Weak C - H ... N≡ C hydrogen bonds in the structures of two poly(cyano)-substituted ring systems

Article abstract of DOI:10.1107/S0108270107052535

In benzene-1,2,3-tricarbonitrile, C9H3N3, the packing of the two independent mol-ecules is three-dimensional and complex, involving inter alia bifurcated (C - H)2...N systems from neighbouring CH groups. In [2.2]paracyclo-phane-4,5,12,13-tetra-carbonitrile, C20H12N4, the [2.2]paracyclo-phane systems display the usual distortions, namely lengthened C - C bonds and widened sp ³ angles in the bridges, narrow angles in the six-membered rings at the bridgehead atoms, and flattened boat conformations of the rings. The mol-ecules are linked by a series of C - H...N inter-actions to form layers parallel to the ab plane. International Union of Crystallography 2007.

Full text of DOI:10.1107/S0108270107052535

organic compounds
Acta Crystallographica Section C
Crystal Structure
Communications
phthalocyanines, dimer (V) should also show interesting
chemical behaviour. Having prepared (V) many years ago
(Hopf & Lenich, 1974), we now report its structure. Since
compounds (II) and (V) display similar CÐHÁ Á ÁN C inter-
actions in the molecular packing, we present the structures
together.
ISSN 0108-2701
Weak CÐHÁ Á ÁN C hydrogen bonds
in the structures of two poly(cyano)-
substituted ring systems
Compound (II) crystallizes with two independent molecules
in the asymmetric unit (Fig. 1); these are, however, essentially
identical. The molecular dimensions are as expected. The
interplanar angle between the two molecules is 68.43 (6)ꢀ.
The main interest centres on the molecular packing. Reddy
et al. (1995) have shown for 1,3,5-tricyanobenzene, the only
other tricyanobenzene for which an X-ray structure analysis
has been performed, that the packing is determined by weak
CÐHÁ Á ÁN C hydrogen bonds (Desiraju & Steiner, 1999)
that in projection give a pseudo-hexagonal pattern. Each
HÁ Á ÁN interaction is simultaneously part of both bifurcated
Peter G. Jones,a* Henning Hopf,b Cornelia Mlynekb and
Vijay Narayanan Swaminathanb
aInstitut fur Anorganische und Analytische Chemie, Technische Universitat
È
È
Braunschweig, Postfach 3329, 38023 Braunschweig, Germany, and bInstitut
fur Organische Chemie, Technische Universitat Braunschweig, Postfach 3329,
È
È
38023 Braunschweig, Germany
Correspondence e-mail: p.jones@tu-bs.de
Received 17 October 2007
Accepted 23 October 2007
Online 14 November 2007
In benzene-1,2,3-tricarbonitrile, C9H3N3, the packing of the
two independent molecules is three-dimensional and complex,
involving inter alia bifurcated (CÐH)2Á Á ÁN systems from
neighbouring CH groups. In [2.2]paracyclophane-4,5,12,13-
tetracarbonitrile, C20H12N4, the [2.2]paracyclophane systems
display the usual distortions, namely lengthened CÐC bonds
and widened sp3 angles in the bridges, narrow angles in the six-
membered rings at the bridgehead atoms, and ¯attened boat
conformations of the rings. The molecules are linked by a
series of CÐHÁ Á ÁN interactions to form layers parallel to the
ab plane.
Figure 1
The two independent molecules of (II). Displacement ellipsoids represent
50% probability levels.
Comment
Heating cyanoacetylene, (I), at 433 K results in the formation
of 1,2,4- and 1,2,3-tricyanobenzene, (II); we have shown that
this trimerization involves the intermediate generation of
tricyano-Dewar benzenes (Witulski et al., 1990). We now
report the crystal structure of (II). For the 1,2,4 isomer, we
have so far been unable to obtain crystals of X-ray quality.
Figure 2
The packing of (II), viewed parallel to the b axis in the region z ' 0
5
8
(bottom) to z '
(top). Molecules generated from the second
independent molecule (atom labels with primes) are drawn with open
bonds. Hydrogen bonds (see Comment and Table 1) are indicated by
dashed lines; one of each independent hydrogen bond is numbered
according to the order of Table 1, but they do not correspond to the
asymmetric unit as de®ned in the coordinate list. The positioning of the
labels is based on the space available in the ®gure; it is not possible to
label all interactions for a given molecule without loss of clarity.
