Crystal structure of ethyl 5-acetyl-2-{[(di­methyl­amino)­methyl­idene]amino}-4-methyl­thio­phene-3-carboxyl­ate

Prasad, N.L.; Krishnamurthy, M.S.; Nagarajaiah, H.; Begum, N.S.

doi:10.1107/S2056989015016217

organic compounds

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ISSN: 2056-9890

Volume 71| Part 10| October 2015| Pages o762-o763

doi:10.1107/S2056989015016217

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Crystal structure of ethyl 5-acetyl-2-{[(dimethylamino)methylidene]amino}-4-methylthiophene-3-carboxylate

N. L. Prasad,^a M. S. Krishnamurthy,^a H. Nagarajaiah ^a and Noor Shahina Begum ^a ^*

^aDepartment of Studies in Chemistry, Central College Campus, Bangalore University, Bangalore 560 001, Karnataka, India
^*Correspondence e-mail: noorsb@rediffmail.com

Edited by W. T. A. Harrison, University of Aberdeen, Scotland (Received 14 August 2015; accepted 31 August 2015; online 17 September 2015)

In the title thiophene derivative, C₁₃H₁₈N₂O₃S, the dihedral angles between the thiophene ring and the [(dimethylamino)methylidene]amino side chain (r.m.s. deviation = 0.009 Å) and the –CO₂ ester group are 3.01 (16) and 59.9 (3)°, respectively. In the crystal, inversion dimers linked by pairs of C—H⋯O hydrogen bonds generate R₂²(16) loops. The dimers are linked by another weak C—H⋯O interaction, forming chains along [001]. In addition, weak C—H⋯π interactions are observed, which link the chains into (001) layers.

Keywords: crystal structure; thiophene derivative; hydrogen bonding; C—H⋯π interactions.

CCDC reference: 1421360

1. Related literature

For background to the applications of thiophene derivatives, see: Sabnis et al. (1999 ). For a related structure, see: Mukhtar et al. (2010 ). For further synthetic details, see: Gewald et al. (1966 ).

2. Experimental

2.1. Crystal data

C₁₃H₁₈N₂O₃S
M_r = 282.35
Orthorhombic, P b c a
a = 12.218 (3) Å
b = 7.332 (2) Å
c = 30.923 (8) Å
V = 2769.9 (13) Å³
Z = 8
Mo Kα radiation
μ = 0.24 mm⁻¹
T = 100 K
0.29 × 0.26 × 0.10 mm

2.2. Data collection

Bruker SMART APEX CCD diffractometer
Absorption correction: multi-scan (SADABS; Bruker, 1998 ) T_min = 0.958, T_max = 0.963
15478 measured reflections
3012 independent reflections
2140 reflections with I > 2σ(I)
R_int = 0.076

2.3. Refinement

R[F² > 2σ(F²)] = 0.058
wR(F²) = 0.173
S = 1.19
3012 reflections
177 parameters
H-atom parameters constrained
Δρ_max = 0.52 e Å⁻³
Δρ_min = −0.34 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

Cg is the centroid of the C2/C3/C4/C5/S1 ring.

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
C9—H9A⋯O2ⁱ	0.99	2.45	3.270 (3)	139
C11—H11⋯O1ⁱⁱ	0.95	2.47	3.312 (4)	147
C7—H7C⋯Cgⁱⁱⁱ	0.98	2.86	3.693 (2)	143
Symmetry codes: (i) $[-x+1, y+{\script{1\over 2}}, -z+{\script{1\over 2}}]$ ; (ii) -x+1, -y, -z+1; (iii) $[x+{\script{1\over 2}}, -y+{\script{3\over 2}}, -z]$ .

Data collection: SMART (Bruker, 1998); cell refinement: SAINT-Plus (Bruker, 1998); data reduction: SAINT-Plus; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012 ) and CAMERON (Watkin et al., 1996 ); software used to prepare material for publication: WinGX (Farrugia, 2012).

