2-Amino­pyrimidinium hydrogen oxalate monohydrate

Eshtiagh-Hosseini, H.; Yousefi, Z.; Mirzaei, M.

doi:10.1107/S1600536809039907

organic compounds

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Volume 65| Part 11| November 2009| Page o2816

https://doi.org/10.1107/S1600536809039907

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2-Aminopyrimidinium hydrogen oxalate monohydrate

Hossein Eshtiagh-Hosseini,^a ^* Zakieh Yousefi ^a and Masoud Mirzaei ^a

^aDepartment of Chemistry, School of Sciences, Ferdowsi University of Mashhad, Mashhad 917791436, Iran
^*Correspondence e-mail: heshtiagh@ferdowsi.um.ac.ir

(Received 3 September 2009; accepted 30 September 2009; online 23 October 2009)

In the title hydrated salt, C₄H₆N₃⁺·C₂HO₄⁻·H₂O, intermolecular N—H⋯O and O—H⋯O hydrogen bonding helps to stabilize the crystal structure.

Related literature

For the biological properties of pyrimidines, see: Rabie et al. (2007 ). For the applications of aminopyrimidines, see: Rospenk & Koll (2007 ). For aminopyrimidine salts, see: Childs et al. (2007 ).

Experimental

Crystal data

C₄H₆N₃⁺·C₂HO₄⁻·H₂O
M_r = 203.16
Triclinic, $[P \overline 1]$
a = 6.295 (2) Å
b = 6.339 (2) Å
c = 11.111 (4) Å
α = 75.045 (6)°
β = 84.302 (6)°
γ = 86.026 (7)°
V = 425.8 (2) Å³
Z = 2
Mo Kα radiation
μ = 0.14 mm⁻¹
T = 120 K
0.35 × 0.15 × 0.07 mm

Data collection

Bruker SMART 1000 CCD area-detector diffractometer
Absorption correction: none
3983 measured reflections
1835 independent reflections
1177 reflections with I > 2σ(I)
R_int = 0.030

Refinement

R[F² > 2σ(F²)] = 0.055
wR(F²) = 0.148
S = 1.02
1835 reflections
151 parameters
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.44 e Å⁻³
Δρ_min = −0.29 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1⋯O2	0.93 (3)	1.75 (3)	2.671 (3)	173 (3)
N2—H2A⋯O1	0.96 (3)	1.87 (3)	2.827 (3)	170 (3)
N2—H2B⋯O2ⁱ	0.91 (4)	1.99 (4)	2.885 (3)	171 (3)
O4—H4O⋯O1Wⁱⁱ	0.89 (3)	1.69 (4)	2.584 (3)	176 (4)
O1W—H1WA⋯O3ⁱⁱⁱ	0.97 (5)	1.91 (5)	2.827 (3)	158 (4)
O1W—H1WB⋯O1	0.82 (5)	2.14 (4)	2.812 (3)	139 (4)
O1W—H1WB⋯O3	0.82 (5)	2.31 (5)	3.002 (3)	144 (4)
Symmetry codes: (i) x, y+1, z; (ii) x, y-1, z; (iii) -x+1, -y+1, -z.

Data collection: SMART (Bruker, 1998 ); cell refinement: SAINT-Plus (Bruker, 1998); data reduction: SAINT-Plus; program(s) used to solve structure: SHELXTL (Sheldrick, 2008 ); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL.

Supporting information

Crystal structure: contains datablocks I, global. DOI: https://doi.org/10.1107/S1600536809039907/xu2606sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536809039907/xu2606Isup2.hkl

checkCIF report

Comment top

Pyrimidines have been attracted special attention because of unique biological properties, such as fungicides, vermicides, inseticides and medicines (Rabie et al., 2007). Among them, aminopyrimidines are as interesting matters for chemists and pharmacist. They are a part of nucleic bases, cystosine, adenine and guanine which are responsible for molecular recognition and replication of DNA, through the formation and breakage of N—H···N hydrogen bonds (Rospenk & Koll, 2007). 2-Aminopyrimidine (2-apym), with amino group as two H-bond donor atoms and two N atoms as two H-bond acceptors atoms is particularly attractive as a very simple self-complementary prototype for chain formation with other organic molecules. Until now, a lot of co-crystals and proton transfer compounds were synthesized using 2-apym and a variety of carboxylic acid derivatives (Childs et al., 2007). In this report, we choose oxalic acid (OxH₂) in according to their difference in pK_a.

In the title compound, the oxalic acid is mono-deprotonated while 2-apym is protonated (Fig. 1). The cation is hydrogen bonded to the anion with a cyclic R₂²(8) pattern (Table 1). The anionic and cationic moieties link with the water molecule into layers by hydrogen bondings, resulting in beautiful picture as Flag-like strucrure. The O1W–H1WA···O3ⁱⁱⁱ hydrogen bond [symmetry code: (iii) 1 - x, 1 - y, -z] between water and carboxyl group produces the three dimensional supra-molecular structure.

