Crystal structure of pencycuron

In the title compound [systematic name: 1-(4-chloro­benz­yl)-1-cyclo­pentyl-3-phenyl­urea], C₁₉H₂₁ClN₂O, which is a urea fungicide, the cyclo­pentyl ring adopts an envelope conformation, with one of the methyl­ene C atoms adjacent to the C atom bonding to the N atom as the flap. The dihedral angles between the mean planes of the central cyclo­pentyl ring (all atoms) and the chloro­benzyl and phenyl rings are 77.96 (6) and 57.77 (7)°, respectively. In the crystal, N—H...O hydrogen bonds link adjacent mol­ecules, forming C(4) chains propagating along the b-axis direction. The chains are linked by weak π–π inter­actions between the chloro­benzene rings [centroid–centroid separation = 3.9942 (9) Å], resulting in two-dimensional networks extending parellel to the (110) plane.

Key indicators

• Single-crystal X-ray study
• T = 173 K
• Mean [sigma](C-C) = 0.002 Å
• R factor = 0.037
• wR factor = 0.095
• Data-to-parameter ratio = 15.9

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT414_ALERT_2_C Short Intra D-H..H-X       H2N    ..  H8      ..       1.97 Ang.
PLAT906_ALERT_3_C Large K value in the Analysis of Variance ......      3.411 Check
PLAT911_ALERT_3_C Missing # FCF Refl Between THmin & STh/L=  0.600          7 Report

Alert level G
PLAT066_ALERT_1_G Predicted and Reported Tmin&Tmax Range Identical          ? Check
PLAT910_ALERT_3_G Missing # of FCF Reflection(s) Below Th(Min) ...          1 Report
PLAT961_ALERT_5_G Dataset Contains no Negative Intensities .......     Please Check

   0 ALERT level A = Most likely a serious problem - resolve or explain
   0 ALERT level B = A potentially serious problem, consider carefully
   3 ALERT level C = Check. Ensure it is not caused by an omission or oversight
   3 ALERT level G = General information/check it is not something unexpected

   1 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   1 ALERT type 2 Indicator that the structure model may be wrong or deficient
   3 ALERT type 3 Indicator that the structure quality may be low
   0 ALERT type 4 Improvement, methodology, query or suggestion
   1 ALERT type 5 Informative message, check

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S1. Comment

Pencycuron, [systematic name: 1-(4-chlorobenzyl)-1-cyclopentyl-3-phenylurea], is a urea fungicide and it has been used for the control of diseases in various crops, including rice (Pal et al., 2005). However, until now its crystal structure has not been reported. In the title compound (Fig. 1), the dihedral angles between the mean planes of the central cyclopentyl ring [r.m.s. deviation = 0.1693] and the chlorobenzyl and phenyl rings are 77.96 (6) and 57.778 (7)°, respectively. All bond lengths and bond angles are normal and comparable to those observed in the crystal structure of a similar compound (Bjerglund et al., 2012).

In the crystal (Fig. 2), N—H···O hydrogen bonds link adjacent molecules, forming a one-dimensional chains along the b axis direction (Table. 1). The chains are linked by weak π–π interactions [Cg1···Cg1ⁱⁱ, 3.9942 (9) Å], resulting in a two-dimensional networks parellel to the (110) plane (Cg1 is the centroid of the C1–C6 ring)[for symmetry codes: (ii), -x, -y, -z].

Related literature

For information on the fungicidal properties of the title compound, see: Pal et al. (2005). For a related crystal structure, see: Bjerglund et al. (2012).

S2. Experimental

The title compound was purchased from the Dr Ehrenstorfer GmbH Company. Slow evaporation of a solution in CH₂Cl₂ gave colourless needles.

S3. Refinement

The N-bound H atom was located in a difference Fourier map and freely refined (N—H = 0.828 (19) Å). The C-bound H atoms were positioned geometrically and refined using a riding model with d(C—H) = 1.00 Å, U_iso = 1.2U_eq(C) for Csp³—H, d(C—H) = 0.99 Å, U_iso = 1.2U_eq(C) for CH₂ groups, d(C—H) = 0.95 Å, U_iso = 1.2U_eq(C) for aromatic C—H.

