Crystal structure of fenclorim

Abstract

In the title compound, C₁₀H₆Cl₂N₂ (systematic name: 4,6-di­chloro-2-phenyl­pyrimidine), which is used commercially as the herbicide safener, fenclorim, the dihedral angle between the di­chloro­pyrimidyl and phenyl rings is 9.45 (10)°. In the crystal, C—H⋯N hydrogen bonds link adjacent mol­ecules, forming chains along the c-axis direction. In addition, weak inter­molecular C—Cl⋯π [3.6185 (10) Å] and π–π [3.8796 (11) Å] inter­actions are present, forming a three-dimensional network.

Related literature  

For information on the herbicidal properties of the title compound, see: Wu et al. (1999 ▸). For a related crystal structure, see: Leban & Polanc (1992 ▸).

Experimental  

Crystal data  

• C₁₀H₆Cl₂N₂

• M _r = 225.07

• Monoclinic,

• a = 5.6210 (6) Å

• b = 17.0659 (18) Å

• c = 10.2582 (12) Å

• β = 99.690 (6)°

• V = 970.00 (19) ų

• Z = 4

• Mo Kα radiation

• μ = 0.62 mm⁻¹

• T = 173 K

• 0.16 × 0.06 × 0.04 mm

Data collection  

• Bruker APEXII CCD diffractometer

• Absorption correction: multi-scan (SADABS; Bruker, 2013 ▸) T _min = 0.690, T _max = 0.746

• 9071 measured reflections

• 2212 independent reflections

• 1750 reflections with I > 2σ(I)

• R _int = 0.034

Refinement  

• R[F ² > 2σ(F ²)] = 0.034

• wR(F ²) = 0.077

• S = 1.07

• 2212 reflections

• 127 parameters

• H-atom parameters constrained

• Δρ_max = 0.28 e Å⁻³

• Δρ_min = −0.23 e Å⁻³

Data collection: APEX2 (Bruker, 2013 ▸); cell refinement: SAINT (Bruker, 2013 ▸); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▸); program(s) used to refine structure: SHELXL2013 (Sheldrick, 2015 ▸); molecular graphics: DIAMOND (Brandenburg, 2010 ▸); software used to prepare material for publication: SHELXTL (Sheldrick, 2008 ▸).

Supplementary Material

CCDC reference: 1421258

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

Table 1. Hydrogen-bond geometry (, ).

DHA	DH	HA	D A	DHA
C2H2N2i	0.95	2.46	3.317(2)	151

Symmetry code: (i) .

supplementary crystallographic information

S1. Comment

Fenclorim [systematic name: 4,6-dichloro-2-phenylpyrimidine] is a herbicide safener that is used in many rice-producing countries to protect rice plants from damage likely to be caused by the chloroacetanilide herbicide pretilachlor. (Wu et al., 1999). The dihedral angle between the dichloropyrimidyl and phenyl rings is 9.45 (10)°. All bond lengths and bond angles are normal and comparable to those observed in a similar crystal structure (Leban & Polanc, 1992).

In the crystal structure (Fig. 2), C–H···N hydrogen bonds (Table 1) link adjacent molecules, forming a one-dimensional chains along the c-axis. In addition, weak intermolecular C3–Cl2···Cg2ⁱⁱⁱ [Cl2···Cg2 = 3.6185 (10) Å] (Cg2 is the centroid of the C5–C10 ring) and Cg1···Cg2^iv [Cg1···Cg2 = 3.8796 (11) Å] interactions are present (Cg1 is the centroid of the N1,N2,C1–C4 ring), forming a three-dimensional network [symmetry codes: (ii), x - 1, y, z; (iii), x - 1, -y + 1/2, z - 1/2; (iv), -x + 1, -y + 1, -z].

S2. Experimental

The title compound was purchased from the Dr. Ehrenstorfer GmbH Company. Slow evaporation of a solution in CH₂Cl₂ gave single crystals suitable for X-ray analysis.

S3. Refinement

All H-atoms were positioned geometrically and refined using a riding model with d(C—H) = 0.95 Å, U_iso = 1.2U_eq(C) for the aromatic C—H.

Figures

Fig. 1.

The asymmetric unit of the title compound with the atom numbering scheme. Displacement ellipsoids are drawn at the 50% probability level. H atoms are shown as small spheres of arbitrary radius.

Fig. 2.

