N-[(Pyridin-2-yl)meth­yl]thio­phene-2-carboxamide

Mohanbabu, M.; Sathishkumar, P.N.; Bhuvanesh, N.S.P.; Karvembu, R.; Aravindhan, S.

doi:10.1107/S2414314619009805

organic compounds

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ISSN: 2414-3146

Volume 4| Part 7| July 2019| x190980

https://doi.org/10.1107/S2414314619009805

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N-[(Pyridin-2-yl)methyl]thiophene-2-carboxamide

M. Mohanbabu,^a P. N. Sathishkumar,^b N. S. P. Bhuvanesh,^c R. Karvembu ^b and S. Aravindhan ^d ^*

^aDepartment of Physics, Sri Malolan College of Arts & Science, Madhurantakam, Kanchipuram - 603 306, India, ^bDepartment of Chemistry, National Institute of Technology, Tiruchirappalli - 620 015, India, ^cDepartment of Chemistry, Texas A & M University, College Station, TX, 77842, USA, and ^dDepartment of Physics, Presidency College (Autonomous), Chennai - 600 005, India
^*Correspondence e-mail: saravindhanpresidency@gmail.com

Edited by W. T. A. Harrison, University of Aberdeen, Scotland (Received 28 June 2019; accepted 9 July 2019; online 26 July 2019)

In the title compound, C₁₁H₁₀N₂OS, the dihedral angle between the thiophene and pyridine rings is 77.79 (8)°. In the crystal, inversion dimers linked by pairs of N—H⋯N hydrogen bonds generate R₂²(10) loops. The dimers are reinforced by pairs of C—H⋯N interactions and C—H⋯O interactions link the dimers into [010] chains.

Keywords: pyridine; methyl; thiophene; carboxamide; hydrogen bonds.; crystal structure.

CCDC reference: 1912193

Structure description

Thiophene and its derivatives have various biological properties including anti-microbial (Russell et al., 1988 ), analgesic and anti-inflammatory (Chen et al., 2008 ), antihypertensive (Monge Vega et al., 1980 ), anti-diabetes mellitus (Abdelhamid et al., 2009 ) and gonadotropin releasing hormone antagonist (Sabins et al., 1944 ) activities. As part of our studies of potential active pharmaceutical ingredients (APIs) based on thiophenes, we report here the synthesis and crystal structure of the title compound (Fig. 1).

Figure 1
The molecular structure of the title compound, with displacement ellipsoids drawn at the 30% probability level.

The key torsion angle of the molecule, S1—C8—C7—O1 and C9—C8—C7—N2 with (−)syn-periplanar conformations and N1—C1—C6—N2 and C1—C6—N2—C7 with (+)syn-clinal conformations are −5.13 (19), −6.4 (2), 79.64 (16) and 73.47 (17)°, respectively. The dihedral angle between the thiophene ring and the pyridine ring is 77.79 (8)°.

In the crystal, the molecules are linked via pairs of N2—H2⋯N1 hydrogen bonds, forming inversion dimers with an R₂²(10) ring motif; the dimers are reinforced by a pair of C9—H9⋯N1 interactions. The dimers are linked into [010] chains by C5—H5⋯O1 interactions (Table 1 and Figs. 2 and 3).

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N2—H2⋯N1ⁱ	0.88	2.11	2.963 (2)	164
C5—H5⋯O1ⁱⁱ	0.95	2.43	3.361 (2)	168
C9—H9⋯N1ⁱ	0.95	2.56	3.441 (2)	155
Symmetry codes: (i) -x+1, -y+1, -z+1; (ii) x, y-1, z.

Figure 2
An inversion dimer with graph-set motif R₂²(10) formed by a pair of N—H⋯N hydrogen bonds. The bottom molecule is generated by the symmetry operation −x + 1, −y + 1, −z + 1.

Figure 3
Packing diagram showing the formation of [010] chains linked by N—H⋯N, C—H⋯N and C—H⋯O hydrogen bonds.

