Role of hydrogen bonding on the self-organization of phenyleneethynylenes on surfaces

Article abstract of DOI:10.1021/la3048592

A series of carboxylic acid substituted phenyleneethynylenes, having a rigid backbone of 2.7 ± 0.1 nm, were synthesized by following the Heck-Cassar-Sonagashira-Hagihara cross-coupling reaction. Hydrogen bonding, through the formation of cyclic dimers of carboxylic acid, is more preferred over catemeric structures in all the molecular systems under investigation. The formation of extended two-dimensional patterns on highly oriented pyrolitic graphite (HOPG) surface is dictated by the position as well as number of the carboxylic acid groups on the phenyleneethynylenes. Highly ordered extended arrangements, in the linear and stepwise fashion, were observed when the carboxylic acid groups are attached in the para and meta positions of phenyleneethynylenes. The vital role of the number of carboxylic acid on the organization of molecules is evident in the case of tetracarboxylic acid derivative wherein a Kagome-type structure was observed. Further, the coassembly of two types of phenyleneethynylenes was achieved on HOPG surface through acid base interaction.

Full text of DOI:10.1021/la3048592

Article
pubs.acs.org/Langmuir
Role of Hydrogen Bonding on the Self-Organization of
Phenyleneethynylenes on Surfaces
Pratap Zalake and K. George Thomas*
School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram (IISER-TVM), CET Campus,
Thiruvananthapuram, 695 016, India
S
* Supporting Information
ABSTRACT: A series of carboxylic acid substituted phenyl-
eneethynylenes, having a rigid backbone of 2.7 0.1 nm, were
synthesized by following the Heck-Cassar-Sonagashira-Hagi-
hara cross-coupling reaction. Hydrogen bonding, through the
formation of cyclic dimers of carboxylic acid, is more preferred
over catemeric structures in all the molecular systems under
investigation. The formation of extended two-dimensional
patterns on highly oriented pyrolitic graphite (HOPG) surface
is dictated by the position as well as number of the carboxylic
acid groups on the phenyleneethynylenes. Highly ordered
extended arrangements, in the linear and stepwise fashion,
were observed when the carboxylic acid groups are attached in
the para and meta positions of phenyleneethynylenes. The vital role of the number of carboxylic acid on the organization of
molecules is evident in the case of tetracarboxylic acid derivative wherein a Kagome-type structure was observed. Further, the
coassembly of two types of phenyleneethynylenes was achieved on HOPG surface through acid base interaction.
resolution, is essential for designing various devices, and
scanning tunneling microscopy is an excellent tool for probing
these aspects.6,16−22 The organization of such molecules on
surfaces can be effectively modulated through hydrogen bond
interactions of cyclic dimers of carboxylic acids. Investigations
on the self-assembled monolayers of various molecular systems
bearing carboxylic acid groups include (i) mono-, di-, and
trisubstituted benzoic acids and alkoxy-substituted benzoic
acids;23−26 (ii) larger ones such as porphyrins;27 and (iii) rigid
molecular systems such as oligothiophenes28−30 and phenylene
ethynylenenes.31−35
Phenyleneethynylene-based rigid rod molecular systems do
not involve any possibility of isomerization and maintains π-
electron conjugation at any degree of rotation.36−38 This
unique property has been utilized to understand the
organization of molecules on the surface by our group35,39,40
and others.31−34,41−46 We have previously demonstrated that
phenyleneethynylenes, even in the absence of any functional
group, can self-organize into wire-like structures in a skewed 1D
fashion on highly oriented pyrolytic graphite (HOPG) surface,
and various modes of alkyl CH−π interaction drive the
organization.39 This organization can be further modulated by
introducing hydroxyl as well as aldehyde groups at the terminal
positions of phenyleneethynylenes.40 More interestingly, the
position of carboxylic acids on phenyleneethynylenes has a
1. INTRODUCTION
Among various noncovalent interactions, hydrogen bonding
remains a topic of great interest due to its continuing relevance
in chemical and biological research.1 Carboxylic acid deriva-
tives, in principle, can form two types of hydrogen bonding
interactions: cyclic dimers and open catemers. Cyclic dimer
formed through the interaction of equivalent hydrogen bonds
