Structural competition between π...π interactions and halogen bonds: A crystallographic study

Article abstract of DOI:10.1039/c2ce26520f

1,3-Diiodotetrafluorobenzene and 1,3,5-trifluoro-2,4,6-triiodobenzene form co-crystals with 4,4′,6,6′-tetramethyl-2,2′-bipyrimidine, 1,2,4,5-tetra(3-pyridyl)benzene and 1,2,4,5-tetra(4-pyridyl)benzene in which the structural competition between π...π interactions and halogen bonds is directly observed. It is found that the strong C-I...N halogen bond competes successfully with the π...π interaction between two 1,3-diiodotetrafluorobenzene molecules while the π...π interaction between two 1,3,5-trifluoro-2,4,6-triiodobenzene molecules can successfully compete with the strong C-I...N halogen bond. Quantum chemical calculations explain the structural competition well.

Full text of DOI:10.1039/c2ce26520f

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Structural competition between πꢀꢀꢀπ interaction and halogen bond: a
crystallographic study†
Baoming Ji,a* Weizhou Wang,a Dongsheng Deng,a Yu Zhang,a Lei Cao,ab Le Zhou,b Chuansheng Ruanac
and Tiesheng Lic
5
Received (in XXX, XXX) Xth XXXXXXXXX 20XX, Accepted Xth XXXXXXXXX 20XX
DOI: 10.1039/b000000x
1,3ꢀDiiodotetrafluorobenzene and 1,3,5ꢀtrifluoroꢀ2,4,6ꢀtriiodobenzene form cocrystals with 4,4’,6,6’ꢀ
tetramethylꢀ2,2’ꢀbipyrimidine, 1,2,4,5ꢀtetra(3ꢀpyridyl)benzene and 1,2,4,5ꢀtetra(4ꢀpyridyl)benzene in
which the structural competition between πꢁꢁꢁπ interaction and halogen bond is directly observed. It is
10 found that the strong C-IꢁꢁꢁN halogen bond competes successfully with the πꢁꢁꢁπ interaction between two
1,3ꢀdiiodotetrafluorobenzene molecules while the πꢁꢁꢁπ interaction between two 1,3,5ꢀtrifluoroꢀ2,4,6ꢀ
triiodobenzene molecules can successfully compete with the strong C-IꢁꢁꢁN halogen bond. Quantum
chemical calculations explain the structural competition well.
NMR and density functional theory method.6 Herein, we address
this issue through a series of cocrystallization reactions between
1,3ꢀdiiodotetrafluorobenzene (1)7 or 1,3,5ꢀtrifluoroꢀ2,4,6ꢀ
50 triiodobenzene (2)8 and 4,4’,6,6’ꢀtetramethylꢀ2,2’ꢀbipyrimidine
(a),9 1,2,4,5ꢀtetra(3ꢀpyridyl)benzene (b)10 or 1,2,4,5ꢀtetra(4ꢀ
pyridyl)benzene (c)11 (Fig. 1).
Introduction
15 The number of crystal structures, in which intermolecular
interactions have been reported to play key roles, has grown
rapidly in recent years.1ꢀ3 These intermolecular interactions
include: hydrogen bonds,1 πꢁꢁꢁπ interactions,2 halogen bonds,3 van
der Waals forces, etc. Evidently, crystal structures cannot be
20 rationalized and predicted from considerations of only one type
of intermolecular interaction and different types of interactions
should be considered jointly in structure analysis. This puts
difficulties in the way of the design and construction of molecular
architectures with desirable connectivity and precisely defined
25 metrics. The only way to overcome such difficulties is to identify
the competition between the directional or nondirectional
intermolecular interactions of different strength.4
I
I
H
H
H
H
H
H
F
F
F
F
F
N
N
H
H
N
N
I
I
I
H
F
H
F
H
H
H
H
2
1
a
H
H
H
H
H
N
N
N
N
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
Besides the hydrogen bond, the πꢁꢁꢁπ interaction also occurs
frequently and makes a substantial contribution to the crystal
30 packing.2 Another important noncovalent driving force for
supramolecular assembly is the halogen bond.3 In supramolecular
chemistry and especially in crystal engineering involving the
halogen bond, aryl or heteroaryl iodide is often used as the
halogen atom donor.4 Along with the formation of the halogen
35 bond between the aryl or heteroaryl iodide and the electron
density donor, the πꢁꢁꢁπ interaction is routinely observed between
the homogeneous dimer of the aryl or heteroaryl iodide.
