Home Crystal structure of diaqua[5,5′-dicarboxy-2,2′-(propane-1,3-diyl)bis(1H-imidazole-4-carboxylato-κ4O,O′,N,N′)]zinc(II) dihydrate, C13H18N4O12Zn
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Crystal structure of diaqua[5,5′-dicarboxy-2,2′-(propane-1,3-diyl)bis(1H-imidazole-4-carboxylato-κ4O,O′,N,N′)]zinc(II) dihydrate, C13H18N4O12Zn

  • Xiao-Fei Li , Li-Gang Ma , Wen-Feng Guo and Wen-Feng Zhao EMAIL logo
Published/Copyright: August 2, 2019

Abstract

C13H18N4O12Zn, triclinic, P1̄ (no. 2), a = 9.0311(3) Å, b = 9.4464(3) Å, c = 12.6951(5) Å, α = 109.2790(11)°, β = 92.6348(12)°, γ = 116.2514(10)°, V = 892.97(5) Å3, Z = 2, Rgt(F) = 0.0263, wRref(F2) = 0.0712, T = 293(2) K.

CCDC no.: 1937016

The molecular structure is shown in the figure (Uncoordinated water molecule and the disorder of the propenyl moiety are omitted for clarity). 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 block
Size:0.21 × 0.18 × 0.14 mm
Wavelength:Mo Kα radiation (0.71073 Å)
μ:1.45 mm−1
Diffractometer, scan mode:Bruker D8, φ and ω
θmax, completeness:27.6°, >99%
N(hkl)measured, N(hkl)unique, Rint:38319, 4132, 0.028
Criterion for Iobs, N(hkl)gt:Iobs > 2 σ(Iobs), 3750
N(param)refined:301
Programs:SHELX [1], [2], Bruker [3], [4]
Table 2:

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

AtomxyzUiso*/Ueq
Zn10.57628(2)0.90902(2)0.72601(2)0.02455(7)
N10.31469(16)0.74953(16)0.69129(11)0.0203(3)
N20.04000(16)0.58174(17)0.65381(11)0.0217(3)
H2A−0.0484960.5013680.6529920.026*
N30.70782(17)0.81796(18)0.79339(12)0.0252(3)
N40.82540(18)0.69593(19)0.85872(13)0.0296(3)
H4A0.8380090.6275460.8793130.036*
O10.49758(14)1.03639(15)0.65041(11)0.0297(3)
O20.26620(15)1.02266(17)0.56788(12)0.0349(3)
O3−0.04767(16)0.83827(19)0.52744(14)0.0422(3)
H30.0553410.8979490.5396520.051*
O4−0.22682(14)0.60709(16)0.55212(12)0.0334(3)
O50.84619(16)1.11732(17)0.76480(12)0.0367(3)
O61.10914(17)1.18466(19)0.83503(15)0.0464(4)
H61.1560331.1388060.8566420.056*
O71.24592(15)1.04756(18)0.90890(12)0.0357(3)
O81.16830(17)0.81224(18)0.94498(12)0.0370(3)
O90.58474(15)0.77476(16)0.55246(10)0.0290(3)
H9A0.6371040.8387410.5179140.035*
H9B0.6363440.7179310.5513540.035*
O100.56749(16)1.07248(19)0.88742(11)0.0391(3)
H10A0.4794881.0751870.9065110.047*
H10B0.6406781.1090970.9479410.047*
O110.71989(17)0.33836(19)0.63106(14)0.0479(4)
H11A0.6533110.2448730.6366920.057*
H11B0.6461310.3300630.5819120.057*
O120.1587(3)0.5603(2)0.08474(18)0.0699(5)
H12A0.2442070.6510440.0877900.084*
H12B0.1051170.6093240.1188900.084*
C10.3401(2)0.9675(2)0.61680(14)0.0234(3)
C20.23509(19)0.8101(2)0.63776(13)0.0202(3)
C30.06323(19)0.7072(2)0.61392(13)0.0208(3)
C4−0.0814(2)0.7137(2)0.56176(14)0.0255(3)
C50.19330(19)0.6113(2)0.70014(13)0.0213(3)
C6a0.2080(9)0.5009(9)0.7564(6)0.031(2)
H6Aa0.1859890.3932550.6971400.037*
H6Ba0.1204150.4750380.7994190.037*
C7a0.3804(3)0.5779(3)0.8377(2)0.0270(7)
H7Aa0.3627850.5372180.8993470.032*
H7Ba0.4303370.7018130.8714250.032*
C8a0.5045(4)0.5293(5)0.7751(4)0.0351(9)
H8Aa0.5073530.4365250.7905950.042*
H8Ba0.4658390.4900860.6930720.042*
C6′b0.2251(18)0.505(2)0.7560(14)0.043(5)
H6′Ab0.1218100.3963410.7354070.052*
H6′Bb0.2523210.5643490.8385990.052*
C7′b0.3686(6)0.4682(6)0.7213(4)0.0281(13)
H7′Ab0.4130890.5183930.6667120.034*
H7′Bb0.3244740.3452880.6842510.034*
C8′b0.5141(8)0.5431(12)0.8271(7)0.042(2)
H8′Ab0.4829740.5930990.8963250.051*
H8′Bb0.5322390.4520010.8332080.051*
C90.6787(2)0.6814(2)0.81480(17)0.0322(4)
C100.9474(2)1.0842(2)0.80588(16)0.0288(4)
C110.88010(19)0.9217(2)0.82321(13)0.0227(3)
C120.9556(2)0.8476(2)0.86483(13)0.0230(3)
C131.1368(2)0.9047(2)0.91013(14)0.0263(3)
  1. aOccupancy: 0.655(5), bOccupancy: 0.345(5).

