Benzylation and nitrosation of 4-amino-2-(methylsulfanyl)pyrimidin-6(1H)-one (see abstract)

Article abstract of DOI:10.1107/S0108270103013465

4-Amino-1-benzyl-2-(methylsulfanyl)pyrimidin-6(1H)-one, C ₁₂H₁₃N₃OS, crystallizes in two polymorphic forms, both having space group P2₁/c, with Z′ = 1 for form (I) and Z′ = 2 for form (II). In (I), the molecules are linked by a single N-H...O hydrogen bond into simple C(6) chains, which are themselves linked into sheets by aromatic π-π interactions, while in (II), chains of edge-fused R₄²(8) and R₄⁴(24) rings are generated by four distinct N-H...O hydrogen bonds. In 4-amino-1-benzyl-2-(methylsulfanyl)-5-nitrosopyrimidin-6(1H)-one, C ₁₂H₁₂N₄O₂S, (III), where Z′ = 2, two independent three-centre N-H...(N,O) hydrogen bonds generate a C(5)C(6)[R₁²(5)] chain of rings. In 4-amino-6-benzyloxy-2-(methylsulfanyl)pyrimidine, C₁₂H ₁₃N₃OS, (IV), which is isomeric with (I) and (II), a combination of N-H...N and N-H...O hydrogen bonds generates a sheet of alternating R₂²(8) and R₆⁶(28) rings.

Full text of DOI:10.1107/S0108270103013465

organic compounds
Acta Crystallographica Section C
Crystal Structure
Communications
Comment
Benzylation of 4-amino-2-(methylsulfanyl)pyrimidin-6(1H)-
one using benzyl chloride yields a mixture of two isomeric
benzyl derivatives, namely 4-amino-1-benzyl-2-(methyl-
sulfanyl)pyrimidin-6(1H)-one, (I), and 4-amino-6-benzyloxy-
2-(methylsulfanyl)pyrimidine, (IV), which result from N- and
O-benzylation, respectively (see reaction Scheme below).
Nitrosation of (I) and (IV) yields the corresponding 5-nitroso
derivatives (III) and (V), respectively. We have reported
previously the molecular and supramolecular structure of (V)
(Low, Quesada, Marchal, Nogueras et al., 2002) and report
ISSN 0108-2701
Benzylation and nitrosation of
4-amino-2-(methylsulfanyl)pyrimidin-
6(1H)-one: two P21/c polymorphs of
4-amino-1-benzyl-2-(methylsulfanyl)-
pyrimidin-6(1H)-one with Z0 = 1 and 2, here on two polymorphs, (I) and (II), of 4-amino-1-benzyl-2-
(methylsulfanyl)pyrimidin-6(1H)-one and on compounds
4-amino-6-benzyloxy-2-(methyl-
sulfanyl)pyrimidine and 4-amino-
1-benzyl-2-(methylsulfanyl)-5-
nitrosopyrimidin-6(1H)-one all give
different hydrogen-bonded supra-
molecular structures
(III) and (IV). The nitrosation of (I), which has Z0 = 1 in space
group P21/c, yielded deep-blue (III) and a second pale-green
product, (II). Compound (II) proved to be a polymorph of (I),
having Z0 = 2 in P21/c, which had cocrystallized with a very
small quantity (less than 3%) of (III).
Christopher Glidewell,a* John N. Low,b²
Antonio Marchalc and Antonio Quesadad³
aSchool of Chemistry, University of St Andrews, Fife KY16 9ST, Scotland,
bDepartment of Chemistry, University of Aberdeen, Meston Walk,
c
Â
Old Aberdeen AB24 3UE, Scotland, Departamento de Quõmica
Â
Â
Â
Â
Inorganica y Organica, Universidad de Jaen, 23071 Jaen, Spain, and
dSchool of Engineering, University of Dundee, Dundee DD1 4HN,
Scotland
Correspondence e-mail: cg@st-andrews.ac.uk
Received 23 May 2003
Accepted 16 June 2003
Online 22 July 2003
4-Amino-1-benzyl-2-(methylsulfanyl)pyrimidin-6(1H)-one,
C12H13N3OS, crystallizes in two polymorphic forms, both
having space group P21/c, with Z0 = 1 for form (I) and Z0 = 2
for form (II). In (I), the molecules are linked by a single
NÐHÁ Á ÁO hydrogen bond into simple C(6) chains, which are
themselves linked into sheets by aromatic ꢀ±ꢀ interactions,
while in (II), chains of edge-fused R24(8) and R44(24) rings are
generated by four distinct NÐHÁ Á ÁO hydrogen bonds.
