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Öğe A theoretical study on cyclometalated iridium (III) complexes by using a density functional theory(World Scientific Publ Co Pte Ltd, 2020) Erkan, Sultan; Karakas, DuranCyclometalated iridium (III) complexes (Ir1-Ir4) are calculated in detail with computational chemistry methods. The calculated structural parameters of Ir3 are compared with experimental values and a good fit is obtained. IR spectra are calculated at B3LYP/LANL2DZ/6-31G(d) level in the gases phase. Calculated H-1-NMR chemical shift values of the mentioned complexes are compared with the experimental data and all chemical shifts are assigned to the respective atoms. The quantum chemical parameters such as absolute hardness (eta), absolute softness (sigma) electronegativity (chi), chemical potential (mu) and electronic charges (Delta N-max) are calculated and are associated with the experimental anti-cancer properties of the related complexes. Nonlinear optic properties of the Ir1-Ir4 were investigated with the average linear polarizability (alpha), the anisotropy of the polarizability (Delta alpha), first hyperpolarizability (beta(0)) values. Hole transfer (t(h)), electron transfer integrals (t(e)), hole reorganization energies (lambda(h)) and electron reorganization energies (lambda(e)) are examined. In addition, molecular docking study was performed. It was found that the molecular docking results are similar to the experimental anti-cancer trend.Öğe Activity of the rocuronium molecule and its derivatives: A theoretical calculation(ELSEVIER SCIENCE BV, 2019) Erkan, SultanIn the present work neuromuscular blocking rocuronium drugs were studied theoretically using the HF and B3LYP methods with the 3-21G, 6-31G, 6-311G, 6-31G (d, p) and CEP-31G basis sets. The transfer integrals (t) and the reorganization energies (lambda) are calculated by applying the Marcus theory. The molecular and electronic properties such as molecular electrostatic potential (MEP) maps, partial state density (PDOS) spectrum and molecular orbitals (HOMO and LUMO) were presented. Molecular docking studies of rocuronium derivatives were performed for provided insights into the mechanism of action on ion channels that mediate rapid chemical neurotransmission at the neuromuscular junction. For the first time, it was found that the rocuronium molecule could be a good electron transfer material with respect to electron and hole reorganization energy values. The forbidden energy values of the rocuronium derivatives are at the range of -1.34 to -9.94 eV and in good agreement with the results for other signalling central nervous drugs. (C) 2019 Elsevier B.V. All rights reserved.Öğe Antiproliferative Evaluation of Some 2-[2-(2-Phenylethenyl)-cyclopent-3-en-1-yl]-1,3-benzothiazoles: DFT and Molecular Docking Study(Wiley-V C H Verlag Gmbh, 2020) Ceylan, Mustafa; Erkan, Sultan; Yaglioglu, Ayse Sahin; Uremis, Nuray Akdogan; Koc, EsraThe 2-[2-(2-phenylethenyl)cyclopent-3-en-1-yl]-1,3-benzothiazoles were synthesized from the reactions of 7-benzylidenebicyclo[3.2.0]hept-2-en-6-ones with 2-aminobenzenethiol. The antiproliferative activities of 2-[2-(2-phenylethenyl)cyclopent-3-en-1-yl]-1,3-benzothiazoles were determined against C6 (rat brain tumor) and HeLa (human cervical carcinoma cells) cell lines using BrdU cell proliferation ELISA assay. Cisplatin and 5-fluorouracil (5-FU) were used as standards. The most active compound was 2-{(1S,2S)-2-[(E)-2-(4-methylphenyl)ethenyl]cyclopent-3-en-1-yl}-1,3-benzothiazole against C6 cell lines with IC50=5.89 mu m value (cisplatin, IC50=14.46 mu m and 5-FU, IC50=76.74 mu m). Furthermore, the most active compound was 2-{(1S,2S)-2-[(E)-2-(2-methoxyphenyl)ethenyl]cyclopent-3-en-1-yl}-1,3-benzothiazole against HeLa cell lines with IC50=3.98 mu m (cisplatin, IC50=37.95 mu m and 5-FU, IC50=46.32 mu m). Additionally, computational studies of related molecules were performed by using B3LYP/6-31G+(d,p) level in the gas phase. Experimental IR and NMR data were compared with the calculated results and were found to be compatible with each other. Molecular electrostatic