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    Anchor Effect on Pedal Motion Observed in Crystal Phase of an Azobenzene Derivative
    (Springer/Plenum Publishers, 2011) Karabiyik, Hasan; Petek, Hande; Iskeleli, Nazan Ocak; Albayrak, Cigdem; Agar, Erbil
    Some molecules having a molecular skeleton similar to that of stilbenes and azobenzenes show orientational disorder in the crystals due to pedal motion. Heretofore, the orientational disorder through pedal motion has been observed for the compounds containing only two aromatic rings in the absence of bulky substituent groups. Here we report that the pedal motion can be detected even in the presence of a bulky substituent group to which orientational disorder becomes invisible as a result of anchor effect arising from phenoxyphtalonitrile group. X-ray crystallographic analysis of the compound, C23H18N4O, reveals the existence of partially overlapped two pedal conformers. The compound crystallizes in the monoclinic space group P2(1)/c with a = 12.9429(11) a<<, b = 8.5075(5) a<<, c = 21.063(2) a<< and beta = 123.155(6)A degrees. Major pedal conformer is stabilized by weak C-H center dot center dot center dot O type hydrogen bond and C-H center dot center dot center dot pi type edge-to-face interactions in solid state. Quantum chemical calculations at B3LYP/6-311G+(d,p) level suggest that the stabilization of the compound decreases with increasing deviation from the planar geometry of trans-azobenzene fragment. Molecular and crystal structure of 4-[2-Methyl-4-(4-ethylphenyldiazenyl)]phenoxyphtalonitrile, C23H18N4O, indicate the existence of partially overlapped two pedal conformers in which orientational disorder becomes invisible as a result of anchor effect arising from phenoxyphtalonitrile group.
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    Experimental (XRD, FTIR, UV-Vis, NMR) and theoretical investigations (chemical activity descriptors, NBO, DNA/ECT) of (E)-2-((2-hydroxy-5-methoxybenzylidene)amino)-4-nitrophenol
    (Taylor & Francis Ltd, 2021) Guzel, Enis; Demircioglu, Zeynep; Cicek, Ceren; Agar, Erbil; Yavuz, Metin
    The new Schiff base of compound was synthesized and characterized by XRD, FTIR, UV-Vis and NMR techniques. The structure with two molecules in its asymmetric unit showed the enol-imine form in one and the keto-amine form in the other. Both tautomeric forms are stabilized by strong O-H horizontal ellipsis N and N-H horizontal ellipsis O intramolecular hydrogen bonds. Optimized geometrical parameters and calculated spectroscopic features obtained by DFT/B3LYP/6-31G(d,p) calculations show a good agreement with the experimental data. Accordingly local and global chemical activity descriptors were investigated.
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    Experimental and DFT Studies of N-2-Methoxyphenyl-2-oxo-5-nitro-1-benzylidenemethylamine: In Gas Phase and Solvent Media.
    (Int Union Crystallography, 2009) Tanak, Hasan; Yavuz, Metin; Buyukgungor, Orhan; Ersahin, Ferda; Agar, Erbil
    [No abstract available]
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    Experimental and theoretical approach: Local and global chemical activity, charge transfer method with DNA bases, spectroscopic, structural and electronic properties of (E)-2-(((4-fluorophenyl)imino) methyl)-4-methoxyphenol
    (Elsevier, 2020) Guzel, Enis; Demircioglu, Zeynep; Cicek, Ceren; Agar, Erbil
    (E)-2-(((4-fluorophenyl)imino) methyl)-4-methoxyphenol compound was synthesized and characterized using FT-IR, UV-Vis, NMR and X-ray diffraction method. Hirshfeld surface analysis was used to show surface contours and two-dimensional fingerprint plots have been used to analyse intermolecular interactions. All theoretical computations were calculated by using density functional theory (DFT) B3LYP method with the help of 6-31G(d,p) basis set. The UV-Vis spectra of the title compund was computed using the Time-Dependent DFT method in DMSO solution phase. H-1 and C-13 NMR chemical shifts have been calculated with WO approximation. In theoretical calculations we obtained detailed information about electrophilic and nucleophilic nature, local and global chemical activity studies. Accordingly, global (FMOs, hardness and softness parameters) and local (MEP, FF, net charges) chemical activity descriptors were investigated. Also, the interactions between the molecule with DNA bases such as adenine, cytosine, guanine, and thymine were investigated by using the ECT (electrophilicity-based charge transfer) method and Delta N (charge transfer) for investigating the charge transfer and electrophilic & nucleophilic nature. (C) 2019 Elsevier B.V. All rights reserved.
