Aza-BODIPY molecular assembly at the liquid-solid interface driven by Br?F[sbnd]BF interactions

Article abstract of DOI:10.1016/j.cclet.2021.02.066

In this work, two aza-BODIPY derivatives, 3,5-diphenyl-1,7-di(p-dodecyloxyphenyl)-aza-BODIPY (CJF) and 3,5-di(p-bromophenyl-1,7-di(p-dodecyloxyphenyl)-aza-BODIPY (2Br-CJF) acted as model molecules to form the self-assembly monolayers on the solid-liquid i

Full text of DOI:10.1016/j.cclet.2021.02.066

G Model
CCLET-6195; No. of Pages 4
Chinese Chemical Letters xxx (xxxx) xxx–xxx
Contents lists available at ScienceDirect
Chinese Chemical Letters
journal homepage: www.elsevier.com/locate/cclet
Communication
Aza-BODIPY molecular assembly at the liquid-solid interface driven
by BrÁ Á ÁFÀÀBF interactions
Yuchuan Xiaoa,c,d,1, Fangjian Caib,1, Xuan Penga,d,1, Xiyuan Kangb, Peng Leia,d, Xin Lie,
a,
a,d,
b,f,**
c,***
*
*
Haijun Xu
, Xiao Xunwen
, Tu Bin , Qingdao Zeng
a
CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience
and Technology (NCNST), Beijing 100190, China
Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University,
b
Nanjing 210037, China
c
School of Materials and Chemical Engineering, Ningbo University of Technology, Ningbo 315211, China
Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
CAS Center for Excellence in Nanoscience, Beijing Key Laboratory of Micro-Nano Energy and Sensor, Beijing Institute of Nanoenergy and Nanosystems,
d
e
Chinese Academy of Sciences, Beijing 100083, China
f
School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang 453002, China
A R T I C L E I N F O
A B S T R A C T
Article history:
In this work, two aza-BODIPY derivatives, 3,5-diphenyl-1,7-di(p-dodecyloxyphenyl)-aza-BODIPY (CJF)
and 3,5-di(p-bromophenyl-1,7-di(p-dodecyloxyphenyl)-aza-BODIPY (2Br-CJF) acted as model molecules
to form the self-assembly monolayers on the solid-liquid interface. With the utilizing of scanning
tunnelling microscope (STM), we demonstrated that intermolecular BrÁ Á ÁFÀÀBF interactions existed in
2Br-CJF self-assembly structure and played an important role in strengthening the stability of 2Br-CJF
self-assembly structure. This result is supported by density functional theory (DFT) calculation.
© 2021 Chinese Chemical Society and Institute of Materia Medica, Chinese Academy of Medical Sciences.
Published by Elsevier B.V. All rights reserved.
Received 11 January 2021
Received in revised form 19 February 2021
Accepted 26 February 2021
Available online xxx
Keywords:
Aza-BODIPY
STM
BrÁ Á ÁF interaction
Self-assembly
Surface assembly
HalogenÁ Á Áhalogen interactions in crystal engineering have
received a massive number of attentions in the past several
decades [1–3]. Though the halogenÁ Á Áhalogen interactions belong
to weak interactions, the intermolecular distances between
halogens in crystals are significantly smaller than those of van
der Waals interaction [4,5]. With this view, halogenÁ Á Áhalogen
interactions play an important role in crystallization [6–8].
With the utilizing of scanning tunnelling microscope (STM), the
halogenÁ Á Áhalogen interactions in two-dimensional (2D) crystal
engineering also have been wildly studied in recent years [9–15].
Currently, most of the recent studies about the halogenÁ Á Áhalogen
interactions at the liquid-solid interface are focused on the
interactions between the same halogen atoms [16–18] and
interactions between halogens and non-halogens [19,20], while
rare studies are related to the halogenÁ Á Áhalogen interactions
between different halogen atoms [21].
4,4-Difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY) and its
derivatives are widely applied to fluorescent sensors, organic solar
cells, and other related areas [22–25] due to their excellent
photoelectric performance and good chemical stability [22,24,25].
