Ethyl 2-meth-oxy-6-[(triphenylphos-phoranylidene)amino]nicotinate and ethyl 2-methylsulfanyl-6-[(triphenylphospho-ranylidene)amino]nicotinate

Article abstract of DOI:10.1107/S0108270108006963

The mol-ecules of ethyl 2-meth-oxy-6-[(triphenyl-phospho-ranyl-idene)amino] nicotinate, C27H25N2O3P, (I), and ethyl 2-methylsulfanyl-6-[(triphenyl-phospho- ranyl-idene)amino]nicotinate, C27H25N2O2PS, (II), have almost identical bond lengths and mol-ecular

Full text of DOI:10.1107/S0108270108006963

organic compounds
Acta Crystallographica Section C
Crystal Structure
While the molecular structures of compounds (I) and (II) are
almost identical, their crystal structures differ considerably.
Communications
ISSN 0108-2701
Ethyl 2-methoxy-6-[(triphenylphos-
phoranylidene)amino]nicotinate and
ethyl 2-methylsulfanyl-6-[(triphenyl-
phosphoranylidene)amino]nicotinate
Justo Cobo,a Christopher Glidewell,b* John N. Lowc and
d
´
Fabıan Orozco
a
´
´
´
´
Departamento de Quımica Inorganica y Organica, Universidad de Jaen, 23071
Jaen, Spain, bSchool of Chemistry, University of St Andrews, Fife KY16 9ST,
´
Scotland, cDepartment of Chemistry, University of Aberdeen, Meston Walk, Old
d
´
Aberdeen AB24 3UE, Scotland, and Departamento de Quımica, Universidad de
Valle, AA 25360 Cali, Colombia
Correspondence e-mail: cg@st-andrews.ac.uk
Received 4 March 2008
Accepted 12 March 2008
Online 20 March 2008
The molecules of ethyl 2-methoxy-6-[(triphenylphosphoranyl-
idene)amino]nicotinate, C27H25N2O3P, (I), and ethyl 2-methyl-
sulfanyl-6-[(triphenylphosphoranylidene)amino]nicotinate,
C27H25N2O2PS, (II), have almost identical bond lengths and
molecular conformations, and both show evidence for
polarized electronic structures. However, the crystal struc-
tures, as illustrated by the weak hydrogen bonds linking the
molecules, are significantly different. The significance of this
study lies in the observation that two compounds which are
almost identical in constitution, configuration and conforma-
tion nonetheless adopt different crystal structures.
Compounds (I) and (II) both crystallize in the P1 space
group and the repeat vectors of the two unit cells are extre-
mely similar, with the maximum difference, in c, being less
than 1%. However, the cell angles in (II) are all close to the
supplementary values in (I), i.e. each angle ꢀ (ꢀ = ꢁ, ꢂ or ꢃ) in
(II) corresponds rather closely to (180ꢀ ꢁ ꢀ) in (I), such that
no transformation can interconvert the two unit cells.
The molecular structures of (I) and (II) (Figs. 1 and 2) are
very similar. The conformations, as defined by the leading
torsion angles (Table 1), are almost identical, with the
Ph3P N fragments adopting approximate local threefold
rotational symmetry, while the chain-extended ester fragment
is, in both compounds, directed away from the MeX (X = O or
S) substituent at C2. In each compound, there is a reasonably
short intramolecular C—Hꢂ ꢂ ꢂN hydrogen bond, with almost
identical dimensions in the two compounds (Table 2), and
these interactions may be of significance in influencing the
overall molecular conformations. No such contacts are
apparent in the structures of (III) and (IV) (Low et al.,
1998).
With the exception of the parameters involving the MeX
substituents, the corresponding bond distances in (I) and (II)
are also very similar. The distances and angles around the P
atoms are similar to the corresponding parameters in the
precursor compounds (III) and (IV) (Low et al., 1998). In
particular, all of (I)–(IV) exhibit wide angles at N6 and all
exhibit a range of ca 10ꢀ in the bond angles at P6. Within each
pyridine ring, the N1—C2 bond is significantly shorter than
N1—C6, while C4—C5 is significantly shorter than all of the
other C—C bonds in this ring. In addition, the C3—C31 bond
Comment
2-Aminopyridines are an important class of heterocyclic
compounds with applications in the agrochemical and
pharmaceutical sectors (Vijn et al., 1993), and an effective
route to substituted 2-aminopyridines has been developed
(Cobo et al., 1994) based on tandem Diels–Alder/retro-Diels–
Alder reactions of 6-aminopyrimidin-4(3H)-ones with acetyl-
enic esters. The structures of two such products have been
reported (Low et al., 1996). The triphenylphosphoranylidene
unit is an effective protecting group for the 6-amino substi-
tuent (Wamhoff et al., 1986), and this is readily introduced by
reaction of the aminopyrimidine precursor with triphenyl-
phosphine in the presence of hexachloroethane (Wamhoff et
al., 1986). The structures of the protected precursors, (III) and
(IV) (see scheme), were reported several years ago (Low et al.,
1998), and we report here the structures of the title com-
pounds, (I) and (II), derived from (III) and (IV), respectively,
using their reactions with ethyl propiolate (ethyl acetylene-
monocarboxylate) conducted under microwave irradiation.
˚
is somewhat short for its type (mean value 1.487 A; Allen et
al., 1987), while C31—O31 is somewhat long (mean value
Acta Cryst. (2008). C64, o233–o236
doi:10.1107/S0108270108006963
# 2008 International Union of Crystallography o233

