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

Yang, S.-H.; Zhai, Z.-W.

doi:10.1107/S1600536812021307

organic compounds

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ISSN: 2056-9890

Volume 68| Part 6| June 2012| Page o1749

doi:10.1107/S1600536812021307

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

Shuang-Hua Yang ^a and Zhi-Wei Zhai ^a ^*

^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 Q_T = 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 ); 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

Crystal data

C₇H₁₂N₂O₂S₂
M_r = 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 ) T_min = 0.863, T_max = 0.961
10308 measured reflections
2346 independent reflections
2099 reflections with I > 2σ(I)
R_int = 0.051

Refinement

R[F² > 2σ(F²)] = 0.043
wR(F²) = 0.090
S = 1.02
2346 reflections
120 parameters
H-atom parameters constrained
Δρ_max = 0.48 e Å⁻³
Δρ_min = −0.39 e Å⁻³
Absolute structure: Flack (1983 ), 963 Friedel pairs
Flack parameter: −0.02 (10)

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	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); cell refinement: CrystalClear; data reduction: CrystalClear; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXL97; software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

Supporting information

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536812021307/hg5213sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536812021307/hg5213Isup2.hkl

Supporting information file. DOI: 10.1107/S1600536812021307/hg5213Isup3.cml

checkCIF report

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) Q_T = 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.

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

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

C₇H₁₂N₂O₂S₂	F(000) = 464
M_r = 220.31	D_x = 1.474 Mg m⁻³
Orthorhombic, P2₁2₁2₁	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2ab	Cell parameters from 3456 reflections
a = 5.927 (4) Å	θ = 1.8–27.8°
b = 11.241 (8) Å	µ = 0.51 mm⁻¹
c = 14.90 (1) Å	T = 113 K
V = 992.7 (11) Å³	Prism, colorless
Z = 4	0.30 × 0.18 × 0.08 mm

Data collection top

Rigaku Saturn CCD area-detector diffractometer	2346 independent reflections
Radiation source: rotating anode	2099 reflections with I > 2σ(I)
Multilayer monochromator	R_int = 0.051
Detector resolution: 14.63 pixels mm^-1	θ_max = 27.8°, θ_min = 2.3°
ω and ϕ scans	h = −6→7
Absorption correction: multi-scan (CrystalClear; Rigaku, 2007)	k = −14→14
T_min = 0.863, T_max = 0.961	l = −19→19
10308 measured reflections

Refinement top

Refinement on F²	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F² > 2σ(F²)] = 0.043	H-atom parameters constrained
wR(F²) = 0.090	w = 1/[σ²(F_o²) + (0.0465P)²] where P = (F_o² + 2F_c²)/3
S = 1.02	(Δ/σ)_max < 0.001
2346 reflections	Δρ_max = 0.48 e Å⁻³
120 parameters	Δρ_min = −0.39 e Å⁻³
0 restraints	Absolute structure: Flack (1983), 963 Friedel pairs
Primary atom site location: structure-invariant direct methods	Absolute structure parameter: −0.02 (10)

Crystal data top

C₇H₁₂N₂O₂S₂	V = 992.7 (11) Å³
M_r = 220.31	Z = 4
Orthorhombic, P2₁2₁2₁	Mo Kα radiation
a = 5.927 (4) Å	µ = 0.51 mm⁻¹
b = 11.241 (8) Å	T = 113 K
c = 14.90 (1) Å	0.30 × 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)
T_min = 0.863, T_max = 0.961	R_int = 0.051
10308 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.043	H-atom parameters constrained
wR(F²) = 0.090	Δρ_max = 0.48 e Å⁻³
S = 1.02	Δρ_min = −0.39 e Å⁻³
2346 reflections	Absolute structure: Flack (1983), 963 Friedel pairs
120 parameters	Absolute 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

