Literature DB >> 27980838

Crystal structure of oxam-yl.

Eunjin Kwon1, Ki-Min Park1, Hyunjin Park1, Tae Ho Kim1.   

Abstract

The title compound, C7H13N3O3S [systematic name: (Z)-methyl 2-di-methyl-amino-N-(methyl-carbamo-yloxy)-2-oxoethanimido-thio-ate], is an oxime carbamate acaride, insecticide and nematicide. The asymmetric unit comprises two independent mol-ecules, A and B. The dihedral angles between the mean planes [r.m.s. deviations = 0.0017 (A) and 0.0016 Å (B)] of the acetamide and oxyimino groups are 88.80 (8)° for A and 87.05 (8)° for B. In the crystal, N/C-H⋯O hydrogen bonds link adjacent mol-ecules, forming chains along the a axis. The chains are further linked by C-H⋯O hydrogen bonds, resulting in a three-dimensional network with alternating rows of A and B mol-ecules in the bc plane stacked along the a-axis direction. The structure was refined as an inversion twin with a final BASF parameter of 0.16 (9).

Entities:  

Keywords:  acaricide; crystal structure; insecticide; nematicide; oxam­yl

Year:  2016        PMID: 27980838      PMCID: PMC5137616          DOI: 10.1107/S2056989016018168

Source DB:  PubMed          Journal:  Acta Crystallogr E Crystallogr Commun


Chemical context

Oxamyl [(N,N-dimethyl-2-methyl­carbamoyloximino-2-(di­methyl­sulfan­yl)acetamide] is a carbamate compound used in a wide range of agricultural situations. It is systemic and active as an insecticide or a nematicide. It is used for the control of nematodes in vegetables, bananas, pineapple, peanuts, cotton, soya beans, tobacco, potatoes, sugar beet, and other crops. It is also used in India for controlling the growth of nematodes on vegetable crops (Mohammad et al., 2015 ▸; Agarwal et al., 2016 ▸). In addition, oxamyl was classified by the World Health Organization (WHO) as highly haza­rdous (class IB) (Al-Dabbas et al., 2014 ▸). Oxamyl can be integrated with horse manure, sesame-oil-cake, or Bacillus thuringiensis to improve eggplant growth response and reduce development of the nematode Meloidogyne incognita (Osman et al., 2009 ▸). Also, oxamyl has a very high water solubility (280 g/L at 298 K) and low sorption solubility affinity to soils. As a result of these properties, oxamyl easily migrates into the water compartment (Mazellier et al., 2010 ▸). Herein, we report the mol­ecular and crystal structure of oxamyl.

Structural commentary

The asymmetric unit of oxamyl comprises two independent mol­ecules, A and B (Fig. 1 ▸). The compound consists of carbamate, acetamide, methyl­thio and oxyimino functional groups. The dihedral angles between the mean planes [r.m.s. deviations = 0.0017 (A) and 0.0016 Å (B)] of the acetamide and oxyimino groups are 88.80 (8) for A and 87.05 (8)° for B. All bond lengths and bond angles are normal and comparable to those observed in methomyl [systematic name: (E)-methyl N-(methyl­carbamo­yl)oxyethanimido­thio­ate] which adopts similar crystal structure (Takusagawa & Jacobson, 1977 ▸).
Figure 1

