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kp2376 scheme

Acta Cryst. (2012). E68, o138    [ doi:10.1107/S1600536811052950 ]

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

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

Abstract top

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].

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%).

Refinement top

The H atoms of both C and N atoms were positioned geometrically and allowed to ride on their parent atoms, with Uiso = 1.2Ueq (C) for CH2 0.97 Å and Uiso(H) = 1.2Ueq(N) for N–H 0.86 Å.

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
[Figure 1] Fig. 1. The molecular structure of (I) with displacement ellipsoids drawn at the 30% probability level.
[Figure 2] 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
C11H12N4SF(000) = 976
Mr = 232.31Dx = 1.351 Mg m3
Monoclinic, C2/cCu Kα radiation, λ = 1.54178 Å
Hall symbol: -C 2ycCell parameters from 1189 reflections
a = 14.1637 (3) Åθ = 3–71°
b = 11.2823 (3) ŵ = 2.33 mm1
c = 14.4413 (3) ÅT = 423 K
β = 98.131 (2)°Plate-like, brown
V = 2284.51 (9) Å30.18 × 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 tube2026 reflections with I > 2σ(I)
graphiteRint = 0.024
ω/2θ scansθmax = 71.2°, θmin = 5.0°
Absorption correction: multi-scan
(CrysAlis PRO; Oxford Diffraction, 2006)
h = 1517
Tmin = 0.679, Tmax = 0.784k = 1213
11636 measured reflectionsl = 1717
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)] = 0.035H-atom parameters constrained
wR(F2) = 0.098 w = 1/[σ2(Fo2) + (0.0635P)2 + 1.3435P]
where P = (Fo2 + 2Fc2)/3
S = 1.05(Δ/σ)max = 0.001
2188 reflectionsΔρmax = 0.36 e Å3
146 parametersΔρmin = 0.29 e Å3
0 restraintsExtinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.00105 (16)
Crystal data top
C11H12N4SV = 2284.51 (9) Å3
Mr = 232.31Z = 8
Monoclinic, C2/cCu Kα radiation
a = 14.1637 (3) ŵ = 2.33 mm1
b = 11.2823 (3) ÅT = 423 K
c = 14.4413 (3) Å0.18 × 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)
Tmin = 0.679, Tmax = 0.784Rint = 0.024
11636 measured reflectionsθmax = 71.2°
Refinement top
R[F2 > 2σ(F2)] = 0.035H-atom parameters constrained
wR(F2) = 0.098Δρmax = 0.36 e Å3
S = 1.05Δρmin = 0.29 e Å3
2188 reflectionsAbsolute structure: ?
146 parametersFlack parameter: ?
0 restraintsRogers parameter: ?
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
xyzUiso*/Ueq
S10.05434 (2)0.13968 (4)0.64677 (2)0.02482 (16)
N10.09012 (9)0.19216 (12)0.39813 (8)0.0267 (3)
H1A0.14720.21380.40390.032*
H1B0.07300.18650.34350.032*
N20.11711 (10)0.11912 (13)0.30576 (9)0.0324 (3)
N30.21230 (9)0.19501 (13)0.61321 (9)0.0305 (3)
N40.21438 (8)0.07773 (11)0.58195 (8)0.0227 (3)
C10.12328 (10)0.11239 (13)0.55838 (10)0.0202 (3)
C20.06959 (10)0.13264 (12)0.47006 (10)0.0193 (3)
C30.02745 (10)0.16710 (12)0.47476 (10)0.0201 (3)
C40.04625 (10)0.17282 (14)0.56599 (10)0.0225 (3)
C50.13693 (10)0.18534 (13)0.59338 (9)0.0229 (3)
C60.09988 (10)0.12325 (13)0.38096 (10)0.0224 (3)
C70.25656 (11)0.08466 (16)0.68138 (10)0.0294 (4)
H7A0.20770.06770.72030.035*
H7B0.27940.16460.69540.035*
C80.33845 (12)0.00184 (17)0.70481 (11)0.0363 (4)
H8A0.31390.08220.70060.044*
H8B0.36850.01140.76860.044*
C90.41251 (11)0.01221 (18)0.63870 (12)0.0394 (4)
H9A0.44140.09020.64640.047*