of two carboxylic acid groups are of particular interest, since
they are relatively strong and directional.1,2 For example, the
enthalpy of association (ΔH) of twofold OH···OC bond
in cyclic dimers of benzoic acids is estimated as −88.7 kJmol−1.3
In contrast, the typical energies of van der Waals interactions
are 10- to 15-fold lower than hydrogen bond interactions in
cyclic dimers.1−4 Often, van der Waals interactions collectively
compete with hydrogen bond interactions; however, the former
one cannot provide any directionality.4 The obvious advantage
of the directionality of hydrogen bonds has been utilized for the
design and effective control of various supramolecular
structures having functional properties.5,6 The hydrogen bond
interactions of carboxylic acids have also been utilized to create
host network, having cavities, which can accommodate guest
molecules such as coronene7−9 and C60.10 It has been also
demonstrated that molecules bearing carboxylic acids can
interact with proton accepting groups to form self-assembled
structures on surfaces.11−13
One of the factors that dictate the efficiency of optoelec-
tronic devices is the way in which photo- as well as electroactive
molecules are organized on surfaces.14,15 An understanding on
the organization of molecules on surfaces, with atomic
Received: December 10, 2012
Revised: January 19, 2013
Published: January 19, 2013
© 2013 American Chemical Society
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Chart 1. Molecular Systems under Investigation
Scheme 1
(i) CuCl, diazabicyclo[5.4.0]undec-7-ene; N,N,N',N'-tetramethylethylenediamine; (ii) Pd(PPh3)2Cl2, CuI, PPh3, disopropyl amine; (iii) KOH,
MeOH.
significant influence on their self-organization: from linear
assembly to rectangular network having periodic cavities35 and
Kagome network.34 These studies clearly indicate that the
directionality of carboxylic acid moiety and the rigid rod
structure of phenyleneethynylenes makes this class of molecules
an ideal candidate for designing programmable monolayers.
Herein, we report the role of hydrogen bonding of carboxylic
acid groups on the organization of phenyleneethynylenes by
systematically varying the position and number of the
carboxylic groups. Further, we report the preliminary results
on the coassembly of two molecules of phenyleneethynylenes,
one bearing carboxylic acids at the terminal position and the
other one bearing proton accepting groups.
2. RESULTS AND DISCUSSION
We have previously investigated the self-organization of
phenyleneethynylenes having three phenyl groups linked
together by acetylenic bridging units as rigid aromatic backbone
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having a dimension of 1.8 0.1 nm (for example, compound 6
in Chart 1 and its derivatives).35,39,40 The rigid aromatic
backbone of these molecular systems can be easily
distinguished in STM as bright rod-like structures due to
high tunneling current. In contrast, the alkyl chain of
phenyleneethynylene derivatives appeared as dark regions due
to the large energy difference between the electronic states of
the aliphatic chain and the Fermi level of the substrate. Various
patterns can be viewed with more clarity if the length of
aromatic rigid backbone is longer. With this objective, we have
further increased the length of the rigid backbone to 2.7 0.1
nm by introducing additional phenyl group and acetylenic
bridging units (1−5; Chart 1).
Synthesis of 1−5 was carried out by following the Heck-
Cassar-Sonagashira-Hagihara cross-coupling reaction, using
Pd(II) as catalyst,36,47,48 as shown in Scheme 1. The
intermediate compound 8 was prepared through the dimeriza-
tion of acetylene by following Glaser reaction, catalyzed by
CuCl.49 Further, on reacting 8 with 2 equiv of respective
phenylacetylene derivative, using Pd(II) as catalyst, yielded 1
and 9a−c. The reaction of 8 with 1 equiv of methyl-4-
ethynylbenzoate give the compound 10, which on further
reaction with 1 equiv of methyl-3-ethynyl-benzoate yielded
product 11. The compound 1 and the precursor of carboxylic
acid derivatives (9a−c, and 11) were purified using recycling
HPLC to maintain high purity of the final products. The
purified products (9a−c and 11) were hydrolyzed using KOH
to yield the corresponding acid derivatives (2−5). The final
products were further characterized through analytical and
spectroscopic techniques and the details are presented as
Supporting Information.
