Supramolecular structures of three isomeric 2-chloro-N-(nitrophenyl) nicotinamides

Article abstract of DOI:10.1107/S0108270105003586

Molecules of 2-chloro-N-(2-nitrophenyl)nicotinamide, C₁₂H ₈ClN₃O₃, are linked by two C-H...O hydrogen bonds into a chain of edge-fused R₂²(14) and R₄⁴(24) rings. In 2-

Full text of DOI:10.1107/S0108270105003586

organic compounds
Acta Crystallographica Section C
Crystal Structure
Communications
some in¯uence on the conformation. The planes of the nitro
groups are all close to the planes of the adjacent aryl rings. The
two independent molecules in (III) adopt very similar
conformations so that for the selected asymmetric unit the two
molecules are nearly enantiomeric (Table 5 and Fig. 3).
ISSN 0108-2701
Supramolecular structures of three
isomeric 2-chloro-N-(nitrophenyl)-
nicotinamides
Marcus V. N. de Souza,a Thatyana R. A. Vasconcelos,a
Solange M. S. V. Wardell,a James L. Wardell,b John N.
Lowc and Christopher Glidewelld*
a
Â
Complexo Tecnologico de Medicamentos Farmanguinhos, Av. Comandante
b
Â
Â
Guaranys 447, Jacarepagua, Rio de Janeiro, RJ, Brazil, Instituto de Quõmica,
Â
Ã
Departamento de Quõmica Inorganica, Universidade Federal do Rio de Janeiro,
CP 68563, 21945-970 Rio de Janeiro, RJ, Brazil, cDepartment of Chemistry,
University of Aberdeen, Meston Walk, Old Aberdeen AB24 3UE, Scotland, and
dSchool of Chemistry, University of St Andrews, Fife KY16 9ST, Scotland
Correspondence e-mail: cg@st-andrews.ac.uk
Received 25 January 2005
Accepted 1 February 2005
Online 11 March 2005
Molecules of 2-chloro-N-(2-nitrophenyl)nicotinamide, C12H8-
ClN3O3, are linked by two CÐHÁ Á ÁO hydrogen bonds
into a chain of edge-fused R22(14) and R44(24) rings. In
2-chloro-N-(3-nitrophenyl)nicotinamide monohydrate, C12H8-
ClN3O3ÁH2O, the molecules are linked by a combination of
NÐHÁ Á ÁO, OÐHÁ Á ÁO and OÐHÁ Á ÁN hydrogen bonds into a
chain of edge-fused rings containing two distinct types of
R44(16) ring. In 2-chloro-N-(4-nitrophenyl)nicotinamide,
C12H8ClN3O3, which crystallizes with Z0 = 2 in space group
P21/n, the molecules are linked by two NÐHÁ Á ÁN hydrogen
bonds into simple C22(12) chains.
Within the spacer units, the backbone CÐCÐN angles are
consistently signi®cantly less than 120ꢀ, while the CÐNÐC
angles are signi®cantly greater than 120ꢀ. There is no evidence
from the bond length in the nitroaniline fragments in
compounds (I) and (III) of any bond ®xation, such as is
typically found in simple 2-nitro- and 4-nitroanilines. Thus,
polarization of types (Ia) and (IIIa) cannot effectively
compete with the normal polarization of the amide units in
these compounds.
The molecules of (I) are linked into a chain of edge-fused
rings by two CÐHÁ Á ÁO hydrogen bonds, involving both the
carbonyl O and one of the nitro O atoms (Table 2). Atom C14
of the heteroaryl ring in the molecule at (x, y, z) acts as a
hydrogen-bond donor to nitro atom O2 in the molecule at
Comment
We report here the molecular and supramolecular structures
of three isomeric 2-chloro-N-(nitrophenyl)nicotinamides
(Figs. 1±3). Of these isomers, the 3-nitrophenyl isomer, (II),
crystallizes from acetone as a monohydrate, whereas the
2-nitrophenyl isomer, (I), crystallizes from the same solvent in
the unsolvated form. The 4-nitrophenyl isomer, (III), crystal-
lizes from ethanol with Z0 = 2 (Fig. 3).
