A hydrogen-bonded chain of rings in 7-amino-5-tert-butyl-2-methyl- pyrazolo[1,5-a]pyrimidine, and a hydrogen-bonded framework structure in 3,7-diamino-2,5-dimethyl-pyrazolo[1,5-a]pyrimidine monohydrate

Article abstract of DOI:10.1107/S0108270106025893

In 7-amino-5-ferf-butyl-2-methylpyrazolo[1,5-a]pyrimidine, C ₁₁H₁₆N₄, which crystallizes with Z' = 2 in the space group P1, the independent molecules are linked by four N-H...N hydrogen bonds into chains containing three types of ring. In 3,7-diamino-2,5-dimethylpyrazolo[1,5-a]pyrimidine monohydrate, C ₈H₁₁N₅.H₂O, the molecular components are linked into a three-dimensional framework structure by a combination of O-H...N, N-H...N and N-H...O hydrogen bonds.

Full text of DOI:10.1107/S0108270106025893

organic compounds
Acta Crystallographica Section C
Crystal Structure
Communications
free cyclocondensation between 5-amino-3-methyl-1H-pyra-
zole and 4,4-dimethyl-3-oxopentanenitrile induced by micro-
wave irradiation. Compound (II) was prepared by nitrosation
of (III) to yield (IV), followed by palladium-catalyzed
reduction with hydrazine.
ISSN 0108-2701
A hydrogen-bonded chain of rings
in 7-amino-5-tert-butyl-2-methyl-
pyrazolo[1,5-a]pyrimidine, and a
hydrogen-bonded framework struc-
ture in 3,7-diamino-2,5-dimethyl-
pyrazolo[1,5-a]pyrimidine mono-
hydrate
a
a
b
Â
Jaime Portilla, Jairo Quiroga, Jose M. de la Torre, Justo
Cobo,b John N. Lowc and Christopher Glidewelld*
The pattern of the bond lengths in both (I) and (II) closely
mimics the pattern found for (III), and it is not necessary to
discuss this in detail again. Following the earlier discussion
(Portilla et al., 2006), it can be concluded that in all three of
these compounds there is a considerable degree of aromatic
10-ꢀ-electron delocalization around the periphery of the
heterocyclic components.
a
Â
Â
Â
Grupo de Investigacion de Compuestos Heterocõclicos, Departamento de Quõmica,
b
Â
Universidad de Valle, AA 25360 Cali, Colombia, Departamento de Quõmica
Inorganica y Organica, Universidad de Jaen, 23071 Jaen, Spain, cDepartment of
Chemistry, University of Aberdeen, Meston Walk, Old Aberdeen AB24 3UE,
Scotland, and dSchool of Chemistry, University of St Andrews, Fife KY16 9ST,
Scotland
Â
Â
Â
Â
Correspondence e-mail: cg@st-andrews.ac.uk
Compound (I) crystallizes with Z0 = 2, and within the
selected asymmetric unit (Fig. 1) the two independent mol-
ecules are linked by two NÐHÁ Á ÁN hydrogen bonds (Table 1),
forming an R22(10) (Bernstein et al., 1995) dimer. Dimers of
this type are then linked by two further NÐHÁ Á ÁN hydrogen
bonds to form a complex chain of rings. Atoms N17 and N27 in
the dimeric unit at (x, y, z) act as hydrogen-bond donors via
atoms H17B and H27B, respectively, to the ring atoms N24 at
Received 4 July 2006
Accepted 5 July 2006
Online 29 July 2006
In 7-amino-5-tert-butyl-2-methylpyrazolo[1,5-a]pyrimidine,
C11H16N4, which crystallizes with Z0 = 2 in the space group
P1, the independent molecules are linked by four NÐHÁ Á ÁN
hydrogen bonds into chains containing three types of ring. In
3,7-diamino-2,5-dimethylpyrazolo[1,5-a]pyrimidine monohy-
drate, C8H11N5ÁH2O, the molecular components are linked
into a three-dimensional framework structure by a combina-
tion of OÐHÁ Á ÁN, NÐHÁ Á ÁN and NÐHÁ Á ÁO hydrogen bonds.
