organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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2-Amino-4,6-dimeth­­oxy­pyrimidin-1-ium 2,2-di­chloro­acetate

aDepartment of Chemistry and Chemical Engineering, Weifang University, Weifang 261061, People's Republic of China, and bJournal Editorial Department, Weifang University, Weifang 261061, People's Republic of China
*Correspondence e-mail: lincuihua2009@126.com

(Received 6 May 2012; accepted 11 May 2012; online 26 May 2012)

In the title salt, C6H10N3O2+·C2HCl2O2, two cations and two anions are linked by N—H⋯O hydrogen bonds, forming chains along the c axis.

Related literature

For the biological activity of heterocyclic compounds, see: Gilchrist (1998[Gilchrist, T. L. (1998). Heterocyclic Chemistry, 3rd ed. London: Addison Wesley Longman Ltd.]). For the bioactivity of pyrimidine derivatives, see: Xue et al. (1993[Xue, S. J., Zhang, A. D. & Wang, H. T. (1993). Chem. Reagents, 15, 181-182.]). For a related structure, see: Hemamalini et al. (2005[Hemamalini, M., Mu­thiah, P. T., Rychlewska, U. & Plutecka, A. (2005). Acta Cryst. C61, o95-o97.]). For standard bond lengths, see: Allen et al. (1987[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.]).

[Scheme 1]

Experimental

Crystal data
  • C6H10N3O2+·C2HCl2O2

  • Mr = 284.10

  • Triclinic, [P \overline 1]

  • a = 6.8502 (14) Å

  • b = 8.6667 (17) Å

  • c = 11.255 (2) Å

  • α = 67.480 (1)°

  • β = 87.320 (2)°

  • γ = 85.970 (2)°

  • V = 615.6 (2) Å3

  • Z = 2

  • Mo Kα radiation

  • μ = 0.53 mm−1

  • T = 293 K

  • 0.45 × 0.43 × 0.35 mm

Data collection
  • Bruker SMART CCD diffractometer

  • Absorption correction: multi-scan (SADABS; Sheldrick, 1996[Sheldrick, G. M. (1996). SADABS. University of Göttingen, Germany.]) Tmin = 0.795, Tmax = 0.835

  • 4710 measured reflections

  • 2173 independent reflections

  • 1806 reflections with I > 2σ(I)

  • Rint = 0.026

Refinement
  • R[F2 > 2σ(F2)] = 0.054

  • wR(F2) = 0.200

  • S = 1.09

  • 2173 reflections

  • 156 parameters

  • H-atom parameters constrained

  • Δρmax = 0.45 e Å−3

  • Δρmin = −0.39 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N3—H3B⋯O3i 0.86 1.97 2.822 (3) 173
N3—H3A⋯O3ii 0.86 2.07 2.848 (3) 149
N2—H2⋯O4i 0.86 1.85 2.692 (3) 168
Symmetry codes: (i) -x, -y+1, -z+1; (ii) x, y+1, z.

Data collection: SMART (Bruker, 1997[Bruker (1997). SMART and SAINT, Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 1997[Bruker (1997). SMART and SAINT, Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (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: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]) and PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]); software used to prepare material for publication: SHELXTL.

Supporting information


Comment top

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, new complexes of pyrimidine have been synthesized (Hemamalini et al., 2005). Herein we report herein the crystal structure of the title compound (I).

The molecular structure of (I) is shown in Fig. 1. There is one cation and one anion in the asymmetric unit of (I). All bond lengths are within the normal ranges (Allen et al., 1987). In the crystal, two cations and two anions are linked by intermolecular N—H···O hydrogen bonds to form centrosymmetric four component aggregates.

Related literature top

For the biological activity of heterocyclic compounds, see: Gilchrist (1998). For the bioactivity of pyrimidine derivatives, see: Xue et al. (1993). For a related structure, see: Hemamalini et al. (2005). For standard bond lengths, see: Allen et al. (1987).

Experimental top

A mixture of 2-amino-4,6-dichloropyrimidine (0.1 mol) and sodium methoxide (0.1 mol) was stirred with methanol (30 ml) for 3 h to afford 2-Amino-4,6-dimethoxypyrimidine (yield 85%). The title compound was crystallized from an aqueous mixture containing 2-Amino-4,6-dimethoxypyrimidine and dichloroacetate in a 1:1 stoichiometric ratio at room temperature by the slow evaporation technique.