potential (MEP) maps of the most active 2-{(1S,2S)-2-[(E)-2-(2-methoxyphenyl)ethenyl]cyclopent-3-en-1-yl}-1,3-benzothiazole against HeLa and the most active 2-{(1S,2S)-2-[(E)-2-(4-methylphenyl)ethenyl]cyclopent-3-en-1-yl}-1,3-benzothiazole against C6 were investigated, aiming to determine the region that the molecule is biologically active. Biological activities of mentioned molecules were investigated with molecular docking analyses. The appropriate target protein (PDB codes: 1 M17 for the HeLa cells and 1JQH for the C6 cells) was used for 2-{(1S,2S)-2-[(E)-2-(2-methoxyphenyl)ethenyl]cyclopent-3-en-1-yl}-1,3-benzothiazole and 2-{(1S,2S)-2-[(E)-2-(4-methylphenyl)ethenyl]cyclopent-3-en-1-yl}-1,3-benzothiazole molecules exhibiting the highest biological activity against HeLa and C6 cells in the docking studies. As a result, it was determined that these molecules are the best candidates for the anticancer drug.Öğe Application of pyrrolidinomethylcalix[4]arene coated silica adsorbent for the removal of Chicago sky blue 6B dye from water samples: Equilibrium and computational modelling studies(Taylor & Francis Ltd, 2021) Junejo, Ranjhan; Jalbani, Nida Shams; Kaya, Savas; Erkan, Sultan; Ebenso, Eno E.In this study, silica surface has been coated using pyrrolidinomethylcalix[4]arene through the chemical modification of silanol groups. The pyrrolidinomethylcalix[4]arene-coated silica (PCS) adsorbent was characterized using the Fourier transform infrared and scanning electron microscopic technique. The adsorptive removal efficiency of PCS adsorbent was checked through batch studies with various effective parameters such adsorbent dose, pH, and temperature. During experiments, it has been observed that maximum adsorption was achieved in acidic to neutral pH and 25 mg.L-1 of PCS dose, while the kinetic models demonstrates that the pseudo 2nd order equation was the best fit (R-2 0.99). The thermodynamic experiments described that the reaction is exothermic and spontaneous. Furthermore, equilibrium models were applied on experimental data and it has been noticed that the equilibrium data was best-fitted with Langmuir isotherm model (R-2 0.99). The DFT analysis of dye molecule is helpful to examine the chemical interaction sites of absorbent and adsorbent using B3LYP/LANL2DZ/6-311++G (d,p) level using G09W software.Öğe Assessing cytotoxic activities, theoretical and in silico molecular docking calculations of phthalocyanines bearing cinnamyloxy-groups(Taylor & Francis Inc, 2023) Ozten, Ozge; Kuznetsov, Aleksey E.; Gokce, Mustafa; Erkan, Sultan; Bulut, Emrah; Taskin, Omer Suat; Kurt, Belma ZenginCancer has been recognized as one of the deadliest diseases in the world in recent years. By chemically tailoring specific properties, anticancer agents can be prepared very effectively for the treatment of various cancer types. In this manner, as anticancer agents, a series of soluble metal-free and metallophthalocyanines carrying cinnamyloxy-groups at peripheral beta-positions have been prepared. All synthesized phthalocyanines were characterized by various spectroscopic approaches such as ultraviolet - visible (UV - Vis), Fourier transform infrared (FT-IR), and matrix-assisted laser deionization/ionization time-of-flight mass spectroscopy (MALDI-TOF MS) techniques. These compounds are highly soluble in dimethyl sulfoxide (DMSO) and soluble in common organic solvents. The spectroscopic properties, cytotoxicity, and theoretical calculations of these complexes have been investigated. In cytotoxicity tests, compounds 1, 4, and 7 are the most active against HT-29 cell lines with IC50 values of 36.9 mu M, 32.5 mu M, and 51.1 mu M, respectively. Also, the most and the least cytotoxic compounds against healthy CCD cell line is compounds 5 and 6 with the IC50 value of 13.4 mu M and >250 mu M, respectively. The PDB ID:4BQG target protein representing the HT-29 cancer cell line and the anti-cancer activities of phthalonitrile and its phthalocyanines were supported by molecular docking studies. Density Functional Theory (DFT) study supported the experimental results, including the spectral data, and implied that the compounds 5-7 are comparable by their characteristics, such as electronic properties, optical properties, electrostatic potentials, reactivity parameters, with the earlier studied compounds 2-4, which were successfully proved to be good candidates for cancer treatment. [GRAPHICS]Öğe Benzaldehyde derivatives with functional propargyl groups as ?