2,6-Diamino-4-oxo-3,4-dihydropyrim­idin-1-ium chloride dihydrate

Suleiman Gwaram, N.; Khaledi, H.; Mohd Ali, H.

doi:10.1107/S1600536810031557

organic compounds

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Volume 66| Part 9| September 2010| Page o2294

https://doi.org/10.1107/S1600536810031557

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2,6-Diamino-4-oxo-3,4-dihydropyrimidin-1-ium chloride dihydrate

Nura Suleiman Gwaram,^a Hamid Khaledi ^a ^* and Hapipah Mohd Ali ^a

^aDepartment of Chemistry, University of Malaya, 50603 Kuala Lumpur, Malaysia
^*Correspondence e-mail: khaledi@siswa.um.edu.my

(Received 1 August 2010; accepted 5 August 2010; online 11 August 2010)

In the crystal structure of the title compound, C₄H₇N₄O⁺·Cl⁻·2H₂O, adjacent cations are connected to one another through N—H⋯O hydrogen bonds, forming infinite chains along the b axis. These chains are further hydrogen bonded to the chloride anions and water molecules, resulting in a three-dimensional network. The pyrimidine rings of adjacent molecules are arranged in an antiparallel manner above each other with centroid–centroid distances of 3.435 (1) Å, indicative of π–π interactions.

Related literature

For related structures, see: Wijaya et al. (2004 ); Muthiah et al. (2004 ).

Experimental

Crystal data

C₄H₇N₄O⁺·Cl⁻·2H₂O
M_r = 198.62
Monoclinic, C 2/c
a = 20.4162 (4) Å
b = 6.6030 (1) Å
c = 12.8876 (2) Å
β = 107.903 (1)°
V = 1653.23 (5) Å³
Z = 8
Mo Kα radiation
μ = 0.44 mm⁻¹
T = 100 K
0.35 × 0.19 × 0.08 mm

Data collection

Bruker APEXII CCD diffractometer
Absorption correction: multi-scan (SADABS; Sheldrick, 1996 ) T_min = 0.862, T_max = 0.966
4405 measured reflections
1488 independent reflections
1352 reflections with (I) > 2.0σ(I)
R_int = 0.022

Refinement

R[F² > 2σ(F²)] = 0.024
wR(F²) = 0.066
S = 1.05
1488 reflections
139 parameters
10 restraints
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.22 e Å⁻³
Δρ_min = −0.25 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O2—H8⋯O3	0.82 (2)	1.97 (2)	2.7503 (17)	161 (2)
O2—H9⋯Cl1ⁱ	0.81 (2)	2.51 (2)	3.2802 (11)	159 (2)
O3—H10⋯Cl1ⁱⁱ	0.83 (2)	2.39 (2)	3.2158 (12)	173 (2)
O3—H11⋯Cl1ⁱⁱⁱ	0.84 (2)	2.35 (2)	3.1831 (13)	173 (2)
N4—H5⋯Cl1^iv	0.85 (1)	2.45 (1)	3.2805 (13)	166 (2)
N4—H6⋯O1ⁱ	0.87 (1)	2.11 (2)	2.8310 (16)	141 (2)
N3—H4⋯O1ⁱ	0.87 (1)	1.88 (2)	2.6806 (15)	151 (2)
N2—H3⋯O2	0.88 (1)	2.05 (1)	2.9151 (17)	167 (2)
N2—H2⋯Cl1	0.87 (1)	2.38 (2)	3.2112 (13)	161 (2)
N1—H1⋯O2^v	0.85 (1)	1.93 (1)	2.7727 (16)	174 (2)
Symmetry codes: (i) x, y+1, z; (ii) $[-x+1, y, -z+{\script{1\over 2}}]$ ; (iii) $[x, -y+1, z+{\script{1\over 2}}]$ ; (iv) $[x+{\script{1\over 2}}, -y+{\script{1\over 2}}, z+{\script{1\over 2}}]$ ; (v) x, y-1, z.

Data collection: APEX2 (Bruker, 2007 ); cell refinement: SAINT (Bruker, 2007); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: X-SEED (Barbour, 2001 ); software used to prepare material for publication: SHELXL97 and publCIF (Westrip, 2010 ).

