Home The crystal structure of 1,2-bis(1H-benzo[d]imidazol-2-yl)ethane-1,2-diol — N-(2-aminophenyl)-3-(1H-benzo[d]imidazol-2-yl)-2,3-dihydroxypropanamide (1/1), C32H30N8O5
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The crystal structure of 1,2-bis(1H-benzo[d]imidazol-2-yl)ethane-1,2-diol — N-(2-aminophenyl)-3-(1H-benzo[d]imidazol-2-yl)-2,3-dihydroxypropanamide (1/1), C32H30N8O5

  • Candyce R. Clark , Eric C. Hosten ORCID logo and Richard Betz ORCID logo
Published/Copyright: February 15, 2021
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Zeitschrift für Kristallographie - New Crystal Structures
From the journal Zeitschrift für Kristallographie - New Crystal Structures Volume 236 Issue 2

Abstract

C32H30N8O5, orthorhombic, P212121 (no. 19), a = 9.1258(4) Å, b = 10.6225(5) Å, c = 30.1870(14) Å, V = 2926.3(2) Å3, Z = 4, Rgt(F) = 0.0367, wRref(F2) = 0.0837, T = 200 K.

CCDC no.: 2045361

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 rod
Size:0.55 × 0.15 × 0.06 mm
Wavelength:Mo Kα radiation (0.71073 Å)
μ:0.10 mm−1
Diffractometer, scan mode:Bruker APEX-II, φ and ω
θmax, completeness:28.3°, >99%
N(hkl)measured, N(hkl)unique, Rint:39064, 7280, 0.034
Criterion for Iobs, N(hkl)gt:Iobs > 2 σ(Iobs), 6175
N(param)refined:446
Programs:Bruker [1], [2], SHELX [3], WinGX/ORTEP [4], Mercury [5], PLATON [6]
Table 2:

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

AtomxyzUiso*/Ueq
O110.14620 (17)0.52437 (13)0.55431 (5)0.0254 (3)
O12−0.04913 (15)0.33833 (14)0.52593 (5)0.0221 (3)
O210.7834 (2)0.71613 (16)0.48936 (5)0.0356 (4)
O220.73500 (15)0.47932 (13)0.45153 (5)0.0201 (3)
O230.47180 (16)0.58894 (14)0.53054 (5)0.0278 (3)
N110.18880 (19)0.21491 (16)0.60449 (6)0.0222 (4)
N120.1950 (2)0.40536 (18)0.63450 (6)0.0273 (4)
N130.26775 (18)0.35960 (16)0.45259 (6)0.0216 (4)
N140.03971 (19)0.43346 (17)0.44705 (6)0.0221 (4)
N210.6082 (2)0.70821 (17)0.38000 (6)0.0254 (4)
N220.8329 (2)0.76985 (17)0.40019 (6)0.0228 (4)
N230.67444 (18)0.46668 (16)0.53706 (5)0.0198 (3)
N240.8680 (2)0.61172 (19)0.58518 (7)0.0300 (4)
C110.1880 (2)0.33647 (18)0.59689 (7)0.0202 (4)
C120.1913 (2)0.39755 (17)0.55193 (7)0.0198 (4)
H120.2956970.3975240.5418400.024*
C130.1030 (2)0.32362 (18)0.51742 (6)0.0182 (4)
H130.1292380.2323910.5193560.022*
C140.1389 (2)0.37158 (18)0.47207 (7)0.0189 (4)
C210.7007 (2)0.72366 (18)0.41284 (7)0.0200 (4)
C220.6637 (2)0.69591 (19)0.46038 (7)0.0227 (4)
H220.5802610.7508630.4697100.027*
C230.6184 (2)0.55756 (17)0.46556 (6)0.0175 (4)
H230.5297940.5405440.4469940.021*
C240.5809 (2)0.53774 (17)0.51421 (6)0.0178 (4)
C1110.1984 (2)0.2035 (2)0.65061 (7)0.0231 (4)
C1120.2029 (2)0.3229 (2)0.66990 (7)0.0263 (5)
C1130.2149 (3)0.3402 (2)0.71540 (8)0.0379 (6)
H1130.2188600.4218920.7281720.045*
C1140.2207 (3)0.2331 (3)0.74101 (8)0.0409 (6)
H1140.2307350.2409890.7722120.049*
C1150.2123 (3)0.1138 (2)0.72231 (8)0.0404 (6)
H1150.2142590.0422040.7411470.049*
C1160.2012 (3)0.0964 (2)0.67706 (8)0.0324 (5)
H1160.1957520.0145300.6645360.039*
C1210.2502 (2)0.41740 (19)0.41123 (7)0.0221 (4)
C1220.1071 (2)0.4637 (2)0.40741 (7)0.0233 (4)
C1230.0568 (2)0.5225 (2)0.36916 (7)0.0317 (5)
H123−0.0409790.5523810.3668000.038*
C1240.1552 (3)0.5354 (2)0.33483 (8)0.0372 (6)
H1240.1249460.5755390.3082450.045*
C1250.2991 (3)0.4905 (2)0.33839 (8)0.0360 (6)
H1250.3646260.5012910.3142260.043*
C1260.3478 (2)0.4308 (2)0.37630 (7)0.0303 (5)
H1260.4452180.3998780.3783920.036*
C2110.6842 (2)0.75012 (19)0.34284 (7)0.0243 (4)
C2120.8252 (2)0.7899 (2)0.35496 (7)0.0239 (4)
C2130.9257 (3)0.8358 (2)0.32441 (9)0.0387 (6)
H2131.0207690.8624660.3331080.046*
C2140.8807 (4)0.8407 (3)0.28080 (9)0.0468 (7)
H2140.9464780.8714790.2589470.056*
C2150.7421 (4)0.8020 (2)0.26809 (8)0.0460 (7)
H2150.7153660.8069000.2377280.055*
C2160.6415 (3)0.7563 (2)0.29834 (8)0.0372 (6)
H2160.5466410.7299350.2892450.045*
C2210.6754 (2)0.45380 (19)0.58432 (7)0.0207 (4)
C2220.7771 (2)0.5266 (2)0.60795 (7)0.0247 (4)
C2230.7911 (3)0.5056 (2)0.65315 (8)0.0339 (5)
H2230.8607000.5523930.6697790.041*
C2240.7040 (3)0.4169 (2)0.67414 (8)0.0380 (6)
H2240.7152660.4029530.7050390.046*
C2250.6012 (3)0.3484 (2)0.65080 (8)0.0350 (5)
H2250.5405280.2892580.6656310.042*
C2260.5873 (2)0.3668 (2)0.60562 (7)0.0263 (5)
H2260.5173050.3196810.5892390.032*
H1A0.826 (3)0.642 (2)0.5593 (9)0.035 (7)*
H1B0.912 (3)0.675 (3)0.6043 (9)0.049 (8)*
H11A0.056 (3)0.526 (3)0.5610 (9)0.040 (8)*
H12A0.200 (3)0.485 (3)0.6350 (9)0.043 (8)*
H12B−0.091 (3)0.270 (3)0.5320 (9)0.036 (7)*
H14A−0.048 (3)0.449 (2)0.4546 (8)0.028 (6)*
H21A0.818 (4)0.788 (3)0.4879 (10)0.059 (10)*
H22A0.708 (3)0.422 (3)0.4327 (9)0.042 (8)*
H22B0.898 (3)0.801 (3)0.4180 (9)0.041 (8)*
H23A0.758 (3)0.440 (2)0.5230 (9)0.035 (7)*

Source of material

Approximately 0.1 mol o-phenylene diamine and 0.1 mol tartaric acid were refluxed in 100 mL 4 M HCl in a round bottomed flask for 1 h. The flask was allowed to cool to room temperature and then the purple solution was neutralized with conc. NH3 solution. The brown precipitate was filtered off and recrystallised from a mixture of water and ethanol. Brown crystals were formed.

Experimental details

Carbon-bound H atoms were placed in calculated positions (C–H 0.95 Å for aromatic carbon atoms) and were included in the refinement in the riding model approximation, with U(H) set to 1.2Ueq(C). All oxygen- and nitrogen-bound H atoms were located on a difference Fourier map and refined freely.