-glucosidase inhibitors(Elsevier, 2020) Gungor, Seyit Ali; Tumer, Mehmet; Kose, Muhammet; Erkan, SultanThe benzaldehyde derivatives (1-6) containing one and/or two propargyl arm(s) attached to the phenolic hydroxyl oxygen atom on the ortho-, meta- or para-positions of the aromatic ring were synthesized and characterized by spectral and microanalytical methods. The molecular structures were of 1, 4-6 determined by the single crystal X-ray crystallography. The benzaldehyde derivatives containing free phenolic groups involved intra- and inter-molecular hydrogen bonding interactions. The electrochemical properties of the compounds were investigated at the different scan rates and it was found that the compounds show different electrochemical behaviors. alpha-Glucosidase inhibitor properties of the carbonyl compounds were investigated and it has been determined that some of them show high activity. Compounds with a free phenolic group (-OH) exhibit better inhibition activity than compounds with no free phenolic group. It was also found that the position of propargyl group played an important role in the alpha-glucosidase inhibition activity. Molecular docking studies were performed to investigate the binding interactions and interaction energies of the (1-6) compounds with the alpha-glucosidase inhibitor. (C) 2020 Elsevier B.V. All rights reserved.Öğe Computational investigation of structural, nonlinear optical and anti-tumor properties of dinuclear metal carbonyls bridged by pyridyl ligands with alkyne unit(Elsevier, 2020) Erkan, Sultan; Karakas, DuranDinuclear metal carbonyls bridged by pyridyl ligands with alkyne unit, [(OC)(5)W-2(mu-DPA) (1), [(OC)(5)W](2)(mu-DPB) (2) and [(OC)(5)W](2)(mu-BPEB) (3), where DPA = 4,4'-dipyridylacetylene, DPB = 4,4'-dipyridylbutadiyne and BPEB = 1,4-bis(4'-pyridylethynyl)benzene, are optimized at B3LYP/(LANL2DZ)(6-31 + G(d)) level. Molecular structures of the complexes are characterized by computational structural parameters, IR, UV-Vis and NMR spectra. According to calculated structural parameters and spectral analysis, the environment geometry of central metal atoms was found to be close to ideal octahedral consistent with C-4v symmetry. Non-linear optical (NLO) properties of the complexes are predicted from energy gap (Delta E), static dipole moment (mu), average linear polarizability (alpha), anisotropy of polarizability (Delta alpha) and first hyperpolarizability (beta) values. Since the mu, alpha and beta values of the complexes are lower than that of reference urea, it is estimated that the complexes don't have NLO characteristics. Anti-tumor activities of the complexes are predicted from the highest occupied molecular orbital energy (E-HOMO), the lowest unoccupied molecular orbital energy (E-LUMO), energy gap (Delta E), hardness (eta), electronegativity (chi), chemical potential (mu(cp)), electrophilicity index (omega) and molecular docking studies. Comparison of the molecular descriptors and molecular docking results of the complexes with cis-platin indicates that all the complexes are the best candidate for anti-tumor drug. (C) 2019 Elsevier B.V. All rights reserved.Öğe Computational Structure Characterization of 1,2,3-Selendiazole Isomers, Investigation of Some Molecular Properties and Biological Activities(2022) Erkan, Sultan; Dikyol, Doğan CanFour different selendiazole compounds were handled by computational chemistry methods. Compounds 1,2,3- selendiazole, 1,2,5-selendiazole, 1,2,4-selendiazole and 1,3,4-selendiazole were optimized at the B3LYP/6- 31G(d) level. Structural parameters were examined. In the structural determination, IR and NMR techniques, which are spectroscopic methods, were applied. Quantum chemical parameters giving global properties such as the highest occupied molecular orbital (HOMO) energy, the lowest unoccupied molecular orbital (LUMO) energy, hardness (?), softness (?), chemical potential (?), electronegativity (?), electrophilicity index (?), nucleophilicity index (?), the electron accepting power (?