İlgi alanları

• MakaleYalnız künye2026Scopus SJRQ2/r/bayburt/10743
  Novel heteroaromatic compounds bearing thiosemicarbazone as anti-cancer and anti-bacterial agents: Synthesis, cytotoxic and biological screening, molecular docking and DFT analysis

  Nartop, Dilek; Ögütcü, Hatice; Özkan, Elvan Hasanoglu; Yetim, Nurdan Kurnaz; Kizil, Hamit Emre; Ekincioglu, Yavuz

  Novel heteroaromatic compounds (Hc1, Hc2, Hc3, Hc4) were obtained, and their structure were confirmed using various spectroscopic methods, including elemental analysis, fourier transform infrared (FT-IR) spectroscopy, proton and carbon nuclear magnetic resonance (1H/13C-NMR) spectroscopy, and molar conductance measurement. The biological activities of the heteroaromatic compounds against several Gram-positive (Micrococcus luteus ATCC9341, Staphylococcus epidermidis ATCC12228, Bacillus cereus RSKK863, Listeria monocytogenes ATCC 19111), and Gram-negative bacterial strains (Pseudomonas aeruginosa ATCC27853, Klebsiella pneumonia ATCC27853, Enterobacter aerogenes ATCC51342, Salmonella typhi H NCTC9018394, Shigella dysenteriae NCTC2966, Proteus vulgaris RSKK96026) were evaluated using the well-diffusion method. In general, the heteroaromatic compounds demonstrated a stronger inhibitory effect against Gram-positive bacteria. Hc1, Hc2 and Hc3 showed the highest inhibitory effect against B. cereus and L. monocytogenes. The compound (Hc4) showed the highest antibacterial activity and antifungal activity against Bacillus cereus and C. albicans, respectively. The cytotoxic activity of the heteroaromatic compounds was assessed against the non-small cell lung cancer cell line (NCI-H460) using the NutriCulture Cell Viability Detection Kit-8 (CVDK-8). Among the synthesized heteroaromatic compounds, Hc3 exhibited significant cytotoxic activity with an IC50 value of 141.3 & micro;g/mL, whereas compounds Hc1, Hc2, and Hc4 did not display significant toxicity at the tested concentrations. The molecular geometry of the heteroaromatic compound (Hc3) was optimized using Gaussian 09 W at the B3LYP/6-311++G (d,p) level of theory. Key structural parameters such as bond lengths, bond angles, and dihedral angles were determined through the same computational framework. Electronic features, including frontier molecular orbitals, global reactivity descriptors, and molecular electrostatic potential surfaces, were analyzed to explore intramolecular charge distribution and predict reactive sites. To evaluate the biological potential of the heteroaromatic compound (Hc3), molecular docking studies were performed. Additionally, drug-likeness assessment based on Lipinski's Rule of Five and ADME profiling revealed favorable pharmacokinetic characteristics. Molecular docking studies revealed that compound Hc3 showed a binding energy of -4.09 kcal/mol against the EGFR target (PDB ID: 1UWH), exhibiting key interactions such as hydrogen bonding and It-interactions with the active site residues. Based on all the results, it can be said that new heteroaromatic compounds have significant potential in the pharmaceutical field.

  AtıfScopus1

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• MakaleYayıncıda açık erişim2026/r/bayburt/11260
  Synthesis and pharmacokinetic profiling of a novel pyrimidine imidazole based thiosemicarbazone derivative for BRAF inhibition in lung cancer therapy

  Ekincioğlu, Yavuz; Kızıl, Hamit Emre; Güllü, Eda; Özkan, Elvan Hasanoğlu; Nartop, Dilek

  This study presents the design, synthesis, and comprehensive evaluation of a novel thiosemicarbazone derivative containing a pyrimidine-imidazole (C11H11N8SCl) as a potential BRAF inhibitor for the treatment of non-small cell lung cancer. The compound was synthesized by a condensation reaction and characterized by elemental analysis, molar conductivity, SEM-EDS, FT-IR, 1H, and 13C-NMR spectral techniques. DFT calculations at the B3LYP/6-311 + + G(d, p) level revealed a HOMO-LUMO gap of 2.8 eV, indicating appropriate molecular stability and reactivity. Molecular docking studies with BRAF (PDB ID: 1UWH) demonstrated favorable binding affinity (-6.85 kcal/mol) with key interactions at ILE512, HIS509, HIS584, GLN529, GLU585, LYS590, VAL510, and LEU587 residues. In vitro cytotoxicity assays revealed that the compound possesses anticancer potential against H-460 cells, with a significant inhibitory effect observed at a concentration of 200 µg/mL. Combined with its favorable binding affinity toward BRAF kinase, these results suggest that the pyrimidine-imidazole thiosemicarbazone may serve as a potential lead scaffold for further development in targeted lung cancer therapy.ADME profiling confirmed the compound’s compliance with Lipinski’s rule of five parameters, supporting its potential as an orally active drug candidate. These findings suggest that our pyrimidine-imidazole thiosemicarbazone represents a promising scaffold for the development of targeted BRAF inhibitors for lung cancer therapy.

