Three-dimensional aggregation in 2-hydroxy-3-iodo-5-nitrobenzaldehyde involving C - H...O, iodo-nitro and aromatic π-π stacking interactions, and isolated dimers in disordered 2,4-diiodo-6-nitroanisole

Article abstract of DOI:10.1107/S0108270103025654

The molecular and supramolecular structures of 2-hydroxy-3-iodo-5-nitrobenzaldehyde (I) and 2,4-diiodo-6-nitroanisole (II) were analyzed. The crystallographic atom numbering scheme differed from the conventional chemical numbering scheme in order that bot

Full text of DOI:10.1107/S0108270103025654

organic compounds
Acta Crystallographica Section C
Crystal Structure
Communications
In compound (I) [Fig. 1, where the crystallographic atom-
numbering scheme differs from the conventional chemical
ISSN 0108-2701
Three-dimensional aggregation in
2-hydroxy-3-iodo-5-nitrobenz-
aldehyde involving CÐHÁ Á ÁO,
iodo±nitro and aromatic p±p
stacking interactions, and isolated
dimers in disordered 2,4-diiodo-
6-nitroanisole
numbering scheme in order that both (I) and (II) have a nitro
group at position 1 and an iodo substituent at position 5], there
is an intramolecular OÐHÁ Á ÁO hydrogen bond, forming an
S(6) motif (Bernstein et al., 1995). There are three distinct
types of intermolecular interactions linking the molecules of
(I). A soft hydrogen bond and an iodo±nitro interaction each
form a chain motif. Thus, aromatic atom C6 in the molecule at
(x, y, z) acts as hydrogen-bond donor to the aldehydic atom
O31 in the molecule at (1 + x, y, z), so generating by trans-
lation a C(7) chain running parallel to the [100] direction
Simon J. Garden,a Fernando R. da Cunha,a Christopher
Glidewell,b* John N. Low,c Janet M. S. Skaklec and
James L. Wardella
a
Â
Ã
Â
Departamento de Quõmica Organica, Instituto de Quõmica, Universidade Federal do
Rio de Janeiro, 21945-970 Rio de Janeiro, RJ, Brazil, bSchool of Chemistry,
University of St Andrews, Fife KY16 9ST, Scotland, and cDepartment of Chemistry,
University of Aberdeen, Meston Walk, Old Aberdeen AB24 3UE, Scotland
Correspondence e-mail: cg@st-andrews.ac.uk
Received 3 November 2003
Accepted 6 November 2003
Online 6 December 2003
In 2-hydroxy-3-iodo-5-nitrobenzaldehyde, C7H4INO4, the
molecules are linked into sheets by a combination of CÐ
HÁ Á ÁO hydrogen bonds and two-centre iodo±nitro interac-
tions, and these sheets are linked by aromatic ꢀ±ꢀ stacking
interactions. Molecules of 2,4-diiodo-6-nitroanisole, C7H5I2-
NO3, are disordered, with the nitro group and one of the I
substituents each occupying common sets of sites with 0.5
occupancy. The molecules are linked into isolated centrosym-
metric dimeric units by a single iodo±nitro interaction.
Figure 1
A view of the molecule of (I), showing the atom-labelling scheme.
Displacement ellipsoids are drawn at the 30% probability level and H
atoms are shown as small spheres of arbitrary radii.
Comment
We have recently reported the supramolecular aggregation of
a wide range of different types of iodo±nitro aromatic
compounds (McWilliam et al., 2001; Garden, da Cunha et al.,
2002; Garden, Fontes et al., 2002; Kelly et al., 2002; Glidewell,
Howie et al., 2002; Glidewell, Low et al., 2002; Glidewell et al.,
2003), in which the patterns of supramolecular aggregation
depend on the interplay of a wide range of weak inter-
molecular forces, including hard and soft (Desiraju & Steiner,
1999) hydrogen bonds of various types, iodo±nitro interactions
and aromatic ꢀ±ꢀ stacking interactions. We report here the
molecular and supramolecular structures of two further
examples of such compounds, viz. 2-hydroxy-3-iodo-5-nitro-
benzaldehyde, (I), and 2,4-diiodo-6-nitroanisole, (II), the
latter being isomeric with 2,6-diiodo-4-nitroanisole, (III)
(Garden, da Cunha et al., 2002).
