Activation and de-activation of fluorine synthons by nitrogen substitution in fluorinated aza-distyrylbenzenes

Article abstract of DOI:10.1039/c0ce00319k

Three derivatives of E,E-1,4-bis[2-(2,3,4,5,6-pentafluorophenyl)ethenyl] benzene, two of which bear nitrogen atoms in the ethenyl spacers, while in a third the central benzene ring is replaced by a pyrazine moiety, have been synthesized. The supramolecula

Full text of DOI:10.1039/c0ce00319k

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Activation and de-activation of fluorine synthons by nitrogen substitution in
fluorinated aza-distyrylbenzenes†
*
Alain Collas, Roeland De Borger, Tatyana Amanova and Frank Blockhuys
Received 18th June 2010, Accepted 10th September 2010
DOI: 10.1039/c0ce00319k
Three derivatives of E,E-1,4-bis[2-(2,3,4,5,6-pentafluorophenyl)ethenyl]benzene, two of which bear
nitrogen atoms in the ethenyl spacers, while in a third the central benzene ring is replaced by a pyrazine
moiety, have been synthesized. The supramolecular structures of the resulting set of four compounds
have been studied using single-crystal X-ray diffraction to gauge the influence of the position of the
nitrogen atoms on the organisation of the molecules in the solid state. The crystal packing patterns were
analyzed in terms of intermolecular interactions involving the fluorine and nitrogen atoms, i.e., CH/F,
F/F, F/p and CH/N interactions. The analysis shows that in two of the three solid-state structures
the main effect of the nitrogen atoms is an indirect one: they do not participate in intermolecular
contacts themselves, but activate nearby hydrogen atoms and phenyl rings in fluorine synthons to form
new interactions.
Whether it be methoxy groups or fluorine atoms, strong
intermolecular interactions can only be obtained when hetero-
atoms (and, consequently, increased polarisation) are introduced
into the molecular structures of (apolar) organic conjugated
systems. Apart from doing this through the introduction of
substituents containing heteroatoms on the carbon backbone, an
alternative approach is based on the substitution of the atoms in
the carbon backbone by heteroatoms. Considering that nitrogen
is the most straightforward choice—the isoelectronic substitu-
tion of a methine (CH) group by a nitrogen atom maintains the
conjugated system—a number of interesting results have been
presented by Ojala et al. who used nitrogen atoms in the
–CH]CH– spacers in DSBs to prepare benzylidene anilines with
–N]CH– or –CH]N– spacers (so-called ‘‘bridge-flipped’’
isomers).17,18 The nitrogen atoms in these systems seem to have
a twofold effect: (1) either they are themselves, through their lone
pairs, directly involved in new intermolecular contacts (e.g.,
strong hydrogen bonds19,20 or interactions with halogen
atoms21,22), or (2) they are not directly involved in new contacts,
but indirectly generate new intermolecular contacts by altering
the electron distribution within the carbon backbone, thereby
activating certain atoms to engage in these new contacts.
1
Introduction
Within the class of oligomeric or low-molecular-weight organic
semiconductors distyrylbenzenes (DSBs) and their derivatives
enjoy a great deal of interest as new materials for opto-electronic
applications such as organic light-emitting diodes (OLEDs),1–6
gas- and ion-selective sensors,7,8 organic memories and non-
linear optics (NLOs).9,10 Since these applications are invariably
based on the organic materials in their solid state, it is clear that
apart from their molecular properties, their bulk properties are
of great importance. In turn, these bulk properties depend on the
three-dimensional organization of the molecules in the solid or
the crystal. Consequently, understanding and manipulating the
crystal structures of organic materials such as DSBs become
a central issue.
A large number of solid-state structures of DSBs have already
been reported11 but relatively few studies have been devoted to
a systematic description of the supramolecular organisation of
the molecules in terms of the presence and position of different
substituents. In this context we refer to the work by Renak et al.
who studied the crystal structures of a number of fluorinated
distyrylbenzene derivatives, amongst which E,E-1,4-bis[2-
(2,3,4,5,6-pentafluorophenyl)ethenyl]benzene (1, Fig. 1), and
confirmed that fluorine synthons such as CH/F interactions
and the vertical stacking of aromatic rings are the main factors
determining the observed packing.12 Equally, our own work on
methoxy-substituted DSBs13–16 led to insight into the occurrence
and relative importance of the different types of inter- and
intramolecular interactions that determine the crystal packing
and which are available for methoxy groups, such as inter- and
intramolecular CH/O interactions and CH/p contacts.
