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Journal logoCRYSTALLOGRAPHIC
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ISSN: 2056-9890
Volume 72| Part 7| July 2016| Pages 964-968
https://doi.org/10.1107/S2056989016008616

Weak inter­actions in the crystal structures of two indole derivatives

CROSSMARK_Color_square_no_text.svg
Jamie R. Kerr,a Laurent Trembleau,a* John M. D. Storey,a James L. Wardella,b and William T. A. Harrisona*

aDepartment of Chemistry, University of Aberdeen, Meston Walk, Aberdeen AB24 3UE, Scotland, and bFundação Oswaldo Cruz, Instituto de Tecnologia em Fármacos-Far Manguinhos, 21041-250 Rio de Janeiro, RJ, Brazil
*Correspondence e-mail: l.trembleau@abdn.ac.uk, w.harrison@abdn.ac.uk

Edited by J. Simpson, University of Otago, New Zealand (Received 24 May 2016; accepted 28 May 2016; online 17 June 2016)

We describe the syntheses and crystal structures of two indole derivatives, namely a second monoclinic polymorph of ethyl 5-chloro-1H-indole-2-carboxyl­ate C11H10ClNO2, (I), and ethyl 5-chloro-3-iodo-1H-indole-2-carboxyl­ate, C11H9ClINO2, (II). In their crystal structures, both compounds form inversion dimers linked by pairs of N—H⋯O hydrogen bonds, which generate R22(10) loops. The dimers are linked into double chains in (I) and sheets in (II) by a variety of weak inter­actions, including π–π stacking, C—I⋯π, C—Cl—π inter­actions and I⋯Cl halogen bonds.

CCDC references: 1482360; 1482359

Similar articles

1. Chemical context

As part of our ongoing synthetic, biological (Kerr, 2013[Kerr, J. R. (2013). PhD Thesis `Allosteric modulation of the CB1 receptor'. University of Aberdeen.]) and structural studies (Kerr et al., 2016[Kerr, J. R., Trembleau, L., Storey, J. M. D., Wardell, J. L. & Harrison, W. T. A. (2016). Acta Cryst. E72, 699-703.]) of variously substituted indole derivatives, we now report the syntheses and crystal structures of ethyl 5-chloro-1H-indole-2-carboxyl­ate (I)[link] and ethyl 5-chloro-3-iodo-1H-indole-2-carboxyl­ate (II)[link], which differ in the substituent (H or I) at the 3-position of the ring system. Compound (I)[link] is a second monoclinic polymorph of the recently described 5-chloro-1H-indole-2-carboxyl­ate (Wu et al., 2013[Wu, J., Liu, Y.-L., Wu, H., Wang, H.-Y. & Zou, P. (2013). Z. Krist. New Cryst. Struct. 228, 185-186.]).

[Scheme 1]

2. Structural commentary

Compound (I)[link] crystallizes in space group P21/n with one mol­ecule in the asymmetric unit (Fig. 1[link]). The dihedral angle between the mean plane of the N1/C1–C8 indole ring system (r.m.s. deviation = 0.010 Å) and the C9/O1/O2 grouping is 2.4 (2)°. The chlorine atom deviates from the indole plane by 0.0625 (14) Å. The C8—C9—O1—C10 torsion angle of −178.86 (11)° indicates an anti conformation about the C9—O1 bond, whereas the C9—O1—C10—C11 torsion angle is −81.73 (14)° and C11 projects from the mean plane of the other non-hydrogen atoms by 1.298 (2) Å.

[Figure 1]
Figure 1
The mol­ecular structure of (I)[link] showing 50% displacement ellipsoids. Also shown with double-dashed lines are the pair of inter­molecular N—H⋯O hydrogen bonds to a nearby mol­ecule related by inversion symmetry, which generate an R22(10) loop. Symmetry code: (i) 1 − x, 2 − y, 1 − z.

In the structure reported by Wu et al. (2013[Wu, J., Liu, Y.-L., Wu, H., Wang, H.-Y. & Zou, P. (2013). Z. Krist. New Cryst. Struct. 228, 185-186.]), (CCDC refcode VIHMUW), the same mol­ecule also crystallizes in space group P21/n [a = 10.570 (3), b = 5.6165 (15), c = 18.091 (5) Å, β = 105.681 (4)°, V = 1034.0 (5) Å3, Z = 4]: the only significant conformational difference compared to (I)[link] is (using our atom-labelling scheme) the C9—O1—C10—C11 torsion angle of 173.19 (12)°, which indicates that the mol­ecule in the Wu et al. polymorph is almost planar (r.m.s. deviation = 0.031 Å for 15 non-hydrogen atoms). The densities of (I)[link] [ρ = 1.438 g cm−1] and the Wu polymorph [ρ = 1.437 g cm−1] are essentially identical.

