Startseite The crystal structure of 1,4-bis((1H-benzimidazol-2-yl)methyl)-piperazine-2,5-dione dihydrate, C20H22N6O4
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The crystal structure of 1,4-bis((1H-benzimidazol-2-yl)methyl)-piperazine-2,5-dione dihydrate, C20H22N6O4

  • Aijun Jia , Zhihai Gong EMAIL logo und Ji Li ORCID logo
Veröffentlicht/Copyright: 4. Januar 2022

Abstract

C20H22N6O4, monoclinic, P21/c (no. 14), a = 11.2208(8) Å, b = 6.0358(4) Å, c = 14.6702(10) Å, β = 92.565(1)°, V = 992.57(12) Å3, Z = 2, R gt (F) = 0.0639, wR ref (F2) = 0.1726, T = 296(2) K.

CCDC no.: 2119281

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: 0.20 × 0.16 × 0.12 mm
Wavelength: Mo Kα radiation (0.71073 Å)
μ: 0.10 mm−1
Diffractometer, scan mode: φ and ω
θmax, completeness: 27.0°, 99%
N(hkl)measured, N(hkl)unique, Rint: 10,383, 2143, 0.033
Criterion for Iobs, N(hkl)gt: Iobs > 2 σ(Iobs), 1623
N(param)refined: 145
Programs: Bruker [1], SHELX [2], [3], [4], Diamond [3], Olex2 [4]
Table 2:

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

Atom x y z Uiso*/Ueq
C1 0.8975 (3) 0.0783 (4) 0.67284 (17) 0.0484 (7)
H1A 0.961332 0.098363 0.718864 0.058*
H1B 0.853067 −0.052909 0.688787 0.058*
C2 0.8158 (2) 0.2759 (4) 0.67395 (15) 0.0395 (6)
C3 0.6863 (2) 0.5290 (4) 0.62803 (17) 0.0421 (6)
C4 0.6078 (3) 0.6729 (5) 0.5818 (2) 0.0601 (8)
H4 0.587237 0.654994 0.520084 0.072*
C5 0.5622 (3) 0.8431 (5) 0.6320 (3) 0.0680 (9)
H5 0.509678 0.942751 0.603315 0.082*
C6 0.5921 (3) 0.8708 (5) 0.7241 (3) 0.0665 (9)
H6 0.559195 0.987950 0.755626 0.080*
C7 0.6694 (2) 0.7284 (5) 0.7696 (2) 0.0537 (7)
H7 0.689858 0.747404 0.831281 0.064*
C8 0.7162 (2) 0.5545 (4) 0.72018 (16) 0.0414 (6)
C9 0.9128 (2) −0.1527 (4) 0.53247 (18) 0.0488 (7)
H9A 0.827063 −0.145699 0.520891 0.059*
H9B 0.929307 −0.281685 0.570366 0.059*
C10 1.0302 (2) 0.1872 (4) 0.55691 (17) 0.0416 (6)
N1 0.94946 (18) 0.0432 (3) 0.58413 (13) 0.0409 (5)
N2 0.75113 (19) 0.3470 (4) 0.60041 (13) 0.0436 (5)
H2 0.758 (2) 0.307 (5) 0.5443 (9) 0.052*
N3 0.79867 (19) 0.3917 (4) 0.74791 (13) 0.0439 (5)
O1 1.05869 (19) 0.3503 (3) 0.60343 (13) 0.0595 (6)
O2 0.7938 (3) 0.2943 (4) 0.42089 (14) 0.0821 (8)
H2A 0.838 (4) 0.401 (5) 0.415 (3) 0.123*
H2B 0.791 (4) 0.230 (7) 0.3716 (17) 0.123*

Source of material

All the reagents and solvents were used as obtained. The title compound was prepared according to a modified method described by Adams et al. [5] in which the molar amount ratio of raw material iminodiacetic acid (13.3 g, 0.10 mol) and 1,2-diaminobenzene (10.8 g, 0.10 mol) being 1/1. A small amount of MnCl2 ·(H2O)4 (1.0 g, 5.0 mmol) was also added as the catalyst (Yield: 9.40 g, 41.5%). Crystals were obtained two weeks later by slow evaporation of the title compound in ethanol (95%).

