Synthesis, crystal structure, Hirshfeld surface and interaction energies analysis of 5-methyl-1,3-bis(3-nitrobenzyl)pyrimidine-2,4(1H,3H)-dione

Abstract

The title compound 5-methyl-1,3-bis(3-nitrobenzyl)pyrimidine-2,4(1H,3H)-dione was obtained by reaction of thymine with 3-nitrobenzylbromide in the presence of cesium carbonate. Characterization of the product was achieved by NMR spectroscopy and its stability was probed in basic condition using UV-Visible analysis. Furthermore, the molecular structure was confirmed by X-ray diffraction analysis. The compound crystallizes in orthorhombic Pna21 space group with unit cell parameters a = 14.9594 (15) Å, b = 25.711 (3) Å, c = 4.5004 (4) Å, V = 1731.0 (3) Å3 and Z = 4. The crystal packing of the title compound is stabilized by intermolecular hydrogen bond, π···π and C−H···π stacking interactions. The intermolecular interactions were furthermore analyzed through the mapping of different Hirshfeld surfaces. The two-dimensional fingerprint revealed that the most important contributions to these surfaces come from O···H (37.1%), H···H (24%) and H···C/C···H (22.6%) interactions. The interaction energies stabilizing the crystal packing were calculated and were presented graphically as framework energy diagrams. Finally, the energy-framework analysis reveals that π···π and C−H···π interactions energies are mainly dispersive and are the most important forces in the crystal.

Describing auxin solid state intermolecular interactions using contact descriptors, shape property and molecular fingerprint: comparison of pure auxin crystal and auxin-TIR1 co-crystal

“…For a best description and measure the weight of the different contacts, the molecular fingerprint is generally used. Indeed, the de and di are combined to generate a 2D histogram named molecular fingerprint (FP) plot [38,39]. Due the molecular diversity in the immediate environment, the fingerprint of a selected molecule is unique.…”

Describing auxin solid state intermolecular interactions using contact descriptors, shape property and molecular fingerprint: comparison of pure auxin crystal and auxin-TIR1 co-crystal

“…For a best description and measure the weight of the different contacts, the molecular fingerprint is generally used. Indeed, the de and di are combined to generate a 2D histogram named molecular fingerprint (FP) plot [38,39]. Due the molecular diversity in the immediate environment, the fingerprint of a selected molecule is unique.…”

Determination of Intermolecular Interactions of Nicotinamide Liganded Complexes of Co(II), Cu(II), Ni(II) and Zn(II) 4-Formilbenzoates by Hirshfeld Surface Analysis and Investigation of Interaction Energies.

“…The computation of energy frames was developed to better understand the topology of the overall interaction energies between the components of a crystal. Total intermolecular interaction energy (E tot) using scale factors of 1.057, 0.740, 0.871 and 0.618, respectively, using four energy terms (electrostatic (E ele ), polarization (E pol ), dispersion (E disp ) and exchangerepulsion (E rep ) ) are added together (Etse et al, 2020;Mackenzie et al, 2017;Madan Kumar, 2019). The closeness of the total energy values calculated in all four isostructural complexes is shown in Table 2.…”

Synthesis, crystal structure, DFT and Hirshfeld surface analysis of 4-fluoro-N-(1,3-dioxoisoindolin-2-yl)benzamide

“…Hirshfeld surface analysis was obtained utilizing the CIF file from single-crystal XRD analysis to quantify and depict multiple intermolecular contacts, and they were used to explore intermolecular interactions and their quantitative contributions [29]. The region on the surface where atoms make intermolecular interactions that are closer together than the sum of their Van der Waals radii is depicted by the color red.…”

Describing auxin solid state intermolecular interactions using contact descriptors, shape property and molecular fingerprint: comparison of pure auxin crystal and auxin-TIR1 co-crystal

“…For a best description and measure the weight of the different contacts, the molecular fingerprint is generally used. Indeed, the de and di are combined to generate a 2D histogram named molecular fingerprint (FP) plot [38,39]. Due the molecular diversity in the immediate environment, the fingerprint of a selected molecule is unique.…”

Determination of Intermolecular Interactions of Nicotinamide Liganded Complexes of Co(II), Cu(II), Ni(II) and Zn(II) 4-Formilbenzoates by Hirshfeld Surface Analysis and Investigation of Interaction Energies.

“…The computation of energy frames was developed to better understand the topology of the overall interaction energies between the components of a crystal. Total intermolecular interaction energy (E tot) using scale factors of 1.057, 0.740, 0.871 and 0.618, respectively, using four energy terms (electrostatic (E ele ), polarization (E pol ), dispersion (E disp ) and exchangerepulsion (E rep ) ) are added together (Etse et al, 2020;Mackenzie et al, 2017;Madan Kumar, 2019). The closeness of the total energy values calculated in all four isostructural complexes is shown in Table 2.…”

Synthesis, crystal structure, DFT and Hirshfeld surface analysis of 4-fluoro-N-(1,3-dioxoisoindolin-2-yl)benzamide

“…Hirshfeld surface analysis was obtained utilizing the CIF file from single-crystal XRD analysis to quantify and depict multiple intermolecular contacts, and they were used to explore intermolecular interactions and their quantitative contributions [29]. The region on the surface where atoms make intermolecular interactions that are closer together than the sum of their Van der Waals radii is depicted by the color red.…”

Describing auxin solid state intermolecular interactions using contact descriptors, shape property and molecular fingerprint: comparison of pure auxin crystal and auxin-TIR1 co-crystal

“…For a best description and measure the weight of the different contacts, the molecular fingerprint is generally used. Indeed, the de and di are combined to generate a 2D histogram named molecular fingerprint (FP) plot [38,39]. Due the molecular diversity in the immediate environment, the fingerprint of a selected molecule is unique.…”

Determination of Intermolecular Interactions of Nicotinamide Liganded Complexes of Co(II), Cu(II), Ni(II) and Zn(II) 4-Formilbenzoates by Hirshfeld Surface Analysis and Investigation of Interaction Energies.

“…The computation of energy frames was developed to better understand the topology of the overall interaction energies between the components of a crystal. Total intermolecular interaction energy (E tot) using scale factors of 1.057, 0.740, 0.871 and 0.618, respectively, using four energy terms (electrostatic (E ele ), polarization (E pol ), dispersion (E disp ) and exchangerepulsion (E rep ) ) are added together (Etse et al, 2020;Mackenzie et al, 2017;Madan Kumar, 2019). The closeness of the total energy values calculated in all four isostructural complexes is shown in Table 2.…”

Synthesis, crystal structure, DFT and Hirshfeld surface analysis of 4-fluoro-N-(1,3-dioxoisoindolin-2-yl)benzamide

“…Hirshfeld surface analysis was obtained utilizing the CIF file from single-crystal XRD analysis to quantify and depict multiple intermolecular contacts, and they were used to explore intermolecular interactions and their quantitative contributions [29]. The region on the surface where atoms make intermolecular interactions that are closer together than the sum of their Van der Waals radii is depicted by the color red.…”