Based on this, we became interested in the combination of the
above mentioned fluorine synthons with the possibilities of new
intermolecular contacts due to nitrogen atoms present in the
backbone, not only in the ethenyl spacers of the original DSBs
but also in the (central) benzene ring, and in studying how the
nitrogen atoms interact with the fluorine synthons. To do this,
three aza-derivatives of the above mentioned decafluoro-DSB (1)
were synthesized and their solid-state structures were investi-
gated. Fig. 1 presents these three additional compounds: two of
them,
E,E-1,4-bis[2-(2,3,4,5,6-pentafluorophenyl)-2-azaethe-
(2) and
E,E-N,N0-bis(2,3,4,5,6-penta-
nyl]benzene
Department of Chemistry, University of Antwerp, Universiteitsplein 1,
B-2610 Wilrijk, Belgium. E-mail: frank.blockhuys@ua.ac.be; Fax: +32 3
820 23 10
fluorobenzylidene)-1,4-phenylenediamine (3), bear the two
nitrogen atoms in the spacers between the phenyl rings, while in
the
third,
E,E-2,5-bis[2-(2,3,4,5,6-pentafluorophenyl)-
† CCDC reference numbers 781116–781118. For crystallographic data in
CIF or other electronic format see DOI: 10.1039/c0ce00319k
ethenyl]pyrazine (4), the nitrogen atoms are located in the central
702 | CrystEngComm, 2011, 13, 702–710
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Fig. 1 The parent DSB (1) and its three aza-derivatives (2–4) under investigation. The structural formula of 1 presents the numbering scheme of the four
compounds; in 2, 3 and 4 N1 replaces C7, C8 and C10, respectively.
aromatic ring. Their experimental molecular and crystal struc-
tures were determined using XRD and the solid-state packings
were analyzed. Crystal packing effects were evaluated through
a comparison of the experimental solid-state molecular struc-
tures with gas-phase structures obtained from quantum chemical
calculations at the DFT/B3LYP level of theory. The nitrogen
atoms located in the central ring in 4 actively participate in
intermolecular contacts, while those in the spacers do not. They
do, however, influence the charge distribution in the backbone to
such an extent that certain fluorine synthons are activated and/or
de-activated.
interaction with a fluorine atom (type II). Consequently, a fluo-
rine atom can act as the electron donor in an interaction with an
electron-poor per- or polyfluorinated phenyl ring (type III). Type
IV contacts can be observed even when a single fluorine atom is
present in the molecular structure: type IVa describes a weak
hydrogen bond with a fluorine atom as acceptor, while type IVb
describes the controversial F/F contacts. Solid-state NMR
measurements and charge-density studies31 have been performed
in an attempt to ascertain whether the latter are stabilizing
interactions or rather caused by close packing,32 but it is not
always clear what their precise nature is. The supramolecular
structures of the four compounds under investigation will be
described in terms of these five types.
2
Results and discussion
2.1 E,E-1,4-Bis[2-(2,3,4,5,6-pentafluorophenyl)ethenyl]ben-
zene (1)
Compounds 2–4 were prepared by standard methods and
completely characterised; note that compounds 2 and 3 are
known but remained uncharacterised until now.23 Details of the
data collection and structural refinement of compounds 2–4 are
collected in Table 1. The necessary data for the 158 K structure of
compound 1 were obtained from the CSD24 (ref. code SER-
QUB25). For all compounds the carbon–hydrogen distances were
Compound 1 crystallizes in the centrosymmetric space group
P21/c.25 As can be seen in the packing diagram shown in Fig. 3,
the molecules adopt the anti conformation in which the two
ethenyl spacers are oriented in opposite directions with respect to
the central phenyl ring: the results of quantum chemical calcu-
lations at the DFT/B3LYP level of theory confirm that this
conformer is slightly more stable (0.42 kJ molꢀ1) than the syn
conformation, with the two ethenyl spacers oriented in the same
direction. The three benzene rings and two ethenyl spacers in 1
are all virtually co-planar, with dihedral angles about the C1–C7
and C8–C9 bonds of about 3ꢁ and 2ꢁ, respectively (Table 3).
Thus, the molecular structure in the crystal is very similar to the
one found in the gas phase, which has C2h symmetry.
ꢀ
normalized to 1.083 A after the refinement and the resulting
geometrical parameters have been used in the following discus-
sion of the different intermolecular short contacts. The details of
these contacts have been summarized in Table 2.
Per- or polyfluorinated aromatic rings and other supramo-
lecular synthons that introduce fluorine atoms into the molecular
structure of organic molecules have proven to be excellent tools
for the manipulation of the crystal structure, through specific
intermolecular interactions involving the fluorine atoms.26
Generally, these interactions can be subdivided into five different
types (Fig. 2). The arene-perfluoroarene stacking synthon (type
I), based on the interaction between an electron-poor per- or
polyfluorinated phenyl ring and an electron-rich (substituted)
phenyl ring, has been used extensively to achieve organization in
the solid state.27–30 On the other hand, an electron-poor
(substituted) phenyl ring can act as an electron acceptor in an
Fig. 3 shows that in one direction the molecules organise
themselves side by side in a ribbon through two type IVa
contacts, i.e., the two weak hydrogen bonds C10–H10/F6 and
C7–H7/F5, and one type IVb contact involving F2 and F5.
