Startseite Crystal structure of 5-bromo-1-(2-iodobenzoyl)-1H-indole-3-carbaldehyde, C16H9BrINO2
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Crystal structure of 5-bromo-1-(2-iodobenzoyl)-1H-indole-3-carbaldehyde, C16H9BrINO2

  • Yue Zhang , Qian-Qian Tang , Jia-Cheng Yuan , Cheng-Sheng Sheng und Wei Cong ORCID logo EMAIL logo
Veröffentlicht/Copyright: 23. November 2023

Abstract

C16H9BrINO2, triclinic, P1̄ (no. 2), a = 7.9305(12) Å, b = 8.2051(10) Å, c = 11.3141(13) Å, α = 85.384(10)°, β = 85.619(11)°, γ = 87.745(11)°, V = 731.27(17) Å3, Z = 2, R gt (F) = 0.0397, wR ref (F2) = 0.0819, T = 293(2) K.

CCDC no.: 2307524

The crystal structure is shown in figure. Displacement ellipsoids are drawn at the 30 % probability level.

Tables 1 and 2 contain details on crystal structure and measurement conditions and a list of the atoms including atomic coordinates and displacement parameters.

Table 1:

Data collection and handling.

Crystal: Colourless block
Size: 0.12 × 0.12 × 0.10 mm
Wavelength: Mo Kα radiation (0.71073 Å)
μ: 4.92 mm−1
Diffractometer, scan mode: SuperNova
θmax, completeness: 25.5°, >99 %
N(hkl)measured, N(hkl)unique, Rint: 4755, 2717, 0.036
Criterion for Iobs, N(hkl)gt: Iobs > 2σ(Iobs), 2200
N(param)refined: 190
Programs: CrysAlisPRO [1], SHELX [2, 3]
Table 2:

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

Atom x y z Uiso*/Ueq
Br1 0.05770 (8) 1.02515 (6) −0.29452 (4) 0.05150 (19)
C1 0.0500 (6) 0.5766 (5) 0.1885 (4) 0.0300 (11)
H1 0.025356 0.500060 0.251976 0.036*
C2 −0.0571 (6) 0.6251 (5) 0.1056 (4) 0.0302 (11)
C3 0.0323 (6) 0.7413 (5) 0.0206 (4) 0.0286 (11)
C4 −0.0112 (6) 0.8206 (5) −0.0863 (4) 0.0321 (11)
H4 −0.116270 0.810052 −0.115700 0.039*
C5 0.1117 (7) 0.9157 (6) −0.1458 (4) 0.0367 (13)
C6 0.2685 (7) 0.9356 (6) −0.1062 (4) 0.0402 (13)
H6 0.345888 1.001913 −0.151113 0.048*
C7 0.3110 (6) 0.8570 (6) 0.0002 (4) 0.0365 (12)
H7 0.415877 0.869423 0.029352 0.044*
C8 0.1899 (6) 0.7584 (5) 0.0622 (4) 0.0288 (11)
C9 0.3337 (6) 0.6401 (6) 0.2417 (4) 0.0351 (12)
C10 0.3341 (6) 0.4842 (6) 0.3209 (4) 0.0349 (12)
C11 0.2931 (6) 0.4771 (6) 0.4414 (4) 0.0350 (12)
C12 0.3017 (6) 0.3305 (6) 0.5105 (5) 0.0429 (14)
H12 0.277281 0.327927 0.592369 0.052*
C13 0.3461 (7) 0.1908 (7) 0.4581 (5) 0.0535 (16)
H13 0.351017 0.091751 0.504058 0.064*
C14 0.3846 (7) 0.1950 (7) 0.3348 (6) 0.0545 (16)
H14 0.410481 0.096925 0.300456 0.065*
C15 0.3855 (6) 0.3344 (6) 0.2643 (5) 0.0405 (13)
H15 0.417242 0.335755 0.183438 0.049*
C16 −0.2265 (7) 0.5685 (6) 0.1017 (5) 0.0407 (13)
H16 −0.264836 0.491862 0.161812 0.049*
I1 0.20158 (4) 0.68494 (4) 0.52463 (3) 0.04539 (15)
N1 0.2014 (5) 0.6546 (4) 0.1677 (3) 0.0286 (9)
O1 0.4414 (5) 0.7402 (5) 0.2382 (3) 0.0526 (10)
O2 −0.3220 (5) 0.6123 (5) 0.0271 (4) 0.0565 (11)

