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Acta Crystallogr Sect E Struct Rep Online. 2008 January 1; 64(Pt 1): o121.
Published online 2007 December 6. doi:  10.1107/S1600536807062071
PMCID: PMC2915191

1-(2-Chloro-1,3-thia­zol-5-ylmeth­yl)-3,5-dimethyl-2-nitrimino-1,2,3,4,5,6-hexa­hydro-1,3,5-triazine

Abstract

In the title compound, C9H13ClN6O2S, all bond lengths and angles are normal. The 1,3,5-triazine ring exhibits a half-chair conformation. In the crystal structure, weak inter­molecular C—H(...)N and C—H(...)O hydrogen bonds link the mol­ecules into layers parallel to the bc plane.

Related literature

For synthesis of the title compound, see: Frank et al. (1990 [triangle]). For related crystal structures, see: Zurn et al. (1982 [triangle]). For useful applications of related compounds, see: Motohiro (2000 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-64-0o121-scheme1.jpg

Experimental

Crystal data

  • C9H13ClN6O2S
  • M r = 304.76
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-64-0o121-efi1.jpg
  • a = 32.864 (7) Å
  • b = 6.4063 (13) Å
  • c = 13.569 (3) Å
  • β = 110.53 (3)°
  • V = 2675.3 (11) Å3
  • Z = 8
  • Mo Kα radiation
  • μ = 0.45 mm−1
  • T = 293 (2) K
  • 0.32 × 0.22 × 0.10 mm

Data collection

  • Rigaku R-AXIS RAPID IP area-detector diffractometer
  • Absorption correction: multi-scan (ABSCOR; Higashi 1995 [triangle]) T min = 0.869, T max = 0.956
  • 9419 measured reflections
  • 2363 independent reflections
  • 1985 reflections with I > 2σ(I)
  • R int = 0.033

Refinement

  • R[F 2 > 2σ(F 2)] = 0.049
  • wR(F 2) = 0.145
  • S = 1.17
  • 2363 reflections
  • 173 parameters
  • H-atom parameters constrained
  • Δρmax = 0.38 e Å−3
  • Δρmin = −0.33 e Å−3

Data collection: RAPID-AUTO (Rigaku 2004 [triangle]); cell refinement: RAPID-AUTO; data reduction: RAPID-AUTO; program(s) used to solve structure: SHELXTL (Sheldrick, 2001 [triangle]); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL.

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536807062071/cv2360sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536807062071/cv2360Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

supplementary crystallographic information

Comment

Crop protection and veterinary pest control have changed greatly with the recent introduction of neonicotinoid insecticides represented by imidacloprid, the only major new class of chemical insecticides of the last three decades. They are increasingly utilized throughout the world (billion-dollar-a-year market), and seven neonicotinoid insecticide are commercialized or nearly on the market at present and expected to become fourth major insecticide group following the organophosphates, methylcarbamates and pyrethroids (Motohiro, 2000). Clothianidin is a neonicotinoid insecticide that was synthesized in Japan by Takeda Chemical. The title compound (I) was synthesized as an intermediate for the synthesis of clothianidin. We report here the crystal structure of (I).

In (I) (Fig. 1), all bond lengths and angles are normal and in a good agreement with those reported previously (Zurn et al., 1982). The title compound contains three planar fragments, which includes thiazole ring C1—C3/N1/S1 and a triazine ring C5—C7/N2/N3. The triazine ring forms two planes - C5/C6/C7/N2 and N3/C5/C7, respectively, with a dihedral angle of 50.8 (2)° between them. The crystal structure is stabilized by intermolecular C—H···O and N—H···O hydrogen bonds (Table 1, Fig. 2).

Experimental

1,5-Dimethyl-2-nitroiminohexahydro-1,3,5-triazine1.72 g (0.01 mol) was dissolved in 20 ml of dried DMF. To the solution, 60% sodium hydride 0.28 g(0.012 mol) was added portionwise with cooling. The mixture was stirred for 1 h at room temperature until evolution of hydrogen was ceased and then the mixture was heated with strring further for 1 h at 50° C. To the mixture, a solution of 2-chloro-5-thiazolymethylchloride1.72 g (0.01 mol) in 8 ml of dried DMF was added dropwise at 40–50° C. After this additon,the reaction mixture was heated with strring for two hours at 70–80° C. The mixture was poured into ice-water and extracted with dichloromethane. The extract was dried over anhydrous magnesium sulfate, and dichloromethane was distilled off. The residue was purified by a column chromatography to obtain the title compound(0.82 g, yield 27%).(Frank et al., 1990). Single crystals suitable for X-ray measurement were obtained by recrystallization from dichloromethane at room temperature.