However, the structural competition between πꢁꢁꢁπ interaction and
halogen bond is very seldom studied.5,6 Lu and coworkers studied
40 the interplay between πꢁꢁꢁπ interaction and halogen bond
employing the Cambridge Structural Database search and
theoretical computation.5 However, they did not conisder the πꢁꢁꢁπ
interaction between the homogeneous dimer of the aryl or
heteroaryl iodide which is the topic of the present study. In a very
45 recent paper, we explored the competition between πꢁꢁꢁπ
H
H
H
H
H
H
H
H
H
H
N
H
H
N
N
H
N
H
H
c
H
b
Fig. 1 The 1 and 2, investigated as coformers with the a, b and c.
Experimental
55 Materials and general methods
All reagents and chemicals, except where indicated, were
purchased from commercial sources and were used without
further purification. NMR experiments were performed using a
1
Bruker Avance spectrometer. H NMR spectra were recorded at
60 400 MHz. 13C NMR spectra were recorded at 100 MHz. The 1, 2
and a were prepared by the methods reported previously.7ꢀ9
Synthesis of b. A mixture of 1,2,4,5ꢀtetrabromobenzene (3.74
g, 10.0 mmol), pyridinꢀ3ꢀylboronic acid (7.40 g, 10.0 mmol),
interaction and halogen bond in solution by using a combined 13
C
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Table 1. Crystallographic data and structure refinement parameters for 1a, 2a, 1b, 2b, 1c and 2c.
1a
2a
C54H28F15I15N8 C32H18F4I2N4
2977.34 788.30
1b
2b
1c
C39H19Cl3F8I4N4 C38H18F6I6N4
1322.55 1405.96
2c
Empirical formula
C18H13F4I2N4
616.13
C38H18F6I6N4
1405.96
formula weight
crystal size (mm3)
0.40×0.22×0.19 0.45×0.28×0.21 0.41×0.22×0.20 0.35×0.31×0.28 0.43×0.21×0.18 0.35×0.27×0.25
crystal system
monoclinic
P21/c
triclinic
Pī
triclinic
Pī
triclinic
Pī
monoclinic
C2/c
triclinic
Pī
space group
a/Å
7.5669(8)
24.046(3)
11.6567(15)
90
9.2428(9)
11.0863(11)
18.8796(19)
87.942(1)
85.311(1)
84.428(1)
1918.2(3)
1
9.2000(11)
9.4032(11)
17.302(2)
82.198(1)
79.011(1)
85.566(1)
1453.7(3)
2
8.9547(11)
11.1438(14)
11.4320(14)
74.690(1)
85.622(1)
69.136(1)
1028.0(2)
1
20.9771(19)
20.4699(18)
10.1640(9)
90
9.3457(10)
10.8381(11)
11.4689(12)
114.173(1)
102.914(1)
91.208(1)
1024.69(19)
1
b/Å
c/Å
α/°
β/°
108.784(1)
90
95.316(1)
90
γ/°
volume/Å3
2008.0(4)
4
4345.6(7)
4
Z
ρcalc/g cmꢀ3
T/K
2.038
2.577
1.801
2.271
2.021
2.278
296(2)
296(2)
296(2)
296(2)
296(2)
296(2)
θ range for data collection (deg) 2.51–25.50
2.39–25.50
14235
2.37–25.50
11130
2.37–25.49
7622
2.37–25.50
15952
2.61–25.50
7614
reflections collected
no. unique data [R(int)]
final R (I > 2σ(I))
final wR2 (all data)
goodnessꢀofꢀfit
14734
3734 [0.0252]
0.0271
7082 [0.0305]
0.0407
5379 [0.0226]
0.0336
3791 [0.0228]
0.0268
4043 [0.0206]
0.0318
3779 [0.0144]
0.0226
0.0597
0.1025
0.0854
0.0659
0.1004
0.0601
1.061
1.057
1.012
1.078
1.021
1.006
K2CO3 (22.00 g, 160.0 mmol), and Pd(PPh3)4 (2.00 g, 1.73
mmol) was weighed into a 500 mL Schlenk flask, to which 1,4ꢀ
dioxane (240 mL) and H2O (80 mL) were added subsequently
under a dry N2 atmosphere. The mixture was heated to reflux
with stirring and maintained at this temperature for 36 h. The
reaction mixture was cooled to room temperature and diluted
with CH2Cl2. The combined organic layers were washed several
Preparation of cocrystals
25 The halogen bond donors and acceptors in a molar ratio of 1:1
were dissolved in approximately 25 mL of chloroform with
gentle stirring at room temperature. The undissolved materials
were removed by filtration. The filtrate was set aside for
crystallization at room temperature. After a few days, the single
30 crystals suitable for Xꢀray analysis were obtained.
