2-Amino-4-(piperidin-1-yl)-11H-pyrimido[4,5-b][1,5]benzodiazepin-6-ium chloride monohydrate and 2-amino-4-[methyl(2-methyl-phenyl)amino]-11H- pyrimido[4,5-b][1,5]benzodiazepin-6-ium chloride-benzene-1,2-diamine (1/1): Complex sheets generated by multiple hydrogen bonds

Article abstract of DOI:10.1107/S0108270110006967

In each of 2-amino-4-(piperidin-1-yl)-11H-pyrimido[4,5-b][1,5] benzodiazepin-6-ium chloride monohydrate, C₁₆H₁₉N ₆ ⁺·Cl^-·H₂O, (I), and 2-amino-4-[methyl(2-methyl-phenyl)amino]-11H-pyrimido[4,5-b][1,5] benzodiazepin-6-ium chloride-ben-zene-1,2-diamine (1/1), C₁₉H ₁₉N₆ ⁺·Cl^-·C ₆H₈N₂, (II), the seven-membered ring in the cation adopts a boat conformation. The pyrimidine ring in (II) adopts a twist-boat conformation, but the corresponding ring in (I) is essentially planar. The amino groups of the benzene-1,2-diamine component of (II) are both pyramidal. The independent components of (I) are linked into complex sheets by a combination of N - H...O, N - H...N, N - H...Cl and O - H...Cl hydrogen bonds. In the crystal structure of (II), one N - H...N hydrogen bond and six independent N - H...Cl hydrogen bonds combine to link the components into complex sheets.

Full text of DOI:10.1107/S0108270110006967

organic compounds
Acta Crystallographica Section C
Crystal Structure
Communications
idin-1-yl)-11H-pyrimido[4,5-b][1,5]benzodiazepin-6-ium
chloride monohydrate, (I) (Fig. 1), and 2-amino-4-[methyl(2-
methylphenyl)amino]-11H-pyrimido[4,5-b][1,5]benzodiaz-
epin-6-ium chloride–benzene-1,2-diamine (1/1), (II) (Fig. 2).
Compounds (I) and (II) were both prepared rapidly and in
satisfactory yield by means of a cyclocondensation reaction
between benzene-1,2-diamine and a 2,4-diamino-6-chloro-5-
formylpyrimidine, mediated by microwave radiation under
solvent-free conditions. The pyrimidine components em-
ployed in the syntheses of (I) and (II) differ in the nature of
the 4-amino substituent: a piperidine unit in the precursor for
(I) and a (2-methylphenyl)amino unit in the precursor for (II)
(see scheme). Both products are fused pyrimidobenzodiaze-
pinium chloride salts, with an additional water molecule
present in (I) and a molecule of benzene-1,2-diamine present
in (II).
ISSN 0108-2701
2-Amino-4-(piperidin-1-yl)-11H-pyri-
mido[4,5-b][1,5]benzodiazepin-6-ium
chloride monohydrate and 2-amino-4-
[methyl(2-methylphenyl)amino]-11H-
pyrimido[4,5-b][1,5]benzodiazepin-6-
ium chloride–benzene-1,2-diamine
(1/1): complex sheets generated by
multiple hydrogen bonds
Jairo Quiroga,a Jorge Trilleras,b Justo Coboc and
Christopher Glidewelld*
a
´
Departamento de Quımica, Universidad de Valle, AA 25360 Cali, Colombia,
b
´
´
´
Departamento de Quımica, Universidad del Atlantico, Km 7 vıa antigua Puerto
c
´
´
Colombia, Barranquilla, Colombia, Departamento de Quımica Inorganica y
Organica, Universidad 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 22 February 2010
Accepted 23 February 2010
Online 6 March 2010
In each of 2-amino-4-(piperidin-1-yl)-11H-pyrimido[4,5-b]-
+
[1,5]benzodiazepin-6-ium chloride monohydrate, C16H19N6 Á-
ClÀÁH2O, (I), and 2-amino-4-[methyl(2-methylphenyl)amino]-
11H-pyrimido[4,5-b][1,5]benzodiazepin-6-ium chloride–ben-
+
zene-1,2-diamine (1/1), C19H19N6 ÁClÀÁC6H8N2, (II), the
seven-membered ring in the cation adopts a boat conforma-
tion. The pyrimidine ring in (II) adopts a twist-boat
conformation, but the corresponding ring in (I) is essentially
planar. The amino groups of the benzene-1,2-diamine
component of (II) are both pyramidal. The independent
components of (I) are linked into complex sheets by a
combination of N—HÁ Á ÁO, N—HÁ Á ÁN, N—HÁ Á ÁCl and O—
HÁ Á ÁCl hydrogen bonds. In the crystal structure of (II), one
N—HÁ Á ÁN hydrogen bond and six independent N—HÁ Á ÁCl
hydrogen bonds combine to link the components into complex
sheets.