Refinement top

H atoms bonded to C atoms were fixed geometrically and and included in a riding-model approximation with C—H = 0.93–0.98 Å and N—H = 0.86Å with Uiso(H)=1.2–1.5Ueq(C).

Computing details top

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

Figures top
[Figure 1] Fig. 1. The structure of the title compound showing 30% probability displacement ellipsoids.
[Figure 2] Fig. 2. Part of the crystal structure with hydrogen bonds shown as dashed lines.
2-Amino-4,6-dimethoxypyrimidin-1-ium 2,2-dichloroacetate top
Crystal data top
C6H10N3O2+·C2HCl2O2Z = 2
Mr = 284.10F(000) = 292
Triclinic, P1Dx = 1.533 Mg m3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71073 Å
a = 6.8502 (14) ÅCell parameters from 3794 reflections
b = 8.6667 (17) Åθ = 3.5–27.5°
c = 11.255 (2) ŵ = 0.53 mm1
α = 67.480 (1)°T = 293 K
β = 87.320 (2)°Block, colorless
γ = 85.970 (2)°0.45 × 0.43 × 0.35 mm
V = 615.6 (2) Å3
Data collection top
Bruker SMART CCD
diffractometer
2173 independent reflections
Radiation source: fine-focus sealed tube1806 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.026
ϕ and ω scansθmax = 25.0°, θmin = 3.5°
Absorption correction: multi-scan
(SADABS; Sheldrick, 1996)
h = 87
Tmin = 0.795, Tmax = 0.835k = 1010
4710 measured reflectionsl = 1313
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)] = 0.054Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.200H-atom parameters constrained
S = 1.09 w = 1/[σ2(Fo2) + (0.1265P)2 + 0.3628P]
where P = (Fo2 + 2Fc2)/3
2173 reflections(Δ/σ)max < 0.001
156 parametersΔρmax = 0.45 e Å3
0 restraintsΔρmin = 0.39 e Å3
Crystal data top
C6H10N3O2+·C2HCl2O2γ = 85.970 (2)°
Mr = 284.10V = 615.6 (2) Å3
Triclinic, P1Z = 2
a = 6.8502 (14) ÅMo Kα radiation
b = 8.6667 (17) ŵ = 0.53 mm1
c = 11.255 (2) ÅT = 293 K
α = 67.480 (1)°0.45 × 0.43 × 0.35 mm
β = 87.320 (2)°
Data collection top
Bruker SMART CCD
diffractometer
2173 independent reflections
Absorption correction: multi-scan
(SADABS; Sheldrick, 1996)
1806 reflections with I > 2σ(I)
Tmin = 0.795, Tmax = 0.835Rint = 0.026
4710 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0540 restraints
wR(F2) = 0.200H-atom parameters constrained
S = 1.09Δρmax = 0.45 e Å3
2173 reflectionsΔρmin = 0.39 e Å3
156 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
Cl10.11057 (16)0.15674 (13)0.03526 (9)0.0641 (4)
Cl20.44050 (14)0.24515 (19)0.14101 (11)0.0804 (5)
N10.5368 (4)0.7901 (3)0.4560 (2)0.0365 (6)
N20.3706 (3)0.6207 (3)0.6442 (2)0.0336 (6)
H20.26670.60430.69240.040*
N30.2252 (4)0.8660 (3)0.5053 (3)0.0450 (7)
H3A0.22640.95420.43560.054*
H3B0.12350.84740.55550.054*
O10.4900 (3)0.3802 (3)0.7880 (2)0.0487 (6)
O20.8446 (3)0.7020 (3)0.4156 (2)0.0530 (7)
O30.0938 (4)0.1810 (3)0.3189 (2)0.0511 (7)
O40.0703 (4)0.4064 (3)0.1873 (2)0.0653 (8)
C10.3790 (4)0.7598 (3)0.5350 (3)0.0332 (6)
C20.5248 (4)0.5073 (4)0.6779 (3)0.0367 (7)
C30.6887 (4)0.5305 (4)0.6026 (3)0.0389 (7)
H30.79620.45400.62320.047*
C40.6855 (4)0.6780 (4)0.4910 (3)0.0384 (7)
C50.6408 (6)0.2493 (5)0.8325 (4)0.0651 (11)
H5A0.67280.20560.76700.098*
H5B0.59560.16140.90890.098*
H5C0.75510.29310.85140.098*
