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Di­methyl[(E)-(2-nitro­methyl­idene-1,3-di­thiolan-4-yl)methyl]amine

aDepartment of Environment Engineering and Chemistry, Luoyang Institute of Science and Technology, Luoyang 471023, People's Republic of China
*Correspondence e-mail: zhaizw2005@126.com

(Received 20 April 2012; accepted 10 May 2012; online 16 May 2012)

In the title compound, C7H12N2O2S2, the conformation of the dithia­cyclo­pentane ring is a half-chair, with a total puckering amplitude QT = 0.473 (5) Å. Inter­molecular C—H⋯N and C—H⋯O inter­actions help to establish the packing.

Related literature

For the crystal structures of related compounds, see: Xu et al. (2005[Xu, L. Z., Li, W. H., Yu, G. P., Qin, Y. Q., Yang, S. H. & Hou, B. R. (2005). Chem. Res. Chin. Univ. 21, 528-530.]); Ortega-Jimenez et al. (2000[Ortega-Jimenez, F., Ortega-Alfaro, M. C., Lopez-Cortes, J. G., Gutierrez-Perez, R., Toscano, R. A., Velasco-Ibarra, L., Pena-Cabrera, E. & Alvarez-Toledano, C. (2000). Organometallics, 19, 4127-4133.]). For the biological activities of heterocyclic compounds, see: Xu et al. (2006[Xu, L. Z., Huang, Y. W., Yu, G. P., Si, G. D. & Zhu, Q. (2006). Struct. Chem. 17, 235-239.]); Yu et al. (2009[Yu, G. P., Xu, L. Z., Yi, X., Bi, W. Z., Zhu, Q. & Zhai, Z. W. (2009). J. Agric. Food Chem. 57, 4854-4860.]). For puckering amplitude, see: Cremer & Pople (1975[Cremer, D. & Pople, J. A. (1975). J. Am. Chem. Soc. 97, 1354-1358.]).

[Scheme 1]

Experimental

Crystal data
  • C7H12N2O2S2

  • Mr = 220.31

  • Orthorhombic, P 21 21 21

  • a = 5.927 (4) Å

  • b = 11.241 (8) Å

  • c = 14.90 (1) Å

  • V = 992.7 (11) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 0.51 mm−1

  • T = 113 K

  • 0.30 × 0.18 × 0.08 mm

Data collection
  • Rigaku Saturn CCD area-detector diffractometer

  • Absorption correction: multi-scan (CrystalClear; Rigaku, 2007[Rigaku (2007). CrystalClear. Rigaku Corporation, Tokyo, Japan.]) Tmin = 0.863, Tmax = 0.961

  • 10308 measured reflections

  • 2346 independent reflections

  • 2099 reflections with I > 2σ(I)

  • Rint = 0.051

Refinement
  • R[F2 > 2σ(F2)] = 0.043

  • wR(F2) = 0.090

  • S = 1.02

  • 2346 reflections

  • 120 parameters

  • H-atom parameters constrained

  • Δρmax = 0.48 e Å−3

  • Δρmin = −0.39 e Å−3

  • Absolute structure: Flack (1983[Flack, H. D. (1983). Acta Cryst. A39, 876-881.]), 963 Friedel pairs

  • Flack parameter: −0.02 (10)

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
C1—H1⋯N2i 0.95 2.44 3.354 (4) 161
C4—H4⋯O1ii 1.00 2.44 3.272 (4) 140
Symmetry codes: (i) [x-{\script{1\over 2}}, -y+{\script{3\over 2}}, -z]; (ii) [-x-{\script{1\over 2}}, -y+2, z+{\script{1\over 2}}].

Data collection: CrystalClear (Rigaku, 2007[Rigaku (2007). CrystalClear. Rigaku Corporation, Tokyo, Japan.]); cell refinement: CrystalClear; data reduction: CrystalClear; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: SHELXL97; software used to prepare material for publication: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]).

Supporting information


Comment top

Many heterocyclic compounds have been widely used as potent and broad-spectrum fungicides (Xu et al., 2006; Yu et al., 2009). In order to search for new heterocylic compounds with higher biological activities, we synthesized the (E)—N,N-dimethyl-1-(2-(nitromethylene)-1,3-dithiolan-4-yl)methanamine and describe its structure here.

In the title compound, all bond lengths in the molecular are normal and in good agreement with those reported previously (Xu et al., 2005; Ortega-Jimenez et al., 2000). The conformation of the dithiacyclopentane ring (C2—C4/S1/S2) is halfchair, with a total puckering amplitude (Cremer & Pople, 1975) QT = 0.456 (3) Å and a pseudo-twofold axis running along the direction through C2 and the mid-point of the C3—C4 bond. The intermolecular C—H···N and C—H···O hydrogen bonds stabilize the structure.

