(E)-3-{2-Amino-4-ethoxy-6-[N-(4-methoxyphenyl)-N-methylamino] pyrimidin-5-yl}-1-phenylprop-2-en-1-one: A boat-shaped pyrimidine ring and a chain of hydrogen-bonded R 4 2(8) and R 2 2(20) rings

Article abstract of DOI:10.1107/S0108270107056569

In the title compound, C23H24N4O3, the pyrimidine ring adopts an almost perfect boat conformation, and the bond distances provide evidence for some polarization of the mol-ecular-electronic structure. Two independent N - H...O hydrogen bonds link the mol-ecules into chains of edge-fused R ² 4(8) and R ² 2(20) rings. International Union of Crystallography 2007.

Full text of DOI:10.1107/S0108270107056569

organic compounds
Acta Crystallographica Section C
Crystal Structure
where n represents zero or an integer. Atoms C2 and C5, at
the stem and stern of the boat, are displaced by 0.061 (2) and
Ê
0.060 (2) A, respectively, on one side of the mean plane of the
pyrimidine ring; the other four ring atoms all lie on the
Communications
ISSN 0108-2701
(E)-3-{2-Amino-4-ethoxy-6-[N-(4-
methoxyphenyl)-N-methylamino]-
pyrimidin-5-yl}-1-phenylprop-2-en-
1-one: a boat-shaped pyrimidine ring
and a chain of hydrogen-bonded R42(8)
and R22(20) rings
Jorge Trilleras,a Jairo Quiroga,a John N. Low,b Justo Coboc
and Christopher Glidewelld*
a
Â
Departamento de Quõmica, Universidad de Valle, AA 25360 Cali, Colombia,
bDepartment of Chemistry, University of Aberdeen, Meston Walk, Old Aberdeen
c
Â
Â
Â
AB24 3UE, Scotland, Departamento de Quõmica Inorganica y Organica,
Universidad de Jaen, 23071 Jaen, Spain, and dSchool of Chemistry, University of
opposite side of the mean plane, displaced from it by distances
Â
Â
Ê
Ê
St Andrews, Fife KY16 9ST, Scotland
ranging from 0.026 (2) A for N1 to 0.034 (2) A for C6. More
striking are the displacements from this plane of the substi-
tuent atoms N2 and C51, bonded to C2 and C5, which are
Correspondence e-mail: cg@st-andrews.ac.uk
Received 7 November 2007
Accepted 8 November 2007
Online 30 November 2007
Ê
0.209 (2) and 0.450 (2) A, respectively; the substituent atoms
O4 and N6, bonded to C4 and C6, are displaced from the
Ê
opposite face of the mean plane by 0.071 (2) and 0.097 (2) A,
respectively, as indicated schematically by A in the scheme.
We have previously observed such nonplanarity in a number
of extensively substituted pyrimidine derivatives exhibiting
boat (Quesada et al., 2004) or twist-boat (Melguizo et al., 2003;
In the title compound, C23H24N4O3, the pyrimidine ring
adopts an almost perfect boat conformation, and the bond
distances provide evidence for some polarization of the
molecular±electronic structure. Two independent NÐHÁ Á ÁO
hydrogen bonds link the molecules into chains of edge-fused
R42(8) and R22(20) rings.
Comment
As part of a programme aimed at the synthesis of new
heterocyclic compounds with potential biological activity, we
have attempted the functionalization of the pyrimidine ring at
position 5 via the modi®cation of 5-formylpyrimidines as a
route to the preparation of intermediates for the synthesis of
polycyclic heterocyclic compounds. We report here the mol-
ecular and supramolecular structures of one such inter-
mediate, (E)-3-{2-amino-4-ethoxy-6-[N-(4-methoxyphenyl)-
N-methylamino]pyrimidin-5-yl}-1-phenylprop-2-en-1-one, (I)
(Fig. 1), formed by a base-catalysed condensation between
acetophenone and 2-amino-4-chloro-6-[N-(4-methoxyphen-
yl)-N-methylamino]pyrimidine-5-carbaldehyde, where the
condensation at the formyl group is accompanied by solvolysis
at position 4 (see scheme).
