Pinning-down molecules in their self-assemblies with multiple weak hydrogen bonds of C[sbnd]H?F and C[sbnd]H?N

Article abstract of DOI:10.1016/j.cclet.2016.11.007

Two-dimensional self-assemblies of four partially fluorinated molecules, 1,4-bis(2,6-difluoropyridin-4-yl)benzene, 4,4′-bis(2,6-difluoropyridin-4-yl)-1,1′-biphenyl, 4,4′-bis(2,6-difluoropyridin-4-yl)-1,1′:4′,1″-terphenyl and 4,4′-bis(2,6-difluoropyridin-3-yl)-1,1′-biphenyl, involving weak intermolecular C[sbnd]H?F and C[sbnd]H?N hydrogen bonds were systematically investigated on Au(111) with low-temperature scanning tunneling microscopy. The inter-molecular connecting modes and binding sites were closely related to the backbones of the building blocks, i.e., the molecule length determines its binding sites with neighboring molecules in the assemblies while the attaching positions of the N and F atoms dictate its approaching and docking angles. The experimental results demonstrate that multiple weak hydrogen bonds such as C[sbnd]H?F and C[sbnd]H?N can be efficiently applied to tune the molecular orientations and the self-assembly structures accordingly.

Full text of DOI:10.1016/j.cclet.2016.11.007

G Model
CCLET 3881 1–6
Chinese Chemical Letters xxx (2016) xxx–xxx
Contents lists available at ScienceDirect
Chinese Chemical Letters
journal homepage: www.elsevier.com/locate/cclet
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Original article
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Pinning-down molecules in their self-assemblies with multiple weak
hydrogen bonds of C ꢀꢀ Hꢁ ꢁ ꢁF and C ꢀꢀ Hꢁ ꢁ ꢁN
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Xin Jin , Jacob R. Cramer , Qi-Wei Chen , Hai-Lin Liang , Jian Shang , Xiang Shao ,
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Wei Chen , Guo-Qin Xu , Kurt V. Gothelf *, Kai Wu
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BNLMS, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
Danish-Chinese Centre for Self-Assembly and Function of Molecular Nanostructures on Surfaces at iNANO, Department of Chemistry, Aarhus University,
000 Aarhus C, Denmark
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Department of Chemical Physics, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei 230026, China
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Department of Chemistry, National University of Singapore, 117543, Singapore
SPURc, 1 CREATE Way, #15-01, CREATE Tower, 138602, Singapore
A R T I C L E I N F O
A B S T R A C T
Article history:
Received 15 June 2016
Two-dimensional self-assemblies of four partially fluorinated molecules, 1,4-bis(2,6-difluoropyridin-4-
yl)benzene, 4,4'-bis(2,6-difluoropyridin-4-yl)-1,1'-biphenyl, 4,4'-bis(2,6-difluoropyridin-4-yl)-1,1':4',
1”-terphenyl and 4,4'-bis(2,6-difluoropyridin-3-yl)-1,1'-biphenyl, involving weak intermolecular
C ꢀꢀ Hꢁ ꢁ ꢁF and C ꢀꢀ Hꢁ ꢁ ꢁN hydrogen bonds were systematically investigated on Au(111) with low-
temperature scanning tunneling microscopy. The inter-molecular connecting modes and binding sites
were closely related to the backbones of the building blocks, i.e., the molecule length determines its
binding sites with neighboring molecules in the assemblies while the attaching positions of the N and F
atoms dictate its approaching and docking angles. The experimental results demonstrate that multiple
weak hydrogen bonds such as C ꢀꢀ Hꢁ ꢁ ꢁF and C ꢀꢀ Hꢁ ꢁ ꢁN can be efficiently applied to tune the molecular
orientations and the self-assembly structures accordingly.
Received in revised form 27 October 2016
Accepted 28 October 2016
Available online xxx
Keywords:
Fluorinated pyridyl molecules
Grouped hydrogen bonds
Molecular self-assembly
Molecular design
Scanning tunneling microscopy
ã 2016 Kurt V. Gothelf, Kai Wu. Chinese Chemical Society and Institute of Materia Medica, Chinese
Academy of Medical Sciences. Published by Elsevier B.V. All rights reserved.
