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Yazar "Kebiroglu, Mehmet Hanifi" seçeneğine göre listele

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6-Amino-5-nitro-1,3-dimetilurasil'in (ANDMU) DFT Tabanlı Teorik Araştırması
(Yozgat Bozok University, 2026) Yılmaz, Mücahit; Kebiroglu, Mehmet Hanifi
Bu çalışma, 6-Amino-5-nitro-1,3-dimetilurasil (ANDMU) molekülünün biyolojik aktivite potansiyelini ve elektronik bir malzeme olarak olası uygulamalarını teorik olarak desteklemekte ve böylece gelecekteki deneysel araştırmalar için temel oluşturmaktadır. ANDMU, benzersiz elektronik ve yapısal özellikleri nedeniyle farmasötik ve malzeme bilimi uygulamalarında önemli potansiyele sahip bir nitro-ikameli urasil türevidir. Bu çalışmada, ANDMU'nun moleküler geometrisi, elektronik yapısı (HOMO-LUMO aralığı, bant enerjisi) ve spektroskopik özellikleri (FT-IR, NMR, UV-Vis), yoğunluk fonksiyonel teorisi (DFT) hesaplamaları kullanılarak incelenmiştir. Optimize edilmiş düzlemsel geometri güçlü π-konjugasyonunu ortaya koyarken, geniş HOMO-LUMO aralığı (5,662 eV) yüksek kimyasal kararlılık ve yalıtkanlık davranışına işaret etmektedir. Titreşimsel spektroskopi, karakteristik fonksiyonel grup tepelerini (nitro yaklaşık 1350-1550 cm-1, amino yaklaşık 3300-3500 cm-1) doğrular ve NMR ve UV-Vis analizleri molekül içi yük transferine dair bilgiler sağlar. Amino ve nitro gruplarının varlığı, potansiyel biyolojik aktiviteye işaret ederek bu bileşiği ilaç geliştirme için umut verici bir aday haline getirir. Farmasötik uygulamaların ötesinde, urasil türevleri malzeme biliminde de kullanılabilir. Moleküler elektrostatik potansiyel (MEP) haritası, elektrofilik/nükleofilik etkileşimler için reaktif bölgeleri vurgular. Bu sonuçlar, ANDMU'nun ilaç tasarımında ve organik yarı iletkenler ve floresan problar gibi malzemelerin geliştirilmesinde çift kullanım potansiyelini desteklemektedir.
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.
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.
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.
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.
Effect of Metal Doping on the Electronic and Optical Properties of Norepinephrine: A DFT Study on Fe, Mg, and Zn Modifications for Enhanced Bioactivity
(Niyazi BULUT, 2025) Hssaın, Ala; Kebiroglu, Mehmet Hanifi
[Abstract Not Available]
Electronic structure perturbation induced by fluorine substitution in methylamine: a comparative DFT, spectroscopic and molecular recognition study
(Springer Int Publ Ag, 2026) Fto, Ahmed Muhsin Mohammed Youns; Tahhan, Omar M. Saeed Younus; Abed, Mahmood Dahham Abed; Hssain, Ala Hamd; Kebiroglu, Mehmet Hanifi; Bulut, Niyazi
This study presents a comparative theoretical investigation of methylamine and fluoromethylamine to explain the electronic and spectroscopic consequences of single fluorine substitution. Geometry optimization and electronic structure calculations were carried out at the B3LYP/6-311G(d, p) level within the framework of density functional theory. Frontier molecular orbital analysis showed that fluorination significantly reduced the HOMO-LUMO energy gap, suggesting enhanced electronic reactivity of the fluorinated derivative. Global reactivity descriptors further revealed an increase in electrophilic character following fluorine substitution. Simulated NMR and UV-Vis spectra showed noticeable spectral changes associated with charge redistribution and fluorine-induced polarization effects. Molecular electrostatic potential and density of states analyses confirmed substantial change in the electronic environment of the molecule. In addition, molecular docking calculations were performed to evaluate the molecular recognition behavior of both compounds toward RhCG, providing insight into their possible interaction propensity. The results show that minimal structural modification by fluorination can induce measurable changes in the electronic structure, spectroscopic response, and exploratory molecular-recognition tendency of methylamine.
