Ethyl 2 amino 6 methyl 4,5,6,7 tetra­hydro­thieno[2,3 c]pyridine 3 carboxyl­ate monohydrate

organic papers

Acta Cryst.(2006). E62, o2457–o2459 doi:10.1107/S1600536806017831 Chandrakumaret al. _C

11H16N2O2SH2O

o2457

Acta Crystallographica Section E

Structure Reports Online

ISSN 1600-5368

Ethyl

2-amino-6-methyl-4,5,6,7-tetrahydrothieno-[2,3-

c

]pyridine-3-carboxylate monohydrate

K. Chandrakumar,aM. K. Kokila,b* Puttaraja,bS. Mohan,c J. Saravanancand M. V.

Kulkarnid

a_{Department of Engineering Physics, HKBK}

College of Engineering, Nagawara, Bangalore 560 045, Karnataka, India,b_{Department of}

Physics, Bangalore University, Bangalore 560 056, Karnataka, India,c_{PES College of}

Pharmacy, Hanumanthanagar, Bangalore 560 050, Karnataka, India, andd_{Department of}

Chemistry, Karnataka University, Dharwad, Karnataka, India

Correspondence e-mail: prmkkgroup@gmail.com

Key indicators

Single-crystal X-ray study

T= 291 K

Mean(C–C) = 0.003 A˚

Rfactor = 0.056

wRfactor = 0.137

Data-to-parameter ratio = 14.7

For details of how these key indicators were automatically derived from the article, see http://journals.iucr.org/e.

Received 24 April 2006 Accepted 15 May 2006

#2006 International Union of Crystallography

All rights reserved

The title compound, C11H16N2O2SH2O, is stabilized by a number of inter- and intramolecular O—H O, O—H N, N—H O and C—H O hydrogen bonds. Delocalization in the thiophene system is indicated by the C—S bond distances.

Comment

The bicyclic tetrahydropyridinothiophenes are an important class of hetrocycles which are known for their wide range of biological activities (Sebniset al., 1999). The title compound, (I), was amongst many compounds which were screened for their antimicrobial and anti-inflammatory activities (Mohan & Saravanan, 2003). Schiff bases (Csaszar & Morvay, 1983; Lakshmiet al., 1985; Cohenet al., 1977) and their thiophene derivatives (El-Maghraby et al., 1984; Dzhurayev et al., 1992; Gewald et al., 1966) possess antibacterial, antitubercular and antifungal activities. The structure of (I) (Fig. 1) was deter-mined with a view to establishing the orientation of the vicinally substituted amino and ester functions in the solid state.

The C—N bond distance in 2-aminothiophenes has been used as a measure of the conjugation across bicyclic thio-phenes (Chandra Kumar et al., 2005). The C2—N2 bond distance of 1.342 (3) A˚ in (I) supports this proposition. Furthermore, the difference between C2—C3 [1.389 (3) A˚ ] and C7—C8 [1.349 (3) A˚ ] shows the compound to have a slightly reduced double-bond character for the C2—C3 bond. The bicyclic system exhibits a non-planar structure, parti-cularly at the ring junction. The ester function has the ethyl group (C10—C11) and the thiophene ring in an S–trans

arrangement across the O2—C9 bond. The N—CH3 group

also shows a significant deviation from the molecular plane.

The water molecules form O—H N and O—H O

non-planar nature of the tetrahydropyridine skeleton, which results in an interaction between C4—H and atom O2 of the ester group (Fig. 2).

Experimental

To a mixture ofN-methylpiperidin-4-one (4.1 ml), ethyl cyanoacetate (4.5 ml) and elemental sulfur (1.2 g) in ethanol (20 ml) was added diethylamine (4 ml) with stirring at a temperature between 318 and 323 K until the sulfur dissolved. Stirring was continued until the product precipitated. The reaction mixture was cooled to room temperature and kept overnight in a refrigerator. The precipitate was filtered off and recrystallized from ethanol to give the title compound, (I) (m.p. 378 K). The source of hydrate water could be the diethy-lamine and ethanol reagents used for the synthesis.