These ribbons are then connected into layers via two type IVb
contacts involving the two remaining fluorine atoms, F3 and F4.
Finally, these layers are organised into the three-dimensional
structure through one type III interaction, in which F4 contacts
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Table 1 Details of the data collection and structural refinement of 2–4
Crystal data
2
3
4
Chemical formula
Chemical formula weight/g molꢀ1
Cell setting
Space group
Monochromator
Crystal form
C20H6F10N2
464.27
Monoclinic
P21/c
Graphite
Plate
C20H6F10N2
464.27
Triclinic
P1
Graphite
Prism
C20H6F10N2
464.27
Monoclinic
P21/c
Graphite
Plate
ꢁ
Crystal size/mm
Crystal colour
No. of reflections for cell param.
q Range/ꢁ
F(0 0 0)
0.18 ꢂ 0.33 ꢂ 0.24
Yellow
25
6.36–10.23
460
293
4.871(2)
6.3980(10)
28.420(6)
90
96.57(2)
90
0.27 ꢂ 0.27 ꢂ 0.27
Orange
25
6.00–14.22
230
293
5.846(2)
7.929(2)
10.331(3)
109.78(2)
102.35(3)
96.13(3)
431.8(2)
1
0.21 ꢂ 0.21 ꢂ 0.21
Yellow
25
5.03–13.01
716
293
6.223(2)
5.9070(10)
24.427(8)
90
103.80(3)
90
T/K
ꢀ
a/A
ꢀ
b/A
ꢀ
c/A
a/ꢁ
b/ꢁ
g/ꢁ
3
ꢀ
V/A
Z
879.9(4)
2
1.752
872.0(4)
2
1.768
Dx/Mg mꢀ3
1.785
0.182
m/mmꢀ1
0.179
0.181
Data collection method
No. of measured reflections
No. of independent reflections
No. of observed reflections [I >
2sꢁ(I)]
u/2q scans
3389
1582
u/2q scans
2612
1571
u/2q scans
3326
1598
1108
1219
778
qmax
/
25.32
25.32
ꢀ7 # h # 3
25.33
Range of h
Range of k
Range of l
No. of standard reflections
Frequency of standard reflections/h
Intensity decay (%)
Refinement on
GoOF
0 # h # 5
ꢀ7 # k # 7
ꢀ32 # l # 30
3
0 # h # 7
ꢀ7 # k # 7
ꢀ29 # l # 28
3
1
19
F2
ꢀ9 # k # 9
ꢀ12 # l # 12
3
1
1
27
F2
1.047
0.1696
0.0562
0.0701
1571
ꢀ1
F2
1.005
1.043
Rw
Ru
0.0963
0.0331
0.0591
1582
0.1738
0.0562
0.1477
1598
Rall
No. of reflections used in
refinement
No. of parameters used
Weighting scheme
145
w ¼ 1/[s2(Fo2) + (AP)2 + BP] where
145
148
2
P ¼ (Fo2 + 2Fc )/3
A
B
0.0427
0.2496
0.00
0.141
ꢀ0.133
0.1172
0.0231
0.00
0.255
ꢀ0.267
0.0827
0.00
0.00
0.274
ꢀ0.294
(D/s)max
Drmax
Drmin
the centroid of a pentafluorophenyl ring, Cg(ArF), and one type
IVb interaction involving F2 and F5 (not shown in Fig. 3). Note
that all fluorine atoms of 1 are involved in intermolecular
contacts.
molecular geometry is also clearly reflected in the calculated
structure which indicates torsion angles of 0.8ꢁ and 38.6ꢁ,
respectively, for the molecule in C2 symmetry. The increased out-
of-plane twist of the peripheral rings is solely due to the presence
of the nitrogen atoms and seems to be unrelated to the presence
of the fluorine atoms. Indeed, in the non-fluorinated derivative
E,E-1,4-bis(2-phenyl-2-azaethenyl)benzene the corresponding
torsion angles are 39.0ꢁ and 2.6ꢁ, i.e., the fluorine atoms do not
introduce additional steric hindrance leading to a further out-of-
plane twist.