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• MakaleYalnız künye2026/r/bayburt/11107
  DFT-based structural and energetic characterisation of nitrogen-rich tetrazine/triazine derivatives with Kamlet-Jacobs performance predictions

  Ekincioğlu, Yavuz; Kepceoğlu, Abdullah; Çakir, Zehra; Şentürk, Şükrü

  Nitrogen-rich heterocycles are attractive candidates for next-generation energetic materials because they can deliver high heats of formation while producing relatively benign, N2-rich decomposition products. In this work, three nitrogen-rich frameworks 3,6-bis(tetrazol-5-yl)−1,2,4,5-tetrazine (H2BTTz), 2,4,6-tris(tetrazol-5-yl)−1,3,5-triazine (H3TTT), and 2,3,5,6-tetra(tetrazol-5-yl)pyrazine (H4TTP) were investigated using a combined conformational sampling and density functional theory (DFT) approach. Initial conformational searches were carried out with the MMFF method, and the lowest-energy structures were optimised at the DFT/B3LYP/6-311++G(d,p) level a widely used compromise between accuracy and computational cost for nitrogen-rich energetic molecules. Electronic structure analyses included frontier molecular orbitals, Mulliken and natural population charges, and molecular electrostatic potential maps. Energetic performance was evaluated through heats of formation, detonation velocity and pressure, and impact sensitivity estimates. Topological descriptors such as ELF, LOL, and NCI were analyzed using Multiwfn program. The calculated HOMO–LUMO gaps (3.54-4.90 eV) indicate electronically stable molecular frameworks. Gas-phase formation enthalpies were converted to condensed-phase values using a sublimation correction, and detonation properties were estimated via the Kamlet–Jacobs equations. The predicted performance follows the order H4TTP > H2BTTz > H3TTT. Although their detonation performance is lower than that of FOX-7 and CL-20, these nitrogen-rich systems remain promising candidates for reduced-sensitivity energetic materials and merit further experimental investigation.

  AtıfScopus1·WoS1

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• MakaleYayıncıda açık erişim2025/r/bayburt/12764
  An Integrated In Vitro and In Silico Investigation of the Bioactive Properties of Wild Glycyrrhiza glabra var. glandulifera

  Kızıl, Hamit Emre; Ulcay, Sibel; Ekincioğlu, Yavuz; Öğütçü, Hatice; Ağar, Güleray

  This investigation examined methanol extracts obtained from the whole plant (encompassing all organs except roots), flowers, and fruits of wild Glycyrrhiza glabra var. glandulifera, a liquorice cultivar indigenous to the Cappadocia region of Türkiye, constituting the first comprehensive in vitro and in silico analysis of this species within the region. Anatomical identification revealed distinctive structural characteristics, including thick-walled epidermal cells in the stem, organized clusters of collenchyma cells, and well-defined sclerenchyma layers encompassing the vascular bundles. The petiole exhibited a characteristic heart-shaped morphology containing three vascular bundles, while foliar analysis demonstrated the presence of stomata on both adaxial and abaxial surfaces, accompanied by a bifacial mesophyll arrangement. The extracts demonstrated remarkable antimicrobial efficacy against both Gram-positive and Gram-negative bacteria, as well as various fungal species. Furthermore, significant cytotoxic activity was observed against non-small cell lung cancer (H460), with the whole plant extract exhibiting IC50 values of 117.8 µg/mL (24 h) and 105.6 µg/mL (48 h). Flower extracts demonstrated IC50 values of 116.8 µg/mL (24 h) and 112.7 µg/mL (48 h), while fruit extracts displayed superior potency with IC50 values of 104.4 µg/mL (24 h) and 63.09 µg/mL (48 h). Molecular docking analyses, conducted utilizing AutoDock Tools 1.5.6 and BIOVIA Discovery Studio Visualizer 4.5, revealed significant protein-ligand interactions, yielding optimal binding energy and inhibition constant values of -9.57 kcal/mol and 96.92 nM, respectively. The RMSD values were calculated based on structural variations between ligand-protein complexes during re-docking procedures. These findings underscore the substantial biological potential of Glycyrrhiza glabra var. glandulifera from Cappadocia, necessitating further comprehensive investigation.