Related literature top

For the biological properties of pyrimidines, see: Rabie et al. (2007). For the applications of aminopyrimidines, see: Rospenk & Koll (2007). For aminopyrimidine salts, see: Childs et al. (2007).

Experimental top

The title compound was synthesized via the reaction of OxH₂ (0.047 g, 0.375 mmol) with 2-apym (0.050 g, 0.5 mmol) in a water solution (5 ml). The solution was stirred for 3 h in 323 K. Colorless crystals were obtained after a week.

Structure description top

For the biological properties of pyrimidines, see: Rabie et al. (2007). For the applications of aminopyrimidines, see: Rospenk & Koll (2007). For aminopyrimidine salts, see: Childs et al. (2007).

Computing details top

Data collection: SMART (Bruker, 1998); cell refinement: SAINT-Plus (Bruker, 1998); data reduction: SAINT-Plus (Bruker, 1998); program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXTL (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

Figures top

Fig. 1. The molecular structure of the title compound, showing the atom-numbering scheme. Displacement ellipsoids are drawn at the 50% probability level. Dashed lines indicate hydrogen bonding.

2-Aminopyrimidinium hydrogen oxalate monohydrate top

Crystal data top

C₄H₆N₃⁺·C₂HO₄⁻·H₂O	Z = 2
M_r = 203.16	F(000) = 212
Triclinic, P1	D_x = 1.585 Mg m⁻³
Hall symbol: -P 1	Melting point: 300 K
a = 6.295 (2) Å	Mo Kα radiation, λ = 0.71073 Å
b = 6.339 (2) Å	Cell parameters from 851 reflections
c = 11.111 (4) Å	θ = 3.3–27.7°
α = 75.045 (6)°	µ = 0.14 mm⁻¹
β = 84.302 (6)°	T = 120 K
γ = 86.026 (7)°	Prism, colorless
V = 425.8 (2) Å³	0.35 × 0.15 × 0.07 mm

Data collection top

Bruker SMART 1000 CCD area-detector diffractometer	1177 reflections with I > 2σ(I)
Radiation source: normal-focus sealed tube	R_int = 0.030
Graphite monochromator	θ_max = 27.0°, θ_min = 1.9°
φ and ω scans	h = −8→8
3983 measured reflections	k = −8→8
1835 independent reflections	l = −14→14

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)] = 0.055	Hydrogen site location: mixed
wR(F²) = 0.148	H atoms treated by a mixture of independent and constrained refinement
S = 1.02	w = 1/[σ²(F_o²) + (0.047P)² + 0.72P] where P = (F_o² + 2F_c²)/3
1835 reflections	(Δ/σ)_max < 0.001
151 parameters	Δρ_max = 0.44 e Å⁻³
0 restraints	Δρ_min = −0.29 e Å⁻³

Crystal data top

C₄H₆N₃⁺·C₂HO₄⁻·H₂O	γ = 86.026 (7)°
M_r = 203.16	V = 425.8 (2) Å³
Triclinic, P1	Z = 2
a = 6.295 (2) Å	Mo Kα radiation
b = 6.339 (2) Å	µ = 0.14 mm⁻¹
c = 11.111 (4) Å	T = 120 K
α = 75.045 (6)°	0.35 × 0.15 × 0.07 mm
β = 84.302 (6)°

Data collection top

Bruker SMART 1000 CCD area-detector diffractometer	1177 reflections with I > 2σ(I)
3983 measured reflections	R_int = 0.030
1835 independent reflections