There is one mol­ecule in the asymmetric unit of (II)[link], which crystallizes in space group P[\overline{1}], as shown in Fig. 2[link]. The C9/O1/O2 grouping is almost coplanar with the mean-plane of the indole ring system (r.m.s. deviation = 0.009 Å), as indicated by the dihedral angle of 3.95 (7)° between C1–C8/N1 and C9/O1/O2. Atoms Cl1 and I1 deviate from the indole plane by −0.106 (2) and 0.081 (2) Å, respectively. The conformation of the C8—C9—O1—C10 bond in (II)[link] [torsion angle = −177.42 (16)°] is almost the same as the equivalent grouping in (I)[link], but the C9—O1—C10—C11 torsion angle of −178.33 (17)° is quite different, and indeed, the complete mol­ecule of (II)[link] is almost planar (r.m.s. deviation = 0.033 Å for 16 non-hydrogen atoms).

[Figure 2]
Figure 2
The mol­ecular structure of (II)[link] showing 50% displacement ellipsoids. Also shown with double-dashed lines are the pair of inter­molecular N—H⋯O hydrogen bonds to a nearby mol­ecule related by inversion symmetry, which generate an R22(10) loop. Symmetry code: (i) −x, 2 − y, 1 − z.

3. Supra­molecular features

In the crystal of (I)[link], inversion dimers linked by pairs of N—H⋯Oi [symmetry code: (i) 1 − x, 2 − y, 1 − z] hydrogen bonds (Table 1[link], Fig. 1[link]) generate R22(10) loops. The first weak inter­action to consider is aromatic π–π stacking between the C1–C6 (π6) ring and the C1/C6/C7/C8/N1 (π5) five-membered ring displaced by translation in the b-axis direction (Fig. 3[link]). The π6–π5ii [symmetry code: (ii) x, 1 + y, z] centroid–centroid separation is 3.7668 (9) Å and the inter-plane angle is 1.30 (7)°. This inter­action appears to be reinforced by a weak C—Cl⋯π5ii bond (Chifotides & Dunbar, 2013[Chifotides, H. T. & Dunbar, K. R. (2013). Acc. Chem. Res. 46, 894-906.]); the chlorine atom lies almost directly above the centre of the six-membered ring displaced in [010] with Cl⋯π = 3.5363 (7) Å and C—Cl⋯π = 86.35 (5)°. This is very slightly shorter than the contact distance of 3.55 Å for a chlorine atom and a benzene ring, assuming a radius of 1.75 Å for Cl and a half-thickness of 1.8 Å for a benzene ring. Thus, each benzene ring faces a chlorine atom on one face and a five-membered ring on the other (Cl⋯π6⋯π5 = 154.5°). The carbonyl oxygen atom (O2) of the ester group lies in a reasonable orientation to partake in a C=O⋯π5 bond (Gao et al., 2009[Gao, X.-L., Lu, L.-P. & Zhu, M.-L. (2009). Acta Cryst. C65, o123-o127.]) but here the O⋯π5iii [symmetry code: (iii) x, y − 1, z] separation of 3.4068 (11) Å is significantly greater than the van der Waals' radius sum of 3.32 Å [C=O⋯π5 = 88.40 (8)° and O⋯π5⋯π6 = 153.9°] and can hardly be considered to be a bond. Taken together, the strong (N—H⋯O) and weak (π–π, Cl⋯π) bonds lead to [010] double chains in the extended structure of (I)[link].

Table 1
Hydrogen-bond geometry (Å, °) for (I)[link]

D—H⋯A D—H H⋯A D⋯A D—H⋯A
N1—H1⋯O2i 0.878 (17) 1.977 (17) 2.8288 (15) 163.0 (15)
Symmetry code: (i) -x+1, -y+2, -z+1.
[Figure 3]
Figure 3
Partial packing diagram for (I)[link], showing the formation of [010] chains linked by π–π and C—Cl⋯π inter­actions (yellow lines). The long C=O⋯π contact is indicated by a cyan line. All hydrogen atoms except H1 are omitted for clarity. Symmetry codes (ii) x, y + 1, z; (iii) x, y – 1, z.

Despite the fact that (I)[link] and the Wu et al. (2013[Wu, J., Liu, Y.-L., Wu, H., Wang, H.-Y. & Zou, P. (2013). Z. Krist. New Cryst. Struct. 228, 185-186.]) polymorph of the same phase crystallize in the same space group, their packing motifs are completely different. In the Wu phase, inversion dimers linked by pairs of N—H⋯O hydrogen bonds also occur but there is no aromatic π–π stacking (the shortest centroid–centroid separation is greater than 4.75 Å) and no C—Cl⋯π contacts. The only significant inter­action indicated by a PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]) analysis of the structure is a weak C—H⋯π5 bond (H⋯π = 2.72 Å). Considered by itself, this inter­action links the mol­ecules into [010] chains; taken together, the N—H⋯O and C—H⋯π inter­actions generate (110) sheets.

