2-Cyano-N-(2,6-dimethoxy-pyrimidin-4-yl)-3-[4-(dimethyl-amino)-phenyl] -acrylamide and dimethyl-ammonium 6-cyano-1,3-dimethyl-2,4,5-trioxo-1,2,3,4,5,8- hexa-hydro-pyrido[2,3-d]pyrimidin-8-ide: A π-stacked dimer and a hydrogen-bonded ribbon containing three types of ring

Article abstract of DOI:10.1107/S0108270109053785

The bond distances in 2-cyano-N-(2,6-dimethoxy-pyrimidin-4-yl)-3-[4- (dimethyl-amino)phenyl]acrylamide, C₁₈H₁₉N ₅O₃, (I), and in the anionic component of the salt dimethyl-ammonium 6-cyano-1,3-dimethyl-2,4,5-trioxo-1,2,3,4,5,8-hexa- hydropyrido[2,3-d]pyrimidin-8-ide, C₂H₈N₂ ⁺·C₁₀H₇N₄O₃ ^-, (II), provide evidence for the occurrence of electronic polarization. There are no hydrogen bonds in the structure of (I), instead pairs of mol-ecules are linked into centrosymmetric dimers by a single π-π stacking inter-action. In (II), a combination of a two-centre N - H...O hydrogen bond, a three-centre N - H...(O)₂ hydrogen bond, together utilizing all three O atoms, and a two-centre C - H...N hydrogen bond, link the components into a ribbon containing R₁²(6), R₂²(10) and R₆⁶(30) rings.

Full text of DOI:10.1107/S0108270109053785

organic compounds
Acta Crystallographica Section C
Crystal Structure
were both synthesized using variations of the recently
reported procedure.
Communications
Within the molecule of (I) (Fig. 1), the spacer unit linking
the two rings adopts an all-trans configuration which is nearly
planar, while the two rings are each twisted out of this plane by
less than 10ꢂ, as shown by the leading torsion angles (Table 1).
Similarly, the C atoms of the methoxy groups are almost
coplanar with the adjacent pyrimidine ring, with deviations
ISSN 0108-2701
2-Cyano-N-(2,6-dimethoxypyrimidin-
4-yl)-3-[4-(dimethylamino)phenyl]-
acrylamide and dimethylammonium
6-cyano-1,3-dimethyl-2,4,5-trioxo-
1,2,3,4,5,8-hexahydropyrido[2,3-d]-
pyrimidin-8-ide: a p-stacked dimer
and a hydrogen-bonded ribbon
˚
from the ring plane of 0.071 (2) A for atom C21 and
˚
0.195 (2) A for atom C61, although the spatial disposition of
these groups differs from that originally suggested (Quiroga et
al., 2009).
containing three types of ring
a
a
b
´
Jairo Quiroga, Jaime Galvez, Michael B. Hursthouse,
Justo Coboc and Christopher Glidewelld*
a
´
Departamento de Quımica, Universidad de Valle, AA 25360 Cali, Colombia,
bSchool of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ,
c
´
´
´
´
England, Departamento de Quımica Inorganica y Organica, Universidad de Jaen,
23071 Jaen, Spain, and dSchool of Chemistry, University of St Andrews, Fife
´
KY16 9ST, Scotland
Correspondence e-mail: cg@st-andrews.ac.uk
Received 10 December 2009
Accepted 14 December 2009
Online 19 December 2009
The bond distances in 2-cyano-N-(2,6-dimethoxypyrimidin-4-
yl)-3-[4-(dimethylamino)phenyl]acrylamide, C18H19N5O3, (I),
and in the anionic component of the salt dimethylammonium
6-cyano-1,3-dimethyl-2,4,5-trioxo-1,2,3,4,5,8-hexahydro-
+
pyrido[2,3-d]pyrimidin-8-ide, C2H8N2 ꢀC10H7N4O3ꢁ, (II),
provide evidence for the occurrence of electronic polarization.