To obtain good STM images, uniform organization of
molecules on HOPG surface is necessary and various attempts
have been made in this direction. Samples for STM
investigations were prepared by dissolving the respective
molecules in a mixture (1:9) of THF and 1,2,4-trichloroben-
zene, and the final concentration of the solution is maintained
at ∼5 μM in all the cases. Attempts to drop-cast the solution on
HOPG surface and drying the solvent by slow evaporation were
not successful. This may be due to the precipitation of the
compound while drying. In the present study, the imaging was
carried out at the liquid−solid interface immediately after drop-
casting the solution on the HOPG surface. Images were
acquired in the constant-height mode, under ambient
conditions, using a multimode scanning probe microscope.
Electrochemically etched Pt/Ir wire (80:20) was used as the
STM tip. The molecules were physically adsorbed on HOPG
surface, and their stability was confirmed by recording the STM
images after a few days. The HOPG surfaces having the self-
assembled molecules were dried and wetted using a mixture
(1:9) of THF and 1,2,4-trichlorobenzene before imaging. STM
images are reproducible, indicating that the molecular systems
are stable on HOPG surface at normal atmospheric condition.
STM images of model compound 1, which does not possess
any functional groups, are presented as Figure 1B,C. Large area
scan showed the presence of well-organized arrangements of
molecules at various locations with clear domain boundaries
(Figure 1B). Organization of 1 on HOPG showed a skewed 1D
wire-like structure similar to that of compound 6. The unit cell
parameters were estimated as a = 1.2 0.1 nm, b = 2.5 0.1
nm, and α = 85 5°.
Figure 1. (A) Molecular structure of 1. (B) STM image of 1 on
HOPG showing skew one-dimensional arrangement: scan size 50 × 50
nm2; Vbias = −852 mV; It = 200 pA; and (C) corresponding high-
resolution image: scan size 8 × 8 nm2; Vbias = −1354 mV; It = 80 pA.
(D) Schematic representation of the organization of 1 on surface.
groups on the organization of phenyleneethynylenes by varying
the (i) position and (ii) number of the carboxylic groups.
Position-dependent organization was investigated by introduc-
ing carboxylic acid at the terminal phenyl rings of phenyl-
eneethynylenes which include para-disubstituted carboxylic acid
derivative (2), meta-disubstituted carboxylic acid derivative (3),
and one having carboxylic acid groups at the para and meta
positions (4). In the case of 2, intermolecular hydrogen
bonding of the carboxylic groups at the para positions leads to
the formation of well-ordered linear arrangement whereas
stepwise arrangement was observed for 3 having carboxylic
acids in the meta positions (Figure 2).
Schematic representation of the various interactions in
compounds 2 and 3 leading to the formation of linear and
stepwise organization are presented in Figure 3. Both molecules
possess four hexyloxy groups which can undergo interaction
with the acetylenic π-bond of the adjacent molecules, leading to
the formation of molecular strips (xy and x′y′ in Figure 2C,F).
A close analysis of STM images further showed that the
adjacent molecules in a strip possess a constant spacing of 1.3
0.1 nm. These results clearly indicate that the interdigitation of
hexyloxy groups which undergo CH−π interaction with
adjacent molecules results in the formation of molecular strips.