Experimental details

H atoms bonded to C atoms were located in difference maps and subsequently treated as riding, with C–H distances of 0.93 Å (aromatic) and 0.97 Å (methylene); Uiso(H) = 1.2Ueq (aromatic and methylene C). H atoms bonded to N and methanol O atoms were also found in difference maps, and refined with restraints of N–H = 0.86(1) Å and O–H = 0.82(1) Å; Uiso(H) values were set equal to 1.2 or 1.5 times of the Ueq of their carrier atoms for N and O atoms, respectively.

Comment

The title compound (BMP) belongs to a new class of bridging ligand containing nitrogen and oxygen donor atoms, which is used in the design and synthesis of very few metal complexes [6]. The mechanism of the synthesis of BMP is still debatable whether it is a byproduct of the synthesis of the bis[N-(benzimidazol-2-ylmethyl)]amine (IDB) or from the IDB ligand decomposition under the catalysis by a metal complex, further producing the semi-condensation product BMP [6]. In this work, we have investigated its formation process by a modified method by using the MnCl2 ·(H2O)4 as the catalyst and the molar ratio of the raw materials iminodiacetic acid and 1,2-diaminobenzene being 1/1. In comparison to the reaction without a catalyst, the product yield of BMP was significantly improved. The colorless crystals can be obtained by a recrystallization of BMP from ethanol solution.

The title compound crystallized in the monoclinic space group P21/c. In its asymmetric unit, there is one half of a BMP and one water molecules with an inversion center residing at the piperazine-2,5-dione centroid. Due to the conjugate effects of the two carbonyl groups, the six-membered piperazine-2,5-dione ring is found to be planar. In comparison with the conformation of a BMP incorporated into a crystal of a metal complex [6], these two benzimidazole groups are also in a trans position to the central piperazine ring, leading to the chair-like conformation. The intermolecular connection between all moieties is furnished by N–H⃛O and O–H⃛O hydrogen bonds. The benzo groups are oriented in a perpendicular arrangement to interact by C–H⃛π interactions.


Corresponding author: Zhihai Gong, Guizhou East China Engineering Co. Ltd., Guiyang 550002, P. R. China, E-mail:

Funding source: Support Plan for Excellent Talents in Colleges and Universities of Anhui Province

Award Identifier / Grant number: qxyqZD2020113

  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 the Support Plan for Excellent Talents in Colleges and Universities of Anhui Province (qxyqZD2020113).

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

References

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Received: 2021-10-30
Accepted: 2021-12-14
Published Online: 2022-01-04
Published in Print: 2022-02-23

