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Acta Cryst. (2007). E63, o3979    [ doi:10.1107/S1600536807042638 ]

(Z)-3-[1-(4-Chlorobenzyl)-1H-indol-3-yl]-2-(3-thienyl)acrylonitrile

V. N. Sonar, S. Parkin and P. A. Crooks

Abstract top

The title compound, C22H15ClN2S, was prepared by the base-catalyzed reaction of 1-(4-chlorobenzyl)indole-3-carboxaldehyde with thiophene-3-acetonitrile and recrystallization of the product from methanol. The double bond connecting the indole and thiophene units has Z geometry. The indole ring system is nearly planar and makes a dihedral angle of 79.81 (4)° with the plane of the 4-chlorophenyl ring. The molecule exhibits orientational disorder of the thienyl fragment, with occupancy factors of 0.65:0.35.

Comment top

We have synthesized a series of novel substituted aryl/heteroaryl-2-(thienyl) acrylonitriles and evaluated them for anticancer activity. The title compound was prepared by the base-catalyzed reaction of 1-(4-chlorobenzyl)indole-3- carboxaldehyde with thiophene-3-acetonitrile and recrystallization of the product from methanol to afford yellow needles. In order to confirm the double bond geometry in the title compound, and to obtain more detailed information of the structural conformation of the molecule, its X-ray structure determination has been carried out.

X-ray crystallography confirmed the molecular structure and atom connectivity for the title compound. In the title molecule the double bond connecting the indole and thiophene moieties has the Z-geometry. The indole ring is nearly planar with bond distances and bond angles comparable with those reported for other indole derivatives (Mason et al., 2003; Zarza et al., 1988). In the molecule, atom N1 lies slightly [0.0640 (16) Å] out of the plane of connecting atoms C2, C9, and C19, the sum of the angles about N1 being 359.36 (13)°. In a previous study, 21 structurally related indole analogues were analyzed (Beddoes et al., 1986) (available in the Cambridge Structural Database; Allen, 2002), and the sum of the three angles around the N atom were determined, to assess planarity. It was found that only two of the 21 compounds had values that were outside the range 359.0–360°, the farthest value from the perfectly planar situation being 357.2°. This is in general agreement with our current observation with the title compound. The plane of the 4-chlorophenyl group is twisted well out of the plane of the indole ring and makes a dihedral angle of 79.81 (4)°. There is an asymmetry of the exocyclic angles at C20 [C19—C20—C21 = 123.19 (14)° and C19—C20—C25 =117.73 (14)°].

Deviations from the ideal bond-angle geometry around the Csp2 atoms of the double bond are observed. The bond angles C2=C3—C10, C3—C10=C11, and C12—C11—C17 [129.95 (14), 129.61 (14), and 114.47 (13)°, respectively] are distorted because of strain induced by the double bond linking the indole and thiophene rings. The vinyl group bearing the three substituents has a double bond length of 1.352 (2)Å and is significantly longer than that observed in the disubstituted vinyl group of 2-styrylbenzimidazoles (1.304 (4) Å; Bacelo et al., 1997). Furthermore, the C3—C10 bond length [1.431 (2) Å] is slightly shorter than a Car—Csp2 single bond (Wilson, 1992). The C2=C3—C10=C11, C3—C10=C11—C12, and C10=C11—C12=C16 torsion angles [4.7 (3), 178.75 (15), and −179.2 (8), respectively] show that the non-H atoms of the indole and thiophene rings are nearly coplanar. The 2-thienyl group exhibits rotational disorder over two sets of sites corresponding to 180° about the C11—C12 bond with occupancy factors of 0.65:0.35.

Related literature top

For related literature, see: Allen (2002); Bacelo et al. (1997); Beddoes et al. (1986); Mason et al. (2003); Sonar et al. (2004); Wilson (1992); Zarza et al. (1988).

Experimental top

The title compound was prepared according to the previously reported procedure of Sonar et al. (2004). Recrystallization from methanol afforded yellow colored needles. 1H NMR (DMSO-d6, p.p.m.): δ 7.22–7.30 (m, 4H), 7.41 (d, 2H), 7.55 (dd, 1H), 7.71 (s, 3H), 8.10 (dd, 1H), 8.15 (s, 1H), 8.45 (s, 1H). 13C NMR (DMSO-d6, p.p.m.): δ 48.90, 99.19, 110.27, 110.89, 119.09, 119.39, 120.82, 121.32, 122.93, 124.69, 127.66, 127.90, 128.55, 128.87, 129.34, 132.10, 132.45, 135.46, 136.18, 136.46.