In a previous work, we used the BODIPY derivative, H-T-BO, as
donor material and C70 molecule as acceptor material to construct
a
host-guest system at the 1-phenyloctane/highly oriented
* Corresponding authors at: CAS Key Laboratory of Standardization and
Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience,
National Center for Nanoscience and Technology (NCNST), Beijing 100190, China.
** Corresponding author at: Jiangsu Co-Innovation Center of Efficient Processing
and Utilization of Forest Resources, College of Chemical Engineering, Nanjing
Forestry University, Nanjing 210037, China.
pyrolytic graphite (HOPG) interface and studied the structure on
the molecular level by STM/STS method [26].
In this work, two aza-BODIPY derivatives, 3,5-di(p-bromo-
phenyl-1,7-di(p-dodecyloxyphenyl)-aza-BODIPY (2Br-CJF) and
3,5-diphenyl-1,7-di(p-dodecyloxyphenyl)-aza-BODIPY (CJF), were
synthesised (Scheme S1 in Supporting information) to investigate
the role of halogenÁ Á Áhalogen interactions in the formation of 2D
molecular self-assembly architectures at 1-phenyloctane/HOPG
*** Corresponding author.
E-mail addresses: xuhaijun@njfu.edu.cn (H. Xu), xunwenxiao@nbut.edu.cn
(X. Xiao), tub@nanoctr.cn (B. Tu), zengqd@nanoctr.cn (Q. Zeng).
1
These authors contributed equally to this work.
https://doi.org/10.1016/j.cclet.2021.02.066
1001-8417/© 2021 Chinese Chemical Society and Institute of Materia Medica, Chinese Academy of Medical Sciences. Published by Elsevier B.V. All rights reserved.
Please cite this article as: Y. Xiao, F. Cai, X. Peng et al., Aza-BODIPY molecular assembly at the liquid-solid interface driven by BrÁ Á ÁFÀÀBF
interactions, Chin. Chem. Lett., https://doi.org/10.1016/j.cclet.2021.02.066

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CCLET-6195; No. of Pages 4
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interface. The chemical structure of aza-BODIPY is similar to that of
BODIPY, but the 8-C atom is replaced by an N atom in aza-BODIPY
[22]. In 2Br-CJF molecules, two 4-bromophenyls are modified on 3
and 5 position of the aza-BODIPY core, and two dodecyloxyphenyls
on 1 and 7 position. The BF2 group of the aza-BODIPY and the
bromine atom provide good sites to form halogenÁ Á Áhalogen
interactions. CJF molecule has a similar structure to 2Br-CJF
molecule, but there is no bromine atom on the benzene ring. With
this difference of molecular structure, we can compare the self-
assembled patterns of these molecules and figure out how the
BrÁ Á ÁFÀÀBF interaction influences the self-assembly. The self-
assembly structures of 2Br-CJF and CJF on HOPG are investigated
by STM. STM is a very important surface analysis technique
because of its capability of capturing the position-specific image on
the molecular level on surface [27–32]. The self-assembly
behaviours and mechanisms are also investigated by density
functional theory (DFT) calculations. The chemical structures of
2Br-CJF and CJF are shown in Scheme 1.
The excremental methods are listed here. First, about the
sample preparation, 1-phenyloctane was purchased from J&K Co.,
Ltd. All these materials were used without further purification. 1-
Phenyloctane functioned as solvent to dissolve CJF and 2Br-CJF, and
the concentrations of CJF and 2Br-CJF were controlled below 10À4
mol/L. The assemblies were prepared by subsequent deposition of
the components onto a freshly cleaned HOPG (grade ZYB, SPI, U. S.
A.) surface. CJF or 2Br-CJF solution was deposited on HOPG, and
detected by STM. All experiments were performed at room
temperature.
adsorption of benzene on graphite and graphene should be very
similar [34], we had performed our calculations on infinite
graphene monolayers using PBC. Considering that the interaction
between adsorbates and substrate was mainly van der Waals
interaction, the Grimme’s dispersion corrections were adopted in
our calculations. In the superlattice, slabs were separated by 35 Å
in the normal direction. When modelling the adsorbates on
graphene, we used graphene supercells and sampled the Brillouin
zone by a 1 Â1Â1 k-point mesh.
