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cv5399 scheme

Acta Cryst. (2013). E69, o713    [ doi:10.1107/S1600536813009513 ]

5-(2-Cyanobenzyl)-4,5,6,7-tetrahydrothieno[3,2-c]pyridin-2-yl acetate

X.-S. Xie, S. Mu, Y. Liu and D.-K. Liu

Abstract top

In the title molecule, C17H16N2O2S, the tetrahydropyridine ring exhibits a half-chair conformation. The mean planes of the ester chain and benzene ring are twisted by 5.5 (1) and 81.32 (5)°, respectively, from the plane of thiophene ring. In the crystal, weak C-H...O interactions link molecules related by translation along [100] into chains.

Comment top

As a continuation of our structural study of tetrahydrothienopyridine derivatives (Yang et al., 2012), herein we present the crystal structure of the title compound (I).

In (I) (Fig. 1), all bond lengths and angles are normal and correspond to those observed in the related compounds 5-[(2-cyclopropylcarbonyl)(2- fluorophenyl)methyl]-4,5,6,7-tetrahydrothieno[3,2-c]pyridin- 2-yl acetate (Prasugrel) (Wang et al., 2010) and 5-(2-chlorobenzyl)-4,5,6,7-tetrahydrothieno[3,2-c]pyridin-2-yl acetate (Yang et al., 2012). The ester chain in (I) is almost planar with a mean deviation of 0.0021 Å. The tetrahydropyridine ring exhibits a half-chair conformation. The mean planes of the ester chain and benzene ring are twisted at 5.5 (1) and 81.32 (5)°, respectively, from the plane of thiophene ring. In the crystal, weak C—H···O interactions (Table 1) link the molecules related by translation in [100] into chains.

Related literature top

For the crystal structures of related compounds, see: Wang et al. (2010); Yang et al. (2012). For details of the synthesis, see: Zhou et al. (2011).

Experimental top

The title compound was prepared according to the method of Zhou et al. (2011). 19.2 g of 5,6,7,7a-tetrahydrothieno[3,2-c]pyridin-2(4H)-one hydrochloride and 29 g of N-methyl morpholine were dissolved in 100 ml of CHCl3. 42.6 g of 2-(bromomethyl)benzonitrile was dropwised into the mixture and then refluxed for 4 h. After filtration, the resulting filtrate was evaporated under reduced pressure. The residue was dissolved in diethyl ether, adjust the pH=5 to get 2-{(2-oxo-7,7a-dihydrothieno [3,2-c]pyridin-5(2H,4H,6H)-yl)methyl} benzonitrile as an intermediate. The intermediate, together with 14.5 g of N-methyl morpholine and 10 g of acetic anhydride was dissolved in 150 ml of acetonitrile and stirred under 30°C for 2 h. The mixture was evaporated under reduced pressure and yellow oil was obtained. The oil was dissolved in CHCl3, washed with saturated brines for 3 times. The crude product was purified by silica gel chromatography to give white powder. Colorless single crystals were grown from a methanol solution.

Refinement top

All H atoms were positioned geometrically and refined using a riding model, with d(C—H) = 0.95 - 0.99 Å, and Uiso (H) = 1.5 or 1.2 Ueq(C).

Computing details top

Data collection: CrystalClear (Rigaku/MSC, 2005); cell refinement: CrystalClear (Rigaku/MSC, 2005); data reduction: CrystalClear (Rigaku/MSC, 2005); 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: CrystalStructure (Rigaku/MSC, 2005).

