organic compounds
pyrimidine ring and those of the C41–C46 and C61–C66 rings,
respectively, are 60.9 (2) and 1.8 (2)ꢁ. Accordingly, the mol-
ecule has no internal symmetry, even though the pattern of
substituents on the pyrimidine ring permits C2v (mm2) mol-
ecular symmetry, or either of its subgroups, C2 or Cs. The fact
that the C61–C66 ring is effectively coplanar with the pyrim-
idine ring indicates that there are no intramolecular factors
preventing the adoption of the full molecular symmetry in the
crystal. Thus, (I) is an example of a crystal structure in which
the molecules exhibit far less than the full molecular
symmetry. Perhaps the most familiar example of this
phenomenon is benzene, where the unperturbed molecule in
the gas phase has D6h (6/mmm) symmetry (Kimura & Kubo,
1960), but only a centre of inversion is retained in the crys-
talline state for both orthorhombic (Cox et al., 1958; Bacon et
al., 1964) and monoclinic (Fourme et al., 1971) polymorphs.
The molecule of dimethoxynitropyrimidine (IV) (Glidewell
et al., 2003) exhibits no crystallographic symmetry, but the
non-H atoms are effectively coplanar, apart from the nitro
group, which is twisted out of the ring plane by some 30ꢁ, so
that this molecule exhibits approximate but noncrystallo-
graphic C2 rotational symmetry. The deviation of the nitro
group from the ring plane in (IV) is best attributed to
nonbonded electronic repulsions between the O atoms of the
nitro group and those of the methoxy groups, in contrast to the
attractive N—Hꢀ ꢀ ꢀO hydrogen bonds in (I), where the nitro
group is effectively coplanar with the pyrimidine ring.
play no role in the intermolecular aggregation. Instead, pairs
of molecules are linked into centrosymmetric dimers by means
of an asymmetric, but effectively planar, three-centre C—
Hꢀ ꢀ ꢀ(O)2 hydrogen bond, in which the O51iꢀ ꢀ ꢀH66ꢀ ꢀ ꢀO52i
[symmetry code: (i) ꢂx, ꢂy + 2, ꢂz + 1] angle is 51ꢁ, giving a
sum of angles at H66 of 359ꢁ. The dimer thus contains two
concentric and centrosymmetric R22(16) motifs together with
two symmetry-related R21(4) rings (Fig. 2). These hydrogen-
bonded dimers are linked into a chain by a single ꢀ–ꢀ stacking
interaction. The planes of the pyrimidine ring in the molecule
at (x, y, z) and the C61–C66 aryl ring in the molecule at (ꢂx + 1,
ꢂy + 1, ꢂz + 1) make a dihedral angle of 1.8 (2)ꢁ, with an
˚
interplanar spacing of ca 3.36 A. The corresponding ring-
˚
centroid separation is 3.6500 (15) A, with a ring-centroid
˚
offset of ca 1.426 A. Propagation of this interaction by inver-
sion thus links the hydrogen-bonded dimers centred at (n,
1 ꢂ n, 12 ), where n represents an integer, into a chain running
parallel to the [110] direction (Fig. 2), where pairs of mol-
ecules centred across (21 + n, 21 ꢂ n, 12 ), where n again represents
an integer, participate in ꢀ–ꢀ stacking interactions. Two chains
of this type, related to one another by the translational
symmetry operations, pass through each unit cell, but there are
no direction-specific interactions between the chains; in
particular, C—Hꢀ ꢀ ꢀꢀ hydrogen bonds are absent.
It is of interest briefly to compare the one-dimensional
supramolecular aggregation in (I) with the corresponding
behaviour in the related compounds (II)–(V). In (II)
(Makarov et al., 1997), there are no significant direction-
specific interactions between the molecules; the closest inter-
molecular contacts involve methyl C—H bonds. By contrast,
in the hydrated salt (III) (Quesada et al., 2003), a combination
of three O—Hꢀ ꢀ ꢀO hydrogen bonds and three N—Hꢀ ꢀ ꢀO
hydrogen bonds link the components into a continuous three-
dimensional structure, but the anion and solvent components
play a dominant role here. Two hydrogen bonds, one each of
the N—Hꢀ ꢀ ꢀO and N—Hꢀ ꢀ ꢀN types, link the molecules of (IV)
into sheets built from alternating R22(8) and R66(32) rings
(Glidewell et al., 2003). Finally, in (V) (Quesada et al., 2004),
two N—Hꢀ ꢀ ꢀN hydrogen bonds generate chains of rings,
which are linked into sheets by an N—Hꢀ ꢀ ꢀO hydrogen bond;
these sheets are themselves linked by a C—Hꢀ ꢀ ꢀO hydrogen
Within the molecule of (I), the C5—N5 bond (Table 1) is
very short for its type [mean value (Allen et al., 1987) =
˚
1.468 A and lower quartile value = 1.460 A], while the N—O
˚
˚
distances are both long (mean value = 1.217 A and upper
˚
quartile value = 1.225 A); similarly, the C4—N4 and C6—N6
˚
bonds are short for their type (mean value = 1.353 A and
˚
lower quartile value = 1.347 A), while the C4—C5 and C5—C6
˚
bonds are both long (mean value in pyrimidines = 1.387 A and
˚
upper quartile value = 1.400 A). These values indicate that
polarized forms such as (Ia) and (Ib) are significant contri-
butors to the overall electronic structure in addition to the
delocalized aromatic form (I). The corresponding distances in
(II) exhibit an exactly analogous pattern of behaviour,
showing firstly that the development of polarized forms
involving electronic delocalization from amine groups to nitro
groups does not depend upon the presence of a planar mol-
ecular skeleton, and secondly that the energy cost of evading
steric clashes between adjacent substituents by rotation of the
amine and nitro groups about the exocyclic C—N bonds, with
concomitant loss of the delocalization, exceeds that of
distorting the formally aromatic ring. Compound (V)
(Quesada et al., 2004) is another close analogue of (I),
containing two primary amine substituents, but with a nitroso
group rather than a nitro group, so that only one intra-
molecular N—Hꢀ ꢀ ꢀO hydrogen bond is present; again the
electronic structure is markedly polarized, with extensive
delocalization involving all three amine substituents.
Figure 2
A stereoview of part of the crystal structure of (I), showing the formation
of a chain along [110] built by the ꢀ stacking of hydrogen-bonded dimers.
For the sake of clarity, H atoms not involved in the motifs shown have
been omitted.
Each of the two independent N—H bonds participates in an
intramolecular hydrogen bond (Table 2), forming two edge-
fused S(6) motifs (Bernstein et al., 1995), but the N—H bonds
ꢃ
´
Acta Cryst. (2009). C65, o438–o440
Rodrıguez et al. C16H13N5O2 o439
Rodriguez, Ricaurte
