(E)-3-Chloro-N′-(2-fluoro­benzyl­idene)thio­phene-2-carbohydrazide

Abstract

The title compound, C₁₂H₈ClFN₂OS, is a hydrazide derivative adopting an E conformation with an azomethine N=C double bond length of 1.272 (2) Å. The mol­ecular skeleton is approximately planar; the terminal five- and six-membered rings form a dihedral angle of 5.47 (9)°. In the crystal, mol­ecules are linked by N—H⋯O and C—H⋯O hydrogen bonds into zigzag chains propagating in [100].

Related literature  

For the applications and biological activity of hydrazones, see: Taha et al. (2013 ▶); Musharraf et al. (2012 ▶); Melnyk et al. (2006 ▶); Terzioglu & Gursoy (2003 ▶). For the crystal structures of related compounds, see: Alanazi et al. (2012a ▶,b ▶).

Experimental  

Crystal data  

• C₁₂H₈ClFN₂OS

• M _r = 282.71

• Orthorhombic,

• a = 5.6833 (3) Å

• b = 13.0817 (6) Å

• c = 16.4001 (8) Å

• V = 1219.30 (10) ų

• Z = 4

• Mo Kα radiation

• μ = 0.48 mm⁻¹

• T = 302 K

• 0.55 × 0.46 × 0.03 mm

Data collection  

• Bruker SMART APEX CCD area-detector diffractometer

• Absorption correction: multi-scan (SADABS; Bruker, 2000 ▶) T _min = 0.776, T _max = 0.985

• 47474 measured reflections

• 2255 independent reflections

• 2210 reflections with I > 2σ(I)

• R _int = 0.028

Refinement  

• R[F ² > 2σ(F ²)] = 0.023

• wR(F ²) = 0.065

• S = 1.09

• 2255 reflections

• 168 parameters

• H atoms treated by a mixture of independent and constrained refinement

• Δρ_max = 0.15 e Å⁻³

• Δρ_min = −0.12 e Å⁻³

• Absolute structure: Flack (1983 ▶), 916 Friedel pairs

• Absolute structure parameter: 0.02 (5)

Data collection: SMART (Bruker, 2000 ▶); cell refinement: SAINT (Bruker, 2000 ▶); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and PLATON (Spek, 2009 ▶).

Supplementary Material

CCDC reference: 1003818

Additional supporting information: crystallographic information; 3D view; checkCIF report

Table 1. Hydrogen-bond geometry (Å, °).

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1A⋯O1i	0.86	2.12	2.9552 (18)	163
C7—H7A⋯O1i	0.93	2.41	3.2268 (19)	147

Symmetry code: (i) .

supplementary crystallographic information

S1. Comment

Hydrazone derivatives are known as good ligands for complexation reactions. They have also displayed a wide spectrum of biological activities including antileishamanial (Taha et al., 2013), antimalarial (Melnyk et al., 2006) and anti-cancer (Terzioglu et al., 2003) properties. Recently the hydrazones are reported to be used as UV-LDI Matrices for measuring the mass of macromolecules (Musharraf et al., 2012) .

The title compound, (I) (Fig. 1), is similar to that of previously reported N'-[(1E)-(2,6-difluorophenyl)methylidene]thiophene-2-carbohydrazide (Alanazi et al., 2012a) and N'-[(1E)-(4-fluorophenyl)methylidene]- thiophene-2-carbohydrazide (Alanazi et al., 2012b) except the thiophene ring is substituted with fluorine atom. The whole molecule is appearently planar with maximum deviation of 0.181 (1)Å for F1 atom from the least square plane. The chlorothiophenecarbonyl O1/C8/S1/(C9-C12)/Cl fragment is trans to the fluorobenzyl, F1/(C1-C7), group across the N1-N2 bond. The bond lengths and angles in (I) are normal and comparable to those in the analogs (Alanazi et al., 2012a,b). The crystal is stablized by N—H···O and C—H···O intermolecular hydrogen bonds (Table 1) to form zigzag chains of molecules extended along the a axis (Fig. 2).

