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Acta Crystallogr Sect E Struct Rep Online. 2009 November 1; 65(Pt 11): o2639.
Published online 2009 October 3. doi:  10.1107/S160053680903880X
PMCID: PMC2971252

2-Amino-4,6-dimethyl­pyrimidinium dihydrogenphosphate

Abstract

In the crystal structure of the title compound, C6H10N3 +·H2PO4 , the cations and anions are linked by inter­molecular O—H(...)O and N—H(...)O hydrogen bonds, forming a two-dimensional network. Additional stabilization is provided by weak inter­molecular C—H(...)O inter­actions. N—H(...)N inter­actions are also present.

Related literature

Five and six-membered heterocyclic compounds often exist in biologically active natural products and synthetic compounds of medicinal inter­est, see: Gilchrist (1998 [triangle]). For methyl­pyrimidines as precursors to potentially bioactive pyrimidine derivatives, see: Xue et al. (1993 [triangle]). For Ru complexes of pyrim­idine with an –NH2 substituent, see: Zhu et al. (2008 [triangle]). For bond-length data, see: Allen et al. (1987 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-65-o2639-scheme1.jpg

Experimental

Crystal data

  • C6H10N3 +·H2PO4
  • M r = 221.16
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-65-o2639-efi1.jpg
  • a = 11.743 (2) Å
  • b = 4.8266 (10) Å
  • c = 16.940 (3) Å
  • β = 95.55 (3)°
  • V = 955.6 (3) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.28 mm−1
  • T = 293 K
  • 0.20 × 0.15 × 0.11 mm

Data collection

  • Bruker SMART CCD diffractometer
  • Absorption correction: none
  • 8743 measured reflections
  • 2193 independent reflections
  • 1973 reflections with I > 2σ(I)
  • R int = 0.021

Refinement

  • R[F 2 > 2σ(F 2)] = 0.035
  • wR(F 2) = 0.108
  • S = 1.08
  • 2193 reflections
  • 133 parameters
  • H-atom parameters constrained
  • Δρmax = 0.40 e Å−3
  • Δρmin = −0.41 e Å−3

Data collection: SMART (Bruker, 1997 [triangle]); cell refinement: SAINT (Bruker, 1997 [triangle]); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: PLATON (Spek, 2009 [triangle]); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S160053680903880X/lh2909sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S160053680903880X/lh2909Isup2.hkl

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

supplementary crystallographic information

Comment

Five and six-membered heterocyclic compounds are important constituents that often exist in biologically active natural products and synthetic compounds of medicinal interest (Gilchrist, 1998). As useful precursors to potentially bioactive pyrimidine derivatives, methylpyrimidine has attracted considerable attention for many years (Xue et al., 1993). In recent years, Ru complexes of pyrimidine with an –NH2 substituent have been synthesized (Zhu et al., 2008). The title compound(I), was synthesized and we report herein its crystal structure.

The molecular structure of the title compound is shown in Fig. 1. There is one 2-Amino-4,6-dimethylpyrimidine cation and one dihydrogenphosphate anion in the asymmetric unit. All bond lengths are within the normal ranges (Allen et al., 1987). In the crystal structure, cations and anions are linked by intermolecular O-H···O and N-H···O hydrogen bonds to form a two-dimensional network. Additional stabilization is provided by weak intermolecular C—H···O interactions.

Experimental

A mixture of guanidine hydrochloride (0.1 mol), acetyl acetone (0.2 mol), sodium carbonate (0.03 mol) and phosphoric acid (0.1 mol) was stirred with water (30 mL) for 5 h to afford the title compound (yield 78%). Single crystals suitable for X-ray measurements were obtained by recrystallization of the title compound from water at room temperature.

Refinement

H atoms bonded to C atoms were fixed geometrically and and included in a riding-model approximation with C—H = 0.93-0.96 Å and Uiso(H)=1.2–1.5Ueq(C). H atoms bonded to N and O atoms were incuded in their 'as found' locations with refined isotropic displacement parameters,

Figures

Fig. 1.
The molecular structure of the title compound showing 30% probability displacement ellipsoids and the atom-numbering scheme.

