CHAPTER 6 CRYSTAL STRUCTURE OF A DEHYDROACETIC ACID SUBSTITUTED SCHIFF BASE DERIVATIVE
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1 139 CHAPTER 6 CRYSTAL STRUCTURE OF A DEHYDROACETIC ACID SUBSTITUTED SCHIFF BASE DERIVATIVE 6.1 INTRODUCTION This chapter describes the crystal and molecular structure of a dehydroacetic acid substituted Schiff base derivative, namely, 3-[1-(4-Bromophenylamino)-ethylidene]-6-methyl-pyran-2,4-dione (BPMP). 6.2 EXPERIMENTAL Crystallization The compound BPMP was synthesized by refluxing an ethanol solution (20ml) of 4-Bromoaniline (2 mmol) and dehydroacetic acid (2 mmol) for 10 hrs. Upon cooling to 0 C, a colourless salt product was obtained. The precipitate was filtered off, washed with ice-cold methanol and dried in vacuum. A prism shaped, colourless single crystals of good diffraction quality were obtained by recrystallization of the compound with ethanol solution. The rate of slow evaporation was controlled by covering the lid of the container with aluminum foil and making small holes in it and placed in a room without much air and mechanical disturbance. BPMP. Figure 6.1 shows the chemical diagram of the molecular compound
2 140 O Br O N OH Enol form O Br O N O H Keto form Figure 6.1 Chemical diagram of the BPMP Intensity Data Collection A single crystal of size mm of BPMP was selected and used for X-ray diffraction experiments. Intensity data for the compound was collected on Bruker AXS Apex-II CCD diffractometer with MoK radiation and ω and φ scan mode at room temperature. Accurate unit cell parameters and orientation matrix for BPMP were obtained by a leastsquares fit of several reflections in the ranges 15< <50. The intensity data for the reflections in the range 1.52 to were collected. Thirty-six initial frames were collected and the reflections were checked for any intensity decay and were no significant decay. A total of reflections were collected, resulting in 4345 independent reflections of which 2374 had I > 2 (I) and were considered as observed. The intensities were corrected for Lorentz and polarization effects. The multi-scan absorption correction was also applied for the compound.
3 Structure Solution and Refinement Crystal structure of BPMP was solved by direct methods procedures as implemented in SHELXS reflections with E > 1.2 reflections were available for phase refinement procedures and 256 phase sets have been refined of which the set with lowest Combined Figure of Merit (CFOM = ) was considered as the best set which revealed the positions of the non-hydrogen atoms and the residual factor calculated based on the point atom model, R E, was Full matrix least squares refinements were carried out based on the trial structure using SHELXL-97 program. Isotropic refinement was carried out initially for the non-hydrogen atoms until convergence. The reliability factor reduced to R = Few cycles of anisotropic refinement were continued and factor further decreased down to After convergence, the position of the hydrogen atom, H12, was deduced from a small peak (0.590 eå -3 ) in a difference Fourier map. The positions of other hydrogen atoms were geometrically fixed and allowed to ride on the corresponding non-hydrogen atoms with C-H = Å and their temperature factors were set equal to 1.2U eq times of the carrier atoms. A suitable weight was given for individual reflections using the formula given in the equation 1.12 with K1 = and K2 = The refinement converged to final R-factors of R1 = , wr2 = The residual electron density was observed in the final difference Fourier map with and eÅ -3 as maximum and minimum values respectively. 6.3 STRUCTURE ANALYSIS Table 6.1 summarizes the crystal data, intensity data collection and refinement details. The atomic coordinates of the non-hydrogen atoms with their equivalent temperature factors are presented in Table 6.2. The bond lengths and bond angles are given in Table 6.3 and 6.4 for the compound. The torsion angles for the non-hydrogen atoms are listed in Table 6.5. The leastsquares planes calculated are tabulated in Table 6.6.