After depositing a droplet of CJF in 1-phenyloctane solution on
the freshly cleaved HOPG, the self-assembly structure of the CJF
molecule was formed at the 1-phenyloctane/HOPG interface. Then
the large-scale domains were detected by STM (Fig. S16a in
Supporting information). The CJF molecules formed a well-aligned
and stable pattern on a large scale. Regular zig-zag lines were
observed on the HOPG surface, and a high-resolution STM image is
resolved for more details (Fig.1a). Single CJF molecule presented as
a bright H-like shaped spot. The CJF molecules alternated with each
other in a dimer (marked by a yellow circle in Fig.1a). As the phenyl
groups are linked with the aza-BODIPY core by a single bond, the
phenyl groups are not parallel to the HOPG strictly. So, the
interactions between the phenyl groups of CJF molecules in a dimer
and the edge-to-face interactions between the phenyl groups
p-p
p-p
and HOPG are the driven forces to the formation of the dimers.
Moreover, different dimers self-assembled into a zig-zag line.
Obviously, the
p-p interactions between the fastigiate phenyl
groups from adjacent dimers facilitated the formation of the zig-
zag lines. On another side of the CJF molecule, the darker strips
staggered with each other in the zig-zag structure and the lengths
were measured to be 1.45 Æ 0.05 nm that were almost identical
with those of dodecyl chains. The intermolecular van der Waals
forces between long alkyl chains also helped to stabilize the zig-
zag structure on the HOPG substrate. Fig. 1b is the corresponding
molecular model given by DFT calculations based on the STM
observations. A measured unit cell was marked in the STM image
and the corresponding model. The measured parameters of unit
Next, is about the STM detection. The STM detection were
performed on a Nanoscope IIIa (Bruker, U. S. A.) under ambient
conditions. All the images were recorded using the constant-
current mode at liquid/solid interface. The STM probes were made
by mechanically cut Pt/Ir wires (80/20).
As for the DFT calculation. All theoretical calculations were
performed using DFT-D scheme provided by DMol3 code. We used
the periodic boundary conditions (PBC) to describe the 2D periodic
structure on the graphite in this work. The Perdew-Burke-
Ernzerhof parameterization of the local exchange correlation
energy was applied in the generalized gradient approximation
(GGA) to describe exchange and correlation [33]. All-electron spin-
unrestricted Kohn-Sham wave functions were expanded in a local
atomic orbital basis. For the large system, the numerical basis set
was applied. All calculations were all-electron ones, and performed
with the medium mesh. Self-consistent field procedure was done
with a convergence criterion of 10À5 a.u. on the energy and
electron density. Combined with the experimental data, we have
optimized the geometry of the adsorbates in the unit cell. When
the energy and density convergence criterion were reached, we
could obtain the optimized parameters and the interaction energy
between adsorbates. To evaluate the interaction between the
adsorbates and HOPG, we design the model system. Since
cell were: a = 2.5 Æ 0.1 nm, b = 3.1 Æ0.1 nm,
g
= 108ꢀ Æ 2ꢀ (Table 1).
To further explore if BrÁ Á ÁFÀÀBF interaction could influence the
self-assembly of CJF molecules, we observed the self-assembly
structure of 2Br-CJF molecules with STM. The same with CJF
molecules, a droplet of the 2Br-CJF solution in 1-phenyloctane was
deposited on the freshly cleaved HOPG. Then the large-scale
structure was detected by STM (Fig. S16b in Supporting informa-
tion). Due to the similar molecular structure with CJF, the 2Br-CJF
molecules formed
a similar self-assembly pattern with CJF
molecules. Each H-like bright spot corresponded to a 2Br-CJF
molecule, and dimers composed of two 2Br-CJF molecules self-
assembled into regular zig-zag lines on the HOPG surface.
