π-stacked hydrogen-bonded sheets in N,N′-bis(4-nitrobenzylidene) ethane1,2-diamine and π-stacked hydrogenbonded chains in N,N′-bis(4- nitrobenzylidene)propane-1,3-diamine

Article abstract of DOI:10.1107/S0108270104030719

Molecules of A,N′-bis(4-nitrobenzylidene)ethane-1,2-diamine, C ₁₆H₁₄N₄O₄, (I), lie across centres of inversion in space group P2₁/n and are linked into (101) sheets by a single C-H...O hydrogen bond [

Full text of DOI:10.1107/S0108270104030719

organic compounds
structure in detail along with that of its homologue N,N0-bis(4-
nitrobenzylidene)propane-1,3-diamine, (II).
Acta Crystallographica Section C
Crystal Structure
Communications
ISSN 0108-2701
p-Stacked hydrogen-bonded sheets in
N,N0-bis(4-nitrobenzylidene)ethane-
1,2-diamine and p-stacked hydrogen-
bonded chains in N,N0-bis(4-nitro-
benzylidene)propane-1,3-diamine
Molecules of (I) (Fig. 1) lie across centres of inversion in
space group P21/n, and the reference molecule was selected to
lie across (12, 21, 12 ). The key torsion angles (Table 1) show that
the N11ÐC11 bond almost eclipses the C12ÐH12A bond; the
C11ÐN11ÐC12ÐH12A angle is only 2.3ꢀ. The two halves of
the molecule are otherwise each nearly planar. The bond
lengths and interbond angles agree closely with those found by
Sun et al. (2004) and show no unusual values.
The molecules of (I) are linked into sheets by a single, fairly
short, CÐHÁ Á ÁO hydrogen bond (Table 2). Atoms C6 at (x, y,
z) and (1 x, 1 y 1 z), which lie in the molecule centred
at (12, 12, 12 ), act as hydrogen-bond donors, respectively, to atoms
O41 at ( 12 + x, 32 y, 21 + z) and (23 x, 21 + y, 32 z), which
themselves lie in the molecules centred at (0, 1, 0) and (1, 0, 1).
In a similar way, atoms O41 at (x, y, z) and (1 x, 1 y,
Joao A. S. Bomfim,a James L. Wardell,a John N. Low,b
Janet M. S. Skakleb and Christopher Glidewellc*
a
Â
Â
Ã
Instituto de Quõmica, Departamento de Quõmica Inorganica, Universidade Federal
do Rio de Janeiro, 21945-970 Rio de Janeiro, RJ, Brazil, bDepartment of Chemistry,
University of Aberdeen, Meston Walk, Old Aberdeen AB24 3UE, Scotland, and
cSchool of Chemistry, University of St Andrews, Fife KY16 9ST, Scotland
Correspondence e-mail: cg@st-andrews.ac.uk
Received 17 November 2004
Accepted 23 November 2004
Online 18 December 2004
Molecules of N,N0-bis(4-nitrobenzylidene)ethane-1,2-diamine,
C16H14N4O4, (I), lie across centres of inversion in space group
P21/n and are linked into (101) sheets by a single CÐHÁ Á ÁO
1
z) accept hydrogen bonds from atoms C6 at (12 + x, 23 y,
1
12 + z) and (12 x, 21 + y,
z), respectively, which lie in the
Ê
Ê
2
hydrogen bond [HÁ Á ÁO = 2.40 A, CÁ Á ÁO = 3.2166 (13) A and
CÐHÁ Á ÁO = 146ꢀ]; these sheets are linked into a three-
dimensional array by a single aromatic ꢀ±ꢀ stacking interac-
tion. Molecules of N,N0-bis(4-nitrobenzylidene)propane-1,3-
diamine, C17H16N4O4, (II), lie across twofold rotation axes in
space group C2/c and are linked into chains of spiro-fused
Ê
rings by a single CÐHÁ Á ÁO hydrogen bond [HÁ Á ÁO = 2.54 A,
ꢀ
Ê
CÁ Á ÁO = 3.267 (2) A and CÐHÁ Á ÁO = 130 ]; these chains are
linked into sheets by a single aromatic ꢀ±ꢀ stacking
interaction.
Comment
As part of a study of the supramolecular structures of
compounds containing nitro groups, the structures of the title
compounds were determined. The structure of N,N0-bis(4-
nitrobenzylidene)ethane-1,2-diamine, (I), has been reported
very recently (Sun et al., 2004) and it is clear that the deter-
mination reported here refers to the same phase as that in the
previous report. A larger data set is employed here (2717
re¯ections as opposed to 1635), leading to slightly higher
precision. Although Sun et al. (2004) drew attention to the
presence in the structure of a CÐHÁ Á ÁO hydrogen bond and
to the occurrence of an aromatic ꢀ±ꢀ stacking interaction, the
structural consequences of these interactions were not
analysed or discussed in detail. In particular, the dimension-
ality of the resulting supramolecular structure was not speci-
®ed. Accordingly, we feel it is justi®able to discuss this
Figure 1
The molecule of (I), showing the atom-labelling scheme. Atoms labelled
with the suf®x `A' are at the symmetry position (1 x, 1 y, 1 z), and
displacement ellipsoids are drawn at the 30% probability level.
Acta Cryst. (2005). C61, o53±o56
DOI: 10.1107/S0108270104030719
# 2005 International Union of Crystallography o53

