A three-dimensional hydrogen-bonded framework in 2-amino-6-(N- methylanilino)pyrimidin-4(3H)-one and a ribbon of fused hydrogen-bonded rings in 2-amino-6-(N-methylanilino)-5-nitropyrimidin-4(3H)-one

Article abstract of DOI:10.1107/S0108270107049931

The mol-ecular dimensions of both 2-amino-6-(N-methyl-anilino)pyrimidin- 4(3H)-one, C11H12N4O, (I), and 2-amino-6-(N-methyl-anilino)-5-nitro-pyrimidin- 4(3H)-one, C11H11N5O3, (II), are consistent with considerable polarization of the mol-ecular-electronic structures. The mol-ecules of (I) are linked into a three-dimensional framework by a combination of one N - H...N hydrogen bond, two independent N - H...O hydrogen bonds and one C - H...π(arene) hydrogen bond. The mol-ecules of (II) are linked into ribbons containing three types of edge-fused ring by the combination of two independent three-centre N - H...(O)2 hydrogen bonds. International Union of Crystallography 2007.

Full text of DOI:10.1107/S0108270107049931

organic compounds
Acta Crystallographica Section C
Crystal Structure
Communications
In compounds (I) and (II) (Figs. 1 and 2), the coordination
at N6 is planar and the methyl atom C67 and the ipso atom of
the phenyl ring, atom C61, are very close to the plane of the
ISSN 0108-2701
A three-dimensional hydrogen-bonded
framework in 2-amino-6-(N-methyl-
anilino)pyrimidin-4(3H)-one and a
ribbon of fused hydrogen-bonded
rings in 2-amino-6-(N-methylanilino)-
5-nitropyrimidin-4(3H)-one
a
a
a
Â
Ricaurte Rodrõguez, ³ Justo Cobo, Manuel Nogueras,
John N. Lowb and Christopher Glidewellc*
a
Â
Â
Â
Â
Departamento de Quõmica Inorganica y Organica, Universidad de Jaen, 23071
Jaen, Spain, bDepartment of Chemistry, University of Aberdeen, Meston Walk, Old
Â
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 10 October 2007
Accepted 11 October 2007
Online 14 November 2007
The molecular dimensions of both 2-amino-6-(N-methyl-
anilino)pyrimidin-4(3H)-one, C11H12N4O, (I), and 2-amino-6-
(N-methylanilino)-5-nitropyrimidin-4(3H)-one, C11H11N5O3,
(II), are consistent with considerable polarization of the
molecular±electronic structures. The molecules of (I) are
linked into a three-dimensional framework by a combination
of one NÐHÁ Á ÁN hydrogen bond, two independent NÐ
HÁ Á ÁO hydrogen bonds and one CÐHÁ Á Áꢀ(arene) hydrogen
bond. The molecules of (II) are linked into ribbons containing
three types of edge-fused ring by the combination of two
independent three-centre NÐHÁ Á Á(O)2 hydrogen bonds.
pyrimidine ring, as indicated by the relevant torsion angles
(Table 3). On the other hand, the planes of the phenyl group in
each compound are well removed from the pyrimidine planes
with dihedral angles between these two planes of 70.1 (2)ꢀ in
(I) and 58.9 (2)ꢀ in (II). In (II), the dihedral angle between the
CNO2 unit and the pyrimidine ring is 47.4 (2)ꢀ.
Comment
As part of a wide-ranging investigation of biologically active
heterocyclic compounds, we have initiated a study of pyri-
mido[4,5-b][1,4]benzodiazepine derivatives that are analogous
to the well known benzodiazepine derivatives and which show
related pharmacological properties, such as anti-anxiety or
antidepressive activity (Dlugosz & Machon, 1990), as well as
being candidates as effective anti-HIV-1 inhibitors (Di Braccio
et al., 2001). We report here the molecular and supramolecular
structures of two compounds, 2-amino-6-(N-methylanilino)-
pyrimidin-4(3H)-one, (I), and 2-amino-6-(N-methylanilino)-5-
nitropyrimidin-4(3H)-one, (II), which were prepared, from the
commercially available pyrimidines, (III) and (IV), respec-
tively, for use as intermediates for the syntheses of
pyrimido[4,5-b][1,4]benzodiazepines, (V).
The molecules in each compound exhibit some unusual
bond distances, which are indicative of polarized molecular±
electronic structures. In compound (I), the C4ÐC5 and C5Ð
C6 distances are identical within experimental uncertainty,
although in the conventional representation these bonds are,
respectively, single and double bonds. In addition, the CÐO
bond is long for its type (Allen et al., 1987), while the C6ÐN6
bond is short. These data together indicate that the polarized
form (Ia) may be a signi®cant contributor to the overall
³ Permanent address: Universidad Nacional de Colombia, Department of
Â
Chemistry, Bogota, AA 14490, Colombia.
Acta Cryst. (2007). C63, o697±o700
DOI: 10.1107/S0108270107049931
# 2007 International Union of Crystallography o697

