(9E)-9-Benzyl-idene-3-methyl-2-methyl-sulfanyl-5-phenyl-5,6,7,8,9, 10-hexa-hydro-pyrimido[4,5-b]quinolin-4(3H)-one: Polarized mol-ecules within hydrogen-bonded bilayers

Article abstract of DOI:10.1107/S0108270110023139

The mol-ecules of the title compound, C₂₆H₂₅N ₃OS, which was prepared by means of an acid-catalysed cyclo-condensation reaction between a 6-amino-pyrimidinone and 2,6-dibenzyl-idene-cyclo-hexa-none, exhibit a polarized ele

Full text of DOI:10.1107/S0108270110023139

organic compounds
Acta Crystallographica Section C
Crystal Structure
Communications
the C5a—C9a bond (Fig. 1) are both nonplanar. The hetero-
cyclic ring containing atom N10 adopts a boat-type confor-
mation, with atoms C5 and N10 acting as the stem and stern of
the boat, respectively. The ring-puckering parameters
(Cremer & Pople, 1975) for the atom sequenꢁce N10/C9a/C5a/
ISSN 0108-2701
ꢁ
˚
C5/C4a/C10a are Q = 0.205 (2) A, ꢁ = 103.8 (6) and ’ = 2.6 (7) ,
whereas the ideal puckering angles for a boat conformation
are ꢁ = 90ꢁ and ’ = 60kꢁ, where k represents an integer.
(9E)-9-Benzylidene-3-methyl-2-methyl-
sulfanyl-5-phenyl-5,6,7,8,9,10-hexa-
hydropyrimido[4,5-b]quinolin-4(3H)-
one: polarized molecules within
hydrogen-bonded bilayers
Diana Becerra,a Braulio Insuasty,a Justo Cobob and
Christopher Glidewellc*
a
´
Departamento de Quımica, Universidad de Valle, AA 25360 Cali, Colombia,
b
´
´
´
´
Departamento de Quımica Inorganica y Organica, Universidad de Jaen, 23071
Jaen, Spain, and cSchool of Chemistry, University of St Andrews, Fife KY16 9ST,
´
Scotland
Correspondence e-mail: cg@st-andrews.ac.uk
Received 10 June 2010
Accepted 15 June 2010
Online 7 July 2010
The molecules of the title compound, C26H25N3OS, which was
prepared by means of an acid-catalysed cyclocondensation
reaction between a 6-aminopyrimidinone and 2,6-dibenzyl-
idenecyclohexanone, exhibit a polarized electronic structure,
namely (9E)-9-benzylidene-3-methyl-2-methylsulfanyl-5-phenyl-
3,5,6,7,8,9-hexahydropyrimido[4,5-b]quinolin-10-ium-4-olate,
involving charge separation in the vinylogous amide portion.
Four hydrogen bonds, two each of the C—Hꢀ ꢀ ꢀO and C—
Hꢀ ꢀ ꢀꢀ(arene) types, link the molecules into bilayers
comprising inversion-related pairs of sheets, each containing
a single type of R34(36) ring.
Comment
In our search for new bioactive compounds based on
heterocyclic frameworks, pyrimido[4,5-b]quinolines have
emerged as interesting targets because of their structural
analogy with flavones. We report here the molecular and
supramolecular structure of the title compound, (I), which was
prepared using an acid-catalysed cyclocondensation between
(2E,6E)-2,6-dibenzylidenecyclohexanone and 6-amino-3-
methyl-2-(methylsulfanyl)pyrimidin-4(3H)-one (see scheme).
This synthetic procedure may be contrasted with the synthesis
of the related compound, (II), which employed a multi-
component cyclocondensation reaction under environmen-
tally friendly solvent-free conditions, mediated by microwave
radiation (Low, Cobo, Cisneros et al., 2004).
The adjacent carbocyclic ring adopts an envelope confor-
mation, folded across the line C6ꢀ ꢀ ꢀC8, with ring-puckering
parameters, for the atom sequence C5a—C6—C7—C8—C9—
ꢁ
ꢁ
˚
C9a, of Q = 0.481 (3) A, ꢁ = 58.6 (4) and ’ = 117.6 (4) . The
angles may be compared with the ideal values for an envelope
conformation of ꢁ = 54.7ꢁ and ’ = 60kꢁ, where k again
represents an integer. By contrast, the pyrimidine component
of the fused ring system is planar. The remainder of the
molecular conformation can be specified in terms of just three
torsion angles (Table 1), defining the orientation of the various
substituents relative to the adjacent components of the fused
ring system. While the C atom of the methylsulfanyl substi-
The molecules of (I) contain a stereogenic centre at C5
(Fig. 1) and the reference molecule was selected as one having
the R configuration at C5. However, the centrosymmetric
space group accommodates equal numbers of the two
enantiomorphs. In addition, the two rings which are fused at
Acta Cryst. (2010). C66, o389–o391
doi:10.1107/S0108270110023139
# 2010 International Union of Crystallography o389