The presence of three independent components in each
structure provides considerable flexibility in the choice of the
asymmetric units. However, for both structures it is possible to
specify rather compact asymmetric units in which the inde-
pendent components are linked by multiple hydrogen bonds
(Figs. 1 and 2, and Table 2). In compound (I), the three
components are linked within the selected asymmetric unit by
a combination of N—HÁ Á ÁO, O—HÁ Á ÁCl and N—HÁ Á ÁCl
hydrogen bonds in a cyclic R23(10) motif (Bernstein et al.,
1995), while in (II), the components within the selected
asymmetric unit are linked by a combination of three inde-
pendent N—HÁ Á ÁCl hydrogen bonds and one N—HÁ Á ÁN
hydrogen bond to form edge-fused R12(7) and R32(10) rings. It
may be noted that the R23(10) rings in (I) and (II) differ only in
the notional replacement of the water O atom in (I) by an
amino N atom in (II).
Comment
Pyrimidine-fused compounds belong to the so-called bicyclic
privileged structures, which may be useful in the field of
medicinal chemistry (Horton et al., 2003). They have shown a
wide variety of biological properties (Gangjee et al., 2004;
McGuigan et al., 2004; Wang et al., 2004). We report here
the structures of two N4-substituted 11H-pyrimido[4,5-b]-
[1,5]benzodiazepine-2,4-diamines, namely 2-amino-4-(piper-
The pyrimidine ring in (I) is effectively planar, but that in
(II) adopts an approximate twist-boat conformation, with a
˚
ring-puckering amplitude of 0.129 (2) A and ring-puckering
o154 # 2010 International Union of Crystallography
doi:10.1107/S0108270110006967
Acta Cryst. (2010). C66, o154–o158

organic compounds
Figure 2
The independent components of (II), showing the atom-labelling scheme
and the 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.
Figure 1
The independent components of (I), showing the atom-labelling scheme
and the 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.
aryl ring plane, and the C—C—N—H torsion angles (Table 1)
indicate that this component has approximate mirror
symmetry, with the mirror normal to the ring plane and
passing through the mid-points of the C21—C22 and C24—
C25 bonds. By contrast, in pure benzene-1,2-diamine
[Cambridge Structural Database (Allen, 2002) refcode
BAGFIY; Stalhandske, 1981], where again the amino groups
are pyramidal with angle sums at the N atoms of 341 and 335ꢀ,
the H atoms of the two amino groups lie on opposite sides of
the ring plane, so that the molecule has approximate twofold
rotation symmetry, with the axis passing through the mid-
points of the bonds corresponding to C21—C22 and C24—C25
in (II).
angles (Cremer & Pople, 1975) of ꢀ = 81.7 (9)ꢀ and ’ =
221.6 (10)ꢀ. The idealized ring-puckering angles for a twist-
boat form are ꢀ = 90ꢀ and ’ = (60k + 30)ꢀ, where k represents
an integer. The seven-membered rings adopt very similar
boat-type conformations in which the ring atoms C5, N6, N11
and C11a are essentially coplanar, with atoms C4a, C6a and
C10a all displaced to the same side of the plane defined by
atoms C5/N6/N11/C11a.
The pattern of the bond distances (Table 1) in the fused
tricyclic cores are very similar for (I) and (II), and a number of
general comments can be made. Firstly, the bond distances in
the C6a/C7–C10/C10a carbocyclic rings span only very small
In addition to the three hydrogen bonds within the selected
asymmetric unit of (I), the crystal structure of (I) contains
three further hydrogen bonds, one each of the N—HÁ Á ÁN, O—
HÁ Á ÁCl and N—HÁ Á ÁCl types, linking the three-component
aggregates comprising the asymmetric units to form complex
sheets. The formation of the sheets is most simply analysed in
terms of two one-dimensional substructures. The first sub-
structure in (I) is a chain of edge-fused rings running parallel
to the [100] direction. Pairs of symmetry-related N—HÁ Á ÁN
hydrogen bonds link pairs of cations related by inversion, via a
centrosymmetric R22(8) motif, while O—HÁ Á ÁCl hydrogen
bonds link pairs of water molecules and pairs of chloride ions
in a centrosymmetric R24(8) motif. Within the chain of rings,
the R22(8) rings are centred at (n + 21, 21, 12), where n represents an
˚
ranges, ca 0.015 A, indicating the occurrence of unperturbed
benzenoid delocalization within this ring in both compounds.