( x, 1
y, 2
z) and N14 at (1
x, 1
y, 1
z), so
generating by inversion two distinct R44(14) motifs centred at
1
1 1
2 2
(0, , 1) and (12, , ), respectively. Propagation by inversion of
2
these two interactions then generates a chain of edge-fused
rings running parallel to the [101] direction, with R44(14) rings
containing pairs of N17 atoms centred at (n, 12, 1 n) (n = zero
Comment
We report here the structures of 7-amino-5-tert-butyl-2-
methylpyrazolo[1,5-a]pyrimidine, (I) (Fig. 1), and 3,7-di-
amino-2,5-dimethylpyrazolo[1,5-a]pyrimidine monohydrate,
(II) (Fig. 2), which we compare with the structure of 7-amino-
2,5-dimethylpyrazolo[1,5-a]pyrimidine hemihydrate, (III).
The structure of (III) was determined many years ago using
diffraction data collected at ambient temperature (Mornon et
al., 1975) and it was recently redetermined using diffraction
data collected at 120 K (Portilla et al., 2006). The heterocyclic
system in (I) differs from that in (III) only in the replacement
of the methyl substituent on the pyrimidine ring by a tert-butyl
substituent, while the heterocyclic system in (II) differs from
that in (III) only by the incorporation of a second amino
group, and this provides an opportunity to observe the effects
of simple changes of substituent upon the supramolecular
aggregation. Compound (I) was prepared in a similar fashion
to compound (III) (Portilla et al., 2006), here using a solvent-
Figure 1
The two independent molecules of compound (I), showing the atom-
labelling scheme and the NÐHÁ Á ÁN hydrogen bonds (dashed lines)
within the selected asymmetric unit. Displacement ellipsoids are drawn at
the 30% probability level and H atoms are shown as small spheres of
arbitrary radii.
Acta Cryst. (2006). C62, o521±o524
DOI: 10.1107/S0108270106025893
# 2006 International Union of Crystallography o521

organic compounds
or integer), R44(14) rings containing pairs of N27 atoms centred
Ê
distant from the reference N3 atom by more than 3.2 A
1
1
at (12 + n, ,
n) (n = zero or integer) and R22(10) rings
(Table 2), and the corresponding DÁ Á ÁA and HÁ Á ÁA distances
are probably too long for signi®cant hydrogen bonding to
occur. Hence, without effective tethering via hydrogen bonds,
the amino group based on N3 is more or less free to rotate
about the N3ÐC3 bond and this possibly accounts for the
observed disorder. Therefore, we analyse the supramolecular
aggregation of compound (II) without reference to the amino
group based on N3.
Two OÐHÁ Á ÁN hydrogen bonds link the bimolecular
aggregates into a sheet, and adjacent sheets are linked by
paired NÐHÁ Á ÁN hydrogen bonds to form a single three-
dimensional framework structure. The water molecule at
(x, y, z) acts as hydrogen-bond donor, via atoms H1A and
H1B, to atoms N1 at (1 x, 12 + y, 23 z) and N4 at (2 x,
2
2
occupying the intermediate locations in the chain (Fig. 3).
Within the selected asymmetric unit of compound (II)
(Fig. 2), the components are linked by an NÐHÁ Á ÁO hydrogen
bond (Table 2). The amino group bonded to atom C3 exhibits
orientational disorder, and this was modelled in terms of one
H-atom site with full occupancy and two H-atom sites each
with 0.5 occupancy. While such disorder undoubtedly
complicates the analysis and the full description of the overall
supramolecular aggregation, it is possible in this case to
demonstrate the occurrence of a three-dimensional hydrogen-
bonded structure without reference to this disordered amino
group. It may be noted here that the only two possible
hydrogen-bond acceptors adjacent to atom N3 in the molecule
at (x, y, z), viz. atoms O1 and N3 in the molecules are (2 x,
1
2
3
2
+ y,
z) and (2 x, 2 y, 1 z), respectively, are both
Figure 4
A stereoview of part of the crystal structure of compound (II), showing
the formation of a sheet of R66(22) rings parallel to (001). For the sake of
clarity, H atoms bonded to C or N atoms which are not involved in the
motif shown have been omitted.
