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Acta Crystallographica Section E: Structure Reports Online logoLink to Acta Crystallographica Section E: Structure Reports Online
. 2010 Dec 24;67(Pt 1):o226. doi: 10.1107/S1600536810051986

Ethyl 2-amino-6-benzyl-4,5,6,7-tetra­hydro­thieno[2,3-c]pyridine-3-carboxyl­ate

Shuang-Ming Meng a, Ke-Wei Wang a, Hai Xie a, Yue-Qin Fan a, Yong Guo a,*
PMCID: PMC3050265  PMID: 21522725

Abstract

In the title compound, C17H20N2O2S, the tetra­hydro­pyridine ring adopts an envelope conformation with the N atom at the flap position; the phenyl ring makes a dihedral angle of 81.06 (10)° with the thio­phene ring. The amino group links with the carbonyl O atom via intra­molecular N—H⋯O hydrogen bonding, forming a six-membered ring. In the crystal, inter­molecular N—H⋯O hydrogen bonds link the mol­ecules into infinite chains running along the b axis.

Related literature

For the biological activity of thio­phene and its derivatives, see: Kidwai & Mishra (2003); Amr et al. (2006); Sherif (1996).graphic file with name e-67-0o226-scheme1.jpg

Experimental

Crystal data

  • C17H20N2O2S

  • M r = 316.41

  • Monoclinic, Inline graphic

  • a = 12.197 (3) Å

  • b = 9.936 (3) Å

  • c = 13.775 (4) Å

  • β = 103.430 (4)°

  • V = 1623.8 (8) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 0.21 mm−1

  • T = 293 K

  • 0.25 × 0.19 × 0.14 mm

Data collection

  • Bruker SMART APEX CCD diffractometer

  • Absorption correction: multi-scan (SADABS; Bruker, 1999) T min = 0.953, T max = 0.977

  • 8867 measured reflections

  • 2875 independent reflections

  • 2122 reflections with I > 2σ(I)

  • R int = 0.030

Refinement

  • R[F 2 > 2σ(F 2)] = 0.042

  • wR(F 2) = 0.107

  • S = 1.04

  • 2875 reflections

  • 205 parameters

  • 3 restraints

  • H atoms treated by a mixture of independent and constrained refinement

  • Δρmax = 0.20 e Å−3

  • Δρmin = −0.17 e Å−3

Data collection: SMART (Bruker, 1999); cell refinement: SAINT (Bruker, 1999); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXTL ; molecular graphics: SHELXTL ; software used to prepare material for publication: SHELXTL .

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536810051986/xu5117sup1.cif

e-67-0o226-sup1.cif (19.9KB, cif)

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810051986/xu5117Isup2.hkl

e-67-0o226-Isup2.hkl (138.3KB, hkl)

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Table 1. Hydrogen-bond geometry (Å, °).

D—H⋯A D—H H⋯A DA D—H⋯A
N2—H1N⋯O1i 0.81 (2) 2.17 (2) 2.972 (2) 171 (2)
N2—H2N⋯O1 0.81 (1) 2.17 (2) 2.777 (2) 132 (2)

Symmetry code: (i) Inline graphic.

Acknowledgments

We thank the Natural Science Foundation of Shanxi Province, China (No. 2010011018) for supporting this work.

supplementary crystallographic information

Comment

As part of an investigation of the thiophene and it's derivatives systems due to their diverse biological activities (Kidwai et al., 2003; Amr et al., 2006; Sherif et al., 1996), we present here the crystal structure of the title compound, (I).

In the crystal structure of title compound (Fig.1), all bond lengths and bond angles have standard dimensions.

The fragments (C8 to C12) of piperidine nearly planar (mean deviation from plane within 0.0632 (1) Å) while the the six-membered piperidine ring exhibits half-chair conformation. The amino group are hydrogen bonded to the carbonyl O atom of another molecule (Table 1), forming a one-dimensional supramolecular structure (Fig. 2). In addition, there are intramolecular N—H···O hydrogen-bonding interactions in the crystal.

Experimental

To the solution containing the ethyl 2-cyanoacetate (10 mmol, 1.06 ml), 1-benzylpiperidin-4-one (10 mmol, 1.80 ml) and powdered sulfur (12 mmol, 0.38 g) in DMF (6 ml), was under stirring triethylamine (1.20 ml) dropwise added. When the reaction was finished (TLC monitoring) the mixture was filtered with charcoal and poured into crushed ice. The formed crystals were filtered off and washed with water. The products were crystallized from ethanol.

