research communications
and Hirshfeld surface analysis of bis(2,6-diaminopyridinium) tetrachloridocobaltate(II)
aUniversity of Tunis El Manar, Faculty of Sciences of Tunis, Laboratory of Materials, Crystal Chemistry and Applied Thermodynamics, 2092 El Manar II, Tunis, Tunisia, and bUniversity of Tunis, Preparatory Institute for Engineering Studies of Tunis, Street Jawaher Lel Nehru, 1089 Montfleury, Tunis, Tunisia
*Correspondence e-mail: medfaouzi.zid57@gmail.com
In the title molecular salt, (C5H8N3)2[CoCl4], the cations are protonated at their pyridine N atoms and the anion is an almost regular tetrahedron. The consists of alternating inorganic layers, built from tetrachloridocobaltate anions, and organic layers formed by protonated cations of 2,6-diaminopyridinium. The crystal packing is governed by C/N—H⋯Cl hydrogen-bonding interactions between the organic and the inorganic ions and Cl⋯Cl interactions. Moreover, the cations show a π–π stacking interaction [intercentroid distance = 3.763 (2) Å]. The prevalence of these interactions is illustrated by an analysis of the three-dimensional Hirshfeld surface and by two-dimensional fingerprint plots.
Keywords: cobalt(II); hybrid organic–inorganic materials; crystal structure; Hirshfeld surface; fingerprint plots.
CCDC reference: 1588020
1. Chemical context
One of the best studied groups of organic–inorganic hybrid materials are the cobalt(II) halide compounds because of their important properties such as fluorescence and magnetism (Decaroli et al., 2015; Kurmoo, 2009). The coordination sphere of CoII is variable, leading to different geometries including octahedral, tetrahedral, square pyramidal, trigonal bipyramidal and square planar (Kurmoo, 2009). Pyridine as an organic heterocyclic molecule has various biological activities (Sellin, 1981; Davidson et al., 1988). As part of our studies in this area, the title compound, (C5H8N3)2[CoCl4] (I), has been investigated.
2. Structural commentary
The is made up of one tetrachloridocobaltate, [CoCl4]2−, anion and two protonated 2,6-diaminopyridinium, (C5H8N3)+, organic cations (Fig. 1). The geometry of the CoCl4 anion is characterized by a range of Co—Cl bond length from 2.2595 (14) to 2.2795 (13) Å and Cl—Co—Cl angles varying from 106.44 (5) to 112.69 (5)°, building a slightly distorted tetrahedron. These data are in agreement with those found in related compounds (Mghandef & Boughzala, 2015). The calculated average values of the distortion indice as described by Baur (1974) corresponding to the different lengths and angles in the CoCl4 tetrahedra [ΔI(Co—Cl) = 0.004 and ΔI(Cl—Co—Cl) = 0.0019] show a slight distortion of the tetrahedra. The interanionic Cl⋯Cl contact distances between the nearest neighbor tetrahedra are 3.986 (2) Å along the a axis and 3.889 (2) Å along the c axis (Fig. 2), compared to a van der Waals contact distance of 3.50 Å. These contacts are sometimes associated with weak antiferromagnetic interactions (Shapiro et al., 2007), which decrease rapidly with increasing Cl⋯Cl separation.
of (I)Pyridinium cations always possess an expanded angle of C—N—C in comparison with the parent pyridine (Ben Nasr et al., 2015). Thus, the observed angles in (I) of C1—N2—C5 and C6—N5—C10 are 124.2 (3) and 124.1 (3)°, respectively, are wider than that in neutral pyridine (116.6°), indicating that protonation takes place on the pyridine ring N2 and N5 atoms. Accordingly, within the cations, we note that the N—C and C—C distances range from 1.332 (5) to 1.393 (6) Å, while the C—C—C, N—C—N, C—C—N and N—C—C angles vary from 116.00 (4) to 126.50 (4)°. The 2,6-diaminopyridinium units are essentially planar, with an r.m.s. deviation from the mean plane of 0.002 and 0.006 Å for the N2 and N5 species, respectively.
