Crystal structure of 3-[({[bis­(2-cyano­eth­yl)carbamo­thio­yl]disulfan­yl}methane­thio­yl)(2-cyano­eth­yl) amino]­propane­nitrile

Sonia, A.S.; Baskaran, R.; Selvanayagam, S.

doi:10.1107/S2414314617003467

organic compounds

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ISSN: 2414-3146

Volume 2| Part 3| March 2017| x170346

https://doi.org/10.1107/S2414314617003467

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Crystal structure of 3-[({[bis(2-cyanoethyl)carbamothioyl]disulfanyl}methanethioyl)(2-cyanoethyl) amino]propanenitrile

A. S. Sonia,^a R. Baskaran ^a ^* and S. Selvanayagam ^b

^aDepartment of Chemistry, Annamalai University, Annamalainagar, Chidambaram 608 002, India, and ^bPG & Research Department of Physics, Government Arts College, Melur 625 106, India
^*Correspondence e-mail: rbaskaran54@gmail.com

Edited by A. J. Lough, University of Toronto, Canada (Received 11 February 2017; accepted 3 March 2017; online 7 March 2017)

In the title compound, C₁₄H₁₆N₆S₄, the molecule resides on a twofold rotation axis, which runs through the central S—S bond. In the crystal, molecules are linked via weak C—H⋯N hydrogen bonds, forming C(5) chains propagating in a helical arrangement along [010].

Keywords: crystal structure; cyano derivatives; weak C—H⋯N hydrogen bonds; short intramolecular contacts; twofold rotation symmetry.

CCDC reference: 1504588

Structure description

In a continuation of the work in our laboratory on the crystal structure analysis of cyano derivatives, we have undertaken the single-crystal X-ray diffraction study of the title compound, and the results are presented herein.

The molecular structure of the title compound is illustrated in Fig. 1. The molecule resides on a crystallographic twofold rotation axis, which runs through the central S—S bond. The molecular structure maybe influenced by a series of very weak intramolecular C—H⋯S hydrogen bonds (Table 1).

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
C2—H2B⋯S1	0.97	2.46	2.857 (2)	105
C3—H3A⋯S1	0.97	2.84	3.332 (2)	112
C5—H5B⋯S2	0.97	2.69	3.028 (2)	101
C2—H2B⋯N2ⁱ	0.97	2.55	3.202 (2)	125
Symmetry code: (i) x, y+1, z.

Figure 1
The molecular structure of the title compound, with the atom labelling. Displacement ellipsoids are drawn at the 30% probability level.

In the crystal, weak C—H⋯N hydrogen bonds link the molecules, forming C(5) chains propagating in a helical arrangement along [010]; see Fig. 2. The structure also forms a cavity consisting of 24 atoms between two molecules in an R₂²(24) graph-set motif.

Figure 2
The crystal packing of the title compound. The weak C—H⋯N hydrogen bonds are shown as dashed lines (see Table 1

). For clarity, H atoms not involved in these hydrogen bonds have been omitted.

Synthesis and crystallization

All chemicals were commercially available and analytical grade materials were used directly without further purification. A stoichiometric amount (0.1732 g, 2 mmol) of carbon disulfide, CS₂, was added dropwise to a methanol solution containing (0.2463 g, 2 mmol) 3,3′-azanediyldipropanenitrile and 0.24 g potassium hydroxide. The mixture was stirred for about 25 minutes until a white precipitate appeared. The clear filtrate was then left at temperature of 278 K for crystallization. After few days, crystals suitable for X-ray analysis were collected (yield = 83%, m.p. 431 K). The presence of the C≡N groups was confirmed by FT–IR analysis.

Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2.

Table 2
Experimental details

Crystal data
Chemical formula	C₁₄H₁₆N₆S₄
M_r	396.57
Crystal system, space group	Monoclinic, C2/c
Temperature (K)	293
a, b, c (Å)	15.4313 (7), 5.6117 (2), 22.8702 (12)
β (°)	108.713 (2)
V (Å³)	1875.77 (15)
Z	4
Radiation type	Mo Kα
μ (mm⁻¹)	0.52
Crystal size (mm)	0.30 × 0.20 × 0.20

Data collection
Diffractometer	Bruker Kappa APEXII CCD
Absorption correction	Multi-scan (SADABS; Bruker, 1999 )
T_min, T_max	0.81, 0.89
No. of measured, independent and observed [I > 2σ(I)] reflections	19984, 3347, 2569
R_int	0.024
(sin θ/λ)_max (Å⁻¹)	0.766

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.037, 0.109, 1.11
No. of reflections	3347
No. of parameters	109
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.34, −0.27
Computer programs: APEX2, SAINT and XPREP (Bruker, 2004 ), SHELXS97 (Sheldrick, 2008 ), ORTEP-3 for Windows (Farrugia, 2012 ), SHELXL2014 (Sheldrick, 2015 ) and PLATON (Spek, 2009 ).

