Startseite Naturwissenschaften The crystal structure of bis(1H-pyrazole-carboxamidine-κN,N′)bis(nitrato-κO)-copper(II), C8H12CuN10O6
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The crystal structure of bis(1H-pyrazole-carboxamidine-κN,N′)bis(nitrato-κO)-copper(II), C8H12CuN10O6

  • Soňa Kohúteková , Irena Matulková ORCID logo EMAIL logo , Ivana Císařová ORCID logo und Ivan Němec ORCID logo
Veröffentlicht/Copyright: 24. Januar 2023

Abstract

C8H12CuN10O6, triclinic, P 1 (no. 2), a = 7.6063(5) Å, b = 9.3072(7) Å, c = 10.8485(8) Å, α = 81.370(2)°, β = 75.503(2)°, γ = 84.756(2)°, V = 733.97(9) Å3, Z = 2, Rgt(F) = 0.0515, wRref(F2) = 0.1194, T = 120(2) K.

CCDC no.: 2225313

The crystal structure (asymmetric unit and packing (1 0 0)) is shown in the figure. Tables 1 and 2 contain details on crystal structure, data collection conditions and a list of the atoms including atomic coordinates and displacement parameters.

Table 1:

Data collection and handling.

Crystal: Blue prism
Size: 0.07 × 0.05 × 0.03 mm
Wavelength: Mo radiation (0.71073 Å)
μ: 1.55 mm−1
Diffractometer, scan mode: Bruker D8 VENTURE Kappa Duo PHOTONIII CMOS, φ and ω
θmax, completeness: 27.5°, >99%
N(hkl)measured, N(hkl)unique, Rint: 3356, 3356
Criterion for Iobs, N(hkl)gt: Iobs > 2 σ(Iobs), 2965
N(param)refined: 230
Programs: SHELX [1, 2], PLATON [3], Bruker [4, 5]
Table 2:

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

Atom x y z Uiso*/Ueq
Cu1A 0.500000 1.000000 0.000000 0.01559 (18)
N1A 0.2170 (5) 0.8167 (4) 0.0294 (3) 0.0144 (7)
N2A 0.3989 (5) 0.8217 (4) −0.0271 (3) 0.0171 (7)
C3A 0.4426 (6) 0.6993 (4) −0.0807 (4) 0.0164 (8)
H3A 0.561363 0.671493 −0.126762 0.020*
C4A 0.2898 (6) 0.6172 (5) −0.0600 (4) 0.0213 (9)
H4A 0.285468 0.526541 −0.089038 0.026*
C5A 0.1486 (6) 0.6941 (4) 0.0105 (4) 0.0188 (9)
H5A 0.026151 0.667165 0.040470 0.023*
C6A 0.1376 (6) 0.9381 (4) 0.0934 (4) 0.0163 (8)
N7A 0.2487 (5) 1.0363 (4) 0.0890 (3) 0.0173 (7)
H7A 0.213008 1.114296 0.123884 0.026*
N8A −0.0389 (5) 0.9353 (4) 0.1499 (4) 0.0199 (8)
H81A −0.080948 0.997644 0.204020 0.030*
H82A −0.112447 0.849344 0.148120 0.030*
N9A 0.5760 (5) 0.7239 (4) 0.2181 (3) 0.0193 (7)
O1A 0.5187 (5) 0.8514 (3) 0.2350 (3) 0.0239 (7)
O2A 0.4732 (5) 0.6209 (4) 0.2500 (4) 0.0311 (8)
O3A 0.7406 (4) 0.6987 (3) 0.1684 (3) 0.0270 (7)
Cu1B 0.000000 0.000000 0.500000 0.01607 (18)
N1B 0.1536 (5) 0.2482 (4) 0.5346 (3) 0.0159 (7)
N2B 0.2047 (5) 0.1264 (4) 0.4747 (3) 0.0167 (7)
C3B 0.3801 (6) 0.1393 (4) 0.4174 (4) 0.0172 (8)
H3B 0.453771 0.069989 0.368287 0.021*
C4B 0.4420 (6) 0.2685 (5) 0.4391 (4) 0.0209 (9)
H4B 0.561098 0.302674 0.408298 0.025*
C5B 0.2936 (6) 0.3352 (5) 0.5143 (4) 0.0186 (9)
H5B 0.290083 0.425462 0.546043 0.022*
C6B −0.0311 (6) 0.2587 (4) 0.6040 (4) 0.0167 (8)
N7B −0.1264 (5) 0.1520 (4) 0.6005 (3) 0.0171 (7)
H7B −0.248342 0.162707 0.635488 0.026*
N8B −0.0857 (5) 0.3765 (4) 0.6625 (4) 0.0217 (8)
H81B −0.208119 0.380560 0.701969 0.033*
H82B −0.002219 0.458359 0.658174 0.033*
N9B −0.0518 (5) 0.2887 (4) 0.2837 (4) 0.0195 (7)
O1B 0.0965 (5) 0.3077 (4) 0.2062 (3) 0.0286 (8)
O2B −0.1335 (4) 0.3870 (3) 0.3471 (3) 0.0247 (7)
O3B −0.1184 (5) 0.1645 (3) 0.3054 (3) 0.0268 (8)

