Home Crystal structure of 1-(2-iodobenzoyl)-6-methoxy-1H-indole-3-carbaldehyde, C17H12INO3
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Crystal structure of 1-(2-iodobenzoyl)-6-methoxy-1H-indole-3-carbaldehyde, C17H12INO3

  • Yi-Fan Sun , Qian-Qian Tang , Yue Zhang , Fan Yang , Yong-Jun Liu and Wei Cong ORCID logo EMAIL logo
Published/Copyright: January 31, 2023

Abstract

C17H12INO3, monoclinic, P21/n (no. 14), a = 7.5319(5) Å, b = 7.9745(5) Å, c = 25.1313(17) Å, β = 98.459(7)°, V = 1493.04(17) Å3, Z = 4, R gt (F) = 0.0272, wR ref (F2) = 0.0595, T = 199.98(10) K.

CCDC no.: 2236467

The crystal structure is shown in the figure. Displacement ellipsoids are drawn at the 50% probability level. Table 1 contains crystallographic data and Table 2 contains the list of the atoms including atomic coordinates and displacement parameters.

Table 1:

Data collection and handling.

Crystal: Colourless block
Size: 0.15 × 0.12 × 0.10 mm
Wavelength: Mo Kα radiation (0.71073 Å)
μ: 2.16 mm−1
Diffractometer, scan mode: SuperNova
θmax, completeness: 25.5°, >99%
N(hkl)measured, N(hkl)unique, Rint: 6746, 2777, 0.020
Criterion for Iobs, N(hkl)gt: Iobs > 2 σ(Iobs), 2585
N(param)refined: 201
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
C1 0.6171 (4) 1.0114 (4) 0.30898 (13) 0.0206 (7)
H1 0.556635 1.052112 0.276628 0.025*
C2 0.5609 (4) 1.0287 (4) 0.35744 (12) 0.0216 (7)
C3 0.6926 (4) 0.9489 (4) 0.39716 (12) 0.0216 (7)
C4 0.7062 (5) 0.9248 (5) 0.45266 (13) 0.0317 (8)
H4 0.617624 0.964856 0.471527 0.038*
C5 0.8520 (5) 0.8415 (5) 0.47869 (14) 0.0370 (9)
H5 0.860964 0.822444 0.515492 0.044*
C6 0.9879 (5) 0.7844 (5) 0.45091 (13) 0.0313 (8)
C7 0.9796 (4) 0.8051 (4) 0.39615 (12) 0.0239 (7)
H7 1.069956 0.766675 0.377713 0.029*
C8 0.8285 (4) 0.8867 (4) 0.37012 (12) 0.0200 (7)
C9 0.8774 (4) 0.8804 (4) 0.27425 (12) 0.0206 (7)
C10 0.7938 (4) 0.9069 (4) 0.21728 (12) 0.0184 (6)
C11 0.8920 (4) 0.9764 (4) 0.17921 (12) 0.0193 (6)
C12 0.8212 (4) 0.9742 (4) 0.12527 (12) 0.0243 (7)
H12 0.884633 1.023135 0.100233 0.029*
C13 0.6572 (5) 0.9001 (4) 0.10826 (13) 0.0300 (8)
H13 0.612329 0.896521 0.071768 0.036*
C14 0.5597 (4) 0.8316 (4) 0.14503 (14) 0.0283 (8)
H14 0.448992 0.781865 0.133484 0.034*
C15 0.6267 (4) 0.8368 (4) 0.19905 (12) 0.0227 (7)
H15 0.558965 0.792706 0.223811 0.027*
C16 0.3977 (5) 1.1145 (4) 0.36499 (15) 0.0312 (8)
H16 0.327604 1.158108 0.334567 0.037*
C17 1.2770 (6) 0.6561 (7) 0.45765 (17) 0.0598 (14)
H17A 1.241793 0.569183 0.431820 0.090*
H17B 1.370215 0.615077 0.484702 0.090*
H17C 1.320657 0.750869 0.439871 0.090*
I1 1.14312 (3) 1.09116 (3) 0.19947 (2) 0.02547 (10)
N1 0.7786 (3) 0.9238 (3) 0.31463 (10) 0.0193 (6)
O1 1.0241 (3) 0.8170 (3) 0.28483 (9) 0.0348 (6)
O2 0.3447 (4) 1.1343 (4) 0.40779 (11) 0.0503 (8)
O3 1.1267 (4) 0.7053 (4) 0.48213 (10) 0.0481 (7)

