Synthesis, enzymes inhibitory properties and characterization of 2- (bis (4-aminophenyl) methyl) butan-1-ol compound: Quantum simulations, and in-silico molecular docking studies

Yıldıko, Ümit; Türkan, Fikret; Tanrıverdı, Aslıhan Aycan; Ata, Ahmet Çağrı; Atalar, Mehmet Nuri; Čakmak, İsmail

doi:10.1016/j.jics.2021.100206

Cited by 12 publications

(10 citation statements)

References 65 publications

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“…MEP indicates the effective localization of electron‐rich regions in the molecular system. Here, interaction power is analyzed using MEP and its topology 61,62 . The surface acquired simultaneously demonstrates the molecular size and shape and the electrostatic potential value.…”

Section: Resultsmentioning

confidence: 99%

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A novel sulfonated aromatic polyimide synthesis and characterization: Energy calculations, QTAIM simulation study of the hydrated structure of one unit

Yıldıko

Tanrıverdı

2022

Bulletin Korean Chem Soc

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A new type of sulfonated polyimide was synthesized from a one‐step polycondensation reaction with perylene‐3,4,9,10‐tetracarboxylic dianhydride and 4,4′‐diamino‐2,2′‐stilbenedisulfonic. Pure characterization of sulfonated polyimide (SPI) was performed by Fourier transform infrared spectroscopy, proton nuclear magnetic resonance, thermogravimetric analysis, differential thermal gravimetric analysis, ultraviolet–visible spectroscopy, and solubility tests. Moreover, the SPI film was prepared by a thermal imidization step heating procedure. Furthermore, quantum chemical calculations of the synthesized SPI were investigated with density functional theory (DFT) and time‐dependent density functional theory. By calculating the frontiers molecular orbital energies of the obtained polyimide, the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO), and the energy gap (Δ) values were found for the one structural unit and three structural units of SPI, respectively. Also, QTAIM was carried out based on the AIMAll program. With the increase in water molecules, the average electronic energy density (HBCP) value decreased according to the results of QTAIM. The SPI can be used as a potential membrane in fuel cells.

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Section: Resultsmentioning

confidence: 99%

“…Here, interaction power is analyzed using MEP and its topology. 61,62 The surface acquired simultaneously demonstrates the molecular size and shape and the electrostatic potential value. Different values of the electrostatic potential on the surface are represented by different colors.…”

Section: Molecular Electrostatic Potential Analysismentioning

confidence: 99%

A novel sulfonated aromatic polyimide synthesis and characterization: Energy calculations, QTAIM simulation study of the hydrated structure of one unit

Yıldıko

Tanrıverdı

2022

Bulletin Korean Chem Soc

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“…Computer‐assisted molecular docking was performed to confirm the interaction of photosensitizing Si−Pc compound with protein‐DNA complexes and to better understand the binding [42–43] . Figure 8 presents the Jablonski diagram of the photosensitizer (PS) and the formation of reactive oxygen species in the target protein‐DNA complexes [44] .…”

Section: Resultsmentioning

confidence: 99%

“…Computer-assisted molecular docking was performed to confirm the interaction of photosensitizing SiÀ Pc compound with protein-DNA complexes and to better understand the binding. [42][43] Figure 8 presents the Jablonski diagram of the photosensitizer (PS) and the formation of reactive oxygen species in the target protein-DNA complexes. [44] Figure 9 represents the pose of the best match of SiÀ Pc as ligand with DNA crystal structures, as analyzed in the visualization software with discovery studio.…”

Section: Molecular Dockingmentioning

confidence: 99%

Synthesis of Axial Bis(benzo[d][1,3]dioxol‐5‐ylmethoxy)phthalocyaninato Silicon (IV): Photophysical and Photochemical Properties and Docking Studies on DNA‐SiPc Interactions

2022

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The synthesis of an axial phthalocyanine compound by the reaction of piperonyl alcohol and SiPcCl2 has been reported. Its structure was characterized by compound 1HNMR,13CNMR, Mass, FTIR and UV visible spectroscopy. Photophysical and photochemical properties of the compound were investigated by fluorescence spectroscopy. The photosensitizer performance of the compound was determined. In addition, with the quantum chemical study, the HOMO ‐ LUMO band gap and the optimized structure of the compound were investigated with two basic sets of the TD‐DFT B3LYP method. The band gap (ΔE) was found to be in the range of 0.6–0.7 eV, and it was determined that the compound would require low energy in the chemotherapeutic interaction with light and in its stimulation. As a chemotherapy drug candidate, its adhesion to protein and DNA structure has been evaluated as in‐silico. In this context, the potential binding and interaction aspects of the new chemotherapeutically effective phthalocyanine compound with two kinds of homo sapiens protein‐DNA complexes were investigated by molecular docking approach. It bonded with the phthalocyanine compound in both crystal structures. A docking score of 6.315 kcal/mol was obtained in the 6DIA encoded DNA polymerase beta substrate complex.

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“…The Maestro Molecular Modeling platform of the Schrödinger (version 11.8), LLC model was implemented via molecular insertion. [34][35][36][37] DNA polymerase beta substrate complex with templating cytosine and incoming Fapy-dGTP analog (DNA1) (PDB: 6DIA) [20], Human Aprataxin (APTX) bound to DNA, AMP, and Zn -product complex (DNA2) (PDB: 4NDH) [21] These DNA complexes, which are high resolution crystal structures, were Downloaded from http://www.rcsb.org/pdb. [37]…”

Section: Simulations Of the Theoretical Studiesmentioning

confidence: 99%

Synthesis of axially silicon phthalocyanine substituted with bis- (3,4-dimethoxyphenethoxy) groups and energy features, charge density analysis and molecular docking studies

Solğun

Tanrıverdı

Yıldıko

et al. 2022

Preprint

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Axially bis-substituted silicon phthalocyanine was synthesized from the reaction of 2-(3,4-dimethoxy phenyl) ethanol and SiPcCl2. The structure of the compound was justified by FT-IR, 1H NMR, 13C NMR, UV-Vis, and mass spectra. The conglomeration action of the phthalocyanine compound was determined by UV-visible spectra at different concentrations and in different solvents. Some parameters of this axial silicon phthalocyanine compound were investigated by computational chemistry. Structural optimization of axial silicon phthalocyanine substituted with compound, HOMO-LUMO energies and MEP maps was performed by density functional theory (DFT) studies. In addition, a chemical bond analysis of the molecule was performed with quantum theory atom in molecules (QTAIM). Finally, a molecular docking study was applied to this new phthalocyanine molecule in its binding mechanism.

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Synthesis, enzymes inhibitory properties and characterization of 2- (bis (4-aminophenyl) methyl) butan-1-ol compound: Quantum simulations, and in-silico molecular docking studies

Cited by 12 publications

References 65 publications

A novel sulfonated aromatic polyimide synthesis and characterization: Energy calculations, QTAIM simulation study of the hydrated structure of one unit

A novel sulfonated aromatic polyimide synthesis and characterization: Energy calculations, QTAIM simulation study of the hydrated structure of one unit

Synthesis of Axial Bis(benzo[d][1,3]dioxol‐5‐ylmethoxy)phthalocyaninato Silicon (IV): Photophysical and Photochemical Properties and Docking Studies on DNA‐SiPc Interactions

Synthesis of axially silicon phthalocyanine substituted with bis- (3,4-dimethoxyphenethoxy) groups and energy features, charge density analysis and molecular docking studies

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