Structural Chemistry & Crystallography Communication

Keywords

Halogen atoms; Epoxides; Xenobiotic compounds

Introduction

Compounds with epoxy group are found to be useful in paints, composite formations, and development of adhesins as well as in many microelectronic applications with biphenyl-type epoxy compounds [1-3]. Epoxides are three-membered oxygen compounds, generated when endogenous as well as xenobiotic compounds undergo oxidative metabolism via chemical and enzymatic oxidation processes. The epoxides are generally unstable in aqueous environments and highly reactive. These epoxide intermediates have been implicated as potential mutagenic and carcinogenic agents [4,5]. In view of the above said properties, structural analyses of such epoxy containing compounds are carried out by many investigators. The present study explains the structural details of three epoxy derivatives.

Experimental

Synthesis of Compound I

The reaction of 5-fluoro-2-nitrobenzaldehyde (0.5 g, 2.95 mmol) with triethyl phosphite (0.98 g, 5.91 mmol) in the presence of ZnBr₂ (0.07 g, 0.29 mmol) at room temperature for 20 min followed by different procedures using the above mentioned general procedure gave trans-epoxide as a colorless solid. Single crystals suitable for X-ray diffraction experiments were obtained by slow evaporation of the compound in chloroform/ethyl acetate. The schematic diagram of compound I is as follows:

Synthesis of Compound II

The reaction of 5-bromo-2-nitrobenzaldehyde (0.5 g, 2.17 mmol) with triethyl phosphite (0.72 g, 4.34 mmol) in the presence of ZnBr₂ (0.05 g, 0.21 mmol) at room temperature for 10 min followed by different procedures using the above mentioned general procedure furnished trans-epoxide as a colorless solid. Single crystals suitable for X-ray diffraction studies were obtained by slow evaporation of the compound in chloroform/ethyl acetate. The schematic diagram of compound II is as follows:

Synthesis of Compound III

The reaction of 4-chloro-2-nitrobenzaldehyde (0.5 g, 2.69 mmol) with triethyl phosphite (0.89 g, 5.39 mmol) in the presence of ZnBr₂ (0.06 g, 0.27 mmol) at room temperature for 10 min followed by different procedures using the above mentioned general procedure furnished trans-epoxide 2b as a colorless solid. Single crystals suitable for X-ray diffraction studies were obtained by slow evaporation of the compound in chloroform/ ethyl acetate. Schematic diagram of compound III is as follows:

Data collection

X-ray diffraction intensity data were collected for all three compounds on Bruker Kappa Apex II single crystal X-ray diffractometer equipped with graphite mono- chromate CuKα (λ=1.54178 Å )radiation and CCD detector. Crystals were cut to suitable size and mounted on a glass fibre using cyano acrylate adhesive. The unit cell parameters were determined from 36 frames measured (0.5° phi-scan) from three different crystallographic zones and using the method of difference vectors. The intensity data were collected with an average fourfold redundancy per reflection and optimum resolution (0.75 Å). The intensity data collection, frames integration, Lorentz and polarization correction and decay correction were done using SAINT-NT (version7.06a) software. Empirical absorption correction (multi-scan) was performed using SADABS program.

Result and Discussion

Structure solving and refinement

Crystal structure was solved by direct methods using SHELXS-97. All the non hydrogen atoms were located without any difficulty. The structure was then refined by full-matrix least-squares method using SHELXL- 97. They arrived model was refined using isotropic thermal parameters followed by anisotropic thermal parameters refinements. After completion of the refinement where R factor is converged with negligible shift/e.s.d and agreeable GooF and other parameters, hydrogen atoms were positioned geometrically C—H=0.93–0.98 Å and allowed to ride on their parent atoms, with U_iso(H) =1.5U_eq(C) for methyl H 1.2U_eq(C) for other H atoms. The relevant details of crystal data table is given in Table 1.

Table 1: Crystal data for Compound I, Compound II and Compound III.

