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Acta Crystallogr Sect E Struct Rep Online. 2009 November 1; 65(Pt 11): o2816.
Published online 2009 October 23. doi:  10.1107/S1600536809039907
PMCID: PMC2971231

2-Amino­pyrimidinium hydrogen oxalate monohydrate

Abstract

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 [triangle]). For the applications of amino­pyrimidines, see: Rospenk & Koll (2007 [triangle]). For amino­pyrimidine salts, see: Childs et al. (2007 [triangle]).

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Object name is e-65-o2816-scheme1.jpg

Experimental

Crystal data

  • C4H6N3 +·C2HO4 ·H2O
  • M r = 203.16
  • Triclinic, An external file that holds a picture, illustration, etc.
Object name is e-65-o2816-efi1.jpg
  • 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[F 2 > 2σ(F 2)] = 0.055
  • wR(F 2) = 0.148
  • S = 1.02
  • 1835 reflections
  • 151 parameters
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.44 e Å−3
  • Δρmin = −0.29 e Å−3

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

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

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

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809039907/xu2606Isup2.hkl

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

supplementary crystallographic information

Comment

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 pKa.

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.

Experimental

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.

Refinement

Nitrogen- and oxygen-bound H atoms were located in a difference Fourier map and refined isotropically. Carbon-bound H atoms were placed in calculated positions and were refined in riding model with Uiso(H) = 1.2Ueq(C).

Figures

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.

Crystal data

C4H6N3+·C2HO4·H2OZ = 2
Mr = 203.16F(000) = 212
Triclinic, P1Dx = 1.585 Mg m3
Hall symbol: -P 1Melting point: 300 K
a = 6.295 (2) ÅMo Kα radiation, λ = 0.71073 Å
b = 6.339 (2) ÅCell parameters from 851 reflections
c = 11.111 (4) Åθ = 3.3–27.7°
α = 75.045 (6)°µ = 0.14 mm1
β = 84.302 (6)°T = 120 K
γ = 86.026 (7)°Prism, colorless
V = 425.8 (2) Å30.35 × 0.15 × 0.07 mm

Data collection

Bruker SMART 1000 CCD area-detector diffractometer1177 reflections with I > 2σ(I)
Radiation source: normal-focus sealed tubeRint = 0.030
graphiteθmax = 27.0°, θmin = 1.9°
[var phi] and ω scansh = −8→8
3983 measured reflectionsk = −8→8
1835 independent reflectionsl = −14→14

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)] = 0.055Hydrogen site location: mixed
wR(F2) = 0.148H atoms treated by a mixture of independent and constrained refinement
S = 1.01w = 1/[σ2(Fo2) + (0.047P)2 + 0.72P] where P = (Fo2 + 2Fc2)/3
1835 reflections(Δ/σ)max < 0.001
151 parametersΔρmax = 0.44 e Å3
0 restraintsΔρmin = −0.29 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
N10.2235 (4)0.3419 (4)0.6301 (2)0.0225 (5)
H10.235 (5)0.290 (5)0.559 (3)0.037 (9)*
N20.2566 (4)0.6890 (4)0.5036 (2)0.0263 (6)
H2A0.270 (5)0.637 (5)0.429 (3)0.027 (8)*
H2B0.258 (5)0.836 (6)0.492 (3)0.040 (9)*
N30.2128 (4)0.6436 (4)0.7189 (2)0.0249 (5)
C20.2305 (4)0.5594 (4)0.6174 (2)0.0232 (6)
C40.1869 (4)0.5030 (5)0.8289 (3)0.0264 (6)
H4A0.17590.55880.90100.032*
C50.1746 (5)0.2770 (5)0.8472 (3)0.0270 (6)
H5A0.15300.18180.92840.032*
C60.1952 (4)0.2013 (5)0.7428 (3)0.0262 (6)
H6A0.18950.04920.74950.031*
O10.2756 (3)0.4892 (3)0.30262 (17)0.0276 (5)
O20.2664 (3)0.1595 (3)0.43700 (17)0.0268 (5)
O30.3456 (3)0.2958 (3)0.11122 (17)0.0316 (5)
O40.3088 (4)−0.0288 (3)0.24753 (19)0.0323 (5)
H4O0.314 (5)−0.099 (6)0.187 (3)0.039 (9)*
C70.2830 (4)0.2859 (4)0.3300 (2)0.0229 (6)
C80.3161 (4)0.1829 (4)0.2173 (2)0.0230 (6)
O1W0.3244 (4)0.7844 (3)0.0656 (2)0.0298 (5)
H1WA0.460 (8)0.772 (7)0.018 (4)0.078 (15)*
H1WB0.306 (7)0.661 (8)0.109 (4)0.070 (14)*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
N10.0308 (13)0.0209 (12)0.0172 (12)−0.0009 (9)−0.0015 (9)−0.0078 (10)
N20.0432 (15)0.0175 (12)0.0176 (12)−0.0027 (10)−0.0019 (10)−0.0035 (10)
N30.0325 (13)0.0240 (12)0.0193 (12)−0.0007 (10)−0.0031 (9)−0.0071 (10)
C20.0284 (15)0.0221 (14)0.0205 (13)−0.0005 (11)−0.0036 (11)−0.0078 (11)
C40.0299 (15)0.0321 (16)0.0192 (14)−0.0013 (12)−0.0026 (11)−0.0100 (12)
C50.0320 (16)0.0273 (15)0.0191 (14)−0.0006 (12)−0.0038 (11)−0.0008 (11)
C60.0316 (16)0.0211 (13)0.0244 (14)−0.0023 (11)−0.0026 (11)−0.0028 (11)
O10.0423 (12)0.0178 (10)0.0224 (10)−0.0008 (8)−0.0025 (8)−0.0050 (8)
O20.0458 (12)0.0174 (9)0.0166 (10)−0.0010 (8)−0.0031 (8)−0.0029 (8)
O30.0544 (14)0.0221 (10)0.0175 (10)−0.0041 (9)−0.0013 (9)−0.0038 (8)
O40.0605 (15)0.0183 (10)0.0196 (10)−0.0015 (9)−0.0015 (9)−0.0080 (8)
C70.0268 (15)0.0228 (14)0.0195 (13)0.0003 (11)−0.0016 (11)−0.0068 (11)
C80.0296 (15)0.0195 (13)0.0208 (14)−0.0010 (11)−0.0022 (11)−0.0065 (11)
O1W0.0455 (14)0.0198 (11)0.0240 (11)−0.0019 (9)−0.0029 (9)−0.0054 (9)