3. Supramolecular features
Examination of the reveals organic layers parallel to the ab plane made of 2,6-diaminopyridinium cations alternating with inorganic layers formed by tetrachloridocobaltate anions (Fig. 3), which is similar to those of related materials: (C5H6Br2N3)2[MBr4] (M = Cd, Mn) (Al-Far et al., 2009) and (C5H7N2)2[CoBr4] (Mhadhbi et al., 2016).
of (I)The construction of the three-dimensional architecture is consolidated by N—H⋯Cl and C—H⋯Cl hydrogen bonds (Table 1), generating R22(4), R22(6), R21(6), R44(8) and R22(8) graph-set motifs (Fig. 4).
As can be seen from Fig. 5, the two nearest neighboring anti-parallel organic cations, which are not connected by hydrogen bonding, are stacked in a face-to-face mode. The centroid–centroid distance is 3.762 (5) Å, slightly less than 3.8 Å, which is the maximum value accepted for π–π interactions (Ben Hassen et al., 2017; Janiak, 2000).
4. Hirshfeld surface analysis
The Hirshfeld surface (Spackman & Jayatilaka, 2009) and the associated two-dimensional fingerprint plots were performed with CrystalExplorer (Wolff et al., 2012). The Hirshfeld surface of the title compound mapped over dnorm is illustrated in Fig. 6. The red spots correspond to the H⋯Cl close contacts, which are due to the N—H⋯Cl hydrogen bonds. Similarly, the presence of H⋯Cl contacts (due to C—H⋯Cl hydrogen bonds) are indicated by a light-red color. The white areas correspond to the places where the distance separating neighboring atoms are close to the sum of the van der Waals radius of the considered atoms and indicate H⋯H interactions. The bluish areas illustrate areas where neighboring atoms are too far apart for there to be interactions between them. In the shape-index map (Fig. 7), the adjacent red and blue triangle-like patches show concave regions that indicate π–π stacking interactions (Bitzer et al., 2017).
The fingerprint plots of (I) (Fig. 8a) (Parkin et al., 2007; Rohl et al., 2008), reveal that the main intermolecular interactions with the highest percentage contributions are: H⋯Cl/Cl⋯H (41.6%, Fig. 8b), H⋯H (30.8%, Fig. 8c) and C⋯H/H⋯C (11.3%, Fig. 8d).
Fig. 9 shows the voids (Wolff et al., 2012) in the of (I). These are based on the sum of spherical atomic electron densities at the appropriate nuclear positions (procrystal electron density). The crystal voids calculation (results under 0.002 a.u. isovalue) shows the void volume of title compound to be of the order of 172 Å3 and surface area in the order of 648 Å2. With the porosity, the calculated void volume of (I) is 10%. There are no large cavities. We note that the electron-density isosurfaces are not completely closed around the components, but are open at those locations where interspecies approaches are found, e.g. N—H⋯Cl and C—H⋯Cl.
5. Synthesis and crystallization
2,6-diaminopyridine and CoCl2·6H2O (molar ratio 1:1) were dissolved in 10 ml of methanol; 3 ml of hydrochloric acid (37%) was added dropwise to the mixture and the resulting blue solution was put aside for crystallization at room temperature. After two weeks, blue crystals of (I) were recovered.