There are no hydrogen bonds in the structure of (I), instead
pairs of molecules are linked into centrosymmetric dimers by a
single ꢀ–ꢀ stacking interaction. In (II), a combination of a
two-centre N—Hꢀ ꢀ ꢀO hydrogen bond, a three-centre N—
Hꢀ ꢀ ꢀ(O)2 hydrogen bond, together utilizing all three O atoms,
and a two-centre C—Hꢀ ꢀ ꢀN hydrogen bond, link the
components into a ribbon containing R21(6), R22(10) and
R66(30) rings.
The bond distances in the molecule of (I) show some values
which are worthy of comment (Table 1). In the C51–C56 aryl
ring, the two bonds C52—C53 and C55—C56 are significantly
shorter than the other four bonds; the exocyclic C54—N54
bond is somewhat short for its type [mean value (Allen et al.,
Comment
˚
1987) = 1.371 A]; the C45—C51 bond is very short for its type
˚
˚
(mean value = 1.470 A, lower quartile value = 1.463 A), while
We report here the structures of the title compounds, (I) and
(II) (Figs. 1 and 2), which result from the reactions of cyano-
acetylpyrimidine derivatives with, respectively, 4-(dimethyl-
amino)benzaldehyde (Quiroga et al., 2009; see scheme 1) and
dimethylformamide dimethylacetal (see scheme 2). The use of
5-cyanoacetylpyrimidines as intermediates for the synthesis of
substituted pyrido[2,3-d]pyrimidin-5-ones has recently been
described (Quiroga et al., 2009), and compounds (I) and (II),
˚
the C43—C45 bond is long for its type (mean value = 1.326 A,
˚
upper quartile value = 1.334 A). Although the C42—C43 and
C42—O42 bonds have lengths typical of their types, the
C43—C44 bond is shorter than those found in a series of
analogous nitriles where electronic conjugation is not possible
[mean value = 1.442 (4) A; Cobo et al., 2005, 2006, 2009] and
the C44—N44 bond is correspondingly longer [mean value =
˚
Acta Cryst. (2010). C66, o39–o43
doi:10.1107/S0108270109053785
# 2010 International Union of Crystallography o39

organic compounds
Figure 1
The molecular structure 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.
˚
1.130 (4) A]. Thus, within the spacer unit, the bond-length
anomalies are concentrated in the carbonitrile fragment,
rather than in the carbonyl fragment and its adjacent C—C
bonds. Taken as a whole, the bond distances in (I) indicate that
form (Ia) (see scheme 1), which is intuitively the more obvious
of the polarized forms, probably makes only a very small
contribution to the overall electronic structure, while form
(Ib) is a significant contributor, in addition to the classical
unpolarized form (I).
Figure 2
The independent components of (II), showing the atom-labelling scheme
and the three-centre N—Hꢀ ꢀ ꢀ(O)2 hydrogen bond (dashed lines) linking
the ions within the selected asymmetric unit. Displacement ellipsoids are
drawn at the 30% probability level and H atoms are shown as small
spheres of arbitrary radii.
C6—C61 bond in (II) is slightly short for its type and
C61—N61 is slightly long. Thus, forms (IIa) and, to a lesser
extent, (IIb) are contributors to the overall electronic struc-
ture, in addition to the simple form (II) (see second scheme).
Despite the polarization of the electronic structure in (I),
neither atom O42 nor N44 acts as a hydrogen-bond acceptor.
Indeed, there are no hydrogen bonds of any kind in the crystal
structure of (I). In particular, the N—H unit does not act as a
Figure 3
In the anion of compound (II) (Fig. 2), it is striking that,
while the C2—O2 and C4—O4 distances are identical and
typical of their type, the C5—O5 distance is significantly
longer (Table 2). As found for the analogous bonds in (I), the
Part of the crystal structure of (I), showing the formation of a
centrosymmetric ꢀ-stacked dimer. For the sake of clarity, H atoms have
been omitted. The atom marked with an asterisk (*) is at the symmetry
position (1 ꢁ x, 1 ꢁ y, 1 ꢁ z).