+), electron donating power (?-) and polarizability were investigated for biological activities of selendiazoles. Local electrophilic and nucleophilic regions were determined using Fukui index functionals. Docking studies of the studied selendiazoles were performed with proteins representing the cervical cancer cell line and the MCF-7 breast cancer cell line.Öğe Copper(II) complexes with N,O-donor azo-Schiff base ligands: Synthesis, structure, DFT studies, molecular docking, anticancer and antimicrobial activity(Pergamon-Elsevier Science Ltd, 2025) Kahraman, Sevgi; Hepokur, Ceylan; Erci, Fatih; Erkan, Sultan; Cetin, Seda; Kose, Muhammet; Kurtoglu, MukerremTwo Schiff base ligands containing 4-(fluoro or bromo)phenylazo group 2, 3 and their Cu(II) complexes 4 and 5 were prepared, and their structures were characterized by analytical, spectral and computational methods. The crystal structures of the ligands 2, 3 and their Cu(II) complexes 4 and 5 were determined by single crystal XRD studies. The XRD data revealed that both ligands 2 and 3 are in phenol-imine tautomeric state in the crystalline form. In the structures of Cu(II) complexes 4 and 5, each Cu(II) is four coordinated binding to NO (imine nitrogen and donor set of two azo-Schiff base ligands with approximately square plane geometry. The elemental analysis data reveal that the azo-Schiff base Cu(II) complexes have 1:2 (M: L) stoichiometry. The electronic absorption spectra and quantum chemical calculations suggest a distorted square planer geometry for the complexes. Antibacterial activities of the azo-Schiff bases and their Cu(II) complexes were screened against of Bacillus cereus and Staphylococcus aureus, Escherichia coli and Salmonella typhimurium. The antitumor activity of the has been investigated across different cancer cell lines, including human breast cancer (MCF-7, MDA-MB-231), human colon colorectal adenocarcinoma (HT-29), rat glioma (C6), human Gastric Adenocarcinoma (AGS) and cisplatin was used as the standard drug. The antiproliferative efficacy of compound 5 was assessed through flow cytometry and annexin-V analysis, while the metabolic pathway active in breast cancer cells was scrutinized to understand its mechanism of action. The cytotoxic effects of synthesized ligands and their Cu(II) complexes were evaluated on multiple cancer cell lines, revealing that Cu(II) complex 5 had the highest potency against MDAMB-231 cells with an IC50 value of 4.45 mu g/mL, demonstrating significant selectivity for cancer cells over healthy cells, and indicating its potential as an effective therapeutic agent in cancer treatment, particularly as it induced cell death while minimally affecting healthy cells. Furthermore, in silico studies were conducted to evaluate the antibacterial and anticancer properties of compounds 1-5. The findings revealed that compound 5 exhibited the highest antibacterial activity against S. aureus and B. cereus, as well as significant cytotoxic effects on breast cancer cells. All in all, two Schiff base ligands containing 4-(fluoro or bromo)phenylazo group 2, 3 and their Cu(II) complexes 4, 5 hold promise as prospective candidates for the development of novel anticancer drugs.Öğe Determination of structural, spectral, computational and OLED properties of Ex2.2Box2+ Cyclophane and its derivatives: Experimental and computational study(Elsevier, 2022) Sayin, Koray; Rezaeivala, Majid; Erkan, Sultan; Guney, ElifEx(2.2)Box(2+) Cyclophane was synthesized, and spectral characterization of this compound was completed by using H-1, (CNMR)-C-13, and ESI-MS spectroscopy. Furthermore, this compound and its seven derivatives were investigated by computational analyses. Initially, these compounds were optimized at B3LYP/631G(d) level in the gas phase and water. Then, IR and NMR spectrum were analyzed. Especially, experimental and computational results are compared with each other in Ex(2.2)Box(2+) Cyclophane. Computational spectral results were presented due to the good harmony between experimental and computational results. These compounds' chemical reactivity and electron mobility were investigated using a contour plot of frontier molecular orbital and molecular electrostatic potential map. Finally, the OLED properties of them were examined, and it was found that compounds (5)-(7) may be suitable candidates for OLED applications. (c) 2021 Published by Elsevier B.V.