6. Refinement
Crystal data, data collection and structure . All hydrogen atoms were found in a difference-Fourier map and refined isotropically.
details are summarized in Table 2
|
Supporting information
CCDC reference: 1588020
https://doi.org/10.1107/S2056989018003171/hb7732sup1.cif
contains datablock I. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989018003171/hb7732Isup2.hkl
Data collection: CAD-4 EXPRESS (Duisenberg, 1992; Macíček & Yordanov, 1992); cell
CAD-4 EXPRESS (Duisenberg, 1992; Macíček & Yordanov, 1992); data reduction: XCAD4 (Harms & Wocadlo, 1995); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015); molecular graphics: DIAMOND (Brandenburg, 2006); software used to prepare material for publication: WinGX (Farrugia, 2012) and publCIF (Westrip, 2010).(C5H8N3)2[CoCl4] | F(000) = 852 |
Mr = 421.02 | Dx = 1.616 Mg m−3 Dm = 1.616 Mg m−3 Dm measured by ? |
Monoclinic, P21/n | Mo Kα radiation, λ = 0.71073 Å |
a = 7.390 (4) Å | Cell parameters from 25 reflections |
b = 15.373 (4) Å | θ = 10.1–14.9° |
c = 15.387 (4) Å | µ = 1.61 mm−1 |
β = 98.203 (4)° | T = 293 K |
V = 1730.1 (11) Å3 | Parallelepiped, blue |
Z = 4 | 0.4 × 0.3 × 0.1 mm |
Enraf–Nonius CAD-4 diffractometer | 2396 reflections with I > 2σ(I) |
Radiation source: fine-focus sealed tube | Rint = 0.038 |
Graphite monochromator | θmax = 27.0°, θmin = 2.7° |
ω/2θ scans | h = −9→1 |
Absorption correction: ψ scan (North et al., 1968) | k = −1→19 |
Tmin = 0.777, Tmax = 0.998 | l = −19→19 |
4367 measured reflections | 2 standard reflections every 120 reflections |
3770 independent reflections | intensity decay: 1% |
Refinement on F2 | Hydrogen site location: difference Fourier map |
Least-squares matrix: full | All H-atom parameters refined |
R[F2 > 2σ(F2)] = 0.044 | w = 1/[σ2(Fo2) + (0.0522P)2] where P = (Fo2 + 2Fc2)/3 |
wR(F2) = 0.110 | (Δ/σ)max = 0.001 |
S = 1.01 | Δρmax = 0.37 e Å−3 |
3770 reflections | Δρmin = −0.42 e Å−3 |
255 parameters | Extinction correction: SHELXL2014 (Sheldrick, 2015), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 |
0 restraints | Extinction coefficient: 0.0049 (8) |
Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes. |
x | y | z | Uiso*/Ueq | ||
Co1 | 0.44824 (7) | 0.51081 (3) | 0.73764 (3) | 0.03878 (16) | |
Cl1 | 0.66787 (14) | 0.61509 (6) | 0.73884 (6) | 0.0497 (2) | |