organic compounds
molecules centred at (1, 1, 1) and (0, 0, 0), respectively. In this
manner, each molecule is linked to four others, forming a
(101) sheet (Fig. 2) in the form of a (4,4)-net (Batten &
Robson, 1998), built from a single type of R44(42) ring (Bern-
stein et al., 1995).
Molecules of (II) (Fig. 4) lie across twofold rotation axes in
space group C2/c, and the reference molecule was selected to
lie across the axis along (21, y, 14 ). The central spacer unit has a
conformation exhibiting almost perfect staggering about the
CÐC bonds (Table 3) and, as in (I), the outer portions of the
molecule are nearly planar.
A single ꢀ±ꢀ stacking interaction links adjacent sheets. The
aryl rings at (x, y, z) and (1 x, 1 y, 2 z) are components
Molecules of (II) are linked into chains of spiro-fused rings
by a single CÐHÁ Á ÁO hydrogen bond (Table 4). Atom C13 at
(12, y, 14 ) acts as a hydrogen-bond donor to nitro atoms O41 at
(x, 1 y, 12 + z) and (1 x, 1 y, 1 z), which themselves
are components of the molecules across the twofold rotation
1
2
1
2
1 3
2 2
of the molecules centred at (12, , ) and (12, , ), respectively.
These rings are strictly parallel, with an interplanar separation
Ê
Ê
of 3.419 (2) A; the ring-centroid separation is 3.696 (2) A,
corresponding to near-ideal ring-centroid offset of
a
3
1.404 (2) A. Propagation of this stacking interaction by
translation and inversion links the molecules into a molecular
ladder running parallel to the [001] direction (Fig. 3), and this
ladder suf®ces to link each (101) sheet to the two adjacent
sheets, hence forming a continuous three-dimensional array.
axes (12, y, 41 ) and (12, y, ), respectively. Propagation by
Ê
4
rotation of this single hydrogen bond then generates a chain of
spiro-fused centrosymmetric R22(22) rings running parallel to
the [001] direction, in which atom C13 is the spiro atom
(Fig. 5).
Two chains of this type, related to one another by the C-
centring operation, pass through each unit cell, and the chains
are linked into sheets by a single aromatic ꢀ±ꢀ stacking
Figure 4
The molecule of (II), showing the atom-labelling scheme. Atoms labelled
Figure 2
A stereoview of part of the crystal structure of (I), showing the formation
of a (101) sheet. For clarity, H atoms not involved in hydrogen bonding
have been omitted.
1
with the suf®x `A' are at the symmetry position (1 x, y,
displacement ellipsoids are drawn at the 30% probability level.
z), and
2
Figure 3
Figure 5
A stereoview of part of the crystal structure of (I), showing the formation
of a ꢀ-stacked molecular ladder along [001]. For clarity, all of the H atoms
have been omitted.
A stereoview of part of the crystal structure of (II), showing the
formation of a [001] chain of spiro-fused R22(22) rings. For clarity, H atoms
not involved in hydrogen bonding have been omitted.
ꢁ
o54 Joao A. S. Bomfim et al.
C16H14N4O4 and C17H16N4O4
Acta Cryst. (2005). C61, o53±o56