2.2 E,E-1,4-Bis[2-(2,3,4,5,6-pentafluorophenyl)-2-
azaethenyl]benzene (2)
Likewise, compound 2 crystallizes in the centrosymmetric space
group P21/c; the packing diagrams are presented in Fig. 4. The
molecules also adopt the anti conformation but they clearly
deviate from planarity: even though the C]N spacers remain
coplanar with the central ring (the torsion angle about the C8–C9
bond is limited to about 4ꢁ), the peripheral rings have now
twisted out of this plane by more than 40ꢁ (Table 3). This
As can be seen in Fig. 4a, the molecules are organised in layers
due to two type IV intermolecular contacts. The ribbons seen in
Fig. 4a are generated through contacts involving the relatively
acidic hydrogen atom on the spacer (H8) and F2 in the [0 1 0]
direction to form the only weak hydrogen bond (type IVa)
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ꢀ
Table 2 Details (distances d in A, angles q in degrees, symmetry codes and type) of the short intermolecular contacts D–X/A given in the text; the lack
of an esd on a number of the parameters is due to the normalisation of the CH distances for 2–4 and to the absence of esds in the CIF of 1
D
X
A
d
q
Symmetry code
Type
1
C10
C7
C2
C3
C4
C4
C2
C8
C4
C5
C4
C3
C7
C10
C10
C11
C2
C5
C5
C11
C2
C4
C5
C5
H10
H7
F2
F3
F4
F4
F2
H8
F4
F5
F4
F3
H7
H10
H10
H11
F2
F5
F5
H11
F2
F4
F5
F5
F6
F5
F5
F4
2.54
2.58
2.814
2.811
2.811
3.431
2.900
2.39
2.847(2)
2.847(2)
3.502(2)
2.831(2)
2.62
2.56
2.62
2.47
2.899(2)
3.333(2)
3.333(2)
2.60
2.912(4)
2.809(4)
2.809(4)
3.150(3)
119
153
140.2
138.7
171.5
103.0
90.6
159
168.29(14)
137.41(13)
102.61(12)
154.24(14)
163
120
120
170
142.76(13)
104.22(13)
104.22(13)
149
95.97(21)
160.8(3)
130.9(3)
132.3(2)
1 + x, 1 + y, z
1 + x, 1 + y, z
1 + x, 1 + y, z
IVa
IVa
IVb
IVb
IVb
III
IVb
IVa
IVb
IVb
III
IVb
IVa
IVa
IVa
IVa
IVb
II
ꢀ1 ꢀ x, 1/2 + y, 1/2 ꢀ z
ꢀ1 ꢀ x, ꢀ1/2 + y, 1/2 ꢀ z
ꢀ1 + x, y, z
F3
Cg(ArF)
F5
F2
F5
F4
Cg(ArF)
F6
F5
F5
F6
F6
F5
Cg(ArH)
Cg(ArH)
N1
F6
F5
F4
Cg(ArF)
x, 1 + y, z
2
3
x, 1 + y, z
ꢀ2 ꢀ x, 1/2 + y, ꢀ1/2 ꢀ z
ꢀ2 ꢀ x, ꢀ1/2 + y, ꢀ1/2 ꢀ z
ꢀ1 + x, y, z
ꢀ1 + x, 1 + y, z
x, ꢀ1 + y, z
x, ꢀ1 + y, z
x, ꢀ1 + y, z
x, 1 ꢀ y, 1 ꢀ z
x, ꢀ1 + y, z
1 + x, 1 + y, z
1 ꢀ x, 1 ꢀ y, 1 ꢀ z
ꢀx, 1 ꢀ y, ꢀz
II
—
IVb
IVb
IVb
III
4
x, ꢀ1 + y, z
3 ꢀ x, ꢀ1/2 + y, 1/2 ꢀ z
3 ꢀ x, 1/2 + y, 1/2 ꢀ z
2 ꢀ x, 1/2 + y, 1/2 ꢀ z
Fig. 2 The five different types of intermolecular interactions involving fluorine atoms.
Fig. 3 View of the packing of 1 showing the CH/F and F/F contacts within the ribbons and layers and the F/Cg(ArF) contacts between the layers.
See text for details.
present in the supramolecular structure. Within the layer, these
ribbons are connected through two type IVb contacts involving
the fluorine atoms in the 4- and 5-positions. Between these layers,
the fluorine atoms in the 4-position contact the centroids of
a fluorinated aromatic ring in an F/Cg(ArF) (type III) contact,
which is accompanied by another type IVb contact between F3
and F6 (Fig. 4b).
2.3 E,E-N,N0-Bis(2,3,4,5,6-pentafluorobenzylidene)-1,4-
phenylenediamine (3)
ꢁ
Compound 3 crystallizes in the centrosymmetric P1 space group.
The packing diagram is presented in Fig. 5. Similar to the
conformations of 1 and 2, the molecules of 3 are found in the
anti conformation and the calculations predict a molecular
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Table 3 Selected geometrical data for compounds 1–4; calculated (DFT)
and experimental (XRD) torsion angles in degrees
Fig. 5) and within these layers four different interactions can be
distinguished in the form of two bifurcated type IVa hydrogen
bonds involving F5 and F6 of one molecule and the two
hydrogen atoms on the central phenyl ring (H10 and H11) and
the one on the C]N spacer (H7) of the next. In addition to these,
there is a single type IVb contact involving F2 and F5. These
layers are then connected via F/Cg(ArH) intermolecular
contacts (type II) with the layers above and below (represented
by the uppermost and lowermost molecules in Fig. 5, respec-
tively).
