Crystal structures and Hirshfeld analysis of 4,6-di­bromo­indole­nine and its quaternized salt

Konovalova, I.S.; Shishkina, S.V.; Kobzev, D.; Semenova, O.; Tatarets, A.

doi:10.1107/S2056989021011385

research communications

CRYSTALLOGRAPHIC
COMMUNICATIONS

ISSN: 2056-9890

Volume 77| Part 12| December 2021| Pages 1203-1207

https://doi.org/10.1107/S2056989021011385

Open

access

Crystal structures and Hirshfeld analysis of 4,6-dibromoindolenine and its quaternized salt

Irina S. Konovalova,^a ^* Svitlana V. Shishkina,^a Dmytro Kobzev,^a,^b Olha Semenova ^a,^b and Anatoliy Tatarets ^a

^aState Scientific Institution Institute for Single Crystals of the National Academy of Sciences of Ukraine, 61001, Kharkov, Ukraine, and ^bDepartment of Chemical Sciences, Ariel University, Ariel, 40700, Israel
^*Correspondence e-mail: ikonovalova0210@gmail.com

Edited by A. Briceno, Venezuelan Institute of Scientific Research, Venezuela (Received 5 October 2021; accepted 28 October 2021; online 2 November 2021)

4,6-Dibromo-2,3,3-trimethyl-3H-indole, C₁₁H₁₁Br₂N, exists as a neutral molecule in the asymmetric unit. The asymmetric unit of 4,6-dibromo-2,3,3-trimethyl-3H-indol-1-ium iodide, C₁₂H₁₄Br₂N⁺·I⁻, contains one organic cation and one iodine anion. The positive charge is localized on the quaternized nitrogen atom. In the crystal, molecules of 4,6-dibromoindolenine are linked by C—Br⋯π halogen bonds, forming zigzag chains propagating in the [001] direction. The molecules of the salt form layers parallel to the (010) plane where they are linked by C—H⋯Br hydrogen bonds, C—Br⋯Br and C—Br⋯I halogen bonds. The Hirshfeld surface analysis and two dimensional fingerprint plots were used to analyse the intermolecular contacts present in both crystals.

Keywords: crystal structure; Hirshfeld surface; 4,6-dibromo-2,3,3-trimethyl-3H-indole; quaternized salt.

CCDC references: 2118325; 2118324

1. Chemical context

The structural analysis of 2,3,3-trimethyl-3H-indole (2,3,3-trimethylindolenine) and its quaternized salts (Lynch et al., 2012 ; Connell et al., 2014 ) plays a crucial role in understanding the mechanisms of the chemical reactions resulting in various functional products. These intermediates are promising scaffolds for the synthesis of indolenine-containing fluorescent dyes, including highly versatile cyanine (Sun et al., 2016 ; Feng et al., 2020 ) and squaraine dyes (Beverina & Salice, 2010 ). The incorporation of heavy atoms in the molecule, such as bromine and iodine, increases the generation of reactive species during photosensitization (Szaciłowski et al., 2005 ; Semenova et al., 2021 ). In particular, fluorescent dyes with bromine atoms are utilized for photodynamic therapy applications (Atchison et al., 2017 ; Liu et al., 2021 ). Moreover, cyanine with the 4,6-dibromoindolenine moiety indicates excellent properties for optical tumor imaging by its fluorescence (Guerrero et al., 2017 ).

In this work, we carried out an X-ray diffraction and Hirshfeld surface analysis of 4,6-dibromoindolenine (1) and its quaternized salt (2), crystals of which were obtained by sequential synthesis starting from 3,5-dibromoaniline (3) by its diazotization with nitrosylsulfuric acid in sulfuric acid followed by reduction of the diazonium salt 4 with tin(II) chloride. The resulting 3,5-dibromophenylhydrazine was refluxed with 3-methyl-2-butanone in acetic acid to give 4,6-dibromoindolenine, 1, which after N-alkylation with the excess of iodomethane in benzene solution forms crystals of the quaternized indolium salt 2 (Fig. 1).

Figure 1
Synthesis of the title compounds 1 and 2.

2. Structural commentary

In the crystal, 4,6-dibromo-2,3,3-trimethyl-3H-indole, 1, exists as one neutral molecule in the asymmetric unit (Fig. 2). The quaternized molecule 2 exists as a salt with an iodine anion in the crystal phase (Fig. 2). All atoms of the quaternized cation, with exception of the C9 atom and the hydrogen atoms of the C10H₃ and C11H₃ methyl groups are located in a special position relative to the symmetry plane. In compound 2, the positive charge is localized on the nitrogen atom, which is caused by its quaternization. The N1—C11 bond is shortened to 1.460 (10) Å in comparison with the mean value of 1.485 Å for an N—Csp³ bond (Burgi & Dunitz, 1994 ). An analysis of the bond lengths in both structures showed that they are typical of those in similar compounds (Seiler et al., 2018 ; Connell et al., 2014; Holliman et al., 2009 ; Bellêtete et al., 1993 ).

Figure 2
Molecular structure of compounds 1 and 2 with the atom labelling. Displacement ellipsoids are drawn at the 50% probability level.