Source of material

1H-Pyrazole carboxamidine hydrochloride (0.10 g; 0.68 mmol; Sigma-Aldrich, 99%) was dissolved in 5 ml of water and stoichiometric amount of silver(I) carbonate (0.094 g; 0.34 mmol; Sigma Aldrich, 99%) was added to the solution. This suspension was stirred approximately 30 min at room temperature until the dark precipitate of silver(I) chloride occurred. Insoluble silver(I) chloride was filtered off using glass frit S4 and the colourless filtrate was spilled into the beaker with copper(II) nitrate trihydrate (0.082 g; 0.34 mmol; Lachema, pure). After two days of crystallisation at room temperature the dark blue product was isolated and characterised. FTIR (Diamond ATR), cm−1: 3373w, 3265m (ν NH), 3146m (ν CH), 3131m (ν CH), 1689s (ν CN3, δ NH2), 1621m (δ NH2), 1534m (δ NH2), 1496m (ν rg, δ CH), 1427sh, 1399s (δ CN3, δ CH), 1372s (ν3 N O 3 ), 1349s (ν3 N O 3 ), 1276m, 1230m, 1124w, 1081m (δ NH2, δ CH), 1072w (δ NH, δ CH), 1051w (ν1 N O 3 ), 986m, 934w, 919w (δ rg, δ CH), 879w, 824m (ν2 N O 3 ), 784m (γ CH), 749w, 723w, 593m (γ rg, γ CN3), 567sh, 534m, 364vw, 349w (ν Cu–O), 235vw, 170w. FT Raman (1064 nm excitation), cm−1: 3260w (ν NH), 3147w (ν CH), 3127w (ν CH), 3114w (ν CH), 1689w (ν CN3, δ NH2), 1621w (δ NH2), 1536w (δ NH2), 1492m (ν rg, δ CH), 1426w, 1403m (δ CN3, δ CH), 1376w (ν3 N O 3 ), 1341m, 1267m, 1226m, 1123w, 1088m (δ NH, δ CH), 1075m (δ NH, δ CH), 1051vs (ν1 N O 3 ), 984w, 917m (δ rg, δ CH), 890vw, 735w (ν4 N O 3 ), 722sh, 708w, 632w, 586m (γ rg, γ CN3), 524w, 340vw (ν Cu–O), 251m, 185m, 134s.

Experimental details

The diffraction experiment for the title structure was performed on Bruker D8 VENTURE Kappa Duo PHOTONIII by IμS micro-focus sealed tube with MoKα (0.71073 Å) radiation at temperature of the sample 120 K. The structure was solved by Direct Methods (XT) [1] and refined by full matrix least squares based on F2 (SHELXL 2018) [2]. The hydrogen atoms on carbon were fixed into idealised positions (riding model) and assigned temperature factors Hiso(H) = 1.2 Ueq (pivot atom), the hydrogen atoms on nitrogen were found on difference Fourier map and kept during refinement under the assumption of rigid-body movement with temperature factor Hiso(H) = 1.5 Ueq (pivot atom). All crystals tested on the diffractometer exhibit extensive twinning [6] and only a very small one could be described as just two component pseudo-merohedral twin. The twin matrix: 0 −0.5 −0.5; −1 −0.5 0.5; −1 0.5 −0.5, refined ratio of twin 0.76:0.24.

X-ray crystallographic data have been deposited with the Cambridge Crystallographic Data Centre (CCDC) as supplementary publication CCDC 2225313 and can be obtained free of charge from the centre via its website (www.ccdc.cam.ac.uk/getstructures).

Comment

The design of novel materials for nonlinear optics (NLO) based on polarizable organic molecules successfully uses several approaches ranging from cocrystallisation with selected hydrogen-bonded anions [7] to utilisation of metal-organic frameworks (MOFs) formation [8]. These crystal engineering approaches involving especially hydrogen bonds formation [9] increase the probability of obtaining desired non-centrosymmetric arrangement of prepared crystal structures. The inspiring work of Hu et al. [10] described preparation of MOFs containing frameworks built by formic acid coordinated to cations of transition metals with incorporated guanidinium cations in the cavities. The product with copper (II) cation exhibits Jahn–Teller effect leading to non-centrosymmetric arrangement of the whole crystal structure. We decided to prepare an analogous product in which guanidinium cations, - successful carriers of NLO properties [11], [12], [13], will be replaced by related planar polarizable molecule of 1H-pyrazole carboxamidine (pcam). However, contrary to our expectations, the reaction resulted in a completely different product which is described in this paper. We have consequently optimised the reaction (by removing the unnecessary formic acid from the reactants) to obtain single crystals of sufficient quality.

The asymmetric unit of the title structure contains two coordination spheres in form of tetragonal bipyramids around copper (II) cations (upper part of the figure). Planar pcam molecules are bidentately coordinated to central ions in the equatorial positions of each bipyramid. Observed lengths of Cu–N coordination bonds are ranging from 1.938(3) to 1.981(3) Å. The nitrogen atom of the pyrazole ring is involved in a slightly longer Cu–N bond compared to Cu–N bond involving the nitrogen atom of the carboxamidine fragment. The axial positions of the coordination bipyramids are occupied by oxygen atoms of unidentately coordinated nitrate anions. The lengths of Cu–O coordination bonds are ranging from 2.742 Å (coordination sphere of Cu1A) to 2.710 Å (coordination sphere of Cu1B). The geometry of Cu(II) coordination polyhedra reflects the presence of two types of donor atoms and is also consistent with expected influence of the Jahn–Teller distortion.

The bonding C–N distances (ranging from 1.288(6) to 1.423(6) Å) and the interatomic N–C–N angles (ranging from 114.8(4) to 128.7(4)°) in the carboxamidine fragment of pcam ligand indicate slight deformation of sp2 hybridization geometry of C6A and C6B atoms. The crystal packing involves an extensive network of N–H···O and C–H···O hydrogen bonds (lower part of the figure).


Corresponding author: Irena Matulková, Department of Inorganic Chemistry, Faculty of Science, Charles University, Hlavova 2030/8, 128 43 Praha 2, Czech Republic, E-mail:

Funding source: CUCAM Centre of Excellence

Award Identifier / Grant number: CZ.02.1.01/0.0/0.0/15_003/0000417

Funding source: Grant Agency of Charles University in Prague

Award Identifier / Grant number: 406922

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

  2. Research funding: Financial support from the Ministry of Education Youth and Sports, CUCAM Centre of Excellence (OP VVV “Excellent Research Teams” project No. CZ.02.1.01/0.0/0.0/15_003/0000417) and Grant Agency of Charles University (Grant No. 406922) are gratefully acknowledged.

