Home The crystal structure of (bis(benzimidazol-2-yl-methyl)amine-κ3N,N′,N″ )-(dihydrogen L-malate-κ2O,O ′)copper(II) perchlorate dihydrate, CuC20H24ClN5O12
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The crystal structure of (bis(benzimidazol-2-yl-methyl)amine-κ3N,N,N )-(dihydrogen L-malate-κ2O,O )copper(II) perchlorate dihydrate, CuC20H24ClN5O12

  • Yu Yang , Huanru Liu , Yuhang Wang and Xianggao Meng ORCID logo EMAIL logo
Published/Copyright: October 10, 2023

Abstract

CuC20H24ClN5O12, monoclinic, P 1 (no. 4), a = 7.4467(4) Å, b = 17.3823(9) Å, c = 9.6974(5) Å, α = 90°, β = 103.373(2)°, γ = 90°, V = 1221.20(11) Å3, Z = 2, Rgt (F) = 0.0642, wRref (F 2) = 0.1757, T = 100(2) K.

CCDC No.: 2289194

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 block
Size: 0.16 × 0.12 × 0.10 mm
Wavelength: Ga Kα radiation (1.34139 Å)
μ: 5.94 mm−1
Diffractometer, scan mode: Bruker Photon III, φ and ω
θ max, completeness: 54.9°, >99 %
N(hkl)measuredN(hkl)uniqueR int: 25,044, 4607, 0.099
Criterion for I obs, N(hkl)gt: I obs > 2σ(I obs), 3932
N(param)refined: 373
Programs: Bruker [1], SHELX [2, 3, 6], Diamond [4], Olex2 [5]
Table 2:

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

Atom x y z U iso*/U eq
C1 0.6343 (13) 0.3976 (5) 0.8240 (9) 0.0458 (19)
H1A 0.536673 0.402955 0.877406 0.055*
H1B 0.745638 0.375556 0.887761 0.055*
C2 0.6775 (11) 0.4737 (5) 0.7694 (9) 0.0407 (18)
C3 0.7466 (11) 0.5585 (5) 0.6256 (9) 0.0429 (19)
C4 0.7391 (11) 0.5968 (5) 0.7502 (10) 0.045 (2)
C5 0.7714 (13) 0.6748 (6) 0.7690 (12) 0.055 (2)
H5 0.765751 0.700269 0.854549 0.066*
C6 0.8128 (13) 0.7138 (6) 0.6549 (12) 0.059 (3)
H6 0.834786 0.767640 0.661520 0.070*
C7 0.8227 (13) 0.6746 (6) 0.5299 (12) 0.055 (2)
H7 0.853594 0.702884 0.454745 0.066*
C8 0.7896 (12) 0.5978 (5) 0.5125 (10) 0.047 (2)
H8 0.795624 0.572243 0.427064 0.057*
C9 0.6120 (14) 0.2649 (5) 0.7188 (9) 0.050 (2)
H9B 0.507455 0.237811 0.744546 0.060*
H9A 0.723289 0.257576 0.796307 0.060*
C10 0.6444 (12) 0.2333 (5) 0.5830 (9) 0.0403 (18)
C11 0.6884 (11) 0.2283 (5) 0.3705 (8) 0.0405 (18)
C12 0.6975 (12) 0.1532 (5) 0.4223 (9) 0.0432 (18)
C13 0.7313 (13) 0.0896 (5) 0.3468 (10) 0.049 (2)
H13 0.738172 0.038900 0.384037 0.059*
C14 0.7544 (13) 0.1060 (6) 0.2121 (10) 0.052 (2)
H14 0.781257 0.064796 0.155650 0.062*
C15 0.7404 (14) 0.1787 (6) 0.1569 (10) 0.054 (2)
H15 0.754667 0.185910 0.062876 0.065*
C16 0.7063 (13) 0.2417 (6) 0.2324 (9) 0.048 (2)
H16 0.695453 0.291871 0.192646 0.058*
C17 0.6145 (12) 0.4388 (5) 0.2397 (8) 0.0386 (17)
C18 0.4088 (10) 0.4368 (5) 0.2403 (8) 0.0367 (16)
H18 0.352877 0.388333 0.193599 0.044*
C19 0.3103 (11) 0.5060 (5) 0.1594 (8) 0.0388 (17)
H19 0.312744 0.500843 0.057115 0.047*
C20 0.1093 (12) 0.5117 (5) 0.1709 (9) 0.0432 (19)
Cu1 0.65223 (15) 0.38791 (7) 0.52418 (11) 0.0379 (3)
N1 0.5700 (12) 0.3473 (4) 0.6979 (7) 0.0505 (18)
H1 0.432310 0.351136 0.673812 0.061*
N2 0.7072 (10) 0.4811 (4) 0.6400 (7) 0.0411 (15)
N3 0.6977 (9) 0.5407 (4) 0.8394 (8) 0.0434 (16)
H3 0.686548 0.547896 0.926919 0.052*
N4 0.6545 (9) 0.2787 (4) 0.4771 (7) 0.0391 (14)
N5 0.6680 (10) 0.1591 (4) 0.5585 (8) 0.0443 (16)
H5A 0.665389 0.120872 0.617484 0.053*
O1 0.7324 (7) 0.4245 (3) 0.3569 (6) 0.0396 (12)
O2 0.6586 (9) 0.4545 (3) 0.1274 (6) 0.0439 (13)
O3 0.3936 (7) 0.4373 (4) 0.3837 (6) 0.0453 (14)
H3A 0.279 (5) 0.429 (7) 0.385 (12) 0.068*
O4 0.3975 (9) 0.5756 (3) 0.2117 (6) 0.0440 (13)
H4 0.497117 0.579858 0.185692 0.066*
O5 0.0426 (9) 0.5700 (4) 0.2072 (9) 0.0608 (18)
O6 0.0183 (9) 0.4470 (4) 0.1397 (7) 0.0491 (14)
H6A 0.019407 0.433993 0.056518 0.074*
Cl1a 0.1526 (5) 0.3263 (2) 0.8571 (4) 0.0460 (8)
O7a 0.0261 (13) 0.3024 (6) 0.9402 (11) 0.079 (3)
O8a 0.1815 (14) 0.4066 (4) 0.8631 (9) 0.068 (3)
O9a 0.3253 (11) 0.2911 (5) 0.9247 (13) 0.076 (3)
O10a 0.091 (3) 0.3002 (8) 0.7186 (10) 0.138 (7)
Cl1Ab 0.150 (4) 0.3403 (14) 0.819 (3) 0.0460 (8)
O7Ab 0.098 (8) 0.356 (3) 0.951 (4) 0.079 (3)
O8Ab 0.224 (7) 0.4098 (18) 0.770 (5) 0.068 (3)
O9Ab 0.288 (7) 0.280 (2) 0.833 (7) 0.076 (3)
O10Ab −0.013 (7) 0.319 (4) 0.712 (6) 0.138 (7)
O1W 0.0989 (9) 0.3964 (5) 0.4683 (8) 0.0634 (18)
H1WA 0.112523 0.375842 0.551277 0.095*
H1WB −0.011267 0.407532 0.419137 0.095*
O2W 0.6867 (9) 0.6229 (4) 0.1044 (7) 0.0492 (14)
H2WA 0.671867 0.669088 0.069096 0.074*
H2WB 0.803817 0.614028 0.137396 0.074*
  1. aOccupancy: 0.867 (10), boccupancy: 0.133 (10).

1 Source of materials

Bis(benzimidazol-2-yl-methyl)amine (IDB) was prepared according to an earlier described method [7]. IDB (0.277 g, 1.0 mmol) and L-malic acid (0.134 g, 1.0 mmol) were firstly dissolved in hot methanol (30.0 mL) and then a solution of Cu(ClO4)2(H2O)6 (0.371 g, 1.0 mmol) in 20.0 mL methanol was added drop by drop. The mixed solution was stirred for 1 h at 60 °C. Then, the reaction mixture was filtered and the filtrate solution was evaporated at room temperature for two weeks. Some blue crystals were obtained at the bottom of the glass vessel (0.40 g, yield: 64 %).