3. Supramolecular features

In the crystal, molecules of 1 form zigzag chains in the [001] direction as a result of the formation of intermolecular C3—Br1⋯N1(π) and C3—Br1⋯C8(π) halogen bonds (Table 1, Fig. 3). Neighbouring chains are linked by weak C11—H11C⋯N1 hydrogen bonds (Table 1). It should be noted that only one of the bromine atoms participates in these interactions. The presence of the iodide anion in compound 2 leads to the complete involvement of both bromine atoms in the formation of intermolecular interactions. As a result, molecules of 2 form chains in the [100] direction as a result of the C2—H2⋯Br2 hydrogen bond and C5—Br2⋯Br1 halogen bond (Table 2, Fig. 4). Neighbouring chains are connected through the bridged iodide anion by the strong C3—Br1⋯I1 halogen bond and C11—H⋯I1 hydrogen bond. Layers parallel to the (010) plane can be recognized as a structural motif in the structure of 2 (Table 2).

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

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
C3—Br1⋯N1ⁱ	1.89 (1)	3.19	5.283 (1)	166
C3—Br1⋯C8ⁱ	1.89 (1)	3.53	5.046 (1)	153
C11—H11C⋯N1ⁱⁱ	0.96	2.69	3.621 (1)	164
Symmetry codes: (i) $[-x+{\script{1\over 2}}, -y+1, z+{\script{1\over 2}}]$ ; (ii) $[x+{\script{1\over 2}}, -y+{\script{3\over 2}}, -z+1]$ .

Table 2
Hydrogen-bond geometry (Å, °) for 2

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
C2—H2⋯Br2ⁱ	0.93	3.05	3.872 (1)	149
C5—Br2⋯Br1ⁱⁱ	1.88 (1)	3.58	5.397 (1)	162
C3—Br1⋯I1ⁱⁱⁱ	1.90 (1)	3.62	5.514 (1)	176
C11—H11A⋯I1^iv	0.96	3.14	3.881 (1)	135
Symmetry codes: (i) ; (ii) x+1, y, z; (iii) ; (iv) .

Figure 3
Zigzag chains in the crystal of compound 1.

Figure 4
The chains (left) and layers (right) in the crystal of compound 2.

4. Hirshfeld surface analysis

Crystal Explorer 17.5 (Turner et al., 2017 ) was used to analyse the interactions in the structures and fingerprint plots mapped over d_norm (Figs. 5–7 ) were generated. The molecular Hirshfeld surfaces were obtained using a standard (high) surface resolution with the three-dimensional d_norm surfaces mapped over a fixed colour scale of −0.1256 (red) to 1.401 (blue). The areas in red on the d_norm-mapped Hirshfeld surfaces (Fig. 5) correspond to contacts that are shorter than van der Waals radii sum of the closest atoms. As can be seen in Fig. 5, short contacts in 1 are present at the nitrogen and Br1 atoms. In 2, the areas of short contacts are located at both the bromine atoms, the iodine atom and the hydrogen atoms of the methyl groups (Fig. 5). All of the intermolecular interactions of the title compounds are shown in the two-dimensional fingerprint plot presented in Figs. 6 and 7. The contribution of the Br⋯H/H⋯Br contacts, corresponding to the C—H⋯Br interaction, is represented by a pair of sharp spikes. The interactions appear in the middle of the scattered points in the two-dimensional fingerprint plot with a contribution to the overall Hirshfeld surface of 30.3% (Fig. 6c) and 18.0% (Fig. 7c). The fingerprint plots indicate that the principal contributions are from H⋯H (38.3% (Fig. 6b) in 1; 41.8% (Fig. 7b) in 2), C⋯H/H⋯C (13.3%; Fig. 6d in structure 1) and I⋯H/H⋯I (17.1%; Fig. 7d in structure 2) contacts. The fingerprint plots also indicate that all intermolecular interactions in the title compounds are rather weak.

Figure 5
The Hirshfeld surface of compounds 1 and 2 mapped over d_norm.

Figure 6
(a) The two-dimensional fingerprint plot for compound 1, and those delineated into (b) H⋯H (38.3%), (c) Br⋯H/H⋯Br (30.3%), (d) C⋯H/H⋯C (13.3%), (e) Br⋯C/C⋯Br (7.4%) and (f) N⋯H/H⋯N (5.8%) contacts.

Figure 7
(a) The two-dimensional fingerprint plot for compound 2, and those delineated into (b) H⋯H (41.8%), (c) Br⋯H/H⋯Br (18.0%), (d) I⋯H/H⋯I (17.1%), (e) Br⋯C/C⋯Br (9.8%) (f) Br⋯I/I⋯Br (4.3%) and Br⋯Br (3.3%) contacts.

5. Database survey

A search of the Cambridge Structural Database (CSD, Version 5.42, update of November 2020; Groom et al., 2016 ) for the 2,3,3-trimethyl-3H-indole skeleton yielded 306 hits. The most similar to the title compounds are 5,7-dibromo-2,3,3-trimethyl-3H-indole (CSD refcode KOFRII; Holliman et al., 2009) and 1,2,3,3-tetramethyl-3H-indolium iodide (NENZAJ01; Connell et al., 2014). These compounds have a very similar molecular structure and differ only in the position of the substituents.