In compounds (I) and (II), and in each of the independent
molecules of (III), the central amide spacer unit is essentially
planar, as demonstrated by the CÐCÐNÐC torsion angles
(Tables 1, 3 and 5). However, the torsion angles describing the
conformations of the two rings relative to the spacer unit show
some variations, particularly for the heteroaryl rings. The
nitroaryl rings do not deviate signi®cantly from the plane of
the amide spacer unit, and in each molecule there is a short
intramolecular CÐHÁ Á ÁO contact involving atom C26 in the
aryl ring [atom C46 in molecule 2 of compound (III)] and the
amide O atom (Tables 2, 4 and 6); this interaction may have
Figure 1
The molecule of (I), showing the atom-labelling scheme. Displacement
ellipsoids are drawn at the 30% probability level.
o204 # 2005 International Union of Crystallography
DOI: 10.1107/S0108270105003586
Acta Cryst. (2005). C61, o204±o208

organic compounds
( 1 + x, y, z), so generating by translation a C(9) chain
(Bernstein et al., 1995) running parallel to the [100] direction.
At the same time, aryl atom C25 in the molecule at (x, y, z)
acts as a donor to carbonyl atom O1 in the molecule at ( x,
(Fig. 4). Two chains of this type pass through each unit cell,
along the lines (x, 0, 0) and (x, 12, 12 ), but there are no direction-
speci®c interactions between adjacent chains.
The independent components in (II) are linked by a
combination of OÐHÁ Á ÁO, OÐHÁ Á ÁN and NÐHÁ Á ÁO
hydrogen bonds (Table 4) into a chain of edge-fused rings.
Water atom O41 acts as a hydrogen-bond donor, via H41, to
carbonyl atom O1 within the asymmetric unit. In addition,
amine atom N21 at (x, y, z) acts as a hydrogen-bond donor to
water atom O4 at (x, 1 + y, z), so generating by translation a
C22(6) chain running parallel to the [010] direction, in which
OÐHÁ Á ÁO hydrogen bonds alternate with NÐHÁ Á ÁO
hydrogen bonds (Fig. 5). Two chains of this type, antiparallel
to one another, pass through each unit cell, and these are
linked by the OÐHÁ Á ÁN hydrogen bonds. Water atom O41 at
(x, y, z) also acts as a hydrogen-bond donor, this time via H42,
to ring atom N11 at (1 x, 1 y, z), so generating a
1
y, 1 z), so forming a centrosymmetric R22(14) ring
centred at (0, 12, 21 ). The combination of these two motifs then
generates a chain of centrosymmetric edge-fused rings along
[100], with R22(14) rings centred at (n, 21, 12 ) (n = zero or integer)
1
1
and R44(24) rings centred at (n + 12, , ) (n = zero or integer)
2
2
1
centrosymmetric R44(16) ring, centred at (12, , 0) (Fig. 5). The
2
combination of these two motifs then generates a chain of
centrosymmetric edge-fused rings along the line (12, y, 0), in
which R44(16) rings containing OÐHÁ Á ÁO and OÐHÁ Á ÁN
hydrogen bonds and centred at (12, n + 21, 0) (n = zero or
integer) alternate with R44(16) rings containing NÐHÁ Á ÁO and
Figure 2
The molecular components of (II), showing the atom-labelling scheme.
Displacement ellipsoids are drawn at the 30% probability level.
Figure 4
A stereoview of part of the crystal structure of (I), showing the formation
of a chain of edge-fused rings along [100]. For clarity, H atoms not
involved in the motifs shown have been omitted.
Figure 3
Figure 5
The two independent molecules of (III), showing the atom-labelling
schemes for (a) molecule 1 and (b) molecule 2. Displacement ellipsoids
are drawn at the 30% probability level.