Supporting information

CCDC reference: 1421360

Crystal structure: contains datablocks global, I. DOI: 10.1107/S2056989015016217/hb7483sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S2056989015016217/hb7483Isup2.hkl

Supporting information file. DOI: 10.1107/S2056989015016217/hb7483Isup3.cml

checkCIF report

Comment top

Thiophene belongs to a class of heterocyclic compounds containing a five membered ring made up of one sulfur as heteroatom, that are widely used as building blocks in many agrochemicals and pharmaceuticals. 2-Aminothiophenes attract special attention because of their applications in pharmaceuticals, agriculture, pesticides and dyes (Sabnis et al., 1999). The most convergent and well established classical approach for the preparation of 2-aminothiophenes is Gewald's method (Gewald et al., 1966), which involves the multicomponent condensation of a ketone with an activated nitrile and elemental sulfur in the presence of diethylamine as a catalyst. Herein, we report the structure of the title compound, (I).

The molecular structure of the compound is shown in Fig. 1. In the title compound, C₁₃H₁₈N₂O₃S, a thiophene derivative with dimethylamino- methyleneamino, acetyl, methyl and ethyl carboxylate substituents attached to a central thiophene ring. The thiophene ring and all the substituents are almost planar except the carboxyl group (C10/C9/O3/C8), it is slightly deviating from the plane at -83.474 (3)°. The carbonyl group of the exocyclic ester at C3 and acetyl at C5 adopts a trans orientation with C3=C2 and C5=C4 double bond respectively. The crystal structure features C—H···O interactions. The C11—H11···O1 hydrogen bonds resulting in a centrosymmetric head to head dimer with graph set R²₂(16) notation, which are in turn linked by another weak C9—H9A···O2 interactions to form chains of rings along [001] (Table.1; Fig. 2). In addition, weak C—H···π interactions of the type C7—H7C···Cg [Cg being the centroid of the thiophene ring (C2/C3/C4/C5/S1)] link the chains into layers parallel to (001) with a distance 2.864 Å is also observed (Fig. 3).

Related literature top

For background to the applications of thiophene derivatives, see: Sabnis et al. (1999). For a related structure, see: Mukhtar et al. (2010). For further synthetic details, see: Gewald et al. (1966).

Experimental top

Step-1: 3.3 g of cyano ethyl acetate was weighed and transferred to RB flask and 5 g of acetyl acetone and 10 to 15 ml of ethanol were added to it. The whole mixture was stirred for 10 min. After stirring 1.6 g of elemental sulfur was added to the mixture and cold condition was maintained by using crushed ice. Later 5 ml of diethyl amine was added drop by drop the solution changes its color to red. After the completion of addition the solution was again kept for stirring (10 min). Ice pack was removed and stirring was continued for about an hour. The precipitated product (1) was filtered, dried and recrystallized from ethanol (yield: 68%, m.p. 430 K)

Step-2: A mixture of compound 1 (10 mmol) and DMF—DMA (5 ml) was stirred at room temperature for 30 minutes. To this was added ethanol and kept in room temperature to give a solid product (title compound) that was collected by filtration. The compound was recrystallized by slow evaporation from ethanol, yielding single crystals suitable for X-ray diffraction studies.

Computing details top

Data collection: SMART (Bruker, 1998); cell refinement: SAINT-Plus (Bruker, 1998); data reduction: SAINT-Plus (Bruker, 1998); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012) and CAMERON (Watkin et al., 1996); software used to prepare material for publication: WinGX (Farrugia, 2012).

Figures top

	Fig. 1. The molecular structure of the title compound with displacement ellipsoids drawn at the 50% probability level. H atoms are presented as small spheres of arbitrary radius.
	Fig. 2. Unit cell packing of the title compound showing intermolecular C—H···O interactions with dotted lines. H-atoms not involved in hydrogen bonding have been excluded.
	Fig. 3. Unit cell packing depicting C—H···π interactions with dotted lines.

