Home The crystal structure of (tris(2-benzimidazolylmethyl)amine)-benzoato-copper(II) perchlorate monohydrate, CuC31H28N7O7Cl
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The crystal structure of (tris(2-benzimidazolylmethyl)amine)-benzoato-copper(II) perchlorate monohydrate, CuC31H28N7O7Cl

  • Ji Li ORCID logo EMAIL logo and Mingzhi Miao
Published/Copyright: October 28, 2022
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Zeitschrift für Kristallographie - New Crystal Structures
From the journal Zeitschrift für Kristallographie - New Crystal Structures Volume 238 Issue 1

Abstract

CuC31H28N7O7Cl, triclinic, P 1 ‾ (no. 2), a = 10.1386(6) Å, b = 12.1155(8) Å, c = 14.1972(8) Å, α = 100.297(2)°, β = 98.411(2)°, γ = 112.744(2)°, V = 1536.78(16) Å3, Z = 2, R gt (F) = 0.0613, wR ref (F 2) = 0.1519, T = 250(2) K.

CCDC no.: 2191213

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: Green block
Size: 0.12 × 0.10 × 0.08 mm
Wavelength: Ga Kα radiation (1.34139 Å)
μ: 4.70 mm−1
Diffractometer, scan mode: Bruker D8 Venture Photon III, φ and ω
θ max, completeness: 57.2°, >99%
N(hkl)measured, N(hkl)unique, R int: 31,453, 6297, 0.075
Criterion for I obs, N(hkl)gt: I obs > 2σ(I obs), 4653
N(param)refined: 428
Programs: Bruker [1], SHELX [2], [3], [4], DIAMOND [5], OLEX2 [6]
Table 2:

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

Atom x y z U iso*/U eq
C1 0.3026 (4) 0.5266 (3) 0.3699 (3) 0.0350 (8)
H1A 0.297624 0.443128 0.349122 0.042*
H1B 0.206706 0.519292 0.380807 0.042*
C2 0.4204 (4) 0.5994 (3) 0.4616 (3) 0.0326 (8)
C3 0.6344 (4) 0.7281 (3) 0.5567 (3) 0.0332 (8)
C4 0.7797 (4) 0.8134 (3) 0.5969 (3) 0.0402 (9)
H4 0.844504 0.843629 0.557056 0.048*
C5 0.8242 (5) 0.8517 (4) 0.6989 (3) 0.0508 (11)
H5A 0.922297 0.908393 0.728621 0.061*
C6 0.7288 (5) 0.8092 (4) 0.7585 (3) 0.0509 (11)
H6 0.763136 0.839019 0.827346 0.061*
C7 0.5849 (5) 0.7243 (4) 0.7189 (3) 0.0453 (10)
H7A 0.520112 0.694888 0.759010 0.054*
C8 0.5399 (4) 0.6841 (3) 0.6169 (3) 0.0338 (8)
C9 0.3050 (4) 0.7030 (3) 0.3081 (3) 0.0359 (8)
H9A 0.312573 0.734895 0.378061 0.043*
H9B 0.203938 0.678292 0.271531 0.043*
C10 0.4109 (4) 0.8008 (3) 0.2710 (3) 0.0324 (8)
C11 0.6102 (4) 0.9108 (3) 0.2333 (3) 0.0347 (8)
C12 0.7501 (4) 0.9592 (4) 0.2140 (3) 0.0444 (10)
H12 0.821665 0.932055 0.235515 0.053*
C13 0.7784 (5) 1.0481 (4) 0.1623 (4) 0.0577 (12)
H13 0.870874 1.081514 0.147311 0.069*
C14 0.6736 (5) 1.0898 (4) 0.1317 (4) 0.0610 (13)
H14 0.697820 1.151439 0.097107 0.073*
C15 0.5357 (5) 1.0440 (4) 0.1502 (3) 0.0507 (11)
H15 0.465434 1.072703 0.129305 0.061*
C16 0.5060 (4) 0.9529 (3) 0.2014 (3) 0.0377 (9)
C17 0.2744 (4) 0.5132 (4) 0.1923 (3) 0.0381 (9)
H17A 0.240182 0.556654 0.149512 0.046*
H17B 0.189293 0.438679 0.192806 0.046*
C18 0.3853 (4) 0.4778 (3) 0.1539 (3) 0.0346 (8)
C19 0.5974 (4) 0.4846 (3) 0.1355 (3) 0.0331 (8)
C20 0.7452 (4) 0.5135 (4) 0.1403 (3) 0.0415 (9)
H20 0.820159 0.582448 0.187506 0.050*
C21 0.7771 (5) 0.4361 (4) 0.0726 (3) 0.0482 (10)
H21 0.876105 0.453620 0.073284 0.058*
C22 0.6668 (5) 0.3330 (4) 0.0035 (3) 0.0514 (11)
H22 0.693218 0.280833 −0.039373 0.062*
C23 0.5210 (5) 0.3053 (4) −0.0038 (3) 0.0459 (10)
H23 0.446714 0.236658 −0.051603 0.055*
C24 0.4879 (4) 0.3839 (3) 0.0630 (3) 0.0356 (8)
C25 1.0259 (4) 0.7569 (3) 0.4409 (3) 0.0344 (8)
C26 1.0934 (4) 0.7230 (4) 0.5154 (3) 0.0453 (10)
H26 1.040880 0.649099 0.532003 0.054*
C27 1.2383 (5) 0.7980 (5) 0.5655 (3) 0.0534 (11)
H27 1.282714 0.776753 0.617947 0.064*
C28 1.3171 (5) 0.9033 (4) 0.5386 (4) 0.0559 (12)
H28 1.415919 0.953354 0.571964 0.067*
C29 1.2519 (4) 0.9357 (4) 0.4632 (4) 0.0538 (12)
H29 1.306816 1.006517 0.443713 0.065*
C30 1.1053 (4) 0.8639 (3) 0.4159 (3) 0.0454 (10)
H30 1.059611 0.888482 0.366336 0.054*
C31 0.8657 (4) 0.6789 (4) 0.3920 (3) 0.0372 (9)
Cl1 −0.02683 (11) 0.20570 (11) −0.06739 (8) 0.0573 (3)
Cu1 0.58207 (5) 0.66700 (5) 0.32064 (4) 0.03158 (19)
N1 0.3424 (3) 0.5950 (3) 0.2939 (2) 0.0305 (6)
N2 0.5550 (3) 0.6740 (3) 0.4580 (2) 0.0327 (7)
N3 0.4067 (3) 0.6014 (3) 0.5544 (2) 0.0362 (7)
H3 0.327868 0.558207 0.572021 0.043*
N4 0.5473 (3) 0.8152 (3) 0.2766 (2) 0.0327 (7)
N5 0.3798 (3) 0.8820 (3) 0.2280 (2) 0.0359 (7)
H5 0.296590 0.888357 0.218795 0.043*
N6 0.5283 (3) 0.5416 (3) 0.1933 (2) 0.0325 (7)
N7 0.3560 (3) 0.3835 (3) 0.0771 (2) 0.0395 (7)
H7 0.268823 0.330854 0.041989 0.047*
O1 0.7955 (3) 0.7341 (2) 0.35524 (19) 0.0408 (6)
O2 0.8106 (3) 0.5669 (3) 0.3910 (2) 0.0524 (8)
O3 −0.0648 (4) 0.2634 (7) −0.1372 (4) 0.172 (3)
O4 0.1035 (4) 0.1932 (5) −0.0742 (4) 0.128 (2)
O5 0.0037 (5) 0.2821 (5) 0.0254 (3) 0.1167 (17)
O6 −0.1499 (4) 0.0938 (4) −0.0786 (4) 0.1058 (15)
O7 0.9594 (5) 0.4327 (5) 0.2954 (4) 0.1051 (14)
H7B 0.897568 0.452785 0.321219 0.158*
H7C 0.912689 0.372704 0.243210 0.158*

Source of material

Tris(2-benzimidazolylmethyl)amine (NTB) was prepared according to an earlier method [7]. Firstly, ligand ntb (0.081 g, 0.20 mmol) was added to an ethanol (20 ml) solution of Cu(ClO4)2·6H2O (0.074 g, 0.20 mmol). The mixture was stirred at room temperature for 20 min to get a clear blue solution. Then, an ethanol solution (5.0 ml) of sodium benzoate (0.0288 g, 0.20 mmol) was added dropwise to this solution and the green suspension was formed. Lastly, the mixture was refluxed for 30 min at 353 K and then gradually cooled to room temperature. The suspension was filtered and a bright green powder was obtained, washed using ether for three times and dried under the infrared light (0.121 g, yield: 85%). The residual filtrate was allowed to stand for one week. Green crystals suitable for X-ray structure analysis were obtained at the bottom of the vessel.

