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Publication Metadata only Structural and spectroscopic investigation on antioxidant dipeptide, L-Methionyl-L-Serine: A combined experimental and DFT study(Elsevier Science Bv, Po Box 211, 1000 AE Amsterdam, Netherlands, 2017-06-05) Kecel Gündüz, Serda; Bıçak, Bilge; Çelik, Sefa; Özel, Ayşen E.; AKYÜZ, SEVİM; 110526; 277135; 110147; 10127; 110745The focus of this study is to determine the conformational, structural and vibrational properties of Methionyl-Serine dipeptide (L-Methionyl-L-Serine, Met-Ser), a biological active molecule. To investigate their energetically preferred conformations, molecular mechanics methods were utilized to determine the optimal conformations of the 3402 different dihedral angle values of the backbone and side chains. It was found that the extended (e) backbone shape in the LB conformational range was the most stable LMethionyl-L-Serine dipeptide conformation, with 3.12 kcal/mol of energy. Density Functional Theory (DFT) was used to determine the optimized geometry, the vibrational wavenumbers and modes of the title dipeptide values, with 6-31G (d,p) and 6-311++G (d,p) basis sets. The potential energy distribution data was used to carry out the assignment of the bands. In addition, the vibrational spectra of the most stable conformer and its dimer form were determined and the obtained results were compared with the experimental IR and Raman spectra in the solid phase. To determine the presence of intramolecular charge transfer, molecular dipole moment, polarizability and hyperpolarizability, the Natural Bond Orbital (NBO), HOMO LUMO calculations, the linear polarizability (alpha) and the first order hyperpolarizability (fio) value analyses of the investigated molecule were carried out using the DFT with the B3LYP/6-31++G(d,p) basis set. This study aims to determine a relatively stable conformation of antioxidant dipeptide and to investigate the molecular geometry, molecular vibrations and hydrogen bonding interactions between monomeric and dimeric forms of Methiony-Serine dipeptide. (C) 2017 Elsevier B.V. All rights reserved.Publication Metadata only The conformational and vibrational behavior of the inhibitory neuropeptide derived from beta-endorphin(Taylor & Francis Inc, 530 Walnut Street, Ste 850, Philadelphia, Pa 19106 USA, 2017) Kecel Gündüz, Serda; Çelik, Sefa; Özel, Ayşen E.; AKYÜZ, SEVİM; 110526; 110147; 110745; 10127In this study, conformational behavior, structural, and vibrational characterization of the carboxy terminal dipeptide of beta-endorphin (glycy-L-glutamine, glycyl-glutamine, beta-endorphin(30-31)), which is an inhibitory neuropeptide synthesized from beta-endorphin(1-31) in brain stem regions, has been investigated. The theoretically possible stable conformers were searched by means of molecular mechanics method to determine their energetically preferred conformations. The 360 different conformations were calculated with the phi, Psi, chi. dihedral angles using the Ramachandran maps. The most stable conformation of the title molecule is characterized by the extended backbone shape (e) in the BR conformational range with -.78 kcal/mol energy. The cis- and trans-dimeric forms of the dipeptide were also formed and energetically preferred conformations of dimers were investigated. The experimental methods (FT-IR, micro-Raman spectroscopies) coupled with quantum chemical calculations based on density functional theory (DFT) have been used to identify the geometrical, energetic, and vibrational characteristics of the dipeptide. The assignment of the vibrational spectra was performed based on the potential energy distribution of the vibrational modes. To investigate the electronic properties, such as nonlinear optical properties, the electric dipole moment, the mean polarizability, the mean first hyperpolarizability, and HOMO-LUMO energy gaps were computed using the DFT with the B3LYP/ 6-31++ G(d, p) basis set combination. The second-order interaction energies were derived from natural bonding orbital analysis. The focus of this study is to determine possible stable conformation on inhibitory neuropeptide and to investigate molecular geometry, molecular vibrations of monomeric and dimeric forms, and hydrogen bonding interactions of glycy-L-glutamine dipeptide.Publication Metadata only Structural and vibrational spectroscopic elucidation of sulpiride in