Crystal structure and Hirshfeld surface analysis of the orthorhombic polymorph of a ZnII complex with 3,5-dinitrobenzoic acid and ethylenediamine

During systematic investigations of the biological action enhancement of well known compounds, a new metal complex, (ethane-1,2-diamine)bis(3,5-dinitrobenzoato)zinc(II), was synthesized and the structure of its orthorhombic form has determined. The zinc ion has a distorted tetrahedral environment formed by two monodentate 3,5-dinitrobenzoato anions and chelating ethylenediamine molecule.


Chemical context
The benzoic acid derivative 3,5-dinitrobenzoic acid (DNBA) is an important corrosion inhibitor that is also applied in photography (Elks & Ganellin, 1990). This aromatic compound is used by chemists in the fluorometric analysis of creatinine (Lewinska et al., 2018;Chandrasekaran et al., 2013). It demonstrates a weak antimicrobial activity against bacteria and yeasts with a minimum inhibitory concentration (MIC) of 3 mmol L À1 , but shows moderate biological action with respect to the filamentous fungi M. gypseum with IC50 = 2.1 mmol L À1 (Vaskova et al., 2009).
Ethylenediamine (En) is widely used in the chemical industry. It is a well-known bidentate chelating ligand that donates lone pairs of electrons of two nitrogen atoms (Matsushita & Taira, 1999). En is not itself biologically active against different strains of microoraganisms, but its Co III complex demonstrates a strong antifungal action relative to a broad spectrum of Candida species (Turecka et al., 2018).
DNBA is poorly water soluble; its solubility is only 1.35 g L À1 at 25 C. In order to enhance its water solubility and antimicrobial activity, we tested some of the presently known approaches (Jain et al., 2015). More promising is a preparation of organic salts of DNBA and En as well as mixed-ligand complexes based on them. Such an approach has been applied for the biopharmaceutical optimization of 4-nitrobenzoic acid (Ibragimov et al., 2017) and 4-aminobenzoic acid (Ibragimov et al., 2016) yielding impressive results.
However, an analysis of the Cambridge Structural Database (CSD Version 5.41, update of November 2019; Groom et al., 2016) attests that organic salts based on DNBA and En have already been obtained as ethylendiammonium bis(3,5-dinitrobenzoate) (refcode VUJXIH; Nethaji et al., 1992) and ethylendiammonium bis(3,5-dinitrobenzoate) bis(3,5-dinitrobenzoic acid) (FONCER; Jones et al., 2005). Therefore, we synthesized two polymorphic forms of the zinc mixed-ligand complex. The synthesis and crystal structure of the monoclinic polymorph has been published recently (Ibragimov et al., 2020), and the present paper is devoted to an orthorhombic polymorph that crystallizes in space group Pbca.

Structural commentary
Two DNBA anions coordinate the Zn II ion in a monodentate mode via the oxygen atoms of the carboxylate groups. As is usual, the En molecule acts as a chelating ligand through the two nitrogen atoms (Fig. 1). The coordination tetrahedron is distorted because of the Zn1Á Á ÁO2 and Zn1Á Á ÁO2 0 interactions, the angles N3-Zn1-N4 [87.09 (7) ] and O1-Zn1-O1 0 [101.82 (5) ] being less than the idealized tetrahedral values. The least-squares planes through the nitro groups are almost parallel to the planes of the aromatic rings. The nitro group N2 0 O5 0 O6 0 subtends the largest dihedral angle to the attached aromatic ring [16.65 (11) ]. The conformation of the complex molecule is fixed due to the intramolecular N4-H4AÁ Á ÁO2 hydrogen bond, which closes a six-membered ring with graph-set notation S(6) (Etter, 1990).

Supramolecular features
In the crystal, complex molecules are linked by three relatively weak hydrogen bonds of the N-HÁ Á ÁO type and two bonds of C-HÁ Á ÁO type ( Table 1). The N3-H3AÁ Á ÁO2 0 , N4-H4AÁ Á ÁO5 0 and N4-H4BÁ Á ÁO1 hydrogen bonds link the complex molecules into a two-dimensional network parallel to the ac plane. Weak C6 0 -H6 0 Á Á ÁO6 0 and C8-H8BÁ Á ÁO3 hydrogen bonds strengthen the association of the complex molecules into this network (Fig. 2). Thus, only the H3B hydrogen on the N3 atom is without an acceptor and five oxygen atoms O1 0 , O3 0 , O4 0 , O4 and O5 do not participate in hydrogen bonding.

Figure 2
A packing diagram for [Zn(DNBA) 2 (En)] showing the two-dimensional networks parallel to (010). For clarity, H atoms not involved in hydrogen bonding are omitted.

Figure 1
Molecular structure of [Zn(DNBA) 2 (En)] with the atom-numbering scheme. Displacement ellipsoids are drawn at the 50% probability level.

Figure 3
View of the three-dimensional Hirshfeld surface of the title compound plotted over d norm in the range À0.4180 to 1.3344 a.u.

Refinement
Crystal data, data collection and structure refinement details are summarized in Table 3. C-bound hydrogen atoms were placed in calculated positions and refined using the ridingmodel approximation with U iso (H) = 1.2U eq (C), C-H = 0.93 and 0.97 Å for aromatic and methylene hydrogen atoms, respectively. N-bound H atoms were located in a difference-Fourier map and refined with bond-length restraints of 0.89 (1) Å .  (Rigaku OD, 2015); cell refinement: CrysAlis PRO (Rigaku OD, 2015); data reduction:

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å 2 )
x y z U iso */U eq  (2)