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Acta Crystallogr Sect E Struct Rep Online. 2009 November 1; 65(Pt 11): o2913.
Published online 2009 October 31. doi:  10.1107/S1600536809044444
PMCID: PMC2971421

2-Amino-4,6-dimethyl­pyrimidinium chloro­acetate

Abstract

There are two cations and two anions in the asymmetric unit of the title compound, C6H10N3 +·C2H2ClO2 . In the crystal, the components are linked by inter­molecular N—H(...)O and N—H(...)N hydrogen bonds to form a two-dimensional network. Additional stabilization is provided by weak inter­molecular C—H(...)O inter­actions.

Related literature

For background to pyrimidine derivatives, see: Xue et al. (1993 [triangle]); Hemamalini et al. (2005 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-65-o2913-scheme1.jpg

Experimental

Crystal data

  • C6H10N3 +·C2H2ClO2
  • M r = 217.66
  • Triclinic, An external file that holds a picture, illustration, etc.
Object name is e-65-o2913-efi1.jpg
  • a = 4.4560 (9) Å
  • b = 12.302 (3) Å
  • c = 19.441 (4) Å
  • α = 92.90 (3)°
  • β = 96.53 (3)°
  • γ = 91.15 (3)°
  • V = 1057.1 (4) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.34 mm−1
  • T = 293 K
  • 0.20 × 0.15 × 0.11 mm

Data collection

  • Bruker SMART CCD diffractometer
  • Absorption correction: none
  • 10303 measured reflections
  • 4761 independent reflections
  • 3452 reflections with I > 2σ(I)
  • R int = 0.028

Refinement

  • R[F 2 > 2σ(F 2)] = 0.055
  • wR(F 2) = 0.195
  • S = 1.08
  • 4761 reflections
  • 253 parameters
  • H-atom parameters constrained
  • Δρmax = 0.42 e Å−3
  • Δρmin = −0.43 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 [triangle]); molecular graphics: SHELXTL (Sheldrick, 2008 [triangle]); 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/S1600536809044444/hb5174sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809044444/hb5174Isup2.hkl

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

supplementary crystallographic information

Comment

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). The title compound(I), was synthesized and we report herein its crystal structure (Fig. 1).

There are two 2-amino-4,6-dimethylpyrimidine cations and two chloracetate anions in the asymmetric unit. In the crystal structure, cations and anions are linked by intermolecular N—H···O and N—H···N 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 2-chloroacetic acid (0.1 mol) was stirred with water (30 ml) for 3 h to afford the title compound (yield 67%). Colourless blocks of (I) 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).

Figures

Fig. 1.
The molecular structure of (I) showing 30% probability displacement ellipsoids.

Crystal data

C6H10N3+·C2H2ClO2Z = 4
Mr = 217.66F(000) = 456
Triclinic, P1Dx = 1.368 Mg m3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71073 Å
a = 4.4560 (9) ÅCell parameters from 3452 reflections
b = 12.302 (3) Åθ = 3.2–27.5°
c = 19.441 (4) ŵ = 0.34 mm1
α = 92.90 (3)°T = 293 K
β = 96.53 (3)°Block, colourless
γ = 91.15 (3)°0.20 × 0.15 × 0.11 mm
V = 1057.1 (4) Å3

Data collection

Bruker SMART CCD diffractometer3452 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.028
graphiteθmax = 27.5°, θmin = 3.2°
ω scansh = −5→5
10303 measured reflectionsk = −15→15
4761 independent reflectionsl = −25→25