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1. Introduction
hexadecafluorophthalocyanine (F16CuPc), a potential molecular
semiconductor serving as an electron acceptor in organic
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Self-assembled molecular architectures on metal surfaces have
attracted great interest due to their structural ordering and
abundance, and potential applications in the field of nanotechnol-
ogy [1–3]. As one of the main driving forces among non-covalent
bonding interactions, hydrogen bond (HB) has been extensively
exploited to form various assembling patterns owing to its unique
properties such as bonding strength, flexibility, directionality and
selectivity [3–7]. Compared with their strong counterparts
photovoltaic (OPV) devices [20–22] and as an n-type organic
semiconducting material in light-emitting diode [23], have
received substantial attention due to their extraordinary air-
stability. Besides the layer thickness, the packing pattern of the
F16CuPc molecules governed by weak intermolecular interactions
including C ꢀꢀ Hꢁ ꢁ ꢁF HBs may have great influence in the perfor-
mance of the OPV devices. In terms of the F16CuPc self-assembly on
metallic substrates [20–22], previous research normally focuses on
its co-assembly with other p-type organic molecules to form
molecular p–n junctions or donor–acceptor pairs [23,24].
While perfluoro-molecules have been generally adopted to
prepare organic semiconducting self-assembled membranes
[29–32], nano-arrays [33] and networks [34,35] at surfaces,
partially fluorinated molecules are less studied in the past. In
our previous report [15], we have successfully assembled a whole
series of 2D molecular porous networks whose pores possess all
possible rotational symmetry, i.e., 2-, 3-, 4- and 6-fold rotations,
by using the same building blocks, 4,4'-bis(pyridin-4-yl)-1,1'-
biphenyl (BPBP) and trimesic acid (TMA). This is achieved by solely
(
7–8 kcal/mol) [8–10], weak HBs [11] are usually more flexible
in bonding geometries which could be employed to control the
orientations of the assembling molecules and hence ultimate
assembling structures [12–14].
Weak HBs like C ꢀꢀ Hꢁ ꢁ ꢁO and C ꢀꢀ Hꢁ ꢁ ꢁN are frequently utilized
to construct two-dimensional (2D) self-assemblies in the past
[15–19]. Meanwhile, perfluoro-molecules such as copper
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Corresponding authors.
E-mail addresses: kvg@chem.au.dk (K.V. Gothelf), kaiwu@pku.edu.cn (K. Wu).
http://dx.doi.org/10.1016/j.cclet.2016.11.007
001-8417/ã 2016 Kurt V. Gothelf, Kai Wu. Chinese Chemical Society and Institute of Materia Medica, Chinese Academy of Medical Sciences. Published by Elsevier B.V. All
1
rights reserved.
Please cite this article in press as: X. Jin , et al., Pinning-down molecules in their self-assemblies with multiple weak hydrogen bonds of
C ꢀꢀ Hꢁ ꢁ ꢁF and C ꢀꢀ Hꢁ ꢁ ꢁN, Chin. Chem. Lett. (2016), http://dx.doi.org/10.1016/j.cclet.2016.11.007

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changing two physical parameters, substrate temperature and
coverage ratio of TMA to BPBP. The driving force is the combined
strong and weak HB networks formed between TMA and BPBP.
(Fig. 1b). In this pattern, one BDFPB molecule perpendicularly
approaches to another at the X sites, as marked in the molecular
model in Fig. 1a. Such a connection mode is termed as Mode X.
Apparently, Pattern X is formed solely via the X mode. One unit
cell of this close-packed structure is schematically modelled in
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Among all possible HBs, the weak ones such as C
¼
O (TMA)ꢁ ꢁ ꢁH ꢀꢀ C
-H in the pyridyl group in BPBP) and N(pyridyl)ꢁ ꢁ ꢁH ꢀꢀ C
pyridyl) play an important role in tuning the final pore symmetry.
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(
(
a- and b
Fig. 1d and defined by the cell parameters: a = (1.2 ꢂ 0.1) nm,
ꢃ
Therefore, it would be very interesting to explore the assembling
behavior of partially fluorinated BPBP derivatives upon substitu-
b = (1.8 ꢂ 0.1) nm, and
a
= (86 ꢂ 2) . Further annealing at 400 K led
to partial desorption of the BDFPB molecules (Fig. 1c). However,
regardless of the surface coverage decrease or temperature
elevation of the sample, Pattern X is the sole structure observed
at surface.
tions of the
a-H in pyridyl with F atoms. The replacing F atoms
would accordingly change the acidity of their neighboring H atoms
in the pyridyl groups. Such a motivation intrigues the present
study of the self-assemblies of 1,4-bis(2,6-difluoropyridin-4-yl)
benzene (BDFPB) and its derivatives which can form weak HBs like
C ꢀꢀ Hꢁ ꢁ ꢁF and C ꢀꢀ Hꢁ ꢁ ꢁN.
