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Öğe A Synthesis of Novel Tetracyclic Azocino[4,3-b]Indole Framework: Combined Spectroscopic, DFT, Molecular Docking, and ADMET Analysis(Wiley-V C H Verlag Gmbh, 2026) Uludag, Nesimi; Serin, Sumeyya; Ustun, Elvan; Serdaroglu, GoncagulThe paper describes a new synthetic method for the 1,5-methanoazocino [4,3-b]indole. Starting from 2,3,4,9-tetrahydrospiro[1H-carbazole-1,2'-[1,3]dithiolan]-4(9H)-one I with (1,3-dithiolan-2-yl)methanamine, reduction of imine II with NaBH4 yielded to the amine and benzoylation, N-((1,3-dithiolan-2-yl)methyl)-N-(2,3,4,9-tetrahydrospiro[carbazole-1,2'-[1,3]dithiolan]-4-yl)benzamide III. Compounds IV and V were completed through several steps from III. The resulting structure V underwent an intramolecular aldol reaction using NaH as a base for the cyclization of 2-benzoyle-4-hydroxy-1,2,3,4,5,7-hexehydro-1,5-methanoazocino[4,3-b]indole-6-one VI, which represents the tetracyclic skeleton of Strychnos alkaloids. Besides, quantum chemical computations were conducted on compounds I-VI. Regarding structural parameters and spectroscopic characterization, the experimental and computational data were found to be in good agreement. Also, ADMET, bioavailability, and drug-likeness properties of the data set were determined to provide comprehensive information on structure-activity relationships. The interactions of I-VI against DNA gyrase of E. coli, CYP51 from Candida glabrata, and leukemia inhibitory factor were evaluated with molecular docking for foresight into the possible bioactivities. This comprehensive work hopefully to provide the structural, physical, and chemical properties, which would be important to optimizing the related properties of the molecular systems for biomedical purposes.Öğe Computational insights into E/Z isomerism of fluoxastrobin, an antifungal agent: A DFT/TD-DFT study(Elsevier, 2023) Serin, SumeyyaHerein, inspired by the success of strobilurins in fungicidal activity bioassays, DFT (Density Functional Theory) -based quantum chemical computations were performed on fluoxastrobin, a fluorinated strobilurin fungicide. Its formulation has E/Z isomerism around the C=N bond. It is highly advantageous to utilize quantum chemical methods to acquire more insights into E/Z isomerism and to gain supplemental confirmations in terms of experimental results. In this respect, the geometries of the E and Z isomers of fluoxastrobin were optimized both in the vacuum and in 1-octanol, acetonitrile, DMSO, and water phases using the DFT/B3LYP/6-311++G (d, p) methodology. Both experimental and theoretical FTIR and UV-vis evaluations were performed for the isomers. TD-DFT/B3LYP/6-311++G (d, p) theory level computations were determined that the observed peaks were mostly caused from the pi ->pi* and n ->pi* transitions. Also, quantum chemical reactivity descriptors and physi-cochemical parameters were calculated for both vacuum and solvent phases. Accordingly, computations in all studied phases estimate the E isomer to be preferred with energy values in the range of 2.51-3.77 kcal/mol. Natural bond orbital (NBO) analysis was also carried out to determine the intermolecular interactions and their corresponding stabilization energies. Last, with the help of Gibbs solvation free energy values, 1-octanol/water partition coefficients were calculated and lipophilicity evaluations of both isomers were performed.Öğe DFT-based computations on some structurally related N-substituted piperazines(Elsevier, 2022) Serin, SumeyyaIn order to focus on more promising drug candidates by reducing the failures that occur in the time-consuming and expensive discovery process of new drugs, it is highly efficient to predict the bioactivity and metabolism behaviors of drug candidates using computational chemistry methods. In this context, this study presents a comparative quantum chemical analysis of the buspirone, used in the treatment of anxiety, and its three structurally related derivatives, kaspar, mesmar, and gepirone, based on Density Functional Theory (DFT) cal-culations. Geometry optimization and frequency calculations of each molecule were implemented at B3LYP/ 6-31G (d, p) and B3LYP/6-311++G (d, p) levels of