© 2021 Aijun Jia et al., 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 (E)-7-hydroxy-2-((6-methoxypyridin-3-yl)methylene)-3, 4-dihydronaphthalen-1(2H)-one, C17H15NO3
  4. Crystal structure of (E)-7-methoxy-2-((2-methoxypyridin-3-yl)methylene)-3,4-dihydronaphthalen-1 (2H)-one, C18H17NO3
  5. The crystal structure of N 6,N 6′-di(pyridin-2-yl)-[2,2′-bipyridine]-6,6′-diamine, C20H16N6
  6. The crystal structure of {N 1,N 2-bis[2,4-dimethyl-6-(4-(tert-butyl)phenyl)(phenyl)methyl]acenaphthylene-1,2-diimino-κ2 N, N′}-dibromido-nickel(II) – dichloromethane(1/2), C64H64Br2Cl4N2Ni
  7. Synthesis and crystal structure of nonacarbonyltris[(2-thia-1,3,5-triaza-7-phosphatricylco[3.3.1.1]decane-κ1 P)-2,2-dioxide]triruthenium(0) – acetonitrile (7/6), C25.71H32.57N9.86O15P3S3Ru3
  8. A new polymorph of 1-(4-nitrophenyl)-1H-benzimidazole (C13H9N3O2)
  9. The crystal structure of 2,2′-((1E,1′E)-(naphthalene-2,3 diylbis(azanylylidene)) bis(methanylylidene))bis(4-methylphenol), C26H22N2O2
  10. The crystal structure of bis(μ2-iodido)-bis(η6-benzene)-bis(iodido)-diosmium(II), C12H12I4Os2
  11. Redetermination of the crystal structure of bis{hydridotris(3,5-dimethylpyrazol-1-yl-κN 3)borato}copper(II), C30H44B2CuN12
  12. Crystal structure of (E)-3-((4-(tert-butyl)phenyl)thio)-4-hydroxypent-3-en-2-one, C15H20O2S
  13. Crystal structure of 2,2′-(p-tolylazanediyl)bis(1-phenylethan-1-one), C23H21NO2
  14. Redetermination of the crystal structure of the crystal sponge the poly[tetrakis(μ3-2,4,6-tris(pyridin-4-yl)-1,3,5-triazine)-dodecaiodidohexazinc(II) nitrobenzene solvate], C72H48I12N24Zn6⋅10(C6H5NO2)
  15. Crystal structure of (4′E)-6′-(diethylamino)-2-[(E)-[(6-methylpyridin-2-yl)methylidene]amino]-4′-{2-[(2E)-1,3,3-trimethyl-2,3-dihydro-1H-indol-2-ylidene]ethylidene}-1′,2,2′,3,3′,4′-hexahydrospiro[isoindole-1,9′-xanthene]-3-one, C44H45N5O2
  16. Crystal structure of (E)-7-fluoro-2-(3-fluorobenzylidene)-3,4-dihydronaphthalen-1(2H)-one, C17H12F2O1
  17. Crystal structure of tetrabutylammonium sulfanilate – 1-(diaminomethylene)thiourea (1/2)
  18. Crystal structure of [2,2′-{azanediyl)bis[(propane-3,1-diyl)(azanylylidene)methylylidene]} bis(3,5-dichlorophenolato)-κ2O,O′]-isothiocyanato-κN-iron(III), C21H19Cl4FeN4O2S
  19. Crystal structure of (4-chlorophenyl)(4-hydroxyphenyl)methanone, C13H9ClO2
  20. Crystal structure of 6,6′-((pentane-1,3-diylbis(azaneylylidene))bis(methaneylylidene))bis(2,4-dibromolphenolato-κ4 N,N′,O,O′)copper(II),) C19H16Br4CuN2O2
  21. Chlorido-(2,2′-(ethane-bis(5-methoxyphenolato))-κ4 N,N,O,O′)manganese(III) monohydrate, C19H18Cl2CuN2O2
  22. Crystal structure of 2,6-di-tert-butyl-4-(4-methoxybenzylidene)cyclohexa-2,5-dien-1-one, C22H28O2
  23. Crystal structure of [6,6′-(((2,2-dimethylpropane-1,3-diyl)bis(azanylylidene))bis(methanylylidene))bis(2-chlorophenolato)-κ4N,N′,O,O′]copper(II)
  24. Crystal structure of 2-chloro-3-((thiophen-2-ylmethyl)amino)naphthalene-1,4-dione, C30H20O4N2Cl2S2
  25. Crystal structure of bis{hydridotris(3-trifluoromethyl-5-methylpyrazolyl-1-yl)borato-κN 3}manganese(II), C30H26B2F18MnN12
  26. Crystal structure of 1-(2-methylphenyl)-2-(2-methylbenzo[b]thienyl)-3,3,4,4,5,5-hexafluorocyclopent-ene, C21H14F6S
  27. Crystal structure of 2-(3-((carbamimidoylthio)methyl)benzyl)isothiouronium hexafluorophosphate monohydrate, C10H17F6N4OPS2
