Home The crystal structure of 4-hydroxy-2,5-bis(1-methyl-1H-imidazol-3-ium-2-ylthio)-3,6-dioxocyclohexa-1,4-dienolate chloride monohydrate, C14H15N4O5S2Cl
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The crystal structure of 4-hydroxy-2,5-bis(1-methyl-1H-imidazol-3-ium-2-ylthio)-3,6-dioxocyclohexa-1,4-dienolate chloride monohydrate, C14H15N4O5S2Cl

  • Ming-zhi Miao and Ji Li ORCID logo EMAIL logo
Published/Copyright: November 16, 2020
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Zeitschrift für Kristallographie - New Crystal Structures
From the journal Zeitschrift für Kristallographie - New Crystal Structures Volume 236 Issue 1

Abstract

C14H15N4O5S2Cl, orthorhombic, Pbca (no. 69), a = 16.1956(11) Å, b = 11.7856(8) Å, c = 18.7814(13) Å, V = 3584.9(4) Å3, Z = 8, Rgt(F) = 0.0459, wRref(F2) = 0.1218, T = 298(2) K.CCDC no.: 2034931

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:Red block
Size:0.30 × 0.25 × 0.10 mm
Wavelength:Mo Kα radiation (0.71073 Å)
μ:0.48 mm−1
Diffractometer, scan mode:Bruker Apex-II, φ and ω
θmax, completeness:28.0°, >99%
N(hkl)measured, N(hkl)unique, Rint:29,558, 4287, 0.064
Criterion for Iobs, N(hkl)gt:Iobs > 2 σ(Iobs), 3527
N(param)refined:252
Programs:Bruker [1], SHELX [2], [3], [4], Diamond [5], Olex2 [6], PLATON [7]
Table 2:

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

AtomxyzUiso*/Ueq
S10.06383 (3)0.60448 (4)0.36616 (3)0.04216 (15)
S20.44740 (3)0.47748 (5)0.39890 (3)0.04839 (16)
Cl10.21156 (3)0.18316 (5)0.55690 (3)0.05259 (17)
C1−0.12646 (13)0.5495 (2)0.36073 (13)0.0585 (6)
H1A−0.11960.54260.41130.088*
H1B−0.18130.52640.34780.088*
H1C−0.11790.62700.34680.088*
C2−0.08418 (14)0.3801 (2)0.28598 (12)0.0523 (6)
H2−0.13650.35080.27730.063*
C3−0.01272(14)0.3364 (2)0.26362 (12)0.0506 (5)
H3−0.00590.27060.23700.061*
C40.01579 (10)0.49152 (16)0.32401 (9)0.0335 (4)
C50.16770 (11)0.56262 (16)0.36799 (9)0.0349 (4)
C60.22462 (11)0.62517 (17)0.32729 (10)0.0375 (4)
C100.19227 (11)0.47866 (19)0.41645 (11)0.0430 (5)
C70.31817 (11)0.59865 (17)0.33721 (10)0.0371 (4)
C90.28374 (11)0.45196 (18)0.42258 (10)0.0412 (4)
C80.34194 (11)0.51137 (17)0.38774 (10)0.0374 (4)
C110.48459 (10)0.60929 (17)0.42523 (9)0.0343 (4)
C120.49932 (13)0.7784 (2)0.47262 (12)0.0493 (5)
H120.48760.84560.49650.059*
C130.57079 (12)0.75110 (19)0.44152 (11)0.0436 (5)
H130.61850.79500.44060.052*
C140.62336 (13)0.5863 (2)0.36916 (12)0.0499 (5)
H14A0.64430.52330.39610.075*
H14B0.66780.63720.35800.075*
H14C0.59900.55900.32580.075*
N1−0.06601 (9)0.47659 (15)0.32436 (9)0.0399 (4)
N20.04898 (10)0.40728 (15)0.28743 (9)0.0404 (4)
H2A0.1006 (7)0.401 (2)0.2771 (12)0.048*
N30.56072 (8)0.64638 (14)0.41122 (8)0.0341 (3)
N40.44674(10)0.68913(17)0.46266(9)0.0443(4)
H40.3973 (8)0.683 (2)0.4790 (12)0.053*
O10.20758 (9)0.70046 (16)0.28457 (10)0.0626 (5)
O40.14684 (9)0.42204 (18)0.45555 (10)0.0676 (5)
O20.36773 (9)0.65319 (15)0.30307 (8)0.0548 (4)
O30.30231 (9)0.36821 (16)0.46595 (10)0.0620 (5)
H3A0.2596 (11)0.344 (2)0.4834 (14)0.074*
O50.20000 (10)0.37036 (14)0.22463 (8)0.0519 (4)
H5A0.2189 (16)0.3157 (16)0.2462 (12)0.078*
H5B0.1925 (18)0.353 (2)0.1824 (6)0.078*