6. Synthesis and crystallization

Synthesis of 4,6-dibromo-2,3,3-trimethyl-3H-indole (1)

3,5-Dibromophenyl)hydrazine hydrochloride (5) (3.3 g, 11 mmol) and 3-methyl-2-butanone (1.8 mL, 16.8 mmol) were refluxed in 15 mL of acetic acid for 5 h. The acetic acid was evaporated and the residue was washed with a 5% aqueous solution Na₂CO₃ (20 mL) and then with water. Indole 1 was extracted using 3 × 25 mL of diethyl ether. The combined organic layers were dried over Na₂SO₄ and the ether was removed under reduced pressure by a rotary evaporator. After recrystallization from acetonitrile, light-brown crystals were obtained. Yield: 1.95 g (57%), ¹H NMR (400 MHz, DMSO-d₆), δ, ppm: 7.66 (1H, s, CH), 7.58 (1H, s, CH), 2.24 (3H, s, CH₃), 1.36 [6H, s, (CH₃)₂]. Analysis, %: found C, 41.69; H, 3.49; N, 4.45, C₁₁H₁₁Br₂N requires C, 41.67; H, 3.50; N, 4.42, ESI–MS m/z found: [M + H]⁺ 317.9; C₁₁H₁₂Br₂N⁺ requires 317.9.

Synthesis of 4,6-dibromo-1,2,3,3-tetramethyl-3H-indol-1-ium iodide (2)

4,6-Dibromo-2,3,3-trimethyl-3H-indole (1) (0.3 g, 0.95 mmol) was dissolved in benzene (5 mL), iodomethane was added (0.5 mL, 8.03 mmol) and the mixture was left at room temperature for 24 h in a sealed tube. The beige crystals that formed were filtered off, washed with diethyl ether, dried, and were used without further purification. Yield: 300 mg (69%), ¹H NMR (400 MHz, DMSO-d₆), δ, ppm: 8.34 (1H, s, CH), 8.11 (1H, s, CH), 3.94 (3H, s, CH₃), 2.81 (3H, s, CH₃), 1.63 [6H, s, (CH₃)₂]. Analysis, %: found C, 31.34; H, 3.01; N, 3.08, C₁₂H₁₄Br₂IN requires C, 31.40; H, 3.07; N, 3.05, ESI–MS m/z found: [M − I]⁺ 331.9; C₁₂H₁₄Br₂N⁺ requires 332.0.

7. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 3. H atoms were included in calculated positions and treated as riding on their parent C atom: C—H = 0.93–0.98 Å with U_iso(H) = 1.5U_eq(C-methyl) or 1.2U_eq(C) for all other H atoms.

Table 3
Experimental details

	1	2
Crystal data
Chemical formula	C₁₁H₁₁Br₂N	C₁₂H₁₄Br₂N⁺·I⁻
M_r	317.03	458.96
Crystal system, space group	Orthorhombic, P2₁2₁2₁	Monoclinic, P2₁/m
Temperature (K)	293	293
a, b, c (Å)	8.7761 (5), 11.3876 (7), 11.8654 (4)	8.3507 (6), 7.3719 (5), 11.7180 (8)
α, β, γ (°)	90, 90, 90	90, 92.755 (6), 90
V (Å³)	1185.81 (11)	720.53 (9)
Z	4	2
Radiation type	Mo Kα	Mo Kα
μ (mm⁻¹)	6.80	7.74
Crystal size (mm)	0.4 × 0.3 × 0.3	0.4 × 0.2 × 0.1

Data collection
Diffractometer	Xcalibur, Sapphire3	Xcalibur, Sapphire3
Absorption correction	Multi-scan (CrysAlis PRO; Rigaku OD, 2018 $[Rigaku OD (2018). CrysAlis PRO. Rigaku Oxford Diffraction, Yarnton, England.]$ )	Multi-scan (CrysAlis PRO; Rigaku OD, 2018 $[Rigaku OD (2018). CrysAlis PRO. Rigaku Oxford Diffraction, Yarnton, England.]$ )
T_min, T_max	0.682, 1.000	0.355, 1.000
No. of measured, independent and observed [I > 2σ(I)] reflections	8516, 2086, 1789	4499, 1374, 1242
R_int	0.081	0.083
(sin θ/λ)_max (Å⁻¹)	0.595	0.595

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.047, 0.121, 1.07	0.046, 0.121, 1.05
No. of reflections	2086	1374
No. of parameters	130	97
H-atom treatment	H-atom parameters constrained	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.44, −0.55	0.86, −0.91
Absolute structure	Flack x determined using 613 quotients [(I⁺)−(I⁻)]/[(I⁺)+(I⁻)] (Parsons et al., 2013 )	–
Absolute structure parameter	0.05 (2)	–
Computer programs: CrysAlis PRO (Rigaku OD, 2018 $[Rigaku OD (2018). CrysAlis PRO. Rigaku Oxford Diffraction, Yarnton, England.]$ ), SHELXT2014/5 (Sheldrick, 2015a ), SHELXL2016/6 (Sheldrick, 2015b ) and OLEX2 (Dolomanov et al., 2009 ).

Supporting information

CCDC references: 2118325; 2118324

Crystal structure: contains datablocks 1, 2. DOI: https://doi.org/10.1107/S2056989021011385/zn2011sup1.cif

Structure factors: contains datablock 1. DOI: https://doi.org/10.1107/S2056989021011385/zn20111sup4.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2056989021011385/zn20111sup4.cml

Structure factors: contains datablock 2. DOI: https://doi.org/10.1107/S2056989021011385/zn20112sup5.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2056989021011385/zn20112sup5.cml

checkCIF report

Computing details top

For both structures, data collection: CrysAlis PRO (Rigaku OD, 2018). Cell refinement: CrysAlis PRO (Rigaku OD, 2018) for (1). For both structures, data reduction: CrysAlis PRO (Rigaku OD, 2018); program(s) used to solve structure: SHELXT2014/5 (Sheldrick, 2015b); program(s) used to refine structure: SHELXL2016/6 (Sheldrick, 2015a); molecular graphics: OLEX2 (Dolomanov et al., 2009); software used to prepare material for publication: OLEX2 (Dolomanov et al., 2009).