Crystal data

C6H10N3+·H2PO4F(000) = 464
Mr = 221.16Dx = 1.537 Mg m3
Monoclinic, P21/nMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ynCell parameters from 1973 reflections
a = 11.743 (2) Åθ = 3.5–27.5°
b = 4.8266 (10) ŵ = 0.28 mm1
c = 16.940 (3) ÅT = 293 K
β = 95.55 (3)°Block, colorless
V = 955.6 (3) Å30.20 × 0.15 × 0.11 mm
Z = 4

Data collection

Bruker SMART CCD diffractometer1973 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.021
graphiteθmax = 27.5°, θmin = 3.5°
[var phi] and ω scansh = −15→15
8743 measured reflectionsk = −6→5
2193 independent reflectionsl = −21→21

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)] = 0.035Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.108H-atom parameters constrained
S = 1.08w = 1/[σ2(Fo2) + (0.0686P)2 + 0.3094P] where P = (Fo2 + 2Fc2)/3
2193 reflections(Δ/σ)max = 0.001
133 parametersΔρmax = 0.40 e Å3
0 restraintsΔρmin = −0.41 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
P10.09666 (3)0.22149 (8)0.74781 (2)0.02327 (14)
O10.17203 (9)0.3129 (2)0.82063 (6)0.0302 (3)
O20.01084 (9)0.4557 (2)0.71860 (7)0.0337 (3)
H2A0.02430.62650.73260.085 (9)*
O30.02931 (10)−0.0362 (2)0.76133 (7)0.0339 (3)
N10.20023 (11)0.0034 (3)0.95145 (7)0.0270 (3)
H1A0.19360.09000.90210.052 (6)*
O40.16964 (11)0.1887 (3)0.67571 (7)0.0381 (3)
H4A0.22410.05080.68220.084 (9)*
N30.02982 (11)−0.2279 (3)0.91928 (8)0.0322 (3)
H3B−0.0198−0.36920.93080.032 (4)*
H3A0.0243−0.15730.87480.044 (6)*
C10.12099 (12)−0.1846 (3)0.96966 (8)0.0252 (3)
N20.13194 (11)−0.3247 (3)1.03924 (7)0.0282 (3)
C40.29458 (13)0.0550 (3)1.00208 (9)0.0300 (3)
C20.22244 (14)−0.2691 (3)1.09017 (9)0.0294 (3)
C30.30667 (13)−0.0793 (4)1.07340 (9)0.0341 (3)
H3D0.3695−0.04531.10990.041*
C60.37991 (16)0.2522 (4)0.97449 (12)0.0417 (4)
H6A0.34270.42400.95940.063*
H6B0.41280.17480.92970.063*
H6C0.43910.28511.01660.063*
C50.23093 (16)−0.4213 (4)1.16774 (9)0.0429 (4)
H5A0.1664−0.54291.16900.064*
H5B0.2315−0.29051.21050.064*
H5C0.3002−0.52801.17340.064*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
P10.0252 (2)0.0188 (2)0.0253 (2)0.00191 (12)−0.00052 (14)0.00042 (12)
O10.0312 (6)0.0308 (6)0.0274 (5)−0.0050 (4)−0.0039 (4)0.0044 (4)
O20.0333 (6)0.0214 (5)0.0437 (6)0.0054 (4)−0.0103 (4)−0.0035 (4)
O30.0404 (6)0.0207 (5)0.0400 (6)−0.0048 (4)0.0005 (5)0.0003 (4)
N10.0281 (6)0.0277 (6)0.0250 (6)−0.0035 (5)0.0012 (4)0.0012 (5)
O40.0470 (7)0.0380 (7)0.0305 (6)0.0135 (5)0.0099 (5)0.0051 (5)
N30.0327 (7)0.0363 (7)0.0263 (7)−0.0087 (5)−0.0031 (5)0.0042 (5)
C10.0265 (7)0.0256 (7)0.0236 (7)−0.0009 (5)0.0026 (5)−0.0008 (5)
N20.0303 (6)0.0310 (7)0.0233 (6)−0.0038 (5)0.0020 (5)0.0020 (5)
C40.0277 (7)0.0296 (7)0.0322 (7)−0.0034 (6)0.0008 (5)−0.0019 (6)
C20.0327 (8)0.0313 (8)0.0239 (7)0.0003 (6)0.0011 (5)−0.0007 (5)
C30.0310 (8)0.0391 (9)0.0308 (7)−0.0049 (7)−0.0040 (6)0.0005 (6)
C60.0346 (9)0.0423 (10)0.0475 (10)−0.0125 (7)−0.0002 (7)0.0068 (7)
C50.0479 (10)0.0532 (11)0.0261 (7)−0.0066 (8)−0.0032 (6)0.0089 (7)