S2. Experimental

The title compound (I) was synthesized by refluxing in methanol a mixture (0.352 g, 2 mmol) of 3-chlorothiophene- 2-carbohydrazide and (0.248 g, 2 mmol) of 2 florobenzaldehyde along with a catalytical amount of acetic acid for 3 h. The progress of reaction was monitored by TLC. After completion of reaction, the solvent was evaporated by vacuum to afford crude material which was purified by repeated recrystallized in methanol to obtain needle like crytals (0.495 g, ° yielded 88). All chemicals (methyl 3-chlorothiophene-2-carboxylate 99%,2-florobenzaldehyde 98%) were purchased from sigma Aldrich.

S3. Refinement

All H atoms except H12A were positioned geometrically (C—H = 0.93 Å and N—H 0.86 Å) and constrained to ride on their parent atoms with U_iso(H) = 1.2U_eq(C, N). Atom H12A attached to C12 was located on a Fourier map and isotropically refined.

Figures

Fig. 1.

The molecular structure of (I) with displacement ellipsoids drawn at the 50% probability level.

Fig. 2.

A portion of the crystal packing viewed down the a axis. Dashed lines denote hydrogen bonds.

Crystal data

C12H8ClFN2OS	F(000) = 576
Mr = 282.71	Dx = 1.540 Mg m−3
Orthorhombic, P212121	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2ab	Cell parameters from 9699 reflections
a = 5.6833 (3) Å	θ = 3.1–25.5°
b = 13.0817 (6) Å	µ = 0.48 mm−1
c = 16.4001 (8) Å	T = 302 K
V = 1219.30 (10) Å3	Slab, colourless
Z = 4	0.55 × 0.46 × 0.03 mm

Data collection

Bruker SMART APEX CCD area-detector diffractometer	2255 independent reflections
Radiation source: fine-focus sealed tube	2210 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.028
Detector resolution: 83.66 pixels mm-1	θmax = 25.5°, θmin = 3.1°
ω scan	h = −6→6
Absorption correction: multi-scan (SADABS; Bruker, 2000)	k = −15→15
Tmin = 0.776, Tmax = 0.985	l = −19→19
47474 measured reflections

Refinement

Refinement on F2	Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: full	H atoms treated by a mixture of independent and constrained refinement
R[F2 > 2σ(F2)] = 0.023	w = 1/[σ2(Fo2) + (0.0388P)2 + 0.1642P] where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.065	(Δ/σ)max < 0.001
S = 1.09	Δρmax = 0.15 e Å−3
2255 reflections	Δρmin = −0.12 e Å−3
168 parameters	Extinction correction: SHELXTL (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
0 restraints	Extinction coefficient: 0.021 (2)
Primary atom site location: structure-invariant direct methods	Absolute structure: Flack (1983), 916 Friedel pairs
Secondary atom site location: difference Fourier map	Absolute structure parameter: 0.02 (5)

Special details

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

	x	y	z	Uiso*/Ueq
S1	0.17368 (8)	0.52165 (3)	0.22226 (3)	0.05051 (13)
Cl1	−0.35177 (8)	0.75148 (4)	0.21939 (3)	0.06171 (15)
F1	0.9968 (2)	0.52634 (9)	−0.05506 (7)	0.0641 (3)
O1	−0.0135 (3)	0.75985 (10)	0.08685 (8)	0.0592 (3)
N1	0.2895 (2)	0.65589 (9)	0.06578 (7)	0.0424 (3)
H1A	0.3269	0.6912	0.0235	0.051*
N2	0.4234 (2)	0.57273 (10)	0.08483 (8)	0.0402 (3)
C1	0.7057 (3)	0.39194 (12)	0.10909 (10)	0.0498 (4)
H1B	0.5728	0.3967	0.1420	0.060*
C2	0.8577 (4)	0.31121 (13)	0.11894 (13)	0.0602 (5)
H2B	0.8273	0.2620	0.1584	0.072*
C3	1.0558 (4)	0.30280 (15)	0.07046 (15)	0.0652 (5)
H3A	1.1577	0.2479	0.0776	0.078*
C4	1.1029 (3)	0.37504 (14)	0.01183 (13)	0.0618 (5)
H4A	1.2357	0.3698	−0.0210	0.074*
C5	0.9492 (3)	0.45490 (13)	0.00305 (10)	0.0484 (4)
C6	0.7486 (3)	0.46727 (12)	0.04998 (9)	0.0428 (3)
C7	0.5958 (3)	0.55497 (12)	0.03748 (9)	0.0430 (4)
H7A	0.6247	0.5989	−0.0059	0.052*
C8	0.1010 (3)	0.68555 (11)	0.11008 (9)	0.0396 (3)
C9	0.0325 (3)	0.62923 (11)	0.18418 (9)	0.0392 (3)
C10	−0.1608 (3)	0.65037 (12)	0.23145 (10)	0.0459 (3)
C11	−0.1957 (4)	0.58121 (15)	0.29608 (10)	0.0599 (5)
H11A	−0.3197	0.5852	0.3330	0.072*
C12	−0.0282 (4)	0.50870 (17)	0.29804 (12)	0.0654 (5)
H12A	−0.005 (5)	0.4586 (17)	0.3352 (16)	0.086 (7)*