However, after detecting the high-resolution STM image
(Fig. 2a), we can clearly distinguish some different details of
2Br-CJF’s self-assembly structure from CJF’s. First of all, the
measured cell parameters were: a = 2.3 Æ 0.1 nm, b = 3.6 Æ 0.1 nm,
Fig. 1. (a) High-resolution STM image of CJF self-assembled structures at PO/HOPG
interface (Iset
=
271.6 pA, Vbias =816.3 mV, 20.4 nm  20.4 nm). (b) Proposed
molecular model of CJF. Inset illuminates that there is no interaction in H atoms and
F atoms.
Scheme 1. Chemical structures of 2Br-CJF and CJF.
2

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Table 1
thermodynamic stability of the different systems should be the
total energy per unit area. All of the calculation results we
mentioned above are listed in Table 2.
The experimental (exptl.) and calculated (calcd.) unit cell parameters for the CJF
cells and 2Br-CJF cells.
Sample
CJF
a (nm)
b (nm)
g (degree)
From Table 2, we notice that the interaction energy between
adsorbates of 2Br-CJF assembled structure is À43.172 kcal/mol,
which is lower than that between adsorbates of CJF assembled
structure (À28.173 kcal/mol). It means that the interaction
between the 2Br-CJF molecules is stronger, which strongly
supports the existence of BrÁ Á ÁF interaction. Combining with the
differences in the cell parameter of the 2Br-CJF and CJF assembled
system we presented above, we suggest the BrÁ Á ÁFÀÀBF interaction
between the 2Br-CJF dimers plays an important role in the self-
assembly process. The BrÁ Á ÁFÀÀBF interaction strengthens the total
interaction between 2Br-CJF dimers and changes the 2Br-CJF self-
assembled structure. There is no significant difference in the
interactions between adsorbates and substrate, which is accept-
able because the molecular structures of these two molecules are
similar. The tiny difference in the interaction between adsorbates
exptl.
calcd.
exptl.
calcd.
2.5 Æ 0.1
2.50
3.1 Æ 0.1
3.02
108 Æ 2
109
2Br-CJF
2.3 Æ 0.1
3.6 Æ 0.1
119 Æ 2
2.34
3.64
119
and substrate may be caused by the Br-
p interactions of 2Br-CJF.
Fig. 2. (a) High-resolution STM image of 2Br-CJF (Iset = 299.1 pA, Vbias =770.3 mV,
21.9 nm  21.9 nm). (b) Proposed molecular model of 2Br-CJF. Inset illuminates the
BrÁ Á ÁFÀÀBF interaction as indicated by dotted lines.
This kind of halogenÁ Á Á interaction has ever been reported in
p
many previous works [35–37]. The total energy per unit area of the
2Br-CJF assembled system is À0.229 kcal molÀ1 ÅÀ2, lower than
that of the CJF assembled system (À0.205 kcal molÀ1 ÅÀ2). It also
means that the 2Br-CJF assembled system is an energetically
favourable structure. In this system, the BrÁ Á ÁFÀÀBF interaction
facilitates the stability of the self-assembled structure. Moreover,
in the optimized molecular model of CJF system and 2Br-CJF
system (Figs. 1b and 2 b, respectively), we can notice that the
distance between the F atoms and H atoms of CJF (marked with a
red circle in Fig. 1b) is 0.51 Æ0.01 nm, which is larger than the van
der Waals radii of these two atoms. So, we think there is no
interaction between the F and H atoms. The distance between the F
atoms and Br atoms of 2Br-CJF (Marked with red dotted lines in the
inset of Fig. 2b) is 0.30 Æ 0.01 nm, this length agreed to the length
of halogenÁ Á Áhalogen interactions reported in the previous article
[20], indicating that there are halogenÁ Á Áhalogen interactions
between the Br atoms and F atoms of BF2 groups.