Geometric parameters (Å, °)

N1—C61.340 (3)C5—H5A0.9500
N1—C21.353 (3)C6—H6A0.9500
N1—H10.93 (4)O1—C71.244 (3)
N2—C21.320 (3)O2—C71.250 (3)
N2—H2A0.96 (3)O3—C81.215 (3)
N2—H2B0.91 (4)O4—C81.299 (3)
N3—C41.316 (4)O4—H4O0.90 (4)
N3—C21.359 (3)C7—C81.545 (4)
C4—C51.400 (4)O1W—H1WA0.97 (5)
C4—H4A0.9500O1W—H1WB0.82 (5)
C5—C61.358 (4)
C6—N1—C2121.5 (2)C6—C5—H5A121.8
C6—N1—H1119 (2)C4—C5—H5A121.8
C2—N1—H1119 (2)N1—C6—C5119.7 (3)
C2—N2—H2A123.4 (18)N1—C6—H6A120.1
C2—N2—H2B120 (2)C5—C6—H6A120.1
H2A—N2—H2B116 (3)C8—O4—H4O119 (2)
C4—N3—C2116.5 (2)O1—C7—O2127.2 (3)
N2—C2—N1118.4 (2)O1—C7—C8115.1 (2)
N2—C2—N3120.5 (2)O2—C7—C8117.7 (2)
N1—C2—N3121.2 (2)O3—C8—O4124.8 (3)
N3—C4—C5124.7 (3)O3—C8—C7121.1 (2)
N3—C4—H4A117.7O4—C8—C7114.1 (2)
C5—C4—H4A117.7H1WA—O1W—H1WB104 (4)
C6—C5—C4116.4 (3)
C6—N1—C2—N2−179.3 (3)C2—N1—C6—C5−0.5 (4)
C6—N1—C2—N31.2 (4)C4—C5—C6—N1−0.6 (4)
C4—N3—C2—N2179.9 (3)O1—C7—C8—O34.3 (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—C61.3 (4)O2—C7—C8—O44.4 (4)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N1—H1···O20.93 (3)1.75 (3)2.671 (3)173 (3)
N2—H2A···O10.96 (3)1.87 (3)2.827 (3)170 (3)
N2—H2B···O2i0.91 (4)1.99 (4)2.885 (3)171 (3)
O4—H4O···O1Wii0.89 (3)1.69 (4)2.584 (3)176 (4)
O1W—H1WA···O3iii0.97 (5)1.91 (5)2.827 (3)158 (4)
O1W—H1WB···O10.82 (5)2.14 (4)2.812 (3)139 (4)
O1W—H1WB···O30.82 (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.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: XU2606).

References

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

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