Hydrogen-bonded chains of rings in methyl 4-[(5-methyl-1H-pyrazol-3-yl) amino]-3-nitrobenzoate and hydrogen-bonded sheets in methyl 1-(5-methyl-1H- pyrazol-3-yl)-1H-benzimidazole-5-carboxylate

Article abstract of DOI:10.1107/S0108270106044611

Molecules of methyl 4-[(5-methyl-1H-pyrazol-3-yl)amino]-3-nitrobenzoate, C₁₂H₁₂N₄O₄, (I), exhibit a polarized (charge-separated) structure in the nitroaniline portion. The molecules are linked into chains of edg

Full text of DOI:10.1107/S0108270106044611

organic compounds
Acta Crystallographica Section C
Crystal Structure
report here the molecular and supramolecular structures of
compounds (I) and (II).
Communications
ISSN 0108-2701
Hydrogen-bonded chains of rings
in methyl 4-[(5-methyl-1H-pyrazol-
3-yl)amino]-3-nitrobenzoate and
hydrogen-bonded sheets in methyl
1-(5-methyl-1H-pyrazol-3-yl)-1H-
benzimidazole-5-carboxylate
Jaime Portilla,a Ernesto G. Mata,b Manuel Nogueras,c
Justo Cobo,c John N. Lowd and Christopher Glidewelle*
a
Â
Departamento de Quõmica, Universidad de Valle, AA 25360 Cali, Colombia,
b
Â
Â
CONICET±Facultad de Ciencias Bioquõmicas y Farmaceuticas, Universidad
Nacional de Rosario, Rosario, Suipacha 531, S2002LRK, Argentina, cDepartamento
Â
Â
Â
Â
Â
de Quõmica Inorganica y Organica, Universidad de Jaen, 23071 Jaen, Spain,
dDepartment of Chemistry, University of Aberdeen, Meston Walk, Old Aberdeen
AB24 3UE, Scotland, and eSchool of Chemistry, University of St Andrews, Fife
KY16 9ST, Scotland
Correspondence e-mail: cg@st-andrews.ac.uk
Received 3 October 2006
Accepted 25 October 2006
Online 12 December 2006
Molecules of methyl 4-[(5-methyl-1H-pyrazol-3-yl)amino]-3-
nitrobenzoate, C12H12N4O4, (I), exhibit a polarized (charge-
separated) structure in the nitroaniline portion. The molecules
are linked into chains of edge-fused R22(16) and R22(22) rings by
a combination of NÐHÁ Á ÁO(carbonyl) and CÐHÁ Á ÁO(nitro)
hydrogen bonds. Methyl 1-(5-methyl-1H-pyrazol-3-yl)-1H-
benzimidazole-5-carboxylate, C13H12N4O2, (II), which is
readily formed from (I) by reduction followed by ring
formation, crystallizes with Z0 = 2 in the space group P1.
Each of the two independent molecular types is linked into
sheets of R44(28) rings by a combination of NÐHÁ Á ÁN and CÐ
HÁ Á ÁO(carbonyl) hydrogen bonds.
The molecule of compound (I) (Fig. 1) is almost planar, as
shown by the key torsion angles (Table 1), and this is possibly
in¯uenced by the intramolecular hydrogen bond (Table 2).
Within the aryl ring, the C1ÐC2 and C5ÐC6 bonds are
signi®cantly shorter than the remainder. In addition, the C3Ð
N3 bond is short for its type (Allen et al., 1987), while the NÐ
O bonds are both long, and the C4ÐN45 bond is signi®cantly
shorter than N45ÐC45. These observations indicate that the
charge-separated form (Ia) (see scheme) is a signi®cant
contributor to the overall molecular electronic structure.
