organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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ISSN: 2414-3146

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

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.

3D view (loading...)
[Scheme 3D1]
Chemical scheme
[Scheme 1]

Structure description

Thio­phene and its derivatives have various biological properties including anti-microbial (Russell et al., 1988[Russell, R. K., Press, J. B., Rampulla, R. A., McNally, J. J., Falotico, R., Keiser, J. A., Bright, D. A. & Tobia, A. (1988). J. Med. Chem. 31, 1786-1793.]), analgesic and anti-inflammatory (Chen et al., 2008[Chen, H. J., Wang, W., l Wang, G. F., Shi, L. P., Gu, M., Ren, Y. D. & Hou, L. F. (2008). Med. Chem. 3, 1316-1321.]), anti­hypertensive (Monge Vega et al., 1980[Monge Vega, A., Aldana, I., Rabbani, M. M. & Fernandez-Alvarez, E. (1980). Heterocycl. Chem. 17, 77-80.]), anti-diabetes mellitus (Abdelhamid et al., 2009[Abdelhamid, A. O. (2009). J. Heterocycl. Chem. 46, 680-686.]) and gonadotropin releasing hormone antagonist (Sabins et al., 1944[Sabins, R. W. (1944). Sulfur Rep. 16, 1.]) 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[link]).

[Figure 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[link] and Figs. 2[link] and 3[link]).

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA 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]
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 operationx + 1, −y + 1, −z + 1.
[Figure 3]
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[link].

Table 2
Experimental details

Crystal data
Chemical formula C11H10N2OS
Mr 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)
V3) 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[Bruker (2013). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.])
Tmin, Tmax 0.539, 0.746
No. of measured, independent and observed [I > 2σ(I)] reflections 11046, 2319, 2058
Rint 0.041
(sin θ/λ)max−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
Δρmax, Δρmin (e Å−3) 0.29, −0.35
Computer programs: APEX2 and SAINT (Bruker, 2013[Bruker (2013). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]), SHELXT (Sheldrick, 2015a[Sheldrick, G. M. (2015a). Acta Cryst. A71, 3-8.]), SHELXL2014 (Sheldrick, 2015b[Sheldrick, G. M. (2015b). Acta Cryst. C71, 3-8.]) and OLEX2 (Dolomanov et al., 2009[Dolomanov, O. V., Bourhis, L. J., Gildea, R. J., Howard, J. A. K. & Puschmann, H. (2009). J. Appl. Cryst. 42, 339-341.]).