Parameter
DFT
XRD
1
2
3
4
C6–C1–C7–C8
C7–C8–C9–C10
C6–C1–N1–C8
N1–C8–C9–C10
C6–C1–C7–N1
C7–N1–C9–C10
C6–C1–C7–C8
C7–C8–C9–C10
0.0
0.0
38.6
0.8
5.1
35.5
0.0
3.21
2.24
42.2(3)
4.2(3)
10.8(3)
11.8(2)
19.6(6)
7.2(4)
0.0
2.4 E,E-2,5-Bis[2-(2,3,4,5,6-pentafluorophenyl)ethenyl]pyra-
zine (4)
conformation with C2 symmetry similar to the one found for 2
(Table 3), but, since the nitrogen atoms have moved to the
central ring, the latter is now twisted by about 36ꢁ out of the
plane formed by the C]N spacer and the peripheral ring (the
torsion angle about the C1–C7 bond is limited to about 5ꢁ).
Again, this particular molecular conformation is not related to
the presence or absence of the fluorine atoms: in the non-fluo-
rinated derivative E,E-N,N0-dibenzylidene-1,4-phenylenedi-
amine the corresponding torsion angles are 1.8ꢁ and 36.5ꢁ.
However, this is not what is observed in the solid state: the
experimental conformation is much more planar, as the two
relevant torsion angles have been reduced to about 12ꢁ and 11ꢁ,
respectively (Table 3).
Compound 4 crystallizes in the centrosymmetric space group
P21/c. Fig. 6 displays the packing schemes. In principle, two anti
conformers with C2h symmetry are possible for compound 4: one
in which the N/N axis in the central ring is aligned with the
orientations of the ethenylic links, and a second in which it is not.
The former, which is found in the solid state, is the more stable
conformer by 14.81 kJ molꢀ1. The corresponding value for the
non-fluorinated derivative E,E-2,5-bis(2-phenylethenyl)pyrazine
is 9.45 kJ molꢀ1 and this indicates that the fluorine atoms shift the
equilibrium more in favour of the experimentally observed
conformer. When incorporated into the supramolecular struc-
ture the planar gas-phase structure is distorted: the central ring
remains almost coplanar with the ethenyl spacers (the torsion
angle about the C8–C9 bond is limited to about 7ꢁ), but the
As can be seen in Fig. 5, the virtually planar molecules are
arranged in layers (represented by the three central molecules in
Fig. 4 View of the packing of 2 showing: (a) the CH/F and F/F contacts within the layer and (b) the F/Cg(ArF) contacts responsible for the
organisation of these layers.
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Fig. 5 View of the packing of 3 showing the CH/F and F/F contacts within the ribbons, as well as the F/Cg(ArH) contacts between them. See text
for details.
Fig. 6 View of the packing of 4 showing: (a) the CH/N dimers forming the ribbons and the F/F contacts between the ribbons and (b) the F/Cg(ArF)
contacts responsible for the three-dimensional packing. See text for details.
peripheral rings are twisted to a somewhat larger extent, with
a torsion angle about the C1–C7 bond of about 20ꢁ.
organisation is due to an F/Cg(ArF) contact (type III)
involving F5.
From Fig. 6 it is clear that this compound displays the CH/N
weak hydrogen bond dimers typical for pyrazine derivatives,
through which the different molecules organise themselves in flat
ribbons in the [0 1 0] direction. In addition to these CH/N
interactions, there is also a short type IVb contact involving the
fluorine atoms in the 2- and 6-positions. Adjacent ribbons are
connected via two type IVb contacts involving the fluorine atoms
in the 4- and 5-positions. Finally, the observed three-dimensional
2.5 The supramolecular structures of fluorinated (aza)
distyrylbenzenes
The supramolecular structures of these compounds can now be
compared to gauge the influence of the position of the nitrogen
atoms. Due to the presence of the ten fluorine atoms on the
peripheral rings the molecules of compound 1 are highly
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polarized and comprise electron-poor peripheral rings and an
electron-rich central ring. This is reflected in the fact that the bulk
of the interactions observed in the solid state involve all five
fluorine atoms on these peripheral rings. One of the hydrogen
atoms on the central ring and one on the spacers become
involved in two weak hydrogen bonds, but the two remaining
hydrogen atoms (H8 and H11) are not used.
ring in 3, or ‘‘de-activating’’ the central ring in 2 and the
peripheral rings in 3. As expected, in 4 the nitrogen atoms are
easily accessible and generate the typical hydrogen bonds.
The previous discussion leads to the following two conclu-
sions. First, interactions involving hydrogen atoms (CH/Y) are
preferable over those involving only fluorine atoms. In all four
structures CH/Y contacts can be found: for compound 4, Y is
the nitrogen atom of the pyrazine ring, while for compounds 1–3
a number of CH/F contacts can be observed. For all three of
the latter compounds the hydrogen atom on the spacer is involved
in a short CH/F contact, while the number of CH/F contacts
involving the central ring is dependent on the (de)activating effect
of the nitrogen atoms. Obviously, the solid-state structure of
compound 4 is a clear illustration of the supremacy of the weak
hydrogen bonds: the molecules are willing to give up part of their
conjugative stabilization to accommodate them. On the other
hand, it is also clear that, even though the weak hydrogen bonds
dominate the organization of the molecules at the first level, the
entire solid-state structures of these systems could not exist
without the presence of the more controversial F/F interactions.