Compound (II) crystallizes with Z0 = 2, and the molecular
geometries of the two independent molecules (Fig. 2) are very
similar. As for compound (I), the molecules of (II) are almost
planar. The dihedral angle between the pyrazole and imida-
zole rings is 5.5 (2)ꢀ in molecule A (containing N11) and
5.9 (2)ꢀ in molecule B (containing N31). There is marked bond
®xation in the imidazole rings (Table 3), with only a modest
variation in the CÐC distances in the aryl rings, indicating that
Comment
As part of our continuing study of biologically active mol-
ecules containing fused pyrazole systems, we have attempted
the preparation of pyrazolo[1,5-a][1,3,5]benzotriazepine,
which is useful for drug, agrochemical or dye intermediates
(Tachibana & Kaneko, 1989), by means of a simple three-step
procedure from 3-amino-5-methyl-1H-pyrazole and methyl
4-¯uoro-3-nitrobenzoate. However, the ®rst step of that
procedure in fact provided not the anticipated compound,
(III) (see scheme), but instead the isomeric compound, methyl
4-[(5-methyl-1H-pyrazol-3-yl)amino]-3-nitrobenzoate, (I),
which afforded methyl 1-(5-methyl-1H-pyrazol-3-yl)-1H-
benzimidazole-5-carboxylate, (II), as the ®nal product instead
of the expected pyrazolo[1,5-a][1,3,5]benzotriazepine. We
o38 # 2007 International Union of Crystallography
DOI: 10.1107/S0108270106044611
Acta Cryst. (2007). C63, o38±o41

organic compounds
the form shown in the scheme is the appropriate representa-
tion for this compound.
1
z), so generating by inversion an R22(22) (Bernstein et al.,
1995) ring centred at (21, 21, 12), and atom C44 at (x, y, z) acts as
hydrogen-bond donor to nitro atom O31 in the molecule at
The molecules of compound (I) are linked into chains of
edge-fused rings by a combination of NÐHÁ Á ÁO(carbonyl)
and CÐHÁ Á ÁO(nitro) hydrogen bonds (Table 2). Pyrazole
atom N42 in the molecule at (x, y, z) acts as hydrogen-bond
donor to carbonyl atom O11 in the molecule at (1 x, 1 y,
Figure 1
Figure 3
The molecular structure of compound (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.
A stereoview of part of the crystal structure of compound (I), showing the
formation of a chain of edge-fused R22(16) and R22(22) rings along [101].
For the sake of clarity, H atoms not involved in the motifs shown have
been omitted.
Figure 2
Figure 4
The two independent molecules in compound (II), viz. (a) a type A
molecule and (b) a type B molecule. Displacement ellipsoids are drawn at
the 30% probability level and H atoms are shown as small spheres of
arbitrary radii.
Stereoviews of parts of the crystal structure of compound (II), showing
the formation of sheets of R44(28) rings parallel to (001) for (a) a sheet of
type A molecules and (b) a sheet of type B molecules. For the sake of
clarity, H atoms not involved in the motifs shown have been omitted.
ꢁ
Acta Cryst. (2007). C63, o38±o41
Portilla et al. C12H12N4O4 and C13H12N4O2 o39

organic compounds
Compound (I)
( x, 1 y, z), so generating a second centrosymmetric ring,
this time of R22(16) type and centred at (0, , 0). The combi-
1
2
Crystal data
nation of these two motifs generates a chain of edge-fused
rings running parallel to the [101] direction, with R22(16) rings
centred at (n, 12, n) (n = zero or integer) alternating with R22(22)
3
Ê
V = 611.51 (6) A
C12H12N4O4
Mr = 276.26
Triclinic, P1
a = 5.9233 (3) A
Ê
b = 8.8858 (6) A
Z = 2
Dx = 1.500 Mg m
Mo Kꢀ radiation
3
Ê
1
1
1
rings centred at (n + , , n + ) (n = zero or integer) (Fig. 3).
2
2
2
1
ꢃ = 0.12 mm
T = 120 (2) K
Within the R22(16) ring, there is a short contact between the
Ê
c = 11.7819 (6) A
Ê
two atoms of type O32, separated by only 2.875 (2) A.
