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    A novel 3-acetoxy-2-methyl-N-(4-methoxyphenyl)benzamide: Molecular structural describe, antioxidant activity with use X-ray diffractions and DFT calculations
    (Elsevier, 2015) Demir, Sibel; Cakmak, Sukriye; Dege, Necmi; Kutuk, Halil; Odabasoglu, Mustafa; Kepekci, R. Aysun
    In this work, the structure of a novel 3-acetoxy-2-methyl-N-(4-methoxyphenyl) benzamide, was analyzed both experimentally and theoretically using three methods, X-ray single crystal diffraction technique, IR spectroscopy, and quantum chemical computation. The X-ray diffraction analysis indicates that 3-acetoxy-2-methyl-N-(4-methoxyphenyl) benzamide molecula crystallizes in a triclinic system (space group P-1) and the calculated lattice constants are, a = 5.1205 +/- 0.0004 angstrom, b = 9.8598 +/- 0.0008 A, c = 15.3398 +/- 0.0013 angstrom, alpha = 80.79(7), beta = 83.142(6)degrees, gamma = 85.411(6)degrees, and Z = 2. In addition, the molecular geometry and vibrational frequencies of the title compound in ground state have been calculated using density functional theory (DFT) at B3LYP level 6-31G+(d,p) basis set. The geometrical parameters of the title compound obtained from XRD studies are good in agreement with the calculated values. The electronic properties, such as HOMO and LUMO energies and thermodynamic properties were calculated with DFT (using B3LYP/6-31G+(d,p) basis set) approach. To estimate the chemical reactivity of the molecule, the molecular electrostatic potential (MEP) surface map of the title molecule and PES scan were investigated with theoretical calculations at the B3LYP/6-31+G(d,p) and B3LYP/3-21G levels, respectively. Antioxidant properties are determined using DPPH free radical scavenging test. (C) 2015 Elsevier B.V. All rights reserved.
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    Crystal structure and Hirshfeld surface analysis of 2,2′{(1 E,1′E)-[ethane-1,2-diyibis(azanylyunene)]-bis(methanylylidene)}bis[4-(traluorometnoxy)-phenol]copper(II) hydroquinone hermsoiyate
    (Int Union Crystallography, 2019) Kansiz, Sevgi; Meral, Seher; Dege, Necmi; Agar, Aysen Alaman; Fritsky, Igor O.
    In the title complex, [Cu(C18H12F6N2O4)]center dot 0.5C(6)H(6)O(2), the Cu-II ion has a square-planar coordination geometry, being ligated by two N and two O atoms of the tetradentate open-chain Schiff base ligand 6,6'-{(1E,1'E)-[ethane-1,2-diyl-bis (azanylylidene)] bis (methanylylidene)}bis [2-(trifluoromethoxy) phenol].The crystal packing is stabilized by intramolecular O-H center dot center dot center dot O and intermolecular C-H center dot center dot center dot F, C-H center dot center dot center dot O and C-H center dot center dot center dot pi hydrogen bonds. In addition, weak pi-pi interactions form a three-dimensional structure. Hirshfeld surface analysis and two-dimensional fingerprint plots were performed and created to analyze the intermolecular interactions present in the crystal, indicating that the most important contributions for the crystal packing are from F center dot center dot center dot H/H center dot center dot center dot F (25.7%), H center dot center dot center dot H (23.5%) and C center dot center dot center dot H/H center dot center dot center dot C (12.6%) interactions.
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    Crystal structure of 2,3-dimethoxy-N-(4-nitrophenyl)benzamide
    (Int Union Crystallography, 2018) Yaman, Mavise; Almarhoon, Zainab M.; Cakmak, Sukriye; Kutuk, Halil; Meral, Gungor; Dege, Necmi
    In the title compound, C15H14N2O5, the benzene rings are nearly coplanar, making a dihedral angle of 4.89 (8)degrees. An intramolecular N-H center dot center dot center dot O hydrogen bond occurs between the imino and methoxy groups. In the crystal, weak C-H center dot center dot center dot O hydrogen bonds link the molecules into supramolecular chains propagating along the a-axis direction. pi-pi stacking is observed between parallel benzene rings of neighbouring chains, the centroid-to-centroid distance being 3.6491 (10) angstrom. Three-dimensional Hirshfeld surface analyses and two-dimensional fingerprint plots have been used to analyse the intermolecular interactions present in the crystal.