Refinement top

H atoms were found in difference Fourier maps and subsequently placed in idealized positions with contrained C—H distances of 0.95 Å and Uiso(H) values set to 1.2Ueq of the attached C atom. The thienyl group was disordered by a 180° rotation over two positions about the C11—C12 bond with occupancy factors of 0.65:0.35, as is common in this type of compound. Refinement of this disorder model required a number of restraints to maintain the similarity and the integrity of the thienyl groups. The restraints used in SHXLEL were:

SAME - helps to maintain similar bond lengths and angles between specified atoms.

SIMU - helps to ensure that the equivalent Uiso of the specified atoms remain similar.

DELU - restrains the components of anisotropic displacement parameters along bonds between specified atoms so that they do not change by any large amount from one atom to the next.

Computing details top

Data collection: APEX2 (Bruker, 2006); cell refinement: APEX2 (Bruker, 2006); data reduction: APEX2 (Bruker, 2006); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: XP in SHELXTL (Sheldrick, 1995); software used to prepare material for publication: SHELXL97 (Sheldrick, 1997) and local procedures.

Figures top
[Figure 1] Fig. 1. A view of molecule (I), with the atom numbering scheme. Displacement ellipsoids are drawn at the 50% probability level and H atoms are shown as small spheres of arbitrary radii. The thienyl ring is disordered with occupancy factors of 0.65:0.35.
(Z)-3-[1-(4-Chlorobenzyl)-1H-indol-3-yl]-2-(3- thienyl)acrylonitrile top
Crystal data top
C22H15ClN2SF000 = 776
Mr = 374.87Dx = 1.424 Mg m−3
Monoclinic, P21/nCu Kα radiation
λ = 1.54178 Å
Hall symbol: -P 2ynCell parameters from 9856 reflections
a = 16.8531 (11) Åθ = 3.3–69.6º
b = 5.5629 (4) ŵ = 3.10 mm−1
c = 18.7889 (13) ÅT = 90.0 (2) K
β = 96.877 (2)ºNeedle, yellow
V = 1748.8 (2) Å30.25 × 0.02 × 0.01 mm
Z = 4
Data collection top
Bruker X8 Proteum
diffractometer		3248 independent reflections
Radiation source: fine-focus rotating anode3020 reflections with I > 2σ(I)
Monochromator: graded multilayer opticsRint = 0.040
T = 90.0(2) Kθmax = 69.7º
φ and ω scansθmin = 3.3º
Absorption correction: multi-scan
(SADABS in APEX2; Bruker, 2006)		h = −20→20
Tmin = 0.657, Tmax = 0.970k = −4→6
24522 measured reflectionsl = −22→22
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.033H-atom parameters constrained
wR(F2) = 0.088  w = 1/[σ2(Fo2) + (0.0351P)2 + 1.6245P]
where P = (Fo2 + 2Fc2)/3
S = 1.05(Δ/σ)max = 0.007
3248 reflectionsΔρmax = 0.34 e Å−3
273 parametersΔρmin = −0.32 e Å−3
162 restraintsExtinction correction: SHELXL97 (Sheldrick, 1997), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.00051 (14)
Crystal data top
C22H15ClN2SV = 1748.8 (2) Å3
Mr = 374.87Z = 4
Monoclinic, P21/nCu Kα
a = 16.8531 (11) ŵ = 3.10 mm−1
b = 5.5629 (4) ÅT = 90.0 (2) K
c = 18.7889 (13) Å0.25 × 0.02 × 0.01 mm
β = 96.877 (2)º
Data collection top
Bruker X8 Proteum
diffractometer		3248 independent reflections
Absorption correction: multi-scan
(SADABS in APEX2; Bruker, 2006)		3020 reflections with I > 2σ(I)
Tmin = 0.657, Tmax = 0.970Rint = 0.040
24522 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.033162 restraints
wR(F2) = 0.088H-atom parameters constrained
S = 1.05Δρmax = 0.34 e Å−3
3248 reflectionsΔρmin = −0.32 e Å−3
273 parameters
Special details top

