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Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 67| Part 4| April 2011| Pages o970-o971

2-Amino­pyrimidinium di­hydrogen phosphate monohydrate

aLaboratoire de Chimie des Matériaux, Faculté des Sciences de Bizerte, 7021 Zarzouna Bizerte, Tunisia, and bPetrochemical Research Chair, College of Science, King Saud University, Riadh, Saudi Arabia
*Correspondence e-mail: houda.marouani@fsb.rnu.tn

(Received 16 March 2011; accepted 22 March 2011; online 26 March 2011)

In the title compound, C4H6N3+·H2O4P·H2O, the pyrimidin­ium ring is essentially planar, with an r.m.s. deviation of 0.0016 Å. In the structure, pairs of symmetry-related anions are connected into centrosymmetric clusters via strong O—H⋯O hydrogen bonds forming six-membered rings with an R22(6) motif. These clusters are inter­connected via water mol­ecules through OW—H⋯O hydrogen bonds, building an infinite layer parallel to the ab plane. Moreover, infinite chains of 2-amino­pyrimidinium cations spread along the a-axis direction. These chains are connected to the inorganic layer through N—H⋯O, C—H⋯O and C—H⋯N hydrogen bonds, which, together with electrostatic and van der Waals inter­actions, contribute to the cohesion and stability of the network in the crystal structure.

Related literature

For the biological activity of amino­pyrimidinium derivatives, see: Grier et al. (1980[Grier, N., Harris, E. H., Joshua, H., Patchett, A. A., Witzel, B. E. & Dybas, R. A. (1980). J. Coat. Technol. A52, 57-63.]); Gueiffier et al. (1996[Gueiffier, A., Lhassani, M., Elhakmaoui, A., Snoeck, R., Andrei, G., Chavignon, O., Teulade, J.-C., Kerbal, A., Essassi, E. M., Debouzy, J.-C., Witvrouw, M., Blache, Y., De Balzarini, J., Clercq, E. & Chapat, J.-P. (1996). J. Med. Chem. 39, 2856-2859.]); Rival et al. (1991[Rival, Y., Grassy, G., Taudou, A. & Ecalle, R. (1991). Eur. J. Med. Chem. 26, 13-18.]); Li et al. (2009[Li, H.-Y., Brooks, H. B., Crich, J. Z., Henry, J. R., Sawyer, J. S. & Wang, Y. (2009). Eur. Patent (Eli Lilly & Company).]). For related structures, see: Cheng et al. (2010[Cheng, X.-L., Gao, S. & Ng, S. W. (2010). Acta Cryst. E66, o127.]); Narayana et al. (2008[Narayana, B., Sarojini, B. K., Prakash Kamath, K., Yathirajan, H. S. & Bolte, M. (2008). Acta Cryst. E64, o117-o118.]). For graph-set notation of hydrogen bonding, see: Bernstein et al. (1995[Bernstein, J., David, R. E., Shimoni, L. & Chang, N. L. (1995). Angew. Chem. Int. Ed. Engl. 34, 1555-1573.]).

[Scheme 1]

Experimental

Crystal data
  • C4H6N3+·H2PO4·H2O

  • Mr = 211.12

  • Triclinic, [P \overline 1]

  • a = 6.212 (3) Å

  • b = 8.600 (4) Å

  • c = 9.462 (2) Å

  • α = 109.56 (3)°

  • β = 106.38 (2)°

  • γ = 95.50 (2)°

  • V = 446.7 (3) Å3

  • Z = 2

  • Ag Kα radiation

  • λ = 0.56083 Å

  • μ = 0.17 mm−1

  • T = 293 K

  • 0.40 × 0.25 × 0.20 mm

Data collection
  • Enraf–Nonius CAD-4 diffractometer

  • 6572 measured reflections

  • 4373 independent reflections

  • 3189 reflections with I > 2σ(I)

