I. INTRODUCTION
5-(3-methoxyphenyl)isatin is a red solid material. Isatin (indole-2,3-dione, C8H5NO2) has been known from ancient times as a pigment in the dye industry. Isatin and 6-bromoisatin were intermediates in the production of indigo and Tyrian purple and probably were minor pigments in these dyes (Ferreira et al., Reference Ferreira, Hulme, McNab and Quye2004). Isatin is widely used as a substrate for organic synthesis (da Silva et al., Reference da Silva, Garden and Pinto2001). Recently, isatin and its derivatives have received more attention due to its diverse biological activity (Medvedev et al., Reference Medvedev, Buneeva and Glover2007), including anticancer properties (Cane et al., Reference Cane, Tournaire, Barritault and Crumeyrolle-Arias2000; Vine et al., Reference Vine, Locke, Ranson, Pyne and Bremner2007). Some aromatic ring-substituted derivatives of isatin are reported to exhibit cytotoxicity on a human monocyte-like histiocytic lymphoma (U937) cell line (Vine et al., Reference Vine, Locke, Ranson, Pyne and Bremner2007). Aryl-substituted isatins are promising inhibitors of matrix metalloproteinases, which are known to affect tumor progression. A two-dimensional (2D) molecular diagram for 5-(3-methoxyphenyl)isatin (C15H11NO3) is shown in Figure 1.
Figure 1. The molecular structure of 5-(3-methoxyphenyl)isatin.
II. EXPERIMENTAL
A. Synthesis
5-Iodoisatin (253 mg, 1.00 mmol) was suspended in a mixture of ethanol (10 ml) and water (10 ml) under constant flow of nitrogen. K2CO3 (0.41 g, 3.00 mmol, 3 equiv) was added and the mixture was heated at reflux until the solution became almost colorless (5–10 min). The solution was cooled to ambient temperature and the 3-methoxyphenylboronic acid (1.30 mmol, 1.3 equiv) was added, followed by the addition of [1,1′-Bis(diphenylphosphino)ferrocene]dichloropalladium(II) (7.30 mg, 0.10 mol. %). The reaction mixture was heated at reflux for 8 h, cooled to ambient temperature and acetic acid (10 ml) was added. The resulting mixture was heated at reflux for 10 min. If precipitate formation was seen after cooling, then it was filtered and recrystallized one more time from a hot solution of acetic acid, filtered and the catalyst residue removed. In all the other cases, the acetic acid was diluted with water (~20 ml) and the product was extracted with ethyl acetate (3 × 10 ml). The combined organic layers were dried over Na2SO4, filtered and evaporated. The residue was purified via chromatography (eluent hexanes/EtOAc, 1:1, 0:1). The product was further recrystallized from ethanol. Yield: 48%, M = 121 mg. Red solid, m.p. 210–212 °C. For more general discussion about synthetic pathways towards 5-aryl-1H-isatins, see recent work (Ivanov et al., Reference Ivanov, Agamennone, Iusupov, Laghezza, Novoselov, Manasova, Altieri, Tortorella, Shtil and Kurkin2022).
B. Powder X-ray diffraction
The powder pattern was measured in variable slit mode on a MiniFLEX 600 powder diffractometer (Rigaku Corp., Tokyo, Japan) equipped with a Cu Kα 1,2 (λ = 1.5418 Å) X-ray tube, a 1D D/teX position-sensitive detector, and variable divergence slits. The goniometer radius was 150 mm. Data were collected at room temperature in the range 3–90° 2θ with a 0.01° 2θ step. Since the diffractometer does not enable to measure pattern within whole range of 2θ in fixed slit mode, the powder pattern was measured in variable slit mode. The obtained pattern was then rescaled as if it had been measured in fixed slit mode with 1° divergence slit.
The pattern was indexed on a primitive orthorhombic unit cell with a = 11.1772(3), b = 7.92536(13), c = 27.0121(7) Å, V = 2392.82(10) Å3, and Z = 8 by SVD-index (Coelho, Reference Coelho2003) as implemented in Bruker TOPAS 5.0 (Coelho, Reference Coelho2018). The space group suggestions were generated with ExtSym (Markvardsen et al., Reference Markvardsen, Shankland, David, Johnston, Ibberson, Tucker, Nowell and Griffin2008); space group Pbca was chosen and confirmed by the successful structure solution and refinement. Parallel tempering, as implemented in FOX (Favre-Nicolin and Černý, Reference Favre-Nicolin and Černý2002), was used to solve the crystal structure in direct space. The Rietveld refinement (with Bruker TOPAS 5.0) was carried out using bond and angle restraints, based on a structure of the similar isatin derivative. Restraint weight was automatically decreased during the refinement, and refinement result of more restrained model served as a starting structure for the next less restrained one.