C60.8456 (6)0.8491 (5)0.3002 (4)0.0614 (10)
H6A0.76880.83390.23670.092*
H6B0.97770.86900.26820.092*
H6C0.79100.94320.31810.092*
C70.0616 (4)0.2935 (4)0.2130 (3)0.0378 (7)
C80.1932 (4)0.2995 (4)0.0968 (3)0.0394 (7)
H80.18320.41270.03020.047*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Cl10.0840 (8)0.0668 (7)0.0495 (6)0.0127 (5)0.0068 (5)0.0292 (5)
Cl20.0425 (6)0.1419 (12)0.0752 (7)0.0083 (6)0.0034 (5)0.0639 (8)
N10.0382 (13)0.0356 (13)0.0345 (13)0.0043 (10)0.0020 (10)0.0121 (10)
N20.0329 (12)0.0350 (13)0.0292 (12)0.0017 (10)0.0014 (9)0.0089 (10)
N30.0435 (14)0.0386 (14)0.0392 (14)0.0085 (11)0.0022 (11)0.0016 (11)
O10.0530 (13)0.0411 (12)0.0371 (12)0.0138 (10)0.0023 (10)0.0015 (9)
O20.0392 (12)0.0607 (16)0.0543 (14)0.0042 (11)0.0145 (10)0.0181 (12)
O30.0588 (15)0.0438 (13)0.0337 (12)0.0107 (10)0.0032 (10)0.0012 (10)
O40.0660 (16)0.0588 (16)0.0430 (13)0.0296 (13)0.0131 (12)0.0046 (11)
C10.0372 (15)0.0319 (14)0.0311 (14)0.0031 (11)0.0025 (11)0.0124 (11)
C20.0424 (16)0.0340 (15)0.0334 (14)0.0028 (12)0.0045 (12)0.0128 (12)
C30.0330 (15)0.0410 (16)0.0416 (16)0.0042 (12)0.0039 (12)0.0152 (13)
C40.0348 (15)0.0445 (17)0.0396 (16)0.0071 (13)0.0019 (12)0.0197 (13)
C50.070 (2)0.059 (2)0.0451 (19)0.0295 (19)0.0043 (18)0.0025 (17)
C60.057 (2)0.068 (3)0.052 (2)0.0141 (18)0.0182 (17)0.0157 (18)
C70.0431 (16)0.0315 (15)0.0340 (15)0.0008 (12)0.0002 (12)0.0076 (12)
C80.0445 (17)0.0375 (16)0.0339 (15)0.0009 (12)0.0003 (12)0.0116 (12)
Geometric parameters (Å, º) top
Cl1—C81.767 (3)O3—C71.234 (4)
Cl2—C81.768 (3)O4—C71.241 (4)
N1—C41.320 (4)C2—C31.353 (4)
N1—C11.342 (4)C3—C41.408 (4)
N2—C21.354 (4)C3—H30.9300
N2—C11.355 (4)C5—H5A0.9600
N2—H20.8600C5—H5B0.9600
N3—C11.315 (4)C5—H5C0.9600
N3—H3A0.8600C6—H6A0.9600
N3—H3B0.8600C6—H6B0.9600
O1—C21.330 (4)C6—H6C0.9600
O1—C51.433 (4)C7—C81.539 (4)
O2—C41.327 (4)C8—H80.9800
O2—C61.430 (5)
C4—N1—C1116.5 (2)O1—C5—H5A109.5
C2—N2—C1120.4 (2)O1—C5—H5B109.5
C2—N2—H2119.8H5A—C5—H5B109.5
C1—N2—H2119.8O1—C5—H5C109.5
C1—N3—H3A120.0H5A—C5—H5C109.5
C1—N3—H3B120.0H5B—C5—H5C109.5
H3A—N3—H3B120.0O2—C6—H6A109.5
C2—O1—C5117.1 (3)O2—C6—H6B109.5
C4—O2—C6117.9 (3)H6A—C6—H6B109.5
N3—C1—N1119.5 (3)O2—C6—H6C109.5
N3—C1—N2118.4 (3)H6A—C6—H6C109.5
N1—C1—N2122.1 (3)H6B—C6—H6C109.5
O1—C2—C3127.8 (3)O3—C7—O4126.9 (3)
O1—C2—N2111.7 (3)O3—C7—C8119.0 (3)
C3—C2—N2120.5 (3)O4—C7—C8114.1 (3)
C2—C3—C4115.5 (3)C7—C8—Cl1108.5 (2)
C2—C3—H3122.2C7—C8—Cl2111.4 (2)
C4—C3—H3122.2Cl1—C8—Cl2109.21 (17)
N1—C4—O2118.7 (3)C7—C8—H8109.3
N1—C4—C3125.0 (3)Cl1—C8—H8109.3
O2—C4—C3116.3 (3)Cl2—C8—H8109.3
C4—N1—C1—N3179.5 (3)C1—N1—C4—O2179.6 (3)
C4—N1—C1—N20.8 (4)C1—N1—C4—C30.9 (4)
C2—N2—C1—N3179.4 (3)C6—O2—C4—N10.1 (4)
C2—N2—C1—N10.7 (4)C6—O2—C4—C3179.0 (3)
C5—O1—C2—C31.4 (5)C2—C3—C4—N10.7 (5)
C5—O1—C2—N2178.5 (3)C2—C3—C4—O2179.5 (3)
C1—N2—C2—O1179.6 (3)O3—C7—C8—Cl181.6 (3)
C1—N2—C2—C30.5 (4)O4—C7—C8—Cl197.9 (3)
O1—C2—C3—C4179.6 (3)O3—C7—C8—Cl238.6 (4)
N2—C2—C3—C40.5 (4)O4—C7—C8—Cl2141.9 (3)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N3—H3B···O3i0.861.972.822 (3)173
N3—H3A···O3ii0.862.072.848 (3)149
N2—H2···O4i0.861.852.692 (3)168
Symmetry codes: (i) x, y+1, z+1; (ii) x, y+1, z.