solid state(Taylor & Francis Inc, 530 Walnut Street, Ste 850, Philadelphia, Pa 19106 USA, 2015-02-01) Kecel Gündüz, Serda; Çelik, Sefa; Özel, Ayşen E.; AKYÜZ, SEVİM; 110526; 110147; 110745; 10127The study on the conformational and vibrational behaviors of sulpiride molecule which is known as a neuroleptic or antipsychotic drug that is widely used clinically in the treatment of schizophrenic or depressive disorders is an important scientific and practical task. In here, a careful enough study of monomer and dimeric forms of sulpiridine {5-(aminosulfonyl)-N-[(1-ethyl-2-pyrrolidinyl) ethyl]-2-methoxy-benzamide (C15H23N3O4S)} is undertaken by density functional theory (DFTB3LYP) method with the B3LYP/6-31G(d,p) basis set. The conformations of free molecule were searched by means of torsion potential energy surfaces scan studies through dihedral angles D-1 (8 N, 18C, 20C, 23 N), D-2 (18C, 20C, 23 N, 25C) and D-3 (28C, 30C, 41S, 44 N) in electronically ground state, employing 6-31G basic set. The final geometrical parameters for the obtained stable conformers were determined by means of geometry optimization, carried out at DFT/B3LYP/6-31G(d,p) theory level. Afterwards, the possible dimer forms of the molecule were formed and their energetically preferred conformations were investigated. Moreover, the effect of basis set superposition error on the structure and energy of the three energetically favourable sulpiride dimers has been determined. The optimized structural parameters of the most stable monomer and three low energy dimer forms were used in the vibrational wavenumber calculations. Raman and IR (4000-400 cm(-1)) spectra of sulpiride have been recorded in the solid state. The assignment of the bands was performed based on the potential energy distribution data. The natural bond orbital analysis has been performed on both monomer and dimer geometries in order to elucidate delocalization of electron density within the molecule. The predicted frontier molecular orbital energies at DFT/B3LYP/6-31G(d,p) theory level show that charge transfer occurs within the molecule. The first-order hyperpolarizability (beta(0)) and related properties (mu and alpha) of the title molecule were also calculated.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 Embargo Structural and Vibrational Study on Monomer and Dimer Forms and Water Clusters of Acetazolamide(Hindawi Ltd, Adam House, 3Rd Flr, 1 Fitzroy Sq, London, W1T 5Hf, England, 2013) Özel, Ayşen; Kecel Gündüz, Serda; Çelik, Sefa; AKYÜZ, SEVİM; 110745; 110526; 110147; 10127Experimental IR and Raman spectra of solid acetazolamide have been analysed by computing the molecular structures and vibrational spectra of monomer and dimer forms and water clusters of acetazolamide. The possible stable conformers of free acetazolamide molecule in the ground state were obtained by scanning the potential energy surface through the dihedral angles, D 1 (1S-2C-6S-9N), D-2 (4N-5C-12N-14C), and D-3 (5C-12N-14C-16C). The final geometry parameters for the obtained stable conformers were determined bymeans of geometry optimization, carried out atDFT/B3LYP/6-31G++(d, p) theory level. Afterwards the possible dimer forms of the molecule and acetazolamide-H2O clusters were formed and their energetically preferred conformations were investigated using the same method and the same level of theory. The effect of BSSE on the structure and energy of acetazolamide dimer has been investigated. The assignment of the vibrational modes was performed based on the potential energy distribution of the vibrational modes, calculated by using GAR2PED program. The experimental vibrational wavenumbers of solid acetazolamide are found to be in better agreement with the calculated wavenumbers of dimer form of acetazolamide than those of its monomeric form. NBO analysis has been performed on both monomer and dimer geometries.Publication Metadata only Investigations of Archaeological Glass Bracelets and Perfume Bottles Excavated in Ancient Ainos (Enez) by Multiple Analytical Techniques(Springer, 233 Spring St, New York, Ny 10013 USA, 2018-03) Özel, Ayşen E.; Kecel Gündüz, Serda; Başaran, Sait; AKYÜZ, SEVİM; AKYÜZ, ZEKİ TANIL; 10127; 110745; 110526Fragments of two perfume bottles belonging to the Hellenistic and Roman periods, and five bracelets belonging to the Roman, Byzantine, and Ottoman periods, excavated in the archaeological site of Enez during the