Dimethyl 6-[1,2-bis-(methoxycarbonyl)-2-(triphenyl-λ5- phosphanylidene)-ethylideneamino]-2-methylsulfanyl-3,4-pyridinedicarboxylate forms a chain of hydrogen-bonded rings

Article abstract of DOI:10.1107/S0108270108016429

In the title compound, C34H31N2O8PS, the intra-molecular distances provide evidence for polarization of the mol-ecular-electronic structure. The mol-ecules are linked into complex chains of rings by three independent C - H...O hydrogen bonds. The significance of this study lies in its finding that two of the four carbonyl O atoms play no role in the hydrogen bonding, despite the large excess of potential hydrogen-bond donors present.

Full text of DOI:10.1107/S0108270108016429

organic compounds
Acta Crystallographica Section C
Crystal Structure
Communications
oxycarbonyl substituents on the pyridine ring are significantly
rotated out of the plane of the ring, with dihedral angles
between the pyridine ring and the Cx/Cx1/Ox1/Ox2 planes (x =
3 or 4, see Fig. 1) of 37.8 (2) and 44.6 (2)ꢁ when x = 3 and 4,
respectively. Such similarity of conformation is not mimicked
by the other pair of carboxylate substituents; the N6—C7—
C8—P9 fragment is markedly nonplanar and the torsion
angles C8—C7—C71—O71 and C7—C8—C81—O81 differ by
ISSN 0108-2701
Dimethyl 6-[1,2-bis(methoxycarbon-
yl)-2-(triphenyl-k5-phosphanylidene)-
ethylideneamino]-2-methylsulfanyl-
3,4-pyridinedicarboxylate forms a
chain of hydrogen-bonded rings
a
b
c
´
Fabian Orozco, John N. Low, Justo Cobo and
Christopher Glidewelld*
a
´
Departamento de Quımica, Universidad de Valle, AA 25360 Cali, Colombia,
bDepartment of Chemistry, University of Aberdeen, Meston Walk, Old Aberdeen
c
´
´
´
AB24 3UE, Scotland, Departamento de Quımica Inorganica y Organica, Univer-
sidad 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 20 May 2008
Accepted 29 May 2008
Online 14 June 2008
In the title compound, C34H31N2O8PS, the intramolecular
distances provide evidence for polarization of the molecular–
electronic structure. The molecules are linked into complex
chains of rings by three independent C—Hꢀ ꢀ ꢀO hydrogen
bonds. The significance of this study lies in its finding that two
of the four carbonyl O atoms play no role in the hydrogen
bonding, despite the large excess of potential hydrogen-bond
donors present.
well over 20ꢁ (Table 1). Associated with this difference in
conformation is a significant difference between the C7—C71
˚
and C8—C81 bond lengths of 0.73 (3) A, whereas C3—C31
˚
and C4—C41 differ by only 0.022 (3) A. These observations
Comment
The triphenylphosphoranylidene unit (Ph3P N) has proven
to be an effective protecting group for the amino substituent
in aminopyrimidines and aminopyrimidinones, which are
themselves useful precursors for the synthesis of substituted
2-aminopyridines (Cobo et al., 1994). We report here the
synthesis and structure of the title compound, (I) (Fig. 1),
prepared by reaction of dimethyl acetylenedicarboxylate
(DMAD) with the protected 6-aminopyrimidin-4(3H)-one
(II), presumably via the intermediate (III). The first step, viz.
conversion of (II) to (III) via a Diels–Alder addition followed
by a retro Diels–Alder elimination, finds a precedent in the
conversion of (II) to the pyridine (IV) (Cobo et al., 2008),
while the second step, also involving cycloaddition followed by
cycloreversion, is closely analogous to the conversion of (V) to
(VI) (Cobo et al., 1999).
taken together indicate a modest contribution to the overall
molecular–electronic structure of the polarized form (Ia) (see
scheme below) involving short-range charge separation, but
The Ph3P N fragment of the molecule of (I) has very
approximate C3 local symmetry, as indicated by the relevant
torsion angles (Table 1), while the methylsulfanyl substituent
is nearly coplanar with the pyridine ring; the displacement of
the long-range polarized form (Ib) is effectively ruled out by
the molecular geometry. A similar conformational arrange-
˚
atom C21 from this plane is only 0.347 (3) A. The two meth-
Acta Cryst. (2008). C64, o379–o381
doi:10.1107/S0108270108016429
# 2008 International Union of Crystallography o379