Comment

Chelate ligands have found widespread use in coordination chemistry due to the increased stability of coordination compounds they can form in comparison to monodentate ligands. The stability of these compounds is enhanced further if the denticity of the ligand is increased upon incorporation of more and more potential donor sites [7]. Especially dicarboxylic acids are interesting in this aspect as chemical factors such as pH values could influence on the protonation/deprotonation of acidic functional groups and fine-tune the denticity of the resulting ligand species. Examples in this aspect are imidazole-dicarboxylic acids that can be synthesized according to a published procedure [8]. The structure of piperazine-1,4-diium bis(hydrogen 2-propyl-1H-imidazole-4,5-dicarboxylate) monohydrate has been reported earlier and confirms the validity of the general synthetic protocol [9]. In continuation of our studies of the structures of polyfunctional carboxylic acids [10], [11], [12], [13], we attempted the synthesis of a novel imidazole-dicarboxylic acid.

The structure solution shows a surprising result confirming that the synthesis reaction was interrupted too early for the complete conversion of the starting materials. The asymmetric unit contains two complete, neutral molecular species 1,2-bis(1H-benzo[d]imidazol-2-yl)ethane-1,2-diol and N-(2-aminophenyl)-3-(1H-benzo[d]imidazol-2-yl)-2,3-dihydroxypropanamide. The latter can be expected as a first step on the conversion pathway of the educts to the intended product. C–N bond lengths in the symmetric molecular entity clearly show the distinction between the imino and the amino-type nitrogen atom with values of 1.312(3) and 1.320(3) Å for the former and 1.352(3) and 1.350(3) Å for the latter with regards to the bond towards the carbon atom connected to both nitrogen atoms within each heterocyclic moiety. These values also tally with the corresponding bond lengths in the benzimidazole motif of the asymmetric second molecular entity present in the asymmetric unit of the crystal structures where values of 1.312(3) and 1.358(3) Å are apparent. In each case, these values are in good agreement with other benzimidazole derivatives whose molecular and crystal structures were determined by means of diffraction studies performed on single crystals and whose metrical parameters have been deposited with the Cambridge Structural Database. The C=O bond in the asymmetric benzimidazol moiety present in the crystal structure is found at 1.237(2) Å. The least-squares planes as defined by the respective non-hydrogen atoms of the two benzimidazole systems present in the 1,2-bis(2-benzimidazyl)-1,2,-dihydroxyethane molecule intersect at an angle of 75.04(7)° while the least-squares planes as defined by the respective non-hydrogen atoms of the benzimidazole moiety on the one hand and the non-hydrogen atoms of the aminophenyl moiety on the other hand in the asymmetric molecule present in the crystal structure intersect at an angle of 23.86(7)° only.

In the crystal, classical hydrogen bonds of the O–H⋯O, O–H⋯N, N–H⋯O and N–H⋯N type are present next to C–H⋯N contacts whose range falls by more than 0.1 Å below the sum of van-der-Waals radii of the atoms participating in them. All hydrogen atoms bonded to heteroatoms act as donors while all imino-type nitrogen atoms as well as all oxygen atoms act as acceptors. These classical hydrogen bonds are established between the two molecular entities of the title compound as well as symmetry-generated equivalents thereof. One intramolecular N–H⋯O hydrogen bond is formed by the amino group of the aminophenyl moiety. The C–H⋯N contact is supported by one of the hydrogen atoms in ortho position to the heterocyclic five-membered ring in the 1,1,2-bis(1H-benzo[d]imidazol-2-yl)ethane-1,2-diol molecule. In terms of graph-set analysis [14], the descriptor for these contacts is S(9)DDDDC11(5)C11(6) C11(7)C11(9)C11(10). In total, the entities present in the asymmetric unit are connected to sheets perpendicular to the crystallographic c axis. Furthermore, a number of N–H⋯π as well as C–H⋯π interactions could be discussed whose metrical details have been tabulated.

