A hydrogen-bonded ribbon in 6-amino-3-methyl-5-nitroso-2-(pyrrol-idin-1-yl) pyrimidin-4(3H)-one monohydrate and hydrogen-bonded sheets in 6-amino-2-dimethyl-amino-3-methyl-5-nitroso-pyrimidin-4(3H)-one monohydrate

Article abstract of DOI:10.1107/S0108270109039018

In each of 6-amino-3-methyl-5-nitroso-2-(pyrrolidin-1-yl)pyri-m-idin-4(3H)- one monohydrate, C₉H₁₃N₅O₂· H₂O, (I), and 6-amino-2-dimethyl-amino-3-methyl-5-nitroso-pyrimidin- 4(3H)-one monohydrate, C

Full text of DOI:10.1107/S0108270109039018

organic compounds
Acta Crystallographica Section C
Crystal Structure
Communications
was aroused by the observation that the structures of amino
acid derivatives (IV)–(VIII) are all characterized by short
intermolecular O—Hꢀ ꢀ ꢀO hydrogen bonds, with the carboxyl
group as donor and the nitrosyl O atom as acceptor, and in
ISSN 0108-2701
˚
which the Oꢀ ꢀ ꢀO distances are all ca 2.50 A. At the same time,
the intramolecular bond distances show a number of unusual
values, and a combination of database analysis and molecular
modelling led to an interpretation of the relationship between
the unusual intramolecular bond lengths and the very short
intermolecular hydrogen bonds in terms of highly polarized
electronic structures (Low et al., 2000).
A hydrogen-bonded ribbon in
6-amino-3-methyl-5-nitroso-2-(pyrrol-
idin-1-yl)pyrimidin-4(3H)-one mono-
hydrate and hydrogen-bonded sheets
in 6-amino-2-dimethylamino-3-
methyl-5-nitrosopyrimidin-4(3H)-one
monohydrate
a
a
b
´
Fabıan Orozco, ‡ Braulio Insuasty, Justo Cobo 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 24 September 2009
Accepted 25 September 2009
Online 7 October 2009
In each of 6-amino-3-methyl-5-nitroso-2-(pyrrolidin-1-yl)pyri-
midin-4(3H)-one monohydrate, C9H13N5O2ꢀH2O, (I), and
6-amino-2-dimethylamino-3-methyl-5-nitrosopyrimidin-4(3H)-
one monohydrate, C7H11N5O2ꢀH2O, (II), the interatomic
distances indicate significant polarization of the electronic
structures of the pyrimidinone molecules. In each compound,
the organic component contains an intramolecular N—Hꢀ ꢀ ꢀO
hydrogen bond. The molecular components in (I) are linked
by a combination of two-centre O—Hꢀ ꢀ ꢀO, O—Hꢀ ꢀ ꢀN and
N—Hꢀ ꢀ ꢀO hydrogen bonds and a three-centre O—Hꢀ ꢀ ꢀ(NO)
hydrogen bond to form a broad ribbon containing five distinct
ring motifs. In compound (II), three intermolecular hydrogen
bonds, one each of the O—Hꢀ ꢀ ꢀO, O—Hꢀ ꢀ ꢀN and N—Hꢀ ꢀ ꢀO
types, link the molecules into sheets containing equal numbers
of centrosymmetric R44(10) and R180(34) rings.
