4-Chloro-6-meth­oxy­pyrimidin-2-amine

Abstract

The title compound, C₅H₆ClN₃O, is essentially planar with a maximum deviation of 0.0256 (11) Å for all non-H atoms. In the crystal, adjacent mol­ecules are linked by a pair of N—H⋯N hydrogen bonds, forming an inversion dimer with an R ₂ ²(8) ring motif. The dimers are further linked via N—H⋯O hydrogen bonds into an undulating sheet structure parallel to the bc plane.

Related literature  

For the biological activity of pyrimidine and amino­pyrimidine derivatives, see: Hunt et al. (1980 ▶); Baker & Santi (1965 ▶). For related structures, see: Schwalbe & Williams (1982 ▶); Hu et al. (2002 ▶); Chinnakali et al. (1999 ▶); Skovsgaard & Bond (2009 ▶). For hydrogen-bond motifs, see: Bernstein et al. (1995 ▶). For bond-length data, see: Allen et al. (1987 ▶). For stability of the temperature controller used for the data collection, see: Cosier & Glazer (1986 ▶).

Experimental  

Crystal data  

• C₅H₆ClN₃O

• M _r = 159.58

• Monoclinic,

• a = 3.7683 (2) Å

• b = 16.4455 (2) Å

• c = 10.7867 (2) Å

• β = 94.550 (1)°

• V = 666.36 (4) ų

• Z = 4

• Mo Kα radiation

• μ = 0.50 mm⁻¹

• T = 100 K

• 0.49 × 0.28 × 0.21 mm

Data collection  

• Bruker SMART APEXII CCD area-detector diffractometer

• Absorption correction: multi-scan (SADABS; Bruker, 2009 ▶) T _min = 0.791, T _max = 0.904

• 9524 measured reflections

• 2436 independent reflections

• 2266 reflections with I > 2σ(I)

• R _int = 0.016

Refinement  

• R[F ² > 2σ(F ²)] = 0.027

• wR(F ²) = 0.070

• S = 1.06

• 2436 reflections

• 100 parameters

• H atoms treated by a mixture of independent and constrained refinement

• Δρ_max = 0.67 e Å⁻³

• Δρ_min = −0.26 e Å⁻³

Data collection: APEX2 (Bruker, 2009 ▶); cell refinement: SAINT (Bruker, 2009 ▶); data reduction: SAINT; 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 and PLATON (Spek, 2009 ▶).

Supplementary Material

Additional supplementary materials: 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—H2N3⋯O1i	0.828 (16)	2.251 (17)	3.0699 (11)	170.1 (15)
N3—H1N3⋯N1ii	0.850 (16)	2.183 (16)	3.0335 (12)	180 (2)

Symmetry codes: (i) ; (ii) .

supplementary crystallographic information

Comment

Pyrimidine and aminopyrimidine derivatives are biologically important compounds as they occur in nature as components of nucleic acids. Some aminopyrimidine derivatives are used as antifolate drugs (Hunt et al., 1980; Baker & Santi, 1965). The crystal structures of aminopyrimidine derivatives (Schwalbe & Williams, 1982), aminopyrimidine carboxylates (Hu et al., 2002) and co-crystal structures (Chinnakali et al., 1999; Skovsgaard & Bond, 2009) have been reported. In order to study some interesting hydrogen bonding interactions, the synthesis and structure of the title compound, (I), is presented here.

The title compound (Fig. 1) is essentially planar, with atom C5 deviating a maximum of 0.0256 (11) Å from a mean plane of non-H atoms. The bond lengths (Allen et al., 1987) and angles are normal. In the crystal structure (Fig. 2), molecules are linked by a pair of N3—H1N3···N1ⁱⁱ hydrogen bonds (symmetry code in Table 1) into an inversion dimer, forming an R₂²(8) (Bernstein et al., 1995) ring motif. These molecules are self-assembled via N3—H2N3···O1ⁱ hydrogen bonds (graph-set notation C(6); symmetry code in Table 1), which interconnect the dimers resulting in a wavy sheet parallel to the bc plane.