In 4-amino-1-benzyl-2-(methylsulfanyl)-5-nitrosopyrimidin-
6(1H)-one, C12H12N4O2S, (III), where Z0 = 2, two indepen-
dent three-centre NÐHÁ Á Á(N,O) hydrogen bonds generate a
C(5)C(6)[R21(5)] chain of rings. In 4-amino-6-benzyloxy-2-
(methylsulfanyl)pyrimidine, C12H13N3OS, (IV), which is
isomeric with (I) and (II), a combination of NÐHÁ Á ÁN and
NÐHÁ Á ÁO hydrogen bonds generates a sheet of alternating
R22(8) and R66(28) rings.
In the molecule of (I) (Fig. 1), the C2ÐN3 and N3ÐC4
distances (Table 1) are typical of those for double and single
bonds of these types (Allen et al., 1987). On the other hand,
the C4ÐC5 distance is very long for a double bond of this type
Ê
Ê
(mean value = 1.326 A and upper quartile value = 1.334 A)
and the C5ÐC6 distance is correspondingly short (mean
Ê
Ê
value = 1.464 A and lower quartile value = 1.453 A; Allen et
al., 1987); at the same time, the C4ÐN4 bond is shorter than
Ê
typical ArÐNH2 bonds (mean value = 1.355 A and lower
Ê
quartile value = 1.340 A), while the C6ÐO6 distance is longer
² Postal address: Department of Electrical Engineering and Physics,
University of Dundee, Dundee DD1 4HN, Scotland.
  Â
³ On leave from the Departamento de Quõmica Inorganica y Organica,
than is typical for C O conjugated with C C (mean
Ê
Ê
value = 1.222 A and upper quartile value = 1.229 A). The two
independent CÐS distances differ as expected. Finally, the
 Â
Universidad de Jaen, 23071 Jaen, Spain.
o454 # 2003 International Union of Crystallography
DOI: 10.1107/S0108270103013465
Acta Cryst. (2003). C59, o454±o460

organic compounds
N1ÐC6 distance is much longer than is usual in amides (mean
molecular±electronic structure of (III). This result is consis-
tent with deductions, on geometrical grounds, of the impor-
tance of the analogous form D in the isomeric compound (V)
(Low, Quesada, Marchal, Nogueras et al., 2002).
The development of form A in both (I) and (II), and of form
C in (III), such that both the potential hydrogen-bond donor
(atom N4) and the potential acceptors [atom O6 in (I) and
(II), and atom O5 in (III)] carry signi®cant partial charges,
suggests that the intermolecular hydrogen bonding may be
dominated by these two components in the formation of so-
called resonance-assisted hydrogen bonds (Gilli et al., 1989,
1994, 2000; Bertolasi et al., 1991).
Ê
Ê
value = 1.346 A and upper quartile value = 1.356 A). All of
these observations point to the importance of the delocalized
form A as a signi®cant contributor to the overall molecular±
electronic structure, while effectively ruling out any signi®cant
contribution from form B (see Scheme below).
The crystal quality of (IV) (Fig. 4) was consistently very
poor, giving very poor diffraction characteristics, with poor
resolution and precision. Accordingly, we do not comment
In polymorph (II), molecule 1 (Fig. 2a) contains no trace of
a 5-nitroso substituent, but there is an approximate 5%
occupancy by a 5-nitroso substituent in molecule 2 (Fig. 2b).
Accordingly, the pattern of the bond distances in both mol-
ecules (Table 3) is very similar to that in (I), which is again
consistent with form A being a signi®cant contributor to the
overall molecular±electronic structure. In (III), which also
crystallizes with Z0 = 2 (Fig. 3), the bond lengths in the two
independent molecules are similar (Table 5) but differ from
those in (I) and (II) in several important respects. Firstly, the
Cn4ÐCn5 and Cn5ÐCn6 bonds (n = 1 or 2) are both signif-
icantly longer than the corresponding bonds in (I) and (II),
while the Cn4ÐNn4 and Cn6ÐOn6 bonds are both shorter,
implying that form C is an important contributor to the
Figure 2
Figure 1
The molecule of (I), showing the atom-labelling scheme. Displacement
ellipsoids are drawn at the 30% probability level.
The two independent molecules of (II), showing the atom-labelling
schemes for (a) molecule 1 and (b) molecule 2. Displacement ellipsoids
are drawn at the 30% probability level.
ꢀ
Acta Cryst. (2003). C59, o454±o460
Christopher Glidewell et al.
