Home Crystal structure of [meso-5,7,7,12,14,14,-hexamethyl-1,4,8,11-tetraazacyclotetradecane]nickel(II) diperchlorate – dimethylsulphoxide (1/2), C20H48Cl2N4NiO10S2
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Crystal structure of [meso-5,7,7,12,14,14,-hexamethyl-1,4,8,11-tetraazacyclotetradecane]nickel(II) diperchlorate – dimethylsulphoxide (1/2), C20H48Cl2N4NiO10S2

  • Saswata Rabi , Lucky Dey , Debashis Palit , Benu Kumar Dey , Ismail M. M. Rahman ORCID logo EMAIL logo , Edward R. T. Tiekink ORCID logo EMAIL logo and Tapashi Ghosh Roy EMAIL logo
Published/Copyright: August 13, 2021

Abstract

C20H48Cl2N4NiO10S2, monoclinic, P21/n (no. 14), a = 8.657(2) Å, b = 15.233(4) Å, c = 11.956(3) Å, β = 102.737(2)°, V = 1537.9(7) Å3, Z = 2, R gt (F) = 0.0237, wR ref (F 2) = 0.0655, T = 93(2) K.

CCDC no.: 2100053

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: Yellow block
Size: 0.25 × 0.25 × 0.15 mm
Wavelength: Mo Kα radiation (0.71073 Å)
μ: 1.00 mm−1
Diffractometer, scan mode: Rigaku Saturn724, ω
θ max, completeness: 27.5°, 99%
N(hkl)measured, N(hkl)unique, R int: 15,153, 3495, 0.012
Criterion for I obs, N(hkl)gt: I obs > 2σ(I obs), 3265
N(param)refined: 189
Programs: Reqab [1], CrystalClear [2], Shelx [3, 4], WinGX/Ortep [5], Diamond [6]
Table 2:

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

Atom x y z U iso*/U eq
Ni 1.000000 0.500000 1.000000 0.01129 (7)
N1 1.10221 (11) 0.45536 (6) 0.88109 (8) 0.0143 (2)
H1N 1.0319 (15) 0.4640 (10) 0.8173 (9) 0.017*
N2 0.94353 (11) 0.37734 (6) 1.02323 (8) 0.01392 (19)
H2N 1.0201 (14) 0.3633 (10) 1.0825 (10) 0.017*
C1 1.12174 (15) 0.35874 (8) 0.89629 (11) 0.0190 (2)
H1A 1.214730 0.345358 0.958593 0.023*
H1B 1.137653 0.331201 0.824676 0.023*
C2 0.97389 (16) 0.32465 (8) 0.92587 (11) 0.0209 (3)
H2A 0.883717 0.330031 0.858998 0.025*
H2B 0.986898 0.261956 0.947715 0.025*
C3 0.79124 (13) 0.35039 (8) 1.05604 (10) 0.0155 (2)
C4 0.80129 (16) 0.25389 (8) 1.09419 (12) 0.0227 (3)
H4A 0.807789 0.216225 1.028930 0.027*
H4B 0.706705 0.238554 1.122385 0.027*
H4C 0.895788 0.245309 1.155587 0.027*
C5 0.65008 (14) 0.36276 (8) 0.95484 (11) 0.0207 (2)
H5A 0.551552 0.360797 0.982359 0.025*
H5B 0.649487 0.315718 0.898830 0.025*
H5C 0.658786 0.419671 0.918521 0.025*
C6 0.77500 (14) 0.40616 (8) 1.15869 (10) 0.0174 (2)
H6A 0.685662 0.382830 1.189061 0.021*
H6B 0.872382 0.398906 1.219412 0.021*
C7 0.74781 (14) 0.50358 (7) 1.13607 (11) 0.0157 (2)
H7 0.664405 0.511041 1.064143 0.019*
C8 0.68932 (15) 0.54592 (9) 1.23515 (11) 0.0217 (3)
H8A 0.598276 0.512952 1.249260 0.026*
H8B 0.657655 0.606710 1.215290 0.026*
H8C 0.774550 0.545212 1.304387 0.026*
Cl1 0.33610 (3) 0.35563 (2) 0.23185 (2) 0.01959 (8)
O1 0.43273 (14) 0.29308 (8) 0.18891 (11) 0.0391 (3)
O2 0.41679 (14) 0.38404 (7) 0.34374 (9) 0.0352 (3)
O3 0.18808 (12) 0.31445 (7) 0.23700 (10) 0.0320 (2)
O4 0.30474 (14) 0.43046 (7) 0.15612 (9) 0.0350 (3)
S1 0.79332 (4) 0.46004 (2) 0.55269 (3) 0.02282 (9)
O5 0.93506 (12) 0.47545 (8) 0.64862 (9) 0.0332 (2)
C9 0.8438 (2) 0.36922 (11) 0.47325 (13) 0.0334 (3)
H9A 0.879134 0.319976 0.525364 0.040*
H9B 0.929250 0.386400 0.435889 0.040*
H9C 0.750831 0.351458 0.414901 0.040*
C10 0.65008 (16) 0.40529 (10) 0.61465 (12) 0.0267 (3)
H10A 0.622941 0.442427 0.674449 0.032*
H10B 0.694032 0.349570 0.648398 0.032*
H10C 0.554645 0.393834 0.555118 0.032*