Similar to the case of BDFPB, BDFPBP also assembled into a
close-packed Pattern X (Fig. 2a) at 1 ML. Two interacting BDFPBP
ꢃ
molecules in adjacent rows formed an angle of about (84 ꢂ 2) . It
As is well known, the structures of the molecular building
blocks are of extreme importance in tailoring and engineering the
molecular self-assemblies. To do this, several strategies including
re-designing the molecular backbones [36–38], introducing
additional functional groups [39–42] and changing the number
and positions of the substituents [43–46] have been developed,
aiming at precisely controlling the assembled architectures on the
substrates.
should be pointed out that these two molecules are not strictly
perpendicular to each other due to the repulsion interaction of the
F atoms in them. Subsequent thermal treatment of the sample led
to several new patterns correspondingly labelled as XYI, XYII and Y
in Fig. 2b–d. The unit cell parameters for the four assembled
patterns are given below: (1) Pattern X, a = (1.1 ꢂ0.1) nm, b = (2.4
ꢃ
ꢂ 0.1) nm, and
a
= (89 ꢂ 2) ; (2) Pattern XYI, a = (2.1 ꢂ0.1) nm,
ꢃ
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b = (2.1 ꢂ0.1) nm, and
a
= (75 ꢂ 2) ; (3) Pattern XYII, a = (1.7 ꢂ 0.1)
ꢃ
ꢃ
To achieve tuning the 2D molecular self-assembly patterns in a
controlled manner, the BPFBP molecule and its three derivatives
such as 4,4'-bis(2,6-difluoropyridin-4-yl)-1,1'-biphenyl (BDFPBP),
nm, b = (1.9 ꢂ 0.1) nm, and
a
a
= (96 ꢂ 2) ; (4) Pattern Y, a = (1.9 ꢂ 0.1)
nm, b = (1.9 ꢂ 0.1) nm, and
= (93 ꢂ 2) . All unit cells are highlight-
ed in the STM images in Fig. 2, and the corresponding schematic
models for the patterns are given in Fig. 2e–h.
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,4”-bis(2,6-difluoropyridin-4-yl)-1,1':4',1”-terphenyl (BDFPTP)
and 4,4'-bis(2,6-difluoropyridin-3-yl)-1,1'-biphenyl (BDFP-3-BP)
were deposited onto an atomically flat Au(111) substrate. Their
corresponding self-assembly patterns were subsequently scruti-
nized in detail with scanning tunneling microscopy (STM), a
powerful tool to unveiling surface molecular assembling structures
at the sub-molecular level. A major experimental observation was
that these molecules could be pinned down in their self-
assemblies by synergic multiple weak HBs of C ꢀꢀ Hꢁ ꢁ ꢁF and
C ꢀꢀ Hꢁ ꢁ ꢁN.
According to the models given in Fig. 2e–h, two distinct
connection modes, namely, X and Y, can be immediately identified.
Obviously, each BDFPB molecule possesses four identical X sites. In
the Y mode, one BDFPBP molecule perpendicularly approaches
another one via the Y sites that bisect the molecule. The distance
between the approaching sites for the Y mode and either end of the
molecule is about 0.71 nm. Again the repulsion interaction of the F
atoms in two connecting BDFPB molecules leads to their docking
angle and distance deviations. The proposed molecular models
suggest that both C ꢀꢀ Hꢁ ꢁ ꢁF and C ꢀꢀ Hꢁ ꢁ ꢁN weak HBs are involved in
either X or Y modes.
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2. Results and discussion
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The close-packed Pattern X is built solely via the X mode
(Fig. 2a), and Pattern Y, solely via the Y mode (Fig. 2d). Pattern XY is
made possible via a mixture of the X and Y modes. In our
experiments, only two large-area ordered XY patterns were
observed, namely Pattern XYI (Fig. 2b) and Pattern XYII (Fig. 2c).
Both possess different X mode/Y mode ratios. For Pattern XYI, there
are six intermolecular binding sites in a unit cell, four of which
adopt the X mode to interact with the nearest molecule, while the
other two adopt the Y mode (Fig. 2b and f). For Pattern XYII, one
unit cell contains four binding sites, two X modes and two Y modes
(Fig. 2c). Accordingly, the ratio of X mode to Y mode is 2:1 for
Pattern XYI and 1:1 for Pattern XYII, respectively.