organic compounds
Figure 3
A stereoview of part of the crystal structure of (VI), showing the
formation of a molecular ladder parallel to the [100] direction in the form
of a ꢀ-stacked pair of hydrogen-bonded chains. The original atomic
coordinates (Cobo et al., 1999) have been used and, 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.
the number of aromatic rings within the molecule, there are no
C—Hꢀ ꢀ ꢀꢀ hydrogen bonds and no ꢀ–ꢀ stacking interactions.
It is notable that, although there are four independent
carbonyl O atoms present in the molecule of (I) (O31, O41,
O71 and O81), two of them play no part in the hydrogen
bonding, despite the large excess of potential hydrogen-bond
donors present, while O71 acts as a double acceptor. By
contrast, in the structure of the related compound (VI), there
is only one C—Hꢀ ꢀ ꢀO hydrogen bond, utilizing the carbonyl O
atom closest to the P atom to form a C(9) chain (Cobo et al.,
1999). Further analysis of the crystal structure of (VI) now
shows that, in addition, pairs of these chains are linked by a
single aromatic ꢀ–ꢀ stacking interaction between the aryl
groups of the benzyl substituents in centrosymmetrically
related molecules to form a molecular ladder running parallel
to the [100] direction (Fig. 3).
ment of the two ester groups was observed in the structure of
(VI) (Cobo et al., 1999). Although the intramolecular
distances in (VI) were not discussed in the original report,
scrutiny of the geometry of (VI) in fact indicates electronic
delocalization precisely analogous to that in (Ia)
The molecules of (I) are linked by three independent C—
Hꢀ ꢀ ꢀO hydrogen bonds (Table 2). Aryl atoms C922 and C934
in the molecule at (x, y, z) act as hydrogen-bond donors,
respectively, to carbonyl atoms O41 and O71, both in the
molecule at (x, y ꢂ 1, z), so forming C(12) and C(10) (Bern-
stein et al., 1995) chains, respectively, generated by translation.
In addition, aryl atom C924 at (x, y, z) acts as a hydrogen-bond
1
donor to carbonyl atom O71 in the molecule at (ꢂx + 12, y ꢂ ,
2
ꢂz + 12), so linking molecules related by the 21 screw axis along
(14, y, 14 ) to form another C(10) chain. The combination of these
three hydrogen bonds then forms a complex chain of rings
running parallel to the [010] direction and containing rings of
R22(18), R32(22) and R33(24) types (Fig. 2). Two chains of this
type pass through each unit cell, but there are no direction-
specific interactions between the chains. In particular, despite
Experimental
A mixture of 3-methyl-2-methylsulfanyl-6-(triphenyl-ꢁ5-phosphanyl-
ideneamino)pyrimidin-4(3H)-one, (II) (0.5 mmol), and dimethyl
acetylenedicarboxylate (1.1 mmol) with dry acetonitrile (0.9 ml) was
subjected to microwave radiation in a CEM monomode microwave
reactor in a sealed tube under magnetic stirring for 12 min (323 K and
100 W maximum power), the progress of the reaction being moni-
tored by thin-layer chromatography. After the mixture had been
cooled to ambient temperature, the solvent was removed under
reduced pressure. The crude product was purified by chromatography
on silica gel using a mixture of dichloromethane and acetone (96:4
v/v) as eluant to give the title compound, which was then crystallized
from dry ethanol to give crystals suitable for single-crystal X-ray
diffraction (yellow blocks, 67% yield, m.p. 444 K). MS m/z (abun-
dance %): 658 (M+, 59), 599 (100), 472 (15), 383 (11), 313 (11), 299
(10), 262 (46), 216 (19), 183 (54), 108 (24), 59 (16), 44 (11).
Crystal data
3
˚
C34H31N2O8PS
Mr = 658.64
V = 3179.7 (5) A
Z = 4
Figure 2
Monoclinic, P21=n
Mo Kꢃ radiation
ꢄ = 0.21 mmꢂ1
T = 120 (2) K
0.32 ꢃ 0.21 ꢃ 0.10 mm
˚
A stereoview of part of the crystal structure of (I), showing the formation
of a hydrogen-bonded chain of rings parallel to [010]. For the sake of
clarity, H atoms not involved in the interactions shown have been
omitted.
a = 14.8046 (12) A
˚
b = 12.0095 (12) A
˚
c = 18.9720 (16) A
ꢂ = 109.499 (8)ꢁ
ꢄ
o380 Orozco et al. C34H31N2O8PS
Acta Cryst. (2008). C64, o379–o381