Related literature top

For the crystal structures of related compounds, see: Xu et al. (2005); Ortega-Jimenez et al. (2000). For the biological activities of heterocyclic compounds, see: Xu et al. (2006); Yu et al. (2009). For puckering amplitude, see: Cremer & Pople (1975).

Experimental top

A mixture of potassium 2-nitroethene-1,1-bis(thiolate) 10 mmol (2.13 g), 2,3-dichloro-N,N-dimethylpropan-1-amine (1.56 g, 10 mmol) is refluxed in absolute ethanol (25 ml) for 3 h. The mixture was filtered to provide crude product. The residue was purified by recrystallized from absolute EtOH, yield 1.89 g (86.0%). Single crystals suitable for X-ray measurements were obtained by recrystallization from acetonitrile at room temperature.

Refinement top

H atoms were positioned geometrically and refined using a riding model, with C—H = 0.95 or 1.00 Å and with Uiso(H) = 1.2 times Ueq(C) for methylene H atoms and 1.5Ueq(C) for the methyl H atoms.

Computing details top

Data collection: CrystalClear (Rigaku, 2007); cell refinement: CrystalClear (Rigaku, 2007); data reduction: CrystalClear (Rigaku, 2007); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXL97 (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

Figures top
[Figure 1] Fig. 1. The molecular structure of (I), with atom labels and 40% probability displacement ellipsoids for non-H atoms.
Dimethyl[(E)-(2-nitromethylidene-1,3-dithiolan-4-yl)methyl]amine top
Crystal data top
C7H12N2O2S2F(000) = 464
Mr = 220.31Dx = 1.474 Mg m3
Orthorhombic, P212121Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2abCell parameters from 3456 reflections
a = 5.927 (4) Åθ = 1.8–27.8°
b = 11.241 (8) ŵ = 0.51 mm1
c = 14.90 (1) ÅT = 113 K
V = 992.7 (11) Å3Prism, colorless
Z = 40.30 × 0.18 × 0.08 mm
Data collection top
Rigaku Saturn CCD area-detector
diffractometer
2346 independent reflections
Radiation source: rotating anode2099 reflections with I > 2σ(I)
Multilayer monochromatorRint = 0.051
Detector resolution: 14.63 pixels mm-1θmax = 27.8°, θmin = 2.3°
ω and ϕ scansh = 67
Absorption correction: multi-scan
(CrystalClear; Rigaku, 2007)
k = 1414
Tmin = 0.863, Tmax = 0.961l = 1919
10308 measured reflections
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.043H-atom parameters constrained
wR(F2) = 0.090 w = 1/[σ2(Fo2) + (0.0465P)2]
where P = (Fo2 + 2Fc2)/3
S = 1.02(Δ/σ)max < 0.001
2346 reflectionsΔρmax = 0.48 e Å3
120 parametersΔρmin = 0.39 e Å3
0 restraintsAbsolute structure: Flack (1983), 963 Friedel pairs
Primary atom site location: structure-invariant direct methodsAbsolute structure parameter: 0.02 (10)
Crystal data top
C7H12N2O2S2V = 992.7 (11) Å3
Mr = 220.31Z = 4
Orthorhombic, P212121Mo Kα radiation
a = 5.927 (4) ŵ = 0.51 mm1
b = 11.241 (8) ÅT = 113 K
c = 14.90 (1) Å0.30 × 0.18 × 0.08 mm
Data collection top
Rigaku Saturn CCD area-detector
diffractometer
2346 independent reflections
Absorption correction: multi-scan
(CrystalClear; Rigaku, 2007)
2099 reflections with I > 2σ(I)
Tmin = 0.863, Tmax = 0.961Rint = 0.051
10308 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.043H-atom parameters constrained
wR(F2) = 0.090Δρmax = 0.48 e Å3
S = 1.02Δρmin = 0.39 e Å3
2346 reflectionsAbsolute structure: Flack (1983), 963 Friedel pairs
120 parametersAbsolute structure parameter: 0.02 (10)
0 restraints
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.