ꢀ = 85.690 (4)ꢀ
ꢁ = 83.500 (4)ꢀ
ꢂ = 84.015 (3)ꢀ
Lath, orange
0.42 Â 0.26 Â 0.15 mm
In the crystal structure of compound (II), there are two
virtually identical substructures, each containing only one of
the two independent molecules and each built from a
combination of NÐHÁ Á ÁN and CÐHÁ Á ÁO(carbonyl) hydrogen
bonds (Table 4). Atoms N12 and C14 in the type A molecule at
(x, y, z) act as hydrogen-bond donors to, respectively, imid-
azole atom N23 in the type A molecule at ( 1 + x, y, z) and
carbonyl atom O251 in the type A molecule at (x, 1 + y, z), so
generating by translation an almost planar sheet parallel to
(001) in the domain 0.05 < z < 0.20 and containing a single
R44(28) ring (Fig. 4a). This sheet lies in the domain 0.05 < z <
0.20, with an inversion-related sheet of type A molecules in the
domain 0.80 < z < 0.95. A very similar sheet is built from type
B molecules (Fig. 4b and Table 4), and inversion-related pairs
of type B sheets lie in the domains 0.36 < z < 0.43 and 0.57 < z
< 0.64. Thus, the overall structure consists of a millefeuille-
style stack of almost planar sheets, with pairs of sheets of type
A molecules alternating with pairs of type B molecules.
However, there are no direction-speci®c interactions between
adjacent sheets. The only stacking contacts between adjacent
sheets all involve the imidazole rings. They exhibit very strong
bond ®xation and hence are non-aromatic, so that such
contacts are unlikely to be energetically and hence structurally
signi®cant.
Data collection
Bruker±Nonius KappaCCD area-
detector diffractometer
' and ! scans
Absorption correction: multi-scan
(SADABS; Sheldrick, 2003)
Tmin = 0.959, Tmax = 0.983
12027 measured re¯ections
2829 independent re¯ections
2117 re¯ections with I > 2ꢄ(I)
Rint = 0.055
ꢅmax = 27.7ꢀ
Re®nement
Re®nement on F2
R[F2 > 2ꢄ(F2)] = 0.046
wR(F2) = 0.128
S = 1.06
2829 re¯ections
w = 1/[ꢄ2(Fo2) + (0.0711P)2
+ 0.097P]
2
where P = (Fo + 2Fc2)/3
(Á/ꢄ)max < 0.001
3
Ê
Áꢆmax = 0.31 e A
3
Ê
0.33 e A
183 parameters
H-atom parameters constrained
Áꢆmin
=
Table 1
Selected geometric parameters (A, ) for (I).
ꢀ
Ê
C1ÐC2
C2ÐC3
C3ÐC4
C4ÐC5
C5ÐC6
1.378 (2)
1.391 (2)
1.420 (2)
1.426 (2)
1.367 (2)
C6ÐC1
1.408 (2)
C3ÐN3
N3ÐO31
N3ÐO32
C4ÐN45
1.4512 (18)
1.2337 (16)
1.2423 (16)
1.3556 (18)
C2ÐC1ÐC11ÐO12
C1ÐC11ÐO12ÐC12
2.0 (2)
178.75 (12)
C2ÐC3ÐN3ÐO31
C4ÐN45ÐC45ÐN41
3.7 (2)
6.5 (2)
Experimental
For the synthesis of compound (I), a solution of 3-amino-5-methyl-
1H-pyrazole (2 mmol) and methyl 4-¯uoro-3-nitrobenzoate (2 mmol)
in dimethyl sulfoxide (2 ml) was stirred at 298 K for 2 h. The resulting
solid product was collected by ®ltration and washed with methanol
(10 ml) to give methyl 4-[(5-methyl-1H-pyrazol-3-yl)amino]-3-nitro-
benzoate, (I). Crystallization of the compound from dimethyl
sulfoxide gave orange crystals suitable for single-crystal X-ray
diffraction (m.p. 498±499 K; yield 93%). MS (m/z, %): 276 (100, M+),
245 (12). For the synthesis of compound (II), a mixture of compound
(I) (1 mmol), hydrazine hydrate (3 mmol) and Raney Nickel (50 mg)
in methanol (10 ml) was heated under re¯ux with magnetic stirring
for 15 min. The Raney Nickel was removed by ®ltration of the hot
solution and the ®ltrate was then cooled. The resulting solid was
collected by ®ltration and recrystallized from methanol to yield the
intermediate methyl 3-amino-4-[(5-methyl-1H-pyrazol-3-yl)amino]-
benzoate as a white solid (m.p. 483±484 K; yield 92%). MS (m/z, %):
246 (33, M+), 215 (100). A mixture of this intermediate (1 mmol) and
trimethyl orthoformate (3 ml) was heated under re¯ux with magnetic
stirring for 1 h. The mixture was then cooled and the resulting solid
product was collected by ®ltration and recrystallized from dimethyl
sulfoxide to yield compound (II) as colourless crystals suitable for
single-crystal X-ray diffraction (m.p. 518±519 K; yield 90%). MS
(m/z, %): 256 (93, M+), 225 (100), 197 (24).
