Home The crystal structure of tert-butyl (E)-3-(2-(benzylideneamino)phenyl)-1H-indole-1-carboxylate, C26H24N2O2
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The crystal structure of tert-butyl (E)-3-(2-(benzylideneamino)phenyl)-1H-indole-1-carboxylate, C26H24N2O2

  • Weihao Da , Haonan Kong , Ruiyao Wang ORCID logo and Yi Lin ORCID logo EMAIL logo
Published/Copyright: June 26, 2023
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Zeitschrift für Kristallographie - New Crystal Structures
From the journal Zeitschrift für Kristallographie - New Crystal Structures Volume 238 Issue 5

Abstract

C26H24N2O2, monoclinic, P21/n (no. 14), a = 10.949(6) Å, b = 9.930(5) Å, c = 20.125(13) Å, β = 98.51(3)°, V = 2164(2) Å3, Z = 4, Rgt(F) = 0.0465, wRref(F2) = 0.1260, T = 296(2) K.

CCDC no.: 2259207

The molecular structure is shown in the figure. 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: Colorless block
Size: 0.30 × 0.25 × 0.15 mm
Wavelength: Mo Kα radiation (0.71073 Å)
μ: 0.08 mm−1
Diffractometer, scan mode: Bruker APEX-II, φ and ω
θmax, completeness: 26.0°, >99 %
N(hkl)measured, N(hkl)unique, Rint: 23,437, 4249, 0.048
Criterion for Iobs, N(hkl)gt: Iobs > 2 σ(Iobs), 3131
N(param)refined: 274
Programs: Bruker [1], SHELX [2, 3]
Table 2:

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

Atom x y z Uiso*/Ueq
O1 0.59035 (13) 0.16789 (12) 0.31150 (6) 0.0497 (3)
O2 0.50419 (16) 0.19822 (15) 0.20392 (7) 0.0714 (5)
N1 0.69809 (13) 0.54819 (14) 0.44105 (7) 0.0409 (4)
N2 0.48904 (13) 0.35892 (14) 0.28235 (7) 0.0375 (3)
C1 1.0379 (2) 0.1985 (3) 0.47627 (15) 0.0773 (7)
H1A 1.095894 0.131131 0.473428 0.093*
C2 0.9761 (2) 0.2560 (3) 0.41880 (13) 0.0736 (7)
H2A 0.993781 0.229011 0.377009 0.088*
C3 0.88803 (19) 0.3538 (2) 0.42298 (10) 0.0593 (6)
H3A 0.846135 0.391699 0.383867 0.071*
C4 0.86142 (16) 0.39588 (19) 0.48468 (9) 0.0438 (4)
C5 0.76297 (17) 0.49321 (19) 0.49095 (9) 0.0437 (4)
H5A 0.747476 0.515623 0.533786 0.052*
C6 0.60100 (16) 0.63551 (16) 0.45176 (8) 0.0367 (4)
C7 0.48946 (16) 0.63197 (16) 0.40647 (8) 0.0356 (4)
C8 0.47230 (15) 0.53928 (16) 0.34880 (8) 0.0353 (4)
C9 0.52280 (16) 0.41520 (17) 0.34555 (8) 0.0369 (4)
H9A 0.573195 0.373478 0.380857 0.044*
C10 0.52764 (18) 0.23438 (18) 0.26077 (9) 0.0446 (4)
C11 0.6464 (2) 0.03439 (19) 0.30093 (11) 0.0567 (5)
C12 0.7014 (3) −0.0053 (3) 0.37129 (13) 0.0869 (9)
H12A 0.745192 −0.088796 0.370052 0.130*
H12B 0.636585 −0.015977 0.398217 0.130*
H12C 0.757348 0.063535 0.390427 0.130*
C13 0.7452 (3) 0.0522 (3) 0.25673 (15) 0.0895 (9)
H13A 0.785547 −0.032423 0.252186 0.134*
H13B 0.804713 0.116988 0.276688 0.134*
H13C 0.708310 0.083445 0.213220 0.134*
C14 0.5452 (3) −0.0629 (2) 0.27220 (16) 0.0908 (9)
H14A 0.578626 −0.152156 0.271720 0.136*
H14B 0.512571 −0.036311 0.227190 0.136*
H14C 0.480349 −0.061583 0.299511 0.136*
C15 0.41353 (15) 0.45163 (17) 0.24304 (8) 0.0366 (4)
C16 0.35770 (17) 0.4439 (2) 0.17694 (9) 0.0453 (4)
H16A 0.367863 0.368996 0.150593 0.054*
C17 0.28633 (18) 0.5518 (2) 0.15161 (10) 0.0519 (5)
H17A 0.246130 0.548182 0.107580 0.062*
C18 0.27263 (18) 0.6658 (2) 0.18993 (10) 0.0511 (5)
H18A 0.224833 0.737425 0.171046 0.061*
C19 0.32921 (16) 0.67355 (19) 0.25551 (9) 0.0433 (4)
H19A 0.320253 0.750071 0.280996 0.052*
C20 0.40043 (15) 0.56494 (17) 0.28347 (8) 0.0352 (4)
C21 1.0137 (2) 0.2408 (3) 0.53745 (14) 0.0757 (7)
H21A 1.056324 0.203107 0.576419 0.091*
C22 0.92624 (18) 0.3393 (2) 0.54186 (11) 0.0572 (5)
H22A 0.910882 0.367831 0.583862 0.069*
C23 0.61276 (18) 0.72731 (19) 0.50465 (9) 0.0467 (5)
H23A 0.686965 0.732066 0.533767 0.056*
C24 0.5172 (2) 0.81110 (19) 0.51482 (9) 0.0524 (5)
H24A 0.527179 0.871415 0.550569 0.063*
C25 0.4069 (2) 0.80566 (19) 0.47210 (10) 0.0511 (5)
H25A 0.341629 0.861028 0.479280 0.061*
C26 0.39393 (18) 0.71765 (18) 0.41864 (9) 0.0438 (4)
H26A 0.319345 0.715148 0.389756 0.053*

