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Publication Open Access Thiabendazole and Thiabendazole-Formic Acid Solvate: A Computational, Crystallographic, Spectroscopic and Thermal Study(2020-07) Tabanez, A.M.; Nogueira, B.A.; Milani, A.; S. Eusébio, M.E.; Paixão, J.A.; Kabuk, H.N.; Jajuga, M.; Fausto, Rui; ILDIZ, GÜLCE ÖĞRÜÇThiabendazole (TBZ) is a substance which has been receiving multiple important applications in several domains, from medicine and pharmaceutical sciences, to agriculture and food industry. Here, a comprehensive multi-technique investigation on the molecular and crystal properties of TBZ is reported. In addition, a new solvate of the compound is described and characterized structurally, vibrationally and thermochemically for the first time. Density functional theory (DFT) calculations were used to investigate the conformational space of thiabendazole (TBZ), revealing the existence of two conformers, the most stable planar trans form and a double-degenerated-by-symmetry gauche form, which is ~30 kJ mol−1 higher in energy than the trans conformer. The intramolecular interactions playing the major roles in determining the structure of the TBZ molecule and its conformational preferences were characterized. The UV-visible and infrared spectra of the isolated molecule (most stable trans conformer) were also calculated, and their assignment undertaken. The information obtained for the isolated molecule provided a strong basis for the understanding of the intermolecular interactions and properties of the crystalline compound. In particular, the infrared spectrum for the isolated molecule was compared with that of crystalline TBZ and the differences between the two spectra were interpreted in terms of the major intermolecular interactions existing in the solid state. The analysis of the infrared spectral data was complemented with vibrational results of up-to-date fully-periodic DFT calculations and Raman spectroscopic studies. The thermal behavior of TBZ was also investigated using differential scanning calorimetry (DSC) and thermogravimetry. Furthermore, a new TBZ–formic acid solvate [2-(1,3-thiazol-4-yl)benzimidazolium formate formic acid solvate] was synthesized and its crystal structure determined by X-ray diffraction. The Hirshfeld method was used to explore the intermolecular interactions in the crystal of the new TBZ solvate, comparing them with those present in the neat TBZ crystal. Raman spectroscopy and DSC studies were also carried out on the solvate to further characterize this species and investigate its temperature-induced desolvation.Publication Restricted The Effects of Conformation and Intermolecular Hydrogen Bonding on the Structure and IR Spectra of Flutamide; A Study Based on the Matrix Isolation Technique, Ab Initio and DFT Calculations(Pergamon-Elsevier Science Ltd., 2023) Arman, C.; Balcı, K.; Akkaya, Y.; AKYÜZ, SEVİM; Reaves-Mckee, T.; Frankamp, AH; Coates, JT; Collier, WB; Ritzhaupt, G.; Klehm, CE; Desman, P.In this study, stable conformers of flutamide referred to as an anticancer drug were searched through a relaxed potential energy surface scan carried out at the B3LYP/6-31G(d) level of theory. This was followed by geometry optimization and thermochemistry calculations performed with the HF-SCF, MP2, B3LYP methods and the 6-31G (d), 6-311++G(d,p), aug-cc-pvTZ basis sets for each of the determined minimum energy conformers. The results revealed that flutamide has at least five stable conformers and two of them provide the major contribution to the observed matrix isolation infrared (IR) spectra of the molecule. The effects of conformational variety and intermolecular hydrogen bonding interactions on the observed IR spectra of flutamide were interpreted in the light of the vibrational spectral data obtained for the most stable monomer and dimer forms of the molecule at the same levels of theory. Pulay's "Scaled Quantum Mechanical-Force Field (SQM-FF)" method was used in the refinement of the calculated harmonic wavenumbers, IR intensities and potential energy distributions. This scaling method which proved its superiority to both anharmonic frequency calculations and other scaling methods helped us to correctly interpret the remarkable differences between the matrix IR spectra of flutamide in argon and the condensed phase IR spectra of the molecule in solvents such as KBr, H2O, D2O, ethanol and methanol.Publication Embargo Counterpoise correction on the geometries and vibrational frequencies of acetazolamide dimers(Asian Journal Of Chemistry, 11/100 Rajendra Nagar, Sector 3,, Sahibabad 201 005, Ghaziabad, India, 2013-10) Özel, Ayşen; Kecel Gündüz, Serda; Çelik, Sefa; AKYÜZ, SEVİM; 110745; 110526; 110147; 10127Acetazolamide (m.f. C4H6N4O3S2) (N-(5-sulfamoyl-1,3,4-thiadiazol-2-yl) acetamide), is a sulfonamide derivative and carbonic anhydrase inhibitor. It is often used in the treatment