Geometric parameters (Å, °)

P1—O31.5033 (12)N2—C21.330 (2)
P1—O11.5128 (12)C4—C31.366 (2)
P1—O21.5626 (11)C4—C61.490 (2)
P1—O41.5665 (12)C2—C31.397 (2)
O2—H2A0.8679C2—C51.500 (2)
N1—C11.3566 (19)C3—H3D0.9300
N1—C41.3568 (19)C6—H6A0.9600
N1—H1A0.9317C6—H6B0.9600
O4—H4A0.9225C6—H6C0.9600
N3—C11.3195 (19)C5—H5A0.9600
N3—H3B0.9302C5—H5B0.9600
N3—H3A0.8243C5—H5C0.9600
C1—N21.3542 (19)
O3—P1—O1113.08 (6)C3—C4—C6124.41 (15)
O3—P1—O2108.30 (7)N2—C2—C3122.50 (14)
O1—P1—O2110.84 (7)N2—C2—C5116.78 (14)
O3—P1—O4111.77 (7)C3—C2—C5120.72 (15)
O1—P1—O4110.13 (7)C4—C3—C2118.42 (14)
O2—P1—O4102.18 (7)C4—C3—H3D120.8
P1—O2—H2A120.4C2—C3—H3D120.8
C1—N1—C4121.00 (13)C4—C6—H6A109.5
C1—N1—H1A120.3C4—C6—H6B109.5
C4—N1—H1A118.5H6A—C6—H6B109.5
P1—O4—H4A113.9C4—C6—H6C109.5
C1—N3—H3B117.8H6A—C6—H6C109.5
C1—N3—H3A120.9H6B—C6—H6C109.5
H3B—N3—H3A119.9C2—C5—H5A109.5
N3—C1—N2119.12 (14)C2—C5—H5B109.5
N3—C1—N1119.36 (13)H5A—C5—H5B109.5
N2—C1—N1121.51 (13)C2—C5—H5C109.5
C2—N2—C1117.81 (13)H5A—C5—H5C109.5
N1—C4—C3118.72 (14)H5B—C5—H5C109.5
N1—C4—C6116.85 (14)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N1—H1A···O10.931.752.667 (2)168
O2—H2A···O3i0.871.702.560 (2)171
N3—H3A···O30.822.022.831 (2)170
N3—H3B···N2ii0.932.073.004 (2)178
O4—H4A···O1iii0.921.682.594 (2)171
C3—H3D···O2iv0.932.403.319 (2)171

Symmetry codes: (i) x, y+1, z; (ii) −x, −y−1, −z+2; (iii) −x+1/2, y−1/2, −z+3/2; (iv) x+1/2, −y+1/2, z+1/2.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: LH2909).

References

  • Allen, F. H., Kennard, O., Watson, D. G., Brammer, L., Orpen, A. G. & Taylor, R. (1987). J. Chem. Soc. Perkin Trans. 2, pp. S1–19.
  • Bruker (1997). SMART and SAINT Bruker AXS Inc., Madison, Wisconsin, USA.
  • Gilchrist, T. L. (1998). Heterocyclic Chemistry, 3rd ed. London: Addison-Wesley Longman Ltd.
  • Sheldrick, G. M. (2008). Acta Cryst A64, 112–122. [PubMed]
  • Spek, A. L. (2009). Acta Cryst. D65, 148–155. [PMC free article] [PubMed]
  • Xue, S. J., Zhang, A. D. & Wang, H. T. (1993). Chem. Reagents, 15, 181.
  • Zhu, W., Liu, X. & Wang, H. (2008). Acta Opt. Sin.28, 1155–1160.

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