Although the pyrimidinone ring in (III) is effectively planar
(Orozco et al., 2008), the rings in both (I) and (II) show a
modest distortion towards a twist-boat conformation. The
ring-puckering parameters (Cremer & Pople, 1975) are ꢀ =
99.5 (1)ꢁ and ’ = 273.9 (10)ꢁ for (I), and ꢀ = 87.1 (10)ꢁ and ’ =
100.2 (11)ꢁ for (II); the ideal values, for rings having all bond
distances equal, are ꢀ = 90ꢁ and ’ = (60k + 30)ꢁ, where k
represents an integer. In both compounds, ring atoms N2 and
C5 are displaced to one side of the mean ring plane, and atoms
N3 and C6 are displaced to the opposite side. While the ring-
Comment
We report here the crystal structures of 6-amino-3-methyl-5-
nitroso-2-(pyrrolidin-1-yl)pyrimidin-4(3H)-one monohydrate,
(I), and 6-amino-2-dimethylamino-3-methyl-5-nitrosopyrim-
idin-4(3H)-one monohydrate, (II) (Figs. 1 and 2), and compare
them with those of 6-amino-3-methyl-2-morpholino-5-
nitrosopyrimidin-4(3H)-one, (III) (Orozco et al., 2008), and of
the amino acid derivatives, (IV)–(VIII) (Low et al., 1997, 1999,
2000). Our interest in the structures of this class of compounds
˚
atom displacements are modest, in the range 0.04–0.07 A, the
displacements of the exocyclic substituent atoms are much
greater, with the maximum displacement being experienced
˚
˚
by atom C31 in each case [0.453 (2) A in (I) and 0.619 (2) A in
(II)]. The twist-boat conformation is not uncommon amongst
highly substituted pyrimidines of this general type (Quesada et
al., 2002; Melguizo et al., 2003). The boat conformation has
also been observed (Quesada et al., 2004), as well as the
expected planar forms.
´
‡ Permanent address: Departamento de Quımica, Pontificia Universidad
Javeriana, Kr 7 No. 43-82, Bogota DC, Colombia.
´
Acta Cryst. (2009). C65, o549–o552
doi:10.1107/S0108270109039018
# 2009 International Union of Crystallography o549

organic compounds
Figure 1
The molecular components of compound (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. The hydrogen
bond linking the two components within the selected asymmetric unit is
indicated by a dashed line.
Figure 3
Part of the crystal structure of (I), showing the formation of a hydrogen-
bonded ribbon running parallel to the [010] direction and containing five
distinct types of ring. For the sake of clarity, H atoms bonded to C atoms
have been omitted. Atoms labelled with an asterisk (*), a hash symbol (#)
or a dollar sign ($) are at the symmetry positions (x, 1 + y, z), (1 ꢃ x, ꢃy,
2 ꢃ z) and (1 ꢃ x, 1 ꢃ y, 2 ꢃ z), respectively.
2008). Of the amino acid derivatives, (IV) crystallizes as a
dihydrate (Low et al., 1997) and (VII) as a monohydrate (Low
et al., 2000), while (V), (VI) and (VIII) all crystallize in the
unsolvated forms (Low et al., 1999, 2000).
Figure 2
In each of (I) and (II), the organic components contain an
intramolecular N—Hꢀ ꢀ ꢀO hydrogen bond forming an S(6)
motif (Bernstein et al., 1995) (Table 2), but the remaining
details of the hydrogen bonding are very different in the two
compounds. In (I), the water molecule acts as a single
acceptor, in an N—Hꢀ ꢀ ꢀO hydrogen bond, and as a triple
donor, forming a two-centre O—Hꢀ ꢀ ꢀN hydrogen bond within
the selected asymmetric unit (Fig. 1) and a three-centre
O—Hꢀ ꢀ ꢀ(N,O) hydrogen bond, which serves to link two
pyrimidinone molecules related by translation (Fig. 3). The
hydrogen bonds involving the water molecules, together with
the intramolecular N—Hꢀ ꢀ ꢀO hydrogen bond, thus generate a
chain of edge-fused S(6), R22(6) and R22(7) rings running
parallel to the [010] direction. Pairs of antiparallel chains,
related to one another by inversion, are linked by an inter-
molecular N—Hꢀ ꢀ ꢀO hydrogen bond involving only the
organic components, so generating a broad ribbon. The central
core of this ribbon consists of R22(4) rings centred at (21, n, 1),
where n represents an integer, alternating with R66(14) rings
The molecular components of compound (II), 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. The hydrogen
bonds linking the components into centrosymmetric four-molecule
aggregates are indicated by dashed lines. Atoms labelled with the
suffixes a and b are at the symmetry position (1 ꢃ x, ꢃy, 1 ꢃ z).
