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Acta Crystallogr Sect E Struct Rep Online. 2010 September 1; 66(Pt 9): o2294.
Published online 2010 August 11. doi:  10.1107/S1600536810031557
PMCID: PMC3007964

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

Abstract

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 [triangle]); Muthiah et al. (2004 [triangle]).

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Object name is e-66-o2294-scheme1.jpg

Experimental

Crystal data

  • C4H7N4O+·Cl·2H2O
  • M r = 198.62
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-66-o2294-efi1.jpg
  • 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 [triangle]) 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[F 2 > 2σ(F 2)] = 0.024
  • wR(F 2) = 0.066
  • S = 1.05
  • 1488 reflections
  • 139 parameters
  • 10 restraints
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.22 e Å−3
  • Δρmin = −0.25 e Å−3

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

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

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

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810031557/pv2317Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Acknowledgments

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

supplementary crystallographic information

Comment

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).

Experimental

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.

Refinement

The C-bound hydrogen atom was placed in idealized location (C—H = 0.95 Å) and refined as riding on its parent carbon atom. The nitrogen- and oxygen-bound hydrogen atoms were located in a difference Fourier map and were refined with distance restraints of N—H 0.88 (2) and O—H 0.84 (2) Å. Uiso(H) were set to 1.2–1.5 × Ueq (parent atom).

Figures

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.

Crystal data

C4H7N4O+·Cl·2H2OF(000) = 832
Mr = 198.62Dx = 1.596 Mg m3
Monoclinic, C2/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -C 2ycCell parameters from 2897 reflections
a = 20.4162 (4) Åθ = 3.3–30.5°
b = 6.6030 (1) ŵ = 0.44 mm1
c = 12.8876 (2) ÅT = 100 K
β = 107.903 (1)°Block, yellow
V = 1653.23 (5) Å30.35 × 0.19 × 0.08 mm
Z = 8

Data collection

Bruker APEXII CCD diffractometer1488 independent reflections
Radiation source: fine-focus sealed tube1352 reflections with (I) > 2.0σ(I)
graphiteRint = 0.022
[var phi] and ω scansθmax = 25.2°, θmin = 2.1°
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)h = −24→24
Tmin = 0.862, Tmax = 0.966k = −7→7
4405 measured reflectionsl = −15→13

Refinement

Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.024Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.066H atoms treated by a mixture of independent and constrained refinement
S = 1.05w = 1/[σ2(Fo2) + (0.0327P)2 + 1.7645P] where P = (Fo2 + 2Fc2)/3
1488 reflections(Δ/σ)max = 0.001
139 parametersΔρmax = 0.22 e Å3
10 restraintsΔρmin = −0.25 e Å3

Special details

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)

xyzUiso*/Ueq
Cl10.485357 (17)0.19327 (5)0.09794 (3)0.01545 (13)
O20.58753 (5)0.85326 (16)0.25118 (9)0.0160 (2)
H80.5728 (9)0.823 (3)0.3011 (14)0.024*
H90.5575 (8)0.910 (3)0.2042 (14)0.024*
O30.55365 (6)0.66656 (18)0.41849 (10)0.0223 (3)
H100.5424 (10)0.545 (2)0.4079 (16)0.033*
H110.5331 (10)0.709 (3)0.4617 (15)0.033*
O10.75583 (5)−0.12955 (15)0.37901 (8)0.0148 (2)
N10.68878 (6)0.14677 (19)0.31998 (10)0.0116 (3)
H10.6566 (8)0.062 (2)0.2953 (13)0.014*
N20.61850 (6)0.4221 (2)0.25253 (10)0.0140 (3)
H20.5846 (8)0.340 (2)0.2242 (14)0.017*
H30.6124 (8)0.554 (2)0.2445 (13)0.017*
N30.73174 (6)0.47140 (18)0.35528 (10)0.0113 (3)
H40.7246 (8)0.601 (2)0.3510 (13)0.014*
N40.84541 (6)0.53639 (19)0.44953 (10)0.0145 (3)
H50.8853 (8)0.496 (3)0.4852 (13)0.017*
H60.8359 (9)0.665 (2)0.4492 (14)0.017*
C10.75285 (7)0.0589 (2)0.37417 (11)0.0118 (3)
C20.67858 (7)0.3467 (2)0.30834 (11)0.0111 (3)
C30.79694 (7)0.3985 (2)0.40909 (11)0.0113 (3)
C40.80775 (7)0.1923 (2)0.41736 (12)0.0125 (3)
H70.85250.14070.45240.015*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
Cl10.0137 (2)0.0141 (2)0.0164 (2)−0.00100 (13)0.00153 (14)−0.00102 (13)
O20.0125 (5)0.0165 (6)0.0180 (6)−0.0001 (4)0.0033 (4)0.0016 (4)
O30.0300 (7)0.0152 (6)0.0253 (6)−0.0055 (5)0.0137 (5)−0.0032 (5)
O10.0153 (5)0.0082 (5)0.0191 (6)0.0004 (4)0.0027 (4)0.0006 (4)
N10.0094 (6)0.0100 (6)0.0137 (6)−0.0021 (5)0.0012 (5)−0.0012 (5)
N20.0106 (6)0.0100 (6)0.0192 (7)−0.0012 (5)0.0016 (5)−0.0003 (5)
N30.0117 (6)0.0077 (6)0.0134 (6)0.0006 (5)0.0025 (5)0.0004 (5)
N40.0114 (6)0.0099 (6)0.0190 (7)0.0000 (5)−0.0003 (5)−0.0007 (5)
C10.0143 (7)0.0125 (7)0.0095 (7)0.0016 (6)0.0049 (5)0.0002 (6)
C20.0128 (7)0.0119 (7)0.0097 (7)−0.0009 (5)0.0050 (6)−0.0007 (5)
C30.0117 (7)0.0136 (7)0.0087 (7)−0.0003 (6)0.0034 (5)0.0001 (5)
C40.0107 (7)0.0127 (7)0.0128 (7)0.0016 (6)0.0014 (6)0.0005 (6)

