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

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].

Key indicators

• Single-crystal X-ray study
• T = 293 K
• Mean [sigma](C-C) = 0.007 Å
• R factor = 0.046
• wR factor = 0.109
• Data-to-parameter ratio = 7.5

checkCIF/PLATON results

No syntax errors found



Alert level B
PLAT915_ALERT_3_B Low Friedel Pair Coverage ......................         15 %

Alert level C
PLAT089_ALERT_3_C Poor Data / Parameter Ratio (Zmax < 18) ........       6.52 Note
PLAT250_ALERT_2_C Large U3/U1 Ratio for Average U(i,j) Tensor ....        2.4 Note
PLAT340_ALERT_3_C Low Bond Precision on  C-C Bonds ...............     0.0073 Ang.

Alert level G
PLAT005_ALERT_5_G No _iucr_refine_instructions_details  in the CIF     Please Do !
PLAT007_ALERT_5_G Number of Unrefined Donor-H Atoms ..............          2 Why ?
PLAT199_ALERT_1_G Reported _cell_measurement_temperature ..... (K)        293 Check
PLAT200_ALERT_1_G Reported   _diffrn_ambient_temperature ..... (K)        293 Check
PLAT912_ALERT_4_G Missing # of FCF Reflections Above STh/L=  0.600          2 Note

   0 ALERT level A = Most likely a serious problem - resolve or explain
   1 ALERT level B = A potentially serious problem, consider carefully
   3 ALERT level C = Check. Ensure it is not caused by an omission or oversight
   5 ALERT level G = General information/check it is not something unexpected

   2 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   1 ALERT type 2 Indicator that the structure model may be wrong or deficient
   3 ALERT type 3 Indicator that the structure quality may be low
   1 ALERT type 4 Improvement, methodology, query or suggestion
   2 ALERT type 5 Informative message, check

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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.

Related literature

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

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.

Computing details

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

	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

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) Å^3	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 F^2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F^2 > 2σ(F^2)] = 0.046	H-atom parameters constrained
wR(F^2) = 0.109	w = 1/[σ^2(Fo^2) + (0.065P)^2] where P = (Fo^2 + 2Fc^2)/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)

	U^11	U^22	U^33	U^12	U^13	U^23
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···N2^i	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.