4,6-Dibromo-2,3,3-trimethyl-3H-indole (1) top

Crystal data top

C₁₁H₁₁Br₂N	D_x = 1.776 Mg m⁻³
M_r = 317.03	Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, P2₁2₁2₁	Cell parameters from 2796 reflections
a = 8.7761 (5) Å	θ = 3.6–24.9°
b = 11.3876 (7) Å	µ = 6.80 mm⁻¹
c = 11.8654 (4) Å	T = 293 K
V = 1185.81 (11) Å³	Prism, red
Z = 4	0.4 × 0.3 × 0.3 mm
F(000) = 616

Data collection top

Xcalibur, Sapphire3 diffractometer	2086 independent reflections
Radiation source: fine-focus sealed X-ray tube, Enhance (Mo) X-ray Source	1789 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.081
Detector resolution: 16.1827 pixels mm^-1	θ_max = 25.0°, θ_min = 2.9°
ω scans	h = −10→10
Absorption correction: multi-scan (CrysAlisPro; Rigaku OD, 2018)	k = −13→13
T_min = 0.682, T_max = 1.000	l = −14→14
8516 measured reflections

Refinement top

Refinement on F²	Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: full	H-atom parameters constrained
R[F² > 2σ(F²)] = 0.047	w = 1/[σ²(F_o²) + (0.0554P)² + 0.295P] where P = (F_o² + 2F_c²)/3
wR(F²) = 0.121	(Δ/σ)_max < 0.001
S = 1.07	Δρ_max = 0.44 e Å⁻³
2086 reflections	Δρ_min = −0.55 e Å⁻³
130 parameters	Absolute structure: Flack x determined using 613 quotients [(I⁺)-(I^-)]/[(I⁺)+(I^-)] (Parsons et al., 2013)
0 restraints	Absolute structure parameter: 0.05 (2)
Primary atom site location: dual

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

	x	y	z	U_iso*/U_eq
Br1	0.24163 (11)	0.35819 (9)	0.83683 (7)	0.0630 (4)
Br2	0.73559 (14)	0.21032 (9)	0.56768 (8)	0.0769 (4)
N1	0.5082 (8)	0.6304 (7)	0.5315 (6)	0.0518 (18)
C1	0.4908 (9)	0.5231 (8)	0.5910 (6)	0.0432 (19)
C2	0.3837 (10)	0.5003 (7)	0.6734 (6)	0.047 (2)
H2	0.312700	0.556729	0.694752	0.056*
C3	0.3861 (9)	0.3912 (8)	0.7227 (6)	0.046 (2)
C4	0.4903 (9)	0.3063 (8)	0.6936 (7)	0.052 (2)
H4	0.489872	0.233692	0.729463	0.062*
C5	0.5979 (10)	0.3311 (8)	0.6085 (7)	0.049 (2)
C6	0.5999 (9)	0.4389 (8)	0.5579 (6)	0.046 (2)
C7	0.6962 (9)	0.4972 (8)	0.4670 (6)	0.050 (2)
C8	0.6202 (9)	0.6146 (8)	0.4635 (7)	0.051 (2)
C9	0.6811 (15)	0.4323 (11)	0.3518 (7)	0.077 (3)
H9A	0.719284	0.353684	0.359071	0.116*
H9B	0.738795	0.473434	0.295515	0.116*
H9C	0.575831	0.429848	0.329832	0.116*
C10	0.8638 (11)	0.5078 (11)	0.5014 (10)	0.079 (3)
H10A	0.870442	0.542173	0.575093	0.119*
H10B	0.916473	0.556660	0.448193	0.119*
H10C	0.909473	0.431228	0.502393	0.119*
C11	0.6680 (12)	0.7123 (9)	0.3846 (8)	0.072 (3)
H11A	0.597667	0.776545	0.390964	0.107*
H11B	0.668219	0.683767	0.308475	0.107*
H11C	0.768433	0.738629	0.404338	0.107*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Br1	0.0625 (6)	0.0687 (6)	0.0578 (5)	−0.0033 (6)	0.0196 (5)	0.0087 (4)
Br2	0.0836 (7)	0.0721 (7)	0.0750 (6)	0.0279 (7)	0.0213 (6)	0.0029 (5)
N1	0.054 (4)	0.052 (4)	0.050 (4)	−0.005 (4)	0.004 (3)	0.000 (4)
C1	0.042 (4)	0.048 (5)	0.040 (4)	−0.006 (4)	−0.002 (3)	−0.005 (4)
C2	0.045 (5)	0.048 (5)	0.047 (4)	0.002 (4)	0.003 (4)	−0.004 (4)
C3	0.039 (4)	0.052 (5)	0.045 (4)	−0.007 (4)	0.004 (4)	−0.004 (4)
C4	0.055 (5)	0.054 (6)	0.046 (4)	0.000 (5)	0.000 (4)	0.008 (4)
C5	0.043 (4)	0.063 (6)	0.041 (4)	−0.001 (4)	0.003 (4)	−0.001 (4)
C6	0.043 (5)	0.058 (5)	0.038 (4)	−0.003 (4)	0.005 (4)	0.001 (4)
C7	0.044 (5)	0.065 (6)	0.040 (4)	0.004 (4)	0.009 (3)	0.004 (4)
C8	0.045 (5)	0.063 (6)	0.047 (5)	−0.014 (4)	0.000 (4)	0.002 (4)
C9	0.095 (8)	0.092 (8)	0.046 (5)	−0.002 (7)	0.020 (5)	−0.016 (5)
C10	0.042 (6)	0.105 (10)	0.090 (7)	−0.003 (6)	0.008 (5)	0.013 (7)
C11	0.080 (7)	0.071 (7)	0.063 (5)	−0.019 (6)	0.023 (5)	0.020 (5)