H9B0.46240.04660.65310.047*
C100.36437 (11)0.00355 (16)0.53838 (12)0.0325 (4)
H10A0.41100.00860.49610.039*
H10B0.34070.08410.52990.039*
C110.28218 (10)0.08241 (15)0.51370 (11)0.0269 (3)
H11A0.30710.16230.51160.032*
H11B0.24900.06340.45200.032*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
S10.0192 (2)0.0380 (3)0.0174 (2)0.00484 (13)0.00300 (14)0.00005 (13)
N10.0193 (6)0.0404 (8)0.0200 (6)0.0078 (5)0.0022 (5)0.0001 (5)
N20.0253 (7)0.0511 (9)0.0213 (7)0.0034 (6)0.0055 (5)0.0012 (6)
N30.0237 (7)0.0427 (8)0.0257 (7)0.0076 (6)0.0057 (5)0.0045 (6)
N40.0163 (6)0.0318 (7)0.0196 (6)0.0015 (5)0.0017 (5)0.0014 (5)
C10.0192 (7)0.0209 (7)0.0211 (7)0.0018 (5)0.0048 (5)0.0001 (5)
C20.0181 (7)0.0213 (7)0.0188 (7)0.0003 (5)0.0036 (5)0.0001 (5)
C30.0192 (7)0.0197 (7)0.0214 (7)0.0006 (5)0.0030 (5)0.0004 (5)
C40.0175 (7)0.0283 (8)0.0213 (7)0.0031 (6)0.0017 (5)0.0005 (6)
C50.0232 (8)0.0263 (8)0.0189 (7)0.0041 (6)0.0017 (6)0.0010 (6)
C60.0171 (7)0.0256 (8)0.0240 (8)0.0010 (5)0.0011 (6)0.0014 (6)
C70.0233 (7)0.0427 (10)0.0212 (7)0.0020 (6)0.0002 (6)0.0022 (6)
C80.0271 (8)0.0510 (11)0.0277 (8)0.0070 (7)0.0065 (7)0.0017 (7)
C90.0192 (8)0.0573 (12)0.0395 (10)0.0081 (7)0.0035 (7)0.0037 (8)
C100.0211 (7)0.0432 (10)0.0328 (9)0.0077 (7)0.0030 (6)0.0009 (7)
C110.0198 (7)0.0339 (9)0.0280 (8)0.0019 (6)0.0065 (6)0.0038 (6)
Geometric parameters (Å, °) top
S1—C11.7407 (14)C7—C81.517 (2)
S1—C41.7493 (14)C7—H7A0.9700
N1—C31.3471 (19)C7—H7B0.9700
N1—H1A0.8600C8—C91.523 (2)
N1—H1B0.8600C8—H8A0.9700
N2—C61.147 (2)C8—H8B0.9700
N3—C51.149 (2)C9—C101.522 (2)
N4—C11.3452 (19)C9—H9A0.9700
N4—C111.4710 (18)C9—H9B0.9700
N4—C71.4773 (18)C10—C111.518 (2)
C1—C21.408 (2)C10—H10A0.9700
C2—C61.417 (2)C10—H10B0.9700
C2—C31.439 (2)C11—H11A0.9700
C3—C41.382 (2)C11—H11B0.9700
C4—C51.403 (2)
C1—S1—C492.14 (7)H7A—C7—H7B107.9
C3—N1—H1A120.0C7—C8—C9111.46 (14)
C3—N1—H1B120.0C7—C8—H8A109.3
H1A—N1—H1B120.0C9—C8—H8A109.3
C1—N4—C11120.92 (12)C7—C8—H8B109.3
C1—N4—C7118.17 (12)C9—C8—H8B109.3
C11—N4—C7115.90 (12)H8A—C8—H8B108.0
N4—C1—C2130.70 (13)C10—C9—C8109.21 (13)
N4—C1—S1118.91 (10)C10—C9—H9A109.8
C2—C1—S1110.39 (10)C8—C9—H9A109.8
C1—C2—C6128.05 (13)C10—C9—H9B109.8
C1—C2—C3113.45 (12)C8—C9—H9B109.8
C6—C2—C3118.50 (13)H9A—C9—H9B108.3
N1—C3—C4125.45 (13)C11—C10—C9111.98 (14)
N1—C3—C2122.72 (13)C11—C10—H10A109.2
C4—C3—C2111.82 (12)C9—C10—H10A109.2
C3—C4—C5125.50 (13)C11—C10—H10B109.2
C3—C4—S1112.16 (11)C9—C10—H10B109.2
C5—C4—S1121.67 (11)H10A—C10—H10B107.9
N3—C5—C4178.05 (15)N4—C11—C10111.79 (12)
N2—C6—C2174.32 (16)N4—C11—H11A109.3
N4—C7—C8111.97 (13)C10—C11—H11A109.3
N4—C7—H7A109.2N4—C11—H11B109.3
C8—C7—H7A109.2C10—C11—H11B109.3
N4—C7—H7B109.2H11A—C11—H11B107.9
C8—C7—H7B109.2
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
N1—H1A···N3i0.862.223.0576 (19)164
N1—H1B···N2ii0.862.293.0293 (17)145
C7—H7A···S10.972.422.9041 (16)110
Symmetry codes: (i) −x−1/2, −y+1/2, −z+1; (ii) −x, y, −z+1/2.
Table 1
Hydrogen-bond geometry (Å, °)
top
D—H···AD—HH···AD···AD—H···A
N1—H1A···N3i0.862.223.0576 (19)164
N1—H1B···N2ii0.862.293.0293 (17)145
Symmetry codes: (i) −x−1/2, −y+1/2, −z+1; (ii) −x, y, −z+1/2.
Acknowledgements top

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
References top

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