  • Rint = 0.018

  • 2 standard reflections every 120 min intensity decay: 3%

Refinement
  • R[F2 > 2σ(F2)] = 0.042

  • wR(F2) = 0.124

  • S = 1.03

  • 4373 reflections

  • 158 parameters

  • 3 restraints

  • All H-atom parameters refined

  • Δρmax = 0.68 e Å−3

  • Δρmin = −0.42 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
O1—H1O⋯O4i 0.83 (3) 1.80 (3) 2.6372 (18) 179 (2)
O2—H2O⋯OW 0.82 (3) 1.80 (3) 2.6132 (18) 175 (2)
OW—H1W⋯O3ii 0.84 (1) 1.96 (1) 2.7882 (17) 166 (2)
OW—H2W⋯O4iii 0.83 (1) 1.95 (1) 2.7843 (16) 177 (2)
N1—H1⋯O4iv 0.83 (2) 2.08 (2) 2.9070 (18) 177 (2)
N1—H2⋯O3v 0.89 (2) 2.00 (2) 2.873 (2) 166 (2)
N2—H3⋯O3iv 0.87 (2) 1.78 (2) 2.6535 (16) 175 (2)
C2—H4⋯N3iii 0.91 (2) 2.62 (2) 3.513 (2) 169 (2)
C3—H5⋯OW 0.95 (2) 2.56 (2) 3.477 (2) 164 (2)
Symmetry codes: (i) -x, -y+1, -z+2; (ii) -x+1, -y+2, -z+2; (iii) x+1, y, z; (iv) x, y-1, z-1; (v) x-1, y-1, z-1.

Data collection: CAD-4 EXPRESS (Enraf–Nonius, 1994)[Enraf-Nonius (1994). CAD-4 EXPRESS. Enraf-Nonius, Delft, The Netherlands.]; cell refinement: CAD-4 EXPRESS[Enraf-Nonius (1994). CAD-4 EXPRESS. Enraf-Nonius, Delft, The Netherlands.]; data reduction: XCAD4 (Harms & Wocadlo, 1995)[Harms, K. & Wocadlo, S. (1995). XCAD4. University of Marburg, Germany.]; program(s) used to solve structure: SHELXS86 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997[Farrugia, L. J. (1997). J. Appl. Cryst. 30, 565.]); software used to prepare material for publication: WinGX (Farrugia, 1999[Farrugia, L. J. (1999). J. Appl. Cryst. 32, 837-838.]).

Supporting information


Comment top

Aminopyrimidinium salts are highly active antimicrobial agents with a low acute mammalian toxicity (Grier et al., 1980). In addition, pyrimidine derivatives possess considerable biological activity and have been widely used in medicinal applications as antiviral agents (Gueiffier et al., 1996), antifungal agents (Rival et al., 1991). Moreover, imidazolidinonyl aminopyrimidine compounds have been investigated for the treatment of cancer (Li et al., 2009). In order to search for new materials for these applications, we have attempted to combine pyrimidine derivatives with phosphate species. In this paper we report the preparation and the crystal structure of the title compound, (I).

The asymmetric unit of (I) contains a H2PO4- anion, a 2-aminopyrimidinium cation and a water molecule (Fig. 1). The pyrimidinium ring is essentially planar with an rms deviation of 0.0016 Å. The interatomic bond lengths and angles in (I) do not show significant deviation from those reported in related 2-aminopyrimidinium salts (Narayana, et al., 2008; Cheng, et al., 2010).

In the structure, pairs of symmetry-related anions are connected into centrosymmetric clusters via strong O—H···O hydrogen bonds forming six-membred rings which may be described as R22(6) motif in the graph-set notation (Bernstein et al., 1995). These clusters are interconnected via water molecules through OW—H···O hydrogen bonds to build an infinite layer parallel to the ab plane. Moreover, infinite chains of 2-aminopyrimidinium cations spread along the a direction. These chains are connected to the inorganic layer through H-bonds: N—H···O, C—H···O and C—H···N (Tab. 1 & Fig. 2).

Related literature top

For the biological activity of aminopyrimidinium derivatives, see: Grier et al. (1980); Gueiffier et al. (1996); Rival et al. (1991); Li et al. (2009). For related structures, see: Cheng et al. (2010); Narayana et al. (2008). For graph-set notation of hydrogen bonding, see: Bernstein et al. (1995).

Experimental top

A small quantity of H3PO4 (3 mmol) was added dropwise to a solution of 2-aminopyrimidine (3 mmol in 20 ml water). A precipitate was formed which was dissolved in water (20 ml) and the solution was allowed to evaporate slowly at room temperature until the formation of colorless prismatic crystals with dimensions suitable for a crystallographic study.

