Home Crystal structure of diaqua[bis(benzimidazol-2-yl-methyl)amine-κ3N,N′,N″]-phthalato-κ1O-nickel(II)-methanol (1/2), C26H31N5NiO8
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Crystal structure of diaqua[bis(benzimidazol-2-yl-methyl)amine-κ3N,N′,N″]-phthalato-κ1O-nickel(II)-methanol (1/2), C26H31N5NiO8

  • Yu-Xiao Chen , Zhong-Ping Luo , He Zhang and Feng-Mei Nie ORCID logo EMAIL logo
Published/Copyright: December 17, 2020
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Zeitschrift für Kristallographie - New Crystal Structures
From the journal Zeitschrift für Kristallographie - New Crystal Structures Volume 236 Issue 2

Abstract

C26H31N5NiO8, monoclinic, P21/n (no. 14), a = 12.554(3) Å, b = 12.401(3) Å, c = 18.718(5) Å, β = 107.844(3)°, V = 2774.0(12) Å3, Z = 4, Rgt(F) = 0.0438, wRref(F2) = 0.1175, T = 153(2) K.

CCDC no.: 2046783

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:Blue platelet
Size:0.27 × 0.20 × 0.07 mm
Wavelength:Mo Kα radiation (0.71073 Å)
μ:0.76 mm−1
Diffractometer, scan mode:AFC10/Saturn724+, φ and ω
θmax, completeness:29.1°, >99%
N(hkl)measured, N(hkl)unique, Rint:30,130, 7431, 0.052
Criterion for Iobs, N(hkl)gt:Iobs > 2 σ(Iobs), 5655
N(param)refined:367
Programs:CrystalClear [1], Olex2 [2], SHELX [3]
Table 2:

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

AtomxyzUiso*/Ueq
Ni10.68986 (2)0.37074 (2)0.63642 (2)0.02025 (8)
O10.60208 (11)0.46465 (10)0.68755 (8)0.0242 (3)
O20.58483 (14)0.37088 (11)0.78566 (9)0.0352 (4)
O30.38114 (11)0.49603 (10)0.57335 (8)0.0253 (3)
O40.47766 (12)0.64950 (11)0.58275 (8)0.0281 (3)
O50.69125 (11)0.51436 (10)0.57738 (8)0.0244 (3)
H5A0.67090.50670.53050.029*
H5B0.64210.55140.58800.029*
O60.53143 (11)0.33192 (11)0.56231 (8)0.0251 (3)
H6A0.47990.36950.56940.030*
H6B0.53290.33870.51800.030*
N10.68523 (15)0.22587 (13)0.69600 (9)0.0240 (3)
N20.83695 (13)0.39126 (13)0.71896 (9)0.0225 (3)
N30.95186 (14)0.33110 (14)0.82708 (10)0.0289 (4)
H30.97940.28900.86620.035*
N40.75799 (13)0.26538 (13)0.57688 (9)0.0243 (3)
N50.77184 (14)0.09276 (14)0.54784 (10)0.0282 (4)
H50.76300.02230.54740.034*
C10.78455 (18)0.21748 (16)0.76292(12)0.0297 (4)
H1A0.82730.15170.75930.036*
H1B0.76050.21140.80840.036*
C20.85745 (16)0.31381 (16)0.76929 (11)0.0239 (4)
C30.99677 (16)0.42765 (17)0.81280 (12)0.0275 (4)
C41.09036 (18)0.48612 (19)0.85326 (13)0.0364 (5)
H41.13910.46070.89970.044*
C51.10900 (18)0.5833 (2)0.82250 (14)0.0396 (5)
H5C1.17160.62600.84870.048*
C61.03829 (18)0.61984 (17)0.75413 (14)0.0330 (5)
H61.05450.68650.73470.040*
C70.94485 (16)0.56188 (16)0.71352 (12)0.0259 (4)
H70.89700.58730.66680.031*
C80.92440 (16)0.46498 (16)0.74421 (11)0.0235 (4)
C90.67222 (18)0.13598 (15)0.64262 (12)0.0288 (4)
H9A0.59200.12430.61540.035*
H9B0.70300.06880.66970.035*
C100.73431 (16)0.16454 (16)0.58837 (12)0.0262 (4)
C110.82695 (17)0.15094 (17)0.50695 (12)0.0289 (4)
C120.88330 (19)0.11935 (19)0.45696 (14)0.0384 (5)
H120.88800.04580.44420.046*
C130.9318 (2)0.1996 (2)0.42700 (15)0.0435 (6)
H130.97050.18130.39230.052*
C140.9254 (2)0.3081 (2)0.44658 (14)0.0414 (6)
H140.96130.36130.42560.050*
C150.86820 (18)0.33948 (19)0.49548 (13)0.0331 (5)
H150.86310.41320.50790.040*
C160.81872 (16)0.25922 (16)0.52546 (11)0.0264 (4)
C170.56180 (16)0.44839 (15)0.74095 (11)0.0237 (4)
C180.48024 (16)0.53347 (15)0.74865 (11)0.0229 (4)
C190.46838 (17)0.55502 (17)0.81888 (12)0.0297 (4)
H190.50880.51330.86100.036*
C200.3985 (2)0.63636 (18)0.82780 (13)0.0363 (5)
H200.39240.65160.87610.044*
C210.33760 (19)0.69563 (19)0.76646 (14)0.0365 (5)
H210.28760.74990.77240.044*
C220.34905 (17)0.67629 (18)0.69661 (13)0.0317 (5)
H220.30790.71820.65470.038*
C230.42075 (15)0.59551 (16)0.68732 (11)0.0238 (4)
C240.42846 (15)0.57785 (16)0.60915 (11)0.0233 (4)
O70.73283 (18)0.37878 (13)0.92406 (11)0.0581 (6)
H7A0.67930.36720.88500.070*
O80.2412 (2)0.35778 (16)0.62579 (15)0.0708 (7)
H80.28740.39510.61220.085*
C250.7492 (3)0.2887 (2)0.97078 (17)0.0705 (9)
H25A0.82820.28411.00070.085*
H25B0.72790.22340.94020.085*
H25C0.70290.29521.00430.085*
C260.1577 (3)0.4251 (3)0.6369 (3)0.0983 (15)
H26A0.10820.38280.65770.118*
H26B0.11400.45660.58890.118*
H26C0.19260.48290.67200.118*
H10.6267 (19)0.2290 (17)0.7133 (13)0.029 (6)*

