organic compounds
2-Amino-4-methyl-4,5,6,7-tetrahydro-1-benzothiophene-3-carbonitrile
aDepartment of Chemistry, Karnatak University, Dharwad 580 003, India, and bDepartment of Studies in Chemistry, Bangalore University, Bangalore 560 001, Karnataka, India
*Correspondence e-mail: dr_imk@yahoo.com
In the title compound, C10H12N2S, the thiophene ring is essentially planar (r.m.s. deviation = 0.0290 Å). The two C atoms of the cyclohexene ring (at positions 6 and 7) are disordered over two sets of sites in a 0.810 (5):0.190 (5) ratio. The cyclohexene rings in both the major and minor occupancy conformers adopt a half-chair conformation. In the crystal, there are two types of N—H⋯N interaction. One of these results in centrosymmetric head-to-head dimers corresponding to an R22(12) graph-set motif and the other forms a 20-membered macrocyclic ring involving six molecules.
Related literature
For biological activities of benzothiophenes, see: Shetty et al. (2009). For the of a closely related compound, see: Ziaulla et al. (2011). For graph-set notation of hydrogen bonds, see: Bernstein et al. (1995).
Experimental
Crystal data
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Refinement
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Data collection: SMART (Bruker, 1998); cell SMART; data reduction: SAINT-Plus (Bruker, 1998); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 (Farrugia, 1997) and CAMERON (Watkin et al., 1996); software used to prepare material for publication: WinGX (Farrugia, 1999).
Supporting information
https://doi.org/10.1107/S160053681204010X/pv2585sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S160053681204010X/pv2585Isup2.hkl
Supporting information file. DOI: https://doi.org/10.1107/S160053681204010X/pv2585Isup3.cml
To a well stirred mixture of 2-methyl cyclohexanone (8 g, 71.4 mmole) and malononitrile (4.712 g, 71.4 mmole) in ethanol (100 ml) was added elemental sulfur (2.3 g, 72 mmole). To this cooled reaction mixture was added diethyl amine (5 ml) with vigorous stirring during 1 min. The reaction mixture was stirred at 333 K for about 1 h. The solvent was evaporated under reduced pressure. The residue was poured into crushed ice and the solid obtained was purified by
(yield = 9.3 g (68%), m.p. = 392–394 K. The crystals suitable for X-ray crystallographic analysis were grown from a solution of dichloromethane.The occupancies were refined individually for the C atoms C6 and C7, the disordered atoms were grouped in Part 1 and Part 2 as Part 1: C6 and C7 with partial occupancy of 0.810 (5) and Part 2: C6' and C7' with partial occupancy 0.190 (5). In this way the occupancy disordered was modelled using the EADP command in SHELXL97. The H atoms were placed at calculated positions in the riding model approximation with N—H = 0.86° A, C—H = 0.97 and 0.96 Å for heterocyclic and methyl H atoms respectively, with Uiso(H) = 1.5Ueq(C) for methyl H atoms and Uiso(H) = 1.2Ueq(N/C).