1 Source of materials

The synthesis consists of two steps. In the first step, tert-butyl 3-bromo-1H-indole-1-carboxylate, 2-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)aniline, and Pd(PPh3)4 were mixed in a dioxane / K2CO3 mixture. The mixture was stirred at 100 °C under argon for 4 h. After cooling to room temperature, the mixture was extracted with ethyl acetate. The organic layer was dried over magnesium sulfate, filtered, and the solvent was removed under reduced pressure. The crude product was purified by column chromatography (silica gel, ethyl acetate/hexane). The final product was obtained as maroon colored oil. In the second step, tert-butyl 3-(2-aminophenyl)-1H-indole-1-carboxylate was added to a mixture of chloroform and acetic acid in presence of molecular sieves. Benzaldehyde was then added dropwise into the mixture. The reaction was stirred at reflux under argon for 5 h. The yellow colored mixture was slowly poured into the NaOH solution. The organic layer was washed with water, dried over magnesium sulfate, filtered, and the solvent was removed under reduced pressure. The crystals were grown using a two solvent system (DCM/hexane) by slow diffusion at room temperature.

2 Experimental details

A crystal was mounted on a glass fiber with epoxy glue. Data collection was performed on a Bruker D8 VENTURE Photon II diffractometer. Data were processed using the Bruker AXS Crystal Structure Analysis Package [1]. Data collection: Bruker Apex2; cell refinement: Bruker Saint; Data reduction: Bruker Saint; Structure solution: Shelxs-97 [2]; Structure refinement: Shelxl-2016/6 [3]; Molecular graphics: Bruker Shelxtl [2]; Publication materials: Bruker Shelxtl [2]. All H-atoms were placed geometrically and refined using a riding model with common isotropic displacement factors Uiso(H) = 1.2 Ueq (parent C-atom) or 1.5 Ueq (methyl C-atom).

3 Comment

The Pictet–Spengler condensation, firstly discovered more than 100 years ago, is a well-known reaction between arylethylamine and aldehyde (or ketone) to create nitrogen containing hetero aromatic compounds such as indole and isoquinoline alkaloids [4, 5]. It has been largely applied in the synthesis of bioactive compounds [6], [7], [8] and recently, it found its application in constructing aza-annulated organic semiconducting materials [9], [10], [11], [12]. In the effort to prepare tert-butyl 6-phenyl-7H-indolo[2,3-c]quinoline-7-carboxylate, we isolated the intermediate tert-butyl (E)-3-(2-(benzylideneamino)phenyl)-1H-indole-1-carboxylate, the precursor for the cyclization.

The crystal structure shows that the compound adopts an E configuration for the imine unit. In the meantime, it’s interesting to note that the tert-butyloxycarbonyl group remains intact in the presence of acetic acid. The angles of C(5)–N(1)–C(6) and N(1)–C(5)–C(4) were measured at 119.39(15)° and 123.34(17)° respectively. The C–N bond lengths were around 1.4 Å in most cases. A slightly shorter value was determined for N(1)–C(5) at 1.265(2) Å, showing a double bond character which is consistent with the imine structure. The bond lengths of the aromatic rings were between 1.356(2) and 1.451(2) Å, while the one that connects the two rings were slightly longer, at 1.471(2) Å.