organic compounds
Data collection
(Duisenberg et al., 2003); program(s) used to solve structure: SIR2004
(Burla et al., 2005); program(s) used to refine structure: OSCAIL
(McArdle, 2003) and SHELXL97 (Sheldrick, 2008); molecular
graphics: PLATON (Spek, 2003); software used to prepare material
for publication: SHELXL97 and PRPKAPPA (Ferguson, 1999).
Bruker–Nonius KappaCCD
diffractometer
Absorption correction: multi-scan
(SADABS; Sheldrick, 2003)
Tmin = 0.942, Tmax = 0.979
68029 measured reflections
7297 independent reflections
4859 reflections with I > 2ꢅ(I)
Rint = 0.075
´
The authors thank ‘Servicios Tecnicos de Investigacion of
Universidad de Jaen’ and the staff for data collection. JC
´
Refinement
´
R[F2 > 2ꢅ(F2)] = 0.055
wR(F2) = 0.104
S = 1.09
420 parameters
H-atom parameteꢂrs3 constrained
´
´
thanks the Consejerıa de Innovacion, Ciencia y Empresa
˚
Áꢆmax = 0.38 e A
´
´
(Junta de Andalucıa, Spain) and Universidad de Jaen for
financial support. FO thanks COLCIENCIAS and
UNIVALLE (Universidad del Valle, Colombia) for financial
support that permitted a short stay at Departamento de
ꢂ3
˚
7297 reflections
Áꢆmin = ꢂ0.36 e A
Table 1
Selected geometric parameters (A, ).
ꢁ
˚
´ ´ ´ ´
Quımica Inorganica y Organica, Universidad de Jaen.
C3—C31
C4—C41
1.483 (3)
1.505 (3)
C7—C71
C8—C81
1.528 (3)
1.455 (3)
Supplementary data for this paper are available from the IUCr electronic
archives (Reference: SK3237). Services for accessing these data are
described at the back of the journal.
C4—C3—C31—O31
C5—C4—C41—O41
C8—C7—C71—O71
C7—C8—C81—O81
ꢂ144.5 (3)
ꢂ130.7 (3)
123.8 (3)
N6—C7—C8—P9
ꢂ22.3 (3)
151.8 (2)
163.91 (17)
116.1 (2)
C8—P9—C911—C912
C8—P9—C921—C922
C8—P9—C931—C932
References
147.6 (2)
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Table 2
Hydrogen-bond geometry (A, ).
ꢁ
˚
´
´
Cobo, J., Garcıa, C., Melguizo, M., Sanchez, A. & Nogueras, M. (1994).
D—Hꢀ ꢀ ꢀA
D—H
Hꢀ ꢀ ꢀA
Dꢀ ꢀ ꢀA
D—Hꢀ ꢀ ꢀA
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C922—H922ꢀ ꢀ ꢀO41i
C924—H924ꢀ ꢀ ꢀO71ii
C934—H934ꢀ ꢀ ꢀO71i
0.95
0.95
0.95
2.50
2.43
2.42
3.225 (3)
3.315 (3)
3.272 (3)
133
155
149
´
1
2
1
2
1
2
Symmetry codes: (i) x; y ꢂ 1; z; (ii) ꢂx þ ; y ꢂ ; ꢂz þ .
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absences. All H atoms were located in difference maps and then
treated as riding atoms, with C—H distances of 0.95 (arene and
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˚
pyridine) or 0.98 A (methyl), and with Uiso(H) = kUiso(C), where k =
1.5 for the methyl groups and k = 1.2 for the other H atoms.
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DIRAX/LSQ (Duisenberg et al., 2000); data reduction: EVALCCD
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ꢄ
Acta Cryst. (2008). C64, o379–o381
Orozco et al. C34H31N2O8PS o381