3-Amino-5-(piperidin-1-yl)thio­phene-2,4-dicarbonitrile

Al-Adiwish, W.M.; Adan, D.; Mohamed Tahir, M.I.; Yaacob, W.A.; Kassim, M.B.

doi:10.1107/S1600536811052950

organic compounds

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ISSN: 2056-9890

Volume 68| Part 1| January 2012| Page o138

doi:10.1107/S1600536811052950

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3-Amino-5-(piperidin-1-yl)thiophene-2,4-dicarbonitrile

Wedad M. Al-Adiwish,^a D. Adan,^a Mohamed Ibrahim Mohamed Tahir,^b W.A. Yaacob ^a and Mohammad B. Kassim ^a,^c ^*

^aSchool of Chemical Sciences and Food Technology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Selangor, Malaysia, ^bDepartment of Chemistry, Faculty of Science, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia, and ^cFuel Cell Institute, Universiti Kebangsaan Malaysia, 43600 Selangor, Malaysia
^*Correspondence e-mail: mbkassim@ukm.my

(Received 7 December 2011; accepted 8 December 2011; online 17 December 2011)

In the title compound, C₁₁H₁₂N₄S, the thiophene ring is roughly planar, with a maximum deviation of 0.012 (1) Å for the S atom, and makes a dihedral angle of 7.89 (8)° with the mean plane of the piperidine ring, which is in a chair conformation. The crystal packing is stabilized by pairs of centrosymmetric intermolecular N—H⋯N hydrogen bonds, which results in the formation of a step-wise chain parallel to [10 $[\overline1]$ ].

Related literature

For the biological activity of aminothiophene derivatives, see: Abdel-Fattah et al. (2006 ). For related structures, see: El-Saghier (2002 ); Eller & Holzer (2006 ); Thomae et al. (2009 ); Al-Adiwish et al. (2011 ). For standard bond lengths, see: Allen et al. (1987 ).

Experimental

Crystal data

C₁₁H₁₂N₄S
M_r = 232.31
Monoclinic, C 2/c
a = 14.1637 (3) Å
b = 11.2823 (3) Å
c = 14.4413 (3) Å
β = 98.131 (2)°
V = 2284.51 (9) Å³
Z = 8
Cu Kα radiation
μ = 2.33 mm⁻¹
T = 423 K
0.18 × 0.14 × 0.11 mm

Data collection

Oxford Diffraction Gemini CCD area-detector' diffractometer
Absorption correction: multi-scan (CrysAlis PRO; Oxford Diffraction, 2006 $[Oxford Diffraction (2006). CrysAlis CCD and CrysAlis RED. Oxford Diffraction, Abingdon, England.]$ ) T_min = 0.679, T_max = 0.784
11636 measured reflections
2188 independent reflections
2026 reflections with I > 2σ(I)
R_int = 0.024

Refinement

R[F² > 2σ(F²)] = 0.035
wR(F²) = 0.098
S = 1.05
2188 reflections
146 parameters
H-atom parameters constrained
Δρ_max = 0.36 e Å⁻³
Δρ_min = −0.29 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1A⋯N3ⁱ	0.86	2.22	3.0576 (19)	164
N1—H1B⋯N2ⁱⁱ	0.86	2.29	3.0293 (17)	145
Symmetry codes: (i) $[-x-{\script{1\over 2}}, -y+{\script{1\over 2}}, -z+1]$ ; (ii) $[-x, y, -z+{\script{1\over 2}}]$ .

Data collection: CrysAlis CCD (Oxford Diffraction, 2006 $[Oxford Diffraction (2006). CrysAlis CCD and CrysAlis RED. Oxford Diffraction, Abingdon, England.]$ ); cell refinement: CrysAlis CCD; data reduction: CrysAlis RED (Oxford Diffraction, 2006 $[Oxford Diffraction (2006). CrysAlis CCD and CrysAlis RED. Oxford Diffraction, Abingdon, England.]$ ); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL, PLATON (Spek, 2009 ) and publCIF (Westrip, 2010 ).