Supporting information

Crystal structure: contains datablocks I, global. DOI: https://doi.org/10.1107/S1600536810031557/pv2317sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536810031557/pv2317Isup2.hkl

checkCIF report

Comment top

The title compound is a chloride salt of 2,4-diamino-6-hydroxypyrimidine, cocrystallized with two molecules of water (Fig. 1). The structures of dimesylamide salt (Wijaya et al., 2004) and sulfate salt (Muthiah et al., 2004) of this cation have been reported previously. In the crystal structure of the title compound, adjacent diaminopyridinium cations are linked together via N—H···O hydrogen bonding into infinite chains along the b-axis. The pyrimidine rings of the adjacent molecules (related by symmetry: –x+3/2, -y + 1/2, -z + 1) are arranged in an antiparallel manner above each other with centroid-centroid distance of 3.435 (1) Å, indicative of a π-π interactions. The cation chains are hydrogen bonded to chloride anions and water molecules to form a three-dimensional hydrogen bonded network, involving O—H···O, O—H···Cl, N—H···Cl and N—H···O type hydrogen bonds (Tab. 1 & Fig. 2).

Related literature top

For related structures, see: Wijaya et al. (2004); Muthiah et al. (2004).

Experimental top

The pale yellow crystals of the title compound were obtained by slow evaporation of an aqueous ethanol (50%) solution of 2,4-diamino-6-hydroxypyrimidine in the presence of a few drops of hydrochloric acid.

Structure description top

For related structures, see: Wijaya et al. (2004); Muthiah et al. (2004).

Computing details top

Data collection: APEX2 (Bruker, 2007); cell refinement: SAINT (Bruker, 2007); data reduction: SAINT (Bruker, 2007); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: X-SEED (Barbour, 2001); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008) and publCIF (Westrip, 2010).

Figures top

	Fig. 1. Thermal ellipsoid plot of the title compound at the 50% probability level. Hydrogen atoms are drawn as spheres of arbitrary radius.
	Fig. 2. Packing view of the crystal structure, looking down the b-axis.

2,6-Diamino-4-oxo-3,4-dihydropyrimidin-1-ium chloride dihydrate top

Crystal data top

C₄H₇N₄O⁺·Cl⁻·2H₂O	F(000) = 832
M_r = 198.62	D_x = 1.596 Mg m⁻³
Monoclinic, C2/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -C 2yc	Cell parameters from 2897 reflections
a = 20.4162 (4) Å	θ = 3.3–30.5°
b = 6.6030 (1) Å	µ = 0.44 mm⁻¹
c = 12.8876 (2) Å	T = 100 K
β = 107.903 (1)°	Block, yellow
V = 1653.23 (5) Å³	0.35 × 0.19 × 0.08 mm
Z = 8

Data collection top

Bruker APEXII CCD diffractometer	1488 independent reflections
Radiation source: fine-focus sealed tube	1352 reflections with (I) > 2.0σ(I)
Graphite monochromator	R_int = 0.022
φ and ω scans	θ_max = 25.2°, θ_min = 2.1°
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)	h = −24→24
T_min = 0.862, T_max = 0.966	k = −7→7
4405 measured reflections	l = −15→13

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F² > 2σ(F²)] = 0.024	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.066	H atoms treated by a mixture of independent and constrained refinement
S = 1.05	w = 1/[σ²(F_o²) + (0.0327P)² + 1.7645P] where P = (F_o² + 2F_c²)/3
1488 reflections	(Δ/σ)_max = 0.001
139 parameters	Δρ_max = 0.22 e Å⁻³
10 restraints	Δρ_min = −0.25 e Å⁻³

Crystal data top

C₄H₇N₄O⁺·Cl⁻·2H₂O	V = 1653.23 (5) Å³
M_r = 198.62	Z = 8
Monoclinic, C2/c	Mo Kα radiation
a = 20.4162 (4) Å	µ = 0.44 mm⁻¹
b = 6.6030 (1) Å	T = 100 K
c = 12.8876 (2) Å	0.35 × 0.19 × 0.08 mm
β = 107.903 (1)°

Data collection top

Bruker APEXII CCD diffractometer	1488 independent reflections
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)	1352 reflections with (I) > 2.0σ(I)
T_min = 0.862, T_max = 0.966	R_int = 0.022
4405 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.024	10 restraints
wR(F²) = 0.066	H atoms treated by a mixture of independent and constrained refinement
S = 1.05	Δρ_max = 0.22 e Å⁻³
1488 reflections	Δρ_min = −0.25 e Å⁻³
139 parameters

Special details top

Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes.

