Concentration dependent halogen-bond density in the 2D self-assembly of a thienophenanthrene derivative at the aliphatic acid/graphite interface

Article abstract of DOI:10.1039/c4cc03687e

The supramolecular patterns of a thienophenanthrene derivative could be switched among dissimilar polymorphs with different halogen-bond densities by solution concentration, which is demonstrated through a combination of STM and density functional theory (DFT) calculations. This journal is the Partner Organisations 2014.

Full text of DOI:10.1039/c4cc03687e

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Concentration dependent halogen-bond density
in the 2D self-assembly of a thienophenanthrene
derivative at the aliphatic acid/graphite interface†
Cite this: Chem. Commun., 2014,
50, 9003
Received 15th May 2014,
Accepted 18th June 2014
Bao Zha, Xinrui Miao,* Pei Liu, Yumeng Wu and Wenli Deng*
DOI: 10.1039/c4cc03687e
www.rsc.org/chemcomm
The supramolecular patterns of a thienophenanthrene derivative could found that different nanostructures could be formed by adjusting
be switched among dissimilar polymorphs with different halogen-bond the DDTD concentration. In addition, the voltage pulse applied to
densities by solution concentration, which is demonstrated through a the STM tip could induce the structural transformation. All the
combination of STM and density functional theory (DFT) calculations.
conjugated moieties of DDTD appear to be triangle features in the
STM images. Our systematic study illustrates that the competition
Rational molecular design and external condition change (such as of interchain van der Waals interactions and halogen bonding of
solvent, concentration and temperature) are considered as powerful the BrÁÁÁBr and BrÁÁÁH bonds along with solvent coadsorption
approaches to tune the ordered pattern and structural transforma- determine the polymorphous structures. The present work provides
tion at the molecular scale for two-dimensional (2D) self-assembly.1 a molecular insight into the 2D assembly of a thienophenanthrene
Many different nanostructures for alkyl chain substituted molecules derivative based on halogen bonding.
have been fabricated involving van der Waals force,2 hydrogen
The DDTD molecule with optical properties (Fig. S1, ESI†) was
bonding,3 dipolar interaction,4 etc. Very recently, halogen bonding home-synthesized (Fig. 1a and ESI†). The calculated electrostatic
has been used to achieve the formation of self-assembled patterns potential of a single DDTD and a dimer is shown in Fig. 1b and c.
for organic molecules, because it is expected to be highly directional, Since Br has both positive and negative electrostatic parts, the
and its binding geometry can adopt a few configurations.5 These positive potential region could point toward the negative part of the
characteristics provide new opportunities for tailing molecular self- other Br atom. Therefore, two DDTD molecules are doubly bonded
assembly and therefore obtaining novel nanopatterns by scanning by BrÁÁÁBr and BrÁÁÁH pairs (Fig. 1c), resulting in a triangular motif.
tunneling microscopy (STM). However, reports describing the for- Electrostatic interactions are identified as the driving forces for
mation of 2D halogen-bonded structures on solid surfaces mainly intermolecular BrÁÁÁBr and BrÁÁÁH bonding.
focus on the rigid molecules.6 As far as we know, the application of
A drop of saturated solution of DDTD was applied to a freshly
halogen bonding in the 2D self-assembly of alkyl chain and bromine cleaved graphite surface under ambient conditions (15 1C). An
substituted organic molecules at the solid–liquid interface has not assembly which we called an alternate pattern occurs fast and mostly
been investigated by STM widely. In addition to the intermolecular covers the whole area (Fig. 2a and Fig. S2, ESI†). In adjacent one-row
interaction, the solvent can drastically affect the structure of halogen- molecular lamellae, the conjugated cores arrange in an antiparallel
bonded architectures at the solid–liquid interfaces.7 The influence of mode as the blue arrows indicate in Fig. 2a. The antiparallel
the solution concentration on halogen-bond density of 2D self- alignment of the molecular dipoles is a consequence of stabilizing
assembly of alkyl chain and bromine substituted organic building
blocks at the solid–liquid interface still remains obscure.
Herein we present the first case of the competition of halogen
bonding and van der Waals interaction on the self-assembly of
DDTD at the aliphatic acid/graphite interface using STM. It was
College of Materials Science and Engineering, South China University of
Technology, Guangzhou, 510640 China. E-mail: msxrmiao@scut.edu.cn,
wldeng@scut.edu.cn; Tel: +86 20-22236708
Fig. 1 (a) Chemical structure of DDTD. (b) Calculated electrostatic
potential map of DDTD under vacuum. (c) Electrostatic potential map of
the DDTD dimer under vacuum showing the transformation of charge due
to dispersion and electrostatic forces of the halogen bonds.