Isomers of C12H13N3OS, and C12H12N4O2S o455

organic compounds
here on the intramolecular geometry, except to note that the
conformation of the MeS substituent differs from that in (I)
and (II).
The importance of form A in (I) is emphasized by the fact
that the molecules of (I) are linked into simple C(6) chains
(Fig. 5) by a single NÐHÁ Á ÁO hydrogen bond (Table 2).
Amino atom N4 acts as a hydrogen-bond donor, via atom
H4B, to atom O6 in the molecule at (1 x, 12 + y, 21 z), and
propagation of this hydrogen bond produces a chain running
parallel to the [010] direction, generated by the 21 screw axis
along (12, y, 14 ). An antiparallel chain is generated by the screw
3
axis along (12, y, ). However, the N4ÐH4A bond partici-
4
pates neither in any conventional hydrogen bond nor in an
NÐHÁ Á Áꢀ(arene) hydrogen bond. Although an adjacent
phenyl ring is available, the H4AÁ Á ÁCg1(x, 1 + y, z) distance
Ê
is ꢁ3.42 A (Cg1 is the centroid of the C11±C16 ring), and atom
N3 does not act as a hydrogen-bond acceptor, although such
Figure 4
The molecule of (IV), showing the atom-labelling scheme. Displacement
ellipsoids are drawn at the 30% probability level.
behaviour is commonly observed in compounds of this type
(Low, Quesada, Marchal, Melguizo et al., 2002; Low, Quesada,
Marchal, Nogueras et al., 2002).
The chains generated by the NÐHÁ Á ÁO hydrogen bonds
are, however, linked by means of aromatic ꢀ±ꢀ-stacking
interactions. The phenyl rings in the molecules at (x, y, z) and
Figure 5
Part of the crystal structure of (I), showing the formation of a C(6) chain
Figure 3
The two independent molecules of (III), showing the atom-labelling
schemes for (a) molecule 1 and (b) molecule 2. Displacement ellipsoids
are drawn at the 30% probability level.
along [010]. Atoms marked with an asterisk (*), a hash (#) or an
1
ampersand (&) are at the symmetry positions (1 x, 12 + y,
(1 x, 12 + y, 12 z) and (x, 1 + y, z), respectively.
z),
2
ꢀ
o456 Christopher Glidewell et al.
Isomers of C12H13N3OS, and C12H12N4O2S
Acta Cryst. (2003). C59, o454±o460

organic compounds
(2 x, 1 y, z) are parallel, with an interplanar spacing of
Ê
3.488 (2) A and a centroid separation of 3.675 (2) A, corre-
Ê
Ê
sponding to a centroid offset of 1.157 (2) A. These two mol-
ecules lie in the chains along (12, y, 41 ) and (23, y, 41 ),
1
2
respectively. Similarly, the molecule at (1 x, 12 + y,
z),
which also lies in the (12, y, ) chain, forms a ꢀ±ꢀ-stacking
1
4
1
2
interaction with the molecule at ( 1 + x,
1
y, 12 + z), which
lies in the chain along (
,
y, 34 ). In this manner, the
2
hydrogen-bonded chains are linked to form a (102) sheet
(Fig. 6).
The two independent molecules in (II) are also linked by
three NÐHÁ Á ÁO hydrogen bonds (Table 4). Amino atom N14
of molecule 1 acts as a hydrogen-bond donor, via atom H14B,
to atom O26 of molecule 2 in the asymmetric unit. Atom N14
also acts as a donor, via atom H14A, to atom O26 in the
molecule at (1 x, 1 y, 1 z), and these two interactions
Figure 7
A stereoview of part of the crystal structure of (II), showing the
formation of a chain of edge-fused rings along [100]. For clarity, H atoms
bonded to C atoms have been omitted.
1
1
H14A, to both atom N25 and atom O26 in the type 2 molecule.
Similarly, atom N24 in the type 2 molecule at (x, y, z) acts as a
hydrogen-bond donor, via atom H24A, to atoms N15 and O16
in the type 1 molecule at (x, y, 1 + z). In this manner, a
C(5)C(6)[R21(5)] chain of rings is generated by translation
along [001] (Fig. 9). Two chains of this type run through each
unit cell, but there are no direction-speci®c interactions
between adjacent chains. The supramolecular structure of
(III) may be contrasted with that of the isomeric compound
(V); in (V), which also crystallizes with Z0 = 2, two indepen-
dent R22(8) dimers are formed by paired NÐHÁ Á ÁN hydrogen
bonds, and these dimers are linked into chains by means of
aromatic ꢀ±ꢀ-stacking interactions (Low, Quesada, Marchal,
Nogueras et al., 2002).
generate a centrosymmetric R24(8) ring centred at (21, ,
)
2
2
(Fig. 7). At the same time, amino atom N24 in molecule 2 at (x,
y, z) acts as a donor to atom O16 in the type 1 molecule at ( x,
1
y, 1 z), so generating an R44(24) ring centred at (0, 21, 12 ).