Figures top
[Figure 1] Fig. 1. The molecular structure of (I) showing the atom-numbering scheme and 50% probability displacement ellipsoids.
5-(2-Cyanobenzyl)-4,5,6,7-tetrahydrothieno[3,2-c]pyridin-2-yl acetate top
Crystal data top
C17H16N2O2SF(000) = 656
Mr = 312.38Dx = 1.329 Mg m3
Monoclinic, P21/nCu Kα radiation, λ = 1.54187 Å
Hall symbol: -P 2ynCell parameters from 2001 reflections
a = 14.174 (3) Åθ = 27.6–72.2°
b = 5.9321 (12) ŵ = 1.91 mm1
c = 18.796 (4) ÅT = 113 K
β = 99.06 (3)°Prism, colourless
V = 1560.7 (5) Å30.26 × 0.24 × 0.22 mm
Z = 4
Data collection top
Rigaku Saturn
diffractometer
3034 independent reflections
Radiation source: fine-focus sealed tube2819 reflections with I > 2σ(I)
Multilayer monochromatorRint = 0.045
Detector resolution: 14.63 pixels mm-1θmax = 72.5°, θmin = 3.6°
ω scansh = 1717
Absorption correction: multi-scan
(CrystalClear; Rigaku/MSC, 2005)
k = 77
Tmin = 0.636, Tmax = 0.678l = 1723
16000 measured reflections
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)] = 0.038H-atom parameters constrained
wR(F2) = 0.098 w = 1/[σ2(Fo2) + (0.0608P)2 + 0.3535P]
where P = (Fo2 + 2Fc2)/3
S = 1.08(Δ/σ)max = 0.001
3034 reflectionsΔρmax = 0.30 e Å3
201 parametersΔρmin = 0.28 e Å3
1 restraintExtinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.0040 (4)
Crystal data top
C17H16N2O2SV = 1560.7 (5) Å3
Mr = 312.38Z = 4
Monoclinic, P21/nCu Kα radiation
a = 14.174 (3) ŵ = 1.91 mm1
b = 5.9321 (12) ÅT = 113 K
c = 18.796 (4) Å0.26 × 0.24 × 0.22 mm
β = 99.06 (3)°
Data collection top
Rigaku Saturn
diffractometer
3034 independent reflections
Absorption correction: multi-scan
(CrystalClear; Rigaku/MSC, 2005)
2819 reflections with I > 2σ(I)
Tmin = 0.636, Tmax = 0.678Rint = 0.045
16000 measured reflectionsθmax = 72.5°
Refinement top
R[F2 > 2σ(F2)] = 0.038H-atom parameters constrained
wR(F2) = 0.098Δρmax = 0.30 e Å3
S = 1.08Δρmin = 0.28 e Å3
3034 reflectionsAbsolute structure: ?
201 parametersFlack parameter: ?
1 restraintRogers parameter: ?
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
xyzUiso*/Ueq
S10.07455 (2)0.16825 (5)0.143145 (17)0.02086 (13)
O10.02603 (6)0.21422 (16)0.06058 (5)0.0237 (2)
O20.09148 (7)0.05922 (19)0.11147 (6)0.0356 (3)
N10.38740 (7)0.30018 (18)0.16585 (6)0.0202 (3)
N20.64150 (12)0.3514 (3)0.02028 (9)0.0527 (4)
C10.09324 (9)0.0540 (2)0.08710 (7)0.0201 (3)
C20.18393 (9)0.0624 (2)0.07280 (7)0.0201 (3)
H20.20640.17150.04250.024*
C30.24163 (9)0.1132 (2)0.10896 (7)0.0187 (3)
C40.19251 (9)0.2503 (2)0.14809 (7)0.0196 (3)
C50.23440 (9)0.4496 (2)0.19049 (7)0.0216 (3)
H5A0.24470.41420.24260.026*
H5B0.19040.57990.18200.026*
C60.32936 (9)0.5055 (2)0.16606 (7)0.0217 (3)
H6A0.31750.57120.11700.026*
H6B0.36430.61830.19900.026*
C70.34597 (9)0.1510 (2)0.10650 (7)0.0206 (3)
H7A0.38000.00470.11060.025*
H7B0.35370.22010.05980.025*
C80.48585 (9)0.3588 (2)0.15919 (8)0.0245 (3)
H8A0.50780.48270.19310.029*
H8B0.48790.41400.10970.029*
