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

Lin, C.-H.; Liu, N.-S.

doi:10.1107/S1600536812021496

organic compounds

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ISSN: 2056-9890

Volume 68| Part 6| June 2012| Page o1898

doi:10.1107/S1600536812021496

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

Cui-Hua Lin ^a ^* and Nai-Sheng Liu ^b

^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 ). 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

Crystal data

C₆H₁₀N₃O₂⁺·C₂HCl₂O₂⁻
M_r = 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 ) T_min = 0.795, T_max = 0.835
4710 measured reflections
2173 independent reflections
1806 reflections with I > 2σ(I)
R_int = 0.026

Refinement

R[F² > 2σ(F²)] = 0.054
wR(F²) = 0.200
S = 1.09
2173 reflections
156 parameters
H-atom parameters constrained
Δρ_max = 0.45 e Å⁻³
Δρ_min = −0.39 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	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 ); cell refinement: SAINT (Bruker, 1997); data reduction: SAINT; 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.

Supporting information

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536812021496/lh5473sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536812021496/lh5473Isup2.hkl

Supporting information file. DOI: 10.1107/S1600536812021496/lh5473Isup3.cml

checkCIF report

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.

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

	Fig. 1. The structure of the title compound showing 30% probability displacement ellipsoids.
	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⁺·C₂HCl₂O₂⁻	Z = 2
M_r = 284.10	F(000) = 292
Triclinic, P1	D_x = 1.533 Mg m⁻³
Hall symbol: -P 1	Mo Kα radiation, λ = 0.71073 Å
a = 6.8502 (14) Å	Cell parameters from 3794 reflections
b = 8.6667 (17) Å	θ = 3.5–27.5°
c = 11.255 (2) Å	µ = 0.53 mm⁻¹
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 tube	1806 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.026
ϕ and ω scans	θ_max = 25.0°, θ_min = 3.5°
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)	h = −8→7
T_min = 0.795, T_max = 0.835	k = −10→10
4710 measured reflections	l = −13→13

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F² > 2σ(F²)] = 0.054	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.200	H-atom parameters constrained
S = 1.09	w = 1/[σ²(F_o²) + (0.1265P)² + 0.3628P] where P = (F_o² + 2F_c²)/3
2173 reflections	(Δ/σ)_max < 0.001
156 parameters	Δρ_max = 0.45 e Å⁻³
0 restraints	Δρ_min = −0.39 e Å⁻³

Crystal data top

C₆H₁₀N₃O₂⁺·C₂HCl₂O₂⁻	γ = 85.970 (2)°
M_r = 284.10	V = 615.6 (2) Å³
Triclinic, P1	Z = 2
a = 6.8502 (14) Å	Mo Kα radiation
b = 8.6667 (17) Å	µ = 0.53 mm⁻¹
c = 11.255 (2) Å	T = 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)
T_min = 0.795, T_max = 0.835	R_int = 0.026
4710 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.054	0 restraints
wR(F²) = 0.200	H-atom parameters constrained
S = 1.09	Δρ_max = 0.45 e Å⁻³
2173 reflections	Δρ_min = −0.39 e Å⁻³
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