Cl2 | 0.36703 (14) | 0.46854 (6) | 0.59572 (6) | 0.0500 (3) | |
Cl3 | 0.20113 (14) | 0.56398 (7) | 0.79102 (6) | 0.0547 (3) | |
Cl4 | 0.58007 (17) | 0.39816 (6) | 0.81784 (7) | 0.0627 (3) | |
N2 | 0.1002 (5) | 0.6175 (2) | 0.4994 (2) | 0.0451 (7) | |
N5 | 0.8682 (4) | 0.6428 (2) | 0.9347 (2) | 0.0425 (7) | |
N4 | 0.9624 (6) | 0.7606 (3) | 0.8611 (3) | 0.0623 (10) | |
N1 | 0.1431 (6) | 0.5199 (3) | 0.3912 (3) | 0.0646 (10) | |
N6 | 0.7523 (6) | 0.5209 (2) | 0.9947 (3) | 0.0678 (12) | |
N3 | 0.0650 (7) | 0.7017 (3) | 0.6196 (3) | 0.0759 (13) | |
C6 | 0.8422 (5) | 0.5964 (2) | 1.0067 (2) | 0.0444 (8) | |
C10 | 0.9484 (5) | 0.7226 (2) | 0.9377 (2) | 0.0434 (8) | |
C1 | 0.0856 (5) | 0.5995 (3) | 0.4122 (2) | 0.0483 (9) | |
C7 | 0.9051 (6) | 0.6309 (3) | 1.0881 (2) | 0.0571 (11) | |
C5 | 0.0425 (6) | 0.6919 (2) | 0.5325 (3) | 0.0489 (9) | |
C9 | 1.0121 (6) | 0.7571 (3) | 1.0189 (3) | 0.0532 (10) | |
C8 | 0.9889 (6) | 0.7105 (3) | 1.0922 (3) | 0.0581 (11) | |
C2 | 0.0069 (6) | 0.6621 (4) | 0.3543 (3) | 0.0630 (12) | |
C3 | −0.0514 (6) | 0.7378 (3) | 0.3851 (3) | 0.0651 (13) | |
C4 | −0.0359 (6) | 0.7541 (3) | 0.4729 (4) | 0.0606 (12) | |
H7 | 0.874 (6) | 0.603 (3) | 1.136 (3) | 0.066 (13)* | |
H2 | 0.000 (6) | 0.648 (3) | 0.298 (3) | 0.074 (14)* | |
H4 | −0.066 (5) | 0.803 (3) | 0.498 (2) | 0.047 (11)* | |
H9 | 1.071 (6) | 0.802 (3) | 1.022 (3) | 0.075 (15)* | |
H8 | 1.035 (6) | 0.735 (3) | 1.146 (3) | 0.062 (12)* | |
H3 | −0.108 (7) | 0.784 (3) | 0.345 (3) | 0.094 (16)* | |
H2N1 | 0.222 (6) | 0.493 (3) | 0.427 (3) | 0.061 (14)* | |
H2N4 | 1.020 (6) | 0.808 (3) | 0.863 (3) | 0.067 (14)* | |
H1N6 | 0.720 (7) | 0.498 (3) | 0.945 (3) | 0.074 (15)* | |
H1N2 | 0.157 (6) | 0.581 (3) | 0.530 (3) | 0.058 (13)* | |
H1N5 | 0.839 (6) | 0.623 (3) | 0.886 (3) | 0.079 (16)* | |
H1N3 | 0.026 (6) | 0.748 (3) | 0.645 (3) | 0.062 (13)* | |
H1N4 | 0.913 (6) | 0.740 (3) | 0.817 (3) | 0.047 (13)* | |
H2N6 | 0.747 (7) | 0.488 (3) | 1.036 (3) | 0.082 (17)* | |
H2N3 | 0.095 (9) | 0.661 (4) | 0.654 (4) | 0.12 (2)* | |
H1N1 | 0.139 (7) | 0.508 (3) | 0.331 (3) | 0.089 (17)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
Co1 | 0.0442 (3) | 0.0358 (3) | 0.0350 (2) | 0.0012 (2) | 0.00079 (19) | 0.00112 (19) |
Cl1 | 0.0558 (6) | 0.0446 (5) | 0.0472 (5) | −0.0080 (4) | 0.0022 (4) | −0.0022 (4) |