Source of material

All reagents and solvents were used as obtained without further purification. Sodium carbonate anhydrous (0.50 g) was firstly dissolved in ethanol (100.0 mL). Then chloranilic acid (0.209 g, 0.1 mmol) and 2-mercapto-1-methylimidazole (0.228 g, 0.2 mmol) were added into the Na2CO3 solution at room temperature. The final mixture was stirred until completion of the reaction. The residue was extracted with chloroform. The organic layer was separated and washed with water (4 × 50 mL) and dried with Na2SO4. The solvent was evaporated and the residue was purified by column chromatography on silica gel. Yield: 0.80 g, (83%). Crystals of the title compound suitable for X-ray diffraction were obtained two weeks later by slow evaporation of the ethanol solution.

Experimental details

Hydrogen atoms bonded to carbon atoms were placed in their geometrically idealized positions and constrained to ride on their parent atoms with C–H = 0.95 Å (aromatic), 0.99 Å (methylene), 0.98 Å (methyl) Uiso(H) = 1.2Ueq(aromatic and methylene) and 1.5Ueq(methyl). Hydrogen atoms bonded to nitrogen, and oxygen atoms were initially found from the difference maps and refined with the restraints of N–H = 0.86(1) Å, O–H = 0.82(1) Å and H⃛H = 1.39(2) Å by using the SHELXL command DFIX. Their Uiso values were set 1.2 (for NH) or 1.5 times (for OH) of their parent atoms.

Comment

2-Mercapto-1-methylimidazole belongs to a class of five-membered heterocyclic nitrogen compounds, which possess various biological activities [8]. Additionally, it has found use as a multidentate ligand in the fields of inorganic and organometallic chemistry, in which the sulfur atom can serve as a soft donor towards a wide variety of transition metals [9]. Quinone derivatives have been also often investigated in cancer therapy and several drug compounds containing the quinone moiety, such as anthracyclines, daunorubicin, mitomycin and saintopin. It was found that the neighbouring ring number, the position and type of heteroatoms around the quinone ring play a crucial synergistic effect in their biological activities. An earlier work indicates that an incorporation of sulfur or nitrogen atoms in the vicinity of the quinone ring may improve biological activity due to their existence in almost all the enzymatic protein [10]. Up to now, there is no work reporting the combination of a 2-mercapto-1-methylimidazole group into a quinone core. Here, we have synthesized the title compound and report its crystal structure in this paper.

The title compound was crystallized in the orthorhombic Pbca space group. In its asymmetric unit, there is one cation, one chloride anion and one water molecule. The X-ray diffraction result indicates that one phenol hydrogen atom was transferred to an imidazole N atom. The other imidazole imine is also protonated. The deprotonation of one phenolic oxygen atom was confirmed by investigating difference Fourier maps and by the value of the C–O bond lengths (dC9–O3 = 1.315(2) Å, dC10–O4 = 1.235(2) Å, dC6–O1 = 1.228(2) Å and dC7–O2 = 1.212(2) Å). This variation is also observed in some analogs [11]. The two imidazolium rings are twisted away from the central quinone ring by 75.5(1)° and 69.3(1)°, respectively.