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    Quantum chemical and X-ray diffraction studies of (E)-3-(((3,4-dimethoxybenzyl)imino)methyl)benzene-1,2-diol
    (Elsevier, 2020) Uzun, Serap; Demircioglu, Zeynep; Tasdogan, Mahmut; Agar, Erbil
    In this study, the target compound, (E)-3-(((3,4-dimethoxybenzyl)imino)methyl)benzene-1,2-diol, has been synthesized and characterized by FT-IR, UV-Vis and H-1 NMR, C-13 NMR methods. It's molecular structure has been experimentally elucidated by single crystal X-ray diffraction method. As a result of the X-ray diffraction experiment, it was found that the title molecule is in zwitterionic form. The minimum energy conformation in the gas phase of the title compound was achieved by density functional theory (DFT) method with the B3LYP hybrid functional using 6-31G(d,p) basis set. Accordingly, global (HOMO, LUMO, hardness and softness parameters) and local (MEP, FF, net charges) chemical activity descriptors were investigated. The stability of the molecule arising from hyperconjugative interactions, charge delocalization were analyzed by using natural bond orbital analysis (NBO) and nonlinear optical properties were investigated. Also, the interactions between the molecule with DNA bases such as adenine, cytosine, guanine, and thymine were investigated by using the ECT (electrophilicity-based charge transfer) method and Delta N (charge transfer) for investigating the charge transfer, electrophilic and nucleophilic nature. (C) 2020 Elsevier B.V. All rights reserved.
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    Spectroscopic and Theoretical Studies and Intramolecular Proton Transfer in (Z)-2-Hydroxy-6-(((2-methoxy-5-(trifluoromethyl)phenyl)amino)methylene)cyclohexa-2,4-dien-1-one
    (Maik Nauka/Interperiodica/Springer, 2021) Tari, Gonca Ozdemir; Kirca, Basak Kosar; Tasdogan, Mahmut; Ozdemir, Namik; Agar, Erbil
    In present work, a new Schiff base compound, (E)-3-(((2-methoxy-5-(trifluoromethyl)phenyl)imino)methyl)benzene-1,2-diol was synthesized and characterized by X-ray diffraction and spectroscopic methods (FT-IR, UV-Vis) and quantum mechanical calculation methods. The obtained structure is monoclinic, space group P2(1)/c, with unit cell parameters a = 15.1881(10) angstrom, b = 14.5816(11) angstrom, c = 6.2023(5) angstrom, beta = 98.008 (6)degrees, and Z = 4. Theoretical calculations were used to investigate the optimized molecular geometry of the title compound. The calculated and experimental results show the title compound tends to the keto-amine form. Besides, the frontier molecular orbital, non-linear optical properties and electronic structure parameters of the title compound were computed in the solvent media using the theoretical methods. The molecular electrostatic potential surface was obtained at the optimized geometry to predict reactive sites for nucleophilic and electrophilic attack for the studied molecule. Statistical thermodynamic functions for the title compound were calculated at 298.15 K temperature and 1 atm pressure by using the HF and DFT/B3LYP methods with the 6-311++G(d,p) basis set.
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    Synthesis and analysis (thermodynamic, electronic, NLO, FMO, NBO, MEP, IR, UV, NMR properties, Hirshfeld surface analysis and molecular docking) of the new Schiff base molecule: (Z)-4-bromo-2-(((2,4-dimethoxypheny) limino)methyl)-5-fluorophenol
    (Elsevier, 2025) Evecen, Meryem; Ersanli, Cem Cueneyt; Dogan, Onur Erman; Bozkurt, Ilhan; Agar, Erbil
    A new Schiff-base (Z)-4-bromo-2-(((2,4-dimethoxyphenyl)imino)methyl)-5-fluorophenol (BDMF) was synthesized and characterized by single-crystal X-ray diffraction, spectroscopic (UV, FT-IR, and NMR), and DFT techniques. Based on DFT computational analysis, Molecular Electrostatic Potential (MESP) 3D plots were used to identify the electrophilic and nucleophilic sites. Based on HOMO-LUMO energies, charge transfer takes place within the molecule, and quantum chemical characteristics were precisely assessed. Additionally, DFT was used to examine charges, molecular orbital contributions, natural bond orbital (NBO), frontier molecular orbital (FMO), nonlinear optic (NLO) analysis, and thermodynamic parameters including enthalpy, entropy, and heat capacity at different temperatures. Values for polarizability, electric dipole moment, and first static hyperpolarizability have been computed. The title compound exhibits nonlinear optical properties, according to the results. In addition, Hirshfeld surface analysis was used to predict molecular interactions. Finally, molecular docking analysis of the title compound was performed.