organic compounds
molecular±electronic structure of this compound, in addition
to the unpolarized form (I).
Despite the large dihedral angle between the pyrimidine
and nitro-group planes in (II), the C5ÐN5 bond is rather short
The molecules of (I) are linked into sheets by three
hydrogen bonds, one of NÐHÁ Á ÁN type and two of NÐHÁ Á ÁO
type (Table 1). It is convenient to consider a centrosymmetric
dimer unit, formed by paired NÐHÁ Á ÁO hydrogen bonds, as
the basic building block forming the sheet. Ring atom N3 in
the molecule at (x, y, z) acts as a donor, in an almost linear
Ê
for its type (mean value 1.486 A; Allen et al., 1987); the C4Ð
O4 bond is signi®cantly shorter in (II) than in (I); and the
N1ÐC2 and C2ÐN2 distances are effectively identical in (II).
These observations indicate that the polarized forms (IIa) and
(IIb) both contribute to the overall molecular±electronic
structure of this compound, in addition to the unpolarized
form (II).
hydrogen bond, to atom O4 in the molecule at (1
1
x, y,
z), so generating by inversion an R22(8) motif (Bernstein et
al., 1995), centred at (12, 0, 21 ). This dimer is linked directly, by
the other two hydrogen bonds, to the four dimers centred at
1
(12, 12, 0), (12, 12, 0), (12, , 1) and (21, 12, 1), and propagation by
2
the space group of these hydrogen bonds then generates a
rather complex sheet parallel to (100) (Fig. 3). Each such sheet
is weakly linked to the two adjacent sheets by a single CÐ
HÁ Á Áꢀ(arene) hydrogen bond (Table 1), so forming a contin-
uous hydrogen-bonded framework structure in three dimen-
sions.
The supramolecular aggregation of (II) is only one-dimen-
sional; despite the presence of the two nitro-group O atoms as
additional sites that are potential hydrogen-bond acceptors,
one of the NÐH bonds of the exocyclic amino group in (II)
plays no part in the hydrogen bonding, and the supra-
molecular aggregation depends entirely on two independent
three-centre NÐHÁ Á Á(O)2 hydrogen-bond systems, both of
them effectively planar (Table 2).
Figure 1
The molecular structure of (I), showing the atom-labelling scheme.
Displacement ellipsoids are drawn at the 30% probability level.
Figure 2
The molecular structure of (II), showing the atom-labelling scheme.
Displacement ellipsoids are drawn at the 30% probability level.
Figure 4
Part of the crystal structure of (II), showing the formation of a hydrogen-
bonded ribbon of edge-fused rings parallel to [100]. For clarity, H atoms
bonded to C atoms have been omitted. Atoms marked with an asterisk
(*), a hash (#), a dollar sign ($) or an ampersand (&) are at the symmetry
positions ( 12 + x, 23 y, 1 z), (21 + x, 32 y, 1 z), (1 + x, y, z) and ( 1 + x,
y, z), respectively.
Figure 3
A stereoview of part of the crystal structure of (I), showing the formation
of a hydrogen-bonded sheet parallel to (100). For clarity, H atoms bonded
to C atoms have been omitted.
ꢁ
Â
o698 Rodrõguez et al. C11H12N4O and C11H11N5O3
Acta Cryst. (2007). C63, o697±o700