In the crystal packing, the component ions are linked mainly by the O–H⋯O/Cl, N–H⋯O/Cl hydrogen bonds into three-dimensional network. In more details, a one-dimensional [010] chain was firstly formed by four intermolecular O3⋯Cl1(3.136(2) Å), N4⋯Cl1(3.116(2) Å), N2⋯O5(2.750(2) Å) and O5⋯O1 (2.742(2) Å) hydrogen bonds. Secondly, these [010] chains were linked together by the O5⋯Cl1 (3.218(2) Å) interactions, giving the two dimensional network parallel to (100) plane. Finally, analysis by the program PLATON indicates these up-and-down (010) layer structures are linked by several intermolecular C–H⋯O and C–H⋯Cl interactions [7].

Corresponding author: Ji Li, School of Biological and Environmental Engineering, Guiyang University, Guiyang550005, P. R. China; and Guizhou Provincial Engineering Research Center for Biological Resources Protection and Efficient Utilization of the Moutainous Region, Guiyang 550005, P. R. China, E-mail:

Funding source: Guiyang Science and Technology Bureau

Funding source: Guiyang University

Award Identifier / Grant number: GYU-KYZ(2019-2020)SH-16

  1. Author contribution: 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 special funding of Guiyang Science and Technology Bureau and Guiyang University GYU-KYZ(2019-2020)SH-16.

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

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Received: 2020-10-01
Accepted: 2020-10-29
Published Online: 2020-11-16
Published in Print: 2021-01-26

© 2020 Ming-zhi Miao and Ji Li, 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-2020-0501
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Articles in the same Issue

