The title compounds, C17H13NO2S, (I), C17H13NO3S, (II), and C24H17ClN2O5S·CHCl3, (III), are indole derivatives. Compounds (I) and (II) crystalize with two independent mol-ecules in the asymmetric unit. The indole ring systems in all three structures deviate only slightly from planarity, with dihedral angles between the planes of the pyrrole and benzene rings spanning the tight range 0.20 (9)-1.65 (9)°. These indole ring systems, in turn, are almost orthogonal to the phenyl-sulfonyl rings [range of dihedral angles between mean planes = 77.21 (8)-89.26 (8)°]. In the three compounds, the mol-ecular structure is stabilized by intra-molecular C-H⋯O hydrogen bonds, generating S(6) ring motifs with the sulfone O atom. In compounds (I) and (II), the two independent mol-ecules are linked by C-H⋯O hydrogen bonds and C-H⋯π inter-actions, while in compound (III), the mol-ecules are linked by C-H⋯O hydrogen bonds, generating R 2 (2)(22) inversion dimers.
The title compounds, C17H13NO2S, (I), C17H13NO3S, (II), and C24H17ClN2O5S·CHCl3, (III), are indole derivatives. Compounds (I) and (II) crystalize with two independent mol-ecules in the asymmetric unit. The indole ring systems in all three structures deviate only slightly from planarity, with dihedral angles between the planes of the pyrrole and benzene rings spanning the tight range 0.20 (9)-1.65 (9)°. These indole ring systems, in turn, are almost orthogonal to the phenyl-sulfonyl rings [range of dihedral angles between mean planes = 77.21 (8)-89.26 (8)°]. In the three compounds, the mol-ecular structure is stabilized by intra-molecular C-H⋯O hydrogen bonds, generating S(6) ring motifs with the sulfone O atom. In compounds (I) and (II), the two independent mol-ecules are linked by C-H⋯O hydrogen bonds and C-H⋯π inter-actions, while in compound (III), the mol-ecules are linked by C-H⋯O hydrogen bonds, generating R 2 (2)(22) inversion dimers.
Indole is an aromatic heterocyclic group, the parent of a large number of important compounds in nature with significant biological activity (Kaushik et al., 2013 ▸). The indole ring system occurs in plants (Nigovic et al., 2000 ▸); for example, indole-3-acetic acid is a naturally occuring auxin that controls several plant growth activities (Moore, 1989 ▸; Fargasova, 1994 ▸). Indole derivatives exhibit antibacterial, antifungal (Singh et al., 2000 ▸), antitumor (Andreani et al., 2001 ▸), antihepatitis B virus (Chai et al., 2006 ▸) and anti-inflammatory (Rodriguez et al., 1985 ▸) activities. They are also used as bioactive drugs (Stevenson et al., 2000 ▸) and have also been proven to display high aldose reductase inhibitory (Rajeswaran et al., 1999 ▸) and antimicrobial activities (Amal Raj et al., 2003 ▸). Indole derivatives are also found to possess hypertensive, muscle relaxant (Hendi & Basangoudar, 1981 ▸) and antiviral (Kolocouris et al., 1994 ▸) activities. Some of the indole alkaloids extracted from plants possess interesting cytotoxic and antiparasitic properties (Quetin-Leclercq, 1994 ▸). Against this background, the X-ray structure determination of 3-ethnyl-2-methyl-1-phenylsulfonyl-1H-indole, (I), 4-phenylsulfonyl-3H,4H-cyclopenta[b]indol-1(2H)-one, (II), and 1-{2-[(E)-2-(5-chloro-2-nitrophenyl)ethenyl]-1-phenylsulfonyl-1H-indol-3-yl}ethan-1-one chloroform monosolvate, (III), has been carried out to study their structural aspects and the results are presented here.
Structural commentary
The molecular structures of title compounds (I), (II) and (III) are shown in Figs. 1 ▸, 2 ▸ and 3 ▸, respectively. Compounds (I) and (II) comprise two crystallographically independent molecules (A and B) in the asymmetric unit. The corresponding bond lengths and bond angles of molecules A and B [in compounds (I) and (II)] agree well with each other, as illustrated in Figs. 4 ▸ and 5 ▸. The indole ring systems depart slightly from planarity, the dihedral angles formed between the pyrrole rings and benzene rings being 1.65 (9) and 0.97 (10) [molecules A and B of compound (I)], 0.20 (9) and 0.86 (9) [molecules A and B of compound (II)], and 1.34 (14)° [compound (III)].