C18H19N5O3 and C2H8N+ꢀC10H7N4O3
Acta Cryst. (2010). C66, o39–o43
ꢁ
ꢃ
o40 Quiroga et al.

organic compounds
dihedral angle of only 2.2 (2)ꢂ. The corresponding ring-
˚
centroid separation is 3.632 (2) A and the interplanar spacing
˚
˚
is ca 3.395 A, with a ring-centroid offset of ca 1.29 A. There
are no direction-specific interactions between these dimers.
In compound (II), the ionic components in the selected
asymmetric unit are linked by a slightly asymmetric but
nonetheless planar three-centre N—Hꢀ ꢀ ꢀ(O)2 hydrogen bond
(Table 3 and Fig. 2), forming an R21(6) motif (Bernstein et al.,
1995). The shorter component of this three-centre system
involves atom O5 as the acceptor and, because of the polar-
ization in form (IIa), this stronger component could be
regarded as a charge-assisted hydrogen bond (Gilli et al.,
1994). In addition, atom N21 in the cation at (x, y, z) acts as
hydrogen-bond donor to atom O2 in the anion at (x, y, 1 + z),
and the combination of all the N—Hꢀ ꢀ ꢀO interactions gener-
ates a hydrogen-bonded C22(8)C22(10)[R21(6)] chain of rings
(Fig. 4). Finally, a single C—Hꢀ ꢀ ꢀN hydrogen bond, which
utilizes the nitrile N atom as the acceptor, links an antiparallel
pair of chains of rings into a ribbon running parallel to the
Figure 4
A stereoview of part of the crystal structure of (II), showing the
formation of a hydrogen-bonded ribbon running parallel to [001] and
containing rings of R21(6), R22(10) and R66(30) types. For the sake of clarity,
H atoms not involved in the motifs shown have been omitted.
1
[001] direction in which R22(10) rings centred at (1, 1, + n),
2
where n represents an integer, alternate with R66(30) rings
centred at (1, 1, n), where n again represents an integer (Fig. 4).
There are no direction-specific interactions between adjacent
ribbons.
hydrogen-bond donor, as the nearest potential hydrogen-bond
acceptor is atom O42 in the molecule at (1 ꢁ x, 1 ꢁ y, 1 ꢁ z)
and the geometric parameters for this contact are
N41ꢀ ꢀ ꢀO42 = 3.501 (2) A, H41ꢀ ꢀ ꢀO42 = 3.51 A and N41—
H41ꢀ ꢀ ꢀO42i = 82ꢂ [symmetry code: (i) 1 ꢁ x, 1 y, 1 ꢁ z]. No
N—Hꢀ ꢀ ꢀꢀ or C—Hꢀ ꢀ ꢀꢀ hydrogen bonds are present either.
Instead, pairs of molecules related by inversion are linked into
centrosymmetric dimers (Fig. 3) by a single ꢀ–ꢀ stacking
The formation of the salt (II) in the reaction of dimethyl-
formamide dimethylacetal with a cyanoacetylpyrimidine
derivative may be contrasted with the reaction (Galvez et al.,
2008) of the same acetal with a cyanoacetylindole derivative to
form the neutral compound, (III) (see scheme 3). Here, the
intramolecular distances indicate that both of the polarized
forms, (IIIa) and (IIIb), are significant contributors to the
overall electronic structure. The formation of these
compounds, and of (I), attests to the synthetic versatility of
cyanoacetyl derivatives as intermediates for the synthesis of
new heterocyclic compounds.
