Crystal structure of (E)-N-phenyl-N′-[1-(thio­phen-2-yl)ethyl­idene]formo­hydrazide

In the title compound, C₁₃H₁₂N₂OS, the planes of the thio­phene and phenyl rings are nearly perpendicular to each other, making a dihedral angle of 86.42 (12)°. In the crystal, mol­ecules are linked by C—H...O hydrogen bonds, forming a helical chain along the b-axis direction.

Key indicators

• Single-crystal X-ray study
• T = 296 K
• Mean [sigma](C-C) = 0.003 Å
• R factor = 0.038
• wR factor = 0.102
• Data-to-parameter ratio = 12.2

checkCIF/PLATON results

No syntax errors found



Alert level C
THETM01_ALERT_3_C  The value of sine(theta_max)/wavelength is less than 0.590
            Calculated sin(theta_max)/wavelength =    0.5860
PLAT029_ALERT_3_C _diffrn_measured_fraction_theta_full Low .......      0.973 Note
PLAT089_ALERT_3_C Poor Data / Parameter Ratio (Zmax < 18) ........       7.30 Note
PLAT911_ALERT_3_C Missing # FCF Refl Between THmin & STh/L=  0.586         33 Why ?
PLAT913_ALERT_3_C Missing # of Very Strong Reflections in FCF ....          1 Note

Alert level G
PLAT005_ALERT_5_G No _iucr_refine_instructions_details  in the CIF     Please Do !
PLAT909_ALERT_3_G Percentage of Observed Data at Theta(Max) still          92 %

   0 ALERT level A = Most likely a serious problem - resolve or explain
   0 ALERT level B = A potentially serious problem, consider carefully
   5 ALERT level C = Check. Ensure it is not caused by an omission or oversight
   2 ALERT level G = General information/check it is not something unexpected

   0 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   0 ALERT type 2 Indicator that the structure model may be wrong or deficient
   6 ALERT type 3 Indicator that the structure quality may be low
   0 ALERT type 4 Improvement, methodology, query or suggestion
   1 ALERT type 5 Informative message, check

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S1. Comment

In medicinal chemistry, thiophene derivatives have been very well known for their therapeutic applications. Many thiophene derivatives have been developed as chemotherapeutic agents and are extensively used. Thiophene nucleus is one of the most important heterocycles exhibiting remarkable pharmacological activities. The great interest in the synthesis of thiophene derivatives due to their diverse biological and chemical properties. Thiophene, as a prominent structural motif, is found in numerous active compounds, which contain 5-membered heterocyclic structure have attracted a lot of interests in many fields, and its rich biological activity in medicinal chemistry owing to their biological properties. Thiophene and thiazole derivatives are known to possess interesting biological properties like anticancer (Bondock et al., 2010; Bellina et al., 2007; Konstantinova et al., 2009). Thiophene or benzothiophene moieties due to the well documented anti-cancer activity of these moieties to study their SAR and their anti-breast cancer activity (Al-Said et al., 2011). In view of their importance as discussed above, thiophene derivatives were taken for their conformational studies to get better structural activity correlation.

In the title compound (Fig. 1), the bond lengths do not show much variation in the core structure of the derivatives, and are similar to the standard values (Allen et al., 2002). The thiophene (S1/C1–C4) and phenyl (C8–C13) rings are nearly perpendicular with a dihedral angle of 86.42 (12)° between their mean planes. The bond lengths and bond angles do not show large deviations and are comparable with those reported for a similar structure (Shan et al., 2011). The conformation of the attachment of the thiophene and phenyl rings can also be characterized by torsion angles of (C4—C5—N1—N2), (C5—N1—N2—C8), (O1—C7—N2—C8) and (S1—C4—C5—C6) being 178.38, 127.73, 171.34 and -170.31°, respectively. The crystal structure has an intermolecular C—H···O hydrogen bond. The molecular packing viewed down the a axis is shown in Fig. 2.

Related literature

For the biological activity of thiophene derivatives, see: Bondock et al. (2010); Bellina et al. (2007); Konstantinova et al. (2009); Al-Said et al. (2011). For the crystal structure of a similar compound, viz. (E)-N'-[1-(thiophen-2-yl)ethylidene]benzohydrazide, see: Shan et al. (2011). For a description of the Cambridge Structural Database, see: Allen (2002).