Crystal data

C11H16N2O2SH2O

Mr= 258.34

Monoclinic,P21=n

a= 9.670 (2) A˚

b= 11.514 (3) A˚

c= 12.219 (3) A˚

= 93.074 (4)

V= 1358.4 (6) A˚3

Z= 4

Dx= 1.263 Mg m3

MoKradiation

= 0.24 mm1

T= 291 (2) K Block, colourless 0.310.280.21 mm

Data collection

Bruker SMART CCD area-detector diffractometer

’and!scans

Absorption correction: multi-scan (SADABS; Sheldrick, 1996)

Tmin= 0.930,Tmax= 0.955

9867 measured reflections 2526 independent reflections 2115 reflections withI> 2(I)

Rint= 0.021

max= 25.5

Refinement

Refinement onF2

R[F2_{> 2(F}2_{)] = 0.056}

wR(F2) = 0.137

S= 1.19 2526 reflections 172 parameters

H atoms treated by a mixture of independent and constrained refinement

w= 1/[2_(F

o2) + (0.0691P)2 + 0.1443P]

whereP= (Fo 2

+ 2Fc 2

)/3 (/)max= 0.001

max= 0.28 e A˚3

min=0.13 e A˚3

Table 1

Selected geometric parameters (A˚ ,_).

N2—C2 1.342 (3)

C2—C3 1.389 (3)

C7—C8 1.349 (3)

C9—C3—C8 128.39 (19)

O1—C9—C3 124.6 (2)

[image:2.610.47.294.72.317.2]

O2—C9—C3 113.53 (19)

Table 2

Hydrogen-bond geometry (A˚ ,_).

D—H A D—H H A D A D—H A

N2—H2A O3i

0.84 (3) 2.02 (3) 2.846 (3) 171 (3)

N2—H2B O1 0.88 (2) 2.10 (3) 2.741 (3) 130 (2)

C4—H4A O2 0.97 (2) 2.52 (3) 2.858 (2) 100 (4)

O3—H3A N1 1.00 (4) 1.80 (4) 2.790 (3) 170 (3)

O3—H3B O1ii 0.71 (3) 2.17 (3) 2.874 (3) 176 (2)

Symmetry codes: (i)xþ1

2;yþ12;zþ21; (ii)xþ1;y;z.

Carbon-bound H atoms were placed in idealized positions, with C—H = 0.93–0.97 A˚ , and constrained to ride on their parent atoms withUiso(H) = 1.2Ueq(C), or 1.5Ueq(C) for methyl H. A

rotating-group model was used for the methyl rotating-groups. The positions of H atoms on N2 (amine) and O3 (hydrate) were located in a difference fourier map and refined isotropically.

organic papers

o2458

Chandrakumaret al. _C

11H16N2O2SH2O Acta Cryst.(2006). E62, o2457–o2459

Figure 1

[image:2.610.45.293.377.651.2]

A view of the title compound (I), with the atom-numbering scheme. Displacement ellipsoids are drawn at the 50% probability level. Dashed lines indicate hydrogen bonds.

Figure 2

[image:2.610.315.565.601.666.2]

Data collection:SMART(Bruker, 1998); cell refinement:SMART; data reduction: SAINT (Bruker, 1998); program(s) used to solve structure:SIR92 (Altomareet al., 1993); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEP-3 for Windows(Farrugia, 1997) andCAMERON(Watkinet al., 1993); software used to prepare material for publication:PARST (Nardelli, 1995) andPLATON(Spek, 2003).

The authors are grateful both to Professor T. N. Guru Row, Indian Institute of Science, and the Department of Science & Technology, India, for data collection on the CCD facility, and Bangalore University. CK thanks the Management, Admin-istrator and Principal of HKBK College of Engineering for encouragement and support.