Synthesis and crystallization

Thiophene 2-carbonyl chloride (1 mmol) and dimethylaminopyridine (DMAP) (1.1 mmol) were dissolved in 10 ml of dry toluene and the mixture was refluxed with stirring for 1 h. The reaction mixture was cooled to room temperature and a solution of 2-aminomethylpyridine (1 mmol) in 5 ml of dry toluene was slowly added to it. The resultant solution was refluxed again for 3 h and the completion of the reaction was confirmed through TLC. The resultant solution was filtered and the filtrate volume was reduced using a rotary evaporator. The residue obtained was dissolved in dichloromethane and washed with water. The organic layer was separated and dried over sodium sulfate and kept for crystallization.

Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2.

Table 2
Experimental details

Crystal data
Chemical formula	C₁₁H₁₀N₂OS
M_r	218.27
Crystal system, space group	Monoclinic, P2₁/c
Temperature (K)	110
a, b, c (Å)	8.681 (3), 8.088 (3), 14.875 (6)
β (°)	103.175 (4)
V (Å³)	1016.8 (7)
Z	4
Radiation type	Mo Kα
μ (mm⁻¹)	0.29
Crystal size (mm)	0.57 × 0.57 × 0.56

Data collection
Diffractometer	Bruker APEXII CCD
Absorption correction	Multi-scan (SADABS; Bruker, 2013 )
T_min, T_max	0.539, 0.746
No. of measured, independent and observed [I > 2σ(I)] reflections	11046, 2319, 2058
R_int	0.041
(sin θ/λ)_max (Å⁻¹)	0.651

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.038, 0.098, 1.04
No. of reflections	2319
No. of parameters	136
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.29, −0.35
Computer programs: APEX2 and SAINT (Bruker, 2013), SHELXT (Sheldrick, 2015a ), SHELXL2014 (Sheldrick, 2015b ) and OLEX2 (Dolomanov et al., 2009 ).

Structural data

CCDC reference: 1912193

Crystal structure: contains datablocks global, I. DOI: https://doi.org/10.1107/S2414314619009805/hb4302sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2414314619009805/hb4302Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2414314619009805/hb4302Isup3.cml

checkCIF report

Computing details top

Data collection: APEX2 (Bruker, 2013); cell refinement: SAINT (Bruker, 2013); data reduction: SAINT (Bruker, 2013); program(s) used to solve structure: SHELXT (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015b); molecular graphics: OLEX2 (Dolomanov et al., 2009); software used to prepare material for publication: OLEX2 (Dolomanov et al., 2009).

N-[(Pyridin-2-yl)methyl]thiophene-2-carboxamide top

Crystal data top

C₁₁H₁₀N₂OS	F(000) = 456
M_r = 218.27	D_x = 1.426 Mg m⁻³
Monoclinic, P2₁/c	Mo Kα radiation, λ = 0.71073 Å
a = 8.681 (3) Å	Cell parameters from 4931 reflections
b = 8.088 (3) Å	θ = 2.4–27.5°
c = 14.875 (6) Å	µ = 0.29 mm⁻¹
β = 103.175 (4)°	T = 110 K
V = 1016.8 (7) Å³	Black, colourless
Z = 4	0.57 × 0.57 × 0.56 mm

Data collection top

Bruker APEXII CCD diffractometer	2058 reflections with I > 2σ(I)
φ and ω scans	R_int = 0.041
Absorption correction: multi-scan (SADABS; Bruker, 2013)	θ_max = 27.6°, θ_min = 2.4°
T_min = 0.539, T_max = 0.746	h = −11→11
11046 measured reflections	k = −10→10
2319 independent reflections	l = −19→19

Refinement top

Refinement on F²	0 restraints
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F² > 2σ(F²)] = 0.038	H-atom parameters constrained
wR(F²) = 0.098	w = 1/[σ²(F_o²) + (0.0462P)² + 0.5739P] where P = (F_o² + 2F_c²)/3
S = 1.04	(Δ/σ)_max = 0.001
2319 reflections	Δρ_max = 0.29 e Å⁻³
136 parameters	Δρ_min = −0.35 e Å⁻³