C90.55298 (9)0.1608 (2)0.17475 (7)0.0207 (3)
C100.62212 (9)0.1119 (2)0.13184 (8)0.0255 (3)
C110.68601 (10)0.0673 (3)0.14838 (9)0.0321 (3)
H110.73270.09800.11850.038*
C120.68115 (10)0.1995 (2)0.20814 (9)0.0311 (3)
H120.72420.32180.21950.037*
C130.61310 (10)0.1526 (2)0.25154 (8)0.0276 (3)
H130.60970.24250.29290.033*
C140.54986 (9)0.0252 (2)0.23487 (8)0.0250 (3)
H140.50350.05510.26510.030*
C150.63104 (11)0.2481 (3)0.06926 (9)0.0351 (4)
C160.06452 (9)0.2078 (2)0.07641 (8)0.0233 (3)
C170.12011 (10)0.4073 (2)0.04513 (8)0.0270 (3)
H17A0.11920.41340.00690.040*
H17B0.18620.39470.05390.040*
H17C0.09140.54510.06780.040*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
S10.01803 (19)0.0246 (2)0.0204 (2)0.00246 (11)0.00426 (13)0.00427 (11)
O10.0176 (5)0.0254 (5)0.0282 (5)0.0002 (4)0.0038 (4)0.0072 (4)
O20.0237 (5)0.0417 (6)0.0437 (7)0.0034 (4)0.0123 (5)0.0190 (5)
N10.0178 (5)0.0186 (5)0.0246 (6)0.0000 (4)0.0041 (4)0.0001 (4)
N20.0543 (10)0.0658 (11)0.0433 (9)0.0074 (8)0.0242 (8)0.0159 (8)
C10.0199 (6)0.0217 (6)0.0185 (6)0.0014 (5)0.0017 (5)0.0015 (5)
C20.0205 (6)0.0205 (6)0.0191 (6)0.0041 (5)0.0028 (5)0.0012 (5)
C30.0197 (6)0.0200 (6)0.0163 (6)0.0024 (5)0.0025 (5)0.0022 (5)
C40.0191 (6)0.0221 (6)0.0174 (6)0.0026 (5)0.0028 (5)0.0005 (5)
C50.0225 (6)0.0216 (6)0.0209 (7)0.0025 (5)0.0046 (5)0.0020 (5)
C60.0250 (6)0.0179 (6)0.0225 (7)0.0009 (5)0.0050 (5)0.0001 (5)
C70.0202 (6)0.0202 (6)0.0219 (7)0.0014 (5)0.0051 (5)0.0013 (5)
C80.0207 (6)0.0224 (6)0.0310 (8)0.0028 (5)0.0063 (5)0.0020 (5)
C90.0167 (6)0.0218 (6)0.0234 (7)0.0039 (5)0.0020 (5)0.0015 (5)
C100.0214 (6)0.0303 (7)0.0255 (7)0.0028 (5)0.0059 (5)0.0009 (6)
C110.0236 (7)0.0369 (8)0.0376 (9)0.0032 (6)0.0103 (6)0.0024 (7)
C120.0217 (7)0.0268 (7)0.0433 (9)0.0026 (5)0.0009 (6)0.0013 (6)
C130.0242 (7)0.0268 (7)0.0303 (8)0.0040 (5)0.0003 (6)0.0052 (6)
C140.0226 (6)0.0275 (7)0.0257 (7)0.0023 (5)0.0058 (5)0.0011 (6)
C150.0322 (8)0.0425 (9)0.0337 (8)0.0026 (7)0.0152 (7)0.0033 (7)
C160.0182 (6)0.0285 (7)0.0231 (7)0.0011 (5)0.0028 (5)0.0003 (5)
C170.0229 (7)0.0270 (7)0.0306 (8)0.0010 (5)0.0029 (6)0.0025 (6)
Geometric parameters (Å, º) top
S1—C41.7297 (13)C7—H7A0.9900
S1—C11.7338 (13)C7—H7B0.9900
O1—C161.3629 (16)C8—C91.5109 (18)
O1—C11.3819 (16)C8—H8A0.9900
O2—C161.1987 (17)C8—H8B0.9900
N1—C81.4625 (16)C9—C141.393 (2)
N1—C61.4702 (16)C9—C101.394 (2)
N1—C71.4716 (17)C10—C111.399 (2)
N2—C151.135 (2)C10—C151.449 (2)
C1—C21.3549 (18)C11—C121.381 (2)
C2—C31.4284 (18)C11—H110.9500
C2—H20.9500C12—C131.386 (2)
C3—C41.3594 (18)C12—H120.9500
C3—C71.5037 (17)C13—C141.388 (2)
C4—C51.4955 (18)C13—H130.9500
C5—C61.5256 (18)C14—H140.9500
C5—H5A0.9900C16—C171.4905 (19)
C5—H5B0.9900C17—H17A0.9800
C6—H6A0.9900C17—H17B0.9800
C6—H6B0.9900C17—H17C0.9800
C4—S1—C190.43 (6)N1—C8—C9112.25 (10)
C16—O1—C1121.43 (10)N1—C8—H8A109.2
C8—N1—C6110.18 (10)C9—C8—H8A109.2
C8—N1—C7110.52 (10)N1—C8—H8B109.2
C6—N1—C7110.09 (10)C9—C8—H8B109.2
C2—C1—O1121.66 (11)H8A—C8—H8B107.9