organic compounds
Table 1
Hydrogen-bond geometry (A, ) for (I).
Amino atom N2 in the molecule at (x, y, z) acts as a
hydrogen-bond donor, via H2B, to atoms O4 and O51 in the
ꢀ
Ê
1
3
Cg is the centroid of the C61±C66 ring.
molecules at (
+ x,
y, 1
z) and ( 1 + x, y, z),
2
2
respectively. In the second three-centre system, ring atom N3
acts as a hydrogen-bond donor to atoms O4 and O51, both in
the molecule at ( 12 + x, 23 y, 1 z). Hence, two of the NÐH
bonds act as double donors of hydrogen bonds, while the third
NÐH bond does not participate in the hydrogen bonding, and
two of the O atoms act as double acceptors of hydrogen bonds,
while the third O atom does not participate in the hydrogen
bonding. The combination of all these hydrogen bonds
produces a ribbon of edge-fused rings running parallel to the
[100] direction and generated by the 21 screw axis along (x, 34,
12 ) (Fig. 4). The ribbon contains an R12(6) ring where the sole
acceptor is an O4 atom, an R21(6) ring where both hydrogen
bonds involve an H3 atom and an R22(6) ring containing both
O4 and O51 atoms as the acceptors. A second ribbon, running
antiparallel to the reference ribbon, is generated by the 21
DÐHÁ Á ÁA
DÐH
HÁ Á ÁA
DÁ Á ÁA
DÐHÁ Á ÁA
N2ÐH2AÁ Á ÁO4i
N2ÐH2BÁ Á ÁN1ii
N3ÐH3Á Á ÁO4iii
C64ÐH64Á Á ÁCgiv
Symmetry codes: (i) x; y ‡ 12; z 21; (ii) x ‡ 1; y
(iv) x ‡ 2; y ‡ 12; z ‡ 23.
0.88
0.88
0.88
0.95
2.07
2.30
1.94
2.82
2.940 (2)
2.998 (2)
2.818 (2)
3.695 (2)
168
136
173
154
1
2
;
z ‡ 12; (iii) x ‡ 1; y; z ‡ 1;
Compound (II)
Crystal data
3
Ê
C11H11N5O3
Mr = 261.25
Orthorhombic, P212121
Ê
a = 8.955 (3) A
b = 11.2165 (15) A
Ê
c = 11.5670 (15) A
V = 1161.8 (4) A
Z = 4
Mo Kꢂ radiation
ꢃ = 0.11 mm
T = 120 (2) K
0.32 Â 0.26 Â 0.09 mm
1
Ê
1
1
screw axis along (x, , ), but there are no direction-speci®c
interactions between adjacent chains.
4
2
Data collection
Bruker±Nonius KappaCCD
diffractometer
Absorption correction: multi-scan
(SADABS; Sheldrick, 2003)
Tmin = 0.923, Tmax = 0.991
15997 measured re¯ections
1447 independent re¯ections
879 re¯ections with I > 2ꢄ(I)
Rint = 0.102
Experimental
For the synthesis of (I), a mixture of 2-amino-4-chloro-6-methoxy-
pyrimidine (1.82 mmol) and N-methylaniline (2.80 mmol) was heated
to fusion between 563 and 573 K for 4 min. The reaction mixture was
cooled to ambient temperature and the resulting solid mass was
broken up; it was washed thrice with ether, and then successively with
a saturated aqueous solution of potassium carbonate, with water and
®nally again with ether. The mixture was then dried in an oven giving
(I) as a pale-beige solid (yield 97%, m.p. 552±554 K). For the
synthesis of (II), a mixture of 2-amino-6-chloro-5-nitropyrimidin-
4(3H)-one (2.78 mmol), N-methylaniline (3.13 mmol) and triethyl-
amine (1 ml) in methanol (20 ml) was stirred magnetically at ambient
temperature for 2 h. The resulting yellow solid was collected by
®ltration, washed with methanol and then dried in an oven to yield
(II) (yield 83%, m.p. 585±588 K). Yellow crystals of (I) and (II)
suitable for single-crystal X-ray diffraction were obtained from
solutions in dimethyl sulfoxide.
Re®nement
R[F2 > 2ꢄ(F2)] = 0.054
wR(F2) = 0.138
S = 1.05
1447 re¯ections
173 parameters
H-atom parameters constrained
3
Ê
Áꢅmax = 0.28 e A
3
Ê
0.32 e A
Áꢅmin
Friedel pairs merged
=
Table 2
Hydrogen-bond geometry (A, ) for (II).
ꢀ
Ê
DÐHÁ Á ÁA
DÐH
HÁ Á ÁA
DÁ Á ÁA
DÐHÁ Á ÁA
N2ÐH2BÁ Á ÁO4i
N2ÐH2BÁ Á ÁO51ii
N3ÐH3Á Á ÁO4i
0.88
0.88
0.88
0.88
1.97
2.40
2.25
2.33
2.783 (4)
2.936 (5)
3.000 (5)
3.093 (4)
153
119
143
145
N3ÐH3Á Á ÁO51i
1
2
Symmetry codes: (i) x
;
y ‡ 32; z ‡ 1; (ii) x 1; y; z.
Compound (I)
Crystal data
Table 3
Selected geometric parameters (A, ).
ꢀ
3
Ê
Ê
C11H12N4O
Mr = 216.25
V = 1042.4 (3) A
Z = 4
Monoclinic, P21=c
Mo Kꢂ radiation
ꢃ = 0.09 mm
T = 120 (2) K
0.52 Â 0.25 Â 0.16 mm
Parameter
(I)
(II)
1
Ê
a = 10.6860 (12) A
Ê
b = 7.1647 (14) A
N1ÐC2
C2ÐN3
N3ÐC4
C4ÐC5
C5ÐC6
C6ÐN1
C2ÐN2
C4ÐO4
C5ÐN5
N5ÐO51
N5ÐO52
C6ÐN6
1.321 (3)
1.355 (2)
1.396 (2)
1.394 (3)
1.396 (3)
1.363 (2)
1.342 (3)
1.268 (2)
±
1.318 (5)
1.357 (5)
1.400 (5)
1.421 (5)
1.403 (5)
1.356 (5)
1.322 (5)
1.235 (5)
1.430 (5)
1.231 (4)
1.243 (4)
1.352 (5)
Ê
c = 14.4911 (12) A
ꢁ = 110.024 (9)ꢀ
Data collection
Bruker±Nonius KappaCCD
diffractometer
Absorption correction: multi-scan
(SADABS; Sheldrick, 2003)
Tmin = 0.962, Tmax = 0.985
23278 measured re¯ections
2396 independent re¯ections
1568 re¯ections with I > 2ꢄ(I)
Rint = 0.057
±
±
1.365 (2)
Re®nement
R[F2 > 2ꢄ(F2)] = 0.050
wR(F2) = 0.137
S = 1.07
146 parameters
H-atom parameters constrained
C4ÐC5ÐN5ÐO51
N1ÐC6ÐN6ÐC61
N1ÐC6ÐN6ÐC67
C6ÐN6ÐC61ÐC62
±
49.4 (5)
161.7 (4)
6.1 (5)
176.53 (17)
6.6 (3)
73.7 (3)
3
Ê
Áꢅmax = 0.35 e A
51.5 (5)
3
Ê
0.26 e A
2396 re¯ections
Áꢅmin
=
ꢁ
Â
Acta Cryst. (2007). C63, o697±o700
Rodrõguez et al. C11H12N4O and C11H11N5O3 o699

