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

Abstract

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].

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,

• a = 3.9110 (8) Å

• b = 10.136 (2) Å

• c = 9.848 (2) Å

• β = 98.71 (3)°

• V = 385.89 (13) ų

• 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[F ² > 2σ(F ²)] = 0.046

• wR(F ²) = 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)

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.

Supplementary Material

CCDC reference: 1013300

Additional supporting information: crystallographic information; 3D view; checkCIF report

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) .

supplementary crystallographic information

S1. Comment

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.

S2. Experimental

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.

S3. Refinement

H atoms were positioned geometrically with N—H = 0.86 and C—H = 0.93–0.96 Å, and refined in riding mode, U_iso(H) = 1.5U_eq(C) for methyl H atoms and 1.2U_eq(C,N) for the others.

Figures

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).

Crystal data

C6H6ClN3O2	F(000) = 192
Mr = 187.59	Dx = 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

Enraf–Nonius CAD-4 diffractometer	Rint = 0.041
Radiation source: fine-focus sealed tube	θmax = 25.4°, θmin = 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

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(Fo2) + (0.065P)2] where P = (Fo2 + 2Fc2)/3
S = 1.01	(Δ/σ)max < 0.001
817 reflections	Δρmax = 0.25 e Å−3
109 parameters	Δρmin = −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)

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 (Ų)

	x	y	z	Uiso*/Ueq
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 (Ų)

	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)

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)

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.