of various diseases. In this study, the effect of the counterpoise correction of the basis set superposition errors (BSSE) on the geometries, interaction energies and vibrational wavenumbers of four more stable acetazolamide dimers have been analyzed at the DFT/B3LYP level of theory, using 6-31++ G(d,p) basis set. The difference in the basis set superposition error corrected (-72.39 kj/mol) and uncorrected (-77.72 kj/mol) interaction energy of the most stable acetazolamide dimer (dimer I) indicates the magnitude of error caused due to the basis set superposition. The counterpoise correction increases the H-bond distance and decreases the wavenumbers of the intermolecular modes compared to the results of calculations without the basis set superposition error-correction.Publication Open Access Structure, Vibrational Spectra, and Cryogenic MatrixPhotochemistry of 6-Bromopyridine-2-Carbaldehyde: From the Single Molecule of the Compound to the Neat Crystalline Material(MDPI, 2023) Brito, Anna Luiza B.; Lopes, Susy; ILDIZ, GÜLCE ÖĞRÜÇ; Fausto, Rui6-Bromopyridine-2-carbaldehyde (abbreviated as BPCA) is used both as a building block in supramolecular chemistry and as a ligand for transition metal catalysts and luminescent complexes. In this study, the structure and vibrational spectra of BPCA were investigated in both the room temperature neat crystalline phase and for the compound isolated in cryogenic Ar, Kr and Xe matrices. The experimental studies were complemented by quantum chemical DFT(B3LYP)/6-311++G(d,p) calculations. For the crystalline compound, infrared and Raman spectra were obtained and interpreted. Comparison of the obtained infrared spectrum of the crystal with those obtained for the isolated molecules of BPCA in the studied cryomatrices helped to conclude that the intermolecular interactions in the crystal do not significantly perturb the intramolecular vibrational potential. Structural analysis further supports the existence of weak coupling between the intermolecular interactions and the structure of the constituting molecular units in crystalline state. The intermolecular interactions in the BPCA crystal were also evaluated by means of Hirshfeld analysis, which revealed that the most important interactions are weak and of the (HN)-N- horizontal ellipsis , (HO)-O- horizontal ellipsis , (HH)-H- horizontal ellipsis , (HBr)-Br- horizontal ellipsis and (BrBr)-Br- horizontal ellipsis types. The conformer of BPCA present in the crystal was found to correspond to the most stable form of the isolated molecule (trans), which bears stabilizing C-(HO)-O- horizontal ellipsis =C and C(=O)(HN)-N- horizontal ellipsis interactions. This conformer was shown to be the single conformer present in the as-deposited cryogenic matrices prepared from the room temperature gaseous compound. Broadband UV irradiation of matrix-isolated BPCA (lambda >= 235 nm) resulted in the conversion of the trans conformer into the higher-energy cis conformer, where repulsive C-(HH)-H- horizontal ellipsis -C(=O) and C=(OLPLPN)-N- horizontal ellipsis (where LP designates a lone electron pair) interactions are present, and decarbonylation of the compound with formation of 2-bromopyridine (plus CO). The decarbonylation reaction was found to be more efficient in the more polarizable Xe matrix, indicating stabilization of the radicals initially formed upon breaking of the C-C(HO) and C-H (aldehyde) bonds in this medium, and testifying the occurrence of the decarbonylation reaction with involvement of radical species. TD-DFT calculations were used to access the nature of the excited states associated with the observed UV-induced reactions. As a whole, this study provides fundamental data to understand the physicochemical behavior of the compound, bridging the properties of the isolated molecule to those of the neat crystalline com-pound. Such information is of fundamental importance for the understanding of the role of BPCA in supramolecular chemistry and to potentiate its applications in synthesis and as a ligand for transition metal catalysts and luminescent complexes.Publication Metadata only Comparative Study of Antitumor Active Cyclo(Gly-Leu) Dipeptide: A Computational and Molecular Modeling Study(Elsevier Science Bv, Po Box 211, 1000 AE Amsterdam, Netherlands, 2016-03) Çelik, Sefa; Özel, Ayşen E.; AKYÜZ, SEVİM; 110745; 10127The conformational behavior and vibrational spectra of cyclo(Gly-Leu) dipeptide, which is an important biological active compound and a therapeudic agent, have been investigated by computational methods. The theoretically possible stable conformers of free cyclo(Gly-Leu) dipeptide in electronic ground state were obtained by performing conformational analysis following DFT calculations. Further, to predict the intermolecular hydrogen bonding interactions in solid phase, various dimer structures were modeled. The optimized geometry and the wavenumbers