Synthesis, X-ray Diffraction, Thermogravimetric and DFT Analyses of Pyrimidine Derivatives

An eco-benign synthesis of pyrimidine derivatives 2a,b containing different functional groups with different electronic character starting from nitroalkenes 1a and 2b has been described. The structures for 1a and 2a,b have been characterized by single crystal X-ray diffraction analysis. The thermal data of the molecules pointed towards important structural aspects of their stability. The mechanism of their thermal decomposition is discussed. The thermodynamic parameters of the dissociation steps were evaluated and discussed. DFT calculations reveal that the compound 1a possesses a high calculated dipole moment value (8.28 D) which indicates its high reactivity towards its surrounding molecules.

SADABS [24]. The structure was solved by direct method using the program SHELXTL [25] and were refined by full-matrix least squares technique on F 2 using anisotropic displacement parameters. The non-hydrogen atoms were refined anisotropically. In these compounds, all the H atoms were calculated geometrically with isotropic displacement parameters set to 1.2 times the equivalent isotropic U values of the parent carbon atoms.
The title compound 1a, C8H5Cl2NO2, which crystallizes in the monoclinic space group P 21/c comprises one crystallographically independent molecule in its asymmetric unit, as depicted in Figure 1. In the crystal structure (Figure 2A), there is an intramolecular C7-H7A· · · O2 hydrogen bond. The crystal is essentially consolidated by Van Der Waals interactions. The crystal data and parameters for structure refinement of the title compound are given in Table 1. Selected geometric parameters are given in Table 2. H-bonding interactions are listed in Table 3.
The title compound 2a, C14H13Cl2N3O5· H2O, which crystallizes in the trigonal space group R-3 comprises one crystallographically independent molecule with disorder in the phenyl ring and a water molecule in its asymmetric unitas shown in Figure 1. Figure 2B shows the crystal packing for the major and minor components of 2a respectively with occupancy ratio 0.755:0.245. There are two intermolecular C6-H6A· · · O2 and C9-H9A· · · O3 hydrogen bonds ( Table 5). The crystal structure is further consolidated by Van Der Waals interactions. The crystal data and parameters for structure refinement of the title compound are given in Table 1. Selected geometric parameters are given in Table 4. H-bonding interactions are listed in Table 5. The title compound 2b, C14H13Cl2N3O5, which crystallizes in the monoclinic space group Cc comprises one crystallographically independent molecule in its asymmetric as shown in Figure 1. In the crystal structure ( Figure 2C), there are two intermolecular C6-H6A· · · O1 and C13-H13C· · · O5 hydrogen bonds ( Table 7). The crystal is further consolidated by Van Der Waals interactions. The crystal data and parameters for structure refinement of the title compound are given in Table 1. Selected geometric parameters are given in Table 6. H-bonding interactions are listed in Table 7.   Table 3. Hydrogen-bond geometry (Å, °) of compound 1a.

Optimized Molecular Geometry
From the XRD data, it is clear that the compounds 1a and 2b possess monoclinic, whereas, 2a has trigonal crystal structures. The cell dimensions and other data are tabulated in Table 1. Selected values of experimental and DFT calculated geometric parameters for the compounds are listed in Tables 2, 4, 6 and 8. Figure 3 shows the optimized structures for 1a and 2a,b.

Experimental and Calculated IR Vibrations
The calculated (B3LYP/6-311G) and experimental C-H, C-Cl, N=O, C=O, and C=C vibration values for all the molecules have good agreement, except for C=O for 2a. For 2a, the computed C=O stretching vibrations at 1894 cm −1 deviated substantially from the experimental result. A plausible reason for this could be the intermolecular interactions present in solid state whereas during DFT calculations the molecule is assumed to be in isolated gaseous state.

Geometric Parameters
The solid state X-ray structure analysis revealed disorder in the phenyl moiety for 2a (see Figure 2). This incongruity noted between the calculated and the experimental vibrational frequencies may be due to the fact that the calculations have been actually performed on a single molecule in the gaseous state contrary to the experimental values recorded in the solid state. In DFT calculations, bond lengths and angles have been reported only for the major component of the phenyl moiety of 2a (designated by the suffix "A"). The selected calculated and experimental geometric parameters for 1a and 2a,b have been tabulated in Tables 2, 4 and 6.

Thermal Gravimetric Analysis (TGA)
The synthesized novel compounds were subjected to thermogravimetric analysis (TGA) to evaluate their thermal stability and degradation patterns (Table 9) and the TGA and DTG patterns are shown in Figure 5. All samples were subjected to analysis in a nitrogen atmosphere in the temperature range from 30 °C to 800 °C with a heating ramp rate of 10 °C per min. It was observed that the different nitrostyrene derivatives displayed different thermal stabilities and degradation patterns. The pyrolysis processes of the materials are characterized by single-stage degradation, with an exception of 2a, which displays two-stage degradation. Interestingly, it was detected that upon the incorporation of the barbituric acid ring into the styrene, the resulting molecule was slightly more thermally stable than its precursor. The weight loss pattern of all the compounds was found to be different at different intervals with 1a,b displaying a weight loss of 70% and 98% respectively at 200 °C, but at the same temperature the weight loss percentage for the barbituric acid derivatives 2a,b were found to be 48% and 18 % respectively. When a comparison of thermal degradation pattern between 1a and 2a was made it was found that 1a undergoes single stage degradation with decomposition range of 100-190 °C (90 °C), while 2a displays two stage degradation with decomposition taking place in the range of 105-195 °C (90 °C) and 200-275 °C (75 °C). The degradation temperature range of 1b and 2b was found to take place at a 162-262 °C (100 °C) and 125-230 °C (105 °C), respectively. The peak temperature of 2b (220.02 °C) was higher than that of 1b (199.38 °C), while the decomposition intensity of 1b was found to be high with 2.35 wt %/°C compared to 1.99 wt %/°C 2b. This behaviour can be attributed to the presence of barbituric acid. However, when the temperature was increased further all the compounds followed similar weight loss patterns with varying percentages of residue at the final temperature of 800 °C. From the residual weight values obtained at ~800 °C it can be concluded that there is no significant thermal stability among any of the four compounds tested, however it can be said that thermal stability of the barbituric acid derivative of the styrene molecule is slightly improved compared to that of its precursor. The weight loss percentage at different temperatures is mentioned in the table below and a comparative graphical representation of the compounds is given in Figure 5. A detailed study into the thermal behaviour of the synthesized compounds shall be carried out the thermal kinetics will be reported separately.