Figure 1
The molecular structure of the compound (I), showing the atom-numbering scheme. The intramolecular C2A—H2A⋯O2A and C2B—H2B⋯O2B interactions (molecules A and B), which generate two S(6) ring motifs, are shown as dashed lines. Displacement ellipsoids are drawn at the 30% probability level.
Figure 2
The molecular structure of the compound (II), showing the atom-numbering scheme. The intramolecular C2A—H2A⋯O2A and C2B—H2B⋯O2B interactions (molecules A and B), which generate two S(6) ring motifs, are shown as dashed lines. Displacement ellipsoids are drawn at the 30% probability level.
Figure 3
The molecular structure of the compound (III), showing the atom-numbering scheme. The intramolecular C2—H2⋯O2 interaction, which generates an S(6) ring motif, is shown as a dashed line. Displacement ellipsoids are drawn at the 30% probability level.
Figure 4
Molecules A (red) and molecule B (black) of title compound (I) overlapping with each other. H atoms are shown as spheres of arbitrary radius.
Figure 5
The molecule A (red) and molecule B (black) of title compound (II) overlapping with each other. H atoms are shown as spheres of arbitrary radius.
The indole ring systems are almost orthogonal to the phenylsulfonyl rings [dihedral angles = 77.21 (8) and 89.26 (8)° in (I), 78.98 (7) and 80.48 (8)° in (II), and 83.17 (13)° in (III)]. In the case of (II), the indole ring systems are nearly coplanar with the cyclopentanone rings [dihedral angles: = 0.58 (9) and 1.52 (8)°].In all three compounds, as a result of the electron-withdrawing character of the phenylsulfonyl group, the N—Csp
2 bond lengths are longer than the mean value of 1.355 (14)Å for the N—C bond length (Allen et al., 1987 ▸). Atom S1 has a distorted tetrahedral configuration. The widening of the angle O1=S1=O2 and the narrowing of the angle N1—S1—C9 from ideal tetrahedral values are attributed to the Thorpe–Ingold effect (Bassindale, 1984 ▸). The widening of the angles may be due to the repulsive interaction between the two short S=O bonds.In all three compounds, the expansion of the ispo angles at atoms C1, C3 and C4, and the contraction of the apical angles at atoms C2, C5 and C6 are caused by fusion of the smaller pyrrole ring with the six-membered benzene ring and the strain is taken up by the angular distortion rather than by bond-length distortion (Allen, 1981 ▸).The sums of the bond angles around atoms N1 are 351.55 and 356.16° in (I), 359.86 and 359.29° in (II), and 352.79° in (III), indicating sp
2 hybridization. In all three compounds, the molecular structure is stabilized by intramolecular C—H⋯O hydrogen bonds which generate S(6) ring motifs with the sulfone O atom (Tables 1 ▸, 2 ▸ and 3 ▸). In addition to these, in compound (III), the molecular structure is characterized by intramolecular C25—Cl3⋯O2 halogen bonding (XB), between the solvent Cl atom (Cl3) and sulfone-group O atom (O2) [Cl3⋯O2 = 3.036 (2) Å and with a bond angle of 164.48 (14)°].
Table 1
Hydrogen-bond geometry (Å, °) for (I)
Cg2 is the centroid of the pyrrole ring N1A/C1A/C6A/C7A/C8A, Cg1 and Cg3 are the centroids of the benzene rings C1B–C6B and C1A–C6A.
D—H⋯A
D—H
H⋯A
D⋯A
D—H⋯A
C2A—H2A⋯O1A
0.93
2.36
2.941 (3)
121
C2B—H2B⋯O1B
0.93
2.38
2.957 (3)
120
C16B—H16B⋯O2Ai
0.93
2.43
3.334 (3)
153
C10A—H10A⋯Cg1ii
0.93
2.95
3.728 (2)
142
C11A—H11A⋯Cg2ii
0.93
2.74
3.546 (2)
145
C16A—H16A⋯Cg3iii
0.93
2.88
3.699 (3)
148
Symmetry codes: (i) ; (ii) ; (iii) .
Table 2
Hydrogen-bond geometry (Å, °) for (II)
Cg1 and Cg2 are the centroids of the benzene rings C9A–C14A and C1A–C6A.