organic compounds
Figure 1
The molecular structure of compound (I), showing the atom-labelling
scheme. Displacement ellipsoids are drawn at the 30% probability level.
Figure 3
A stereoview of part of the crystal structure of compound (I), showing the
formation of a chain of rings along [101], built from C—Hꢂ ꢂ ꢂO hydrogen
bonds only. For the sake of clarity, H atoms not involved in the motifs
shown have been omitted.
Figure 2
The molecular structure of compound (II), showing the atom-labelling
scheme. Displacement ellipsoids are drawn at the 30% probability level.
˚
1.196 A). These observations, taken all together, support a
degree of quinonoidal bond fixation within the pyridine rings,
corresponding to the polarized forms (Ia) and (IIa) (see
scheme). The bond distances in the precursor compounds (III)
and (IV) similarly show clear evidence for polarization of the
molecular–electronic structures, with the short exocyclic C—N
bonds, the long carbonyl C—O bonds and the similarity of the
two C—C distances in the polarized fragments all pointing
towards the significance of forms (IIIa) and (IVa) in addition
to the classical forms (III) and (IV).
Figure 4
A stereoview of part of the crystal structure of compound (II), showing
the formation of a chain of rings along [001], built from C—Hꢂ ꢂ ꢂO and
C—Hꢂ ꢂ ꢂꢄ(pyridyl) hydrogen bonds. For the sake of clarity, H atoms
bonded to C atoms not involved in the motifs shown have been omitted.
The molecules of (I) are linked, albeit rather weakly, by
three C—Hꢂ ꢂ ꢂO hydrogen bonds, all involving the polarized
carbonyl atom O31 as acceptor. Atoms C64 and C65 in the
molecule at (x, y, z) both act as hydrogen-bond donors to atom
O31 in the molecule at (ꢁ1 + x, y, 1 + z), so forming a
C(12)C(13)[R12(5)] (Bernstein et al., 1995) chain of rings
running parallel to the [101] direction. Antiparallel pairs of
such chains are linked by the third C—Hꢂ ꢂ ꢂO hydrogen bond
to form a more complex chain containing three types of ring,
with alternating centrosymmetric R22(26) and R42(24) rings and
pairs of R12(5) rings flanking the R24(24) rings (Fig. 3).
bond (Table 2), with the former generating C(12) chains
running parallel to the [001] direction and the latter linking
antiparallel pairs of such chains into a chain of edge-fused
centrosymmetric rings (Fig. 4). Hence, despite the almost
identical intramolecular geometries of (I) and (II), their
patterns of supramolecular aggregation are different. Such a
contrast between the similarity in molecular structures and the
difference in crystal structures could provide an interesting
test for methods for crystal structure prediction from first
principles.
The original report on the structures of the precursor
compounds (III) and (IV) did not discuss the intermolecular
interactions (Low et al., 1998). Analysis using the original atom
By contrast, the molecules of (II) are linked by one C—
Hꢂ ꢂ ꢂO hydrogen bond and one C—Hꢂ ꢂ ꢂꢄ(pyridyl) hydrogen
ꢃ
o234 Cobo et al. C27H25N2O3P and C27H25N2O2PS
Acta Cryst. (2008). C64, o233–o236