theory. Linear correlation coefficients (R2) were calculated for each piperazine derivative to detect the power of the relationship between theoretical and experimental structural parameters. Subsequently, frontier molecular orbital (FMO) analysis, quantum chemical reactivity descriptors, electrostatic surface properties (ESP), and natural bond orbital (NBO) analysis were examined in detail. The lipophilicity evaluations of mentioned piperazine derivatives were interpreted not only according to the data obtained from the DFT calculations, but also according to the results obtained from the Molinspiration software. As a result of both methods, the order of lipophilicity emerged as kaspar > mesmar > buspirone > gepirone. It is revealed that on account of the substitution of the pyrimidine ring in buspirone and gepirone with the quinoline ring, both lipophilicity increased and the direction of the lipophilic interaction predominantly changed. Based on all the obtained results, it is concluded that although the studied molecules are structurally very similar, they support different lipophilic interactions. Therefore, their pharmacological activities differ.Öğe (E)-3-(4-Hydroxyphenyl)-1-(4-methoxyphenyl)prop-2-en-1-one: DFT/TD-DFTbased investigations with distinct solvents and in silico ADME profiling(Natl Inst Science Communication & Policy Research-Niscpr, 2024) Serin, SumeyyaThe chalcone scaffold has become one of the privileged structures frequently encountered in medicinal chemistry for the discovery of new and effective drug candidates. In recent years, chalcone derivatives have attracted intense attention from both experimental and theoretical researchers due to their ease of synthesis and wide range of biological activities. Herein, quantum chemical-based calculations have been performed on chalcone derivative (E)-3-(4-hydroxyphenyl)-1-(4methoxyphenyl)prop-2-en-1-one. Density functional theory (DFT) method has been applied with the B3LYP hybrid functional and 6-311++G (d, p) basis set. The structural, electronic, energetic and reactivity properties of the mentioned chalcone derivative have been examined. Bond parameters and vibrational analysis results are compatible with experimental data. The energy gap (triangle E) values corresponding to acetonitrile, DMSO and water phases have been calculated as 3.753, 3.750 and 3.747 eV, respectively. Also, the reactive regions of the molecule have been visualized with molecular electrostatic potential (MEP) maps. The excited state characteristics of the title compound in water, acetonitrile and DMSO environments have been calculated by the TD-DFT method. All absorption wavelengths could be qualified as pi ->pi* and n ->pi* transition type. A bioavailability radar has been created by calculating some physicochemical parameters such as lipophilicity, TPSA, and water solubility. ADME properties have been predicted from pharmacokinetics and drug likeness data.Öğe Integrated experimental-computational elucidation of a new Ag(I)-NHC complex: Synthesis, spectroscopic profiling, DFT/TD-DFT calculations, and QTAIM topological analysis(Elsevier, 2026) Balazghem, Nour-Elhouda; Ulu, Oznur Dogan; Serin, Sumeyya; Sekkoum, Khaled; Yildirim, Ilkay; Ozdemir, Namik; Ozdemir, IsmailIn this study, the electronic structures, bonding properties, and reactivity profiles of the benzimidazolium salt (1) and its Ag(I) complex (2) were investigated using DFT-based analyses. The structures of the compounds were elucidated by using spectroscopic methods including FT-IR, NMR, and LC-MS. Furthermore, the structure of the Ag(I)-NHC complex was determined by single-crystal X-ray diffraction. The results reveal that, compared to complex 2, 1 possesses a smaller energy gap, enhanced electronic delocalization, and more accessible donoracceptor regions, indicating higher chemical softness and reactivity. In contrast, Ag(I) coordination induces a more stabilized and localized electronic distribution, reduces polarity, and increases structural rigidity. NBO second-order perturbation analysis further demonstrates that while precursor 1 exhibits strong pi ->pi* and lonepair-driven delocalization pathways, complex 2 displays additional ligand-metal donor-acceptor interactions with moderate stabilization energies, confirming the electron-accepting role of the metal center.