Crystal structure of 4,6-di­chloro-5-methyl­pyrimidine

Abstract

The title compound, C₅H₄Cl₂N₂, is essentially planar with an r.m.s. deviation for all non-H atoms of 0.009 Å. The largest deviation from the mean plane is 0.016 (4) Å for an N atom. In the crystal, mol­ecules are linked by pairs of C—H⋯N hydrogen bonds, forming inversion dimers, enclosing an R ² ₂(6) ring motif.

Related literature  

For the applications of pyrimidine derivatives as pesticides and pharmaceutical agents, see: Condon et al. (1993 ▸); as agrochemicals, see: Maeno et al. (1990 ▸); as anti­viral agents, see: Gilchrist (1997 ▸); as herbicides, see: Selby et al. (2002 ▸); Zhu et al. (2007 ▸); and for applications of organoselenide compounds, see: Ip et al. (1997 ▸). For the crystal structure of 5-methyl­pyrimidine, see: Furberg et al. (1979 ▸).

Experimental  

Crystal data  

• C₅H₄Cl₂N₂

• M _r = 163.00

• Monoclinic,

• a = 7.463 (5) Å

• b = 7.827 (5) Å

• c = 11.790 (5) Å

• β = 93.233 (5)°

• V = 687.6 (7) ų

• Z = 4

• Mo Kα radiation

• μ = 0.85 mm⁻¹

• T = 293 K

• 0.11 × 0.10 × 0.08 mm

Data collection  

• Oxford Diffraction Xcalibur, Eos diffractometer

• Absorption correction: multi-scan (CrysAlis PRO; Oxford Diffraction, 2013 ▸) T _min = 0.922, T _max = 0.934

• 2347 measured reflections

• 1228 independent reflections

• 791 reflections with I > 2σ(I)

• R _int = 0.099

Refinement  

• R[F ² > 2σ(F ²)] = 0.068

• wR(F ²) = 0.173

• S = 1.01

• 1228 reflections

• 83 parameters

• H-atom parameters constrained

• Δρ_max = 0.39 e Å⁻³

• Δρ_min = −0.38 e Å⁻³

Data collection: CrysAlis PRO (Oxford Diffraction, 2013 ▸); cell refinement: CrysAlis PRO; data reduction: CrysAlis PRO; program(s) used to solve structure: SIR97 (Altomare et al., 1999 ▸); program(s) used to refine structure: SHELXL2014/6 (Sheldrick, 2015 ▸); molecular graphics: PLATON (Spek, 2009 ▸) and Mercury (Macrae et al., 2008 ▸); software used to prepare material for publication: SHELXL2014/6 and PLATON.

Supplementary Material

CCDC reference: 1442378

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
C2—H2⋯N3i	0.93	2.66	3.468 (6)	146

Symmetry code: (i) .

supplementary crystallographic information

S1. Comments

Pyrimidines have inter­esting biological properties with applications as pesticides, pharmaceutical agents (Condon et al., 1993; Maeno et al., 1990) and are also inter­esting from a biochemical pint of view and applications of organoselenide compounds (Ip et al., 1997). Pyrimidine derivatives have been developed as anti­viral agents, such as AZT, which is the anti-AIDS drug most widely used (Gilchrist, 1997). Recently, a new series of highly substituted pyrimidine herbicides have been reported (Selby et al., 2002; Zhu et al., 2007). In the present study, we were inter­ested in examining a derivative of pyrimidine with a methyl substituent surrounded by two chlorine atoms.

The molecular structure of the title compound is shown in Fig. 1. The molecule is planar, as is typical in benzenes substituted by halogen atoms and methyl groups, with an r.m.s. deviation for all non-H atoms of 0.009 Å. The largest deviation from the mean plane is 0.016 (4) Å for atom N3. The bond distances and bond angles in the molecule are similar to those reported for 5-methyl­pyrimidine (Furberg et al., 1979).

In the crystal, molecules are linked by a pair of C—H···N hydrogen bonds forming inversion dimers (Table 1 and Fig. 2), enclosing an R²₂(6) ring motif.

S2. Synthesis and crystallization

The commercially available title compound (Sigma-Aldrich) was recrystallized from ethanol giving colourless prismatic crystals.

S3. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2. A l l H atoms were localized in a difference Fourier map but introduced in calculated positions and treated as riding: C—H = 0.93–0.96 Å with U_iso(H) = 1.5U_eq(C-methyl) and 1.2U_eq(C) for other H atoms.

Figures

Fig. 1.

The molecular structure of the title compound, with atom labelling. Displacement ellipsoids drawn at the 50% probability level.

Fig. 2.

The crystal packing of the title compound, viewed along the b axis. Hydrogen bonds are shown as dashed lines (see Table 1).