organic compounds
The space groups P21/c, for (I), and P212121, for (II), were both
uniquely assigned from the systematic absences. All H atoms were
located in difference maps and then treated as riding atoms, with CÐ
Supplementary data for this paper are available from the IUCr electronic
archives (Reference: SK3172). Services for accessing these data are
described at the back of the journal.
Ê
H distances of 0.95 (aromatic or heteroaromatic) or 0.98 A (methyl),
Ê
and NÐH distances of 0.88 A, and with Uiso(H) = kUeq(carrier),
where k = 1.5 for the methyl groups and k = 1.2 for all other H atoms.
For both compounds, data collection: COLLECT (Hooft, 1999);
cell re®nement: DIRAX/LSQ (Duisenberg et al., 2000); data reduc-
tion: EVALCCD (Duisenberg et al., 2003); program(s) used to solve
structure: SIR2004 (Burla et al., 2005); program(s) used to re®ne
structure: OSCAIL (McArdle, 2003) and SHELXL97 (Sheldrick,
1997); molecular graphics: PLATON (Spek, 2003); software used to
prepare material for publication: SHELXL97 and PRPKAPPA
(Ferguson, 1999).
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Â
The authors thank Servicios Tecnicos de Investigacion of
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Â
Â
Â
Â
MN thank the Consejerõa de Innovacion, Ciencia y Empresa
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(Junta de Andalucõa, Spain) and the Universidad de Jaen for
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Â
Fundacion Carolina for a Fellowship to carry out postgraduate
studies at Departamento de Quõmica Inorganica y Organica,
Â
Universidad de Jaen.
È
Â
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o700 Rodrõguez et al. C11H12N4O and C11H11N5O3
Acta Cryst. (2007). C63, o697±o700