	x	y	z	U_iso*/U_eq
S1	0.16147 (11)	0.88829 (5)	0.02451 (4)	0.02114 (16)
S2	−0.05675 (11)	1.12418 (5)	0.02804 (4)	0.02176 (16)
O1	−0.4710 (3)	0.96345 (17)	−0.18337 (13)	0.0307 (5)
O2	−0.3988 (3)	1.10926 (16)	−0.09091 (12)	0.0276 (4)
N1	−0.3632 (4)	1.00756 (17)	−0.12006 (14)	0.0222 (5)
N2	0.4568 (4)	0.81812 (18)	0.18117 (14)	0.0196 (5)
C1	−0.1909 (5)	0.9375 (2)	−0.08113 (16)	0.0203 (5)
H1	−0.1734	0.8573	−0.0999	0.024*
C2	−0.0496 (4)	0.9819 (2)	−0.01767 (17)	0.0192 (5)
C3	0.1989 (5)	1.1078 (2)	0.09357 (18)	0.0256 (6)
H3A	0.3319	1.1288	0.0566	0.031*
H3B	0.1945	1.1617	0.1461	0.031*
C4	0.2158 (4)	0.9797 (2)	0.12456 (17)	0.0225 (6)
H4	0.0973	0.9636	0.1708	0.027*
C5	0.4449 (5)	0.9457 (2)	0.16155 (18)	0.0247 (6)
H5A	0.5630	0.9667	0.1173	0.030*
H5B	0.4743	0.9914	0.2172	0.030*
C6	0.3446 (5)	0.7885 (2)	0.26605 (17)	0.0255 (6)
H6A	0.3518	0.7023	0.2759	0.038*
H6B	0.1865	0.8137	0.2634	0.038*
H6C	0.4206	0.8295	0.3156	0.038*
C7	0.6931 (4)	0.7797 (3)	0.18472 (18)	0.0261 (6)
H7A	0.7689	0.8189	0.2352	0.039*
H7B	0.7688	0.8014	0.1286	0.039*
H7C	0.6995	0.6933	0.1928	0.039*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
S1	0.0270 (3)	0.0141 (3)	0.0223 (3)	0.0024 (3)	−0.0050 (3)	−0.0022 (3)
S2	0.0298 (4)	0.0134 (3)	0.0220 (3)	0.0023 (3)	−0.0032 (3)	−0.0015 (3)
O1	0.0375 (12)	0.0268 (10)	0.0279 (10)	−0.0037 (9)	−0.0164 (9)	−0.0017 (8)
O2	0.0313 (11)	0.0185 (9)	0.0330 (10)	0.0037 (8)	−0.0065 (8)	−0.0030 (8)
N1	0.0268 (12)	0.0167 (10)	0.0231 (11)	−0.0006 (9)	−0.0035 (10)	0.0016 (8)
N2	0.0235 (11)	0.0156 (10)	0.0198 (11)	0.0034 (9)	−0.0015 (9)	0.0023 (8)
C1	0.0270 (14)	0.0140 (11)	0.0198 (12)	0.0031 (11)	−0.0008 (11)	0.0006 (9)
C2	0.0219 (13)	0.0180 (11)	0.0177 (12)	−0.0001 (10)	0.0007 (11)	0.0028 (10)
C3	0.0344 (15)	0.0145 (11)	0.0279 (13)	−0.0005 (11)	−0.0100 (12)	−0.0005 (10)
C4	0.0263 (15)	0.0189 (12)	0.0221 (13)	−0.0007 (11)	−0.0016 (11)	−0.0007 (10)
C5	0.0296 (15)	0.0167 (12)	0.0277 (14)	−0.0022 (12)	−0.0055 (13)	−0.0007 (10)
C6	0.0291 (15)	0.0226 (13)	0.0248 (13)	0.0045 (12)	0.0021 (12)	0.0015 (11)
C7	0.0252 (15)	0.0266 (14)	0.0265 (14)	0.0027 (12)	0.0022 (12)	−0.0005 (11)

Geometric parameters (Å, º) top

S1—C2	1.752 (2)	C3—H3A	0.9900
S1—C4	1.839 (3)	C3—H3B	0.9900
S2—C2	1.739 (3)	C4—C5	1.514 (4)
S2—C3	1.812 (3)	C4—H4	1.0000
O1—N1	1.243 (3)	C5—H5A	0.9900
O2—N1	1.241 (3)	C5—H5B	0.9900
N1—C1	1.414 (3)	C6—H6A	0.9800
N2—C5	1.466 (3)	C6—H6B	0.9800
N2—C7	1.466 (3)	C6—H6C	0.9800
N2—C6	1.467 (3)	C7—H7A	0.9800
C1—C2	1.358 (3)	C7—H7B	0.9800
C1—H1	0.9500	C7—H7C	0.9800
C3—C4	1.516 (4)

