Home 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
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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

  • Tian-Xu Qiao , Yu-Xiao Chen , Jing-Yi An and Feng-Mei Nie ORCID logo EMAIL logo
Published/Copyright: January 12, 2021

Abstract

C32H41N7NiO8, monoclinic, P21/c (no. 14), a = 10.0076(5) Å, b = 18.6561(10) Å, c = 19.0893(18) Å, β = 108.532(6)°, V = 3378.4(4) Å3, Z = 4, Rgt(F) = 0.0607, wRref(F2) = 0.1340, T = 111.9(1) K.

CCDC no.: 2050294

The molecular structure is shown in the figure (four solvent molecules which belong to the asymmetric unit are not shown). 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 block
Size:0.34 × 0.32 × 0.30 mm
Wavelength:Mo Kα radiation (0.71073 Å)
μ:0.64 mm−1
Diffractometer, scan mode:Xcalibur, ω
θmax, completeness:26.0°, >99%
N(hkl)measured, N(hkl)unique, Rint:16175, 6632, 0.055
Criterion for Iobs, N(hkl)gt:Iobs > 2 σ(Iobs), 4640
N(param)refined:448
Programs:CrysAlisPRO [1], Olex2 [2], SHELX [3]
Table 2:

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

AtomxyzUiso*/Ueq
C1−0.2079 (3)0.35410 (19)0.13583 (18)0.0209 (7)
H1A−0.2732280.3954960.1244520.025*
H1B−0.2652620.3097620.1254650.025*
C2−0.1232 (3)0.35589 (17)0.21544 (18)0.0156 (7)
C30.0529 (4)0.35991 (18)0.31572 (19)0.0225 (8)
C4−0.0697 (4)0.35832 (18)0.33607 (19)0.0223 (8)
C5−0.0652 (5)0.3596 (2)0.4096 (2)0.0378 (10)
H5A−0.1488470.3583060.4229160.045*
C60.0653 (5)0.3629 (3)0.4619 (2)0.0605 (15)
H60.0728300.3636750.5128090.073*
C70.1876 (5)0.3651 (3)0.4415 (2)0.0640 (16)
H7A0.2762410.3677280.4792180.077*
C80.1849 (4)0.3636 (2)0.3690 (2)0.0385 (11)
H80.2690260.3649860.3560230.046*
C9−0.1369 (4)0.42405 (18)0.04423 (19)0.0233 (8)
H9A−0.2363490.4398250.0306010.028*
H9B−0.1129590.416519−0.0017190.028*
C10−0.0420 (4)0.47997 (18)0.09122 (19)0.0216 (8)
C110.1407 (3)0.52716 (18)0.17066 (19)0.0205 (8)
C120.0514 (4)0.58354 (18)0.1359 (2)0.0220 (8)
C130.0850 (4)0.65469 (19)0.1541 (2)0.0287 (9)
H130.0234880.6925400.1306170.034*
C140.2115 (4)0.6679 (2)0.2079 (2)0.0367 (10)
H140.2385490.7160000.2215460.044*
C150.3014 (4)0.6119 (2)0.2430 (2)0.0338 (9)
H150.3883100.6231730.2796040.041*
C160.2673 (4)0.54087 (19)0.2258 (2)0.0261 (8)
H160.3276350.5031150.2505810.031*
C17−0.1357 (4)0.29061 (19)0.0414 (2)0.0321 (9)
H17A−0.0940320.2971070.0012000.039*
H17B−0.2369860.2790550.0191200.039*
C18−0.0617 (4)0.23234 (19)0.0923 (2)0.0279 (9)
C190.0899 (4)0.18070 (18)0.1843 (2)0.0243 (8)
C20−0.0109 (4)0.12876 (19)0.1504 (2)0.0280 (9)
C21−0.0043 (4)0.05951 (19)0.1778 (2)0.0314 (9)
H21−0.0724490.0243290.1543160.038*
C220.1054 (4)0.0443 (2)0.2404 (2)0.0359 (10)
H220.113444−0.0026610.2606600.043*
C230.2057 (4)0.0961 (2)0.2753 (3)0.0382 (10)
H230.2795700.0835340.3188700.046*
C240.2001 (4)0.1647 (2)0.2480 (2)0.0356 (10)
H240.2686940.1996050.2717300.043*
C250.4248 (4)0.33511 (18)0.2196 (2)0.0246 (8)
C260.2643 (5)0.3365 (2)0.0444 (2)0.0411 (11)
