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    A comprehensive study of experimental and theoretical characterization and in silico toxicity analysis of new molecules
    (Taylor & Francis Ltd, 2024) Cankaya, Nevin; Kebiroglu, Mehmet Hanifi; Temuz, Mehmet Muersit
    In this study, for the first time in the literature, a 2-(3-methoxyphenylamino)-2-oxoethyl acrylate (3MPAEA) molecule was synthesized in two steps, and a 2-chloro-N-(3-methoxyphenyl)acetamide (m-acetamide) was obtained in the first step. Experimental results were obtained using FTIR, 1H, and 13C NMR spectroscopy methods for m-acetamide and 3MPAEA compounds created in the laboratory environment and compared with theoretical results. Band gap (BG) energy, chemical hardness, electronegativity, chemical potential, and electrophilicity index were calculated. With vibration spectroscopic analysis, atom-molecule vibrations of the theoretical and experimental peaks of the spectrum were observed. The locations of C and H atoms were determined by nuclear magnetic resonance spectroscopy. The green, blue, and red regions of the potential energy map (MEP) map were examined. Some observed that the energy thermal, heat capacity, and entropy graphs increased in direct proportion to increasing the temperature in Kelvin, which is known as thermochemistry. The changes in the rotation, translation, and vibration of the molecule as its temperature increased were examined. When the thermochemistry surface map was examined, some observed that the temperature was high in the middle binding site of the molecules. Covalent interactions were graphed using the non-covalent interactions (NCIs) calculation method. In silico toxicity studies were carried out for m-acetamide and 3MPAEA molecules: fathead minnow LC50 (96 h), Daphnia magna LC50 (48 h), Tetrahymena pyriformis IGC50 (48 h), oral rat LD50, water solubility, bioconcentration factor, developmental toxicity, mutation, normal boiling point, flash point, melting point, density, thermal conductivity, viscosity, vapor pressure, etc. parameters were investigated.
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    Comprehensive Assessment of 2-(3-Methoxyphenylamino)-2-Oxoethyl Methacrylate: Spectroscopic, Computational, Toxicological, Molecular Docking and Dynamic Studies with STAT3 Protein
    (Springer, 2025) Cankaya, Nevin; Kebiroglu, Mehmet Hanifi; Azarkan, Serap Yalcin
    In this study, we successfully resynthesized the compound 2-(3-methoxyphenylamino)-2-oxoethyl methacrylate (3MPAEMA) and characterized it using experimental spectroscopic methods and advanced computational analyses. Theoretical investigations encompassed Natural Bond Orbital (NBO) analysis, Band Gap (BG) calculations, Molecular Electrostatic Potential (MEP) mapping, and Density of States (DOS) evaluations, offering a comprehensive understanding of the molecule's electronic structure. We also employed thermochemical parameters, electronic descriptors, and Non-Covalent Interaction (NCI) analyses to assess the compound's stability, reactivity, and intramolecular interactions. We performed toxicological profiling through in silico oral toxicity prediction models, validating model performance metrics. We conducted molecular docking and 50-ns molecular dynamics (MD) simulations to elucidate the binding behavior of 3MPAEMA with the oncogenic transcription factor STAT3, specifically targeting its SH2 domain. Docking studies revealed a strong binding affinity, while MD simulations confirmed the structural stability of the 3MPAEMA-STAT3 complex. Collectively, these results underscore the promising potential of 3MPAEMA as a STAT3-targeting agent in anticancer therapy. However, further in vitro and in vivo investigations must confirm its therapeutic potential. This comprehensive study offers valuable insights into the physicochemical, toxicological, and biological attributes of 3MPAEMA, supporting its candidacy for future biomedical applications.