Source of material

Hexamethyl tetrazacyclotetradecane (tet-a) was synthesized as per the literature procedure and exhibited the expected spectroscopic characteristics [7]. The tet-a macrocycle reacted with CH2=CH–CN to form the N-pendent bis-cyanoethyl derivative, hereafter tet-ax. The nickel(II) perchlorate salt of tet-ax, i.e. [Ni(tet-ax)](ClO4)2, was synthesised from the reaction of tet-ax with Ni(CH3COO)2·4H2O followed by the addition of NaClO4·6H2O. Then, [Ni(tet-ax)](ClO4)2 was dissolved in a solvent mixture of DMSO and H2O (1:1 v/v) followed by the addition of triethylamine and HClO4 with the aim to prepare [Ni(tet-am)](ClO4)2 (tet-am is the N-bound bis-carbamoylethyl derivative of isomeric ligand tet-a) by converting the cyanoethyl branches to carbamoylethyl branches, but a few yellow crystals of the unexpected product, [Ni(tet-a)](ClO4)2·2(CH3)2S=O, without any branches, was identified by X-ray crystallography.

Experimental details

The C-bound H atoms were geometrically placed (C–H = 0.98–1.00 Å) and refined as riding with U iso(H) = 1.2–1.5U eq(C). The N-bound atoms were located from a Fourier difference map and refined with N–H = 0.88 ± 0.01 Å, and with U iso(H) = 1.2U eq(N).

Comment

Some new N-pendent derivative macrocycles bearing bis-cyanoethyl branches were recently synthesised by combining certain macrocyclic ligands with an alkylating agent, acrylonitrile [8, 9]. In continuation of this work, an attempt was made to prepare a new N-pendent derivative containing N-bound bis-carbamoylethyl branches employing a different procedure [10]. It was observed during these investigations that a small quantity of yellow crystals were obtained (see Source of material) which were shown by X-ray crystallography to be [Ni(C16H36N4)](ClO4)2·2(CH3)2S=O, hereafter (I).

The crystallographic asymmetric unit of (I) comprises half a complex cation, as this is disposed about a centre of inversion, a perchlorate anion and a molecule of DMSO of crystallisation. The molecular structure of the complex cation is shown in the upper part of the Figure (70% probability displacement ellipsoids). The nickel(II) centre is coordinated by four amine-nitrogen atoms with the two independent Ni–N1, N2 bond lengths of 1.9548(10) and 1.9665(11) Å differing insignificantly. The resulting N4 donor set defines a square-planar geometry. The isomeric form of the tet-a ligand in (I) is meso and this has been characterised previously as the perchlorate salt [11] as have other configurational isomeric forms of tet-a [12]. The closest related structure to (I) is the isostructural copper(II) salt [13].