Geometric parameters (Å, º) top

Br1—C3	1.893 (8)	C7—C8	1.494 (13)
Br2—C5	1.894 (9)	C7—C9	1.560 (12)
N1—C1	1.419 (11)	C7—C10	1.531 (13)
N1—C8	1.284 (10)	C8—C11	1.514 (12)
C1—C2	1.381 (11)	C9—H9A	0.9600
C1—C6	1.411 (11)	C9—H9B	0.9600
C2—H2	0.9300	C9—H9C	0.9600
C2—C3	1.374 (11)	C10—H10A	0.9600
C3—C4	1.375 (11)	C10—H10B	0.9600
C4—H4	0.9300	C10—H10C	0.9600
C4—C5	1.412 (11)	C11—H11A	0.9600
C5—C6	1.367 (12)	C11—H11B	0.9600
C6—C7	1.522 (11)	C11—H11C	0.9600

C8—N1—C1	105.9 (8)	C8—C7—C10	111.5 (8)
C2—C1—N1	126.0 (8)	C10—C7—C9	110.6 (7)
C2—C1—C6	122.1 (8)	N1—C8—C7	116.7 (8)
C6—C1—N1	111.9 (7)	N1—C8—C11	119.8 (9)
C1—C2—H2	121.3	C7—C8—C11	123.4 (8)
C3—C2—C1	117.5 (8)	C7—C9—H9A	109.5
C3—C2—H2	121.3	C7—C9—H9B	109.5
C2—C3—Br1	118.3 (6)	C7—C9—H9C	109.5
C2—C3—C4	122.6 (7)	H9A—C9—H9B	109.5
C4—C3—Br1	119.1 (6)	H9A—C9—H9C	109.5
C3—C4—H4	120.5	H9B—C9—H9C	109.5
C3—C4—C5	119.0 (8)	C7—C10—H10A	109.5
C5—C4—H4	120.5	C7—C10—H10B	109.5
C4—C5—Br2	117.7 (7)	C7—C10—H10C	109.5
C6—C5—Br2	122.2 (6)	H10A—C10—H10B	109.5
C6—C5—C4	120.2 (8)	H10A—C10—H10C	109.5
C1—C6—C7	106.1 (7)	H10B—C10—H10C	109.5
C5—C6—C1	118.7 (7)	C8—C11—H11A	109.5
C5—C6—C7	135.2 (8)	C8—C11—H11B	109.5
C6—C7—C9	111.5 (8)	C8—C11—H11C	109.5
C6—C7—C10	112.3 (8)	H11A—C11—H11B	109.5
C8—C7—C6	99.3 (7)	H11A—C11—H11C	109.5
C8—C7—C9	111.2 (8)	H11B—C11—H11C	109.5

Br1—C3—C4—C5	−180.0 (6)	C3—C4—C5—Br2	−178.1 (6)
Br2—C5—C6—C1	178.3 (6)	C3—C4—C5—C6	1.4 (13)
Br2—C5—C6—C7	−1.3 (14)	C4—C5—C6—C1	−1.2 (12)
N1—C1—C2—C3	−179.1 (7)	C4—C5—C6—C7	179.2 (9)
N1—C1—C6—C5	179.6 (7)	C5—C6—C7—C8	179.9 (9)
N1—C1—C6—C7	−0.6 (9)	C5—C6—C7—C9	62.6 (13)
C1—N1—C8—C7	−0.7 (10)	C5—C6—C7—C10	−62.2 (13)
C1—N1—C8—C11	178.8 (8)	C6—C1—C2—C3	−0.3 (12)
C1—C2—C3—Br1	179.5 (6)	C6—C7—C8—N1	0.3 (9)
C1—C2—C3—C4	0.5 (12)	C6—C7—C8—C11	−179.2 (8)
C1—C6—C7—C8	0.2 (8)	C8—N1—C1—C2	179.8 (8)
C1—C6—C7—C9	−117.1 (8)	C8—N1—C1—C6	0.8 (9)
C1—C6—C7—C10	118.1 (9)	C9—C7—C8—N1	117.9 (8)
C2—C1—C6—C5	0.7 (12)	C9—C7—C8—C11	−61.7 (11)
C2—C1—C6—C7	−179.6 (7)	C10—C7—C8—N1	−118.2 (9)
C2—C3—C4—C5	−1.0 (13)	C10—C7—C8—C11	62.3 (11)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C3—Br1···N1ⁱ	1.89	3.19	5.283 (1)	166
C3—Br1···C8ⁱ	1.89	3.53	5.046 (1)	153
C11—H11C···N1ⁱⁱ	0.96	2.69	3.621 (1)	164

Symmetry codes: (i) −x+1/2, −y+1, z+1/2; (ii) x+1/2, −y+3/2, −z+1.