Experimental details

Crystal data
Chemical formulaC6H10N3O2+·C2HCl2O2
Mr284.10
Crystal system, space groupTriclinic, P1
Temperature (K)293
a, b, c (Å)6.8502 (14), 8.6667 (17), 11.255 (2)
α, β, γ (°)67.480 (1), 87.320 (2), 85.970 (2)
V3)615.6 (2)
Z2
Radiation typeMo Kα
µ (mm1)0.53
Crystal size (mm)0.45 × 0.43 × 0.35
Data collection
DiffractometerBruker SMART CCD
diffractometer
Absorption correctionMulti-scan
(SADABS; Sheldrick, 1996)
Tmin, Tmax0.795, 0.835
No. of measured, independent and
observed [I > 2σ(I)] reflections
4710, 2173, 1806
Rint0.026
(sin θ/λ)max1)0.595
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.054, 0.200, 1.09
No. of reflections2173
No. of parameters156
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.45, 0.39

Computer programs: SMART (Bruker, 1997), SAINT (Bruker, 1997), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2009), SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N3—H3B···O3i0.861.972.822 (3)173.1
N3—H3A···O3ii0.862.072.848 (3)149.4
N2—H2···O4i0.861.852.692 (3)167.8
Symmetry codes: (i) x, y+1, z+1; (ii) x, y+1, z.
 

Acknowledgements

The authors thank the Natural Science Foundation of Shandong Province (No. ZR2010BL011), and Weifang University for a research grant (2012Z06).

References

First citationAllen, F. H., Kennard, O., Watson, D. G., Brammer, L., Orpen, A. G. & Taylor, R. (1987). J. Chem. Soc. Perkin Trans. 2, pp. S1–19.  CrossRef Web of Science Google Scholar
First citationBruker (1997). SMART and SAINT, Bruker AXS Inc., Madison, Wisconsin, USA.  Google Scholar
First citationGilchrist, T. L. (1998). Heterocyclic Chemistry, 3rd ed. London: Addison Wesley Longman Ltd.  Google Scholar
First citationHemamalini, M., Mu­thiah, P. T., Rychlewska, U. & Plutecka, A. (2005). Acta Cryst. C61, o95–o97.  Web of Science CSD CrossRef CAS IUCr Journals Google Scholar
First citationSheldrick, G. M. (1996). SADABS. University of Göttingen, Germany.  Google Scholar
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationSpek, A. L. (2009). Acta Cryst. D65, 148–155.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationXue, S. J., Zhang, A. D. & Wang, H. T. (1993). Chem. Reagents, 15, 181–182.  CAS Google Scholar

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