C. DFT calculations
PW-DFT-D calculations carried out in Quantum Espresso 7.1 (Giannozzi et al., Reference Giannozzi, Baroni, Bonini, Calandra, Car, Cavazzoni, Ceresoli, Chiarotti, Cococcioni, Dabo, Corso, de Gironcoli, Fabris, Fratesi, Gebauer, Gerstmann, Gougoussis, Kokalj, Lazzeri, Martin-Samos, Marzari, Mauri, Mazzarello, Paolini, Pasquarello, Paulatto, Sbraccia, Scandolo, Sclauzero, Seitsonen, Smogunov, Umari and Wentzcovitch2009, Reference Giannozzi, Andreussi, Brumme, Bunau, Buongiorno Nardelli, Calandra, Car, Cavazzoni, Ceresoli, Cococcioni, Colonna, Carnimeo, Dal Corso, de Gironcoli, Delugas, DiStasio, Ferretti, Floris, Fratesi, Fugallo, Gebauer, Gerstmann, Giustino, Gorni, Jia, Kawamura, Ko, Kokalj, Küçükbenli, Lazzeri, Marsili, Marzari, Mauri, Nguyen, Nguyen, Otero-de-la-Roza, Paulatto, Poncé, Rocca, Sabatini, Santra, Schlipf, Seitsonen, Smogunov, Timrov, Thonhauser, Umari, Vast, Wu and Baroni2017) using the PBE functional (Perdew et al., Reference Perdew, Burke and Ernzerhof1996), Grimme D3 van der Waals correction (Grimme et al., Reference Grimme, Antony, Ehrlich and Krieg2010) with Becke-Johnson damping (Grimme et al., Reference Grimme, Ehrlich and Goerigk2011), and a plane-wave basis set with projector augmented wave (PAW) pseudopotentials (Blöchl, Reference Blöchl1994; Kresse and Joubert, Reference Kresse and Joubert1999) from PSLibrary (Corso, Reference Corso2014). Constant cell optimization was performed with the recommended cutoff of 640 eV; for variable cell optimization, the cutoff was increased by a factor of 1.3. Default 0.5 Å−1 k-point mesh and 2 k-points were used in all calculations. Root-mean-square (RMS) Cartesian displacement between the Rietveld refined structure and the PW-DFT-D optimized one was calculated as suggested by Neumann (van de Streek and Neumann, Reference van de Streek and Neumann2014). Pairwise intermolecular interaction energies were estimated using CE-B3LYP approximation (Mackenzie et al., Reference Mackenzie, Spackman, Jayatilaka and Spackman2017) in CrystalExplorer (Spackman et al., Reference Spackman, Turner, McKinnon, Wolff, Grimwood, Jayatilaka and Spackman2021).
III. RESULTS AND DISCUSSION
The pattern calculated from the initial structure obtained from FOX showed poor agreement with the experimental pattern, until preferred orientation was taken into account. Platy morphology with {001} as the major faces was suggested by the BFDH (Donnay and Harker, Reference Donnay and Harker1937) method in Mercury (Macrae et al., Reference Macrae, Bruno, Chisholm, Edgington, McCabe, Pidcock, Rodriguez-Monge, Taylor, van de Streek and Wood2008). The March coefficient was close to 0.9. As only 30 mg of the title compound was available, we were not able to prepare less textured sample. The texture was added to the FOX model, and the direct-space search was repeated; the difference between the initial structure and the new one was minor. We used the new structure as a starting model for DFT optimization and Rietveld refinement.