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

Supra­molecular features

The crystal structure is stabilized by several N—H⋯O and C—H⋯O hydrogen bonds (Table 1 ▸). Adjacent A mol­ecules form inter­molecular N1—H1N⋯O1 hydrogen bonds. In addition, C6—H6B⋯O2 and C7—H7B⋯O1 hydrogen bonds between the carbamate and di­methyl­amine groups generate (8) inversion dimers. These contacts link the A mol­ecules into double chains along the a axis. A closely similar situation obtains for the B mol­ecules, with inter­molecular N4—H4N⋯O4 hydrogen bonds together with C13—H13B⋯O4 and C14—H14B⋯O5 (8) inversion dimers also forming a double chain, this time solely of B mol­ecules, parallel to the one described previously, again along the a axis, Fig. 2 ▸. The A and B double chains are further linked by C4—H4B⋯O6 and C11—H11B⋯O3 contacts, Table 1 ▸, to give a three-dimensional network with alternating rows of A and B mol­ecules in the bc plane stacked along the a-axis direction, Fig. 3 ▸.
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯A D—HH⋯A DA D—H⋯A
N1—H1N⋯O1i 0.882.132.871 (3)142
N4—H4N⋯O4ii 0.882.042.794 (3)142
C4—H4B⋯O6iii 0.982.543.075 (4)114
C6—H6B⋯O2iv 0.982.603.518 (4)156
C7—H7B⋯O1iv 0.982.523.431 (4)155
C11—H11B⋯O3v 0.982.533.042 (4)113
C13—H13B⋯O4iv 0.982.533.440 (4)155
C14—H14B⋯O5iv 0.982.593.554 (4)168

Symmetry codes: (i) ; (ii) ; (iii) ; (iv) ; (v) .

Figure 2

The double chains formed through inter­molecular N—H⋯O (black dashed lines) and C—H⋯O (sky-blue dashed lines) hydrogen bonds. The A and B mol­ecules are shown in green and yellow, respectively. H atoms not involved in inter­molecular inter­actions have been omitted for clarity.

Figure 3

The three-dimensional network made up of mol­ecules A (green) and B (yellow). Black dashed lines represent inter­molecular N—H⋯O hydrogen bonds. The C—H⋯O hydrogen bonds are shown as sky-blue (between each mol­ecule A or B) and red (between mol­ecules A and B) dashed lines, respectively. H atoms not involved in inter­molecular inter­actions have been omitted for clarity.

Synthesis and crystallization

The title compound was purchased from Dr Ehrenstorfer GmbH. Slow evaporation of its solution in CH3OH gave single crystals suitable for X-ray analysis.

Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2 ▸. All C-bound H atoms were positioned geometrically [with d(N—H) = 0.88 Å, U iso = 1.2U eq(C) for N—H group, U iso = 1.5U eq(C) for methyl group, d(C—H) = 0.98 Å]. The crystal studied was an inversion twin with a 0.84 (9):0.16 (9) domain ratio.
Table 2

Experimental details

Crystal data
Chemical formulaC7H13N3O3S
M r 219.26
Crystal system, space groupOrthorhombic, P c a21
Temperature (K)173
a, b, c (Å)8.3367 (4), 10.7752 (5), 24.1016 (12)
V3)2165.04 (18)
Z 8
Radiation typeMo Kα
μ (mm−1)0.29
Crystal size (mm)0.50 × 0.14 × 0.11
 
Data collection
DiffractometerBruker APEXII CCD
Absorption correctionMulti-scan (SADABS; Bruker, 2014)
T min, T max 0.665, 0.746
No. of measured, independent and observed [I > 2σ(I)] reflections19300, 5238, 4655
R int 0.035
(sin θ/λ)max−1)0.667
 
Refinement
R[F 2 > 2σ(F 2)], wR(F 2), S 0.037, 0.090, 1.04
No. of reflections5238
No. of parameters262
No. of restraints1
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å−3)0.21, −0.23
Absolute structureRefined as an inversion twin
Absolute structure parameter0.16 (9)

Computer programs: APEX2 and SAINT (Bruker, 2014 ▸), SHELXS97 and SHELXTL (Sheldrick, 2008 ▸), SHELXL2014 (Sheldrick, 2015 ▸), DIAMOND (Brandenburg, 2010 ▸) and publCIF (Westrip, 2010 ▸).