The combined effect of these hydrogen bonds is the formation
of a chain of edge-fused rings running parallel to the [100]
direction, with R24(8) rings centred at (n + 12, , ) (n = zero or
1
1
2
2
1
2
1
integer) alternating with R44(24) rings centred at (n, ,
)
2
(n = zero or integer) (Fig. 7). The formation of this chain is
reinforced by the overlap of centrosymmetrically related pairs
of highly polarized pyrimidinone rings (Fig. 8). The inter-
planar spacing between these rings in the type 2 molecules at
Ê
(x, y, z) and ( x, 1 y, 1 z) is 3.444 (2) A, and the centroid
Ê
separation is 3.514 (2) A, corresponding to a centroid offset of
In compound (IV), the molecules are linked into centro-
symmetric dimer units by pairs of strong NÐHÁ Á ÁN hydrogen
bonds (Table 7), and these units are linked into sheets by a
weaker NÐHÁ Á ÁO hydrogen bond. Amino atom N4 in the
molecule at (x, y, z) acts as a hydrogen-bond donor, via atom
H4A, to ring atom N3 in the molecule at (1 x, 1 y, 1 z),
Ê
only 0.698 (2) A.
Each of the two independent molecules of (III) contains an
intramolecular NÐHÁ Á ÁO hydrogen bond, de®ning an S(6)
motif, as is usual in molecules of this type with adjacent amino
and nitroso substituents. The molecules of (III) are linked into
chains by two independent three-centre NÐHÁ Á Á(N,O)
hydrogen bonds, each of which is asymmetric but essentially
planar (Table 6). In the asymmetric unit, amino atom N14 in
the type 1 molecule acts as a hydrogen-bond donor, via atom
Figure 8
Figure 6
Part of the crystal structure of (II), showing the overlap of pairs of type 2
molecules. Atoms marked with an asterisk (*) are at the symmetry
position ( x, 1 y, 1 z). For clarity, the unit-cell box and H atoms
bonded to C atoms have been omitted.
A stereoview of part of the crystal structure of (I), showing the linking of
the [010] chains into a (102) sheet by means of aromatic ꢀ±ꢀ-stacking
interactions. For clarity, H atoms bonded to C atoms have been omitted.
ꢀ
Acta Cryst. (2003). C59, o454±o460
Christopher Glidewell et al.
Isomers of C12H13N3OS, and C12H12N4O2S o457

organic compounds
entirely different from those of (I) and (II), it is, in fact, similar
to that of 4-amino-2,6-dimethoxypyrimidine, (VI) (Glidewell
et al., 2003), as indeed the overall conformation of (IV) is
similar to that of both (V) and (VI).
Thus, in summary, no two isomeric or polymorphic
compounds in this series adopt the same pattern of
supramolecular aggregation. The two polymorphs (I) and (II)
form ꢀ-stacked chains and chains of edge-fused rings,
respectively, while the isomeric compound (IV) forms sheets.
Compound (III) forms a simple chain of rings, while its isomer
(V) forms chains of ꢀ-stacked dimers.
Experimental
A suspension of 6-amino-2-(methylsulfanyl)pyrimidin-4(3H)-one
(10.00 g, 63.62 mmol) and ®nely ground K2CO3 (11.89 g, 86 mmol) in
dimethyl sulfoxide (90 ml) was stirred at room temperature for 1 h.