Refinement. Refinement of F² against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F², conventional R-factors R are based on F, with F set to zero for negative F². The threshold expression of F² > σ(F²) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F² are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
Cl1	0.485357 (17)	0.19327 (5)	0.09794 (3)	0.01545 (13)
O2	0.58753 (5)	0.85326 (16)	0.25118 (9)	0.0160 (2)
H8	0.5728 (9)	0.823 (3)	0.3011 (14)	0.024*
H9	0.5575 (8)	0.910 (3)	0.2042 (14)	0.024*
O3	0.55365 (6)	0.66656 (18)	0.41849 (10)	0.0223 (3)
H10	0.5424 (10)	0.545 (2)	0.4079 (16)	0.033*
H11	0.5331 (10)	0.709 (3)	0.4617 (15)	0.033*
O1	0.75583 (5)	−0.12955 (15)	0.37901 (8)	0.0148 (2)
N1	0.68878 (6)	0.14677 (19)	0.31998 (10)	0.0116 (3)
H1	0.6566 (8)	0.062 (2)	0.2953 (13)	0.014*
N2	0.61850 (6)	0.4221 (2)	0.25253 (10)	0.0140 (3)
H2	0.5846 (8)	0.340 (2)	0.2242 (14)	0.017*
H3	0.6124 (8)	0.554 (2)	0.2445 (13)	0.017*
N3	0.73174 (6)	0.47140 (18)	0.35528 (10)	0.0113 (3)
H4	0.7246 (8)	0.601 (2)	0.3510 (13)	0.014*
N4	0.84541 (6)	0.53639 (19)	0.44953 (10)	0.0145 (3)
H5	0.8853 (8)	0.496 (3)	0.4852 (13)	0.017*
H6	0.8359 (9)	0.665 (2)	0.4492 (14)	0.017*
C1	0.75285 (7)	0.0589 (2)	0.37417 (11)	0.0118 (3)
C2	0.67858 (7)	0.3467 (2)	0.30834 (11)	0.0111 (3)
C3	0.79694 (7)	0.3985 (2)	0.40909 (11)	0.0113 (3)
C4	0.80775 (7)	0.1923 (2)	0.41736 (12)	0.0125 (3)
H7	0.8525	0.1407	0.4524	0.015*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Cl1	0.0137 (2)	0.0141 (2)	0.0164 (2)	−0.00100 (13)	0.00153 (14)	−0.00102 (13)
O2	0.0125 (5)	0.0165 (6)	0.0180 (6)	−0.0001 (4)	0.0033 (4)	0.0016 (4)
O3	0.0300 (7)	0.0152 (6)	0.0253 (6)	−0.0055 (5)	0.0137 (5)	−0.0032 (5)
O1	0.0153 (5)	0.0082 (5)	0.0191 (6)	0.0004 (4)	0.0027 (4)	0.0006 (4)
N1	0.0094 (6)	0.0100 (6)	0.0137 (6)	−0.0021 (5)	0.0012 (5)	−0.0012 (5)
N2	0.0106 (6)	0.0100 (6)	0.0192 (7)	−0.0012 (5)	0.0016 (5)	−0.0003 (5)
N3	0.0117 (6)	0.0077 (6)	0.0134 (6)	0.0006 (5)	0.0025 (5)	0.0004 (5)
N4	0.0114 (6)	0.0099 (6)	0.0190 (7)	0.0000 (5)	−0.0003 (5)	−0.0007 (5)
C1	0.0143 (7)	0.0125 (7)	0.0095 (7)	0.0016 (6)	0.0049 (5)	0.0002 (6)
C2	0.0128 (7)	0.0119 (7)	0.0097 (7)	−0.0009 (5)	0.0050 (6)	−0.0007 (5)
C3	0.0117 (7)	0.0136 (7)	0.0087 (7)	−0.0003 (6)	0.0034 (5)	0.0001 (5)
C4	0.0107 (7)	0.0127 (7)	0.0128 (7)	0.0016 (6)	0.0014 (6)	0.0005 (6)

Geometric parameters (Å, º) top

O2—H8	0.815 (15)	N2—H3	0.882 (14)
O2—H9	0.809 (15)	N3—C2	1.3484 (18)
O3—H10	0.832 (16)	N3—C3	1.3845 (18)
O3—H11	0.841 (15)	N3—H4	0.870 (14)
O1—C1	1.2467 (18)	N4—C3	1.3279 (19)
N1—C2	1.3379 (19)	N4—H5	0.846 (14)
N1—C1	1.4048 (18)	N4—H6	0.868 (14)
N1—H1	0.846 (14)	C1—C4	1.399 (2)
N2—C2	1.3142 (18)	C3—C4	1.378 (2)
N2—H2	0.867 (14)	C4—H7	0.9500

H8—O2—H9	108.9 (19)	H5—N4—H6	119.3 (17)
H10—O3—H11	105.1 (19)	O1—C1—C4	125.98 (13)
C2—N1—C1	123.52 (12)	O1—C1—N1	117.43 (13)
C2—N1—H1	122.2 (11)	C4—C1—N1	116.59 (13)
C1—N1—H1	114.3 (11)	N2—C2—N1	121.48 (13)
C2—N2—H2	118.8 (11)	N2—C2—N3	120.10 (13)
C2—N2—H3	120.8 (11)	N1—C2—N3	118.43 (12)
H2—N2—H3	120.4 (16)	N4—C3—C4	124.39 (13)
C2—N3—C3	121.99 (12)	N4—C3—N3	116.34 (13)
C2—N3—H4	118.6 (11)	C4—C3—N3	119.27 (13)
C3—N3—H4	119.4 (11)	C3—C4—C1	120.08 (13)
C3—N4—H5	118.1 (12)	C3—C4—H7	120.0
C3—N4—H6	121.9 (12)	C1—C4—H7	120.0