Figure 2
Part of the crystal structure of (I), showing the formation of an (001)
sheet built from CÐHÁ Á ÁO hydrogen bonds and iodo±nitro interactions.
Atoms marked with an asterisk (*), a hash (#) or a dollar sign ($) are at
the symmetry positions (1 + x, y, z), (1 x, 12 + y, 21 z) and (x, 1 + y, z),
respectively.
o12 # 2004 International Union of Crystallography
DOI: 10.1107/S0108270103025654
Acta Cryst. (2004). C60, o12±o14

organic compounds
1
axis along (12, y, ). The combination of the [100] and [010]
4
chains generates an elegant sheet parallel to (001) in the form
of a (4,4)-net (Batten & Robson, 1998) containing equal
numbers of S(6) and R45(22) rings (Fig. 2).
Two sheets of this type pass through each unit cell of (I),
lying in the domains 0.09 < z < 0.41 and 0.59 < z < 0.91, and
adjacent sheets are weakly linked by the third type of inter-
molecular interaction, an aromatic ꢀ±ꢀ stacking interaction.
The aryl ring in the molecule at (x, y, z), which lies in the 0.09 <
1
z < 0.41 sheet, and those in the molecules at (x,
1
y, 12 + z)
2
and (x,
y, z 12), which lie in the domains 0.59 < z < 0.91
and 0.41 < z < 0.09, respectively, are nearly parallel, with
2
Figure 3
A stereoview of part of the crystal structure of (I), showing the ꢀ±ꢀ
stacking interaction which links adjacent (001) sheets. For the sake of
clarity, H atoms have been omitted.
an intꢀerplanar angle between rings in adjacent sheets of only
Ê
ca 1.3 . The centroid separations are both 3.767 (3) A and the
Ê
interplanar separations are ca 3.46 A, corresponding to
Ê
centroid offsets of ca 1.49 A (Fig. 3).
(Fig. 2). At the same time, atom I5 in the molecule at (x, y, z)
forms a short two-centre iodo±nitro interaction with nitro
atom O11 in the molecule at (1 x, 12 + y, 21 z), with IÁ Á ÁO =
In the disordered structure of (II) (Fig. 4, where again the
crystallographic atom-numbering scheme differs from the
conventional chemical numbering scheme, see above), in
contrast with (I), there are neither CÐHÁ Á ÁO hydrogen bonds
nor aromatic ꢀ±ꢀ stacking interactions. The only direction-
speci®c intermolecular interaction is a two-centre iodo±nitro
interaction involving the fully occupied I5 site and the half-
occupied O1 site in the molecules at (x, y, z) and (12 x, 21 y,
ꢀ
ꢀ
Ê
3.054 (3) A, CÐIÁ Á ÁO = 167.8 (2) and IÁ Á ÁOÐN = 116.0 (2) ,
so producing a C(6) chain (Starbuck et al., 1999) running
parallel to the [010] direction and generated by the 21 screw
ꢀ
Ê
1
z), with IÁ Á ÁO = 3.339 (13) A, CÐIÁ Á ÁO = 148.5 (2) and
IÁ Á ÁOÐN = 135.3 (13)ꢀ. If the O11 sites in both of these
molecules were fully occupied, the resulting dimer would
contain an R22(14) motif (Fig. 5). However, each such pair of
molecules may, in fact, contain two, one or zero IÁ Á ÁO inter-
actions, depending upon the local occupancy of the O11 sites,
with an average value of one. There are four of these dimeric
aggregates in each unit cell of (II), but there are no direction-
speci®c interactions between them. In the isomeric compound,
(III), the fully ordered molecules are linked into isolated
chains by a single two-centre iodo±nitro interaction (Garden,
da Cunha et al., 2002). The intramolecular distances and angles
in (I) and (II) present no unusual features.
Figure 4
Aview of the molecule of (II), showing the atom-labelling scheme and the
disorder (see text). Displacement ellipsoids are drawn at the 30%
probability level and H atoms are shown as small spheres of arbitrary
radii.