Refinement

All H atoms bound to C atoms were positioned geometrically and refined as riding, with C—H = 0.93 Å (CH), C—H = 0.97 Å (CH2) and Uiso(H) = 1.2Ueq(C), C—H = 0.96 Å (CH3) and Uiso(H) = 1.5Ueq(C). The H atoms bound to N atoms were located in a difference Fourier map and refined with Uiso(H) = 1.2Ueq(N). The N—H distances were restrained.

Figures

Fig. 1.

Fig. 1.

Molecular structure of the title compound. Displacement ellipsoids are drawn at the 30% probabilitylevel.

Fig. 2.

Fig. 2.

View of the one-dimensional supra-molecular chain of the title compound formed by hydrogen bonding (dashed lines). H atoms of C omitted for clarity.

Crystal data

C17H20N2O2S F(000) = 672
Mr = 316.41 Dx = 1.294 Mg m3
Monoclinic, P21/n Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2yn Cell parameters from 2875 reflections
a = 12.197 (3) Å θ = 2.2–25.1°
b = 9.936 (3) Å µ = 0.21 mm1
c = 13.775 (4) Å T = 293 K
β = 103.430 (4)° Block, yellow
V = 1623.8 (8) Å3 0.25 × 0.19 × 0.14 mm
Z = 4

Data collection

Bruker SMART APEX CCD diffractometer 2875 independent reflections
Radiation source: fine-focus sealed tube 2122 reflections with I > 2σ(I)
graphite Rint = 0.030
ω scans θmax = 25.1°, θmin = 2.0°
Absorption correction: multi-scan (SADABS; Bruker, 1999) h = −14→14
Tmin = 0.953, Tmax = 0.977 k = −10→11
8867 measured reflections l = −16→14

Refinement

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)] = 0.042 Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.107 H atoms treated by a mixture of independent and constrained refinement
S = 1.04 w = 1/[σ2(Fo2) + (0.0533P)2 + 0.2035P] where P = (Fo2 + 2Fc2)/3
2875 reflections (Δ/σ)max < 0.001
205 parameters Δρmax = 0.20 e Å3
3 restraints Δρmin = −0.17 e Å3

Special details

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)

x y z Uiso*/Ueq
C1 0.15299 (16) 0.6448 (2) 0.47716 (17) 0.0480 (5)
H1 0.1593 0.6354 0.4115 0.058*
C2 0.14619 (18) 0.7720 (2) 0.51559 (19) 0.0583 (6)
H2 0.1477 0.8472 0.4757 0.070*
C3 0.13735 (19) 0.7877 (2) 0.6113 (2) 0.0610 (6)
H3 0.1325 0.8734 0.6370 0.073*
C4 0.1356 (2) 0.6766 (3) 0.67014 (19) 0.0630 (6)
H4 0.1300 0.6873 0.7359 0.076*
C5 0.14210 (18) 0.5487 (2) 0.63200 (17) 0.0539 (6)
H5 0.1408 0.4740 0.6724 0.065*
C6 0.15054 (15) 0.5310 (2) 0.53451 (16) 0.0416 (5)
C7 0.15136 (17) 0.3930 (2) 0.48984 (17) 0.0503 (6)
H7A 0.0800 0.3494 0.4889 0.060*
H7B 0.1577 0.4022 0.4212 0.060*
C8 0.23336 (17) 0.17339 (19) 0.49528 (17) 0.0480 (5)
H8A 0.2476 0.1822 0.4292 0.058*
H8B 0.1571 0.1401 0.4878 0.058*
C9 0.31573 (15) 0.07232 (19) 0.55515 (16) 0.0441 (5)
H9A 0.2875 0.0412 0.6115 0.053*
H9B 0.3216 −0.0049 0.5136 0.053*
C10 0.43028 (15) 0.13375 (19) 0.59228 (14) 0.0372 (5)
C11 0.44382 (15) 0.26693 (19) 0.58452 (15) 0.0409 (5)
C12 0.35245 (15) 0.36571 (19) 0.54262 (17) 0.0471 (5)
H12A 0.3633 0.4473 0.5824 0.057*
H12B 0.3552 0.3890 0.4748 0.057*
C13 0.53359 (15) 0.06514 (18) 0.64255 (14) 0.0371 (4)
C14 0.62303 (15) 0.15380 (19) 0.66948 (15) 0.0405 (5)
C15 0.54785 (16) −0.07575 (19) 0.66775 (14) 0.0400 (5)
C16 0.45439 (19) −0.28970 (19) 0.65815 (19) 0.0562 (6)
H16A 0.5239 −0.3251 0.6456 0.067*
H16B 0.3921 −0.3307 0.6106 0.067*
C17 0.4472 (2) −0.3267 (2) 0.7607 (2) 0.0746 (8)
H17A 0.4497 −0.4229 0.7676 0.112*
H17B 0.3777 −0.2935 0.7730 0.112*
H17C 0.5095 −0.2877 0.8080 0.112*
O1 0.63729 (11) −0.12830 (13) 0.70893 (11) 0.0503 (4)
O2 0.45118 (11) −0.14512 (13) 0.64303 (12) 0.0540 (4)
S1 0.58197 (4) 0.31782 (5) 0.63602 (5) 0.0502 (2)
N1 0.24303 (12) 0.30618 (15) 0.54336 (13) 0.0417 (4)
N2 0.73186 (14) 0.12651 (18) 0.71338 (16) 0.0544 (5)
H1N 0.7738 (18) 0.1883 (17) 0.7340 (17) 0.065*
H2N 0.7441 (19) 0.0488 (15) 0.7300 (17) 0.065*