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) top
xyzUiso*/Ueq
S10.16147 (11)0.88829 (5)0.02451 (4)0.02114 (16)
S20.05675 (11)1.12418 (5)0.02804 (4)0.02176 (16)
O10.4710 (3)0.96345 (17)0.18337 (13)0.0307 (5)
O20.3988 (3)1.10926 (16)0.09091 (12)0.0276 (4)
N10.3632 (4)1.00756 (17)0.12006 (14)0.0222 (5)
N20.4568 (4)0.81812 (18)0.18117 (14)0.0196 (5)
C10.1909 (5)0.9375 (2)0.08113 (16)0.0203 (5)
H10.17340.85730.09990.024*
C20.0496 (4)0.9819 (2)0.01767 (17)0.0192 (5)
C30.1989 (5)1.1078 (2)0.09357 (18)0.0256 (6)
H3A0.33191.12880.05660.031*
H3B0.19451.16170.14610.031*
C40.2158 (4)0.9797 (2)0.12456 (17)0.0225 (6)
H40.09730.96360.17080.027*
C50.4449 (5)0.9457 (2)0.16155 (18)0.0247 (6)
H5A0.56300.96670.11730.030*
H5B0.47430.99140.21720.030*
C60.3446 (5)0.7885 (2)0.26605 (17)0.0255 (6)
H6A0.35180.70230.27590.038*
H6B0.18650.81370.26340.038*
H6C0.42060.82950.31560.038*
C70.6931 (4)0.7797 (3)0.18472 (18)0.0261 (6)
H7A0.76890.81890.23520.039*
H7B0.76880.80140.12860.039*
H7C0.69950.69330.19280.039*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
S10.0270 (3)0.0141 (3)0.0223 (3)0.0024 (3)0.0050 (3)0.0022 (3)
S20.0298 (4)0.0134 (3)0.0220 (3)0.0023 (3)0.0032 (3)0.0015 (3)
O10.0375 (12)0.0268 (10)0.0279 (10)0.0037 (9)0.0164 (9)0.0017 (8)
O20.0313 (11)0.0185 (9)0.0330 (10)0.0037 (8)0.0065 (8)0.0030 (8)
N10.0268 (12)0.0167 (10)0.0231 (11)0.0006 (9)0.0035 (10)0.0016 (8)
N20.0235 (11)0.0156 (10)0.0198 (11)0.0034 (9)0.0015 (9)0.0023 (8)
C10.0270 (14)0.0140 (11)0.0198 (12)0.0031 (11)0.0008 (11)0.0006 (9)
C20.0219 (13)0.0180 (11)0.0177 (12)0.0001 (10)0.0007 (11)0.0028 (10)
C30.0344 (15)0.0145 (11)0.0279 (13)0.0005 (11)0.0100 (12)0.0005 (10)
C40.0263 (15)0.0189 (12)0.0221 (13)0.0007 (11)0.0016 (11)0.0007 (10)
C50.0296 (15)0.0167 (12)0.0277 (14)0.0022 (12)0.0055 (13)0.0007 (10)
C60.0291 (15)0.0226 (13)0.0248 (13)0.0045 (12)0.0021 (12)0.0015 (11)
C70.0252 (15)0.0266 (14)0.0265 (14)0.0027 (12)0.0022 (12)0.0005 (11)
Geometric parameters (Å, º) top
S1—C21.752 (2)C3—H3A0.9900
S1—C41.839 (3)C3—H3B0.9900
S2—C21.739 (3)C4—C51.514 (4)
S2—C31.812 (3)C4—H41.0000
O1—N11.243 (3)C5—H5A0.9900
O2—N11.241 (3)C5—H5B0.9900
N1—C11.414 (3)C6—H6A0.9800
N2—C51.466 (3)C6—H6B0.9800
N2—C71.466 (3)C6—H6C0.9800
N2—C61.467 (3)C7—H7A0.9800
C1—C21.358 (3)C7—H7B0.9800
C1—H10.9500C7—H7C0.9800
C3—C41.516 (4)
C2—S1—C494.61 (12)C3—C4—S1105.80 (18)
C2—S2—C395.60 (12)C5—C4—H4109.5
O2—N1—O1123.1 (2)C3—C4—H4109.5
O2—N1—C1119.5 (2)S1—C4—H4109.5
O1—N1—C1117.4 (2)N2—C5—C4111.3 (2)
C5—N2—C7110.0 (2)N2—C5—H5A109.4
C5—N2—C6111.9 (2)C4—C5—H5A109.4
C7—N2—C6109.6 (2)N2—C5—H5B109.4
C2—C1—N1121.8 (2)C4—C5—H5B109.4
C2—C1—H1119.1H5A—C5—H5B108.0
N1—C1—H1119.1N2—C6—H6A109.5
C1—C2—S2126.56 (19)N2—C6—H6B109.5
C1—C2—S1118.00 (19)H6A—C6—H6B109.5
S2—C2—S1115.43 (14)N2—C6—H6C109.5
C4—C3—S2108.41 (18)H6A—C6—H6C109.5
C4—C3—H3A110.0H6B—C6—H6C109.5
S2—C3—H3A110.0N2—C7—H7A109.5
C4—C3—H3B110.0N2—C7—H7B109.5
S2—C3—H3B110.0H7A—C7—H7B109.5
H3A—C3—H3B108.4N2—C7—H7C109.5
C5—C4—C3114.2 (2)H7A—C7—H7C109.5
C5—C4—S1108.15 (18)H7B—C7—H7C109.5
O2—N1—C1—C25.7 (4)S2—C3—C4—C5166.65 (18)
O1—N1—C1—C2173.5 (2)S2—C3—C4—S147.8 (2)
N1—C1—C2—S21.8 (4)C2—S1—C4—C5161.36 (17)
N1—C1—C2—S1178.79 (18)C2—S1—C4—C338.61 (19)
C3—S2—C2—C1174.4 (2)C7—N2—C5—C4159.4 (2)
C3—S2—C2—S16.22 (17)C6—N2—C5—C478.6 (3)
C4—S1—C2—C1162.7 (2)C3—C4—C5—N2173.9 (2)
C4—S1—C2—S216.82 (16)S1—C4—C5—N256.4 (2)
C2—S2—C3—C433.5 (2)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C1—H1···N2i0.952.443.354 (4)161
C4—H4···O1ii1.002.443.272 (4)140
Symmetry codes: (i) x1/2, y+3/2, z; (ii) x1/2, y+2, z+1/2.