D—H⋯A
D—H
H⋯A
D⋯A
D—H⋯A
C2A—H2A⋯O1A
0.93
2.44
3.007 (2)
119
C2B—H2B⋯O1B
0.93
2.44
3.010 (2)
120
C12B—H12B⋯O2Ai
0.93
2.46
3.369 (3)
166
C5A—H5A⋯Cg1ii
0.93
2.65
3.550 (2)
164
C17B—H17C⋯Cg2ii
0.97
2.85
3.729 (2)
151
Symmetry codes: (i) ; (ii) .
Table 3
Hydrogen-bond geometry (Å, °) for (III)
D—H⋯A
D—H
H⋯A
D⋯A
D—H⋯A
C2—H2⋯O1
0.93
2.32
2.903 (4)
121
C22—H22⋯O2i
0.93
2.51
3.412 (4)
162
C25—H25⋯O3ii
0.98
2.49
3.283 (4)
138
Symmetry codes: (i) ; (ii) .
Supramolecular features
In the crystal packing of compound (I), the molecules are linked via intermolecular C16B—H16B⋯O2A(−x + 1, y + , −z + 1) hydrogen bonds running parallel to the [101] direction. The crystal packing is further stabilized by intermolecular C10A—H10A⋯Cg1, C11A—H11A⋯Cg2 and C16A—H16A⋯Cg3 interactions, with separations of 3.727 (2), 3.546 (2) and 3.699 (3) Å at (−x + 2, y − , −z + 1) and (−x + 1, y + , −z), respectively. Cg2 is the centre of gravity of pyrrole ring N1B/C1B/C6B/C7B/C8B, and Cg1 and Cg3 are the centres of gravity of benzene rings C1B–C6B and C1A–C6A, respectively. C—H⋯π interactions run parallel to the [210] direction (Table 1 ▸ and Fig. 6 ▸).
Figure 6
The crystal packing of compound (I), viewed down the b axis, showing C12B—H12B⋯O2A
i intermolecular hydrogen bond link the independent molecules running parallel to the [101] direction and further interconnected by C10A—H10A⋯Cg1ii, C11A—H11A⋯Cg2ii and C16A—H16A⋯Cg3iii interactions. Cg2 is the centre of the gravity of the pyrrole ring (atoms N1B/C1B/C6B/C7B/C8B), and Cg1 and Cg3 are the centres of the gravity of benzene rings C1B–C6B and C1A–C6A, respectively. [Symmetry codes: (i) −x + 1, y + , −z + 1; (ii) −x + 2, y − , −z + 1; (iii) −x + 1, y + , −z.]
In the crystal packing of compound (II), the independent molecules (A and B) are linked by intermolecular C12B—H12B⋯O2A(x + 1, y, z − 1) hydrogen bonds and are further connected by C5A—H5A⋯Cg1 and C17B—H17C⋯Cg2 interactions, with separations of 3.550 (2) and 3.729 (2) Å at (−x + 1, −y + 1, -z+1) (1 and Cg2 are the centres of gravity of benzene rings C9A–C14A and C1A–C6A), respectively). The C12B—H12B⋯O2A and C17B—H17C⋯Cg2 interactions run parallel to the [101] direction and C5A—H5A⋯Cg1 interactions run along the [01] direction (Table 2 ▸ and Fig. 7 ▸), respectively.
Figure 7
The crystal packing of compound (II), viewed down the b axis, showing C12B—H12B⋯O2A
i intermolecular hydrogen bond running parallel to the [101] direction and further intercomnnected by C5A—H5A⋯Cg1ii and C17B—H17C⋯Cg2ii interactions. H atoms not involved in the hydrogen bonding have been omitted for clarity. Cg1 and Cg2 are the centres of the gravity of benzene rings C9A–C14A and C1A–C6A, respectively. [Symmetry codes: (i) x + 1, y, z − 1; (ii) −x + 1, −y + 1, −z + 1.]
In the crystal of compound (III), molecules are linked via C22—H22⋯O2(−x + 1, −y + 1, −z + 1) intermolecular hydrogen bonds which generates (22) inversion dimers. In addition, the chloroform solvent molecule is linked to the organic molecule by a C25—H25⋯O3 hydrogen bond (Bernstein et al., 1995 ▸) involving the O atom of the ethanone group (Table 3 ▸ and Fig. 8 ▸).