Refinement top

R[F² > 2σ(F²)] = 0.055	0 restraints
wR(F²) = 0.148	H atoms treated by a mixture of independent and constrained refinement
S = 1.02	Δρ_max = 0.44 e Å⁻³
1835 reflections	Δρ_min = −0.29 e Å⁻³
151 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
N1	0.2235 (4)	0.3419 (4)	0.6301 (2)	0.0225 (5)
H1	0.235 (5)	0.290 (5)	0.559 (3)	0.037 (9)*
N2	0.2566 (4)	0.6890 (4)	0.5036 (2)	0.0263 (6)
H2A	0.270 (5)	0.637 (5)	0.429 (3)	0.027 (8)*
H2B	0.258 (5)	0.836 (6)	0.492 (3)	0.040 (9)*
N3	0.2128 (4)	0.6436 (4)	0.7189 (2)	0.0249 (5)
C2	0.2305 (4)	0.5594 (4)	0.6174 (2)	0.0232 (6)
C4	0.1869 (4)	0.5030 (5)	0.8289 (3)	0.0264 (6)
H4A	0.1759	0.5588	0.9010	0.032*
C5	0.1746 (5)	0.2770 (5)	0.8472 (3)	0.0270 (6)
H5A	0.1530	0.1818	0.9284	0.032*
C6	0.1952 (4)	0.2013 (5)	0.7428 (3)	0.0262 (6)
H6A	0.1895	0.0492	0.7495	0.031*
O1	0.2756 (3)	0.4892 (3)	0.30262 (17)	0.0276 (5)
O2	0.2664 (3)	0.1595 (3)	0.43700 (17)	0.0268 (5)
O3	0.3456 (3)	0.2958 (3)	0.11122 (17)	0.0316 (5)
O4	0.3088 (4)	−0.0288 (3)	0.24753 (19)	0.0323 (5)
H4O	0.314 (5)	−0.099 (6)	0.187 (3)	0.039 (9)*
C7	0.2830 (4)	0.2859 (4)	0.3300 (2)	0.0229 (6)
C8	0.3161 (4)	0.1829 (4)	0.2173 (2)	0.0230 (6)
O1W	0.3244 (4)	0.7844 (3)	0.0656 (2)	0.0298 (5)
H1WA	0.460 (8)	0.772 (7)	0.018 (4)	0.078 (15)*
H1WB	0.306 (7)	0.661 (8)	0.109 (4)	0.070 (14)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
N1	0.0308 (13)	0.0209 (12)	0.0172 (12)	−0.0009 (9)	−0.0015 (9)	−0.0078 (10)
N2	0.0432 (15)	0.0175 (12)	0.0176 (12)	−0.0027 (10)	−0.0019 (10)	−0.0035 (10)
N3	0.0325 (13)	0.0240 (12)	0.0193 (12)	−0.0007 (10)	−0.0031 (9)	−0.0071 (10)
C2	0.0284 (15)	0.0221 (14)	0.0205 (13)	−0.0005 (11)	−0.0036 (11)	−0.0078 (11)
C4	0.0299 (15)	0.0321 (16)	0.0192 (14)	−0.0013 (12)	−0.0026 (11)	−0.0100 (12)
C5	0.0320 (16)	0.0273 (15)	0.0191 (14)	−0.0006 (12)	−0.0038 (11)	−0.0008 (11)
C6	0.0316 (16)	0.0211 (13)	0.0244 (14)	−0.0023 (11)	−0.0026 (11)	−0.0028 (11)
O1	0.0423 (12)	0.0178 (10)	0.0224 (10)	−0.0008 (8)	−0.0025 (8)	−0.0050 (8)
O2	0.0458 (12)	0.0174 (9)	0.0166 (10)	−0.0010 (8)	−0.0031 (8)	−0.0029 (8)
O3	0.0544 (14)	0.0221 (10)	0.0175 (10)	−0.0041 (9)	−0.0013 (9)	−0.0038 (8)
O4	0.0605 (15)	0.0183 (10)	0.0196 (10)	−0.0015 (9)	−0.0015 (9)	−0.0080 (8)
C7	0.0268 (15)	0.0228 (14)	0.0195 (13)	0.0003 (11)	−0.0016 (11)	−0.0068 (11)
C8	0.0296 (15)	0.0195 (13)	0.0208 (14)	−0.0010 (11)	−0.0022 (11)	−0.0065 (11)
O1W	0.0455 (14)	0.0198 (11)	0.0240 (11)	−0.0019 (9)	−0.0029 (9)	−0.0054 (9)

Geometric parameters (Å, º) top

N1—C6	1.340 (3)	C5—H5A	0.9500
N1—C2	1.353 (3)	C6—H6A	0.9500
N1—H1	0.93 (4)	O1—C7	1.244 (3)
N2—C2	1.320 (3)	O2—C7	1.250 (3)
N2—H2A	0.96 (3)	O3—C8	1.215 (3)
N2—H2B	0.91 (4)	O4—C8	1.299 (3)
N3—C4	1.316 (4)	O4—H4O	0.90 (4)
N3—C2	1.359 (3)	C7—C8	1.545 (4)
C4—C5	1.400 (4)	O1W—H1WA	0.97 (5)
C4—H4A	0.9500	O1W—H1WB	0.82 (5)
C5—C6	1.358 (4)