Computing details

Data collection: APEX2 (Bruker, 2009); cell refinement: SAINT (Bruker, 2009); data reduction: SAINT (Bruker, 2009); 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

	Fig. 1. The asymmetric unit of the title compound with displacement ellipsoids drawn at the 50% probability level.
	Fig. 2. Crystal packing viewed along the a axis. The intermolecular N—H···O hydrogen bonds and weak π–π interactions are shown as dashed lines.

1-(4-Chlorobenzyl)-1-cyclopentyl-3-phenylurea

Crystal data

C19H21ClN2O	Dx = 1.270 Mg m^−3
Mr = 328.83	Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, Pbca	Cell parameters from 6227 reflections
a = 12.1585 (5) Å	θ = 2.5–27.3°
b = 8.6721 (4) Å	µ = 0.23 mm^−1
c = 32.6152 (12) Å	T = 173 K
V = 3438.9 (2) Å^3	Needle, colourless
Z = 8	0.50 × 0.11 × 0.09 mm
F(000) = 1392

Data collection

Bruker APEX-II CCD diffractometer	2698 reflections with I > 2σ(I)
φ and ω scans	Rint = 0.039
Absorption correction: multi-scan (SADABS; Bruker, 2009)	θmax = 26.0°, θmin = 2.1°
Tmin = 0.894, Tmax = 0.980	h = −14→14
27037 measured reflections	k = −6→10
3374 independent reflections	l = −40→40

