Yazar "Ekincioglu, Yavuz" seçeneğine göre listele

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    An Integrated In Vitro and In Silico Investigation of the Bioactive Properties of Wild Glycyrrhiza glabra var. glandulifera
    (Springer, 2025) Kizil, Hamit Emre; Ulcay, Sibel; Ekincioglu, Yavuz; Ogutcu, Hatice; Agar, Guleray
    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 T & uuml;rkiye, 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 mu g/mL (24 h) and 105.6 mu g/mL (48 h). Flower extracts demonstrated IC50 values of 116.8 mu g/mL (24 h) and 112.7 mu g/mL (48 h), while fruit extracts displayed superior potency with IC50 values of 104.4 mu g/mL (24 h) and 63.09 mu g/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.
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    Analysis of the nonlinear optical properties, vibrational spectra, DFT method and photovoltaic performance of cyanidin-3-rutinoside chloride
    (Springer, 2024) Sarikaya, Ebru Karakas; Ekincioglu, Yavuz; Bahceli, Semiha; Dereli, Omer
    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, \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\:{V}_{oc}$$\end{document}, \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\:{{\Delta\:}\text{G}}_{\text{i}\text{n}\text{j}\text{e}\text{c}\text{t}}$$\end{document}, \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\:{E}_{b}$$\end{document}, \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\:{\lambda\:}_{h}$$\end{document}, \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\:{\lambda\:}_{e}$$\end{document} and \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\:{\lambda\:}_{total}$$\end{document} : 0.06, 2.45 eV, 0.20 eV, 0.56 eV, 0.50 eV, 0.57 eV and 1.06 eV, respectively.
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    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
    (Wiley, 2025) Sarikaya, Ebru Karakas; Pehlivanoglu, Suray; Turkmen, Merve Ozcan; Ekincioglu, Yavuz; Kostak, Feyza; Celik, Sultan; Dereli, Omer
    Background InformationThe 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. ResultsSubsequently, 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. ConclusionIdentifying 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. SignificanceThis work analyzes 3,5-DBSA's conformational search, characterization, molecular docking, and structural and anticancer properties.
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    DFT-based structural and energetic characterisation of nitrogen-rich tetrazine/triazine derivatives with Kamlet-Jacobs performance predictions
    (Taylor & Francis Ltd, 2026) Ekincioglu, Yavuz; Kepceoglu, Abdullah; Cakir, Zehra; Senturk, Sukru
    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 > H(2)BTTz > 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.
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    Electronic structure and adsorption behavior of 2PANI with selected gases: a DFT approach
    (Walter De Gruyter Gmbh, 2025) Ekincioglu, Yavuz
    This study examines the adsorption properties of C2H4, F-2, 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-F-2 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, F-2, HCl, and H2S can be physically adsorbed onto 2PANI. The recovery time and conductivity were evaluated to determine gas sensitivity performance.
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    Nonlinear optical properties of KnCl (n=2-7) superalkali clusters
    (Iop Publishing Ltd, 2024) Senturk, Sukru; Fardad, Fraidoon; Ekincioglu, 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 (beta(o)) values are in the range of 2.33 x 10(-2.87)(3) x 10(4) au and the second static hyperpolarizability varies between 5.74 x 10(6) au and 38.9 x 10(6) au for the cluster. The nonlinear optical response is due to the superalkali nature of KnCl (n = 2-7) clusters. From computed beta(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 (lambda< 300 nm).
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    Nonlinear optical response of Lin ClK (n=1-6) superalkali clusters
    (Walter De Gruyter Gmbh, 2024) Senturk, Suekrue; Ekincioglu, Yavuz; Dogan, Umit
    The geometrical structures, stabilities, electronic properties and nonlinear optical response of the halogen doped bimetallic Li-n ClK (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 Lin ClK (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 (beta(o)) values are in the range of 1.56 x 10(4) - 4.33 x 10(4) au while the second static hyperpolarizability vary within 2.47 x 10(6) au to 13.9 x 10(6) au for the Li-n ClK (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 (lambda < 300 nm) among the superalkalis indicating that the Li5ClK superalkali can be a candidate structure as new member of NLO materials.
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    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
    (Maik Nauka/Interperiodica/Springer, 2023) Ekincioglu, Yavuz
    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, pi-stacking, and hydrophobic interactions.