References

Altomare, A., Cascarano, G., Giacovazzo, C. & Guagliardi, A. (1993).J. Appl. Cryst.26, 343–350.

Bruker (1998).SMART(Version 5.0) andSAINT(Version 4.0). Bruker AXS Inc., Madison, Wisconsin, USA.

Chandra Kumar, K., Kokila, M. K., Puttaraja, Mohan, S., Manjunath Shetty, K. S. & Kulkarni, M. V. (2005).Acta Cryst.E61, o304–o306.

Cohen, V. I., Rist, N. & Duponchel, C. (1977).J. Pharm. Sci.66, 1332–1334. Csaszar, J. & Morvay, J. (1983).Acta Pharm. Hung.53, 121–128.

Dzhurayev, A. D., Karimkulov, K. M., Makshsumov, A. G. & Amanov, N. (1992).Khim. Farm. Zh.26, 73–75.

El-Maghraby, A. A., Haroun, B. & Mohamed, N. A. (1984).Egypt. J. Pharm. Sci.23, 327–336.

Farrugia, L. J. (1997).J. Appl. Cryst.30, 565.

Gewald, K., Schinke, E. & Botcher, H. (1966).Chem. Ber.99, 94–100. Lakshmi, V. V., Sridhar, P. & Polsa, H. (1985).Indian J. Pharm. Sci.23, 327–

336.

Mohan, S. & Saravanan, J. (2003).Asian J. Chem.15, 67–70. Nardelli, M. (1995).J. Appl. Cryst.28, 659.

Sebnis, R. W., Rangnekar, D. W. & Sonawane, N. D. (1999).J. Heterocycl. Chem.36, 333–345.

Sheldrick, G. M. (1996).SADABS. University of Go¨ttingen, Germany. Sheldrick, G. M. (1997).SHELXL97. University of Go¨ttingen, Germany. Spek, A. L. (2003).J. Appl. Cryst.36, 7–13.

Watkin, D. M., Pearce, L. & Prout, C. K. (1993).CAMERON. Chemical Crystallography Laboratory, University of Oxford, England.

organic papers

Acta Cryst.(2006). E62, o2457–o2459 Chandrakumaret al. _C

supporting information

sup-1 Acta Cryst. (2006). E62, o2457–o2459

supporting information

Acta Cryst. (2006). E62, o2457–o2459 [https://doi.org/10.1107/S1600536806017831]

Ethyl 2-amino-6-methyl-4,5,6,7-tetrahydrothieno[2,3-

c

]pyridine-3-carboxylate

monohydrate

K. Chandrakumar, M. K. Kokila, Puttaraja, S. Mohan, J. Saravanan and M. V. Kulkarni

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

Crystal data

C11H16N2O2S·H2O

Mr = 258.34 Monoclinic, P21/n Hall symbol: -P 2yn a = 9.670 (2) Å b = 11.514 (3) Å c = 12.219 (3) Å β = 93.074 (4)° V = 1358.4 (6) Å3

Z = 4

F(000) = 552 Dx = 1.263 Mg m−3

Mo Kα radiation, λ = 0.71073 Å Cell parameters from 260 reflections θ = 2.2–27.5°

µ = 0.24 mm−1

T = 291 K Block, colourless 0.31 × 0.28 × 0.21 mm

Data collection

Bruker SMART CCD area-detector diffractometer

Radiation source: fine-focus sealed tube Graphite monochromator

φ and ω scans

Absorption correction: multi-scan (SADABS; Sheldrick, 1996) Tmin = 0.930, Tmax = 0.955

9867 measured reflections 2526 independent reflections 2115 reflections with I > 2σ(I) Rint = 0.021