Source of material

The target compound 1-(2-iodobenzoyl)-6-methoxy-1H-indole-3-carbaldehyde could be prepared by acylation of 6-methoxy-1H-indole-3-formaldehyde with corresponding acyl chloride. First, sodium hydride (2.2 g, 54 mmol) and anhydrous N,N-dimethylformamide (DMF, 4 mL) were added into a 250 mL round bottom flask, and stirred in an ice water bath for 5 min. Second, a solution of 6-methoxy-1H-indole-3-formaldehyde (2.63 g, 15 mmol) in anhydrous DMF (20 mL) was added dropwise into the above reaction solution, and continued stirring for another 15 min. Next, a solution prepared by 2-iodobenzoyl chloride (7.2 g, 27 mmol) and anhydrous DMF (15 mL) was added dropwise. After addition, the reaction solution was slowly raised to room temperature and stirred for 3 h. The reaction process was monitored by TLC (UV, 254 nm). The crude product was purified by column chromatography (silica gel), eluting with petroleum ether/ethyl acetate (6:1, v/v) to obtain the white solid product (5.40 g, yield 89%). Single crystals were obtained from n-hexane/ethyl acetate (2:1, v/v) solution.

Experimental details

The H atoms were placed in idealized positions and treated as riding on their parent atoms, with d(C–H) = 0.96 Å (methyl), Uiso(H) = 1.5Ueq(C), and d(C–H) = 0.93 Å (aromatic), Uiso(H) = 1.2Ueq(C).

Comment

Indole is a kind of common skeleton exists widely in natural products and drugs, and has been researched in both organic chemistry and medicinal chemistry fields [4]. Especially in the field of organic synthesis, many researchers have extensively studied the reaction characteristics of the N(1), C(2) and C(3) positions of indole [5], [6], [7]. Among them, the most classic reaction is that after being treated with strong base, the negatively charged nitrogen atom shows high nucleophilic activity, so it is easy to acylate with acyl chloride or other reagents to form amide. Many anti-inflammatory drugs containing N-acyl substitution indoles, such as indomethacin, could be synthesized or structurally modified through the above acylation reaction [8]. Therefore, this acylation reaction of indole has important applications in drug synthesis [9]. Based on the previous research on the synthetic methodology of indole derivatives [10], we have designed and synthesized a series of compounds with N-acyl indole structures, which are expected to exhibit anti-inflammatory or anti-tumor activities. Recently, a series of N-acyl indole compounds with active functional groups such as methoxy, aldehyde and iodide substituents have been synthesized by acylation reaction. In this work, the crystals of 1-(2-iodobenzoyl)-6-methoxy-1H-indole-3-carbaldehyde were obtained and its structure is reported here.

Single-crystal structure analysis reveals that there are four molecules in the asymmetric unit. Bond lengths and angles are in the expected ranges [11], [12], [13]. In title molecule, the iodobenzene part and indole part are bridged by carbonyl group. Due to the conjugation of amide bond in the molecule, the bond length of C(9)–N(1) (1.387(4) Å), is similar to the C(1)–N(1) bond in the indole ring (1.392(4) Å) and is shortened as compared to the C(8)–N(1) bond (1.421(4) Å). The torsion angle O(1)–C(9)–N(1)–C(8) is −5.9(5)°, which indicate the amide moiety and indole ring are almost coplanar. On the contrary, the amide part and the benzene ring of the side chain are not coplanar, because the torsion angles of O(1)–C(9)–C(10)–C(11) is −46.2(4)°. The dihedral angle between the indole ring and the benzene ring is about 55.5(4)°. In addition, as a key intermediate, the title molecule contains methoxy, aldehyde and iodine substituents, which providing plenty of active reaction sites for further modification.


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:

Funding source: National Science Foundation of China

Award Identifier / Grant number: 21702018

Funding source: Key Research and Development Program of Shandong Province

Award Identifier / Grant number: 2019GSF108031

  1. Author contributions: 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: 2022-12-24
Accepted: 2023-01-20
Published Online: 2023-01-31
Published in Print: 2023-04-25

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

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

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  76. The crystal structure of hexalithium decavanadate hexadecahydrate, H32Li6O44V10
  77. Crystal structure of ethyl 4-{[5-(adamantan-1-yl)-2-sulfanylidene-2,3-dihydro-1,3,4-oxadiazol-3-yl]methyl}piperazine-1-carboxylate, C20H30N4O3S
  78. Crystal structure of aqua(μ2-2,2′,2″-((nitrilo)tris(ethane-2,1-diyl(nitrilo)methylylidene))tris (6-ethoxyphenolato))(pentane-2,4-dionato-κ2O,O′)-dinickel(II), C38H48N4Ni2O9
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