Structural data


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
C11H10N2OSF(000) = 456
Mr = 218.27Dx = 1.426 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
a = 8.681 (3) ÅCell parameters from 4931 reflections
b = 8.088 (3) Åθ = 2.4–27.5°
c = 14.875 (6) ŵ = 0.29 mm1
β = 103.175 (4)°T = 110 K
V = 1016.8 (7) Å3Black, colourless
Z = 40.57 × 0.57 × 0.56 mm
Data collection top
Bruker APEXII CCD
diffractometer
2058 reflections with I > 2σ(I)
φ and ω scansRint = 0.041
Absorption correction: multi-scan
(SADABS; Bruker, 2013)
θmax = 27.6°, θmin = 2.4°
Tmin = 0.539, Tmax = 0.746h = 1111
11046 measured reflectionsk = 1010
2319 independent reflectionsl = 1919
Refinement top
Refinement on F20 restraints
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) + (0.0462P)2 + 0.5739P]
where P = (Fo2 + 2Fc2)/3
S = 1.04(Δ/σ)max = 0.001
2319 reflectionsΔρmax = 0.29 e Å3
136 parametersΔρmin = 0.35 e Å3
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
xyzUiso*/Ueq
S10.48410 (5)1.06177 (5)0.27924 (3)0.02145 (13)
O10.27142 (13)0.92442 (13)0.38710 (8)0.0201 (3)
N10.25034 (15)0.41563 (15)0.44501 (9)0.0164 (3)
N20.44226 (14)0.74541 (15)0.47523 (9)0.0149 (3)
H20.53920.70580.48970.018*
C10.20492 (17)0.57130 (18)0.45674 (10)0.0138 (3)
C20.05897 (18)0.63262 (19)0.41132 (11)0.0195 (3)
H2A0.02900.74240.42240.023*
C30.04294 (19)0.5317 (2)0.34950 (12)0.0245 (4)
H30.14320.57140.31690.029*
C40.00436 (19)0.3724 (2)0.33628 (12)0.0238 (4)
H40.06250.30060.29410.029*
C50.15017 (19)0.3193 (2)0.38527 (11)0.0210 (3)
H50.18140.20910.37630.025*
C60.32272 (17)0.68000 (18)0.52048 (10)0.0162 (3)
H6A0.26610.77310.54180.019*
H6B0.37540.61520.57540.019*
C70.40555 (17)0.86572 (17)0.41170 (10)0.0143 (3)
C80.53409 (18)0.92391 (17)0.36918 (10)0.0141 (3)
C90.69193 (18)0.88705 (19)0.38810 (11)0.0176 (3)
H90.74210.81360.43570.021*
C100.77229 (19)0.9712 (2)0.32843 (11)0.0213 (3)
H100.88240.96070.33170.026*
C110.6740 (2)1.0683 (2)0.26630 (11)0.0208 (3)
H110.70721.13260.22070.025*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
S10.0171 (2)0.0242 (2)0.0209 (2)0.00174 (15)0.00019 (15)0.00863 (15)
O10.0139 (5)0.0177 (6)0.0278 (6)0.0023 (4)0.0029 (5)0.0045 (4)
N10.0146 (6)0.0150 (6)0.0199 (7)0.0009 (5)0.0046 (5)0.0026 (5)
N20.0101 (6)0.0151 (6)0.0194 (6)0.0001 (5)0.0029 (5)0.0018 (5)
C10.0124 (7)0.0155 (7)0.0149 (7)0.0001 (5)0.0061 (5)0.0032 (5)
C20.0132 (7)0.0178 (7)0.0283 (9)0.0020 (6)0.0065 (6)0.0048 (6)
C30.0112 (7)0.0306 (9)0.0296 (9)0.0014 (6)0.0003 (6)0.0080 (7)
C40.0194 (8)0.0268 (9)0.0236 (8)0.0102 (7)0.0018 (6)0.0008 (6)
C50.0223 (8)0.0166 (7)0.0252 (8)0.0024 (6)0.0074 (7)0.0013 (6)
C60.0158 (7)0.0168 (7)0.0172 (7)0.0009 (6)0.0063 (6)0.0009 (6)
C70.0148 (7)0.0110 (6)0.0169 (7)0.0012 (5)0.0032 (6)0.0025 (5)
C80.0175 (7)0.0112 (6)0.0131 (7)0.0001 (5)0.0023 (5)0.0002 (5)
C90.0176 (8)0.0168 (7)0.0197 (8)0.0027 (6)0.0069 (6)0.0033 (6)
C100.0197 (8)0.0223 (8)0.0249 (8)0.0026 (6)0.0110 (6)0.0030 (6)
C110.0225 (8)0.0226 (8)0.0187 (8)0.0036 (6)0.0075 (6)0.0030 (6)
Geometric parameters (Å, º) top
S1—C81.7195 (16)C3—C41.380 (3)
S1—C111.7031 (18)C4—H40.9500
O1—C71.2331 (18)C4—C51.377 (2)
N1—C11.3425 (19)C5—H50.9500
N1—C51.342 (2)C6—H6A0.9900
N2—H20.8800C6—H6B0.9900
N2—C61.4587 (18)C7—C81.479 (2)
N2—C71.3431 (19)C8—C91.367 (2)
C1—C21.385 (2)C9—H90.9500
C1—C61.509 (2)C9—C101.421 (2)
C2—H2A0.9500C10—H100.9500
C2—C31.387 (2)C10—C111.356 (2)
C3—H30.9500C11—H110.9500
C11—S1—C891.66 (8)N2—C6—H6A109.2
C5—N1—C1117.73 (13)N2—C6—H6B109.2
C6—N2—H2119.7C1—C6—H6A109.2
C7—N2—H2119.7C1—C6—H6B109.2
C7—N2—C6120.51 (13)H6A—C6—H6B107.9
N1—C1—C2122.39 (14)O1—C7—N2122.98 (13)
N1—C1—C6116.81 (13)O1—C7—C8120.25 (13)
C2—C1—C6120.77 (14)N2—C7—C8116.75 (13)
C1—C2—H2A120.4C7—C8—S1117.25 (11)
C1—C2—C3119.16 (15)C9—C8—S1111.40 (11)
C3—C2—H2A120.4C9—C8—C7131.35 (14)
C2—C3—H3120.7C8—C9—H9123.9
C4—C3—C2118.57 (15)C8—C9—C10112.24 (14)
C4—C3—H3120.7C10—C9—H9123.9
C3—C4—H4120.6C9—C10—H10123.8
C5—C4—C3118.90 (15)C11—C10—C9112.37 (15)
C5—C4—H4120.6C11—C10—H10123.8
N1—C5—C4123.23 (15)S1—C11—H11123.8
N1—C5—H5118.4C10—C11—S1112.33 (12)
C4—C5—H5118.4C10—C11—H11123.8
N2—C6—C1111.90 (12)
S1—C8—C9—C100.32 (17)C5—N1—C1—C21.5 (2)
O1—C7—C8—S15.13 (19)C5—N1—C1—C6176.95 (13)
O1—C7—C8—C9175.25 (15)C6—N2—C7—O11.4 (2)
N1—C1—C2—C31.8 (2)C6—N2—C7—C8179.75 (12)
N1—C1—C6—N279.64 (16)C6—C1—C2—C3176.59 (14)
N2—C7—C8—S1173.26 (11)C7—N2—C6—C173.47 (17)
N2—C7—C8—C96.4 (2)C7—C8—C9—C10179.31 (15)
C1—N1—C5—C40.2 (2)C8—S1—C11—C100.70 (13)
C1—C2—C3—C40.8 (2)C8—C9—C10—C110.2 (2)
C2—C1—C6—N298.81 (16)C9—C10—C11—S10.64 (19)
C2—C3—C4—C50.4 (2)C11—S1—C8—C7179.12 (12)
C3—C4—C5—N10.7 (2)C11—S1—C8—C90.58 (12)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H2···N1i0.882.112.963 (2)164
C5—H5···O1ii0.952.433.361 (2)168
C9—H9···N1i0.952.563.441 (2)155
Symmetry codes: (i) x+1, y+1, z+1; (ii) x, y1, z.
 