Atomic displacement parameters (Ų)

	U11	U22	U33	U12	U13	U23
S1	0.0573 (2)	0.0498 (2)	0.0445 (2)	0.00003 (18)	−0.00151 (19)	0.01644 (17)
Cl1	0.0550 (2)	0.0632 (3)	0.0670 (3)	0.0061 (2)	0.0052 (2)	−0.0115 (2)
F1	0.0649 (6)	0.0732 (7)	0.0542 (6)	−0.0086 (6)	0.0104 (5)	−0.0038 (5)
O1	0.0655 (8)	0.0571 (7)	0.0551 (7)	0.0185 (6)	0.0050 (6)	0.0202 (6)
N1	0.0472 (7)	0.0429 (6)	0.0370 (6)	0.0018 (6)	0.0005 (6)	0.0104 (5)
N2	0.0439 (7)	0.0378 (6)	0.0389 (6)	−0.0010 (5)	−0.0040 (5)	0.0050 (5)
C1	0.0503 (9)	0.0459 (8)	0.0533 (9)	0.0002 (7)	−0.0053 (8)	0.0012 (7)
C2	0.0631 (11)	0.0470 (9)	0.0706 (11)	0.0036 (8)	−0.0161 (10)	0.0002 (8)
C3	0.0560 (11)	0.0507 (10)	0.0889 (15)	0.0117 (8)	−0.0153 (11)	−0.0148 (10)
C4	0.0455 (10)	0.0655 (11)	0.0746 (12)	0.0037 (8)	−0.0020 (9)	−0.0256 (10)
C5	0.0493 (9)	0.0503 (9)	0.0457 (8)	−0.0072 (7)	−0.0041 (7)	−0.0125 (7)
C6	0.0420 (8)	0.0443 (8)	0.0421 (7)	−0.0034 (6)	−0.0059 (6)	−0.0059 (6)
C7	0.0474 (8)	0.0436 (8)	0.0380 (7)	−0.0045 (6)	−0.0026 (6)	0.0026 (6)
C8	0.0437 (8)	0.0395 (7)	0.0355 (7)	−0.0019 (6)	−0.0057 (6)	0.0051 (6)
C9	0.0430 (8)	0.0401 (7)	0.0345 (7)	−0.0050 (6)	−0.0064 (6)	0.0026 (6)
C10	0.0476 (8)	0.0497 (8)	0.0406 (8)	−0.0089 (7)	−0.0018 (7)	−0.0049 (6)
C11	0.0673 (11)	0.0673 (11)	0.0452 (9)	−0.0139 (10)	0.0113 (8)	0.0027 (8)
C12	0.0806 (14)	0.0708 (12)	0.0447 (9)	−0.0108 (11)	0.0056 (9)	0.0191 (9)

Geometric parameters (Å, º)