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    Crystal Structure of 3-Acetoxy-2-methyl-N-(4-nitrophenyl)benzamide
    (Japan Soc Analytical Chemistry, 2018) Kansiz, Sevgi; Cakmak, Sukriye; Dege, Necmi; Meral, Gungor; Kutuk, Halil
    The structure of 3-acetoxy-2-methyl-N-(4-nitrophenyl)benzamide was determined by X-ray crystallography. The compound crystallized in a monoclinic system and it was characterized in the space group P2(1)/c with cell parameters a = 5.8658(3), b = 17.1661(10), c = 15.1938(7) angstrom, beta = 103.182(4)degrees, Z = 4, V = 1489.60(14) angstrom(3). The R1 [I > 2 sigma(I)] and wR2 (all data) values are 0.046 and 0.093, respectively, for all 2932 independent reflections. Intramolecular C3-H3 center dot center dot center dot O3 and intermolecular N2-H2 center dot center dot center dot O1, C5-H5 center dot center dot center dot O1 interactions were observed in the crystal lattice.
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    Exploring crystal structure, Hirshfeld surface and quantum mechanical attributes of symmetric thiophene Schiff base
    (Springer, 2023) Meral, Seher; Agar, Aysen Alaman; Cinar, Emine Berrin; Dege, Necmi; Kanmazalp, Sibel Demir; Vidya, V. G.; Kumar, V. G. Viju
    A novel compound (1E,1 ' E)-N,N '-(ethane-1,2-diyl)bis(1-(5-nitrothiophen-2-yl)methanimine) [EDNM] was synthesized from thiophene derivative in view to get multidentate ligand with potential biological activity. EDNM is characterized by FT-IR, 1H and 13C NMR and UV-Vis spectroscopic techniques and confirmed by SCXRD. EDNM crystallizes in the monoclinic system with P21/c space group with Z value 4 and unit cell parameters a = 5.6540(3) angstrom, b = 17.9249(8) angstrom and c = 7.5077(5) angstrom. DFT was employed for theoretical evaluations using B3LYP with the basis set 6-311 + + G (d,p). Geometry optimization, vibrational analysis, NMR, electronic absorption, MEP, FMO, Mulliken charges and NBO analysis were performed, thereby establishing the nature of reactive sites, band energy gap and atomic charges of EDNM. Theoretical values matched well with the experimental findings. NBO analysis revealed the donor acceptor interactions in molecule. Analysis of global reactivity descriptors along with Fukui indices outlines the elaborate scheme of reactive sites of the molecule, and Hirshfeld surface investigation revealed the intermolecular interactions in crystal packing.
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    Solvothermal synthesis, crystal structure, thermal, magnetic properties and DFT computations of a Ytterbium(III) complex derived from pyridine-2,6-dicarboxylic acid
    (Elsevier, 2022) Sharif, Shahzad; Saeed, Maham; Dege, Necmi; Bano, Rehana; Ahmad, Saeed; Gilani, Mazhar Amjad; Sahin, Onur
    A new ytterbium(III) complex, (DMAH(2))(3)[Yb(Pydc)(3)].4H(2)O (1) {Pydc = Pyridine-2,6-dicarboxylate anion, DMAH(2) = Dimethylammonium} has been prepared under mild solvothermal conditions and character-ized by elemental analysis, IR spectroscopy, thermal analysis and single crystal X-ray diffraction. The DMAH2 molecules in 1 , generated in situ from hydrolysis of N,N-dimethylformamide are responsible to assemble 2D coordination polymer through N-H center dot center dot center dot O and O-H center dot center dot center dot O h ydrogen bonding. Magnetic suscepti-bility measurements indicate that the complex ( 1 ) obeys the Curie Weiss law and the overall magnetic behavior is typical for the presence of weak antiferromagnetic exchange coupling interactions. Theoretical data for geometrical parameters of complex 1 agree well with the experimental data. Large HOMO-LUMO energy gap of 4.33 eV has provided kinetic stability to the complex 1 . NBO analysis reflects that in-tramolecular charge transfer occurred between ligand and metal orbitals with the highest stabilization energy of 1024.04 kcal/mol. The negative electrostatic potential at the nitrogen and dianionic pyridine-2,6-dicarboxylate regions confirms that these are dynamic locations for Yb(III) binding. (c) 2022 Elsevier B.V. All rights reserved.