Experimental
To prepare compound (I), 5-nitrosalicylaldehyde (10 mmol) was
dissolved in warm methanol (30 ml) and a solution of K[ICl2] in
methanol (2 M, 10 ml) was added with stirring. After a few hours, the
reaction mixture was diluted with water (100 ml) and compound (I)
was collected by ®ltration, washed with water and crystallized from
aqueous ethanol (yield 83%, m.p. 432±433 K). To prepare compound
(II), a solution of K[ICl2] in methanol (2 M, 25 ml) was added to a
methanol solution (50 ml) of 2-nitrophenol (20 mmol) and the
mixture was gently warmed. Water (100 ml) was added to the reac-
tion mixture and the 2,4-diiodo-6-nitrophenol which precipitated out
was collected by ®ltration and washed with water. This material was
dissolved in acetone (50 ml) and to this solution was added K2CO3
(30 mmol) followed by an excess of Me2SO4 (10 ml). The resulting
mixture was stirred at room temperature for 3 d, after which time the
reaction mixture was concentrated by evaporation of the volatiles.
The addition of water (100 ml) prompted the precipitation of
compound (II), which was collected by ®ltration and crystallized from
aqueous ethanol (yield 93%, m.p. 385±386 K).
Figure 5
Part of the crystal structure of (II), showing the formation of an R22(14)
dimer. For the sake of clarity, only one orientation of the disordered
components is shown, and the H atoms and the unit-cell box have been
omitted. Atoms marked with an asterisk (*) are at the symmetry position
1
1
(
x,
y, 1 z).
2
2
ꢁ
Acta Cryst. (2004). C60, o12±o14
Simon J. Garden et al.
C7H4INO4 and C7H5I2NO3 o13

organic compounds
The crystals of (I) and (II) are monoclinic. For (I), the space group
P21/c was uniquely assigned from the systematic absences, while for
(II), the systematic absences permitted Cc and C2/c as possible space
groups; C2/c was selected, and con®rmed by the subsequent structure
analysis. It was apparent at an early stage that the molecules of (II)
were disordered over two sets of sites such that all atoms except one
nitro group and one I atom were common to both orientations. When
the site-occupancy factors for these disordered substituents were
re®ned they gave values of 0.48 (3) and 0.52 (3), and hence they were
both thereafter ®xed at 0.50. When full anisotropic re®nement was
attempted for (II), the behaviour of the disordered nitro groups was
erratic and not satisfactory. Accordingly, the atoms in these substi-
tuents were constrained to have the same anisotropic displacement
parameters and the re®nement then behaved satisfactorily. All H
atoms were located from difference maps and then treated as riding
Compound (I)
Crystal data
3
C7H4INO4
Mr = 293.01
Dx = 2.348 Mg m
Mo Kꢂ radiation
Monoclinic, P21=c
Cell parameters from 1901
re¯ections
Ê
a = 8.2556 (3) A
ꢃ = 3.0±27.5ꢀ
ꢄ = 3.84 mm
T = 120 (2) K
Ê
b = 15.3414 (8) A
1
Ê
c = 7.2521 (4) A
ꢁ = 115.496 (3)ꢀ
Ê
V = 829.05 (7) A
Z = 4
3
Lath, colourless
0.36 Â 0.05 Â 0.02 mm
Data collection
Nonius KappaCCD diffractometer
' scans, and ! scans with ꢅ offsets
Absorption correction: multi-scan
(DENZO±SMN; Otwinowski &
Minor, 1997)
1901 independent re¯ections
1482 re¯ections with I > 2ꢆ(I)
Rint = 0.065
ꢃ
max = 27.5ꢀ
Ê
atoms, with CÐH distances of 0.93 (aromatic and CHO) and 0.96 A
Ê
(methyl), and OÐH distances of 0.82 A.
h = 10 ! 10
k = 19 ! 19
l = 9 ! 9
Tmin = 0.339, Tmax = 0.927
8251 measured re¯ections
For both compounds, data collection: KappaCCD Server Software
(Nonius, 1997); cell re®nement: DENZO±SMN (Otwinowski &
Minor, 1997); data reduction: DENZO±SMN; program(s) used to
solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to
re®ne structure: SHELXL97 (Sheldrick, 1997); molecular graphics:
PLATON (Spek, 2003); software used to prepare material for
publication: SHELXL97 and PRPKAPPA (Ferguson, 1999).