Source of material

The reagents and solvents used in this work were purchased from commercial sources and used without further purification. A mixture of Zn(NO3)2⋅6H2O (0.05 mmol), 2,2′-(propane-1,3-diyl)bis(1H-imidazole-4,5-dicarboxylic acid (H6pbidc, 0.05 mmol), methanol (1 mL) and distilled water (4 mL) was sealed in a 25 mL Teflon-lined stainless steel container and heated at 393 K for 72 hours. After the mixture was cooled to room temperature at a rate of 5 K h−1, colourless crystals of [Zn(H4pbidc)(H2O)2]⋅2H2O were obtained (yield 57%, based on Zn).

Experimental details

The propyl group was modelled by splitting it into two parts (C6—C8 and C6′—C8′), the site-occupation factors of which refined in a ratio of 0.655(5): 0.345(5). Hydrogen atoms on carbon and nitrogen atoms were positioned geometrically and refined as riding atoms, with C—H = 0.97 Å and N—H = 0.82 Å. H atoms of the nondeprotonated carboxylic acid groups of H4pbidc2− were refined as riding atoms, with O—H = 0.82 Å. The H atoms of the water molecules were located in a difference Fourier map and the O—H distance was constrained to 0.85 Å. All H atoms were refined with Uiso(H) = 1.2 Ueq(C, N, O).

Comment

Careful choice of the organic ligands is one of the most important parameters in the rational design and synthesis of complexes [5]. Imidazole-4,5-dicarboxylic acid (H3idc) and its derivatives have been used widely as ligands for the construction of complexes since they contain N-donors as well as O-donors and can exhibit various coordination modes and high binding capacity with almost all soft and hard metal ions [6], [7], [8]. To the best of our knowledge, most of the imidazole-4,5-dicarboxylates used in the construction of complexes only contain one imidazole-ligand. Only a few N-heterocyclic carboxylate ligands containing two imidazole-4,5-dicarboxylic acid motifs has been used in the preparation of complexes [9], [10], [11], [12].