Crystal packing viewed along the a axis. The intermolecular interactions are shown as dashed lines.

Crystal data

C10H6Cl2N2	F(000) = 456
Mr = 225.07	Dx = 1.541 Mg m−3
Monoclinic, P21/c	Mo Kα radiation, λ = 0.71073 Å
a = 5.6210 (6) Å	Cell parameters from 2286 reflections
b = 17.0659 (18) Å	θ = 2.3–25.9°
c = 10.2582 (12) Å	µ = 0.62 mm−1
β = 99.690 (6)°	T = 173 K
V = 970.00 (19) Å3	Plate, colourless
Z = 4	0.16 × 0.06 × 0.04 mm

Data collection

Bruker APEXII CCD diffractometer	1750 reflections with I > 2σ(I)
φ and ω scans	Rint = 0.034
Absorption correction: multi-scan (SADABS; Bruker, 2013)	θmax = 27.5°, θmin = 2.3°
Tmin = 0.690, Tmax = 0.746	h = −6→7
9071 measured reflections	k = −19→22
2212 independent reflections	l = −13→9

Refinement

Refinement on F2	0 restraints
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.034	H-atom parameters constrained
wR(F2) = 0.077	w = 1/[σ2(Fo2) + (0.0277P)2 + 0.269P] where P = (Fo2 + 2Fc2)/3
S = 1.07	(Δ/σ)max < 0.001
2212 reflections	Δρmax = 0.28 e Å−3
127 parameters	Δρmin = −0.23 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
Cl1	0.65642 (9)	0.34546 (3)	−0.36827 (4)	0.04016 (15)
Cl2	0.00001 (9)	0.21187 (3)	−0.11631 (4)	0.03800 (15)
N1	0.6078 (2)	0.37521 (8)	−0.12511 (13)	0.0265 (3)
N2	0.3094 (2)	0.31826 (8)	−0.01497 (13)	0.0251 (3)
C1	0.5151 (3)	0.33485 (10)	−0.23126 (16)	0.0266 (4)
C2	0.3205 (3)	0.28518 (10)	−0.24028 (16)	0.0274 (4)
H2	0.2551	0.2580	−0.3190	0.033*
C3	0.2296 (3)	0.27863 (10)	−0.12406 (16)	0.0258 (4)
C4	0.4978 (3)	0.36583 (9)	−0.01979 (15)	0.0239 (4)
C5	0.5944 (3)	0.41068 (10)	0.10104 (15)	0.0248 (4)
C6	0.4715 (3)	0.41288 (10)	0.20807 (16)	0.0294 (4)
H6	0.3240	0.3851	0.2044	0.035*
C7	0.5644 (4)	0.45554 (11)	0.31979 (17)	0.0355 (4)
H7	0.4809	0.4566	0.3929	0.043*
C8	0.7773 (4)	0.49654 (12)	0.32573 (18)	0.0381 (5)
H8	0.8395	0.5259	0.4026	0.046*
C9	0.9000 (3)	0.49498 (12)	0.22019 (19)	0.0391 (5)
H9	1.0460	0.5236	0.2239	0.047*
C10	0.8099 (3)	0.45159 (11)	0.10867 (18)	0.0332 (4)
H10	0.8964	0.4498	0.0367	0.040*

Atomic displacement parameters (Ų)

	U11	U22	U33	U12	U13	U23
Cl1	0.0519 (3)	0.0482 (3)	0.0248 (2)	−0.0100 (2)	0.0192 (2)	−0.0056 (2)
Cl2	0.0424 (3)	0.0384 (3)	0.0344 (3)	−0.0145 (2)	0.0099 (2)	−0.00277 (19)
N1	0.0314 (8)	0.0280 (8)	0.0213 (7)	−0.0007 (7)	0.0077 (6)	−0.0002 (6)
N2	0.0290 (8)	0.0250 (8)	0.0217 (7)	−0.0008 (6)	0.0056 (6)	0.0012 (6)
C1	0.0352 (10)	0.0268 (9)	0.0194 (8)	0.0042 (8)	0.0095 (7)	0.0021 (7)
C2	0.0346 (10)	0.0265 (9)	0.0210 (8)	−0.0003 (8)	0.0042 (7)	−0.0027 (7)
C3	0.0296 (9)	0.0234 (9)	0.0244 (8)	−0.0008 (7)	0.0043 (7)	0.0021 (7)
C4	0.0278 (9)	0.0240 (9)	0.0200 (8)	0.0047 (7)	0.0046 (7)	0.0033 (6)
C5	0.0307 (9)	0.0226 (9)	0.0209 (8)	0.0032 (7)	0.0035 (7)	0.0011 (6)
C6	0.0375 (10)	0.0264 (9)	0.0253 (9)	0.0013 (8)	0.0080 (7)	0.0005 (7)
C7	0.0500 (12)	0.0366 (11)	0.0206 (9)	0.0080 (9)	0.0078 (8)	−0.0013 (7)
C8	0.0442 (12)	0.0383 (11)	0.0276 (9)	0.0086 (10)	−0.0063 (8)	−0.0079 (8)
C9	0.0323 (10)	0.0415 (12)	0.0406 (11)	−0.0028 (9)	−0.0019 (8)	−0.0081 (9)
C10	0.0316 (10)	0.0375 (11)	0.0311 (9)	−0.0021 (8)	0.0073 (8)	−0.0037 (8)

