Crystal structure of (3E)-5-nitro-3-(2-phenylhydrazinylidene)-1H-indol-2(3H)-one

The molecule of 5-nitroisatin-3-phenylhydrazone deviates slightly from a planar geometry. In the crystal, molecules are linked by hydrogen bonding into a two-dimensional polymer along (120), forming rings of graph-set motifs (8), (26), (32) and S(6). In addition, molecules are stacked along the [100] through C=O⋯Cg interactions, as suggested by the Hirshfeld surface, which also indicates that the most important contributions for the crystal structure cohesion are O⋯H (28.5%) and H⋯H (26.7%) interactions. An in silico evaluation of the title compound with the dihydrofolate reductase enzyme was performed and N—H⋯O and Cg⋯Cg interactions were found.

The reaction between 5-nitroisatin and phenylhydrazine in acidic ethanol yields the title compound, C 14 H 10 N 4 O 3 , whose molecular structure deviates slightly from a planar geometry (r.m.s. deviation = 0.065 Å for the mean plane through all non-H atoms). An intramolecular N-HÁ Á ÁO hydrogen bond is present, forming a ring of graph-set motif S(6). In the crystal, molecules are linked by N-HÁ Á ÁO and C-HÁ Á ÁO hydrogen-bonding interactions into a two-dimensional network along (120), and rings of graph-set motif R 2 2 (8), R 2 2 (26) and R 4 4 (32) are observed. Additionally, a Hirshfeld surface analysis suggests that the molecules are stacked along [100] through C OÁ Á ÁCg interactions and indicates that the most important contributions for the crystal structure are OÁ Á ÁH (28.5%) and HÁ Á ÁH (26.7%) interactions. An in silico evaluation of the title compound with the DHFR enzyme (dihydrofolate reductase) was performed. The isatin-hydrazone derivative and the active site of the selected enzyme show N-HÁ Á ÁO(ASP29), N-HÁ Á ÁO(ILE96) and CgÁ Á ÁCg(PHE33) interactions.

Chemical context
The first reports on isatin and the synthesis of isatin derivatives were published independently in Germany and France over 170 years ago (Erdmann, 1841a,b;Laurent, 1841). After the 19th Century, isatin chemistry changed rapidly into a major group of compounds with a wide range of applications in different scientific disciplines, with special attention to medicinal chemistry. For example, the synthesis, in silico evaluation and in vitro inhibition of Chikungunya virus replication by an isatin-thiosemicarbazone derivative was performed recently (Mishra et al., 2016). Other isatin derivatives synthesized in the 1950s (Campaigne & Archer, 1952) had their pharmacological properties in vitro successfully tested against Cruzain, Falcipain-2 and Rhodesian in the 2000s (Chiyanzu et al., 2003), and the crystal structure of one of the derivatives was determined by X-ray diffraction in the 2010s (Pederzolli et al., 2011). The crystal structure determination of isatin-based molecules is an intensive research field, especially in medicinal chemistry. As part of our studies in this area, we now describe the synthesis and structure of the title compound, (I).

Structural commentary
For the title compound, the molecular structure matches the asymmetric unit and one intramolecular N4-H5Á Á ÁO1 inter- ISSN 2056-9890 action of graph-set S(6) is observed (Fig. 1). The molecule is nearly planar with an r.m.s. deviation from the mean plane of the non-H atoms of 0.065 Å and a maximum deviation of 0.1907 (9) Å for atom O2 of the nitro group. The dihedral angle between the indole unit and the phenyl ring is 0.9 (4) . The plane through the nitro group is rotated by 6.21 (6) with respect to the indole ring.