organic compounds
Figure 2
A stereoview of part of the crystal structure of (I), showing the formation
of a hydrogen-bonded sheet of R34(36) rings lying parallel to (010) and
built from two independent C—Hꢀ ꢀ ꢀO hydrogen bonds. For the sake of
clarity, H atoms not involved in the motif shown have been omitted.
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.
again related by translation, into a C(13) chain running
parallel to the [101] direction. The combination of these two
chain motifs generates a sheet lying parallel to (010) and built
from a single type of R34(36) ring (Fig. 2). Of the two C—
Hꢀ ꢀ ꢀꢀ(arene) hydrogen bonds, that having the longer
Hꢀ ꢀ ꢀcentroid distance lies within the (010) sheet and hence
provides a modest reinforcement of the sheet formation, while
the shorter of these two interactions weakly links an inversion-
related pair of sheets into a bilayer parallel to (010). Aromatic
ꢀ–ꢀ stacking interactions, however, are absent from the
structure.
It is of interest briefly to compare the supramolecular
aggregation in (I) with those in the related compounds, (II)
and (III). In (II), which crystallizes as a stoichiometric 1:1
solvate with dimethylformamide (Low, Cobo, Cisneros et al.,
2004), inversion-related pairs of pyrimidinedione molecules
are linked by pairs of N—Hꢀ ꢀ ꢀO hydrogen bonds to form
centrosymmetric R22(8) dimers, from which the dimethyl-
formamide molecules are pendent, and these dimers are
linked into chains by a single C—Hꢀ ꢀ ꢀꢀ(arene) hydrogen
bond.
tuent is almost coplanar with the adjacent ring, the C51–C56
aryl ring is nearly orthogonal to the mean plane of the reduced
pyridine ring (Table 1), with a dihedral angle between the
mean planes of 83.0 (2)ꢁ.
Within the fused heterocyclic ring system, the bond
distances are fairly similar to those found in the related
methylsulfanylpyrimidinone (III), where the polarized form
(IIIa) was deduced to be important (Low, Cobo, Cruz et al.,
2004). In particular, in (I), the N10—C10a bond is significantly
longer than the N10—C9a bond, while the C4—C4a bond is
significantly shorter than the analogous C9—C9a bond. The
C5a—C9a and C9—C90 bonds are localized double bonds.
These observations point to a contribution to the electronic
structure of (I) from the polarized form (Ia). By contrast, in
(II) (Low, Cobo, Cisneros et al., 2004), the polarization of the
structure involves the carbonyl unit in the five-membered
carbocyclic ring, rather than that in the pyrimidone ring (see
scheme).
The supramolecular aggregation in (I) is determined by two
C—Hꢀ ꢀ ꢀO hydrogen bonds and two C—Hꢀ ꢀ ꢀꢀ(arene)
hydrogen bonds (Table 2), but the N—H group in the reduced
pyridine ring plays no part in the hydrogen bonding. The only
potential acceptor within plausible hydrogen-bonding
distance of atom N10 in the reference molecule at (x, y, z) is
the corresponding atom N10 in the molecule at (1 ꢂ x, 1 ꢂ y,
By contrast, (III) crystallizes in a solvent-free form (Low,
Cobo, Cruz et al., 2004) and, while the structure contains three
hydrogen bonds, one of the O—Hꢀ ꢀ ꢀO type and two of the
N—Hꢀ ꢀ ꢀO type, two of them are intramolecular. The
remaining N—Hꢀ ꢀ ꢀO hydrogen bond links molecules related
by translation into simple C(9) chains, and antiparallel pairs of
these chains are weakly linked by a single ꢀ–ꢀ stacking
interaction involving pyrimidine rings.
˚
1 ꢂ z), but the Nꢀ ꢀ ꢀN distance is 3.163 (2) A and, more
significantly, the N—Hꢀ ꢀ ꢀN angle is only 91ꢁ.
The two C—Hꢀ ꢀ ꢀO hydrogen bonds form a simple sheet.
The hydrogen bond having atom C53 as the donor links
molecules related by translation into a C(8) (Bernstein et al.,
1995) chain running parallel to the [100] direction, while the
hydrogen bond having atom C94 as the donor links molecules,
Experimental
A catalytic quantity of boron trifluoride etherate was added to an
ethanol solution containing equimolar quantities of (2E,6E)-2,6-di-
benzylidenecyclohexanone and 6-amino-3-methyl-2-(methylsulfan-
ꢃ
o390 Becerra et al. C26H25N3OS
Acta Cryst. (2010). C66, o389–o391