Öğe DFT investigation and molecular docking studies on dinuclear metal carbonyls containing pyridyl ligands with alkyne unit(SPRINGER INTERNATIONAL PUBLISHING AG, 2019) Erkan, Sultan; Karakas, DuranCO-releasing (CORM) complexes ([(CO)(4)LW](2)(mu-DPB) (L=CO, PMe3, P(OMe)(3), PPh3 and P(OPh)(3)) were optimized using various methods and basis sets. The most suitable level according to the correlation between the calculated and experimental structural parameters was found at B3LYP/LANL2DZ/6-31G(d)level for [(CO)(4)LW](2)(mu-DPB) [L=CO, PPh3, P(OPh)(3)]. [(CO)(4)LW](2)(mu-DPB) (L=PMe3, P(OMe)(3)) are hypothetical complexes which have been not synthesized yet. Experimental IR, NMR and UV-Vis spectra for [(CO)(4)LW](2)(mu-DPB) [L=CO, PPh3, P(OPh)(3)] were compared with the calculated values. At the same time, IR, H-1-NMR chemical shift values and UV-Vis spectra were estimated for the hypothetical complexes. Polarizability (alpha) and first hyperpolarizability (beta(0)) values were calculated for nonlinear optical properties (NLO). To investigate the therapeutic effects of complexes such as CO-releasing reagents, the target protein was identified as the empty coordination domain in the data bank and the soluble sGC and hemoglobin coordination code was determined as PDB ID:2O0G and molecular docking was performed between target protein and mentioned complexes. The calculated structural parameters, stretching frequencies, H-1-NMR chemical shift values and UV-Vis spectra for [(CO)(4)LW](2)(mu-DPB) [L=CO, PPh3, P(OPh)(3)] complexes were found to be in agreement with the experimental values. When the [(CO)(4)LW](2)(mu-DPB) (L=PMe3, P(OMe)(3)) complexes are synthesized, it is considered that there will be a good fit between the experimental results and the calculated values. All complexes can be used as optical material according to their polarizability (alpha) and first hyperpolarizability (beta(0)) values. In addition, the binding energy of the [(CO)(5)W](2)(mu-DPB), [(CO)(4)PMe3W](2)(mu-DPB), [(CO)(4)P(OMe)(3)W](2)(mu-DPB), [(CO)(4)PPh3W](2)(mu-DPB) and [(CO)(4)P(OPh)(3)W](2)(mu-DPB) complexes to the target protein was calculated to be -385.18, -423.89, -496.95, -479.73 and -538.31kcal/mol, respectively.Öğe Evaluation of carbonic anhydrase and paraoxonase inhibition activities and molecular docking studies of highly water-soluble sulfonated phthalocyanines(Tubitak Scientific & Technological Research Council Turkey, 2020) Guzel, Emre; Sonmez, Fatih; Erkan, Sultan; Cikrikci, Kubra; Ergun, Adem; Gencer, Nahit; Arslan, OktayThe investigation of carbonic anhydrase and paraoxonase enzyme inhibition properties of water-soluble zinc and gallium phthalocyanine complexes (1 and 2) are reported for the first time. The binding of p-sulfonylphenoxy moieties to the phthalocyanine structure favors excellent solubilities in water, as well as providing an inhibition effect on carbonic anhydrase (CA) I and II isoenzymes and paraoxonase (PON I) enzyme. According to biological activity results, both complexes inhibited hCA I, hCA II, and PON1. Whereas 1 and 2 showed moderate hCA I and hCA II (off-target cytosolic isoforms) inhibitory activity (K-i values of 26.09 mu M and 43.11 mu M for hCA I and 30.95 mu M and 33.19 mu M for hCA II, respectively), they exhibited strong PON1 (associated with high-density lipoprotein [HDL]) inhibitory activity (K-i values of 0.37 mu M and 0.27 mu M, respectively). The inhibition kinetics were analyzed by Lineweaver-Burk double reciprocal plots. It revealed that 1 and 2 were noncompetitive inhibitors against PON1, hCA I, and hCA II. These complexes can be snore advantageous than other synthetic CA and PON inhibitors due to their water solubility. Docking studies were carried out to examine the interactions between hCA I, hCA II, and PON1 inhibitors and metal complexes at a molecular level and to predict binding energies.