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Öğe 2-kloro-1-(6-floro-3,4-dihidro-2H-kromen-2yl)ethanon Yapısının Yoğunluk Fonksiyonel Kuramı İle Kimyasal Aktivite Hesaplamaları(2022) Demircioğlu, Zeynep; Uzun, SerapBu çalışmada, sentezi yapılmış ve X-ışını kırınımı yöntemi ile yapısı aydınlatılmış 2-kloro-1-(6-floro-3,4-dihidro-2H-kromen-2yl) ethanon molekülünün kimyasal aktivitesi, ikinci dereceden lineer olmayan optik özellikleri ve DNA bazları ile etkileşimi üzerine kuramsal çalışmalar yapılmıştır. Kuramsal yöntem olarak, deneysel çalışmalara yakın ve anlamlı değerler vermesi ayrıca hesapsal maliyeti nedeniyle Yoğunluk Fonksiyonel Kuramı (YFK) seçildi. Çalışılan molekülün kararlı moleküler geometrisi optimizasyon yapılarak elde edildi. Tüm kuramsal hesaplamalarda YFK/B3LYP/6-311++G(d,p) baz seti kullanıldı. Optimize edilmiş molekülün geometrik parametre değerlerinin deneysel verilerle uyumlu olduğu görüldü. Frekans hesaplamaları sonucunda sanal frekans verisinin gözlenmemesi de yapının başarılı olarak optimize edildiğini destekledi. Böylece optimize yapı üzerinden elde edilen diğer özellikler hesaplanarak yorumlandı. Molekülün kimyasal aktivitesinin hesaplanmasında sınır moleküler orbital (HOMO, LUMO) enerjileri kullanılarak sertlik, yumuşaklık ve diğer kimyasal aktivite parametreleri elde edildi. Moleküler elektrostatik potansiyel (MEP), yük popülasyon ve Fukui fonsiyon analizleri ile yapının hangi bölgelerde kimyasal etkileşime yatkın olduğu belirlendi. Bunların yanı sıra Hirshfeld yüzey analizi ile moleküler etkileşimler, Hirshfeld yüzey haritaları, atomların birbirleriyle etkileşim yüzdeleri 2 boyutlu-parmak izi tayini ile incelendi.Öğe Bis[2-(metilamino)troponato]bakır(II) Molekülünün Yapısal ve Elektronik Özelliklerinin Deneysel ve Kuramsal Analizleri(2020) Uzun, Serap; Demircioğlu, ZeynepBis[2-(metilamino)troponato]bakır(II) molekülünün moleküler, elektronik ve kimyasal yapısı incelendi. Hesaplamalı kimya yöntemlerinden yoğunluk fonksiyonel kuramı kullanılarak molekülün deneysel olarak elde edilemeyen lokal ve global kimyasal aktivite parametreleri ve elektrofilik ve nükleofilik doğasının belirlenmesi amaçlandı. Bunun yanı sıra çalışılan molelükün optik bir materyal olma eğilimi incelenmiştir. Yapının kararlılık enerjisi, konjüge etkileşimler, yörünge orbitallerinin stabilizasyonu, hibritleşme yüzdeleri ve geçiş durumları incelendi.Öğe Chemical Activity Determination of 4-Ethoxy-3-methoxybenzaldehyde Molecule by Computational Chemical Method(Giresun Üniversitesi, 2019) Uzun, Serap; Demircioglu, ZeynepThe 4-ethoxy-3-methoxybenzaldehyde molecule is of great importance in the synthesis of hetero-ring compounds as well as biological activities. X-ray diffraction analysis is made by Leka and friends and theoretical results are calculated by density funct,onal theory, B3LYP model and 6-311G(d,p) bases set. The geometric parameters obtained as a result of the optimization of the structure were successfully represented by X-ray diffraction method and all theoretical calculations are used by the the same method of DFT/B3LYP/6-311G(d,p). Chemical activity parameters of the optimized structure, molecular electrostatic potential map, Fukui functions and net charge analysis were used to obtain electrophilic and nucleophilic nature of the structure as well as hardness and softness information. Nonlinear optical properties were examined and the tendency of the structure to be an optical material was discussed. In addition, the interactions of DNA bases adenine, guanine, cytosine and thymine with the studied molecule were determined by electrophilic charge transfer (ECT) method.Öğe Combined X-Ray, Ir, Intramolecular Proton Transfer and Quantum Chemical Studies on (E)-2-Bromo-4-Methoxy-6-[(P-Tolylimino)Methyl]Phenol(2017) Uzun, Serap; Albayrak Kaştaş, Çiğdem; Büyükgüngör, Orhan; Şenel, IsmetIn this work, molecular structure of (E)-2-Bromo-4-methoxy-6-[(p-tolylimino) methyl] phenol which is an o-hydroxy Schiff basederivative was characterized by X-ray single crystal diffraction, IR spectroscopy. In the quantum mechanical calculations, the densityfunctional theory (B3LYP) with 6-31G (d, p) was used to support our studies. According to the X-ray crystallographic data, it wasobserved that adopts the phenol-imine tautomeric form of the compound in solid state.The two possible tautomeric forms of the title compound were investigated using DFT method with B3LYP applying 6-31G(d,p) basis set. A relaxed potantial energy surface (PES) scan was performed based on the optimized geometry of the OH tautomericform and O–H bond distances were used as the redundant internal coordinate. PES scan process helped us for understand the effectsof transfer on the molecular geometry. At the same time, in this study, nonlinear optical properties (NLO) of the molecule wereinvestigated.