organic compounds
1-(4-Bromo-3-chlorophenyl)-3-methoxy-3-methylurea (chlorbromuron)
aDepartment of Chemistry, Truman State University, Kirksville, MO 63501-4221, USA
*Correspondence e-mail: baughman@truman.edu
In the title urea-based herbicide, C9H10BrClN2O2, there exist multiple inter- and intramolecular interactions. Most notably, the intramolecular hydrogen bond between the urea carbonyl O atom and an aromatic H atom affects the planarity and torsion angles of the molecule by restricting rotations about the Ar—secondary amine N and the secondary amine N and the carbonyl C. The two N atoms in the urea fragment are in different environments. One is planar; the other, pseudo-C3v. It is likely that the different nitrogen-atom geometries and the restricted rotations within the molecule impact the bioactivity of chlorbromuron.
Related literature
The structure of the title compound, chlorbromuron, was determined as part of a larger project on the crystal and molecular structures of a series of herbicides, see: Baughman & Yu (1988 and references cited therein). Chlorbromuron is a urea-based herbicide that acts to inhibit photosynthesis and the oxidation of water to oxygen during the Hill reaction, see: Metcalf (1971). Typically one or more hydrogen bonds form between the –NH– or C=O groups in the urea-based herbicides and an active site in the protein, see: Good (1961).
Experimental
Crystal data
|
Refinement
|
|
Data collection: XSCANS (Bruker, 1996); cell XSCANS; data reduction: XSCANS; program(s) used to solve structure: SHELXS86 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL/PC (Sheldrick, 2008); software used to prepare material for publication: SHELXTL/PC and SHELXL97.
Supporting information
https://doi.org/10.1107/S1600536810030606/bv2148sup1.cif
contains datablocks I, global. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536810030606/bv2148Isup2.hkl
Approximate positions of all H's were first obtained from a difference map, then placed into "ideal" positions. Bond lengths were constrained at 0.93 Å (AFIX 43) for aromatic C—H's, at 0.96 Å (AFIX 137) for methyl C—H's, and 0.86 Å (AFIX 43) for the N—H.
Uiso(H) were fixed at 1.5Ueq(parent) for OH and methyl H's, and 1.2 Ueq(parent) for all other H's.
In the final stages of
for (I), 14 very small or negative Fo's were deemed to be in high disagreement and were eliminated from final refinement.Percent decay of the three standards was calculated as the average of their σ(I)'s.
The
of 3-(4-bromo-3-chlorophenyl)-1-methoxy-1- methylurea, chlorbromuron (I), was determined as part of a larger project (Baughman and Yu, 1988 and references cited therein) that has focused on the crystal and molecular structures of a series of herbicides. Chlorbromuron is a urea-based herbicide that acts to inhibit photosynthesis and the oxidation of water to oxygen during the Hill reaction (Metcalf, 1971). Typically one or more hydrogen bonds form between the –NH– or C=O groups in the urea-based herbicides and an active site in the protein (Good, 1961).Molecules in the
utilize intermolecular hydrogen bonds, while the molecule contains intramolecular hydrogen bonds. The O1···H1 intermolecular hydrogen bond and the O2···H1 and O1···H2 intramolecular hydrogen bonds affect the torsion angles (Table 1). The O1···H2 hydrogen bond is interesting because it likely causes H2/C2/C1/N1/C7/O1 to be nearly planar (r.m.s. deviation = 0.167 Å). Similarly, the O2—N2—C7—N1 torsion angle of 20.2 (7)° and near planarity of H1A/N1/C7/N2/O2 (r.m.s. = 0.100 Å) indicate the effect of the O2···H1 hydrogen bond.Since the O1···H2 and O2···H1 intramolecular hydrogen bonds limit rotation, the structure of (I) presented here may also be close to that in vitro and/or in vivo. The limiting of the rotational
about the C1—N1, N1—C7, and C7—N2 bonds may influence the bioactivity of (I). A very weak intermolecular interaction between Cl1 and H9A likely exists, but, at a distance of 3.15 Å, is a little too long to be considered a true hydrogen bond, but may have some impact on packing.Structurally significant angles around N2 indicate a pseudo-C3v shape (Fig. 1, Table 1). However, the geometry around N1 is planar. Although the C4—C3—Cl1 angle [121.1 (5)°] is ~2σ greater than the ideal angle of 120°, the C3—C4—Br1 angle [122.3 (5)°] is ~5σ greater than ideal angle, which indicates some steric and charge repulsion in this portion of the molecule.