Öğe Exploring the Antioxidant, Antimicrobial, Antidiabetic, and Anticancer Properties of Capsicum annuum L. (Samandağ Pepper): Biochemical and In Silico Insights(Wiley-V C H Verlag Gmbh, 2024) Tunc, Tutku; Ozpinar, Hulya; Kocyigit, Umit Muhammet; Erkan, SultanCapsicum annuum L. species from the Samanda & gbreve; district of Hatay/Turkey was used in our study. Phytochemical analysis of seed and fruit ethanol extracts of this plant was carried out by GC-MS method. Total Antioxidant Status (TAS) and Total Oxidant Status (TOS) levels were determined to calculate the Oxidative Stress Index to determine antioxidant activity. MIC method was used to evaluate antimicrobial properties against pathogenic bacteria and fungi. Anticancer activity was determined by the XTT assay on breast (MCF-7), lung (A549) and brain (C6) cancer cells and healthy fibroblast (WI-38) cell lines. The effects of the extracts on acetylcholinesterase and alpha-amylase activities were investigated. It was found that C. annuum fruit extract had a lower OSI value than the seed extract. Fruit and seed extracts showed antimicrobial activity on microorganisms at MIC values of 200 mu g/mL. Molecular docking studies were conducted to analyze the antibacterial properties of plant active ingredients. These studies are chemical components that are determined to be more abundant in the plant extract. Thus, it aimed to evaluate the effects of active compounds on various bacterial species. The results revealed the potential antibacterial properties of plants and provided important data that these ingredients can be used in future treatment methods. The anticancer activity in all cancer cell lines was very high in both seed and fruit extracts with a selectivity index (SI) well above SI >= 3. Furthermore, no deleterious effect on healthy fibroblast (WI-38) cells was observed. The extracts were found to decrease acetylcholinesterase activity but increase alpha-amylase activity. As a result, these plant extracts were found to have anticholinergic potential.Öğe Investigation of Anticancer Properties of 2-benzylidene-1-indanone and Its Derivatives by DFT and Molecular Docking(DergiPark, 2024) Yildiz, Ceylan Alkaya; Erkan, SultanIn this study, 2-benzylidene-1-indanone and its derivatives, which is a chalcone compound and contains indanone in its structure, were examined. Quantum chemical parameters for these compounds were calculated with the B3LYP method and the 6-31G(d) basis set and evaluated for their biological activity. The effect of different functional groups (F, Cl, Br, CF3, CH3 and OCH3) attached to the 2-benzylidene-1-indanone compound on biological activity was investigated. Some quantum chemical parameters such as highest energy filled molecule orbital energy (EHOMO), lowest non-bonding empty molecule orbital energy (ELUMO), energy gap (?E), hardness (?), softness (?), global molecular electrophilicity (?) index, global molecular nucleophilicity (?) index, electron-accepting (?+) and electron-donating (?-) electrophilicity index were calculated for the biological activities of the compounds. Frontier molecular orbitals and molecular electrostatic potential (MEP) maps were interpreted. The biological activities of 2-benzylidine-1-indanone and some of its derivatives bearing the 1-indanone skeleton were evaluated by performing molecular docking studies with the target protein PDB ID = 1HJD corresponding to the melanoma cell line. The activity ranking obtained with quantum chemical parameters was found to be compatible with the binding energies obtained from docking results. © (2024), (DergiPark). All rights reserved.