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

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890

2-Amino-4,6-di­methyl­pyrimidinium chloro­acetate

aMicroscale Science Institute, Department of Chemistry and Chemical Engineering, Weifang University, Weifang 261061, People's Republic of China, bJournal Editorial Department, Weifang University, Weifang 261061, People's Republic of China, and cMicroscale Science Institute, Weifang University, Weifang 261061, People's Republic of China
*Correspondence e-mail: ffjian2008@163.com

(Received 23 October 2009; accepted 26 October 2009; online 31 October 2009)

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[Xue, S. J., Zhang, A. D. & Wang, H. T. (1993). Chemical Reagents, 15, 181.]); Hemamalini et al. (2005[Hemamalini, M., Mu­thiah, P. T., Rychlewska, U. & Plutecka, A. (2005). Acta Cryst. C61, o95-o97.]).

[Scheme 1]

Experimental

Crystal data
  • C6H10N3+·C2H2ClO2

  • Mr = 217.66

  • Triclinic, [P \overline 1]

  • 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)

  • Rint = 0.028

Refinement
  • R[F2 > 2σ(F2)] = 0.055

  • wR(F2) = 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

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N1—H1A⋯N3i 0.86 2.14 2.999 (3) 177
N1—H1B⋯O3ii 0.86 1.98 2.830 (3) 173
N2—H2A⋯O4ii 0.86 1.74 2.593 (3) 175
N4—H4A⋯N6iii 0.86 2.19 3.046 (3) 175
N4—H4B⋯O1iv 0.86 2.00 2.851 (3) 173
N5—H5A⋯O2iv 0.86 1.75 2.606 (3) 174
C1—H1C⋯O4ii 0.96 2.56 3.355 (4) 140
C7—H7A⋯O2iv 0.96 2.57 3.355 (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.

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.]); software used to prepare material for publication: SHELXTL.

Supporting information


Comment top

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.

Related literature top

For background o pyrimidine derivatives, see: Xue et al. (1993); Hemamalini et al. (2005).

Experimental top

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 top

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).

Structure description top

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.

For background o pyrimidine derivatives, see: Xue et al. (1993); Hemamalini et al. (2005).

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); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

Figures top
[Figure 1] Fig. 1. The molecular structure of (I) showing 30% probability displacement ellipsoids.
2-Amino-4,6-dimethylpyrimidinium chloroacetate top
Crystal data top
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 top
Bruker SMART CCD
diffractometer
3452 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.028
Graphite monochromatorθmax = 27.5°, θmin = 3.2°
ω scansh = 55
10303 measured reflectionsk = 1515
4761 independent reflectionsl = 2525
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)] = 0.055Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.195H-atom parameters constrained
S = 1.08 w = 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
Crystal data top
C6H10N3+·C2H2ClO2γ = 91.15 (3)°
Mr = 217.66V = 1057.1 (4) Å3
Triclinic, P1Z = 4
a = 4.4560 (9) ÅMo Kα radiation
b = 12.302 (3) ŵ = 0.34 mm1
c = 19.441 (4) ÅT = 293 K
α = 92.90 (3)°0.20 × 0.15 × 0.11 mm
β = 96.53 (3)°
Data collection top
Bruker SMART CCD
diffractometer
3452 reflections with I > 2σ(I)
10303 measured reflectionsRint = 0.028
4761 independent reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0550 restraints
wR(F2) = 0.195H-atom parameters constrained
S = 1.08Δρmax = 0.42 e Å3
4761 reflectionsΔρmin = 0.43 e Å3
253 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
Cl10.92264 (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)
H15A0.73200.02430.05960.074*
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)
N40.0552 (6)0.15065 (18)0.47176 (12)0.0610 (6)
H4A0.10120.10750.50260.073*
H4B0.11450.21670.47290.073*
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)
H11A0.38410.17210.41180.103*
H11B0.67150.14000.37700.103*
H11C0.37190.17680.33080.103*
N20.0615 (5)0.69331 (16)0.07225 (10)0.0457 (5)
H2A0.10880.74700.04860.055*
N30.2359 (5)0.53279 (17)0.07940 (11)0.0489 (5)
C60.0956 (6)0.5215 (2)0.14272 (13)0.0493 (6)
N10.2951 (5)0.63311 (18)0.01745 (11)0.0566 (6)
H1A0.43490.58760.03540.068*
H1B0.24640.68780.04010.068*
C40.1547 (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*
C50.1883 (8)0.4234 (2)0.17923 (16)0.0657 (8)
H5B0.34220.38210.14990.099*
H5C0.26540.44660.22160.099*
H5D0.01620.37880.18960.099*
Atomic displacement parameters (Å2) top
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, º) top
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, º) top
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) x1, y+1, z; (ii) x+1, y+1, z; (iii) x, y, z+1; (iv) x1, y, z.

Experimental details

Crystal data
Chemical formulaC6H10N3+·C2H2ClO2
Mr217.66
Crystal system, space groupTriclinic, P1
Temperature (K)293
a, b, c (Å)4.4560 (9), 12.302 (3), 19.441 (4)
α, β, γ (°)92.90 (3), 96.53 (3), 91.15 (3)
V3)1057.1 (4)
Z4
Radiation typeMo Kα
µ (mm1)0.34
Crystal size (mm)0.20 × 0.15 × 0.11
Data collection
DiffractometerBruker SMART CCD
Absorption correction
No. of measured, independent and
observed [I > 2σ(I)] reflections
10303, 4761, 3452
Rint0.028
(sin θ/λ)max1)0.649
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.055, 0.195, 1.08
No. of reflections4761
No. of parameters253
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.42, 0.43

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

Hydrogen-bond geometry (Å, º) top
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) x1, y+1, z; (ii) x+1, y+1, z; (iii) x, y, z+1; (iv) x1, y, z.
 

References

First citationBruker (1997). SMART and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.  Google Scholar
First citationHemamalini, M., Mu&shy;thiah, 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. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationXue, S. J., Zhang, A. D. & Wang, H. T. (1993). Chemical Reagents, 15, 181.  Google Scholar

This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Follow Acta Cryst. E
Sign up for e-alerts
Follow Acta Cryst. on Twitter
Follow us on facebook
Sign up for RSS feeds