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 = 0.94 Å (aromatic), 0.98 Å (methylene) and U iso(H) = 1.2U eq (aromatic and methylene). Hydrogen atoms bonded to nitrogen, water oxygen atoms were initially found from the difference maps and then refined to be at their ideal positions with N–H = 0.87 Å and O–H = 0.86 Å. Their thermal factors were set as U iso(H) = 1.2U eq(N) and 1.5U eq(O).

Comment

Multi-benzimidazole ligand tris(2-benzimidazolylmethyl)-amine (NTB) has been often used as a histidine-like mimic to model the active sites of metalloproteins [8], [9], [10], [11], [12], [13]. A number of mononuclear copper complexes related with NTB have been synthesized and reported. In these analogs, there may be a coligand such as nitrate, chloride, azide and water molecule around the copper coordination sphere, which can regulate its redox properties and further influence the enzymatic-mimicking activities. As a continuation of our studies [14].

In the crystal of the title compound(I), its asymmetric unit was composed of each one [Cu(NTB)(PhCOO)]+, one perchlorate anion and one water solvent molecule. In (I), NTB acts as a tetradentate ligand, coordinating through the tertiary N atom and three benzimidazole (bzim) N atoms to the metal ion. There is also a benzoate oxygen atom mono-dentated coordinated to the copper atom, forming a distorted trigonal bipyramidal coordination configuration with a τ parameter of 0.608 [15]. The three benzimidazole N2, N4 and N6 atoms constitute of the equatorial plane, and the amine N1 and carboxylated O1 atoms reside at the axial positions. The tertiary N1 atom presents the Cu–N1 bond length about 0.14 Å longer than the mean value of the three Cu–Nbzim bond lengths. This should result from steric requirements of the trigonal ligand NTB. The cis angles around the copper center are ranging from 79.09(1)° to 107.83(1)° and the two larger trans angles are 139.08(1)° and 175.55(1)° for N2–Cu1–N6 and N1–Cu1–O1, respectively, which are very similar to some analogs [16], [17], [18].

In the crystal packing, the component ions are linked into a complex structure by a combination of N–H⋯O, O–H⋯O, π⋯π and C–H⋯π interactions [19].

Corresponding author: Ji Li, School of Biological and Environmental Engineering, Guiyang University, Guiyang 550005, P. R. China, E-mail:

Funding source: Guiyang University

Award Identifier / Grant number: 2020

Acknowledgments

This work was financially supported by Discipline and Master’s Site Construction Project of Guiyang University by Guiyang City Financial Support Guiyang University [2020].

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

  2. Research funding: Discipline and Master’s Site Construction Project of Guiyang University by Guiyang City Financial Support Guiyang University [2020].

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

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Received: 2022-08-23
Accepted: 2022-10-10
Published Online: 2022-10-28
Published in Print: 2023-01-27

© 2022 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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  43. The crystal structure of 3,3′-disulfanediyldi(1H-1,2,4-triazol-5-amine) monohydrate, C4H8N8OS2
  44. The crystal structure of trans-[bis(4-methylpyridine-κN)bis(quinoline-2-carboxylato- κ 2 N,O)cadmium(II)], C32H26CdN4O4
  45. The crystal structure of ethyl 2′-hydroxy-4′,6′-dimethoxy-3-(4-methoxynaphthalen-1-yl)-5-oxo-2,3,4,5-tetrahydro-[1,1′-biphenyl]-4-carboxylate, C28H28O7
https://doi.org/10.1515/ncrs-2022-0426
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Articles in the same Issue