Refinement

Refinement on F^2	0 restraints
Least-squares matrix: full	Hydrogen site location: mixed
R[F^2 > 2σ(F^2)] = 0.037	H atoms treated by a mixture of independent and constrained refinement
wR(F^2) = 0.095	w = 1/[σ^2(Fo^2) + (0.0384P)^2 + 1.2518P] where P = (Fo^2 + 2Fc^2)/3
S = 1.04	(Δ/σ)max < 0.001
3374 reflections	Δρmax = 0.17 e Å^−3
212 parameters	Δρmin = −0.24 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	0.23590 (4)	−0.16966 (8)	−0.05434 (2)	0.06131 (19)
O1	0.15878 (8)	−0.14846 (11)	0.15909 (3)	0.0287 (2)
N1	0.08966 (10)	0.07872 (15)	0.13656 (4)	0.0278 (3)
N2	0.23017 (10)	0.07453 (16)	0.18515 (4)	0.0288 (3)
H2N	0.2489 (14)	0.162 (2)	0.1777 (5)	0.039 (5)*
C1	0.17668 (14)	−0.1232 (2)	−0.00710 (5)	0.0384 (4)
C2	0.22919 (13)	−0.0213 (2)	0.01841 (5)	0.0397 (4)
H2	0.2975	0.0233	0.0106	0.048*
C3	0.18127 (12)	0.0160 (2)	0.05576 (5)	0.0355 (4)
H3	0.2173	0.0863	0.0736	0.043*
C4	0.08150 (12)	−0.04807 (17)	0.06739 (4)	0.0277 (3)
C5	0.03091 (13)	−0.15110 (19)	0.04097 (5)	0.0327 (4)
H5	−0.0373	−0.1962	0.0486	0.039*
C6	0.07769 (14)	−0.1895 (2)	0.00376 (5)	0.0390 (4)
H6	0.0423	−0.2604	−0.0141	0.047*
C7	0.02356 (12)	−0.00774 (19)	0.10708 (4)	0.0298 (3)
H7A	−0.0428	0.0535	0.1005	0.036*
H7B	−0.0012	−0.1045	0.1203	0.036*
C8	0.06470 (12)	0.24352 (18)	0.14250 (5)	0.0315 (4)
H8	0.1190	0.2854	0.1627	0.038*
C9	0.07296 (15)	0.3403 (2)	0.10377 (5)	0.0436 (4)
H9A	0.0381	0.2873	0.0802	0.052*
H9B	0.1506	0.3629	0.0969	0.052*
C10	0.01105 (17)	0.4869 (2)	0.11481 (6)	0.0532 (5)
H10A	−0.0149	0.5406	0.0898	0.064*
H10B	0.0584	0.5579	0.1307	0.064*
C11	−0.08580 (17)	0.4315 (2)	0.14061 (7)	0.0565 (5)
H11A	−0.1520	0.4182	0.1233	0.068*
H11B	−0.1027	0.5070	0.1625	0.068*
C12	−0.05145 (14)	0.2774 (2)	0.15928 (6)	0.0421 (4)
H12A	−0.1033	0.1949	0.1511	0.050*
H12B	−0.0502	0.2841	0.1896	0.050*
C13	0.15966 (11)	−0.00577 (17)	0.16037 (4)	0.0249 (3)
C14	0.29239 (11)	0.00718 (17)	0.21711 (4)	0.0255 (3)
C15	0.39770 (12)	0.06323 (18)	0.22439 (5)	0.0300 (3)
H15	0.4283	0.1387	0.2066	0.036*
C16	0.45819 (13)	0.0096 (2)	0.25737 (5)	0.0357 (4)