Special details top

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
S1	0.48410 (5)	1.06177 (5)	0.27924 (3)	0.02145 (13)
O1	0.27142 (13)	0.92442 (13)	0.38710 (8)	0.0201 (3)
N1	0.25034 (15)	0.41563 (15)	0.44501 (9)	0.0164 (3)
N2	0.44226 (14)	0.74541 (15)	0.47523 (9)	0.0149 (3)
H2	0.5392	0.7058	0.4897	0.018*
C1	0.20492 (17)	0.57130 (18)	0.45674 (10)	0.0138 (3)
C2	0.05897 (18)	0.63262 (19)	0.41132 (11)	0.0195 (3)
H2A	0.0290	0.7424	0.4224	0.023*
C3	−0.04294 (19)	0.5317 (2)	0.34950 (12)	0.0245 (4)
H3	−0.1432	0.5714	0.3169	0.029*
C4	0.00436 (19)	0.3724 (2)	0.33628 (12)	0.0238 (4)
H4	−0.0625	0.3006	0.2941	0.029*
C5	0.15017 (19)	0.3193 (2)	0.38527 (11)	0.0210 (3)
H5	0.1814	0.2091	0.3763	0.025*
C6	0.32272 (17)	0.68000 (18)	0.52048 (10)	0.0162 (3)
H6A	0.2661	0.7731	0.5418	0.019*
H6B	0.3754	0.6152	0.5754	0.019*
C7	0.40555 (17)	0.86572 (17)	0.41170 (10)	0.0143 (3)
C8	0.53409 (18)	0.92391 (17)	0.36918 (10)	0.0141 (3)
C9	0.69193 (18)	0.88705 (19)	0.38810 (11)	0.0176 (3)
H9	0.7421	0.8136	0.4357	0.021*
C10	0.77229 (19)	0.9712 (2)	0.32843 (11)	0.0213 (3)
H10	0.8824	0.9607	0.3317	0.026*
C11	0.6740 (2)	1.0683 (2)	0.26630 (11)	0.0208 (3)
H11	0.7072	1.1326	0.2207	0.025*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
S1	0.0171 (2)	0.0242 (2)	0.0209 (2)	−0.00174 (15)	−0.00019 (15)	0.00863 (15)
O1	0.0139 (5)	0.0177 (6)	0.0278 (6)	0.0023 (4)	0.0029 (5)	0.0045 (4)
N1	0.0146 (6)	0.0150 (6)	0.0199 (7)	0.0009 (5)	0.0046 (5)	0.0026 (5)
N2	0.0101 (6)	0.0151 (6)	0.0194 (6)	−0.0001 (5)	0.0029 (5)	0.0018 (5)
C1	0.0124 (7)	0.0155 (7)	0.0149 (7)	−0.0001 (5)	0.0061 (5)	0.0032 (5)
C2	0.0132 (7)	0.0178 (7)	0.0283 (9)	0.0020 (6)	0.0065 (6)	0.0048 (6)
C3	0.0112 (7)	0.0306 (9)	0.0296 (9)	−0.0014 (6)	0.0003 (6)	0.0080 (7)
C4	0.0194 (8)	0.0268 (9)	0.0236 (8)	−0.0102 (7)	0.0018 (6)	0.0008 (6)
C5	0.0223 (8)	0.0166 (7)	0.0252 (8)	−0.0024 (6)	0.0074 (7)	−0.0013 (6)
C6	0.0158 (7)	0.0168 (7)	0.0172 (7)	−0.0009 (6)	0.0063 (6)	0.0009 (6)
C7	0.0148 (7)	0.0110 (6)	0.0169 (7)	−0.0012 (5)	0.0032 (6)	−0.0025 (5)
C8	0.0175 (7)	0.0112 (6)	0.0131 (7)	−0.0001 (5)	0.0023 (5)	−0.0002 (5)
C9	0.0176 (8)	0.0168 (7)	0.0197 (8)	0.0027 (6)	0.0069 (6)	0.0033 (6)
C10	0.0197 (8)	0.0223 (8)	0.0249 (8)	0.0026 (6)	0.0110 (6)	0.0030 (6)
C11	0.0225 (8)	0.0226 (8)	0.0187 (8)	−0.0036 (6)	0.0075 (6)	0.0030 (6)