organic compounds
Compound (I)
Crystal data
C27H25N2O3P
Mr = 456.46
Triclinic, P1
ꢃ = 85.93 (2)ꢀ
V = 1159.5 (5) A
Z = 2
Mo Kꢁ radiation
ꢅ = 0.15 mmꢁ1
T = 120 (2) K
0.22 ꢄ 0.20 ꢄ 0.15 mm
3
˚
˚
a = 8.5336 (18) A
˚
b = 11.063 (3) A
˚
c = 13.426 (3) A
ꢁ = 73.722 (18)ꢀ
ꢂ = 72.389 (16)ꢀ
Data collection
Bruker–Nonius KappaCCD area-
detector diffractometer
Absorption correction: multi-scan
(SADABS; Sheldrick, 2003)
Tmin = 0.972, Tmax = 0.978
30925 measured reflections
5321 independent reflections
3750 reflections with I > 2ꢆ(I)
Rint = 0.080
Figure 5
A stereoview of part of the crystal structure of compound (III), showing
the formation of a hydrogen-bonded R22(20) dimer. The original atom
coordinates (Low et al., 1998) have been used and, for the sake of clarity,
H atoms not involved in the motif shown have been omitted.
Refinement
R[F2 > 2ꢆ(F2)] = 0.054
wR(F2) = 0.120
S = 1.08
300 parameters
H-atom parameteꢁrs3 constrained
˚
Áꢇmax = 0.32 e A
ꢁ3
˚
5321 reflections
Áꢇmin = ꢁ0.40 e A
Compound (II)
Crystal data
C27H25N2O2PS
Mr = 472.52
Triclinic, P1
a = 8.5671 (14) A
˚
b = 11.0617 (6) A
ꢃ = 94.596 (10)ꢀ
3
˚
V = 1185.7 (3) A
Z = 2
˚
Mo Kꢁ radiation
ꢅ = 0.23 mmꢁ1
T = 120 (2) K
0.46 ꢄ 0.31 ꢄ 0.29 mm
˚
c = 13.547 (2) A
ꢁ = 102.987 (8)ꢀ
ꢂ = 106.417 (12)ꢀ
Table 1
Selected geometric parameters (A, ) for compounds (I) and (II).
ꢀ
˚
(I)
(II)
Figure 6
N1—C2
C2—C3
C3—C4
C4—C5
C5—C6
C6—N1
C3—C31
C31—O31
C6—N6
N6—P6
P6—C61
P6—C71
P6—C81
1.319 (3)
1.406 (3)
1.401 (3)
1.365 (3)
1.413 (3)
1.359 (3)
1.466 (3)
1.207 (3)
1.359 (3)
1.5975 (18)
1.792 (2)
1.814 (2)
1.807 (2)
1.335 (2)
1.403 (2)
1.403 (2)
1.369 (2)
1.410 (2)
1.3581 (19)
1.470 (2)
1.212 (2)
1.3637 (19)
1.5944 (13)
1.7959 (16)
1.8148 (17)
1.8050 (16)
A stereoview of part of the crystal structure of compound (IV), showing
the formation of a hydrogen-bonded C(9) chain along [010]. The original
atom coordinates (Low et al., 1998) have been used and, for the sake of
clarity, H atoms not involved in the motif shown have been omitted.
coordinates shows that the molecules of (III) are linked by
paired C—Hꢂ ꢂ ꢂO hydrogen bonds to form a centrosymmetric
R22(20) dimer (Fig. 5), while in (IV) a single C—Hꢂ ꢂ ꢂO
hydrogen bond links molecules related by translation into a
C(9) chain (Fig. 6).
C6—N6—P6
124.01 (15)
105.47 (10)
115.46 (10)
114.99 (10)
105.61 (10)
107.39 (10)
107.20 (10)
124.59 (11)
104.98 (7)
115.61 (7)
115.68 (7)
106.30 (7)
106.87 (7)
106.65 (7)
N6—P6—C61
N6—P6—C71
N6—P6—C81
C61—P6—C71
C71—P6—C81
C81—P6—C61
Experimental
For the synthesis of compounds (I) and (II), mixtures of the
precursors (III) or (IV) (0.5 mmol), respectively, and ethyl propiolate
(2.5 mmol) in dry acetonitrile (0.9 ml) were subjected to microwave
irradiation (100 W for 0.5 h) in sealed tubes under magnetic stirring.
The resulting mixtures were evaporated to dryness under reduced
pressure, and the products were purified by chromatography on silica
using dichloromethane–acetone (98:2 v/v) as eluent. After removal of
the solvent, crystallization from ethanol gave samples of (I) and (II)
suitable for single-crystal X-ray diffraction. Compound (I): yellow
blocks, m.p. 483–484 K, yield 54%; compound (II): yellow blocks,
m.p. 492 K, yield 18%.
N6—P6—C61—C62
N6—P6—C71—C72
N6—P6—C81—C82
P6—N6—C6—N1
N1—C2—X21—C21†
C2—C3—C31—O32
C3—C31—O32—C32
C31—O32—C32—C33
158.42 (18)
124.5719)
136.53 (19)
ꢁ11.1 (3)
4.8 (3)
156.65 (13)
128.28 (14)
141.77 (13)
ꢁ7.7 (2)
11.65 (14)
165.7 (2)
ꢁ176.17 (19)
165.35 (14)
ꢁ176.39 (13)
ꢁ179.24 (15)
ꢁ177.9 (2)
† The X21 site represents atom O21 in compound (I) and S21 in compound (II).
ꢃ
Acta Cryst. (2008). C64, o233–o236
Cobo et al. C27H25N2O3P and C27H25N2O2PS o235