Ethyl 5-acetyl-2-{[(dimethylamino)methylidene]amino}-4-methylthiophene-3-carboxylate top

Crystal data top

C₁₃H₁₈N₂O₃S	F(000) = 1200
M_r = 282.35	D_x = 1.354 Mg m⁻³
Orthorhombic, Pbca	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ac 2ab	Cell parameters from 3012 reflections
a = 12.218 (3) Å	θ = 2.1–27.0°
b = 7.332 (2) Å	µ = 0.24 mm⁻¹
c = 30.923 (8) Å	T = 100 K
V = 2769.9 (13) Å³	Block, colorless
Z = 8	0.29 × 0.26 × 0.10 mm

Data collection top

Bruker SMART APEX CCD diffractometer	3012 independent reflections
Radiation source: fine-focus sealed tube	2140 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.076
ω scans	θ_max = 27.0°, θ_min = 2.1°
Absorption correction: multi-scan (SADABS; Bruker, 1998)	h = −14→15
T_min = 0.958, T_max = 0.963	k = −9→9
15478 measured reflections	l = −39→35

Refinement top

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)] = 0.058	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.173	H-atom parameters constrained
S = 1.19	w = 1/[σ²(F_o²) + (0.0811P)² + 0.3374P] where P = (F_o² + 2F_c²)/3
3012 reflections	(Δ/σ)_max < 0.001
177 parameters	Δρ_max = 0.52 e Å⁻³
0 restraints	Δρ_min = −0.33 e Å⁻³

Crystal data top

C₁₃H₁₈N₂O₃S	V = 2769.9 (13) Å³
M_r = 282.35	Z = 8
Orthorhombic, Pbca	Mo Kα radiation
a = 12.218 (3) Å	µ = 0.24 mm⁻¹
b = 7.332 (2) Å	T = 100 K
c = 30.923 (8) Å	0.29 × 0.26 × 0.10 mm

Data collection top

Bruker SMART APEX CCD diffractometer	3012 independent reflections
Absorption correction: multi-scan (SADABS; Bruker, 1998)	2140 reflections with I > 2σ(I)
T_min = 0.958, T_max = 0.963	R_int = 0.076
15478 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.058	0 restraints
wR(F²) = 0.173	H-atom parameters constrained
S = 1.19	Δρ_max = 0.52 e Å⁻³
3012 reflections	Δρ_min = −0.33 e Å⁻³
177 parameters

Special details top

Geometry. All s.u.'s (except the s.u. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell s.u.'s are taken into account individually in the estimation of s.u.'s in distances, angles and torsion angles; correlations between s.u.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell s.u.'s is used for estimating s.u.'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 > 2σ(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) top