Secondly, it appears that these distyrylbenzenes, with their
particular rod-like shape, are organised more efficiently in
a three-dimensional superstructure when they are more planar.
This is illustrated by the packing efficiencies of the four
compounds under investigation: 75.1% (1@158 K), 73.6%
(1@190 K), 71.7% (2), 73.1% (3) and 72.6% (4). The more planar
compounds (1 and 3) clearly have a higher packing efficiency.
Table 3 also clearly shows that compounds 1 and 3 display the
largest numbers of intermolecular contacts of the four systems
under investigation, which must be a direct consequence of the
more favourable three-dimensional organisation.
When nitrogen atoms are introduced in the 2-positions of the
ethenyl spacers (compound 2), the peripheral rings become even
more electron-poor than in 1 due to the inductively accepting ꢀI
effect of the nitrogen atom, resulting in a further polarization of
the molecule. As a result, the central ring does not participate
anymore in intermolecular contacts and the corresponding CH/
F (type IVa) synthon is de-activated. All five fluorine atoms of
the peripheral rings continue to be involved in the intermolecular
network and they generate four of the five observed short
contacts (F/F and F/p). The fifth, a single weak hydrogen
bond, is a result of the further activation of the one remaining
hydrogen atom on the spacer and its corresponding CH/F (type
IVa) synthon.
Shifting the nitrogen atom towards the central ring in
compound 3 reshuffles the electron distribution throughout the
carbon backbone and now the central ring becomes considerably
electron-poorer than in 1. This leads to three effects. First, the
peripheral rings lose part of the activation they enjoyed in 2, due
to the absence of the nitrogen atom: only three of the five fluorine
atoms on these rings are involved in intermolecular contacts, and
just one F/F (type IVb) and no F/pF (type III) contacts
remain. Secondly, as in 2, a single weak hydrogen bond, the
result of the further activation of the one remaining hydrogen
atom on the spacer and its corresponding CH/F (type IVa)
synthon, is observed. Thirdly, the fact that the central ring has
become more electron-poor leads to the activation of three CH/
F (type IVa) synthons and two type II synthons, with the central
ring being contacted from below and above. In effect, moving the
nitrogen from the 2- to the 1-position in the ethenyl spacer has
switched off the type III contact in 2 and switched on the type II
contacts in 3. Apparently, in order to maximize the number of
weak CH/F hydrogen bonds the non-planar molecular struc-
ture of the isolated molecule has to become more planar, but this
is achieved without too great a destabilization.33
Conspicuously absent from these solid-state structures are the
typical cooperative interactions labelled type I in Fig. 2. The
phenyl-perfluorophenyl stacking synthon has been used as a tool
to bring about solid-state topochemical [2 + 2] photodimerisations
and photopolymerizations in molecular crystals or co-crystals of
stilbene-type systems.25 The typical face-to-face stacking, resulting
from the non-covalent interactions between the aromatic moieties,
generates the necessary conditions (in particular, a distance of 3.5–
ꢀ
4.2 A between the ethenyl fragments) for the cycloaddition to
proceed. These conditions are met in the structures of E-2,3,4,5,6-
pentafluorostilbene25 and its 40-methyl derivative.34 In these
systems the ratio of the number of electron-rich phenyl rings to the
number of electron-deficient perfluorophenyl rings is 1 : 1—the
dependence of the occurrence of intermolecular interactions on
the hydrogen–fluorine ratio has been discussed for fluorinated
azines.35 When this ratio is altered, such as in compounds 1–4, in
which it is 1 : 2, the ArH/ArF synthon is not observed. However,
when aromatic solvent molecules such as o-xylene are incorpo-
rated into the structure of 1 (CSD ref. code SERRIQ), they can act
as the missing phenyl moieties and return the ratio to 1 : 1, at
which point the ArH/ArF synthon is again seen.25
Finally, in the solid-state structure of compound 4 the CH/N
interactions typical for pyrazine derivatives dominate the struc-
ture, but, since they are relatively short, stacking the planar
conformation found for the isolated molecule would lead to
intermolecular repulsion between the fluorine atoms on the
peripheral rings. Therefore, a part of the stabilization associated
with the planar structure is sacrificed to accommodate the per-
fluorophenyl rings and the latter are twisted out of the molecular
plane. Once the ribbons based on the CH/N interactions are
formed, they are organised into the three-dimensional structure
via three F/F and one F/Cg contacts, the latter again
involving the peripheral rings, as in 1.