Cl2 | 0.0553 (6) | 0.0531 (5) | 0.0382 (5) | 0.0072 (4) | −0.0049 (4) | −0.0042 (4) |
Cl3 | 0.0573 (6) | 0.0547 (6) | 0.0547 (5) | 0.0058 (5) | 0.0170 (5) | 0.0013 (5) |
Cl4 | 0.0892 (8) | 0.0407 (5) | 0.0511 (6) | 0.0053 (5) | −0.0141 (5) | 0.0073 (4) |
N2 | 0.0487 (19) | 0.0386 (16) | 0.0468 (17) | 0.0056 (15) | 0.0027 (15) | 0.0068 (14) |
N5 | 0.0458 (18) | 0.0446 (17) | 0.0360 (16) | −0.0034 (14) | 0.0023 (13) | −0.0017 (14) |
N4 | 0.068 (3) | 0.059 (2) | 0.059 (2) | −0.015 (2) | 0.006 (2) | 0.010 (2) |
N1 | 0.061 (2) | 0.077 (3) | 0.054 (2) | 0.011 (2) | 0.0023 (19) | −0.011 (2) |
N6 | 0.103 (3) | 0.053 (2) | 0.045 (2) | −0.028 (2) | 0.001 (2) | −0.0006 (18) |
N3 | 0.122 (4) | 0.047 (2) | 0.063 (3) | 0.011 (2) | 0.030 (3) | −0.001 (2) |
C6 | 0.051 (2) | 0.0416 (19) | 0.0397 (19) | −0.0056 (17) | 0.0037 (16) | −0.0002 (15) |
C10 | 0.040 (2) | 0.041 (2) | 0.049 (2) | 0.0030 (16) | 0.0073 (16) | 0.0048 (16) |
C1 | 0.039 (2) | 0.057 (2) | 0.048 (2) | −0.0024 (18) | 0.0032 (16) | 0.0011 (18) |
C7 | 0.078 (3) | 0.057 (3) | 0.035 (2) | −0.015 (2) | 0.004 (2) | −0.0021 (18) |
C5 | 0.054 (2) | 0.041 (2) | 0.053 (2) | 0.0032 (18) | 0.0151 (18) | 0.0070 (18) |
C9 | 0.050 (2) | 0.046 (2) | 0.062 (3) | −0.013 (2) | 0.002 (2) | −0.0082 (19) |
C8 | 0.070 (3) | 0.058 (3) | 0.044 (2) | −0.014 (2) | −0.002 (2) | −0.0083 (19) |
C2 | 0.054 (3) | 0.085 (3) | 0.047 (2) | −0.006 (2) | 0.000 (2) | 0.016 (2) |
C3 | 0.060 (3) | 0.061 (3) | 0.073 (3) | 0.001 (2) | 0.005 (2) | 0.029 (2) |
C4 | 0.059 (3) | 0.040 (2) | 0.085 (3) | 0.009 (2) | 0.019 (2) | 0.015 (2) |
Co1—Cl3 | 2.2595 (14) | N6—H2N6 | 0.82 (5) |
Co1—Cl4 | 2.2645 (11) | N3—C5 | 1.335 (6) |
Co1—Cl2 | 2.2754 (11) | N3—H1N3 | 0.88 (4) |
Co1—Cl1 | 2.2795 (13) | N3—H2N3 | 0.83 (6) |
N2—C5 | 1.346 (5) | C6—C7 | 1.379 (5) |
N2—C1 | 1.359 (5) | C10—C9 | 1.378 (5) |
N2—H1N2 | 0.82 (4) | C1—C2 | 1.382 (6) |
N5—C6 | 1.355 (4) | C7—C8 | 1.369 (6) |
N5—C10 | 1.360 (5) | C7—H7 | 0.91 (4) |
N5—H1N5 | 0.82 (5) | C5—C4 | 1.393 (6) |
N4—C10 | 1.332 (5) | C9—C8 | 1.367 (6) |
N4—H2N4 | 0.84 (5) | C9—H9 | 0.82 (5) |
N4—H1N4 | 0.79 (4) | C8—H8 | 0.93 (4) |
N1—C1 | 1.349 (5) | C2—C3 | 1.350 (7) |
N1—H2N1 | 0.84 (5) | C2—H2 | 0.89 (4) |
N1—H1N1 | 0.94 (5) | C3—C4 | 1.362 (7) |
N6—C6 | 1.337 (5) | C3—H3 | 0.99 (5) |
N6—H1N6 | 0.85 (5) | C4—H4 | 0.89 (4) |
