Research Article | Open Access
Hakan Bülbül, Yavuz Köysal, Necmi Dege, Sümeyye Gümüş, Erbil Ağar, "Crystal Structure, Spectroscopy, SEM Analysis, and Computational Studies of N-(1,3-Dioxoisoindolin-2yl)benzamide", Journal of Crystallography, vol. 2015, Article ID 232036, 6 pages, 2015. https://doi.org/10.1155/2015/232036
Crystal Structure, Spectroscopy, SEM Analysis, and Computational Studies of N-(1,3-Dioxoisoindolin-2yl)benzamide
The compound N-(1,3-dioxoisoindolin-2yl)benzamide, C15H10N2O3, was prepared by the heating of an ethanolic solution of 2-hydroxy-1H-isoindole-1,3(2H)-dione and 4-chloroaniline. The product was characterised using a combination of IR spectroscopy, SEM, and single crystal X-ray diffraction techniques. In addition to the experimental analysis, theoretical calculations were used to investigate the crystal structure in order to compare experimental and theoretical values. The X-ray diffraction analysis shows that the compound crystallises in the monoclinic space group with the geometric parameters of , , , and °. The crystal structure is held together by a network of N-H⋯O hydrogen bonds involving the carboxamide group.
The molecular structure of N-(1,3-dioxoisoindolin-2yl)benzamide contains isoindoline and benzamide moieties. Benzamide groups show various pharmaceutical activities including antiemetic, antipsychotic, and antiarrythmic , anti-inflammatory, immunomodulatory, antitumoral, and antiallergic activities  and are also known to have important bioactive frameworks . Isoindoline derivatives show anti-inflammatory, antipsychotic, antileukemic, antiviral, and antiulcer properties [4–6]. It is reported that disubstituted isoindolines display antibacterial, diuretic, and antitumor activity. Isoindolines, substituted with carboxylic acid groups, have been employed in SAR studies and also as candidates for organic light emitting diodes . As a part of our ongoing research on benzamide and isoindoline derivatives, the title compound was synthesized and characterized by various methods.
2.1. Synthesis and Crystallization
The compound N-(1,3-dioxoisoindolin-2yl)benzamide (Scheme 1) was prepared by a refluxing mixture of a solution containing 2-hydroxy-1H-isoindole-1,3(2H)-dione (0.0095 g 0.058 mmol) in 20 mL ethanol and a solution containing 4-chloroaniline (0.0158 g 0.116 mmol) in 20 mL ethanol. The reaction mixture was stirred for 1 h under reflux. The crystals of N-(1,3-dioxoisoindolin-2yl) benzamide suitable for X-ray analysis were obtained from ethylalcohol by slow evaporation (yield 53%; m.p = 471–479 K).
Data collection of the title compound, C15H10N2O3, was performed with STOE IPDS II single crystal X-ray diffractometer using graphite monochromated Mo radiation (λ = 0.71073 Å) at room temperature (293 K). Cell parameters were obtained by using X-AREA  and data reduction was achieved with X-RED32  software. In total, 12087 reflections were collected with angles in the range using the ω scan mode. The structure was solved and refined with SHELXS97  and SHELXL-97  software. Molecular graphics were created using ORTEP-3 . WinGX  was used to prepare the data for publication.
All nonhydrogen atoms were refined anisotropically. The carboxamide hydrogen atom (H2A), bonded to (N2), was located in the Fourier difference map and refined isotropically. All other H atoms were placed geometrically and refined with their parent atoms with usable riding model C-H = 0.93 Å for aromatic ring, ]. The details of the experimental and refinement process are shown in Table 1.
3. Results and Discussion
3.1. Crystal Structure Description
The location the hydrogen atom on the N2 atom confirms that the structure adopts the amide form rather than the enolic form (Figure 1). The amide links the dioxoisoindolin and arene groups. The individual aromatic rings in structure are essentially planar. The fused isoindoline ring is perfectly planar with a maximum deviation of 0.018(2) Å for C8, while the arene ring (C10–C15) is also planar with a maximum deviation of −0.007(4) Å for C13. The fused isoindoline ring makes a dihedral angle of 65.45 (7)° to the arene ring. The bond parameters in the structure are closely related to values in closely related structures [12–14]. The torsion angle C10-C9-N2-N1 is 179.68(18)° which confirms that the side chain conformation of the molecule is defined as the anticonformation. The independent molecules within the crystal are linked by N-H⋯O hydrogen bonds [N2-H2A⋯O3 with symmetry code (i): x, −y + 1/2, z + 1/2] that generate C4 motif  which links the molecules infinite chain along the c axis (Figure 2). The detail of the hydrogen bond is shown in Table 2.
3.2. Computational Methods
In order to obtain the most optimized geometry, theoretical calculations were performed with ab initio HF and DFT(B3LYP) method by using the standard basis set of 6-31+G(d) [16–19] in the Gaussian03 software package  and Gaussview4.1 visualization program .