organic compounds
yl)pyrimidin-4(3H)-one, and this mixture was then stirred for 3 d at
ambient temperature. The resulting solid product was collected by
filtration and recrystallized from an ethanol–dimethylformamide
mixture (1:1 v/v) to give yellow crystals of (I) suitable for single-
crystal X-ray diffraction [yield 56%, m.p. 490–493 K (decomposi-
tion)]. MS (EI) m/z: 427 [M+] (6), 350 (100), 302 (8).
with C—H = 0.95 (aromatic and alkenyl), 0.98 (CH3), 0.99 (CH2) or
˚
1.00 A (aliphatic CH), and with Uiso(H) = kUeq(C), 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 bonded to C atoms. The H atom bonded to
atom N10 was permitted to ride at the position found in a difference
˚
map, with Uiso(H) = 1.2Ueq(N), giving an N—H distance of 0.92 A
and a sum of the bond angles at atom N10 of 359ꢁ. There is a short
˚
(1.80 A) nonbonded intramolecular contact between atoms H10 and
Crystal data
H90, but the mutual disposition of the carrier atoms N10 and C90 is
determined by the rigidity imposed on this part of the molecular
skeleton by the ꢀ-system (see scheme). PLATON (Spek, 2009)
C26H25N3OS
Mr = 427.55
Triclinic, P1
ꢄ = 76.43 (3)ꢁ
V = 1071.1 (5) A
Z = 2
Mo Kꢂ radiation
ꢅ = 0.18 mmꢂ1
T = 120 K
0.27 ꢄ 0.20 ꢄ 0.10 mm
3
˚
3
˚
˚
a = 8.382 (2) A
reports a void volume of 54.3 A centred at the origin, but none of the
˚
b = 10.777 (3) A
maxima in the final difference map is particularly close to the origin,
while the SQUEEZE option in PLATON reported only one addi-
tional electron per unit cell. We conclude that there is no significant
electron density within this void volume.
˚
c = 12.745 (4) A
ꢂ = 73.18 (3)ꢁ
ꢃ = 85.13 (4)ꢁ
Data collection
Data collection: COLLECT (Nonius, 1999); cell refinement:
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 refine structure: SHELXL97
(Sheldrick, 2008); molecular graphics: PLATON (Spek, 2009); soft-
ware used to prepare material for publication: SHELXL97 and
PLATON.
Bruker–Nonius KappaCCD area-
detector diffractometer
Absorption correction: multi-scan
(SADABS; Sheldrick, 2003)
Tmin = 0.942, Tmax = 0.983
22289 measured reflections
3983 independent reflections
2998 reflections with I > 2ꢆ(I)
Rint = 0.060
Refinement
R[F2 > 2ꢆ(F2)] = 0.053
wR(F2) = 0.104
S = 1.10
282 parameters
H-atom parameteꢂrs3 constrained
´
´
The authors thank the Centro de Instrumentacion Cientı-
˚
Áꢇmax = 0.25 e A
´
´
fico-Tecnica of the Universidad de Jaen and the staff for the
data collection. DB and BI thank COLCIENCIAS, Univer-
sidad del Valle and Universidad de los Andes for financial
ꢂ3
˚
3983 reflections
Áꢇmin = ꢂ0.33 e A
´
support. JC thanks the Consejerıa de Innovacion, Ciencia y
Empresa (Junta de Andalucıa, Spain), the Universidad de
´
Table 1
Selected geometric parameters (A, ).
ꢁ
˚
´
´
Jaen (project No. UJA_07_16_33) and the Ministerio de
Ciencia e Innovacion (project No. SAF2008-04685-C02-02) for
financial support.
N1—C2
C2—N3
N3—C4
C4—C4a
C4a—C10a
C10a—N1
1.296 (3)
1.362 (3)
1.408 (3)
1.417 (3)
1.355 (3)
1.361 (3)
C4—O4
1.228 (3)
1.339 (3)
1.341 (3)
1.467 (3)
1.401 (3)
1.357 (3)
´
C9—C90
C5a—C9a
C9—C9a
C9a—N10
N10—C10a
Supplementary data for this paper are available from the IUCr electronic
archives (Reference: SK3376). Services for accessing these data are
described at the back of the journal.
N1—C2—S2—C21
C9—C90—C91—C92
1.6 (2)
ꢂ23.7 (4)
C4a—C5—C51—C52
ꢂ84.5 (3)
References
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Int. Ed. Engl. 34, 1555–1573.
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Table 2
Hydrogen-bond geometry (A, ).
ꢁ
˚
Cg1 and Cg2 are the centroids of the C51–C56 and C91–C96 rings,
respectively.
D—Hꢀ ꢀ ꢀA
D—H
Hꢀ ꢀ ꢀA
Dꢀ ꢀ ꢀA
D—Hꢀ ꢀ ꢀA
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Nonius (1999). COLLECT. Nonius BV, Delft, The Netherlands.
C53—H53ꢀ ꢀ ꢀO4i
C94—H94ꢀ ꢀ ꢀO4ii
C54—H54ꢀ ꢀ ꢀCg2iii
C96—H96ꢀ ꢀ ꢀCg1iv
0.95
0.95
0.95
0.95
2.50
2.48
2.93
2.89
3.440 (3)
3.325 (3)
3.772 (3)
3.765 (3)
170
148
149
154
Symmetry codes: (i) x ꢂ 1; y; z; (ii) x ꢂ 1; y; z þ 1; (iii) x; y; z ꢂ 1; (iv) ꢂx þ 1; ꢂy þ 1,
ꢂz þ 1.
¨
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Germany.
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All H atoms were located in difference maps. H atoms bonded to C
atoms were then treated as riding in geometrically idealized positions,
ꢃ
Acta Cryst. (2010). C66, o389–o391
Becerra et al. C26H25N3OS o391