The crystal of (II)[link] also features inversion dimers linked by pairs of N—H⋯Oi [symmetry code: (i) −x, 2 − y, 1 − z] hydrogen bonds (Table 2[link], Fig. 2[link]) involving the equivalent atoms to (I)[link] with the same graph-set motif. Aromatic π–π stacking also occurs in the crystal of (II)[link], but this time the mol­ecules are related by inversion, rather than translation, symmetry: this operation `flips' one of the mol­ecules such that the six-membered ring in each mol­ecule overlaps the five-membered ring in the other (Fig. 6): the π6–π5ii [symmetry code: (ii) −x, 1 − y, 1 − z] separation of the centroids of the six- and five-membered rings is 3.6365 (14) Å and the inter-planar angle is 0.92 (13)°. The iodine atom of a mol­ecule displaced in the [100] direction lies above the inversion-generated five-membered ring to form a C—I⋯π5 bond with I1⋯π5iii [symmetry code: (iii) 1 − x, 1 − y, 1 − z] = 3.6543 (11) Å and C7—I1⋯π5iii = 87.00 (7)°. Thus, the five-membered ring faces a six-membered ring on one face and an I atom on the other (I⋯π5⋯π6 = 148.6°). The I atom also participates in a halogen bond (Desiraju et al., 2013[Desiraju, G. R., Ho, P. S., Kloo, L., Legon, A. C., Marquardt, R., Metrangolo, P., Politzer, P., Resnati, G. & Rissanen, K. (2013). Pure Appl. Chem. 85, 1711-1713.]) to the chlorine atom of an inversion-related mol­ecule with I1⋯Cl1iv [symmetry code: (iv) 1 − x, −y, 1 − z] = 3.6477 (6) Å (van der Waals contact distance = 3.73 Å), C7—I1⋯Cl1iv = 173.28 (5)° and C4iv—Cl1iv⋯I1 = 104.34 (5)°. These angles clearly define this inter­action as a type-II halogen bond (Pedireddi et al., 1994[Pedireddi, V. R., Reddy, D. S., Goud, B. S., Craig, D. C., Rae, A. D. & Desiraju, G. R. (1994). J. Chem. Soc. Perkin Trans. 2, pp. 2353-2360.]). Taken together, the weak and strong inter­actions lead to (001) sheets, with the centrosymmetric pairs of I⋯Cl halogen bonds and pairs of N—H⋯O hydrogen bonds alternating with respect to the [100] direction (Fig. 4[link]).

Table 2
Hydrogen-bond geometry (Å, °) for (II)[link]

D—H⋯A D—H H⋯A D⋯A D—H⋯A
N1—H1⋯O2i 0.77 (3) 2.06 (3) 2.821 (2) 168 (3)
Symmetry code: (i) -x, -y+2, -z+1.
[Figure 4]
Figure 4
Partial packing diagram for (II)[link], showing part of an (001) sheet. N—H⋯O hydrogen bonds are indicated by crimson lines, π–π and I⋯π inter­actions by yellow lines and I⋯Cl halogen bonds by green lines. All hydrogen atoms except H1 are omitted for clarity. Symmetry codes (i) −x, 2 − y, 1 − z; (ii) −x, 1 − y, 1 − z; (iii) 1 − x, 1 − y, 1 − z.

4. Database survey

A search of the Cambridge Structural Database (CSD; Groom et al., 2016[Groom, C. R., Bruno, I. J., Lightfoot, M. P. & Ward, S. C. (2016). Acta Cryst. B72, 171-179.]) revealed 24 indole derivatives with an ester group at the 2-position of the ring system. In terms of halogen substitution, there were 58 5-chloro and just two 3-iodo deriv­atives. As noted above, VIHMUW (Wu et al., 2013[Wu, J., Liu, Y.-L., Wu, H., Wang, H.-Y. & Zou, P. (2013). Z. Krist. New Cryst. Struct. 228, 185-186.]) is a polymorph of (I)[link]: crystals of this phase in the form of colourless prisms were obtained by recrystallization from ethanol solution at room temperature, compared to colourless needles obtained from methanol solution at room temperature in the present study.

There has recently been debate on the significance – or otherwise – of weak inter­molecular inter­actions in establishing the packing in mol­ecular crystals (Dunitz, 2015[Dunitz, J. D. (2015). IUCrJ, 2, 157-158.]; Thakur et al., 2015[Thakur, T. S., Dubey, R. & Desiraju, G. R. (2015). IUCrJ, 2, 159-160.]). The latter authors mentioned the role of weak inter­actions in establishing the structures of polymorphs and it is striking to us how different the packing motifs of (I)[link] and VIHMUW are.