Structural data

CCDC reference: 1504588

Crystal structure: contains datablocks I, global. DOI: https://doi.org/10.1107/S2414314617003467/lh4017sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2414314617003467/lh4017Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2414314617003467/lh4017Isup3.cml

checkCIF report

Computing details top

Data collection: APEX2 (Bruker, 2004); cell refinement: APEX2 and SAINT (Bruker, 2004); data reduction: SAINT and XPREP (Bruker, 2004); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012) and PLATON (Spek, 2009); software used to prepare material for publication: SHELXL2014 (Sheldrick, 2015) and PLATON (Spek, 2009).

3-[({[bis(2-Cyanoethyl)carbamothioyl]disulfanyl}methanethioyl)(2-cyanoethyl)amino]propanenitrile top

Crystal data top

C₁₄H₁₆N₆S₄	F(000) = 824
M_r = 396.57	D_x = 1.404 Mg m⁻³
Monoclinic, C2/c	Mo Kα radiation, λ = 0.71073 Å
a = 15.4313 (7) Å	Cell parameters from 8307 reflections
b = 5.6117 (2) Å	θ = 2.3–31.7°
c = 22.8702 (12) Å	µ = 0.52 mm⁻¹
β = 108.713 (2)°	T = 293 K
V = 1875.77 (15) Å³	Block, brown
Z = 4	0.30 × 0.20 × 0.20 mm

Data collection top

Bruker Kappa APEXII CCD diffractometer	2569 reflections with I > 2σ(I)
Radiation source: Sealed tube	R_int = 0.024
ω and φ scan	θ_max = 33.0°, θ_min = 2.8°
Absorption correction: multi-scan (SADABS; Bruker, 1999)	h = −23→19
T_min = 0.81, T_max = 0.89	k = −8→8
19984 measured reflections	l = −34→34
3347 independent reflections

Refinement top

Refinement on F²	0 restraints
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F² > 2σ(F²)] = 0.037	H-atom parameters constrained
wR(F²) = 0.109	w = 1/[σ²(F_o²) + (0.0427P)² + 1.4682P] where P = (F_o² + 2F_c²)/3
S = 1.11	(Δ/σ)_max < 0.001
3347 reflections	Δρ_max = 0.34 e Å⁻³
109 parameters	Δρ_min = −0.27 e Å⁻³

Special details top

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.

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

	x	y	z	U_iso*/U_eq
S1	−0.00264 (3)	0.57876 (7)	0.20581 (2)	0.03874 (11)
S2	0.13996 (3)	0.20336 (9)	0.26542 (2)	0.05086 (14)
N1	0.06850 (8)	0.2800 (2)	0.14508 (5)	0.0328 (2)
N2	−0.09703 (13)	−0.1278 (3)	0.02598 (9)	0.0644 (5)
N3	0.21226 (12)	0.6016 (3)	0.08156 (8)	0.0610 (4)
C1	0.07351 (10)	0.3344 (3)	0.20300 (6)	0.0325 (3)
C2	0.00524 (10)	0.3986 (3)	0.09077 (6)	0.0351 (3)
H2A	0.0289	0.3838	0.0565	0.042*
H2B	0.0027	0.5669	0.0997	0.042*
C3	−0.09148 (10)	0.2961 (3)	0.07169 (7)	0.0388 (3)
H3A	−0.1125	0.2922	0.1074	0.047*
H3B	−0.1322	0.3997	0.0411	0.047*
C4	−0.09592 (11)	0.0566 (3)	0.04630 (8)	0.0429 (3)
C5	0.12945 (11)	0.0991 (3)	0.13344 (8)	0.0389 (3)
H5A	0.1026	0.0367	0.0920	0.047*
H5B	0.1356	−0.0318	0.1622	0.047*
C6	0.22415 (11)	0.2006 (3)	0.14036 (9)	0.0487 (4)
H6A	0.2567	0.2279	0.1838	0.058*
H6B	0.2586	0.0851	0.1252	0.058*
C7	0.21877 (11)	0.4242 (4)	0.10651 (8)	0.0455 (4)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
S1	0.0506 (2)	0.03350 (19)	0.03374 (19)	0.00673 (15)	0.01572 (16)	0.00523 (14)
S2	0.0572 (3)	0.0543 (3)	0.0332 (2)	0.0171 (2)	0.00349 (17)	0.00587 (17)
N1	0.0318 (5)	0.0356 (6)	0.0300 (5)	0.0003 (5)	0.0086 (4)	0.0007 (5)
N2	0.0730 (12)	0.0457 (9)	0.0650 (11)	−0.0021 (8)	0.0088 (9)	−0.0066 (8)
N3	0.0552 (9)	0.0645 (11)	0.0605 (10)	−0.0191 (8)	0.0146 (8)	0.0024 (9)
C1	0.0335 (6)	0.0312 (6)	0.0306 (6)	−0.0009 (5)	0.0071 (5)	0.0013 (5)
C2	0.0367 (7)	0.0390 (7)	0.0283 (6)	−0.0023 (6)	0.0084 (5)	0.0035 (5)
C3	0.0332 (7)	0.0430 (8)	0.0360 (7)	−0.0003 (6)	0.0054 (5)	−0.0027 (6)
C4	0.0407 (8)	0.0437 (8)	0.0386 (8)	−0.0027 (7)	0.0047 (6)	0.0008 (7)
C5	0.0408 (7)	0.0349 (7)	0.0422 (8)	0.0006 (6)	0.0150 (6)	−0.0045 (6)
C6	0.0360 (7)	0.0490 (9)	0.0610 (11)	0.0050 (7)	0.0155 (7)	−0.0001 (8)
C7	0.0346 (7)	0.0570 (10)	0.0456 (9)	−0.0093 (7)	0.0140 (6)	−0.0090 (8)