Secondly, the bond distances in the pyrimidine rings are
typical of their types and again are consistent with aromatic-
type delocalization in these rings. Thirdly, in the seven-
membered rings, there is not even approximate equivalence
between the distances in the two halves of the ring (defined by
the local pseudo-mirror through atom C4a and the mid-point
of the C6a—C10a bond), as expected for a simple benzodia-
zepinium cation and, in particular, there are some marked
differences in the C—N distances. Thus, the C5—N6 bond is
markedly shorter than the N6—C6a bond in both compounds,
consistent with C5—N6 being a localized double bond. Hence,
it may be concluded that there is no electronic delocalization
between the fused rings, nor around the periphery, so that the
outer rings both behave as closed 6ꢁ systems, while the central
ring contains a localized double bond.
1
1
integer, and the R24(8) rings are centred at (n, , ), where n
2
2
again represents an integer, and these two centrosymmetric
motifs are linked by the R23(10) ring within the asymmetric
unit, giving a continuous chain of edge-fused rings parallel to
[100] (Fig. 3). In the second substructure in (I), atom N6 in the
cation at (x, y, z) acts as hydrogen-bond donor to the chloride
In the benzene-1,2-diamine component of (II), the N atoms
are both markedly pyramidal, with angle sums at N21 and N22
of 340.1 and 336.1ꢀ, respectively, and the C—N distances in
this component (Table 1) are typical of those in aryl–NH2
fragments containing pyramidal N atoms (Allen et al., 1987).
All of the amino-group H atoms lie on the same side of the
1
1
ion at (32 À x, À + y, À z), so linking the three-component
2
2
1
4
aggregates related by the 21 screw axis along (34, y, ) into a
C32(9)C21(10)[R23(10)] chain of rings running parallel to the
[010] direction (Fig. 4). The combination of [100] and [010]
C16H19N6 ÁClÀÁH2O and C19H19N6 ÁClÀÁC6H8N2 o155
+
+
ꢁ
Acta Cryst. (2010). C66, o154–o158
Quiroga et al.

organic compounds
Figure 5
A stereoview of part of the crystal structure of (II), showing the
formation of a hydrogen-bonded chain of edge-fused R24(8) and R42(20)
rings along [010] and containing only the ionic components. Hydrogen
bonds are shown as dashed lines. For the sake of clarity, H atoms bonded
to C atoms have been omitted.
Figure 3
A stereoview of part of the crystal structure of (I), showing the formation
of a hydrogen-bonded chain along [100] and containing three types of
edge-fused ring. Hydrogen bonds are shown as dashed lines. For the sake
of clarity, H atoms bonded to C atoms have been omitted.
Figure 4
A stereoview of part of the crystal structure of (I), showing the formation
of a hydrogen-bonded C32(9)C21(10)[R23(10)] chain of rings along [010].
Hydrogen bonds are shown as dashed lines. For the sake of clarity, H
atoms bonded to C atoms have been omitted.
chains of rings generates a sheet of some complexity lying
parallel to (001).
In compound (II), there are four N—H bonds exterior to
the three-component aggregate comprising the selected
asymmetric unit. As in (I), the hydrogen-bonded structure of
(II) is two-dimensional and again it is readily analysed in terms
of two substructures, one involving only the ionic components
and the other involving all three components. In the first and
simpler of the two substructures, the cations and anions are
linked by three independent N—HÁ Á ÁCl hydrogen bonds
involving atoms N2 and N6 as donors (Table 2) to form a chain
of edge-fused centrosymmetric rings running parallel to the
Figure 6
A stereoview of part of the crystal structure of (II), showing the
formation of a chain along [110] containing four types of hydrogen-
bonded ring. Hydrogen bonds are shown as dashed lines. For the sake of
clarity, H atoms bonded to C atoms have been omitted.
