European Journal of Chemistry 2020, 11(2), 91-99 | doi: | Get rights and content

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

Koffi Senam Etse (1,*) orcid , Laura Comeron Lamela (2) orcid , Guillermo Zaragoza (3) orcid , Bernard Pirotte (4) orcid

(1) Laboratory of Medicinal Chemistry, Center for Interdisciplinary Research on Medicines (CIRM), University of Liège, Quartier Hôpital B36 Av. Hippocrate 15 B-4000 Liège, Belgium
(2) Laboratory of Medicinal Chemistry, Center for Interdisciplinary Research on Medicines (CIRM), University of Liège, Quartier Hôpital B36 Av. Hippocrate 15 B-4000 Liège, Belgium
(3) Unidade de Difracción de Raios X, RIAIDT, Universidade de Santiago de Compostela, Campus VIDA, 15782 Santiago de Compostela, Spain
(4) Laboratory of Medicinal Chemistry, Center for Interdisciplinary Research on Medicines (CIRM), University of Liège, Quartier Hôpital B36 Av. Hippocrate 15 B-4000 Liège, Belgium
(*) Corresponding Author

Received: 19 Feb 2020 | Revised: 22 Mar 2020 | Accepted: 24 Mar 2020 | Published: 30 Jun 2020 | Issue Date: June 2020


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.


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European Journal of Chemistry


Thymine; Crystal structure; Hirshfeld surfaces; Hydrogen bonding; Interaction energies; 3-Nitrobenzylbromide

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DOI: 10.5155/eurjchem.11.2.91-99.1973

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How to cite

Etse, K.; Lamela, L.; Zaragoza, G.; Pirotte, B. Eur. J. Chem. 2020, 11(2), 91-99. doi:10.5155/eurjchem.11.2.91-99.1973
Etse, K.; Lamela, L.; Zaragoza, G.; Pirotte, B. Synthesis, crystal structure, Hirshfeld surface and interaction energies analysis of 5-methyl-1,3-bis(3-nitrobenzyl)pyrimidine-2,4(1H,3H)-dione. Eur. J. Chem. 2020, 11(2), 91-99. doi:10.5155/eurjchem.11.2.91-99.1973
Etse, K., Lamela, L., Zaragoza, G., & Pirotte, B. (2020). Synthesis, crystal structure, Hirshfeld surface and interaction energies analysis of 5-methyl-1,3-bis(3-nitrobenzyl)pyrimidine-2,4(1H,3H)-dione. European Journal of Chemistry, 11(2), 91-99. doi:10.5155/eurjchem.11.2.91-99.1973
Etse, Koffi, Laura Comeron Lamela, Guillermo Zaragoza, & Bernard Pirotte. "Synthesis, crystal structure, Hirshfeld surface and interaction energies analysis of 5-methyl-1,3-bis(3-nitrobenzyl)pyrimidine-2,4(1H,3H)-dione." European Journal of Chemistry [Online], 11.2 (2020): 91-99. Web. 3 Oct. 2023
Etse, Koffi, Lamela, Laura, Zaragoza, Guillermo, AND Pirotte, Bernard. "Synthesis, crystal structure, Hirshfeld surface and interaction energies analysis of 5-methyl-1,3-bis(3-nitrobenzyl)pyrimidine-2,4(1H,3H)-dione" European Journal of Chemistry [Online], Volume 11 Number 2 (30 June 2020)

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