Refinement top

All H atoms were located in difference Fourier maps and were allowed to refine with isotropic displacement parameters Uiso. The H-atoms of water molecule were refined with a distance restraint of O—H = 0.85 (1) Å.

Computing details top

Data collection: CAD-4 EXPRESS (Enraf–Nonius, 1994); cell refinement: CAD-4 EXPRESS (Enraf–Nonius, 1994); data reduction: XCAD4 (Harms & Wocadlo, 1995); program(s) used to solve structure: SHELXS86 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997); software used to prepare material for publication: WinGX (Farrugia, 1999).

Figures top
[Figure 1] Fig. 1. An ORTEP view of of the title compound with the atom-labelling scheme. Displacement ellipsoids are drawn at the 30% probability level. H atoms are represented by small spheres of arbitrary radii.
[Figure 2] Fig. 2. Projection of (I) along the b axis.
2-Aminopyrimidinium dihydrogen phosphate monohydrate top
Crystal data top
C4H6N3+·H2PO4·H2OZ = 2
Mr = 211.12F(000) = 220
Triclinic, P1Dx = 1.570 Mg m3
Hall symbol: -P 1Ag Kα radiation, λ = 0.56083 Å
a = 6.212 (3) ÅCell parameters from 25 reflections
b = 8.600 (4) Åθ = 9–11°
c = 9.462 (2) ŵ = 0.17 mm1
α = 109.56 (3)°T = 293 K
β = 106.38 (2)°Prism, colorless
γ = 95.50 (2)°0.40 × 0.25 × 0.20 mm
V = 446.7 (3) Å3
Data collection top
Enraf–Nonius CAD-4
diffractometer
Rint = 0.018
Radiation source: fine-focus sealed tubeθmax = 28.0°, θmin = 2.0°
Graphite monochromatorh = 1010
non–profiled ω scansk = 1414
6572 measured reflectionsl = 515
4373 independent reflections2 standard reflections every 120 min
3189 reflections with I > 2σ(I) intensity decay: 3%
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.042Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.124All H-atom parameters refined
S = 1.03 w = 1/[σ2(Fo2) + (0.0745P)2 + 0.0087P]
where P = (Fo2 + 2Fc2)/3
4373 reflections(Δ/σ)max = 0.002
158 parametersΔρmax = 0.68 e Å3
3 restraintsΔρmin = 0.42 e Å3
Crystal data top
C4H6N3+·H2PO4·H2Oγ = 95.50 (2)°
Mr = 211.12V = 446.7 (3) Å3
Triclinic, P1Z = 2
a = 6.212 (3) ÅAg Kα radiation, λ = 0.56083 Å
b = 8.600 (4) ŵ = 0.17 mm1
c = 9.462 (2) ÅT = 293 K
α = 109.56 (3)°0.40 × 0.25 × 0.20 mm
β = 106.38 (2)°
Data collection top
Enraf–Nonius CAD-4
diffractometer
Rint = 0.018
6572 measured reflections2 standard reflections every 120 min
4373 independent reflections intensity decay: 3%
3189 reflections with I > 2σ(I)
Refinement top
R[F2 > 2σ(F2)] = 0.0423 restraints
wR(F2) = 0.124All H-atom parameters refined
S = 1.03Δρmax = 0.68 e Å3
4373 reflectionsΔρmin = 0.42 e Å3
158 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
xyzUiso*/Ueq
P10.16874 (4)0.74641 (3)1.06016 (4)0.02665 (8)
O30.30367 (14)0.91480 (10)1.18597 (11)0.03404 (18)
O40.07714 (13)0.70387 (10)1.05045 (11)0.03351 (18)
O10.30374 (15)0.61277 (12)1.09639 (14)0.0442 (3)
O20.16298 (17)0.73861 (14)0.89151 (12)0.0433 (2)
OW0.56449 (16)0.79100 (13)0.85902 (13)0.0406 (2)
N20.15897 (16)0.12980 (13)0.39597 (13)0.03242 (19)
N30.14127 (17)0.21993 (14)0.48619 (13)0.0348 (2)
