Home Physical Sciences The crystal structure of dichlorido-(tris(2-benzimidazolylmethyl)amine-κ4N,N′,N′′,N′′′)chromium(III) chloride — methanol (1/3), CrC27H33Cl3N7O3
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The crystal structure of dichlorido-(tris(2-benzimidazolylmethyl)amine-κ4N,N′,N′′,N′′′)chromium(III) chloride — methanol (1/3), CrC27H33Cl3N7O3

  • Ji Li ORCID logo EMAIL logo and Siqi Wu
Published/Copyright: December 5, 2019

Abstract

CrC27H33Cl3N7O3, triclinic, P1̄ (no. 2), a = 9.7862(13) Å, b = 12.4690(17) Å, c = 12.8413(17), α = 84.163(2)°, β = 73.602(3)°, γ = 85.524(2)°, V = 1493.4(3) Å3, Z = 2, Rgt(F) = 0.0472, wRref(F2) = 0.1524, T = 100(2) K.

CCDC no.: 1947955

The asymmetric unit of the title crystal 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:Block, green
Size:0.15 × 0.12 × 0.10 mm
Wavelength:Mo Kα radiation (0.71073 Å)
μ:0.69 mm−1
Diffractometer, scan mode:Bruker APEX-II, φ and ω-scans
θmax, completeness:28.3°, >99%
N(hkl)measured, N(hkl)unique, Rint:13443, 7221, 0.036
Criterion for Iobs, N(hkl)gt:Iobs > 2 σ(Iobs), 5873
N(param)refined:391
Programs:Bruker programs [1], SHELX [2], [3], [4], DIAMOND [5], OLEX2 [6]
Table 2:

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

AtomxyzUiso*/Ueq
Cr10.87932(4)0.24696(3)0.35537(3)0.01037(12)
O10.5572(2)0.10643(17)1.08021(17)0.0294(5)
H10.597(4)0.0454(16)1.087(3)0.044*
O20.9564(2)0.19453(16)0.86432(15)0.0232(4)
H21.030(2)0.157(2)0.866(3)0.035*
O3a0.4809(3)0.1332(2)0.7181(2)0.0396(8)
H3Aa0.42510.14190.77990.059*
O3′b0.5987(13)0.1141(7)0.6653(9)0.0396(8)
H3′b0.68770.10250.64730.059*
Cl10.82188(6)0.39065(4)0.45741(4)0.01619(14)
Cl20.91378(6)0.13139(5)0.50164(4)0.01610(14)
Cl30.23008(6)0.09169(5)0.92587(5)0.01804(14)
N10.9336(2)0.11276(15)0.25366(15)0.0117(4)
N20.8550(2)0.32773(15)0.21376(16)0.0127(4)
N30.8637(2)0.31986(16)0.03942(16)0.0151(4)
H30.895(3)0.294(2)−0.0247(13)0.018*
N41.0931(2)0.26305(15)0.29001(16)0.0123(4)
N51.3009(2)0.19395(16)0.19269(16)0.0148(4)
H5A1.367(2)0.1476(19)0.161(2)0.018*
N60.6845(2)0.18585(15)0.38087(15)0.0129(4)
N70.5594(2)0.04882(16)0.36851(16)0.0145(4)
H7A0.534(3)−0.0141(13)0.358(2)0.017*
C10.9177(3)0.14815(18)0.14170(19)0.0152(5)
H1A1.00850.13230.08620.018*
H1B0.84280.10720.12780.018*
C20.8787(2)0.26562(19)0.13211(18)0.0127(4)
C30.8258(2)0.43219(18)0.17069(18)0.0126(4)
C40.7961(3)0.53062(19)0.2178(2)0.0159(5)
H40.79160.53530.29210.019*
C50.7736(3)0.6211(2)0.1513(2)0.0195(5)
H50.75410.68930.18070.023*
C60.7787(3)0.6146(2)0.0420(2)0.0207(5)
H60.76240.6786−0.00070.025*
C70.8067(3)0.5180(2)−0.0053(2)0.0199(5)
H70.80940.5135−0.07930.024*
C80.8309(3)0.4276(2)0.0608(2)0.0156(5)
C91.0847(2)0.07642(19)0.2481(2)0.0148(5)
H9A1.12760.03640.18290.018*
H9B1.08900.02870.31370.018*
C101.1626(2)0.17676(18)0.24190(18)0.0132(4)
C111.1930(2)0.34181(19)0.27076(19)0.0133(4)
C121.1792(3)0.44687(19)0.30174(19)0.0147(4)
H121.09050.47700.34280.018*
C131.3013(3)0.5055(2)0.2697(2)0.0185(5)
H131.29610.57700.29040.022*
C141.4323(3)0.4623(2)0.2076(2)0.0209(5)
H141.51260.50590.18590.025*
C151.4469(3)0.3571(2)0.1772(2)0.0197(5)
H151.53570.32700.13640.024*
C161.3246(3)0.29844(19)0.20976(19)0.0148(5)
C170.8306(2)0.02783(18)0.30757(19)0.0142(4)
H17A0.8242−0.02230.25430.017*
H17B0.8616−0.01420.36740.017*
C180.6898(3)0.08606(19)0.35124(18)0.0139(4)
C190.5399(2)0.21641(19)0.42022(18)0.0127(4)
C200.4731(3)0.3126(2)0.46055(19)0.0159(5)
H200.52630.37210.46390.019*
C210.3258(3)0.3171(2)0.4954(2)0.0189(5)
H210.27670.38100.52430.023*
C220.2464(3)0.2297(2)0.48932(19)0.0189(5)
H220.14530.23640.51380.023*
C230.3115(3)0.1343(2)0.44872(19)0.0162(5)
H230.25790.07530.44490.019*
C240.4607(3)0.12970(19)0.41353(18)0.0140(4)
C250.5900(3)0.1465(3)0.9689(2)0.0290(6)
H25A0.53020.21200.96110.043*
H25B0.57170.09170.92560.043*
H25C0.69070.16360.94310.043*
C260.9777(3)0.2404(2)0.7549(2)0.0297(6)
H26A0.93760.31490.75520.045*
H26B0.93010.19800.71650.045*
H26C1.08010.23980.71790.045*
C270.5644(3)0.2223(2)0.6994(2)0.0305(6)
H27Aa0.50390.28770.69300.046*
H27Ba0.64110.21660.63170.046*
H27Ca0.60380.22460.76120.046*
H27Db0.64960.26440.67230.046*
H27Eb0.48850.25630.66920.046*
H27Fb0.53350.21960.77910.046*
  1. Occupancies: a0.800(4), b0.200(4).

Source of materials

Tris(2-benzimidazolylmethyl)amine (NTB) was prepared according to an earlier reported method [7]. NTB (0.408 g, 1.0 mmol) was dissolved in hot methanol (50.0 mL) and then a solution of CrCl3 (0.158 g, 1.0 mmol) in 20.0 mL methanol was added drop by drop. The mixed solution was stirred for 30 min at 50 °C. Finally, the reaction mixture was filtered and the filtrate solution was evaporated at room temperature for ten days. Some green block crystals were obtained at the bottom of the vessel (0.50 g, yield: 75%).

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, O1 and O2 atoms were initially found from the difference maps and refined with the restraints of N—H = 0.88(1) Å, O—H = 0.84(1) Å. The positions of hydrogen atoms bonded to disordered O3 and O3′ were constrained to be at the ‘best’ positions, forming hydrogen bonds to neighboring chloride anions [3]. Commands DFIX and SADI were used in the refinement to restrain C—O, N—H and O—H distances, and EADP was used to restrain the thermal factor of O3′ being similar to O3. For the N and O atoms, Uiso(H) = 1.2Ueq(N) and 1.5Ueq(O).

Comment

The multi-benzimidazole ligand tris(2-benzimidazolylmethyl)amine (NTB) has been often used in the design and synthesis of metal-containing compounds due to their potential application in the fields of biological and bioinorganic chemistry [8], [9], [10]. NTB has been often seen to be a tetradentate ligand coordinating a late transition metal. Compared to these metal complexes, early transition metal complexes of NTB are rarely reported.