To explore the influence of the ratio of donor to acceptor on
the formation of these compounds, a series of coꢀcrystallization
experiments between halogen compound and nitrogenꢀcontaining
aromatic compound were performed by altering the ratio of the
35 two reactants from 1:1 to 1:2. It was found that the same crystals
were always obtained in CHCl3 regardless of donor/acceptor
molar ratio of the two components. The stoichiometry of the
compounds (1a, 2a, 1b, 2b, 1c, and 2c) in the coꢀcrystal is
different from that of the solution. However, this is not
40 uncommon. A similar phenomenon can be documented by recent
reports by van der Boom.12 In addition, as a consequence of the
low solubility of the base and acid species in other organic
solvent such as acetone, acetonitrile, benzene, and methanol, the
5
10 times with brine, dried over anhydrous Na2SO4, and then
concentrated under reduced pressure. The crude product was
purified by column chromatography on silica gel (1:35
CH3OH/CH2Cl2) to afford b (2.38 g, 61.0 % yield) as a white
1
solid. H NMR (CDCl3): δ 8.53 (s, 8H, ArH), 7.58 (s, 2H, ArH),
15 7.51 (d, J = 8.0 Hz, 4H, ArH), 7.22 (d, J = 4.0 Hz, 4H, ArH). 13
C
NMR (CDCl3): δ 150.34, 148.71, 137.59, 137.05, 135.44, 133.15,
123.17.
Synthesis of c. Synthesis of c was the same as that of b except
that the pyridinꢀ4ꢀylboronic acid not the pyridinꢀ3ꢀylboronic acid
20 was used. The yield of c is about 82.0 % (3.16 g, white solid). 1H
NMR (CDCl3): δ 8.55 (d, J = 4.0 Hz, 8H, ArH), 7.55 (s, 2H,
ArH), 7.14 (s, 8H, ArH). 13C NMR (CDCl3): δ 150.08, 147.23,
138.58, 132.64, 124.42.
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combination of them only led to the formation of a lot of
precipitates. Consequently, in CHCl3, the donor/acceptor 1:1 was
selected as the optimal reaction conditions.
asymmetric bifurcated halogen bond constructs a 1ꢀD chain, as
depicted in Fig. 3 (top). The 1ꢀD chains are then held together
two by weak C–HꢁꢁꢁF (C13ꢁꢁꢁF3: 3.365(2), 154.4°; C8ꢁꢁꢁF1:
50 3.502(2) Å, 134.9°) interactions, resulting in a 2ꢀD sheet. There is
no πꢁꢁꢁπ stacking interaction between two 1 molecules. The value
of θ shown in Fig. 3 (top) is about 10º, which shows little
deviation from linearity. The case in 2a is totally different from
that in 1a. The molecules organize themselves into linear ribbons
55 through four halogen bonds and the πꢁꢁꢁπ stacking interactions.
Perpendicular to these ribbons, the πꢁꢁꢁπ stacking interactions
based on the 2 molecules with parallel alignment are formed
which are responsible for the formation of 2ꢀD layer structure. As
shown in Fig. 3 (bottom), one halogen bond is strong (θ=3º); the
60 other halogen bond is very weak (θ=58º). Evidently, it is the
formation of the πꢁꢁꢁπ stacking interaction between two 2
molecules that makes it impossible to form two strong halogen
bonds like that in 1a. Comparing the cocrystal structures of 1a
and 2a, we can see that the strong C-IꢁꢁꢁN halogen bond
65 competes successfully with the πꢁꢁꢁπ interaction between two 1
molecules while the πꢁꢁꢁπ interaction between two 2 molecules
can successfully compete with the strong C-IꢁꢁꢁN halogen bond.