5. Synthesis and crystallization

To prepare (I)[link], a mixture of ethyl 2-(2-[4-chloro­phen­yl]hydrazono)propano­ate (2.29 g, 9.51 mmol), prepared from p-chloro­phenyl­hydrazine hydro­chloride and ethyl pyruvate according to a published method (Zhang et al., 2011[Zhang, F., Zhao, Y., Sun, L., Ding, L., Gu, Y. & Gong, P. (2011). Eur. J. Med. Chem. 46, 3149-3157.]) and PPA (22.54 g) were refluxed in toluene (40 ml) for 3 h. After cooling, the solvent was deca­nted off and the solid residue was washed with toluene (3 × 50 ml). Evaporation of the combined organic phases under reduced pressure gave a yellow solid, flash chromatography of which (1:6 ethyl acetate, hexa­nes) afforded ethyl 5-chloro-1H-indole-2-carboxyl­ate as a yellow solid (1.34 g, 63%). Colourless needles of (I)[link] were recrystallized from methanol solution at room temperature. δC(101 MHz; CDCl3) 162.0 (Cq), 135.2 (Cq), 128.9 (Cq), 128.6 (Cq), 126.7 (Cq), 126.0 (CH), 121.9 (CH), 113.1 (CH), 108.1 (CH), 61.5 (CH2) and 14.5 (CH3); δH(400 MHz; CDCl3) 8.91 (1 H, br s), 7.67 (1 H, s), 7.35–7.28 (2 H, m), 7.15 (1 H, s), 4.41 (2 H, q, J 7.1) and 1.41 (3 H, t, J 7.1); Rf 0.29 (1:6 EtOAc, hexa­nes); m.p. 440–441 K; IR (Nujol, cm−1) 3310, 1728, 1697, 1264, 1080 and 877; HRMS (ESI) for C11H1135ClNO2 [M + H]+ calculated 224.0479, found 224.0466.

To prepare (II)[link], potassium hydroxide (1.804 g, 32.2 mmol) was added to a solution of (I)[link] (1.215 g, 5.43 mmol) in dry DMF (6.0 ml) at 273 K and stirred for 10 min. Separately, a solution of iodine (1.710 g, 6.74 mmol) in dry DMF (6.75 ml) was prepared. The two liquids were combined and stirred over ice for 90 min. Pouring the reaction mixture into a saturated aqueous solution of ammonium chloride and sodium thio­sulfate (60 ml) precipitated a brown solid. This was collected by filtration and purified by flash chromatography (1:8 ethyl acetate, hexa­nes) to afford ethyl 5-chloro-3-iodo-1H-indole-2-carboxyl­ate as a yellow solid (1.825 g, 80%). Pale-yellow plates of (II)[link] were recrystallized from methanol solution at room temperature. δC(101 MHz; DMSO-d6) 160.5 (Cq), 135.8 (Cq), 132.1 (Cq), 128.9 (Cq), 126.5 (CH), 126.3 (Cq), 121.8 (CH), 115.4 (CH), 65.2 (Cq), 61.4 (CH2) and 14.6 (CH3); δH(400 MHz; DMSO-d6) 12.42 (1 H, br s), 7.47 (1 H, d, J 8.4), 7.39 (1 H, d, J 1.6), 7.31 (1 H, dd, J 2.0, 9.2), 4.36 (2 H, q, J 7.2) and 1.36 (3 H, t, J 7.0); Rf 0.13 (1:8 ethyl acetate, hexa­nes); m.p. 412 K, IR (KBr, cm−1) 3291, 2977, 1744, 1683, 1514, 1332, 1115, 1080, 772, 749 and 604; HRMS (ESI) for C11H1035ClINO2 [M + H]+ calculated 349.9445, found 349.9453.

6. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 3[link]. The N-bound H atoms were located in difference maps and their positions freely refined. The C-bound H atoms were placed geometrically (C—H = 0.93–0.98 Å) and refined as riding atoms. The constraint Uiso(H) = 1.2Ueq(carrier) or 1.5Ueq(methyl carrier) was applied in all cases. The –CH3 groups were allowed to rotate, but not to tip, to best fit the electron density.

Table 3
Experimental details

  (I) (II)
Crystal data
Chemical formula C11H10ClNO2 C11H9ClINO2
Mr 223.65 349.54
Crystal system, space group Monoclinic, P21/n Triclinic, P[\overline{1}]
Temperature (K) 100 100
a, b, c (Å) 13.7168 (6), 4.5783 (1), 16.5929 (11) 7.7733 (5), 7.8240 (5), 10.4594 (7)
α, β, γ (°) 90, 97.464 (7), 90 86.085 (8), 80.575 (7), 71.308 (6)
V (Å3) 1033.20 (9) 594.35 (7)
Z 4 2
Radiation type Mo Kα Mo Kα
μ (mm−1) 0.35 2.90
Crystal size (mm) 0.70 × 0.04 × 0.03 0.17 × 0.10 × 0.02
 
Data collection
Diffractometer Rigaku Mercury CCD Rigaku Mercury CCD
Absorption correction Multi-scan (CrystalClear; Rigaku, 2012[Rigaku (2012). CrystalClear. Rigaku Corporation, Tokyo, Japan.]) Multi-scan (CrystalClear; Rigaku, 2012[Rigaku (2012). CrystalClear. Rigaku Corporation, Tokyo, Japan.])
Tmin, Tmax 0.793, 0.990 0.638, 0.944
No. of measured, independent and observed [I > 2σ(I)] reflections 7035, 2340, 2051 7837, 2739, 2640
Rint 0.022 0.031
(sin θ/λ)max (Å−1) 0.649 0.650
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.031, 0.082, 1.09 0.022, 0.058, 1.04
No. of reflections 2340 2739
No. of parameters 139 149
H-atom treatment H atoms treated by a mixture of independent and constrained refinement H atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å−3) 0.33, −0.23 1.18, −0.44
Computer programs: CrystalClear (Rigaku, 2012[Rigaku (2012). CrystalClear. Rigaku Corporation, Tokyo, Japan.]), SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]), SHELXL2014 (Sheldrick, 2015[Sheldrick, G. M. (2015). Acta Cryst. C71, 3-8.]), ORTEP-3 for Windows (Farrugia, 2012[Farrugia, L. J. (2012). J. Appl. Cryst. 45, 849-854.]), ATOMS (Dowty, 2006[Dowty, E. W. (2006). ATOMS. Shape Software, Kingsport, Tennessee, USA.]) and publCIF (Westrip, 2010[Westrip, S. P. (2010). J. Appl. Cryst. 43, 920-925.]).