Tetrahydro-benzothiophenes are important class of compounds which exhibits antibacterial and antifungal activities (Shetty et al.,2009). In the title compound, the tetrahydro-benzothiophene ring is substituted with the methyl group at C8, amine at C2 and carbonitrile group at C3 positions. The thiophene ring is essentially planar (r.m.s. deviation = 0.03 Å). The atoms C6 and C7 are disordered over two sites (C6/C6' and C7/C7') with site occupancy factors 0.810 (5) and 0.190 (5) resulting in a major and a minor conformers, respectively. The cyclohexene ring in both the conformers is in the half-chair conformation with C6 and C7 atoms being deviated from the rest of the ring atoms by 0.3330 (3) and -0.3132 (3) Å for the major conformer. The C6' and C7' atoms are deviated by -0.3738 (2) and 0.3546 (2) Å for the minor conformer respectively. The methyl group of the cyclohexene ring is oriented axially which is characterized by the bond angles C6—C8—C11 = 112.50 (2)° and C10—C8—C11 = 115.02 (2)°. The
is stabilized by two types of N—H···N intermolecular interactions generating centrosymmetric head-to-head dimers corresponding to graph-set R22(12) motif (Bernstein et al., 1995) and a 20-membered macrocyclic ring involving six molecules (Fig. 2). The bond distances and angles in the title compound agree very well with the corresponding bond distances and angles reported in a closely related compound (Ziaulla et al., 2011).For biological activities of benzothiophenes, see: Shetty et al. (2009). For the
of a closely related compound, see: Ziaulla et al. (2011). For graph-set notation of hydrogen bonds, see: Bernstein et al. (1995).Data collection: SMART (Bruker, 1998); cell
SMART (Bruker, 1998); data reduction: SAINT-Plus (Bruker, 1998); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 (Farrugia, 1997) and CAMERON (Watkin et al., 1996); software used to prepare material for publication: WinGX (Farrugia, 1999).C10H12N2S | F(000) = 408 |
Mr = 192.28 | Dx = 1.271 Mg m−3 |
Monoclinic, P21/c | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2ybc | Cell parameters from 2195 reflections |
a = 9.6771 (2) Å | θ = 2.1–27.0° |
b = 7.6364 (2) Å | µ = 0.28 mm−1 |
c = 13.8156 (3) Å | T = 296 K |
β = 100.221 (2)° | Block, yellow |
V = 1004.75 (4) Å3 | 0.18 × 0.16 × 0.16 mm |
Z = 4 |
Bruker SMART APEX CCD detector diffractometer | 2195 independent reflections |
Radiation source: fine-focus sealed tube | 1812 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.024 |
ω scans | θmax = 27.0°, θmin = 2.1° |
Absorption correction: multi-scan (SADABS; Bruker, 1998) | h = −12→12 |
Tmin = 0.952, Tmax = 0.957 | k = −9→9 |
8861 measured reflections | l = −17→17 |
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.039 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.118 | H-atom parameters constrained |
S = 1.06 | w = 1/[σ2(Fo2) + (0.0678P)2 + 0.1371P] where P = (Fo2 + 2Fc2)/3 |
2195 reflections | (Δ/σ)max < 0.001 |
125 parameters | Δρmax = 0.16 e Å−3 |
0 restraints | Δρmin = −0.25 e Å−3 |
C10H12N2S | V = 1004.75 (4) Å3 |
Mr = 192.28 | Z = 4 |
Monoclinic, P21/c | Mo Kα radiation |
a = 9.6771 (2) Å | µ = 0.28 mm−1 |
b = 7.6364 (2) Å | T = 296 K |
c = 13.8156 (3) Å | 0.18 × 0.16 × 0.16 mm |
β = 100.221 (2)° |
Bruker SMART APEX CCD detector diffractometer | 2195 independent reflections |
Absorption correction: multi-scan (SADABS; Bruker, 1998) | 1812 reflections with I > 2σ(I) |
Tmin = 0.952, Tmax = 0.957 | Rint = 0.024 |
8861 measured reflections |
R[F2 > 2σ(F2)] = 0.039 | 0 restraints |
wR(F2) = 0.118 | H-atom parameters constrained |
