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Communication

Heteroleptic Zn(II)–Pentaiodobenzoate Complexes: Structures and Features of Halogen–Halogen Non-Covalent Interactions in Solid State

by
Mikhail A. Bondarenko
1,
Alexander S. Novikov
2,3,
Maxim N. Sokolov
1 and
Sergey A. Adonin
1,*
1
Nikolaev Institute of Inorganic Chemistry SB RAS, Lavrentieva St., 3, 630090 Novosibirsk, Russia
2
Institute of Chemistry, Saint Petersburg State University, Universitetskaya Nab., 7/9, 199034 Saint Petersburg, Russia
3
Research Institute of Chemistry, Peoples’ Friendship University of Russia, Miklukho-Maklaya St., 6, 117198 Moscow, Russia
*
Author to whom correspondence should be addressed.
Inorganics 2022, 10(10), 151; https://doi.org/10.3390/inorganics10100151
Submission received: 25 August 2022 / Revised: 9 September 2022 / Accepted: 16 September 2022 / Published: 22 September 2022
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Abstract

:
Reactions between Zn(II) nitrate, pentaiodobenzoic acid (HPIBA) and different pyridines in dimethylformamide (DMF) result in the formation of the heteroleptic neutral complexes [Zn(3,5-MePy)2PIBA2] (1) and [Zn(DMF)3(NO3)PIBA] (2). Both compounds were isolated in pure form, as shown by the PXRD data. The features of specific non-covalent interactions involving halogen atoms (halogen bonding) were examined by means of DFT calculations (QTAIM analysis and the estimation of corresponding energies).

1. Introduction

Complexes with halogen-polysubstituted organic (in particular, aromatic) ligands constitute a not very large, but important and interesting, field of coordination chemistry. The lion’s share of them are those containing perfluorinated substituents [1,2,3,4,5,6,7,8], mostly due to their potential applications in luminescent materials [8,9,10,11,12] (it is commonly assumed that the replacement of protons by F reduces quenching [13]). At the same time, the ligands polysubstituted by other halogens are much less studied. Here, we give some examples illustrating this current misbalance. Pentachlorobenzoic acid has been known about since at least 1887 [14] and, since then, authors have published optimized protocols of its quantitative preparation [15]; however, its structure was only reported in 2018 [16], and there is only one article on the corresponding structurally characterized complex [17]. Works on ligands with heavier halogens (especially iodine) are rare, despite the fact that some of these compounds—in particular, pentaiodobenzoic acid (HPIBA), known about for several decades [18]—can be of interest in terms of design of contrast media for tomography (a very interesting paper demonstrating the potential of this pathway was recently presented by Lin et al. [19]).
A few years ago, we performed structural characterization of HPIBA and its several salts, [20] noting that it features very strong (as shown by the DFT calculation) halogen bonding (XB) [21,22,23]. We assumed that this feature must also persist in hypothetic PIBA metal complexes. Soon after, we reported the first examples of such compounds (heteroleptic Cu(II) PIBA complexes [24]), and an analysis of the corresponding structural data confirmed our hypothesis.
Continuing this work, we hereby present the first PIBA complexes of Zn(II)—[Zn(3,5-MePy)2PIBA2] (1) and [Zn(DMF)3(NO3)PIBA] (2). Both of these compounds were characterized using X-ray diffractometry and obtained as pure phases (as shown by the PXRD data). The features of non-covalent interactions in both crystal structures were investigated by means of DFT calculations.

2. Materials and Methods

All reagents were obtained from commercial sources and used as purchased. HPIBA was synthesized according to the previously published procedure [18].

2.1. Synthesis of 1

A total of 80 mg (0.106 mmol) of HPIBA was dissolved in 2 mL of DMF, followed by addition of 24 μL (0.212 mmol) of 3,5-MePy and solution of 16 mg (0.053 mmol) of Zn(NO3)2·6H2O in 1 mL of DMF. Slow diffusion of diethyl ether at r.t. (≈18 h) resulted in formation of transparent pale-yellow crystals of 1. Yield, 79%. For C28H18I10N2O4Zn, calcd %: C, 18.89; H, 1.02; and N, 1.57; found %: C, 19.01; H, 1.10; and N, 1.65. IR (4000–400 cm−1, KBr): 1610 s, 1578 m, 1485 m, 1358 s, 1250 s, 1175 s, 1150 m, 1009 m, 859 m, 775 m and 695 s.