Corresponding author: Yi Lin, Department of Chemistry, Xi’an Jiaotong–Liverpool University, Suzhou, Jiangsu, 215000, P. R. China, E-mail:

Funding source: Xi’an Jiaotong–Liverpool University Key Program Special Fund

Award Identifier / Grant number: KSF–E-55

Funding source: Xi’an Jiaotong–Liverpool University Postgraduate Research Scholarship Fund

Award Identifier / Grant number: PGRS1912016

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

  2. Research funding: This work was financially supported by Xi’an Jiaotong–Liverpool University Key Program Special Fund (KSF–E-55) and Xi’an Jiaotong–Liverpool University Postgraduate Research Scholarship Fund (PGRS1912016).

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

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Received: 2023-05-04
Accepted: 2023-06-01
Published Online: 2023-06-26
Published in Print: 2023-10-26

© 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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https://doi.org/10.1515/ncrs-2023-0213
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Articles in the same Issue

  1. Frontmatter
  2. New Crystal Structures
  3. The crystal structure of (N-([1,1′:4′,1″-terphenyl]-4,4′-diethyl)-2-(bis(pyridin-2-ylmethyl)amino)acetamide-κ4N,N,N″, O)tri(nitrato-kO, O′) samarium(III) - methanol - acetonitrile (1/1/1), C40H39SmN8O14
  4. The crystal structure of 6,6′-(((2-(dimethylamino)ethyl)azanediyl)bis(methylene))bis(2-chloro-4-methyl phenolate-κ4N,N′,O,O′)-(pyridine-2,6-dicarboxylato-N,O,O′)-titanium(IV), C27H27Cl2N3O6Ti
  5. N′-[(1E)-(4–Fluorophenyl)methylidene]adamantane-1-carbohydrazide, C18H21FN2O
  6. Crystal structure of 4-bromo-3-nitro-1H-pyrazole-5-carboxylic acid monohydrate, C4H2N3BrO4·H2O
  7. Crystal structure of dipyridine-k1N-tris(2,2,6,6-tetramethyl-5-oxohept-3-en-3-olato-k2O,O′)dysprosium(III), DyC43H67O6N2
  8. Crystal structure of cyclo[tetraiodido-bis{μ2-1-[(benzotriazol-1-yl)methyl]-1-H-1,3-(2-isopropyl-imidazol)-k2N:N}dicadmiun(II)], C26H30N10Cd2I4
  9. The crystal structure of tert-butyl (E)-3-(2-(benzylideneamino)phenyl)-1H-indole-1-carboxylate, C26H24N2O2
  10. The crystal structure of 4-(3-carboxy-1-cyclopropyl-6-fluoro-8-methoxy-4-oxo-1,4- dihydroquinolin-7-yl)-2-methylpiperazin-1-ium 2,5-dihydroxybenzoate methanol solvate, C27H32FN3O9
  11. Crystal structure of (μ2-1-(4,4′-bipyridine-κ2N:N′)-bis[diaqua-(4-iodopyridine-2,6-dicarboxylato-κ3O,N,O′)–cobalt(II)], C24H20Co2I2N4O12
  12. The crystal structure of dimethyl 4,4′-(10,20-diphenylporphyrin-5,15-diyl)dibenzoate dichloromethane solvate, C49H36N4O4Cl2
  13. (E)-2-((E)-4-(2,6,6-trimethylcyclohex-1-en-1-yl)but-3-en-2-ylidene)hydrazine-1-carbothioamide C14H23N3S1
  14. The crystal structure of [1-(4-(trifluoromethyl)phenyl)-3,4-dihydroquinolin-2(1H)-one], C16H12F3NO
  15. Crystal structure of (E)-2-amino-N′-((3-hydroxy-5-(hydroxymethyl)-2-methylpyridin-4-yl)methylene)benzohydrazide – dimethylformamide – water (1/1/2), C15H16N4O3·C3H7NO·2H2O
  16. Crystal structure of 3-(4-bromophenyl)-5-methyl-1H-pyrazole, C10H9BrN2