  1. Frontmatter
  2. New Crystal Structures
  3. Crystal structure of undecacalcium decaarsenide, Ca11As10
  4. Crystal structure of catena-poly[diiodido-(μ2-1,5-dimethyl-2-phenyl-4-((pyridin-4- ylmethylene)amino)-1,2-dihydro-3H -pyrazol-3-one-κ2 N: O)zinc(II)], C17H16I2N4OZn
  5. The crystal structure of 5,10,15,20-tetrakis(4-(tert-butyl)phenyl)porphyrin-21,23-diido-κ4 N 4-naphthalocyanido-κ4 N 4-neodymium(IV) - chloroform (1/6) C114H90N12Cl18Nd
  6. The crystal structure of 1-(4-bromophenyl)-3-(2-chlorobenzyl)urea, C14H12BrClN2O
  7. Crystal structure of bis[benzyl(methyl)carbamodithioato-κ 2 S,S′]-di-n-butyltin(IV), C26H38N2S4Sn
  8. Crystal structure of (E)-3-(2-(4-(diethylamino)-2-hydroxystyryl)-3,3-dimethyl-3H-indol-1-ium-1-yl)propane-1-sulfonate – methanol (1/2), C25H32N2O4S⋅2CH3OH
  9. Synthesis and crystal structure of {(N′,N″-(((ethane-1,2-diylbis(oxy))bis(2,1-phenylene))-bis(methaneylylidene))bis(2-hydroxybenzohydrazonato)-κ6 N 2 O 4}copper(II), C30H24CuN4O6
  10. The crystal structure of ((E)-2,4-dibromo-6-(((5-(nitro)-2-oxidophenyl)imino)methyl)phenolato-κ 3 N,O,O′)tris(pyridine-κN)manganese(II), C28H21Br2MnN5O4
  11. Synthesis and crystal structure of 1-((3R,10S,13R,17S)-10,13-dimethyl-3-(p-tolylamino)hexadecahydro-1H-cyclopenta-[a]phenanthren-17-yl)ethan-1-one, C28H41NO
  12. The crystal structure of 3-nitrobenzene-1,2-dicarboxylic acid—pyrazine-2-carboxamide(1/1), C13H10N4O7
  13. Crystal structure of poly[tetrakis(μ3-2-aminonicotinato-κ3N,O,O′)-(μ2-oxalato-κ4 O,O′:O″,O′″)-(μ4-oxalato-κ6 N:N′:O,O′:O″,O′″)dicopper(I)-disamarium(III)], [SmCu(C6N2H5O2)2(C2O4)] n
  14. The crystal structure of 2,3,4-trihydroxybenzoic- acid—pyrazine-2-carboxamide—water (1/1/1), C12H13N3O7
  15. Crystal structure of N-ethyl-4-[3-(trifluoromethyl)-phenyl]piperazine-1-carbothioamide, C14H18F3N3S
  16. The crystal structure of 3-anilino-1,4-diphenyl-4H-1,2,4-triazol-1-ium iodide, C20H17N4I
  17. The crystal structure of (tris(2-benzimidazolylmethyl)amine)-benzoato-copper(II) perchlorate monohydrate, CuC31H28N7O7Cl
  18. Crystal structure of [2-hydroxy-3-methyl-benzoato-k1 O-triphenyltin(IV)], C26H22O3Sn
  19. Crystal structure of diaqua-bis(4-(hydroxymethyl)-benzoato-k1 O)zinc(II), C16H18O8Zn
  20. The crystal structure of dicarbonyl-(N-nitroso-N-oxido-phenylamine-κ 2 O,O)-rhodium(I), C8H5N2O4Rh
  21. The crystal structure of oxalic acid – 2-ethoxybenzamide (2/1), C20H24N2O8
  22. The crystal structure of ethyl 7-ethyl-5-methyl-4,7-dihydrotetrazolo[1,5-a]pyrimidine-6-carboxylate, C10H15N5O2
  23. Crystal structure of poly[(N,N-dimethylacetamide-κO) (μ4-2-nitroisophthalato-κ 4 O:O′:O″:O′″)manganese(II)], C11H10N2O7Mn
  24. Crystal structure of 14-O-acetyldelcosine, C26H41NO8