Geometric parameters (Å, º)

Cl1—C1	1.7362 (17)	C5—C6	1.393 (2)
Cl2—C3	1.7333 (17)	C6—C7	1.384 (2)
N1—C1	1.319 (2)	C6—H6	0.9500
N1—C4	1.342 (2)	C7—C8	1.379 (3)
N2—C3	1.320 (2)	C7—H7	0.9500
N2—C4	1.342 (2)	C8—C9	1.378 (3)
C1—C2	1.375 (2)	C8—H8	0.9500
C2—C3	1.379 (2)	C9—C10	1.385 (2)
C2—H2	0.9500	C9—H9	0.9500
C4—C5	1.480 (2)	C10—H10	0.9500
C5—C10	1.389 (2)
C1—N1—C4	115.52 (14)	C6—C5—C4	120.90 (15)
C3—N2—C4	115.88 (14)	C7—C6—C5	119.93 (17)
N1—C1—C2	125.22 (15)	C7—C6—H6	120.0
N1—C1—Cl1	116.28 (13)	C5—C6—H6	120.0
C2—C1—Cl1	118.49 (13)	C8—C7—C6	120.49 (17)
C1—C2—C3	113.49 (15)	C8—C7—H7	119.8
C1—C2—H2	123.3	C6—C7—H7	119.8
C3—C2—H2	123.3	C9—C8—C7	120.06 (17)
N2—C3—C2	124.69 (16)	C9—C8—H8	120.0
N2—C3—Cl2	116.58 (13)	C7—C8—H8	120.0
C2—C3—Cl2	118.70 (13)	C8—C9—C10	119.83 (18)
N1—C4—N2	125.13 (15)	C8—C9—H9	120.1
N1—C4—C5	117.31 (15)	C10—C9—H9	120.1
N2—C4—C5	117.55 (14)	C9—C10—C5	120.63 (17)
C10—C5—C6	119.06 (16)	C9—C10—H10	119.7
C10—C5—C4	120.04 (15)	C5—C10—H10	119.7
C4—N1—C1—C2	−0.4 (2)	N1—C4—C5—C10	−8.8 (2)
C4—N1—C1—Cl1	−179.46 (12)	N2—C4—C5—C10	170.39 (16)
N1—C1—C2—C3	−1.8 (3)	N1—C4—C5—C6	170.99 (15)
Cl1—C1—C2—C3	177.25 (12)	N2—C4—C5—C6	−9.9 (2)
C4—N2—C3—C2	−2.3 (2)	C10—C5—C6—C7	0.1 (3)
C4—N2—C3—Cl2	175.70 (12)	C4—C5—C6—C7	−179.64 (15)
C1—C2—C3—N2	3.2 (3)	C5—C6—C7—C8	0.5 (3)
C1—C2—C3—Cl2	−174.72 (13)	C6—C7—C8—C9	−0.3 (3)
C1—N1—C4—N2	1.6 (2)	C7—C8—C9—C10	−0.6 (3)
C1—N1—C4—C5	−179.38 (14)	C8—C9—C10—C5	1.2 (3)
C3—N2—C4—N1	−0.3 (2)	C6—C5—C10—C9	−1.0 (3)
C3—N2—C4—C5	−179.36 (14)	C4—C5—C10—C9	178.79 (16)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
C2—H2···N2i	0.95	2.46	3.317 (2)	151

Symmetry code: (i) x, −y+1/2, z−1/2.