organic compounds
Re®nement
Re®nement on F2
R[F2 > 2ꢅ(F2)] = 0.050
wR(F2) = 0.158
S = 1.05
2717 re¯ections
w = 1/[ꢅ2(F2o) + (0.095P)2
+ 0.0285P]
where P = (F2o + 2Fc2)/3
(Á/ꢅ)max < 0.001
3
Ê
Áꢆmax = 0.21 e A
3
Ê
0.24 e A
109 parameters
H-atom parameters constrained
Áꢆmin
=
Table 1
Selected torsion angles (ꢀ) for (I).
C12iÐC12ÐN11ÐC11
C12ÐN11ÐC11ÐC1
118.31 (13)
176.58 (8)
N11ÐC11ÐC1ÐC2
C3ÐC4ÐN4ÐO41
177.91 (9)
5.86 (15)
Symmetry code: (i) 1 x; 1 y; 1 z.
Figure 6
Table 2
Hydrogen-bonding geometry (A, ) for (I).
A stereoview of part of the crystal structure of (II), showing the
formation of a [101] ꢀ-stacked chain, which links the hydrogen-bonded
chains into (010) sheets. For clarity, all of the H atoms have been omitted.
ꢀ
Ê
DÐHÁ Á ÁA
DÐH
HÁ Á ÁA
DÁ Á ÁA
DÐHÁ Á ÁA
C6ÐH6Á Á ÁO41ii
0.93
2.40
3.2166 (13)
146
interaction. The aryl rings at (x, y, z) and (32 x, 23 y, 1 z),
1
2
3
1
Symmetry code: (ii) x
;
y; z
.
2
3
which lie in molecules across the axes (12, y, 41 ) and (1, y, ),
2
4
respectively, are strictly parallel, with an interplanar separa-
Ê
Ê
tion of 3.366 (2) A; the ring-centroid separation is 3.664 (2) A,
Ê
corresponding to a near-ideal centroid offset of 1.447 (2) A.
Compound (II)
Propagation of this interaction by inversion and rotation then
generates a ꢀ-stacked [101] chain (Fig. 6). Since each molecule
in this chain is also a component of a hydrogen-bonded chain
along [001], the overall supramolecular structure takes the
form of a (010) sheet.
Crystal data
C17H16N4O4
Mr = 340.34
Monoclinic, C2=c
Mo Kꢁ radiation
Cell parameters from 1827
re¯ections
ꢃ = 3.2±27.6ꢀ
ꢄ = 0.11 mm
T = 120 (2) K
Ê
a = 12.9412 (6) A
1
Ê
b = 7.3062 (3) A
Ê
c = 16.9061 (8) A
ꢂ = 99.559 (2)ꢀ
V = 1576.29 (12) A
Needle, orange
0.20 Â 0.09 Â 0.04 mm
Experimental
3
Ê
The title compounds were prepared by the reactions of 4-nitro-
benzaldehyde with the appropriate ꢁ,!-diaminoalkane (2:1 molar
ratio) in re¯uxing methanol; crystals suitable for single-crystal X-ray
diffraction were grown from solutions in ethanol. For (I), m.p. 470±
Z = 4
Dx = 1.434 Mg m
3
Data collection
N), 1520 and 1340 cmÐ1 (NO2); for (II), m.p.
Nonius KappaCCD diffractometer
' and ! scans
1306 re¯ections with I > 2ꢅ(I)
Rint = 0.052
ꢃmax = 27.6ꢀ
474 K; IR: 1640 (C
466±467 K (melts with decomposition to black liquid): IR: 1644
(C
N), 1518 and 1341 cmÐ1 (NO2).
ꢂ
Absorption correction: multi-scan
(SADABS; Sheldrick, 2003)
Tmin = 0.984, Tmax = 0.996
8695 measured re¯ections
1827 independent re¯ections
ꢂ
h = 16 ! 16
k = 9 ! 9
l = 21 ! 21
Compound (I)
Crystal data
Re®nement
3
C16H14N4O4
Mr = 326.31
Monoclinic, P21=n
Dx = 1.433 Mg m
Mo Kꢁ radiation
Re®nement on F2
R[F2 > 2ꢅ(F2)] = 0.052
wR(F2) = 0.158
S = 1.06
1827 re¯ections
w = 1/[ꢅ2(F2o) + (0.0884P)2
+ 0.3187P]
Cell parameters from 2717
re¯ections
where P = (F2o + 2Fc2)/3
(Á/ꢅ)max < 0.001
Ê
Ê
a = 9.1606 (5) A
b = 7.2295 (4) A
ꢃ = 2.7±32.6ꢀ
3
Ê
Áꢆmax = 0.21 e A
1
Ê
c = 11.5201 (6) A
ꢄ = 0.11 mm
T = 291 (2) K
3
Ê
0.25 e A
114 parameters
H-atom parameters constrained
Áꢆmin
=
ꢂ = 97.515 (1)ꢀ
V = 756.38 (7) A
Z = 2
3
Ê
Block, colourless
0.47 Â 0.37 Â 0.25 mm
Data collection
Table 3
Selected torsion angles (ꢀ) for (II).
Bruker SMART 1000 CCD area-
detector diffractometer
' and ! scans
Absorption correction: multi-scan
(SADABS; Bruker, 2000)
Tmin = 0.946, Tmax = 0.974
7869 measured re¯ections
2717 independent re¯ections
2008 re¯ections with I > 2ꢅ(I)
Rint = 0.020
C12iiiÐC13ÐC12ÐN11
C13ÐC12ÐN11ÐC11
C12ÐN11ÐC11ÐC1
67.65 (11)
121.50 (17)
179.33 (14)
N11ÐC11ÐC1ÐC2
C3ÐC4ÐN4ÐO41
174.52 (17)
2.4 (2)
ꢃmax = 32.6ꢀ
h = 13 ! 13
k = 10 ! 10
Symmetry code: (iii) 1 x; y; 12 z.
l = 13 ! 17
ꢁ
Acta Cryst. (2005). C61, o53±o56
Joao A. S. Bomfim et al. C16H14N4O4 and C17H16N4O4 o55