Despite the nonplanarity of the pyrimidinone rings, the
bond distances in (I) and (II) (Table 1) provide evidence for
polarization of the electronic structure, but in a manner which
differs slightly from that in (III). The key indicators for
compounds of this type have been identified (Low et al., 2000)
as: (i) the C—N distances in the sequence N21—C2—N1—
C6—N6; (ii) the similarity of the distances C4—C5 and
C5—C6; (iii) the distances C5—N5 and N5—O5 and, perhaps
most importantly, the difference between these distances. On
this basis, the extent of the polarization can be identified as
greatest in (II) and least in (III), with the extent of the de-
localization greater in (I) and (II) than in (III), all indicating
the importance of the polarized forms (Ia) and (IIa) in addi-
tion to the localized forms (I) and (II), compared with form
(IIIa) (Orozco et al., 2008). Accordingly, in both (I) and (II),
hydrogen bonds involving atom N6 as the donor or atom O5 as
the acceptor can be regarded as charge-assisted hydrogen
bonds (Gilli et al., 1994). In (II), where all of the inter-
molecular hydrogen bonds are of the two-centre type, those
involving atoms N6 or O5 exhibit almost linear D—Hꢀ ꢀ ꢀA
fragments.
1
centred at (12, n + , 1), where n again represents an integer.
2
This central core is flanked by two outer strips, each
containing S(6), R22(6) and R22(7) rings, so that, overall, the
ribbon contains five different ring motifs (Fig. 3).
The hydrogen bonding in (II) is simpler than that in (I)
(Table 2). In particular, the water molecule does not act as an
acceptor of hydrogen bonds. As a double donor, it forms only
two-centre hydrogen bonds, one each of the O—Hꢀ ꢀ ꢀN and
O—Hꢀ ꢀ ꢀO types, which link a pair of organic components
which are related to one another by inversion, thus forming a
Compounds (I) and (II) both crystallize as monohydrates,
while (III) crystallizes in the unsolvated form (Orozco et al.,
1
centrosymmetric four-molecule aggregate centred at (12, 0, )
2
ꢂ
o550 Orozco et al. C9H13N5O2ꢀH2O and C7H11N5O2ꢀH2O
Acta Cryst. (2009). C65, o549–o552

organic compounds
Experimental
To a suspension of 6-amino-2-methylsulfanyl-3-methyl-5-nitroso-
pyrimidin-4(3H)-one (25 mmol) in methanol (80 ml), the appropriate
secondary amine (100 mmol), viz. pyrrolidine for (I) and dimethyl-
amine for (II), was added dropwise with magnetic stirring. The
reactions proceeded for 6 h with a change of colour from blue to
violet and the liberation of methanethiol. The resulting solid products
were collected by filtration and washed with cold ethanol, and then
recrystallized from dimethylformamide–water (3:1 v/v) to give red–
violet crystals suitable for single-crystal X-ray diffraction. Analysis
for (I): 87% yield, m.p. 484 K; MS (70 eV) m/z (%): 223 (M+, 100),
209 (4), 150 (20), 123 (17), 97 (24). Analysis for (II): 52% yield, m.p.
504 K; MS (70 eV) m/z (%): 197 (M+, 90), 183 (32), 152 (56), 92 (100),
42 (73).
Figure 4
Compound (I)
A stereoview of part of the crystal structure of (II), showing the
formation of a hydrogen-bonded sheet parallel to (101) and containing
three types of ring. For the sake of clarity, H atoms bonded to C atoms
have been omitted.
Crystal data
C9H13N5O2ꢀH2O
ꢃ = 64.436 (16)ꢁ
3
˚
Mr = 241.26
Triclinic, P1
V = 523.46 (19) A
Z = 2
˚
a = 7.9734 (18) A
Mo Kꢁ radiation
ꢄ = 0.12 mmꢃ1
T = 120 K
0.41 ꢄ 0.18 ꢄ 0.15 mm
and containing an R44(10) motif (Fig. 2). This aggregate can
conveniently be regarded as the basic building block for the
supramolecular structure. The intermolecular N—Hꢀ ꢀ ꢀO
hydrogen bond links the four-molecule aggregate centred at
˚
b = 8.452 (2) A
˚
c = 8.9099 (2) A
ꢁ = 75.158 (9)ꢁ
ꢂ = 84.727 (7)ꢁ
(12, 0, 12) to four similar aggregates centred at (0, 12, 0), (0, ꢃ , 0),
1
2
Data collection
1
2
1
2
(1, , 1) and (1, ꢃ , 1), so generating a sheet parallel to (101)
and containing S(6), R44(10) and R180(34) rings (Fig. 4). Thus,
although there are fewer independent hydrogen bonds in the
structure of (II) than in (I), the hydrogen-bonded supra-
molecular structure of (II) is two-dimensional, as opposed to
the one-dimensional hydrogen-bonded structure of (I).