A stereoview of part of the crystal structure of (II), showing the
formation of a chain of edge-fused rings along [010]. For clarity, H atoms
bonded to C atoms have been omitted.
ꢁ
Acta Cryst. (2005). C61, o204±o208
de Souza et al.
Three isomers of C12H8ClN3O3 o205

organic compounds
OÐHÁ Á ÁN hydrogen bonds and centred at (12, n, 0) (n = zero or
integer) (Fig. 5).
Experimental
For the synthesis of each of compounds (I)±(III), a solution of
2-chloronicotinoyl chloride (5.68 mmol), the appropriate nitroaniline
(5.78 mmol) and triethylamine (12 mmol) in anhydrous tetrahydro-
furan (30 ml) was stirred at ambient temperature for 8 h; water
(20 ml) and ethyl acetate (20 ml) were added, and the organic layer
was separated. This was washed with a saturated aqueous Na(HCO3)
solution (2 Â 20 ml), dried over sodium sulfate and the solvent
removed. The resulting solids were puri®ed by chromatography on
alumina, with ethyl acetate and hexane (7:3 v/v) as eluant.
Compounds (I) and (II) were recrystallized from acetone [m.p. 430±
432 and 428±429 K (darkens at 407 K)], while compound (III) was
recrystallized from ethanol (m.p. 479±481 K).
The hydrogen-bonded chains in compound (II) are linked
by three distinct aromatic ꢀ±ꢀ stacking interactions, all of
them centrosymmetric but some of them fairly weak, into a
continuous three-dimensional array. The heteroaryl ring in the
molecule at (x, y, z) is parallel to the corresponding ring in the
molecule at ( x, 1 y, z), which itself forms part of the
hydrogen-bonded chain along ( 12, y, 0); the interplanar
Ê
spacing is 3.546 (2) A, with a ring-centroid separation of
Ê
Ê
3.795 (2) A, corresponding to a ring offset of 1.352 (2) A. This
interaction thus links the [010] chains into (001) sheets. In a
similar fashion, the aryl rings of the molecules at (x, y, z) and
(1 x, y, 1 z), where the latter forms part of the
hydrogen-bonded chain along (12, y, 1), are also parallel, with
Compound (I)
Ê
Crystal data
an interplanar spacing of 3.707 (2) A, a ring-centroid separa-
3
Ê
Ê
C12H8ClN3O3
Mr = 277.66
Dx = 1.633 Mg m
Mo Kꢂ radiation
Cell parameters from 2580
re¯ections
tion of 3.917 (2) A and a ring offset of 1.264 (2) A. Finally, the
aryl rings of the molecules at (x, y, z) and ( x, y, 1 z),
which forms part of the hydrogen-bonded chain along ( 12, y,
Monoclinic, P21=c
Ê
a = 6.9964 (1) A
ꢃ = 3.4±27.5ꢀ
ꢄ = 0.35 mm
T = 120 (2) K
Ê
Ê
b = 22.4244 (4) A
1), are also parallel, with an interplanar spacing of 3.384 (2) A,
Ê
a ring-centroid separation of 3.793 (2) A and a ring offset of
Ê
1.715 (2) A. These latter interactions connect the (001) sheets,
so linking all of the hydrogen-bonded chains into a continuous
framework.
1
Ê
c = 7.2085 (1) A
ꢁ = 93.0910 (11)ꢀ
3
Ê
V = 1129.30 (3) A
Z = 4
Block, colourless
0.54 Â 0.44 Â 0.36 mm
Data collection
The two independent molecules in (III) are linked into
simple chains by two NÐHÁ Á ÁN hydrogen bonds (Table 6).