Figure 2
The independent components of compound (II), showing the atom-
labelling scheme and the NÐHÁ Á ÁO hydrogen bond (dashed line) within
the selected asymmetric unit. Displacement ellipsoids are drawn at the
30% probability level and H atoms are shown as small spheres of
arbitrary radii. The atoms bonded to atom N3 are disordered; see
Comment for discussion.
Figure 5
A part of the crystal structure of compound (II), showing the formation of
the R22(10) motif linking the (001) sheets. For the sake of clarity, the water
molecules and H atoms bonded to C or N atoms which are not involved in
the motif shown have been omitted. Atoms marked with an asterisk (*)
are at the symmetry position (1 x, 1 y, 1 z).
Figure 3
A stereoview of part of the crystal structure of compound (I), showing the
formation of a chain along [101] built from R22(10) rings and two types of
R44(14) ring. For the sake of clarity, H atoms bonded to C or N atoms
which are not involved in the motifs shown have been omitted.
ꢀ
o522 Portilla et al. C11H16N4 and C8H11N5ÁH2O
Acta Cryst. (2006). C62, o521±o524

organic compounds
12 + y, 32 z), so forming a sheet parallel to (001) built from a
single type of R66(22) ring (Fig. 4). Two sheets of this type pass
through each unit cell, generated by the 21 screw axes at y = 41
and y = 34, and lying in the domains 0.04 < z < 0.54 and 0.46 <
z < 1.04, respectively. The (001) sheets are linked by a
centrosymmetric R22(10) motif, in which paired NÐHÁ Á ÁN
hydrogen bonds link the heterocyclic molecules at (x, y, z) and
(1 x, 1 y, 1 z) (Fig. 5). Propagation of this motif links
each (001) sheet to the two adjacent sheets, so forming a
continuous framework.
In compound (III), where the water molecules lie across
twofold rotation axes in the space group C2, the molecular
components are linked by a combination of OÐHÁ Á ÁN, NÐ
HÁ Á ÁN and NÐHÁ Á ÁO hydrogen bonds into a three-dimen-
sional framework structure (Portilla et al., 2006). Within that
structure, it is possible to identify a centrosymmetric R22(10)
motif, precisely similar to that found here in compound (II)
(Fig. 5), but there are no further similarities between the
supramolecular structures of (I), (II) and (III).
Data collection
Bruker±Nonius KappaCCD area-
detector diffractometer
' and ! scans
Absorption correction: multi-scan
(SADABS; Sheldrick, 2003)
Tmin = 0.982, Tmax = 0.997
22882 measured re¯ections
4863 independent re¯ections
2931 re¯ections with I > 2ꢅ(I)
Rint = 0.066
ꢆmax = 26.8ꢁ
Re®nement
Re®nement on F2
R[F2 > 2ꢅ(F2)] = 0.056
wR(F2) = 0.150
S = 1.04
4863 re¯ections
w = 1/[ꢅ2(Fo2) + (0.0716P)2
+ 0.1822P]
2
where P = (Fo + 2Fc2)/3
(Á/ꢅ)max < 0.001
3
Ê
Áꢇmax = 0.22 e A
3
Ê
0.23 e A
280 parameters
H-atom parameters constrained
Áꢇmin
=
Extinction correction: SHELXL97
(Sheldrick, 1997)
Extinction coef®cient: 0.015 (3)
Table 1
Hydrogen-bond geometry (A, ) for (I).