The pyrimidine ring in (I) adopts an almost perfect boat
conformation; the ring-puckering parameters (Cremer &
Pople, 1975) for the atom sequence N1ÐC2ÐN3ÐC4ÐC5Ð
C6 are ꢀ = 88 (2)ꢀ and ' = 241 (2)ꢀ, with a total puckering
amplitude Q of 0.105 (2) A. The ideal values of the puckering
angles for a boat conformation are ꢀ = 90ꢀ and ' = (60n)ꢀ,
Figure 1
The molecular structure of (I), showing the atom-labelling scheme.
Displacement ellipsoids are drawn at the 30% probability level.
Ê
o758 # 2007 International Union of Crystallography
DOI: 10.1107/S0108270107056569
Acta Cryst. (2007). C63, o758±o760

organic compounds
Quesada et al., 2002, 2003) conformations, and by comparison
with less extensively substituted analogues, the distortions
from planarity were ascribed to steric factors (Melguizo et al.,
2003). The occurrence here of a nonplanar pyrimidine ring in
the presence of three adjacent substituents on the ring is
certainly consistent with the earlier interpretation.
The propenone side chain is effectively planar, as indicated
by the relevant torsion angles (Table 1). Although the steric
effects arising from the three adjacent substituents at atoms
C4, C5 and C6 appear to be responsible for the puckering of
the pyrimidine ring, the conformational arrangement of the
methyl and aryl substituents at atom N6 is somewhat
surprising, particularly as there appear to be no intramolecular
CÐHÁ Á Áꢁ(arene) interactions that could lock the C61±C66
ring into position. The exocyclic angles at atoms C4 and C64
show the usual deviations from 120ꢀ observed for alkoxy
groups, with the alkyl C atom effectively coplanar with the
adjacent ring, but similar effects are found at none of the other
substituent sites.
Despite the nonplanarity of the pyrimidine ring, the bond
distances in (I) (Table 1) provide some evidence for polar-
ization of the molecular±electronic structure. The C4ÐN3
bond is signi®cantly shorter than any other CÐN bond
present; the N2ÐC2, C2ÐN1 and N1ÐC6 bonds are very
similar in length; the C51ÐC52 and C53ÐO53 bonds are both
long for their types (Allen et al., 1987), and the C6ÐN6, C5Ð
C51 and C52ÐC53 bonds are somewhat short for their types.
These observations taken together indicate a modest contri-
bution from the polarized form (Ia).
The molecules of (I) are linked by two independent NÐ
HÁ Á ÁO hydrogen bonds (Table 2) into a chain of edge-fused
rings along [100]. Amino atom N2 in the molecule at (x, y, z)
acts as a hydrogen-bond donor to atoms O53 in the two
molecules at ( 1 + x, y, z) and (1 x, 1 y, 1 z). Propa-
gation of these two hydrogen bonds by translation and
inversion forms a chain in which R24(8) (Bernstein et al., 1995)
rings centred at (n, 12, 21 ), where n represents zero or an integer,
1
1 1
2 2
alternate with R22(20) rings centred at (n + , , ), where n
2
represents zero or an integer (Fig. 2). In these two hydrogen
bonds, both donor atom N2 and acceptor atom O53 carry
partial charges arising from the polarization of the molecular±
electronic structure [see (Ia) in the scheme], and hence they
can be regarded as charge-assisted or resonance-assisted
hydrogen bonds (Gilli et al., 1994).