g
= 119ꢀ Æ 2ꢀ (Table 1). The differences in cell parameters indicated
that the driven force may be different in the 2Br-CJF self-assembly
structure. Except for the p-p interactions we mentioned above, the
halogenÁ Á Áhalogen interactions between Br atoms and F atoms of
BF2 groups also affected 2Br-CJF’s self-assembly structure. A pair of
BrÁ Á ÁFÀÀBF interactions exist between the Br atoms of 4-
bromophenyls and the F atoms of BF2 groups on two adjacent
molecules. The BF2 group is an electron-deficient group, and the Br
atom has a lone electron pair. So, in two 2Br-CJF molecules, there
are two antiparallel BrÁ Á ÁFÀÀBF interactions. One is formed by one F
atom of the BF2 group on the first 2Br-CJF molecule and one Br
atom on the second 2Br-CJF molecule. Another one is formed by the
Br atom of the first 2Br-CJF molecule and one F atom of the BF2
group on the second2Br-CJF molecule. Next, we measured the
angle in the zig-zag lines (α, Marked with blue lines in Figs.1a and 2
a). In the CJF self-assembly structures, the angle α was measured to
be 114ꢀ Æ 2ꢀ. While in the self-assembly structure of 2Br-CJF, the
angle α was measured to be 104ꢀ Æ 2ꢀ. The smaller angle of the zig-
zag lines indicated that the phenyl group of a 2Br-CJF molecule was
closer to the axis of symmetry of another 2Br-CJF molecule. This
further demonstrated that the BrÁ Á ÁFÀÀBF interaction has changed
the self-assembly structure of the aza-BODIPY molecules.
In order to further demonstrate the result, DFT calculations for
the CJF’s and the 2Br-CJF’s assembly system were conducted based
on the observed phenomena. The calculated parameters are listed
in Table 1. The calculated parameter agreed with the experimental
data. In the surface-assisted self-assembly system, the interaction
between adsorbates and the interaction between adsorbates and
substrates are important. Therefore, we presented the total energy
including the interaction energy between adsorbates and the
interaction energy between adsorbates and the substrate. These
results are the total energy of a cell. We could compare the total
energy to evaluate the thermodynamic stability of different
systems in general. However, if we need to compare two systems
with different unit cells precisely, we should consider the effect of
the unit area. So, a more reasonable way to compare the
In addition, the energy analysis based on the whole unit cell
provides limited information about the BrÁ Á ÁFÀÀBF halogen
interaction, as it may be overwhelmed by the contribution from
the difference at the alkyl chains, aromatic part. In order to exclude
the possibility that the structure is only driven by close-packing
and the interactions between alkyl chains and aromatics, based on
the previous work we build a high-quality DFT calculation model
with only key atoms (Fig. S17 in Supporting information) for such
interaction motif [38]. In this DFT calculation, we calculated the
energy of the BrÁ Á ÁFÀÀBF interaction is À1.256 kcal/mol. This means
the BrÁ Á ÁFÀÀBF interaction is a week interaction in this self-
assembly system.
In conclusion, we investigated self-assembled structures of two
aza-BODIPY derivatives, CJF molecule and 2Br-CJF molecule with
STM and demonstrated that the BrÁ Á ÁF interactions exist and can
adjust the 2D self-assembly behaviour of the aza-BODIPY
derivatives at the 1-phenyloctane/HOPG interface. This result
was supported by the DFTcalculation. We expect that this research
can enrich the method of designing the 2D molecular networks
and provide a new idea to explain some self-assembly behaviours
of halides on the solid-liquid interface.
Table 2
Total energies and energies per unit area of the assembled structures of CJF and 2Br-CJF.
Interactions between
adsorbates (kcal/mol)
Interactions between adsorbates
and substrate (kcal/mol)
Total energy (kcal/mol)
Total energy per unit
area (kcal molÀ1 ÅÀ2
)
CJF
2Br-CJF
À28.173
À43.172
À118.235
À126.749
À146.408
À169.921
À0.205
À0.229
3

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Declaration of competing interest
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The authors declare that they have no known competing
financial interests or personal relationships that could have
appeared to influence the work reported in this paper.
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Appendix A. Supplementary data
Supplementary material related to this article can be found,
in the online version, at doi:https://doi.org/10.1016/j.
cclet.2021.02.066.
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