	x	y	z	U_iso*/U_eq
Cl1	0.11057 (16)	0.15674 (13)	0.03526 (9)	0.0641 (4)
Cl2	0.44050 (14)	0.24515 (19)	0.14101 (11)	0.0804 (5)
N1	0.5368 (4)	0.7901 (3)	0.4560 (2)	0.0365 (6)
N2	0.3706 (3)	0.6207 (3)	0.6442 (2)	0.0336 (6)
H2	0.2667	0.6043	0.6924	0.040*
N3	0.2252 (4)	0.8660 (3)	0.5053 (3)	0.0450 (7)
H3A	0.2264	0.9542	0.4356	0.054*
H3B	0.1235	0.8474	0.5555	0.054*
O1	0.4900 (3)	0.3802 (3)	0.7880 (2)	0.0487 (6)
O2	0.8446 (3)	0.7020 (3)	0.4156 (2)	0.0530 (7)
O3	0.0938 (4)	0.1810 (3)	0.3189 (2)	0.0511 (7)
O4	−0.0703 (4)	0.4064 (3)	0.1873 (2)	0.0653 (8)
C1	0.3790 (4)	0.7598 (3)	0.5350 (3)	0.0332 (6)
C2	0.5248 (4)	0.5073 (4)	0.6779 (3)	0.0367 (7)
C3	0.6887 (4)	0.5305 (4)	0.6026 (3)	0.0389 (7)
H3	0.7962	0.4540	0.6232	0.047*
C4	0.6855 (4)	0.6780 (4)	0.4910 (3)	0.0384 (7)
C5	0.6408 (6)	0.2493 (5)	0.8325 (4)	0.0651 (11)
H5A	0.6728	0.2056	0.7670	0.098*
H5B	0.5956	0.1614	0.9089	0.098*
H5C	0.7551	0.2931	0.8514	0.098*
C6	0.8456 (6)	0.8491 (5)	0.3002 (4)	0.0614 (10)
H6A	0.7688	0.8339	0.2367	0.092*
H6B	0.9777	0.8690	0.2682	0.092*
H6C	0.7910	0.9432	0.3181	0.092*
C7	0.0616 (4)	0.2935 (4)	0.2130 (3)	0.0378 (7)
C8	0.1932 (4)	0.2995 (4)	0.0968 (3)	0.0394 (7)
H8	0.1832	0.4127	0.0302	0.047*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Cl1	0.0840 (8)	0.0668 (7)	0.0495 (6)	−0.0127 (5)	−0.0068 (5)	−0.0292 (5)
Cl2	0.0425 (6)	0.1419 (12)	0.0752 (7)	0.0083 (6)	−0.0034 (5)	−0.0639 (8)
N1	0.0382 (13)	0.0356 (13)	0.0345 (13)	−0.0043 (10)	0.0020 (10)	−0.0121 (10)
N2	0.0329 (12)	0.0350 (13)	0.0292 (12)	0.0017 (10)	0.0014 (9)	−0.0089 (10)
N3	0.0435 (14)	0.0386 (14)	0.0392 (14)	0.0085 (11)	0.0022 (11)	−0.0016 (11)
O1	0.0530 (13)	0.0411 (12)	0.0371 (12)	0.0138 (10)	0.0023 (10)	−0.0015 (9)
O2	0.0392 (12)	0.0607 (16)	0.0543 (14)	−0.0042 (11)	0.0145 (10)	−0.0181 (12)
O3	0.0588 (15)	0.0438 (13)	0.0337 (12)	0.0107 (10)	0.0032 (10)	0.0012 (10)
O4	0.0660 (16)	0.0588 (16)	0.0430 (13)	0.0296 (13)	0.0131 (12)	0.0046 (11)
C1	0.0372 (15)	0.0319 (14)	0.0311 (14)	−0.0031 (11)	−0.0025 (11)	−0.0124 (11)
C2	0.0424 (16)	0.0340 (15)	0.0334 (14)	0.0028 (12)	−0.0045 (12)	−0.0128 (12)
C3	0.0330 (15)	0.0410 (16)	0.0416 (16)	0.0042 (12)	−0.0039 (12)	−0.0152 (13)
C4	0.0348 (15)	0.0445 (17)	0.0396 (16)	−0.0071 (13)	0.0019 (12)	−0.0197 (13)
C5	0.070 (2)	0.059 (2)	0.0451 (19)	0.0295 (19)	−0.0043 (18)	−0.0025 (17)
C6	0.057 (2)	0.068 (3)	0.052 (2)	−0.0141 (18)	0.0182 (17)	−0.0157 (18)
C7	0.0431 (16)	0.0315 (15)	0.0340 (15)	0.0008 (12)	0.0002 (12)	−0.0076 (12)
C8	0.0445 (17)	0.0375 (16)	0.0339 (15)	0.0009 (12)	0.0003 (12)	−0.0116 (12)

Geometric parameters (Å, º) top

Cl1—C8	1.767 (3)	O3—C7	1.234 (4)
Cl2—C8	1.768 (3)	O4—C7	1.241 (4)
N1—C4	1.320 (4)	C2—C3	1.353 (4)
N1—C1	1.342 (4)	C3—C4	1.408 (4)
N2—C2	1.354 (4)	C3—H3	0.9300
N2—C1	1.355 (4)	C5—H5A	0.9600
N2—H2	0.8600	C5—H5B	0.9600
N3—C1	1.315 (4)	C5—H5C	0.9600
N3—H3A	0.8600	C6—H6A	0.9600
N3—H3B	0.8600	C6—H6B	0.9600
O1—C2	1.330 (4)	C6—H6C	0.9600
O1—C5	1.433 (4)	C7—C8	1.539 (4)
O2—C4	1.327 (4)	C8—H8	0.9800
O2—C6	1.430 (5)