Experimental
Sodium hydroxide (two pellets) was added to a solution containing
1 mmol each of 2-amino-4-chloro-6-[N-(4-methoxyphenyl)-N-methyl-
amino]pyrimidine-5-carbaldehyde and acetophenone in ethanol
(10 ml). The solution was stirred for 2 h at room temperature and
then heated under re¯ux for 20 h. The resulting precipitate of sodium
chloride was removed by ®ltration. The ®ltrate was diluted with water
(2 ml), brie¯y heated and then allowed to cool to ambient tempera-
ture. The solid product (I) was collected by ®ltration, washed with
ethanol and dried. Crystallization from ethanol gave yellow block-
shaped crystals suitable for single-crystal X-ray diffraction (yield
20%, m.p. 427±428 K). HRMS: m/z found: 404.1848; C23H24N4O3
requires: 404.1832.
Crystal data
C23H24N4O3
Mr = 404.46
Triclinic, P1
ꢄ = 113.339 (10)ꢀ
3
Ê
V = 1035.5 (3) A
Z = 2
Mo Kꢂ radiation
Ê
a = 10.1975 (14) A
Ê
1
b = 10.959 (2) A
Ê
ꢅ = 0.09 mm
T = 120 (2) K
c = 11.046 (2) A
ꢂ = 94.079 (16)ꢀ
ꢃ = 109.845 (11)ꢀ
0.49 Â 0.29 Â 0.24 mm
Data collection
Bruker±Nonius KappaCCD
diffractometer
Absorption correction: multi-scan
(SADABS; Sheldrick, 2003)
Tmin = 0.963, Tmax = 0.979
28433 measured re¯ections
4750 independent re¯ections
3263 re¯ections with I > 2ꢆ(I)
Rint = 0.052
Re®nement
R[F2 > 2ꢆ(F2)] = 0.047
wR(F2) = 0.113
S = 1.05
274 parameters
H-atom parameters constrained
3
Ê
Áꢇmax = 0.26 e A
3
Ê
0.30 e A
4750 re¯ections
Áꢇmin
=
Table 1
Selected geometric parameters (A, ).
ꢀ
Ê
N1ÐC2
C2ÐN3
N3ÐC4
C4ÐC5
C5ÐC6
C6ÐN1
1.344 (2)
1.351 (2)
1.317 (2)
1.418 (2)
1.428 (2)
1.338 (2)
C2ÐN2
1.339 (2)
1.435 (2)
1.354 (2)
1.450 (2)
1.242 (2)
1.373 (2)
C5ÐC51
C51ÐC52
C52ÐC53
C53ÐO53
N6ÐC6
N3ÐC4ÐO4
C5ÐC4ÐO4
118.79 (14)
115.85 (14)
C63ÐC64ÐO64
C65ÐC64ÐO64
116.22 (15)
124.14 (15)
N1ÐC6ÐN6ÐC61
N1ÐC6ÐN6ÐC68
N3ÐC4ÐO4ÐC41
C4ÐO4ÐC41ÐC42
C63ÐC64ÐO64ÐC67
150.48 (15)
4.8 (2)
2.2 (2)
96.99 (18)
176.96 (16)
C6ÐC5ÐC51ÐC52
C5ÐC51ÐC52ÐC53
C51ÐC52ÐC53ÐO53
C51ÐC52ÐC53ÐC531 176.08 (15)
C52ÐC53ÐC531ÐC532 29.6 (2)
175.61 (17)
170.18 (16)
5.9 (3)
Figure 2
A stereoview of part of the crystal structure of (I), showing the formation
of a hydrogen-bonded chain of edge-fused R24(8) and R22(20) rings along
[100]. For the sake of clarity, H atoms bonded to C atoms have been
omitted.
ꢁ
Acta Cryst. (2007). C63, o758±o760
Trilleras et al. C23H24N4O3 o759

organic compounds
Table 2
Hydrogen-bond geometry (A, ).
  Â
amento de Quõmica Inorganica y Organica, Universidad de
Â
Jaen.