The structure of the title compound, chlorbromuron, was determined as part of a larger project on the crystal and molecular structures of a series of herbicides, see: Baughman & Yu (1988 and references cited therein). Chlorbromuron is a urea-based herbicide that acts to inhibit photosynthesis and the oxidation of water to oxygen during the Hill reaction, see: Metcalf (1971). Typically one or more hydrogen bonds form between the –NH– or C=O groups in the urea-based herbicides and an active site in the protein, see: Good (1961).
Data collection: XSCANS (Bruker, 1996); cell
XSCANS (Bruker, 1996); data reduction: XSCANS (Bruker, 1996); program(s) used to solve structure: SHELXS86 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL/PC (Sheldrick, 2008); software used to prepare material for publication: SHELXTL/PC (Sheldrick, 2008) and SHELXL97 (Sheldrick, 2008).Fig. 1. The asymmetric unit of (I). Displacement ellipsoids are drawn at the 50% probability levels; H atoms are drawn as small spheres of arbitrary radius. |
C9H10BrClN2O2 | F(000) = 1168 |
Mr = 293.55 | Dx = 1.675 Mg m−3 |
Orthorhombic, Pbca | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2ac 2ab | Cell parameters from 100 reflections |
a = 11.3872 (7) Å | θ = 10.0–15.8° |
b = 9.5037 (5) Å | µ = 3.74 mm−1 |
c = 21.512 (2) Å | T = 295 K |
V = 2328.0 (3) Å3 | Rectangular prism, colorless |
Z = 8 | 0.44 × 0.44 × 0.42 mm |
Bruker P4 diffractometer | 1230 reflections with I > 2σ(I) |
Radiation source: normal-focus sealed tube | Rint = 0.107 |
Graphite monochromator | θmax = 25.0°, θmin = 1.9° |
Ω scans | h = −1→13 |
Absorption correction: integration (XSHELL; Bruker, 1999) | k = −11→1 |
Tmin = 0.224, Tmax = 0.331 | l = −25→1 |
2643 measured reflections | 3 standard reflections every 100 reflections |
2017 independent reflections | intensity decay: 1.3% |
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)] = 0.065 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.173 | H-atom parameters constrained |
S = 0.99 | w = 1/[σ2(Fo2) + (0.1011P)2 + 0.010P] where P = (Fo2 + 2Fc2)/3 |
2017 reflections | (Δ/σ)max < 0.001 |
136 parameters | Δρmax = 1.13 e Å−3 |
0 restraints | Δρmin = −0.63 e Å−3 |
C9H10BrClN2O2 | V = 2328.0 (3) Å3 |
Mr = 293.55 | Z = 8 |
Orthorhombic, Pbca | Mo Kα radiation |
a = 11.3872 (7) Å | µ = 3.74 mm−1 |
b = 9.5037 (5) Å | T = 295 K |
c = 21.512 (2) Å | 0.44 × 0.44 × 0.42 mm |
Bruker P4 diffractometer | 1230 reflections with I > 2σ(I) |
Absorption correction: integration (XSHELL; Bruker, 1999) | Rint = 0.107 |
Tmin = 0.224, Tmax = 0.331 | 3 standard reflections every 100 reflections |
2643 measured reflections | intensity decay: 1.3% |
2017 independent reflections |
R[F2 > 2σ(F2)] = 0.065 | 0 restraints |
wR(F2) = 0.173 | H-atom parameters constrained |
S = 0.99 | Δρmax = 1.13 e Å−3 |
2017 reflections | Δρmin = −0.63 e Å−3 |
136 parameters |