  1. Frontmatter
  2. New Crystal Structures
  3. The crystal structure of 3-oxo-urs-12-en-28-oic acid, C30H46O3·1/6H2O
  4. The crystal structure of (3S,12R,20R,24R)-3,12-diacetyl-20,24-epoxy-dammarane-3,12,25–triol–ethyl acetate (4/1), C34H56O6⋅ 0.25(C4H8O2)
  5. A new polymorph of tetrakis(dimethylammonium) catena-poly[tetrakis(μ2-sulfato-κ2O:O′)dizinc(II)], Zn2C8H32N4O16S4
  6. Crystal structure of 10-oxysophoridine, C15H22N2O2
  7. The crystal structure of (5R,8R,9R,10R,12R,13R,14R)-12-hydroxy-4,4,8,10,14-pentamethyl-17-((R)-2,6,6-trimethyltetrahydro-2H-pyran-2-yl)tetradecahydro-3H-cyclopenta[a]phenanthrene-3,6(2H)-dione, C30H48O4
  8. Synthesis, crystal structure and optical property of 1,6-bis(p-tolylthio)pyrene, C30H22S2
  9. The crystal structure of hexakis(2-(pyridin-2-ylamino)pyridin-1-ium) decavanadate(V) dihydrate, C60H64N18O30V10
  10. Preparation and crystal structure of a cationic olefin polymerization precatalyst: (1,7-bis(2,6–dichlorophenyl)-1,7-di-aza-4-oxo-heptan-1,4,7-triyl)dimethyl zirconium(IV), C18H20Cl4N2OZr
  11. The crystal structure of fac-tricarbonyl(4,4-dimethyl-2,2-dipyridyl-κ2N,N′)- (pyrazole-κN)rhenium(I) nitrate, C18H16O3N4Re
  12. Synthesis and crystal structure of hexaaquacopper(II) 2,5-dicarboxyterephthalate, C10H16O14Cu
  13. The crystal structure of (8R,10R,12R,14R)- 12-hydroxy-16-(5-(2-hydroxypropan-2-yl)-2-methyltetrahydrofuran-2-yl)- 4,4,8,10,14-pentamethyltetradecahydro-3H- cyclopenta[a]phenanthrene-3,6(2H)-dione, C30H48O5
  14. Structure of the mixed crystal (S)-(6-(bromo/chloro)-2-methoxy-2,6-dihydroquinolin-3-yl)(phenyl)methanol, C17H14Br0.5Cl0.5NO2
  15. The crystal structure of trans-tetraaqua-bis(4-acetylphenoxyacetato-κ1O)manganese(II), C20H26O12Mn
  16. Crystal structure of (E)-2-(4-fluoro-3-(trifluoromethyl)benzylidene)-7-methoxy-3,4-dihydronaphthalen-1(2H)-one, C19H14F4O2
  17. Crystal structure of DL-α-(methylaminomethyl)benzyl alcohol, C9H13NO
  18. The crystal structure of dipentaerthritol hexanitrate, C10H16N6O19
  19. Crystal structure of N,N-diphenylformamide, C13H11NO
  20. Crystal structure of (E)-2-(3,5-bis(trifluoromethyl)benzylidene)-7-methoxy-3,4-dihydronaphthalen- 1(2H)-one, C20H14F6O2
  21. Crystal structure of ortho-methoxy benzaldehyde, C8H8O2 – a second polymorph and deposition of 3D coordinates
  22. Crystal structure of catena-poly[diaqua-bis(μ2-2-(4-(2,4,4-trimethylpentan-2-yl)phenoxy)propanoato-κ2O:O')-(2-(4-(2,4,4-trimethylpentan-2-yl)phenoxy)propanoato-κ2O,O')yttrium(III)], C51H79O11Y
  23. Crystal structure of benzylthiouronium chloride, C8H11ClN2S
  24. Synthesis and crystal structure of tert-butyl (2′R,3R,3′R,4a′R,9a′S)-1-acetyl-5-chloro-3″-methyl-2,5″,9′-trioxo-1″-phenyl-1″,4a′,5″,9a′-tetrahydro-1′H,3′H,9′H-dispiro[indoline-3,4′-xanthene-2′,4″-pyrazole]-3′-carboxylate, C36H32ClN3O7
  25. Crystal structure of 2-hydroxy-4-methoxy benzaldehyde, C8H8O3
  26. Crystal structure of poly[diaqua-(m3-3′,5′-dicarboxy-[1,1′-biphenyl]-3,4-dicarboxylato-K4O,O′:O″:O‴) cadmium(II)], C16H11O10Cd
