2-Amino­pyrimidinium dihydrogen phosphate monohydrate

Marouani, H.; Al-Deyab, S.S.; Rzaigui, M.

doi:10.1107/S1600536811010658

organic compounds

CRYSTALLOGRAPHIC
COMMUNICATIONS

ISSN: 2056-9890

Volume 67| Part 4| April 2011| Pages o970-o971

doi:10.1107/S1600536811010658

Open

access

2-Aminopyrimidinium dihydrogen phosphate monohydrate

Houda Marouani,^a ^* Salem S. Al-Deyab ^b and Mohamed Rzaigui ^a

^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 ); 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

Crystal data

C₄H₆N₃⁺·H₂PO₄⁻·H₂O
M_r = 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)
R_int = 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
Δρ_max = 0.68 e Å⁻³
Δρ_min = −0.42 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	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⋯O4^iv	0.83 (2)	2.08 (2)	2.9070 (18)	177 (2)
N1—H2⋯O3^v	0.89 (2)	2.00 (2)	2.873 (2)	166 (2)
N2—H3⋯O3^iv	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); cell refinement: CAD-4 EXPRESS; 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 ).

Supporting information

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536811010658/pv2399sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536811010658/pv2399Isup2.hkl

checkCIF report

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.

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

	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.
	Fig. 2. Projection of (I) along the b axis.

2-Aminopyrimidinium dihydrogen phosphate monohydrate top

Crystal data top

C₄H₆N₃⁺·H₂PO₄⁻·H₂O	Z = 2
M_r = 211.12	F(000) = 220
Triclinic, P1	D_x = 1.570 Mg m⁻³
Hall symbol: -P 1	Ag Kα radiation, λ = 0.56083 Å
a = 6.212 (3) Å	Cell parameters from 25 reflections
b = 8.600 (4) Å	θ = 9–11°
c = 9.462 (2) Å	µ = 0.17 mm⁻¹
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	R_int = 0.018
Radiation source: fine-focus sealed tube	θ_max = 28.0°, θ_min = 2.0°
Graphite monochromator	h = −10→10
non–profiled ω scans	k = −14→14
6572 measured reflections	l = −5→15
4373 independent reflections	2 standard reflections every 120 min
3189 reflections with I > 2σ(I)	intensity decay: 3%

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)] = 0.042	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.124	All H-atom parameters refined
S = 1.03	w = 1/[σ²(F_o²) + (0.0745P)² + 0.0087P] where P = (F_o² + 2F_c²)/3
4373 reflections	(Δ/σ)_max = 0.002
158 parameters	Δρ_max = 0.68 e Å⁻³
3 restraints	Δρ_min = −0.42 e Å⁻³

Crystal data top

C₄H₆N₃⁺·H₂PO₄⁻·H₂O	γ = 95.50 (2)°
M_r = 211.12	V = 446.7 (3) Å³
Triclinic, P1	Z = 2
a = 6.212 (3) Å	Ag Kα radiation, λ = 0.56083 Å
b = 8.600 (4) Å	µ = 0.17 mm⁻¹
c = 9.462 (2) Å	T = 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	R_int = 0.018
6572 measured reflections	2 standard reflections every 120 min
4373 independent reflections	intensity decay: 3%
3189 reflections with I > 2σ(I)

Refinement top

R[F² > 2σ(F²)] = 0.042	3 restraints
wR(F²) = 0.124	All H-atom parameters refined
S = 1.03	Δρ_max = 0.68 e Å⁻³
4373 reflections	Δρ_min = −0.42 e Å⁻³
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