1 Source of material

The title compound 5-bromo-1-(2-iodobenzoyl)-1H-indole-3-carbaldehyde was prepared from 5-bromo-1H-indole-3-formaldehyde through N-acylation reaction. In a dry 25 mL flask, sodium hydride (0.24 g, 6 mmol) was suspended in anhydrous N,N-dimethylformamide (DMF, 3 mL) and stirred in an ice water bath for 2 min. Then, a solution composed of 5-methoxy-1H-indole-3-formaldehyde (0.26 g, 1.5 mmol) and anhydrous DMF (2 mL) was dropped into the reaction solution and continued to stir for 5 min. Subsequently, 2-iodobenzoyl chloride (0.72 g, 2.7 mmol) dissolved in anhydrous DMF (2 mL) was added dropwise to the reaction solution. After addition, the reaction solution was slowly rose to room temperature and continued stirring for 2 h. Thin-layer chromatography (UV, 254 nm) was used to detect the reaction process. The crude product was dispersed and washed with petroleum ether/ethyl acetate (2:1, v/v) to obtain a pure product (0.35 g, yield 54.3 %). Single crystals were obtained from n-hexane/ethyl acetate (6:1, v/v) solution.

2 Experimental details

The H atoms were placed in idealized positions and treated as riding on their parent atoms, d (C–H) = 0.93 Å (aromatic), Uiso (H) = 1.2Ueq (C).

3 Comment

Nitrogen-containing aromatic heterocycles are common structural fragments in many natural products and drug molecules, and are also useful molecular building blocks in organic synthesis [4, 5]. Among them, indole has attracted much attention due to its unique organic chemical characteristics and biological activities [6, 7]. The most classic reactions of indole included electrophilic reactions at the C(3) position and alkylation or acylation reactions at the N(1) position [8]. Meanwhile, in recent decades, the cross-coupling reactions of indole became a more popular research field [9]. Especially at the C(2) and C(3) positions of indole, due to its high reactivity, it could efficiently couple with olefins or aromatic hydrocarbons to generate a variety of products [10]. In addition, compounds containing indole fragments also exhibited important biological activity. For example, the endogenous active substance 5-hydroxytryptamine, the anti-inflammatory drug indomethacin, and the anti-tumor drug osimertinib contained indole fragments all [11]. On the basis of previous research on the synthesis methodology and pharmaceutical chemistry of indole derivatives, we designed and synthesized a series of compounds with N-acyl indole structures, which could serve as key intermediates for synthesizing other anti-inflammatory or anti-tumor active molecules [12].

Single-crystal structure analysis reveals that there is one molecule in the asymmetric unit (cf. figure). Bond lengths and angles are within a reasonable range [13], [14], [15]. The 5-bromoindole part and iodobenzene part are bridged by a carbonyl group. There is a significant conjugation effect between the carbonyl group and N(1) atom in this molecule, resulting in a significantly shortened bond length for C(9)–N(1) (1.388(6) Å), which is similar to the C–N bonds within the indole ring (1.378(6) Å for C(1)–N(1) and 1.416(6) Å for C(8)–N(1), respectively). The torsion angles of O(1)–C(9)–C(10)–C(11) and O(1)–C(9)–C(10)–C(15) are 75.0(7)° and −103.6(6)° respectively, indicating that the iodobenzene ring and carbonyl group are close to perpendicular. In contrast, the indole ring and carbonyl group are approximately coplanar, because the torsion angles of O(1)–C(9)–N(1)–C(1) and O(1)–C(9)–N(1)–C(8) are −159.3(5)° and 16.1(7)° respectively. In summary, due to the steric hindrance of carbonyl group and iodine atom of this molecule, the indole and iodobenzene rings are not only non-coplanar but nearly perpendicular, with a dihedral angle of approximately 84.7(3)° between them. Moreover, functional groups such as aldehyde, bromine, and iodine provide a wide range of possibilities for this molecule to serve as a key intermediate in the synthesis active compounds.


Corresponding author: Wei Cong, School of Pharmacy, The Key Laboratory of Prescription Effect and Clinical Evaluation of State Administration of Traditional Chinese Medicine of China, Binzhou Medical University, Yantai, 264003, P.R. China, E-mail:

  1. Author contribution: All the authors have accepted responsibility for the entire content of this submitted manuscript and approved submission.

  2. Research funding: National Science Foundation of China (No. 21702018), a Key Research and Development Program of Shandong Province (No. 2019GSF108031).