Supporting information

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536811052950/kp2376sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536811052950/kp2376Isup2.hkl

Supporting information file. DOI: 10.1107/S1600536811052950/kp2376Isup3.cml

checkCIF report

Comment top

Recent studies have shown that aminothiophene derivatives are potential antibacterial and antifungal substances [Abdel-Fattah et al. (2006)]. The title compound (I), is a derivative of piperidine containing aminothiophene, was reported earlier [Al-Adiwish et al. (2011); Eller & Holzer (2006); El-Saghier et al. (2002)]. However, its crystal structure is reported here. The thiophene fragment (S1/N1/N2/N4/C1/C2/C3/C4/C6) is close to be planar with the largest deviation of 0.034 (1)Å for S1. The two C(sp²)–C(sp²) bond lengths in the carbonitrile fragments differ slightly with C2–C6 1.417 (2)Å and C4–C5 1.403 (2) Å, respectively. Electron donation of the S atom may contribute to the increase in the former bond length. Angles in the respective fragments, C6–C2–C3 [118.50 (13) °] and C3–C4–C5 [125.50 (13) °]are different from the value typical for this hybridisation. Other bond lengths and angles in the molecule are in the normal ranges (Allen et al., 1987).

In the crystal molecules are linked by two intermolecular N1–H1A···N2 and N1–H1B···N3 hydrogen bonds forming a centro-symmetric dimers along the crystallographic (010) direction (Table 1, Fig. 2).The intramolecular contact C-H···S between the pyperidine and thiophene rings was observed (Table 1).

Related literature top

For the biological activity of aminothiophene derivatives, see: Abdel-Fattah et al. (2006). For related structures, see: El-Saghier et al. (2002); Eller & Holzer (2006); Thomae et al. (2009); Al-Adiwish et al. (2011). For standard bond lengths, see: Allen et al. (1987).

Experimental top

The title compound was prepared according to previously report (Thomae et al., 2009) with some modifications. 2-[Bis(methylthio)methylene]propanedinitrile (0.01 mol) was dissolved in DMF (15 mL) prior to addition of piperidine (0.01 mol). The mixture was heated at 343 K for 75 min and then Na₂S.9H₂O (0.01 mol) was added and heated for another 2 h. Then, chloroacetonitrile (0.02 mol) was added slowly and was left at 343 K for another 2 h. Subsequently, potassium carbonate (0.02 mol) was added and left for another 90 min. Finally, the reaction mixture was poured into water (100 mL) and stirred vigorously to give a white precipitate. The residue was filtered, washed with water, and dried at room temperature until a constant weight. A slow evaporation of the compound from methanol solution gave single crystals suitable for X-ray diffraction (yield = 74.0%).

Computing details top

Data collection: CrysAlis CCD (Oxford Diffraction, 2006); cell refinement: CrysAlis RED (Oxford Diffraction, 2006); data reduction: CrysAlis RED (Oxford Diffraction, 2006); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008), PLATON (Spek, 2009) and publCIF (Westrip, 2010).

Figures top

	Fig. 1. The molecular structure of (I) with displacement ellipsoids drawn at the 30% probability level.
	Fig. 2. Crystal packing of (I) viewed down the a-axis. Hydrogen bonds are drawn as dashed lines.

3-Amino-5-(piperidin-1-yl)thiophene-2,4-dicarbonitrile top

Crystal data top

C₁₁H₁₂N₄S	F(000) = 976
M_r = 232.31	D_x = 1.351 Mg m⁻³
Monoclinic, C2/c	Cu Kα radiation, λ = 1.54178 Å
Hall symbol: -C 2yc	Cell parameters from 1189 reflections
a = 14.1637 (3) Å	θ = 3–71°
b = 11.2823 (3) Å	µ = 2.33 mm⁻¹
c = 14.4413 (3) Å	T = 423 K
β = 98.131 (2)°	Plate-like, brown
V = 2284.51 (9) Å³	0.18 × 0.14 × 0.11 mm
Z = 8