  17. Crystal structure of 1,10-phenanthrolinium bromide dihydrate, C12H9N2Br
  18. Crystal structure of N-(4′-chloro-[1,1′-biphenyl]-2-yl)formamide, C13H10ClNO
  19. The crystal structure of nitroterephthalic acid, C8H5NO6
  20. Crystal structure of (2-((4-bromo-2,6-dichlorophenyl)amino)phenyl) (morpholino)methanone, C17H15BrCl2N2O2
  21. Crystal structure of tetraaqua-bis(ethanol-κO)-tetrakis(μ2-trifluoroacetate-κ2O:O′)-bis(trifluoroacetate-κ2O)digadolinium(III) Gd2C16H20O18F18
  22. The crystal structure of dimethyl 4,4′-[10,20-bis(2,6-difluorophenyl)porphyrin-5,15-diyl]dibenzoate chloroform solvate, C50H32Cl6F4N4O4
  23. The crystal structure of N,N′-((nitroazanediyl)bis(methylene))diacetamide, C6H12O4N4
  24. The crystal structure of [bis(2,2′-bipyridine-6-carboxylato-κ3N,N,O)magnesium(II)]dihydrate, C22H18N4O6Mg
  25. Crystal structure of poly[diaqua-(bis(μ2-1,4-bis(imidazol-1-ylmethyl)benzene)-κ2N,N′] cobalt(II)-tetraqua-bis(1,4-bis(imidazol-1-ylmethyl)benzene)-κ1N)-cobalt(II) di(2,5-thiophenedicarboxylate) dihydrate, C68H76Co2N16O16S2
  26. Crystal structure of poly[chlorido-μ2-chlorido-(μ2-1-[(2-ethyl-4-methyl-1H-imidazol-1-yl)methyl]-1H-benzotriazole-κN:N’)cadmium(II)], C13H15CdN5Cl2
  27. The crystal structure of (4-hydroxybenzenesulfonate)-k1O-6,6′-((1E,1′E)- (ethane-1,2-diylbis(azaneylylidene))bis(methaneylylidene)) bis(2-methoxyphenol)-κ2N,N,μ2O,O,κ2O, O)-(methanol)-cobalt(II) sodium(I), C25H27CoN2NaO9S
  28. Crystal structure of (1-methyl-3-(trifluoromethyl)-1H-pyrazol-4-yl)(4-((2-methyl-6-(trifluoromethyl)pyrimidin-4-yl)amino)piperidin-1-yl)methanone, C17H18F6N6O
  29. Crystal structure of bis{[(cyclohexylimino)(phenylimino)-l5-(methyl)diethylazane-κ2N:N′]-(ethyl)-zinc(II)]}, C38H62N6Zn2
  30. Crystal structure of 2-[(4-bromobenzyl)thio]-5-(5-bromothiophen-2-yl)-1,3,4-oxadiazole, C13H8Br2N2OS2
  31. Crystal structure of 10-methoxy-7,11b,12,13-tetrahydro-6H-pyrazino [2′,3′:5,6]pyrazino[2,1-a]isoquinoline, C15H16N4O
  32. The crystal structure of 1-propyl-2-nitro-imidazole oxide, C6H9N3O3
  33. The crystal structure of 3-nitrobenzene-1,2-dicarboxylic acid–2-ethoxybenzamide (1/1), C17H16N2O8
  34. The structure of RUB-1, (C8H16N)6[B6Si48O108], a boron containing levyne-type zeolite, occluding N-methyl-quinuclidinium in the cage-like pores
  35. The crystal structure of diaqua-(naphthalene-4,5-dicarboxylate-1,8-dicarboxylic anhydride-κ1O)-(4′-(4-(1H-benzimidazolyl-1-yl)phenyl)-2,2′:6′,2″-terpyridine-κ3N,N′,N″)–manganese(II) dihydrate, C42H27MnN5O9·2H2O
  36. Crystal structure of 6,6′-((1E,1′E)-hydrazine-1,2-diylidenebis(methanylylidene))bis (3-(3-bromopropoxy)phenol), C20H22Br2N2O4
  37. The crystal structure of 3-(2-hydroxyphenyl)-4-phenyl-6-(p-tolyl)-2H-pyran-2-one, C24H18O3
  38. Crystal structure of bis(μ2-2-(1,5-dimethyl–3-oxo-2-phenyl-2,3-dihydro-1H-pyrazol-4-yl)imino)methyl)phenolato-κ4O:O,N,O′)-(nitrato-κ2O,O′)dicobalt(II), C36H32Co2N8O4
