Crystal structure of fenclorim

Kwon, E.; Kim, J.; Kang, G.; Kim, T.H.

doi:10.1107/S2056989015016187

organic compounds

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ISSN: 2056-9890

Volume 71| Part 10| October 2015| Page o714

doi:10.1107/S2056989015016187

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Crystal structure of fenclorim

Eunjin Kwon,^a Jineun Kim,^a ^* Gihaeng Kang ^a and Tae Ho Kim ^a ^*

^aDepartment of Chemistry and Research Institute of Natural Sciences, Gyeongsang National University, Jinju 660-701, Republic of Korea
^*Correspondence e-mail: thkim@gnu.ac.kr, jekim@gnu.ac.kr

Edited by J. Simpson, University of Otago, New Zealand (Received 27 August 2015; accepted 31 August 2015; online 12 September 2015)

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.

Keywords: crystal structure; herbicide; fenclorim; pyrimidine; C—Cl⋯π interactions; π–π interactions; hydrogen bonding.

CCDC reference: 1421258

1. 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 ).

2. Experimental

2.1. Crystal data

C₁₀H₆Cl₂N₂
M_r = 225.07
Monoclinic, P 2₁ /c
a = 5.6210 (6) Å
b = 17.0659 (18) Å
c = 10.2582 (12) Å
β = 99.690 (6)°
V = 970.00 (19) Å³
Z = 4
Mo Kα radiation
μ = 0.62 mm⁻¹
T = 173 K
0.16 × 0.06 × 0.04 mm

2.2. 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

2.3. Refinement

R[F² > 2σ(F²)] = 0.034
wR(F²) = 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

Table 1
Hydrogen-bond geometry (Å, °)

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) $[x, -y+{\script{1\over 2}}, z-{\script{1\over 2}}]$ .

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).

Supporting information

CCDC reference: 1421258

Crystal structure: contains datablocks global, I. DOI: 10.1107/S2056989015016187/sj5469sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S2056989015016187/sj5469Isup2.hkl

Supporting information file. DOI: 10.1107/S2056989015016187/sj5469Isup3.cml

checkCIF report

Comment top

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].

Related literature top

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 top

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.

Computing details top

Data collection: APEX2 (Bruker, 2013); cell refinement: SAINT (Bruker, 2013); data reduction: SAINT (Bruker, 2013); 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).

Figures top

	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.

4,6-Dichloro-2-phenylpyrimidine top

Crystal data top

C₁₀H₆Cl₂N₂	F(000) = 456
M_r = 225.07	D_x = 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 top

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

Refinement top

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(F_o²) + (0.0277P)² + 0.269P] where P = (F_o² + 2F_c²)/3
S = 1.07	(Δ/σ)_max < 0.001
2212 reflections	Δρ_max = 0.28 e Å⁻³
127 parameters	Δρ_min = −0.23 e Å⁻³

Crystal data top

C₁₀H₆Cl₂N₂	V = 970.00 (19) Å³
M_r = 225.07	Z = 4
Monoclinic, P2₁/c	Mo Kα radiation
a = 5.6210 (6) Å	µ = 0.62 mm⁻¹
b = 17.0659 (18) Å	T = 173 K
c = 10.2582 (12) Å	0.16 × 0.06 × 0.04 mm
β = 99.690 (6)°

Data collection top

Bruker APEXII CCD diffractometer	2212 independent reflections
Absorption correction: multi-scan (SADABS; Bruker, 2013)	1750 reflections with I > 2σ(I)
T_min = 0.690, T_max = 0.746	R_int = 0.034
9071 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.034	0 restraints
wR(F²) = 0.077	H-atom parameters constrained
S = 1.07	Δρ_max = 0.28 e Å⁻³
2212 reflections	Δρ_min = −0.23 e Å⁻³
127 parameters

Special details top

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 (Å²) top

	x	y	z	U_iso*/U_eq
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 (Å²) top

	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) top

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) top

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.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C2—H2···N2ⁱ	0.95	2.46	3.317 (2)	150.5

Symmetry code: (i) x, −y+1/2, z−1/2.

Acknowledgements

This research was supported by the Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education, Science and Technology (No. 2015R1D1A4A01020317).

References

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