Corresponding author: Dr. Richard Betz, Department of Chemistry, Nelson Mandela University, Summerstrand Campus (South), University Way, Summerstrand, PO Box 77000, Port Elizabeth6031, South Africa, E-mail:

Funding source: National Research Foundation

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

  2. Researchfunding: CRC thanks the National Research Foundation for financial support in connection with the Thuthuka funding initiative.

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

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Received: 2020-10-08
Accepted: 2020-11-19
Published Online: 2021-02-15
Published in Print: 2021-03-26

© 2020 Candyce R. Clark et al., published by De Gruyter, Berlin/Boston

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

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  56. Crystal structure of {tris((1H-benzo[d]imidazol-2- yl)methyl)amine-κ4N,N′,N′′,N′′′}-(succinato-κ2O,O′)nickel(II) – methanol (1/4), C32H41N7NiO8
  57. Crystal structure of catena-poly[trans-tetraaqua(μ2-1,1′-(biphenyl-4,4′-diyl)bis(1H-imidazol)-k2N:N′)cobalt(II)] dinitrate – 1,1′-(biphenyl-4,4′-diyl)bis(1H-imidazol) – water (1/3/2), C72H68CoN18O12
  58. Crystal structure of bis(μ2-2-oxido-2-phenylacetate-κ3O:O,O′)-bis(1-isopropoxy-2-oxo-2-phenylethan-1-olato-κ2O,O′)-bis(propan-2-olato-κ1O)dititanium(IV), C44H52O14Ti2
  59. The crystal structure of 5-carboxy-2-(hydroxymethyl)-1H-imidazol-3-ium-4-carboxylate, C6H8N2O6
  60. The crystal structure of 2,6-dibromo-4-fluoroaniline, C6H4Br2FN
  61. The crystal structure of 4-chloro-N-(2-phenoxyphenyl)benzamide, C19H14ClNO2
  62. The crystal structure of 2-methyl-β-naphthothiazole, C12H9NS
https://doi.org/10.1515/ncrs-2020-0529
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Articles in the same Issue