We used a closely related structure of 5-(4-hexylphenyl)isatin (CSD Ref. code EWUVAU) (Porada et al., Reference Porada, Neudörfl and Blunk2011) as a source of bond and angle restraints for the Rietveld refinement. We did not use DFT-optimized values to keep refinement and validation procedures separate. We also abandoned the idea of using mean values from Mogul check as restraints. N-unsubstituted isatins have a peculiar bond length alternation comparing to other indole derivatives (with an elongated C7–C8 bond as the main difference). Although there are 40 of them in the CSD, Mogul finds more than 3000 of (not so) similar compounds. As a result, even accurate isatin structures determined from single crystal experiments have unusual bonds and angles according to the Mogul check with default parameters.
Final refinement yielded R p/R ′p/R wp/R ′wp = 1.86/4.85/2.34/5.37%, GOF = 2.29. The March coefficient for the final structure is 0.87. The RMS Cartesian displacement of non-hydrogen atoms between free-cell energy-optimized structure and final Rietveld refined structure is 0.311 Å, which is higher than expected for a high-quality powder structure but has not surpassed the upper RMS limit for a corect structure (van de Streek and Neumann, Reference van de Streek and Neumann2014). We believe that the main source of the error is preferred orientation. Comparison of the final Rietveld refined structure with variable cell energy-minimized structure is shown in Figure 2.
Figure 2. Comparison of the Rietveld-refined (red) and energy-optimized (blue) structures of 5-(3-methoxyphenyl)isatin.
Mogul check (2020 version, with default parameters) indicates that the C2–N1 and C2–C3 bond distances in the structure of 5-(3-methoxyphenyl)isatin are unusual, with Z-scores of 4.8 and 4.6. The deviation from Mogul's mean values was not unexpected as corresponding bond distances of the significant number of N-unsubstituted isatins are also marked as unusual.
Platon/checkCIF yields an alert on the long (1.58 Å) C1(sp2)–C4(sp2) bond. The elongation of this bond compared with mean values is also intrinsic for N-unsubstituted isatin derivatives.
Figure 3 depicts the asymmetric unit (with atom numbering) and the packing of 5-(3-methoxyphenyl)isatin is presented in Figure 4.
Figure 3. The asymmetric unit of 5-(3-methoxyphenyl)isatin, with the atom numbering. The atoms are represented by 50% probability spheroids.
Figure 4. Fragment of the crystal packing of 5-(3-methoxyphenyl)isatin.
The isatin molecule contains one classical hydrogen bond donor (N1–H4) and two hydrogen bond acceptors (O1, O2). Therefore, the structure motifs of isatin derivatives are diverse, compared to other small rigid molecules. It forms H-bonded centrosymmetric dimers (Golen and Manke, Reference Golen and Manke2016), two types of chains (N1–H⋯O1 (Wei et al., Reference Wei, Tian, Zhou, Sun and Wang2010) and N1–H⋯O2 (Manley-King et al., Reference Manley-King, Bergh and Petzer2011)) and cyclic tetramers with Z′ = 2 (Mohamed et al., Reference Mohamed, Barnett, Tocher, Price, Shankland and Leech2008).
The structure of title compound contains H-bonded N1–H⋯O2 (Figure 5) chains along the a direction. The chain is almost flat and additionally stabilized by a weak hydrogen bond C15–H8⋯O1. Corresponding pairwise interaction energy is 36 kJ/mol. The chains are arranged into layers by π-stacking; the corresponding pairwise energy is even higher –44 kJ/mol. The layers are connected with weaker C–H⋯π and C–H⋯O contacts (Figure 6).
Figure 5. The principal classical hydrogen bonds of 5-(3-methoxyphenyl)isatin.
Figure 6. The bilayers of 5-(3-methoxyphenyl)isatin chains, connected with C–H⋯π and C–H⋯O contacts.
The Rietveld plot is included in Figure 7. Observed diffraction patterns are in good agreement with the calculated pattern. The largest errors in the fit are in the positions of some of the low-angle peaks and probably represent the changes in the specimen during the measurement.
Figure 7. Final observed (black), calculated (red), and difference profiles for the Rietveld refinement.
IV. DEPOSITED DATA
The Crystallographic Information File containing the results of the Rietveld refinement and the raw powder diffraction pattern was deposited with ICDD and can be requested at pdj@icdd.com. The crystal structure is also available from CCDC 2223458.
ACKNOWLEDGEMENTS
The study was funded by RFBR according to the research project 1933-60075. A.V.K. acknowledges financial support from the RFBR (project 20-33-90131) for the synthesis of the title compound.