S1—C12	1.700 (2)	C3—C4	1.375 (3)
S1—C9	1.7362 (15)	C3—H3A	0.9300
Cl1—C10	1.7224 (18)	C4—C5	1.369 (3)
F1—C5	1.362 (2)	C4—H4A	0.9300
O1—C8	1.2304 (19)	C5—C6	1.385 (2)
N1—C8	1.351 (2)	C6—C7	1.453 (2)
N1—N2	1.3639 (17)	C7—H7A	0.9300
N1—H1A	0.8600	C8—C9	1.474 (2)
N2—C7	1.272 (2)	C9—C10	1.373 (2)
C1—C2	1.374 (2)	C10—C11	1.408 (2)
C1—C6	1.404 (2)	C11—C12	1.344 (3)
C1—H1B	0.9300	C11—H11A	0.9300
C2—C3	1.382 (3)	C12—H12A	0.90 (2)
C2—H2B	0.9300
C12—S1—C9	91.82 (10)	C5—C6—C7	120.37 (15)
C8—N1—N2	123.24 (12)	C1—C6—C7	123.21 (15)
C8—N1—H1A	118.4	N2—C7—C6	121.23 (14)
N2—N1—H1A	118.4	N2—C7—H7A	119.4
C7—N2—N1	115.83 (13)	C6—C7—H7A	119.4
C2—C1—C6	120.76 (17)	O1—C8—N1	118.68 (14)
C2—C1—H1B	119.6	O1—C8—C9	120.69 (14)
C6—C1—H1B	119.6	N1—C8—C9	120.63 (13)
C1—C2—C3	120.37 (18)	C10—C9—C8	125.21 (14)
C1—C2—H2B	119.8	C10—C9—S1	109.27 (11)
C3—C2—H2B	119.8	C8—C9—S1	125.43 (12)
C4—C3—C2	120.41 (18)	C9—C10—C11	114.11 (16)
C4—C3—H3A	119.8	C9—C10—Cl1	126.46 (13)
C2—C3—H3A	119.8	C11—C10—Cl1	119.42 (14)
C5—C4—C3	118.29 (18)	C12—C11—C10	111.83 (17)
C5—C4—H4A	120.9	C12—C11—H11A	124.1
C3—C4—H4A	120.9	C10—C11—H11A	124.1
F1—C5—C4	118.06 (17)	C11—C12—S1	112.96 (14)
F1—C5—C6	118.18 (16)	C11—C12—H12A	129.0 (18)
C4—C5—C6	123.76 (18)	S1—C12—H12A	117.9 (18)
C5—C6—C1	116.41 (16)
C8—N1—N2—C7	−179.62 (14)	N2—N1—C8—C9	1.4 (2)
C6—C1—C2—C3	−0.2 (3)	O1—C8—C9—C10	2.1 (2)
C1—C2—C3—C4	0.0 (3)	N1—C8—C9—C10	−177.17 (14)
C2—C3—C4—C5	0.1 (3)	O1—C8—C9—S1	178.35 (13)
C3—C4—C5—F1	179.92 (17)	N1—C8—C9—S1	−0.9 (2)
C3—C4—C5—C6	0.1 (3)	C12—S1—C9—C10	0.39 (13)
F1—C5—C6—C1	179.91 (14)	C12—S1—C9—C8	−176.37 (14)
C4—C5—C6—C1	−0.2 (2)	C8—C9—C10—C11	176.15 (14)
F1—C5—C6—C7	−0.6 (2)	S1—C9—C10—C11	−0.62 (18)
C4—C5—C6—C7	179.24 (15)	C8—C9—C10—Cl1	−5.0 (2)
C2—C1—C6—C5	0.3 (2)	S1—C9—C10—Cl1	178.22 (10)
C2—C1—C6—C7	−179.19 (15)	C9—C10—C11—C12	0.6 (2)
N1—N2—C7—C6	−178.51 (13)	Cl1—C10—C11—C12	−178.35 (14)
C5—C6—C7—N2	−173.37 (14)	C10—C11—C12—S1	−0.3 (2)
C1—C6—C7—N2	6.1 (2)	C9—S1—C12—C11	−0.07 (17)
N2—N1—C8—O1	−177.85 (14)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1A···O1i	0.86	2.12	2.9552 (18)	163
C7—H7A···O1i	0.93	2.41	3.2268 (19)	147

Symmetry code: (i) x+1/2, −y+3/2, −z.