Öğe Investigation of Antiviral Activities of Nickel and Copper Complexes with Macrocyclic Ligands against Crimean-Congo Hemorrhagic Fever by In Silico Calculations(2023) Erkan, Sultan; Bulut, Niyazi; Karakaş, DuranFor the first time, electronic characteristics of potential drug candidates and their inhibitory activities have been linked thanks to this work. Synthesized copper and nickel complexes with trans-N1,N8-bis(2-cyanoethyl)-2,4,4,9,11,11-hexamethyl-1,5,8,12-tetraazacyclotetradecane (tet-bx) ligand, as well as the proposed hypothetical complexes, were properly examined by the appropriate calculation method in atomic and molecular dimensions. The appropriate calculation level was achieved by using the IR spectroscopic data of the tet-bx ligand. The experimental and calculated bond stretching frequencies were compared for synthesized complexes [Ni(tet-bx)](ClO4)2 (1), [Cu(tet-bx)](ClO4)2 (2), [Ni(tet-bx)(NCS)2] (3), and [Ni(tet-bx)(ClO4)Cl] (5). Some bond stretching frequencies of hypothetical complexes [Cu(tet-bx)(NCS)2] (4) and [Cu(tet-bx)(ClO4)Cl] (6) have also been proposed and their molecular structure were determined. To analyze the electronic behavior of the examined complexes at the atomic level, Fukui function indices (nucleophilic f+ and electrophilic f- populations) were determined. Furthermore, antibacterial and antiviral inhibition efficiency of the complexes against Crimean-Congo hemorrhagic fever has been investigated by docking studiesÖğe Investigation of the Effect of Main Components of Wild Thyme on Covid-19 by Computational Methods(2023) Kaya, Serpil; Erkan, Sultan; Karakaş, DuranAromatic plant species of the genus thymus have an important role as they have therapeutic properties such as antirheumatic, antiseptic, antispasmodic, antimicrobial, cardiac, carminative, diuretic and expectorant. It is also known that such plants strengthen the immune system and help cope with infectious diseases such as colds and flu. In this study, the effects of thymol, p-cymene, ?-terpinene, bornyl acetate, borneol, carvacrol, thymol methyl ether, thymol acetate, which are the main components of wild thyme (thymus serpyllum L.), on Covid-19 were investigated at the molecular level. Optimizations and molecular docking were done in Docking Server with the MMFF94 method. Major components of wild thyme were docked separately against 6LU7 protein representing the first gene form of Covid-19 and 7KDL protein representing the mutated form. Docking poses and binding energies between target proteins and wild thyme components were calculated. The results were compared with favipiravir, an antiviral drug developed against influenza virus and also used in the treatment of Covid-19. It was found that the thymol molecule, one of the main components of wild thyme, has the highest biological activity against both 6LU7 and 7KDL protein chains of Covid-19.Öğe Investigations of structural, spectral (IR and NMR) and in silico analyses of boron compounds as SERM inhibitor(Elsevier, 2022) Kaya, Serpil; Sayin, Koray; Erkan, Sultan; Karakas, DuranComputational analyses of selected boron compounds are performed at M06-2X/6-31+G(d,p) level in vacuum and water. Simulated X-Ray structure and structural parameters are reported. In spectral analyses, IR spectrum are examined with VEDA program and vibration modes of selected peaks in IR spectrum are revealed. As for the NMR spectrum, chemical shift value of carbon, hydrogen, nitrogen and boron atoms are calculated for studied compounds. In addition to characterization studies, electronic properties of studied boron compounds are investigated by the calculation of contour plots and MEP maps of mentioned compounds. Finally, anticancer properties of studied compounds are investigated by molecular docking calculations. 6VPK, estrogen receptor, is selected as target protein in this study. Selective estrogen receptor modulator (SERM) properties of studied compounds are investigated due to the fact that inhibiting of the estrogen receptor is one of the cancer preventions. As a result, compound (2) and (4) are the best drug candidates due to the fact that their results are similar to each other. Amino acids between 525 and 539 in target protein are determined as effective in targeted drug development. Finally, leucine is identified as the most interacting amino acid.