In each of (I) and (II), the water component is firmly
embedded in the hydrogen-bonded structure. By contrast,
(III) contains no water component and its very simple
hydrogen-bonded structure is built from just two inter-
molecular N—Hꢀ ꢀ ꢀO hydrogen bonds, in which the ketonic
and morpholine O atoms are the acceptors, giving a sheet
containing only S(6) and R44(26) rings. Had the morpholine O
atom not been available to accept a hydrogen bond in the
structure of (III), then, without further reorganization, the
hydrogen-bonded structure would consist of simple C(6)
chains, with one of the amino N—H bonds finding no acceptor
site. This suggests that the presence of water in (I) and (II),
versus its absence in (III), may be connected with the overall
ratio of hydrogen-bond donors and acceptors.
Bruker–Nonius KappaCCD area-
detector diffractometer
Absorption correction: multi-scan
(SADABS; Sheldrick, 2003)
Tmin = 0.953, Tmax = 0.983
12137 measured reflections
2051 independent reflections
1629 reflections with I > 2ꢅ(I)
Rint = 0.054
Refinement
R[F2 > 2ꢅ(F2)] = 0.046
wR(F2) = 0.116
S = 1.05
155 parameters
H-atom parameteꢃrs3 constrained
˚
Áꢆmax = 0.26 e A
Áꢆmin = ꢃ0.28 e A
ꢃ3
˚
2051 reflections
Compound (II)
Crystal data
3
˚
V = 951.34 (19) A
Z = 4
C7H11N5O2ꢀH2O
Mr = 215.22
Monoclinic, P21=n
Mo Kꢁ radiation
ꢄ = 0.12 mmꢃ1
T = 120 K
0.16 ꢄ 0.16 ꢄ 0.12 mm
˚
a = 11.8125 (6) A
˚
b = 7.1372 (7) A
˚
c = 11.8588 (19) A
ꢂ = 107.910 (4)ꢁ
Three-dimensional hydrogen-bonded structures are formed
by each of (IV)–(VI) and (VIII), despite the fact that, whereas
(IV) crystallizes as a dihydrate (Low et al., 1997), the other
three compounds all crystallize in the solvent-free forms (Low
et al., 1999, 2000), while the monohydrate, (VII), forms only a
two-dimensional hydrogen-bonded structure (Low et al.,
2000). The contrast between the two-dimensional structure of
(VII) and the three-dimensional structures of (V) and (VI) is
both striking and unexpected in view of the considerably
greater number of potential hydrogen-bonding donor and
acceptor sites available in the asymmetric unit of (VII)
compared with (V) and (VI).
Data collection
Bruker–Nonius KappaCCD area-
detector diffractometer
Absorption correction: multi-scan
(SADABS; Sheldrick, 2003)
Tmin = 0.971, Tmax = 0.986
9096 measured reflections
1873 independent reflections
1304 reflections with I > 2ꢅ(I)
Rint = 0.049
Refinement
R[F2 > 2ꢅ(F2)] = 0.046
wR(F2) = 0.109
S = 1.05
139 parameters
H-atom parameteꢃrs3 constrained
˚
Áꢆmax = 0.22 e A
Áꢆmin = ꢃ0.27 e A
ꢃ3
˚
1873 reflections
ꢂ
Acta Cryst. (2009). C65, o549–o552
Orozco et al.
C9H13N5O2ꢀH2O and C7H11N5O2ꢀH2O o551

organic compounds
Table 1
Selected bond distances (A) for compounds (I)–(III).
PLATON (Spek, 2009); software used to prepare material for
publication: SHELXL97 and PLATON.
˚
Á represents the bond-length difference d(C5—N5) ꢃ d(N5—O5).