Geometry. All s.u.'s (except the s.u. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell s.u.'s are taken into account individually in the estimation of s.u.'s in distances, angles and torsion angles; correlations between s.u.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell s.u.'s is used for estimating s.u.'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 > 2σ(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. |
x | y | z | Uiso*/Ueq | ||
Br1 | 0.99321 (6) | 0.13975 (8) | 0.40066 (3) | 0.0648 (4) | |
Cl1 | 0.75978 (19) | −0.0374 (2) | 0.44369 (7) | 0.0690 (6) | |
O1 | 0.6655 (4) | 0.0148 (4) | 0.6675 (2) | 0.0571 (12) | |
O2 | 0.6463 (4) | 0.3363 (4) | 0.7430 (2) | 0.0560 (12) | |
N1 | 0.7597 (4) | 0.2249 (5) | 0.6520 (2) | 0.0424 (12) | |
H1 | 0.7741 | 0.3050 | 0.6690 | 0.051* | |
N2 | 0.6419 (5) | 0.1877 (5) | 0.7384 (2) | 0.0501 (14) | |
C1 | 0.8124 (5) | 0.1972 (6) | 0.5945 (3) | 0.0389 (14) | |
C2 | 0.7677 (6) | 0.1002 (6) | 0.5513 (3) | 0.0449 (15) | |
H2 | 0.7011 | 0.0479 | 0.5609 | 0.054* | |
C3 | 0.8216 (5) | 0.0839 (6) | 0.4948 (3) | 0.0457 (15) | |
C4 | 0.9200 (5) | 0.1589 (6) | 0.4788 (3) | 0.0443 (15) | |
C5 | 0.9659 (5) | 0.2525 (7) | 0.5221 (3) | 0.0506 (17) | |
H5 | 1.0328 | 0.3040 | 0.5121 | 0.061* | |
C6 | 0.9133 (6) | 0.2707 (6) | 0.5784 (3) | 0.0466 (15) | |
H6 | 0.9457 | 0.3331 | 0.6070 | 0.056* | |
C7 | 0.6870 (6) | 0.1363 (7) | 0.6830 (3) | 0.0429 (15) | |
C8 | 0.5314 (7) | 0.1313 (8) | 0.7610 (4) | 0.074 (2) | |
H8A | 0.5320 | 0.0306 | 0.7571 | 0.111* | |
H8B | 0.5204 | 0.1565 | 0.8038 | 0.111* | |
H8C | 0.4684 | 0.1693 | 0.7366 | 0.111* | |
C9 | 0.7083 (8) | 0.3723 (8) | 0.7985 (3) | 0.079 (2) | |
H9A | 0.7121 | 0.4729 | 0.8023 | 0.118* | |
H9B | 0.6691 | 0.3336 | 0.8341 | 0.118* | |
H9C | 0.7864 | 0.3348 | 0.7960 | 0.118* |
U11 | U22 | U33 | U12 | U13 | U23 | |
Br1 | 0.0657 (5) | 0.0802 (6) | 0.0485 (5) | 0.0019 (4) | 0.0147 (4) | 0.0053 (4) |
Cl1 | 0.0940 (14) | 0.0718 (12) | 0.0412 (9) | −0.0225 (10) | 0.0052 (10) | −0.0125 (9) |
O1 | 0.084 (3) | 0.038 (3) | 0.049 (3) | −0.006 (2) | 0.007 (3) | −0.005 (2) |
O2 | 0.071 (3) | 0.047 (2) | 0.051 (3) | 0.007 (2) | 0.003 (2) | −0.013 (2) |
N1 | 0.049 (3) | 0.037 (3) | 0.041 (3) | 0.003 (2) | −0.001 (3) | −0.008 (2) |
N2 | 0.065 (4) | 0.042 (3) | 0.043 (3) | 0.006 (3) | 0.009 (3) | −0.007 (2) |
C1 | 0.043 (3) | 0.033 (3) | 0.041 (3) | 0.008 (3) | −0.001 (3) | 0.000 (3) |
C2 | 0.051 (4) | 0.042 (3) | 0.042 (3) | −0.002 (3) | 0.005 (3) | 0.005 (3) |
C3 | 0.053 (4) | 0.043 (3) | 0.041 (4) | 0.000 (3) | −0.002 (3) | 0.001 (3) |
C4 | 0.041 (4) | 0.051 (4) | 0.040 (3) | 0.009 (3) | 0.005 (3) | 0.002 (3) |
C5 | 0.039 (3) | 0.047 (4) | 0.065 (5) | −0.006 (3) | 0.000 (3) | 0.009 (3) |
C6 | 0.050 (4) | 0.046 (4) | 0.045 (4) | −0.003 (3) | −0.003 (3) | −0.002 (3) |
C7 | 0.052 (4) | 0.042 (4) | 0.035 (3) | 0.007 (3) | −0.004 (3) | 0.000 (3) |
C8 | 0.077 (5) | 0.074 (5) | 0.070 (5) | −0.009 (4) | 0.024 (4) | −0.009 (4) |
C9 | 0.094 (6) | 0.088 (6) | 0.054 (5) | −0.018 (5) | 0.003 (4) | −0.023 (4) |
Br1—C4 | 1.885 (6) | C2—H2 | 0.9303 |
Cl1—C3 | 1.741 (6) | C3—C4 | 1.372 (9) |