Crystal structure: contains datablock(s) I, New_Global_Publ_Block. DOI: 10.1107/S2056989016018168/sj5514sup1.cif Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989016018168/sj5514Isup2.hkl Click here for additional data file. Supporting information file. DOI: 10.1107/S2056989016018168/sj5514Isup3.cml CCDC reference: 1516996 Additional supporting information: crystallographic information; 3D view; checkCIF report
C7H13N3O3SDx = 1.345 Mg m3
Mr = 219.26Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, Pca21Cell parameters from 6335 reflections
a = 8.3367 (4) Åθ = 2.5–27.8°
b = 10.7752 (5) ŵ = 0.29 mm1
c = 24.1016 (12) ÅT = 173 K
V = 2165.04 (18) Å3Plate, colourless
Z = 80.50 × 0.14 × 0.11 mm
F(000) = 928
Bruker APEXII CCD diffractometer4655 reflections with I > 2σ(I)
φ and ω scansRint = 0.035
Absorption correction: multi-scan (SADABS; Bruker, 2014)θmax = 28.3°, θmin = 1.7°
Tmin = 0.665, Tmax = 0.746h = −11→11
19300 measured reflectionsk = −14→14
5238 independent reflectionsl = −32→31
Refinement on F2Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: fullH-atom parameters constrained
R[F2 > 2σ(F2)] = 0.037w = 1/[σ2(Fo2) + (0.0432P)2 + 0.3998P] where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.090(Δ/σ)max < 0.001
S = 1.04Δρmax = 0.21 e Å3
5238 reflectionsΔρmin = −0.23 e Å3
262 parametersAbsolute structure: Refined as an inversion twin
1 restraintAbsolute structure parameter: 0.16 (9)
Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.
Refinement. Refined as a 2-component inversion twin.
xyzUiso*/Ueq
S10.55678 (10)0.32807 (7)0.87717 (3)0.0373 (2)
S20.97239 (10)0.16264 (7)0.54545 (3)0.0376 (2)
O10.8636 (3)0.13823 (18)0.74085 (9)0.0308 (5)
O20.6589 (2)0.17413 (17)0.79576 (8)0.0270 (4)
O30.2966 (3)0.0966 (2)0.91570 (10)0.0431 (6)
O41.2851 (3)0.36802 (18)0.67471 (9)0.0307 (5)
O51.0771 (3)0.32628 (17)0.62210 (9)0.0282 (5)
O60.7167 (3)0.3997 (2)0.50123 (10)0.0403 (6)
N10.6479 (3)0.0112 (2)0.73350 (10)0.0290 (5)
H1N0.5497−0.00370.74510.035*
N20.5009 (3)0.1328 (2)0.81132 (10)0.0272 (5)
N30.1571 (3)0.2143 (2)0.85463 (10)0.0303 (6)
N41.0729 (3)0.4993 (2)0.67852 (10)0.0287 (5)
H4N0.97640.51510.66550.034*
N50.9217 (3)0.3683 (2)0.60490 (10)0.0261 (5)
N60.5764 (3)0.2808 (2)0.56227 (10)0.0291 (6)
C10.7188 (4)−0.0672 (3)0.69115 (14)0.0348 (7)
H1A0.7844−0.01640.66620.052*
H1B0.6335−0.10790.66990.052*
H1C0.7863−0.13040.70880.052*