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 > 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
xyzUiso*/UeqOcc. (<1)
N10.60215 (8)0.8954 (2)0.37437 (7)0.0171 (3)
C20.55429 (9)0.6994 (3)0.37495 (8)0.0170 (3)
H20.53120.64350.41560.020*
C30.54388 (9)0.5928 (3)0.30821 (8)0.0164 (3)
C40.58888 (9)0.7374 (3)0.26350 (8)0.0168 (3)
C50.60044 (9)0.7306 (3)0.19122 (8)0.0203 (3)
H50.57830.60440.16110.024*
C60.64460 (10)0.9105 (3)0.16452 (9)0.0229 (4)
H60.65240.90820.11530.027*
C70.67814 (10)1.0960 (3)0.20821 (9)0.0223 (3)
H70.70821.21760.18810.027*
C80.66845 (9)1.1062 (3)0.27981 (9)0.0200 (3)
H80.69151.23140.30980.024*
C90.62347 (9)0.9253 (3)0.30613 (8)0.0168 (3)
C100.49692 (9)0.3884 (3)0.28348 (8)0.0171 (3)
H100.50210.33910.23580.021*
C110.44630 (9)0.2549 (3)0.31782 (8)0.0168 (3)
C120.39941 (9)0.0499 (3)0.28704 (8)0.0181 (3)0.652 (2)
C130.4007 (10)−0.034 (2)0.2194 (7)0.0193 (13)0.652 (2)
H130.43240.03660.18640.023*0.652 (2)
S140.33986 (9)−0.2784 (3)0.19900 (6)0.0198 (3)0.652 (2)
C150.3100 (7)−0.266 (2)0.2821 (6)0.0279 (18)0.652 (2)
H150.2722−0.37440.29790.034*0.652 (2)
C160.3446 (8)−0.0911 (19)0.3232 (6)0.0187 (12)0.652 (2)
H160.3343−0.06230.37110.022*0.652 (2)
C12'0.39941 (9)0.0499 (3)0.28704 (8)0.0181 (3)0.348 (2)
C13'0.4009 (19)−0.059 (4)0.2181 (13)0.020 (2)0.348 (2)
H13'0.4334−0.00940.18270.024*0.348 (2)
C14'0.3494 (8)−0.239 (2)0.2119 (6)0.029 (2)0.348 (2)
H14'0.3407−0.33280.16950.034*0.348 (2)
S15'0.2997 (3)−0.2935 (10)0.2838 (2)0.0211 (7)0.348 (2)
C16'0.3492 (16)−0.058 (4)0.3271 (11)0.020 (2)0.348 (2)
H16'0.3420−0.00870.37430.024*0.348 (2)
C170.43384 (9)0.3125 (3)0.38978 (8)0.0189 (3)
N180.42323 (8)0.3528 (3)0.44772 (7)0.0243 (3)
C190.61814 (9)1.0662 (3)0.43239 (8)0.0185 (3)
H19A0.58521.02250.47070.022*
H19B0.60061.22730.41440.022*
C200.70410 (9)1.0828 (3)0.46485 (8)0.0171 (3)
C210.75987 (10)0.9063 (3)0.45686 (8)0.0207 (3)
H210.74450.76710.42930.025*
C220.83803 (10)0.9300 (3)0.48858 (9)0.0245 (4)
H220.87640.80870.48280.029*
C230.85917 (10)1.1319 (3)0.52860 (8)0.0240 (4)
C240.80456 (10)1.3088 (3)0.53802 (9)0.0244 (4)
H240.81991.44610.56650.029*
C250.72715 (10)1.2843 (3)0.50554 (8)0.0211 (3)
H250.68921.40700.51110.025*
Cl10.95722 (3)1.16827 (10)0.56800 (2)0.03730 (15)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
N10.0194 (7)0.0150 (6)0.0176 (6)−0.0007 (5)0.0048 (5)0.0005 (5)
C20.0160 (7)0.0160 (7)0.0197 (7)0.0016 (6)0.0048 (6)0.0040 (6)
C30.0159 (7)0.0166 (7)0.0172 (7)0.0013 (6)0.0033 (6)0.0033 (6)
C40.0147 (7)0.0156 (7)0.0206 (8)0.0024 (6)0.0037 (6)0.0032 (6)
C50.0205 (8)0.0209 (8)0.0199 (8)−0.0004 (6)0.0045 (6)0.0003 (6)
C60.0237 (8)0.0262 (9)0.0201 (8)0.0006 (7)0.0084 (6)0.0032 (7)