XꢁRay crystallography
5
Crystallographic data were collected on a Bruker Smart ApexꢀII
CCD area detector equipped with a graphiteꢀmonochromatic Mo
Kα radiation (λ = 0.71073 Å) at room temperature. An empirical
absorption correction was applied. All structures were solved and
refined by a combination of direct methods and difference
10 Fourier syntheses, using SHELXTL.13,14 Anisotropic thermal
parameters were assigned to all nonꢀhydrogen atoms. The
hydrogen atoms were set in calculated positions and refined as
riding atoms with a common isotropic thermal parameter. The
crystallographic data and structure refinement parameters are
15 listed in Table 1.
Notably, the methyl (C9) H atoms in compound 2a were found
at the difference Fourier map and subsequently constrained with
HFIX 123 constraint. In the case of C25, C26, C27, C28, C29,
C30, F7, F8, I7, I8, and I9, these atoms are disordered about the
20 mirror plane, and upon generation of the mirror symmetry, their
disordered counterpart is generated. Thus, these atoms are
modelled with occupancy of 50%. Further, C20, Cl1, Cl2, and
Cl3 in compound 1c were refined by using the ‘‘ISOR’’ restraint
to make the ADP values of the disordered atoms.
11º
25
Xꢀray powder diffraction patterns were collected at 293 K on a
Bruker AXS DiffracPlus D8 Advance diffractometer using a Cu
generator with wavelength of the Kα,Cu radiation of 1.5406 Å.
The 2θ angle was scanned between 5° and 50°, and the counting
time was 2 seconds at each angle step (0.01052°) without using
10º
30 delay time (see ESI†).
Results and discussion
3º
3.09
58º
3.24
Experiments have proved that the interaction between the highly
polarized iodine and the nitrogen atom is strong.3a It is generally
accepted that the strong halogen bond is an electrostaticallyꢀ
35 driven highly directional noncovalent interaction.15 Hence, we
can use the angle (θ) to describe the strength of halogen bond in
the crystal structure: smaller values of θ mean much stronger
halogen bonds (Fig. 2). As shown below, the values of θ are in
proportional to the values of the corresponding IꢁꢁꢁN distances,
40 which proves again the rationality of using θ to describe the
strength of halogen bond.
Fig. 3 Partial view (ellipsoid representation) of the crystal
packing of 1a (top) and 2a (bottom). Dashed lines indicate
70 halogen bonds. Colour code: Carbon: gray; Nitrogen: blue;
Fluorine: yellow; Iodine: purple; Hydrogen: light gray.Theꢁvalues
of θ are shown in red numbers. The corresponding IꢁꢁꢁN distances
(Å) are shown in black numbers.
C(sp2)
In chloroform solvent, compound 1 forms a 1:1 cocrystal with
75 b, to give 1b, in the monoclinic space group Pī, and 2 with b
forms a 2:1 cocrystal 2b, in the triclinic space group Pī. The
structural competition between πꢁꢁꢁπ interaction and halogen bond
in 1b and 2b is similar to that in 1a and 2a (Fig. 4). In 1b, the C–
IꢁꢁꢁN halogen bonds, with the help of weak C–IꢁꢁꢁI and C–HꢁꢁꢁN
80 interactions, may be effective in the stabilization of the 2ꢀD layer
structure. In order to form the strong C-IꢁꢁꢁN halogen bond
(θ=13º), the molecules of 1 are separated a great distance from
one another in space (distance between two ring centroids=9.485
Å), such that there is no πꢁꢁꢁπ interaction between two 1
85 molecules. In 2b, in order to form the πꢁꢁꢁπ interaction between
two 2 molecules, one halogen bond (θ=58º) becomes much
I
¦È
N
Fig. 2 The angle (θ) used to describe the strength of halogen
bond.