	x	y	z	U_iso*/U_eq
P1	0.16874 (4)	0.74641 (3)	1.06016 (4)	0.02665 (8)
O3	0.30367 (14)	0.91480 (10)	1.18597 (11)	0.03404 (18)
O4	−0.07714 (13)	0.70387 (10)	1.05045 (11)	0.03351 (18)
O1	0.30374 (15)	0.61277 (12)	1.09639 (14)	0.0442 (3)
O2	0.16298 (17)	0.73861 (14)	0.89151 (12)	0.0433 (2)
OW	0.56449 (16)	0.79100 (13)	0.85902 (13)	0.0406 (2)
N2	0.15897 (16)	0.12980 (13)	0.39597 (13)	0.03242 (19)
N3	−0.14127 (17)	0.21993 (14)	0.48619 (13)	0.0348 (2)
N1	−0.20502 (17)	−0.03637 (13)	0.28151 (13)	0.0352 (2)
C1	−0.06315 (18)	0.10520 (14)	0.38722 (13)	0.02783 (19)
C2	0.3116 (2)	0.27019 (17)	0.50499 (18)	0.0419 (3)
C4	0.0099 (2)	0.35703 (17)	0.59250 (17)	0.0401 (3)
C3	0.2421 (3)	0.38927 (18)	0.60766 (19)	0.0467 (3)
H1W	0.608 (3)	0.8881 (14)	0.862 (2)	0.052 (5)*
H1	−0.164 (3)	−0.111 (2)	0.218 (2)	0.049 (5)*
H1O	0.232 (4)	0.513 (3)	1.051 (3)	0.075 (7)*
H3	0.201 (3)	0.054 (2)	0.327 (2)	0.049 (5)*
H6	−0.051 (3)	0.439 (2)	0.662 (2)	0.044 (4)*
H5	0.347 (4)	0.487 (3)	0.689 (3)	0.064 (6)*
H2	−0.355 (4)	−0.047 (2)	0.269 (2)	0.053 (5)*
H4	0.455 (4)	0.272 (3)	0.499 (2)	0.060 (6)*
H2W	0.668 (3)	0.761 (2)	0.916 (2)	0.065 (6)*
H2O	0.289 (4)	0.761 (3)	0.883 (3)	0.078 (7)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
P1	0.01938 (11)	0.02235 (12)	0.03390 (15)	0.00234 (8)	0.00888 (9)	0.00599 (9)
O3	0.0271 (3)	0.0257 (3)	0.0406 (5)	−0.0005 (3)	0.0135 (3)	0.0018 (3)
O4	0.0216 (3)	0.0284 (3)	0.0472 (5)	0.0027 (3)	0.0124 (3)	0.0102 (3)
O1	0.0261 (4)	0.0291 (4)	0.0649 (7)	0.0059 (3)	0.0023 (4)	0.0132 (4)
O2	0.0328 (4)	0.0556 (6)	0.0366 (5)	0.0013 (4)	0.0123 (4)	0.0130 (4)
OW	0.0297 (4)	0.0428 (5)	0.0520 (6)	0.0031 (3)	0.0113 (4)	0.0244 (4)
N2	0.0256 (4)	0.0323 (4)	0.0358 (5)	0.0064 (3)	0.0124 (4)	0.0068 (4)
N3	0.0295 (4)	0.0376 (5)	0.0353 (5)	0.0116 (4)	0.0132 (4)	0.0080 (4)
N1	0.0256 (4)	0.0340 (5)	0.0374 (5)	0.0050 (3)	0.0100 (4)	0.0038 (4)
C1	0.0244 (4)	0.0311 (4)	0.0284 (5)	0.0080 (3)	0.0093 (3)	0.0108 (4)
C2	0.0274 (5)	0.0376 (6)	0.0513 (8)	0.0022 (4)	0.0116 (5)	0.0079 (5)
C4	0.0398 (6)	0.0363 (5)	0.0388 (6)	0.0132 (5)	0.0132 (5)	0.0061 (5)
C3	0.0373 (6)	0.0356 (6)	0.0484 (8)	0.0031 (5)	0.0081 (5)	−0.0006 (5)

Geometric parameters (Å, º) top

P1—O4	1.5055 (11)	N3—C4	1.3207 (18)
P1—O3	1.5056 (12)	N3—C1	1.3473 (15)
P1—O1	1.5583 (11)	N1—C1	1.3194 (16)
P1—O2	1.5645 (11)	N1—H1	0.83 (2)
O1—H1O	0.83 (3)	N1—H2	0.89 (2)
O2—H2O	0.82 (3)	C2—C3	1.354 (2)
OW—H1W	0.843 (9)	C2—H4	0.91 (2)
OW—H2W	0.834 (9)	C4—C3	1.399 (2)
N2—C2	1.3473 (17)	C4—H6	0.98 (2)
N2—C1	1.3503 (15)	C3—H5	0.95 (2)
N2—H3	0.87 (2)

