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

Yilmaz, Zeynep; Odabaşoğlu, Hakkı Yasin; Şenel, Pelin; Adımcılar, Veselina; Erdoğan, Taner; Özdemir, Ayşe; Gölcü, Ayşegül; Odabaşoğlu, Mustafa

doi:10.1016/j.molstruc.2019.127585

Cited by 19 publications

(17 citation statements)

References 67 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…To study the band gap, the structural features of the polymers, we have used the DMol3 in the copyrighted Material Studio software combined with the Density Function Theory (DFT) method. To investigate band gap, the structural, calculates the thermodynamic properties of many different polymer systems [ 65–71 ], and polythiophenes [ 72 , 73 ]. Besides, use the GGA package [ 74 ] with takes the combined parameters of the PW91 exchange, correlation functional [ 75 , 76 ], and the K-point grid according to the Monkhorst–Pack diagram [ 77 ] was directed into a three-dimensional unit cell with definite dimensions a, b, c, α, β and γ as follows: P1: C 11 H 7 NS-O (a = 10 Å, b = 10 Å, c = 25 Å), P2: C 11 H 7 NS-S (a = 10 Å, b = 10 Å, c = 6 Å), P3: C 18 H 9 ON 2 S 2 -H (a = 10 Å, b = 10 Å, c = 40 Å), P4: C 18 H 9 ON 2 S 2 -OCH 3 (a = 10 Å, b = 15 Å, c = 40 Å) and P5: C 18 H 9 ON 2 S 2 -Cl (a = 10 Å, b = 15 Å, c = 40 Å) and α = β = γ = 90°.…”

Section: Methodsmentioning

confidence: 99%

DFT study on some polythiophenes containing benzo[d]thiazole and benzo[d]oxazole: structure and band gap

Quoc

Thuy

et al. 2021

Designed Monomers and Polymers

View full text Add to dashboard Cite

The content of this paper focuses/shed light on the effects of X (X = S in P1 and X = O in P2) in C 11 H 7 NSX and R (R = H in P3, R = OCH 3 in P4, and R = Cl in P5) in C 18 H 9 ON 2 S 2 -R on structural features and band gaps of the polythiophenes containing benzo[ d ]thiazole and benzo[ d ]oxazole by the Density Function Theory (DFT) method/calculation. The structural features including the electronic structure lattice constant (a), shape, total energy (E tot ) per cell, and link length (r), are measured via band gap (E g ) prediction with the package of country density (PDOS) and total country density (DOS) of material studio software. The results obtained showed that the link angle and the link length between atoms were not changed significantly while the E tot was decreased from E tot = – 1904 eV (in P1) to E tot = – 2548 eV (in P2) when replacing O with S; and the E tot of P3 was decreased from E tot = – 3348 eV (in P3) when replacing OCH 3 , Cl on H of P3 corresponding to E tot = – 3575 eV (P4), – 4264 eV (P5). Similarly, when replacing O in P1 with – S to form P2, the E g of P1 was dropped from E g = 0.621 eV to E g = 0.239 eV for P2. The E g of P3, P4, and P5 is E g = 0.006 eV, 0.064 eV, and 0.0645 eV, respectively. When a benzo[ d ]thiazole was added in P1 (changing into P3), the E g was extremely strongly decreased, nearly 100 times (from E g = 0.621 eV to E g = 0.006 eV). The obtained results serve as a basis for future experimental work and used to fabricate smart electronic device.

show abstract

Section: Methodsmentioning

confidence: 99%

DFT study on some polythiophenes containing benzo[d]thiazole and benzo[d]oxazole: structure and band gap

Quoc

Thuy

et al. 2021

Designed Monomers and Polymers

View full text Add to dashboard Cite

show abstract

“…(Default grid spacing= 0.375 Å) [38] . In order to prepare the ligand for docking, the CIF data obtained from the X-ray crystal structure [39] was converted to mol2 format. The partial charge and torsion angels were changed and saved in pdbqt format with AutoDock Tools.…”