Compound 1 forms a 1:1 cocrystal with a, to give 1a, in the
45 monoclinic space group P21/c and 2 with a forms a 5:2 cocrystal
2a in the triclinic space group Pī. In 1a, the propagation of the
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weaker than the other halogen bond (θ=14º). The crystal
structures of 1b and 2b also reflect the structural advantage of the
strong C-IꢁꢁꢁN halogen bond over the πꢁꢁꢁπ interaction between
two 1 molecules and the structural advantage of the πꢁꢁꢁπ
interaction between two 2 molecules over the strong C-IꢁꢁꢁN
halogen bond. Inevitably, there are many other noncovalent
interactions such as C-HꢁꢁꢁN, C-Hꢁꢁꢁπ and C-IꢁꢁꢁI in 1b and 2b,
but these noncovalent interactions are very weak and have little
effect on the structural competition between πꢁꢁꢁπ interaction and
35 (Fig. 6). Again, the structural competition between πꢁꢁꢁπ
interaction and halogen bond results in that there is no πꢁꢁꢁπ
interaction between two 1 molecules in 1c and the weak C-IꢁꢁꢁN
halogen bonds (θ=32º) exists in 2c.
5
12º
4º
10 halogen bond.
12º
4º
13º
13º
2.95
32º
2.90
8º
32º
8º
14º
Fig. 5 Partial view (ellipsoid representation) of the crystal
40 packing of 1c (top) and 2c (bottom). Dashed lines indicate
halogen bonds. Colour code: Carbon: gray; Nitrogen: blue;
Fluorine: yellow; Iodine: purple; Hydrogen: light gray.Theꢁvalues
of θ are shown in red numbers. The corresponding IꢁꢁꢁN distances
(Å) are shown in black numbers.
58º
58º
3.30
14º
2.89
Fig. 4 Partial view (ellipsoid representation) of the crystal
packing of 1b (top) and 2b (bottom). Dashed lines indicate
halogen bonds. Colour code: Carbon: gray; Nitrogen: blue;
Fluorine: yellow; Iodine: purple; Hydrogen: light gray.Theꢁvalues
15 of θ are shown in red numbers. The corresponding IꢁꢁꢁN distances
(Å) are shown in black numbers.
As shown in Fig. 5, the crystal packing of 1c (the 2:1 cocrystal
of 1 and c) is governed mainly by the strong C-IꢁꢁꢁN halogen
bonds (θ=4º and θ=12º). The C–IꢁꢁN halogen bonds generate the
20 main building blocks of the crystal. These building blocks are
then organized into the 3ꢀD structure with 1D channels along the
c axis (Fig. 6). In the structure, C–HꢁꢁꢁF weak interactions can
also be formed as those in cocrystal 1a, which further consolidate
the crystal packing. It is interesting to note that the 1D channels
25 are filled with chloroform molecules. The guest molecules
interact with the host also through the weak C-HꢁꢁꢁF hydrogen
bonds. Hence, the effect of the solvent molecules on the
structural competition between the strong πꢁꢁꢁπ interaction and the
strong halogen bond can be neglected. For the 1 molecules in 1c,
30 the shortest distance between two ring centroids is 5.437 Å.
Obviously, there is no πꢁꢁꢁπ interaction between two 1 molecules
in 1c. 2c (the 2:1 cocrystal of 2 and c) has assembled into a 2ꢀD
sheet structure via a combination of strong C-IꢁꢁꢁN halogen bonds
(θ=8º), weak C-IꢁꢁꢁN halogen bonds (θ=32º) and πꢁꢁꢁπ interactions
(a)
(b)
45 Fig. 6. (a) Mercury view of 3ꢀD architecture of 1c. The C–IꢁꢁꢁN
and C–HꢁꢁꢁF interactions are indicated as blue dashed lines. (b)
4
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Mercury view of 2ꢀD sheet of 2c in the ab plane. The C–IꢁꢁꢁN and
C–HꢁꢁꢁF interactions are indicated as blue dashed lines.
In this contribution, we have revealed that the πꢁꢁꢁπ interaction
between two 1 molecules is unlikely to be very competitive for
the strong C-IꢁꢁꢁN halogen bond while the πꢁꢁꢁπ interaction
between two 2 molecules can successfully compete with the
50 strong C-IꢁꢁꢁN halogen bond. As shown above, with the
increasing of the number of iodine atoms, the πꢁꢁꢁπ interaction
between two C6FxI(6ꢀx) (x =0, 1, 2, 3, 4 or 5) molecules becomes
stronger. So it is expected that the πꢀπ interaction between two
C6FxI(6ꢀx) (x =0, 1 or 2) molecules also can successfully compete
55 with the strong C-IꢁꢁꢁN halogen bond. The corresponding
cocrystallization reactions and calculations are in progress in our
laboratory and will be reported in due course.