Similar molecular packing was observed earlier by our group for
molecule 6 and related compounds having three phenyl group
and two acetylenic bridging units.35,39,40 In these systems, the
alkoxy chain of the adjacent molecules interacts with the
acetylenic moiety, from either the ortho or meta position,
leading to two types of arrangements with an angle of
orientation of 65
5° and 85
5°, respectively. However,
only one type of arrangement was observed in the present case,
having an angle >85 5°, favoring meta interaction. The angle
of orientation (α) of phenyleneethynylene core for compounds
1−3 was estimated from the high-resolution STM images as 85
5° (1), 99 5° (2), and 103 5° (3).
The main objective of the present investigation is to
understand the role of hydrogen bonding of carboxylic acid
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modulating their organization. For example, 2 having both
carboxylic groups at the para positions form intermolecular
hydrogen bonding in an end-to-end fashion leading to the
formation of parallel stacks (PS-a; Figure 3). Interestingly, an
extended 2D organization, in a stepwise fashion (Figure 2F),
was observed in the case of 3 wherein both carboxylic groups
are at the meta positions. The phenyl group can freely rotate,
along the alkyne-aryl single bonds leading to the formation of
two types of rotamers on surface having carboxylic acids located
in the opposite side PS-b or in the same side PS-c. Thus, the
alkyl CH−acetylenic π-interaction can lead to the formation of
two types of molecular strips as shown in Figure 3 (PS-b and
PS-c). These molecular strips can further interlock through
intermolecular hydrogen bonding of carboxylic acids leading to
the formation of extended organization (EO-b and EO-c).
However, it is difficult to distinguish the way in which
phenyleneethynylenes undergo hydrogen bonding in 3 using
STM. A recent report on the crystal structure of biphenyl-3,3′-
dicaboxylic acid showed the formation of zigzag arrangements
wherein one-dimensional chains of molecules are formed
through intermolecular hydrogen bonding. In this case, it was
found that the carboxylic acid groups are located in the
opposite sides.50 In the present case, a similar arrangement
having carboxylic acid on the opposite sides (EO-b) may be
more preferred. The unit cell parameters were further
Figure 2. (A,D) Molecular structure of 2 and 3, respectively. (B) STM
image of 2 showing linear arrangement: scan size 20 × 20 nm2; Vbias
=
−1732 mV; It = 60 pA; and (C) corresponding high-resolution image:
scan size 10 × 10 nm2; Vbias = −1925 mV; It = 58 pA. (E) STM image
of 3 showing stepwise arrangement: scan size 50 × 50 nm2; Vbias
=
−753 mV; It = 610 pA; and (F) corresponding high resolution image
calculated from STM images: for 2, a = 1.3
0.1 nm; b =
scan size: 10 × 10 nm2; Vbias = −841 mV; It = 100 pA.
3.2 0.1 nm; α = 99 5°; and for 3, a = 1.2 0.1 nm; b = 3
0.1 nm; α =103 5°.
Various possibilities of hydrogen bonding exist in the case of
phenyleneethynylene 4 having carboxylic acid groups at the
para and meta positions. For example, it can be seen from the
STM images that the carboxylic groups at the para position
underwent intermolecular hydrogen bonding leading to the
formation of linear assembly, while the carboxylic acid groups at
the meta positions result in a stepwise organization. Irregularity
in the STM image of 4 arises from the existence of various
modes of hydrogen bonding (Figure 4). Thus, the positions of
carboxylic acid groups play a significant role in the organization
phenyleneethynylenes on surfaces.
The organization of phenyleneethynylenes on surfaces was
further investigated systematically by increasing the number of
carboxylic acid groups. Compound 3, which possesses two
Figure 3. Schematic representation of parallel stacks (PS) of 2 and 3
formed through CH−π interaction and extended organization (EO)
through hydrogen bonding (note: the phenyl ring of the phenyl-
eneethynylenes can freely rotate along the alkyne-aryl single bonds
leading to the formation of two types of rotamers on surface having
carboxylic acids located in the opposite side PS-b or in the same side
PS-c).
It is also clear from the STM images that the formation of the
extended organization (EO) is dictated by the functional
groups present on the terminal phenyl rings in the case of 2−4.