  1. Frontmatter
  2. New Crystal Structures
  3. The crystal structure of 4-hydroxybenzene-1,3-diaminium dichloride, C6H10Cl2N2O
  4. The crystal structure of 3-chloropropylammonium chloride, C3H9Cl2N
  5. The crystal structure of 1-chloro-2-(dimethylamino)ethane hydrochloride, C4H11Cl2N
  6. Crystal structure of N-(2-(trifluoromethyl)phenyl)hexanamide, C13H16F3NO
  7. Redetermination of the crystal structure of para-toluidine, C7H9N 
  8. The crystal structure of bis(1,3-dihydroxy-2-methylpropan-2-aminium) carbonate, C9H24N2O7
  9. The crystal structure of 4-chloro-1-methylpiperidin-1-ium chloride, C6H13Cl2N
  10. Crystal structure of (Z)-3-(6-bromo-1H-indol-3-yl)-1,3-diphenylprop-2-en-1-one, C23H16BrNO
  11. The crystal structure of ethyl 2-amino-4-(3,5-difluorophenyl)-7,7-dimethyl-5-oxo-5,6,7,8-tetrahydro-4H-chromene-3-carboxylate, C20H21F2NO4
  12. Crystal structure of 6,6'‐((1E,1'E)‐(propane‐1,3‐diylbis(azaneylylidene))bis(methaneylylidene))bis(3‐bromophenol), C34H32Br4N4O4
  13. The crystal structure of (E)-2-(2-((2-picolinoylhydrazono)methyl)phenoxy)acetic acid dihydrate, C15H17N3O6
  14. Crystal structure of (E)-4-bromo-N′-(3-chloro-2-hydroxybenzylidene)benzohydrazide, C14H10BrClN2O2
  15. Crystal structure of N,N′-bis(4-bromosalicylidene) ethylene-1,2-diaminopropan, C34H32Br4N4O4
  16. Crystal structure of 4-bromo-N′-[(3-bromo-2-hydroxyphenyl)methylidene]benzohydrazide methanol solvate, C15H14Br2N2O3
  17. The crystal structure of 1,2-bis(1H-benzo[d]imidazol-2-yl)ethane-1,2-diol — N-(2-aminophenyl)-3-(1H-benzo[d]imidazol-2-yl)-2,3-dihydroxypropanamide (1/1), C32H30N8O5
  18. The crystal structure of para-trifluoromethyl-aniline hemihydrate, C14H14F6N2O
  19. Redetermination of the crystal structure of 2-amino-2-methyl-propane-1,3-diole, C4H11NO2
  20. The crystal structure of methacholine chloride, C8H18ClNO2
  21. Crystal structure of 5,7,7-trimethyl-4,6,7,8-tetrahydrocyclopenta[g]isochromen-1(3H)-one, C15H18O2
  22. Crystal structure of poly[diammine-bis(μ4-4-hydroxypyridine-3-sulfonato-κ5N:O, O′:O′′:O′′)(μ2-pyrazinyl-κ2N:N′)tetrasilver(I)], C7H8Ag2N3O4S
  23. Crystal structure of ethyl (E)-5-(((3′,6′-bis(ethylamino)-3-oxospiro[isoindoline-1,9′-xanthen]-2-yl)imino)methyl)-2,4-dimethyl-1H-pyrrole-3-carboxylate — ethanol (1/1), C38H45N5O5
  24. Crystal structure of 4-bromo-N′-[(3-chloro-2-hydroxyphenyl)methylidene]benzohydrazide, C14H7Br2N2O2
  25. Redetermination of the crystal structure of 3,3,3-triphenylpropanoic acid, C21H18O2 – Deposition of hydrogen atomic coordinates
  26. Structure redetermination of dextromethorphan hydrobromide monohydrate, C18H28BrNO2 – localization of hydrogen atoms
  27. Crystal structure of tris(azido-κ1N)-(N-(2-aminoethyl)-N-methyl-1,3-propanediamine-κ3N,N′,N′′)cobalt(III), C7H19CoN12
  28. Crystal structure of tetraaqua-bis(1H-indazole-6-carboxylate-κN)cadmium (II), C16H18CdN4O8
  29. Crystal structure of dichloride-bis(1-propylimidazole-κ1N)zinc(II), C12H20Cl2N4Zn
  30. Crystal structure of (E)-resveratrol 3-O-β-D-xylopyranoside, C19H22O8
  31. Crystal structure of 3,3′-(1,2-phenylene-bis(methylene))bis(1-vinyl- 1H-imidazol-3-ium) bis(hexafluoro phosphate)(V), C18H20F12N4P2
  32. Crystal structure of diaqua[bis(benzimidazol-2-yl-methyl)amine-κ3N,N′,N″]-phthalato-κ1O-nickel(II)-methanol (1/2), C26H31N5NiO8
  33. Crystal structure of 6,7-difluoro-1-methyl-3-(trifluoromethyl)quinoxalin-2(1H)-one, C10H5F5N2O
  34. Crystal structure of dichlorido-bis(1-hexyl-1H-benzotriazole-k1N)zinc(II), C24H34N6Cl2Zn