excavations in 2000, have been investigated. The samples were analyzed using micro-Raman, FTIR, and energy dispersive X-ray fluorescence techniques, in order to study the ancient technology of glass production and to determine chemical compositions of the basic components and coloring elements of the glassware. All the investigated glasses can be characterized as low-magnesia-soda-lime silicate glasses, whose colors are induced by metal ions. The melting points of the investigated glasses are estimated to be quite close to each other and around 1000A degrees C.Publication Metadata only Vibrational Analysis and Quantum Chemical Calculations of 2,2′-Bipyridine Zinc(II) Halide Complexes(Elsevier, 2007-05-27) Özel, Ayşen E.; Kecel Gündüz, Serda; AKYÜZ, SEVİM; 110745; 110526; 10127In this study the molecular structure and vibrational spectra of Zn(2,2′-bipyridine)X2 (X = Cl and Br) complexes were studied in their ground states by computational vibrational study and scaled quantum mechanical (SQM) analysis. The geometry optimization, vibrational wavenumber and intensity calculations of free and coordinated 2,2′-bipyridine were carried out with the Gaussian03 program package by using Hartree–Fock (HF) and Density Functional Theory (DFT) with B3LYP functional and 6-31G (d,p) basis set. The total energy distributions (TED) of the vibrational modes were calculated by using Scaled Quantum Mechanical (SQM) analysis. Fundamentals were characterised by their total energy distributions. Coordination sensitive modes of 2,2′-bipyridine were determined.Publication Metadata only Structural analysis, spectroscopic characterization and molecular docking studies of the cyclic heptapeptide(Taylor and Francis Online, 2018) Kecel Gündüz, Serda; Özel, Ayşen E.; AKYÜZ, SEVİM; 110526; 10127; 110745The theoretically possible stable conformer of the cyclic heptapeptide, that has significant anti-metastatic activity, was examined by conformational analysis followed by DFT calculations. Experimental infrared and Raman spectroscopy, together with theoretical DFT (6-31G (d,p) basis set)-based quantum chemical calculations, have been used to understand the structural and spectral characteristics of cyclo(Gly-Arg-Gly-Asp-Ser-Pro-Ala) {cyclo(GRGDSPA)}. A complete analysis of the vibrational spectrum has been reported on the basis of potential energy distribution (PED%) data of the vibrational modes. Finally, the calculation results were applied to simulate infrared and Raman spectra of the title compound. The simulated spectra satisfactorily coincide with the experimental spectra. In addition, molecular electrostatic potential and frontier molecular orbital analysis were investigated using theoretical calculations. The stability of the molecule, arising from hyperconjugative interaction and charge delocalization, has been analyzed using natural bond orbital analysis and a high E(2) value reveals the presence of strong interaction between donors and acceptors. Molecular docking studies with fibronectin were performed on cyclo(GRGDSPA) in order to understand its inhibitory nature. The results indicate that the docked ligand {cyclo(GRGDSPA)} forms a stable complex with human fibronectin and gives a binding affinity value of −7.7 kcal/mol, which points out that cyclo(GRGDSPA) might exhibit inhibitory activity against the attachment of melanoma cells to human fibronectin.Publication Metadata only Molecular Structure and Vibrational Assignment of 2-,4-,6-Methylquinoline by Density Functional Theory (DFT) and Ab Initio Hartree-Fock (HF) Calculations(Elsevier, 2006-11-24) Özel, Ayşen E.; Kecel Gündüz, Serda; AKYÜZ, SEVİM; 110745; 110526; 10127The molecular geometry, the normal mode frequencies and corresponding vibrational assignments of 2-,4-,6-methylquinoline (2-,4-,6-mq) in the ground state were performed by HF and DFT/B3LYP levels of theory using the 6-31++G(d,p) basis set. Harmonic and anharmonic vibrational frequencies were calculated. The complete assignments were performed on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method by using parallel quantum mechanic solutions program. The general agreements between the observed and calculated frequencies are shown.Publication Metadata only Theoretical Vibrational Spectra and Molecular docking studies with protein and DNA on cyclo-heptapeptide(2017) Çelik, Sefa; Kecel Gündüz, Serda; Özel, Ayşen; AKYÜZ, SEVİM; 110147; 110526; 10127; 110745