 molecules within the rows.
To probe the recognition properties between the different
molecular modules, we have studied the hybrid assemblies
resulting from the co-deposition of 2 and 3, 1 and 2, and 1–3,
respectively. As expected, the uracil-bearing molecules 2 and
3 do not assemble in an ordered layer, but instead form
disordered phases consisting of only 3 as well as mixed but
disordered assemblies of 2 and 3.[13] In contrast, the subse-
quent deposition of linear modules 1 and 2 resulted in the
formation of extended linear bimolecular wires, [(1·2)n],
where the two modules alternate within the linear assembly
(Figure 3). As both modules are geometrically symmetric and
bear complementary recognition groups (DAD and ADA for
1 and 2, respectively), the development of the wires unam-
biguously confirms the formation of the expected intermo-
lecular triple H bonds. The two different molecules can be
easily distinguished within the wires as bis-(DAD) 1 is
visualized as three aligned lobes and four lateral spokes, the
latter corresponding to the acetyl residues, whereas bis-ADA
2
features two lateral protrusions in a cis or a trans
Figure 4. STM images of multicomponent submonolayers constructed
by a sequential sublimation of molecules 1, 2, and 3 on Ag(111)
surfaces. a) STM image (scan range: 50”40 nm2, Vbias =À1.7 V,
It =20 pA) of the anthracene-terminated supramolecular wires. The
inset in the upper left (13”6.5 nm2) highlights how molecule 3
interrupts the self-assembly of 1 and 2 while the surroundings still
show the closed-packed [(1·2)n] assemblies, thus creating energetically
disfavored voids (see text). Inset in the upper right (7.7”7.7 nm2):
aggregate of 3. b) Left: proposed model for the assembly of pentame-
ric [3·1·2·1·3] miniatures; Right: zoomed STM image of the assembly.
c) Left: proposed model for the assembly. Right: zoomed STM image
of some trimeric [3·1·3] miniatures.
Figure 3. STM images for a mixture of molecules 1 and 2 on Ag(111)
after annealing at 383 K: a) scan range: 41.5”41.5 nm2, Vbias =À1.3 V,
It =12 pA; b) scan range: 12”12 nm2, Vbias =À1.3 V, It =12 pA. The
unit cell, which contains four molecules, together with some molecules
has been drawn in the STM image. c) Proposed model for the
observed [(1·2)n] assembly, in which molecules 1 and 2 are alternately
arranged in a linear fashion through triple H bonds. The intra- and
inter-row distances between two neighboring central 1,4-disubstituted
phenyl rings are (1.7Æ0.2) nm and (1.2Æ0.1) nm, respectively. The
numbered lines (i–iii) show the different periodic distances between
neighboring rows (see text).
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(as observed for the mixture of 1 and 2), in this case the
supramolecular structures are terminated with the monour-
acil conjugate 3, exposing the anthracenyl moiety as the end
point of the assembly [3·1·(2·1)m·3]. The structural finger-
prints of molecule 3 can be easily distinguished in the STM
images of Figure 4a. Each molecule 3 exhibits a characteristic
mushroom-like shape with the anthracenyl group as cap and
the hexyl chain as lateral protrusion. Conjugate 3 terminates
the supramolecular linear assembly [(1·2)n] by complemen-
tary interactions with a 1-derived free DAD site, ultimately
acting as a molecular stopper. Apart from the long oligomers,
short linear trimeric and pentameric miniatures have also
been observed by STM as displayed in Figure 4b-c. Whereas
in the trimeric structure, [3·1·3] (Figure 4c), two molecular
stoppers are H-bonded to one central bis-(DAD) unit 1, in the
pentameric architecture, [3·1·2·1·3] (Figure 4b and Figure 5),
one central bis-(ADA) module 2 axially interacts with two
units of 1 through one of their two DAD sites and the other
DAD recognition site is H-bonded to molecular stopper 3.
H bonds with the carbonyl group of the acetyl residues. This
observation could account for a pre-recognition event that
organizes the anthracene derivatives at the triply H-bonded
1–2 junctions. Consequently, if the molecules obtain enough
energy (by thermal annealing, for example) molecule 3 will
compete equally with 2 to form a triple H bond with molecule
1, terminating the long linear assembly.
In summary, the first example of a simultaneous three-
component assembly on surfaces mediated by triple H-
bonding interactions, which yields the formation of linear
supramolecular miniatures, has been studied on Ag(111)
surfaces by STM. Two linear modules, 1 and 2, and an
anthracenyl-capped unit 3 (which can act as a molecular
stopper) were assembled complementarily, to form discrete
linear oligomeric assemblies. Although strict control of the
length of the linear assemblies has not yet been achieved, our
findings suggest that by controlling the ratio of the molecular
modules, as well as the post-annealing treatment of the
sample, the preparation of monodisperse auto-assembling
architectures on surfaces could be achieved. Additionally,
further control over the resulting H-bonded structures could
be gained with a slight modification of the molecular building
blocks by, for example, varying the length or the chemical
nature of the alkyl moieties for 2 and/or 3 or by attaching
other functional groups to 1. This approach would lead to a
large library of versatile molecular modules that could be
ultimately used as single-molecule devices.
Received: May 19, 2008
Published online: August 27, 2008
Keywords: hydrogen bonding · molecular wires ·
.
scanning probe microscopy · self-assembly · surface analysis
Figure 5. STM image (scan range: 44”29 nm2, Vbias =À1.7 V,
It =20 pA) of two pentameric miniatures in which four molecules 3
(dotted circles) have pre-recognized the complementary DAD unit.
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