	x	y	z	U_iso*/U_eq
C1	0.8067 (2)	0.2414 (4)	0.37436 (9)	0.0219 (6)
H1A	0.8527	0.3124	0.3942	0.033*
H1B	0.7973	0.3089	0.3473	0.033*
H1C	0.8419	0.1240	0.3684	0.033*
C2	0.5031 (2)	0.1973 (4)	0.39447 (9)	0.0194 (6)
C3	0.5979 (2)	0.2312 (4)	0.37104 (9)	0.0193 (6)
C4	0.6967 (2)	0.2091 (4)	0.39477 (9)	0.0196 (6)
C5	0.6764 (2)	0.1574 (4)	0.43709 (9)	0.0190 (6)
C6	0.7476 (2)	0.1108 (4)	0.47350 (9)	0.0211 (6)
C7	0.8697 (2)	0.1198 (4)	0.46853 (9)	0.0252 (7)
H7A	0.9048	0.0694	0.4944	0.038*
H7B	0.8923	0.2471	0.4648	0.038*
H7C	0.8919	0.0488	0.4431	0.038*
C8	0.5956 (2)	0.2660 (4)	0.32370 (9)	0.0203 (6)
C9	0.5315 (2)	0.4612 (4)	0.26762 (9)	0.0251 (7)
H9A	0.4661	0.5384	0.2628	0.030*
H9B	0.5215	0.3467	0.2511	0.030*
C10	0.6313 (2)	0.5590 (5)	0.25110 (10)	0.0321 (7)
H10A	0.6411	0.6730	0.2672	0.048*
H10B	0.6219	0.5864	0.2203	0.048*
H10C	0.6958	0.4814	0.2550	0.048*
C11	0.3149 (2)	0.1822 (4)	0.40202 (9)	0.0216 (6)
H11	0.3262	0.1544	0.4317	0.026*
C13	0.1194 (2)	0.1650 (4)	0.41533 (10)	0.0287 (7)
H13A	0.1452	0.1305	0.4442	0.043*
H13B	0.0736	0.0673	0.4035	0.043*
H13C	0.0765	0.2776	0.4173	0.043*
C12	0.1888 (2)	0.2409 (5)	0.34251 (10)	0.0323 (8)
H12A	0.2567	0.2747	0.3277	0.048*
H12B	0.1377	0.3439	0.3418	0.048*
H12C	0.1558	0.1356	0.3280	0.048*
N1	0.40009 (18)	0.2074 (3)	0.37699 (7)	0.0216 (5)
N2	0.21291 (18)	0.1943 (3)	0.38709 (7)	0.0218 (5)
O1	0.70690 (16)	0.0608 (3)	0.50809 (6)	0.0285 (5)
O2	0.63937 (18)	0.1686 (3)	0.29724 (6)	0.0308 (5)
O3	0.54047 (16)	0.4187 (3)	0.31356 (6)	0.0244 (5)
S1	0.53616 (5)	0.13387 (10)	0.44751 (2)	0.0202 (2)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
C1	0.0151 (15)	0.0206 (15)	0.0301 (16)	−0.0008 (11)	0.0015 (11)	−0.0017 (12)
C2	0.0147 (14)	0.0169 (14)	0.0267 (15)	0.0005 (11)	−0.0003 (11)	−0.0026 (11)
C3	0.0166 (15)	0.0142 (14)	0.0270 (15)	0.0008 (10)	0.0002 (11)	−0.0016 (11)
C4	0.0154 (15)	0.0127 (14)	0.0308 (15)	−0.0002 (10)	−0.0009 (11)	−0.0039 (11)
C5	0.0125 (14)	0.0223 (15)	0.0220 (14)	0.0018 (11)	0.0012 (11)	−0.0017 (11)
C6	0.0176 (15)	0.0189 (15)	0.0268 (15)	0.0001 (11)	−0.0015 (12)	−0.0001 (11)
C7	0.0170 (15)	0.0281 (16)	0.0304 (16)	−0.0015 (12)	−0.0037 (12)	0.0031 (12)
C8	0.0133 (14)	0.0197 (15)	0.0278 (16)	−0.0041 (11)	−0.0025 (12)	−0.0015 (12)
C9	0.0231 (16)	0.0261 (16)	0.0262 (15)	−0.0016 (12)	−0.0041 (12)	0.0043 (12)
C10	0.0262 (17)	0.0424 (19)	0.0276 (16)	−0.0008 (14)	−0.0002 (14)	0.0053 (14)
C11	0.0165 (15)	0.0236 (15)	0.0248 (15)	0.0010 (11)	−0.0026 (12)	0.0007 (12)
C13	0.0131 (15)	0.0363 (18)	0.0368 (18)	−0.0005 (12)	0.0015 (13)	0.0009 (14)
C12	0.0196 (16)	0.043 (2)	0.0341 (18)	0.0057 (13)	−0.0040 (13)	−0.0024 (15)
N1	0.0140 (13)	0.0235 (13)	0.0275 (13)	0.0013 (10)	−0.0003 (10)	0.0009 (10)
N2	0.0130 (12)	0.0285 (14)	0.0240 (12)	0.0006 (10)	0.0000 (10)	0.0005 (10)
O1	0.0216 (11)	0.0385 (13)	0.0254 (11)	−0.0008 (9)	−0.0010 (9)	0.0059 (9)
O2	0.0307 (12)	0.0372 (13)	0.0245 (11)	0.0088 (10)	−0.0012 (9)	−0.0060 (9)
O3	0.0225 (11)	0.0257 (11)	0.0251 (11)	0.0029 (8)	0.0001 (8)	0.0028 (9)
S1	0.0121 (4)	0.0250 (4)	0.0237 (4)	−0.0003 (3)	0.0004 (3)	0.0017 (3)