Supporting information

CCDC references: 1482360; 1482359

Crystal structure: contains datablocks I, II, global. DOI: https://doi.org/10.1107/S2056989016008616/sj5499sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989016008616/sj5499Isup2.hkl

Structure factors: contains datablock II. DOI: https://doi.org/10.1107/S2056989016008616/sj5499IIsup3.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2056989016008616/sj5499Isup4.cml

Supporting information file. DOI: https://doi.org/10.1107/S2056989016008616/sj5499IIsup5.cml

checkCIF report


Computing details top

For both compounds, data collection: CrystalClear (Rigaku, 2012); cell refinement: CrystalClear (Rigaku, 2012); data reduction: CrystalClear (Rigaku, 2012); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012) and ATOMS (Dowty, 2006); software used to prepare material for publication: publCIF (Westrip, 2010).

(I) Ethyl 5-chloro-1H-indole-2-carboxylate top
Crystal data top
C11H10ClNO2F(000) = 464
Mr = 223.65Dx = 1.438 Mg m−3
Monoclinic, P21/nMo Kα radiation, λ = 0.71073 Å
a = 13.7168 (6) ÅCell parameters from 6396 reflections
b = 4.5783 (1) Åθ = 3.0–27.5°
c = 16.5929 (11) ŵ = 0.35 mm−1
β = 97.464 (7)°T = 100 K
V = 1033.20 (9) Å3Rod, colourless
Z = 40.70 × 0.04 × 0.03 mm
Data collection top
Rigaku Mercury CCD
diffractometer		2051 reflections with I > 2σ(I)
ω scansRint = 0.022
Absorption correction: multi-scan
(CrystalClear; Rigaku, 2012)		θmax = 27.5°, θmin = 3.0°
Tmin = 0.793, Tmax = 0.990h = −17→17
7035 measured reflectionsk = −4→5
2340 independent reflectionsl = −19→21
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullHydrogen site location: mixed
R[F2 > 2σ(F2)] = 0.031H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.082 w = 1/[σ2(Fo2) + (0.0408P)2 + 0.4177P]
where P = (Fo2 + 2Fc2)/3
S = 1.09(Δ/σ)max < 0.001
2340 reflectionsΔρmax = 0.33 e Å−3
139 parametersΔρmin = −0.23 e Å−3
0 restraints
Special details top