Öğe NHC based Pd-PEPPSI complexes: synthesis, computational studies and application for Suzuki and direct arylation reactions(Springer/Plenum Publishers, 2026) Belazghem, Nour-Elhouda; Ulu, Oznur Dogan; Serin, Sumeyya; Yildirim, Ilkay; Sekkoum, Khaled; Ozdemir, Namik; Ozdemir, IsmailA series of novel air- and moisture-resistant NHC-based pyridine containing palladium PEPPSI-type Pd(II) complexes (2a-e) were synthesized and characterized. The structures of all synthesized complexes were determined by various spectroscopic techniques. In addition, the structure of 2b was elucidated by single X-ray crystallography. The structural and electronic properties of 2a-e were further investigated using DFT calculations, which provided valuable insights into thermodynamic parameters, frontier molecular orbitals, and natural bond orbital interactions. The experimental and theoretical data showed strong agreement, confirming the robustness of the applied methodology. The complexes were successfully employed in the Suzuki cross-coupling of phenylboronic acid with aryl chlorides using green solvents. Also, the complexes were tested for direct arylation reactions and obtained mild to good yields.Öğe NHC-based Pd-PEPPSI complexes: Synthesis, characterization, DFT studies and catalytic activity in Suzuki-Miyaura cross coupling(Elsevier, 2025) Ulu, Oznur Dogan; Serin, Sumeyya; Ozdemir, IsmailThree new Pd-PEPPSI complexes (2a-c) with the general formula [PdBr2(NHC)(Py)] were prepared via unsymmetrical benzimidazolium salts containing a 1-3-dioxane group on one of the nitrogen atoms and cyanopropyl, cyclobutyl or 2-methylbenzyl on the other side. All the compounds were isolated in excellent yields (68-85 %) and fully characterized using 1H and 13C NMR, FT-IR, and elemental analysis. Additionally, the DFT (Density functional Theory) calculations carried out on complexes 2a-c offers valuable insights on topics like physicochemical characteristics and reactivity tendencies, as well as further validations to the experimentally obtained data of examined Pd complexes. With regard to structural parameters, experimental and computational findings were revealed to be in alignment. A comparative analysis was conducted of the electronic properties, possible donor-acceptor interactions, and electrostatic surface properties of 2a-c. A close examination of the computational findings reveals that cyanopropyl substitution leads to a relative increase in structural stability. Also, Pd-PEPPSI-type complexes with NHC ligands were applied as catalyst precursors in Suzuki cross-coupling reactions forming a wide range of biaryls with high yields. Therefore, the catalytic activities of the synthesized complexes in the Suzuki reaction were tested. The reactions were carried out at very low catalyst loading (0.25 mol%) in the presence of air using a green water-based solvent (i-PrOH:H2O/1:3). The results demonstrated that the catalysts exhibited high activity in this reaction.Öğe Novel fluorinated benzimidazole-based N-heterocyclic carbene precursor and its silver (I) and selenium adducts: synthesis, spectral characterization, DFT/TD-DFT, QTAIM, and in silico ADME investigations(Taylor & Francis Ltd, 2025) Serin, SumeyyaN-heterocyclic carbenes (NHCs) are a highly versatile type of ligand, offering a unique ability to modify their electronic and steric characteristics with relative ease. In light of the encouraging outcomes observed with fluorinated NHCs in pharmacological applications, this study aims to explore the potential of a novel fluorinated benzimidazole-based NHC precursor (1) and its associated silver(I) (2) and selenium adducts (3). The syntheses of compounds were conducted in inert atmosphere using the Schlenk technique. The characterization of synthesized compounds was carried out using a combination of spectroscopic methods, including 1H,13C,19F NMR, FT-IR, and UV-vis spectroscopy. Furthermore, DFT calculations were conducted on compounds 1-3 with the aim of gaining insight into reactivity trends, donor-acceptor interactions, and physicochemical properties. This approach also served to provide additional validation of the experimental data obtained for these compounds. In terms of structural parameters and spectroscopic characterization, the experimental and computational data were found to be compatible. To determine the main binding areas and weak interactions of 1-3, QTAIM analyses were utilized. Given the importance of benzimidazole derivatives as a heterocyclic motif with activity across a range of pharmaceutical applications, an investigation was also conducted into the ADME characteristics of the synthesized compounds.