  AtıfScopus6·WoS6

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• MakaleYayıncıda açık erişim2025/r/bayburt/11532
  Anticancer (cytotoxic, anticlonogenic, antimetastatic, immunomodulatory actions) properties of 3,5-dibromosalicylaldehyde against glioblastoma cells and DFT analyses (FT-IR, Raman, NMR, UV) as well as a molecular docking study

  Karakaş Sarıkaya, Ebru; Pehlivanoğlu, Suray; Türkmen, Merve Özcan; Ekincioğlu, Yavuz; Kostak, Feyza; Çelik, Sultan; Dereli, Ömer

  Background Information: The primary objectives of this study were to characterize 3,5-dibromosalicylaldehyde (3,5-DBSA) and, investigate its antiproliferative, antimetastatic, cytotoxic, and immunoregulatory properties. NMR, Raman, UV, and FT-IR spectroscopies were used to characterize 3,5-DBSA. Potential conformations of 3,5-DBSA were evaluated using Spartan's MMFF method. Geometry optimization calculations using Gaussian software calculated conformation energy values. Results: Subsequently, Raman, FT-IR, UV (ethanol) and NMR (DMSO) parameters were calculated. The experimental spectrum was compared to theoretical spectroscopic data. The present investigation investigated 3,5-DBSA's anticancer properties; therefore, docking was done once the stable structure had been identified. Conclusion: Identifying stable structure is crucial to molecular docking studies. In order to identify the mechanism by which 3,5-DBSA binds to PI3K as a therapeutic target, molecular docking was utilized. This work is the first to show that 3,5-DBSA is cytotoxic, anticlonogenic, antimetastatic, and immunomodulatory in glioblastoma cell line U87MG compared to healthy fibroblast L929 cells. Cytotoxicity and anti-clonogenicity studies investigated 3,5-DBSA's antiproliferative activities, whereas wound healing assays assessed cell migration. The immunomodulatory effects of 3,5-DBSA in glioblastoma were assessed by measuring Netrin-1 and IL-6 protein levels. According to our findings, 3,5-DBSA may treat glioblastoma. Significance: This work analyzes 3,5-DBSA's conformational search, characterization, molecular docking, and structural and anticancer properties.

  İncele
• MakaleYalnız künye2025/r/bayburt/11475
  Electronic structure and adsorption behavior of 2PANI with selected gases: A DFT approach

  Ekincioglu, Yavuz

  This study examines the adsorption properties of C2H4, F2, HCl, and H2S gases on 2PANI using density functional theory (B3LYP/6-311++G(d,p)). Adsorption energies follow the order: 2PANI-HCl > 2PANI-H2S > 2PANI-C2H4 > 2PANI-F2 including the BSSE corrections. Geometry optimizations and topological analyses (electrostatic potential, localized orbital locator and electron localization function) were performed using Multiwfn software. Mulliken charge analysis assessed the sensing potential of 2PANI for each gas. Time-dependent DFT was used to analyze molecular orbitals, reactivity indices, density of states, and UV-Vis spectra, revealing red or blue shifts depending on the gas type. The results confirm that C2H4, F2, HCl, and H2S can be physically adsorbed onto 2PANI. The recovery time and conductivity were evaluated to determine gas sensitivity performance.

  AtıfScopus1·WoS1

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• MakaleYayıncıda açık erişim2024/r/bayburt/11840
  Nonlinear optical properties of KnCl (n = 2-7) superalkali clusters

  Şentürk, Şükrü; Fardad, Fraidoon; Ekincioğlu, Yavuz

  The lowest energy structures along with the low lying isomer, stabilities, electronic properties, optical properties and nonlinear optical responses of KnCl (n = 2-7) clusters were studied within the density functional theory. The second order energy difference, dissociation energy and GH-L (HOMO-LUMO gap) point out that KnCl (n = 3, 5, 7) clusters are more stable. The calculated adiabatic ionization energies (AIE) for the KnCl (n = 2-6) clusters are in agreement with the measured ionization energies. The optical properties, namely optical electronegativity and refractive index, depends on the GH-L energy values. The K atom capped planar rhombus geometry of the K4Cl causes the noticeable vibrational frequency shift compared to the rest of IR spectra of the clusters. The first static hyperpolarizability (β o) values are in the range of 2.33 × 103-2.87 × 104 au and the second static hyperpolarizability varies between 5.74 × 106 au and 38.9 × 106 au for the cluster. The nonlinear optical response is due to the superalkali nature of KnCl (n = 2-7) clusters. From computed β vec values, the hyperpolarizability has projection on the dipole moment vector for the superalkalis except the K2Cl and K5Cl. The absorption spectra point out that KnCl (n = 6-7) clusters can be suitable as a NLO material since they have transparency in the deep UV region (λ< 300 nm).