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
C10.52594 (9)0.5040 (3)0.35005 (8)0.0142 (3)
C20.62255 (10)0.4033 (3)0.35004 (8)0.0176 (3)
H20.67420.46690.38990.021*
C30.63988 (9)0.2090 (3)0.29013 (8)0.0171 (3)
H30.70440.13600.28830.021*
C40.56188 (10)0.1181 (3)0.23127 (8)0.0153 (3)
C50.46670 (9)0.2127 (3)0.23045 (8)0.0146 (3)
H50.41570.14590.19050.017*
C60.44761 (9)0.4121 (3)0.29091 (8)0.0134 (3)
C70.36151 (9)0.5605 (3)0.30827 (8)0.0136 (3)
H70.29720.54340.27950.016*
C80.38999 (9)0.7341 (3)0.37519 (7)0.0135 (3)
C90.33337 (9)0.9388 (3)0.41806 (7)0.0133 (3)
C100.17639 (10)1.1516 (3)0.42258 (8)0.0174 (3)
H10A0.11861.20250.38290.021*
H10B0.21341.33340.43760.021*
C110.14202 (11)1.0204 (4)0.49746 (9)0.0271 (3)
H11A0.10021.16100.52140.041*
H11B0.10440.84210.48250.041*
H11C0.19910.97280.53710.041*
N10.48871 (8)0.6981 (3)0.40047 (7)0.0147 (2)
H10.5235 (12)0.789 (4)0.4411 (10)0.018*
O10.23886 (6)0.9493 (2)0.38517 (5)0.0152 (2)
O20.36753 (7)1.0841 (2)0.47654 (6)0.0184 (2)
Cl10.58935 (2)−0.12275 (8)0.15557 (2)0.01929 (11)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.0137 (6)0.0138 (6)0.0147 (6)−0.0016 (5)−0.0002 (5)0.0003 (5)
C20.0128 (6)0.0196 (7)0.0193 (6)−0.0010 (5)−0.0026 (5)−0.0010 (5)
C30.0123 (6)0.0175 (7)0.0213 (7)0.0013 (5)0.0012 (5)0.0009 (6)
C40.0175 (6)0.0126 (6)0.0164 (6)−0.0001 (5)0.0040 (5)−0.0007 (5)
C50.0144 (6)0.0146 (6)0.0140 (6)−0.0017 (5)−0.0008 (5)0.0004 (5)
C60.0134 (6)0.0126 (6)0.0135 (6)−0.0014 (5)−0.0007 (5)0.0020 (5)
C70.0130 (6)0.0140 (6)0.0134 (6)−0.0011 (5)−0.0004 (4)0.0008 (5)
C80.0122 (6)0.0149 (6)0.0129 (6)−0.0012 (5)−0.0007 (4)0.0014 (5)
C90.0142 (6)0.0132 (6)0.0122 (6)−0.0014 (5)0.0007 (4)0.0025 (5)
C100.0149 (6)0.0169 (7)0.0203 (7)0.0043 (5)0.0013 (5)−0.0010 (5)
C110.0248 (7)0.0318 (9)0.0265 (8)0.0035 (7)0.0106 (6)0.0017 (7)
N10.0125 (5)0.0175 (6)0.0130 (5)−0.0004 (5)−0.0023 (4)−0.0027 (4)
O10.0126 (4)0.0171 (5)0.0154 (4)0.0015 (4)−0.0005 (3)−0.0023 (4)
O20.0164 (5)0.0218 (5)0.0158 (5)−0.0001 (4)−0.0018 (4)−0.0050 (4)
Cl10.01786 (17)0.01983 (19)0.02054 (18)0.00168 (13)0.00388 (12)−0.00493 (13)
Geometric parameters (Å, º) top
C1—N11.3644 (18)C7—H70.9500
C1—C21.4032 (18)C8—N11.3744 (16)
C1—C61.4215 (17)C8—C91.4599 (19)
C2—C31.3774 (19)C9—O21.2187 (16)
C2—H20.9500C9—O11.3405 (15)
C3—C41.4145 (19)C10—O11.4543 (16)
C3—H30.9500C10—C111.5098 (19)
C4—C51.3739 (18)C10—H10A0.9900
C4—Cl11.7488 (14)C10—H10B0.9900
C5—C61.4059 (18)C11—H11A0.9800
C5—H50.9500C11—H11B0.9800
C6—C71.4240 (18)C11—H11C0.9800
C7—C81.3800 (18)N1—H10.878 (17)
N1—C1—C2130.00 (12)N1—C8—C9119.57 (11)