i
i
˚
˚
Experimental
For the synthesis of (I), a solution of 2-cyano-N-(2,6-dimethoxy-
pyrimidin-4-yl)acetamide (1.0 mmol) and 4-(dimethylamino)benz-
aldehyde (1.0 mmol) in ethanol (10 ml) containing a catalytic
quantity of sodium hydroxide (20% w/v aqueous solution, 5 drops)
was stirred for 3 h at ambient temperature. The resulting precipitate
was collected by filtration, washed with ethanol, and crystallized by
slow evaporation, at ambient temperature and in air, of a solution in a
mixture of dimethylformamide and ethanol (1:1, v/v) to give yellow
crystals of (I) suitable for single-crystal X-ray diffraction (yield 76%,
m.p. 526–527 K). MS (70 eV): 354 (17), 353 (76, M+), 352 (16),
199 (65), 182 (100), 172 (20), 171 (58), 156 (12).
For the synthesis of compound (II), a solution of 3-(6-amino-1,3-
dimethyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-3-oxopropane-
nitrile (1.9 mmol) and dimethylformamide dimethyl acetal
(3.0 mmol) in toluene (5.3 ml) was heated at 393 K for 30 min. The
resulting solid product was collected by filtration, washed and crys-
tallized by slow evaporation, at ambient temperature and in air, of a
solution in ethanol to give yellow crystals of (II) suitable for single-
crystal X-ray diffraction (yield 70%, m.p. 532–534 K). MS (70 eV):
232 {M+ ꢁ 45 [HN(CH3)2]} (37), 204 (12), 120 (35).
interaction. The aryl ring of the molecule at (x, y, z) and the
pyrimidine ring of the molecule at (1 ꢁ x, 1 ꢁ y, 1 ꢁ z) make a
C18H19N5O3 and C2H8N+ꢀC10H7N4O3
o41
ꢁ
ꢃ
Acta Cryst. (2010). C66, o39–o43
Quiroga et al.

organic compounds
Table 1
Selected geometric parameters (A, ) for (I).
Table 2
Selected bond lengths (A) for (II).
ꢂ
˚
˚
C42—O42
C42—C43
C43—C44
C44—N44
C43—C45
C45—C51
C54—N54
1.2276 (18)
1.489 (2)
1.430 (2)
1.152 (2)
1.361 (2)
1.434 (2)
1.363 (2)
C51—C52
C52—C53
C53—C54
C54—C55
C55—C56
C56—C51
1.410 (2)
1.373 (2)
1.418 (2)
1.412 (2)
1.375 (2)
1.411 (2)
N1—C2
C2—N3
N3—C4
C4—C4a
C4a—C5
C5—C6
C6—C7
C7—N8
1.368 (4)
1.381 (4)
1.401 (3)
1.447 (4)
1.449 (4)
1.444 (4)
1.379 (4)
1.346 (4)
N8—C8a
C8a—N1
C4a—C8a
C2—O2
C4—O4
C5—O5
1.340 (4)
1.393 (4)
1.408 (4)
1.225 (3)
1.225 (4)
1.258 (3)
1.438 (4)
1.151 (4)
C6—C61
C61—N61
N3—C4—N41—C42
ꢁ170.16 (13)
N1—C2—O2—C21
N1—C6—O6—C61
C53—C54—N54—C57
C53—C54—N54—C58 ꢁ178.89 (13)
ꢁ178.19 (12)
ꢁ4.43 (19)
ꢁ3.2 (2)
C4—N41—C42—C43 ꢁ177.93 (13)
N41—C42—C43—C45
C42—C43—C45—C51
C43—C45—C51—C52
178.81 (12)
178.03 (15)
ꢁ8.9 (3)
Table 3
Hydrogen-bond geometry (A, ) for (II).
