Methyl 4-amino-2-chloro­pyrimidine-5-carboxyl­ate

Wu, Y.-M.

doi:10.1107/S1600536814016080

organic compounds

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ISSN: 2056-9890

Volume 70| Part 8| August 2014| Page o869

doi:10.1107/S1600536814016080

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Methyl 4-amino-2-chloropyrimidine-5-carboxylate

Ya-Ming Wu ^a ^*

^aDepartment of Applied Chemistry, Nanjing College of Chemical Technology, Nanjing 210048, People's Republic of China
^*Correspondence e-mail: adsony05@163.com

Edited by D.-J. Xu, Zhejiang University (Yuquan Campus), China (Received 12 June 2014; accepted 10 July 2014; online 17 July 2014)

In the title compound, C₆H₆ClN₃O₂, all non-H atoms are approximately coplanar [maximum deviation = 0.012 (4) Å]; an intramolecular N—H⋯O hydrogen bond occurs between the amino group and the carbonyl group. In the crystal, molecules are linked by N—H⋯N hydrogen bonds into supramolecular chains propagated along [101].

Keywords: crystal structure.

CCDC reference: 1013300

Related literature

For related structures, see: He & Kang (2006 ); He et al. (2007 ). For the synthesis, see: Ballard & Johnson (1942 ).

Experimental

Crystal data

C₆H₆ClN₃O₂
M_r = 187.59
Monoclinic, P c
a = 3.9110 (8) Å
b = 10.136 (2) Å
c = 9.848 (2) Å
β = 98.71 (3)°
V = 385.89 (13) Å³
Z = 2
Mo Kα radiation
μ = 0.45 mm⁻¹
T = 293 K
0.20 × 0.20 × 0.15 mm

Data collection

Enraf–Nonius CAD-4 diffractometer
1474 measured reflections
817 independent reflections
673 reflections with I > 2σ(I)
R_int = 0.041
3 standard reflections every 200 reflections intensity decay: 1%

Refinement

R[F² > 2σ(F²)] = 0.046
wR(F²) = 0.109
S = 1.01
817 reflections
109 parameters
2 restraints
H-atom parameters constrained
Δρ_max = 0.25 e Å⁻³
Δρ_min = −0.36 e Å⁻³
Absolute structure: Flack (1983 ), 106 Friedel pairs
Absolute structure parameter: 0.07 (17)

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N3—H3A⋯N2ⁱ	0.86	2.10	2.955 (7)	171
N3—H3B⋯O2	0.86	2.11	2.745 (7)	130
Symmetry code: (i) $[x+1, -y, z+{\script{1\over 2}}]$ .

Data collection: CAD-4 EXPRESS (Enraf–Nonius, 1994 ); cell refinement: CAD-4 EXPRESS; data reduction: XCAD4 (Harms & Wocadlo, 1995 ); program(s) used to solve structure: SHELXTL (Sheldrick, 2008 ); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL.

Supporting information

CCDC reference: 1013300

Crystal structure: contains datablocks I, New_Global_Publ_Block. DOI: 10.1107/S1600536814016080/xu5799sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536814016080/xu5799Isup2.hkl

Supporting information file. DOI: 10.1107/S1600536814016080/xu5799Isup3.cml

checkCIF report

Comment top

The title compound,(I), is an intermediate for preparation of tuberculosis. We herein report its crystal structure.

The molecular structure of (I) is shown in Fig. 1. The bond lengths and angles are within normal ranges (He & Kang, 2006; He et al., 2007). The pyrimidine ring is almost planar.

In the crystal, molecules are linked each other to form chains framework via intermolecular N—H···N hydrogen bonds, which with intramolecular N—H···O hydrogen bonds may be effective in the stabilization of the crystal structure.

Related literature top

For related structures, see: He & Kang (2006); He et al. (2007). For the synthesis, see: Ballard & Johnson (1942).

Experimental top

The title compound was synthesized according to the reported procedure (Ballard & Johnson, 1942). Crystals suitable for X-ray analysis were obtained by dissolving it (0.5 g) in dichloromethane (50 ml) and evaporating the solvent slowly at room temperature for about 5 d.

Computing details top

Data collection: CAD-4 EXPRESS (Enraf–Nonius, 1994); cell refinement: CAD-4 EXPRESS (Enraf–Nonius, 1994); data reduction: XCAD4 (Harms & Wocadlo, 1995); program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXTL (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

Figures top

	Fig. 1. The molecular structure of (I), with the atom-numbering scheme. Displacement ellipsoids are drawn at the 50% probability level.
	Fig. 2. A packing diagram of (I).