N1—C1—C6107.86 (11)C7—C8—C9130.46 (12)
C2—C1—C6122.13 (13)O2—C9—O1123.78 (12)
C3—C2—C1117.63 (12)O2—C9—C8124.37 (12)
C3—C2—H2121.2O1—C9—C8111.85 (11)
C1—C2—H2121.2O1—C10—C11111.24 (12)
C2—C3—C4120.17 (12)O1—C10—H10A109.4
C2—C3—H3119.9C11—C10—H10A109.4
C4—C3—H3119.9O1—C10—H10B109.4
C5—C4—C3123.13 (12)C11—C10—H10B109.4
C5—C4—Cl1119.00 (10)H10A—C10—H10B108.0
C3—C4—Cl1117.87 (10)C10—C11—H11A109.5
C4—C5—C6117.55 (12)C10—C11—H11B109.5
C4—C5—H5121.2H11A—C11—H11B109.5
C6—C5—H5121.2C10—C11—H11C109.5
C5—C6—C1119.38 (12)H11A—C11—H11C109.5
C5—C6—C7133.66 (12)H11B—C11—H11C109.5
C1—C6—C7106.95 (11)C1—N1—C8108.85 (11)
C8—C7—C6106.38 (11)C1—N1—H1124.7 (11)
C8—C7—H7126.8C8—N1—H1126.4 (11)
C6—C7—H7126.8C9—O1—C10116.19 (10)
N1—C8—C7109.96 (12)
N1—C1—C2—C3−178.66 (14)C1—C6—C7—C80.37 (15)
C6—C1—C2—C3−0.1 (2)C6—C7—C8—N1−0.63 (15)
C1—C2—C3—C40.2 (2)C6—C7—C8—C9178.10 (13)
C2—C3—C4—C5−0.5 (2)N1—C8—C9—O2−0.4 (2)
C2—C3—C4—Cl1178.63 (11)C7—C8—C9—O2−178.99 (14)
C3—C4—C5—C60.8 (2)N1—C8—C9—O1179.38 (11)
Cl1—C4—C5—C6−178.38 (10)C7—C8—C9—O10.8 (2)
C4—C5—C6—C1−0.67 (19)C2—C1—N1—C8178.35 (14)
C4—C5—C6—C7178.26 (14)C6—C1—N1—C8−0.40 (15)
N1—C1—C6—C5179.20 (11)C7—C8—N1—C10.65 (15)
C2—C1—C6—C50.3 (2)C9—C8—N1—C1−178.23 (12)
N1—C1—C6—C70.01 (15)O2—C9—O1—C100.89 (18)
C2—C1—C6—C7−178.85 (12)C8—C9—O1—C10−178.86 (11)
C5—C6—C7—C8−178.65 (14)C11—C10—O1—C9−81.73 (14)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···O2i0.878 (17)1.977 (17)2.8288 (15)163.0 (15)
Symmetry code: (i) −x+1, −y+2, −z+1.
(II) Ethyl 5-chloro-3-iodo-1H-indole-2-carboxylate top
Crystal data top
C11H9ClINO2Z = 2
Mr = 349.54F(000) = 336
Triclinic, P1Dx = 1.953 Mg m−3
a = 7.7733 (5) ÅMo Kα radiation, λ = 0.71073 Å
b = 7.8240 (5) ÅCell parameters from 7985 reflections
c = 10.4594 (7) Åθ = 2.7–27.5°
α = 86.085 (8)°µ = 2.90 mm−1
β = 80.575 (7)°T = 100 K
γ = 71.308 (6)°Plate, colourless
V = 594.35 (7) Å30.17 × 0.10 × 0.02 mm
Data collection top
Rigaku Mercury CCD
diffractometer		2640 reflections with I > 2σ(I)
ω scansRint = 0.031
Absorption correction: multi-scan
(CrystalClear; Rigaku, 2012)		θmax = 27.5°, θmin = 2.8°
Tmin = 0.638, Tmax = 0.944h = −8→10
7837 measured reflectionsk = −10→10
2739 independent reflectionsl = −12→13
Refinement top
Refinement on F20 restraints
Least-squares matrix: fullHydrogen site location: mixed
R[F2 > 2σ(F2)] = 0.022H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.058 w = 1/[σ2(Fo2) + (0.0409P)2 + 0.1325P]
where P = (Fo2 + 2Fc2)/3
S = 1.04(Δ/σ)max = 0.002
2739 reflectionsΔρmax = 1.18 e Å−3
149 parametersΔρmin = −0.44 e Å−3
Special details top