Source of material

Bis(benzimidazol-2-yl-methyl)amine (bbma) was synthesized according to a literature procedure [4]. A methanol solution (25 ml) of Ni(NO3)2·6H2O (58 mg, 0.2 mmol) and bbma (55 mg 0.2 mmol) was mixed. Then a methanol solution (20 ml) of phthalic acid (33 mg, 0.2 mmol) and triethylamine (40 mg, 0.4 mmol) was dropped to the above solution. After being stirred at room temperature for 5 h, the solution was filtered for slow evaporation. Light blue crystals formed.

Experimental details

The structure was solved with the Olex2 program [2]. The methyl groups were idealized and refined using rigid groups allowed to rotate about the C–O bond (with the SHELX program [3]). The Uiso values of all the hydrogen atoms were set to 1.2 Ueq.

Comment

Phthalate (pht) is a versatile ligand which adopts many coordination modes due to a variety of its bonding abilities [5], [6], [7], [8]. It is used in the design of coordination compounds. Bis(benzimidazol-2-yl-methyl)amine (bbma) is a tridentate ligand with two benzimidazole groups attached to a nitrogen atom. This ligand is often used to prepare metal complexes in the use of modeling the active sites of relevant metalloenzymes. Compared to other metal complexes, nickel(II) complexes of bbma are rare. Several nickel(II) complexes with bis(bbma) have been structurally characterized [9]. To the best of our knowledge, only three nickel(II) complexes of bbma containing picolinate, thiocyanate and dicyandiamide as coligands have been reported [10], [11], [12].

The title compound consists of a neutral [Ni(bbma)(pht)(H2O)2] and two methanol molecules. The Ni(II) atom is coordinated by three nitrogen atoms (N1, N2, N4) of bbma, one carboxylate oxygen atom (O1) of phthalate and two oxygen atoms (O5, O6) of water molecules, adopting a distorted octahedral geometry (see the Figure). The equatorial plane of Ni(II) is constructed by N2, N4, O1, O6 with the bond angles from 84.38(6)° to 93.89(6)°. The axial positions are occupied by N1 and O5 with bond angle of 178.92(6)°. The phthalate coordinates to nickel(II) by one of its carboxylate groups in an unidentate way, with the bond length of 2.0331(13) Å, which is shorter than Ni–Owater=2.0990(14) Å for Ni1–O5 and 2.1026(14) Å for Ni1–O6. In this complex, bbma behaves as a tridentate ligand, where the three Ni–N distances are ranging from 2.0281(17) Å to 2.1248(17) Å, with the Ni–Nalkylamine significantly longer than the Ni–Nbenzimidzole. The most striking feature is that two benzimidazole groups of bbma are not coplanar. They are bent with a dihedral angle of 98.18°. This is quite different from the reported copper(II) complex [Cu(bbma)(pht)]CH3OH·2H2O, in which the two benzimidazole groups of bbma are nearly coplanar with the dihedral angel to be 170.72° [13]. The copper(II) is coordinated in a distorted square pyramidal geometry with τ value of 0.19. Phthalate coordinates to the central copper(II) ion through only one of its carboxylate groups in bidentate cheating way.

In this complex, hydrogen bonding interactions play an important role in the crystal packing, while no π–π interactions between the aromatic rings were observed. Two intramolecular hydrogen bonding interactions can be observed between the NH(N1) of bbma and the carboxylate group O2 of phthalate, and between the uncoordinated carboxylate O3 atom and O6 (coordinated water molecule). Two neighbouring molecules are linked by O–H⋯O intermolecular hydrogen bonds to form a dinuclear unit, involving the uncoordinated carboxylate group (O3, O4) of phathlate and two coordinating aqua molecules (O5, O6). These dinuclear units are hydrogen bonded by the NH(N3) group of bbma and O4 to form a 1D chain structure. The 1D chain are further expanded into 2D network structure involving the NH(N5) group of bbma, methanol molecule (O7) and O2 through N–H⋯O and O–H⋯O hydrogen bonds.

Corresponding author: Feng-Mei Nie, Department of Chemistry, Capital Normal University, Beijing100048, PR China, E-mail:

Funding source: Scientific Research Base Development Program of the Beijing Municipal Commission of Education

Award Identifier / Grant number: KM201910028013

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

  2. Research funding: This study was supported by Scientific Research Base Development Program of the Beijing Municipal Commission of Education (KM201910028013).

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

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Received: 2020-10-02
Accepted: 2020-11-27
Published Online: 2020-12-17
Published in Print: 2021-03-26

© 2020 Yu-Xiao Chen 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-2020-0502
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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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