S2. Experimental

A mixture of (E)-1-phenyl-2-[(1-thiophen-2-yl)ethylidene]hydrazine (0.176 mmol) were added to the Vilsmeier-Haack reagent prepared by drop-wise addition of POCl₃ (1.2 ml) in ice cooled DMF (5 ml). The mixture was stirred at 60–65 °C for 6 h. The progress of the reaction was monitored by TLC. After completion of the reaction, the mixture was poured into ice cold water, neutralized with NaHCO₃, the solid separated was filtered, washed with water and recrystallized from ethanol to get the compound in 93% yield.

S3. Refinement

All H atoms were located from difference maps and were positioned geometrically and refined using a riding model with C—H = 0.93–0.96 Å and U_iso(H) = 1.2U_eq(C).

Computing details

Data collection: APEX2 (Bruker, 2013); cell refinement: SAINT (Bruker, 2013); data reduction: SAINT (Bruker, 2013); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: Mercury (Macrae et al., 2006); software used to prepare material for publication: PLATON (Spek, 2009).

Figures

	Fig. 1. ORTEP view of the molecule with the atom-labeling scheme. The displacement ellipsoids are drawn at the 50% probability level.
	Fig. 2. A molecular packing view of the title compound down the a-axis.

(E)-N-Phenyl-N'-[1-(thiophen-2-yl)ethylidene]formohydrazide.

Crystal data

C13H12N2OS	F(000) = 512
Mr = 244.32	Dx = 1.324 Mg m^−3
Orthorhombic, P212121	Cu Kα radiation, λ = 1.54178 Å
Hall symbol: P 2ac 2ab	Cell parameters from 6298 reflections
a = 5.4960 (7) Å	θ = 4.4–64.6°
b = 11.0177 (13) Å	µ = 2.22 mm^−1
c = 20.249 (2) Å	T = 296 K
V = 1226.1 (2) Å^3	Block, pale yellow
Z = 4	0.25 × 0.22 × 0.20 mm

Data collection

Bruker X8 Proteum diffractometer	2010 independent reflections
Radiation source: Bruker MicroStar microfocus rotating anode	1904 reflections with I > 2σ(I)
Helios multilayer optics monochromator	Rint = 0.042
Detector resolution: 10.7 pixels mm^-1	θmax = 64.6°, θmin = 4.4°
ϕ and ω scans	h = −2→6
Absorption correction: multi-scan (SADABS; Bruker, 2013)	k = −12→12
Tmin = 0.604, Tmax = 0.662	l = −23→22
6298 measured reflections

Refinement

Refinement on F^2	Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: full	H-atom parameters constrained
R[F^2 > 2σ(F^2)] = 0.038	w = 1/[σ^2(Fo^2) + (0.0605P)^2 + 0.0861P] where P = (Fo^2 + 2Fc^2)/3
wR(F^2) = 0.102	(Δ/σ)max = 0.001
S = 1.10	Δρmax = 0.21 e Å^−3
2010 reflections	Δρmin = −0.20 e Å^−3
165 parameters	Extinction correction: SHELXL, FC^*=KFC[1+0.001XFC^2Λ^3/SIN(2Θ)]^-1/4
0 restraints	Extinction coefficient: 0.0158 (16)
Primary atom site location: structure-invariant direct methods	Absolute structure: Flack (1983), 805 Friedel pairs
Secondary atom site location: difference Fourier map	Absolute structure parameter: 0.02 (2)

Special details

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 e.s.d.'s 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 > σ(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 (Ų)