Crystal data

C5H4Cl2N2	F(000) = 328
Mr = 163.00	Dx = 1.575 Mg m−3
Monoclinic, P21/n	Mo Kα radiation, λ = 0.71073 Å
a = 7.463 (5) Å	Cell parameters from 776 reflections
b = 7.827 (5) Å	θ = 4.2–27.8°
c = 11.790 (5) Å	µ = 0.85 mm−1
β = 93.233 (5)°	T = 293 K
V = 687.6 (7) Å3	Prism, colourless
Z = 4	0.11 × 0.10 × 0.08 mm

Data collection

Oxford Diffraction Xcalibur, Eos diffractometer	1228 independent reflections
Radiation source: Enhance (Mo) X-ray Source	791 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.099
CCD rotation images, thin slices ω scans	θmax = 25.2°, θmin = 3.1°
Absorption correction: multi-scan (CrysAlis PRO; Oxford Diffraction, 2013)	h = −8→8
Tmin = 0.922, Tmax = 0.934	k = −9→4
2347 measured reflections	l = −14→10

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)] = 0.068	Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.173	H-atom parameters constrained
S = 1.01	w = 1/[σ2(Fo2) + (0.0729P)2] where P = (Fo2 + 2Fc2)/3
1228 reflections	(Δ/σ)max < 0.001
83 parameters	Δρmax = 0.39 e Å−3
0 restraints	Δρmin = −0.38 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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq
Cl14	0.47393 (16)	0.21816 (17)	0.57181 (8)	0.0686 (5)
Cl16	0.45631 (17)	0.4430 (2)	0.13763 (9)	0.0853 (6)
N1	0.2066 (5)	0.4832 (6)	0.2775 (3)	0.0604 (11)
N3	0.2153 (5)	0.3882 (5)	0.4695 (3)	0.0579 (10)
C2	0.1383 (6)	0.4657 (7)	0.3784 (4)	0.0661 (14)
H2	0.0251	0.5123	0.3865	0.079*
C4	0.3744 (5)	0.3225 (5)	0.4544 (3)	0.0458 (10)
C5	0.4659 (5)	0.3309 (6)	0.3546 (3)	0.0458 (10)
C6	0.3650 (6)	0.4175 (6)	0.2685 (3)	0.0514 (11)
C51	0.6464 (6)	0.2553 (7)	0.3426 (4)	0.0666 (14)
H51A	0.7041	0.3121	0.2823	0.100*
H51B	0.6344	0.1359	0.3252	0.100*
H51C	0.7175	0.2692	0.4124	0.100*

Atomic displacement parameters (Ų)

	U11	U22	U33	U12	U13	U23
Cl14	0.0846 (9)	0.0601 (9)	0.0604 (6)	−0.0009 (7)	−0.0019 (6)	0.0089 (5)
Cl16	0.0934 (11)	0.1053 (14)	0.0592 (7)	−0.0109 (9)	0.0219 (6)	0.0116 (6)
N1	0.057 (2)	0.061 (3)	0.063 (2)	0.005 (2)	0.0033 (16)	0.0012 (19)
N3	0.057 (2)	0.057 (3)	0.0602 (19)	0.000 (2)	0.0160 (15)	−0.0040 (17)
C2	0.050 (2)	0.074 (4)	0.075 (3)	0.008 (3)	0.005 (2)	−0.008 (3)
C4	0.045 (2)	0.039 (3)	0.0537 (19)	−0.003 (2)	0.0041 (16)	−0.0034 (18)
C5	0.042 (2)	0.039 (3)	0.057 (2)	−0.005 (2)	0.0089 (16)	−0.0056 (17)
C6	0.054 (2)	0.053 (3)	0.0475 (18)	−0.004 (2)	0.0070 (16)	−0.0023 (18)
C51	0.051 (3)	0.070 (4)	0.081 (3)	0.007 (3)	0.016 (2)	−0.002 (2)

Geometric parameters (Å, º)

Cl14—C4	1.737 (4)	C4—C5	1.395 (5)
Cl16—C6	1.733 (4)	C5—C6	1.403 (6)
N1—C6	1.299 (6)	C5—C51	1.486 (6)
N1—C2	1.327 (5)	C51—H51A	0.9600
N3—C4	1.315 (5)	C51—H51B	0.9600
N3—C2	1.335 (5)	C51—H51C	0.9600
C2—H2	0.9300
C6—N1—C2	115.4 (3)	C6—C5—C51	125.2 (4)
C4—N3—C2	114.8 (3)	N1—C6—C5	125.9 (3)
N1—C2—N3	126.8 (4)	N1—C6—Cl16	115.6 (3)
N1—C2—H2	116.6	C5—C6—Cl16	118.5 (3)
N3—C2—H2	116.6	C5—C51—H51A	109.5
N3—C4—C5	125.7 (4)	C5—C51—H51B	109.5
N3—C4—Cl14	115.1 (3)	H51A—C51—H51B	109.5
C5—C4—Cl14	119.2 (3)	C5—C51—H51C	109.5
C4—C5—C6	111.4 (4)	H51A—C51—H51C	109.5
C4—C5—C51	123.4 (4)	H51B—C51—H51C	109.5
C6—N1—C2—N3	−0.2 (8)	Cl14—C4—C5—C51	−0.2 (6)
C4—N3—C2—N1	−0.7 (8)	C2—N1—C6—C5	0.5 (8)
C2—N3—C4—C5	1.3 (7)	C2—N1—C6—Cl16	−179.0 (4)
C2—N3—C4—Cl14	−178.9 (4)	C4—C5—C6—N1	0.1 (7)
N3—C4—C5—C6	−1.1 (6)	C51—C5—C6—N1	179.5 (5)
Cl14—C4—C5—C6	179.2 (3)	C4—C5—C6—Cl16	179.6 (3)
N3—C4—C5—C51	179.5 (4)	C51—C5—C6—Cl16	−1.0 (7)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
C2—H2···N3i	0.93	2.66	3.468 (6)	146

Symmetry code: (i) −x, −y+1, −z+1.