Halogen-dependent electronic regulation of reactivity and acetylcholinesterase recognition in halomethyl acetates: a predictive DFT-docking framework
(Springer, 2026) Abed, Mahmood Dahham Abed; Tahhan, Omar M. Saeed Younus; Fto, Ahmed Muhsin Mohammed Youns; Kebiroglu, Mehmet Hanifi; Bulut, Niyazi
In this work, we propose a halogen-tuning framework that links electronic reactivity descriptors to enzyme recognition for halomethyl acetates (fluoromethyl, chloromethyl, and bromomethyl acetate). Density Functional Theory calculations were performed at the B3LYP/6-311G(d, p) level to explain structure property relationships across the F/Cl/Br substitution axis. Geometry optimization shows a systematic elongation of the C5-X bond (F < Cl < Br), while the ester carbonyl remains nearly invariant, suggesting a localized substituent effect. Frontier orbital energies analysis and global descriptors reveal that bromomethyl acetate is the softest and most electronically labile derivative, exhibiting the smallest HOMO-LUMO energy gap, whereas the fluorinated analogue demonstrates the highest kinetic stability. Simulated FT-IR, H-1/C-13 NMR (GIAO), and TD-DFT UV-Vis spectra provide complementary fingerprints showing halogen-driven electronic modulation. Topological analyses (MEP, DOS, RDG/NCI/DORI) map the redistribution of electron density and weak interaction regions that rationalize the observed trends. Molecular docking against acetylcholinesterase (AChE; PDB: 1EVE) indicates a monotonic enhancement of binding affinity with increasing halogen polarizability, with bromomethyl acetate exhibiting the strongest predicted affinity. Collectively, these results establish a predictive structure reactivity recognition reasoning for halomethyl acetates and support their consideration as electrophile-tuned model systems for exploring substituent-dependent recognition tendencies.
Integrated DFT Mapping of Structural, Thermochemical, Non-covalent, and Toxicological Profiles of 2-(Tetrahydro-2H-pyran-4-ylmethoxy)-4-pyrimidinecarboxylic Acid (THPMPCA)
(Springer Heidelberg, 2025) Kebiroglu, Mehmet Hanifi
Using density functional theory (B3LYP/LanL2MB), we studied 2-(tetrahydro-2H-pyran-4-ylmethoxy)-4-pyrimidinecarboxylic acid (THPMPCA, C11H14N2O4). Geometry optimization, OPDOS, thermochemical surface mapping, non-covalent interaction analysis, and ProTox 3.0 toxicity modeling were carried out. To the best of our knowledge, this study provides the first comprehensive theoretical assessment of THPMPCA combining structural, thermochemical, electronic, non-covalent, and toxicological analyses in an integrated framework. THPMPCA displays a moderate HOMO-LUMO gap of 0.63 eV, retains structural integrity up to 900 K, and is predicted to fall in toxicity class IV (LD50 > 2000 mg kg(-)(1)). This multi-pronged computational framework has not been applied to THPMPCA, demonstrating its structural robustness and suggesting its potential as a multifunctional platform for bioelectronic devices and pharmaceutical development. The findings pave the way for future in vitro/in vivo validation, and the molecule's favorable physicochemical and toxicological profile supports its potential use in CNS-targeted drug delivery systems and organic electronics.
Potential Benefits and Opportunities of AI-Enabled Software Programs for Opticians: A study in Türkiye
(Niyazi BULUT, 2024) Ak, Fermin; Kebiroglu, Mehmet Hanifi
[Abstract Not Available]
Spectroscopic Characterization, Electronic Structure Analysis, and DFT Investigation of C₁₁H₁₄N₂O₄
(Niyazi BULUT, 2025) Kebiroglu, Mehmet Hanifi; Yılmaz, Mücahit
In this study, the electronic properties of 2-(Tetrahydro-2H-pyran-4-ylmethoxy)-4-pyrimidinecarboxylic acid (THPMPCA, C₁₁H₁₄N₂O₄) were investigated using density functional theory (DFT) calculations with the LanL2MB basis set (0.625 eV). Spectroscopic methods including Ultraviolet-visible (UV-vis), Fourier Transform Infrared (FTIR), and Nuclear Magnetic Resonance (NMR) were employed to characterize the structural and electronic properties of THPMPCA. Detailed electronic structure analyses such as density of states (DOS), highest occupied molecular orbital (HOMO), and lowest unoccupied molecular orbital (LUMO) calculations were performed to elucidate the electronic transitions and stability of the molecule. The results revealed significant improvements in electronic properties, suggesting enhanced applicability of THPMPCA in electronic and medical fields. This comprehensive investigation provides insight into optimizing THPMPCA for future technological and pharmaceutical applications.