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O2—H8···O3	0.82 (2)	1.97 (2)	2.7503 (17)	161 (2)
O2—H9···Cl1ⁱ	0.81 (2)	2.51 (2)	3.2802 (11)	159 (2)
O3—H10···Cl1ⁱⁱ	0.83 (2)	2.39 (2)	3.2158 (12)	173 (2)
O3—H11···Cl1ⁱⁱⁱ	0.84 (2)	2.35 (2)	3.1831 (13)	173 (2)
N4—H5···Cl1^iv	0.85 (1)	2.45 (1)	3.2805 (13)	166 (2)
N4—H6···O1ⁱ	0.87 (1)	2.11 (2)	2.8310 (16)	141 (2)
N3—H4···O1ⁱ	0.87 (1)	1.88 (2)	2.6806 (15)	151 (2)
N2—H3···O2	0.88 (1)	2.05 (1)	2.9151 (17)	167 (2)
N2—H2···Cl1	0.87 (1)	2.38 (2)	3.2112 (13)	161 (2)
N1—H1···O2^v	0.85 (1)	1.93 (1)	2.7727 (16)	174 (2)

Symmetry codes: (i) x, y+1, z; (ii) −x+1, y, −z+1/2; (iii) x, −y+1, z+1/2; (iv) x+1/2, −y+1/2, z+1/2; (v) x, y−1, z.

Experimental details

Crystal data
Chemical formula	C₄H₇N₄O⁺·Cl⁻·2H₂O
M_r	198.62
Crystal system, space group	Monoclinic, C2/c
Temperature (K)	100
a, b, c (Å)	20.4162 (4), 6.6030 (1), 12.8876 (2)
β (°)	107.903 (1)
V (Å³)	1653.23 (5)
Z	8
Radiation type	Mo Kα
µ (mm⁻¹)	0.44
Crystal size (mm)	0.35 × 0.19 × 0.08

Data collection
Diffractometer	Bruker APEXII CCD
Absorption correction	Multi-scan (SADABS; Sheldrick, 1996)
T_min, T_max	0.862, 0.966
No. of measured, independent and observed [(I) > 2.0σ(I)] reflections	4405, 1488, 1352
R_int	0.022
(sin θ/λ)_max (Å⁻¹)	0.600

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.024, 0.066, 1.05
No. of reflections	1488
No. of parameters	139
No. of restraints	10
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.22, −0.25

Computer programs: APEX2 (Bruker, 2007), SAINT (Bruker, 2007), SHELXS97 (Sheldrick, 2008), X-SEED (Barbour, 2001), SHELXL97 (Sheldrick, 2008) and publCIF (Westrip, 2010).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O2—H8···O3	0.815 (15)	1.967 (15)	2.7503 (17)	160.9 (18)
O2—H9···Cl1ⁱ	0.809 (15)	2.511 (16)	3.2802 (11)	159.3 (18)
O3—H10···Cl1ⁱⁱ	0.832 (16)	2.389 (16)	3.2158 (12)	172.7 (18)
O3—H11···Cl1ⁱⁱⁱ	0.841 (15)	2.346 (16)	3.1831 (13)	173.4 (19)
N4—H5···Cl1^iv	0.846 (14)	2.453 (14)	3.2805 (13)	166.0 (16)
N4—H6···O1ⁱ	0.868 (14)	2.105 (16)	2.8310 (16)	140.8 (15)
N3—H4···O1ⁱ	0.870 (14)	1.884 (15)	2.6806 (15)	151.4 (15)
N2—H3···O2	0.882 (14)	2.049 (14)	2.9151 (17)	167.4 (16)
N2—H2···Cl1	0.867 (14)	2.380 (15)	3.2112 (13)	160.7 (15)
N1—H1···O2^v	0.846 (14)	1.929 (14)	2.7727 (16)	174.4 (16)

Symmetry codes: (i) x, y+1, z; (ii) −x+1, y, −z+1/2; (iii) x, −y+1, z+1/2; (iv) x+1/2, −y+1/2, z+1/2; (v) x, y−1, z.

Acknowledgements

The authors thank University of Malaya for funding this study (FRGS grant FP009/2008 C).

References

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