C27a0.4526 (10)0.2907 (5)0.1503 (5)0.0196 (14)
H27Aa0.5095960.3219240.1287710.024*
H27Ba0.5111850.2483530.1713200.024*
C27′b0.4153 (10)0.2781 (5)0.1700 (5)0.0196 (14)
H27Cb0.3277820.2505410.1637230.024*
H27Db0.4965970.2453840.1895020.024*
C28a0.3269 (7)0.2649 (4)0.0875 (4)0.0204 (11)
H28Aa0.2570680.2410010.1065180.024*
H28Ba0.3563240.2310490.0551970.024*
C28′b0.4148 (7)0.3092 (4)0.0950 (4)0.0204 (11)
H28Cb0.4486150.2719250.0677900.024*
H28Db0.4820060.3497710.1041650.024*
C290.6529 (5)0.5039 (2)0.3587 (2)0.0454 (11)
H29A0.5999860.5329940.3162750.068*
H29B0.7326290.4809660.3482180.068*
H29C0.6881290.5345610.4024200.068*
C300.5114 (5)0.2784 (4)−0.0970 (3)0.0788 (19)
H30A0.5053140.307451−0.1406110.118*
H30B0.4228050.252236−0.1050070.118*
H30C0.5892010.244113−0.0884280.118*
C31−0.4254 (7)0.0810 (6)0.0464 (4)0.173 (5)
H31A−0.5158240.0625270.0142710.259*
H31B−0.4422100.1188980.0780690.259*
H31C−0.3720330.0419510.0771590.259*
C320.4594 (4)0.4982 (3)0.1160 (2)0.0477 (12)
H32A0.3668580.4750680.0973560.072*
H32B0.4475730.5503770.1128120.072*
H32C0.5049370.4843240.1676460.072*
N1−0.1174 (3)0.35652 (14)0.08711 (15)0.0203 (6)
N20.0154 (3)0.35792 (14)0.23932 (14)0.0165 (6)
N3−0.1805 (3)0.35595 (14)0.27041 (15)0.0183 (6)
H3−0.2708650.3547200.2655590.022*
N40.0787 (3)0.46250 (15)0.14095 (15)0.0193 (6)
N5−0.0646 (3)0.55125 (15)0.08568 (15)0.0217 (7)
H5−0.1389370.5731460.0558880.026*
N60.0550 (3)0.24494 (15)0.14593 (17)0.0245 (7)
N7−0.1068 (4)0.16396 (16)0.09182 (17)0.0336 (8)
H7−0.1829980.1452810.0601940.040*
Ni10.10551 (5)0.35324 (2)0.15663 (3)0.02142 (14)
O10.3085 (2)0.35461 (14)0.22464 (16)0.0396 (7)
O20.5401 (2)0.35651 (13)0.26313 (12)0.0253 (6)
O30.1566 (3)0.35167 (13)0.05988 (15)0.0345 (7)
O40.2918 (3)0.36258 (15)−0.00957 (14)0.0347 (7)
O50.5632 (3)0.45025 (15)0.37227 (14)0.0376 (7)
H5B0.5430870.4202150.3376950.056*
O60.5354 (4)0.3229 (4)−0.0354 (3)0.148 (3)
H6A0.4578700.335828−0.0312190.222*
O7−0.3525 (5)0.1073 (2)0.00527 (18)0.0793 (13)
H7B−0.3838610.090430−0.0376610.119*
O80.5417 (4)0.4769 (3)0.0743 (3)0.118 (2)
H8A0.4921910.4539890.0372720.178*
  1. aOccupancy: 0.497(5), bOccupancy: 0.503(5).

Source of material

Tris(benzimidazol-2-yl-methyl)amine (ntb) was synthesized according to a literature procedure [4]. A methanol solution (50 mL) of Ni(ClO4)2⋅6H2O (73 mg, 0.2 mmol) and ntb (82 mg, 0.2 mmol) was stirred for 10 min. Then a methanol solution (40 mL) of disodium succinate hexahydrate (54 mg, 0.2 mmol) was added dropwise to the aforementioned solution. After being stirred at room temperature for 2 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 N–C bond (with the SHELX program [3]). The Uiso values of the hydrogen atoms of methyl groups were set to 1.5 Ueq and the values of all other hydrogen atoms were set to 1.2 Ueq. The disordered C27 and C28 atoms of succinate including H atoms on them were located at two sites with occupancies to be 0.503(5) for C27, C28 and 0.497(5) for C27′, C28′ (Table 2).