† Electronic supplementary information (ESI) available: STM experimental con-
ditions, synthesis and characterization of DDTD and DPTD, additional STM
images and packing parameters and binding energy calculation. See DOI:
10.1039/c4cc03687e
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images (Fig. S6, ESI†) display the assembled pattern changing
from an alternate motif to a dislocated linear pattern, which is
driven by the change in the van der Waals force and halogen
bonding. Compared with extensively studied hydrogen bonding,
BrÁÁÁBr and BrÁÁÁH halogen bonding is weaker in energy which leads
to faster dissociation dynamics.6a The phase transition was not
observed between the dislocated linear pattern and the tetramer
structure (Fig. S7, ESI†). The relative occurrence of three phases and
structural transition on the surface reflects that at low concentra-
tions, the dislocated linear pattern and the tetramer structure are the
stable arrangements, whereas the alternate pattern is a stable phase
at high concentrations. In the linear pattern, the coadsorption of
solvent enhances the adlayer stability.
At the 1-heptoic acid or 1-nonoic acid/graphite interface, the
alternate, dislocated linear and tetramer patterns are observed
(Fig. S8 and S11, ESI†), which are similar to those in 1-octanoic acid.
Moreover, the structural transition was recorded at high concentra-
tions (Fig. S9, S10 and S12, ESI†). However, at low concentrations,
another matrix pattern was obtained (Fig. 3 and Fig. S13, ESI†),
in which no solvent molecule coadsorbs. The systematic results
indicate that the solvent polarity affects the proportion of different
structures (Fig. S8e and S11e, ESI†) and the amount of solvent is
important for the formation of a coadsorbed structure.
Fig. 2 STM images of the DDTD adlayers in 1-octanoic acid. (a) Alternate
pattern (1.1 Â 10À3 M). (b) Dislocated linear pattern (10À3–10À5 M). (c)
Tetramer structure (10À4–10À5 M). Inset shows the halogen bonding of the
tetramer. (d) Linear pattern (3.4 Â 10À5 M). Vbias = 500–600 mV, It = 400–
450 pA. Schematic representations of DDTD overlayed on each image to
illustrate the molecular arrangements.
In order to confirm the crucial role of halogen bonding in the
dipole–dipole forces, which govern the 2D structure formation.8 Only structural polymorph of DDTD, the DPTD without the bromine
in such lamellae the side chains of DDTD stretch on both sides of atoms was home-synthesized (ESI†). The packing details show the
the conjugated core and interdigitate with those of neighboring conjugated cores of DPTD displaying triangle features arranged in
molecules. In the two-row molecular lamellae, the DDTD molecules pairs in a helix fashion and give a windmill-shaped tetramer as the
pack in a head-to-head fashion via BrÁÁÁBr and BrÁÁÁH interactions. green rectangles indicate in Fig. 4. Since the side chains interdigitate
With the decreasing concentration, the alternate pattern and lie along the graphite lattices (Fig. S14, ESI†), it can be inferred
disappeared gradually and a dislocated linear pattern and a tetramer that the featured adlayer is influenced by the maximized molecule–
pattern were observed (Fig. 2b and c). In Fig. 2b, two DDTD substrate interaction. No solution concentration-dependence was
molecules form a dimer and arrange in a dislocated head-to-head observed (Fig. S15, ESI†). The results demonstrate that the self-
fashion via a pair of halogen bonds. In each dimer, the alkyl chains assembled structure of DPTD is mainly dominated by the interchain
of two DDTD molecules pack in the opposite direction. In Fig. 2c, van der Waals force and shape complementarity of cores. Compared
four DDTD molecules arrange head-to-head, resulting from three with the self-assembly of DPDT, the halogen bonding plays an
pairs of halogen bonds. The side chains in adjacent lamellae important role in the structural formation and transformation
arrange in a tail-to-tail fashion, indicating the stronger halogen of DDTD.
bonding between the conjugated cores compared with the alternate
It is commonly known that the concentration dependence is
and dislocated linear patterns.9 When the DDTD concentration was directly related to the difference in stability of different polymorphs
decreased to 3.4 Â 10À5 M, only the linear pattern was observed and their respective molecular density. In principle, high-density
(Fig. 2d). Two DDTD molecules form a dimer according to a single structures are optimal from a free-energy point of view.
halogen bond. Two solvent molecules forming a dimer with a head-
to-head motif via hydrogen bonding coadsorb with DDTD due to
the space matching as the superimposed molecular model shown
in Fig. 2d.