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: inferred from neighbouring sites
wR(F2) = 0.195H-atom parameters constrained
S = 1.08w = 1/[σ2(Fo2) + (0.1056P)2 + 0.3945P] where P = (Fo2 + 2Fc2)/3
4761 reflections(Δ/σ)max < 0.001
253 parametersΔρmax = 0.42 e Å3
0 restraintsΔρmin = −0.43 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
Cl10.92264 (17)0.01264 (6)0.17209 (4)0.0623 (2)
O40.7689 (5)0.14297 (17)−0.00572 (10)0.0681 (6)
C160.8811 (6)0.13347 (19)0.05672 (13)0.0463 (5)
O31.0794 (5)0.19170 (18)0.08873 (11)0.0742 (7)
C150.7353 (7)0.0407 (2)0.09016 (14)0.0616 (7)
H15A0.7320−0.02430.05960.074*
H15B0.52760.05840.09540.074*
Cl20.8148 (2)0.60659 (7)0.34169 (5)0.0862 (3)
O20.9854 (5)0.38470 (15)0.37047 (10)0.0594 (5)
C140.8160 (6)0.4192 (2)0.41493 (13)0.0497 (6)
O10.7445 (6)0.36870 (18)0.46320 (12)0.0798 (7)
C130.6862 (8)0.5308 (2)0.40795 (16)0.0632 (7)
H13A0.73420.57220.45180.076*
H13B0.46800.52300.39930.076*
N50.1724 (4)0.18552 (15)0.37450 (10)0.0418 (4)
H5A0.10930.25110.37620.050*
N60.1954 (5)0.01175 (16)0.42234 (10)0.0467 (5)
C100.1065 (6)0.11536 (19)0.42261 (12)0.0436 (5)
C90.4323 (6)0.0461 (2)0.32177 (13)0.0502 (6)
H9A0.54460.02100.28700.060*
C120.3572 (6)−0.02223 (19)0.37232 (13)0.0477 (5)
C80.3363 (5)0.15178 (19)0.32440 (12)0.0430 (5)
N4−0.0552 (6)0.15065 (18)0.47176 (12)0.0610 (6)
H4A−0.10120.10750.50260.073*
H4B−0.11450.21670.47290.073*
C70.4002 (7)0.2310 (2)0.27171 (13)0.0554 (6)
H7A0.31490.29980.28290.083*
H7B0.31190.20380.22660.083*
H7C0.61460.24020.27180.083*
C110.4550 (8)−0.1383 (2)0.37303 (18)0.0689 (8)
H11A0.3841−0.17210.41180.103*
H11B0.6715−0.14000.37700.103*
H11C0.3719−0.17680.33080.103*
N20.0615 (5)0.69331 (16)0.07225 (10)0.0457 (5)
H2A0.10880.74700.04860.055*
N3−0.2359 (5)0.53279 (17)0.07940 (11)0.0489 (5)
C6−0.0956 (6)0.5215 (2)0.14272 (13)0.0493 (6)
N1−0.2951 (5)0.63311 (18)−0.01745 (11)0.0566 (6)
H1A−0.43490.5876−0.03540.068*
H1B−0.24640.6878−0.04010.068*
C4−0.1547 (5)0.61899 (19)0.04524 (12)0.0443 (5)
C20.2013 (5)0.6821 (2)0.13654 (13)0.0472 (5)
C30.1249 (6)0.5956 (2)0.17351 (14)0.0520 (6)
H3B0.21830.58680.21810.062*
C10.4302 (6)0.7682 (2)0.16441 (15)0.0594 (7)
H1C0.44850.82040.13000.089*
