Investigation of Molecular Structures, Basicity Constants and their Interactions with Tumor-Associated Proteins of 2-((phenylimino)methyl)phenol Derivative Schiff Bases by Computational Methods

Burcu Çöpcü; Sultan Erkan; Duran Karakaş

doi:10.17776/csj.1686893

Investigation of Molecular Structures, Basicity Constants and their Interactions with Tumor-Associated Proteins of 2-((phenylimino)methyl)phenol Derivative Schiff Bases by Computational Methods

Abstract

HL1–HL5 Schiff bases were designed by attaching methyl, ethyl, isopropyl, and chloro substituents to the imine group of the 2-((phenylimino)methyl)phenol structure. The experimentally determined basicity constant of the Schiff bases were calculated at various computational levels and a comparative analysis was performed. The B3LYP/6-31G(d) level was determined as the optimal level. The geometries of HL1–HL5 Schiff bases were optimized at the B3LYP/6-31G(d) level. IR and NMR spectra were calculated. The ground state molecular structures of Schiff bases were characterized from IR stretching frequencies, 1H-NMR and 13C-NMR chemical shift values obtained from the optimized structures. Some molecular descriptors, basicity constants (pKb), and proton affinities (PA) of the HL1–HL5 Schiff bases were calculated from aqueous-phase and gas-phase optimizations, respectively. It was found that there is an almost linear proportional relationship between the pKb values of Schiff bases and their HOMO energies and proton affinities. Schiff bases were docked to protein chains with PDB codes 3HY3 and 1M17 in cell lines and their docking poses, binding energies (BE), interaction energies (IE) and total interaction energies (TIE) were calculated. To investigate whether there is a relationship between basicity strength and antitumor activity, BE, IE and TIE graphs were drawn against pKb values of Schiff bases. It was found that the antitumor activity of Schiff bases with high pKb values was generally high. However, it was determined that there was no linear relationship between pKb value and antitumor activity.

Keywords

Supporting Institution

Sivas Cumhuriyet Üniversitesi Bilimsel Araştırma Projeleri

Project Number

F-2022-662

Thanks

Sivas Cumhuriyet Üniversitesi Bilimsel Araştırma projeleri komisyonuna verdikleri destek için teşekkür ederiz.

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Details

Primary Language

English

Subjects

Bioinorganic Chemistry

Journal Section

Research Article

Authors

Burcu Çöpcü ^*
0000-0001-9372-1867
Türkiye

Sultan Erkan
0000-0001-6744-929X
Türkiye

Duran Karakaş
0000-0002-6770-3726
Türkiye

Publication Date

December 30, 2025

Submission Date

April 30, 2025

Acceptance Date

November 9, 2025

Published in Issue

Year 2025 Volume: 46 Number: 4

DOI

https://doi.org/10.17776/csj.1686893

IZ

https://izlik.org/JA65MX83XL

Cite

RIS / Bibtex

APA

Çöpcü, B., Erkan, S., & Karakaş, D. (2025). Investigation of Molecular Structures, Basicity Constants and their Interactions with Tumor-Associated Proteins of 2-((phenylimino)methyl)phenol Derivative Schiff Bases by Computational Methods. Cumhuriyet Science Journal, 46(4), 812-824. https://doi.org/10.17776/csj.1686893