O4—P1—O3	114.86 (5)	C1—N1—H2	118.5 (12)
O4—P1—O1	111.37 (6)	H1—N1—H2	118.3 (17)
O3—P1—O1	106.04 (6)	N1—C1—N3	119.50 (10)
O4—P1—O2	106.56 (6)	N1—C1—N2	118.97 (10)
O3—P1—O2	110.54 (6)	N3—C1—N2	121.51 (10)
O1—P1—O2	107.27 (7)	N2—C2—C3	119.76 (12)
P1—O1—H1O	115.6 (18)	N2—C2—H4	112.8 (13)
P1—O2—H2O	115.0 (18)	C3—C2—H4	127.4 (13)
H1W—OW—H2W	112.2 (18)	N3—C4—C3	124.26 (12)
C2—N2—C1	121.10 (11)	N3—C4—H6	115.4 (10)
C2—N2—H3	120.4 (13)	C3—C4—H6	120.3 (10)
C1—N2—H3	118.5 (13)	C2—C3—C4	116.54 (13)
C4—N3—C1	116.83 (11)	C2—C3—H5	121.6 (14)
C1—N1—H1	122.7 (13)	C4—C3—H5	121.8 (13)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	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···O4^iv	0.83 (2)	2.08 (2)	2.9070 (18)	177 (2)
N1—H2···O3^v	0.89 (2)	2.00 (2)	2.873 (2)	166 (2)
N2—H3···O3^iv	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.

Experimental details

Crystal data
Chemical formula	C₄H₆N₃⁺·H₂PO₄⁻·H₂O
M_r	211.12
Crystal system, space group	Triclinic, 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)
V (Å³)	446.7 (3)
Z	2
Radiation type	Ag Kα, λ = 0.56083 Å
µ (mm⁻¹)	0.17
Crystal size (mm)	0.40 × 0.25 × 0.20

Data collection
Diffractometer	Enraf–Nonius CAD-4 diffractometer
Absorption correction	–
No. of measured, independent and observed [I > 2σ(I)] reflections	6572, 4373, 3189
R_int	0.018
(sin θ/λ)_max (Å⁻¹)	0.836

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.042, 0.124, 1.03
No. of reflections	4373
No. of parameters	158
No. of restraints	3
H-atom treatment	All H-atom parameters refined
Δρ_max, Δρ_min (e Å⁻³)	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···A	D—H	H···A	D···A	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	0.843 (9)	1.962 (10)	2.7882 (17)	166 (2)
OW—H2W···O4ⁱⁱⁱ	0.834 (9)	1.952 (10)	2.7843 (16)	177 (2)
N1—H1···O4^iv	0.83 (2)	2.08 (2)	2.9070 (18)	177 (2)
N1—H2···O3^v	0.89 (2)	2.00 (2)	2.873 (2)	166 (2)
N2—H3···O3^iv	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.

Acknowledgements

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

References

Bernstein, J., David, R. E., Shimoni, L. & Chang, N. L. (1995). Angew. Chem. Int. Ed. Engl. 34, 1555–1573. CrossRef CAS Web of Science Google Scholar
Cheng, X.-L., Gao, S. & Ng, S. W. (2010). Acta Cryst. E66, o127. Web of Science CSD CrossRef IUCr Journals Google Scholar
Enraf–Nonius (1994). CAD-4 EXPRESS. Enraf–Nonius, Delft, The Netherlands. Google Scholar
Farrugia, L. J. (1997). J. Appl. Cryst. 30, 565. CrossRef IUCr Journals Google Scholar
Farrugia, L. J. (1999). J. Appl. Cryst. 32, 837–838. CrossRef CAS IUCr Journals Google Scholar
Grier, N., Harris, E. H., Joshua, H., Patchett, A. A., Witzel, B. E. & Dybas, R. A. (1980). J. Coat. Technol. A52, 57–63. Google Scholar
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. CrossRef CAS PubMed Web of Science Google Scholar
Harms, K. & Wocadlo, S. (1995). XCAD4. University of Marburg, Germany. Google Scholar
Li, H.-Y., Brooks, H. B., Crich, J. Z., Henry, J. R., Sawyer, J. S. & Wang, Y. (2009). Eur. Patent (Eli Lilly & Company). Google Scholar
Narayana, B., Sarojini, B. K., Prakash Kamath, K., Yathirajan, H. S. & Bolte, M. (2008). Acta Cryst. E64, o117–o118. Web of Science CSD CrossRef IUCr Journals Google Scholar
Rival, Y., Grassy, G., Taudou, A. & Ecalle, R. (1991). Eur. J. Med. Chem. 26, 13–18. CrossRef CAS Web of Science Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar