Home The crystal structure of cis-diaqua-bis (N-butyl-N-(pyridin-2-yl)pyridin-2-amine-κ2N,N′)cobalt(II)] dichloride trihydrate, C28H44Cl2N6O5Co
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The crystal structure of cis-diaqua-bis (N-butyl-N-(pyridin-2-yl)pyridin-2-amine-κ2N,N′)cobalt(II)] dichloride trihydrate, C28H44Cl2N6O5Co

  • Orbett T. Alexander ORCID logo EMAIL logo , Roger Alberto and Andreas Roodt
Published/Copyright: July 14, 2021

Abstract

C28H44Cl2N6O5Co, triclinic, P 1 (no. 2), a = 11.20(2) Å, b = 12.70(3) Å, c = 12.80(4) Å, α = 100.30(12)°, β = 103.18(9)°, γ = 106.77(6)°, V = 1638(8) Å3, Z = 2, R gt (F) = 0.0372, wR ref (F2) = 0.0890, T = 100 K.

CCDC no.: 2086847

The molecular structure is shown in figure (the chloride counter anions and uncoordinated water molecules are omitted for clarity). 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: Colourless cuboid
Size: 0.27 × 0.22 × 0.16 mm
Wavelength: Mo Kα radiation (0.71073 Å)
μ: 0.73 mm−1
Diffractometer, scan mode: Bruker Apex-II, φ and ω
θmax, completeness: 28.6°, >99%
N(hkl)measured, N(hkl)unique, Rint: 26,921, 8038, 0.049
Criterion for Iobs, N(hkl)gt: Iobs > 2σ(Iobs), 6746
N(param)refined: 421
Programs: Bruker [1], SIR97 [2], WinGX [3], Shelx [4], Diamond [5]
Table 2:

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

Atom x y z Uiso*/Ueq
C1 0.44687(18) 0.21909(17) 0.34586(16) 0.0219(4)
H1 0.437968 0.291082 0.344727 0.026*
C2 0.36548(19) 0.14787(18) 0.38800(17) 0.0277(4)
H2 0.303145 0.170000 0.417329 0.033*
C3 0.37728(19) 0.04307(18) 0.38632(17) 0.0277(4)
H3 0.322273 −0.009110 0.414668 0.033*
C4 0.46914(19) 0.01331(17) 0.34342(16) 0.0232(4)
H4 0.476677 −0.059649 0.341019 0.028*
C5 0.55030(17) 0.09108(15) 0.30388(14) 0.0176(3)
C6 0.65536(16) 0.07428(15) 0.15508(15) 0.0169(3)
C7 0.65246(17) −0.01831(15) 0.07429(15) 0.0191(4)
H7 0.640584 −0.090435 0.089785 0.023*
C8 0.66678(17) −0.00493(16) −0.02730(15) 0.0208(4)
H8 0.664981 −0.067276 −0.081922 0.025*
C9 0.68366(17) 0.09999(16) −0.04821(15) 0.0200(4)
H9 0.696205 0.112818 −0.116441 0.024*
C10 0.68174(17) 0.18639(15) 0.03383(15) 0.0178(3)
H10 0.689847 0.258200 0.018501 0.021*
C11 0.69594(19) −0.02121(16) 0.30369(16) 0.0218(4)
H11A 0.643870 −0.098037 0.253643 0.026*
H11B 0.684834 −0.020932 0.378278 0.026*
C12 0.83923(19) 0.00300(16) 0.31130(17) 0.0239(4)
H12A 0.852723 0.016742 0.240425 0.029*
H12B 0.892490 0.073398 0.371081 0.029*
C13 0.8862(2) −0.0927(2) 0.3346(2) 0.0365(5)
H13A 0.832480 −0.163421 0.275422 0.044*
H13B 0.874393 −0.105671 0.406135 0.044*
C14 1.0291(2) −0.0673(2) 0.3401(3) 0.0487(7)
H14A 1.040989 −0.056057 0.268893 0.073*
H14B 1.055558 −0.131489 0.355519 0.073*
H14C 1.082908 0.001901 0.399539 0.073*
C15 0.83187(19) 0.31527(16) 0.47229(15) 0.0208(4)
H15 0.751412 0.306097 0.488534 0.025*
C16 0.9373(2) 0.31636(16) 0.55451(16) 0.0243(4)
H16 0.928799 0.306468 0.624612 0.029*
C17 1.0552(2) 0.33221(17) 0.53185(17) 0.0269(4)
H17 1.129187 0.332552 0.586001 0.032*
C18 1.06387(18) 0.34758(17) 0.42907(17) 0.0244(4)
H18 1.144667 0.360566 0.412734 0.029*
C19 0.95238(17) 0.34384(15) 0.34905(15) 0.0177(3)
C20 0.91515(17) 0.43934(15) 0.20201(14) 0.0176(3)
C21 0.99754(19) 0.51915(16) 0.16566(16) 0.0227(4)
H21 1.083005 0.519026 0.168582 0.027*
C22 0.9532(2) 0.59821(17) 0.12544(17) 0.0280(4)
H22 1.007423 0.652870 0.098787 0.034*
C23 0.8286(2) 0.59823(17) 0.12373(17) 0.0269(4)
H23 0.796912 0.653197 0.097105 0.032*
C24 0.75329(19) 0.51762(16) 0.16112(15) 0.0217(4)
H24 0.668243 0.517561 0.160271 0.026*
C25 1.05597(18) 0.32351(16) 0.19778(17) 0.0222(4)
H25A 1.144388 0.370681 0.247691 0.027*
H25B 1.049360 0.338889 0.123906 0.027*
C26 1.03853(19) 0.19962(16) 0.18676(18) 0.0247(4)
H26A 0.946759 0.152703 0.144892 0.030*
H26B 1.056676 0.186184 0.261697 0.030*
C27 1.1294(2) 0.16229(18) 0.12673(18) 0.0285(4)
H27A 1.219657 0.216334 0.162739 0.034*
H27B 1.128310 0.086180 0.135547 0.034*
C28 1.0923(3) 0.1567(2) 0.0033(2) 0.0398(6)
H28A 1.148355 0.125078 −0.031284 0.060*
H28B 1.103878 0.233584 −0.006140 0.060*
H28C 1.000858 0.107930 −0.032088 0.060*
Cl1 0.47781(5) 0.31888(4) −0.11558(4) 0.02823(11)
Cl2 0.64532(5) 0.43755(5) 0.60652(4) 0.03053(12)
Co1 0.66479(2) 0.31584(2) 0.25061(2) 0.01468(7)
H1A 0.493(2) 0.307(2) 0.066(2) 0.035(7)*
H1B 0.452(3) 0.357(3) 0.145(3) 0.062(9)*
H2A 0.643(2) 0.448(2) 0.428(2) 0.030(6)*
H2B 0.639(3) 0.509(3) 0.358(2) 0.051(9)*
H3A 0.386(3) 0.501(3) 0.128(2) 0.049(8)*
H3B 0.359(3) 0.476(3) 0.215(3) 0.056(9)*
H4A 0.562(3) 0.643(2) 0.377(2) 0.053(9)*
H4B 0.615(3) 0.670(2) 0.302(3) 0.048(8)*
H5A 0.683(3) 0.298(3) −0.284(2) 0.046(9)*
H5B 0.635(4) 0.285(3) −0.200(3) 0.087(12)*
N1 0.53957(14) 0.19313(13) 0.30556(12) 0.0175(3)
N2 0.64645(15) 0.06351(13) 0.26165(12) 0.0181(3)
N3 0.66903(14) 0.17531(12) 0.13467(12) 0.0154(3)
N4 0.83724(14) 0.32653(12) 0.37037(12) 0.0167(3)
N5 0.95761(15) 0.35721(13) 0.24248(13) 0.0188(3)
N6 0.79397(15) 0.43790(13) 0.19929(12) 0.0176(3)
O1 0.49629(13) 0.31181(12) 0.13010(12) 0.0216(3)
O2 0.64032(14) 0.44669(12) 0.36299(12) 0.0225(3)
O3 0.35491(15) 0.44747(13) 0.15145(14) 0.0269(3)
O4 0.63318(15) 0.65980(13) 0.36378(13) 0.0263(3)
O5 0.6914(2) 0.26774(17) −0.2365(2) 0.0541(5)

Source of material

To a stirred solution of N-butyl-N-(pyridin-2-yl)pyridin-2-amine (nBut-DPA) (50 mg, 0.2 mmol) in methanol/water (80/20 ratio), a stoichiometric amount of sodium hydroxide (NaOH) was added at room temperature. After stirring for ca. 10 min, a solution of cobalt(II) chloride (52.3 mg, 0.2 mmol) was added drop-wise over 5 min. The reaction was left to stir for another hour. The reaction mixture was filtered and dried in vacuo. The dried product yielded reddish crystals, from a methanol/DCM solvent mixture, suitable for X-ray diffraction analysis.

Experimental details

The aromatic H atoms were placed in geometrically idealized positions and constrained to ride on their parent atoms, with C–H = 0.95 and 0.98 Å and Uiso(H) = 1.5 Ueq(C) and 1.2 Ueq(C), respectively. The placement of the H atoms on the butyl groups was that of an idealised methylene and methyl group according to the electron-density map (HFIX 23, 137).

Comment

The use of organometallic complexes across many scientific disciplines, in attempt to analyse potential synergistic effects therein, has become a norm. Moreover, derivatizing organic compounds as ligand systems has become a necessity to allow appropriate functionalities to be built-in [6], [7], [8], [9]. Herein, N-butyl-N-(pyridin-2-yl)pyridin-2-amine (nBut-DPA), a derivative of 2,2′-dipyridylamine is used. This ligand and its derivative analogs with metal centres have been found to be efficient in many biological media [10], [11], [12]. Its complexes with different transition metal ions cover broad scientific fields [12], [13], [14], [15], [16], [17].

The crystal structure is comprised of two nBut-DPA bidentate ligands inducing a distorted octahedral coordination mode to a cobalt(II) metal ion. Furthermore, there are two coordinated aqua ligands in a cis configuration completing the distorted octahedral molecular geometry for the tittle structure. In the second coordination sphere, there are further three water molecules and two charge balancing chloride anions in the asymmetric unit. The structure is further held in tact by intramolecular hydrogen interactions between the water (O1 and O2) molecules in the first coordination sphere and the chloride anions (Cl1 and Cl2) and other water molecules (O3, O4 and O5) in the second coordination sphere.


Corresponding author: Orbett T. Alexander, Department of Chemistry, Tshwane University of Technology, 0001 Pretoria, South Africa, E-mail:

Funding source: Swiss National Science Foundation 10.13039/501100001711

Award Identifier / Grant number: IZLSZ2_149029/1

Funding source: South African National Research Foundation (NRF)

Funding source: Research Fund of the University of the Free State

Funding source: Swiss-South Africa joint research program (SSAJRP)

Award Identifier / Grant number: 107802

Funding source: Competitive Program for Rated Researchers

Award Identifier / Grant number: 111698

Acknowledgements

RAA thanks the Swiss National Science Foundation (SNF Project IZLSZ2_149029/1 within the SSAJRP program), while AR and OTA acknowledge financial assistance from the South African National Research Foundation (NRF), and the Research Fund of the University of the Free State. This includes funding under the Swiss-South Africa joint research program (SSAJRP) from the SA NRF (AR: UID: 107802) as well as from the Competitive Program for Rated Researchers of the SA NRF (AR: UID 111698). Opinions, findings, conclusions, or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the NRF nor the SNF.

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

  2. Research funding: Swiss National Science Foundation (SNF Project IZLSZ2_149029/1 within the SSAJRP program), South African National Research Foundation (NRF), and the Research Fund of the University of the Free State, Swiss-South Africa joint research program (SSAJRP) from the SA NRF (AR: UID: 107802), Competitive Program for Rated Researchers of the SA NRF (AR: UID 111698).

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

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Received: 2021-06-01
Accepted: 2021-06-28
Published Online: 2021-07-14
Published in Print: 2021-09-27

© 2021 Orbett T. Alexander 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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  40. Crystal structure of 3-(2-ethoxy-2-oxoethyl)-1-ethyl-1H-imidazol-3-ium hexafluoridophos-phate(V), C9H15F6N2O2P
  41. Crystal structure of (1,10-phenanthroline-κ2N,N′)-bis(3-thiophenecarboxylato-κ2O,O′)copper(II), C22H14N2O4S2Cu
  42. The crystal structure of 2-amino-3-carboxypyridin-1-ium iodide hemihydrate, C6H8IN2O2.5
  43. Crystal structure of (E)-7-methoxy-2-((6-methoxypyridin-2-yl)methylene)-tetralone, C18H17NO3
  44. The crystal structure of [μ-hydroxido-bis[(5,5′-dimethyl-2,2′-bipyridine-κ2N,N′)-tricarbonylrhenium(I)] bromide hemihydrate, C30H26N4O9Re2Br
  45. The crystal structure of 2,5-bis(3,5-dimethylphenyl)thiazolo[5,4-d]thiazole, C20H18N2S2
  46. The crystal structure of 5-benzoyl-1-[(E)-(4-fluorobenzylidene)amino]-4-phenylpyrimidin-2(1H)-one, C24H16FN3O2
  47. Crystal structure of monocarbonyl(N-nitroso-N-oxido-phenylamine-κ 2 O,O′)(tricyclohexylphosphine-κP)rhodium(I), C25H39N2O3PRh
  48. Crystal structure of poly[bis[μ3-1,3,5-tris[(1H-imidazol-1-yl)methyl]benzene-κ3N:N′:N″]nickel(II)] hexafluorosilicate, C36H36N12NiSiF6
  49. The crystal structure of 13-(pyrazole-1-yl-4-carbonitrile)-matrine, C19H25N5O
  50. Crystal structure of 3,5-bis((E)-4-methoxy-2-(trifluoromethyl)benzylidene)-1-methylpiperidin-4-one, C24H21F6NO3
  51. The crystal structure of N,N′-(Disulfanediyldi-2,1-phenylene)di(6′-methylpyridine)-2-carboxamide, C26H22N4O2S2
  52. Crystal structure of (E)-7-fluoro-2-(4-methoxy-2-(trifluoromethyl)benzylidene)-3,4-dihydronaphthalen-1(2H)-one, C19H14F4O2
  53. Crystal structure of ethyl 1-(4-fluorophenyl)-4-phenyl-1H-pyrrole-3-carboxylate, C19H16FNO2
  54. The crystal structure of cis-diaqua-bis (N-butyl-N-(pyridin-2-yl)pyridin-2-amine-κ2N,N′)cobalt(II)] dichloride trihydrate, C28H44Cl2N6O5Co
  55. Crystal structure of (E)-7-methoxy-2-((6-methoxypyridin-3-yl)methylene)-3,4-dihydronaphthalen-1(2H)-one, C18H17NO3
  56. Crystal structure of (E)-2-((3-fluoropyridin-4-yl)methylene)-7-methoxy-3,4-dihydronaphthalen-1(2H)-one, C17H14FNO2
  57. The crystal structure of 6-bromohexanoic acid, C6H11BrO2
  58. The crystal structure of 4-chloro-thiophenol, C6H5ClS
  59. The crystal structure of 4-bromobenzyl chloride, C7H6BrCl
  60. The crystal structure of di-tert-butyl dicarbonate, C10H18O5
  61. The crystal structure of (2-(4-chlorophenyl)-5-methyl-1,3-dioxan-5-yl)methanol, C12H15ClO3
  62. The crystal structure of the co-crystal: 2-hydroxybenzoic acid – N′-(butan-2-ylidene)pyridine-4-carbohydrazide, C10H13N3O·C7H6O3
  63. Crystal structure and anti-inflammatory activity of (E)-7-fluoro-2-((5-methoxypyridin-3-yl)methylene)-3,4-dihydronaphthalen-1(2H)-one, C17H14FNO2
  64. Crystal structure of (E)-7-fluoro-2-((6-methoxypyridin-3-yl)methylene)-3,4-dihydronaphthalen-1(2H)-one, C17H14FNO2
  65. Crystal structure of 1,1′-(butane-1,4-diyl)bis(3-propyl-1H-imidazol-3-ium) bis(hexafluoridophosphate), C32H56F24N8P4
  66. The crystal structure of dichlorido-bis(3-methyl-3-imidazolium-1-ylpropionato-κ2)-cadmium(II), C14H20CdCl2N4O4
  67. Crystal structure of 1-(2-cyanobenzyl)-3-cyano-4-phenyl-4-(2-cyanobenzyl)-1,4-dihydropyridine monohydrate, C56H42N8O
  68. The crystal structure of 3-(carboxymethyl)-1-ethenyl-1H-imidazol-3-ium chloride, C7H9N2O2Cl
  69. The crystal structure of adamantylmethoxydiphenylsilane, C23H28OSi
  70. Redetermination of the crystal structure of (2E,4Z,13E,15Z)-3,5,14,16-tetramethyl-2,6,13,17-tetraazatricyclo[16.4.0.07,12]docosa-1(22),2,4,7,9,11,13,15,18,20-decaene, C22H24N4
  71. Crystal structure of (E)-7-hydroxy-2-((6-methoxypyridin-2-yl)methylene)-3,4-dihydronaphthalen-1(2H)-one, C17H15NO3
  72. Crystal structure of catena-poly[diaqua-bis(μ2-1,3-di(1H-imidazol-1-yl)propane-κ2 N:N′)cobalt(II)] dinitrate, C18H28N10O8Co
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