S = 1.06 | Δρmax = 0.16 e Å−3 |
2195 reflections | Δρmin = −0.25 e Å−3 |
125 parameters |
Geometry. All s.u.'s (except the s.u. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell s.u.'s are taken into account individually in the estimation of s.u.'s in distances, angles and torsion angles; correlations between s.u.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell s.u.'s is used for estimating s.u.'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 > 2σ(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. |
x | y | z | Uiso*/Ueq | Occ. (<1) | |
S1 | 0.71234 (4) | 0.00203 (5) | 0.83213 (3) | 0.05244 (18) | |
C3 | 0.65478 (15) | 0.14987 (19) | 0.98594 (10) | 0.0421 (3) | |
C1 | 0.59583 (16) | 0.2640 (2) | 1.04856 (10) | 0.0472 (4) | |
N2 | 0.54845 (17) | 0.3532 (2) | 1.10080 (11) | 0.0653 (4) | |
C2 | 0.63578 (15) | 0.17225 (19) | 0.88557 (10) | 0.0439 (3) | |
C9 | 0.76862 (16) | −0.0986 (2) | 0.94522 (11) | 0.0481 (4) | |
C8 | 0.73216 (16) | −0.00656 (18) | 1.01974 (11) | 0.0420 (3) | |
N1 | 0.57113 (16) | 0.3034 (2) | 0.82953 (10) | 0.0650 (4) | |
H1A | 0.5345 | 0.3890 | 0.8566 | 0.078* | |
H1B | 0.5666 | 0.3014 | 0.7668 | 0.078* | |
C10 | 0.8661 (2) | 0.0583 (3) | 1.18824 (14) | 0.0791 (6) | |
H10A | 0.8837 | 0.0168 | 1.2549 | 0.119* | |
H10B | 0.8258 | 0.1734 | 1.1861 | 0.119* | |
H10C | 0.9528 | 0.0626 | 1.1637 | 0.119* | |
C4 | 0.76560 (17) | −0.0641 (2) | 1.12553 (12) | 0.0528 (4) | |
H4 | 0.6773 | −0.0591 | 1.1509 | 0.063* | 0.810 (5) |
C5 | 0.8427 (2) | −0.2719 (2) | 0.95380 (14) | 0.0663 (5) | |
H5A | 0.9131 | −0.2740 | 0.9118 | 0.080* | 0.810 (5) |
H5B | 0.7762 | −0.3655 | 0.9336 | 0.080* | 0.810 (5) |
C7 | 0.8107 (4) | −0.2568 (4) | 1.1298 (2) | 0.0708 (8) | 0.810 (5) |
H7A | 0.8542 | −0.2857 | 1.1966 | 0.085* | 0.810 (5) |
H7B | 0.7281 | −0.3300 | 1.1123 | 0.085* | 0.810 (5) |
C6 | 0.9126 (4) | −0.2970 (4) | 1.06146 (19) | 0.0730 (8) | 0.810 (5) |
H6A | 0.9452 | −0.4168 | 1.0715 | 0.088* | 0.810 (5) |
H6B | 0.9934 | −0.2202 | 1.0766 | 0.088* | 0.810 (5) |
C4' | 0.76560 (17) | −0.0641 (2) | 1.12553 (12) | 0.0528 (4) | 0.00 |
H4A | 0.6823 | −0.0925 | 1.1538 | 0.063* | 0.190 (5) |
C5' | 0.8427 (2) | −0.2719 (2) | 0.95380 (14) | 0.0663 (5) | 0.00 |
H5C | 0.9410 | −0.2557 | 0.9498 | 0.080* | 0.190 (5) |
H5D | 0.8009 | −0.3485 | 0.9006 | 0.080* | 0.190 (5) |
C7' | 0.8760 (17) | −0.2149 (18) | 1.1356 (10) | 0.0708 (8) | 0.190 (5) |
H7C | 0.8836 | −0.2697 | 1.1996 | 0.085* | 0.190 (5) |
H7D | 0.9673 | −0.1679 | 1.1297 | 0.085* | 0.190 (5) |
C6' | 0.8294 (17) | −0.3534 (17) | 1.0531 (9) | 0.0730 (8) | 0.190 (5) |
H6C | 0.8883 | −0.4567 | 1.0650 | 0.088* | 0.190 (5) |
H6D | 0.7329 | −0.3882 | 1.0528 | 0.088* | 0.190 (5) |
U11 | U22 | U33 | U12 | U13 | U23 | |
S1 | 0.0652 (3) | 0.0563 (3) | 0.0354 (2) | 0.01326 (18) | 0.00757 (18) | −0.00553 (16) |
C3 | 0.0464 (7) | 0.0441 (8) | 0.0358 (7) | −0.0006 (6) | 0.0074 (5) | −0.0036 (6) |
C1 | 0.0574 (9) | 0.0472 (8) | 0.0362 (7) | 0.0016 (7) | 0.0063 (6) | −0.0003 (6) |
N2 | 0.0859 (11) | 0.0645 (9) | 0.0477 (8) | 0.0141 (8) | 0.0176 (7) | −0.0073 (7) |
C2 | 0.0486 (8) | 0.0458 (8) | 0.0369 (7) | 0.0041 (6) | 0.0062 (6) | −0.0016 (6) |
C9 | 0.0532 (8) | 0.0470 (9) | 0.0435 (8) | 0.0064 (7) | 0.0073 (6) | 0.0019 (6) |