Atomic displacement parameters (Å2)

U11 U22 U33 U12 U13 U23
C1 0.0413 (11) 0.0530 (14) 0.0484 (13) −0.0033 (10) 0.0078 (10) 0.0019 (10)
C2 0.0566 (14) 0.0454 (14) 0.0690 (17) −0.0080 (11) 0.0066 (12) 0.0068 (12)
C3 0.0595 (15) 0.0463 (14) 0.0756 (19) −0.0028 (11) 0.0125 (13) −0.0119 (12)
C4 0.0689 (16) 0.0696 (17) 0.0550 (15) 0.0006 (13) 0.0232 (12) −0.0077 (13)
C5 0.0573 (14) 0.0506 (14) 0.0553 (15) 0.0017 (11) 0.0157 (11) 0.0094 (11)
C6 0.0290 (10) 0.0431 (12) 0.0510 (13) 0.0035 (8) 0.0058 (9) 0.0013 (10)
C7 0.0397 (11) 0.0476 (13) 0.0586 (14) 0.0062 (10) 0.0012 (10) −0.0040 (10)
C8 0.0384 (11) 0.0411 (12) 0.0595 (14) −0.0027 (9) 0.0009 (10) −0.0071 (10)
C9 0.0378 (11) 0.0329 (11) 0.0592 (14) −0.0022 (8) 0.0063 (10) −0.0038 (9)
C10 0.0346 (10) 0.0327 (10) 0.0445 (12) −0.0012 (8) 0.0100 (9) −0.0014 (8)
C11 0.0332 (10) 0.0334 (11) 0.0561 (13) −0.0011 (8) 0.0100 (9) 0.0031 (9)
C12 0.0373 (11) 0.0359 (11) 0.0667 (15) 0.0017 (9) 0.0090 (10) 0.0065 (10)
C13 0.0356 (10) 0.0296 (10) 0.0459 (12) −0.0007 (8) 0.0090 (9) −0.0015 (8)
C14 0.0355 (10) 0.0358 (11) 0.0495 (13) 0.0015 (8) 0.0087 (9) 0.0003 (9)
C15 0.0387 (11) 0.0353 (11) 0.0456 (12) −0.0004 (9) 0.0088 (9) −0.0041 (9)
C16 0.0553 (14) 0.0261 (11) 0.0791 (18) −0.0048 (9) −0.0010 (12) −0.0014 (10)
C17 0.0791 (18) 0.0546 (15) 0.083 (2) −0.0141 (13) 0.0051 (15) 0.0115 (14)
O1 0.0399 (8) 0.0375 (8) 0.0689 (10) 0.0062 (6) 0.0032 (7) 0.0037 (7)
O2 0.0413 (8) 0.0291 (8) 0.0841 (11) −0.0039 (6) −0.0006 (7) 0.0050 (7)
S1 0.0357 (3) 0.0324 (3) 0.0794 (4) −0.0055 (2) 0.0068 (3) 0.0047 (3)
N1 0.0319 (8) 0.0328 (9) 0.0576 (11) 0.0020 (7) 0.0048 (8) −0.0008 (8)
N2 0.0363 (10) 0.0392 (10) 0.0810 (15) −0.0036 (8) −0.0002 (9) 0.0014 (10)