Structural, Electronic, and Spectroscopic Insights Into Pralsetinib via Density Functional Theory and in Silico Toxicity Assessment
(Wiley-V C H Verlag Gmbh, 2026) Kebiroglu, Mehmet Hanifi; Hssain, Ala; Allame, Sara Sabah Khaeoon; Kaygili, Omer; Bulut, And Niyazi
This study investigates the structural, electronic, and toxicological properties of Pralsetinib using DFT at the PBEPBE/6-31G level. Topological analyses (NCI and ELF) confirmed stable non-planar geometry supported by weak interactions. FMO analysis revealed a narrow energy gap (Delta E = 2.126 eV), characterizing Pralsetinib as a chemically soft and reactive molecule, consistent with DOS and Fukui function calculations. Spectroscopic properties (FT-IR, NMR, UV-vis) were simulated to explain the molecular framework. In silico toxicity assessments (ProTox-3.0 and T.E.S.T.) predicted an LD50 of 800 mg/kg (GHS Class 4). While the molecule was non-mutagenic and non-carcinogenic, potential risks for neurotoxicity and respiratory toxicity were identified. These findings provide a comprehensive profile for future pharmacological evaluations.
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.
Theoretical insights into the optoelectronic and charge-transfer characteristics of 5-(1H-1,2,4-triazol-1-yl)-2-thiophenecarboxylic acid
(Springer, 2026) Kebiroglu, Mehmet Hanifi
This study elucidates the electronic and structural interplay of 5-(1 H-1,2,4-triazol-1-yl)-2-thiophenecarboxylic acid (TTCA) to assess its potential as a multifunctional heteroaromatic scaffold. Using DFT and TD-DFT calculations at the B3LYP/6-311 + + G(d, p) level, we demonstrate that intramolecular hydrogen bonding locks the triazole and thiophene rings into a highly rigid, planar configuration. This structural coplanarity facilitates extensive pi-electron delocalization, which is critical for the molecule's observed optoelectronic behavior. The analysis reveals a dual electronic character: a chemically stable ground state with a HOMO-LUMO gap of 3.13 eV, contrasted by significant visible-light photoactivity evidenced by a narrow optical transition energy of 1.7 eV. Molecular Electrostatic Potential (MEP) and Non-Covalent Interaction (NCI) analyses identify specific nucleophilic sites and weak interactions that empower TTCA to act as a versatile ligand. Validated by high statistical agreement with experimental literature data for structurally related analogs (FT-IR, NMR, UV-Vis), these results confirm TTCA as a promising candidate for charge-transfer applications, coordination chemistry, and optoelectronic material design.
Unveiling the Pharmacological Potential of a Pyrazole-Benzodioxole Hybrid Computational Analysis, ADMET Screening, and Molecular Docking Against ABL Tyrosine Kinase
(Wiley-V C H Verlag Gmbh, 2026) Yilmaz, Mucahit; Kebiroglu, Mehmet Hanifi
In this study, the physicochemical, electronic, and interaction properties of a pyrazole-benzodioxole hybrid molecule, 3-(1,3-benzodioxol-5-yl)-1H-pyrazole-5-carboxylic acid (C11H8N2O4), were systematically investigated using integrated in silico approaches. The novelty of this work lies in combining density functional theory (DFT), noncovalent interaction analysis (NCI/RDG), electron localization function (ELF), thermochemical evaluation, multiplatform toxicity prediction, and molecular docking within a unified computational framework. The results indicate that weak noncovalent interactions play a key role in stabilizing molecular conformation, while thermodynamic behavior is primarily governed by vibrational contributions. Toxicity predictions suggest a mixed safety profile, including potential mutagenicity and developmental toxicity, highlighting important limitations. Molecular docking against ABL tyrosine kinase reveals a moderate binding affinity (-6.588 kcal/mol), which is lower than that typically reported for strong inhibitors, indicating that the compound does not exhibit high inhibitory potency. Overall, the findings suggest that the investigated molecule may serve as a preliminary scaffold for further structural optimization, and its pharmacological relevance requires comprehensive experimental validation.

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