Home Crystal structure of 3-((1H-benzo[d]imidazol-2-yl)amino)-2-(1H-benzo[d]imidazol-2-yl)isoindolin-1-one, C22H16N6O
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Crystal structure of 3-((1H-benzo[d]imidazol-2-yl)amino)-2-(1H-benzo[d]imidazol-2-yl)isoindolin-1-one, C22H16N6O

  • Dai Zeng , Ai-Ping Xing , Jun-Jun Wei , Yi-Xin Chu and Shu-Ling Zhang EMAIL logo
Published/Copyright: October 25, 2018

Abstract

C22H16N6O, monoclinic, P21/c (no. 14), a = 13.2081(5) Å, b = 23.3620(11) Å, c = 12.2769(5) Å, β = 102.345(4)°, V = 3700.7(3) Å3, Z = 8, Rgt(F) = 0.0648, wRref(F2) = 0.1730, T = 293(2) K.

CCDC no.: 1851055

The asymmetric unit of the title crystal structure containing two independent molecules is shown in the figure (hydrogen atoms are omitted for clarity). 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:Colorless prism
Size:0.1 × 0.09 × 0.08 mm
Wavelength:Cu Kα radiation (1.54184Å)
μ:0.72 mm−1
Diffractometer, scan mode:Xcalibur, ω-scans
θmax, completeness:67.1°, >99%
N(hkl)measured, N(hkl)unique, Rint:16853, 6602, 0.039
Criterion for Iobs, N(hkl)gt:Iobs > 2 σ(Iobs), 3589
N(param)refined:544
Programs:CrysAlisPRO [1], SHELX [2], OLEX2 [3]
Table 2:

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

AtomxyzUiso*/Ueq
N10.1148(2)0.54550(11)0.2065(2)0.0592(7)
N20.1934(2)0.48418(14)0.0902(2)0.0677(8)
H20.248(3)0.5084(16)0.093(3)0.113(16)*
N30.0355(2)0.46189(11)0.1159(2)0.0598(7)
N40.0062(2)0.52544(11)0.3452(2)0.0596(7)
H40.04680.52810.40980.072*
N5−0.1199(2)0.46600(11)0.2304(2)0.0586(7)
H5−0.080(3)0.4685(15)0.172(3)0.101(13)*
N6−0.10730(19)0.46445(11)0.4175(2)0.0573(7)
N1′0.4194(2)0.48286(11)0.3265(2)0.0625(7)
N2′0.2631(3)0.45256(15)0.3781(3)0.0764(9)
H2′0.254(3)0.4847(14)0.411(3)0.081(13)*
N3′0.3425(2)0.39144(12)0.2826(2)0.0646(7)
N4′0.4679(2)0.47268(11)0.1448(2)0.0568(7)
H4′0.471(2)0.5046(12)0.108(2)0.063(10)*
N5′0.4545(2)0.37164(11)0.1178(2)0.0579(7)
H5′0.425(2)0.3693(15)0.177(3)0.082(12)*
N6′0.50950(19)0.42455(10)−0.0116(2)0.0553(7)
O10.2657(2)0.58563(12)0.1736(2)0.0966(9)
O1′0.3712(2)0.54895(11)0.4465(2)0.1011(9)
C10.2005(3)0.68776(17)0.3055(3)0.0926(13)
H10.26240.69760.28570.111*
C20.1527(4)0.72488(17)0.3658(4)0.1004(14)
H2A0.18210.76050.38640.121*
C30.0615(3)0.70973(16)0.3960(3)0.0876(12)
H30.03090.73510.43760.105*
C40.0146(3)0.65705(14)0.3651(3)0.0708(10)
H4A−0.04660.64680.38600.085*
C50.0616(3)0.62050(14)0.3027(3)0.0604(9)
C60.1536(3)0.63508(15)0.2749(3)0.0684(10)
C70.1888(3)0.58847(16)0.2134(3)0.0726(10)
C80.0265(2)0.56201(13)0.2593(3)0.0577(8)
H8−0.03670.56580.20110.069*
C90.1121(3)0.49821(15)0.1383(3)0.0603(9)
C100.1661(3)0.43344(15)0.0332(3)0.0645(9)
C110.0683(3)0.41969(14)0.0505(2)0.0596(9)
C120.0196(3)0.36940(15)0.0080(3)0.0714(10)
H12−0.04580.36000.01910.086*
C130.0709(3)0.33397(16)−0.0510(3)0.0804(11)
H130.04020.2997−0.07910.096*
C140.1685(3)0.34842(17)−0.0696(3)0.0831(12)
H140.20110.3237−0.11060.100*
C150.2178(3)0.39868(17)−0.0285(3)0.0769(11)
H150.28230.4086−0.04170.092*
C16−0.0725(2)0.48660(13)0.3331(3)0.0549(8)
C17−0.1854(2)0.42250(13)0.2513(3)0.0568(8)
C18−0.1784(2)0.42272(13)0.3669(3)0.0553(8)
C19−0.2358(2)0.38377(14)0.4137(3)0.0667(9)
H19−0.23350.38390.48990.080*
C20−0.2967(3)0.34473(15)0.3440(3)0.0729(10)
H20−0.33490.31790.37440.087*
C21−0.3020(3)0.34466(15)0.2295(3)0.0732(10)
H21−0.34290.31760.18500.088*
C22−0.2475(3)0.38419(15)0.1809(3)0.0687(10)
H22−0.25240.38500.10420.082*
C1′0.5709(4)0.61141(15)0.4154(3)0.0849(12)
H1′0.54140.63350.46350.102*
C2′0.6610(4)0.62809(18)0.3852(3)0.0923(13)
H2′A0.69270.66230.41230.111*
C3′0.7048(3)0.59438(16)0.3149(3)0.0856(12)
H3′0.76620.60610.29620.103*
C4′0.6589(3)0.54342(15)0.2715(3)0.0722(10)
H4′A0.68830.52130.22340.087*
C5′0.5693(3)0.52668(13)0.3015(3)0.0599(9)
C6′0.5255(3)0.56030(14)0.3714(3)0.0655(9)
C7′0.4312(3)0.53296(15)0.3886(3)0.0734(10)
C8′0.5037(2)0.47405(13)0.2649(3)0.0572(8)
H8′0.54280.43920.29090.069*
C9′0.3445(3)0.44209(16)0.3286(3)0.0644(9)
C10′0.2023(3)0.40383(18)0.3621(3)0.0757(11)
C11′0.2509(3)0.36669(17)0.3015(3)0.0683(10)
C12′0.2088(3)0.31345(18)0.2679(3)0.0876(12)
H12′0.24170.28820.22830.105*
C13′0.1156(4)0.2997(2)0.2959(3)0.1013(15)
H13′0.08420.26480.27290.122*
C14′0.0682(3)0.3367(2)0.3574(4)0.1057(17)
H14′0.00600.32590.37530.127*
C15′0.1106(3)0.3893(2)0.3931(4)0.1007(15)
H15′0.07930.41380.43570.121*
C16′0.4794(2)0.42445(13)0.0847(3)0.0520(8)
C17′0.4671(2)0.33389(13)0.0353(3)0.0548(8)
C18′0.5025(2)0.36689(13)−0.0434(3)0.0530(8)
C19′0.5266(2)0.34096(14)−0.1366(3)0.0631(9)
H19′0.55300.3621−0.18840.076*
C20′0.5102(3)0.28292(15)−0.1497(3)0.0727(10)
H20′0.52460.2648−0.21210.087*
C21′0.4726(3)0.25102(14)−0.0717(3)0.0751(10)
H21′0.46160.2120−0.08350.090*
C22′0.4510(3)0.27567(14)0.0230(3)0.0698(10)
H22′0.42670.25410.07580.084*