Geometric parameters (Å, °)

C1—C2 1.380 (3) C10—C11 1.341 (3)
C1—C6 1.383 (3) C10—C13 1.458 (3)
C1—H1 0.9300 C11—C12 1.497 (3)
C2—C3 1.357 (3) C11—S1 1.7445 (19)
C2—H2 0.9300 C12—N1 1.462 (2)
C3—C4 1.372 (3) C12—H12A 0.9700
C3—H3 0.9300 C12—H12B 0.9700
C4—C5 1.384 (3) C13—C14 1.384 (3)
C4—H4 0.9300 C13—C15 1.443 (3)
C5—C6 1.382 (3) C14—N2 1.352 (2)
C5—H5 0.9300 C14—S1 1.736 (2)
C6—C7 1.505 (3) C15—O1 1.224 (2)
C7—N1 1.468 (2) C15—O2 1.340 (2)
C7—H7A 0.9700 C16—O2 1.451 (2)
C7—H7B 0.9700 C16—C17 1.482 (3)
C8—N1 1.469 (2) C16—H16A 0.9700
C8—C9 1.521 (3) C16—H16B 0.9700
C8—H8A 0.9700 C17—H17A 0.9600
C8—H8B 0.9700 C17—H17B 0.9600
C9—C10 1.501 (3) C17—H17C 0.9600
C9—H9A 0.9700 N2—H1N 0.807 (15)
C9—H9B 0.9700 N2—H2N 0.809 (14)
C2—C1—C6 121.2 (2) C10—C11—C12 125.70 (17)
C2—C1—H1 119.4 C10—C11—S1 112.26 (14)
C6—C1—H1 119.4 C12—C11—S1 121.95 (14)
C3—C2—C1 120.2 (2) N1—C12—C11 109.34 (16)
C3—C2—H2 119.9 N1—C12—H12A 109.8
C1—C2—H2 119.9 C11—C12—H12A 109.8
C2—C3—C4 119.8 (2) N1—C12—H12B 109.8
C2—C3—H3 120.1 C11—C12—H12B 109.8
C4—C3—H3 120.1 H12A—C12—H12B 108.3
C3—C4—C5 120.3 (2) C14—C13—C15 120.63 (17)
C3—C4—H4 119.9 C14—C13—C10 111.72 (17)
C5—C4—H4 119.9 C15—C13—C10 127.61 (17)
C6—C5—C4 120.6 (2) N2—C14—C13 128.54 (18)
C6—C5—H5 119.7 N2—C14—S1 119.99 (15)
C4—C5—H5 119.7 C13—C14—S1 111.45 (14)
C5—C6—C1 117.87 (19) O1—C15—O2 122.38 (18)
C5—C6—C7 121.5 (2) O1—C15—C13 124.76 (18)
C1—C6—C7 120.6 (2) O2—C15—C13 112.84 (16)
N1—C7—C6 114.01 (16) O2—C16—C17 112.14 (19)
N1—C7—H7A 108.8 O2—C16—H16A 109.2
C6—C7—H7A 108.8 C17—C16—H16A 109.2
N1—C7—H7B 108.8 O2—C16—H16B 109.2
C6—C7—H7B 108.8 C17—C16—H16B 109.2
H7A—C7—H7B 107.6 H16A—C16—H16B 107.9
N1—C8—C9 112.02 (16) C16—C17—H17A 109.5
N1—C8—H8A 109.2 C16—C17—H17B 109.5
C9—C8—H8A 109.2 H17A—C17—H17B 109.5
N1—C8—H8B 109.2 C16—C17—H17C 109.5
C9—C8—H8B 109.2 H17A—C17—H17C 109.5
H8A—C8—H8B 107.9 H17B—C17—H17C 109.5
C10—C9—C8 111.19 (16) C15—O2—C16 118.70 (15)
C10—C9—H9A 109.4 C14—S1—C11 91.59 (9)
C8—C9—H9A 109.4 C12—N1—C7 110.42 (15)
C10—C9—H9B 109.4 C12—N1—C8 109.76 (16)
C8—C9—H9B 109.4 C7—N1—C8 109.22 (15)
H9A—C9—H9B 108.0 C14—N2—H1N 118.7 (16)
C11—C10—C13 112.98 (16) C14—N2—H2N 114.6 (16)
C11—C10—C9 119.74 (17) H1N—N2—H2N 124 (2)
C13—C10—C9 127.21 (17)
C6—C1—C2—C3 0.3 (3) C9—C10—C13—C15 −0.3 (3)
C1—C2—C3—C4 0.2 (4) C15—C13—C14—N2 5.0 (3)
C2—C3—C4—C5 −0.4 (4) C10—C13—C14—N2 −177.1 (2)
C3—C4—C5—C6 0.1 (4) C15—C13—C14—S1 −176.97 (15)
C4—C5—C6—C1 0.4 (3) C10—C13—C14—S1 0.9 (2)
C4—C5—C6—C7 −176.62 (19) C14—C13—C15—O1 −3.6 (3)
C2—C1—C6—C5 −0.6 (3) C10—C13—C15—O1 178.95 (19)
C2—C1—C6—C7 176.49 (19) C14—C13—C15—O2 175.16 (18)
C5—C6—C7—N1 −58.6 (3) C10—C13—C15—O2 −2.3 (3)
C1—C6—C7—N1 124.5 (2) O1—C15—O2—C16 −5.2 (3)
N1—C8—C9—C10 −43.7 (2) C13—C15—O2—C16 176.01 (18)
C8—C9—C10—C11 10.4 (3) C17—C16—O2—C15 86.3 (2)
C8—C9—C10—C13 −172.76 (19) N2—C14—S1—C11 177.73 (18)
C13—C10—C11—C12 −175.99 (19) C13—C14—S1—C11 −0.45 (17)
C9—C10—C11—C12 1.2 (3) C10—C11—S1—C14 −0.11 (17)
C13—C10—C11—S1 0.6 (2) C12—C11—S1—C14 176.65 (18)
C9—C10—C11—S1 177.86 (15) C11—C12—N1—C7 −171.98 (17)
C10—C11—C12—N1 19.4 (3) C11—C12—N1—C8 −51.5 (2)
S1—C11—C12—N1 −156.87 (15) C6—C7—N1—C12 −61.0 (2)
C11—C10—C13—C14 −1.0 (3) C6—C7—N1—C8 178.23 (18)
C9—C10—C13—C14 −177.97 (19) C9—C8—N1—C12 66.7 (2)
C11—C10—C13—C15 176.68 (19) C9—C8—N1—C7 −172.09 (18)