Experimental

A hot ethanol solutions (20 ml) of 2-amino-4-chloro-6-methoxypyrimidine (36 mg, Aldrich) was warmed over a heating magnetic stirrer hotplate for a few minutes. The resulting solution was allowed to cool slowly at room temperature. Single crystals of the title compound (I) appeared from the mother liquor after a few days.

Refinement

N-bound H atoms were located in a difference Fourier maps and refined freely [N—H = 0.828 (16) and 0.850 (16) Å]. The remaining H atoms were positioned geometrically (C–H = 0.95–0.98 Å) and were refined using a riding model, with U_iso(H) = 1.2U_eq(C) or 1.5U_eq(methyl C). A rotating group model was used for the methyl group. Two outliers were omitted (1 8 14 and 0 1 2) in the final refinement.

Figures

Fig. 1.

The molecular structure of the title compound with atom labels with 50% probability displacement ellipsoids.

Fig. 2.

The crystal packing of the title compound. The H atoms not involved in the intermolecular interactions (dashed lines) have been omitted for clarity.

Crystal data

C5H6ClN3O	F(000) = 328
Mr = 159.58	Dx = 1.591 Mg m−3
Monoclinic, P21/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 6060 reflections
a = 3.7683 (2) Å	θ = 3.8–32.6°
b = 16.4455 (2) Å	µ = 0.50 mm−1
c = 10.7867 (2) Å	T = 100 K
β = 94.550 (1)°	Block, colourless
V = 666.36 (4) Å3	0.49 × 0.28 × 0.21 mm
Z = 4

Data collection

Bruker SMART APEXII CCD area-detector diffractometer	2436 independent reflections
Radiation source: fine-focus sealed tube	2266 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.016
φ and ω scans	θmax = 32.6°, θmin = 2.3°
Absorption correction: multi-scan (SADABS; Bruker, 2009)	h = −5→5
Tmin = 0.791, Tmax = 0.904	k = −24→21
9524 measured reflections	l = −16→14

Refinement

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)] = 0.027	Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.070	H atoms treated by a mixture of independent and constrained refinement
S = 1.06	w = 1/[σ2(Fo2) + (0.0306P)2 + 0.3355P] where P = (Fo2 + 2Fc2)/3
2436 reflections	(Δ/σ)max = 0.001
100 parameters	Δρmax = 0.67 e Å−3
0 restraints	Δρmin = −0.26 e Å−3

Special details

Experimental. The crystal was placed in the cold stream of an Oxford Cryosystems Cobra open-flow nitrogen cryostat (Cosier & Glazer, 1986) operating at 100.0 (1) K.

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
Cl1	1.11362 (6)	0.546310 (13)	0.64838 (2)	0.01425 (6)
O1	0.57563 (19)	0.80520 (4)	0.79576 (6)	0.01449 (13)
N1	0.9448 (2)	0.57688 (5)	0.87272 (7)	0.01299 (14)
N2	0.6906 (2)	0.70257 (5)	0.93883 (7)	0.01284 (14)
N3	0.8057 (3)	0.59594 (5)	1.07440 (8)	0.01996 (17)
C1	0.8338 (2)	0.68624 (5)	0.72638 (8)	0.01284 (15)
H1A	0.8437	0.7075	0.6448	0.015*
C2	0.9490 (2)	0.60954 (5)	0.76040 (8)	0.01137 (14)
C3	0.8137 (2)	0.62570 (5)	0.95924 (8)	0.01305 (15)
C4	0.7000 (2)	0.73004 (5)	0.82415 (8)	0.01155 (15)
C5	0.4336 (3)	0.85141 (6)	0.89378 (9)	0.01568 (16)
H5A	0.3073	0.8992	0.8583	0.024*
H5B	0.6286	0.8691	0.9532	0.024*
H5C	0.2680	0.8174	0.9366	0.024*
H2N3	0.722 (4)	0.6245 (10)	1.1281 (15)	0.027 (4)*
H1N3	0.876 (4)	0.5475 (10)	1.0891 (15)	0.023 (4)*

Atomic displacement parameters (Ų)