Öğe 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, ErbilIn 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.Öğe Synthesis, crystal structure, theoretical chemical activitiy, electrophilicity-based charge transfer (ECT) with DNA bases and molecular docking studies of 2-amino-4-(2,4-dimethoxyphenyl)-5,6-dihydrobenzo[H]quinoline-3-carbonitrile(Elsevier, 2023) Uzun, Serap; Kelesoglu, Zeynep; Koc, Esra; Ceylan, MustafaIn this study, the title compound is synthesized and characterized by X-ray diffraction method, FT-IR, UV-Vis, TGA and NMR spectroscopy. The crystal packing is mainly controlled by N-H...N, C-H...N hy-drogen bonds and C-H...pi interactions. Hirshfeld surface analysis reveals the presence of intermolecular interactions in the crystal. All theoretical computations (NBO, FMOs, MEP, FF, ECT) are calculated by Den-sity Functional Theory (DFT) at B3LYP level by using 6-311G(d,p) basis set. The stability of the molecule arising from hyperconjugative interactions, charge delocalization was analyzed by using natural bond or-bital analysis (NBO). Also, the interactions between the title molecule and DNA bases are investigated by using the ECT (electrophilicity-based charge transfer) method. Calculations show that the title molecule interacts with the guanine more than other DNA bases. Furthermore, the interactions states between the guanine DNA (PDB:4ENM) and the studied molecule is determined by molecular docking study.(c) 2022 Elsevier B.V. All rights reserved.Öğe 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, ErbilThe 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.Öğe Synthesis, X-ray structure, antimicrobial activity, DFT and molecular docking studies of N-(thiophen-2-ylmethyl)thiophene-2-carboxamide(Int Union Crystallography, 2022) Cakmak, Sukriye; Demircioglu, Zeynep; Uzun, Serap; Veyisoglu, Aysel; Yakan, Hasan; Ersanli, Cem CuneytIn the present study, N-(thiophen-2-ylmethyl)thiophene-2-carboxamide, C10H9-NOS2, (I), was obtained by the reaction of thiophene-2-carbonyl chloride and thiophen-2-ylmethanamine. Characterization of (I) was carried out using X-ray diffraction, spectroscopic techniques and elemental analyses. The DFT/B3LYP/ 6-311++G(d,p) theoretical level was successfully applied to calculate the optimized geometry and the local and global chemical activity parameters. The results obtained show good agreement between the experimental and theoretical geometrical parameters. The local and global chemical activity parameters were examined to determine the electrophilic and nucleophilic sites in (I). The natural bond orbital (NBO) analysis of (I) gives an efficient methodology for investigating the inter- and intramolecular bonding, as well as giving a convenient basis for investigating charge transfer or conjugative interactions in molecular systems. Also, the antimicrobial activity of (I) was investigated against eight microorganisms using the microdilution method and it is found to have an effective antibacterial activity. In addition, molecular docking studies were calculated in order to understand the nature of the binding of (I) with a lung cancer protein (PDB entry 1x2j).Öğe 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, NecmiCu(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.Öğe X-ray, DFT (Chemical activity, Charge transfer and Non-linear optical properties) and Spectroscopic Studies on 2-amino-4-(4-bromophenyl)-5,6[H]quinoline-3-carbonitrile (I) and 2-amino-4-(2-bromophenyl)-5,6[H]quinoline-3-carbonitrile (II)(Elsevier, 2022) Uzun, Serap; Demircioglu, Zeynep; Koc, Esra; Ceylan, Mustafayyy The title compounds of (I) and (II) have been synthesized and characterized by FT-IR and NMR spectroscopic techniques. Solid state crystal structures have been determined by X-ray diffraction technique. The Hirshfeld and 2D fingerprint analyses are used to investigate the intermolecular interactions in the crystal structure. The molecular geometries have also been optimized by using density functional theory (DFT/B3LYP) methods with the 6-31 + G(d,p) basis set and geometric parameters have been compared with the experimental datas. Additionally, molecular electrostatic potential (MEP), chemical activity parameters, non-linear optical (NLO) properties, ECT analysis of the title compounds have been investigated. (C) 2021 Elsevier B.V. All rights reserved.