Table 2
Hydrogen-bond geometry (A, ) for (I).
ꢀ
Ê
DÐHÁ Á ÁA
DÐH
HÁ Á ÁA
DÁ Á ÁA
DÐHÁ Á ÁA
N45ÐH45Á Á ÁO32
N42ÐH42Á Á ÁO11i
C44ÐH44Á Á ÁO31ii
0.88
0.88
0.95
1.92
1.98
2.49
2.6221 (16)
2.8400 (17)
3.4180 (18)
136
164
164
Symmetry codes: (i) x ‡ 1; y ‡ 1; z ‡ 1; (ii) x; y ‡ 1; z.
Compound (II)
Crystal data
3
Ê
V = 1197.75 (10) A
Z = 4
Dx = 1.421 Mg m
Mo Kꢀ radiation
ꢃ = 0.10 mm
T = 120 (2) K
Block, colourless
0.46 Â 0.45 Â 0.40 mm
C13H12N4O2
Mr = 256.27
Triclinic, P1
a = 8.3646 (3) A
b = 11.5735 (6) A
3
Ê
1
Ê
Ê
c = 12.7953 (7) A
ꢀ = 88.328 (3)ꢀ
ꢁ = 88.526 (3)ꢀ
ꢂ = 75.362 (3)ꢀ
ꢁ
o40 Portilla et al.
C12H12N4O4 and C13H12N4O2
Acta Cryst. (2007). C63, o38±o41

organic compounds
Data collection
Data collection: COLLECT (Nonius, 1999) for (I); KappaCCD
Server Software (Nonius, 1997) for (II). Cell re®nement: DENZO
(Otwinowski & Minor, 1997) and COLLECT for (I); DENZO±SMN
for (II). Data reduction: DENZO and COLLECT for (I); DENZO±
SMN for (II). Program(s) used to solve structure: OSCAIL
(McArdle, 2003) and SHELXS97 (Sheldrick, 1997) for (I);
SHELXS97 for (II). Program(s) used to re®ne structure: OSCAIL
and SHELXL97 (Sheldrick, 1997) for (I); SHELXL97 for (II). For
both compounds, molecular graphics: PLATON (Spek, 2003); soft-
ware used to prepare material for publication: SHELXL97 and
PRPKAPPA (Ferguson, 1999).
Bruker±Nonius KappaCCD area-
detector diffractometer
' and ! scans
Absorption correction: multi-scan
(SADABS; Sheldrick, 2003)
Tmin = 0.945, Tmax = 0.961
25906 measured re¯ections
5488 independent re¯ections
3945 re¯ections with I > 2ꢄ(I)
Rint = 0.051
ꢅmax = 27.7ꢀ
Re®nement
Re®nement on F2
R[F2 > 2ꢄ(F2)] = 0.068
wR(F2) = 0.173
S = 1.20
5488 re¯ections
w = 1/[ꢄ2(Fo2) + (0.0417P)2
+ 1.6885P]
where P = (Fo2 + 2Fc2)/3
(Á/ꢄ)max < 0.001
3
Ê
Áꢆmax = 0.38 e A
The X-ray data were collected at the EPSRC National
Crystallography Service, University of Southampton,
England; the authors thank the staff for all their help and
3
Ê
0.33 e A
347 parameters
H-atom parameters constrained
Áꢆmin
=
Â
Â
advice. MN and JC thank the Consejerõa de innovadõon,
Â
Ciencia y Empresa (Junta de Andalucõa, Spain) and the
Table 3
Selected geometric parameters (A, ) for (II).