Öğe Synthesis and characterization of novel Rh-NHC complexes: addition of phenylboronic acid to aldehydes, DFT/TD-DFT, and QTAIM studies(Elsevier Science Sa, 2026) Ulu, Oznur Dogan; Serin, Sumeyya; Ozdemir, IsmailHerein, three new Rh(I)-NHC complexes (2a-c) were synthesized by reacting benzimidazolium salts with the [Rh (OMe)(COD)]2 compound. The structures of the synthesized compounds were elucidated by various spectroscopic methods such as 1H, 13C NMR, FT-IR, and UV-vis spectroscopies, and the elemental analysis technique. A thorough theoretical investigation was conducted to explore the electronic structure, reactivity, donor-acceptor interactions, and thermodynamic properties of newly synthesized Rh-NHC complexes. To this end, Density Functional Theory (DFT) calculations were utilized. The findings reveal that the 3,4,5-trimethoxybenzyl substitution contributes to the formation of a more stable and rigid structure in the Rh complex. Additionally, TDDFT calculations were performed to assess the potential electronic transitions of the complexes 2a-c within a chloroform environment. It is possible to interpret the observed peaks of the three complexes as predominantly associated with intra-ligand pi -> pi* transitions and metal-ligand charge-transfer (MLCT) transitions. The quantum theory of atoms in molecules (QTAIM) was employed to facilitate comprehension of bond characteristics and intermolecular interaction strengths in 2a-c complexes. Furthermore, the complexes were evaluated in the reaction of phenylboronic acid to aldehydes, and satisfactory yields were obtained for the desired products.Öğe Synthesis, characterization, computational studies and biological activities of novel NHC precursor and its silver (I) and selenium compounds(Elsevier, 2025) Serin, Sumeyya; Karakas, Gulsen; Mumcu, Akin; Ulu, Oznur Dogan; Dik, Gamze; Utku, Tugba; Ates, BurhanThe potential applications of fluorine in drug design are expanding rapidly. The evolution of synthetic methodologies has engendered the conception of novel fluorinated motifs. In the present study, the effective use of N-heterocyclic carbenes (NHCs) in pharmaceutical chemistry was combined with the enhancing role of fluorine groups in bioactivity, and the synthesis of a new NHC precursor (1) containing 2,6-difluorobenzyl group was achieved. Respective Ag-NHC (2) and Se-NHC (3) compounds were prepared from the synthesized NHC precursor. Structural characterization of each compound (1-3) was conducted by H-1, C-13 and F-19 NMR, FT-IR, UV-visible spectroscopy, and elemental analysis methods. The antioxidant activity of these compounds was evaluated by using ABTS and DPPH radical scavenging assays as well as their ability to inhibit the acetylcholine esterase (AChE) enzyme. Besides, density functional theory (DFT) computations were performed in order to comparatively peruse the molecular structures, electronic properties, reactivity tendencies, donor-acceptor interactions, and electrostatic surface properties of compounds 1-3 for both vacuum and CHCl3 phase. The reactivity ranking for the gas phase was clearly determined to be 3 < 2 < 1, based on the calculated energy gap values. The excited state characteristics of 1-3 in CHCl3 were calculated by the TD-DFT method. The antioxidant activity showed that the compounds, particularly compound 3 displayed effective antioxidant activities. According to the enzyme inhibition outcomes, compound 2 (IC50 value 8.43 +/- 0.71 mu M) had the most effective AChE inhibition among the synthesized compounds. Taken together, this investigation revealed the synthesis, characterization of various novel compounds (1-3) with, antioxidant potentials, AChE inhibitory activities, and quantum chemical calculations.