In the crystal, the perchlorate-O4 atom forms a weak contact with the nickel(II) atom [Ni⋯O4 i  = 3.0651(14) Å for symmetry operation (i): 1 − x, 1 − y, 1 − z] leading to a tetragonally distorted 4 + 2 coordination geometry. Further links between the complex cation and the perchlorate anion are mediated by amine-N–H⋯O(perchlorate) [N2–H2n⋯O3 ii : H2n⋯O3 ii  = 2.213(12) Å, N2⋯O3 ii  = 3.0897(17) Å with angle at H2n = 171.9(13)° for (ii): 1 + x, y, 1 + z] hydrogen bonds. The DMSO molecules are also associated with the complex cation, via amine-N–H⋯O(DSMO) hydrogen bonds [N1–H1n⋯O5: H1n⋯O5 = 2.014(11) Å, N1⋯O5 = 2.8529(16) Å with angle at H1n = 160.5(12)°]. The aforementioned contacts lead to the formation of a five-molecule aggregate, as represented in the lower part of the figure (the Ni⋯O and N–H⋯O interactions are shown as black and blue dashed lines, respectively, and non-participating H atoms are omitted). The aggregates are assembled into the crystal via a combination of DMSO-methyl-, methylene-, methyl-C–H⋯O(perchlorate) and methyl-C–H⋯O(DMSO) interactions.

Finally, the Hirshfeld surfaces and of the full and delineated two-dimensional fingerprint plots were calculated with the program Crystal Explorer 17 [14] in accord with literature methods [15]. For the complex cation, the surface contacts are clearly dominated by H⋯H [62.8%] and O⋯H/H⋯O [35.1%] contacts, with minor contributions from S⋯H/H⋯S [1.5%] and Ni⋯O/O⋯Ni [0.5%] contacts. For the DMSO molecule, H⋯H contacts also predominate, contributing 51.1% followed by O⋯H/H⋯O [36.1%] and S⋯H/H⋯S [9.5%] contacts. Minor contributions to the Hirshfeld surface of DMSO are contributed by O⋯O [1.7%] and S⋯O/O⋯S [1.6%] contacts. By contrast, the surface contacts for the perchlorate anion are dominated by O⋯H/H⋯O contacts, at 95.2%. This is followed by small contributions from O⋯O [2.4%], S⋯O/O⋯S [1.3%] and Ni⋯O/O⋯Ni [1.0%] contacts.


Corresponding author: Edward R. T. Tiekink, Research Centre for Crystalline Materials, School of Science and Technology, Sunway University, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia, E-mail: ; and Ismail M. M. Rahman, Institute of Environmental Radioactivity, Fukushima University, 1 Kanayagawa, Fukushima City, Fukushima 960-1296, Japan, ; and Tapashi Ghosh Roy, Department of Chemistry, Faculty of Science, University of Chittagong, Chattogram 4331, Bangladesh, E-mail:

Funding source: Japan International Cooperation Agency

Award Identifier / Grant number: JPMJSA1603

Funding source: Fukushima University

Award Identifier / Grant number: I-19-08

Award Identifier / Grant number: I-20-09

Award Identifier / Grant number: I-21-09

Funding source: Japan Society for the Promotion of Science doi.org/10.13039/501100001691

Award Identifier / Grant number: 21K12287

Funding source: Sunway University doi.org/10.13039/501100010798

Award Identifier / Grant number: GRTIN-IRG-01-2021

  1. Author contributions: 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 the Science and Technology Research Partnership for Sustainable Development (SATREPS) in collaboration between the Japan Science and Technology Agency (JST) and the Japan International Cooperation Agency (JICA) (Grant No. JPMJSA1603), the Environmental Radioactivity Research Network Center at Fukushima University, Japan (Grant Nos. I-19-08, I-20-09, I-21-09), the Grants-in -Aid for Scientific Research from the Japan Society for the Promotion of Science (JSPS) (Grant No. 21K12287) and Sunway University Sdn Bhd (Grant No. GRTIN-IRG-01-2021).