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In a previous study [5], a porous honeycomb network was
prepared by grouped HBs, exhibiting a much stronger hetero- as
opposed to homo-molecular hydrogen bonding between perylene
tetra-carboxylic di-imide (PTCDI) and melamine (1,3,5-triazine-
,4,6-triamine) on a silver-terminated silicon surface. Such a
honeycomb network contains vertices formed by melamine and
straight edges formed by PTCDI. Here, we adopt grouped weak HBs
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formed by bent F ꢀꢀ C ꢀꢀ N¼C ꢀꢀ F and H ꢀꢀ C¼C ꢀꢀ C¼C ꢀꢀ H in the
F-containing molecules to govern the assembling structures.
At the coverage of one monolayer (ML), the BDFPB molecules
assembled into a close-packed structure denoted Pattern X
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Fig. 1. (a) Schematic model of BDFPB, in which the HB acceptor groups and HB donor groups are marked by short lines and arrows. (b–c) STM images of the self-assembled
Pattern X at full coverage (b) and after partial desorption (c). The yellow rods highlight the arrangements of BDFPB in within a unit cell, as marked by the black rectangle for eye
guidance. (d) Schematic model for Pattern X superimposed onto an enlarged STM image. Imaging conditions: (b–c) bias voltage (V) = 1.5 V, feedback current (I) = 50 pA. (For
interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)
Please cite this article in press as: X. Jin , et al., Pinning-down molecules in their self-assemblies with multiple weak hydrogen bonds of
C ꢀꢀ Hꢁ ꢁ ꢁF and C ꢀꢀ Hꢁ ꢁ ꢁN, Chin. Chem. Lett. (2016), http://dx.doi.org/10.1016/j.cclet.2016.11.007

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Fig. 2. Molecular structure of BDFPBP is schematically shown by the model in left panel, and HB acceptor and donor groups are marked by short lines and arrows. STM images
of the four assembled patterns: (a) Pattern X, (b) Pattern XYI, (c) Pattern XYII, and (d) Pattern Y. Different connection modes in Patterns XYI and XYII are marked in (c) and (d).
(
e–h) Schematic models superimposed on enlarged STM images, corresponding to (a–d) respectively. Imaging conditions: (a–d) V = 1.5 V, I = 50 pA.
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As revealed by the STM images, Pattern XYII and Pattern Y are
and XYII are similar to the corresponding patterns achieved with
porous molecular networks with rectangular and square pores, and
BDFPBP. Due to the elongated molecular backbone, the pore area in
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the pore areas are measured to be 0.66 and 0.36 nm , respectively.
Pattern XYII (1.04 nm ) is larger than that in Pattern XYII of BDFPBP.
As mentioned above, Patterns XYI, XYII and Y were experimen-
tally obtained by thermally annealing of Pattern X. In our
experiments, large-area Pattern X appeared at 1 ML. At 450 K,
Pattern XYI was formed on the substrate. When the temperature
rose up to 460 K, Patterns XYII and Y coexisted at the surface. The
domain size of Pattern Y increased with the annealing tempera-
ture. Above 500 K, all BDFPBP molecules completely desorbed from
the substrate.
For BDFPTP, the increasing number of the phenyl rings in the
assembling molecule doubles the number of the identical sites for
the Y mode, as depicted by the molecular structural model in Fig. 3.
Similar to the densely packed structures of BDFPB and BDFPBP,
zigzag-like Pattern X appeared at 1 ML (Fig. 3a). Afterwards,
sample annealing resulted in four new structures, namely, XYI,
XYII, Y and XYIII (Fig. 3b–e). Among these patterns, Patterns XYI
Pattern XYIII is constructed via mixed X and Y modes at an X
mode/Y mode ratio of 1:1. Though being identical to the X/Y ratio
for Pattern XYII, the differences between Patterns XYIII and XYII are
feasibly noticeable: In Pattern XYII, for a half of the molecules, both
ends of an individual molecule are connected to the nearest
molecule via the X mode and for the other half, via the Y mode;
however, in Pattern XYIII, for all the molecules, one end of an
individual molecule interacts with the nearest molecule by the X
mode and the other end, by the Y mode. In addition, Pattern XYIII
contains two different kinds of pores labelled as A and B in Fig. 3e,
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and the pore areas were measured to be 1.38 and 0.67 nm ,
respectively.
The unit cell of each structure is marked in corresponding STM
image in Fig. 3, and the unit cell parameters are: (1) Pattern X,
ꢃ
a = (3.0 ꢂ 0.1) nm, b = (1.1 ꢂ0.1) nm, and
a
= (90 ꢂ 2) ; (2) Pattern
Fig. 3. Molecular structure of BDFPTP is schematically shown by the model in left panel, and HB acceptor groups and HB donor groups are marked by short lines and arrows. (a
e) STM images of its assembled structures: (a) Pattern X, (b) Pattern XYI, (c) Pattern XYII (d) Pattern Yand (e) Pattern XYIII. (f–j) Schematic models of each assembled patterns
–
respectively. In (e), two different pores are marked as A and B. Imaging conditions: V = 1.5 V, I = 50pA.