2.2. Synthesis of 2

A total of 120 mg (0.160 mmol) of HPIBA was dissolved in 2 mL of DMF, followed by addition of 30 μL (0.32 mmol) of 3-ClPy or equimolar amount of some other substituted pyridines (see Results and Discussion for details) and solution of 24 mg (0.08 mmol) of Zn(NO3)2·6H2O in 1 mL of DMF. Slow diffusion of diethyl ether at r.t. (≈18 h) resulted in formation of transparent pale-yellow crystals of 1. Yield, 84%. For C16H21I5N4O8Zn, calcd %: C, 17.52; H, 1.93; and N, 5.11; found %: C, 17.69; H, 2.01; and N, 5.27.

2.3. X-ray Diffractometry

Crystallographic data and refinement details for 1 and 2 are given in Table 1. The diffraction data were collected using a Bruker D8 Venture diffractometer with a CMOS PHOTON III detector and IµS 3.0 source (Mo Kα radiation, λ = 0.71073 Å) at 150 K. The φ- and ω-scan techniques were employed. Absorption correction was applied via SADABS (Bruker Apex3 software suite, Apex3, SADABS-2016/2 and SAINT, version 2018.7-2; Bruker AXS Inc., Madison, WI, USA, 2017). Structures were solved via SHELXT [25] and refined via full-matrix least-squares treatment against |F|2 in anisotropic approximation with SHELX 2014/7 [26] in ShelXle program [27]. H-atoms were refined in the geometrically calculated positions. The crystallographic data have been deposited in the Cambridge Crystallographic Data Centre under the deposition codes CCDC 2203477-2203478. These data can be obtained free of charge via www.ccdc.cam.ac.uk/data_request/cif, accessed on 24 August 2022 or by emailing [email protected].

2.4. Powder X-ray Diffractometry

XRD analysis of polycrystals was performed using Shimadzu XRD-7000 diffractometer (CuK alpha radiation, Ni filter, linear One Sight detector, 0.0143° 2θ step, 2s per step). Plotting of PXRD patterns and data treatment were performed using X’Pert Plus software (see Supplementary Materials).

2.5. Computational Details

See Supplementary Materials.