Benzyl chloride (10 ml, 86 mmol) was then added and the mixture
was stirred at room temperature for 9 h. Cold water (270 ml) was
added to the mixture, with continuous stirring, to precipitate the
water-insoluble reaction products. The resulting mixture was stirred
for a further 2 h, and a white solid was then collected by ®ltration,
washed with water and dried in vacuo. The dried solid was suspended
in diethyl ether (300 ml) and stirred for 24 h. The solid in suspension
was collected by ®ltration, washed with diethyl ether and recrys-
tallized from ethanol to afford the pure N-benzyl isomer (I) (2.23 g,
9.02 mmol, 14%). The ethereal ®trate was evaporated under reduced
pressure and the residue was chromatographed on silica gel with
mixed dichloromethane±acetone to afford the corresponding
O-benzyl isomer (IV) (5.42 g, 22.4 mmol, 35%) and further crystals of
(I) (0.378 g, 1.53 mmol, 2.4%). Crystals of (I) and (IV) suitable for
single-crystal X-ray diffraction were obtained by slow evaporation of
solutions in ethyl acetate for (I) (m.p. 478 K) and in tert-butanol for
(IV) [m.p.: 397 K; literature value for (IV): 396±397 K (Ward &
Baker, 1977)]. The nitrosation methodology described by Low,
Quesada, Marchal, Nogueras et al. (2002), using (I) as starting
material, provided a mixture of green (II) and blue (III). Crystals of
(II) and (III) suitable for single-crystal X-ray diffraction were
obtained by slow evaporation of a solution in acetone±water (1:1 v/v)
and manual separation.
Figure 9
A stereoview of part of the crystal structure of (III), showing the
formation of a chain of rings along [001]. For clarity, H atoms bonded to C
atoms have been omitted.
so generating a dimer centred at (12, , ) and containing an
1
2
1
2
R22(8) ring. Amino atom N4 at (x, y, z) also acts as a hydrogen-
bond donor, this time via atom H4B, to atom O6 in the mol-
ecule at (1 z, 12 + y, 21 z), which lies in the dimer centred at
(12, 1, 0), while atom O6 at (x, y, z) accepts a hydrogen bond
from atom N4 at (1 z, 21 + y, 12 z), which lies in the dimer
centred at (12, 0, 0). At the same time, atom N4 at (1 x, 1 y,
1
z) acts as a donor to atom O6 at (x, 12 y, 21 + z), which lies
in the dimer centred at (21, 0, 1), while atom O6 at (1 x,
3
2
1
y, 1 z) acts as an acceptor from atom N4 at (x,
y,
12 + z), part of the dimer centred at (12, 1, 1). In this manner, the
molecules are linked into a (100) sheet built from R22(8) and
R66(28) rings alternating in a checkerboard fashion (Fig. 10). If
the individual molecules are regarded as the nodes of the
resulting net then this is a (6,3)-net, while if the R22(8) dimers
are taken as the nodes it is a (4,4)-net (Batten & Robson,
1998). Thus, although the supramolecular structure of (IV) is
Compound (I)
Crystal data
3
C12H13N3OS
Mr = 247.31
Monoclinic, P21=c
a = 9.7139 (2) A
b = 9.5846 (2) A
Dx = 1.435 Mg m
Mo Kꢂ radiation
Cell parameters from 2600
re¯ections
Ê
Ê
ꢃ = 3.0±27.5ꢂ
ꢄ = 0.27 mm
T = 120 (1) K
1
Ê
c = 12.6431 (2) A
ꢁ = 103.4465 (13)ꢂ
3
Ê
V = 1144.85 (4) A
Z = 4
Block, colourless
0.30 Â 0.26 Â 0.20 mm
Data collection
Nonius KappaCCD diffractometer
' scans, and ! scans with ꢅ offsets
Absorption correction: multi-scan
(DENZO±SMN; Otwinowski &
Minor, 1997)
2600 independent re¯ections
2249 re¯ections with I > 2ꢆ(I)
Rint = 0.032
ꢃmax = 27.5ꢂ
Figure 10
A stereoview of part of the crystal structure of (IV), showing the
formation of a (100) sheet of R22(8) and R66(28) rings. For clarity, H atoms
bonded to C atoms have been omitted.
h = 12 ! 11
Tmin = 0.902, Tmax = 0.943
7564 measured re¯ections
k = 11 ! 12
l = 14 ! 16
ꢀ
o458 Christopher Glidewell et al.
Isomers of C12H13N3OS, and C12H12N4O2S
Acta Cryst. (2003). C59, o454±o460

organic compounds
Re®nement
Table 4
Hydrogen-bonding geometry (A, ) for (II).
ꢂ
Ê
Re®nement on F2
R[F2 > 2ꢆ(F2)] = 0.035
wR(F2) = 0.091
S = 1.06
2600 re¯ections
w = 1/[ꢆ2(F2o) + (0.0415P)2
+ 0.4958P]
DÐHÁ Á ÁA
DÐH
HÁ Á ÁA
DÁ Á ÁA
DÐHÁ Á ÁA
where P = (F2o + 2Fc2)/3
(Á/ꢆ)max = 0.001
N14ÐH14AÁ Á ÁO26ii
N14ÐH14BÁ Á ÁO26
N24ÐH24AÁ Á ÁO16iii
N24ÐH24BÁ Á ÁO16iv
0.88
0.88
0.88
0.88
2.28
2.10
2.29
2.62
3.029 (2)
2.896 (2)
3.124 (2)
3.330 (2)
143
151
157
138
3
Ê
Áꢇmax = 0.24 e A
3
Ê
0.31 e A
155 parameters
H-atom parameters constrained
Áꢇmin
=
Symmetry codes: (ii) 1 x; 1 y; 1 z; (iii) x; 1 y; 1 z; (iv) x; y 1; z.