  3. Conflict of interest statement: The authors declare no conflicts of interest regarding this article.

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Received: 2023-10-11
Accepted: 2023-11-13
Published Online: 2023-11-23
Published in Print: 2024-02-26

© 2023 the author(s), published by De Gruyter, Berlin/Boston

This work is licensed under the Creative Commons Attribution 4.0 International License.

Artikel in diesem Heft

  1. Frontmatter
  2. New Crystal Structures
  3. Crystal structure of poly[diaqua-(μ4-3,3′-di(1H-1,2,4-triazol-1-yl)-[1,1′-biphenyl]-4,4′-dicarboxylate-N:N′:O:O′)cadmium(II)], C18H14N6O6Cd
  4. Crystal structure of (8R,8′S,13S,13′R)-8,8′-bis(hydroxymethyl)-9,9′,10,10′-tetramethoxy-5,5′,6,6′,8,8′,13,13′-octahydro-[13,13′-bi[1,3]dioxolo[4,5-g]isoquinolino[3,2-a]isoquinoline]-7,7′-diium chloride-methanol (1/2), C46H58N2O14Cl2
  5. The crystal structure of 8-methoxy-2,2-diphenyl-tosyl-1,2-dihydro-2λ4,3λ4-[1,3,2]diazaborolo[4,5,1-ig]quinoline, C29H25BN2O3S
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  9. The crystal structure of 1-(3-oxo-1-phenyl-3-(p-tolyl) propylidene)-1,3-dihydro-2H-inden-2-one, C25H20O2
  10. Crystal structure of tricyclohexyl[4-(4H-1,2,4-triazol-4-yl)-benzoato-κO]tin(IV), C27H39N3O2Sn
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  13. The crystal structure of 2-(hydroxymethyl)-2-(4H-1,2,4-triazol-4-yl)propane-1,3-diol, C6H11N3O3
  14. The crystal structure of 1,2-bis(2,4-dinitrophenyl) hydrazine, C12H8N6O8
  15. Crystal structure of 1-(2,6-dichloro-4-(3,5-dimethylisoxazol-4-yl)phenyl)-1,2-dihydro-4H-benzo[d][1,3]oxazin-4-one, C19H14Cl2N2O3
  16. The crystal structure of 5-amino-5-oxo-4-(1-oxo-4-(2-oxopyrrolidin-1-yl)isoindolin-2-yl)pentanoic acid, C17H19N3O5
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  18. The crystal structure of (E)-2-methoxy-6-(((5-methyl-1,3,4-thiadiazol-2-yl)imino)methyl)phenol, C11H11N3O2S
  19. The crystal structure of 3-((tert-butyldiphenylsilyl)methyl)-5,5-diphenyl-6-(p-tolyl) tetrahydro-2H-pyran-2-one, C41H42O2Si
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  28. Crystal structure of langite from Mine du Pradet (France)
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  30. Synthesis and crystal structure of bis{2-(((4-acetophenone)imino)methyl)-4-fluorophenolato-κ2N,O}zinc(II), C30H22F2N2O4Zn
  31. The crystal structure of poly[(tripyridine-κ3N,N′,N″) μ3-(pyridine-3,4-dicarboxylate-κ3N:O:O′) manganese(II)], C22H22N4O8Mn
  32. The crystal structure of (E)-4-chloro-N′-(1-(4-hydroxyphenyl)propylidene)benzohydrazide, C16H15ClN2O2
  33. Synthesis and crystal structure of bis{2-(tert-butyl)-6-((E)-((4-((E)-1-(methoxyimino) ethyl)phenyl)imino)methyl)phenolato-κ2N,O}cobalt(II), C40H46CoN4O4
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  35. (6R,7S)-2,3,13-trimethoxy-6,7-dimethyl-5,6,7,8-tetrahydrobenzo[3′,4′]cycloocta [1′,2′:4,5]benzo[1,2-d][1,3]dioxol-1-ol, C22H26O6
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  37. Crystal structure of (5aS,6aS,8aR,9R,11aS, 11bS,13R,13aS)-1,1,8a,11a-tetramethyl-9-((S)-1-((S)-5-methyl-6-oxo-3,6-dihydro-2H-pyran-2-yl)ethyl)-3-oxo-1,7,8,8a,9,10,11,11a,11b,12,13,13a-dodecahydro-3H,6H-cyclopenta[5,6]cyclopropa[1,8a]naphtho[2,1-c]oxepin-13-yl acetate, C32H44O6
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