Geometric parameters (Å, °)

O2—H80.815 (15)N2—H30.882 (14)
O2—H90.809 (15)N3—C21.3484 (18)
O3—H100.832 (16)N3—C31.3845 (18)
O3—H110.841 (15)N3—H40.870 (14)
O1—C11.2467 (18)N4—C31.3279 (19)
N1—C21.3379 (19)N4—H50.846 (14)
N1—C11.4048 (18)N4—H60.868 (14)
N1—H10.846 (14)C1—C41.399 (2)
N2—C21.3142 (18)C3—C41.378 (2)
N2—H20.867 (14)C4—H70.9500
H8—O2—H9108.9 (19)H5—N4—H6119.3 (17)
H10—O3—H11105.1 (19)O1—C1—C4125.98 (13)
C2—N1—C1123.52 (12)O1—C1—N1117.43 (13)
C2—N1—H1122.2 (11)C4—C1—N1116.59 (13)
C1—N1—H1114.3 (11)N2—C2—N1121.48 (13)
C2—N2—H2118.8 (11)N2—C2—N3120.10 (13)
C2—N2—H3120.8 (11)N1—C2—N3118.43 (12)
H2—N2—H3120.4 (16)N4—C3—C4124.39 (13)
C2—N3—C3121.99 (12)N4—C3—N3116.34 (13)
C2—N3—H4118.6 (11)C4—C3—N3119.27 (13)
C3—N3—H4119.4 (11)C3—C4—C1120.08 (13)
C3—N4—H5118.1 (12)C3—C4—H7120.0
C3—N4—H6121.9 (12)C1—C4—H7120.0

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
O2—H8···O30.82 (2)1.97 (2)2.7503 (17)161.(2)
O2—H9···Cl1i0.81 (2)2.51 (2)3.2802 (11)159.(2)
O3—H10···Cl1ii0.83 (2)2.39 (2)3.2158 (12)173.(2)
O3—H11···Cl1iii0.84 (2)2.35 (2)3.1831 (13)173.(2)
N4—H5···Cl1iv0.85 (1)2.45 (1)3.2805 (13)166.(2)
N4—H6···O1i0.87 (1)2.11 (2)2.8310 (16)141.(2)
N3—H4···O1i0.87 (1)1.88 (2)2.6806 (15)151.(2)
N2—H3···O20.88 (1)2.05 (1)2.9151 (17)167.(2)
N2—H2···Cl10.87 (1)2.38 (2)3.2112 (13)161.(2)
N1—H1···O2v0.85 (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.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: PV2317).

References

  • Barbour, L. J. (2001). J. Supramol. Chem.1, 189–191.
  • Bruker (2007). APEX2 and SAINT Bruker AXS Inc., Madison, Wisconsin, USA.
  • Muthiah, P. T., Hemamalini, M., Bocelli, G. & Cantoni, A. (2004). Acta Cryst. E60, o2038–o2040.
  • Sheldrick, G. M. (1996). SADABS University of Göttingen, Germany.
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]
  • Westrip, S. P. (2010). J. Appl. Cryst.43, 920–925.
  • Wijaya, K., Moers, O., Blaschette, A. & Jones, P. G. (2004). Z. Naturforsch. Teil B, 59, 17–26.

Articles from Acta Crystallographica Section E: Structure Reports Online are provided here courtesy of International Union of Crystallography