Hydrogen bond 4 is not included in this view.
The tetrasubstituted [2.2]paracyclophane (V) is formally a
dimer of phthalonitrile, in which the two aromatic halves are
held in ®xed orientation by the ethano bridges. Considering
that the monomer is, for example, the starting material for
Acta Cryst. (2007). C63, o723±o725
DOI: 10.1107/S0108270107052535
# 2007 International Union of Crystallography o723

organic compounds
(two H-atom donors to the same acceptor) and three-centre
(one H-atom donor to two acceptors) hydrogen-bond systems;
each H atom donates to two N atoms, and each N atom accepts
two H-atom donors. The packing of (II), as might be expected
in space group P212121 and with two independent molecules,
is three-dimensional and complicated, but a reasonably
comprehensible overview can be obtained (Table 1 and Fig. 2)
in terms of CÐHÁ Á ÁN interactions; there are no CÐHÁ Á Á(ring
other molecule; these (hydrogen bonds 6 and 7, and 1 and 2)
are shown as thicker bonds in Fig. 2, and one such system (6/7)
is implicitly recognizable in Fig. 1. In both molecules, atom H4
forms one reasonably linear hydrogen bond (4 and 5), whereas
atoms H5 and H6 participate in rather nonlinear but two-
centre hydrogen bonds (8 and 9, and 3 and 10) in addition to
the bifurcated interactions. The (uncorrected) hydrogen-bond
Ê
length limit HÁ Á ÁN has to be set at ca 2.9 A to ®nd all the
Ê
centroid) contacts shorter than 3.49 A.
interactions; this seems to be normal for the analysis of CÐ
HÁ Á ÁN C systems (e.g. Reddy et al., 1995). The correct
compromise between the use of high or low contact radii,
which may lead, respectively, either to a mass of unimportant
detail or to an apparent lack of signi®cant contacts, is not
always easy to ®nd.
Molecule 1 occupies the regions at z ' 0, 12, etc., and forms
layers connected by hydrogen bond 4 (numbering according to
the order in Table 1) via the 21 screw axis parallel to a. Mol-
1
3
ecule 2 occupies the regions z ' , , etc., and forms layers
4
4
connected by hydrogen bond 10 via the 21 screw axis parallel
to b. The main interest thus involves the interplay in the region
The acceptor properties of the N atoms differ. Atoms N1
and N10 accept only the bifurcated interactions, atoms N2 and
N30 each accept one branch of a three-centre system, atom N20
accepts one branch from each of two three-centre systems, and
atom N3 accepts the two linear two-centre interactions. The
topological difference between the two independent mol-
ecules is thus established.
3
8
at z ' , which is shown in Fig. 2; nine of the ten independent
hydrogen bonds can be accommodated in this view.
The neighbouring CH groups C5ÐH5 and C6ÐH6 in both
molecules form bifurcated hydrogen bonds to atom N1 of the
The molecule of compound (V) (Fig. 3) has no imposed
symmetry, but its noncrystallographic symmetry is close to 2/m
Ê
(the r.m.s. deviation of the non-H atoms is 0.034 A). The
molecular dimensions are largely as expected; in particular,
the usual distortions of [2.2]paracyclophanes are observed
(lengthened CÐC bonds and widened sp3 angles in the
bridges, narrow angles in the six-membered rings at the
bridgehead atoms, and ¯attened boat conformation of the
rings; Table 2).
Despite the more complicated nature of the molecule of
(V), the molecular packing is conceptually much simpler than
that of (II). It involves layers parallel to the ab plane, in which
N atoms act as acceptors for weak CÐHÁ Á ÁN C hydrogen
bonds (Table 3 and Fig. 4; hydrogen-bond numbers in Fig. 4
correspond to the order of Table 3). It is noteworthy that
hydrogen bonds 5, 6, 7 and 8 form a concerted system of
bifurcated and three-centre bonds; hydrogen bonds 1 and 2
form a further bifurcated system. As for (II), some of the
Figure 3
The molecule of (V). Displacement ellipsoids represent 50% probability
levels.