C8 | 0.0429 (7) | 0.0449 (8) | 0.0373 (8) | −0.0026 (6) | 0.0044 (6) | 0.0023 (6) |
N1 | 0.0891 (11) | 0.0662 (9) | 0.0391 (7) | 0.0320 (8) | 0.0095 (7) | 0.0061 (6) |
C10 | 0.0743 (13) | 0.1082 (17) | 0.0479 (11) | −0.0107 (12) | −0.0082 (9) | 0.0044 (11) |
C4 | 0.0556 (9) | 0.0618 (10) | 0.0413 (8) | −0.0008 (8) | 0.0095 (7) | 0.0107 (8) |
C5 | 0.0798 (12) | 0.0545 (10) | 0.0669 (12) | 0.0193 (9) | 0.0196 (9) | 0.0058 (9) |
C7 | 0.083 (2) | 0.0661 (16) | 0.0646 (14) | 0.0052 (14) | 0.0166 (15) | 0.0268 (12) |
C6 | 0.0775 (19) | 0.0668 (16) | 0.0730 (15) | 0.0256 (14) | 0.0090 (14) | 0.0181 (12) |
C4' | 0.0556 (9) | 0.0618 (10) | 0.0413 (8) | −0.0008 (8) | 0.0095 (7) | 0.0107 (8) |
C5' | 0.0798 (12) | 0.0545 (10) | 0.0669 (12) | 0.0193 (9) | 0.0196 (9) | 0.0058 (9) |
C7' | 0.083 (2) | 0.0661 (16) | 0.0646 (14) | 0.0052 (14) | 0.0166 (15) | 0.0268 (12) |
C6' | 0.0775 (19) | 0.0668 (16) | 0.0730 (15) | 0.0256 (14) | 0.0090 (14) | 0.0181 (12) |
S1—C2 | 1.7256 (14) | C4—C7 | 1.533 (3) |
S1—C9 | 1.7397 (16) | C4—H4 | 0.9800 |
C3—C2 | 1.3768 (19) | C5—C6 | 1.533 (3) |
C3—C1 | 1.417 (2) | C5—H5A | 0.9700 |
C3—C8 | 1.443 (2) | C5—H5B | 0.9700 |
C1—N2 | 1.146 (2) | C7—C6 | 1.513 (5) |
C2—N1 | 1.3499 (19) | C7—H7A | 0.9700 |
C9—C8 | 1.345 (2) | C7—H7B | 0.9700 |
C9—C5 | 1.500 (2) | C6—H6A | 0.9700 |
C8—C4 | 1.505 (2) | C6—H6B | 0.9700 |
N1—H1A | 0.8600 | C7'—C6' | 1.56 (2) |
N1—H1B | 0.8600 | C7'—H7C | 0.9700 |
C10—C4 | 1.507 (3) | C7'—H7D | 0.9700 |
C10—H10A | 0.9600 | C6'—H6C | 0.9700 |
C10—H10B | 0.9600 | C6'—H6D | 0.9700 |
C10—H10C | 0.9600 | ||
C2—S1—C9 | 92.20 (7) | C10—C4—H4 | 106.5 |
C2—C3—C1 | 122.84 (14) | C7—C4—H4 | 106.5 |
C2—C3—C8 | 113.43 (13) | C9—C5—C6 | 108.02 (16) |
C1—C3—C8 | 123.61 (13) | C9—C5—H5A | 110.1 |
N2—C1—C3 | 178.40 (17) | C6—C5—H5A | 110.1 |
N1—C2—C3 | 129.43 (14) | C9—C5—H5B | 110.1 |
N1—C2—S1 | 120.27 (11) | C6—C5—H5B | 110.1 |
C3—C2—S1 | 110.29 (11) | H5A—C5—H5B | 108.4 |
C8—C9—C5 | 125.99 (15) | C6—C7—C4 | 112.5 (2) |
C8—C9—S1 | 111.95 (12) | C6—C7—H7A | 109.1 |
C5—C9—S1 | 122.00 (12) | C4—C7—H7A | 109.1 |
C9—C8—C3 | 112.13 (14) | C6—C7—H7B | 109.1 |
C9—C8—C4 | 123.39 (14) | C4—C7—H7B | 109.1 |
C3—C8—C4 | 124.46 (14) | H7A—C7—H7B | 107.8 |
C2—N1—H1A | 120.0 | C7—C6—C5 | 110.9 (3) |
C2—N1—H1B | 120.0 | C7—C6—H6A | 109.5 |
H1A—N1—H1B | 120.0 | C5—C6—H6A | 109.5 |
C4—C10—H10A | 109.5 | C7—C6—H6B | 109.5 |
C4—C10—H10B | 109.5 | C5—C6—H6B | 109.5 |
H10A—C10—H10B | 109.5 | H6A—C6—H6B | 108.1 |
C4—C10—H10C | 109.5 | C6'—C7'—H7C | 109.8 |
H10A—C10—H10C | 109.5 | C6'—C7'—H7D | 109.8 |
H10B—C10—H10C | 109.5 | H7C—C7'—H7D | 108.3 |
C8—C4—C10 | 112.49 (15) | C7'—C6'—H6C | 110.0 |
C8—C4—C7 | 109.16 (16) | C7'—C6'—H6D | 110.0 |
C10—C4—C7 | 115.0 (2) | H6C—C6'—H6D | 108.4 |
C8—C4—H4 | 106.5 | ||
C2—C3—C1—N2 | 158 (6) | C2—C3—C8—C9 | −0.47 (19) |
C8—C3—C1—N2 | −17 (6) | C1—C3—C8—C9 | 175.63 (14) |
C1—C3—C2—N1 | 5.0 (3) | C2—C3—C8—C4 | −178.94 (14) |
C8—C3—C2—N1 | −178.86 (16) | C1—C3—C8—C4 | −2.8 (2) |
C1—C3—C2—S1 | −176.09 (12) | C9—C8—C4—C10 | 114.82 (19) |
C8—C3—C2—S1 | 0.05 (16) | C3—C8—C4—C10 | −66.9 (2) |
C9—S1—C2—N1 | 179.29 (14) | C9—C8—C4—C7 | −14.1 (3) |
C9—S1—C2—C3 | 0.28 (12) | C3—C8—C4—C7 | 164.16 (19) |
C2—S1—C9—C8 | −0.56 (13) | C8—C9—C5—C6 | −18.6 (3) |
C2—S1—C9—C5 | 176.80 (15) | S1—C9—C5—C6 | 164.40 (18) |