Experimental details

Crystal data
Chemical formulaC7H12N2O2S2
Mr220.31
Crystal system, space groupOrthorhombic, P212121
Temperature (K)113
a, b, c (Å)5.927 (4), 11.241 (8), 14.90 (1)
V3)992.7 (11)
Z4
Radiation typeMo Kα
µ (mm1)0.51
Crystal size (mm)0.30 × 0.18 × 0.08
Data collection
DiffractometerRigaku Saturn CCD area-detector
diffractometer
Absorption correctionMulti-scan
(CrystalClear; Rigaku, 2007)
Tmin, Tmax0.863, 0.961
No. of measured, independent and
observed [I > 2σ(I)] reflections
10308, 2346, 2099
Rint0.051
(sin θ/λ)max1)0.656
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.043, 0.090, 1.02
No. of reflections2346
No. of parameters120
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.48, 0.39
Absolute structureFlack (1983), 963 Friedel pairs
Absolute structure parameter0.02 (10)

Computer programs: CrystalClear (Rigaku, 2007), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C1—H1···N2i0.952.443.354 (4)161.4
C4—H4···O1ii1.002.443.272 (4)140.2
Symmetry codes: (i) x1/2, y+3/2, z; (ii) x1/2, y+2, z+1/2.
 

Acknowledgements

The authors thank Dr Haibin Song, Nankai University, for the X-ray crystallographic determination.

References

First citationCremer, D. & Pople, J. A. (1975). J. Am. Chem. Soc. 97, 1354–1358.  CrossRef CAS Web of Science Google Scholar
First citationFlack, H. D. (1983). Acta Cryst. A39, 876–881.  CrossRef CAS Web of Science IUCr Journals Google Scholar
First citationOrtega-Jimenez, F., Ortega-Alfaro, M. C., Lopez-Cortes, J. G., Gutierrez-Perez, R., Toscano, R. A., Velasco-Ibarra, L., Pena-Cabrera, E. & Alvarez-Toledano, C. (2000). Organometallics, 19, 4127–4133.  Web of Science CSD CrossRef CAS Google Scholar
First citationRigaku (2007). CrystalClear. Rigaku Corporation, Tokyo, Japan.  Google Scholar
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationXu, L. Z., Huang, Y. W., Yu, G. P., Si, G. D. & Zhu, Q. (2006). Struct. Chem. 17, 235–239.  Web of Science CSD CrossRef CAS Google Scholar
First citationXu, L. Z., Li, W. H., Yu, G. P., Qin, Y. Q., Yang, S. H. & Hou, B. R. (2005). Chem. Res. Chin. Univ. 21, 528–530.  CAS Google Scholar
First citationYu, G. P., Xu, L. Z., Yi, X., Bi, W. Z., Zhu, Q. & Zhai, Z. W. (2009). J. Agric. Food Chem. 57, 4854–4860.  Web of Science CrossRef PubMed CAS Google Scholar

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