ꢀ
Ê
Â
Universidad de Jaen for ®nancial support. JP thanks
N21ÐC22
C22ÐN23
N23ÐC23A
C23AÐC27A
C27AÐN21
1.385 (3)
1.301 (3)
1.392 (3)
1.400 (4)
1.393 (3)
N41ÐC42
C42ÐN43
N43ÐC43A
C43AÐC47A
C47AÐN41
1.380 (3)
1.295 (3)
1.395 (3)
1.398 (4)
1.395 (3)
COLCIENCIAS and UNIVALLE (Universidad del Valle,
Colombia) for ®nancial support that has also supported a
short stay at Instituto de Quõmica Organica de Sõntesis,
Universidad Nacional de Rosario. EGM thanks CONICET
and Universidad Nacional de Rosario for ®nancial support.
Â
Â
Â
N11ÐC15ÐN21ÐC22
C24ÐC25ÐC251ÐO252
C25ÐC251ÐO252ÐC252 177.1 (2)
173.5 (2)
15.7 (4)
N31ÐC35ÐN41ÐC42
C44ÐC45ÐC451ÐO452
C45ÐC451ÐO452ÐC452 177.1 (2)
173.1 (2)
14.2 (4)
Supplementary data for this paper are available from the IUCr electronic
archives (Reference: SQ3044). Services for accessing these data are
described at the back of the journal.
Table 4
Hydrogen-bond geometry (A, ) for (II).
ꢀ
Ê
References
Allen, F. H., Kennard, O., Watson, D. G., Brammer, L., Orpen, A. G. & Taylor,
R. (1987). J. Chem. Soc. Perkin Trans. 2, pp. S1±19.
Bernstein, J., Davis, R. E., Shimoni, L. & Chang, N.-L. (1995). Angew. Chem.
Int. Ed. Engl. 34, 1555±1573.
Ferguson, G. (1999). PRPKAPPA. University of Guelph, Canada.
McArdle, P. (2003). OSCAIL for Windows. Version 10. Crystallography
Centre, Chemistry Department, NUI Galway, Ireland.
Nonius (1997). KappaCCD Server Software. Windows 3.11 Version. Nonius
BV, Delft, The Netherlands.
DÐHÁ Á ÁA
DÐH
HÁ Á ÁA
DÁ Á ÁA
DÐHÁ Á ÁA
N12ÐH12Á Á ÁN23i
N32ÐH32Á Á ÁN43ii
C14ÐH14Á Á ÁO251iii
C34ÐH34Á Á ÁO451iv
0.96
0.96
0.95
0.95
1.88
1.88
2.46
2.45
2.836 (4)
2.840 (4)
3.269 (3)
3.248 (3)
173
174
143
141
Symmetry codes: (i) x 1; y; z; (ii) x ‡ 1; y; z; (iii) x; y 1; z; (iv) x; y ‡ 1; z.
Nonius (1999). COLLECT. Nonius BV, Delft, The Netherlands.
Otwinowski, Z. & Minor, W. (1997). Methods in Enzymology, Vol. 276,
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Sweet, pp. 307±326. New York: Academic Press.
Crystals of both (I) and (II) are triclinic. For each compound, the
space group P1 was selected and con®rmed by the successful struc-
ture re®nement. All H atoms were located in difference maps and
then treated as riding atoms. For H atoms bonded to C atoms, CÐH =
Sheldrick, G. M. (1997). SHELXS97 and SHELXL97. University of
È
Gottingen, Germany.
Ê
0.95 A and Uiso(H) = 1.2Ueq(C) for aromatic and heteroaromatic H
Ê
atoms or CÐH = 0.98 A and Uiso(H) = 1.5Ueq(C) for methyl H atoms.
H atoms bonded to N atoms were permitted to ride at the NÐH
Sheldrick, G. M. (2003). SADABS. Version 2.10. University of GoÈttingen,
Germany.
Spek, A. L. (2003). J. Appl. Cryst. 36, 7±13.
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01003187 A2, Jpn Patent Application 87-159281, 1987; Chem. Abstr. (1989),
111, 97297.
Ê
distances deduced from the difference maps [0.88 A in (I) and 0.96 A
Ê
in (II)], with Uiso(H) = 1.2Ueq(N).
ꢁ
Acta Cryst. (2007). C63, o38±o41
Portilla et al. C12H12N4O4 and C13H12N4O2 o41