Geometric parameters (Å, º) top

C1—C4	1.504 (4)	C9—O3	1.458 (3)
C1—H1A	0.9800	C9—C10	1.504 (4)
C1—H1B	0.9800	C9—H9A	0.9900
C1—H1C	0.9800	C9—H9B	0.9900
C2—N1	1.372 (3)	C10—H10A	0.9800
C2—C3	1.388 (4)	C10—H10B	0.9800
C2—S1	1.752 (3)	C10—H10C	0.9800
C3—C4	1.422 (4)	C11—N1	1.310 (3)
C3—C8	1.486 (4)	C11—N2	1.332 (3)
C4—C5	1.385 (4)	C11—H11	0.9500
C5—C6	1.464 (4)	C13—N2	1.454 (4)
C5—S1	1.752 (3)	C13—H13A	0.9800
C6—O1	1.235 (3)	C13—H13B	0.9800
C6—C7	1.501 (4)	C13—H13C	0.9800
C7—H7A	0.9800	C12—N2	1.450 (4)
C7—H7B	0.9800	C12—H12A	0.9800
C7—H7C	0.9800	C12—H12B	0.9800
C8—O2	1.210 (3)	C12—H12C	0.9800
C8—O3	1.343 (3)

C4—C1—H1A	109.5	C10—C9—H9A	109.2
C4—C1—H1B	109.5	O3—C9—H9B	109.2
H1A—C1—H1B	109.5	C10—C9—H9B	109.2
C4—C1—H1C	109.5	H9A—C9—H9B	107.9
H1A—C1—H1C	109.5	C9—C10—H10A	109.5
H1B—C1—H1C	109.5	C9—C10—H10B	109.5
N1—C2—C3	123.4 (3)	H10A—C10—H10B	109.5
N1—C2—S1	126.5 (2)	C9—C10—H10C	109.5
C3—C2—S1	110.1 (2)	H10A—C10—H10C	109.5
C2—C3—C4	114.7 (3)	H10B—C10—H10C	109.5
C2—C3—C8	122.0 (2)	N1—C11—N2	121.9 (3)
C4—C3—C8	122.9 (2)	N1—C11—H11	119.0
C5—C4—C3	111.5 (2)	N2—C11—H11	119.0
C5—C4—C1	126.8 (2)	N2—C13—H13A	109.5
C3—C4—C1	121.6 (3)	N2—C13—H13B	109.5
C4—C5—C6	133.2 (3)	H13A—C13—H13B	109.5
C4—C5—S1	112.1 (2)	N2—C13—H13C	109.5
C6—C5—S1	114.7 (2)	H13A—C13—H13C	109.5
O1—C6—C5	119.7 (3)	H13B—C13—H13C	109.5
O1—C6—C7	120.2 (2)	N2—C12—H12A	109.5
C5—C6—C7	120.1 (2)	N2—C12—H12B	109.5
C6—C7—H7A	109.5	H12A—C12—H12B	109.5
C6—C7—H7B	109.5	N2—C12—H12C	109.5
H7A—C7—H7B	109.5	H12A—C12—H12C	109.5
C6—C7—H7C	109.5	H12B—C12—H12C	109.5
H7A—C7—H7C	109.5	C11—N1—C2	119.2 (2)
H7B—C7—H7C	109.5	C11—N2—C12	122.3 (2)
O2—C8—O3	123.7 (3)	C11—N2—C13	121.1 (2)
O2—C8—C3	123.8 (3)	C12—N2—C13	116.5 (2)
O3—C8—C3	112.5 (2)	C8—O3—C9	116.3 (2)
O3—C9—C10	111.8 (2)	C2—S1—C5	91.56 (13)
O3—C9—H9A	109.2