N10.20502 (17)0.03637 (13)0.28151 (13)0.0352 (2)
C10.06315 (18)0.10520 (14)0.38722 (13)0.02783 (19)
C20.3116 (2)0.27019 (17)0.50499 (18)0.0419 (3)
C40.0099 (2)0.35703 (17)0.59250 (17)0.0401 (3)
C30.2421 (3)0.38927 (18)0.60766 (19)0.0467 (3)
H1W0.608 (3)0.8881 (14)0.862 (2)0.052 (5)*
H10.164 (3)0.111 (2)0.218 (2)0.049 (5)*
H1O0.232 (4)0.513 (3)1.051 (3)0.075 (7)*
H30.201 (3)0.054 (2)0.327 (2)0.049 (5)*
H60.051 (3)0.439 (2)0.662 (2)0.044 (4)*
H50.347 (4)0.487 (3)0.689 (3)0.064 (6)*
H20.355 (4)0.047 (2)0.269 (2)0.053 (5)*
H40.455 (4)0.272 (3)0.499 (2)0.060 (6)*
H2W0.668 (3)0.761 (2)0.916 (2)0.065 (6)*
H2O0.289 (4)0.761 (3)0.883 (3)0.078 (7)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
P10.01938 (11)0.02235 (12)0.03390 (15)0.00234 (8)0.00888 (9)0.00599 (9)
O30.0271 (3)0.0257 (3)0.0406 (5)0.0005 (3)0.0135 (3)0.0018 (3)
O40.0216 (3)0.0284 (3)0.0472 (5)0.0027 (3)0.0124 (3)0.0102 (3)
O10.0261 (4)0.0291 (4)0.0649 (7)0.0059 (3)0.0023 (4)0.0132 (4)
O20.0328 (4)0.0556 (6)0.0366 (5)0.0013 (4)0.0123 (4)0.0130 (4)
OW0.0297 (4)0.0428 (5)0.0520 (6)0.0031 (3)0.0113 (4)0.0244 (4)
N20.0256 (4)0.0323 (4)0.0358 (5)0.0064 (3)0.0124 (4)0.0068 (4)
N30.0295 (4)0.0376 (5)0.0353 (5)0.0116 (4)0.0132 (4)0.0080 (4)
N10.0256 (4)0.0340 (5)0.0374 (5)0.0050 (3)0.0100 (4)0.0038 (4)
C10.0244 (4)0.0311 (4)0.0284 (5)0.0080 (3)0.0093 (3)0.0108 (4)
C20.0274 (5)0.0376 (6)0.0513 (8)0.0022 (4)0.0116 (5)0.0079 (5)
C40.0398 (6)0.0363 (5)0.0388 (6)0.0132 (5)0.0132 (5)0.0061 (5)
C30.0373 (6)0.0356 (6)0.0484 (8)0.0031 (5)0.0081 (5)0.0006 (5)
Geometric parameters (Å, º) top
P1—O41.5055 (11)N3—C41.3207 (18)
P1—O31.5056 (12)N3—C11.3473 (15)
P1—O11.5583 (11)N1—C11.3194 (16)
P1—O21.5645 (11)N1—H10.83 (2)
O1—H1O0.83 (3)N1—H20.89 (2)
O2—H2O0.82 (3)C2—C31.354 (2)
OW—H1W0.843 (9)C2—H40.91 (2)
OW—H2W0.834 (9)C4—C31.399 (2)
N2—C21.3473 (17)C4—H60.98 (2)
N2—C11.3503 (15)C3—H50.95 (2)
N2—H30.87 (2)
O4—P1—O3114.86 (5)C1—N1—H2118.5 (12)
O4—P1—O1111.37 (6)H1—N1—H2118.3 (17)
O3—P1—O1106.04 (6)N1—C1—N3119.50 (10)
O4—P1—O2106.56 (6)N1—C1—N2118.97 (10)
O3—P1—O2110.54 (6)N3—C1—N2121.51 (10)
O1—P1—O2107.27 (7)N2—C2—C3119.76 (12)
P1—O1—H1O115.6 (18)N2—C2—H4112.8 (13)
P1—O2—H2O115.0 (18)C3—C2—H4127.4 (13)
H1W—OW—H2W112.2 (18)N3—C4—C3124.26 (12)
C2—N2—C1121.10 (11)N3—C4—H6115.4 (10)
C2—N2—H3120.4 (13)C3—C4—H6120.3 (10)
C1—N2—H3118.5 (13)C2—C3—C4116.54 (13)
C4—N3—C1116.83 (11)C2—C3—H5121.6 (14)
C1—N1—H1122.7 (13)C4—C3—H5121.8 (13)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1—H1O···O4i0.83 (3)1.80 (3)2.6372 (18)179 (2)
O2—H2O···OW0.82 (3)1.80 (3)2.6132 (18)175 (2)
OW—H1W···O3ii0.84 (1)1.96 (1)2.7882 (17)166 (2)
OW—H2W···O4iii0.83 (1)1.95 (1)2.7843 (16)177 (2)
N1—H1···O4iv0.83 (2)2.08 (2)2.9070 (18)177 (2)
N1—H2···O3v0.89 (2)2.00 (2)2.873 (2)166 (2)
N2—H3···O3iv0.87 (2)1.78 (2)2.6535 (16)175 (2)
C2—H4···N3iii0.91 (2)2.62 (2)3.513 (2)169 (2)
C3—H5···OW0.95 (2)2.56 (2)3.477 (2)164 (2)
Symmetry codes: (i) x, y+1, z+2; (ii) x+1, y+2, z+2; (iii) x+1, y, z; (iv) x, y1, z1; (v) x1, y1, z1.

