Synthesis, crystal structure, Hirshfeld surface and interaction energies analysis of 5-methyl-1,3-bis(3-nitrobenzyl)pyrimidine-2,4(1H,3H)-dione
- 30 June 2020
- journal article
- Published by European Journal of Chemistry in European Journal of Chemistry
- Vol. 11 (2), 91-99
- https://doi.org/10.5155/eurjchem.11.2.91-99.1973
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.Keywords
This publication has 22 references indexed in Scilit:
- Crystal structure refinement withSHELXLActa Crystallographica Section C Structural Chemistry, 2015
- Energy frameworks: insights into interaction anisotropy and the mechanical properties of molecular crystalsChemical Communications, 2014
- WinGXandORTEP for Windows: an updateJournal of Applied Crystallography, 2012
- Hirshfeld surface analysisCrystEngComm, 2008
- Synthesis and Biological Activity of Mustard Derivatives of ThymineNucleosides, Nucleotides and Nucleic Acids, 2008
- Mercury CSD 2.0– new features for the visualization and investigation of crystal structuresJournal of Applied Crystallography, 2008
- Structure−Activity Relationship Studies on N3-Substituted Willardiine Derivatives Acting as AMPA or Kainate Receptor AntagonistsJournal of Medicinal Chemistry, 2006
- Pyrimidine as Constituent of Natural Biologically Active CompoundsChemistry & Biodiversity, 2005
- Differential activities of 1-[(2-hydroxyethoxy)methyl]-6-(phenylthio)thymine derivatives against different human immunodeficiency virus type 1 mutant strainsAntimicrobial Agents and Chemotherapy, 1995
- (o- and p-Nitrobenzyloxycarbonyl)-5-fluorouracil derivatives as potential conjugated bioreductive alkylating agentsJournal of Medicinal Chemistry, 1986