θmax = 25.5°, θmin = 2.4°

h = −11→11 k = −13→13 l = −14→14

Refinement

Refinement on F2 Least-squares matrix: full R[F2 _{> 2σ(F}2_{)] = 0.056}

wR(F2_{) = 0.137}

S = 1.19 2526 reflections 172 parameters 0 restraints

Primary atom site location: structure-invariant direct methods

Secondary atom site location: difference Fourier map

Hydrogen site location: inferred from neighbouring sites

H atoms treated by a mixture of independent and constrained refinement

w = 1/[σ2_(F

o2) + (0.0691P)2 + 0.1443P] where P = (Fo2 + 2Fc2)/3

supporting information

sup-2 Acta Cryst. (2006). E62, o2457–o2459

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 F}2_,

conventional R-factors R are based on F, with F set to zero for negative F2_{. The threshold expression of F}2 _{> σ(F}2_{) 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

N1 0.29415 (18) 0.39444 (15) 0.08467 (15) 0.0548 (5)

N2 0.6910 (3) 0.0207 (2) 0.2670 (2) 0.0760 (7)

O1 0.51741 (18) −0.12967 (14) 0.15275 (14) 0.0674 (5)

O2 0.32274 (16) −0.05708 (12) 0.07172 (13) 0.0595 (4)

O3 0.4169 (2) 0.36935 (18) −0.11546 (17) 0.0645 (5)

S1 0.60326 (7) 0.24039 (5) 0.26417 (5) 0.0636 (3)

C1 0.2309 (3) 0.5103 (2) 0.0740 (2) 0.0744 (7)

H1A 0.1751 0.5244 0.1353 0.112*

H1B 0.1739 0.5140 0.0073 0.112*

H1C 0.3024 0.5680 0.0725 0.112*

C2 0.5909 (2) 0.0942 (2) 0.23095 (18) 0.0556 (6)

C3 0.4703 (2) 0.07060 (18) 0.16800 (16) 0.0480 (5)

C4 0.2522 (2) 0.18358 (19) 0.08182 (19) 0.0549 (6)

H4A 0.1883 0.1256 0.1069 0.066*

H4B 0.2669 0.1683 0.0053 0.066*

C5 0.1891 (2) 0.3036 (2) 0.0930 (2) 0.0613 (6)

H5A 0.1168 0.3147 0.0358 0.074*

H5B 0.1475 0.3096 0.1632 0.074*

C6 0.3918 (2) 0.39054 (19) 0.17991 (19) 0.0582 (6)

H6A 0.3457 0.4132 0.2452 0.070*

H6B 0.4675 0.4441 0.1700 0.070*

C7 0.4462 (2) 0.27006 (18) 0.19256 (18) 0.0524 (5)

C8 0.3876 (2) 0.17382 (18) 0.14745 (16) 0.0472 (5)

C9 0.4422 (2) −0.04625 (19) 0.13153 (17) 0.0502 (5)

C10 0.2851 (3) −0.1725 (2) 0.0343 (2) 0.0657 (7)

H10A 0.2792 −0.2247 0.0962 0.079*

H10B 0.3540 −0.2024 −0.0132 0.079*

C11 0.1480 (3) −0.1631 (3) −0.0268 (3) 0.0921 (9)

H11A 0.0799 −0.1372 0.0221 0.138*

H11B 0.1217 −0.2377 −0.0562 0.138*

H11C 0.1541 −0.1083 −0.0855 0.138*

H3B 0.434 (3) 0.311 (3) −0.127 (2) 0.071 (10)*

H3A 0.379 (4) 0.370 (3) −0.041 (3) 0.139 (14)*

H2A 0.763 (3) 0.047 (2) 0.299 (2) 0.085 (9)*

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Atomic displacement parameters (Å2₎

U11 _U22 _U33 _U12 _U13 _U23

N1 0.0553 (11) 0.0434 (10) 0.0660 (12) −0.0003 (8) 0.0069 (9) −0.0039 (8)

N2 0.0734 (15) 0.0617 (15) 0.0895 (16) 0.0030 (12) −0.0266 (13) −0.0063 (12)