O1—C7 | 1.227 (7) | C4—C5 | 1.390 (9) |
O2—N2 | 1.417 (6) | C5—C6 | 1.363 (9) |
O2—C9 | 1.428 (8) | C5—H5 | 0.9302 |
N1—C7 | 1.356 (8) | C6—H6 | 0.9302 |
N1—C1 | 1.401 (7) | C8—H8A | 0.9604 |
N1—H1 | 0.8602 | C8—H8B | 0.9599 |
N2—C7 | 1.385 (7) | C8—H8C | 0.9601 |
N2—C8 | 1.452 (9) | C9—H9A | 0.9605 |
C1—C6 | 1.388 (8) | C9—H9B | 0.9600 |
C1—C2 | 1.404 (8) | C9—H9C | 0.9602 |
C2—C3 | 1.372 (8) | ||
N2—O2—C9 | 108.4 (5) | C6—C5—H5 | 119.9 |
C7—N1—C1 | 125.4 (5) | C4—C5—H5 | 119.3 |
C7—N1—H1 | 117.2 | C5—C6—C1 | 121.4 (6) |
C1—N1—H1 | 117.4 | C5—C6—H6 | 119.6 |
C7—N2—O2 | 113.5 (5) | C1—C6—H6 | 119.0 |
C7—N2—C8 | 118.6 (6) | O1—C7—N1 | 124.9 (5) |
O2—N2—C8 | 112.0 (5) | O1—C7—N2 | 119.5 (6) |
C6—C1—N1 | 118.7 (5) | N1—C7—N2 | 115.4 (5) |
C6—C1—C2 | 117.8 (6) | N2—C8—H8A | 109.4 |
N1—C1—C2 | 123.5 (5) | N2—C8—H8B | 110.0 |
C3—C2—C1 | 119.9 (6) | H8A—C8—H8B | 109.5 |
C3—C2—H2 | 120.1 | N2—C8—H8C | 109.0 |
C1—C2—H2 | 120.0 | H8A—C8—H8C | 109.5 |
C4—C3—C2 | 121.9 (6) | H8B—C8—H8C | 109.5 |
C4—C3—Cl1 | 121.1 (5) | O2—C9—H9A | 109.4 |
C2—C3—Cl1 | 117.0 (5) | O2—C9—H9B | 110.2 |
C3—C4—C5 | 118.1 (6) | H9A—C9—H9B | 109.5 |
C3—C4—Br1 | 122.3 (5) | O2—C9—H9C | 108.8 |
C5—C4—Br1 | 119.6 (5) | H9A—C9—H9C | 109.5 |
C6—C5—C4 | 120.8 (6) | H9B—C9—H9C | 109.5 |
C9—O2—N2—C7 | −124.6 (6) | C3—C4—C5—C6 | −1.1 (9) |
C9—O2—N2—C8 | 97.8 (7) | Br1—C4—C5—C6 | 178.5 (5) |
C7—N1—C1—C6 | −157.8 (6) | C4—C5—C6—C1 | −0.1 (9) |
C7—N1—C1—C2 | 23.3 (9) | N1—C1—C6—C5 | −177.4 (5) |
C6—C1—C2—C3 | −1.8 (9) | C2—C1—C6—C5 | 1.6 (9) |
N1—C1—C2—C3 | 177.0 (5) | C1—N1—C7—O1 | 6.7 (10) |
C1—C2—C3—C4 | 0.7 (9) | C1—N1—C7—N2 | −178.0 (5) |
C1—C2—C3—Cl1 | −179.4 (5) | O2—N2—C7—O1 | −164.2 (5) |
C2—C3—C4—C5 | 0.8 (9) | C8—N2—C7—O1 | −29.6 (9) |
Cl1—C3—C4—C5 | −179.1 (5) | O2—N2—C7—N1 | 20.2 (7) |
C2—C3—C4—Br1 | −178.8 (5) | C8—N2—C7—N1 | 154.8 (6) |
Cl1—C3—C4—Br1 | 1.3 (8) |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···O1i | 0.86 | 2.11 | 2.902 (7) | 153 |
N1—H1···O2 | 0.86 | 2.18 | 2.573 (6) | 108 |
C2—H2···O1 | 0.93 | 2.35 | 2.873 (7) | 115 |
Symmetry code: (i) −x+3/2, y+1/2, z. |
Experimental details
Crystal data | |
Chemical formula | C9H10BrClN2O2 |
Mr | 293.55 |
Crystal system, space group | Orthorhombic, Pbca |
Temperature (K) | 295 |
a, b, c (Å) | 11.3872 (7), 9.5037 (5), 21.512 (2) |
V (Å3) | 2328.0 (3) |
Z | 8 |
Radiation type | Mo Kα |
µ (mm−1) | 3.74 |
Crystal size (mm) | 0.44 × 0.44 × 0.42 |
Data collection | |
Diffractometer | Bruker P4 diffractometer |
Absorption correction | Integration (XSHELL; Bruker, 1999) |
Tmin, Tmax | 0.224, 0.331 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 2643, 2017, 1230 |
Rint | 0.107 |
(sin θ/λ)max (Å−1) | 0.594 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.065, 0.173, 0.99 |
No. of reflections | 2017 |
No. of parameters | 136 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 1.13, −0.63 |
Computer programs: XSCANS (Bruker, 1996), SHELXS86 (Sheldrick, 2008), SHELXTL/PC (Sheldrick, 2008) and SHELXL97 (Sheldrick, 2008).