Geometric parameters (Å, º) top

S1—C1	1.8201 (15)	C2—H2B	0.9700
S1—S1ⁱ	1.9968 (7)	C3—C4	1.457 (2)
S2—C1	1.6405 (14)	C3—H3A	0.9700
N1—C1	1.3375 (18)	C3—H3B	0.9700
N1—C5	1.4651 (19)	C5—C6	1.529 (2)
N1—C2	1.4699 (18)	C5—H5A	0.9700
N2—C4	1.132 (2)	C5—H5B	0.9700
N3—C7	1.136 (3)	C6—C7	1.462 (3)
C2—C3	1.527 (2)	C6—H6A	0.9700
C2—H2A	0.9700	C6—H6B	0.9700

C1—S1—S1ⁱ	102.62 (5)	C2—C3—H3B	109.2
C1—N1—C5	120.13 (12)	H3A—C3—H3B	107.9
C1—N1—C2	123.03 (12)	N2—C4—C3	177.8 (2)
C5—N1—C2	116.82 (12)	N1—C5—C6	111.78 (13)
N1—C1—S2	125.50 (11)	N1—C5—H5A	109.3
N1—C1—S1	111.98 (10)	C6—C5—H5A	109.3
S2—C1—S1	122.52 (8)	N1—C5—H5B	109.3
N1—C2—C3	113.23 (12)	C6—C5—H5B	109.3
N1—C2—H2A	108.9	H5A—C5—H5B	107.9
C3—C2—H2A	108.9	C7—C6—C5	112.02 (14)
N1—C2—H2B	108.9	C7—C6—H6A	109.2
C3—C2—H2B	108.9	C5—C6—H6A	109.2
H2A—C2—H2B	107.7	C7—C6—H6B	109.2
C4—C3—C2	112.20 (14)	C5—C6—H6B	109.2
C4—C3—H3A	109.2	H6A—C6—H6B	107.9
C2—C3—H3A	109.2	N3—C7—C6	177.1 (2)
C4—C3—H3B	109.2

C5—N1—C1—S2	−3.8 (2)	C1—N1—C2—C3	−82.14 (17)
C2—N1—C1—S2	177.86 (11)	C5—N1—C2—C3	99.48 (15)
C5—N1—C1—S1	175.66 (10)	N1—C2—C3—C4	−69.60 (17)
C2—N1—C1—S1	−2.67 (17)	C1—N1—C5—C6	−81.15 (18)
S1ⁱ—S1—C1—N1	170.16 (9)	C2—N1—C5—C6	97.28 (16)
S1ⁱ—S1—C1—S2	−10.36 (10)	N1—C5—C6—C7	−48.7 (2)

Symmetry code: (i) −x, y, −z+1/2.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C2—H2B···S1	0.97	2.46	2.857 (2)	105
C3—H3A···S1	0.97	2.84	3.332 (2)	112
C5—H5B···S2	0.97	2.69	3.028 (2)	101
C2—H2B···N2ⁱⁱ	0.97	2.55	3.202 (2)	125

Symmetry code: (ii) x, y+1, z.

References

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