C20.7298 (4)0.1050 (2)0.75477 (12)0.0244 (6)
C30.4493 (4)0.2044 (3)0.84969 (11)0.0242 (6)
C40.4197 (5)0.3917 (4)0.92805 (16)0.0481 (10)
H4A0.32550.42600.90910.072*
H4B0.47360.45760.94900.072*
H4C0.38580.32590.95360.072*
C50.2909 (3)0.1659 (3)0.87589 (13)0.0271 (6)
C60.0028 (4)0.1835 (4)0.88024 (16)0.0398 (8)
H6A0.01710.11380.90590.060*
H6B−0.07420.16040.85130.060*
H6C−0.03760.25570.90070.060*
C70.1526 (4)0.3046 (3)0.80973 (14)0.0372 (7)
H7A0.11880.38530.82430.056*
H7B0.07640.27700.78130.056*
H7C0.25970.31220.79330.056*
C81.1426 (4)0.5816 (3)0.71943 (13)0.0348 (7)
H8A1.18340.53260.75070.052*
H8B1.06070.63960.73270.052*
H8C1.23110.62810.70260.052*
C91.1516 (4)0.4014 (2)0.66055 (11)0.0242 (6)
C100.8681 (4)0.2936 (2)0.56845 (11)0.0240 (6)
C110.8379 (5)0.0982 (3)0.49430 (15)0.0462 (9)
H11A0.74310.06410.51290.069*
H11B0.89280.03200.47390.069*
H11C0.80490.16350.46840.069*
C120.7109 (4)0.3295 (2)0.54159 (13)0.0267 (6)
C130.5720 (4)0.1938 (3)0.60790 (14)0.0366 (7)
H13A0.53640.11260.59440.055*
H13B0.49720.22380.63630.055*
H13C0.67950.18610.62400.055*
C140.4231 (4)0.3106 (4)0.53622 (15)0.0420 (8)
H14A0.43010.39220.51840.063*
H14B0.33860.31200.56450.063*
H14C0.39760.24760.50830.063*
U11U22U33U12U13U23
S10.0356 (4)0.0368 (4)0.0393 (4)−0.0072 (3)0.0091 (4)−0.0137 (4)
S20.0352 (4)0.0330 (4)0.0447 (5)0.0083 (3)−0.0103 (4)−0.0155 (4)
O10.0210 (10)0.0284 (10)0.0428 (12)−0.0018 (9)0.0060 (9)−0.0027 (9)
O20.0212 (10)0.0271 (10)0.0325 (11)−0.0017 (8)0.0047 (9)−0.0055 (8)
O30.0392 (14)0.0478 (13)0.0423 (13)0.0036 (11)0.0085 (11)0.0196 (11)
O40.0246 (11)0.0275 (10)0.0401 (12)−0.0007 (9)−0.0058 (10)0.0029 (9)
O50.0211 (10)0.0257 (10)0.0379 (12)0.0023 (8)−0.0061 (9)−0.0072 (9)
O60.0342 (13)0.0476 (12)0.0393 (12)0.0008 (11)−0.0035 (10)0.0185 (11)
N10.0227 (12)0.0282 (11)0.0360 (13)−0.0003 (10)0.0061 (10)−0.0077 (10)
N20.0233 (13)0.0265 (12)0.0318 (13)−0.0011 (11)0.0054 (11)0.0001 (10)
N30.0269 (13)0.0338 (13)0.0303 (13)−0.0022 (11)0.0031 (11)0.0026 (10)
N40.0259 (12)0.0261 (11)0.0343 (12)0.0015 (10)−0.0078 (10)−0.0065 (10)
N50.0204 (12)0.0268 (11)0.0310 (13)0.0025 (10)−0.0039 (10)−0.0028 (10)
N60.0242 (13)0.0338 (12)0.0293 (13)−0.0019 (10)−0.0014 (10)−0.0019 (10)
C10.0351 (17)0.0295 (15)0.0398 (17)0.0018 (13)0.0061 (14)−0.0103 (12)
C20.0232 (15)0.0219 (12)0.0281 (14)0.0057 (11)0.0031 (12)0.0023 (11)
C30.0265 (15)0.0235 (13)0.0225 (13)0.0020 (12)0.0005 (11)0.0021 (11)