Please cite this article in press as: X. Jin , et al., Pinning-down molecules in their self-assemblies with multiple weak hydrogen bonds of
C ꢀꢀ Hꢁ ꢁ ꢁF and C ꢀꢀ Hꢁ ꢁ ꢁN, Chin. Chem. Lett. (2016), http://dx.doi.org/10.1016/j.cclet.2016.11.007

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ꢃ
XYI, a = (2.4 ꢂ 0.1) nm, b = (2.5 ꢂ 0.1) nm, and
a
= (77 ꢂ2) ;
(
3) Pattern XYII, a = (2.2 ꢂ 0.1) nm, b = (1.9 ꢂ 0.1) nm, and
ꢃ
a
= (88 ꢂ 2) ; (4) Pattern Y, a = (2.0 ꢂ 0.1) nm, b = (2.2 ꢂ 0.1) nm,
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and
a
= (92 ꢂ 2) ; (5) Pattern XYIII, a = (3.2 ꢂ 0.1) nm, b = (3.4 ꢂ 0.1)
ꢃ
nm, and
a
= (85 ꢂ 2) .
All other self-assembled structures were experimentally
achieved by thermal treatments of Pattern X for the BDFPTP
molecule. At 450 K, the original Pattern X turned into XYI. At 500 K,
Patterns XYII and Y became dominant while some small domains
of Pattern XYI co-existed. After extended thermal treatment of the
sample at 500 K, Pattern Y faded in and became larger and larger at
the expense of Pattern XYII. Finally, Pattern XYIII formed after
further annealing at 500 K.
According to above-described results, one can straightforward
conclude that there are two binding modes in all self-assembled
structures for the three molecules studied above. It is the length of
the linear molecule that determines the number of the connection
sites for different modes. All experimentally observed patterns are
formed by the molecules connected by sole X(Y) mode or a mixture
of both modes at different ratios.
For the BDFPBP molecule, the continuous changes of the
assembled structures sequentially occurred during the tempera-
ture elevation as follows: Pattern X ! Pattern XYI ! Pattern XY
II ! Pattern Y. The surface molecular density for Patterns X, XYI,
XYII and Y decreased with the annealing temperature, corre-
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spondingly being 0.76, 0.70, 0.62 and 0.55 molecules/nm . The
decrease in the surface molecule density can be rationalized by the
fact that more and more molecules desorb from the substrate
during the annealing process. In another set of experiments, we
started from a sample at the sub-monolayer coverage and then
added up more and more BDFPBP molecules onto the substrate. As
a result, the evolution of the molecularly assembled patterns was
inversed with respect to the annealing experiment starting from
Fig. 4. (a) Models of three molecular conformations for the BDFP-3-BP molecule at
surface, labelled as A, B and C. (b) STM image of the zigzag structure. The black
parallelogram marks the unit cell: a = (1.3 ꢂ 0.1) nm, b = (1.9 ꢂ 0.1) nm, and
a= (70
ꢃ
ꢂ 2) . (c) STM image of triangular structure. The black parallelogram marks the unit
ꢃ
cell with parameters: a = (1.7 ꢂ 0.1) nm, b = (4.2 ꢂ 0.1) nm, and
a
= (73ꢂ 2) . (d-e)
Proposed models for the assembled structures. Red dashed lines indicate possible
HBs. The pink, orange and red rods correspondingly represent Conformation A, B
and C. Imaging conditions: (a), V = 2.3 V, I = 30 pA; (b), V = 1.6 V, I = 150 pA. (For
interpretation of the references to color in this figure legend and in the text, the
reader is referred to the web version of this article.)
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ML. Such a comparison of the above two sets of experiments
implies that the structural transformation of the 2D BDFPBP
molecular assemblies is solely governed by the surface coverage.
For the BDFPTP molecule, warm-up of the substrate gave rise to
the sequential pattern change from Pattern X to XYI, then to XYII, Y
and finally to XYIII as the molecular density decreased with the
substrate temperature. The molecular density for Pattern X, XYI,
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shown in Fig. 4b and c. According to the structural symmetry, we
can infer that the molecules in Conformation A mingle with those
in Conformation B at a ratio of 1:1 in the zigzag structure (Fig. 4b),
but in the triangular structure (Fig. 4c), all three molecular
conformations are involved and the conformational ratio of A:B:C
is 1:1:2. Both self-assembled structures share the similarity that
XYII and XYIII is correspondingly 0.61, 0.51, 0.48, 0.45 and
2
0
.37 molecules/nm . All these results suggest again that the
surface coverage dictates self-assembled structures for all three
molecules.
