Crystal structures of four indole derivatives with a phenyl substituent at the 2-position and a carbonyl group at the 3-position: the C(6) N—H⋯O chain remains the same, but the weak reinforcing interactions are different

Four related indole derivatives crystallize with a consistent C(6) N—H⋯O chain motif, but in each case the reinforcing interactions and crystal symmetries are different.

As we discuss below, each structure features C(6) N-HÁ Á ÁO hydrogen-bonded chains but with different crystal symmetries and weak reinforcing effects (C-HÁ Á ÁO and C-HÁ Á Á interactions and aromaticstacking).
Compound (IV) crystallizes with two molecules in the asymmetric unit, as shown in Fig. 4. The molecules have similar but not identical conformations, as indicated by the r.m.s. overlay fit of 0.102 Å for the 23 non-hydrogen atoms. The main differences are a slightly different twist of the benzene ring at the 2-position and the fact that atoms C10 and C31 deviate slightly from the indole ring plane, but in opposite 364 Kerr  The molecular structure of (I), showing 50% displacement ellipsoids.

Supramolecular features
In each structure, as might be expected, the dominant supramolecular motif is an N-HÁ Á ÁO C hydrogen bond, which generates a C(6) chain in every case. However, it is notable that the same chain motif is reinforced by different weak interactions in these structures, as described below and listed in Tables 1-4, for (I)-(IV), respectively.
In the triclinic crystal of (I), the N1-H1Á Á ÁO1 i [symmetry code: (i) x -1, y, z] hydrogen bond links the molecules into [100] chains with the aforementioned C(6) chain motif in which adjacent molecules are related by translational symmetry. In addition, a C12-H12Á Á ÁO1 ii [symmetry code: (ii) 1 -x, 1 -y, 1 -z] interaction is seen. By itself, this generates inversion dimers ( Fig. 5) with an R 2 2 (14) motif: the twisting of the C11 ring relative to the indole skeleton appears to optimize the geometry for this interaction. Taken together, the N-HÁ Á ÁO and C-HÁ Á ÁO bonds in (I) lead to double chains propagating in [100] (Fig. 6). Inversion symmetry means that the sense of the N-HÁ Á ÁO bonds are opposed in the two chains. Packing between the chains does not feature any directional interactions beyond typical van der Waals contacts and there is no aromaticstacking in (I).
In the orthorhombic crystal of (II), the molecules are linked by N1-H1-O2 i [symmetry code: (i) x + 1, y, z] hydrogen bonds into [100] chains ( Fig. 7) characterized by a C(6) motif: adjacent molecules are again related by simple unit-cell translation. There is no reinforcement of the chain bonding in this case, but a pair of weak C-HÁ Á Á interactions occur,

Figure 5
An inversion dimer in the crystal of (I) linked by a pair of C-HÁ Á ÁO interactions (double-dashed lines). Symmetry code as in Table 1.    (001) sheets. The extended structure in (III) conforms to rhombohedral (trigonal) crystal symmetry. Once again, adjacent molecules are linked into C(6) chains by N1-H1Á Á ÁO2 i [symmetry code: (i) 1 3 À x + y, 2 3 À x, z À 1 3 ] and symmetry-equivalent hydrogen bonds. The chain propagates in the [001] direction ( Fig. 9) and the chain that incorporates the asymmetric molecule describes an anticlockwise helix, when viewed from above, about the 3 1 symmetry element at ( 1 3 , 1 3 , z). The centrosymmetric space group leads, of course, to an equal number of clockwise and anticlockwise helices in the crystal. The chains are reinforced by aromaticstacking between the pendant C15-C20 ring and the C1-C6 ring of the indole system with the same symmetry relation as the N-HÁ Á ÁO hydrogen bond: the centroid separation is 3.7565 (8) Å and the inter-plane angle is 0.00 (6) ]. There appears to be no directional interactions between the chains beyond van der Waals contacts.  Table 2 Hydrogen-bond geometry (Å , ) for (II).

Figure 7
Partial packing diagram for (II), showing the formation of [100] chains linked by N-HÁ Á ÁO hydrogen bonds (double-dashed lines). Symmetry code as in Table 2.   Table 2.

Figure 9
Partial packing diagram for (III), showing the formation of [001] chains linked by N-HÁ Á ÁO hydrogen bonds (double-dashed lines) and reinforced by aromaticstacking contacts. Symmetry code as in Table 3.
Compound (IV) crystallizes in a monoclinic space group. The C(6) chain motif (Fig. 10) is built up from alternating N1and N2-molecules, with simple translation in the [100] direction generating the chain from the starting pair. In this case, the chain is consolidated by C-HÁ Á Á interactions (involving both the N1 and N2 molecules) with the donor C-H group lying syn (i.e., C2-H2A and C23-H23, compare Fig. 4) to the N-H group in the indole ring system and the acceptor ring being the pendant phenyl group attached to the carbonyl group at the 3-position of the ring system (i.e., the C10 and C31 rings). Adjacent N1-and N2-molecules in the chain are 'flipped' by approximately 180 with respect to each other, so the chain has approximate local 2 1 symmetry. The packing for (IV) also features two C-HÁ Á ÁO and three inter-chain C-HÁ Á Á interactions, which generate a three-dimensional network.