Refinement

All H atoms were placed in idealized positions and constrained to ride on their parent atoms (C—H 0.93–0.97 Å), with Uiso(H) values set at 1.5 Ueq(C)(for CH3) or 1.2 Ueq(C)(for CH2, thiazole CH).

Figures

Fig. 1.
View of the title compound (I), with displacement ellipsoids drawn at the 30% probability level.
Fig. 2.
A packing diagram viewed down the b axis. Hydrogen bonds are shown as dashed lines.

Crystal data

C9H13ClN6O2SF000 = 1264
Mr = 304.76Dx = 1.513 Mg m3
Monoclinic, C2/cMo Kα radiation λ = 0.71073 Å
Hall symbol: -C 2ycCell parameters from 2652 reflections
a = 32.864 (7) Åθ = 2.6–25.6º
b = 6.4063 (13) ŵ = 0.45 mm1
c = 13.569 (3) ÅT = 293 (2) K
β = 110.53 (3)ºBlock, colourless
V = 2675.3 (11) Å30.32 × 0.22 × 0.10 mm
Z = 8

Data collection

Rigaku R-AXIS RAPID IP area-detector diffractometer2363 independent reflections
Radiation source: Rotating Anode1985 reflections with I > 2σ(I)
Monochromator: graphiteRint = 0.033
T = 153(2) Kθmax = 25.0º
ω Oscillation scansθmin = 3.0º
Absorption correction: multi-scan(ABSCOR; Higashi 1995)h = −38→38
Tmin = 0.869, Tmax = 0.956k = −7→7
9419 measured reflectionsl = −16→14

Refinement

Refinement on F2Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: fullH-atom parameters constrained
R[F2 > 2σ(F2)] = 0.049  w = 1/[σ2(Fo2) + (0.0788P)2 + 1.7911P] where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.145(Δ/σ)max < 0.001
S = 1.17Δρmax = 0.38 e Å3
2363 reflectionsΔρmin = −0.33 e Å3
173 parametersExtinction correction: SHELXL, Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.0107 (11)
Secondary atom site location: difference Fourier map

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.
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 > σ(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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2)