H16	0.5295	0.0500	0.2625	0.043*
C17	0.41528 (14)	−0.1025 (2)	0.28280 (5)	0.0381 (4)
H17	0.4569	−0.1396	0.3054	0.046*
C18	0.31135 (14)	−0.16039 (19)	0.27514 (5)	0.0354 (4)
H18	0.2822	−0.2390	0.2923	0.043*
C19	0.24920 (12)	−0.10478 (18)	0.24270 (4)	0.0293 (3)
H19	0.1772	−0.1434	0.2381	0.035*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
Cl1	0.0543 (3)	0.0950 (5)	0.0346 (2)	0.0261 (3)	0.0028 (2)	−0.0022 (3)
O1	0.0304 (5)	0.0214 (5)	0.0343 (6)	−0.0008 (5)	−0.0029 (4)	−0.0001 (5)
N1	0.0293 (6)	0.0238 (7)	0.0303 (6)	0.0018 (6)	−0.0084 (5)	−0.0012 (6)
N2	0.0295 (7)	0.0207 (6)	0.0361 (7)	−0.0033 (6)	−0.0097 (5)	0.0054 (6)
C1	0.0388 (9)	0.0465 (10)	0.0298 (8)	0.0157 (8)	−0.0022 (7)	0.0049 (8)
C2	0.0300 (8)	0.0476 (11)	0.0414 (9)	0.0029 (8)	0.0011 (7)	0.0082 (9)
C3	0.0303 (8)	0.0365 (9)	0.0396 (9)	−0.0018 (7)	−0.0046 (7)	−0.0005 (8)
C4	0.0274 (7)	0.0269 (8)	0.0290 (7)	0.0030 (7)	−0.0073 (6)	0.0041 (7)
C5	0.0300 (8)	0.0331 (9)	0.0350 (8)	−0.0003 (7)	−0.0070 (6)	0.0014 (7)
C6	0.0408 (9)	0.0412 (10)	0.0352 (8)	0.0044 (8)	−0.0113 (7)	−0.0056 (8)
C7	0.0254 (7)	0.0316 (9)	0.0324 (8)	−0.0024 (7)	−0.0056 (6)	−0.0017 (7)
C8	0.0354 (8)	0.0245 (8)	0.0345 (8)	0.0026 (7)	−0.0091 (7)	0.0022 (7)
C9	0.0495 (10)	0.0358 (10)	0.0454 (10)	0.0022 (8)	−0.0033 (8)	0.0120 (9)
C10	0.0705 (13)	0.0338 (10)	0.0552 (11)	0.0087 (10)	−0.0153 (10)	0.0118 (9)
C11	0.0532 (11)	0.0433 (12)	0.0730 (14)	0.0190 (10)	−0.0099 (10)	0.0020 (11)
C12	0.0459 (10)	0.0343 (9)	0.0459 (10)	0.0084 (8)	0.0025 (8)	−0.0006 (8)
C13	0.0231 (7)	0.0246 (8)	0.0269 (7)	−0.0011 (6)	0.0017 (6)	0.0016 (7)
C14	0.0265 (7)	0.0211 (7)	0.0290 (7)	0.0047 (6)	−0.0049 (6)	−0.0033 (6)
C15	0.0278 (8)	0.0253 (8)	0.0369 (8)	0.0015 (6)	−0.0026 (6)	−0.0027 (7)
C16	0.0271 (7)	0.0346 (9)	0.0454 (9)	0.0065 (7)	−0.0104 (7)	−0.0104 (8)
C17	0.0430 (9)	0.0375 (10)	0.0339 (8)	0.0145 (8)	−0.0141 (7)	−0.0038 (8)
C18	0.0440 (9)	0.0297 (9)	0.0326 (8)	0.0073 (8)	−0.0023 (7)	0.0018 (7)
C19	0.0286 (7)	0.0249 (8)	0.0342 (8)	0.0023 (7)	−0.0038 (6)	−0.0013 (7)