Experimental details

Crystal data
Chemical formulaC4H6N3+·H2PO4·H2O
Mr211.12
Crystal system, space groupTriclinic, P1
Temperature (K)293
a, b, c (Å)6.212 (3), 8.600 (4), 9.462 (2)
α, β, γ (°)109.56 (3), 106.38 (2), 95.50 (2)
V3)446.7 (3)
Z2
Radiation typeAg Kα, λ = 0.56083 Å
µ (mm1)0.17
Crystal size (mm)0.40 × 0.25 × 0.20
Data collection
DiffractometerEnraf–Nonius CAD-4
diffractometer
Absorption correction
No. of measured, independent and
observed [I > 2σ(I)] reflections
6572, 4373, 3189
Rint0.018
(sin θ/λ)max1)0.836
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.042, 0.124, 1.03
No. of reflections4373
No. of parameters158
No. of restraints3
H-atom treatmentAll H-atom parameters refined
Δρmax, Δρmin (e Å3)0.68, 0.42

Computer programs: CAD-4 EXPRESS (Enraf–Nonius, 1994), XCAD4 (Harms & Wocadlo, 1995), SHELXS86 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), ORTEP-3 for Windows (Farrugia, 1997), WinGX (Farrugia, 1999).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1—H1O···O4i0.83 (3)1.80 (3)2.6372 (18)179 (2)
O2—H2O···OW0.82 (3)1.80 (3)2.6132 (18)175 (2)
OW—H1W···O3ii0.843 (9)1.962 (10)2.7882 (17)166 (2)
OW—H2W···O4iii0.834 (9)1.952 (10)2.7843 (16)177 (2)
N1—H1···O4iv0.83 (2)2.08 (2)2.9070 (18)177 (2)
N1—H2···O3v0.89 (2)2.00 (2)2.873 (2)166 (2)
N2—H3···O3iv0.87 (2)1.78 (2)2.6535 (16)175 (2)
C2—H4···N3iii0.91 (2)2.62 (2)3.513 (2)169 (2)
C3—H5···OW0.95 (2)2.56 (2)3.477 (2)164 (2)
Symmetry codes: (i) x, y+1, z+2; (ii) x+1, y+2, z+2; (iii) x+1, y, z; (iv) x, y1, z1; (v) x1, y1, z1.
 

Acknowledgements

We would like to acknowledge the support provided by the Secretary of State for Scientific Research and Technology of Tunisia.

References

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First citationCheng, X.-L., Gao, S. & Ng, S. W. (2010). Acta Cryst. E66, o127.  Web of Science CSD CrossRef IUCr Journals Google Scholar
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ISSN: 2056-9890
Volume 67| Part 4| April 2011| Pages o970-o971
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