Methyl 4-amino-2-chloropyrimidine-5-carboxylate top

Crystal data top

C₆H₆ClN₃O₂	F(000) = 192
M_r = 187.59	D_x = 1.614 Mg m⁻³
Monoclinic, Pc	Melting point: 433 K
Hall symbol: p -2yc	Mo Kα radiation, λ = 0.71073 Å
a = 3.9110 (8) Å	Cell parameters from 25 reflections
b = 10.136 (2) Å	θ = 9–13°
c = 9.848 (2) Å	µ = 0.45 mm⁻¹
β = 98.71 (3)°	T = 293 K
V = 385.89 (13) Å³	Block, colorless
Z = 2	0.20 × 0.20 × 0.15 mm

Data collection top

Enraf–Nonius CAD-4 diffractometer	R_int = 0.041
Radiation source: fine-focus sealed tube	θ_max = 25.4°, θ_min = 2.0°
Graphite monochromator	h = 0→4
ω/2θ scans	k = −12→12
1474 measured reflections	l = −11→11
817 independent reflections	3 standard reflections every 200 reflections
673 reflections with I > 2σ(I)	intensity decay: 1%

Refinement top

Refinement on F²	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F² > 2σ(F²)] = 0.046	H-atom parameters constrained
wR(F²) = 0.109	w = 1/[σ²(F_o²) + (0.065P)²] where P = (F_o² + 2F_c²)/3
S = 1.01	(Δ/σ)_max < 0.001
817 reflections	Δρ_max = 0.25 e Å⁻³
109 parameters	Δρ_min = −0.36 e Å⁻³
2 restraints	Absolute structure: Flack (1983), 106 Friedel pairs
Primary atom site location: structure-invariant direct methods	Absolute structure parameter: 0.07 (17)

Crystal data top

C₆H₆ClN₃O₂	V = 385.89 (13) Å³
M_r = 187.59	Z = 2
Monoclinic, Pc	Mo Kα radiation
a = 3.9110 (8) Å	µ = 0.45 mm⁻¹
b = 10.136 (2) Å	T = 293 K
c = 9.848 (2) Å	0.20 × 0.20 × 0.15 mm
β = 98.71 (3)°

Data collection top

Enraf–Nonius CAD-4 diffractometer	R_int = 0.041
1474 measured reflections	3 standard reflections every 200 reflections
817 independent reflections	intensity decay: 1%
673 reflections with I > 2σ(I)

Refinement top

R[F² > 2σ(F²)] = 0.046	H-atom parameters constrained
wR(F²) = 0.109	Δρ_max = 0.25 e Å⁻³
S = 1.01	Δρ_min = −0.36 e Å⁻³
817 reflections	Absolute structure: Flack (1983), 106 Friedel pairs
109 parameters	Absolute structure parameter: 0.07 (17)
2 restraints

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
Cl	1.0210 (5)	−0.25325 (18)	0.5060 (2)	0.0602 (4)
O1	0.6389 (12)	0.3421 (3)	0.3059 (4)	0.0559 (11)
C1	1.1205 (14)	0.1186 (6)	0.5586 (5)	0.0363 (14)
N1	1.1550 (12)	−0.0104 (6)	0.5759 (4)	0.0411 (11)
O2	0.9976 (15)	0.3988 (3)	0.4968 (5)	0.0597 (12)
C2	0.9749 (16)	−0.0851 (5)	0.4819 (5)	0.0399 (13)
N2	0.7645 (13)	−0.0485 (4)	0.3675 (5)	0.0423 (12)
N3	1.3017 (15)	0.1949 (5)	0.6544 (5)	0.0480 (12)
H3A	1.4322	0.1594	0.7229	0.058*
H3B	1.2878	0.2793	0.6476	0.058*
C3	0.7362 (14)	0.0804 (4)	0.3525 (5)	0.0381 (13)
H3C	0.5923	0.1118	0.2754	0.046*
C4	0.9020 (14)	0.1715 (5)	0.4414 (5)	0.0339 (12)
C5	0.8591 (15)	0.3139 (6)	0.4214 (6)	0.0409 (13)
C6	0.576 (2)	0.4789 (6)	0.2751 (8)	0.0626 (18)
H6A	0.4174	0.4871	0.1911	0.094*
H6B	0.7904	0.5215	0.2650	0.094*
H6C	0.4795	0.5199	0.3485	0.094*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Cl	0.0703 (9)	0.0469 (7)	0.0553 (8)	−0.0003 (8)	−0.0160 (6)	0.0032 (7)
O1	0.067 (3)	0.051 (2)	0.040 (2)	0.008 (2)	−0.023 (2)	0.000 (2)
C1	0.031 (3)	0.046 (3)	0.029 (3)	−0.002 (3)	−0.006 (2)	−0.003 (2)
N1	0.041 (3)	0.052 (3)	0.026 (2)	0.002 (2)	−0.008 (2)	0.000 (2)
O2	0.070 (3)	0.046 (2)	0.053 (2)	−0.008 (3)	−0.023 (2)	−0.007 (2)
C2	0.039 (3)	0.050 (3)	0.030 (3)	0.003 (3)	0.002 (3)	−0.003 (2)
N2	0.041 (3)	0.051 (3)	0.031 (2)	−0.003 (2)	−0.008 (2)	−0.003 (2)
N3	0.057 (3)	0.049 (2)	0.031 (2)	−0.004 (3)	−0.016 (2)	−0.004 (2)
C3	0.039 (3)	0.046 (3)	0.026 (3)	0.001 (3)	−0.006 (2)	−0.003 (3)
C4	0.032 (3)	0.040 (3)	0.028 (3)	0.006 (2)	−0.003 (2)	0.006 (2)
C5	0.040 (3)	0.048 (3)	0.032 (3)	0.004 (3)	−0.005 (2)	0.004 (2)
C6	0.060 (4)	0.051 (3)	0.067 (4)	0.008 (3)	−0.023 (3)	0.012 (3)