running parallel to the [110] direction (Fig. 6). The R24(8) and
R24(20) rings in the chain along [110] are spiro-fused, in
contrast with the edge-fused R24(8) and R42(20) rings in the
chain along [010]. In addition, the chain along [110] also
contains the R12(7) and R32(10) rings which lie within the
selected asymmetric unit, so that the chain along [110]
contains four distinct ring types, as opposed to just two ring
types in the chain along [010]. The combination of chains of
rings along [010] and [110] generates a complex sheet parallel
to (001). Unlike that of (I), the structure of (II) contains a
single rather weak C—HÁ Á Áꢁ(arene) hydrogen bond (Table 2)
but this lies within the (001) sheet, rather than linking adjacent
1
[010] direction, in which R24(8) rings are centred at (12, n, ),
2
1
2
1
2
alternating with R24(20) rings centred at (12, n + , ), where in
both cases n represents an integer (Fig. 5). The second, more
complex, substructure again contains centrosymmetric R24(20)
rings built from pairs of cations and anions and centred at
1
1 1
(n + , n + , ), where n represents an integer. These rings
2
2 2
alternate with centrosymmetric R24(8) rings built from chloride
ions and benzene-1,2-diamine molecules which are centred at
1
2
(n, n, ), where n represents an integer, so forming a chain
o156 Quiroga et al. C16H19N6 ÁClÀÁH2O and C19H19N6 ÁClÀÁC6H8N2
Acta Cryst. (2010). C66, o154–o158
+
+
ꢁ

organic compounds
Table 1
Selected bond distances (A) for (I) and (II), and selected torsion angles
sheets, so that the hydrogen-bonded structures of (I) and (II)
are both strictly two-dimensional.
˚
(ꢀ) for (II).
(I)
(II)
Experimental
N1—C2
C2—N3
N3—C4
C4—C4a
C4a—C5
C5—N6
N6—C6a
C6a—C7
C7—C8
1.345 (3)
1.338 (3)
1.331 (4)
1.428 (3)
1.389 (3)
1.307 (3)
1.418 (3)
1.378 (3)
1.377 (3)
1.373 (3)
1.377 (3)
1.380 (3)
1.401 (3)
1.348 (3)
1.308 (3)
1.426 (3)
1.388 (3)
1.329 (3)
1.342 (2)
1.334 (2)
1.316 (3)
1.432 (3)
1.389 (3)
1.298 (2)
1.412 (2)
1.374 (3)
1.374 (3)
1.375 (3)
1.366 (3)
1.377 (3)
1.397 (2)
1.347 (2)
1.315 (2)
1.416 (3)
1.381 (3)
1.319 (2)
1.350 (2)
An intimate mixture of benzene-1,2-diamine (0.2 mmol) with the
appropriate N4-substituted 2,4-diamino-6-chloropyrimidine-5-carb-
aldehyde (0.2 mmol) [2-amino-6-chloro-4-piperidinopyrimidine-5-
carbaldehyde for (I) and 2-amino-6-chloro-4-(2-methylphenyl-
amino)pyrimidine-5-carbaldehyde for (II)] was subjected to micro-
wave irradiation in the absence of solvent (maximum power 300 W
over 3 min at a controlled temperature of 378 K) using a focused
microwave reactor (CEM Discover). After cooling to ambient
temperature, the solid products were washed with ethanol and then
with diethyl ether to give red crystals of (I) and (II) suitable for
single-crystal X-ray diffraction. For (I), yield 70%, m.p. 524–526 K;
MS (70 eV) m/z (%): 294 (M+, 100), 293 (34), 251 (19), 237 (17),
169 (11), 84 (16), 36 (15). For (II), yield 70%, m.p. 525–527 K; MS
(70 eV) m/z (%): 330 (M+, 27), 315 (14), 108 (19), 81 (54), 69 (100),
41 (28).
C8—C9
C9—C10
C10—C10a
C10a—N11
N11—C11a
C11a—N1
C4a—C11a
C6a—C10a
C2—N2
C4—N4
C4—N41
C21—N21
C22—N22
1.350 (3)
1.391 (3)
1.404 (2)
Compound (I)
C22—C21—N21—H21A
C22—C21—N21—H21B
C21—C22—N22—H22A
C21—C22—N22—H22B
39
171
Crystal data
+
À32
C16H19N6 ÁClÀÁH2O
3
˚
V = 1582.4 (3) A
Z = 4
À159
Mr = 348.84
Monoclinic, P21=n
Mo Kꢃ radiation
ꢄ = 0.26 mmÀ1
T = 120 K
0.32 Â 0.28 Â 0.10 mm
˚
a = 13.7831 (14) A
Table 2
Hydrogen-bond parameters (A, ) for (I) and (II).
˚
b = 7.5324 (9) A
ꢀ
˚
˚
c = 15.2987 (12) A
ꢂ = 94.925 (8)ꢀ
Cg1 is the centroid of the C41–C46 ring.