C40.047 (2)0.052 (2)0.045 (2)0.0018 (18)0.0094 (18)−0.0225 (17)
C50.0276 (15)0.0256 (13)0.0282 (14)−0.0014 (11)0.0051 (13)−0.0014 (12)
C60.0255 (15)0.055 (2)0.0388 (17)−0.0041 (15)0.0053 (16)−0.0005 (16)
C70.0364 (18)0.0385 (17)0.0368 (17)0.0014 (14)−0.0027 (15)0.0072 (14)
C80.0439 (19)0.0293 (14)0.0311 (15)−0.0019 (14)−0.0055 (14)−0.0050 (12)
C90.0236 (14)0.0225 (13)0.0266 (13)−0.0036 (11)−0.0002 (12)0.0020 (11)
C100.0262 (15)0.0210 (12)0.0249 (13)0.0001 (12)0.0008 (11)0.0001 (11)
C110.048 (2)0.0461 (19)0.045 (2)0.0003 (17)−0.0105 (17)−0.0213 (16)
C120.0277 (15)0.0253 (12)0.0271 (14)0.0005 (11)−0.0025 (13)−0.0024 (12)
C130.0346 (18)0.0368 (16)0.0383 (18)−0.0050 (14)0.0050 (14)0.0040 (14)
C140.0240 (15)0.057 (2)0.045 (2)0.0030 (15)−0.0041 (15)0.0001 (16)
S1—C31.737 (3)C1—H1A0.9800
S1—C41.811 (3)C1—H1B0.9800
S2—C101.748 (3)C1—H1C0.9800
S2—C111.805 (3)C3—C51.521 (4)
O1—C21.218 (4)C4—H4A0.9800
O2—C21.371 (3)C4—H4B0.9800
O2—N21.440 (3)C4—H4C0.9800
O3—C51.216 (4)C6—H6A0.9800
O4—C91.219 (4)C6—H6B0.9800
O5—C91.378 (3)C6—H6C0.9800
O5—N51.434 (3)C7—H7A0.9800
O6—C121.233 (4)C7—H7B0.9800
N1—C21.323 (4)C7—H7C0.9800
N1—C11.451 (4)C8—H8A0.9800
N1—H1N0.8800C8—H8B0.9800
N2—C31.279 (4)C8—H8C0.9800
N3—C51.334 (4)C10—C121.512 (4)
N3—C71.455 (4)C11—H11A0.9800
N3—C61.464 (4)C11—H11B0.9800
N4—C91.315 (4)C11—H11C0.9800
N4—C81.448 (4)C13—H13A0.9800
N4—H4N0.8800C13—H13B0.9800
N5—C101.272 (4)C13—H13C0.9800
N6—C121.334 (4)C14—H14A0.9800
N6—C131.445 (4)C14—H14B0.9800
N6—C141.460 (4)C14—H14C0.9800
C3—S1—C4102.89 (16)N3—C6—H6C109.5
C10—S2—C11102.61 (16)H6A—C6—H6C109.5
C2—O2—N2114.5 (2)H6B—C6—H6C109.5
C9—O5—N5114.6 (2)N3—C7—H7A109.5
C2—N1—C1120.5 (2)N3—C7—H7B109.5
C2—N1—H1N119.8H7A—C7—H7B109.5
C1—N1—H1N119.8N3—C7—H7C109.5
C3—N2—O2108.1 (2)H7A—C7—H7C109.5
C5—N3—C7124.6 (3)H7B—C7—H7C109.5
C5—N3—C6118.9 (3)N4—C8—H8A109.5
C7—N3—C6116.3 (3)N4—C8—H8B109.5
C9—N4—C8121.0 (3)H8A—C8—H8B109.5
C9—N4—H4N119.5N4—C8—H8C109.5
C8—N4—H4N119.5H8A—C8—H8C109.5
C10—N5—O5108.5 (2)H8B—C8—H8C109.5
C12—N6—C13124.1 (3)O4—C9—N4126.9 (3)
C12—N6—C14119.2 (3)O4—C9—O5115.2 (2)
C13—N6—C14116.6 (3)N4—C9—O5117.9 (3)
N1—C1—H1A109.5N5—C10—C12116.0 (2)
N1—C1—H1B109.5N5—C10—S2123.7 (2)
H1A—C1—H1B109.5C12—C10—S2120.1 (2)
N1—C1—H1C109.5S2—C11—H11A109.5
H1A—C1—H1C109.5S2—C11—H11B109.5
H1B—C1—H1C109.5H11A—C11—H11B109.5
O1—C2—N1126.2 (3)S2—C11—H11C109.5
O1—C2—O2115.7 (2)H11A—C11—H11C109.5
N1—C2—O2118.1 (3)H11B—C11—H11C109.5
N2—C3—C5115.3 (2)O6—C12—N6124.7 (3)