4 Intramolecular Features Figure 6.2 shows the thermal ellipsoid plot of the compound BPMP drawn at 50% probability level with atom numbering scheme. Two types of intramolecular hydrogen bonds (either N-H O or N H O) can exist in Schiff bases and these hydrogen bonds form five-or six-membered rings, of which the latter is found to be stronger than the former one due to the acquisition of a quasi-aromatic type in the latter case (Garnovskii et al 1993). X-ray structural analysis of BPMP reveals that the proton from the hydroxyl group of the pyrone moiety has been transferred to the nitrogen atom facilitating the formation of intramolecular N-H O hydrogen bond, rather than the N H O hydrogen bond. The present investigation indicates that the keto-amine tautomer is favoured for the compound BPMP over the phenolimine tautomer. The bond lengths with in the vicinity of the N and O atoms are consistent with this interpretation. The C2 O7 bond is the most sensitive indicator of the type of tautomeric form. This is a single bond for the enol-imino tautomer, while it is shortened in the keto-amino tautomers. In contrast, C10 N12 bond is lengthened to a single bond in the keto-tautomer, while in the enol tautomer it is a double bond. The C2 O7 and C10 N12 bond lengths of the compound BPMP are 1.254(3)Å and 1.312(3)Å, respectively and correspond to the keto-amine tautomer. These values are comparable to those found in 3-[1-(4- Methoxyphenylamino)ethylidene]-6-methyl-3H-pyran-2,4-dione and 3-[1-(4- Chlorophenylamino)ethylidene]-6-methyl-3H-pyran-2,4-dione (Gilli et al 2000). This is also supported by the conjugation observed in the localized intramolecular loop comprising O7-C2-C3-C10-N12-H. The bond lengths in this section are, O7-C2, 1.254(3)Å; C2-C3, 1.439(3)Å; C3-C10, 1.426(3)Å;
5 143 C10-N12, 1.312(3)Å showing conjugated alternating single and double bonds allowing pi-electron movement (Gilli et al 2000). The bond lengths C4-O8 [1.206(3)Å], C4-O5 [1.394(3)Å], O5-C6 [1.359(3)Å], C1-C6 [1.316(4)Å], C1-C2 [1.483(3)Å] agree well with the related α-pyrone derivatives (Kakehi et al 1993; Thailambal and Vasantha Pattabhi, 1985). The C-C bond lengths in the phenyl ring are normal and have an average value of 1.377(4)Å while C-Br bond length is 1.894(3)Å for the compound BPMP. In the compound BPMP, the C2, C3, C4, C6, C10, C13 and C16 atoms take sp 2 hybridization state with the sum of valence angles around them is approximately 360. The widening of the angle C3-C2-O7 [129.38(25) ] in the pyrone moiety is probably enhanced by the steric interactions between the methyl group C11 and O7 atom. Such widening has been observed in the case of 3-acetyl-4-hydroxy-6-phenyl-2-pyrone (Thailambal and Vasantha Pattabhi 1985). The torsion angle C10-N12-C13-C18 is 52.4(4) which is mainly responsible for the twist between the pyrone ring and phenyl ring. The bridge atoms C3, C10, N12 and C13 lie in the same plane. The pyrone ring is planar with keto oxygen atoms O7 and O8 and the methyl carbon atom C9 lying in the same plane. The bromine substituted phenyl ring plane is inclined to the plane of the pyrone ring by 52.7(1) Intermolecular Features In this crystal structure, a C-H O intermolecular hydrogen bond between O7 and C11 atoms [C11-H11A O7 (symmetry code: x, -y, z+1/2)] connects molecules into an infinite chain running along the c-axis as shown in Figure 6.3. The details are C11-H11A = 0.96Å; H11A...O7 = 2.53Å; C11...O7 = 3.280(3)Å; C11-H11A O7 =
6 Figure 6.2 Thermal Ellipsoid plot (50% probability level) of BPMP 144
7 Figure 6.3 Packing of molecules of BPMP viewed down b-axis 145