for cyclo(Gly-Leu) and its dimers have been calculated by DFT method with B3LYP functional, 6-31++G(d,p) basis set. The complete assignment of the bands was performed based on the potential energy distributions (PED%) and experimental wavenumber shifts upon N-deuteration. General agreements between the observed and calculated frequencies are shown. Chemical interpretation of hyperconjugative interactions was carried out by natural bond orbital (NBO) analysis. Finally, HOMO and LUMO energy levels have been calculated. (C) 2016 Elsevier B.V. All rights reserved.Publication Restricted Synthesis, Characterization and Sensing Mechanism of a Novel Fluorescence Probe for Fe(III) in Semi-Aqueous Solution Based on a Schiff Base Hexadentate Receptor(Elsevier Science SA, 2023) Ooshall, Farkhondeh; Jamehbozorgi, Saeed; Golbedaghi, Reza; Justino, Licinia L. G.; Feshalame, Keyvan Mirzaei; Liyaghati-Delshad, Mozhdeh; Anaraki-Ardakani, Hossein; Jaleh, Babak; FAUSTO, RUIA new acyclic Schiff base chemosensor L was synthesized by the one pot condensation reaction of 2-[3-(formyl phenoxy)2-hydroxypropoxy]benzaldehyde and 2-aminophenol in a 1:2 molar ratio and was characterized by elemental analysis, FTIR, 1H- and 13C NMR, and fluorescence spectroscopies. These studies were complemented with a thorough conformational study at the molecular mechanics and density functional theory (DFT) levels of theory to further elucidate the structure of the compound in solution. The chemosensor L displays high sensitivity and selectivity for Fe3+ in semi-aqueous (H2O-DMF, 1:1) solution, except in the presence of a significant amount of Ni2+, with the presence of Fe3+ being signaled through the total fluorescence quenching of the fluorophore when Fe3+ binds to the recognition unit. The synthesized ligand also shows high selectivity for Fe3+ compared to the metal ions Cu2+, Zn2+, Mg2+, Mn2+, Pb2+, Hg2+, Na+, Ba2+ and Cd2+, and reasonable selectivity in the presence of Ag+, Co2+ and Cr3+. The stoichiometry and structure of the complex formed between Fe3+ and the probe L were determined from a Job's plot and DFT calculations, respectively. The complex was characterized as a high-spin 1:1 octahedral species, in which the ligand coordinates to the metal through the two ether oxygen atoms, two nitrogen atoms and two terminal hydroxyl groups. Time dependent (TD-DFT) calculations were performed to provide information on the type of mechanism causing the quenching of the fluorescence in the presence of Fe3+.Publication Restricted Synthesis, FT-IR and NMR Characterization, Antibacterial and Antioxidant Activities, and DNA Docking Analysis of a New Vanillin-Derived imine Compound(Elsevier, 2021) Çelik, Sefa; Özkök, Funda; Özel, Ayşen E.; Çakır, Elif; AKYÜZ, SEVİMA new vanillin-derived imine compound, [5-((1E,15E)-16-(3-methoxy-4-hydroxyphenyl)hexadeca-1',15'-diimine)-2-methoxyphenol], was synthesized and characterized by DFT calculations, experimental and theoretical vibrational spectroscopy and NMR techniques. The most stable molecular structure of the title compound has been calculated by optimizing the molecular structures using DFT/B3LYP/6-311+G(d,p) level of theory. The fundamental vibrational wavenumbers, IR and Raman intensities for the optimized geometry of the compound under investigation were determined and compared to the experimental vibrational spectra. The vibration assignment of the molecule was made in accord with the potential energy distribution (PED) of the vibration modes and using the group frequencies. The molecular electrostatic potential (MEP), HOMO and LUMO orbitals were also calculated. The antibacterial activities of the new vanillin-derived imine compound against gram-positive and gram-negative bacteria was determined. The antioxidant activity of the title compound was also examined. Moreover, the molecular docking studies have been performed to understand the nature of binding of the compound with DNA. The results indicated that the investigated compound has a good binding affinity with DNA and interacted with the DG4 and DT7 residues via the intermolecular hydrogen bonds.Publication Open Access Synthesis, Molecular Modelling, FT-IR, Raman and NMR Characterization, Molecular Docking and ADMET Study of New Nickel(II) Complex with an N4-Tetradentate Thiosemicarbazone(Taylor and Francis Ltd., 2021) Eğlence-Bakır, Songül; Çelik, Sefa; Şahin, Musa; Ozel, Ayşen E.; AKYÜZ, SEVİM; Ülküseven, BahriA new nickel(II) complex was synthesized by using S-propyl-thiosemicarbazide and 2-amino-3,5-dibromobenzaldehyde. The complex, obtained by the template effect of nickel ions, was structurally analysed by experimental and theoretical vibrational spectroscopy, NMR and density functional theory (DFT) calculations. By using DFT/B3LYP method with 6-311++G(d, p) basis set, the most stable molecular structure of the title molecule was calculated. The fundamental vibrational