The asymmetric unit of the title structure contains one Zn(II) ion, one 5,5′-dicarboxy-2,2′-(propane-1,3-diyl)bis(1H-imidazole-4-carboxylate anion, two coordination water molecules and two uncoordination water molecules. The Zn1 ion is six-coordinated by two N atoms and two O atoms from the tetradentate anion in equatorial positions and by two water O atoms in axial positions, leading to a distorted octahedral environment. The Zn—N bond lengths are 2.0443(13) and 2.0886(13) Å, while the Zn—O bond lengths are in the range of 2.0810(11)–2.2501(13) Å, all of which are in the normal range of those observed in the reported Zn(II) complexes [13], [14]. The two imidazole rings are nearly co-planar, with a dihedral angle between the two least-square planes N1, N2, C2, C3, C5 and N3, N4, C9, C11, C12 of 8.2(1)°. Intramolecular O—H⋯O hydrogen bonds between carboxyl and carboxylate groups stabilize the molecular configuration. In addition, there are two N—H⋯O hydrogen bonds and eight O—H⋯O hydrogen bonds involving imidazoles, coordinated water molecules, uncoordinated water molecules and carboxylate/carboxylic groups of adjacent molecules. In the crystal, adjacent molecules are linked through the above hydrogen-bonding interactions into a three-dimensional supramolecular architecture, which is very similar to a literature known one [15].

Funding source: Science and Technology Innovation Talents of Henan University of Chinese Medicine

Award Identifier / Grant number: 2014XCXRC04

Funding source: Henan University of Chinese Medicine, Provincial Scientific Research Business

Award Identifier / Grant number: 2014KYYWF-QN03

Funding statement: This study was supported by Science and Technology Innovation Talents of Henan University of Chinese Medicine (2014XCXRC04) and Henan University of Chinese Medicine, Provincial Scientific Research Business (2014KYYWF-QN03).

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Received: 2019-05-10
Accepted: 2019-06-28
Published Online: 2019-08-02
Published in Print: 2019-11-26

©2019 Xiao-Fei Li 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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  56. Crystal structure of poly[(μ7-4-(3,5-dicarboxylatophenoxy)phthalato)-(1,10-phenanthroline-κ2N,N′)dizinc(II)], C28H14N2O9Zn2
  57. The crystal structure of methyl 2-(benzylamino)-5-(benzyloxy)benzoate, C22H21NO3
  58. Crystal structure of (1,4,8,11-tetraazacyclotetradecane)palladium(II) tetracyanoplatinate(II), C14H24N8PdPt
  59. Crystal structure of (pyridine-2-carboxylato-κ2N,O)-[2-(2-pyridyl)phenyl-κ2N,C1]palladium(II), C17H12N2O2Pd
  60. Crystal structure of (cyclohexane-1,4-diammonium) 4-[(4-carboxylatophenyl)disulfanyl]benzoate dimethylsulphoxide hydrate (1/1/1/1), [C6H16N2]2+[C14H8O4S2]2−⋅C2H6OS⋅H2O
  61. Crystal structure of the 2:1 co-crystal 2-[(2-carboxyphenyl)disulfanyl]benzoic acid – 3-bromobenzoic acid, 2(C14H10O4S2)⋅C7H5BrO2
  62. Crystal structure of chlorido-dimethyl-(phenylpiperazine-1-carbodithioato-κ2S,S′)tin(IV), C13H19ClN2S2Sn
  63. Crystal structure of (N-n-butyl, N-methyl-dithiocarbamato-κ2 S,S′)-chlorido-dimethyl-tin(IV), C8H18ClNS2Sn
  64. Crystal structure of (2,2′-bipyridyl)bis(4-bromobenzyl)dibromidotin(IV), C24H20Br4N2Sn
  65. Crystal structure of (2,2′-bipyridyl)bis(4-chlorobenzyl)dichloridotin(IV), C24H20Cl4N2Sn
  66. Crystal structure of N-methyl-N-phenyl(methylsulfanyl)carbothioamide, C9H11NS2
  67. Crystal structure of 4-phenylpiperazin-1-ium (4-phenylpiperazin-1-yl)carbothioylsulfanide, [C10H15N2][C11H13N2S2]
  68. Crystal structure of catena-{di-aqua-sodium [n-butyl(methyl)carbamothioyl]sulfanide}n, [C6H16NNaO2S2]n
  69. Crystal structure of (2-([1,1-bis(hydroxymethyl)-2-oxyethyl]iminomethyl)-5-(n-decyl)phenolato)-dimethyl-tin(IV), C23H39NO5Sn
  70. Crystal structure of 4-chloro-N′-[(1E)-(3-ethoxy-2-hydroxyphenyl)methylidene]benzohydrazide – a Z′ = 3 structure, C16H15ClN2O3
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