3. Results and Discussion

For designing the synthetic procedures for 1 and 2, we followed the same straightforward scheme—“source of Zn(II) + HPIBA + substituted pyridine”—expecting that the latter would play the roles of both the base, for the deprotonation of HPIBA, and the ligand, to complete the coordination environment of Zn. This idea worked well in the case of 1, resulting in a pure phase, as shown by the PXRD data (see Supplementary Materials, Figures S1 and S2). At the same time, we found that the use of several substituted pyridines, namely 3-chloro, 2,5-diiodo, 2,6-dibromo, 2-iodo, 3-bromo, 2-bromo and 2-chloro derivatives, results in the formation of pure 2 with minor variations in yields (the nature of product was confirmed by means of element analysis and PXRD in all cases).
In 1, the coordination environment of Zn(II) is tetrahedral (Figure 1). It consists of two 3,5-MePy ligands (Zn-N = 2.025 Å) and two PIBAs coordinated in monodentate mode (Zn-O = 1.950 Å).
The 3D system of halogen bonds in the structure of 1 is rather sophisticated (Figure 2). It involves O atoms of carboxylic groups in which each O interacts simultaneously with two iodine atoms. All 3-I and 5-I substituents participate in the formation of XB; the corresponding distances are 3.045 and 3.320 Å, which are much less than the sum of the related Bondi’s van der Waals Radii (3.50 Å [28,29]; those are 87% and 94.8%, respectively). Additionally, there are I–I contacts (3.829–3.908 Å) involving 2-, 4- and 5-I atoms of PIBA ligands (Figure 3). This system of non-covalent interactions is very different from the one found in the similar complex [24] of Cu(II) with the same ligands due to the fundamentally different geometry of the coordination units.
Unlike in 1, Zn(II) features hexa-coordination in the structure of 2 (Figure 4). There is one PIBA ligand (Zn-O = 2.018 Å), three DMF ligands (Zn-O = 2.034–2.084 Å) and one nitrate ligand; the latter is coordinated in bidentate mode (Zn-O = 2.116 and 2.473 Å, respectively).
Complex 2 also features multiple I–O halogen bonds, yielding a 3D structure (Figure 5). These involve O atoms of carboxylate groups (2.997–3.181 Å) and of nitrate ligands (3.079–3.129 Å, respectively). It must be noticed that XBs involving a nitrate anion or ligand are rather rare; as shown by the CSD data, there are fewer than 10 of such examples [30,31,32,33,34,35]. I–I non-covalent interactions are absent in this structure. Comparing the XBs in 1 and in relevant Cu(II) complexes which were reported by us recently [24], it can be seen that the lengths of non-covalent interactions are rather similar, likely corresponding to rather strong bonding.
To investigate the nature of non-covalent interactions in the structures of 1 and 2, we used the approach which was previously used by us [36,37,38,39,40] and demonstrated its high efficiency: atomic coordinates were extracted from the XRD data and used for DFT calculations without optimization, followed by topological analysis of the electron density distribution (ωB97XD/DZP-DKH; see Supplementary Materials for details and visualization (Figures S3 and S4). The results are summarized in Table 2. It can be seen that the highest XB energies (5.1 kcal/mol) are comparable with those found in the structures of the corresponding Cu(II) complexes [24] and PIBA salts [20]).
The balance between the Lagrangian kinetic energy G(r) and potential energy density V(r) at the bond’s critical points (3, –1) reveals [41] that a covalent contribution in the intermolecular interactions I–I and I–O in 1 and 2 is absent.
Table
Table 2. Values of the density of all electrons ρ(r), Laplacian of electron density ∇2ρ(r) and appropriate λ2 eigenvalues; energy density Hb, potential energy density V(r), and Lagrangian kinetic energy G(r); and electron localization function ELF (a.u.) at the bond’s critical points (3, –1) for intermolecular interactions in 1 and 2, and their estimated strength Eint (kcal/mol).
Table 2. Values of the density of all electrons ρ(r), Laplacian of electron density ∇2ρ(r) and appropriate λ2 eigenvalues; energy density Hb, potential energy density V(r), and Lagrangian kinetic energy G(r); and electron localization function ELF (a.u.) at the bond’s critical points (3, –1) for intermolecular interactions in 1 and 2, and their estimated strength Eint (kcal/mol).
ContactLength ρ (r)∇2ρ (r)−λ2Hb−V (r)G (r)Eint *
1
I–I3.9080.0070.0290.0070.0020.0040.0061.7
I–I3.8290.0090.0330.0090.0010.0060.0072.6
I–O3.3210.0080.0350.0080.0020.0050.0072.1
I–O3.0450.0150.0540.0150.0010.0110.0124.7
2
I–O3.1810.0110.0470.0110.0020.0080.0103.4
I–O3.1290.0120.0470.0120.0010.0090.0103.8
I–O3.0790.0140.0530.0140.0020.0100.0124.3
I–O2.9970.0170.0600.0170.0020.0120.0145.1
* Eint = 0.88 (−V (r)) (this empirical correlation between the interaction energy and the potential energy density of electrons at the bond’s critical points (3, –1) was specifically developed for non-covalent interactions involving bromine atoms) [42].

4. Conclusions

Our results confirm that PIBA can indeed be utilized as a ligand, and its complexes readily form halogen bonds in solid state. These findings can be applied for the preparation of other carboxylate complexes (this is a very large family of coordination compounds demonstrating fascinating structural diversity [43,44,45,46,47,48]); these could potentially be applicable in the design of contrast agents. Corresponding experiments are underway.

Supplementary Materials

The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/inorganics10100151/s1, Figures S1 and S2. Comparison of experimental and calculated PXRD patterns for 1 and 2; Computational details; Figures S3 and S4. Contour line diagrams of the Laplacian of electron density distribution, bond paths, and selected zero-flux surfaces, visualization of electron localization function and reduced density gradient analyses for intermolecular interactions I···I and I···O in 1 and 2; Table S1. Cartesian atomic coordinates for model supramolecular associates.

Author Contributions

Conceptualization, S.A.A.; methodology, S.A.A. and A.S.N.; validation, A.S.N. and M.N.S., formal analysis, S.A.A., A.S.N. and M.N.S.; investigation, M.A.B. and A.S.N.; resources, S.A.A.; data curation, M.A.B. and A.S.N.; writing—original draft preparation, S.A.A.; writing—review and editing, M.N.S.; visualization, A.S.N. and S.A.A.; supervision, S.A.A.; project administration, S.A.A.; funding acquisition, S.A.A. All authors have read and agreed to the published version of the manuscript.

Funding

This research was funded by the Ministry of Science and Higher Education of the Russian Federation (121031700313-8). A.S.N. is grateful to the RUDN University Strategic Academic Leadership Program.