ꢁ
Ê
DÐHÁ Á ÁA
DÐH
HÁ Á ÁA
DÁ Á ÁA
DÐHÁ Á ÁA
N17ÐH17AÁ Á ÁN21
N17ÐH17BÁ Á ÁN24i
N27ÐH27AÁ Á ÁN11
N27ÐH27BÁ Á ÁN14ii
0.88
0.88
0.88
0.88
2.20
2.20
2.23
2.10
3.017 (3)
3.054 (2)
3.021 (3)
2.951 (2)
155
165
150
162
Experimental
Symmetry codes: (i) x; y ‡ 1; z ‡ 2; (ii) x ‡ 1; y ‡ 1; z ‡ 1.
For the synthesis of compound (I), equimolar quantities (2 mmol
of each component) of 5-amino-3-methyl-1H-pyrazole and 4,4-di-
methyl-3-oxopentanenitrile were placed in an open Pyrex glass vessel
and irradiated in a domestic microwave oven for 2.5 min at 600 W.
The reaction mixture was extracted with ethanol. After removal of
the solvent, the resulting product, (I), was crystallized from a solution
in ethanol to give colourless crystals suitable for single-crystal X-ray
diffraction (m.p. 490±491 K, yield 90%). MS (30 eV) m/z (%): 204
(100, M+), 189 (12). For the synthesis of compound (II), a solution of
sodium nitrite (30 mmol) in water (10 ml) was added to a solution of
7-amino-2,5-dimethylpyrazolo[1,5-a]pyrimidine (Portilla et al., 2006)
(10 mmol) in ethanol (20 ml). To this solution was then added,
dropwise at 273±283 K with magnetic stirring, a mixture of concen-
trated sulfuric acid (5 ml), water (10 ml) and ethanol (10 ml). The
resulting solid was collected by ®ltration and crystallized from a
solution in ethanol to yield 7-amino-2,5-dimethyl-3-nitrosopyra-
zolo[1,5-a]pyrimidine as green crystals (m.p. 501±502 K, yield 95%).
MS (30 eV) m/z (%): 191 (100, M+), 150 (27), 135 (42). To a solution
of this nitroso compound (2 mmol) in methanol (20 ml) was added
hydrazine hydrate (6 mmol) and a catalytic amount (50 mg) of
palladium on activated carbon. This mixture was then heated under
re¯ux with magnetic stirring for 3 h. After removal of the catalyst
from the hot solution by ®ltration, the ®ltrate was cooled and the
resulting solid product, (II), was collected by ®ltration and crystal-
lized from a solution in ethanol to yield yellow crystals suitable for
single-crystal X-ray diffraction (m.p. 484±486 K, yield 80%). MS
(30 eV) m/z (%): 177 (57, M+), 136 (31), 109 (100).
Compound (II)
Crystal data
C8H11N5ÁH2O
Z = 4
Dx = 1.362 Mg m
Mo Kꢁ radiation
ꢄ = 0.10 mm
T = 120 (2) K
Plate, yellow
0.50 Â 0.36 Â 0.10 mm
3
Mr = 195.23
Monoclinic, P21=c
1
Ê
a = 8.0970 (2) A
Ê
b = 9.8881 (3) A
Ê
c = 11.9661 (3) A
ꢂ = 96.230 (5)ꢁ
V = 952.40 (5) A
3
Ê
Data collection
Bruker±Nonius KappaCCD area-
detector diffractometer
' and ! scans
Absorption correction: multi-scan
(SADABS; Sheldrick, 2003)
Tmin = 0.938, Tmax = 0.990
12664 measured re¯ections
2188 independent re¯ections
1631 re¯ections with I > 2ꢅ(I)
Rint = 0.034
ꢆmax = 27.5ꢁ
Re®nement
Re®nement on F2
R[F2 > 2ꢅ(F2)] = 0.048
wR(F2) = 0.151
w = 1/[ꢅ2(Fo2) + (0.0821P)2
+ 0.2832P]
2
where P = (Fo + 2Fc2)/3
S = 1.06
2188 re¯ections
129 parameters
H-atom parameters constrained
(Á/ꢅ)max < 0.001
3
Ê
Áꢇmax = 0.26 e A
3
Ê
0.20 e A
Áꢇmin
=
Extinction correction: SHELXL97
(Sheldrick, 1997)
Extinction coef®cient: 0.034 (7)
Table 2
Hydrogen-bond geometry (A, ) for (II).
