A novel 3-((5-methylpyridin-2-yl)amino)isobenzofuran-1(3H)-one: Molecular structure describe, X-ray diffractions and DFT calculations, antioxidant activity, DNA binding and molecular docking studies

Z. T. Yılmaz, H. Yasin Odabaşoğlu, P. Şenel, V. Adımcılar, T. Erdoğan, A. D. Özdemir, A. Gölcü*, M. Odabaşoğlu

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

18 Citations (Scopus)

Abstract

In this work, the structure of a novel phthalide derivative, 3-((5-methylpyridin-2-yl) amino) isobenzofuran-1(3H)-one, was analyzed both experimentally and theoretically by X-ray single crystal diffraction technique, IR spectroscopy, and quantum chemical computation. The X-ray diffraction analysis indicates that 3-((5-methylpyridin-2-yl) amino) isobenzofuran-1(3H)-one crystallizes in a monoclinic space group P21/n with unit-cell parameters a = 8.0712(7) Å, b = 6.6762(4) Å, c = 23.005(2) Å, β = 98.813(7)° and Z = 4. Additionally, DFT method at B3LYP level by using the hybrid functional with 6-311G (d, p) basis set have been used in the geometry optimizations and vibrational frequencies calculations of the title compound in ground state. The geometrical parameters obtained from XRD studies and the calculated values are in good agreement to each other. In addition, the electronic properties, such as HOMO and LUMO energies, and thermodynamic properties were calculated with the same method. The chemical reactivity estimation, the molecular electrostatic potential (MEP) surface map and PES scan of the related molecule were investigated with theoretical calculations at the B3LYP/6-31þG(d,p) and B3LYP/3-21G levels, respectively. The Folin-Ciocalteu's method have been used to determine the total phenolic (TP) content of the compound under study and it was found to be 0.14 (±0.0) mg gallic acid equivalents (GAE)/g. Antioxidant activities were evaluated by 1,1-diphenyl-2-picryl-hydrazyl (DPPH) radical scavenging activity and ferric reducing anti-oxidant power assay (FRAP). Metal chelating assay was based on the measurement of iron-ferrozine absorbance at 562 nm. The DNA binding affinity for double strain fish sperm DNA (dsFSDNA) was investigated by electronic absorption titration, thermal denaturation measurement and viscosity techniques which indicate that the title compound binds to dsFSDNA by minor groove and has a binding constant of 9.59 × 104. Additionally, in molecular docking studies, it has been observed that the lowest energy docking pose binds to minor groove of DNA and 1-DNA complex has been stabilized by several hydrogen bonds. The binding affinity of the lowest energy docking pose was found to be −8.3 kcal/mol.

Original languageEnglish
Article number127585
JournalJournal of Molecular Structure
Volume1205
DOIs
Publication statusPublished - 5 Apr 2020

Bibliographical note

Publisher Copyright:
© 2019 Elsevier B.V.

Funding

The authors wish to thank Istanbul Technical University for some experimental conditions and Dr. Filiz ALTAY (Department of Food Engineering, Faculty of Chemical and Metallurgical Engineering, Istanbul Technical University, Maslak, Istanbul 34469, Turkey.) for viscosity measurements and her valuable comments.

FundersFunder number
Istanbul Teknik Üniversitesi34469

    Keywords

    • Antioxidant property
    • Crystal structure
    • DFT
    • DNA binding
    • Molecular docking
    • Phthalide

    Fingerprint

    Dive into the research topics of 'A novel 3-((5-methylpyridin-2-yl)amino)isobenzofuran-1(3H)-one: Molecular structure describe, X-ray diffractions and DFT calculations, antioxidant activity, DNA binding and molecular docking studies'. Together they form a unique fingerprint.

    Cite this