Ê
contacts involve long HÁ Á ÁN distances (up to 2.9 A uncor-
rected), but their striking combined effect is that of a series of
intermolecular links roughly parallel to the b axis. Only the
contact H1BÁ Á ÁN2ii (hydrogen bond 3) is not observed within
the layers; instead, it serves to connect the layers. There are no
Ê
CÐHÁ Á Á(ring centroid) contacts shorter than 3.18 A.
Experimental
Compound (II) was prepared from cyanoacetylene, (I), as previously
described (Witulski et al., 1990); the spectroscopic and analytical data
were consistent with those reported previously. Single crystals were
obtained by slow cooling from carbon tetrachloride. Cyclophane (V)
was prepared as described by Hopf & Lenich (1974) by the cyclo-
addition of dicyanoacetylene, (III) (Hopf, 1995), to 1,2,4,5-hexa-
tetraene, (IV) (Hopf et al., 1981). All spectroscopic and analytical
data agreed with those reported in the literature (Hopf & Lenich,
1974). Single crystals were obtained from acetonitrile.
Figure 4
The packing of (V), viewed perpendicular to the ab plane in the region
1
z ' . Hydrogen bonds are indicated by dashed lines, drawn thicker for
4
the bifurcated systems, and are numbered for one molecule according to
their order in Table 3, but they do not correspond to the asymmetric unit
as de®ned in the coordinate list. H atoms not involved in hydrogen bonds
have been omitted. Hydrogen bond 3 is not included in this view.
ꢁ
o724 Jones et al. C9H3N3 and C20H12N4
Acta Cryst. (2007). C63, o723±o725

organic compounds
Table 2
Selected geometric parameters (A, ) for (V).
Compound (II)
ꢀ
Ê
Crystal data
3
C1ÐC2
1.5877 (15)
C9ÐC10
1.5856 (15)
Ê
V = 1520.1 (5) A
C9H3N3
Mr = 153.14
Z = 8
Mo Kꢀ radiation
Orthorhombic, P212121
Ê
C14ÐC1ÐC2
C3ÐC2ÐC1
C4ÐC3ÐC8
112.60 (8)
112.28 (8)
116.84 (9)
C5ÐC6ÐC7
C16ÐC11ÐC12
C15ÐC14ÐC13
116.37 (9)
116.70 (9)
116.57 (9)
1
a = 6.7083 (12) A
ꢁ = 0.09 mm
T = 133 (2) K
Ê
b = 7.8650 (14) A
Ê
c = 28.811 (5) A
0.23 Â 0.15 Â 0.10 mm
Data collection
Table 3
Hydrogen-bond and short-contact geometry (A, ) for (V).
Bruker SMART 1000 CCD area-
detector diffractometer
17402 measured re¯ections
2581 independent re¯ections
2067 re¯ections with I > 2ꢂ(I)
Rint = 0.089
ꢀ
Ê
DÐHÁ Á ÁA
DÐH
HÁ Á ÁA
DÁ Á ÁA
DÐHÁ Á ÁA
C8ÐH8Á Á ÁN1i
0.95
0.95
0.99
0.99
0.99
0.95
0.95
0.95
2.69
2.90
2.50
2.55
2.60
2.78
2.82
2.90
3.3654 (15)
3.4710 (15)
3.3569 (15)
3.4380 (15)
3.4606 (15)
3.4221 (15)
3.4403 (15)
3.7133 (15)
129
120
145
149
145
125
124
145
Re®nement
C7ÐH7Á Á ÁN1i
R[F2 > 2ꢂ(F2)] = 0.054
wR(F2) = 0.115
S = 1.07
217 parameters
H-atom parameters constrained
C1ÐH1BÁ Á ÁN2ii
C2ÐH2BÁ Á ÁN2i
C10ÐH10AÁ Á ÁN4iii
C15ÐH15Á Á ÁN3iii
C16ÐH16Á Á ÁN3iii
C16ÐH16Á Á ÁN4iii
3
Ê
Áꢃmax = 0.31 e A
3
Ê
0.32 e A
2581 re¯ections
Áꢃmin
=
Table 1
Hydrogen-bond and short-contact geometry (A, ) for (II).