Furthermore, it should be mentioned that in all STM images, the
angle between two adjacent weakly-bounded molecules is
ꢃ
the angle between two interacting molecules is nearly 30 , as
ꢃ
approximately 90 , but slightly deviates from the right angle
expected from our molecular design. Such an orientational
arrangement ensures that the “donor line” formed by C and N
atoms is parallel to the “acceptor line” including multiple H atoms.
due to the repulsing F atoms in involved molecules. Nevertheless,
this can still be ascribed to the directional formation of the weak
HBs. The “donor line” formed by the C and N atoms at the
molecular terminal tends to be parallel to the “acceptor line”
composed entirely of the H atoms in the side of the molecules,
making the lengths of the intermolecular HBs shortest. To testify
this, we designed and synthesized the BDFP-3-BP molecule, and
explored its self-assembling behavior on Au(111). Due to the
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267
268
269
In summary, 2D self-assemblies of three partially fluorinated
molecules including BDFPB, BDFPBP and BDFPTP via weak
C ꢀꢀ Hꢁ ꢁ ꢁF and C ꢀꢀ Hꢁ ꢁ ꢁN HBs have been systematically studied on
p
rotational freedom of the
s-bond connecting the pyridyls, BDFP-3-
the atomically flat Au(111)-(22 ꢄ 3) substrate. The inter-molecu-
BP may have three possible conformations after deposition,
labelled as A (blue rod), B (pink rod) and C (red rod) in Fig. 4.
It’s noticed that, although experimentally captured, Conformation
C did not very often appear in the assemblies, possibly due to
energy optimization of the assemblies because Conformations A
and B in total overtook in their appearance probability and
suppressed the occurrence of Conformation C. Nonetheless,
Conformation C looks like the half moon and thus can be easily
identified in the STM image (red rods in Fig. 4b). Two close-packed
structures were experimentally observed on the substrate, as
lar binding sites become abundant as the length of the assembling
molecule increases. In comparison with the BDFP-3-BP molecule,
the “donor line” involving the F atom and N atom in the molecule
endings is attributed to govern that two neighboring and weakly
bounded molecules in the assembled structures are perpendicular
to each other. For each molecule, various self-assembled structures
could be achieved by careful annealing treatments at different
temperatures. Our experimental findings demonstrate that by
rational design of molecular structures and corresponding weak
HBs such as C ꢀꢀ Hꢁ ꢁ ꢁF and C ꢀꢀ Hꢁ ꢁ ꢁN, the 2D self-assemblies of
Please cite this article in press as: X. Jin , et al., Pinning-down molecules in their self-assemblies with multiple weak hydrogen bonds of
C ꢀꢀ Hꢁ ꢁ ꢁF and C ꢀꢀ Hꢁ ꢁ ꢁN, Chin. Chem. Lett. (2016), http://dx.doi.org/10.1016/j.cclet.2016.11.007

G Model
CCLET 3881 1–6
X. Jin et al. / Chinese Chemical Letters xxx (2016) xxx–xxx
5
2
2
70
71
J = 250, 16, 2C), 115.6 (dd, J = 24, 10, 2C), 110.3. 19F NMR (376 MHz,
320
321
322
323
semiconducting molecules can be tuned, which may possibly lead
to a drastic performance change of the devised molecular devices.
+
CDCl
3
):
d
ꢀ68.1. GC–MS m/z calcd. for C
5
2
H F
2
IN [M ]: 241, found:
ꢃ
2
41. MP: 78–80 C.
2
2
72
73
4. Experimental
BDFPB: A mixture of 1,4-phenylenediboronic acid (80 mg,
3
24
325
26
0.48 mmol) and 2,6-difluoro-4-iodopyridine (233 mg, 0.97 mmol)
4.1. Molecule syntheses
was added to a suspension of Pd (PPh
,2-dimethoxyethane (5 mL) and aqueous Na
The mixture was subsequently maintained at reflux for 14 h,
allowed to cool and then poured into H O (20mL) and extracted
with CH Cl ),
(3 ꢄ15 mL). The organic extracts were dried (MgSO
concentrated in vacuo and the residue was purified by column
chromatography (CH Cl /pentane = 1:9, v/v) to give the product as a
white powder (113 mg, 77%). H NMR (400 MHz, CDCl
3
)
4
(56 mg, 0.048 mmol) in
3
1
2
CO (1.0 mL, 2 mol/L).