References

First citationAbdelhamid, A. O. (2009). J. Heterocycl. Chem. 46, 680–686.  Web of Science CrossRef CAS Google Scholar
First citationBruker (2013). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.  Google Scholar
First citationChen, H. J., Wang, W., l Wang, G. F., Shi, L. P., Gu, M., Ren, Y. D. & Hou, L. F. (2008). Med. Chem. 3, 1316–1321.  Google Scholar
First citationDolomanov, O. V., Bourhis, L. J., Gildea, R. J., Howard, J. A. K. & Puschmann, H. (2009). J. Appl. Cryst. 42, 339–341.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationMonge Vega, A., Aldana, I., Rabbani, M. M. & Fernandez-Alvarez, E. (1980). Heterocycl. Chem. 17, 77–80.  CrossRef CAS Web of Science Google Scholar
First citationRussell, R. K., Press, J. B., Rampulla, R. A., McNally, J. J., Falotico, R., Keiser, J. A., Bright, D. A. & Tobia, A. (1988). J. Med. Chem. 31, 1786–1793.  CrossRef CAS PubMed Web of Science Google Scholar
First citationSabins, R. W. (1944). Sulfur Rep. 16, 1.  Google Scholar
First citationSheldrick, G. M. (2015a). Acta Cryst. A71, 3–8.  Web of Science CrossRef IUCr Journals Google Scholar
First citationSheldrick, G. M. (2015b). Acta Cryst. C71, 3–8.  Web of Science CrossRef IUCr Journals Google Scholar

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