ꢀ
Ê
DÐHÁ Á ÁA
DÐH
HÁ Á ÁA
DÁ Á ÁA
DÐHÁ Á ÁA
Supplementary data for this paper are available from the IUCr electronic
archives (Reference: SK3178). Services for accessing these data are
described at the back of the journal.
N2ÐH2AÁ Á ÁO53i
0.86
0.86
2.17
2.16
2.9836 (19)
2.9806 (19)
157
160
N2ÐH2BÁ Á ÁO53ii
Symmetry codes: (i) x 1; y; z; (ii) x ‡ 1; y ‡ 1; z ‡ 1.
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.
Burla, M. C., Caliandro, R., Camalli, M., Carrozzini, B., Cascarano, G. L., De
Caro, L., Giacovazzo, C., Polidori, G. & Spagna, R. (2005). J. Appl. Cryst. 38,
381±388.
Cremer, D. & Pople, J. A. (1975). J. Am. Chem. Soc. 97, 1354±1358.
Duisenberg, A. J. M., Hooft, R. W. W., Schreurs, A. M. M. & Kroon, J. (2000).
J. Appl. Cryst. 33, 893±898.
Duisenberg, A. J. M., Kroon-Batenburg, L. M. J. & Schreurs, A. M. M. (2003).
J. Appl. Cryst. 36, 220±229.
Ferguson, G. (1999). PRPKAPPA. University of Guelph, Canada.
Gilli, P., Bertolasi, V., Ferretti, V. & Gilli, G. (1994). J. Am. Chem. Soc. 116,
909±915.
Hooft, R. W. W. (1999). COLLECT. Nonius BV, Delft, The Netherlands.
McArdle, P. (2003). OSCAIL for Windows. Version 10. Crystallography
Centre, Chemistry Department, NUI Galway, Ireland.
Melguizo, M., Quesada, A., Low, J. N. & Glidewell, C. (2003). Acta Cryst. B59,
263±276.
Crystals of compound (I) are triclinic; the space group P1 was
selected and con®rmed by the structure analysis. All H atoms were
located in difference maps and then treated as riding atoms in
geometrically idealized positions, with CÐH distances of 0.95
Ê
(aromatic and alkene), 0.98 (CH3) or 0.99 A (CH2), and NÐH
Ê
distances of 0.86 A, and with Uiso(H) = kUeq(carrier), where k = 1.5
for the methyl groups and k = 1.2 for all other H atoms.
Data collection: COLLECT (Hooft, 1999); cell re®nement:
DIRAX/LSQ (Duisenberg et al., 2000); data reduction: 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).
Quesada, A., Marchal, A., Low, J. N. & Glidewell, C. (2003). Acta Cryst. C59,
o102±o104.
Â
The authors thank Servicios Tecnicos de Investigacion of
Universidad de Jaen and the staff for data collection. JC
Â
Quesada, A., Marchal, A., Melguizo, M., Low, J. N. & Glidewell, C. (2004).
Acta Cryst. B60, 76±89.
Â
Quesada, A., Marchal, A., Melguizo, M., Nogueras, M., Sanchez, A., Low, J. N.,
Cannon, D., Farrell, D. M. M. & Glidewell, C. (2002). Acta Cryst. B58, 300±
Â
Â
Â
thanks the Consejerõa de Innovacion, Ciencia y Empresa
Â
Â
(Junta de Andalucõa, Spain) and the Universidad de Jaen for
®nancial support. JT and JQ thank COLCIENCIAS and
UNIVALLE (Universidad del Valle, Colombia) for ®nancial
support and for supporting a short stay by JT at Depart-
315.
Sheldrick, G. M. (1997). SHELXL97. University of Gottingen, Germany.
È
Sheldrick, G. M. (2003). SADABS. Version 2.10. University of Gottingen,
È
Germany.
Spek, A. L. (2003). J. Appl. Cryst. 36, 7±13.
ꢁ
o760 Trilleras et al. C23H24N4O3
Acta Cryst. (2007). C63, o758±o760