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
C10.0847 (3)0.5746 (3)0.6457 (2)0.0165 (4)
C2−0.0166 (3)0.5738 (3)0.7698 (2)0.0190 (4)
H2−0.09560.68240.80970.023*
C30.0037 (3)0.4078 (3)0.8316 (2)0.0204 (4)
H3−0.06310.40130.91540.024*
C40.1227 (3)0.2486 (3)0.7712 (2)0.0185 (4)
C50.2249 (3)0.2468 (3)0.6505 (2)0.0176 (4)
H50.30450.13740.61220.021*
C60.2064 (3)0.4142 (3)0.5863 (2)0.0160 (4)
C70.2860 (3)0.4665 (3)0.46397 (19)0.0144 (4)
C80.2117 (3)0.6518 (3)0.45207 (19)0.0155 (4)
C90.2427 (3)0.7849 (3)0.3534 (2)0.0162 (4)
C100.4005 (3)0.8407 (3)0.1517 (2)0.0196 (4)
H10A0.45840.91850.18790.023*
H10B0.28630.91830.12110.023*
C110.5308 (3)0.7311 (3)0.0411 (2)0.0260 (5)
H11A0.56870.8125−0.02470.039*
H11B0.46860.66120.00240.039*
H11C0.63920.64880.07400.039*
N10.0899 (2)0.7153 (2)0.56278 (17)0.0159 (3)
H10.030 (4)0.814 (4)0.576 (3)0.019*
O10.3601 (2)0.71212 (19)0.24936 (14)0.0179 (3)
O20.1685 (2)0.9465 (2)0.36622 (16)0.0232 (3)
Cl10.14126 (8)0.04416 (8)0.85625 (5)0.02534 (12)
I10.48122 (2)0.28666 (2)0.33716 (2)0.01543 (6)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.0128 (9)0.0169 (9)0.0192 (10)−0.0027 (7)−0.0041 (7)−0.0020 (8)
C20.0143 (9)0.0213 (10)0.0191 (10)−0.0020 (8)−0.0017 (7)−0.0036 (8)
C30.0156 (9)0.0278 (11)0.0163 (10)−0.0053 (8)−0.0015 (7)0.0002 (8)
C40.0171 (9)0.0168 (9)0.0207 (10)−0.0044 (8)−0.0049 (8)0.0049 (8)
C50.0139 (9)0.0160 (9)0.0207 (10)−0.0013 (8)−0.0038 (7)0.0001 (8)
C60.0135 (9)0.0170 (9)0.0168 (9)−0.0027 (7)−0.0038 (7)−0.0015 (7)
C70.0126 (8)0.0125 (8)0.0171 (9)−0.0024 (7)−0.0021 (7)−0.0009 (7)
C80.0129 (8)0.0163 (9)0.0169 (9)−0.0031 (7)−0.0033 (7)−0.0016 (7)
C90.0144 (9)0.0143 (9)0.0195 (10)−0.0038 (7)−0.0025 (7)−0.0004 (7)
C100.0222 (10)0.0162 (9)0.0197 (10)−0.0068 (8)−0.0013 (8)0.0043 (8)
C110.0347 (12)0.0227 (11)0.0205 (11)−0.0121 (10)0.0024 (9)−0.0009 (8)
N10.0139 (8)0.0129 (8)0.0186 (8)−0.0010 (6)−0.0016 (6)−0.0018 (6)
O10.0206 (7)0.0125 (6)0.0188 (7)−0.0044 (6)−0.0001 (6)0.0020 (5)
O20.0240 (8)0.0135 (7)0.0268 (8)−0.0018 (6)0.0023 (6)−0.0001 (6)
Cl10.0254 (3)0.0228 (3)0.0242 (3)−0.0060 (2)−0.0008 (2)0.0092 (2)
I10.01470 (9)0.01248 (9)0.01706 (9)−0.00172 (6)−0.00130 (6)−0.00153 (6)
Geometric parameters (Å, º) top
C1—N11.361 (3)C7—I12.0660 (19)
C1—C21.405 (3)C8—N11.380 (3)
C1—C61.417 (3)C8—C91.463 (3)
C2—C31.384 (3)C9—O21.216 (3)
C2—H20.9500C9—O11.330 (2)
C3—C41.409 (3)C10—O11.453 (2)
C3—H30.9500C10—C111.515 (3)
C4—C51.376 (3)C10—H10A0.9900
C4—Cl11.752 (2)C10—H10B0.9900
C5—C61.406 (3)C11—H11A0.9800
C5—H50.9500C11—H11B0.9800
C6—C71.421 (3)C11—H11C0.9800
C7—C81.383 (3)N1—H10.77 (3)
N1—C1—C2129.80 (19)N1—C8—C9117.43 (17)
N1—C1—C6108.08 (18)C7—C8—C9133.80 (19)
C2—C1—C6122.11 (19)O2—C9—O1123.5 (2)
C3—C2—C1117.05 (19)O2—C9—C8122.96 (19)
C3—C2—H2121.5O1—C9—C8113.50 (17)
C1—C2—H2121.5O1—C10—C11106.61 (17)
C2—C3—C4120.58 (19)O1—C10—H10A110.4
C2—C3—H3119.7C11—C10—H10A110.4
C4—C3—H3119.7O1—C10—H10B110.4
C5—C4—C3123.23 (19)C11—C10—H10B110.4
C5—C4—Cl1119.08 (16)H10A—C10—H10B108.6
C3—C4—Cl1117.69 (16)C10—C11—H11A109.5
C4—C5—C6117.06 (19)C10—C11—H11B109.5
C4—C5—H5121.5H11A—C11—H11B109.5
C6—C5—H5121.5C10—C11—H11C109.5
C5—C6—C1119.95 (19)H11A—C11—H11C109.5
C5—C6—C7133.51 (19)H11B—C11—H11C109.5
C1—C6—C7106.53 (18)C1—N1—C8109.37 (17)
C8—C7—C6107.32 (17)C1—N1—H1124 (2)
C8—C7—I1129.30 (15)C8—N1—H1127 (2)
C6—C7—I1123.36 (14)C9—O1—C10115.06 (16)
N1—C8—C7108.70 (18)
N1—C1—C2—C3179.0 (2)C1—C6—C7—I1178.14 (13)
C6—C1—C2—C3−1.6 (3)C6—C7—C8—N10.2 (2)
C1—C2—C3—C40.5 (3)I1—C7—C8—N1−178.26 (13)
C2—C3—C4—C50.4 (3)C6—C7—C8—C9176.9 (2)
C2—C3—C4—Cl1179.75 (16)I1—C7—C8—C9−1.5 (3)
C3—C4—C5—C6−0.2 (3)N1—C8—C9—O21.2 (3)
Cl1—C4—C5—C6−179.59 (15)C7—C8—C9—O2−175.3 (2)
C4—C5—C6—C1−0.8 (3)N1—C8—C9—O1−179.20 (16)
C4—C5—C6—C7−179.7 (2)C7—C8—C9—O14.3 (3)
N1—C1—C6—C5−178.72 (18)C2—C1—N1—C8179.1 (2)
C2—C1—C6—C51.7 (3)C6—C1—N1—C8−0.4 (2)
N1—C1—C6—C70.5 (2)C7—C8—N1—C10.1 (2)
C2—C1—C6—C7−179.05 (18)C9—C8—N1—C1−177.20 (17)
C5—C6—C7—C8178.7 (2)O2—C9—O1—C102.2 (3)
C1—C6—C7—C8−0.4 (2)C8—C9—O1—C10−177.42 (16)
C5—C6—C7—I1−2.8 (3)C11—C10—O1—C9−178.33 (17)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···O2i0.77 (3)2.06 (3)2.821 (2)168 (3)
Symmetry code: (i) −x, −y+2, −z+1.
 

Acknowledgements

We thank the EPSRC National Crystallography Service (University of Southampton) for the data collections and the EPSRC National Mass Spectrometry Service (University of Swansea) for the HRMS data.

References

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ISSN: 2056-9890
Volume 72| Part 7| July 2016| Pages 964-968
https://doi.org/10.1107/S2056989016008616
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