H1D0.62200.73550.17590.089*
H1E0.36730.80390.20520.089*
C5−0.1883 (8)0.4234 (2)0.17923 (16)0.0657 (8)
H5B−0.34220.38210.14990.099*
H5C−0.26540.44660.22160.099*
H5D−0.01620.37880.18960.099*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
Cl10.0689 (4)0.0673 (4)0.0516 (4)−0.0052 (3)0.0041 (3)0.0202 (3)
O40.0883 (15)0.0633 (12)0.0497 (11)−0.0230 (11)−0.0076 (10)0.0170 (9)
C160.0500 (13)0.0415 (12)0.0478 (13)−0.0017 (10)0.0065 (10)0.0057 (10)
O30.0887 (15)0.0727 (14)0.0573 (12)−0.0334 (12)−0.0100 (11)0.0213 (10)
C150.0666 (17)0.0649 (17)0.0515 (15)−0.0184 (14)−0.0035 (12)0.0182 (13)
Cl20.1195 (7)0.0527 (4)0.0972 (7)0.0286 (4)0.0432 (5)0.0302 (4)
O20.0773 (13)0.0450 (10)0.0609 (11)0.0132 (9)0.0229 (10)0.0130 (8)
C140.0569 (14)0.0407 (12)0.0512 (14)0.0017 (11)0.0031 (11)0.0057 (10)
O10.1139 (19)0.0612 (13)0.0750 (14)0.0228 (12)0.0437 (13)0.0261 (11)
C130.0779 (19)0.0520 (15)0.0638 (17)0.0163 (14)0.0193 (14)0.0105 (13)
N50.0532 (11)0.0323 (9)0.0405 (10)0.0009 (8)0.0054 (8)0.0097 (7)
N60.0617 (12)0.0356 (10)0.0449 (10)0.0052 (9)0.0101 (9)0.0118 (8)
C100.0554 (13)0.0375 (11)0.0387 (11)0.0014 (10)0.0054 (9)0.0096 (9)
C90.0628 (15)0.0461 (13)0.0436 (12)0.0069 (11)0.0116 (11)0.0071 (10)
C120.0581 (14)0.0393 (12)0.0463 (13)0.0068 (10)0.0044 (10)0.0076 (9)
C80.0476 (12)0.0429 (12)0.0383 (11)−0.0006 (9)0.0008 (9)0.0096 (9)
N40.0932 (17)0.0420 (11)0.0545 (13)0.0128 (11)0.0300 (12)0.0158 (9)
C70.0702 (16)0.0512 (14)0.0475 (13)−0.0013 (12)0.0140 (12)0.0159 (11)
C110.094 (2)0.0426 (14)0.074 (2)0.0197 (14)0.0196 (17)0.0118 (13)
N20.0515 (11)0.0420 (10)0.0458 (11)−0.0001 (9)0.0120 (8)0.0094 (8)
N30.0563 (12)0.0423 (10)0.0505 (12)0.0016 (9)0.0129 (9)0.0112 (9)
C60.0574 (14)0.0451 (12)0.0490 (13)0.0119 (11)0.0147 (11)0.0138 (10)
N10.0679 (14)0.0504 (12)0.0507 (12)−0.0145 (11)0.0014 (10)0.0147 (9)
C40.0480 (12)0.0426 (12)0.0443 (12)0.0013 (10)0.0116 (10)0.0070 (9)
C20.0444 (12)0.0497 (13)0.0494 (13)0.0098 (10)0.0111 (10)0.0051 (10)
C30.0547 (14)0.0561 (14)0.0472 (13)0.0110 (12)0.0089 (11)0.0118 (11)
C10.0571 (15)0.0599 (16)0.0599 (16)0.0006 (13)0.0025 (12)0.0015 (13)
C50.085 (2)0.0530 (15)0.0628 (17)0.0037 (14)0.0126 (15)0.0231 (13)