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

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Received: 2022-12-14
Accepted: 2023-01-10
Published Online: 2023-01-24
Published in Print: 2023-04-25

© 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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  60. Crystal structure of bis(2,5,5,7-tetramethyl-1,4-diazepane-1,4-diium) diaqua-bis(1,2-diaminopropane)copper(II) bis(μ6-oxido)tetrakis(μ3-oxido)-tetradecakis(μ2-oxido)-octaoxido-decavanadium(V) – water (1/4), C24H76CuN8V10O34
  61. Crystal structure of 1,2,3,5,13-pentamethoxy-6,7-dimethyl-1,2,3,4,4a,5,6,7,8,13b-decahydrobenzo[3′,4′]cycloocta[1′,2′:4,5]benzo[1,2-d][1,3]dioxole, C24H30O7
  62. Crystal structure of bis(6-carboxyhexyl)-4,4′-bipyridinium dibromide – 2,6-dihydroxynaphthalene (1/2), C42H46Br2N2O8
  63. Crystal structure of methyl 2-(2-chloroacetyl)-1-(4-(methoxycarbonyl)phenyl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b] indole-3-carboxylate, C23H21ClN2O5
  64. Crystal structure of bis(dimethylammonium) poly[{μ4-1,1ʹ-(1,4-phenylenebis(methylene))bis(1H-pyrazole-3,5-dicarboxylato)-κ6N4O2}zinc(II)], C22H26N6O8Zn
  65. Crystal structure of 2-(2-(4-methoxyphenyl)-2H-indazol-3-yl)acetonitrile, C16H13N3O
  66. Crystal structure of (E)-7-methoxy-2-(4-morpholinobenzylidene)-3,4-dihydronaphthalen-1(2H)-one, C22H23NO3
  67. The crystal structure of N′1,N′2-bis((E)-3-(tert-butyl)-2-hydroxybenzylidene)oxalohydrazide, C24H30N4O4
  68. The crystal structure of trimethyl 2,2′,2′′-(benzene-1,3,5-triyltris(oxy))triacetate, C15H18O9
  69. Crystal structure of bis(N,N-dimethylformamide-κO)-bis(pyridine-2-carboxylato-κ2N,O)-bis(μ2-pyridine-2-carboxylato-κ2N,O)-dinickel(II), C30H30N6Ni2O10
  70. Crystal structure of bis(μ2-1-pyrenecarboxylato-κ3O,O′:O′)-bis(1-pyrenecarboxylato-κ2O,O′)-(benzimidazole-κ1N)dicadmium(II), C82H48Cd2N4O8
  71. One-pot synthesis and crystal structure of diethyl 2,6-dimethyl-4-(1-(2-nitrophenyl)-1H-1,2,3-triazol-4-yl)-1,4-dihydropyridine-3,5-dicarboxylate, C21H23N5O6
  72. The crystal structure of 1-(2-fluorobenzoyl)-5-methoxy-2-methyl-1H-indole-3-carbonitrile, C18H13FN2O2
  73. Crystal structure of bis(trimethylphenylammonium) aqua-oxido-octathiotritungstate, (Me3PhN)2[W3OS8(H2O)]
  74. The crystal structure of trichlorido[N-[(2-oxyphenyl)methylidene]phenylglycinemethylester-κ3O,N,O′]-tin(IV) – methylene chloride (1/1), C16H14Cl3NO3Sn·CH2Cl2
  75. The crystal structure of furan-2,5-diylbis((4-chlorophenyl)methanol), C18H14Cl2O3
  76. The crystal structure of hexalithium decavanadate hexadecahydrate, H32Li6O44V10
  77. Crystal structure of ethyl 4-{[5-(adamantan-1-yl)-2-sulfanylidene-2,3-dihydro-1,3,4-oxadiazol-3-yl]methyl}piperazine-1-carboxylate, C20H30N4O3S
  78. Crystal structure of aqua(μ2-2,2′,2″-((nitrilo)tris(ethane-2,1-diyl(nitrilo)methylylidene))tris (6-ethoxyphenolato))(pentane-2,4-dionato-κ2O,O′)-dinickel(II), C38H48N4Ni2O9
Heruntergeladen am 4.2.2026 von https://www.degruyterbrill.com/document/doi/10.1515/ncrs-2022-0586/html
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