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    Synthesis, crystal structure, spectroscopic features and Hirshfeld surfaces of 2-methyl-3-[(2-methylphenyl)carbamoyl]phenyl acetate
    (Int Union Crystallography, 2019) Yaman, Mavise; Cakmak, Sukriye; Dege, Necmi; Odabasoglu, Mustafa; Pavlenko, Vadim A.; Kutuk, Halil
    The title compound, C17H17NO3, was synthesized, characterized by IR spectroscopy and its crystal structure was determined from single-crystal diffraction data. The asymmetric unit contains two molecules, which adopt different conformations. In one molecule, the acetoxy and the terminal 2-methylphenyl groups are positioned on opposite sides of the plane formed by the central benzene ring, whereas in the other molecule they lie on the same side of this plane. In the crystal, the molecules are linked through strong N-H center dot center dot center dot O hydrogen bonds into chains along [010]. Hirshfeld surface analysis and fingerprint plots were used to investigate the intermolecular interactions in the solid state.
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    Synthesis, structure, supramolecular assembly inspection by Hirshfeld surface analysis, DFT study and molecular docking inspection of 4,5-bis (2-chlorophenyl)-8a-phenylhexahydropyrimido[4,5-d]pyrimidine-2,7 (1H,3H)-dithione
    (Elsevier, 2025) Ahsin, Atazaz; Kurbanova, Malahat; Ahmad, Sajjad; Qamar, Aamna; Ashfaq, Muhammad; Tahir, Muhammad Nawaz; Dege, Necmi
    We studied the three-component condensation of 2-chloraldehyde, acetophenone, and thiourea in conjunction with HCl, resulting in the formation of a new compound: 4,5-bis(2-chlorophenyl)-8a-phenylhexahydropyrimido [4,5-d]pyrimidine-2,7(1H,3H)-dithione (CPPD). The compound's structure was affirmed via X-ray diffraction study. The asymmetric unit contained two molecules that were independent relative to crystallography and an ethanol solvent. The difference between independent molecules was explored by dihedral angles between similar rings in both molecular. The difference between molecules was further explored by molecular overlay plot. The supramolecular assembly was supported via diverse intermolecular interactions which were studied through the use of Hirshfeld surface analysis. Electronic structure computations were carried out at the omega b97xd/tzvp level. Natural bonding orbital (NBO), and FMO study reveal reactivity and charge transfer mechanisms within the compound. Furthermore, the nature of bonding in the present molecule is characterized through quantum theory of atoms in molecules (QTAIM), ELF, and LOL studies. Ab-initio molecular dynamic (AIMD) revealed the kinetic and thermodynamic stability at 300 K. The DFT results have excellent correlation with experimental data. The molecular docking and molecular dynamics simulation further revealed the compound to get deep access in the active pocket of type 2 anti-diabetes GLUT4 protein. This was validated by the stable dynamics as demonstrated by the uniform behavior of the root mean square deviation (RMSD) plot. The root mean square fluctuation (RMSF) also showed stable interactions with amino acids in the presence of the compound. Further, simulation trajectories on the basis of binding free energies indicate the significant role of van der Waals force in the formation of the intermolecular docked complex. This concluded the compound might be a potent structure for the development of anti-diabetic compounds.