Öğe Synthesis, characterization, DFT quantum chemical calculations and catalytic properties of azobenzene-bearing Schiff base palladium(II) complexes for the Suzuki-Miyaura Cross-Coupling reaction in aqueous solvent(Elsevier, 2025) Duyar, Ayse Inan; Sunbul, Ali Burak; Serin, Sumeyya; Ulu, Oznur Dogan; Ozdemir, Ismail; Ikiz, Mesut; Kose, MuhammetA series of azobenzene-bearing Schiff base ligands, 4-((E)-(4-ethylphenyl)diazenyl)-2-((E)-(p-tolylimino)methyl) phenol (2), 4-((E)-(4-ethylphenyl)diazenyl)-2-((E)-((4-methoxyphenyl)imino)methyl)phenol (3), 2-((E)-((3,4dimethoxyphenyl)imino)methyl)-4-((E)-(4-ethylphenyl)diazenyl)phenol (4), 2-((E)-((4-chlorophenyl)imino) methyl)-4-((E)-(4-ethylphenyl)diazenyl)phenol (5), 2-((E)-((4-bromophenyl)imino)methyl)-4-((E)-(4-ethylphenyl)diazenyl)phenol (6), 2-((E)-(tert-butylimino)methyl)-4-((E)-(4-ethylphenyl)diazenyl)phenol (7), 2-((E)(cyclohexylimino)methyl)-4-((E)-(4-ethylphenyl)diazenyl)phenol (8) and their homoleptic Pd(II) complexes have been synthesized. Ligand structures were characterized by the combination of 13CNMR , 1HNMR , FTIR, UV-Visible spectroscopy and elemental analyses. According to the UV-visible, FTIR, elemental analyses and HRMS data, the Pd(II) complexes 9-15 are formed by the coordination of N, O atoms of the ligands. Examining the coordination of the free ligands with the central metal ion, the new weak bands observed in the 633-581 and 543-481 cm-1 ranges in the spectra of the Pd(II) metal complexes can be attributed to M-O and M-N stretching peaks, respectively. DFT calculations were performed to determine the optimized structures of Pd(II) complexes utilizing the GAUSSIAN 16 software package with appropriate basis sets. The HOMO and LUMO energies of complexes 9-15 were calculated at the studied theory level in the gas phase. The Delta E values were found to be 3.136-3.239 eV range suggests the high chemical reactivity for those of Pd(II) complexes. In addition, Pd(II) complexes were used as catalysts for Suzuki-Miyaura coupling reactions of phenylboronic acid with aryl bromide in aqueous media. All complexes exhibited notably high catalytic properties in the Suzuki-Miyaura coupling reactions. It was found that the substit & uuml;e groups in the aryl bromide has an impact on the catalytic reaction. In the presence of an electron-withdrawing group such as 4-bromobenzaldehyde, the highest yields were obtained with catalysts 12 and 15, while the lowest yield was observed when catalyst 11 was used with 86 % efficiency.Öğe Synthesis, crystal structure, and DFT studies of NHC mediated Pd-PEPPSI complex: Application for Suzuki reaction(Elsevier, 2025) Ulu, Oznur Dogan; Serin, Sumeyya; Ozdemir, Namik; Ozdemir, IsmailA novel air and moisture resistant Pd-PEPPSI (pyridine-enhanced precatalyst preparation, stabilization, and initiation) complex was synthesized via the reaction of benzimidazolium salt, PdCl2, KBr, K2CO3, and pyridine. The structure was characterized by spectroscopic methods such as 1H and 13C NMR, FT-IR, UV-vis. and single Xray diffraction techniques. In order to evaluate the synthesized Pd complex in a detailed manner in terms of structural, bonding, electronic, and thermodynamic characteristics, DFT-based calculations were carried out at the B3LYP/6-311++G (d, p)/LANL2TZ theory level. Natural bond orbital (NBO) analysis was implemented to provide more insights about the possible donor-acceptor interactions and types of hybridization. Also, TD-DFT calculations were performed to rationalize the nature of the observed electronic transitions. The complex showed high catalytic activity in the Suzuki-Miyaura cross coupling of aryl chlorides with phenylboronic acid. Aryl chlorides bearing either electron- donating or withdrawing substituents afforded a wide range of biaryl derivatives that were isolated in the range of 55-97 % yields (7 examples). The reactions were carried out at very low catalyst loading (0.25 mol%) in the presence of air using a green water-based solvent (ipr:H2O/ 1:3). The palladium complex was found to be efficient for the coupling of aryl chlorides with arylboronic acids under aerobic conditions, affording the corresponding biaryls in high yields.