Section: Methodsmentioning

confidence: 99%

Synthesis, X-ray crystal structure, IR and Raman spectroscopic analysis, quantum chemical computational and molecular docking studies on hydrazone-pyridine compound: As an insight into the inhibitor capacity of main protease of SARS-CoV2

Topal

Zorlu

Karapınar

2021

Journal of Molecular Structure

View full text Add to dashboard Cite

The characterization and synthesis of 3-chloro-2-{(2E)-2-[1-(4-chlorophenyl)ethylidene]hydrazinyl}pyridine (CCPEHP) was investigated in our study. Mass and UV-visible spectra were recorded in chloroform solvent. The CCPEHP molecule containing pyridine and chlorophenyl rings and hydrazone group crystallized in the triclinic system and P-1 space group. FTRaman and FTIR spectra were performed in the solid state. The optimized geometry of CCPEHP was computed by DFT/B3LYP method with 6-311G (d, p) and 6-31G (d, p) levels. The computed vibrational analysis, electronic absorption spectrum, electronic properties, molecular electrostatic potential, natural bond orbitals analysis and other calculated structural parameters were determined by using the DFT/B3LYP/6-31G (d, p) basis set. The correlation of fundamental modes of the compound and the complete vibrational assignments analysis were studied. The strong and weak contacts were identified by using Hirshfeld surface analysis. The molecular modeling results showed that CCPEHP structure strongly binds to COVID-19 main protease by relative binding affinity of -6.4 kcal/mol.

show abstract

“…Upon increasing the temperature of the DNA solution, hydrogen bonding of the DNA double helix was affected, resulting in the disruption of the helical structure. The damage which caused the transformation of ds-DNA into ss-DNA can be distinguished as the "hyperchromic effect" [70]. The range of ∆Tm is the midpoint between the values triggered by different binding modes.…”

Section: Uv Optical Meltingmentioning

confidence: 99%

Depicting the DNA Binding and Cytotoxicity Studies against Human Colorectal Cancer of Aquabis (1-Formyl-2-Naphtholato-k2O,O′) Copper(II): A Biophysical and Molecular Docking Perspective

Alolayqi¹,

Afzal²,

Alarifi³

et al. 2021

Crystals

View full text Add to dashboard Cite

In this study, we attempted to examine the biological activity of the copper(II)–based small molecule aquabis (1-formyl-2-naphtholato-k2O,O′)copper(II) (1) against colon cancer. The characterization of complex 1 was established by analytical and spectral methods in accordance with the single-crystal X-ray results. A monomeric unit of complex 1 exists in an O4 (H2O) coordination environment with slightly distorted square pyramidal geometry (τ = ~0.1). The interaction of complex 1 with calf thymus DNA (ctDNA) was determined by employing various biophysical techniques, which revealed that complex 1 binds to ctDNA at the minor groove with a binding constant of 2.38 × 105 M–1. The cytotoxicity of complex 1 towards human colorectal cell line (HCT116) was evaluated by the MTT assay, which showed an IC50 value of 11.6 μM after treatment with complex 1 for 24 h. Furthermore, the apoptotic effect induced by complex 1 was validated by DNA fragmentation pattern, which clarified that apoptosis might be regulated through the mitochondrial-mediated production of reactive oxygen species (ROS) causing DNA damage pathway. Additionally, molecular docking was also carried out to confirm the recognition of complex 1 at the minor groove.

show abstract

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

Cited by 19 publications

References 67 publications

DFT study on some polythiophenes containing benzo[d]thiazole and benzo[d]oxazole: structure and band gap

DFT study on some polythiophenes containing benzo[d]thiazole and benzo[d]oxazole: structure and band gap

Synthesis, X-ray crystal structure, IR and Raman spectroscopic analysis, quantum chemical computational and molecular docking studies on hydrazone-pyridine compound: As an insight into the inhibitor capacity of main protease of SARS-CoV2

Depicting the DNA Binding and Cytotoxicity Studies against Human Colorectal Cancer of Aquabis (1-Formyl-2-Naphtholato-k2O,O′) Copper(II): A Biophysical and Molecular Docking Perspective

Contact Info

Product

Resources

About