C2—C1—S1112.89 (10)C14—C9—C10117.63 (12)
O1—C1—S1125.42 (9)C14—C9—C8120.42 (12)
C1—C2—C3111.65 (11)C10—C9—C8121.90 (12)
C1—C2—H2124.2C9—C10—C11121.26 (13)
C3—C2—H2124.2C9—C10—C15120.83 (13)
C4—C3—C2112.94 (11)C11—C10—C15117.90 (13)
C4—C3—C7121.15 (12)C12—C11—C10119.92 (13)
C2—C3—C7125.90 (11)C12—C11—H11120.0
C3—C4—C5124.54 (12)C10—C11—H11120.0
C3—C4—S1112.08 (10)C11—C12—C13119.56 (14)
C5—C4—S1123.38 (9)C11—C12—H12120.2
C4—C5—C6107.86 (10)C13—C12—H12120.2
C4—C5—H5A110.1C12—C13—C14120.29 (14)
C6—C5—H5A110.1C12—C13—H13119.9
C4—C5—H5B110.1C14—C13—H13119.9
C6—C5—H5B110.1C13—C14—C9121.34 (13)
H5A—C5—H5B108.4C13—C14—H14119.3
N1—C6—C5109.95 (10)C9—C14—H14119.3
N1—C6—H6A109.7N2—C15—C10177.32 (17)
C5—C6—H6A109.7O2—C16—O1122.22 (12)
N1—C6—H6B109.7O2—C16—C17127.33 (12)
C5—C6—H6B109.7O1—C16—C17110.45 (11)
H6A—C6—H6B108.2C16—C17—H17A109.5
N1—C7—C3110.09 (10)C16—C17—H17B109.5
N1—C7—H7A109.6H17A—C17—H17B109.5
C3—C7—H7A109.6C16—C17—H17C109.5
N1—C7—H7B109.6H17A—C17—H17C109.5
C3—C7—H7B109.6H17B—C17—H17C109.5
H7A—C7—H7B108.2
C16—O1—C1—C2178.55 (12)C4—C3—C7—N116.65 (17)
C16—O1—C1—S10.90 (18)C2—C3—C7—N1163.09 (12)
C4—S1—C1—C20.56 (11)C6—N1—C8—C9167.62 (11)
C4—S1—C1—O1177.27 (12)C7—N1—C8—C970.50 (14)
O1—C1—C2—C3176.86 (11)N1—C8—C9—C1446.34 (17)
S1—C1—C2—C31.06 (14)N1—C8—C9—C10136.16 (13)
C1—C2—C3—C41.16 (16)C14—C9—C10—C110.2 (2)
C1—C2—C3—C7178.60 (12)C8—C9—C10—C11177.72 (13)
C2—C3—C4—C5179.07 (12)C14—C9—C10—C15178.76 (13)
C7—C3—C4—C51.2 (2)C8—C9—C10—C151.2 (2)
C2—C3—C4—S10.74 (15)C9—C10—C11—C120.0 (2)
C7—C3—C4—S1179.03 (10)C15—C10—C11—C12178.99 (14)
C1—S1—C4—C30.12 (11)C10—C11—C12—C130.3 (2)
C1—S1—C4—C5179.69 (11)C11—C12—C13—C140.4 (2)
C3—C4—C5—C614.85 (18)C12—C13—C14—C90.2 (2)
S1—C4—C5—C6164.94 (10)C10—C9—C14—C130.1 (2)
C8—N1—C6—C5166.73 (11)C8—C9—C14—C13177.70 (12)
C7—N1—C6—C571.13 (13)C9—C10—C15—N2162 (4)
C4—C5—C6—N149.11 (14)C11—C10—C15—N217 (4)
C8—N1—C7—C3173.55 (10)C1—O1—C16—O23.0 (2)
C6—N1—C7—C351.61 (13)C1—O1—C16—C17176.31 (11)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C11—H11···O2i0.952.533.3346 (19)143
Symmetry code: (i) x+1, y, z.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C11—H11···O2i0.952.533.3346 (19)142.9
Symmetry code: (i) x+1, y, z.
Acknowledgements top

This project was supported by the National Major Scientific and Technological Special Project for "Significant New Drugs Development" (No. 2013ZX09102014). The authors also thank Mr Hai-Bin Song of Nankai University for the X-ray crystallographic determination and helpful suggestions.

references
References top

Rigaku/MSC (2005). CrystalClear and CrystalStructure. Rigaku/MSC Inc., The Woodlands, Texas, USA.

Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122.

Wang, Z.-M., Zhao, J. & Xu, G. (2010). Acta Cryst. E66, o1354.

Yang, J., Chen, N., Sun, H., Cao, X.-X. & Liu, D.-K. (2012). Acta Cryst. E68, o1053.

Zhou, Y. S., Wang, P. B., Liu, Y., Chen, J. F., Yue, N. & Liu, D. K. (2011). Acta Pharm. Sin. 46, 70–74.