ꢀ
Ê
1
2
1
1
Symmetry codes: (i)
y ‡ 12; z ‡ 12.
x ‡ 12; y
;
z ‡ 12; (ii)
x
;
y ‡ 32; z
; (iii)
2
x ‡ 32,
2
DÐHÁ Á ÁA
DÐH
HÁ Á ÁA
DÁ Á ÁA
DÐHÁ Á ÁA
C50ÐH50Á Á ÁN1i
C60ÐH60Á Á ÁN1i
C50ÐH50Á Á ÁN2ii
C4ÐH4Á Á ÁN3iii
C40ÐH40Á Á ÁN3iv
C5ÐH5Á Á ÁN10
C6ÐH6Á Á ÁN10
0.95
0.95
0.95
0.95
0.95
0.95
0.95
0.95
0.95
0.95
2.71
2.64
2.55
2.63
2.60
2.64
2.65
2.57
2.78
2.89
3.320 (3)
3.288 (3)
3.380 (3)
3.566 (3)
3.528 (3)
3.262 (3)
3.261 (3)
3.430 (3)
3.650 (3)
3.758 (3)
123
125
146
169
167
124
123
150
154
152
H atoms were included, starting from calculated positions, using a
Ê
riding model with CÐH distances of 0.95 (aromatic) and 0.99 A
(CH2). Uiso(H) values were ®xed at 1.2Ueq of the parent C atom.
Compound (II) crystallizes by chance in a chiral space group,
although the molecule is achiral. In the absence of signi®cant
anomalous scattering, Friedel opposite re¯ections were merged.
For both compounds, data collection: SMART (Bruker, 1998); cell
re®nement: SAINT (Bruker, 1998); data reduction: SAINT;
program(s) used to solve structure: SHELXS97 (Sheldrick, 1997);
program(s) used to re®ne structure: SHELXL97 (Sheldrick, 1997);
molecular graphics: XP (Siemens, 1994); software used to prepare
material for publication: SHELXL97.
v
C5ÐH5Á Á ÁN30
vi
C6ÐH6Á Á ÁN20
vii
C60ÐH60Á Á ÁN20
1
2
Symmetry codes: (i) x; y
;
z ‡ 32; (ii) x ‡ 21; y ‡ 1; z ‡ 12; (iii) x ‡ 21, y ‡ 12,
z ‡ 1; (iv) x ‡ 32; y ‡ 1; z ‡ 12; (v) x ‡ 2; y
;
z ‡ 32; (vi)
x
1; y; z; (vii)
1
2
1
2
x ‡ 1; y
;
z ‡ 32.
Compound (V)
Supplementary data for this paper are available from the IUCr electronic
archives (Reference: HJ3057). Services for accessing these data are
described at the back of the journal.
Crystal data
3
Ê
C20H12N4
Mr = 308.34
V = 1479.1 (2) A
Z = 4
References
Monoclinic, P21=n
Mo Kꢀ radiation
ꢁ = 0.09 mm
T = 133 (2) K
0.40 Â 0.22 Â 0.12 mm
1
Ê
a = 7.0277 (6) A
b = 15.1197 (14) A
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Chemistry and Biology. Oxford University Press.
Ê
Ê
c = 14.3219 (14) A
ꢄ = 103.603 (4)ꢀ
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È
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Bruker SMART 1000 CCD area-
detector diffractometer
16873 measured re¯ections
4321 independent re¯ections
3137 re¯ections with I > 2ꢂ(I)
Rint = 0.032
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(1995). Acta Cryst. C51, 2352±2354.
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È
Re®nement
Gottingen, Germany.
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R[F2 > 2ꢂ(F2)] = 0.043
wR(F2) = 0.130
S = 1.06
217 parameters
H-atom parameters constrained
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2022.
3
Ê
Áꢃmax = 0.44 e A
3
Ê
0.22 e A
4321 re¯ections
Áꢃmin
=
ꢁ
Acta Cryst. (2007). C63, o723±o725
Jones et al. C9H3N3 and C20H12N4 o725