Data collection top

Oxford Diffraction Gemini CCD area-detector' diffractometer	2188 independent reflections
Radiation source: fine-focus sealed tube	2026 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.024
ω/2θ scans	θ_max = 71.2°, θ_min = 5.0°
Absorption correction: multi-scan (CrysAlis PRO; Oxford Diffraction, 2006)	h = −15→17
T_min = 0.679, T_max = 0.784	k = −12→13
11636 measured reflections	l = −17→17

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)] = 0.035	H-atom parameters constrained
wR(F²) = 0.098	w = 1/[σ²(F_o²) + (0.0635P)² + 1.3435P] where P = (F_o² + 2F_c²)/3
S = 1.05	(Δ/σ)_max = 0.001
2188 reflections	Δρ_max = 0.36 e Å⁻³
146 parameters	Δρ_min = −0.29 e Å⁻³
0 restraints	Extinction correction: SHELXL97 (Sheldrick, 2008), Fc^*=kFc[1+0.001xFc²λ³/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.00105 (16)

Crystal data top

C₁₁H₁₂N₄S	V = 2284.51 (9) Å³
M_r = 232.31	Z = 8
Monoclinic, C2/c	Cu Kα radiation
a = 14.1637 (3) Å	µ = 2.33 mm⁻¹
b = 11.2823 (3) Å	T = 423 K
c = 14.4413 (3) Å	0.18 × 0.14 × 0.11 mm
β = 98.131 (2)°

Data collection top

Oxford Diffraction Gemini CCD area-detector' diffractometer	2188 independent reflections
Absorption correction: multi-scan (CrysAlis PRO; Oxford Diffraction, 2006)	2026 reflections with I > 2σ(I)
T_min = 0.679, T_max = 0.784	R_int = 0.024
11636 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.035	0 restraints
wR(F²) = 0.098	H-atom parameters constrained
S = 1.05	Δρ_max = 0.36 e Å⁻³
2188 reflections	Δρ_min = −0.29 e Å⁻³
146 parameters

Special details top

Experimental. The crystal was placed in the cold stream of an Oxford Cryosystems open-flow nitrogen cryostat (Cosier & Glazer, 1986) with a nominal stability of 0.1 K.

Cosier, J. & Glazer, A.M., 1986. J. Appl. Cryst. 105 107.