For Compound I

The molecular structure (ORTEP diagram) of compound I is shown in Figure 1. The bond lengths and bond angles are listed in Table 2. The epoxy ring (O12/C11/C13) plane is oriented axially with two fluro phenyl rings (C1—C6) and (C14—C19) makes dihedral angles of 66.75(19)° and 64.79\(18)°, respectively. The dihedral angle between the two fluro phenyl rings is 55.89(11)°. The nitro group (N20/O21/O22) is lie in a plane with one of the fluro phenyl ring (C14-C19/F23) which evidenced by the torsion angle values are [C14/C15/N20/O21=] 3.2(3)° and [C16/C15/ N20/O22=] 2.3(3)° and another nitro group (N7/O8/O9) is not lie in a plane with the fluro phenyl ring (C1-C6/F10). C-H…O types of intermolecular interaction makes R²₂(22) dimer ring motifs. C-H…O and C-H…F types hydrogen bond stabilize the crystal packing (Figure 2). Relevant hydrogen bond details are given in Table 3.

Table 2: Selected bond lengths (Å) and bond angles (°) for Compound I.

Table 3: Hydrogen bond interactions for Compound I [Å and =]. Symmetry codes: i) -1+x,y,z ii) -x,1/2+y,1/2-z iii) 1-x,2-y,-z and iv) 1-x,-1/2+y,1/2-z.

Figure 1: The molecular structure of compound I, showing the atomic numbering and displacement ellipsoids drawn at the 30% probability level.

Figure 2: The packing of the molecules compound I viewed down c-axis.

For Compound II

The molecular structure (ORTEP diagram) of compound II is shown in Figure 3. The bond lengths and bond angles are listed in Table 4. The epoxy ring (O3/C5/C6) plane is oriented axially with two bromo phenyl rings (C1—C4/C11/C12/Br2) and (C7—C14/ Br1) makes dihedral angles of 66.5(3)° and 70.3(3)°, respectively. The dihedral angle between the two bromo phenyl rings is 71.01(2)°. The nitro group (N1/O1/O2) is oriented with one of the bromo phenyl ring (C1-C4/C11/C12/Br2) the values of 32.0(2)° and another nitro group (N2/O4/O5) is oriented with the bromo phenyl ring (C7-C14/Br1) the values of 32.1(2)°. C-H…O types of intermolecular interaction makes R²₂ (22) dimer ring motifs. C-H…O types intra and inter molecular hydrogen bond stabilize the crystal packing (Figure 4). Relevant hydrogen bond details are given in Table 5 [6-12].

Table 4: Selected bond lengths (Å) and bond angles (°) for compound III.

Table 5: Hydrogen bond interactions for Compound II [Å and =]. Symmetry code: i) 2-x, -y, -z and ii) 1-x, 1-y, 1-z.

Figure 3: The molecular structure of compound II. Displacement ellipsoids are drawn at the 30% probability level. H atoms have been omitted for clarity.

Figure 4: The crystal packing of Compound II. H atoms not involved in hydrogen bonding (dashed lines) have been omitted for clarity.

For Compound III

The molecular structure (ORTEP diagram) of compound III is shown in Figure 5. The bond lengths and bond angles are listed in Table 6. The epoxy ring (O12/C11/C13) plane is oriented axially with two chloro phenyl rings (C1—C6/Cl7) and (C14—C19/Cl20) makes dihedral angles of 68.6(4) and 68.0(4)°, respectively. The dihedral angle between the two chloro phenyl rings is 63.6(3)°. The nitro group (N8/O9/O10) is oriented with one of the chloro phenyl ring (C1-C6/Cl7) with the angle of 10.6(4)° and another nitro group (N21/O22/O23) is oriented with the chloro phenyl ring (C14-C19/Cl20) with the angle of 10.2(3)°. C-H…O types of intermolecular interaction makes R²₂ (20) and R²₂ (10) dimer ring motifs. C-H…O types intra and inter molecular hydrogen bond stabilize the crystal packing (Figure 6). Relevant hydrogen bond details are given in Table 7.

Table 6: Bond Length and Bond Angle of Compound III.

Table 7: Hydrogen bond interactions for Compound III [Å and =]. Symmetry code: i) 1-x, 2-y, 1-z and ii) 2-x, 1-y, 1-z.

Figure 5: Perspective view of Compound III showing the thermal ellipsoids are drawn at 30% probability level. H atoms have been omitted for clarity.

Figure 6: The crystal packing of Compound III. Showing H atoms not involved in hydrogen bonding (dashed lines) have been omitted for clarity.

Acknowledgements

The authors are thankful to Institution of Excellence, University of Mysore for providing the single-crystal X-ray diffraction facility.

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