Source of material

A Mixture of 2-aminobenzimidazole (10 mmol, 1.3315 g) and 2-carboxybenzaldehyde (10 mmol, 1.4912 g) in 25 mL ethanol was refluxed for 3 h. The resulting solution was cooled to room temperature and the light yellow precipitate was isolated. The crude product was recrystallized in a methanol-dimethylsulfoxide mixture and afforded colorless crystals suitable for crystal structure analysis. IR (cm−1, KBr): 3368 (m), 2843 (br), 1716 (s), 1635(s), 1586 (s), 1550 (s), 1485 (m), 1450 (s), 1416 (m), 1362 (s), 1319 (m), 1305 (m), 1233 (w), 1209 (m), 1139 (m), 1108 (w), 1049 (m), 1028 (m), 1008 (w), 992 (w), 952 (w), 929 (w), 916 (w), 871 (w), 797 (m), 763 (m), 745 (s), 715 (w), 705 (m), 684 (s), 603 (s), 591(s), 583 (s), 560 (w), 537 (w), 481 (w), 441 (w), 416 (w).

Experimental details

All hydrogen atoms were placed geometrically and refined using a riding model with Uiso set to 1.5Ueq of the parent atom.

Discussion

Isoindolinone derivatives with lactam five-membered heterocyclic skeleton have become a hot topic of current interest due to its high pharmacological and biological activities and potential applications in medicine, materials and organic pigments [4], [5], [6], [7]. As a class of indole alkaloids, isoindolinone compounds can be extracted and isolated from plants [8], [9], [10]. In view of the structural diversity and important significance of isoindolinone derivatives, the construction of such a motif has attracted great attention over the past decades [11], [12], [13]. It is noteworthy that the traditional way of synthesizing the designed compounds would suffer from multistep reactions and high cost. Thus, it is highly desirable to explore more efficient and convenient synthetic methods of isoindolinone derivatives. Herein we report the facile synthesis and crystal structure of a new isoindolinone-containing compound.

Single crystal structure analysis reveals that the title compound crystallizes in the monoclinic P21/c space group with two crystallographically independent molecules in the asymmetric unit (cf. the figure). The molecule consists of a isoindolin-1-one group, a benzimidazole group and a 2-aminobenzimidazole group. The latter two groups lie to the same side of the plane through the isoindolin-1-one moiety and locate in 2- and 3-position of the isoindolin-1-one moiety, respectively. The isoindolin-1-one moiety is effectively planar with the maximum deviation from the least-squares plane through the atoms being 0.0262 Å for the C8 atom. The dihedral angles between the plane of isoindolin-1-one moiety and the planes through the C10—C15 and C17—C22 rings are 6.3° and 53.0°, respectively. The C8—N4 distance of 1.449 Å is consistent with a C—N single bond, as in 2-benzyl-3-(benzylamino)-6-nitroisoindolin-1-one (C—N: 1.434 Å) and 3-(Thiazol-2-ylamino)isobenzofuran-1(3H)-one (C—N: 1.418 Å) [14], [15] .

The imidazole nitrogen atoms (N6 and N6′) are involved in the intermolecular hydrogen bond interactions with N4 and N4′ atoms [N4⋯N6: 2.107 Å, N4′⋯N6′: 2.083 Å], forming a dimer. Face to face π⋯π interactions are observed between adjacent dimers with the centroid-centroid distance between the other two imidazole rings of 3.50 Å. Thus a supramolecular chain structure which lies in the ac plane is constructed. Van der Waals forces are responsible to construct a three-dimensional architecture. All these interactions stabilize the solid state of the title compound.

Acknowledgements

This work was financially supported by the Doctoral Research Fund of Henan University of Chinese Medicine (No. BSJJ2015−20).