Öğe Light-Emitting Properties of Pyrimidine-5-Carbonitrile Derivatives: a Theoretical Calculation(2022) Karakoyun, Necdet; Erkan, SultanIn this study, 4,6-Di (9H-carbazol-9-yl) pyrimidine-5-carbonitrile (C1), 4,6-bis (3,6-di-tert-butyl-9H-carbazol-9-yl) pyrimidine-5-carbonitrile (C2), 4,6-bis (3,6-dimethoxy-9H-carbazol-9-yl) pyrimidine-5-carbonitrile (C3) compounds were optimized at the B3LYP/6-31G(d) level. Energy densities of frontier molecular orbitals were investigated with molecular properties. Vertical ionization potentials (IPv), adiabatic ionization potential (IPa) (in eV), vertical electron affinity (EAv), adiabatic electron affinity (EAa), the hole reorganization energy (?h )and electron reorganization energy (?e ) were calculated (in eV)for C1, C2 and C3 compounds. ?e values of the C1 and C3 compounds are 0.29 and 0.30 eV and the ?h value is 0.18 and 0.20 eV, respectively.It can be said that the C1 and C3 compounds are not suitable as an electron bearing layers (ETL) material since its ?e values are greater than 0.276 eV and that its ?h value is less than 0.290 eV, so they are a suitable material for the hole bearing layers (HTL). The C2 compound is suitable for both ETL and HTL materials.Öğe Light-Emitting Properties of Pyrimidine-5-Carbonitrile Derivatives: a Theoretical Calculation(Niyazi ÖZDEMİR, 2022) Karakoyun, Necdet; Erkan, SultanIn this study, 4,6-Di (9H-carbazol-9-yl) pyrimidine-5-carbonitrile (C1), 4,6-bis (3,6-di-tert-butyl-9H-carbazol-9-yl) pyrimidine-5-carbonitrile (C2), 4,6-bis (3,6-dimethoxy-9H-carbazol-9-yl) pyrimidine-5-carbonitrile (C3) compounds were optimized at the B3LYP/6-31G(d) level. Energy densities of frontier molecular orbitals were investigated with molecular properties. Vertical ionization potentials (IPv), adiabatic ionization potential (IPa) (in eV), vertical electron affinity (EAv), adiabatic electron affinity (EAa), the hole reorganization energy (h )and electron reorganization energy (e ) were calculated (in eV) for C1, C2 and C3 compounds. e values of the C1 and C3 compounds are 0.29 and 0.30 eV and the h value is 0.18 and 0.20 eV, respectively. It can be said that the C1 and C3 compounds are not suitable as an electron bearing layers (ETL) material since its e values are greater than 0.276 eV and that its h value is less than 0.290 eV, so they are a suitable material for the hole bearing layers (HTL). The C2 compound is suitable for both ETL and HTL materials.Öğe Manganese(III) Acetate-Based Radical Cyclization Reactions for Pyranocoumarin and Pyranoquinoline Compounds: Synthesis, DFT and Molecular Docking Studies(Wiley-V C H Verlag Gmbh, 2022) Yakut, Mehtap; Yilmaz, Mehmet; Pekel, Tarik; Erkan, Sultan; Katirci, Ramazan; Bicer, EmrePyranofuroquinoline and pyranofurocoumarin derivatives are significant class of compounds due to being useful in many diverse applications. The synthesis of the compounds are succeeded in one step by radical cyclization reaction in the presence of manganese(III) acetate. Furoquinoline and furocoumarin reactants were used together with 1,1-disubstituted-, 1,2-disubstituted and cyclic alkenes giving pyranofuroquinoline and pyranofurocoumarin compounds in moderate to high yields. Also, we were able to isolate alkenyl and acetoxy- side-products in minor low yields. The electronic and optical features of furoquinoline and furocoumarin reactants and pyranofuroquinoline products were inquired using theoretical approaches (DFT and TD-DFT). Their excitation and emission spectrums were computed. The results revealed that the pyranofuroquinoline molecules did not show the energy transfer feature. It was observed that the behavior of nonlinear optic of furoquinoline is higher than the pyranofuroquinoline and furocoumarin molecules. But the average polarization and the anisotropy of the polarizability of pyranofuroquinoline increased and was found to be 262.7 and 141.9 respectively. Also, according to the calculated docking parameters, the investigated pyranofuroquinoline and pyranofurocoumarin compounds were found to have higher activity than the substances with anticancer and antibacterial standards.