The surface phases show clear concentration dependence
(Fig. S3, ESI†): in the saturated solution (1.1 Â 10À3 M), the
alternate and dislocated linear patterns show phases separate
on the surface (Fig. S4a, ESI†). In the concentration range
(10À3–10À5 M), the alternated pattern disappeared gradually
and the dislocated linear and tetramer patterns coexist, in
which the percentage of the tetramer pattern increases gradually
(Fig. S4b–4d, ESI†). At the low concentration (3.4 Â 10À5 M), only
Fig. 3 STM image (17 Â 17 nm2) of the DDTD adlayer in 1-heptoic acid at a
the linear pattern was formed resulting from the coadsorption of
low concentration (2.5 Â 10À5 M). Vbias = 600 mV, It = 400 pA.
DDTD and 1-octanoic acid (Fig. S5, ESI†). Consecutive STM
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Fig. 5 Atomic structure of (a) dislocated, a1 E 901, a2 E 1801, (b) tetrameric,
a1 E 901, a2 E 1801 and (c) linear configuration obtained (a1 = a2) from DFT
calculations. Dotted lines indicate possible intermolecular bonds, BrÁÁÁBr (red)
and BrÁÁÁH (green).
Fig. 4 High-resolution STM image (16 Â 16 nm2) of the DPTD adlayer at
the 1-octanoic acid/graphite interface. Vbias = 570 mV, It = 420 pA.
by changing the solution concentration. Four different molecular
structures – alternate, dislocated linear, tetrameric, and linear – were
observed. Based on the STM images, the proposed molecular models
are in good agreement with the DFT calculations, and can be
explained by a triangular structure consisting of the BrÁÁÁBr and
BrÁÁÁH bonds. Without the solvent coadsorption, the higher the
halogen-bond density, the more stable the structure is. The DDTD
molecule has long side chains and Br atoms, so the van der Waals
interactions of molecule–molecule and halogen bonding of the
BrÁÁÁBr and BrÁÁÁH bonds along with solvent coadsorption deter-
mine the polymorphous structures. Our results open up new
opportunities for tailoring molecular self-assembly by changing the
intermolecular van der Waals interaction and halogen bonding. We
will further investigate the position of halogen atoms, chain-length
and solvent effects on the 2D molecular self-assembly.
The calculated molecular densities of the alternate, dislocated
linear, tetrameric and linear patterns are 3.13, 3.75, 3.75 and
4.50 nm2 per molecule, respectively (Table S1, ESI†). In our
system, the alternate pattern with the highest packing density
is thermodynamically stable in saturated solution. In all the
phases, the side chains of DDTD molecules lie along the graphite
lattice (Fig. S16, ESI†), indicating the same molecule–substrate
interactions. However, only the side chains in adjacent lamellae
are interdigitated in the alternate pattern, which illustrates the
strongest intermolecular van der Waals interactions. With
deceasing concentration, the DDTD molecules form a dimer or
a tetramer, in which the coupled halogen bonds enhance the
intermolecular interactions. When the carbon atom number of
DDTD side chains is decreased down to 14, only the alternate
pattern was obtained at different concentrations (Fig. S17 and
S18, ESI†). The results demonstrate that the van der Waals
interaction between the side chains and halogen bonding
between the bromine atoms for DDTD adlayers either compete
or cooperate in constructing polytypic intermolecular structures.
We performed DFT calculations to gain deeper insights into
the intermolecular binding mechanisms within the adlayers.
The molecular aggregations are stabilized by the BrÁ Á ÁBrÁ Á ÁH
triangular structure between neighboring molecules, which has
been observed in 3D crystal structures of other halogenated
molecules.10 Besides the van der Waals interaction between the
side chains, the intermolecular halogen bonding plays an
important role in the self-assembly of DDTD. The C–BrÁÁÁBr angles
a1 and a2 in dislocated and tetrameric patterns are about 901 and
1801, which are understood as charge-polarization induced halogen
bonds. While a1 and a2 in the linear structure are the same
indicating that the halogen bond is of the van der Waals type
(Fig. 5 and Fig. S19, ESI†).7,11 The calculated binding energies for
dislocated, tetrameric and linear structures are À0.32, À0.96, and
À0.11 eV, respectively (Fig. 5 and Fig. S20, ESI†). The binding energy
of the tetramer is three times that of the dimer, indicating that two
halogen bonds exist between the dimers. In the linear structure, only
one halogen bond between two molecules results in two nonplanar
molecules under vacuum. Considering the molecule–substrate and
molecule–solvent interactions, such a pattern is also stable and all
molecules are coplanar on the surface.
Financial support from the National Program on the Key
Basic Research Project (2012CB932900), the National Natural
Science Foundation of China (21103053, 51373055) and the
Fundamental Research Funds for the Central Universities
(SCUT) is gratefully acknowledged.
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