8 146 Table 6.1 Crystal data and other relevant details for BPMP Identification code BPMP Empirical formula C14 H12 Br N O3 Formula weight Temperature (K) 293(2) Wavelength (Å) Crystal system Orthorhombic Space group P b c n Unit cell dimensions a(å) (7) b(å) (3) c(å) 9.710(2) α( ) 90 β( ) 90 γ( ) 90 Volume (Å 3 ) (1) Molecules/Unit cell, Z 8 Density calculated, D c (Mgm -3 ) Absorption coefficient (mm -1 ) F(000) 1296 Crystal size (mm) range for data collection ( ) 1.52 to Limiting indices h -39 to 37 k -14 to 14 l -14 to 14 Reflections collected / unique / 4345 R(int) / R(sigma) / Completeness to theta = % Absorption correction method Multi-scan absorption correction Data / restraints / parameters 4345 / 0 / 177 Goodness-of-fit on F Final R indices [I>2sigma(I)] R1 = , wr2 = R indices (all data) R1 = , wr2 = Largest diff. peak and hole(eå -3 ) and
9 147 Table 6.2 Atomic co-ordinates ( 10 4 ) and equivalent isotropic displacement parameters (Å ) of BPMP Atom x y z U(eq) C1 1596(1) -267(3) -2708(3) 46(1) C2 2077(1) 170(2) -2247(2) 36(1) C3 2089(1) 1278(2) -1324(2) 34(1) C4 1631(1) 1910(3) -944(3) 42(1) O5 1187(1) 1390(2) -1468(2) 54(1) C6 1182(1) 329(3) -2320(3) 53(1) O7 2461(1) -414(2) -2669(2) 44(1) O8 1563(1) 2844(2) -200(2) 66(1) C9 660(1) -27(4) -2724(4) 86(1) C (1) 1745(2) -778(2) 35(1) C (1) 2876(2) 176(2) 43(1) N (1) 1126(2) -1172(2) 41(1) C (1) 1338(2) -772(2) 39(1) C (1) 1427(3) -1801(3) 47(1) C (1) 1585(3) -1470(3) 54(1) C (1) 1656(3) -109(3) 48(1) C (1) 1546(3) 925(3) 51(1) C (1) 1376(3) 590(3) 48(1) Br (1) 1935(1) 323(1) 70(1) U (eq) = (1/3) i j U ij a i * a j * a i. a j
10 148 Table 6.3 Bond lengths (Å) for non-hydrogen atoms for BPMP Atoms BPMP C1 C (4) C1 C (3) C2 O (3) C2 C (3) C3 C (3) C3 C (3) C4 O (3) C4 O (3) O5 C (3) C6 C (4) C10 N (3) C10 C (3) N12 C (3) N12 H (3) C13 C (3) C13 C (3) C14 C (4) C15 C (4) C16 C (4) C16 Br (3) C17 C (4)
11 149 Table 6.4 Bond Angles (º) for non-hydrogen atoms of BPMP Atoms BPMP C6 C1 C (2) O7 C2 C (2) O7 C2 C (2) C1 C2 C (2) C10 C3 C (2) C10 C3 C (2) C4 C3 C (2) O8 C4 O (2) O8 C4 C (3) O5 C4 C (2) C6 O5 C (2) C1 C6 O (2) C1 C6 C (3) O5 C6 C (3) N12 C10 C (2) N12 C10 C (2) C3 C10 C (2) C10 N12 C (2) C10 N12 H (18) C13 N12 H (18) C14 C13 C (2) C14 C13 N (2) C18 C13 N (2) C15 C14 C (2) C14 C15 C (3) C17 C16 C (3) C17 C16 Br (2) C15 C16 Br (2) C16 C17 C (2) C17 C18 C (2)
12 150 Table 6.5 Torsion angles (º) for non-hydrogen atoms of BPMP Atoms BPMP C6 C1 C2 O (3) C6 C1 C2 C3 0.9(4) O7 C2 C3 C10 2.8(3) C1 C2 C3 C (2) O7 C2 C3 C (2) C1 C2 C3 C4 1.8(3) C10 C3 C4 O8 0.9(4) C2 C3 C4 O (3) C10 C3 C4 O (2) C2 C3 C4 O5 1.7(3) O8 C4 O5 C (2) C3 C4 O5 C6 0.5(4) C2 C1 C6 O5 0.2(4) C2 C1 C6 C (3) C4 O5 C6 C1 0.4(4) C4 O5 C6 C (3) C4 C3 C10 N (2) C2 C3 C10 N12 0.7(3) C4 C3 C10 C11 0.3(3) C2 C3 C10 C (2) C3 C10 N12 C (2) C11 C10 N12 C13 2.9(4) C10 N12 C13 C (3) C10 N12 C13 C (4) C18 C13 C14 C15 1.5(4) N12 C13 C14 C (3) C13 C14 C15 C16 0.2(5) C14 C15 C16 C17 1.3(5) C14 C15 C16 Br (2) C15 C16 C17 C18 0.7(5) Br19 C16 C17 C (2) C16 C17 C18 C13 0.9(5) C14 C13 C18 C17 2.0(4) N12 C13 C18 C (3)
13 151 Table 6.6 Mean planes through various groups of atoms and deviation (Å) from the plane for BPMP The equation of the plane: m1x+m2y+m3z-d=0, where m1, m2, m3 and D are constants Plane m1 m2 m3 D Atoms Deviation (1) (9) (7) 2.209(4) C (3) C (2) C (2) C (3) O (2) C (3) O7* 0.040(2) O8* 0.005(2) C9* (4) (9) 0.631(3) (2) 2.380(6) C (2) C (2) N (2) C (3) (1) (6) (5) 2.274(7) C (2) C (2) C (2) N (2) H (3) O (2) (1) (2) (1) 0.24(1) C (3) C (3) C (3) C (3) C (3) C (3) Br19* (4) *Starred atoms are not included for plane calculation Dihedral angles ( ) Plane Plane Angle (1) (6) (1) (1) (2)
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