Data collection
Compound D—HÁ Á ÁA
D—H
HÁ Á ÁA
DÁ Á ÁA
D—HÁ Á ÁA
Bruker–Nonius KappaCCD area-
detector diffractometer
Absorption correction: multi-scan
(SADABS; Sheldrick, 2003)
Tmin = 0.933, Tmax = 0.975
22943 measured reflections
3122 independent reflections
2253 reflections with I > 2ꢅ(I)
Rint = 0.066
(I)
N2—H2AÁ Á ÁCl1
0.88
0.88
2.59
1.92
3.422 (2) 159
2.782 (3) 167
N11—H11Á Á ÁO1
O1—H1AÁ Á ÁCl1
O1—H1BÁ Á ÁCl1i
N2—H2BÁ Á ÁN3ii
N6—H6Á Á ÁCl1iii
N2—H2AÁ Á ÁCl1
N11—H11Á Á ÁN22
N21—H21AÁ Á ÁCl1
N22—H22AÁ Á ÁCl1
N2—H2BÁ Á ÁCl1iv
N6—H6Á Á ÁCl1ii
0.88 (3) 2.29 (3) 3.151 (2) 165 (3)
0.89 (2) 2.19 (2) 3.078 (2) 171 (3)
0.88
0.88
0.88
0.88
0.88
0.88
0.88
0.92
2.33
2.41
2.65
2.09
2.60
2.51
2.37
2.14
2.56
2.96
3.198 (3) 169
3.281 (2) 169
3.521 (2) 171
2.922 (3) 158
3.477 (2) 179
3.380 (2) 172
3.209 (2) 161
3.050 (2) 172
3.418 (2) 167
3.770 (3) 144
(II)
Refinement
R[F2 > 2ꢅ(F2)] = 0.044
wR(F2) = 0.111
S = 1.07
3122 reflections
223 parameters
2 restraints
H atoms treated by a mixture of
independent and constrained
refinement
À3
˚
Áꢆmax = 0.26 e A
À3
˚
N21—H21BÁ Á ÁCl1v 0.88
Áꢆmin = À0.32 e A
C9—H9Á Á ÁCg1vi
0.95
Symmetry codes: (i) 2 À x, 1 À y, 1 À z; (ii) 1 À x, 1 À y, 1 À z; (iii) 32 À x, À + y, 21 À z; (iv)
1
2
1 À x, 2 À y, 1 À z; (v) 2 À x, 2 À y, 1 À z; (vi) 1 + x, y, z.
Compound (II)
Crystal data
C19H19N6 ÁClÀÁC6H8N2
Refinement
+
ꢇ = 107.512 (10)ꢀ
3
˚
V = 1149.0 (3) A
Z = 2
R[F2 > 2ꢅ(F2)] = 0.042
wR(F2) = 0.103
S = 1.06
309 parameters
H-atom parameteÀrs3 constrained
Mr = 475.00
Triclinic, P1
a = 10.9559 (13) A
˚
˚
˚
Áꢆmax = 0.37 e A
Mo Kꢃ radiation
ꢄ = 0.20 mmÀ1
T = 120 K
0.42 Â 0.35 Â 0.12 mm
À3
˚
4532 reflections
Áꢆmin = À0.26 e A
b = 11.2372 (13) A
˚
c = 11.432 (2) A
ꢃ = 102.894 (12)ꢀ
ꢂ = 112.176 (14)ꢀ
All H atoms were located in difference maps. H atoms bonded to C
atoms were then treated as riding in geometrically idealized positions,
˚
with C—H = 0.95 (aromatic or alkenyl), 0.98 (CH3) or 0.99 A (CH2),
Data collection
and with Uiso(H) = kUeq(C), where k = 1.5 for the methyl groups,
which were permitted to rotate but not to tilt, and 1.2 for all other H
atoms bonded to C atoms. H atoms bonded to N atoms were treated
as riding at the positions located in difference maps, with Uiso(H) =
Bruker–Nonius KappaCCD area-
detector diffractometer
Absorption correction: multi-scan
(SADABS; Sheldrick, 2003)
Tmin = 0.941, Tmax = 0.977
30475 measured reflections
4532 independent reflections
3349 reflections with I > 2ꢅ(I)
Rint = 0.057
˚
1.2Ueq(N), giving N—H distances in the range 0.88–0.92 A. The
C16H19N6 ÁClÀÁH2O and C19H19N6 ÁClÀÁC6H8N2 o157
+
+
ꢁ
Acta Cryst. (2010). C66, o154–o158
Quiroga et al.

organic compounds
coordinates of the H atoms of the water molecule in (I) were refined
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˚
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´
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´
´
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