C4—N1—C1	116.5 (2)	O1—C5—H5A	109.5
C2—N2—C1	120.4 (2)	O1—C5—H5B	109.5
C2—N2—H2	119.8	H5A—C5—H5B	109.5
C1—N2—H2	119.8	O1—C5—H5C	109.5
C1—N3—H3A	120.0	H5A—C5—H5C	109.5
C1—N3—H3B	120.0	H5B—C5—H5C	109.5
H3A—N3—H3B	120.0	O2—C6—H6A	109.5
C2—O1—C5	117.1 (3)	O2—C6—H6B	109.5
C4—O2—C6	117.9 (3)	H6A—C6—H6B	109.5
N3—C1—N1	119.5 (3)	O2—C6—H6C	109.5
N3—C1—N2	118.4 (3)	H6A—C6—H6C	109.5
N1—C1—N2	122.1 (3)	H6B—C6—H6C	109.5
O1—C2—C3	127.8 (3)	O3—C7—O4	126.9 (3)
O1—C2—N2	111.7 (3)	O3—C7—C8	119.0 (3)
C3—C2—N2	120.5 (3)	O4—C7—C8	114.1 (3)
C2—C3—C4	115.5 (3)	C7—C8—Cl1	108.5 (2)
C2—C3—H3	122.2	C7—C8—Cl2	111.4 (2)
C4—C3—H3	122.2	Cl1—C8—Cl2	109.21 (17)
N1—C4—O2	118.7 (3)	C7—C8—H8	109.3
N1—C4—C3	125.0 (3)	Cl1—C8—H8	109.3
O2—C4—C3	116.3 (3)	Cl2—C8—H8	109.3

C4—N1—C1—N3	−179.5 (3)	C1—N1—C4—O2	179.6 (3)
C4—N1—C1—N2	−0.8 (4)	C1—N1—C4—C3	0.9 (4)
C2—N2—C1—N3	179.4 (3)	C6—O2—C4—N1	0.1 (4)
C2—N2—C1—N1	0.7 (4)	C6—O2—C4—C3	179.0 (3)
C5—O1—C2—C3	−1.4 (5)	C2—C3—C4—N1	−0.7 (5)
C5—O1—C2—N2	178.5 (3)	C2—C3—C4—O2	−179.5 (3)
C1—N2—C2—O1	179.6 (3)	O3—C7—C8—Cl1	81.6 (3)
C1—N2—C2—C3	−0.5 (4)	O4—C7—C8—Cl1	−97.9 (3)
O1—C2—C3—C4	−179.6 (3)	O3—C7—C8—Cl2	−38.6 (4)
N2—C2—C3—C4	0.5 (4)	O4—C7—C8—Cl2	141.9 (3)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	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.

Experimental details

Crystal data
Chemical formula	C₆H₁₀N₃O₂⁺·C₂HCl₂O₂⁻
M_r	284.10
Crystal system, space group	Triclinic, 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)
V (Å³)	615.6 (2)
Z	2
Radiation type	Mo Kα
µ (mm⁻¹)	0.53
Crystal size (mm)	0.45 × 0.43 × 0.35

Data collection
Diffractometer	Bruker SMART CCD diffractometer
Absorption correction	Multi-scan (SADABS; Sheldrick, 1996)
T_min, T_max	0.795, 0.835
No. of measured, independent and observed [I > 2σ(I)] reflections	4710, 2173, 1806
R_int	0.026
(sin θ/λ)_max (Å⁻¹)	0.595

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.054, 0.200, 1.09
No. of reflections	2173
No. of parameters	156
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	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···A	D—H	H···A	D···A	D—H···A
N3—H3B···O3ⁱ	0.86	1.97	2.822 (3)	173.1
N3—H3A···O3ⁱⁱ	0.86	2.07	2.848 (3)	149.4
N2—H2···O4ⁱ	0.86	1.85	2.692 (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

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