C70.0216 (8)0.0190 (8)0.0280 (8)−0.0007 (6)0.0102 (6)0.0056 (7)
C80.0181 (8)0.0165 (8)0.0261 (8)−0.0002 (6)0.0059 (6)0.0006 (6)
C90.0157 (7)0.0158 (7)0.0194 (7)0.0030 (6)0.0045 (6)0.0027 (6)
C100.0176 (7)0.0174 (8)0.0166 (7)0.0024 (6)0.0027 (6)0.0021 (6)
C110.0163 (7)0.0175 (8)0.0165 (7)0.0024 (6)0.0020 (6)0.0034 (6)
C120.0159 (7)0.0159 (7)0.0220 (8)0.0019 (6)0.0007 (6)0.0049 (6)
C130.020 (2)0.013 (3)0.024 (2)−0.002 (2)0.0019 (17)0.0015 (17)
S140.0220 (5)0.0171 (5)0.0203 (5)−0.0011 (3)0.0023 (4)−0.0002 (3)
C150.026 (3)0.021 (3)0.037 (3)−0.001 (2)0.006 (2)0.0089 (19)
C160.017 (2)0.017 (3)0.023 (2)−0.0039 (18)0.0053 (18)0.0060 (17)
C12'0.0159 (7)0.0159 (7)0.0220 (8)0.0019 (6)0.0007 (6)0.0049 (6)
C13'0.021 (3)0.020 (4)0.020 (3)0.007 (3)0.004 (3)−0.002 (3)
C14'0.027 (3)0.026 (4)0.030 (3)0.008 (3)−0.004 (3)−0.006 (3)
S15'0.0206 (12)0.0173 (12)0.0253 (10)−0.0030 (9)0.0021 (7)0.0016 (8)
C16'0.019 (4)0.015 (4)0.026 (3)−0.002 (3)−0.004 (3)0.003 (3)
C170.0153 (7)0.0180 (8)0.0236 (9)−0.0007 (6)0.0035 (6)0.0052 (6)
N180.0234 (7)0.0283 (8)0.0223 (7)−0.0017 (6)0.0064 (6)0.0031 (6)
C190.0205 (8)0.0154 (7)0.0203 (8)0.0012 (6)0.0056 (6)−0.0010 (6)
C200.0215 (8)0.0157 (7)0.0149 (7)0.0005 (6)0.0059 (6)0.0030 (6)
C210.0239 (8)0.0181 (8)0.0205 (8)0.0023 (6)0.0046 (6)−0.0013 (6)
C220.0246 (9)0.0265 (9)0.0231 (8)0.0092 (7)0.0059 (6)0.0003 (7)
C230.0212 (8)0.0346 (10)0.0165 (7)0.0019 (7)0.0032 (6)−0.0002 (7)
C240.0277 (9)0.0253 (9)0.0203 (8)−0.0006 (7)0.0036 (7)−0.0057 (7)
C250.0231 (8)0.0194 (8)0.0217 (8)0.0032 (6)0.0057 (6)−0.0010 (6)
Cl10.0219 (2)0.0607 (3)0.0282 (2)0.0056 (2)−0.00151 (16)−0.0154 (2)
Geometric parameters (Å, °) top
N1—C21.357 (2)S14—C151.698 (10)
N1—C91.3823 (19)C15—C161.334 (15)
N1—C191.447 (2)C15—H150.9500
C2—C31.379 (2)C16—H160.9500
C2—H20.9500C13'—C14'1.32 (2)
C3—C101.431 (2)C13'—H13'0.9500
C3—C41.442 (2)C14'—S15'1.701 (11)
C4—C51.395 (2)C14'—H14'0.9500
C4—C91.401 (2)S15'—C16'1.707 (17)
C5—C61.377 (2)C16'—H16'0.9500
C5—H50.9500C17—N181.146 (2)
C6—C71.396 (2)C19—C201.506 (2)
C6—H60.9500C19—H19A0.9900
C7—C81.375 (2)C19—H19B0.9900
C7—H70.9500C20—C211.380 (2)
C8—C91.386 (2)C20—C251.386 (2)
C8—H80.9500C21—C221.385 (2)
C10—C111.352 (2)C21—H210.9500
C10—H100.9500C22—C231.375 (3)
C11—C171.429 (2)C22—H220.9500
C11—C121.466 (2)C23—C241.373 (2)
C12—C131.355 (11)C23—Cl11.7397 (17)
C12—C161.442 (9)C24—C251.379 (2)
C13—S141.721 (10)C24—H240.9500
C13—H130.9500C25—H250.9500
C2—N1—C9108.95 (13)C15—S14—C1389.9 (5)
C2—N1—C19125.38 (13)C16—C15—S14113.8 (8)
C9—N1—C19125.03 (13)C16—C15—H15123.1
N1—C2—C3110.44 (13)S14—C15—H15123.1
N1—C2—H2124.8C15—C16—C12112.7 (8)
C3—C2—H2124.8C15—C16—H16123.7