In the absence of any functional group, the parallel stacks of
phenyleneethynylenes interlock through aromatic CH−aro-
matic π-interaction leading to the formation of a skewed 1D
arrangement. However, the presence of carboxylic acid groups
at the terminal positions has a significant influence in
Figure 4. (A) Molecular structure of 4. (B) STM image of 4: scan size
50 × 50 nm2; Vbias = −500 mV; It = 653 pA and (C) corresponding
high-resolution image: scan size 10 × 10 nm2; Vbias = −1653 mV; It =
150 pA.
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carboxylic groups in the meta positions of phenyleneethyny-
lene, forms beautiful a stepwise arrangement on the surface
(Figure 2F). It is interesting to investigate the organization of
phenyleneethynylenes by attaching two more carboxylic acid
groups at the meta positions. With this objective, a phenyl-
eneethynylene derivative 5 which possess four carboxylic acid
groups at the meta positions was synthesized. Surprisingly,
STM images showed network-like organization (Figure 5B,C),
presented in Figure 6C,D. A linear assembly of molecules with
alternate regions of low and high tunneling currents was
Figure 6. (A,B) Molecular structures of 2 and 7, respectively. (C)
STM image showing coassembly of 2 and 7: scan size 20 × 20 nm2;
Vbias = −900 mV; It = 150 pA and (D) corresponding high-resolution
image: scan size 15 × 15 nm2; Vbias = −800 mV; It = 170 pA. (E)
Schematic representation of the formation coassembly on surface.
Figure 5. (A) Molecular structure of 5. (B) STM image of 5 showing
Kagome arrangement: scan size 30 × 30 nm2; Vbias = −850 mV; It = 50
pA; and (C) corresponding high-resolution image: scan size 12 × 12
nm2; Vbias = −1400 mV; It = 140 pA. (D) Schematic representation of
the organization of 5 on surface.
observed throughout. The difference in tunneling current leads
to regions of varying contrast having dimensions of 1.8 0.1
nm and 2.7 0.1 nm. The dimensions of these strips match
well with the molecular lengths of 2 (2.7 0.1 nm) and 7 (1.8
0.1 nm). Compound 2 has an extended aromatic backbone
compared to 7 and possesses higher tunneling current, resulting
in regions of higher contrast. The lone pair of electrons on the
nitrogen atom of the pyridine moieties in compound 7 can
undergo strong interaction with the carboxylic acid group at the
terminal positions of 2 through intermolecular N···H−O−
C(O)-type hydrogen bonds leading to the formation of
coassembled linear structures.52−54 From the STM image, it
is clear that two coassembled linear structures maintain a
with a regular pattern on the surface. The unit cell parameters
were estimated from STM images for 5: a = b = 4.2 0.1 nm
and α = 64
5°. Close analysis of the image (Figure 5C)
showed that six phenyleneethynylene molecules interact
through intermolecular hydrogen bonding leading to Ka-
gome-type structure. Schematic representation of the hydrogen
bonding interactions in compound 5 leading to the formation
of Kagome-type structure is presented in Figure 5D. Thus,
compound 3 which possess two carboxylic acids at the meta
positions forms a stepwise arrangement, which transforms to a
Kagome-type structure by incorporating two additional
carboxylic acid groups in the meta positions. These results
clearly indicate that, in the absence any functional groups,
CH−π interaction is the main driving force for the organization
of phenyleneethynylenes. However, as the number of carboxylic
group increases, intermolecular hydrogen bonding between
carboxylic acids dominates, leading to the formation of various
types of organization.
constant distance of 1.3
0.1 nm throughout, further
indicating the role of CH−π acetylene interaction in forming
2D assembly.