  25. The crystal structure of poly[(1,10-phenanthroline-κ2 N,N′)-(μ 4-2-chlorobenzene-1,3-dicarboxylato-κ5 O:O′:O″:O‴) cadmium(II)] monohydrate, C20H13CdClN2O5
  26. Crystal structure of propane-1,3-diylbis(diphenylphosphine sulfide) ethanol solvate, C27H26P2S2
  27. Crystal structure of bis{[(4-diethylamino-2-hydroxy-benzylidene)-hydrazinocarbonylmethyl]-trimethylammonium} tetrabromozincate, C32H54N8O4ZnBr4
  28. Synthesis and crystal structure of dimethyl 2,2′-(2,5-bis(4-hydroxyphenyl)-2,5-dihydrofuran-3,4-diyl)dibenzoate, C34H30O7
  29. Synthesis and crystal structure of 2-(2-oxo-2-phenylethyl)-4H-chromen-4-one, C17H12O3
  30. The crystal structure of tetra(imidazole-κ1 N)zinc(II) μ2-oxido-hexaoxido-divanadium(VI) C12H16N8O6V2Zn
  31. Crystal structure of S-2-(1-(5-methylpyridin-2-ylamino)octyl)-3-hydroxynaphthalene-1,4-dione, C24H28N2O3
  32. Crystal structure of bis(μ2-5-chloro-2-oxido-N-(1-oxido-2-oxo-2-phenylethylidene)-benzohydrazonato-κ5 N,O,O′:N′,O′′)-oktakis(pyridine-κ1 N)trinickel(II) – methanol – pyridine (1/1/1) C76H65N13Cl2Ni3O9
  33. The crystal structure of methyl 3,5-diaminobenzoate, C8H10N2O2
  34. Crystal structure of 10-(9H-carbazol-9-yl)-5H-dibenzo[a,d][7]annelen-5-one, C27H17NO
  35. Crystal structure of ethyl 1-(2-hydroxyethyl)-4-((4-methoxyphenyl)amino)-5-oxo-2,5-dihydro-1H-pyrrole-3-carboxylate, C16H20N2O5
  36. The crystal structure of 1-(4-bromophenyl)-3-cycloheptylurea, C14H19BrN2O
  37. The crystal structure of 1,4-bis(1,2,3,4,5-pentamethylcyclopenta-2,4-dien-1-yl)-3,6-bis ((4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)methylene)-1,4-dialuminacyclohexane – benzene (1/2), C50H72Al2B2O4
  38. Crystal structure of bis(μ 3-diphenylphosphinato)-tetrakis(μ 2-diphenylphosphinato)-bis(diphenylphosphinato)-bis(μ 2-hydroxo)dicopper(II)-ditin(IV), C104H100O18P8Cu2Sn2
  39. Crystal structure of 3-((3,4-dichloroisothiazol-5-yl)methoxy)benzo[d] isothiazole 1,1-dioxide, C11H6Cl2N2O3S2
  40. Synthesis and crystal structure of 2-(2-(2-fluorophenyl)-2-oxoethyl)-4H-chromen-4-one, C17H11FO3
  41. The crystal structure of tris(carbonyl)-bis(carbonyl)-[μ-propane-1,2- dithiolato]-(benzyldiphenylphosphine)diiron (Fe—Fe), C27H23Fe2O5PS2
  42. Crystal structure of 1-(2-(4-chlorophenethyl)-2-hydroxy-3,3-dimethylbutyl)-1H-1,2,4-triazol-4-ium nitrate, C16H23N4O4Cl
  43. The crystal structure of 3,3′-disulfanediyldi(1H-1,2,4-triazol-5-amine) monohydrate, C4H8N8OS2
  44. The crystal structure of trans-[bis(4-methylpyridine-κN)bis(quinoline-2-carboxylato- κ 2 N,O)cadmium(II)], C32H26CdN4O4
  45. The crystal structure of ethyl 2′-hydroxy-4′,6′-dimethoxy-3-(4-methoxynaphthalen-1-yl)-5-oxo-2,3,4,5-tetrahydro-[1,1′-biphenyl]-4-carboxylate, C28H28O7
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