Table 1
Selected bond lengths (A) for (I).
Ê
Re®nement
N1ÐC2
C2ÐN3
N3ÐC4
C4ÐC5
C5ÐC6
C6ÐN1
1.364 (2)
1.303 (3)
1.375 (2)
1.376 (2)
1.401 (2)
1.424 (2)
N1ÐC17
C2ÐS2
C21ÐS2
C4ÐN4
C6ÐO6
1.463 (2)
1.757 (2)
1.798 (2)
1.344 (2)
1.241 (2)
Re®nement on F2
R[F2 > 2ꢆ(F2)] = 0.047
wR(F2) = 0.119
S = 1.06
5325 re¯ections
w = 1/[ꢆ2(F2o) + (0.0447P)2
+ 1.7296P]
where P = (F2o + 2Fc2)/3
(Á/ꢆ)max = 0.001
3
Ê
Áꢇmax = 0.51 e A
3
Ê
0.41 e A
318 parameters
H-atom parameters constrained
Áꢇmin
=
Table 2
Hydrogen-bonding geometry (A, ) for (I).
ꢂ
Ê
Compound (III)
DÐHÁ Á ÁA
DÐH
HÁ Á ÁA
DÁ Á ÁA
DÐHÁ Á ÁA
Crystal data
N4ÐH4BÁ Á ÁO6i
Symmetry code: (i) 1 x; y
0.88
1.95
2.823 (2)
170
C12H12N4O2S
Mr = 276.33
Triclinic, P1
a = 10.5035 (3) A
b = 10.8741 (3) A
Z = 4
Dx = 1.461 Mg m
Mo Kꢂ radiation
3
1
2
1
2
;
z.
Ê
Ê
Ê
Cell parameters from 4417
re¯ections
c = 11.8261 (4) A
ꢃ = 3.0±25.0ꢂ
ꢄ = 0.26 mm
T = 120 (1) K
1
ꢂ = 109.6510 (13)ꢂ
ꢁ = 96.4203 (14)ꢂ
ꢈ = 93.7181 (14)ꢂ
Compound (II)
Plate, blue
0.30 Â 0.22 Â 0.04 mm
3
Crystal data
Ê
V = 1256.49 (7) A
3
C12H13N3OS
Mr = 247.31
Dx = 1.400 Mg m
Mo Kꢂ radiation
Data collection
Monoclinic, P21=c
Cell parameters from 5325
re¯ections
Nonius KappaCCD diffractometer
' scans, and ! scans with ꢅ offsets
Absorption correction: multi-scan
(DENZO±SMN; Otwinowski &
Minor, 1997)
4417 independent re¯ections
3498 re¯ections with I > 2ꢆ(I)
Rint = 0.094
Ê
a = 11.4629 (2) A
b = 10.2603 (2) A
ꢃ = 3.1±27.5ꢂ
Ê
Ê
1
ꢃmax = 25.0ꢂ
c = 20.9303 (4) A
ꢄ = 0.26 mm
T = 120 (1) K
ꢁ = 107.0920 (14)ꢂ
h = 12 ! 12
3
Ê
V = 2352.95 (8) A
Z = 8
Block, green
0.47 Â 0.22 Â 0.14 mm
Tmin = 0.920, Tmax = 0.991
24 784 measured re¯ections
k = 12 ! 12
l = 14 ! 14
Re®nement
Data collection
Re®nement on F2
R[F2 > 2ꢆ(F2)] = 0.044
wR(F2) = 0.107
S = 1.05
4417 re¯ections
w = 1/[ꢆ2(F2o) + (0.0461P)2
+ 0.5677P]
Nonius KappaCCD diffractometer
' scans, and ! scans with ꢅ offsets
Absorption correction: multi-scan
(DENZO±SMN; Otwinowski &
Minor, 1997)
5325 independent re¯ections
4389 re¯ections with I > 2ꢆ(I)
Rint = 0.064
where P = (F2o + 2Fc2)/3
(Á/ꢆ)max = 0.001
max = 27.5ꢂ
3
ꢃ
Ê
Áꢇmax = 0.21 e A
3
h = 14 ! 14
k = 13 ! 12
l = 27 ! 27
Ê
0.31 e A
345 parameters
H-atom parameters constrained
Áꢇmin
=
Tmin = 0.887, Tmax = 0.957
21 205 measured re¯ections
Table 5
Selected bond lengths (A) for (III).