On the basis of the present investigations and earlier
reports,35,39,40 some important generalizations can be made on
the self-organization of rigid rod molecular systems such as
phenyleneethynylenes. Schematic representation of the role of
hydrogen bonding in the organization of compounds 2, 3 and 5
is illustrated in Figure 7. As mentioned earlier, carboxylic
groups can, in principle, form cyclic dimeric as well as extended
structures (catamers).1,2 However cyclic dimeric arrangement
of carboxylic acids, formed through twofold OH···OC
bonding, is favored due to their higher enthalpy of association
compared to that of catamers.3 In the case of monosubstituted
carboxylic acid derivatives, independent of whether the
substitution is at the para or meta position of phenyl ring,
Further, we have investigated the coassembly between two
phenyleneethynylene molecules: para-disubstituted carboxylic
acid derivative 2 and a phenyleneethynylene having pyridine
groups at the terminal position 7.51 Equimolar concentrations
(5 μM) of 2 and 7 were dissolved in a mixture (1:9) of THF
and 1,2,4-trichlorobenzene. The solution was drop-cast onto
HOPG and the STM investigations were carried out at the
liquid−solid interface. The images of the coassembly are
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observed for 2 and 3, respectively (Figure 2). Earlier, we
demonstrated that the self-organization of a meta-substituted
phenyleneethynylene derivative having short rigid aromatic
backbone (1.8
0.1 nm) yielded a rectangular network
through multiple hydrogen bonding. Stepwise arrangement was
observed in the case of 3 on increasing the length of the rigid
backbone to 2.7 0.1 nm, further indicating the role of the
phenyleneethynylene core on the self-organization. In contrast,
compound 5 having four carboxylic acid groups results in the
formation of highly stable hexagonal arrangement through
twofold OH···OC bonds.
3. CONCLUSION
Engineering of two-dimensional supramolecular structures on
surfaces was achieved by the design of molecular systems
having two important structural motifs: (i) phenyleneethyny-
lene core providing rigidity and (ii) carboxylic acid moiety
providing directionality. In the present case, two types of
noncovalent forces, namely, CH−π and hydrogen bonding
interactions are mainly operative. In the absence of functional
groups, collective CH−π interactions drive the self-organization
of phenyleneethynylene. However, incorporation of carboxylic
acid moieties significantly influences their organization from
linear assembly to stepwise arrangement by varying the position
of carboxylic acid group. As the number of carboxylic groups
increases, intermolecular hydrogen bonding between the
phenyleneethynylenes becomes more dominant and stable
Kagome-type structures were observed. Strong enthalpy of
association of twofold OH···OC bond in cyclic dimers,
compared to that of open catemers, may be responsible for the
formation of periodic patterns. Coassembly of donor−acceptor
molecules, in an ordered fashion, was achieved on surface, and
such systems can show interesting charge transfer properties.
Investigations of the optical and electrical properties of these
well-organized molecular assemblies on surfaces are in progress.
These studies may pave the way toward the design of next-
generation optoelectronic devices with tunable functional
properties.
ASSOCIATED CONTENT
■
S
* Supporting Information
Details on the synthesis and characterization of all new
compounds. This material is available free of charge via the
Internet at http://pubs.acs.org.
AUTHOR INFORMATION
■
Corresponding Author
*E-mail: kgt@iisertvm.ac.in.
Present Address
Figure 7. Schematic representation of basic hydrogen bonding
interactions leading to various types of self-organization of molecules
on HOPG surface as shown in Figures 2, 3 and 5: (a) 2 forming linear
assembly, (b) 3 forming stepwise arrangement, (c) 5 forming
hexagonal pattern and Kagome-type arrangement, and (d) coassembly
of 2 and 7.
School of Chemistry, Indian Institute of Science Education and
Research Thiruvananthapuram (IISER-TVM), CET Campus,
Thiruvananthapuram, 695 016, India.
Notes
The authors declare no competing financial interest.
dimerization of molecules is preferred. These structures can be
further extended into periodic patterns by proper substitution
at the other end of the molecule. For example, well-organized
linear and stepwise arrangements over a large area were
ACKNOWLEDGMENTS
■
We acknowledge IISER-TVM, for financial support and P.Z. for
fellowship from CSIR.
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