4,6-Dibromo-2,3,3-trimethyl-3H-indol-1-ium iodide (2) top

Crystal data top

C₁₂H₁₄Br₂N⁺·I⁻	F(000) = 432
M_r = 458.96	D_x = 2.115 Mg m⁻³
Monoclinic, P2₁/m	Mo Kα radiation, λ = 0.71073 Å
a = 8.3507 (6) Å	Cell parameters from 1781 reflections
b = 7.3719 (5) Å	θ = 3.8–28.6°
c = 11.7180 (8) Å	µ = 7.74 mm⁻¹
β = 92.755 (6)°	T = 293 K
V = 720.53 (9) Å³	Needle, red
Z = 2	0.4 × 0.2 × 0.1 mm

Data collection top

Xcalibur, Sapphire3 diffractometer	1374 independent reflections
Radiation source: fine-focus sealed X-ray tube, Enhance (Mo) X-ray Source	1242 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.083
Detector resolution: 16.1827 pixels mm^-1	θ_max = 25.0°, θ_min = 2.9°
ω scans	h = −9→9
Absorption correction: multi-scan (CrysAlisPro; Rigaku OD, 2018)	k = −8→8
T_min = 0.355, T_max = 1.000	l = −12→13
4499 measured reflections

Refinement top

Refinement on F²	Primary atom site location: dual
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F² > 2σ(F²)] = 0.046	H-atom parameters constrained
wR(F²) = 0.121	w = 1/[σ²(F_o²) + (0.0732P)² + 0.1443P] where P = (F_o² + 2F_c²)/3
S = 1.05	(Δ/σ)_max = 0.001
1374 reflections	Δρ_max = 0.86 e Å⁻³
97 parameters	Δρ_min = −0.91 e Å⁻³
0 restraints

Special details top

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq	Occ. (<1)
I1	0.70649 (6)	0.750000	0.12215 (4)	0.0481 (3)
Br1	0.57546 (9)	0.250000	0.65282 (7)	0.0477 (3)
Br2	1.19756 (8)	0.250000	0.49523 (7)	0.0455 (3)
N1	0.7083 (7)	0.250000	0.2129 (5)	0.0333 (13)
C1	0.7464 (7)	0.250000	0.3305 (5)	0.0310 (15)
C2	0.6429 (8)	0.250000	0.4171 (6)	0.0339 (15)
H2	0.532393	0.250000	0.402939	0.041*
C3	0.7113 (9)	0.250000	0.5275 (6)	0.0361 (16)
C4	0.8733 (8)	0.250000	0.5472 (6)	0.0334 (15)
H4	0.915491	0.250000	0.622086	0.040*
C5	0.9763 (8)	0.250000	0.4585 (6)	0.0321 (14)
C6	0.9130 (8)	0.250000	0.3468 (6)	0.0317 (15)
C7	0.9823 (9)	0.250000	0.2291 (6)	0.0328 (15)
C8	0.8337 (9)	0.250000	0.1513 (6)	0.0347 (16)
C9	1.0830 (6)	0.4194 (8)	0.2084 (5)	0.0446 (12)
H9A	1.017880	0.525689	0.215897	0.067*
H9B	1.122463	0.414922	0.132876	0.067*
H9C	1.171753	0.423837	0.263544	0.067*
C10	0.8300 (11)	0.250000	0.0265 (7)	0.0483 (19)
H10A	0.929629	0.203613	0.001073	0.073*	0.5
H10B	0.814457	0.371640	−0.001140	0.073*	0.5
H10C	0.743463	0.174747	−0.002504	0.073*	0.5
C11	0.5431 (10)	0.250000	0.1659 (8)	0.051 (2)
H11A	0.541464	0.284350	0.086856	0.077*	0.5
H11B	0.480906	0.334906	0.207372	0.077*	0.5
H11C	0.498349	0.130744	0.172659	0.077*	0.5

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
I1	0.0529 (4)	0.0457 (4)	0.0464 (4)	0.000	0.0092 (3)	0.000
Br1	0.0410 (5)	0.0658 (6)	0.0376 (5)	0.000	0.0156 (4)	0.000
Br2	0.0282 (5)	0.0547 (5)	0.0532 (5)	0.000	−0.0025 (4)	0.000
N1	0.034 (3)	0.038 (3)	0.028 (3)	0.000	−0.006 (2)	0.000
C1	0.024 (4)	0.042 (4)	0.027 (3)	0.000	−0.001 (3)	0.000
C2	0.028 (3)	0.041 (4)	0.033 (4)	0.000	0.004 (3)	0.000
C3	0.036 (4)	0.041 (4)	0.033 (4)	0.000	0.009 (3)	0.000
C4	0.038 (4)	0.038 (4)	0.024 (3)	0.000	−0.004 (3)	0.000
C5	0.031 (4)	0.034 (3)	0.032 (3)	0.000	0.001 (3)	0.000
C6	0.029 (4)	0.033 (4)	0.033 (4)	0.000	0.005 (3)	0.000
C7	0.038 (4)	0.031 (3)	0.030 (4)	0.000	0.014 (3)	0.000
C8	0.040 (4)	0.035 (4)	0.030 (4)	0.000	0.007 (3)	0.000
C9	0.046 (3)	0.047 (3)	0.042 (3)	−0.002 (2)	0.012 (2)	0.007 (2)
C10	0.058 (5)	0.052 (5)	0.036 (4)	0.000	0.006 (4)	0.000
C11	0.038 (5)	0.070 (6)	0.045 (5)	0.000	0.000 (4)	0.000