Ê
Table 3
Selected bond lengths (A) for (II).
Ê
N11ÐC12
C12ÐN13
N13ÐC14
C14ÐC15
C15ÐC16
C16ÐN11
N11ÐC117
C12ÐS12
S12ÐC121
C14ÐN14
C15ÐN15
N15ÐO15
C16ÐO16
1.372 (3)
1.306 (3)
1.362 (3)
1.433 (3)
1.452 (3)
1.419 (3)
1.483 (3)
1.743 (2)
1.804 (2)
1.312 (3)
1.353 (3)
1.273 (2)
1.218 (3)
N21ÐC22
C22ÐN23
N23ÐC24
C24ÐC25
C25ÐC26
C26ÐN21
N21ÐC217
C22ÐS22
S22ÐC221
C24ÐN24
C25ÐN25
N25ÐO25
C26ÐO26
1.372 (3)
1.305 (3)
1.368 (3)
1.422 (3)
1.445 (3)
1.420 (3)
1.466 (3)
1.747 (2)
1.796 (2)
1.316 (3)
1.352 (3)
1.272 (2)
1.223 (3)
N11ÐC12
C12ÐN13
N13ÐC14
C14ÐC15
C15ÐC16
C16ÐN11
N11ÐC117
C12ÐS12
S12ÐC121
C14ÐN14
C16ÐO16
1.366 (2)
1.304 (2)
1.374 (2)
1.390 (3)
1.401 (3)
1.435 (2)
1.469 (2)
1.759 (2)
1.794 (2)
1.342 (2)
1.245 (2)
N21ÐC22
C22ÐN23
N23ÐC24
C24ÐC25
C25ÐC26
C26ÐN21
N21ÐC217
C22ÐS22
S22ÐC221
C24ÐN24
C26ÐO26
1.376 (2)
1.311 (3)
1.373 (3)
1.381 (3)
1.400 (3)
1.420 (3)
1.464 (3)
1.747 (2)
1.791 (2)
1.353 (3)
1.246 (3)
ꢀ
Acta Cryst. (2003). C59, o454±o460
Christopher Glidewell et al.
Isomers of C12H13N3OS, and C12H12N4O2S o459

organic compounds
Table 6
Hydrogen-bonding geometry (A, ) for (III).
crystals; those obtained were always of extremely poor quality and
very ®ne hair-like habit, giving no detectable diffraction beyond a ꢃ
value of 20ꢂ, so that the overall resolution was poor. Nonetheless, the
overall conformation and supramolecular structure of (IV) were
determined as being clearly different from those of the isomeric (I)
and (II). For each compound, all H atoms were treated as riding
ꢂ
Ê
DÐHÁ Á ÁA
DÐH
HÁ Á ÁA
DÁ Á ÁA
DÐHÁ Á ÁA
N14ÐH14AÁ Á ÁN25
N14ÐH14AÁ Á ÁO26
N14ÐH14BÁ Á ÁO15
N24ÐH24AÁ Á ÁN15v
N24ÐH24AÁ Á ÁO16v
N24ÐH24BÁ Á ÁO25
0.88
0.88
0.88
0.88
0.88
0.88
2.23
2.40
2.01
2.09
2.50
2.01
3.100 (3)
2.879 (2)
2.642 (2)
2.970 (3)
2.938 (2)
2.631 (2)
168
114
128
177
112
127
Ê
atoms, with CÐH distances of 0.95 (aromatic), 0.98 (CH3) or 0.99 A
Ê
(CH2), and NÐH distances of 0.88 A.
For all compounds, data collection: KappaCCD Server Software
(Nonius, 1997); cell re®nement: DENZO±SMN (Otwinowski &
Minor, 1997); data reduction: DENZO±SMN; program(s) used to
solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to
re®ne structure: SHELXL97 (Sheldrick, 1997); molecular graphics:
PLATON (Spek, 2003); software used to prepare material for
publication: SHELXL97 and PRPKAPPA (Ferguson, 1999).
Symmetry code: (v) x; y; z 1.