C6—N1—C2	121.5 (2)	C6—C5—H5A	121.8
C6—N1—H1	119 (2)	C4—C5—H5A	121.8
C2—N1—H1	119 (2)	N1—C6—C5	119.7 (3)
C2—N2—H2A	123.4 (18)	N1—C6—H6A	120.1
C2—N2—H2B	120 (2)	C5—C6—H6A	120.1
H2A—N2—H2B	116 (3)	C8—O4—H4O	119 (2)
C4—N3—C2	116.5 (2)	O1—C7—O2	127.2 (3)
N2—C2—N1	118.4 (2)	O1—C7—C8	115.1 (2)
N2—C2—N3	120.5 (2)	O2—C7—C8	117.7 (2)
N1—C2—N3	121.2 (2)	O3—C8—O4	124.8 (3)
N3—C4—C5	124.7 (3)	O3—C8—C7	121.1 (2)
N3—C4—H4A	117.7	O4—C8—C7	114.1 (2)
C5—C4—H4A	117.7	H1WA—O1W—H1WB	104 (4)
C6—C5—C4	116.4 (3)

C6—N1—C2—N2	−179.3 (3)	C2—N1—C6—C5	−0.5 (4)
C6—N1—C2—N3	1.2 (4)	C4—C5—C6—N1	−0.6 (4)
C4—N3—C2—N2	179.9 (3)	O1—C7—C8—O3	4.3 (4)
C4—N3—C2—N1	−0.6 (4)	O2—C7—C8—O3	−175.8 (3)
C2—N3—C4—C5	−0.7 (4)	O1—C7—C8—O4	−175.5 (2)
N3—C4—C5—C6	1.3 (4)	O2—C7—C8—O4	4.4 (4)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···O2	0.93 (3)	1.75 (3)	2.671 (3)	173 (3)
N2—H2A···O1	0.96 (3)	1.87 (3)	2.827 (3)	170 (3)
N2—H2B···O2ⁱ	0.91 (4)	1.99 (4)	2.885 (3)	171 (3)
O4—H4O···O1Wⁱⁱ	0.89 (3)	1.69 (4)	2.584 (3)	176 (4)
O1W—H1WA···O3ⁱⁱⁱ	0.97 (5)	1.91 (5)	2.827 (3)	158 (4)
O1W—H1WB···O1	0.82 (5)	2.14 (4)	2.812 (3)	139 (4)
O1W—H1WB···O3	0.82 (5)	2.31 (5)	3.002 (3)	144 (4)

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

Experimental details

Crystal data
Chemical formula	C₄H₆N₃⁺·C₂HO₄⁻·H₂O
M_r	203.16
Crystal system, space group	Triclinic, P1
Temperature (K)	120
a, b, c (Å)	6.295 (2), 6.339 (2), 11.111 (4)
α, β, γ (°)	75.045 (6), 84.302 (6), 86.026 (7)
V (Å³)	425.8 (2)
Z	2
Radiation type	Mo Kα
µ (mm⁻¹)	0.14
Crystal size (mm)	0.35 × 0.15 × 0.07

Data collection
Diffractometer	Bruker SMART 1000 CCD area-detector
Absorption correction	–
No. of measured, independent and observed [I > 2σ(I)] reflections	3983, 1835, 1177
R_int	0.030
(sin θ/λ)_max (Å⁻¹)	0.639

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.055, 0.148, 1.02
No. of reflections	1835
No. of parameters	151
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.44, −0.29

Computer programs: SMART (Bruker, 1998), SAINT-Plus (Bruker, 1998), SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···O2	0.93 (3)	1.75 (3)	2.671 (3)	173 (3)
N2—H2A···O1	0.96 (3)	1.87 (3)	2.827 (3)	170 (3)
N2—H2B···O2ⁱ	0.91 (4)	1.99 (4)	2.885 (3)	171 (3)
O4—H4O···O1Wⁱⁱ	0.89 (3)	1.69 (4)	2.584 (3)	176 (4)
O1W—H1WA···O3ⁱⁱⁱ	0.97 (5)	1.91 (5)	2.827 (3)	158 (4)
O1W—H1WB···O1	0.82 (5)	2.14 (4)	2.812 (3)	139 (4)
O1W—H1WB···O3	0.82 (5)	2.31 (5)	3.002 (3)	144 (4)

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

References

Bruker (1998). SMART and SAINT-Plus. Bruker AXS Inc., Madison, Wisconsin, USA. Google Scholar
Childs, S. L., Stahly, G. P. & Park, A. (2007). Mol. Pharm. 4, 323–338. Web of Science CSD CrossRef PubMed CAS Google Scholar
Rabie, U. M., Abou-El-Wafa, M. H. & Mohamed, R. A. (2007). J. Mol. Struct. 871, 6–13. Web of Science CrossRef CAS Google Scholar
Rospenk, M. & Koll, A. (2007). J. Mol. Struct. 844–845, 232–241. Web of Science CrossRef CAS Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar

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CRYSTALLOGRAPHIC
COMMUNICATIONS

ISSN: 2056-9890

Volume 65| Part 11| November 2009| Page o2816

https://doi.org/10.1107/S1600536809039907

Open

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