Amide atom N21 acts as a hydrogen-bond donor to ring atom
N31 within the asymmetric unit; similarly, amide atom N41 at
(x, y, z) acts as a donor to ring atom N11 at ( 1 + x, y, z), so
generating by translation a C22(12) chain running parallel to
the [100] direction (Fig. 6). There are number of short CÐ
HÁ Á ÁO contacts within this chain (Table 6), although it is
doubtful if any of them could be regarded as a hydrogen bond;
it is likely that these contacts are simply adventitious conse-
quences of the NÐHÁ Á ÁN hydrogen bonds. Two C22(12) chains,
antiparallel to one another, pass through each unit cell, but
there are no direction-speci®c interactions between adjacent
chains.
Nonius KappaCCD diffractometer
' and ! scans
2355 re¯ections with I > 2ꢅ(I)
Rint = 0.029
Absorption correction: multi-scan
(SADABS; Sheldrick, 2003)
Tmin = 0.835, Tmax = 0.886
13 129 measured re¯ections
2580 independent re¯ections
ꢃmax = 27.5ꢀ
h = 9 ! 9
k = 29 ! 28
l = 9 ! 9
Re®nement
Re®nement on F2
R[F2 > 2ꢅ(F2)] = 0.038
wR(F2) = 0.104
S = 1.19
2580 re¯ections
w = 1/[ꢅ2(F2o) + (0.0562P)2
+ 0.4042P]
where P = (F2o + 2Fc2)/3
(Á/ꢅ)max = 0.001
3
Ê
Áꢆmax = 0.57 e A
Áꢆmin
3
Ê
0.47 e A
174 parameters
H-atom parameters constrained
=
Extinction correction: SHELXL97
Extinction coef®cient: 0.078 (6)
It is thus striking that modest changes in the geometric
position of a single substituent are associated with signi®cant
changes in crystallization characteristics, in the direction-
speci®c intermolecular interactions manifested and hence in
the overall supramolecular structures; none of these changes is
readily predictable.
Table 1
Selected geometric parameters (A, ) for (I).
ꢀ
Ê
N21ÐC21
1.4052 (17)
114.40 (12)
C22ÐN22
1.4618 (18)
127.03 (12)
N21ÐC17ÐC13
C17ÐN21ÐC21
C12ÐC13ÐC17ÐN21
C13ÐC17ÐN21ÐC21
62.93 (18)
178.88 (13)
C17ÐN21ÐC21ÐC22
C21ÐC22ÐN22ÐO2
157.61 (14)
15.1 (2)
Table 2
Hydrogen-bond parameters and short intramolecular contacts (A,
for (I).
ꢀ
Ê
)
DÐHÁ Á ÁA
DÐH
HÁ Á ÁA
DÁ Á ÁA
DÐHÁ Á ÁA
N21ÐH21Á Á ÁO2
C14ÐH14Á Á ÁO2i
C25ÐH25Á Á ÁO1ii
C26ÐH26Á Á ÁO1
0.88
0.95
0.95
0.95
2.01
2.49
2.53
2.30
2.6416 (16)
3.4084 (17)
3.2921 (18)
2.8771 (18)
128
162
137
119
Figure 6
A stereoview of part of the crystal structure of (III), showing the
formation of a C22(12) chain along [100]. For clarity, H atoms bonded to C
atoms have been omitted.
Symmetry codes: (i) x 1; y; z; (ii) x; y ‡ 1; z ‡ 1.
Acta Cryst. (2005). C61, o204±o208
ꢁ
o206 de Souza et al. Three isomers of C12H8ClN3O3

organic compounds
Table 3
Selected geometric parameters (A, ) for (II).
Table 5
Selected geometric parameters (A, ) for (III).