Br1—C4 | 1.885 (6) | O1—C7 | 1.227 (7) |
Cl1—C3 | 1.741 (6) | O2—N2 | 1.417 (6) |
C7—N1—C1 | 125.4 (5) | C7—N2—O2 | 113.5 (5) |
C7—N1—H1 | 117.2 | C7—N2—C8 | 118.6 (6) |
C1—N1—H1 | 117.4 | O2—N2—C8 | 112.0 (5) |
C9—O2—N2—C7 | −124.6 (6) | C7—N1—C1—C2 | 23.3 (9) |
C9—O2—N2—C8 | 97.8 (7) | O2—N2—C7—N1 | 20.2 (7) |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···O1i | 0.86 | 2.11 | 2.902 (7) | 153 |
N1—H1···O2 | 0.86 | 2.18 | 2.573 (6) | 108 |
C2—H2···O1 | 0.93 | 2.35 | 2.873 (7) | 115 |
Symmetry code: (i) −x+3/2, y+1/2, z. |
Acknowledgements
This material is based upon work supported by the National Science Foundation under grant No. DUE-0431664.
References
Baughman, R. G. & Yu, P.-J. (1988). J. Agric. Food Chem. 36, 1294–6. CSD CrossRef CAS Web of Science Google Scholar
Bruker (1996). XSCANS. Bruker AXS Inc., Madison, Wisconsin, USA. Google Scholar
Bruker (1999). XSHELL. Bruker AXS Inc., Madison, Wisconsin, USA. Google Scholar
Good, N. E. (1961). Plant Physiol. 36, 788–803. CrossRef PubMed CAS Web of Science Google Scholar
Metcalf, R. L. (1971). Pesticides in the Environment, Vol. 1, Part 1, edited by R. White-Stevens, p. 51. New York: Marcel Dekker. Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar
This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.
The crystal structure of 3-(4-bromo-3-chlorophenyl)-1-methoxy-1- methylurea, chlorbromuron (I), was determined as part of a larger project (Baughman and Yu, 1988 and references cited therein) that has focused on the crystal and molecular structures of a series of herbicides. Chlorbromuron is a urea-based herbicide that acts to inhibit photosynthesis and the oxidation of water to oxygen during the Hill reaction (Metcalf, 1971). Typically one or more hydrogen bonds form between the –NH– or C=O groups in the urea-based herbicides and an active site in the protein (Good, 1961).
Molecules in the unit cell utilize intermolecular hydrogen bonds, while the molecule contains intramolecular hydrogen bonds. The O1···H1 intermolecular hydrogen bond and the O2···H1 and O1···H2 intramolecular hydrogen bonds affect the torsion angles (Table 1). The O1···H2 hydrogen bond is interesting because it likely causes H2/C2/C1/N1/C7/O1 to be nearly planar (r.m.s. deviation = 0.167 Å). Similarly, the O2—N2—C7—N1 torsion angle of 20.2 (7)° and near planarity of H1A/N1/C7/N2/O2 (r.m.s. = 0.100 Å) indicate the effect of the O2···H1 hydrogen bond.
Since the O1···H2 and O2···H1 intramolecular hydrogen bonds limit rotation, the structure of (I) presented here may also be close to that in vitro and/or in vivo. The limiting of the rotational degrees of freedom about the C1—N1, N1—C7, and C7—N2 bonds may influence the bioactivity of (I). A very weak intermolecular interaction between Cl1 and H9A likely exists, but, at a distance of 3.15 Å, is a little too long to be considered a true hydrogen bond, but may have some impact on packing.
Structurally significant angles around N2 indicate a pseudo-C3v shape (Fig. 1, Table 1). However, the geometry around N1 is planar. Although the C4—C3—Cl1 angle [121.1 (5)°] is ~2σ greater than the ideal angle of 120°, the C3—C4—Br1 angle [122.3 (5)°] is ~5σ greater than ideal angle, which indicates some steric and charge repulsion in this portion of the molecule.