Investigations on crystal structure of a novel 3-((4,6-dimethylpyrimidin-2-yl)amino)isobenzofuran-1(3H)-one, and related theoretical studies

Zeynep Tanrıkulu Yılmaz, H. Yasin Odabaşoğlu, Pelin Şenel, Veselina Adımcılar, Taner Erdoğan, Ayşe Daut Özdemir, Ayşegül Gölcü*, Mustafa Odabaşoğlu, Orhan Büyükgüngör

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

7 Citations (Scopus)


In this report, 3-((4,6-dimethylpyrimidin-2-yl)amino)isobenzofuran-1(3H)-one have been synthesized via reaction between phthalaldehydic acid and 2-amino-4,6-dimethylpyrimidine in 90% yields and characterized by Infrared (IR), Nuclear Magnetic Resonance (NMR), Ultraviolet–visible (UV–Vis), X-ray single crystal diffraction techniques. The single-crystal X-ray analysis shows that the title compound crystallizes in the triclinic space group P-1 with unit-cell parameters a = 7.9351(4) Å, b = 11.1687(6) Å, c = 16.1281(9) Å, α = 73.713(5)°, β = 80.362(5)°, γ = 72.882(4)° and Z = 4. A theoretical study with hybrid functional B3LYP 6-311G (d, p) basis set have been used in calculations. The structural and electronic properties have been detailed. The title compound was screened for its antioxidant activity by (1,1-diphenyl-2-picryl hydrazyl) free radical scavenging (DPPH), Ferric ion reducing antioxidant power (FRAP), total phenolic contents (TP) assays and its ferrous ions chelating property. Electronic absorption titration, thermal denaturation measurement and viscosity techniques were used to determine the interaction between double stranded DNA (dsDNA) and compound 1. In three techniques, the mode of binding of compound 1 to dsDNA is minor groove. The UV–Vis measurement results allowed the calculation of the binding constant showing the binding strength of compound 1 to dsDNA was calculated as 8.13 × 104 ± 0.07 L mol−1. Moreover, the molecular docking calculations have been performed to investigate the compound–DNA interactions, computationally. In molecular docking calculations, it was observed that for the title compound, the lowest energy docking pose takes place in the minor groove of DNA and in addition to minor groove binding, interactions between the compound and the consecutive base pairs of DNA which may cause a partial intercalation were also observed. Results showed that title compound – DNA complex is stabilized by several hydrogen bonds, and Pi-alkyl interactions also take part in the stabilization of the complex. Binding affinities of the lowest energy docking pose of the title compound was found to be −8.3 kcal/mol.

Original languageEnglish
Pages (from-to)5564-5580
Number of pages17
JournalArabian Journal of Chemistry
Issue number6
Publication statusPublished - Jun 2020

Bibliographical note

Publisher Copyright:
© 2020


The authors wish to thank Istanbul Technical University, Faculty of Science and Letters, Department of Chemistry for some experimental conditions, and Dr. Filiz ALTAY (Istanbul Technical University, Department of Food Engineering, Faculty of Chemical and Metallurgical Engineering) for viscosity measurements and her valuable comments.

FundersFunder number
Istanbul Teknik Üniversitesi


    • Crystal structure
    • DFT calculations
    • DNA binding
    • Molecular docking
    • Phthalide


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