´
The authors thank the Servicios Tecnicos de Investigacion
of the Universidad de Jaen and the staff for the data collec-
´
Parameter
(I)
(II)
(III)†
´
tions. BI and FO thank COLCIENCIAS and the Universidad
del Valle for financial support, and for supporting a short stay
N1—C2
C2—N3
N3—C4
C4—C5
C5—C6
C6—N1
C2—N21
C4—O4
C5—N5
N5—O5
C6—N6
Á
1.326 (2)
1.376 (2)
1.401 (2)
1.446 (3)
1.429 (3)
1.338 (2)
1.325 (2)
1.209 (2)
1.336 (2)
1.273 (2)
1.313 (2)
0.063 (3)
1.320 (3)
1.377 (3)
1.388 (3)
1.438 (3)
1.438 (3)
1.333 (3)
1.328 (3)
1.226 (2)
1.332 (3)
1.278 (2)
1.311 (3)
0.054 (3)
1.315 (3)
1.376 (3)
1.415 (3)
1.447 (3)
1.435 (3)
1.357 (3)
1.358 (3)
1.221 (3)
1.358 (3)
1.275 (3)
1.316 (3)
0.083 (3)
´
by FO at the Departamento de Quımica Inorganica y
Organica, Universidad de Jaen. JC thanks the Consejerıa de
´
´
´
´
´
Innovacion, Ciencia y Empresa (Junta de Andalucıa, Spain),
the Universidad de Jaen (project reference UJA_07_16_33)
´
´
´
and the Ministerio de Ciencia e Innovacion (project reference
SAF2008-04685-C02-02) for financial support.
† Data for (III) are taken from Orozco et al. (2008).
Supplementary data for this paper are available from the IUCr electronic
archives (Reference: SK3349). Services for accessing these data are
described at the back of the journal.
Table 2
Hydrogen-bonding parameters (A, ) for compounds (I) and (II).
ꢁ
˚
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Compound
(I)
D—Hꢀ ꢀ ꢀA
D—H
Hꢀ ꢀ ꢀA
Dꢀ ꢀ ꢀA
D—Hꢀ ꢀ ꢀA
N6—H6Aꢀ ꢀ ꢀO5
0.88
0.88
0.88
0.86
0.86
0.86
0.88
0.88
0.86
0.86
2.00
2.25
1.99
2.00
2.48
2.57
1.97
2.01
2.15
2.08
2.630 (2)
2.989 (2)
2.808 (2)
2.860 (2)
2.946 (2)
3.082 (2)
2.641 (2)
2.874 (2)
2.995 (2)
2.921 (2)
128
142
154
177
114
119
132
168
168
166
N6—H6Aꢀ ꢀ ꢀO5i
N6—H6Bꢀ ꢀ ꢀO41ii
O41—H41Aꢀ ꢀ ꢀN5
O41—H41Bꢀ ꢀ ꢀO4†
O41—H41Bꢀ ꢀ ꢀN1iii
N6—H6Aꢀ ꢀ ꢀO5
(II)
N6—H6Bꢀ ꢀ ꢀO4iv
O41—H41Aꢀ ꢀ ꢀN5
O41—H41Bꢀ ꢀ ꢀO5v
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† The O4ꢀ ꢀ ꢀH41Bꢀ ꢀ ꢀN1iii angle is 125ꢁ. Symmetry codes: (i) 1 ꢃ x; ꢃy; 2 ꢃ z; (ii)
´
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´
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1
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1
2
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´
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´
´
´
´
All H atoms were located in difference maps and then treated as
riding atoms. H atoms bonded to C or N atoms were allowed to ride
in geometrically idealized positions, with C—H = 0.98 (CH3) or
˚
˚
0.99 A (CH2) and N—H = 0.88 A, and with Uiso(H) = kUeq(C,N),
where k = 1.5 for the methyl groups, which were permitted to rotate
but not to tilt, and 1.2 otherwise. Water H atoms were permitted to
ride at the positions deduced from the difference maps, with O—H =
˚
0.86 A and Uiso(H) = 1.5Ueq(O).
´
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–
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tion: 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:
315.
Sheldrick, G. M. (2003). SADABS. Version 2.10. University of Gottingen,
¨
Germany.
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ꢂ
o552 Orozco et al. C9H13N5O2ꢀH2O and C7H11N5O2ꢀH2O
Acta Cryst. (2009). C65, o549–o552