  AtıfScopus2·WoS2

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• MakaleYalnız künye2024/r/bayburt/11665
  Nonlinear optical response of LinClK (n = 1–6) superalkali clusters

  Şentürk, Şükrü; Ekincioğlu, Yavuz; Doğan, Ümit

  The geometrical structures, stabilities, electronic properties and nonlinear optical response of the halogen doped bimetallic LinClK (n = 1–6) clusters were studied within the density functional theory. Based on the dissociation energy, second order energy difference and GH-L (HOMO-LUMO gap), the LinClK (n = 2, 4, 6) clusters are more stable. According to their ionization energies, the clusters can be classified as a superalkali. From the NBO analysis, the clusters are excess electron systems. The obtained first static hyperpolarizability (o) values are in the range of 1.56 × 104 − 4.33 × 104 au while the second static hyperpolarizability vary within 2.47 × 106 au to 13.9 × 106 au for the LinClK (n = 1–6) superalkalis that are slightly higher than the nonlinear optical response of halogen doped monometallic clusters. More importantly, the Li5ClK is transparent in the deep UV region ( < 300 nm) among the superalkalis indicating that the Li5ClK superalkali can be a candidate structure as new member of NLO materials.

  AtıfScopus1·WoS1

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• MakaleYayıncıda açık erişim2024/r/bayburt/11223
  Analysis of the nonlinear optical properties, vibrational spectra, DFT method and photovoltaic performance of cyanidin-3-rutinoside chloride

  Sarıkaya, Ebru Karakaş; Ekincioğlu, Yavuz; Bahçeli, Semiha; Dereli, Ömer

  This study aims to identify a cyanidin-3-rutinoside chloride that exhibits both photovoltaic performance and nonlinear optical properties, which may be utilized in the field of optoelectronics. Prior to investigating these properties, the stable structure must be determined. For this purpose, its conformational analysis is performed by the Molecular Force Field method with the spartan program. The exact nature of the stable configuration has been ascertained by empirical evidence. The energy of the stable configuration is -1654184.76 kcal/mol, and its dipole moment is 9.94 Debye. Cyanidin-3-rutinoside chloride has been investigated using experimental FT-IR and Raman spectroscopies. Meanwhile, the DFT method at the B3LYP/6-311 + + G(d, p) level was employed in order to study the simulated FT-IR and Raman spectra, the HOMO-LUMO analysis, the molecular electrostatic potentials (MEP), and the non-linear optical (NLO) characteristics of the title molecule. The HOMO and LUMO energies are − 6.45 and − 3.64 electron volts (eV), respectively, with a gap value of 2.81 eV. Additionally, the title compound’s open-circuit voltage, the transition density matrix light-harvesting efficiency, driving force, and binding energy were calculated with by taking photovoltaic cell properties into account. Furthermore, investigations of hole reorganization energy, electron reorganization energy, and total reorganization energy were carried out at the B3LYP/6-31G(d, p) level for the cyanidin-3-rutinoside chloride of interest. In addition, density of state calculations and NBO were made at the B3LYP/6-31G(d, p) level. We calculated the following values for LHE,,,,, and : 0.06, 2.45 eV, 0.20 eV, 0.56 eV, 0.50 eV, 0.57 eV and 1.06 eV, respectively.

  AtıfScopus9·WoS10

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• MakaleYayıncıda açık erişim2023/r/bayburt/12903
  Theoretical Investigation of (E)-1-(2,4-Dichlorophenyl)-3-[4-(morpholin-4-yl)phenyl]prop-2-en-1-one Molecule As a Possible Potential COVID-19 Drug Candidate: Molecular Docking and DFT Calculations

  Ekíncíoğlu, Yavuz

  Abstract: In this study, a potential new drug to fight against the COVID-19 virus, (E)-1-(2,4-dichlorophen-yl)-3-[4-(morpholin-4-yl)phenyl]prop-2-en-1-one molecule has been investigated via computational assessment and molecular docking approach. From the conformer analysis and optimization, the most stable structure is determined. For this structure, geometrical parameters, Frontier molecular orbitals analysis, chemical reactivity descriptors, nonlinear optical properties, natural bond orbital, mulliken population analysis, molecular electrostatic potential map and thermodynamic properties of molecule were calculated with standard functional at the B3LYP/6-311++G(d,p) method. The geometric parameters (bond lengths and bond angles) are in good agreement with the experimental values available in the literature. The stability, structural and electronic properties obtained for the molecule can be a significant contribution to the future experimental and theoretical studies. The molecular docking mechanisms between the molecule and 7ALI protein points out that the protein-ligand systems are hydrogen bonding, π-stacking, and hydrophobic interactions.

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