  27. Crystal structure of {tetraaqua-bis(1-(4-hydroxy-2-oxotetrahydrofuran-3-yl)-2-((4aS,6R,8aS)-6-hydroxy-5-(hydroxymethyl)-5,8a-dimethyl-2-methylenedecahydronaphthalen-1-yl)ethane-1-sulfonato-k2O,O') calcium(II)}-{triaqua-bis(1-(4-hydroxy-2-oxotetrahydrofuran-3-yl)-2-((4aS,6R,8aS)-6-hydroxy-5-(hydroxymethyl)-5,8a-dimethyl-2-methylenedecahydronaphthalen-1-yl)ethane-1-sulfonato-k2O,O') calcium(II)} – water – acetone (1/1/8/2)
  28. Synthesis and crystal structure of bis{2-bromo-6-((E)-((4-((E)-1-(methoxy-imino)ethyl)phenyl)imino)methyl)phenolato- κ2N,O}zinc(II)-methanol(1/2), C65H60Br4N8O9Zn2
  29. Crystal structure of benzenesulphonic acid
  30. Crystal structure of N-benzyl-N-nicotinoyl-nicotine amide C19H15N3O2
  31. Crystal structure of poly[aqua(μ3-2,4-diamino-benzenesulfonato-κ4N:N′,O:O′)silver(I)], C12H18O8N4S2Ag2
  32. Crystal structure of 1,4-bis(methylpyridinium benzene) bis(1,2-dicyanoethene-1,2-dithiolato-κ2S:S)nickel(II), C26H18N6NiS4
  33. Crystal structure of the Cu(II) complex chlorido-(6-oxo-2-phenyl-1,6-dihydropyrimidine-4-carboxylato-k2N,O)-(phenanthroline-k2N,N')copper(II), C23H15ClCuN4O3
  34. Crystal structure of phenarsazine chloride acetic acid solvate, C14H13AsClNO2
  35. Crystal structure of poly[aqua-(μ2-3,3′,4,5′-biphenyl tetracarboxylate- κ3O,O′:O′′) -(μ2-4,4′-bis(pyrid-4-yl)biphenyl-κ2N:N′)zinc(II)], C27H18NO9Zn
  36. Crystal structure of catena-poly[(μ2-3-amino-benzenedisulfonato-κ2N:O)-bis (3-methyl-isoquinoline-κN)silver(I)], C26H24N3O3SAg
  37. Crystal structure of 2-((4-Aminophenyl)thio)acetic acid, C8H9NO2S
  38. Crystal structure of phenarsazine chloride dimethylsulfoxide solvate, C14H15AsClNOS
  39. Synthesis and crystal structure of 2-azido-N-phenylacetamide, C8H8N4O
  40. Crystal structure of chlorido{hydridotris[3-phenyl-5-methylpyrazol-1-yl-κN3]borato}copper(II), C30H28BClCuN6
  41. Crystal structure of benzanthrone – a redetermination for correct molecular geometry and localization of hydrogen atoms
  42. Crystal structure of 4-bromobenzaldehyde – complete redetermination at 200 K, C7H5BrO
  43. Crystal structure and spectroscopic properties of chlorido{hydridotris[3-,5-dimethylpyrazol-1-yl-κN3]borato}(3-,5-dimethylpyrazol-1-yl-κN)copper(II), C20H30BClCuN8
  44. The crystal structure of 4-((2-hydroxynaphthalen-1-yl)(pyrrolidin-1-yl)methyl)benzonitrile, C22H20N2O
  45. Crystal structure of 4-ethyl-3-phenylisoquinolin-1(2H)-one, C17H15NO
  46. Crystal structure of (tricyclohexylphosphane-κP)-[(Z)-N-(3-fluorophenyl)-O-methylthiocarbamato-k1S]gold(I), C26H40AuFNOPS
  47. Crystal structure of (3S,8R,10R,12R,14R)-12-hydroxy-4,4,8,10,14-pentamethyl-17-((R)-2,6,6-trimethyltetrahydro-2H-pyran-2-yl) hexadecahydro-1H-cyclopenta[a]phenanthren-3-yl acetate, C32H54O4
  48. The crystal structure of 2-[(S)-1-(naphthalen-1-yl)ethyl]-2,3,7,7a- tetrahydro-3a,6-epoxyisoindol-1(6H)-one, C19H20NO2
  49. Crystal structure of {hydridotris[3-(t-butyl)-5-isopropylpyrazol-1-yl-κN3]borato}thallium(I), C30H52BN6Tl
  50. Synthesis and crystal structure of 1-octyl-3-phenylquinoxalin-2(1H)-one, C22H26N2O
  51. The crystal structure of 2,6-difluorophenol, C6H4F2O
  52. 4-(9H-Fluoren-9-yl)-4-methylmorpholin-4-ium bromide, C18H20BrNO
  53. The crystal structure of 2,4-dimethylimidazole monohydrate, C5H10N2O