Figure 8
The crystal packing of compound (III), viewed down the c axis, showing C22—H22⋯O2i intermolecular hydrogen bonds, which results in (22) inversion dimers forms a sheet lying parallel to the [1
] direction. In addition, the solvent molecule interacts with the organic molecule linked via a C25—H25⋯O3ii hydrogen bond. H atoms not involved in the hydrogen bonding have been omitted for clarity. [Symmetry codes: (i) −x + 1, −y + 1, −z + 1; (ii) −x + 1, −y + 1, −z.]
Synthesis and crystallization
Compound (I)
A solution of [(3-acetyl-1-phenylsulfanyl-1H-indol-2-yl)methyl]triphenylphosphonium ylide (0.5 g, 9 mmol) in dry toluene (20 ml) was refluxed for 12 h under an N2 atmosphere. After consumption of the starting material [monitered by thin-layer chromatography (TLC)], removal of the solvent in vacuo followed by column chromatographic purification (silica gel, EtOAc–hexane 1:9 v/v) gave (I) (yield 1.30 g, 29%) as a colourless solid. Single crystals suitable for X-ray diffraction were prepared by slow evaporation of a solution of compound (I) in ethyl acetate at room temperature (m.p. 383–385 K).
Compound (II)
Reaction of 2-bromomethyl-1-(1-phenylsulfonyl-1H-indol-3-yl)ethan-1-one (0.2 g, 5 mmol) with K2CO3 (0.35 g, 5 mmol) in acetonitrile was carried out under reflux for 8 h under an N2 atmosphere. After the consumption of the starting material (monitered by TLC), the reaction mass was poured over crushed ice and extracted with dichloromethane (2 × 15 ml). The organic layers were combined and washed with brine solution (2 × 20 ml) and dried (Na2SO4). The crude product was purified by column chromatography (silica gel, EtOAc–hexane 1:4 v/v) to give (II) (yield 1.40 g, 88%) as a white solid. Single crystals suitable for X-ray diffraction were prepared by slow evaporation of a solution of compound (II) in ethyl acetate at room temperature (m.p. 475–481 K).
Compound (III)
A solution of [(3-acetyl-1-phenylsufanyl-1H-indol-2-yl)methyl]triphenylphosphonium ylide (3 g, 5.23 mmol) and 5-chloronitrobenzaldehyde (1.06 g, 5.75 mmol) in dry chloroform (50 ml) was refluxed for 10 h under an N2 atmosphere. Removal of the solvent in vacuo followed by titration of the crude product with methonal (10 ml), gave (III) (yield 2.29 g, 91%) as a yellow solid. Single crystals suitable for X-ray diffraction were prepared by slow evaporation of a solution of compound (III) in chloroform at room temperature (m.p. 439–441 K).
Refinement
Crystal data, data collection and structure refinement details for compounds (I), (II) and (III) are summarized in Table 4 ▸. The positions of the H atoms were localized from the difference electron-density maps and their distances were geometrically constrained. H atoms bound to the C atoms were treated as riding atoms, with C—H = 0.93, 0.96, 0.97 and 0.98 Å for aryl, methyl, methylene and methine H atoms, respectively, with U
iso(H) = 1.5U
eq(methyl C) and 1.2U
eq(nonmethyl C). The rotation angles for methyl groups were optimized by least squares.