xyzUiso*/Ueq
S10.06171 (2)0.27878 (12)0.16669 (7)0.0561 (3)
Cl1−0.03042 (2)0.41507 (14)0.09448 (8)0.0715 (3)
C10.00747 (8)0.2188 (4)0.1269 (2)0.0456 (6)
N1−0.00266 (8)0.0260 (4)0.1214 (2)0.0551 (6)
O10.15917 (9)0.4743 (4)0.2334 (2)0.0874 (9)
N20.14362 (6)−0.0081 (3)0.15051 (14)0.0355 (5)
C20.03521 (9)−0.0889 (5)0.1509 (2)0.0541 (7)
H2A0.0346−0.23400.15200.065*
O20.19505 (9)0.4278 (4)0.40121 (19)0.0825 (8)
N30.14082 (7)0.0518 (3)−0.02674 (15)0.0415 (5)
C30.07300 (8)0.0158 (4)0.17781 (18)0.0378 (6)
N40.20026 (6)0.1676 (3)0.12543 (16)0.0403 (5)
C40.11820 (8)−0.0718 (4)0.21546 (19)0.0408 (6)
H4A0.1332−0.02650.28730.049*
H4B0.1165−0.22300.21570.049*
N50.19224 (7)0.1754 (3)0.29169 (16)0.0456 (6)
C50.13045 (9)−0.0922 (4)0.04226 (19)0.0470 (7)
H5B0.1452−0.22360.04320.056*
H5C0.0994−0.11890.01600.056*
C60.17769 (7)0.1185 (4)0.18622 (17)0.0333 (5)
N60.18187 (8)0.3633 (4)0.30871 (19)0.0527 (6)
C70.18655 (8)0.0946 (4)0.01513 (19)0.0454 (6)
H7A0.19350.2005−0.02750.054*
H7B0.2025−0.03110.01180.054*
C80.11418 (10)0.2411 (5)−0.0471 (2)0.0559 (8)
H8A0.12250.3313−0.09320.084*
H8B0.11840.31200.01810.084*
H8C0.08410.2041−0.07950.084*
C90.23765 (9)0.3080 (5)0.1597 (3)0.0594 (8)
H9A0.24350.34820.23150.089*
H9B0.23150.43010.11590.089*
H9C0.26260.23800.15410.089*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
S10.0366 (4)0.0366 (4)0.0967 (6)−0.0027 (3)0.0252 (4)−0.0049 (3)
Cl10.0430 (4)0.0628 (6)0.1085 (7)0.0110 (3)0.0262 (4)0.0014 (4)
C10.0374 (13)0.0489 (16)0.0538 (15)−0.0002 (12)0.0200 (12)−0.0001 (12)
N10.0405 (12)0.0520 (15)0.0704 (15)−0.0082 (11)0.0165 (11)0.0040 (12)
O10.105 (2)0.0537 (14)0.0933 (18)0.0394 (15)0.0215 (16)−0.0055 (13)
N20.0382 (11)0.0361 (11)0.0352 (10)−0.0033 (9)0.0167 (8)−0.0010 (8)
C20.0520 (17)0.0361 (15)0.0735 (18)−0.0093 (12)0.0211 (14)0.0036 (13)
O20.1016 (19)0.0792 (18)0.0685 (14)−0.0091 (14)0.0320 (13)−0.0434 (13)
N30.0451 (12)0.0470 (13)0.0362 (10)−0.0016 (10)0.0188 (9)−0.0025 (9)
C30.0409 (13)0.0387 (14)0.0375 (12)−0.0007 (11)0.0183 (10)0.0041 (10)
N40.0339 (10)0.0429 (12)0.0461 (11)−0.0048 (9)0.0165 (9)−0.0043 (9)
C40.0444 (14)0.0400 (14)0.0426 (13)0.0043 (11)0.0209 (11)0.0103 (11)
N50.0539 (14)0.0410 (12)0.0371 (11)0.0073 (10)0.0098 (10)−0.0071 (9)
C50.0559 (16)0.0464 (16)0.0426 (13)−0.0155 (13)0.0223 (12)−0.0121 (11)
C60.0331 (12)0.0303 (12)0.0352 (11)0.0089 (10)0.0104 (9)0.0018 (9)
N60.0506 (13)0.0488 (14)0.0603 (14)0.0043 (12)0.0213 (11)−0.0158 (12)
C70.0460 (14)0.0533 (16)0.0440 (13)−0.0004 (12)0.0247 (11)−0.0040 (11)
C80.0573 (18)0.067 (2)0.0438 (14)0.0142 (15)0.0177 (13)0.0042 (13)
C90.0440 (15)0.064 (2)0.0733 (19)−0.0178 (14)0.0239 (14)−0.0106 (15)

Geometric parameters (Å, °)