3
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
00
01
02
03
04
05
06
07
08
09
10
11
12
13
14
15
16
17
18
19
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
The molecular models of the fluorinated molecules including
BDFPB, BDFPBP, BDFPTP and BDFP-3-BP are schematically shown in
Scheme 1. These molecules were not commercially available and
hence laboratory-synthesized starting from the precursors of 2,6-
difluoro-3-iodopyridine (DFIP) and 2,6-difluoro-4-iodopyridine
2
2
2
4
2
2
1
(
DFIDP). Such a series of the fluorinated molecules served two
3
):
ꢀ67.6. HRMS m/z
Na [M + Na ]: 304.0624, found: 304.0624. MP:
d 7.77
19
aims: (1) The BDFPB, BDFPBP and BDFPTP molecules were
designed to study the similarity of and length effect on the final
assembling structures; (2) The BDFP-3-BP molecule was designed
to explore the orientation effect of the synergic multiple weak HBs
3
(s, 4H), 7.07 (s, 4H). F NMR (376 MHz, CDCl ): d
+
calcd. for C16
8
H F
4
N
2
ꢃ
308–310 C.
BDFPBP: A mixture of 4,4-biphenyldiboronic acid (25 mg,
0.10 mmol) and 2,6-difluoro-4-iodopyridine (50 mg, 0.21 mmol)
ꢃ
of C ꢀꢀ Hꢁ ꢁ ꢁF and C ꢀꢀ Hꢁ ꢁ ꢁN at an angle of 60 with respect to its long
axial direction, in comparison to the BDFPB, BDFPBP and BDFPTP
ones whose grouped C ꢀꢀ Hꢁ ꢁ ꢁF and C ꢀꢀ Hꢁ ꢁ ꢁN HBs pointing along
their long axial directions.
was added to a suspension of Pd (PPh
1,2-dimethoxyethane (4 mL) and aqueous Na
The mixture was subsequently maintained at reflux for 14 h,
allowed to cool, poured into H O (10 mL), and extracted with
CH Cl ),
(3 ꢄ 30 mL). The organic extracts were dried (MgSO
concentrated in vacuo, and the residue was purified by column
chromatography (CH Cl /pentane = 1:9, v/v) to give the product as
a white powder (32 mg, 82%). H NMR (400 MHz, DMSO):
3
)
4
(14 mg, 0.012 mmol) in
2
CO (0.5 mL, 2 M).
3
The synthesized molecules were separated, purified and finally
2
1
19
confirmed by H and F nuclear magnetic resonance (NMR),
combined gas chromotograph and mass spectroscopy (GC–MS),
and melting point (MP) measurements. The synthesis procedures
and characterization data of the synthesized precurosors and
molecules are listed below.
2
2
4
2
2
1
d
8.00
(dd, 8H, J = 8.5, 38.9), 7.65 (s, 4H). F NMR (376 MHz, CDCl ):
[M ]: 380.094,
19
3
+
DFIP: Diisopropylamine (7.0 mL, 50 mmol) and 2,6-difluoropyr-
idine (4.5 mL, 50 mmol) were added consecutively to a solution of
n-butyllithium (20 mL, 50 mmol, 2.5 mol/L in hexane) in THF
d
-68.6. MALDI-TOF-MS m/z calcd. for C22
H
12
F
4
N
2
ꢃ
found: 379.848. MP: 240–242 C.
BDFPTP:
(200 mg, 0.52 mmol) and (2,6-difluoropyridin-4-yl)boronic acid
(164 mg, 1.03 mmol) was added to a solution of Pd(PPh (60 mg,
0.052 mmol) in DMF (5 mL) at room temperature. The suspension
was stirred and to it was added aqueous Na CO (0.5 mL, 2 mol/L).
A
mixture of 4,4”-dibromo-1,1':4',1”-terphenyl
ꢃ
ꢃ
(
100 mL) and pentane (30 mL) at ꢀ78 C. After 1 h at ꢀ78 C, the
mixture was treated with a solution of iodine (13 g, 5.0 mmol) in
THF (50 mL) before being washed with 10% aqueous Na SO
25 mL). The organic phase was dried and the volatiles evaporated.