ꢀ
ꢀ
Ê
Ê
N21ÐC21
1.4122 (18)
114.31 (13)
C23ÐN23
1.465 (2)
N21ÐC21
C24ÐN24
1.410 (3)
1.467 (3)
N41ÐC41
C44ÐN44
1.412 (3)
1.471 (3)
N21ÐC17ÐC13
C17ÐN21ÐC21
127.89 (13)
N21ÐC17ÐC13
C17ÐN21ÐC21
114.8 (2)
127.75 (19)
N41ÐC37ÐC33
C37ÐN41ÐC41
114.6 (2)
127.63 (19)
C12ÐC13ÐC17ÐN21
C13ÐC17ÐN21ÐC21
123.99 (17)
174.38 (15)
C17ÐN21ÐC21ÐC22
C22ÐC23ÐN23ÐO2
178.35 (16)
3.2 (2)
C12ÐC13ÐC17ÐN21
C13ÐC17ÐN21ÐC21
C17ÐN21ÐC21ÐC22
C25ÐC24ÐN24ÐO13
78.1 (3)
173.29 (19)
179.8 (2)
8.1 (3)
C32ÐC33ÐC37ÐN41
C33ÐC37ÐN41ÐC41
C37ÐN41ÐC41ÐC42
C43ÐC44ÐN44ÐO22
71.5 (3)
173.4 (2)
173.6 (2)
5.2 (3)
Table 4
Hydrogen-bond parameters and short intramolecular contacts (A,
for (II).
ꢀ
Ê
)
DÐHÁ Á ÁA
DÐH
HÁ Á ÁA
DÁ Á ÁA
DÐHÁ Á ÁA
Table 6
Hydrogen-bond parameters and short intramolecular contacts (A,
for (III).
ꢀ
N21ÐH21Á Á ÁO4iii
O4ÐH41Á Á ÁO1
O4ÐH42Á Á ÁN11iv
C26ÐH26Á Á ÁO1
0.88
0.85
0.88
0.95
2.03
2.07
2.06
2.25
2.907 (2)
2.916 (2)
2.935 (2)
2.864 (2)
173
173
170
121
Ê
)
DÐHÁ Á ÁA
DÐH
HÁ Á ÁA
DÁ Á ÁA
DÐHÁ Á ÁA
Symmetry codes: (iii) x; y 1; z; (iv) x ‡ 1; y ‡ 1; z.
N21ÐH21Á Á ÁN31
N41ÐH41Á Á ÁN11i
C22ÐH22Á Á ÁO11i
C23ÐH23Á Á ÁO11i
C26ÐH26Á Á ÁO11
C43ÐH43Á Á ÁO21i
C46ÐH46Á Á ÁO21
0.92
0.95
0.95
0.95
0.95
0.95
0.95
2.08
2.14
2.58
2.37
2.25
2.57
2.27
2.999 (3)
3.067 (3)
3.117 (3)
3.011 (3)
2.861 (3)
3.166 (3)
2.874 (3)
178
164
116
124
121
121
121
Compound (II)
Crystal data
C12H8ClN3O3ÁH2O
Z = 2
Dx = 1.547 Mg m
Mo Kꢂ radiation
Cell parameters from 2891
re¯ections
ꢃ = 3.3±27.6ꢀ
ꢄ = 0.32 mm
T = 120 (2) K
Block, colourless
0.2 Â 0.2 Â 0.2 mm
Symmetry code: (i) x 1; y; z.