Data Availability Statement

Not applicable.

Acknowledgments

The authors thank Ilya V. Korolkov (NIIC SB RAS) for his assistance with PXRD experiments.

Conflicts of Interest

The authors declare no conflict of interest.

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Inorganics 10 00151 g001 550
Figure 1. Structure of 1 (thermal ellipsoids, 50% probability). Here, and below: Zn—black, N—deep blue, C—grey, I—purple, O—red. H atoms are omitted for clarity.
Figure 1. Structure of 1 (thermal ellipsoids, 50% probability). Here, and below: Zn—black, N—deep blue, C—grey, I—purple, O—red. H atoms are omitted for clarity.
Inorganics 10 00151 g001
Inorganics 10 00151 g002 550
Figure 2. The system of I–O interactions (dashed) in the structure of 1. Only N atoms of Py ligands are shown.
Figure 2. The system of I–O interactions (dashed) in the structure of 1. Only N atoms of Py ligands are shown.
Inorganics 10 00151 g002
Inorganics 10 00151 g003 550
Figure 3. The system of I–I interactions (dashed) in the structure of 1. Only N atoms of Py ligands are shown.
Figure 3. The system of I–I interactions (dashed) in the structure of 1. Only N atoms of Py ligands are shown.
Inorganics 10 00151 g003
Inorganics 10 00151 g004 550
Figure 4. Structure of 2 (thermal ellipsoids, 50% probability).
Figure 4. Structure of 2 (thermal ellipsoids, 50% probability).
Inorganics 10 00151 g004
Inorganics 10 00151 g005 550
Figure 5. The system of I–O interactions (dashed) in the structure of 2. Only O atoms of DMF ligands are shown.
Figure 5. The system of I–O interactions (dashed) in the structure of 2. Only O atoms of DMF ligands are shown.
Inorganics 10 00151 g005
Table
Table 1. XRD experimental details.
Table 1. XRD experimental details.
(1)(2)
Chemical formulaC28H18I10N2O4ZnC16H21I5N4O8Zn
Mr1780.811097.24
Crystal system, space groupOrthorhombic, Fdd2Monoclinic, P21/n
α, β, γ (°)90, 90, 9090, 94.011 (1), 90
V (Å3)8048.2 (3)2922.66 (10)
Z84
µ (mm−1)8.326.17
Tmin, Tmax0.642, 0.7460.616, 0.746
No. of measured, independent and observed [I > 2σ(I)] reflections49,070, 6155, 608833,369, 5530, 5174
Rint0.0290.030
θ values (°)θmax = 30.5, θmin = 2.4θmax = 25.7, θmin = 2.3
(sin θ/λ)max (Å−1)0.7150.610
Range of h, k, lh = −72→72, k = −14→14, l = −21→21h = −13→13, k = −11→11, l = −32→32
R[F2 > 2σ(F2)], wR(F2), S0.014, 0.036, 0.990.025, 0.058, 1.07
No. of reflections, parameters and restraints6155, 204, 15530, 307, 0
Δρmax, Δρmin (e Å−3)0.74, −0.841.97, −1.20
Absolute structureFlack x determined using 2891 quotients [(I+)−(I-)]/[(I+)+(I-)]
Absolute structure parameter0.000 (7)
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Bondarenko, M.A.; Novikov, A.S.; Sokolov, M.N.; Adonin, S.A. Heteroleptic Zn(II)–Pentaiodobenzoate Complexes: Structures and Features of Halogen–Halogen Non-Covalent Interactions in Solid State. Inorganics 2022, 10, 151. https://doi.org/10.3390/inorganics10100151

AMA Style

Bondarenko MA, Novikov AS, Sokolov MN, Adonin SA. Heteroleptic Zn(II)–Pentaiodobenzoate Complexes: Structures and Features of Halogen–Halogen Non-Covalent Interactions in Solid State. Inorganics. 2022; 10(10):151. https://doi.org/10.3390/inorganics10100151

Chicago/Turabian Style

Bondarenko, Mikhail A., Alexander S. Novikov, Maxim N. Sokolov, and Sergey A. Adonin. 2022. "Heteroleptic Zn(II)–Pentaiodobenzoate Complexes: Structures and Features of Halogen–Halogen Non-Covalent Interactions in Solid State" Inorganics 10, no. 10: 151. https://doi.org/10.3390/inorganics10100151

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