N1—C2—C3—C4	−178.5 (2)	C2—C3—C8—O2	−117.1 (3)
S1—C2—C3—C4	−0.6 (3)	C4—C3—C8—O2	55.5 (4)
N1—C2—C3—C8	−5.4 (4)	C2—C3—C8—O3	63.5 (3)
S1—C2—C3—C8	172.5 (2)	C4—C3—C8—O3	−124.0 (3)
C2—C3—C4—C5	0.0 (3)	N2—C11—N1—C2	178.5 (2)
C8—C3—C4—C5	−173.0 (2)	C3—C2—N1—C11	−176.6 (3)
C2—C3—C4—C1	−179.7 (2)	S1—C2—N1—C11	5.8 (4)
C8—C3—C4—C1	7.3 (4)	N1—C11—N2—C12	−1.7 (4)
C3—C4—C5—C6	177.1 (3)	N1—C11—N2—C13	179.7 (3)
C1—C4—C5—C6	−3.2 (5)	O2—C8—O3—C9	2.1 (4)
C3—C4—C5—S1	0.6 (3)	C3—C8—O3—C9	−178.4 (2)
C1—C4—C5—S1	−179.8 (2)	C10—C9—O3—C8	−83.4 (3)
C4—C5—C6—O1	−176.9 (3)	N1—C2—S1—C5	178.6 (2)
S1—C5—C6—O1	−0.4 (3)	C3—C2—S1—C5	0.7 (2)
C4—C5—C6—C7	1.8 (5)	C4—C5—S1—C2	−0.8 (2)
S1—C5—C6—C7	178.2 (2)	C6—C5—S1—C2	−178.0 (2)

Hydrogen-bond geometry (Å, º) top

Cg is the centroid of the C2/C3/C4/C5/S1 ring .

D—H···A	D—H	H···A	D···A	D—H···A
C9—H9A···O2ⁱ	0.99	2.45	3.270 (3)	139
C11—H11···O1ⁱⁱ	0.95	2.47	3.312 (4)	147
C7—H7C···Cgⁱⁱⁱ	0.98	2.86	3.693 (2)	143

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

Hydrogen-bond geometry (Å, º) top

Cg is the centroid of the C2/C3/C4/C5/S1 ring .

D—H···A	D—H	H···A	D···A	D—H···A
C9—H9A···O2ⁱ	0.99	2.45	3.270 (3)	139
C11—H11···O1ⁱⁱ	0.95	2.47	3.312 (4)	147
C7—H7C···Cgⁱⁱⁱ	0.98	2.86	3.693 (2)	143

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

Acknowledgements

NLP thanks the University Grants Commission (UGC), India for a CSIR–NET fellowship and MSK thanks the UGC for a UGC–BSR Meritorious fellowship.

References

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Volume 71| Part 10| October 2015| Pages o762-o763

doi:10.1107/S2056989015016217

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

Crystal structure of ethyl 5-acetyl-2-{[(di­methyl­amino)­methyl­­idene]amino}-4-methyl­thio­phene-3-carboxyl­ate

1. Related literature

2. Experimental

2.1. Crystal data

2.2. Data collection

2.3. Refinement

Supporting information

Acknowledgements

References

organic compounds

Crystal structure of ethyl 5-acetyl-2-{[(dimethylamino)methylidene]amino}-4-methylthiophene-3-carboxylate