2-Chloro­pyrimidin-4-amine

Abstract

In the title pyrimidine derivative, C₄H₄ClN₃, the 2-chloro and 4-amino substituents almost lie in the mean plane of the pyrimidine ring, with deviations of 0.003 (1) Å for the Cl atom, and 0.020 (1) Å for the N atom. In the crystal, molecules are linked via pairs of N—H⋯N hydrogen bonds, forming inversion dimers. These dimers are further linked via N—H⋯N hydrogen bonds, forming an undulating two-dimensional network lying parallel to (100).

Related literature

For compounds related to pyrimidin-4-amine, see: Van Albada et al. (1999 ▶, 2003 ▶); Van Meervelt & Uytterhoeven (2003 ▶); Kožíšek et al. (2005 ▶). For the agricultural and pharmaceutical relevance of 2-chloro­pyrimidin-4-amine, see: Zunszain et al. (2005 ▶). For graph-set analysis of hydrogen bonds, see: Etter et al. (1990 ▶); Bernstein et al. (1995 ▶).

Experimental

Crystal data

• C₄H₄ClN₃

• M _r = 129.55

• Monoclinic,

• a = 3.83162 (19) Å

• b = 11.8651 (7) Å

• c = 12.7608 (7) Å

• β = 100.886 (2)°

• V = 569.70 (5) ų

• Z = 4

• Mo Kα radiation

• μ = 0.55 mm⁻¹

• T = 294 K

• 0.40 × 0.20 × 0.20 mm

Data collection

• Rigaku R-AXIS RAPID diffractometer

• Absorption correction: multi-scan (CrystalClear; Rigaku, 2007 ▶) T _min = 0.840, T _max = 0.888

• 9506 measured reflections

• 1296 independent reflections

• 962 reflections with I > 2σ(I)

• R _int = 0.038

Refinement

• R[F ² > 2σ(F ²)] = 0.035

• wR(F ²) = 0.092

• S = 1.14

• 1296 reflections

• 82 parameters

• 2 restraints

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

• Δρ_max = 0.17 e Å⁻³

• Δρ_min = −0.27 e Å⁻³

Data collection: CrystalClear (Rigaku, 2007 ▶); cell refinement: CrystalClear; data reduction: CrystalClear; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: DIAMOND (Brandenburg, 2007 ▶); software used to prepare material for publication: publCIF (Westrip, 2010 ▶).

Supplementary Material

Supplementary material file. DOI: 10.1107/S1600536811055863/zj2047Isup3.cml

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
N2—H2A⋯N3i	0.90 (2)	2.17 (2)	3.069 (2)	174 (2)
N2—H2B⋯N1ii	0.87 (2)	2.16 (2)	3.024 (2)	170 (2)

Symmetry codes: (i) ; (ii) .

supplementary crystallographic information

Comment

The molecule of 2-chloropyrimidin-4-amine is relevant for agrochemistry as a plant growth regulator and as a pharmaceutical intermediate (Zunszain et al. 2005). It could also be an interesting precursor for chelating ligands after chlorine substitution. Pyrimidin-amines are interesting bridging ligands, as they contain two nitrogen coordination donor atoms, and an amine as a hydrogen bond donor group (Van Albada et al. 1999, 2003). The ligands pyrimidin-4-amine and 2-amine can easily bridge two metal ions (Kožíšek et al. 2005). With the presence of two donor atoms, the title compound might serve as a building block in the formation of coordination polymers. Due to the position of a chloride atom in-between the two donor N atoms of the pyrimidin-4-amine, the bridging would be likely to change. In fact, coordination complexes with the 2-chloropyrimidin-4-amine are yet unreachable. We here present the molecular structure of this compound, (Figure 1).

The 2-chloropyrimidin-4-amine molecule is nearly planar, with r.m.s. deviation of the pyrimidine heterocyclic non-hydrogen atoms is 0.002 (2) Å. In the crystal, molecules are arranged with two N—H···N hydrogen bond motifs, where the amine group serves as a twofold donor of the hydrogen atoms for the two pyrimidine nitrogen atoms. Considering graph-set analysis (Etter et al., 1990; Bernstein et al., 1995), the descriptors are R²₂(8) loops and C(5) chain motifs along the [001] and [010] vectors, respectively. The network can be described as a wobbled two-dimensional network extending in the (100) plane, (Figure 2). It is worth to note that the related pyrimidin-4-amine molecule (Van Meervelt et al. 2003), crystallizes in the orthorhombic Pcab space group and exhibits only the N—H···N hydrogen bond with C(5) chain motif of a one-dimensional zigzag chain.

Experimental

The ligand was used as commercially available. 0.5 mg of the compound was dissolved in 10 ml of methanol. The solution was stand at room temperature in a closed vessel. After two weeks, colourless blocks appeared and separated by filtration.

Refinement

Carbon-bound H-atoms were placed in ideal calculated positions [aromatic C—H 0.93 Å, U_iso(H) = 1.2U_eq(C)] and refined as riding atoms. The amine H-atoms were constrained into their positions using two distance restraints [N—H 0.91 Å, U_iso(H) = 1.2U_eq(N)].

Figures

Fig. 1.

Atomic numbering scheme and thermal ellipsoidal (50% probability level) of the title compound. Hydrogen atoms are presented as spheres of arbitrary radii.

Fig. 2.

bc-plane projection showing the N—H···N hydrogen bonds as dotted line of R22(8) loop (presented in blue color), and C(5) chain (presented in red color). Symmetry codes: (i) -x, -y + 1, -z + 1; (ii) x, -y + 1/2, z + 1/2.