Hydrogen-bond geometry (Å, °)

D—H···A D—H H···A D···A D—H···A
N2—H1N···O1i 0.81 (2) 2.17 (2) 2.972 (2) 171 (2)
N2—H2N···O1 0.81 (1) 2.17 (2) 2.777 (2) 132 (2)

Symmetry codes: (i) −x+3/2, y+1/2, −z+3/2.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: XU5117).

References

  1. Amr, A. G. E., Mohamed, A. M., Mohamed, S. F., Abdel-Hafez, N. A. & Hammam, A. E. F. G. (2006). Bioorg. Med. Chem. 14, 5481–5488. [DOI] [PubMed]
  2. Bruker (1999). SMART, SAINT and SADABS Bruker AXS Inc., Madison, Wisconsin, USA.
  3. Kidwai, M. & Mishra, A. D. (2003). Bull Korean Chem. Soc 24, 1038–1040.
  4. Sheldrick, G. M. (2008). Acta Cryst A64, 112–122. [DOI] [PubMed]
  5. Sherif, S. M. (1996). Monatsh. Chem. 127, 955–962.

Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536810051986/xu5117sup1.cif

e-67-0o226-sup1.cif (19.9KB, cif)

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810051986/xu5117Isup2.hkl

e-67-0o226-Isup2.hkl (138.3KB, hkl)

Additional supplementary materials: crystallographic information; 3D view; checkCIF report


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