Synthesis and crystallization
To prepare (I), 2-phenylindole (2.129 g, 11.0 mmol) was suspended in dry dichloromethane (45 ml) at 273 K and a 1.0 M solution of Et 2 AlCl in hexanes (16.5 ml, 16.5 mmol) was added slowly with stirring. A solution of benzoyl chloride (1.919 ml, 16.5 mmol) in dry dichloromethane (20 ml) was then added dropwise and the mixture was stirred at 273 K for a further 2 h. Water (30 ml) was added to quench the reaction then the solution was poured into 1.0 M HCl(aq) (100 ml) and the organic layer collected after shaking. The organic solution was washed with water (30 ml, twice) and saturated NaCl(aq) (30 ml) then dried over sodium sulfate, filtered and reduced under vacuum. Flash chromatography (1:4 EtOAc, hexanes) afforded 1-(2-phenyl-1H-indol-3-yl)ethanone as a colourless solid (2.257 g, 69%). Colourless slabs of (I) were recrystallized from ethanol solution at room temperature.    Table 4. Table 4 Hydrogen-bond geometry (Å , ) for (IV).

Refinement
Crystal data, data collection and structure refinement details for (I)-(IV) are summarized in Table 5. The N-bound H atoms were located in difference maps and their positions freely refined [for (IV) they were refined as riding atoms in their asfound relative positions]. The C-bound H atoms were geometrically placed (C-H = 0.93-0.98 Å ) and refined as riding atoms. The constraint U iso (H) = 1.2U eq (carrier) or 1.5U eq (methyl carrier) was applied in all cases. The methyl H atoms (if any) were allowed to rotate, but not to tip, to best fit the electron density. Compound (II) crystallizes in space group P2 1 2 1 2 1 but the absolute structure was indeterminate in the present experiment. The crystal of (III) was found to contain highly disordered solvent molecules. Attempts to model the disorder were ineffective and the contribution to the scattering was removed with the SQUEEZE (Spek, 2015) option in PLATON (Spek, 2009), which revealed a solventaccessible volume of 244.3 Å 3 per unit cell and 19 'solvent' electrons per unit cell. The stated formula, molecular mass, density, etc. for (III) in Table 5 do not take the solvent into account.

(I) 1-(2-Phenyl-1H-indol-3-yl)ethanone
Special details Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes. Refinement. Refinement of F 2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F 2 , conventional R-factors R are based on F, with F set to zero for negative F 2 . The threshold expression of F 2 > 2sigma(F 2 ) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F 2 are statistically about twice as large as those based on F, and R-factors based on ALL data will be even larger.

Special details
Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes. Refinement. Refinement of F 2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F 2 , conventional R-factors R are based on F, with F set to zero for negative F 2 . The threshold expression of F 2 > 2sigma(F 2 ) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F 2 are statistically about twice as large as those based on F, and R-factors based on ALL data will be even larger.

Refinement
Refinement on F 2 Least-squares matrix: full R[F 2 > 2σ(F 2 )] = 0.036 wR(F 2 ) = 0.092 S = 1.08 3690 reflections 205 parameters 0 restraints Primary atom site location: structure-invariant direct methods Secondary atom site location: difference Fourier map Hydrogen site location: inferred from neighbouring sites H atoms treated by a mixture of independent and constrained refinement w = 1/[σ 2 (F o 2 ) + (0.0448P) 2 + 4.7609P] where P = (F o 2 + 2F c 2 )/3 (Δ/σ) max < 0.001 Δρ max = 0.28 e Å −3 Δρ min = −0.18 e Å −3 Special details Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes. Refinement. Refinement of F 2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F 2 , conventional R-factors R are based on F, with F set to zero for negative F 2 . The threshold expression of F 2 > 2sigma(F 2 ) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F 2 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 (Å 2 )
x y z U iso */U eq C1 0.31613 (5) 0.41861 (  Special details Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes. Refinement. Refinement of F 2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F 2 , conventional R-factors R are based on F, with F set to zero for negative F 2 . The threshold expression of F 2 > 2sigma(F 2 ) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F 2 are statistically about twice as large as those based on F, and R-factors based on ALL data will be even larger. Symmetry codes: (i) x+1, y, z; (ii) −x, y−1/2, −z+1/2; (iii) −x+1, y+1/2, −z+1/2; (iv) −x+1, −y+1, −z+1.