	x	y	z	Uiso*/Ueq
S1	0.05502 (12)	0.12455 (6)	0.72104 (3)	0.0539 (2)
O1	0.0434 (4)	−0.24121 (15)	0.55887 (8)	0.0526 (6)
N1	0.0078 (3)	0.00557 (16)	0.59394 (8)	0.0348 (5)
N2	0.0086 (3)	−0.04249 (15)	0.52882 (8)	0.0344 (5)
C1	−0.0682 (6)	0.1399 (3)	0.79702 (12)	0.0623 (10)
C2	−0.2635 (6)	0.0712 (3)	0.80591 (13)	0.0648 (10)
C3	−0.3227 (5)	0.0016 (2)	0.74907 (11)	0.0513 (8)
C4	−0.1639 (4)	0.02325 (18)	0.69777 (10)	0.0358 (6)
C5	−0.1724 (4)	−0.02503 (18)	0.63061 (10)	0.0331 (6)
C6	−0.3905 (4)	−0.0972 (2)	0.61062 (13)	0.0509 (8)
C7	0.0373 (4)	−0.16179 (19)	0.51733 (10)	0.0410 (7)
C8	0.0373 (4)	0.04484 (17)	0.47710 (9)	0.0325 (6)
C9	0.2273 (4)	0.0366 (2)	0.43330 (11)	0.0397 (6)
C10	0.2429 (4)	0.1192 (2)	0.38203 (12)	0.0479 (7)
C11	0.0710 (5)	0.2091 (2)	0.37516 (11)	0.0469 (7)
C12	−0.1151 (5)	0.2185 (2)	0.41975 (12)	0.0463 (8)
C13	−0.1322 (4)	0.1365 (2)	0.47156 (11)	0.0413 (6)
H1	−0.00560	0.19130	0.82930	0.0750*
H2	−0.35200	0.06880	0.84500	0.0780*
H3	−0.45300	−0.05220	0.74680	0.0620*
H6A	−0.39060	−0.10770	0.56360	0.0760*
H6B	−0.53550	−0.05510	0.62380	0.0760*
H6C	−0.38540	−0.17530	0.63170	0.0760*
H7	0.05420	−0.18570	0.47350	0.0490*
H9	0.34410	−0.02390	0.43800	0.0480*
H10	0.37060	0.11400	0.35200	0.0570*
H11	0.08130	0.26340	0.34010	0.0560*
H12	−0.23010	0.27990	0.41530	0.0560*
H13	−0.25720	0.14340	0.50230	0.0500*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
S1	0.0546 (4)	0.0703 (5)	0.0368 (3)	−0.0147 (3)	−0.0029 (3)	−0.0071 (3)
O1	0.0729 (11)	0.0375 (9)	0.0474 (9)	0.0049 (8)	0.0049 (8)	0.0096 (7)
N1	0.0402 (10)	0.0379 (9)	0.0263 (8)	−0.0024 (8)	−0.0012 (7)	−0.0037 (6)
N2	0.0452 (10)	0.0313 (8)	0.0266 (8)	0.0006 (8)	−0.0005 (7)	−0.0022 (7)
C1	0.085 (2)	0.0689 (17)	0.0330 (12)	0.0037 (16)	−0.0059 (13)	−0.0095 (11)
C2	0.0757 (18)	0.0819 (19)	0.0368 (13)	0.0055 (16)	0.0152 (13)	0.0000 (13)
C3	0.0524 (14)	0.0590 (15)	0.0426 (13)	−0.0041 (12)	0.0127 (11)	−0.0022 (11)
C4	0.0373 (10)	0.0370 (11)	0.0332 (10)	0.0038 (9)	0.0009 (8)	0.0026 (8)
C5	0.0317 (10)	0.0314 (10)	0.0362 (11)	0.0037 (8)	−0.0030 (8)	0.0008 (8)
C6	0.0372 (12)	0.0564 (15)	0.0592 (14)	−0.0111 (10)	0.0008 (11)	−0.0119 (12)
C7	0.0511 (12)	0.0353 (11)	0.0366 (11)	0.0020 (9)	0.0024 (10)	−0.0018 (9)
C8	0.0388 (10)	0.0296 (10)	0.0291 (9)	−0.0017 (8)	−0.0051 (8)	−0.0012 (8)
C9	0.0355 (10)	0.0392 (11)	0.0444 (12)	0.0049 (9)	0.0011 (9)	0.0016 (10)
C10	0.0456 (12)	0.0511 (13)	0.0469 (13)	−0.0056 (11)	0.0089 (10)	0.0094 (11)
C11	0.0604 (14)	0.0365 (11)	0.0439 (12)	−0.0080 (11)	−0.0054 (11)	0.0088 (9)
C12	0.0536 (14)	0.0350 (12)	0.0503 (13)	0.0084 (11)	−0.0087 (11)	0.0024 (10)
C13	0.0429 (11)	0.0416 (11)	0.0395 (11)	0.0083 (10)	0.0012 (10)	−0.0035 (10)

Geometric parameters (Å, º)