Geometric parameters (Å, º) top

Cl—C2	1.726 (5)	N2—C3	1.318 (6)
O1—C5	1.350 (7)	N3—H3A	0.8600
O1—C6	1.433 (7)	N3—H3B	0.8600
C1—N1	1.324 (8)	C3—C4	1.367 (7)
C1—N3	1.337 (7)	C3—H3C	0.9300
C1—C4	1.432 (7)	C4—C5	1.464 (7)
N1—C2	1.315 (7)	C6—H6A	0.9600
O2—C5	1.210 (7)	C6—H6B	0.9600
C2—N2	1.343 (8)	C6—H6C	0.9600

C5—O1—C6	116.7 (5)	C4—C3—H3C	117.5
N1—C1—N3	116.6 (5)	C3—C4—C1	115.5 (4)
N1—C1—C4	120.7 (5)	C3—C4—C5	123.1 (4)
N3—C1—C4	122.7 (5)	C1—C4—C5	121.3 (4)
C2—N1—C1	116.4 (5)	O2—C5—O1	122.4 (5)
N1—C2—N2	128.8 (5)	O2—C5—C4	126.0 (5)
N1—C2—Cl	116.0 (4)	O1—C5—C4	111.6 (4)
N2—C2—Cl	115.2 (4)	O1—C6—H6A	109.5
C3—N2—C2	113.5 (5)	O1—C6—H6B	109.5
C1—N3—H3A	120.0	H6A—C6—H6B	109.5
C1—N3—H3B	120.0	O1—C6—H6C	109.5
H3A—N3—H3B	120.0	H6A—C6—H6C	109.5
N2—C3—C4	125.0 (5)	H6B—C6—H6C	109.5
N2—C3—H3C	117.5

N3—C1—N1—C2	179.6 (6)	N3—C1—C4—C3	179.6 (6)
C4—C1—N1—C2	−1.1 (9)	N1—C1—C4—C5	179.5 (5)
C1—N1—C2—N2	1.9 (10)	N3—C1—C4—C5	−1.3 (8)
C1—N1—C2—Cl	−179.8 (4)	C6—O1—C5—O2	0.4 (10)
N1—C2—N2—C3	−1.5 (10)	C6—O1—C5—C4	−179.9 (6)
Cl—C2—N2—C3	−179.9 (5)	C3—C4—C5—O2	179.7 (7)
C2—N2—C3—C4	0.5 (8)	C1—C4—C5—O2	0.6 (9)
N2—C3—C4—C1	0.0 (8)	C3—C4—C5—O1	0.0 (8)
N2—C3—C4—C5	−179.2 (6)	C1—C4—C5—O1	−179.1 (6)
N1—C1—C4—C3	0.4 (8)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N3—H3A···N2ⁱ	0.86	2.10	2.955 (7)	171
N3—H3B···O2	0.86	2.11	2.745 (7)	130

Symmetry code: (i) x+1, −y, z+1/2.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N3—H3A···N2ⁱ	0.86	2.10	2.955 (7)	171
N3—H3B···O2	0.86	2.11	2.745 (7)	130

Symmetry code: (i) x+1, −y, z+1/2.

Acknowledgements

Diffraction data were collected at the Center of Testing and Analysis, Nanjing University, China.

References

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