For confirming the phase purity and homogeneity of the
cocrystals, Xꢀray powder diffraction measurements for 1a, 2a,
1b, 2b, 1c and 2c were performed at room temperature. The
peaks displayed in the measured patterns for each cocrystal
closely match those in the simulated patterns generated from
singleꢀcrystal diffraction data, indicating a good phase purity of
the bulk crystal products. The few discrepancies in intensity
10 between experimental and simulated values may be the
consequence of preferred orientations of the crystal powder
samples (see ESI†).
5
To rationalize the experimental observations, quantum
chemical calculations were carried out on the model systems with
15 the Gaussian09 suite of programs16 at the SCSꢀMP2/SDD** level
of theory.17,18 The reliability of SCSꢀMP2 method for the study of
the weak molecular interactions can be found elsewhere.19
SDD** is the core basis sets (D95V for C, F and [2s3p] for I)
augmented by two sets of polarization functions at carbons and
20 halogens [(C, F, I) = 0.8, 0.25; 0.8, 0.25; 0.4, 0.07].20 The
structures of the complexes (Fig. 7) were optimized in the gas
phase and the binding energies of the complexes were calculated
using the supermolecule method. All binding energies reported
are corrected for basis set superposition error using the
25 counterpoise method of Boys and Bernardi.21 The binding
energies of the πꢁꢁꢁπ interactions and halogen bonds investigated
in this study are shown in Fig. 7. It is noticed in Fig. 7 that the
strengths of the πꢁꢁꢁπ interactions and halogen bonds are all larger
than 5.30 kcal/mol. Let us add here that the binding energy of the
30 πꢁꢁꢁπ interaction in the benzene dimer is just 2.78 kcal/mol.22
More importantly, Fig. 7 clearly shows that the halogen bond in
the dimer C5H5Nꢀꢀꢀ1 is stronger than the πꢁꢁꢁπ interaction in the
dimer 1ꢀꢀꢀ1 while the halogen bond in the dimer C5H5Nꢀꢀꢀ2 is
much weaker than the πꢁꢁꢁπ interaction in the dimer 2ꢀꢀꢀ2. Based
35 on the calculations, it appears that the strength of the halogen
bond and the πꢁꢁꢁπ interaction is comparable in 1, but the πꢁꢁꢁπ
interaction is significantly stronger in the case of 2. This is
consistent with the observed crystal structures where the πꢁꢁꢁπ
interaction is the primary force in the crystal structures obtained
40 with compound 2. Theoretical calculations explain the
competition between πꢁꢁꢁπ interaction and halogen bond in the
reported crystal structures.
Acknowledgements
The authors gratefully acknowledge financial support from the
60 Natural Science Foundation of China (21072089, 21173113) and
the science and technology innovation team support programs of
Henan Province University (2012IRTSTHN019). This work is
also partly supported by the Aid Project for the Leading Young
Teachers in Henan Provincial Institutions of Higher Education of
65 China (2010GGJSꢀ166) and the Natural Science Foundation of
Henan Educational Committee (2010A150017, 2011B150024).
Notes and references
a
College of Chemistry and Chemical Engineering, Luoyang Normal
University, Luoyang 471022, P. R. China. Fax: 86 379 65523821; Tel: 86
70 379 65523821; Eꢀmail: lyhxxjbm@126.com
b Northwest Agriculture and Forest University, Yangling 712100, P. R.
China
c Department of Chemistry, Zhengzhou University, Zhengzhou 450052, P.
R. China
75 † Electronic Supplementary Information (ESI) available: Cif files with
Xꢀray powder diffraction patterns of cocrystals are presented as
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Structural competition between πꢀꢀꢀπ interaction and halogen bond: a
crystallographic study
Baoming Ji, Weizhou Wang, Dongsheng Deng, Yu Zhang, Lei Cao, Le Zhou, Chuansheng Ruan
and Tiesheng Li
The structural competition between πꢀꢀꢀπ interaction and halogen bond is directly
observed in six designed cocrystals.
¦Ð¡¡¤¡¤¦¤Ðinteraction
versus
Halogen bond
F
I
(F)
I
F
F
I
I
I
F
F
F
I
N
R
(F)