S1—C1	1.690 (3)	C10—C11	1.376 (3)
S1—C4	1.707 (2)	C11—C12	1.368 (4)
O1—C7	1.214 (3)	C12—C13	1.388 (3)
N1—N2	1.421 (2)	C1—H1	0.9300
N1—C5	1.283 (3)	C2—H2	0.9300
N2—C7	1.344 (3)	C3—H3	0.9300
N2—C8	1.431 (2)	C6—H6A	0.9600
C1—C2	1.326 (5)	C6—H6B	0.9600
C2—C3	1.421 (4)	C6—H6C	0.9600
C3—C4	1.378 (3)	C7—H7	0.9300
C4—C5	1.461 (3)	C9—H9	0.9300
C5—C6	1.494 (3)	C10—H10	0.9300
C8—C9	1.373 (3)	C11—H11	0.9300
C8—C13	1.379 (3)	C12—H12	0.9300
C9—C10	1.383 (3)	C13—H13	0.9300
C1—S1—C4	91.96 (13)	C2—C1—H1	123.00
N2—N1—C5	116.20 (17)	C1—C2—H2	124.00
N1—N2—C7	121.70 (16)	C3—C2—H2	124.00
N1—N2—C8	115.40 (15)	C2—C3—H3	124.00
C7—N2—C8	121.19 (16)	C4—C3—H3	124.00
S1—C1—C2	113.0 (2)	C5—C6—H6A	109.00
C1—C2—C3	112.6 (2)	C5—C6—H6B	109.00
C2—C3—C4	111.9 (2)	C5—C6—H6C	109.00
S1—C4—C3	110.58 (16)	H6A—C6—H6B	109.00
S1—C4—C5	121.16 (16)	H6A—C6—H6C	109.00
C3—C4—C5	128.2 (2)	H6B—C6—H6C	109.00
N1—C5—C4	114.73 (19)	O1—C7—H7	117.00
N1—C5—C6	127.04 (19)	N2—C7—H7	117.00
C4—C5—C6	118.13 (19)	C8—C9—H9	120.00
O1—C7—N2	126.02 (19)	C10—C9—H9	120.00
N2—C8—C9	120.81 (18)	C9—C10—H10	120.00
N2—C8—C13	118.53 (18)	C11—C10—H10	120.00
C9—C8—C13	120.65 (19)	C10—C11—H11	120.00
C8—C9—C10	119.2 (2)	C12—C11—H11	120.00
C9—C10—C11	120.5 (2)	C11—C12—H12	120.00
C10—C11—C12	120.1 (2)	C13—C12—H12	120.00
C11—C12—C13	120.0 (2)	C8—C13—H13	120.00
C8—C13—C12	119.5 (2)	C12—C13—H13	120.00
S1—C1—H1	124.00
C4—S1—C1—C2	0.9 (3)	C2—C3—C4—C5	−176.1 (2)
C1—S1—C4—C3	−1.3 (2)	C2—C3—C4—S1	1.4 (3)
C1—S1—C4—C5	176.4 (2)	S1—C4—C5—N1	6.3 (3)
C5—N1—N2—C7	−67.0 (2)	C3—C4—C5—N1	−176.4 (2)
C5—N1—N2—C8	127.7 (2)	C3—C4—C5—C6	7.0 (3)
N2—N1—C5—C4	178.38 (16)	S1—C4—C5—C6	−170.31 (16)
N2—N1—C5—C6	−5.3 (3)	N2—C8—C9—C10	176.94 (19)
C7—N2—C8—C13	135.3 (2)	C13—C8—C9—C10	−2.1 (3)
N1—N2—C7—O1	6.9 (3)	N2—C8—C13—C12	−176.7 (2)
C8—N2—C7—O1	171.3 (2)	C9—C8—C13—C12	2.3 (3)
N1—N2—C8—C9	121.6 (2)	C8—C9—C10—C11	0.4 (3)
C7—N2—C8—C9	−43.7 (3)	C9—C10—C11—C12	1.0 (4)
N1—N2—C8—C13	−59.4 (2)	C10—C11—C12—C13	−0.7 (4)
S1—C1—C2—C3	−0.3 (4)	C11—C12—C13—C8	−0.9 (3)
C1—C2—C3—C4	−0.7 (4)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
C1—H1···O1^i	0.93	2.39	3.202 (3)	145

Symmetry code: (i) −x, y+1/2, −z+3/2.