Startseite The crystal structure of 5-carboxy-2-(hydroxymethyl)-1H-imidazol-3-ium-4-carboxylate, C6H8N2O6
Artikel Open Access

The crystal structure of 5-carboxy-2-(hydroxymethyl)-1H-imidazol-3-ium-4-carboxylate, C6H8N2O6

  • Candyce R. Clark , Eric C. Hosten ORCID logo und Richard Betz ORCID logo EMAIL logo
Veröffentlicht/Copyright: 15. Februar 2021

Abstract

C6H8N2O6, monoclinic, P21/c (no. 14), a = 7.4709(4) Å, b = 14.2051(9) Å, c = 7.3198(4) Å, β = 97.096(4)°, V = 770.86(8) Å3, Z = 4, Rgt(F) = 0.0346, wRref(F2) = 0.0946, T = 200 K.

CCDC no.: 2053160

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:Yellow platelet
Size:0.56 × 0.14 × 0.05 mm
Wavelength:Mo Kα radiation (0.71073 Å)
μ:0.16 mm−1
Diffractometer, scan mode:Bruker APEX-II, φ and ω
θmax, completeness:28.3°, >99%
N(hkl)measured, N(hkl)unique, Rint:9388, 1919, 0.020
Criterion for Iobs, N(hkl)gt:Iobs > 2 σ(Iobs), 1567
N(param)refined:148
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
O10.46258 (14)0.88897 (7)0.73947 (15)0.0252 (2)
O20.69777 (13)0.83834 (7)0.60857 (14)0.0232 (2)
O30.82914 (14)0.68678 (7)0.54187 (15)0.0244 (2)
H30.770 (3)0.7617 (19)0.575 (3)0.069 (8)*
O40.77886 (14)0.53446 (7)0.58178 (15)0.0282 (3)
O50.05073 (15)0.63360 (8)0.93659 (16)0.0316 (3)
H50.0691760.6353101.0520920.047*
O60.10691 (14)0.85018 (7)0.82943 (17)0.0281 (3)
N10.33934 (15)0.70842 (8)0.78531 (16)0.0178 (2)
N20.46211 (15)0.57430 (8)0.73756 (16)0.0179 (2)
C10.32162 (17)0.61548 (9)0.79985 (18)0.0178 (3)
C20.49649 (17)0.72716 (9)0.71056 (18)0.0166 (3)
C30.57351 (17)0.64241 (9)0.68025 (18)0.0166 (3)
C40.16598 (19)0.56707 (10)0.8709 (2)0.0250 (3)
H4A0.0984210.5297690.7708460.030*
H4B0.2114490.5234130.9714240.030*
C50.55545 (18)0.82539 (9)0.68500 (18)0.0179 (3)
C60.73946 (18)0.61706 (9)0.59758 (19)0.0194 (3)
H10.254 (3)0.7565 (15)0.815 (3)0.041 (5)*
H20.485 (3)0.5086 (17)0.736 (3)0.046 (6)*
H6A0.019 (2)0.8416 (15)0.892 (3)0.052 (6)*
H6B0.151 (3)0.9033 (9)0.864 (3)0.047 (6)*

Source of material

The compound was synthesized in analogy to a published procedure [7]. 0.1 mol of o-phenylenediamine and 0.1 mol of glycolic acid were placed in a round bottomed flask and refluxed in 100 mL of 4 M HCl solution for 2 h. The resultant dark blue solution was neutralised with aqueous ammonia and the resultant light purple precipitate was filtered on a Buchner funnel. The precipitate was recrystallised from boiling ethanol. A small amount of the purified compound was dissolved in aqueous ethanol, and crystals suitable for single crystal X-ray diffraction were obtained after slow evaporation of the mother liquor.

Experimental details

Carbon-bound H atoms were placed in calculated positions (C–H 0.95 Å for aromatic carbon atoms, C–H 0.99 Å for the methylene group) and were included in the refinement in the riding model approximation, with U(H) set to 1.2Ueq(C).

The H atom of the hydroxyl groups was allowed to rotate with a fixed angle around the C–O bond to best fit the experimental electron density (HFIX 147 in the SHELX program suite [3]), with U(H) set to 1.5Ueq(O).

Both nitrogen-bound H atoms as well as the H atoms of the water molecule and the H atom of the carboxyl group were located on a difference Fourier map and refined freely. The position of the aforementioned carboxyl H atom was refined approximately midway between the two O atoms, suggesting H atom disorder.

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 [8]. Especially dicarboxylic acids are interesting in this aspect as chemical factors such as pH values could have an influence on the protonation/deprotonation of acidic functional groups and fine-tune the denticity of the resulting ligand species. One such example are imidazole-dicarboxylic acids that can be synthesized according to a published procedure [7]. In continuation of our studies of the structures of polyfunctional carboxylic acids [9], [10], [11], [12], [13], [14], [15] the title compound was synthesized. To ensure the successful generation of the desired compound, the molecular and crystal structure of the latter was determined. Structural information about barium salts of the title compound has been published earlier [16]. Furthermore, the structures of three related compounds have been reported in the literature [17], [18], [19].

The structure solutions shows the presence of an imidazole-4,5-dicarboxylic acid bearing a hydroxymethyl substituent in the 2-position. Furthermore, one molecule of solvent water is present in the asymmetric unit. The acid is present in a zwitterionic form with one of the carboxyl groups having protonated the imine-type nitrogen atom. The hydrogen atom of the remaining carboxyl group is disordered over both carboxyl moieties. C–N bond lengths are measured at 1.3303(17)–1.3811(17) Å which is in good agreement with other compounds found in the Cambridge Structural Database [20]. Intracyclic angles cover a range of 106.74(11)–109.15(11)° with the largest two angles found on the pnicogen atoms.

In the crystal, classical hydrogen bonds of the N–H⋯O and O–H⋯O type are present. The hydrogen bonds stemming from the protons on the water molecule invariably employ one of the carboxylate-type oxygen atoms as acceptor. The carboxyl groups are linked by an intramolecular hydrogen bond. The N–H supported hydrogen bonds see either the oxygen atom of the water molecule or another carboxyl group oxygen atom as acceptor. The hydroxymethyl group gives rise to a hydrogen bond to the water molecule. In terms of graph-set analysis [21], [22], the descriptor for the hydrogen bonds is S(6)DDDDC11(6) at the unitary level. Furthermore one C–H⋯O contact whose range falls by more than 0.1 Å below the sum of van-der–Waals radii is observed between one of the hydrogen atoms of the methylene group and a carboxylate oxygen atom as acceptor. The graph-set descriptor for the latter contact is C11(7) at the unitary level. In total, the molecular species present in the asymmetric unit are connected to a three-dimensional network. π-Stacking is not a stabilizing feature of the crystal structure with the shortest distance in between two centers of gravity measured at 4.5719(8) Å.


Corresponding author: Richard Betz, Department of Chemistry, Nelson Mandela University, Summerstrand Campus (South), University Way, Summerstrand, PO Box 77000, Port Elizabeth, 6031, South Africa, E-mail:

Funding source: National Research Foundation

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

  2. Research funding: The corresponding author thanks the National Research Foundation for financial support.

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

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Received: 2020-11-12
Accepted: 2020-12-30
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.

Artikel in diesem Heft

  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, C7H9
  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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