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	0.05434 (2)	0.13968 (4)	0.64677 (2)	0.02482 (16)
N1	−0.09012 (9)	0.19216 (12)	0.39813 (8)	0.0267 (3)
H1A	−0.1472	0.2138	0.4039	0.032*
H1B	−0.0730	0.1865	0.3435	0.032*
N2	0.11711 (10)	0.11912 (13)	0.30576 (9)	0.0324 (3)
N3	−0.21230 (9)	0.19501 (13)	0.61321 (9)	0.0305 (3)
N4	0.21438 (8)	0.07773 (11)	0.58195 (8)	0.0227 (3)
C1	0.12328 (10)	0.11239 (13)	0.55838 (10)	0.0202 (3)
C2	0.06959 (10)	0.13264 (12)	0.47006 (10)	0.0193 (3)
C3	−0.02745 (10)	0.16710 (12)	0.47476 (10)	0.0201 (3)
C4	−0.04625 (10)	0.17282 (14)	0.56599 (10)	0.0225 (3)
C5	−0.13693 (10)	0.18534 (13)	0.59338 (9)	0.0229 (3)
C6	0.09988 (10)	0.12325 (13)	0.38096 (10)	0.0224 (3)
C7	0.25656 (11)	0.08466 (16)	0.68138 (10)	0.0294 (4)
H7A	0.2077	0.0677	0.7203	0.035*
H7B	0.2794	0.1646	0.6954	0.035*
C8	0.33845 (12)	−0.00184 (17)	0.70481 (11)	0.0363 (4)
H8A	0.3139	−0.0822	0.7006	0.044*
H8B	0.3685	0.0114	0.7686	0.044*
C9	0.41251 (11)	0.01221 (18)	0.63870 (12)	0.0394 (4)
H9A	0.4414	0.0902	0.6464	0.047*
H9B	0.4624	−0.0466	0.6531	0.047*
C10	0.36437 (11)	−0.00355 (16)	0.53838 (12)	0.0325 (4)
H10A	0.4110	0.0086	0.4961	0.039*
H10B	0.3407	−0.0841	0.5299	0.039*
C11	0.28218 (10)	0.08241 (15)	0.51370 (11)	0.0269 (3)
H11A	0.3071	0.1623	0.5116	0.032*
H11B	0.2490	0.0634	0.4520	0.032*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
S1	0.0192 (2)	0.0380 (3)	0.0174 (2)	0.00484 (13)	0.00300 (14)	−0.00005 (13)
N1	0.0193 (6)	0.0404 (8)	0.0200 (6)	0.0078 (5)	0.0022 (5)	−0.0001 (5)
N2	0.0253 (7)	0.0511 (9)	0.0213 (7)	0.0034 (6)	0.0055 (5)	0.0012 (6)
N3	0.0237 (7)	0.0427 (8)	0.0257 (7)	0.0076 (6)	0.0057 (5)	0.0045 (6)
N4	0.0163 (6)	0.0318 (7)	0.0196 (6)	0.0015 (5)	0.0017 (5)	0.0014 (5)
C1	0.0192 (7)	0.0209 (7)	0.0211 (7)	−0.0018 (5)	0.0048 (5)	0.0001 (5)
C2	0.0181 (7)	0.0213 (7)	0.0188 (7)	−0.0003 (5)	0.0036 (5)	0.0001 (5)
C3	0.0192 (7)	0.0197 (7)	0.0214 (7)	−0.0006 (5)	0.0030 (5)	−0.0004 (5)
C4	0.0175 (7)	0.0283 (8)	0.0213 (7)	0.0031 (6)	0.0017 (5)	−0.0005 (6)
C5	0.0232 (8)	0.0263 (8)	0.0189 (7)	0.0041 (6)	0.0017 (6)	0.0010 (6)
C6	0.0171 (7)	0.0256 (8)	0.0240 (8)	0.0010 (5)	0.0011 (6)	0.0014 (6)
C7	0.0233 (7)	0.0427 (10)	0.0212 (7)	0.0020 (6)	−0.0002 (6)	−0.0022 (6)
C8	0.0271 (8)	0.0510 (11)	0.0277 (8)	0.0070 (7)	−0.0065 (7)	0.0017 (7)
C9	0.0192 (8)	0.0573 (12)	0.0395 (10)	0.0081 (7)	−0.0035 (7)	−0.0037 (8)
C10	0.0211 (7)	0.0432 (10)	0.0328 (9)	0.0077 (7)	0.0030 (6)	−0.0009 (7)
C11	0.0198 (7)	0.0339 (9)	0.0280 (8)	0.0019 (6)	0.0065 (6)	0.0038 (6)

Geometric parameters (Å, º) top

S1—C1	1.7407 (14)	C7—C8	1.517 (2)
S1—C4	1.7493 (14)	C7—H7A	0.9700
N1—C3	1.3471 (19)	C7—H7B	0.9700
N1—H1A	0.8600	C8—C9	1.523 (2)
N1—H1B	0.8600	C8—H8A	0.9700
N2—C6	1.147 (2)	C8—H8B	0.9700
N3—C5	1.149 (2)	C9—C10	1.522 (2)
N4—C1	1.3452 (19)	C9—H9A	0.9700
N4—C11	1.4710 (18)	C9—H9B	0.9700
N4—C7	1.4773 (18)	C10—C11	1.518 (2)
C1—C2	1.408 (2)	C10—H10A	0.9700
C2—C6	1.417 (2)	C10—H10B	0.9700
C2—C3	1.439 (2)	C11—H11A	0.9700
C3—C4	1.382 (2)	C11—H11B	0.9700
C4—C5	1.403 (2)