N2—C3—S1124.4 (2)O6—C12—C10117.4 (3)
C5—C3—S1119.9 (2)N6—C12—C10117.9 (3)
S1—C4—H4A109.5N6—C13—H13A109.5
S1—C4—H4B109.5N6—C13—H13B109.5
H4A—C4—H4B109.5H13A—C13—H13B109.5
S1—C4—H4C109.5N6—C13—H13C109.5
H4A—C4—H4C109.5H13A—C13—H13C109.5
H4B—C4—H4C109.5H13B—C13—H13C109.5
O3—C5—N3125.1 (3)N6—C14—H14A109.5
O3—C5—C3117.4 (3)N6—C14—H14B109.5
N3—C5—C3117.4 (3)H14A—C14—H14B109.5
N3—C6—H6A109.5N6—C14—H14C109.5
N3—C6—H6B109.5H14A—C14—H14C109.5
H6A—C6—H6B109.5H14B—C14—H14C109.5
C2—O2—N2—C3179.8 (2)S1—C3—C5—N393.6 (3)
C9—O5—N5—C10178.1 (2)C8—N4—C9—O40.0 (5)
C1—N1—C2—O13.0 (5)C8—N4—C9—O5179.2 (2)
C1—N1—C2—O2−178.2 (3)N5—O5—C9—O4−178.6 (2)
N2—O2—C2—O1179.9 (2)N5—O5—C9—N42.1 (3)
N2—O2—C2—N11.0 (3)O5—N5—C10—C12−174.7 (2)
O2—N2—C3—C5−173.4 (2)O5—N5—C10—S20.4 (3)
O2—N2—C3—S1−0.5 (3)C11—S2—C10—N5−179.2 (3)
C4—S1—C3—N2179.3 (3)C11—S2—C10—C12−4.2 (3)
C4—S1—C3—C5−8.0 (3)C13—N6—C12—O6176.8 (3)
C7—N3—C5—O3175.0 (3)C14—N6—C12—O60.1 (4)
C6—N3—C5—O3−0.1 (5)C13—N6—C12—C10−1.4 (4)
C7—N3—C5—C3−2.4 (4)C14—N6—C12—C10−178.1 (3)
C6—N3—C5—C3−177.5 (3)N5—C10—C12—O685.8 (3)
N2—C3—C5—O389.3 (3)S2—C10—C12—O6−89.5 (3)
S1—C3—C5—O3−84.0 (3)N5—C10—C12—N6−95.9 (3)
N2—C3—C5—N3−93.1 (3)S2—C10—C12—N688.8 (3)
D—H···AD—HH···AD···AD—H···A
N1—H1N···O1i0.882.132.871 (3)142
N4—H4N···O4ii0.882.042.794 (3)142
C4—H4B···O6iii0.982.543.075 (4)114
C6—H6B···O2iv0.982.603.518 (4)156
C7—H7B···O1iv0.982.523.431 (4)155
C11—H11B···O3v0.982.533.042 (4)113
C13—H13B···O4iv0.982.533.440 (4)155
C14—H14B···O5iv0.982.593.554 (4)168
  4 in total

1.  A short history of SHELX.

Authors:  George M Sheldrick
Journal:  Acta Crystallogr A       Date:  2007-12-21       Impact factor: 2.290

2.  Crystal and molecular structure of carbamate insecticides. 3. Methomyl.

Authors:  F Takusagawa; R A Jacobson
Journal:  J Agric Food Chem       Date:  1977 May-Jun       Impact factor: 5.279

3.  Adsorption of toxic carbamate pesticide oxamyl from liquid phase by newly synthesized and characterized graphene quantum dots nanomaterials.

Authors:  Shilpi Agarwal; Nima Sadeghi; Inderjeet Tyagi; Vinod Kumar Gupta; Ali Fakhri
Journal:  J Colloid Interface Sci       Date:  2016-06-10       Impact factor: 8.128

4.  Crystal structure refinement with SHELXL.

Authors:  George M Sheldrick
Journal:  Acta Crystallogr C Struct Chem       Date:  2015-01-01       Impact factor: 1.172

  4 in total

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