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

• Published in: Journal of molecular structure 2020-04, Vol.1205, p.127585, Article 127585
• Main Authors: Yılmaz, Z.T., Odabaşoğlu, H. Yasin, Şenel, P., Adımcılar, V., Erdoğan, T., Özdemir, A.D., Gölcü, A., Odabaşoğlu, M.
• Format: Article
• Language: English
• Subjects: Antioxidant property; Crystal structure; DFT; DNA binding; Molecular docking; Phthalide
• ISSN: 0022-2860; 1872-8014
• DOI: 10.1016/j.molstruc.2019.127585

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. [Display omitted] •A new phthalide derivative has been synthesized and characterized by X-ray single crystal diffraction technique.•The DFT calculations were performed to confirm experimental data.•Antioxidant activities and metal chelating activ