  28. Crystal structure of 4,5-diiodo-1,3-dimesityl-1H-1,2,3-triazol-3-ium chloride – chloroform (1/1), C21H23Cl4I2N3
  29. Crystal structure of azido-k1 N-{6,6′-((((methylazanediyl)bis(propane-3,1-diyl))bis(azanylylidene))bis(methanylylidene))bis(2,4-dibromophenolato)k5 N,N′,N″,O,O′}cobalt(III)-methanol (1/1)), C21H23Br4CoN6O3
  30. The crystal structure of 2-(4-((carbamimidoylthio)methyl)benzyl)isothiouronium hexafluorophosphate monohydrate, C10H17F6N4OPS2
  31. Crystal structure of 1,1′-(methane-1,1-diyl)bis(3-methyl-1H-imidazol-3-ium) bis(hexafluoridophosphate), C9H14F12N4P2
  32. Crystal structure of (4′E)-6′-(diethylamino)-2-[(E)-[(pyren-1-yl)methylidene]amino]-4′-{2-[(2E)-1,3,3-trimethyl-2,3-dihydro-1H-indol-2-ylidene]ethylidene}-1′,2,2′,3,3′,4′-hexahydrospiro[isoindole-1,9′-xanthene]-3-one, C54H48N4O2
  33. Crystal structure of poly[bis(μ2-2,6-bis(1-imidazoly)pyridine-κ2 N,N′)-bis(thiocyanato-κ1 N)copper(II)] dithiocyanate, C24H18CuN12S2
  34. Cones with a three-fold symmetry constructed from three hydrogen bonded theophyllinium cations that coat [FeCl4] anions in the crystal structure of tris(theophyllinium) bis(tetrachloridoferrate(III)) chloride trihydrate, C21H33Cl9Fe2N12O9
  35. Crystal structure of 14-O-[(4-(4-hydroxypiperidine-1-yl)-6-methylpyrimidine-2-yl)thioacetyl]-mutilin monohydrate, C32H49N3O6S
  36. The crystal structure of (E)-3-chloro-2-(2-(4-methylbenzylidene)hydrazinyl)pyridine, C13H12ClN3
  37. The crystal structure of 4-phenyl-4-[2-(pyridine-4-carbonyl)hydrazinylidene]butanoic acid, C16H15N3O3
  38. The crystal structure of 6-amino-5-carboxypyridin-1-ium pentaiodide monohydrate C6H9I5N2O3
  39. Crystal structure of bis(μ3-oxido)-bis(μ2-2-formylbenzoato-k2O:O′)-bis(2-(dimethoxymethyl)-benzoato-κO)-oktakismethyl-tetratin(IV)
  40. Crystal structure of 2-((E)-(((E)-2-hydroxy-4-methylbenzylidene) hydrazineylidene)methyl)-4-methylphenol, C16H16N2O2
  41. Crystal structure of (E)-amino(2-((5-methylfuran-2-yl)methylene)hydrazinyl) methaniminium nitrate monohydrate, C14H26N10O10
  42. The crystal structure of N′-(2-chloro-6-hydroxybenzylidene)thiophene-2-carbohydrazide monohydrate, C12H11ClN2O3S
  43. Crystal structure of catena-poly[(μ2-1,1′-(biphenyl-4,4-diyl)bis(1H-imidazol)-κ2N:N′)-bis(4-bromobenzoate-κ1O)zinc(II)], C64H44Br4N8O8Zn2
  44. The crystal structure of catena-poly[(1-(4-carboxybenzyl)pyridin-1-ium-4-carboxylato-κ1O)-(μ2-oxalato-κ4 O:O′:O″:O‴)dioxidouranium(VI)], C16H11NO10U
  45. Crystal structure of 3-allyl-4-(2-bromoethyl)-5-(4-methoxyphenyl)-2-phenylfuran, C22H21BrO2
  46. Halogen bonds in the crystal structure of 4,3′:5′,4″-terpyridine — 1,3-diiodotetrafluorobenzene (1/1), C21H11F4I2N3
  47. Crystal structure of 2-(1H-indol-3-yl)ethan-1-aminium 2-(4-acetylphenoxy)acetate, C20H22N2O4
  48. Chalcogen bonds in the crystal structure of 4,7-dibromo-2,1,3-benzoselenadiazole, C6H2Br2N2Se
  49. The crystal structure of 1,4-bis((1H-benzimidazol-2-yl)methyl)-piperazine-2,5-dione dihydrate, C20H22N6O4
  50. The crystal structure of C19H20O8
  51. The crystal structure of KNa3Te8O18·5H2O exhibiting a 2[Te4O9]2− layer
  52. Erratum
  53. Erratum to: Crystal structure of (Z)-3-(6-bromo-1H-indol-3-yl)-1,3-diphenylprop-2-en-1-one, C23H16BrNO
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