Hirshfeld surface analysis
The Hirshfeld surface analysis of the crystal structure indicates that the contribution of OÁ Á ÁH intermolecular interactions to the crystal packing amounts to 28.5% and the HÁ Á ÁH interactions amount to 26.7%. Other important intermolecular contacts for the cohesion of the structure are (in %): HÁ Á ÁC = 17.7, HÁ Á ÁN = 8.9, CÁ Á ÁO = 8.2, CÁ Á ÁC = 5.5 and CÁ Á ÁN = 3.3. The Hirshfeld surface graphical representation with transparency and labelled atoms (Figs. 4 and 5) indicates, in magenta, the locations of the strongest intermolecular contacts. The H1, H8, O1 and O2 atoms are the most important for the intermolecular hydrogen bonding, while the C1 and C14 atoms are the most important for CÁ Á ÁC interactions. The OÁ Á ÁH contribution to the crystal packing is shown as a Hirshfeld surface fingerprint two-dimensional plot with cyan dots (Wolff et al., 2012). The d e (y axis) and d i (x axis) values are the closest external and internal distances (in Å ) from given points on the Hirshfeld surface ( The molecular structure of the title compound, showing displacement ellipsoids drawn at the 50% probability level. The intramolecular hydrogen bond is shown as a dashed line. Table 1 Hydrogen-bond geometry (Å , ). Symmetry codes: (i) Àx þ 2; Ày; Àz þ 1; (ii) x; y; z þ 1; (iii) Àx; Ày þ 1; Àz þ 1.

Molecular docking evaluation
Finally, for a lock-and-key supramolecular analysis, a molecular docking evaluation between the title compound and the DHFR enzyme (dihydrofolate reductase) was carried out. Initially, the semi-empirical equilibrium energy of the small molecule was obtained using the PM6 Hamiltonian, but the experimental bond lengths were conserved. The calculated parameters were: heat of formation = 149.41 kJ mol À1 , gradient normal = 0.763, HOMO = À8.96 eV, LUMO =-1.66 eV and energy gap = 7.30 eV. The target prediction for 5-nitroisatin-3-phenylhydrazone was calculated with the SwissTargetPrediction webserver based on the bioisosteric similarity to the isatin entity (Gfeller et al., 2013). As result of this screening, the title compound showed a promising theo- A Hirshfeld surface graphical representation (d norm ) for the title compound. The surface is drawn with transparency and all atoms are labelled. The surface regions with strongest intermolecular interactions for atoms H1, O1 and C14 are shown in magenta.

Figure 5
A Hirshfeld surface graphical representation (d norm ) for the title compound. The surface is drawn with transparency and all atoms are labelled. The surface regions with strongest intermolecular interactions for atoms H8, O2 and C1 are shown in magenta.

Comparison with a related structure
A recently published article (Bittencourt et al., 2016) reports the structure of (3E)-5-nitro-3-(2-phenylhydrazinylidene)-1Hindol-2(3H)-one, which may be compared with that of the title compound. The molecular structure deviates slightly from the ideal planar geometry and the CÁ Á ÁC contacts between the planes are observed. The molecules are linked by N-HÁ Á ÁO and C-HÁ Á ÁCl interactions into a two-dimensional hydrogenbonded polymer, a quite similar structure to the title compound. The in silico evaluation of 5-chloroisatin-phenylhydrazone, a molecule with similar crystal packing to the title compound, with and the DNA topoisomerase II enzyme was performed and the global free energy of À26.59 kJ mol À1 was found. The evaluation agrees with the literature data for molecular docking and cytotoxic activity of hydrazone derivatives against breast cancer cells (Dandawate et al., 2012) and supports research on the structural determination of other isatin-based molecules. The title compound is commercially available, but its structural analysis by X-ray single crystal diffraction, Hirshfeld surface calculation and molecular docking evaluation are presented in this work for the first time.

Synthesis and crystallization
All starting materials are commercially available and were used without further purification. The synthesis of the title compound was adapted from a procedure reported previously (Fonseca et al., 2011). The glacial acetic acid-catalysed reaction of 5-nitroisatin (2.6 mmol) and phenylhydrazine (2.6 mmol) in ethanol (40 mL) was refluxed for 4 h. After cooling and filtering, an irregular solid was isolated. Single crystals suitable for X-ray diffraction were obtained from a DMF/methanol solution (1:1 v/v) on slow evaporation of the solvent.

(3E)-5-nitro-3-(2-phenylhydrazinylidene)-1H-indol-2(3H)-one
Crystal data Special details 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. Refinement. Refinement of F 2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F 2 , conventional R-factors R are based on F, with F set to zero for negative F 2 . The threshold expression of F 2 > 2sigma(F 2 ) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F 2 are statistically about twice as large as those based on F, and R-factors based on ALL data will be even larger.