2-Amino-N-(furan-2-ylmeth­yl)-5,6-di­hydro-4H-cyclo­penta­[b]thio­phene-3-carboxamide

Chandra Kumar, K.; Balasaraswathy, S.; Rajesh, B.M.; Chandra

doi:10.1107/S2414314617012111

organic compounds

IUCrDATA

ISSN: 2414-3146

Volume 2| Part 8| August 2017| x171211

https://doi.org/10.1107/S2414314617012111

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2-Amino-N-(furan-2-ylmethyl)-5,6-dihydro-4H-cyclopenta[b]thiophene-3-carboxamide

K. Chandra Kumar,^a S. Balasaraswathy,^a B. M. Rajesh ^b and Chandra ^c ^*

^aDepartment of Engineering Physics, HKBK College of Engineering, Bengaluru 560 045, India, ^bDepartment of Physics, RV College of Engineering, Bengaluru 560 059, India, and ^cDepartment of Physics, The National Institute of Engineering (NIE), Mysore 570 008, India
^*Correspondence e-mail: mychandru.10@gmail.com

Edited by W. T. A. Harrison, University of Aberdeen, Scotland (Received 19 August 2017; accepted 22 August 2017; online 30 August 2017)

In the title compound, C₁₃H₁₄N₂O₂S, the dihedral angle between the furan and cyclopentathiophene groups is 89.88 (14)°. The carboximidamide unit is in an anticlinal conformation with respect to the cycloheptathiophene moiety and an intramolecular N—H⋯O hydrogen bond closes an S(6) ring. In the crystal, N—H⋯O hydogen bonds link the molecules into [010] C(6) chains and a very weak C—H⋯O interaction is also observed.

Keywords: crystal structure; thiophene derivative; hydrogen bonding; biological activities.

CCDC reference: 1570199

Structure description

Tetrahydrothieno derivatives are studied extensively in medicinal chemistry due to their various biological activities (Lopez-Rodriguez et al., 2001 ). As part of our interest in these compounds, we have synthesized the title compound (Fig. 1) and determined its crystal structure.

Figure 1
The molecular structure of (I), shown with 50% probability displacement ellipsoids.

The mean plane of the furan moiety (O1/C10–C13) is oriented at a dihedral angle of 89.88 (14)° with respect to the plane of the almost planar (r.m.s. deviation = 0.014 Å) cyclopentathiophene ring (S1–C7). The carboximidamide unit is in an antiperiplanar conformation with respect to the cycloheptathiophene moiety, as indicated by the torsion angle of 177.07 (18)° for N2—C8—C7—C6. An intramolecular N1—H1A⋯O2 hydrogen bond (Table 1) closes an S(6) ring.

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1A⋯O2	0.86	2.15	2.738 (3)	125
N1—H1B⋯O2ⁱ	0.86	2.06	2.902 (3)	167
C9—H9B⋯O1ⁱⁱ	0.97	2.59	3.224 (4)	123
Symmetry codes: (i) $[-x+{\script{1\over 2}}, y-{\script{1\over 2}}, -z+{\script{1\over 2}}]$ ; (ii) $[-x, y, -z+{\script{1\over 2}}]$ .

In the crystal, N1—H1B⋯O2ⁱ hydrogen bonds link the molecules into C(6) chains propagating in the [010] direction (Fig. 2). A very weak C—H⋯O interaction is also observed. The amide N2—H1N group does not participate in hydrogen bonding, perhaps due to steric crowding.

Figure 2
Packing diagram viewed down [010].

Synthesis and crystallization

Cyclopentanone (0.8 equivalents), diethylamine (0.9 equivalents) and N-(2-methoxyphenyl)acetamide (1.2 equivalents) were taken in 15 ml ethanol and mixed thoroughly in a microwave tube. The tube was sealed and irradiated at 325 K for 15 min. After cooling, ethyl acetate was added to the reaction mixture and the solid residue was removed by filtration. The reaction mixture was poured into ice-cold water, and the separated solid was filtered off and recrystallized from ethyl alcohol solution to give pale-yellow blocks of the title compound.

Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2. The H atoms were positioned geometrically and allowed to ride on their parent atom, with N—H = 0.86 Å and C—H = 0.93–0.97 Å, and with U_iso(H) = 1.2–1.5U_eq(carrier) for all H atoms.

Table 2
Experimental details

Crystal data
Chemical formula	C₁₃H₁₄N₂O₂S
M_r	262.32
Crystal system, space group	Monoclinic, C2/c
Temperature (K)	273
a, b, c (Å)	21.694 (2), 9.8547 (11), 15.1162 (16)
β (°)	131.661 (2)
V (Å³)	2414.3 (4)
Z	8
Radiation type	Mo Kα
μ (mm⁻¹)	0.26
Crystal size (mm)	0.28 × 0.25 × 0.22

Data collection
Diffractometer	Bruker APEXII CCD
No. of measured, independent and observed [I > 2σ(I)] reflections	9118, 2375, 1950
R_int	0.026
(sin θ/λ)_max (Å⁻¹)	0.617

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.043, 0.120, 0.94
No. of reflections	2375
No. of parameters	167
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.25, −0.27
Computer programs: APEX2 (Bruker, 2009 ), SAINT (Bruker, 2009), SHELXS97 (Sheldrick, 2008 ), SHELXL97 (Sheldrick, 2008) and PLATON (Spek, 2009 ).

Structural data

CCDC reference: 1570199

Crystal structure: contains datablocks global, I. DOI: https://doi.org/10.1107/S2414314617012111/hb4165sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2414314617012111/hb4165Isup2.hkl

checkCIF report

Computing details top

Data collection: APEX2 (Bruker, 2009); cell refinement: SAINT (Bruker, 2009); data reduction: SAINT (Bruker, 2009); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: PLATON (Spek, 2009); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008).

2-Amino-N-(furan-2-ylmethyl)-5,6-dihydro-4H-cyclopenta[b]thiophene-3-carboxamide top

Crystal data top

C₁₃H₁₄N₂O₂S	F(000) = 1104
M_r = 262.32	D_x = 1.443 Mg m⁻³
Monoclinic, C2/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -C 2yc	Cell parameters from 2375 reflections
a = 21.694 (2) Å	θ = 2.4–26.0°
b = 9.8547 (11) Å	µ = 0.26 mm⁻¹
c = 15.1162 (16) Å	T = 273 K
β = 131.661 (2)°	Block, pale yellow
V = 2414.3 (4) Å³	0.28 × 0.25 × 0.22 mm
Z = 8

Data collection top

Bruker APEXII CCD diffractometer	R_int = 0.026
Detector resolution: 18.4 pixels mm^-1	θ_max = 26.0°, θ_min = 2.4°
ω and φ scans	h = −25→26
9118 measured reflections	k = −11→12
2375 independent reflections	l = −18→18
1950 reflections with I > 2σ(I)

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Hydrogen site location: mixed
R[F² > 2σ(F²)] = 0.043	H atoms treated by a mixture of independent and constrained refinement
wR(F²) = 0.120	W = 1/[Σ²(FO²) + (0.0768P)² + 1.5332P] WHERE P = (FO² + 2FC²)/3
S = 0.94	(Δ/σ)_max < 0.001
2375 reflections	Δρ_max = 0.25 e Å⁻³
167 parameters	Δρ_min = −0.27 e Å⁻³
0 restraints

Special details top

Geometry. Bond distances, angles etc. have been calculated using the rounded fractional coordinates. All su's are estimated from the variances of the (full) variance-covariance matrix. The cell esds are taken into account in the estimation of distances, angles and torsion angles