Cl3—Co1—Cl4 | 112.69 (5) | N4—C10—N5 | 117.1 (4) |
Cl3—Co1—Cl2 | 109.64 (5) | N4—C10—C9 | 125.0 (4) |
Cl4—Co1—Cl2 | 109.80 (4) | N5—C10—C9 | 117.9 (3) |
Cl3—Co1—Cl1 | 110.73 (5) | N1—C1—N2 | 116.0 (4) |
Cl4—Co1—Cl1 | 106.44 (5) | N1—C1—C2 | 126.5 (4) |
Cl2—Co1—Cl1 | 107.37 (4) | N2—C1—C2 | 117.4 (4) |
C5—N2—C1 | 124.2 (3) | C8—C7—C6 | 118.5 (4) |
C5—N2—H1N2 | 123 (3) | C8—C7—H7 | 123 (3) |
C1—N2—H1N2 | 113 (3) | C6—C7—H7 | 118 (3) |
C6—N5—C10 | 124.1 (3) | N3—C5—N2 | 118.3 (4) |
C6—N5—H1N5 | 120 (3) | N3—C5—C4 | 124.4 (4) |
C10—N5—H1N5 | 116 (3) | N2—C5—C4 | 117.3 (4) |
C10—N4—H2N4 | 117 (3) | C8—C9—C10 | 118.7 (4) |
C10—N4—H1N4 | 120 (3) | C8—C9—H9 | 121 (3) |
H2N4—N4—H1N4 | 123 (4) | C10—C9—H9 | 120 (3) |
C1—N1—H2N1 | 119 (3) | C9—C8—C7 | 122.7 (4) |
C1—N1—H1N1 | 117 (3) | C9—C8—H8 | 117 (3) |
H2N1—N1—H1N1 | 118 (4) | C7—C8—H8 | 121 (3) |
C6—N6—H1N6 | 124 (3) | C3—C2—C1 | 120.0 (4) |
C6—N6—H2N6 | 121 (4) | C3—C2—H2 | 125 (3) |
H1N6—N6—H2N6 | 114 (4) | C1—C2—H2 | 115 (3) |
C5—N3—H1N3 | 122 (3) | C2—C3—C4 | 121.4 (4) |
C5—N3—H2N3 | 123 (4) | C2—C3—H3 | 122 (3) |
H1N3—N3—H2N3 | 114 (5) | C4—C3—H3 | 117 (3) |
N6—C6—N5 | 118.1 (3) | C3—C4—C5 | 119.7 (4) |
N6—C6—C7 | 123.7 (4) | C3—C4—H4 | 127 (2) |
N5—C6—C7 | 118.1 (3) | C5—C4—H4 | 114 (3) |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H2N1···Cl2 | 0.84 (5) | 2.69 (5) | 3.432 (4) | 147 (4) |
N4—H2N4···Cl2i | 0.84 (5) | 2.65 (5) | 3.465 (5) | 162 (4) |
N6—H1N6···Cl4 | 0.85 (5) | 2.58 (5) | 3.406 (4) | 165 (4) |
N2—H1N2···Cl2 | 0.82 (4) | 2.44 (4) | 3.240 (3) | 168 (4) |
N5—H1N5···Cl1 | 0.82 (5) | 2.43 (5) | 3.191 (3) | 156 (4) |
N3—H1N3···Cl4ii | 0.88 (4) | 2.53 (5) | 3.390 (5) | 166 (4) |
N4—H1N4···Cl1 | 0.79 (4) | 2.79 (4) | 3.481 (5) | 147 (4) |
N6—H2N6···Cl3iii | 0.82 (5) | 2.75 (5) | 3.516 (4) | 156 (4) |
N3—H2N3···Cl3 | 0.83 (6) | 2.61 (6) | 3.420 (5) | 166 (6) |
N1—H1N1···Cl1iv | 0.94 (5) | 2.69 (5) | 3.326 (4) | 126 (4) |
C7—H7···Cl3iii | 0.91 (4) | 2.89 (4) | 3.669 (4) | 145 (3) |
Symmetry codes: (i) −x+3/2, y+1/2, −z+3/2; (ii) −x+1/2, y+1/2, −z+3/2; (iii) −x+1, −y+1, −z+2; (iv) −x+1, −y+1, −z+1. |
Funding information
The authors acknowledge financial support from the Ministry of Higher Education and Scientific Research of Tunisia.
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