Compound (I)
ꢁ
Ê
Crystal data
DÐHÁ Á ÁA
DÐH
HÁ Á ÁA
DÁ Á ÁA
DÐHÁ Á ÁA
3
Ê
C11H16N4
V = 1147.66 (12) A
Z = 4
O1ÐH1AÁ Á ÁN1i
O1ÐH1BÁ Á ÁN4ii
N3ÐH3AÁ Á ÁO1iii
N3ÐH3CÁ Á ÁN3iv
N7ÐH7AÁ Á ÁO1
N7ÐH7BÁ Á ÁN1v
0.90
0.90
0.86
0.86
0.86
0.86
2.17
1.94
2.57
2.43
2.10
2.45
3.059 (2)
2.817 (2)
3.386 (2)
3.279 (2)
2.933 (2)
3.205 (2)
168
166
158
171
163
147
Mr = 204.28
Triclinic, P1
a = 9.8216 (5) A
3
Dx = 1.182 Mg m
Mo Kꢁ radiation
Ê
1
Ê
Ê
b = 11.3582 (7) A
ꢄ = 0.08 mm
T = 120 (2) K
c = 12.2783 (8) A
ꢁ = 70.429 (3)ꢁ
ꢂ = 69.895 (4)ꢁ
ꢃ = 66.454 (4)ꢁ
Plate, colourless
0.15 Â 0.10 Â 0.04 mm
1
2
1
2
Symmetry codes: (i) x ‡ 1; y
;
z ‡ 32; (ii) x ‡ 2; y
;
z ‡ 32; (iii) x ‡ 2,
y ‡ 12; z ‡ 32; (iv) x ‡ 2; y ‡ 2; z ‡ 1; (v) x ‡ 1; y ‡ 1; z ‡ 1.
ꢀ
Acta Cryst. (2006). C62, o521±o524
Portilla et al. C11H16N4 and C8H11N5ÁH2O o523

organic compounds
Compound (I) crystallized in the triclinic system; space group P1
was assumed and con®rmed by the analysis. For compound (II), the
space group P21/c was uniquely assigned from the systematic
absences. All H atoms were located in difference maps, and then
treated as riding atoms. For compound (I), the distances were CÐH =
short stay at the EPSRC X-ray Crystallographic Service,
University of Southampton. JP and JQ thank COLCIENCIAS
and UNIVALLE (Universidad del Valle, Colombia) for
®nancial support.
Ê
0.95 (aromatic) or 0.98 A (methyl) and NÐH = 0.88 A, and for
Ê
compound (II), the distances were CÐH = 0.93 (aromatic) or 0.96 A
Ê
Supplementary data for this paper are available from the IUCr electronic
archives (Reference: SK3040). Services for accessing these data are
described at the back of the journal.
Ê
Ê
(methyl), NÐH = 0.86±0.87 A and OÐH = 0.90 A, with Uiso(H) =
kUeq(C, N,O), where k = 1.5 for OÐH or methyl groups and 1.2 for all
other H atoms. In compound (II), the amino group containing N3 was
modelled using three sites, with one, labelled H3A, of unit occupancy
and two others, labelled H3B and H3C, each with 0.5 occupancy.
For both compounds, data collection: COLLECT (Nonius, 1999);
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Â
ꢀ
o524 Portilla et al. C11H16N4 and C8H11N5ÁH2O
Acta Cryst. (2006). C62, o521±o524