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

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Received: 2021-07-17
Published Online: 2021-08-13
Published in Print: 2021-12-20

© 2021 Saswata Rabi 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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  52. The crystal structure of (E)-2-((tert-butylimino)methyl)-4-chlorophenol, C11H14ClNO
  53. Crystal structure of all-cis-2,4,6-trihydroxycyclohexane- 1,3,5-triaminium chloride sulfate, C6H18ClN3O7S
  54. Crystal structure of dichlorido-bis(dimethyl sulfoxide-κO)bis(4-methylphenyl-κC 1)tin(IV), C18H26Cl2O2S2Sn
  55. Crystal structure of dichlorido-bis(4-chlorophenyl-κC 1)(2,2′-bipyridyl-κ 2 N,N′)tin(IV), C22H16Cl4N2Sn
  56. Redetermination of the crystal structure of (E)-5-bromo-2-hydroxybenzaldehyde oxime, C 7 H 6 BrNO 2
  57. The crystal structure of (E)-amino(2-(4-methylbenzylidene)hydrazineyl)methaniminium 4-methylbenzoate, C9H13N4 + C8H7O2
  58. Crystal structure of 2-chloro-3-(isopentylamino)naphthalene-1,4-dione, C 15 H 16 ClNO 2
  59. The crystal structure of bis(2-acetyl-5-methoxyphenyl)carbonate 1.5 hydrate, C19H18O7
  60. The crystal structure of poly[(μ 4-4,4′-(azanediylbis(methylene))dibenzoato-κ 4 O:N:O′:Oʺ)zinc(II)], C16H13NO4Zn
  61. The crystal structure of catena-poly[(1,10-phenanthroline-k2N,N′)-(μ3-tetraoxidomoybdato(VI)-k3O:O′:O″)manganese(II)] C12H8N2O4MoMn
  62. Crystal structure of catena-poly[(4-hydroxyl-5-(methoylcarbonyl)thiophene-2-carboxylato-κ1 O)-(μ2-piperazine-1,4-diylbis(pyridin-4-ylmethanone)-κ2 N:N′)silver(I)] monohydrate, C23H23AgN4O8S
  63. Crystal structure of bis(4-bromo-2-(((3-bromopropyl)imino)methyl)phenolato-κ2N,O)-oxido-vanadium(IV), C20H20Br4N2O3V
  64. The crystal structure of (2a′S,2a1′S,3R,5a′S,7′R)-5-(furan-3-yl)-2a′,2a1′-dihydroxy-7′-methyldecahydro-2H-spiro[furan-3,6′-naphtho[1,8-bc]furan]-2,2′(2a′H)-dione, C19H22O7
  65. The crystal structure of 3-bromopicolinic acid, C6H4BrNO2
  66. Crystal structure of 1,1′-(1,4-phenylenebis(methylene))bis(pyridin-1-ium) bis(1,2-dicyanoethene-1,2-dithiolato-κ2 S,S) platinum(II), C26H18N6PtS4
  67. Synthesis and crystal structure of 5-(8-((3-carboxyazetidin-1-ium-1-yl)methyl)-7-hydroxy-4-oxo-4H-chromen-3-yl)-2-hydroxybenzenesulfonate monohydrate, C20H19NO10S
  68. The crystal structure of 3-amino-5-carboxypyridin-1-ium bromide, C6H7BrN2O2
  69. The crystal structure of (2-hydroxy-5-methyl-phenyl)-(1H-pyrazol-4-yl)-methanone hemihydrate, C11H10.5N2O2.5
  70. Crystal structure of tetraaqua-(2-(4-formylphenoxy)acetato-k1O)cadmium(II), C18H22O12Cd
  71. Crystal structure of diethyl 6,12-dimethyl-3,9-di-p-tolyl-3,9-diazapentacyclo[6.4.0.02,7.04,11.05,10]dodecane-1,5-dicarboxylate, C32H38N2O4
  72. Crystal structure of (E)-N′-(1-(3-chloro-4-fluorophenyl)ethylidene)-4-hydroxy – tetrahydrofuran (2/1), C17H16ClFN2O2.5
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