2 Experimental details

Hydrogen atoms bonded to carbon atoms were placed in their geometrically idealized positions and restrained to ride on their parent atoms with C–H = 0.95 Å (aromatic), 0.99 Å (methylene), 1.00 Å (methine) and U iso(H) = 1.2U eq (aromatic, methylene and methine). Hydrogen atoms bonded to nitrogen and oxygen atoms were initially found from the difference maps and restrained to be at their indicative positions using command ’AFIX′. The thermal factors of these hydrogen atoms were set 1.2 times (for N) or 1.5 times (for O) of their parent atoms. During the refinement, the perchlorate anion was found to be disordered over two positions with the final occupancies being 0.87(1):0.13(1) for the major and minor components. Commands DFIX, DANG and EADP were used to constrain the Cl–O,O···O distances and thermal factors.

3 Comment

Cu(II)-containing complexes are of great interest in relation of the active site of natural superoxidase dismutase (SOD), hemerythrin and nuclease [8], [9], [10]. These model compounds can be used as mimics aiming to provide further insight into the mechanism of metal sites in complex biological systems. Some of the important considerations in the preparation of model compounds include donor atoms and the resulting geometry around the metal center. Although there is each one copper(II) and one zinc(II) ions in the active site of the natural SOD, research indicates the two back-to-back single-electron redox reactions occur only around the Cu(II) ion which plays a decisive role in the whole catalytic process, and the metal zinc ion only stabilize the skeleton of the enzymatic protein. Therefore, much synthesis of superoxide dismutase model compounds have mainly focused on the micking of copper metal complexes containing imidazole or benzimidazole ligands due to their structurally similarity.

The crystal of the title compund (I) crystallized in the chiral space group P21 because of the use of the chiral ligand L-malic acid. Its asymmetric unit was composed of each one [Cu(IDB)(L-mal)]+ cation, one counter perchlorate anion and two water molecules. In (I), IDB acts as a tridentate ligand coordinating through one tertiary N atom (N1) and two benzimidazole (bzim) N atoms (N2 and N4) to copper. And the L-malate anion coordinates to the central copper ion in a way of bidentated ligand via the O1 and O3 atoms. Thus, a distorted five-coordinated environment was formed around the copper center with a τ parameter of 0.35 showing a moderately distortion of the square-pyramidal polyhedron [11]. The donor sets of N1/N2/N4/O1 constitute the basic plane and O3 atom resides at the apical position. The Cu1–N1 (2.049(7) Å) bond distance is slightly longer that the other two Cu–N2 (1.957(7) Å) and Cu1–N4 (1.954(7) Å), which should be ascribed to the steric hindrance originating from the IDB ligand. The Cu1–O1 of 1.960(5) Å is apparently shorter than the Cu1–O3 (2.256(5) Å) which also meets the requirement of the copper center. The bond angles around Cu1 atom from 76.0(2) to 178.8(2)° are comparable to some analogs [12], [13], [14].

Analysis by Platon [15] indicates that in this component [Cu(IDB)(L-mal)]+, the ClO 4 ions and two water solvent molecules are linked into a complex three-dimensional hydrogen-bonded network by the extensive N–H···O and O–H···O hydrogen bonds. Also there are two intermolecular π···π interactions observed between the benzene ring (C3–C8) and the adjacent imidazole ring [N4/N5/C10–C12, (1 − x, 1/2 + y, 1 − z)] and the benzene ring [C11–C16, (2 − x, 1/2 + y, 1 − z)]. Their centroid-to-centroid distances are of 3.538(4) and 3.664(4) Å, respectively, showing moderate non-covalent interactions, which further consolidate the crystal structure.