Crystallization of the residue from pentane afforded the product as
3 4
)
2
3
(
2
3
ꢃ
The mixture was subsequently heated to 95 C for 6 h followed by a
1
colorless crystals (8.0 g, 66%). H NMR (400 MHz, CDCl
3
):
d
8.20 (td,
):
filtration of the hot precipitate. The greyish precipitate was washed
13
1
H, J = 8.1, 7.3), 6.70 (dd, 1H, J = 8.3, 3.0). C NMR (100 MHz, CDCl
3
with H
2
O and pentane to furnish the product as a white powder
1
1
61.9 (dd, J = 248, 13), 160.1 (dd, J = 242, 14), 153.5 (dd, J = 7, 2), 108.2
(188 mg, 80%). H NMR (400 MHz, DMSO):
(d, 4H, J = 8.6,), 7.91 (s, 4H), 7.64 (s, 4H). F NMR (376 MHz, DMSO):
d
8.05 (d, 4H, J = 8.4),7.93
19
19
(
dd, J = 35, 6), 69.1 (dd, J = 41, 6). F NMR (376 MHz, CDCl
3
):
d
ꢀ69.1,
+
+
ꢀ
81.5. GC–MS m/z calcd. for C
5
2
H F
2
IN [M ]: 241, found: 241. MP:
d
ꢀ69.8. MALDI-TOF-MS m/z calcd. for C28
16 4 2
H F N [M ]: 456.125,
ꢃ
ꢃ
359
360
361
362
363
364
365
366
367
368
369
370
371
40–42 C.
found: 456.105. MP: 400 C (decomp.).
DFIDP: n-Butyllithium (1.66 mL, 4.15 mmol, 2.5 mol/L in hex-
BDFP-3-BP: A mixture of 4,4-biphenyldiboronic acid (25 mg,
0.10 mmol) and 2,6-difluoro-3-iodopyridine (50 mg, 0.21 mmol)
ane) was added dropwise to a solution of diisopropylamine
ꢃ
(
1.30 mL, 4.15 mmol) in THF (2 mL) at ꢀ78 C. After 25 min 2,6-
was added to a suspension of Pd (PPh
in 1,2-dimethoxyethane (4 mL) and aqueous Na
2 mol/L). The mixture was subsequently maintained at reflux for
12 h, allowed to cool and then poured into H O (10 mL) and
extracted with CH Cl
(3 ꢄ 30 mL). The organic extracts were dried
(MgSO ), concentrated in vacuo and the residue was purified by
column chromatography (CH Cl /pentane = 1:9, v/v) to give the
product as a white powder (29 mg, 76%). H NMR (400 MHz,
CDCl ): 8.03 (dd, 2H, J = 7.9, 17.3), 7.75 (d, 4H, J = 8.5), 7.64 (d, 4H,
J = 8.4), 6.96 (dd, 2H, J = 2.9, 8.1). F NMR (376 MHz, CDCl
3
)
4
(14 mg, 0.012 mmol)
difluoro-3-iodopyridine (1.00 g, 4.15 mmol) in THF (5 mL) was
2
CO (0.5 mL,
3
ꢃ
added dropwise into this mixture by cannula. After 12 h at ꢀ78 C,
H
2
O (0.2 mL, 11 mmol) in THF (2 mL) was added and the mixture
2
was warmed to room temperature during 1 h. The mixture was
washed with 10% aqueous Na SO (5 mL) and extracted with ethyl
) and
2
2
2
3
4
acetate (3 ꢄ 50 mL). The organic extracts were dried (MgSO
4
2
2
1
concentrated in vacuo. Crystallization from hexane afforded the
1
product as colorless crystals (740 mg, 74%). H NMR (400 MHz,
3
d
13
19
CDCl
3
):
d
7.22 (t, 2H,J = 1.2). C NMR (100 MHz, CDCl
3
): 161.1 (dd,
3
):
d
ꢀ69.8,
Scheme 1. Structural models of the four molecules studied.
Please cite this article in press as: X. Jin , et al., Pinning-down molecules in their self-assemblies with multiple weak hydrogen bonds of
C ꢀꢀ Hꢁ ꢁ ꢁF and C ꢀꢀ Hꢁ ꢁ ꢁN, Chin. Chem. Lett. (2016), http://dx.doi.org/10.1016/j.cclet.2016.11.007

G Model
CCLET 3881 1–6
6
X. Jin et al. / Chinese Chemical Letters xxx (2016) xxx–xxx
3
3
72
73
+
ꢀ
70.8. HRMS m/z calcd. for C22
found: 403.0837. MP: 193–195 C.
H
12
4
F N
2
Na [M + Na ]: 403.0834,
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3
3
3
3
3
3
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3
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77
78
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80
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83
84
85
86
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All assembly experiments were performed with a UNISOKU
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431
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