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Received: 2018-08-04
Accepted: 2018-10-09
Published Online: 2018-10-25
Published in Print: 2019-03-26

©2019 Dai Zeng et al., published by De Gruyter, Berlin/Boston

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

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  43. Crystal structure of (E)-2-(((6-bromopyridin-2-yl)methylene)amino)-3′,6′-bis(diethylamino)spiro[isoindoline-1,9′-xanthen]-3-one, C34H34N5O2Br
  44. Crystal structure of (Z)-2-((adamantan-1-ylimino)methyl)-5-methoxyphenol, C18H23NO2
  45. Crystal structure of bis((E)-2-ethoxy-6-(((2-hydroxyethyl)imino)methyl)phenolato-κ2N,O)copper(II), C22H28N2CuO6
  46. Crystal structure of 2,3-diphenyl-5,6-bis(4-methoxyphenyl)pyrazine, C30H24N2O2
  47. Crystal structure of dichlorido bis[1-((2,4-dimethyl-1H-imidazol-1-yl)methyl)-1H-benzo[d][1,2,3]triazole-κN]cadmium(II), Cd(C12H13N5)2Cl2
  48. The crystal structure of 1,5-di(naphthalen-2-yl)-3-(pyridin-2-yl)pentane-1,5-dione, C30H23NO2
  49. The crystal structure of 2-((3-methylthiophen-2-yl)methylene)malononitrile, C9H6N2S
  50. The crystal structure of 1,4-dinitroso-2,3,5,6-tetraacetoxy-piperazine, C12H16N4O10
  51. Crystal structure of bis(2,4,6-trichlorophenyl) malonate, C15H6Cl6O4
  52. The crystal structure of trans-dichlorido-bis(pyridine-2-carboxylato-κ2N,O)platinum(IV), C12H8Cl2N2O4Pt
  53. Crystal structure of 3-nitroquinoline 1-oxide, C9H6N2O3
  54. Crystal structure of 2-(piperidin-1-ium-4-yl)-1H-benzo[d]imidazol-3-ium dichloride dihydrate, C12H21Cl2N3O2
  55. Crystal structure of (4S,4aS,6aR,6bR,12aS,12bR,14aS,14bR)-3,3,6a,6b,9,9,12a-heptamethyloctadecahydro-1H,3H-4,14b-ethanophenanthro[1,2-h]isochromene, C30H50O
  56. Crystal structure of (E)-4-((2-fluoro-3-(trifluoromethyl)benzylidene)amino)-3-methyl-1H-1,2,4-triazole-5(4H)-thione, C11H8F4N4S
  57. Crystal structure of 5-(4-fluorophenyl)-4-methyl-2,4-dihydro-3H-1,2,4-triazole-3-thione, C9H8FN3S
  58. Crystal structure of catena-poly[(1-(4-fluorophenyl)-N–(5-((trimethylstannyl)thio)-1,3,4-thiadiazol-2-yl)methanimine], (C12H14FN3S2Sn)n
  59. The crystal structure of 4-(methoxycarbonyl)benzoic acid, C9H8O4
  60. The crystal structure of N,N′-(6-(thiophen-2-yl)-1,3,5-triazine-2,4-diyl)bis(2-methylpropane-2-sulfonamide) – ethyl acetate(2/1), C34H54N10O6S6
  61. Crystal structure of N′-(1-(2-hydroxyphenyl)ethylidene)-5-methyl-1-phenyl-1H-1,2,3-triazole-4-carbohydrazide, C18H17N5O2
  62. Crystal structure of 3-(4-methoxyphenyl)-1-phenylprop-2-yn-1-one, C16H12O2
  63. Crystal structure of N′-(1-(benzofuran-2-yl)ethylidene)-2-cyanoacetohydrazide, C13H11N3O2
  64. Crystal structure of hexa-μ2-chlorido-μ4-oxido-tetrakis(1-vinyl-1H-imidazole-κN)tetracopper(II), C20H24Cu4Cl6N8O
  65. Crystal structure of N′-((1E,2E)-4-(7-methoxy-2-oxo-2H-chromen-8-yl)-2-methylbut-2-en-1-ylidene)-4-methylbenzenesulfonohydrazide, C22H22O5N2S
  66. Crystal structure of 2-acetyl pyrene, C18H12O
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