Corresponding author: Xianggao Meng, College of Chemistry, Central China Normal University, Wuhan 430079, P.R. China, E-mail:

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

  2. Competing interests: The authors declare no conflicts of interest regarding this article.

  3. Research funding: None declared.

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Received: 2023-08-21
Accepted: 2023-09-27
Published Online: 2023-10-10
Published in Print: 2023-12-15

© 2023 the author(s), published by De Gruyter, Berlin/Boston

This work is licensed under the Creative Commons Attribution 4.0 International License.

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  48. Crystal structure of (1E,1′E)-4,4′-(9,9-diethyl-9H-fluorene-2,7-diyl)dibenzaldehyde dioxime, C31H28N2O2
  49. Crystal structure of diethyl 1,9-bis(4-fluorophenyl)-4,6-diphenylhexahydro-3H-2,7,3,5-(epimethanetriyliminomethanetriyl)cyclopenta [b]pyridine-3,7(2H)-dicarboxylate, C40H36F2N2O4
  50. Crystal structure of bis(benzene-1 carboxylato-O 3,5-carboxyl-κ1O)-[(5,5,7,12,12,14-hexamethyl-1,4,8,11-tetraazacyclotetradecane-κ4N,N′,N′′,N′′′)nickel(II) ─ benzene-1,3,5-tricarboxylic acid ─ water (1/2/4), C52H66N4NiO28
  51. Crystal structure of 1,4-dibromo-2,5-bis(2-methoxyethoxy)benzene-1,4-diol, C12H16Br2O4
  52. Crystal structure of dicarbonyl[N,N′-(1,2-dimethyl-1,2-ethanediylidene)bis[2,6-bis(1-methylethyl)benzenamine]-N,N′]nickel(0), C30H40N2NiO2
  53. Crystal structure of 1,4-dibromo-2,5-bis(prop-2-yn-1-yloxy)benzene, C12H8Br2O2
  54. Crystal structure of O-(3-(benzo[d]thiazol-2-yl)naphthalen-2-yl) O-phenyl carbonothioate, C24H15NO2S2
  55. The crystal structure of (E)-4-fluoro-N′-(1-(4-hydroxyphenyl)propylidene)benzohydrazide, C16H15FN2O2
  56. Crystal structure of (E)-1-(benzo[d]thiazol-2-yl)-N-(4,5-dihydropyren-2-yl)methanimine, C24H16N2S
  57. Crystal structure of 3-((4-bromophenyl)thio)-1H-indole, C14H10BrNS
  58. Synthesis and crystal structure of 1-((7-hydroxy-3-(4-hydroxy-3-nitrophenyl)-4-oxo-4H-chromen-8-yl)methyl)piperidin-1-ium-4-carboxylate monohydrate, C22H22N2O9
  59. Synthesis and crystal structure of (3E,5S,10S,13S,14S,17Z)-17-ethylidene-10,13-dimethylhexadecahydro-3H-cyclopenta[α]phenanthren-3-one O-(methacryloyl) oxime, C50H74N2O4
  60. Crystal structure of the hydrogen storage active phase La12Mg46LiMn
  61. The crystal structure of the salt: 4-((1,3-dioxoisoindolin-2-yl)carbamoyl)pyridine-1-ium 2-carboxybenzoate, C14H10N3O3·C8H5O4
  62. Crystal structure of (2-(2-pyridine)-benzimidazole-κ2 N,N′)-bis(1-phenylpyrazole-κ2 C,N)iridium(III) hexafluorophosphate, C30H22F6IrN7P
  63. Crystal structure of dichlorido-bis[2-(2,4-difluorophenyl)pyridine-κ1N]platinum(II), C22H14Cl2F4N2Pt
  64. Crystal structure of (5R,8R,9R,10R,12R,13R,14R, 17S,17Z)-2-((3-fluoropyridin-4-yl)methylene)-12-hydroxy-4,4,8,10,14-pentamethyl-17-((R)-2,6,6-trimethyltetrahydro-2H-pyran-2-yl)hexadecahydro-3H-cyclopenta[a]phenanthren-3-one, C36H52FNO3
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