C5—C9—C8—C3 | −176.56 (16) | C8—C4—C7—C6 | 44.6 (3) |
S1—C9—C8—C3 | 0.67 (17) | C10—C4—C7—C6 | −82.9 (3) |
C5—C9—C8—C4 | 1.9 (3) | C4—C7—C6—C5 | −64.8 (4) |
S1—C9—C8—C4 | 179.16 (12) | C9—C5—C6—C7 | 47.9 (3) |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1A···N2i | 0.86 | 2.24 | 3.088 (2) | 167 |
N1—H1B···N2ii | 0.86 | 2.56 | 3.349 (2) | 153 |
Symmetry codes: (i) −x+1, −y+1, −z+2; (ii) x, −y+1/2, z−1/2. |
Experimental details
Crystal data | |
Chemical formula | C10H12N2S |
Mr | 192.28 |
Crystal system, space group | Monoclinic, P21/c |
Temperature (K) | 296 |
a, b, c (Å) | 9.6771 (2), 7.6364 (2), 13.8156 (3) |
β (°) | 100.221 (2) |
V (Å3) | 1004.75 (4) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.28 |
Crystal size (mm) | 0.18 × 0.16 × 0.16 |
Data collection | |
Diffractometer | Bruker SMART APEX CCD detector |
Absorption correction | Multi-scan (SADABS; Bruker, 1998) |
Tmin, Tmax | 0.952, 0.957 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 8861, 2195, 1812 |
Rint | 0.024 |
(sin θ/λ)max (Å−1) | 0.639 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.039, 0.118, 1.06 |
No. of reflections | 2195 |
No. of parameters | 125 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.16, −0.25 |
Computer programs: SMART (Bruker, 1998), SAINT-Plus (Bruker, 1998), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), ORTEP-3 (Farrugia, 1997) and CAMERON (Watkin et al., 1996), WinGX (Farrugia, 1999).
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1A···N2i | 0.86 | 2.243 | 3.088 (2) | 167 |
N1—H1B···N2ii | 0.86 | 2.558 | 3.349 (2) | 153 |
Symmetry codes: (i) −x+1, −y+1, −z+2; (ii) x, −y+1/2, z−1/2. |
Acknowledgements
IMK is grateful to the University Grants Commission (UGC), India, for financial assistance.
References
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Tetrahydro-benzothiophenes are important class of compounds which exhibits antibacterial and antifungal activities (Shetty et al.,2009). In the title compound, the tetrahydro-benzothiophene ring is substituted with the methyl group at C8, amine at C2 and carbonitrile group at C3 positions. The thiophene ring is essentially planar (r.m.s. deviation = 0.03 Å). The atoms C6 and C7 are disordered over two sites (C6/C6' and C7/C7') with site occupancy factors 0.810 (5) and 0.190 (5) resulting in a major and a minor conformers, respectively. The cyclohexene ring in both the conformers is in the half-chair conformation with C6 and C7 atoms being deviated from the rest of the ring atoms by 0.3330 (3) and -0.3132 (3) Å for the major conformer. The C6' and C7' atoms are deviated by -0.3738 (2) and 0.3546 (2) Å for the minor conformer respectively. The methyl group of the cyclohexene ring is oriented axially which is characterized by the bond angles C6—C8—C11 = 112.50 (2)° and C10—C8—C11 = 115.02 (2)°. The crystal structure is stabilized by two types of N—H···N intermolecular interactions generating centrosymmetric head-to-head dimers corresponding to graph-set R22(12) motif (Bernstein et al., 1995) and a 20-membered macrocyclic ring involving six molecules (Fig. 2). The bond distances and angles in the title compound agree very well with the corresponding bond distances and angles reported in a closely related compound (Ziaulla et al., 2011).