organic compounds
Table 4
Hydrogen-bonding geometry (A, ) for (II).
funding the purchase of the diffractometer. X-ray data for (II)
were collected at the EPSRC X-ray Crystallographic Service,
University of Southampton, England; the authors thank the
staff for all their help and advice. JNL thanks NCR Self-
Service, Dundee, for grants which have provided computing
facilities for this work. JLW thanks CNPq and FAPERJ for
®nancial support.
ꢀ
Ê
DÐHÁ Á ÁA
DÐH
HÁ Á ÁA
DÁ Á ÁA
DÐHÁ Á ÁA
C13ÐH13AÁ Á ÁO42iv
0.99
2.54
3.267 (2)
130
1
2
Symmetry code: (iv) x; 1 y; z
.
For compound (I), the space group P21/n was uniquely assigned
from the systematic absences. For compound (II), the systematic
absences permitted Cc and C2/c as possible space groups; C2/c was
selected and con®rmed by the successful structure analysis. All H
atoms were located from difference maps and then treated as riding
Supplementary data for this paper are available from the IUCr electronic
archives (Reference: SK1795). Services for accessing these data are
described at the back of the journal.
Ê
atoms, with CÐH distances in (I) of 0.97 (CH2) or 0.93 A (all other H
References
Ê
atoms) and in (II) of 0.99 (CH2) or 0.95 A (all other H atoms), and
with Uiso(H) values of 1.2Ueq(C).
Batten, S, R. & Robson, R. (1998). Angew. Chem. Int. Ed. 37, 1460±1494.
Bernstein, J., Davis, R. E., Shimoni, L. & Chang, N.-L. (1995). Angew. Chem.
Int. Ed. Engl. 34, 1555±1573.
Bruker (2000). SMART (Version 5.624), SAINT-Plus (Version 6.02A) and
SADABS (Version 2.03). Bruker AXS Inc., Madison, Wisconsin, USA.
Ferguson, G. (1999). PRPKAPPA. University of Guelph, Canada.
Hooft, R. W. W. (1999). COLLECT. Nonius BV, Delft, The Netherlands.
McArdle, P. (2003). OSCAIL for Windows. Version 10. Crystallography
Centre, Chemistry Department, NUI Galway, Ireland.
For compound (I), data collection: SMART (Bruker, 2000); cell
re®nement: SAINT-Plus (Bruker, 2000); data reduction: SAINT-
Plus. For compound (II), data collection: COLLECT (Hooft, 1999);
cell re®nement: DENZO (Otwinowski
& Minor, 1997) and
COLLECT; data reduction: DENZO and COLLECT. For both
compounds, program(s) used to solve structure: OSCAIL (McArdle,
2003) and SHELXS97 (Sheldrick, 1997); program(s) used to re®ne
structure: OSCAIL and SHELXL97 (Sheldrick, 1997); molecular
graphics: PLATON (Spek, 2003); software used to prepare material
for publication: SHELXL97 and PRPKAPPA (Ferguson, 1999).
Otwinowski, Z. & Minor, W. (1997). Methods in Enzymology, Vol 276,
Macromolecular Crystallography, Part A, edited by C. W. Carter Jr & R. M.
Sweet, pp. 307±326. New York: Academic Press.
Sheldrick, G. M. (1997). SHELXS97 and SHELXL97. University of
È
Gottingen, Germany.
Sheldrick, G. M. (2003). SADABS. Version 2.10. University of Gottingen,
È
Germany.
Spek, A. L. (2003). J. Appl. Cryst. 36, 7±13.
Sun, Y.-X., You, Z.-L. & Zhu, H.-L. (2004). Acta Cryst. E60, o1707±o1708.
X-ray data for (I) were collected at the University of
Aberdeen; the authors thank the University of Aberdeen for
ꢁ
o56 Joao A. S. Bomfim et al.
C16H14N4O4 and C17H16N4O4
Acta Cryst. (2005). C61, o53±o56