Geometric parameters (Å, °)

Cl1—C151.766 (3)C7—H7A0.9600
O4—C161.271 (3)C7—H7B0.9600
C16—O31.219 (3)C7—H7C0.9600
C16—C151.512 (3)C11—H11A0.9600
C15—H15A0.9700C11—H11B0.9600
C15—H15B0.9700C11—H11C0.9600
Cl2—C131.767 (3)N2—C21.347 (3)
O2—C141.273 (3)N2—C41.357 (3)
C14—O11.220 (3)N2—H2A0.8600
C14—C131.507 (4)N3—C61.331 (3)
C13—H13A0.9700N3—C41.344 (3)
C13—H13B0.9700C6—C31.389 (4)
N5—C81.337 (3)C6—C51.505 (3)
N5—C101.356 (3)N1—C41.326 (3)
N5—H5A0.8600N1—H1A0.8600
N6—C121.331 (3)N1—H1B0.8600
N6—C101.342 (3)C2—C31.372 (4)
C10—N41.322 (3)C2—C11.493 (4)
C9—C81.378 (4)C3—H3B0.9300
C9—C121.389 (3)C1—H1C0.9600
C9—H9A0.9300C1—H1D0.9600
C12—C111.501 (4)C1—H1E0.9600
C8—C71.495 (3)C5—H5B0.9600
N4—H4A0.8600C5—H5C0.9600
N4—H4B0.8600C5—H5D0.9600
O3—C16—O4126.0 (2)C8—C7—H7C109.5
O3—C16—C15121.5 (2)H7A—C7—H7C109.5
O4—C16—C15112.5 (2)H7B—C7—H7C109.5
C16—C15—Cl1113.42 (19)C12—C11—H11A109.5
C16—C15—H15A108.9C12—C11—H11B109.5
Cl1—C15—H15A108.9H11A—C11—H11B109.5
C16—C15—H15B108.9C12—C11—H11C109.5
Cl1—C15—H15B108.9H11A—C11—H11C109.5
H15A—C15—H15B107.7H11B—C11—H11C109.5
O1—C14—O2125.4 (2)C2—N2—C4119.3 (2)
O1—C14—C13116.1 (2)C2—N2—H2A120.4
O2—C14—C13118.5 (2)C4—N2—H2A120.4
C14—C13—Cl2115.3 (2)C6—N3—C4117.5 (2)
C14—C13—H13A108.5N3—C6—C3122.1 (2)
Cl2—C13—H13A108.5N3—C6—C5116.2 (2)
C14—C13—H13B108.5C3—C6—C5121.7 (2)
Cl2—C13—H13B108.5C4—N1—H1A120.0
H13A—C13—H13B107.5C4—N1—H1B120.0
C8—N5—C10119.4 (2)H1A—N1—H1B120.0
C8—N5—H5A120.3N1—C4—N3118.6 (2)
C10—N5—H5A120.3N1—C4—N2118.3 (2)
C12—N6—C10117.6 (2)N3—C4—N2123.1 (2)
N4—C10—N6118.5 (2)N2—C2—C3119.7 (2)
N4—C10—N5118.3 (2)N2—C2—C1116.9 (2)
N6—C10—N5123.2 (2)C3—C2—C1123.4 (2)
C8—C9—C12118.4 (2)C2—C3—C6118.4 (2)
C8—C9—H9A120.8C2—C3—H3B120.8
C12—C9—H9A120.8C6—C3—H3B120.8
N6—C12—C9121.8 (2)C2—C1—H1C109.5
N6—C12—C11116.7 (2)C2—C1—H1D109.5
C9—C12—C11121.5 (2)H1C—C1—H1D109.5
N5—C8—C9119.7 (2)C2—C1—H1E109.5
N5—C8—C7117.8 (2)H1C—C1—H1E109.5
C9—C8—C7122.5 (2)H1D—C1—H1E109.5
C10—N4—H4A120.0C6—C5—H5B109.5
C10—N4—H4B120.0C6—C5—H5C109.5
H4A—N4—H4B120.0H5B—C5—H5C109.5
C8—C7—H7A109.5C6—C5—H5D109.5
C8—C7—H7B109.5H5B—C5—H5D109.5
H7A—C7—H7B109.5H5C—C5—H5D109.5

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N1—H1A···N3i0.862.142.999 (3)177
N1—H1B···O3ii0.861.982.830 (3)173
N2—H2A···O4ii0.861.742.593 (3)175
N4—H4A···N6iii0.862.193.046 (3)175
N4—H4B···O1iv0.862.002.851 (3)173
N5—H5A···O2iv0.861.752.606 (3)174
C1—H1C···O4ii0.962.563.355 (4)140
C7—H7A···O2iv0.962.573.355 (4)139

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

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: HB5174).

References

  • Bruker (1997). SMART and SAINT Bruker AXS Inc., Madison, Wisconsin, USA.
  • Hemamalini, M., Mu&shy;thiah, P. T., Rychlewska, U. & Plutecka, A. (2005). Acta Cryst. C61, o95–o97. [PubMed]
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]
  • Xue, S. J., Zhang, A. D. & Wang, H. T. (1993). Chemical Reagents, 15, 181.

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