C2—S1—C4	94.61 (12)	C3—C4—S1	105.80 (18)
C2—S2—C3	95.60 (12)	C5—C4—H4	109.5
O2—N1—O1	123.1 (2)	C3—C4—H4	109.5
O2—N1—C1	119.5 (2)	S1—C4—H4	109.5
O1—N1—C1	117.4 (2)	N2—C5—C4	111.3 (2)
C5—N2—C7	110.0 (2)	N2—C5—H5A	109.4
C5—N2—C6	111.9 (2)	C4—C5—H5A	109.4
C7—N2—C6	109.6 (2)	N2—C5—H5B	109.4
C2—C1—N1	121.8 (2)	C4—C5—H5B	109.4
C2—C1—H1	119.1	H5A—C5—H5B	108.0
N1—C1—H1	119.1	N2—C6—H6A	109.5
C1—C2—S2	126.56 (19)	N2—C6—H6B	109.5
C1—C2—S1	118.00 (19)	H6A—C6—H6B	109.5
S2—C2—S1	115.43 (14)	N2—C6—H6C	109.5
C4—C3—S2	108.41 (18)	H6A—C6—H6C	109.5
C4—C3—H3A	110.0	H6B—C6—H6C	109.5
S2—C3—H3A	110.0	N2—C7—H7A	109.5
C4—C3—H3B	110.0	N2—C7—H7B	109.5
S2—C3—H3B	110.0	H7A—C7—H7B	109.5
H3A—C3—H3B	108.4	N2—C7—H7C	109.5
C5—C4—C3	114.2 (2)	H7A—C7—H7C	109.5
C5—C4—S1	108.15 (18)	H7B—C7—H7C	109.5

O2—N1—C1—C2	−5.7 (4)	S2—C3—C4—C5	166.65 (18)
O1—N1—C1—C2	173.5 (2)	S2—C3—C4—S1	47.8 (2)
N1—C1—C2—S2	1.8 (4)	C2—S1—C4—C5	−161.36 (17)
N1—C1—C2—S1	−178.79 (18)	C2—S1—C4—C3	−38.61 (19)
C3—S2—C2—C1	−174.4 (2)	C7—N2—C5—C4	159.4 (2)
C3—S2—C2—S1	6.22 (17)	C6—N2—C5—C4	−78.6 (3)
C4—S1—C2—C1	−162.7 (2)	C3—C4—C5—N2	−173.9 (2)
C4—S1—C2—S2	16.82 (16)	S1—C4—C5—N2	−56.4 (2)
C2—S2—C3—C4	−33.5 (2)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	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−1/2, −y+3/2, −z; (ii) −x−1/2, −y+2, z+1/2.

Experimental details

Crystal data
Chemical formula	C₇H₁₂N₂O₂S₂
M_r	220.31
Crystal system, space group	Orthorhombic, P2₁2₁2₁
Temperature (K)	113
a, b, c (Å)	5.927 (4), 11.241 (8), 14.90 (1)
V (Å³)	992.7 (11)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.51
Crystal size (mm)	0.30 × 0.18 × 0.08

Data collection
Diffractometer	Rigaku Saturn CCD area-detector diffractometer
Absorption correction	Multi-scan (CrystalClear; Rigaku, 2007)
T_min, T_max	0.863, 0.961
No. of measured, independent and observed [I > 2σ(I)] reflections	10308, 2346, 2099
R_int	0.051
(sin θ/λ)_max (Å⁻¹)	0.656

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.043, 0.090, 1.02
No. of reflections	2346
No. of parameters	120
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.48, −0.39
Absolute structure	Flack (1983), 963 Friedel pairs
Absolute structure parameter	−0.02 (10)

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

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C1—H1···N2ⁱ	0.95	2.44	3.354 (4)	161.4
C4—H4···O1ⁱⁱ	1.00	2.44	3.272 (4)	140.2

Symmetry codes: (i) x−1/2, −y+3/2, −z; (ii) −x−1/2, −y+2, z+1/2.

Acknowledgements

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

References

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