ꢂ
˚
D—Hꢀ ꢀ ꢀA
D—H
Hꢀ ꢀ ꢀA
Dꢀ ꢀ ꢀA
D—Hꢀ ꢀ ꢀA
N21—H21Aꢀ ꢀ ꢀO2i
N21—H21Bꢀ ꢀ ꢀO4
N21—H21Bꢀ ꢀ ꢀO5
C7—H7ꢀ ꢀ ꢀN61ii
0.92
0.92
0.92
0.95
1.88
2.12
1.89
2.54
2.735 (4)
2.757 (3)
2.699 (3)
3.483 (4)
153
126
146
172
Compound (I)
Crystal data
C18H19N5O3
Mr = 353.38
Triclinic, P1
ꢃ = 99.196 (2)ꢂ
V = 849.80 (6) A
Z = 2
Mo Kꢁ radiation
ꢄ = 0.10 mmꢁ1
T = 120 K
Symmetry codes: (i) x; y; z þ 1; (ii) ꢁx þ 2; ꢁy þ 2; ꢁz þ 1.
3
˚
˚
a = 7.9772 (2) A
˚
b = 10.0023 (4) A
˚
c = 10.8409 (5) A
All H atoms were located in difference maps and then treated as
riding atoms in geometrically idealized positions, with C—H
˚
distances of 0.98 A for methyl H atoms or 0.95 A for aromatic,
ꢁ = 93.693 (2)ꢂ
ꢂ = 93.562 (3)ꢂ
0.23 ꢄ 0.12 ꢄ 0.12 mm
˚
˚
heteroaromatic and alkenyl H atoms, and an N—H distance of 0.88 A
˚
for the N—H group in (I) or 0.92 A for the ammonium N—H
Data collection
distances in (II), and with Uiso(H) = kUeq(carrier), where k = 1.5 for
the methyl groups, which were permitted to rotate but not to tilt, and
1.2 for all other H atoms.
Bruker–Nonius KappaCCD area-
detector diffractometer
Absorption correction: multi-scan
(SADABS; Sheldrick, 2003)
Tmin = 0.978, Tmax = 0.988
15270 measured reflections
3350 independent reflections
2512 reflections with I > 2ꢅ(I)
Rint = 0.055
For both compounds, data collection: COLLECT (Nonius, 1999);
cell refinement: 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 refine
structure: SHELXL97 (Sheldrick, 2008); molecular graphics:
PLATON (Spek, 2009); software used to prepare material for
publication: SHELXL97 and PLATON.
Refinement
R[F2 > 2ꢅ(F2)] = 0.047
wR(F2) = 0.133
S = 1.04
239 parameters
H-atom parameteꢁrs3 constrained
˚
Áꢆmax = 0.30 e A
Áꢆmin = ꢁ0.28 e A
ꢁ3
˚
3350 reflections
JQ and JG thank COLCIENCIAS and Universidad del
Compound (II)
´
Valle for financial support. JC thanks the Consejerıa de
Innovacion, Ciencia y Empresa (Junta de Andalucıa, Spain),
´
´
Crystal data
C2H8N+ꢀC10H7N4O3
´
the Universidad de Jaen (project reference UJA_07_16_33)
and the Ministerio de Ciencia e Innovacion (project reference
ꢁ
ꢃ = 79.447 (5)ꢂ
V = 650.69 (9) A
Z = 2
Mo Kꢁ radiation
ꢄ = 0.11 mmꢁ1
T = 120 K
´
3
˚
Mr = 277.29
Triclinic, P1
a = 8.1520 (5) A
SAF2008-04685-C02-02) for financial support.
˚
˚
b = 9.2984 (8) A
˚
c = 9.7299 (8) A
Supplementary data for this paper are available from the IUCr electronic
archives (Reference: FA3211). Services for accessing these data are
described at the back of the journal.
ꢁ = 69.609 (3)ꢂ
ꢂ = 70.741 (4)ꢂ
0.12 ꢄ 0.05 ꢄ 0.03 mm
Data collection
References
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Absorption correction: multi-scan
(SADABS; Sheldrick, 2003)
Tmin = 0.988, Tmax = 0.997
9719 measured reflections
2419 independent reflections
1538 reflections with I > 2ꢅ(I)
Rint = 0.077
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˚
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ꢁ3
˚
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C18H19N5O3 and C2H8N+ꢀC10H7N4O3
Acta Cryst. (2010). C66, o39–o43
ꢁ
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