Re®nement
Re®nement on F2
R[F2 > 2ꢆ(F2)] = 0.033
wR(F2) = 0.074
S = 1.03
1901 re¯ections
119 parameters
H-atom parameters constrained
w = 1/[ꢆ2(Fo2) + (0.0348P)2]
where P = (Fo2 + 2Fc2)/3
(Á/ꢆ)max = 0.001
3
Ê
Áꢇmax = 1.13 e A
3
Ê
1.08 e A
Áꢇmin
=
The X-ray data were collected at the EPSRC X-ray Crys-
tallographic 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.
Table 1
Hydrogen-bonding geometry (A, ) for (I).
ꢀ
Ê
DÐHÁ Á ÁA
DÐH
HÁ Á ÁA
DÁ Á ÁA
DÐHÁ Á ÁA
O41ÐH41Á Á ÁO31
0.82
0.93
1.92
2.48
2.629 (5)
3.351 (6)
145
155
C6ÐH6Á Á ÁO31i
Supplementary data for this paper are available from the IUCr electronic
archives (Reference: GG1198). Services for accessing these data are
described at the back of the journal.
Symmetry code: (i) 1 ‡ x; y; z.
Compound (II)
References
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Bernstein, J., Davis, R. E., Shimoni, L. & Chang, N.-L. (1995). Angew. Chem.
Int. Ed. Engl. 34, 1555±1573.
Desiraju, G. R. & Steiner, T. (1999). The Weak Hydrogen Bond, pp. 86±89.
Oxford University Press.
Ferguson, G. (1999). PRPKAPPA. University of Guelph, Canada.
Garden, S. J., da Cunha, F. R., Wardell, J. L., Skakle, J. M. S., Low, J. N. &
Glidewell, C. (2002). Acta Cryst. C58, o463±o466.
Garden, S. J., Fontes, S. P., Wardell, J. L., Skakle, J. M. S., Low, J. N. &
Glidewell, C. (2002). Acta Cryst. B58, 701±709.
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(2002). Acta Cryst. C58, o487±o490.
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Crystal data
3
C7H5I2NO3
Mr = 404.92
Monoclinic, C2=c
Dx = 2.609 Mg m
Mo Kꢂ radiation
Cell parameters from 3712
re¯ections
Ê
a = 32.999 (2) A
ꢃ = 2.5±32.6ꢀ
ꢄ = 6.08 mm
T = 120 (2) K
Ê
b = 4.2305 (3) A
1
Ê
c = 14.8328 (11) A
ꢁ = 95.225 (2)ꢀ
V = 2062.1 (2) A
Z = 8
3
Ê
Needle, colourless
0.34 Â 0.04 Â 0.04 mm
Data collection
Nonius KappaCCD diffractometer
' scans, and ! scans with ꢅ offsets
Absorption correction: multi-scan
(DENZO±SMN; Otwinowski &
Minor, 1997)
3712 independent re¯ections
1520 re¯ections with I > 2ꢆ(I)
Rint = 0.044
ꢃ
max = 32.6ꢀ
h = 49 ! 33
McWilliam, S. A., Skakle, J. M. S., Low, J. N., Wardell, J. L., Garden, S. J., Pinto,
A. C., Torres, J. C. & Glidewell, C. (2001). Acta Cryst. C57, 942±945.
Nonius (1997). KappaCCD Server Software. Windows 3.11 Version. Nonius
BV, Delft, The Netherlands.
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.
Tmin = 0.232, Tmax = 0.793
10 606 measured re¯ections
k = 6 ! 6
l = 22 ! 22
Re®nement
Re®nement on F2
R[F2 > 2ꢆ(F2)] = 0.053
wR(F2) = 0.154
S = 0.89
3712 re¯ections
126 parameters
H-atom parameters constrained
w = 1/[ꢆ2(Fo2) + (0.0721P)2]
where P = (Fo2 + 2Fc2)/3
(Á/ꢆ)max < 0.001
Sheldrick, G. M. (1997). SHELXS97 and SHELXL97. University of
È
Gottingen, Germany.
Spek, A. L. (2003). J. Appl. Cryst. 36, 7±13.
Starbuck, J., Norman, N. C. & Orpen, A. G. (1999). New J. Chem. 23, 969±972.
3
Ê
Áꢇmax = 1.07 e A
3
Ê
1.29 e A
Áꢇmin
=
ꢁ
o14 Simon J. Garden et al.
C7H4INO4 and C7H5I2NO3
Acta Cryst. (2004). C60, o12±o14