Compound (IV)
Crystal data
3
C12H13N3OS
Mr = 247.31
Dx = 1.367 Mg m
Mo Kꢂ radiation
X-ray data were collected at the EPSRC X-ray Crystal-
lographic Service, University of Southampton, England; the
authors thank the staff for all their help and advice. JNL
thanks NCR Self-Service, Dundee, for grants that have
provided computing facilities for this work. We thank Dr
Monoclinic, P21=c
Cell parameters from 1177
re¯ections
Ê
a = 15.747 (2) A
b = 5.1044 (7) A
ꢃ = 2.7±20.5ꢂ
Ê
1
Ê
c = 15.501 (3) A
ꢄ = 0.26 mm
T = 120 (1) K
ꢁ = 105.286 (5)ꢂ
Ê
V = 1201.9 (3) A
Z = 4
3
Â
Manuel Melguizo, Universidad de Jaen, Spain, for his advice,
support and encouragement.
Needle, colourless
0.60 Â 0.04 Â 0.03 mm
Data collection
Supplementary data for this paper are available from the IUCr electronic
archives (Reference: GG1172). Services for accessing these data are
described at the back of the journal.
Nonius KappaCCD diffractometer
' scans, and ! scans with ꢅ offsets
Absorption correction: multi-scan
(DENZO±SMN; Otwinowski &
Minor, 1997)
1177 independent re¯ections
1006 re¯ections with I > 2ꢆ(I)
Rint = 0.147
ꢃ
max = 20.5ꢂ
h = 15 ! 15
Tmin = 0.862, Tmax = 0.992
9738 measured re¯ections
k = 5 ! 5
References
l = 14 ! 15
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.
Batten, S. R. & Robson, R. (1998). Angew. Chem. Int. Ed. 37, 1460±1494.
Bertolasi, V., Gilli, P., Ferretti, V. & Gilli, G. (1991). J. Am. Chem. Soc. 113,
4917±4925.
Ferguson, G. (1999). PRPKAPPA. University of Guelph, Canada.
Gilli, G., Bellucci, F., Ferretti, V. & Bertolasi, V. (1989). J. Am. Chem. Soc. 111,
1023±1028.
Re®nement
Re®nement on F2
R[F2 > 2ꢆ(F2)] = 0.077
wR(F2) = 0.155
S = 1.22
1177 re¯ections
155 parameters
H-atom parameters constrained
w = 1/[ꢆ2(F2o) + 5.5293P]
where P = (F2o + 2Fc2)/3
(Á/ꢆ)max < 0.001
3
Ê
Áꢇmax = 0.32 e A
3
Ê
0.35 e A
Áꢇmin
=
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909±915.
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10405±10417.
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o202±o204.
Table 7
Hydrogen-bonding geometry (A, ) for (IV).
ꢂ
Ê
Low, J. N., Quesada, A., Marchal, A., Melguizo, M., Nogueras, M. & Glidewell,
C. (2002). Acta Cryst. C58, o289±o294.
Â
Low, J. N., Quesada, A., Marchal, A., Nogueras, M., Sanchez, A. & Glidewell,
C. (2002). Acta Cryst. C58, o284±o286.
Nonius (1997). KappaCCD Server Software. Windows 3.11 Version. Nonius
BV, Delft, The Netherlands.
DÐHÁ Á ÁA
DÐH
HÁ Á ÁA
DÁ Á ÁA
DÐHÁ Á ÁA
N4ÐH4AÁ Á ÁN3ii
0.88
0.88
2.16
2.40
3.044 (8)
3.209 (7)
177
154
N4ÐH4BÁ Á ÁO6vi
Symmetry codes: (ii) 1 x; 1 y; 1 z; (vi) 1 x; 12 ‡ y; 21 z.
Otwinowski, Z. & Minor, W. (1997). Methods in Enzymology, Vol. 276,
Macromolecular Crystallography, Part A, edited by C. W. Carter Jr & R. M.
Sweet, pp. 307±326. New York: Academic Press.
For (I), (II) and (IV), the space group P21/c was determined
uniquely from the systematic absences. Crystals of (III) are triclinic,
and space group P1 was selected and con®rmed by successful struc-
ture analysis. For (IV), it proved extremely dif®cult to obtain single
Sheldrick, G. M. (1997). SHELXS97 and SHELXL97. University of
È
Gottingen, Germany.
Spek, A. L. (2003). J. Appl. Cryst. 36, 7±13.
Ward, D. A. & Baker, B. R. (1977). J. Med. Chem. 20, 88±92.
ꢀ
o460 Christopher Glidewell et al.
Isomers of C12H13N3OS, and C12H12N4O2S
Acta Cryst. (2003). C59, o454±o460