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    Synthesis, spectroscopic, and molecular structure characterizations of some azo derivatives of 2-hydroxyacetophenone
    (Elsevier, 2009) Albayrak, Cigdem; Gumrukcuoglu, Ismail E.; Odabasoglu, Mustafa; Iskeleli, Nazan Ocak; Agar, Erbil
    Some novel azo compounds were prepared by the reaction of 2-hydroxyacetophenone with aniline and its substituted derivatives. The structures of synthesized azo compounds were determined by IR, UV-Vis, H-1 NMR and C-13 NMR spectroscopic techniques and the structures of some of these compounds were also determined by X-ray diffraction studies. Structural analysis using IR in solid state shows that the azo form is favoured in the azo compounds whereas UV-Vis analysis of the azo compounds in solution has shown that there is a azo and ionic form. The azo compounds in the basic solvents dimethylformamide (DMF) and dimethylsulfoxide (DMSO) are both azo and ionic form while these compounds in ethyl alcohol (EtOH) and chloroform (CHCl3) are only azo form. (C) 2009 Elsevier B.V. All rights reserved.
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    Synthesis, spectroscopic, X-ray diffraction, molecular modelling and ADME Studies of (E)-2-(((4-bromo-2-(trifluoromethyl)phenyl)imino) methyl)-6-methoxyphenol
    (Elsevier, 2025) Kalkan, Selami; Yesilbag, Semanur; Kelessglu, Zeynep; Guzel, Enis; Agar, Erbil; Yavuz, Metin
    The title compund is characterized by single-crystal X-ray diffraction, FT-IR, UV-Vis and NMR analyses. The molecular geometry and spectroscopic analyses (UV-Vis, 1HNMR , 13CNMR and vibrational frequencies) in the ground state have been calculated by using the density functional hybrid function of DFT/B3LYP/6-311G(d,p) basis set. The presence and species of the intra-molecular hyperconjugative interactions are studied by NBO study. Moreover, molecular orbitals, molecular electrostatic potential (MEP), chemical activity parametrs and Fukui function analyses are determined with the computational method. Hirshfeld surface (HS) analysis followed by two-dimensional fingerprint plots provides insights into the intermolecular interactions within the crystalline structure. ADME analysis is to access the physicochemical properties, lipophilicity values, pharmacokinetic properties, liquid solubility data, medicinal chemistry and drug similarity data obtained for the ligand. Also, in the molecular docking study, the interaction between the studied compound structure and Tyrosine-protein kinase (SYK) is investigated. The selected protein (SYK) is chosen because it provides control and change of cell functions and plays an important role in the development of cancer and the spreads of cancerous cells to other regions directly or through blood and lymph vessels. In the biological activity analysis, the extracts prepared in solvent were tested against the microorganism Bacillus subtilis.
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    Synthesis, X-ray diffraction, spectroscopic (FT-IR, UV-Vis, 1H-NMR, 13C-NMR and TGA), DFT and molecular docking studies of (E)-3-(((3-chloro-4-(4-chlorphenoxy) phenyl) imino) methyl) benzene-1,2-diol
    (Taylor & Francis Ltd, 2022) Uzun, Serap; Demircioglu, Zeynep; Tasdogan, Mahmut; Agar, Erbil
    The title compound has been synthesized and characterized by FT-IR, UV-Vis, TGA, H-1-NMR and C-13-NMR spectroscopic techniques. Solid state of title structure has been determined by XRD. The molecular properties of title compound have performed by Density functional theory (DFT) using B3LYP/6-31G(d,p) method. Also, the interactions between the title molecule with DNA bases have been calculated by using the electrophilicity-based charge transfer (ECT) method for investigating the charge transfer. Finally, molecular docking study has also performed to investigate the binding pattern of the title compound with PDB ID: 2QDJ inhibitor targets and showed good insights on the possible interactions.
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    Synthesis, X-ray Molecular Structure, and Computational Study of (E)-2-[tris(hydroximethyl)methy]aminomethylen-4-methylphenol
    (Int Union Crystallography, 2009) Tari, Gonca Ozdemir; Isik, Samil; Tanak, Hasan; Ersahin, Ferda; Agar, Erbil
    [No abstract available]
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    Theoretical modeling and experimental studies on N-n-Decyl-2-oxo-5-nitro-1-benzylidene-methylamine
    (Springer, 2009) Tanak, Hasan; Ersahin, Ferda; Koysal, Yavuz; Agar, Erbil; Isik, Samil; Yavuz, Metin
    The Schiff base compound, N-n-Decyl-2-oxo-5-nitro-1-benzylidene-methylamine, has been -synthesized and characterized by IR, electronic spectroscopy, and X-ray single-crystal determination. Molecular geometry from X-ray experiment of the title compound in the ground state have been compared using the Hartree-Fock (HF) and density functional method (B3LYP) with 6-31G(d) basis set. Calculated results show that density functional theory (DFT) at B3LYP/6-31G(d) level can well reproduce the structure of the title compound. To investigate the solvent effect for the atomic charge distributions of the title compound, self-consistent reaction field theory with Onsager reaction field model was used. In addition, DFT calculations of the title compound, molecular electrostatic potential and thermodynamic properties were performed at B3LYP/6-31G(d) level of theory.