It is clear that nitrogen atoms in 2 and 3 do not participate
directly in the interactions that determine the crystal packing:
they are too well ‘‘buried’’ inside the backbone of the molecules
to reach any other atom in a short contact. These nitrogen atoms
do develop an indirect effect through ‘‘activating’’ the azome-
thine hydrogens on the spacer in 2 and 3, as well as the central
3
Experimental
3.1 Syntheses
All reagents and solvents were obtained from ACROS and used
as received. Pentafluorobenzaldehyde was purchased from
708 | CrystEngComm, 2011, 13, 702–710
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View Article Online
Fluorochem Ltd. All NMR spectra except the 19F NMR spectra
were recorded in CDCl3 with a Bruker AV-600 spectrometer at
frequencies of 600.30 MHz for 1H and 150.95 MHz for 13C
(broadband decoupling was applied) with tetramethylsilane
(TMS) as internal standard. 19F NMR spectra were recorded in
CDCl3 with a Bruker AV-300 spectrometer at a frequency of
282.40 MHz and the signals were referenced to C6F6. Chemical
shifts are given in ppm and coupling constants in Hz. UV/Vis
absorption spectra were recorded on a Cary 5 spectrometer for
solutions (about 20 ꢂ 10ꢀ6 M) of the oligomers in CH2Cl2.
Melting points were obtained with an open capillary electro-
thermal melting point apparatus and are uncorrected.
CAD-4 EXPRESS36 software was used for data collection and
cell refinement and XCAD-437 for data reduction. The structures
were solved by direct methods using SHELXS-9738 and refined
using SHELXL-97:38 hydrogen atoms were restrained to occupy
ꢀ
the calculated positions and defined as riding [CH ¼ 0.93 A and
Uiso(H) ¼ 1.2Ueq(C) for aromatic CH]. For the analysis of the
supramolecular structures, CH bond lengths were normalised to
ꢀ
the value derived from neutron diffraction (1.083 A). After this
normalisation procedure, PLATON39 was used to calculate all
intra- and intermolecular contacts. Figures were prepared using
MERCURY (version 2.3).40 The experimental details including
the results of the refinements are given in Table 1. The numbering
scheme can be found in Fig. 1.
3.1.1 E,E-1,4-Bis[2-(2,3,4,5,6-pentafluorophenyl)-2-azaethe-
nyl]benzene (2). A mixture of 2,3,4,5,6-pentafluoroaniline (1.8 g,
10 mmol) and terephthalic aldehyde (0.6 g, 5 mmol) in ethanol
(100 ml) was refluxed overnight. After cooling, the residue was
concentrated to 50 ml and the precipitated yellow product was
collected by filtration and washed with cold ethanol. The yield is
196 mg (8.4%). Mp 185 ꢁC. UV/Vis lmax ¼ 332 nm (log 3 ¼ 4.28).
3.3 Electrochemical measurements
Electrochemical measurements were performed using an AUTO-
LAB potentiostat/galvanostat connected to a PC equipped with
the ‘‘General Purpose Electrochemical System’’ (GPES) soft-
ware. Cyclic voltammetric (CV) measurements were carried out
in dry acetonitrile at 298 K under an argon atmosphere. Tetra-
butylammonium tetrafluoroborate obtained from ALDRICH was
used as the supporting electrolyte. Concentrations of 0.4 mM
and 80 mM for the oligomer and electrolyte, respectively, were
used. Extra dry acetonitrile (<50 ppm water) was purchased from
1
d H 8.7 (s, H8), 7.2 (s, H10 and H11). d 13C 167.2 (C8), 140.9
(C4), 139.3 (C2 and C6), 138.8 (C3 and C5), 138.6 (C9), 129.6
(C10), 126.1 (C1). d 19F 9.0 (dd, J ¼ 21.5 and 6.0, F2 and F6), 2.4
(t, J ¼ 21.5, F4), ꢀ1.1 (td, J ¼ 21.1 and 6.0, F3 and F5). Crystals
suitable for a diffraction experiment were grown by diffusion of
hexane in a saturated CH3CN solution.
ꢀ
ACROS and stored on 3 A sieves. Standard voltammograms were
recorded at a scan rate of 0.1 Vꢀ1 sꢀ1 using the ferrocene/ferro-
cenium (Fc/Fc+) couple as reference. The working electrode was
a BASi stationary voltammetry electrode comprising a platinum
electrode disc with a diameter of 3 mm. A platinum plate was
used as the auxiliary electrode and a silver wire as the pseudo-
reference electrode. The large number of fluorine atoms makes
the oxidation of compounds 1–4 virtually impossible. Reduction
potentials could not be determined due to the irreversible nature
of the systems, but forward and reverse peak potentials (in V vs.
Fc/Fc+ with standard deviations between brackets), respectively,
are reported for 1 [ꢀ1.634(8) and ꢀ0.958(36)], 2 [ꢀ1.649(21) and
ꢀ0.971(8)], 3 [–1.528(23) and ꢀ1.095(51)] and 4 [–1.544(54) and
ꢀ0.987(37)].
3.1.2 E,E-N,N0-Bis(2,3,4,5,6-pentafluorobenzylidene)-1,4-
phenylenediamine (3).