  35. The crystal structre of 2-(4-bromophenyl)-2,3-dihydro-1H-naphtho[1,8-de][1,3,2]diazaborinine, C16H12BBrN2
  36. Crystal structure of diethyl 3,9-bis(4-fluorophenyl)-6,12-diphenyl-3,9-diazapentacyclo[6.4.0.02,7.04,11]dodecane-1,5-dicarboxylate, C40H36F2N2O4
  37. Crystal structure of (E)-7-methoxy-2-((5-methoxypyridin-3-yl)methylene)-3,4- dihydronaphthalen-1(2H)-one, C18H17NO3
  38. Crystal structure of (E)-2-chloro-6-(((1,3-dihydroxy-2-(oxidomethyl)propan-2-yl)imino)methyl)phenolate-κ3N,O,O’)manganese(IV), C22H24Cl2MnN2O8
  39. The crystal structure of α-(meta-methoxyphenoxy)-ortho-tolylic acid, C15H14O4
  40. The crystal structure of N-(2-chloroethyl)-N,N-diethylammonium chloride, C6H15Cl2N
  41. The crystal structure of tris(2,3,4,6,7,8,9,10-octahydro-1H-pyrimido[1,2-a]azepin-5-ium) trihydrodecavanadate(V), C27H54N6O28V10
  42. Crystal structure of 1,3-bis(octyl)benzimidazolium perchlorate C23H39ClN2O4
  43. Crystal structure of tetrakis[(Z)-(2-(1-(furan-2-yl)-2-methylpropylidene)-1-phenylhydrazin-1-ido-κ2N,N′)] zirconium(IV), C56H60N8O4Zr
  44. The crystal structure of 2-(naphthalen-2-yloxy)-4-phenyl-6-(prop-2-yn-1-yloxy)-1,3,5-triazine, C22H15N3O2
  45. The crystal structure of trimethylsulfonium tris(trifluoromethylsulfonyl)methanide, C7H9F9O6S4
  46. Crystal structure of 4-bromo-N′-[3,5-dichloro-2-hydroxyphenyl)methylidene]benzohydrazide methanol solvate, C15H13BrCl2N2O3
  47. The crystal structure of 4-(4-bromophenyl)-2-(3-(4-bromophenyl)-5-(4-fluorophenyl)-4,5-dihydro-1H-pyrazol-1-yl)thiazole, C24H16Br2FN3S
  48. The crystal structure of N-(adamantan-1-yl)-piperidine-1-carbothioamide, C16H26N2S
  49. The crystal structure of 1-phenyl-N-(4,5,6,7-tetrabromo-1,3-dioxoisoindolin-2-yl)-5-(thiophen-2-yl)-1H-pyrazole-3-carboxamide-dimethylformamide (1/1) C22H10Br4N4O3S
  50. The crystal structure of benzeneseleninic acid anhydride, C12H10O3Se2
  51. The crystal structure of diphenyalmine hydrochloride antimony trichloride co-crystallizate, C12H12Cl4NSb – Localization of hydrogen atoms
  52. The crystal structure of para-nitrobenzylbromide, C7H6BrNO2 – A second polymorph and correction of 3D coordinates
  53. Crystal structure of catena-poly[(5H-pyrrolo[3,2-b:4,5-b′]dipyridine-κ2N,N′)-(μ4-hexaoxidodivanadato)dizinc(II)],C10H9N3O6V2Zn
  54. Crystal structure of N,N′-(2-hydroxypropane-1,3-diyl)bis(pyridine-2-aldimine)-κ5N,N′,N′′,N′′′,O]-tris(nitrato-κ2O,O′) cerium(III), C15H16CeN7O10
  55. Synthesis and crystal structure of oktakis(dimethylsulphoxide-κ1O)gadolinium(III) [tetrabromido-μ2-bromido-μ2-sulfido-di-μ3-sulfido-μ4-sulfido-tetracopper(I)-tungsten(VI)], C16H48O8S12Br5Cu4GdW
  56. Crystal structure of {tris((1H-benzo[d]imidazol-2- yl)methyl)amine-κ4N,N′,N′′,N′′′}-(succinato-κ2O,O′)nickel(II) – methanol (1/4), C32H41N7NiO8
  57. Crystal structure of catena-poly[trans-tetraaqua(μ2-1,1′-(biphenyl-4,4′-diyl)bis(1H-imidazol)-k2N:N′)cobalt(II)] dinitrate – 1,1′-(biphenyl-4,4′-diyl)bis(1H-imidazol) – water (1/3/2), C72H68CoN18O12
  58. Crystal structure of bis(μ2-2-oxido-2-phenylacetate-κ3O:O,O′)-bis(1-isopropoxy-2-oxo-2-phenylethan-1-olato-κ2O,O′)-bis(propan-2-olato-κ1O)dititanium(IV), C44H52O14Ti2
  59. The crystal structure of 5-carboxy-2-(hydroxymethyl)-1H-imidazol-3-ium-4-carboxylate, C6H8N2O6
  60. The crystal structure of 2,6-dibromo-4-fluoroaniline, C6H4Br2FN
  61. The crystal structure of 4-chloro-N-(2-phenoxyphenyl)benzamide, C19H14ClNO2
  62. The crystal structure of 2-methyl-β-naphthothiazole, C12H9NS
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