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    Computational and experimental study of terpolymers: spectroscopic, thermal, thermochemical, molecular property, and in silico toxicity analysis
    (Taylor & Francis Ltd, 2025) Cankaya, Nevin; Kebiroglu, Mehmet Hanifi; Soykan, Cengiz
    In this study, a comprehensive analysis of the CMA2OEM-co-DVB-co-AMPS (2-(bis(cyanomethyl)amino)-2-oxoethyl methacrylate-co-divinylbenzene-co-2-acrylamido-2-methyl-1-propanesulfonic acid) and CMA2OEM-co-DVB-co-VIM (2-(bis(cyanomethyl)amino)-2-oxoethyl methacrylate-co-divinylbenzene-co-vinylimidazole) terpolymers was conducted. The structural and chemical properties of the terpolymers were examined using Fourier transform infrared (FT-IR) spectroscopy, frontier molecular orbital analysis, molecular electrostatic potential (MEP) maps, 1H, and 13C NMR spectroscopy, thermochemistry surface maps (TCSM), toxicity assessments, physical properties, electron localization function (ELF), and total electrostatic potential (ESP) analyses. In silico toxicity analyses, a quantitative structure-activity relationship (QSAR) model was used for Toxicity Estimation Software Tool (TEST) and ProTox 3.0, a web-based virtual toxicity laboratory, was used for oral toxicity prediction. Toxicity estimates using TEST showed that both terpolymers exhibited low toxicity profiles. Oral toxicity prediction emphasizes that CMA2OEM-co-DVB-co-VIM may pose a greater risk compared to CMA2OEM-co-DVB-co-AMPS. In addition, experimental thermal characterization of these terpolymers was also performed. These comprehensive analyses have provided significant insights into the potential applications and functional properties of the terpolymers.
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    Computational investigation of m-acetamide and 3MPAEA: Characterization, toxicity, and molecular docking and dynamic analyses
    (Taylor & Francis Ltd, 2025) Cankaya, Nevin; Kebiroglu, Mehmet Hanifi; Azarkan, Serap Yalcin
    In this study, 2-(3-methoxyphenylamino)-2-oxoethyl acrylate (3MPAEA) molecule was synthesized in two steps. In the first step, 2-chloro-N-(3-methoxyphenyl)acetamide (m-acetamide) was obtained. Density functional theory (DFT) calculations were performed to obtain information about the electronic and structural properties of the synthesized molecules. The Raman Spectrum and UV-Visible analysis were calculated using the Gaussian package program. Additionally, Natural Bond Orbital (NBO) Analysis, Electron Localization Function (ELF), Electrostatic Potential Map (ESP), Average Local Ionization Energy (ALIE), and the toxicological properties of the molecules were examined. Simultaneously, molecular docking and dynamic analyses were conducted to investigate the interaction of m-acetamide and 3MPAEA with proteins involved in nuclear receptor signaling pathways, stress response pathways, molecular initiating events, and metabolism, as identified in the protox analysis. The findings aligned with the protox analysis results. The results obtained provide new insights into the electronic and toxicological properties of these molecules.
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    Synthesis, Characterization and Molecular Modeling of Novel Oxoethyl methacrylate Polymers
    (Amer Chemical Soc, 2025) Kayacik Bilir, Seray; Cankaya, Nevin; Kebiroglu, Mehmet Hanifi
    The monomer 2-(2-methoxyphenylamino)-2-oxoethyl methacrylate (2MPAEMA) was synthesized and polymerized for the first time into its homopolymer and a copolymer with methyl methacrylate via free-radical polymerization. Structural verification was conducted using FT-IR and NMR spectroscopy, while thermal analysis confirmed the two-stage decomposition of both polymers. Quantum chemical calculations at the B3LYP/LanL2DZ level supported the experimental data, revealing significant intramolecular interactions, electronic delocalization, and thermal stability. The homopolymer exhibited a narrower HOMO-LUMO gap (4.954 eV) than the copolymer (5.207 eV), implying enhanced charge-transport potential. Molecular Electrostatic Potential and Density of States analyses further confirmed well-defined charge distribution and greater orbital overlap in the homopolymer. These results provide new insights into the structure-property relationships of 2MPAEMA-based polymers, highlighting their potential for optoelectronic, sensing, and thermoresponsive applications. Future studies will explore their biological activity and functional performance in targeted environments. FT-IR/NMR, thermal analysis, and DFT collectively indicate that 2MPAEMA polymers are wide-band gap and thermally robust, suggesting their suitability as dielectric matrices or UV-absorbing hosts.