A
mixture of 2,3,4,5,6-penta-
fluorobenzaldehyde (2.0 g, 10 mmol) and p-phenylenediamine
(0.6 g, 5 mmol) in ethanol (100 ml) was refluxed for 2 hours. After
cooling, the orange crystals were collected by filtration and
ꢁ
washed with cold ethanol. The yield is 1.2 g (54%). Mp 175 C.
UV/Vis lmax ¼ 361 nm (log 3 ¼ 4.3). d 1H 8.6 (s, H7), 7.3 (s, H10
and H11). d 13C 159.7 (C7), 150.3 (C9), 148.1 (C1), 143.4 (C2 and
C6), 141.7 (C4), 136.9 (C3 and C5), 121.9 (C10). d 19F 20.1 (td, J ¼
19.8 and 6.4, F2 and F6), 12.5 (t, J ¼ 20.6, F4), 0.4 (td, J ¼ 20.3
and 6.4, F3 and F5). Crystals suitable for a diffraction experiment
were grown by slow evaporation of a CHCl3 solution.
3.1.3 E,E-2,5-Bis[2-(2,3,4,5,6-pentafluorophenyl)ethenyl]pyra-
zine (4). A mixture of 2,3,4,5,6-pentafluorobenzaldehyde (3.9 g,
20 mmol) and 2,5-dimethylpyrazine (1.1 g, 10 mmol) in DMSO
(250 ml) was refluxed with ZnCl2 for 8 hours. After cooling, the
precipitated yellow product was collected by filtration and washed
with cold ethanol. After refluxing for 4 hours in p-xylene with
a catalytic amount of I2 the pure E,E oligomer was filtered off and
washed with cold ethanol. The yield is 2.5 g (54%). Mp 204 ꢁC. UV/
Vis lmax ¼ 369 nm (log 3 ¼ 4.7). d 1H 8.6 (s, H10), 7.7 (d, J ¼ 16.3,
H8), 7.5 (d, J ¼ 16.3, H7). d 13C 148.9 (C9), 144.2 (C10), 141.5 (C2
and C6), 139.8 (C4), 137.0 (C3 and C5), 131.4 (C8), 128.8 (C7),
119.1 (C1). d 19F 20.1 (td, J ¼ 21 and 7.3, F2 and F6), 12.5 (t, J ¼
20.7, F4), ꢀ0.4 (td, J ¼ 20.7 and 7.3, F3 and F5). Crystals suitable
for a diffraction experiment were grown by slow evaporation of
a solution in 1,10-dichloroethane.
3.4 Quantum chemical calculations
The molecular structures of different conformers of compounds
1–4 were optimized at the DFT/B3LYP/6-31G* level of theory
using the Gaussian 03 program package,41 adding diffuse func-
tions to the nitrogen and fluorine atoms only; the basis sets were
used as they are implemented in the program. Frequency calcu-
lations were performed to ascertain that the resulting struc-
tures—C2h symmetry for 1 and 4, and C2 symmetry for 2 and
3—are minima on the Potential Energy Surface (PES).
4
Conclusions
The crystal structures of three derivatives of E,E-1,4-bis[2-
(2,3,4,5,6-pentafluorophenyl)ethenyl]benzene, i.e., E,E-1,4-bis[2-
(2,3,4,5,6-pentafluorophenyl)-2-azaethenyl]benzene, E,E-N,N0-
bis(2,3,4,5,6-pentafluorobenzylidene)-1,4-phenylenediamine and
E,E-2,5-bis[2-(2,3,4,5,6-pentafluorophenyl)ethenyl]pyrazine,
have been analysed in terms of the different intermolecular
interactions involving the heteroatoms. The analysis shows
3.2 X-Ray crystallography
Data collection was performed on a Enraf-Nonius Mach 3
ꢀ
diffractometer using Mo-Ka radiation (l ¼ 0.71073 A). The
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that when the nitrogen atoms are not available to participate
directly in intermolecular interactions (i.e., when they are
positioned in the spacers between the phenyl rings), they
indirectly generate new contacts by activating synthons
involving nearby hydrogen atoms and phenyl rings. The
supramolecular structures are dominated by CH/N and
CH/F hydrogen bonds, as a result of which additional
weaker F/F and F/p contacts can be observed. The latter
are, however, indispensable for the formation of the three-
dimensional structure.
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Acknowledgements
A.C. and R.D.B. wish to thank the Institute for the Promotion of
Innovation by Science and Technology in Flanders (IWT) for
their predoctoral grants. The authors are grateful to Dr A. Yu.
Makarov (Institute of Organic Chemistry, Russian Academy of
Sciences, Novosibirsk) for recording the NMR data. Financial
support by FWO-Vlaanderen under grant G.0129.05 and by the
University of Antwerp under Grant GOA-2404 is gratefully
acknowledged. The authors gratefully acknowledge the Univer-
sity of Antwerp for access to the university’s computer cluster
CalcUA.
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This journal is ª The Royal Society of Chemistry 2011