3.3. Optimized Geometry
The total energy of the title compound was calculated using the B3LYP/6-31+G(d) which is (−912,84239530 a.u.) lower than that calculated by the HF/6-31+G(d) method (−907.39330891 a.u.). Selected optimized parameters (bond lengths, bond angles, and torsion angles) are listed in Table 3 with related experimental and theoretical values. All of these optimized parameters are obtained from experimental X-ray analysis and theoretically calculated by HF/6-31+G (d) and B3LYP/6-31+G (d) methods. It is seen that obtained optimized parameters show a good approximation with X-ray results. But some of these optimized parameters are somewhat different from experimental values. It is because the theoretical calculations are made for isolated molecules in gaseous phase while experimental results are based on solid phase of the molecule [22, 23]. The most notable discrepancy occurs at C8-N1-N2-C9 torsion angle (−91.2(3)° for X-ray, −74.3417° for DFT, and −72.6382° for HF) which is partially involved in the hydrogen bond. It can be considered that intermolecular interaction affects the crystal system. The bridged C10-C9-N2-N1 torsion angle was obtained as 179.68(18)° for X-ray results. This torsion angle has been calculated as 174.620° and 174.582° for DFT and HF levels, respectively. Root-mean-square-error (RMSE) was obtained with selected theoretical values. Calculated RMSE for selected bond lengths and bond angles are 0,0198 Å, 0,606° for B3LYP/6-31+G(d) level, and 0,0145 Å, 0,753° for HF/6-31+G(d) level, respectively. As a result of these calculations, it can be interpreted that B3LYP/6-31+G(d) level is giving more consistent results with X-ray experimental values.
3.4. Molecular Electrostatic Potential (MEP)
To illustrate the charge distribution of the title compound, the molecular electrostatic potential (MEP) was investigated by B3YLP function theory with the standard basis set of 6-31+G(d). Electrostatic potential, , that is formed by nuclei and electrons of the system at given point is defined as where is the charge of nucleus that is located at , is electron density function of molecule, and is the dummy integration variable. Molecular electrostatic potential (MEP) gives information of electrophilic attack and nucleophilic reactions besides hydrogen bonding interactions [25–28]. To interpret the molecular electrostatic potential (MEP) easily, a colored spectrum was used. From this spectrum the blue regions indicate positive molecular electrostatic potentials which are the preferred sites for nucleophilic attack while the red regions indicate negative molecular electrostatic potentials which are the preferred sites for electrophilic attack. As seen from Figure 3, the negative regions were mainly condensed on O atoms of the molecule with the maximum value of −0.053 a.u. for atom O3 whereas positive regions were localized on N2-H2A bond of the amide group in the studied molecule with maximum value of 0.0548 a.u. These values give information where the molecule tends to have hydrogen bond interactions. The obtained MEP results would help in understanding intermolecular hydrogen bond N2-H2A⋯O3 which is obtained from X-ray analysis.
3.5. Scanning Electron Micrography (SEM)
Surface morphology of the grown crystal, N-(1,3-dioxoisoindolin-2yl)benzamide, was investigated by scanning electron microscope. SEM measurements were performed at FEI-Quanta FEG 250. The surface morphology and particle size of the title compound, C15H10N2O3, have been shown in Figure 4. From the SEM micrographs, it can be seen that particles have nonuniform distribution. The structural morphology consists of foam-like shape. SEM images were taken 20000x and 5000x magnifications with acceleration voltage of 3-4 kV.
3.6. IR Spectra
The experimental FTIR spectra were collected by using KBr Pellets on Schmadzu 8900 FT-IR spectrophotometer and shown in Figure 5. Obtained frequencies were recorded in wave number cm−1. In this section of the study, vibrational frequencies calculated at B3YLP/6-31+G(d) and HF/6-31+G(d) levels and scaled by 0.9613 and 0.8929, respectively [29, 30]. As seen from Table 4, calculated and experimental values are in good agreement to each other. The broadest absorption was observed at 3350 cm−1 due to the N-H stretching of bridged moiety. Theoretically this band calculated at 3460 cm−1 and 3462 cm−1 for B3YLP and HF methods, respectively. N-H stretching vibration was observed at 2500–3500 cm−1 band range with related structure . Aromatic rings have the C-H stretching vibrations assigned to 3100–3000 cm−1 . For the title molecule, C-H stretching vibration was observed at 3100 cm−1 while theoretical values have been calculated at 3098 cm−1 for B3YLP/6-31+G(d) and 3038 cm−1 for HF/6-31+G(d) methods. For the title compound, C=O symmetric stretching mode and asymmetric stretching mode were observed at 1790 cm−1 and 1749 cm−1 for dioxoisoindolin group, respectively. All these experimental vibrational assignments are in agreement with related compound . Calculated values of the C=O symmetric stretching mode were 1778 cm−1 and 1843 cm−1 for B3YLP and HF, respectively. These asymmetric stretching frequencies were computed at 1734 cm−1 and 1788 cm−1 for B3YLP and HF, respectively. C=O vibration of the amide group was observed at 1716 cm−1 experimentally. Presence of these spectroscopic values (N-H and C=O vibrations) shows that the title molecule has ketoamine tautomeric form [34, 35]. The details of the spectral values are shown in Table 4.
|Note: ν, stretching; γ, rocking; , wagging; s, symmetric; as, asymmetric; R, ring.|
In this paper we have investigated the molecular structure of N-(1,3-dioxoisoindolin-2yl)benzamide, using single crystal X-ray diffraction, IR spectroscopy, and computational methods. The results obtained show that the X-ray crystal structure and computational methods are consistent with each other. There was particularly good agreement using the DFT (B3LYP) with the 6-31+G(d) basis set. The structural X-ray analysis has indicated that the crystal structure is stabilized by N-H⋯O hydrogen bonding. These results were consistent with those obtained by a MEP analysis. The calculated and observed N-H and C=O vibrations in the IR spectrum confirm the ketoamine tautomeric form of the structure. The surface morphology was also studied by SEM analysis and the results indicate a nonuniform distribution for the sample.
Conflict of Interests
The authors declare that there is no conflict of interests regarding the publication of this paper.
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