	U11	U22	U33	U12	U13	U23
Cl1	0.01773 (10)	0.01199 (10)	0.01346 (10)	0.00039 (7)	0.00388 (7)	−0.00276 (7)
O1	0.0206 (3)	0.0093 (3)	0.0136 (3)	0.0025 (2)	0.0019 (2)	0.0013 (2)
N1	0.0169 (3)	0.0103 (3)	0.0119 (3)	0.0017 (2)	0.0022 (2)	0.0000 (2)
N2	0.0170 (3)	0.0092 (3)	0.0124 (3)	0.0018 (2)	0.0017 (2)	0.0004 (2)
N3	0.0359 (5)	0.0129 (4)	0.0119 (3)	0.0084 (3)	0.0069 (3)	0.0022 (3)
C1	0.0171 (4)	0.0105 (3)	0.0110 (3)	0.0002 (3)	0.0014 (3)	0.0003 (3)
C2	0.0128 (3)	0.0099 (3)	0.0116 (3)	−0.0006 (3)	0.0018 (3)	−0.0018 (3)
C3	0.0171 (4)	0.0103 (3)	0.0118 (3)	0.0014 (3)	0.0020 (3)	0.0005 (3)
C4	0.0130 (3)	0.0086 (3)	0.0130 (3)	−0.0001 (3)	0.0004 (3)	0.0003 (3)
C5	0.0176 (4)	0.0115 (4)	0.0182 (4)	0.0029 (3)	0.0026 (3)	−0.0013 (3)

Geometric parameters (Å, º)

Cl1—C2	1.7449 (9)	N3—H2N3	0.828 (16)
O1—C4	1.3485 (10)	N3—H1N3	0.850 (16)
O1—C5	1.4393 (11)	C1—C2	1.3743 (12)
N1—C2	1.3266 (11)	C1—C4	1.4035 (12)
N1—C3	1.3539 (11)	C1—H1A	0.9500
N2—C4	1.3201 (11)	C5—H5A	0.9800
N2—C3	1.3584 (11)	C5—H5B	0.9800
N3—C3	1.3378 (12)	C5—H5C	0.9800
C4—O1—C5	117.38 (7)	N3—C3—N1	117.35 (8)
C2—N1—C3	114.89 (8)	N3—C3—N2	117.28 (8)
C4—N2—C3	115.86 (8)	N1—C3—N2	125.37 (8)
C3—N3—H2N3	118.7 (11)	N2—C4—O1	119.46 (8)
C3—N3—H1N3	119.1 (11)	N2—C4—C1	124.50 (8)
H2N3—N3—H1N3	122.1 (15)	O1—C4—C1	116.04 (8)
C2—C1—C4	113.28 (8)	O1—C5—H5A	109.5
C2—C1—H1A	123.4	O1—C5—H5B	109.5
C4—C1—H1A	123.4	H5A—C5—H5B	109.5
N1—C2—C1	126.09 (8)	O1—C5—H5C	109.5
N1—C2—Cl1	114.95 (6)	H5A—C5—H5C	109.5
C1—C2—Cl1	118.96 (7)	H5B—C5—H5C	109.5
C3—N1—C2—C1	−0.18 (13)	C4—N2—C3—N1	0.61 (14)
C3—N1—C2—Cl1	−179.36 (6)	C3—N2—C4—O1	178.63 (8)
C4—C1—C2—N1	−0.63 (13)	C3—N2—C4—C1	−1.55 (13)
C4—C1—C2—Cl1	178.52 (6)	C5—O1—C4—N2	−0.73 (12)
C2—N1—C3—N3	−179.55 (9)	C5—O1—C4—C1	179.44 (8)
C2—N1—C3—N2	0.22 (13)	C2—C1—C4—N2	1.55 (13)
C4—N2—C3—N3	−179.62 (9)	C2—C1—C4—O1	−178.62 (8)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N3—H2N3···O1i	0.828 (16)	2.251 (17)	3.0699 (11)	170.1 (15)
N3—H1N3···N1ii	0.850 (16)	2.183 (16)	3.0335 (12)	180 (2)

Symmetry codes: (i) x, −y+3/2, z+1/2; (ii) −x+2, −y+1, −z+2.