  39. Synthesis and crystal structure of (3E,5S,10S,13S,14S,17Z)-17-ethylidene-10,13-dimethylhexadecahydro-3H-cyclopenta[α] phenanthren-3-one O-(4-fluorobenzoyl) oxime, C28H36FNO2
  40. The crystal structure of 4-aminiumbiphenyl benzenesulfonate, C18H17NO3S
  41. Synthesis and crystal structure of 1-(7-hydroxy-3-(4-hydroxy-3-nitrophenyl)-4-oxo-4H-chromen-8-yl)-N,N-dimethylmethanaminiumnitrate, C18H17N3O9
  42. Crystal structure of N-(Ar)-N′-(Ar′)-formamidine, C14H12Br2N2O
  43. The crystal structure of 4-(2,4-dichlorophenyl)-2-(4-fluorophenyl)-5-methyl-1H-imidazole, C16H11Cl2FN2
  44. Crystal structure of 1-(4–chlorophenyl)-4-benzoyl-3-methyl-1H-pyrazol-5-ol, C17H13ClN2O2
  45. The crystal structure of 5-amino-1-methyl-4-nitroimidazole, C4H6O2N4
  46. Crystal structure of 1,3-diisopropyl-4,5-dimethylimidazol-2-ylidene-N,N′-bis(1,3-bis(2,6-diisopropylphenyl)-1,3-dihydro-2H-1,3,2-diazaborol-2-yl)-l2-germenediamine, C63H94B2GeN8
  47. The crystal structure of (bromido, chlorido)-tricarbonyl-(5,5′-dimethyl-2,2′-bipyridine)-rhenium(I), C15H12Br0.2Cl0.8N2O3Re1
  48. Crystal structure of [N(E),N′(E)]-N,N′-(1,4-phenylenedimethylidyne)bis-3,5-bis(propan-2-yl)-1H-pyrazol-4-amine, C26H36N6
  49. The crystal structure of poly[2-(4-carboxypyridin-3-yl)terephthalpoly[diaqua-(μ4-2-(6-carboxylatopyridin-3-yl)terephthalato-κ5O,N:O′:O″,O‴)]) cadmium(II)] dihydrate, C28H20Cd3N2O16
  50. Crystal structure of [tetraaqua-bis((3-carboxy-5-(pyridin-4-yl)benzoate-κ1N)cobalt(II)] tetrahydrate, C26H32CoN2O16
  51. Crystal structure of bis(μ2-azido-κ2N:N)-tetrakis(azido-κ1N)-tetrakis(1,10-phenanthroline-κ2N,N′)dibismuth(III), C48H32N26Bi2
  52. Crystal structure of (Z)-N-(4-(4-(4-((4,5,6-trimethoxy-3-oxobenzofuran-2(3H)-ylidene)methyl)phenoxy)butoxy)phenyl)acetamide, C30H31NO8
  53. Crystal structure of poly[diaqua-(μ2-1,3-di(1H-imidazol-1-yl)propane-κ2N:N′)-bis(μ2-5-carboxybenzene-1,3-dicarboxylato-O,O′:O″)-aqua-di-zinc dihydrate solvate], C27H28N4O16Zn2
  54. Crystal structure of 2-(3,5,5-trimethylcyclohex-2-en-1-ylidene)malononitrile, C12H14N2
  55. Crystal structure of chlorido-(5-nitro-2-phenylpyridine-κ2N,C)-[(methylsulfinyl)methane-κ1S]platinum(II), C13H13ClN2O3PtS
  56. The crystal structure of the co-crystal 1,4-dioxane–4,6-bis(nitroimino)-1,3,5-triazinan-2-one(2/1), C11H19N7O9
  57. Crystal structure of [N(E),N′(E)]-N,N′-(1,4-phenylenedimethylidyne)bis-3,5-dimethyl-1H-pyrazol-4-amine di-methanol solvate, C18H20N6·2(CH3OH)
  58. Crystal structure of catena-poly[bis(μ2-azido-k2N:N′)-(nitrato-K2N:N′)-bis(1,10-phenanthroline-K2N:N′)samarium(III)], C24H16N11O3Sm
  59. Crystal structure of (Z)-2-(4-((5-bromopentyl)oxy)benzylidene)-4,5,6-trimethoxybenzofuran-3(2H)-one, C23H25BrO6
  60. Crystal structure of bis(3,5-dimethyl-1H-pyrazol-4-ammonium) tetrafluoroterephthate, 2[C5H10N3][C8F4O4]
  61. Crystal structure of 2-amino-4-(2-fluoro-4-(trifluoromethyl)phenyl)-9-methoxy-1,4,5,6-tetrahydrobenzo[h]quinazolin-3-ium chloride, C20H18ClF4N3O
  62. Crystal structure of 6-(pyridin-3-yl)-1,3,5-triazine-2,4-diamine-sebacic acid (2/1), C13H17N6O2
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