O1 0.0744 (11) 0.0465 (9) 0.0806 (11) 0.0017 (8) −0.0019 (9) −0.0031 (8)

O2 0.0606 (10) 0.0441 (9) 0.0736 (10) −0.0110 (7) −0.0005 (8) −0.0063 (7)

O3 0.0686 (12) 0.0515 (11) 0.0735 (13) 0.0030 (9) 0.0053 (9) 0.0063 (9)

S1 0.0661 (4) 0.0559 (4) 0.0670 (4) −0.0067 (3) −0.0126 (3) −0.0123 (3)

C1 0.0796 (17) 0.0527 (14) 0.0915 (18) 0.0134 (13) 0.0109 (14) −0.0028 (13)

C2 0.0606 (14) 0.0526 (13) 0.0535 (12) −0.0029 (11) 0.0006 (10) −0.0010 (10)

C3 0.0527 (12) 0.0452 (12) 0.0466 (11) −0.0081 (10) 0.0068 (9) 0.0000 (9)

C4 0.0480 (12) 0.0495 (13) 0.0668 (14) −0.0112 (10) 0.0004 (10) −0.0005 (10)

C5 0.0512 (13) 0.0578 (14) 0.0750 (15) −0.0005 (11) 0.0052 (11) −0.0018 (12)

C6 0.0631 (15) 0.0486 (13) 0.0634 (14) −0.0058 (11) 0.0076 (11) −0.0088 (10)

C7 0.0541 (13) 0.0489 (13) 0.0541 (12) −0.0056 (10) 0.0029 (10) −0.0060 (10)

C8 0.0480 (12) 0.0474 (12) 0.0468 (11) −0.0073 (9) 0.0076 (9) 0.0002 (9)

C9 0.0532 (12) 0.0478 (12) 0.0500 (12) −0.0061 (10) 0.0082 (10) 0.0014 (10)

C10 0.0719 (16) 0.0493 (14) 0.0762 (16) −0.0177 (12) 0.0075 (13) −0.0135 (11)

C11 0.0702 (18) 0.091 (2) 0.114 (2) −0.0284 (15) 0.0012 (16) −0.0259 (17)

Geometric parameters (Å, º)

N1—C6 1.460 (3) C3—C8 1.447 (3)

N1—C1 1.470 (3) C4—C8 1.503 (3)

N1—C5 1.465 (3) C4—C5 1.519 (3)

N2—C2 1.342 (3) C4—H4A 0.9700

N2—H2A 0.84 (3) C4—H4B 0.9700

N2—H2B 0.87 (3) C5—H5A 0.9700

O1—C9 1.224 (3) C5—H5B 0.9700

O2—C9 1.339 (2) C6—C7 1.489 (3)

O2—C10 1.445 (2) C6—H6A 0.9700

O3—H3B 0.70 (3) C6—H6B 0.9700

O3—H3A 0.99 (4) C7—C8 1.349 (3)

S1—C2 1.734 (2) C10—C11 1.490 (4)

S1—C7 1.745 (2) C10—H10A 0.9700

C1—H1A 0.9600 C10—H10B 0.9700

C1—H1B 0.9600 C11—H11A 0.9600

C1—H1C 0.9600 C11—H11B 0.9600

C2—C3 1.389 (3) C11—H11C 0.9600

C3—C9 1.439 (3)

C6—N1—C1 110.30 (18) N1—C5—H5B 109.4

C6—N1—C5 110.12 (18) C4—C5—H5B 109.4

C1—N1—C5 111.54 (19) H5A—C5—H5B 108.0

C2—N2—H2A 119.5 (19) N1—C6—C7 108.74 (18)

C2—N2—H2B 115.7 (17) N1—C6—H6A 109.9

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C9—O2—C10 116.95 (18) N1—C6—H6B 109.9