Geometric parameters (Å, º) top

Br1—C3	1.899 (7)	C7—C8	1.504 (10)
Br2—C5	1.877 (7)	C7—C9	1.532 (7)
N1—C1	1.399 (8)	C7—C9ⁱ	1.532 (7)
N1—C8	1.301 (9)	C8—C10	1.461 (10)
N1—C11	1.460 (10)	C9—H9A	0.9600
C1—C2	1.364 (10)	C9—H9B	0.9600
C1—C6	1.395 (9)	C9—H9C	0.9600
C2—H2	0.9300	C10—H10A	0.9600
C2—C3	1.389 (10)	C10—H10B	0.9600
C3—C4	1.361 (10)	C10—H10C	0.9600
C4—H4	0.9300	C11—H11A	0.9600
C4—C5	1.381 (10)	C11—H11B	0.9600
C5—C6	1.387 (10)	C11—H11C	0.9600
C6—C7	1.522 (9)

C1—N1—C11	122.5 (6)	C8—C7—C9	110.3 (4)
C8—N1—C1	113.3 (6)	C8—C7—C9ⁱ	110.3 (4)
C8—N1—C11	124.2 (7)	C9—C7—C9ⁱ	109.3 (6)
C2—C1—N1	127.6 (6)	N1—C8—C7	109.0 (6)
C2—C1—C6	124.1 (6)	N1—C8—C10	125.2 (7)
C6—C1—N1	108.3 (6)	C10—C8—C7	125.7 (6)
C1—C2—H2	121.7	C7—C9—H9A	109.5
C1—C2—C3	116.5 (6)	C7—C9—H9B	109.5
C3—C2—H2	121.7	C7—C9—H9C	109.5
C2—C3—Br1	119.1 (5)	H9A—C9—H9B	109.5
C4—C3—Br1	119.6 (5)	H9A—C9—H9C	109.5
C4—C3—C2	121.3 (6)	H9B—C9—H9C	109.5
C3—C4—H4	119.3	C8—C10—H10A	109.5
C3—C4—C5	121.5 (6)	C8—C10—H10B	109.5
C5—C4—H4	119.3	C8—C10—H10C	109.5
C4—C5—Br2	118.0 (5)	H10A—C10—H10B	109.5
C4—C5—C6	119.1 (6)	H10A—C10—H10C	109.5
C6—C5—Br2	122.9 (5)	H10B—C10—H10C	109.5
C1—C6—C7	107.2 (6)	N1—C11—H11A	109.5
C5—C6—C1	117.5 (6)	N1—C11—H11B	109.5
C5—C6—C7	135.3 (6)	N1—C11—H11C	109.5
C6—C7—C9ⁱ	112.3 (4)	H11A—C11—H11B	109.5
C6—C7—C9	112.3 (4)	H11A—C11—H11C	109.5
C8—C7—C6	102.2 (5)	H11B—C11—H11C	109.5

Br1—C3—C4—C5	180.000 (2)	C4—C5—C6—C1	0.000 (1)
Br2—C5—C6—C1	180.000 (1)	C4—C5—C6—C7	180.000 (1)
Br2—C5—C6—C7	0.000 (2)	C5—C6—C7—C8	180.000 (1)
N1—C1—C2—C3	180.000 (1)	C5—C6—C7—C9	−61.8 (4)
N1—C1—C6—C5	180.000 (1)	C5—C6—C7—C9ⁱ	61.8 (4)
N1—C1—C6—C7	0.000 (1)	C6—C1—C2—C3	0.000 (1)
C1—N1—C8—C7	0.000 (1)	C6—C7—C8—N1	0.000 (1)
C1—N1—C8—C10	180.000 (1)	C6—C7—C8—C10	180.000 (1)
C1—C2—C3—Br1	180.000 (1)	C8—N1—C1—C2	180.000 (1)
C1—C2—C3—C4	0.000 (2)	C8—N1—C1—C6	0.000 (1)
C1—C6—C7—C8	0.000 (1)	C9ⁱ—C7—C8—N1	119.6 (4)
C1—C6—C7—C9ⁱ	−118.2 (4)	C9—C7—C8—N1	−119.6 (4)
C1—C6—C7—C9	118.2 (4)	C9ⁱ—C7—C8—C10	−60.4 (4)
C2—C1—C6—C5	0.000 (1)	C9—C7—C8—C10	60.4 (4)
C2—C1—C6—C7	180.000 (1)	C11—N1—C1—C2	0.000 (1)
C2—C3—C4—C5	0.000 (2)	C11—N1—C1—C6	180.000 (1)
C3—C4—C5—Br2	180.000 (1)	C11—N1—C8—C7	180.000 (1)
C3—C4—C5—C6	0.000 (2)	C11—N1—C8—C10	0.000 (1)

Symmetry code: (i) x, −y+1/2, z.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C2—H2···Br2ⁱⁱ	0.93	3.05	3.872 (1)	149
C5—Br2···Br1ⁱⁱⁱ	1.88 (1)	3.58	5.397 (1)	162
C3—Br1···I1^iv	1.90 (1)	3.62	5.514 (1)	176
C11—H11A···I1^v	0.96	3.14	3.881 (1)	135

Symmetry codes: (ii) x−1, y, z; (iii) x+1, y, z; (iv) −x+1, −y+1, −z+1; (v) −x+1, −y+1, −z.

Funding information

Funding for this research was provided by: National Academy of Sciences of Ukraine (grant No. 0120U102660).