  54. The crystal structure of 1,2-dimethylimidazole, C5H8N2
  55. The crystal structure of 3-ammonio-4-aminobenzoate, C7H8N2O2 – a second polymorph
  56. The crystal structure of 4-hydroxy-2,5-bis(1-methyl-1H-imidazol-3-ium-2-ylthio)-3,6-dioxocyclohexa-1,4-dienolate chloride monohydrate, C14H15N4O5S2Cl
  57. The crystal structure of butyrylferrocene, C14H16FeO
  58. The crystal structure of bi-1,1′-cyclopentane-1,1′-diol, C10H18O2
  59. The crystal structure of 2-iso-propylimidazole, C6H10N2
  60. The crystal structure of aqua-tris (1,3-diphenylpropane-1,3-dionato-κ2O,O′)-lanthanum(III), C45H35LaO7
  61. Crystal structure of (3E,5E)-3,5-bis-4-methoxy-3-(trifluoromethyl)benzylidene)-1-methylpiperidin-4-one, C24H21F6NO3
  62. The crystal structure of 3,5-dichloro-6-diazo-2,4-dinitrocyclohexa-2,4-dien-1-one, C6Cl2N4O5
  63. Crystal structure of carbonyl(2-methylquinolin-8-olato-κ2N,O)(triphenylarsine-κAs)rhodium(I), C29H23AsNO2Rh
  64. Crystal structure of (1aS,1a1S,2S)-4a-butoxy-1a,1a1,2,4a,5,6-hexahydro-1H-cyclobuta[de]naphthalen-2-yl-4-nitrobenzoate, C22H25NO5
  65. Crystal structure of carbonyl(2-oxopyridin-1(2H)-olato-k2O,O′)(triphenylarsine-κAs)rhodium(I), C24H19AsNO3Rh
  66. Crystal structure of catena-poly[triqua-bis(μ2-4-carboxy-2-(1H-tetrazol-1-yl)-1H-imidazole-5-carboxylato-k3N,O:O′)barium(II)] tetrahydrate, C14H14BaN12O15
  67. Crystal structure of (E)-3′,6′-bis(ethylamino)-2-((quinoxalin-2-ylmethylene)amino)spiro[isoindoline-1,9′-xanthen]-3-one, C35H32N6O2
  68. Crystal structure of diaqua-bis(μ2-5-chloro-salicylato-κ3O,O′:O′)-bis(5-chloro-salicylato-κ2O,O′)-bis(1,10-phenanthroline-κ2N,N′) dilead(II) – water (1/2), C52H36C14N4O14Pb2·2(H2O)
  69. Crystal structure of (E)-2-(4-ethoxycarbonyl-3,5-dimethyl-2-(pyrrole-2-ylmethyleneamino)-3′,6′-dihydroxylspiro[isoindoline-1,9′-xanthen]-3-one-methanol (1/1), C31H29N3O7
  70. The crystal structure of 5H-dibenzo[b,e]azepine-6,11-dione, C14H9NO2
  71. Crystal structure of (E)-2-(4-fluoro-2-(trifluoromethyl)benzylidene)-7-methoxy-3,4-dihydronaphthalen-1(2H)-one, C19H14F4O2
  72. The crystal structure of N-(2-methoxy-4,5-bis[phenylselanyl]phenyl)picolinamide, C25H20N2O2Se2
  73. The crystal structure of (E)-2-(5-bromo-2-hydroxybenzylidene)-N-phenylhydrazine-1- carboxamide monohydrate, C14H14BrN3O3
  74. Crystal structure of fac-tricarbonyl-(nitrato-k1O)-bis(pyridine-κN)-rhenium, C13H10O6N3Re
  75. Crystal structure of (E)-2-(((1H-pyrrol-2-yl)methylene)amino)-3′,6′-dihydroxyspiro[isoindoline-1,9′-xanthen]-3-one — methanol (1/2), C27H25N3O6
  76. The crystal structure of 4-amino-N′-(4-aminobenzoyl)benzohydrazide monohydrate, C14H16N4O3
  77. Crystal structure of bis(amino(carbamothioylamino)methaniminium) 5-hydroxyisophthalate monohydrate, C12H20N8O6S2
  78. The crystal structure of 2-(chloromethyl)pyridine, C6H6ClN
  79. The crystal structure of 1-bromo-4-iodo-benzene, C6H4BrI
  80. The crystal structure of 2,6-dimethyl-4-nitro-phenol, C8H9NO3
  81. The crystal structure of 3-chloropropionic acid, C3H5ClO2
  82. The crystal structure of 2-(2-methoxyphenyl)acetic acid, C9H10O3
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