Refinement. Refinement on F² for ALL reflections except those flagged by the user for potential systematic errors. Weighted R-factors wR and all goodnesses of fit S are based on F², conventional R-factors R are based on F, with F set to zero for negative F². The observed criterion of F² > 2sigma(F²) is used only for calculating -R-factor-obs 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

	x	y	z	U_iso*/U_eq
S1	0.20078 (3)	0.46023 (5)	0.33918 (5)	0.0417 (2)
O1	−0.01010 (9)	1.03238 (16)	0.12373 (13)	0.0494 (5)
O2	0.20894 (9)	0.91283 (14)	0.28657 (13)	0.0419 (5)
N1	0.24893 (11)	0.65497 (18)	0.27274 (16)	0.0460 (6)
N2	0.13634 (11)	0.94561 (16)	0.34213 (16)	0.0369 (6)
C1	0.09466 (13)	0.6855 (2)	0.42005 (18)	0.0387 (6)
C2	0.13894 (11)	0.64691 (19)	0.37874 (15)	0.0315 (5)
C3	0.07541 (17)	0.5480 (2)	0.4461 (3)	0.0579 (9)
C4	0.11271 (15)	0.4340 (2)	0.4249 (2)	0.0481 (8)
C5	0.14820 (12)	0.5112 (2)	0.38300 (17)	0.0374 (6)
C6	0.20996 (11)	0.62804 (19)	0.31246 (16)	0.0323 (6)
C7	0.17454 (11)	0.71866 (18)	0.33821 (15)	0.0296 (5)
C8	0.17492 (11)	0.86383 (19)	0.32061 (15)	0.0307 (5)
C9	0.12394 (12)	1.08935 (19)	0.31397 (17)	0.0357 (6)
C10	0.05629 (11)	1.11794 (19)	0.18473 (17)	0.0341 (6)
C11	0.04371 (14)	1.2137 (2)	0.11172 (19)	0.0488 (7)
C12	−0.03482 (14)	1.1888 (2)	−0.00186 (19)	0.0520 (8)
C13	−0.06404 (14)	1.0795 (3)	0.0094 (2)	0.0530 (8)
H1A	0.25426	0.73747	0.26020	0.0550*
H1B	0.26842	0.58963	0.25995	0.0550*
H1D	0.04431	0.73478	0.35898	0.0460*
H1E	0.12945	0.74105	0.49084	0.0460*
H1N	0.1123 (15)	0.914 (2)	0.359 (2)	0.047 (7)*
H3A	0.09891	0.54570	0.52755	0.0700*
H3B	0.01619	0.53591	0.39458	0.0700*
H4A	0.15513	0.38489	0.49735	0.0580*
H4B	0.07068	0.37072	0.36516	0.0580*
H9A	0.17493	1.12798	0.34037	0.0430*
H9B	0.11115	1.13391	0.35731	0.0430*
H11	0.07968	1.28374	0.13150	0.0590*
H12	−0.06040	1.23942	−0.07033	0.0620*
H13	−0.11455	1.03962	−0.05200	0.0640*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
S1	0.0525 (3)	0.0264 (3)	0.0565 (4)	−0.0005 (2)	0.0405 (3)	−0.0038 (2)
O1	0.0473 (9)	0.0544 (10)	0.0507 (9)	−0.0160 (7)	0.0344 (8)	−0.0103 (7)
O2	0.0565 (9)	0.0323 (7)	0.0596 (9)	−0.0007 (6)	0.0481 (8)	0.0022 (6)
N1	0.0646 (12)	0.0324 (9)	0.0711 (12)	0.0011 (8)	0.0578 (11)	−0.0032 (8)
N2	0.0517 (10)	0.0271 (9)	0.0492 (10)	0.0024 (7)	0.0408 (9)	0.0029 (7)
C1	0.0446 (11)	0.0370 (11)	0.0448 (11)	−0.0010 (9)	0.0340 (10)	−0.0001 (9)
C2	0.0326 (9)	0.0309 (10)	0.0309 (9)	−0.0025 (7)	0.0211 (8)	−0.0023 (7)
C3	0.0780 (17)	0.0436 (14)	0.0860 (18)	−0.0057 (11)	0.0687 (16)	0.0008 (12)
C4	0.0580 (13)	0.0365 (12)	0.0608 (14)	−0.0056 (10)	0.0441 (12)	0.0013 (10)
C5	0.0424 (11)	0.0311 (10)	0.0430 (11)	−0.0037 (8)	0.0302 (10)	−0.0023 (8)
C6	0.0346 (10)	0.0287 (10)	0.0345 (9)	−0.0025 (7)	0.0234 (8)	−0.0038 (7)
C7	0.0314 (9)	0.0283 (10)	0.0306 (9)	−0.0017 (7)	0.0213 (8)	−0.0022 (7)
C8	0.0324 (9)	0.0300 (10)	0.0297 (9)	−0.0003 (7)	0.0207 (8)	−0.0014 (7)
C9	0.0449 (11)	0.0256 (10)	0.0430 (11)	0.0003 (8)	0.0319 (10)	−0.0029 (8)
C10	0.0374 (10)	0.0280 (9)	0.0438 (11)	−0.0017 (8)	0.0299 (9)	−0.0061 (8)
C11	0.0503 (13)	0.0365 (12)	0.0469 (12)	−0.0049 (10)	0.0270 (11)	0.0013 (9)
C12	0.0537 (14)	0.0502 (14)	0.0418 (12)	0.0107 (11)	0.0274 (11)	0.0032 (10)
C13	0.0396 (12)	0.0718 (17)	0.0449 (13)	−0.0038 (11)	0.0269 (11)	−0.0131 (11)