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    X-ray diffraction, Hirshfeld surface, local and global chemical activity studies of a Bis{(E)-2,4-di-tert-butyl-6-((3-iodo-4-methylphenylimino)methyl)phenolato-N,O-}copper(II) complex
    (Elsevier, 2020) Demircioglu, Zeynep; Uzun, Serap; Macit, Mustafa; Dege, Necmi
    Cu(II) complex of (BINO)Cu, (E)-2,4-di-tert-butyl-6-((3-iodo-4-methylphenylimino)methyl)phenol, has been synthesized and characterized by FT-IR, UV-Vis and X-ray diffraction techniques. The (BINO)Cu complex crystallizes in the triclinic space group P-1 with a = 14.0545 (5) angstrom, b = 18.5744 (8) angstrom, c = 20.0541 (7) angstrom, alpha = 93.317 (3)degrees, beta = 109.053 (3)degrees, gamma = 95.229 (3)degrees, Z = 4 and Z' = 2, the asymmetric unit contains 2 molecules. X-ray diffraction technique results showed that title complex is in a distorted square environment with tau=0.0436. Also, Hirshfeld surface (HS) analysis is carried out to understand the molecular interactions (fingerprint plots) and molecular surface contours. The close contacts of H center dot center dot center dot H/H center dot center dot center dot H (61.9%) and Cl center dot center dot center dot H/H center dot center dot center dot Cl (15.8%) shows a largest portion of total HS. Optimization of the title molecule was studied using B3LYP and M05-2X functionals in DFT method at the LANL2DZ basis set. Theoretical calculations is a good way for obtaining detailed information about local and global chemical activity, molecular and chemical properties which are reveal the electrophilic and nucleophilic nature. According to local chemical activity results (MEP, Fukui function and net charge analyses), the optimized structure shows more electrophilic nature than nucleophilic one. Optimized structure is a soft molecule (eta=1.689 eV for spin alpha and eta = 1.131eV for spin beta and s = 0.296 eV(-1) for spin alpha and s = 0.442 eV(-1) for spin (3) so it shows very high chemical reactivity, low kinetic stability and displays higher intramolecular charge transfer. The stability of the molecule arising from hyperconjugative interactions, charge delocalization was analyzed by using natural bond orbital analysis (HBO). (C) 2020 Elsevier B.V. All rights reserved.
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    Zinc(II) coordination compound with N ′-(pyridin-2-ylmethylene) nicotinohydrazide: Synthesis, crystal structure, computational and cytotoxicity studies
    (Elsevier Science Inc, 2024) Adhikari, Suman; Nath, Sourav; Kansiz, Sevgi; Balidya, Nabajyoti; Paul, Anirban Kumar; Dege, Necmi; Sahin, Onur
    In this work, we report on the synthesis of a novel zinc(II) coordination compound [ZnL 2 ] ( 1 ), which was readily obtained from the reaction of Zn(OAc) & sdot; 2H 2 O and N ' -(pyridin-2-ylmethylene)nicotinohydrazide ( HL ) in methanol. Recrystallization of 1 from dimethylformamide under ambient conditions allowed to produce yellow blocklike crystals of 1 & sdot; H 2 O. Complex 1 & sdot; H 2 O was characterized by FT-IR and 1 H NMR spectroscopy, while its optical properties were studied by UV - vis and spectrofluorimetry in methanol. The crystal structure of the title complex was revealed by single crystal X-ray diffraction and further explored in detail by the Hirshfeld surface analysis. Theoretical investigations based on the DFT calculations have also been applied to show the electronic properties of complex 1 . The antitumor activities of the parent ligand HL and complex 1 were studied using Dalton ' s lymphoma malignant cancer model. Both compounds were found to induce concentration -dependent cytotoxicity and apoptotic cell death, leading to a decrease in cell viability, body weight, and tumor volume in mice with the superior activity of complex 1 over HL . Mice treated with complex 1 demonstrated an increase in life span with a survival period of 23 days. Finally, using a molecular docking approach, we have probed complex 1 to inhibit the recombinant mouse tumor -necrosis factor alpha (mTNF).