H3B—O3—H3A 107 (3) C7—C6—H6B 109.9

C2—S1—C7 91.46 (10) H6A—C6—H6B 108.3

N1—C1—H1A 109.5 C8—C7—C6 125.8 (2)

N1—C1—H1B 109.5 C8—C7—S1 112.28 (17)

H1A—C1—H1B 109.5 C6—C7—S1 121.83 (16)

N1—C1—H1C 109.5 C7—C8—C3 112.8 (2)

H1A—C1—H1C 109.5 C7—C8—C4 119.4 (2)

H1B—C1—H1C 109.5 C3—C8—C4 127.72 (18)

N2—C2—C3 128.8 (2) O1—C9—O2 121.9 (2)

N2—C2—S1 119.76 (19) O1—C9—C3 124.6 (2)

C3—C2—S1 111.41 (17) O2—C9—C3 113.53 (19)

C2—C3—C9 119.6 (2) O2—C10—C11 107.1 (2)

C2—C3—C8 112.02 (19) O2—C10—H10A 110.3

C9—C3—C8 128.39 (19) C11—C10—H10A 110.3

C8—C4—C5 111.25 (17) O2—C10—H10B 110.3

C8—C4—H4A 109.4 C11—C10—H10B 110.3

C5—C4—H4A 109.4 H10A—C10—H10B 108.6

C8—C4—H4B 109.4 C10—C11—H11A 109.5

C5—C4—H4B 109.4 C10—C11—H11B 109.5

H4A—C4—H4B 108.0 H11A—C11—H11B 109.5

N1—C5—C4 111.12 (18) C10—C11—H11C 109.5

N1—C5—H5A 109.4 H11A—C11—H11C 109.5

C4—C5—H5A 109.4 H11B—C11—H11C 109.5

C7—S1—C2—N2 −179.7 (2) S1—C7—C8—C3 −1.0 (2)

C7—S1—C2—C3 −0.32 (17) C6—C7—C8—C4 −2.8 (3)

N2—C2—C3—C9 −1.2 (4) S1—C7—C8—C4 −179.47 (15)

S1—C2—C3—C9 179.50 (15) C2—C3—C8—C7 0.7 (3)

N2—C2—C3—C8 179.1 (2) C9—C3—C8—C7 −178.9 (2)

S1—C2—C3—C8 −0.2 (2) C2—C3—C8—C4 179.1 (2)

C6—N1—C5—C4 −68.2 (2) C9—C3—C8—C4 −0.5 (4)

C1—N1—C5—C4 169.03 (19) C5—C4—C8—C7 −9.6 (3)

C8—C4—C5—N1 43.8 (3) C5—C4—C8—C3 172.2 (2)

C1—N1—C6—C7 176.08 (19) C10—O2—C9—O1 0.9 (3)

C5—N1—C6—C7 52.5 (2) C10—O2—C9—C3 −178.43 (18)

N1—C6—C7—C8 −18.6 (3) C2—C3—C9—O1 0.7 (3)

N1—C6—C7—S1 157.76 (16) C8—C3—C9—O1 −179.7 (2)

C2—S1—C7—C8 0.75 (18) C2—C3—C9—O2 179.97 (18)

C2—S1—C7—C6 −176.0 (2) C8—C3—C9—O2 −0.4 (3)

C6—C7—C8—C3 175.7 (2) C9—O2—C10—C11 178.3 (2)

Hydrogen-bond geometry (Å, º)

D—H···A D—H H···A D···A D—H···A

N2—H2A···O3i _{0.84 (3) 2.02 (3) 2.846 (3) 171.00}

N2—H2B···O1 0.88 (2) 2.10 (3) 2.741 (3) 130 (2)

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O3—H3A···N1 1.00 (4) 1.80 (4) 2.790 (3) 170 (3)

O3—H3B···O1ii _{0.71 (3) 2.17 (3) 2.874 (3) 176.00}