References

Atchison, J., Kamila, S., Nesbitt, H., Logan, K. A., Nicholas, D. M., Fowley, C., Davis, J., Callan, B., McHale, A. P. & Callan, J. F. (2017). Chem. Commun. 53, 2009–2012. Web of Science CrossRef CAS Google Scholar
Belletête, M., Brisse, F., Durocher, G., Gravel, D., Héroux, A. & Popowycz, A. (1993). J. Mol. Struct. 297, 63–80. Google Scholar
Beverina, L. & Salice, P. (2010). Eur. J. Org. Chem. pp. 1207–1225. Web of Science CrossRef Google Scholar
Burgi, H.-B. & Dunitz, J. D. (1994). Structure correlation, vol. 2, pp. 741–784. Weinheim: VCH. Google Scholar
Connell, A., Holliman, P. J., Davies, M. L., Gwenin, Ch. D., Weiss, S., Pitak, M. B., Horton, P. N., Coles, S. J. & Cooke, G. (2014). J. Mater. Chem. A, 2, 4055–4066. Web of Science CSD CrossRef CAS Google Scholar
Dolomanov, O. V., Bourhis, L. J., Gildea, R. J., Howard, J. A. K. & Puschmann, H. (2009). J. Appl. Cryst. 42, 339–341. Web of Science CrossRef CAS IUCr Journals Google Scholar
Feng, L., Chen, W., Ma, X., Liu, S. H. & Yin, J. (2020). Org. Biomol. Chem. 18, 9385–9397. Web of Science CrossRef CAS PubMed Google Scholar
Groom, C. R., Bruno, I. J., Lightfoot, M. P. & Ward, S. C. (2016). Acta Cryst. B72, 171–179. Web of Science CrossRef IUCr Journals Google Scholar
Guerrero, Y., Singh, S. P., Mai, T., Murali, R. K., Tanikella, L., Zahedi, A., Kundra, V. & Anvari, B. (2017). Appl. Mater. Interfaces, 9, 19601–19611. Web of Science CrossRef CAS Google Scholar
Holliman, P. J., Tizzard, G. J., Hursthouse, M. B. & Lamond, S. J. (2009). University of Southampton, Crystal Structure Report Archive, 1229. Google Scholar
Liu, H., Yin, J., Xing, E., Du, Y., Su, Y., Feng, Y. & Meng, S. (2021). Dyes Pigments, 190, 109327. Web of Science CrossRef Google Scholar
Lynch, D. E., Kirkham, A. N., Chowdhury, M. Z. H., Wane, E. S. & Heptinstall, J. (2012). Dyes Pigments, 94, 393–402. Web of Science CSD CrossRef CAS Google Scholar
Parsons, S., Flack, H. D. & Wagner, T. (2013). Acta Cryst. B69, 249–259. Web of Science CSD CrossRef CAS IUCr Journals Google Scholar
Rigaku OD (2018). CrysAlis PRO. Rigaku Oxford Diffraction, Yarnton, England. Google Scholar
Seiler, V. K., Callebaut, K., Robeyns, K., Tumanov, N., Wouters, J., Champagne, B. & Leyssens, T. (2018). CrystEngComm, 20, 3318–3327. Web of Science CSD CrossRef CAS Google Scholar
Semenova, O., Kobzev, D., Yazbak, F., Nakonechny, F., Kolosova, O., Tatarets, A., Gellerman, G. & Patsenker, L. (2021). Dyes Pigments, 195, 109745–109746. Web of Science CrossRef CAS Google Scholar
Sheldrick, G. M. (2015a). Acta Cryst. A71, 3–8. Web of Science CrossRef IUCr Journals Google Scholar
Sheldrick, G. M. (2015b). Acta Cryst. C71, 3–8. Web of Science CrossRef IUCr Journals Google Scholar
Sun, W., Guo, Sh., Hu, Ch., Fan, J. & Peng, X. (2016). Chem. Rev. 116, 7768–7817. Web of Science CrossRef CAS PubMed Google Scholar
Szaciłowski, K., Macyk, W., Drzewiecka-Matuszek, A., Brindell, M. & Stochel, G. (2005). Chem. Rev. 105, 2647–2694. Web of Science PubMed Google Scholar
Turner, M. J., McKinnon, J. J., Wolff, S. K., Grimwood, D. J., Spackman, P. R., Jayatilaka, D. & Spackman, M. A. (2017). CrystalExplorer17. University of Western Australia. https://Hirshfeldsurface.net Google Scholar

This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.

CRYSTALLOGRAPHIC
COMMUNICATIONS

ISSN: 2056-9890

Volume 77| Part 12| December 2021| Pages 1203-1207

https://doi.org/10.1107/S2056989021011385

Open

access

Format		BIBTeX
		EndNote
		RefMan
		Refer
		Medline
		CIF
		SGML
		Plain Text
		Text

Format		BIBTeX
		EndNote
		RefMan
		Refer
		Medline
		CIF
		SGML
		Plain Text
		Text

Search IUCr Journals		doi		Advanced search
Author		volume	page

research communications\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Crystal structures and Hirshfeld analysis of 4,6-di­bromo­indole­nine and its quaternized salt

1. Chemical context

2. Structural commentary

3. Supra­molecular features

4. Hirshfeld surface analysis

5. Database survey

6. Synthesis and crystallization

7. Refinement

Supporting information

Funding information

References

research communications

Crystal structures and Hirshfeld analysis of 4,6-dibromoindolenine and its quaternized salt

3. Supramolecular features