S1—C11.715 (3)N4—C91.461 (3)
S1—C31.720 (3)N4—C71.479 (3)
Cl1—C11.715 (3)C4—H4A0.9700
C1—N11.275 (4)C4—H4B0.9700
N1—C21.379 (4)N5—N61.294 (3)
O1—N61.254 (3)N5—C61.389 (3)
N2—C61.329 (3)C5—H5B0.9700
N2—C41.469 (3)C5—H5C0.9700
N2—C51.480 (3)C7—H7A0.9700
C2—C31.344 (4)C7—H7B0.9700
C2—H2A0.9300C8—H8A0.9600
O2—N61.246 (3)C8—H8B0.9600
N3—C71.434 (3)C8—H8C0.9600
N3—C51.438 (3)C9—H9A0.9600
N3—C81.464 (3)C9—H9B0.9600
C3—C41.500 (3)C9—H9C0.9600
N4—C61.326 (3)
C1—S1—C388.66 (13)N2—C5—H5B109.4
N1—C1—Cl1123.0 (2)N3—C5—H5C109.4
N1—C1—S1117.2 (2)N2—C5—H5C109.4
Cl1—C1—S1119.85 (17)H5B—C5—H5C108.0
C1—N1—C2108.0 (2)N4—C6—N2120.1 (2)
C6—N2—C4122.32 (19)N4—C6—N5120.9 (2)
C6—N2—C5120.00 (19)N2—C6—N5118.5 (2)
C4—N2—C5117.67 (19)O2—N6—O1122.0 (3)
C3—C2—N1117.8 (3)O2—N6—N5117.9 (3)
C3—C2—H2A121.1O1—N6—N5120.1 (2)
N1—C2—H2A121.1N3—C7—N4111.47 (19)
C7—N3—C5108.6 (2)N3—C7—H7A109.3
C7—N3—C8113.0 (2)N4—C7—H7A109.3
C5—N3—C8113.1 (2)N3—C7—H7B109.3
C2—C3—C4128.0 (3)N4—C7—H7B109.3
C2—C3—S1108.3 (2)H7A—C7—H7B108.0
C4—C3—S1123.62 (19)N3—C8—H8A109.5
C6—N4—C9122.7 (2)N3—C8—H8B109.5
C6—N4—C7121.1 (2)H8A—C8—H8B109.5
C9—N4—C7116.1 (2)N3—C8—H8C109.5
N2—C4—C3113.29 (19)H8A—C8—H8C109.5
N2—C4—H4A108.9H8B—C8—H8C109.5
C3—C4—H4A108.9N4—C9—H9A109.5
N2—C4—H4B108.9N4—C9—H9B109.5
C3—C4—H4B108.9H9A—C9—H9B109.5
H4A—C4—H4B107.7N4—C9—H9C109.5
N6—N5—C6114.3 (2)H9A—C9—H9C109.5
N3—C5—N2111.0 (2)H9B—C9—H9C109.5
N3—C5—H5B109.4
C3—S1—C1—N10.1 (2)C9—N4—C6—N2179.1 (2)
C3—S1—C1—Cl1−178.89 (18)C7—N4—C6—N24.0 (3)
Cl1—C1—N1—C2178.9 (2)C9—N4—C6—N5−9.2 (4)
S1—C1—N1—C2−0.1 (3)C7—N4—C6—N5175.6 (2)
C1—N1—C2—C30.0 (4)C4—N2—C6—N4178.4 (2)
N1—C2—C3—C4178.0 (2)C5—N2—C6—N4−0.8 (3)
N1—C2—C3—S10.1 (3)C4—N2—C6—N56.5 (3)
C1—S1—C3—C2−0.1 (2)C5—N2—C6—N5−172.7 (2)
C1—S1—C3—C4−178.1 (2)N6—N5—C6—N484.1 (3)
C6—N2—C4—C3112.1 (3)N6—N5—C6—N2−104.1 (3)
C5—N2—C4—C3−68.7 (3)C6—N5—N6—O2−177.7 (2)
C2—C3—C4—N2123.3 (3)C6—N5—N6—O12.4 (4)
S1—C3—C4—N2−59.1 (3)C5—N3—C7—N4−54.3 (3)
C7—N3—C5—N257.2 (3)C8—N3—C7—N472.1 (3)
C8—N3—C5—N2−69.0 (3)C6—N4—C7—N324.6 (3)
C6—N2—C5—N3−30.6 (3)C9—N4—C7—N3−150.9 (2)
C4—N2—C5—N3150.1 (2)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
C4—H4A···N3i0.972.453.314 (3)148
C4—H4B···O1ii0.972.363.178 (3)142
C7—H7A···O2iii0.972.583.483 (4)156

Symmetry codes: (i) x, −y, z+1/2; (ii) x, y−1, z; (iii) x, −y+1, z−1/2.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: CV2360).

References

  • Frank, W., Noriyoshi, K., Kiyoshi, T., Shigenori, S. & Junko, S. (1990). EP Patent 0 428 941.
  • Higashi, T. (1995). ABSCOR Rigaku Corporation, Tokyo, Japan.
  • Motohiro, T. (2000). Pestic. Outlook, 6, 238–240.
  • Rigaku (2004). RAPID-AUTO Version 3.0. Rigaku Corporation, Tokyo, Japan.
  • Sheldrick, G. M. (2001). SHELXTL Version 5.0. Bruker AXS Inc., Madison, Wisconsin, USA.
  • Zurn, V., Schwarz, W., Rozdzinski, W. & Schmidt, A. (1982). Z. Naturforsch. Teil B, 37, 81–85.

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