The asymmetric unit of the title structure is composed of each one [Cr(NTB)Cl2]+, one Cl anion and three methanol solvent molecules. NTB acts as a tetradentate ligand, coordinating through the tertiary N atom and three benzimidazole (bzim) N atoms to metal ion. Two chlorido ligands are in a cis configuration. The N4Cl2 donor set constructs an octahedral polyhedron around the central Cr(III). The tertiary N1 atom presents a bond length about 0.10 Å longer than those for the three bzim N atoms. To retain the octahedral geometry, ligand NTB adopts a planar geometry with a dihedral angle of 11.9(1)° between the N4/N5 and N6/N7-containing bzim groups. However, the angles of these moieties with the third one are 79.9(1) and 88.3(1)°, respectively, which are very similar to its analogous structure with different solvent [11]. By considering some NTB-containing analogs as a whole, it can be found NTB can adopt many spatial arrangements to meet the coordination preference of a metal ion or solvent molecules [12], [13], [14]. On the other hand, the Cr(III) ion lies in the plane formed by N1, N4, N6 and CL1 atoms (maximal deviation: 0.025 Å for Cr1). As a result of these features, the deviations from an ideal octahedral geometry around Cr (III) ion are the following: trans angles range from 158.09(8) to 178.29(5)° and cis angles from 78.92(7) to 101.19(6)°.

A detailed geometrically analysis using the program PLATON [15] indicates that these adjacent [Cr(NTB)Cl2]+ ions are firstly linked into two-dimensional layers parallel to the (011) plane by three π⋯π interactions. These layers are further linked by three N—H⋯O and three O—H⋯Cl hydrogen bonds into the final three-dimensional network.

Acknowledgements

This work was financially supported by Discipline and Master’s Site Construction Project of Guiyang University by Guiyang City Financial Support Guiyang University (SH-2019).

References

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Received: 2019-08-21
Accepted: 2019-11-11
Published Online: 2019-12-05
Published in Print: 2020-02-25