Comment

The ligand ntb is often used in the construction of a variety of metal complexes [5]. Some mononuclear nickel(II) complexes have been reported which use monocarboxylate (isonicotinate, picolinate and 3, 5-dinitrobenzoate), azide and 2-(2′-pyridyl)-4, 4, 5, 5-tetramethylimidazoline-1-oxyl-3-oxide (NIT2Py) [6], [7], [8] as coligands, respectively. Two dinuclear nickel(II) complexes of ntb were prepared and characterized using dicarboxylate (terephthalate and fumarate) as bridging ligands by our group [9]. Succinic acid is a saturated aliphatic dicarboxylic acid. It shows conformational freedom and coordination versatility due to the single-bonded carbon chains, coordinating metal ions in various modes [10], [11], [12], [13]. As an extension of our work, succinate was selected for the construction of a nickel(II) complex of ntb. At this time, the effort to get a dinickel(II) complex failed, while a mononuclear complex was obtained.

The title complex was obtained by the reaction of Ni(ClO4)2⋅6H2O, ntb and disodium succinate hexahydrate in the ratio of 2:2:1 in methanol. The asymmetric unit of the title structure consists of one [Ni(ntb)(suc)] unit and four methanol molecules. The central Ni(II) is six-coordinate in a N4O2 donor set formed by four nitrogen atoms of ntb and two oxygen atoms of succinate. The equatorial plane is defined by N2, N4, N6 of ntb and O3 of succinate. Equatorial bond angles are in the range 86.68(10)−91.14(11)°. The apical positions are occupied by O1 of succinate and tertiary amine N1 of ntb with O1–Ni1–N1 bond angle to be 176.64°, showing a distorted octahedral environment. As expected, the tripodal ntb ligand coordinates nickel(II) with the three benzimidazole groups in a T-shaped fashion. This can be observed almost in all nickel(II) complexes of ntb [7], [8], [9], [14], [15]. The three benzimidazole Ni–N bond lengths are in the range of 2.054(3)–2.077(3) Å, while the Ni–N(tertiary amine) bond length is 2.205(3) Å. The succinate anion shows a bidentate chelating mode. Each carboxylate provides one oxygen atom (O1, O3) to coordinate with nickel(II) to form a seven-membered ring. The two Ni–O bond lengths are 2.033(3) Å for Ni1–O1 and 2.067(2) Å for Ni1–O3, respectively. The O1–Ni–O3 bond angle is 95.16(11)°. This coordination is different to previously reported dicarboxylato-nickel(II) complexes of ntb. In the complexes [Ni2(ntb)2(μ-tp)(H2O)2](NO3)2⋅4CH3OH⋅H2O and [Ni2(ntb)2(μ-fum)(H2O)(CH3OH)](NO3)2⋅6CH3OH⋅H2O, two [Ni(ntb)]2+ units are bridged by terephthalate and fumarate in bis(monodentate) mode [7]. Thus, we showed that the single-bonded carbon chain of succinate is flexible enough to adopt the bidentate chelating mode.

In the complex, two of the [Ni(ntb)(suc)] units are interlinked by H-bonds to form a dimolecular unit [N5–H5⃛O4, d(D⃛A) = 2.786(4) Å]. These dimolecular units are interacted to form a chain structure by H-bonds through the carboxylate (O2) of succinate and the benzimidazole NH(N3) groups of ntb [N3–H3⃛O2, d(D⃛A) = 2.756(3) Å]. The chains are further expanded into a 2D network structure by weak π-π interaction between benzimidazole groups.


Corresponding author: Feng-Mei Nie, Department of Chemistry, Capital Normal University, Beijing, 100048, P.R. China, E-mail:

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

Award Identifier / Grant number: KM201910028013

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

  2. Research funding: 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: 2020-11-21
Accepted: 2020-12-15
Published Online: 2021-01-12
Published in Print: 2021-03-26

© 2020 Tian-Xu Qiao 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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  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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