wavenumbers, IR and Raman intensities for the optimized structure of the molecule under investigation were determined and compared with the experimental vibrational spectra. The vibrational assignment was achieved using the calculated potential energy distributions of the vibrational modes. Moreover, the molecular electrostatic potential (MEP), the highest occupied molecular orbital (HOMO) and the lowest occupied molecular orbital (LUMO) energies were calculated, Molecular docking of the molecule was carried out against DNA in order to identify the potential inhibitory action of the title compound. The findings suggested that the aforementioned compound has a strong binding affinity to interact with DNA residues DT8, DC9, DG12, DG16, DA17, and DA18 through the intermolecular hydrogen bonds. Also the performed in silico ADMET analysis was the prediction of the synthesized molecule’s pharmacokinetic and toxicity profile expressing good oral drug like actions and non-toxic nature. The complex has been shown to have the possibility to become a model molecule for drug development processes. Communicated by Ramaswamy H. Sarma. © 2020 Informa UK Limited, trading as Taylor & Francis Group.Publication Restricted Structural and Spectral Analysis of Anticancer Active Cyclo(Ala-His) Dipeptide(Taylor & Francis Inc., 2020) Çelik, Sefa; YILMAZ, GÖZDE; Özel, Ayşen E.; AKYÜZ, SEVİMThe theoretically possible most stable conformation of the cyclic dipeptide, which has a significant anticancer activity, was examined by conformational analysis method and then by DFT calculations. With DFT calculations, cyclo(Ala-His) dipeptide was found to be more stable in boat form than in planar conformation. Moreover, conformations of the dimeric forms of the title molecule were investigated. The dimeric forms of the cyclo(Ala-His) dipeptide were created by combining two identical cyclo(Ala-His) monomers, in lowest energy configuration and as a result three energetically possible dimeric structures were obtained. The solid phase FTIR and Raman spectra of cyclo(Ala-His) have been recorded. The spectra were interpreted with the aid of quantum chemical calculations based on density functional theory, using B3LYP and wb97xd methods with 6-311++G(d,p) basis set, in order to elucidate structural and spectral properties of the investigated molecule. Experimental vibrational spectra are found to be in accord with the simulated vibrational spectra. The assignment of the vibrational modes was performed depending on the calculated potential energy distribution (PED).In slicomolecular docking of cyclo(Ala-His) was also carried out with DNA. The drug likeness and ADMET properties were analyzed for the prediction of pharmacokinetic profiles. The results revealed that the compound has the potential to be the leading molecule in the drug discovery process.Publication Restricted Molecular and Crystal Structure, Spectroscopy, and Photochemistry of a Dispiro Compound Bearing the Tetraoxane Pharmacophore(Wiley-VCH Verlag GmbH, 2023) Amado, Patricia S. M.; Lopes, Susy; Bras, Elisa M.; Paixao, Jose A.; Takano, Ma-aya; Abe, Manabu; FAUSTO, RUI; Cristiano, Maria L. S.The molecular structure and photochemistry of dispiro[cyclohexane-1,3 & PRIME;-[1,2,4,5]tetraoxane-6 & PRIME;,2 & PRIME;& PRIME;-tricyclo[3.3.1.1(3,7)]decan]-4-one (TX), an antiparasitic 1,2,4,5-tetraoxane was investigated using matrix isolation IR and EPR spectroscopies, together with quantum chemical calculations undertaken at the DFT(B3LYP)/6-311++G(3df,3pd) level of theory, with and without Grimme's dispersion correction. Photolysis of the matrix-isolated TX, induced by in situ broadband (& lambda;>235 nm) or narrowband (& lambda; in the range 220-263 nm) irradiation, led to new bands in the infrared spectrum that could be ascribed to two distinct photoproducts, oxepane-2,5-dione, and 4-oxohomoadamantan-5-one. Our studies show that these photoproducts result from initial photoinduced cleavage of an O-O bond, with the formation of an oxygen-centered diradical that regioselectivity rearranges to a more stable (secondary carbon-centered)/(oxygen-centered) diradical, yielding the final products. Formation of the diradical species was confirmed by EPR measurements, upon photolysis of the compound at & lambda;=266 nm, in acetonitrile ice (T=10-80 K). Single-crystal X-ray diffraction (XRD) studies demonstrated that the TX molecule adopts nearly the same conformation in the crystal and matrix-isolation conditions, revealing that the intermolecular interactions in the TX crystal are weak. This result is in keeping with observed similarities between the infrared spectrum of the crystalline material and that of matrix-isolated TX. The detailed structural, vibrational, and photochemical data reported here appear relevant to the practical uses of TX in medicinal chemistry, considering its efficient and broad parasiticidal properties.