Geometric parameters (Å, º) top

S1—C5	1.731 (3)	C6—C7	1.392 (3)
S1—C6	1.745 (2)	C7—C8	1.456 (3)
O1—C10	1.368 (3)	C9—C10	1.496 (3)
O1—C13	1.372 (3)	C10—C11	1.335 (3)
O2—C8	1.244 (3)	C11—C12	1.422 (3)
N1—C6	1.349 (4)	C12—C13	1.317 (4)
N2—C8	1.348 (4)	C1—H1D	0.9700
N2—C9	1.452 (2)	C1—H1E	0.9700
C1—C2	1.502 (4)	C3—H3A	0.9700
C1—C3	1.544 (4)	C3—H3B	0.9700
N1—H1A	0.8600	C4—H4A	0.9700
N1—H1B	0.8600	C4—H4B	0.9700
N2—H1N	0.78 (4)	C9—H9A	0.9700
C2—C5	1.348 (3)	C9—H9B	0.9700
C2—C7	1.449 (4)	C11—H11	0.9300
C3—C4	1.538 (5)	C12—H12	0.9300
C4—C5	1.490 (4)	C13—H13	0.9300

C5—S1—C6	91.10 (12)	C10—C11—C12	107.4 (2)
C10—O1—C13	106.0 (2)	C11—C12—C13	106.2 (2)
C8—N2—C9	122.4 (2)	O1—C13—C12	111.0 (2)
C2—C1—C3	103.9 (2)	C2—C1—H1D	111.00
C6—N1—H1B	120.00	C2—C1—H1E	111.00
H1A—N1—H1B	120.00	C3—C1—H1D	111.00
C6—N1—H1A	120.00	C3—C1—H1E	111.00
C1—C2—C5	110.4 (2)	H1D—C1—H1E	109.00
C1—C2—C7	136.07 (18)	C1—C3—H3A	110.00
C8—N2—H1N	119.8 (18)	C1—C3—H3B	110.00
C9—N2—H1N	116.8 (19)	C4—C3—H3A	110.00
C5—C2—C7	113.6 (2)	C4—C3—H3B	110.00
C1—C3—C4	108.6 (3)	H3A—C3—H3B	108.00
C3—C4—C5	102.0 (2)	C3—C4—H4A	111.00
C2—C5—C4	115.1 (2)	C3—C4—H4B	111.00
S1—C5—C2	112.6 (2)	C5—C4—H4A	111.00
S1—C5—C4	132.26 (17)	C5—C4—H4B	111.00
S1—C6—N1	119.41 (17)	H4A—C4—H4B	109.00
S1—C6—C7	111.98 (19)	N2—C9—H9A	109.00
N1—C6—C7	128.61 (19)	N2—C9—H9B	109.00
C2—C7—C6	110.71 (17)	C10—C9—H9A	109.00
C6—C7—C8	120.5 (2)	C10—C9—H9B	109.00
C2—C7—C8	128.7 (2)	H9A—C9—H9B	108.00
O2—C8—C7	122.3 (2)	C10—C11—H11	126.00
N2—C8—C7	117.6 (2)	C12—C11—H11	126.00
O2—C8—N2	120.13 (18)	C11—C12—H12	127.00
N2—C9—C10	113.35 (16)	C13—C12—H12	127.00
O1—C10—C9	116.34 (18)	O1—C13—H13	125.00
O1—C10—C11	109.48 (19)	C12—C13—H13	124.00
C9—C10—C11	134.2 (2)