Geometric parameters (Å, º) top

S1—C8	1.7195 (16)	C3—C4	1.380 (3)
S1—C11	1.7031 (18)	C4—H4	0.9500
O1—C7	1.2331 (18)	C4—C5	1.377 (2)
N1—C1	1.3425 (19)	C5—H5	0.9500
N1—C5	1.342 (2)	C6—H6A	0.9900
N2—H2	0.8800	C6—H6B	0.9900
N2—C6	1.4587 (18)	C7—C8	1.479 (2)
N2—C7	1.3431 (19)	C8—C9	1.367 (2)
C1—C2	1.385 (2)	C9—H9	0.9500
C1—C6	1.509 (2)	C9—C10	1.421 (2)
C2—H2A	0.9500	C10—H10	0.9500
C2—C3	1.387 (2)	C10—C11	1.356 (2)
C3—H3	0.9500	C11—H11	0.9500

C11—S1—C8	91.66 (8)	N2—C6—H6A	109.2
C5—N1—C1	117.73 (13)	N2—C6—H6B	109.2
C6—N2—H2	119.7	C1—C6—H6A	109.2
C7—N2—H2	119.7	C1—C6—H6B	109.2
C7—N2—C6	120.51 (13)	H6A—C6—H6B	107.9
N1—C1—C2	122.39 (14)	O1—C7—N2	122.98 (13)
N1—C1—C6	116.81 (13)	O1—C7—C8	120.25 (13)
C2—C1—C6	120.77 (14)	N2—C7—C8	116.75 (13)
C1—C2—H2A	120.4	C7—C8—S1	117.25 (11)
C1—C2—C3	119.16 (15)	C9—C8—S1	111.40 (11)
C3—C2—H2A	120.4	C9—C8—C7	131.35 (14)
C2—C3—H3	120.7	C8—C9—H9	123.9
C4—C3—C2	118.57 (15)	C8—C9—C10	112.24 (14)
C4—C3—H3	120.7	C10—C9—H9	123.9
C3—C4—H4	120.6	C9—C10—H10	123.8
C5—C4—C3	118.90 (15)	C11—C10—C9	112.37 (15)
C5—C4—H4	120.6	C11—C10—H10	123.8
N1—C5—C4	123.23 (15)	S1—C11—H11	123.8
N1—C5—H5	118.4	C10—C11—S1	112.33 (12)
C4—C5—H5	118.4	C10—C11—H11	123.8
N2—C6—C1	111.90 (12)

S1—C8—C9—C10	−0.32 (17)	C5—N1—C1—C2	1.5 (2)
O1—C7—C8—S1	−5.13 (19)	C5—N1—C1—C6	−176.95 (13)
O1—C7—C8—C9	175.25 (15)	C6—N2—C7—O1	−1.4 (2)
N1—C1—C2—C3	−1.8 (2)	C6—N2—C7—C8	−179.75 (12)
N1—C1—C6—N2	79.64 (16)	C6—C1—C2—C3	176.59 (14)
N2—C7—C8—S1	173.26 (11)	C7—N2—C6—C1	73.47 (17)
N2—C7—C8—C9	−6.4 (2)	C7—C8—C9—C10	179.31 (15)
C1—N1—C5—C4	−0.2 (2)	C8—S1—C11—C10	−0.70 (13)
C1—C2—C3—C4	0.8 (2)	C8—C9—C10—C11	−0.2 (2)
C2—C1—C6—N2	−98.81 (16)	C9—C10—C11—S1	0.64 (19)
C2—C3—C4—C5	0.4 (2)	C11—S1—C8—C7	−179.12 (12)
C3—C4—C5—N1	−0.7 (2)	C11—S1—C8—C9	0.58 (12)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N2—H2···N1ⁱ	0.88	2.11	2.963 (2)	164
C5—H5···O1ⁱⁱ	0.95	2.43	3.361 (2)	168
C9—H9···N1ⁱ	0.95	2.56	3.441 (2)	155

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

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