C2—C3—C10129.95 (14)C12—C16—H16123.7
C2—C3—C4105.73 (13)C14'—C13'—H13'125.8
C10—C3—C4124.27 (14)C13'—C14'—S15'116.6 (11)
C5—C4—C9118.68 (14)C13'—C14'—H14'121.7
C5—C4—C3134.10 (15)S15'—C14'—H14'121.7
C9—C4—C3107.15 (13)C14'—S15'—C16'88.9 (8)
C6—C5—C4118.64 (15)S15'—C16'—H16'123.8
C6—C5—H5120.7N18—C17—C11178.23 (17)
C4—C5—H5120.7N1—C19—C20115.37 (13)
C5—C6—C7121.44 (15)N1—C19—H19A108.4
C5—C6—H6119.3C20—C19—H19A108.4
C7—C6—H6119.3N1—C19—H19B108.4
C8—C7—C6121.23 (15)C20—C19—H19B108.4
C8—C7—H7119.4H19A—C19—H19B107.5
C6—C7—H7119.4C21—C20—C25119.08 (15)
C7—C8—C9116.95 (15)C21—C20—C19123.19 (14)
C7—C8—H8121.5C25—C20—C19117.73 (14)
C9—C8—H8121.5C20—C21—C22120.70 (15)
N1—C9—C8129.21 (15)C20—C21—H21119.7
N1—C9—C4107.71 (13)C22—C21—H21119.7
C8—C9—C4123.06 (14)C23—C22—C21118.93 (15)
C11—C10—C3129.61 (14)C23—C22—H22120.5
C11—C10—H10115.2C21—C22—H22120.5
C3—C10—H10115.2C24—C23—C22121.48 (16)
C10—C11—C17120.07 (14)C24—C23—Cl1118.61 (14)
C10—C11—C12125.45 (14)C22—C23—Cl1119.90 (13)
C17—C11—C12114.47 (13)C23—C24—C25119.02 (16)
C13—C12—C16109.8 (4)C23—C24—H24120.5
C13—C12—C11124.6 (4)C25—C24—H24120.5
C16—C12—C11125.6 (4)C24—C25—C20120.78 (15)
C12—C13—S14113.8 (7)C24—C25—H25119.6
C12—C13—H13123.1C20—C25—H25119.6
S14—C13—H13123.1
C9—N1—C2—C31.06 (17)C10—C11—C12—C130.1 (10)
C19—N1—C2—C3172.28 (14)C17—C11—C12—C13178.9 (10)
N1—C2—C3—C10−177.97 (15)C10—C11—C12—C16−179.2 (8)
N1—C2—C3—C4−0.34 (17)C17—C11—C12—C16−0.4 (8)
C2—C3—C4—C5−177.53 (17)C16—C12—C13—S14−1.1 (15)
C10—C3—C4—C50.3 (3)C11—C12—C13—S14179.5 (5)
C2—C3—C4—C9−0.48 (17)C12—C13—S14—C151.2 (13)
C10—C3—C4—C9177.32 (14)C13—S14—C15—C16−0.9 (14)
C9—C4—C5—C6−0.8 (2)S14—C15—C16—C120.4 (17)
C3—C4—C5—C6176.00 (16)C13—C12—C16—C150.5 (17)
C4—C5—C6—C70.6 (2)C11—C12—C16—C15179.8 (9)
C5—C6—C7—C80.1 (3)C13'—C14'—S15'—C16'1(2)
C6—C7—C8—C9−0.5 (2)C2—N1—C19—C20117.63 (16)
C2—N1—C9—C8176.85 (15)C9—N1—C19—C20−72.53 (19)
C19—N1—C9—C85.6 (3)N1—C19—C20—C21−18.7 (2)
C2—N1—C9—C4−1.35 (17)N1—C19—C20—C25162.34 (13)
C19—N1—C9—C4−172.60 (13)C25—C20—C21—C22−0.4 (2)
C7—C8—C9—N1−177.66 (15)C19—C20—C21—C22−179.32 (14)
C7—C8—C9—C40.3 (2)C20—C21—C22—C230.4 (2)
C5—C4—C9—N1178.70 (13)C21—C22—C23—C240.4 (3)
C3—C4—C9—N11.11 (17)C21—C22—C23—Cl1−179.11 (13)
C5—C4—C9—C80.4 (2)C22—C23—C24—C25−1.0 (3)
C3—C4—C9—C8−177.21 (14)Cl1—C23—C24—C25178.44 (13)
C2—C3—C10—C114.7 (3)C23—C24—C25—C201.0 (2)
C4—C3—C10—C11−172.51 (15)C21—C20—C25—C24−0.3 (2)
C3—C10—C11—C170.0 (3)C19—C20—C25—C24178.69 (14)
C3—C10—C11—C12178.75 (15)
Acknowledgements top

This investigation was supported by the National Institute of Alcohol Abuse and Alcoholism (grant No. AA12600).

references
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