Crystal data

C4H4ClN3	F(000) = 264
Mr = 129.55	Dx = 1.510 Mg m−3
Monoclinic, P21/c	Mo Kα radiation, λ = 0.71075 Å
Hall symbol: -P 2ybc	Cell parameters from 342 reflections
a = 3.83162 (19) Å	θ = 3.3–27.5°
b = 11.8651 (7) Å	µ = 0.55 mm−1
c = 12.7608 (7) Å	T = 294 K
β = 100.886 (2)°	Block, colourless
V = 569.70 (5) Å3	0.40 × 0.20 × 0.20 mm
Z = 4

Data collection

Rigaku R-AXIS RAPID diffractometer	1296 independent reflections
Radiation source: fine-focus sealed tube	962 reflections with I > 2σ(I)
graphite	Rint = 0.038
ω scans	θmax = 27.5°, θmin = 3.3°
Absorption correction: multi-scan (CrystalClear; Rigaku, 2007)	h = −4→4
Tmin = 0.840, Tmax = 0.888	k = −15→15
9506 measured reflections	l = −16→16

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)] = 0.035	Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.092	H atoms treated by a mixture of independent and constrained refinement
S = 1.14	w = 1/[σ2(Fo2) + (0.0422P)2 + 0.0697P] where P = (Fo2 + 2Fc2)/3
1296 reflections	(Δ/σ)max < 0.001
82 parameters	Δρmax = 0.17 e Å−3
2 restraints	Δρmin = −0.27 e Å−3

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
Cl1	0.05814 (13)	0.43867 (4)	0.20898 (3)	0.0586 (2)
N1	0.3425 (4)	0.25622 (13)	0.29987 (11)	0.0500 (4)
N2	0.2112 (5)	0.37262 (14)	0.59166 (12)	0.0522 (4)
H2B	0.277 (5)	0.3340 (17)	0.6504 (14)	0.065 (6)*
H2A	0.103 (5)	0.4395 (14)	0.5959 (17)	0.061 (6)*
C2	0.2035 (4)	0.35294 (14)	0.32044 (13)	0.0419 (4)
N3	0.1530 (4)	0.39673 (11)	0.41103 (10)	0.0407 (3)
C4	0.2612 (4)	0.33227 (13)	0.49910 (12)	0.0400 (4)
C5	0.4177 (5)	0.22616 (15)	0.48826 (14)	0.0480 (4)
H5	0.4961	0.1806	0.5473	0.058*
C6	0.4495 (5)	0.19310 (16)	0.38937 (16)	0.0531 (5)
H6	0.5506	0.1230	0.3818	0.064*

Atomic displacement parameters (Ų)

	U11	U22	U33	U12	U13	U23
Cl1	0.0718 (4)	0.0665 (4)	0.0379 (3)	0.0003 (2)	0.0113 (2)	0.0060 (2)
N1	0.0570 (9)	0.0502 (9)	0.0447 (9)	0.0005 (7)	0.0143 (7)	−0.0103 (7)
N2	0.0775 (11)	0.0455 (9)	0.0345 (8)	0.0079 (8)	0.0130 (7)	0.0007 (7)
C2	0.0431 (9)	0.0456 (9)	0.0379 (9)	−0.0055 (7)	0.0101 (7)	−0.0045 (7)
N3	0.0496 (8)	0.0380 (7)	0.0357 (7)	−0.0010 (6)	0.0112 (6)	−0.0019 (6)
C4	0.0439 (9)	0.0395 (9)	0.0372 (8)	−0.0034 (7)	0.0092 (7)	−0.0013 (7)
C5	0.0533 (10)	0.0429 (10)	0.0472 (10)	0.0047 (8)	0.0075 (8)	0.0027 (8)
C6	0.0550 (11)	0.0442 (10)	0.0610 (12)	0.0047 (8)	0.0132 (9)	−0.0092 (9)

Geometric parameters (Å, °)

Cl1—C2	1.7518 (17)	C2—N3	1.315 (2)
N1—C2	1.312 (2)	N3—C4	1.358 (2)
N1—C6	1.363 (2)	C4—C5	1.412 (2)
N2—C4	1.322 (2)	C5—C6	1.349 (2)
N2—H2B	0.874 (15)	C5—H5	0.9300
N2—H2A	0.902 (16)	C6—H6	0.9300
C2—N1—C6	112.47 (15)	N2—C4—C5	123.11 (16)
C4—N2—H2B	120.6 (14)	N3—C4—C5	119.33 (15)
C4—N2—H2A	121.3 (14)	C6—C5—C4	117.77 (16)
H2B—N2—H2A	118 (2)	C6—C5—H5	121.1
N1—C2—N3	130.85 (16)	C4—C5—H5	121.1
N1—C2—Cl1	115.10 (12)	C5—C6—N1	123.94 (17)
N3—C2—Cl1	114.05 (13)	C5—C6—H6	118.0
C2—N3—C4	115.64 (14)	N1—C6—H6	118.0
N2—C4—N3	117.56 (15)

Hydrogen-bond geometry (Å, °)

D—H···A	D—H	H···A	D···A	D—H···A
N2—H2A···N3i	0.90 (2)	2.17 (2)	3.069 (2)	174 (2)
N2—H2B···N1ii	0.87 (2)	2.16 (2)	3.024 (2)	170 (2)

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