Geometric parameters (Å, º)

Cl1—C1	1.7478 (17)	C8—H8	1.0000
O1—C13	1.2382 (17)	C9—C10	1.521 (3)
N1—C13	1.3654 (18)	C9—H9A	0.9900
N1—C7	1.4604 (18)	C9—H9B	0.9900
N1—C8	1.474 (2)	C10—C11	1.525 (3)
N2—C13	1.3686 (19)	C10—H10A	0.9900
N2—C14	1.4141 (18)	C10—H10B	0.9900
N2—H2N	0.828 (19)	C11—C12	1.527 (3)
C1—C2	1.371 (2)	C11—H11A	0.9900
C1—C6	1.380 (2)	C11—H11B	0.9900
C2—C3	1.389 (2)	C12—H12A	0.9900
C2—H2	0.9500	C12—H12B	0.9900
C3—C4	1.387 (2)	C14—C19	1.384 (2)
C3—H3	0.9500	C14—C15	1.390 (2)
C4—C5	1.385 (2)	C15—C16	1.384 (2)
C4—C7	1.515 (2)	C15—H15	0.9500
C5—C6	1.381 (2)	C16—C17	1.380 (2)
C5—H5	0.9500	C16—H16	0.9500
C6—H6	0.9500	C17—C18	1.382 (2)
C7—H7A	0.9900	C17—H17	0.9500
C7—H7B	0.9900	C18—C19	1.387 (2)
C8—C9	1.520 (2)	C18—H18	0.9500
C8—C12	1.543 (2)	C19—H19	0.9500
C13—N1—C7	116.23 (12)	H9A—C9—H9B	109.0
C13—N1—C8	125.02 (12)	C9—C10—C11	104.42 (15)
C7—N1—C8	118.11 (12)	C9—C10—H10A	110.9
C13—N2—C14	124.07 (13)	C11—C10—H10A	110.9
C13—N2—H2N	117.8 (12)	C9—C10—H10B	110.9
C14—N2—H2N	116.5 (12)	C11—C10—H10B	110.9
C2—C1—C6	121.24 (15)	H10A—C10—H10B	108.9
C2—C1—Cl1	119.44 (13)	C10—C11—C12	106.55 (15)
C6—C1—Cl1	119.32 (14)	C10—C11—H11A	110.4
C1—C2—C3	119.13 (15)	C12—C11—H11A	110.4
C1—C2—H2	120.4	C10—C11—H11B	110.4
C3—C2—H2	120.4	C12—C11—H11B	110.4
C4—C3—C2	120.91 (15)	H11A—C11—H11B	108.6
C4—C3—H3	119.5	C11—C12—C8	105.99 (14)
C2—C3—H3	119.5	C11—C12—H12A	110.5
C5—C4—C3	118.45 (14)	C8—C12—H12A	110.5
C5—C4—C7	118.30 (13)	C11—C12—H12B	110.5
C3—C4—C7	123.23 (14)	C8—C12—H12B	110.5
C6—C5—C4	121.28 (15)	H12A—C12—H12B	108.7
C6—C5—H5	119.4	O1—C13—N1	120.78 (13)
C4—C5—H5	119.4	O1—C13—N2	122.27 (13)
C1—C6—C5	118.98 (16)	N1—C13—N2	116.96 (13)
C1—C6—H6	120.5	C19—C14—C15	119.46 (13)
C5—C6—H6	120.5	C19—C14—N2	122.10 (13)
N1—C7—C4	115.17 (12)	C15—C14—N2	118.31 (14)
N1—C7—H7A	108.5	C16—C15—C14	120.32 (15)
C4—C7—H7A	108.5	C16—C15—H15	119.8
N1—C7—H7B	108.5	C14—C15—H15	119.8
C4—C7—H7B	108.5	C17—C16—C15	120.21 (15)
H7A—C7—H7B	107.5	C17—C16—H16	119.9
N1—C8—C9	114.36 (13)	C15—C16—H16	119.9
N1—C8—C12	114.81 (13)	C16—C17—C18	119.51 (15)
C9—C8—C12	104.49 (13)	C16—C17—H17	120.2
N1—C8—H8	107.6	C18—C17—H17	120.2
C9—C8—H8	107.6	C17—C18—C19	120.64 (16)
C12—C8—H8	107.6	C17—C18—H18	119.7
C8—C9—C10	103.43 (14)	C19—C18—H18	119.7
C8—C9—H9A	111.1	C14—C19—C18	119.83 (14)
C10—C9—H9A	111.1	C14—C19—H19	120.1
C8—C9—H9B	111.1	C18—C19—H19	120.1
C10—C9—H9B	111.1
C6—C1—C2—C3	−0.2 (3)	C9—C10—C11—C12	24.7 (2)
Cl1—C1—C2—C3	179.54 (13)	C10—C11—C12—C8	−1.9 (2)
C1—C2—C3—C4	−0.2 (3)	N1—C8—C12—C11	−147.64 (15)
C2—C3—C4—C5	0.4 (2)	C9—C8—C12—C11	−21.56 (18)
C2—C3—C4—C7	−177.90 (15)	C7—N1—C13—O1	−6.1 (2)
C3—C4—C5—C6	−0.3 (2)	C8—N1—C13—O1	164.53 (14)
C7—C4—C5—C6	178.12 (14)	C7—N1—C13—N2	173.51 (12)
C2—C1—C6—C5	0.4 (3)	C8—N1—C13—N2	−15.8 (2)
Cl1—C1—C6—C5	−179.41 (12)	C14—N2—C13—O1	−13.1 (2)
C4—C5—C6—C1	−0.1 (2)	C14—N2—C13—N1	167.32 (13)
C13—N1—C7—C4	−81.80 (16)	C13—N2—C14—C19	−40.2 (2)
C8—N1—C7—C4	106.87 (15)	C13—N2—C14—C15	144.02 (15)
C5—C4—C7—N1	169.45 (13)	C19—C14—C15—C16	−1.1 (2)
C3—C4—C7—N1	−12.2 (2)	N2—C14—C15—C16	174.79 (14)
C13—N1—C8—C9	131.17 (15)	C14—C15—C16—C17	1.4 (2)
C7—N1—C8—C9	−58.34 (18)	C15—C16—C17—C18	−0.2 (2)
C13—N1—C8—C12	−108.04 (16)	C16—C17—C18—C19	−1.3 (2)
C7—N1—C8—C12	62.45 (18)	C15—C14—C19—C18	−0.3 (2)
N1—C8—C9—C10	163.14 (14)	N2—C14—C19—C18	−176.06 (14)
C12—C8—C9—C10	36.79 (18)	C17—C18—C19—C14	1.5 (2)
C8—C9—C10—C11	−38.08 (18)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N2—H2N···O1^i	0.828 (19)	2.081 (19)	2.8838 (17)	163.1 (17)

Symmetry code: (i) −x+1/2, y+1/2, z.