Table 4
Experimental details
(I)
(II)
(III)
Crystal data
Chemical formula
C17H13NO2S
C17H13NO3S
C24H17ClN2O5S·CHCl3
Mr
295.34
311.34
600.27
Crystal system, space group
Monoclinic, P21
Triclinic, P
Triclinic, P
Temperature (K)
296
296
296
a, b, c (Å)
12.1786 (5), 10.2422 (5), 12.6306 (5)
9.8708 (6), 12.3914 (7), 13.1457 (12)
9.5856 (3), 11.2767 (4), 13.1782 (4)
α, β, γ (°)
90, 113.082 (2), 90
102.706 (3), 96.552 (3), 111.989 (2)
104.9070 (11), 108.2350 (9), 91.581 (1)
V (Å3)
1449.36 (11)
1419.70 (18)
1298.31 (7)
Z
4
4
2
Radiation type
Mo Kα
Mo Kα
Mo Kα
μ (mm−1)
0.23
0.24
0.58
Crystal size (mm)
0.35 × 0.30 × 0.25
0.35 × 0.30 × 0.25
0.35 × 0.30 × 0.25
Data collection
Diffractometer
Bruker Kappa APEXII CCD diffractometer
Bruker Kappa APEXII CCD diffractometer
Bruker Kappa APEXII CCD diffractometer
Absorption correction
Multi-scan (SADABS; Bruker, 2008 ▸)
Multi-scan (SADABS; Bruker, 2008 ▸)
Multi-scan (SADABS; Bruker, 2008 ▸)
Tmin, Tmax
0.924, 0.945
0.919, 0.942
0.817, 0.866
No. of measured, independent and observed [I > 2σ(I)] reflections
12944, 5750, 5372
20747, 5869, 4993
25757, 4579, 4054
Rint
0.024
0.028
0.019
(sin θ/λ)max (Å−1)
0.639
0.628
0.595
Refinement
R[F2 > 2σ(F2)], wR(F2), S
0.029, 0.080, 1.02
0.038, 0.105, 1.04
0.049, 0.136, 1.05
No. of reflections
5750
5869
4579
No. of parameters
389
397
335
No. of restraints
1
0
0
H-atom treatment
H-atom parameters constrained
H-atom parameters constrained
H-atom parameters constrained
Δρmax, Δρmin (e Å−3)
0.16, −0.25
0.22, −0.46
0.99, −0.77
Absolute structure
Flack (1983 ▸), 2406 Friedel pairs
–
–
Absolute structure parameter
0.01 (4)
–
–
Computer programs: APEX2 (Bruker, 2008 ▸), SAINT (Bruker, 2008 ▸), SHELXS97 (Sheldrick, 2008 ▸), ORTEP-3 for Windows (Farrugia, 2012 ▸) and Mercury (Macrae et al., 2008 ▸), SHELXL97 (Sheldrick, 2008 ▸) and PLATON (Spek, 2009 ▸).
Crystal structure: contains datablock(s) I, II, III, global. DOI: 10.1107/S2056989015014917/bg2558sup1.cifStructure factors: contains datablock(s) I. DOI: 10.1107/S2056989015014917/bg2558Isup2.hklStructure factors: contains datablock(s) II. DOI: 10.1107/S2056989015014917/bg2558IIsup3.hklStructure factors: contains datablock(s) III. DOI: 10.1107/S2056989015014917/bg2558IIIsup4.hklClick here for additional data file.Supporting information file. DOI: 10.1107/S2056989015014917/bg2558IIsup5.cmlClick here for additional data file.Supporting information file. DOI: 10.1107/S2056989015014917/bg2558IIIsup6.cmlCCDC references: 1417660, 1417659, 1417658Additional supporting information: crystallographic information; 3D view; checkCIF report
Primary atom site location: structure-invariant direct methods
Absolute structure parameter: 0.01 (4)
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.
Primary atom site location: structure-invariant direct methods
Least-squares matrix: full
Secondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.038
Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.105
H-atom parameters constrained
S = 1.04
w = 1/[σ2(Fo2) + (0.0542P)2 + 0.3752P] where P = (Fo2 + 2Fc2)/3
5869 reflections
(Δ/σ)max < 0.001
397 parameters
Δρmax = 0.22 e Å−3
0 restraints
Δρmin = −0.46 e Å−3
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.
Primary atom site location: structure-invariant direct methods
Least-squares matrix: full
Secondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.049
Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.136
H-atom parameters constrained
S = 1.05
w = 1/[σ2(Fo2) + (0.0647P)2 + 1.2652P] where P = (Fo2 + 2Fc2)/3
4579 reflections
(Δ/σ)max < 0.001
335 parameters
Δρmax = 0.99 e Å−3
0 restraints
Δρmin = −0.77 e Å−3
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.
Authors: A Andreani; M Granaiola; A Leoni; A Locatelli; R Morigi; M Rambaldi; G Giorgi; L Salvini; V Garaliene Journal: Anticancer Drug Des Date: 2001 Apr-Jun
Authors: N Kolocouris; G B Foscolos; A Kolocouris; P Marakos; N Pouli; G Fytas; S Ikeda; E De Clercq Journal: J Med Chem Date: 1994-09-02 Impact factor: 7.446