C6—S1—C5—C2	−0.58 (17)	C1—C2—C7—C6	179.0 (2)
C6—S1—C5—C4	−179.9 (2)	C1—C2—C7—C8	−2.5 (4)
C5—S1—C6—N1	−179.91 (18)	C1—C3—C4—C5	−2.3 (3)
C5—S1—C6—C7	0.76 (16)	C3—C4—C5—S1	−179.6 (2)
C13—O1—C10—C9	178.8 (2)	C3—C4—C5—C2	1.1 (3)
C13—O1—C10—C11	0.3 (3)	S1—C6—C7—C2	−0.7 (2)
C10—O1—C13—C12	−0.8 (3)	N1—C6—C7—C8	1.4 (3)
C9—N2—C8—O2	7.5 (3)	S1—C6—C7—C8	−179.33 (14)
C9—N2—C8—C7	−172.27 (18)	N1—C6—C7—C2	−180.0 (2)
C8—N2—C9—C10	76.0 (3)	C2—C7—C8—O2	179.03 (19)
C2—C1—C3—C4	2.7 (3)	C2—C7—C8—N2	−1.2 (3)
C3—C1—C2—C5	−2.1 (3)	C6—C7—C8—O2	−2.7 (3)
C3—C1—C2—C7	179.2 (2)	C6—C7—C8—N2	177.07 (18)
C1—C2—C5—S1	−178.78 (14)	N2—C9—C10—O1	35.1 (4)
C1—C2—C5—C4	0.7 (3)	N2—C9—C10—C11	−147.0 (3)
C7—C2—C5—S1	0.3 (2)	O1—C10—C11—C12	0.2 (3)
C7—C2—C5—C4	179.70 (18)	C9—C10—C11—C12	−177.8 (3)
C5—C2—C7—C8	178.76 (19)	C10—C11—C12—C13	−0.7 (4)
C5—C2—C7—C6	0.3 (2)	C11—C12—C13—O1	0.9 (4)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1A···O2	0.86	2.15	2.738 (3)	125
N1—H1B···O2ⁱ	0.86	2.06	2.902 (3)	167
C9—H9B···O1ⁱⁱ	0.97	2.59	3.224 (4)	123

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

Acknowledgements

The authors thank HKBK College of Engineering, Bengaluru, R. V. College of Engineering, Bengaluru, and The National Institute of Engineering (NIE), Mysuru, for support.

References

Bruker (2009). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA. Google Scholar
Lopez-Rodriguez, M. L., Murcia, M., Benhamu, B., Viso, A., Campillo, M. & Pardo, L. (2001). Bioorg. Med. Chem. Lett. 11, 2807–2811. Web of Science PubMed CAS Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar
Spek, A. L. (2009). Acta Cryst. D65, 148–155. Web of Science CrossRef CAS IUCr Journals Google Scholar

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