©2019 Ji 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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  52. Crystal structure and anti-inflammatory activity of (3E,5E)-1-((4-chlorophenyl)sulfonyl)-3-(pyridin-4-ylmethylene)-5-(2-(trifluoromethyl)benzylidene)piperidin-4-one, C25H18ClF3N2O3S
  53. The crystal structure of 3-((1R,2S)-1-methylpyrrolidin-1-ium-2-yl)pyridin-1-ium tetrachloridomanganate(II), C10H16Cl4MnN2
  54. The crystal structure of 3-carboxy-5-methylpyridin-1-ium-2-carboxylate, C8H7NO4
  55. Crystal structure of bis(3-methoxy-N-(1-(pyridin-2-yl)ethylidene)benzohydrazonato κ3O,N,N′)zinc(II), C30H28N6O4Zn
  56. Crystal structure of dichlorido-(4,4′-dichloro-2,2′-bipyridine-κ2N,N′)platinum(II) — acetone (1/1), C13H12Cl4N2PtO
  57. Crystal structure of diethyl 6,12-bis(4-fluorophenyl)-2,10-dimethoxy-3,9-diphenyl-3,9-diazatetracyclo[6.4.0.02,7.04,11]dodecane-1,5-dicarboxylate, C42H42F2N2O6
  58. Synthesis and crystal structure of (1E,3E)-2-hydroxy-5-methylisophthalaldehyde O,O-di(2-((((E)-(2-hydroxynaphthalen-1-yl)methylene)amino)oxy)ethyl) dioxime, C35H32N4O7
  59. The crystal structure of 2-phenyl-4,6-bis(prop-2-yn-1-yloxy)-1,3,5-triazine, C15H11N3O2
  60. Crystal structure of 7-(2-{4-[(4-bromophenyl)methyl]piperazin-1-yl}ethoxy)-2H-chromen-2-one, C22H23BrN2O3
  61. Crystal structure of bis-[N-(3-ethyl-1-pyrazin-2-yl-ethylidene)-3-bromo-benzoic acid-hydrazonato-κ3O,N,N′)]-cadmium(II), C30H28N8O2Br2Cd
  62. Crystal structure of 6-(4-fluorophenyl)-4-methoxy-2H-pyran-2-one, C12H9FO3
  63. Crystal structure of 3-methyl-3-(2,4,5-trimethyl-3,6-dioxocyclohexa-1,4-dien-1-yl)butanoic acid, C14H18O4
  64. The crystal structure of 3-bromo-6-methoxy-2-methyl-5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)pyridine, C13H19BBrNO3
  65. The crystal structure of 6-methyl-3,20-dioxo-19-norpregna-4,6-dien-17-yl acetate–2,4-dihydroxybenzoic acid (1/1), C30H36O8
  66. The crystal structure of (5-chloro-2-hydroxy-N-(4-methoxy-2-oxidobenzylidene)benzohydrazonato-κ3N,O,O′)-(pyridine-κ1N)copper(II), C20H16ClCuN3O4
  67. Crystal structure of (E)-2-cyano-N′-(1-(3-ethylpyrazin-2-yl)ethylidene)acetohydrazide, C11H3N5O
  68. Crystal structure of (2,7-dihexyl-9,9-dimethyl-9H-xanthene-4,5-diyl)bis(diphenylphosphane), C51H56OP2
  69. Crystal structure of 5-((bis(pyridin-2-ylmethyl)amino)methyl)quinolin-8-ol, C22H20N4O
  70. Crystal structure of 3-(2-(5-(4-fluorophenyl)-3-(4-methylphenyl)-4,5-dihydro-1H-pyrazol-1-yl)thiazol-4-yl)-2H-chromen-2-one, C28H20FN3O2S
  71. The crystal structure of [(tetra-μ2-2,6-difluorobenzoato-κ2O:O′)-bis-(2,6-difluorobenzoato-κ2O:O′)-bis-(1,10-phenanthroline-κ2N:N′)]dierbium(III) C66H34N4O12F12Er2
  72. Crystal structure of bis(3-chloro-N-(1-(pyrazin-2-yl)ethylidene)benzohydrazonato-k3N,N′,O)nickel(II), C26H20N8O2Cl2Ni
  73. Crystal structure of (E)-3-(3-(5-methyl-1-phenyl-1H-1,2,3-triazol-4-yl)-1-phenyl-1H-pyrazol-4-yl)-1-phenylprop-2-en-1-one, C27H21N5O
  74. Crystal structure of (E)-N′-((4-aminophenyl)sulfonyl)-N,N-dimethylformimidamide, C9H13N3O2S
  75. Crystal structure of η6-p-cymene-iodido-(N-isopropyl-1-(pyridin-2-yl)methanimine-κ2N,N′)ruthenium(II) hexafluorophosphate(V), C19H26IN2F6Ru
  76. Crystal structure of 6-iodo-3-phenyl-2-propylquinazolin-4(3H)-one, C17H15IN2O
  77. Low temperature redetermination of the crystal structure of catena-poly[[tri-4-fluorobenzyltin(IV)]μ2-pyridine-4-carboxylato-κ2N:O], {C27H22F3NO2Sn}n
  78. Crystal structure of bis(2-propyl-1H-benzo[d]imidazol-3-ium) tetrachloridozincate(II), C10H13Cl4N2Zn
  79. The crystal structure of (Z)-3-hydrazono-5-nitroindolin-2-one – dimethyl sulfoxide (1/1), C8H6N4O3
  80. Crystal structure of bis-[N-(1-pyrazin-2-yl-ethylidene)-cyanoacetic acid-hydrazonato-κ3O,N,N′)]-zinc(II), C18H16N10O2Zn
  81. Crystal structure and photochromism of 1-(2,5-dimethyl-3-thienyl)-2-[2-methyl-5-(benzaldoxime)-3-thienyl] perfluorocyclopentene, C23H17F6NOS2
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