3
Mr = 295.68
Triclinic, P1
a = 7.5607 (4) A
Ê
Ê
b = 7.6518 (3) A
Data collection
Ê
c = 12.6775 (5) A
1
ꢂ = 81.177 (3)ꢀ
ꢁ = 84.367 (2)ꢀ
ꢇ = 61.172 (2)ꢀ
Nonius KappaCCD diffractometer
' and ! scans
3366 re¯ections with I > 2ꢅ(I)
Rint = 0.079
Absorption correction: multi-scan
(SADABS; Sheldrick, 2003)
Tmin = 0.945, Tmax = 0.968
5494 measured re¯ections
5494 independent re¯ections
ꢃmax = 27.6ꢀ
3
Ê
h = 9 ! 9
V = 634.69 (5) A
k = 31 ! 30
l = 17 ! 17
Data collection
Nonius KappaCCD diffractometer
' and ! scans
2318 re¯ections with I > 2ꢅ(I)
Rint = 0.028
ꢃmax = 27.6ꢀ
Re®nement
Absorption correction: multi-scan
(SADABS; Sheldrick, 2003)
Tmin = 0.926, Tmax = 0.938
12 769 measured re¯ections
2891 independent re¯ections
Re®nement on F2
R[F2 > 2ꢅ(F2)] = 0.051
wR(F2) = 0.143
S = 1.00
5494 re¯ections
w = 1/[ꢅ2(Fo2) + (0.073P)2]
h = 9 ! 9
2
where P = (Fo + 2Fc2)/3
k = 9 ! 9
(Á/ꢅ)max = 0.001
l = 16 ! 16
3
Ê
Áꢆmax = 0.29 e A
3
Ê
0.44 e A
Áꢆmin
=
Re®nement
343 parameters
H-atom parameters constrained
Re®nement on F2
R[F2 > 2ꢅ(F2)] = 0.044
wR(F2) = 0.129
S = 1.08
2891 re¯ections
w = 1/[ꢅ2(F2o) + (0.074P)2
+ 0.1161P]
where P = (F2o + 2Fc2)/3
(Á/ꢅ)max < 0.001
For isomers (I) and (III), the space groups P21/c and P21/n were
uniquely assigned from the systematic absences. Crystals of
compound (II) are triclinic; space group P1 was selected and
con®rmed by the successful structure analysis. All H atoms were
located from difference maps. H atoms bonded to C atoms were
3
Ê
Áꢆmax = 0.27 e A
3
Ê
0.43 e A
183 parameters
H-atom parameters constrained
Áꢆmin
=
Ê
treated as riding atoms, with CÐH distances of 0.95 A and Uiso(H)
Compound (III)
values of 1.2Ueq(C). H atoms bonded to N atoms were allowed to ride
at the positions located from the difference maps, with NÐH
Ê
distances of 0.88±0.95 A and Uiso(H) values of 1.2Ueq(N). H atoms
Crystal data
C12H8ClN3O3
Mr = 277.66
Mo Kꢂ radiation
Cell parameters from 5494
re¯ections
bonded to atom O4 in (II) were allowed to ride at the positions
located from the difference maps, with OÐH distances of 0.85 and
Ê
0.88 A and individual isotropic displacement parameters.
Monoclinic, P21=n
a = 7.2385 (2) A
ꢃ = 2.9±27.6ꢀ
Ê
1
Ê
b = 24.5094 (6) A
ꢄ = 0.33 mm
T = 120 (2) K
For all compounds, data collection: COLLECT (Hooft, 1999); cell
re®nement: DENZO (Otwinowski & Minor, 1997) and COLLECT;
data reduction: DENZO and COLLECT; structure solution:
OSCAIL (McArdle, 2003) and SHELXS97 (Sheldrick, 1997); struc-
ture re®nement: OSCAIL and SHELXL97 (Sheldrick, 1997); mol-
Ê
c = 13.5018 (4) A
ꢁ = 92.834 (2)ꢀ
V = 2392.44 (11) A
Block, colourless
0.2 Â 0.1 Â 0.1 mm
3
Ê
Z = 8
Dx = 1.542 Mg m
3
ꢁ
Acta Cryst. (2005). C61, o204±o208
de Souza et al.
Three isomers of C12H8ClN3O3 o207

organic compounds
ecular graphics: PLATON (Spek, 2003); software used to prepare
material for publication: SHELXL97 and PRPKAPPA (Ferguson,
1999).
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X-ray data were collected at the EPSRC X-ray Crystal-
lographic Service, University of Southampton, England; the
authors thank the staff for all their help and advice. JLW
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Supplementary data for this paper are available from the IUCr electronic
archives (Reference: SK1812). Services for accessing these data are
described at the back of the journal.
ꢁ
o208 de Souza et al. Three isomers of C12H8ClN3O3
Acta Cryst. (2005). C61, o204±o208