organic compounds
Table 2
Hydrogen bonds and short intramolecular contacts (A, ) for compounds
(I) and (II).
´
The authors thank the Servicios Tecnicos de Investigacion
of the Universidad de Jaen and the staff for data collection. JC
´
ꢀ
˚
´
´
´
thanks the Consejerıa de Innovacion, Ciencia y Empresa
Cg represents the centroid of the N1/C2–C6 ring.
´
´
(Junta de Andalucıa, Spain) and the Universidad de Jaen
for financial support. FO thanks COLCIENCIAS and
UNIVALLE (Universidad del Valle, Colombia) for financial
support that enabled a short stay at the Departamento de
D—Hꢂ ꢂ ꢂA
D—H
Hꢂ ꢂ ꢂA
Dꢂ ꢂ ꢂA
D—Hꢂ ꢂ ꢂA
(I)
C76—H76ꢂ ꢂ ꢂN1
C64—H64ꢂ ꢂ ꢂO31i
C65—H65ꢂ ꢂ ꢂO31i
C74—H74ꢂ ꢂ ꢂO31ii
C76—H76ꢂ ꢂ ꢂN1
C65—H65ꢂ ꢂ ꢂO31iii
C33—H33Bꢂ ꢂ ꢂCgiv
0.95
0.95
0.95
0.95
0.95
0.95
0.99
2.48
2.55
2.46
2.54
2.43
2.50
2.73
3.284 (3)
3.138 (3)
3.096 (3)
3.466 (3)
3.246 (3)
3.170 (2)
3.560 (2)
142
120
124
164
143
128
141
´ ´ ´ ´
Quımica Inorganica y Organica, Universidad de Jaen.
(II)
Supplementary data for this paper are available from the IUCr electronic
archives (Reference: SK3213). Services for accessing these data are
described at the back of the journal.
Symmetry codes: (i) ꢁ1 þ x; y; 1 þ z; (ii) 1 ꢁ x; 2 ꢁ y; ꢁz; (iii) x; y; ꢁ1 þ z; (iv) 2 ꢁ x,
1 ꢁ y; 2 ꢁ z.
Data collection
References
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24840 measured reflections
5400 independent reflections
4362 reflections with I > 2ꢆ(I)
Rint = 0.033
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˚
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˚
5400 reflections
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ꢃ
o236 Cobo et al. C27H25N2O3P and C27H25N2O2PS
Acta Cryst. (2008). C64, o233–o236