C1—S1—C4	92.14 (7)	H7A—C7—H7B	107.9
C3—N1—H1A	120.0	C7—C8—C9	111.46 (14)
C3—N1—H1B	120.0	C7—C8—H8A	109.3
H1A—N1—H1B	120.0	C9—C8—H8A	109.3
C1—N4—C11	120.92 (12)	C7—C8—H8B	109.3
C1—N4—C7	118.17 (12)	C9—C8—H8B	109.3
C11—N4—C7	115.90 (12)	H8A—C8—H8B	108.0
N4—C1—C2	130.70 (13)	C10—C9—C8	109.21 (13)
N4—C1—S1	118.91 (10)	C10—C9—H9A	109.8
C2—C1—S1	110.39 (10)	C8—C9—H9A	109.8
C1—C2—C6	128.05 (13)	C10—C9—H9B	109.8
C1—C2—C3	113.45 (12)	C8—C9—H9B	109.8
C6—C2—C3	118.50 (13)	H9A—C9—H9B	108.3
N1—C3—C4	125.45 (13)	C11—C10—C9	111.98 (14)
N1—C3—C2	122.72 (13)	C11—C10—H10A	109.2
C4—C3—C2	111.82 (12)	C9—C10—H10A	109.2
C3—C4—C5	125.50 (13)	C11—C10—H10B	109.2
C3—C4—S1	112.16 (11)	C9—C10—H10B	109.2
C5—C4—S1	121.67 (11)	H10A—C10—H10B	107.9
N3—C5—C4	178.05 (15)	N4—C11—C10	111.79 (12)
N2—C6—C2	174.32 (16)	N4—C11—H11A	109.3
N4—C7—C8	111.97 (13)	C10—C11—H11A	109.3
N4—C7—H7A	109.2	N4—C11—H11B	109.3
C8—C7—H7A	109.2	C10—C11—H11B	109.3
N4—C7—H7B	109.2	H11A—C11—H11B	107.9
C8—C7—H7B	109.2

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1A···N3ⁱ	0.86	2.22	3.0576 (19)	164
N1—H1B···N2ⁱⁱ	0.86	2.29	3.0293 (17)	145
C7—H7A···S1	0.97	2.42	2.9041 (16)	110

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

Experimental details

Crystal data
Chemical formula	C₁₁H₁₂N₄S
M_r	232.31
Crystal system, space group	Monoclinic, C2/c
Temperature (K)	423
a, b, c (Å)	14.1637 (3), 11.2823 (3), 14.4413 (3)
β (°)	98.131 (2)
V (Å³)	2284.51 (9)
Z	8
Radiation type	Cu Kα
µ (mm⁻¹)	2.33
Crystal size (mm)	0.18 × 0.14 × 0.11

Data collection
Diffractometer	Oxford Diffraction Gemini CCD area-detector' diffractometer
Absorption correction	Multi-scan (CrysAlis PRO; Oxford Diffraction, 2006)
T_min, T_max	0.679, 0.784
No. of measured, independent and observed [I > 2σ(I)] reflections	11636, 2188, 2026
R_int	0.024
(sin θ/λ)_max (Å⁻¹)	0.614

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.035, 0.098, 1.05
No. of reflections	2188
No. of parameters	146
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.36, −0.29

Computer programs: CrysAlis CCD (Oxford Diffraction, 2006), CrysAlis RED (Oxford Diffraction, 2006), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008), PLATON (Spek, 2009) and publCIF (Westrip, 2010).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1A···N3ⁱ	0.86	2.22	3.0576 (19)	164
N1—H1B···N2ⁱⁱ	0.86	2.29	3.0293 (17)	145

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

Acknowledgements

The authors thank University Kebangsaan Malaysia for providing facilities and the Ministry of Science, Technology and Innovation for the research fund No. UKM-GGPM-KPB-098–2010. A PhD scholarship from the Libyan Government for WMA is greatly appreciated.

References

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