Fizik Bölümü / Department of Physics

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Now showing 1 - 20 of 416
  • Publication
    The Importance of Polymers in Medicine and their FTIR and Raman Spectroscopic Investigations
    (IGI Global, 2023) Çelik, Sefa; AKYÜZ, SEVİM; Özel, Ayşen E.
    Polymers are macromolecules with a very high molecular weight that are formed as a result of one or more small molecules bonding to each other, typically by covalent bonds. The concept of macromolecules consisting of many repeating units are published in the article titled "Uber Polymerization," which was first published in 1920 by Hermann Staudinger. The idea of polymers, which have been in our lives for a long time, has thus become an important field of study. Polymers are commonly used in tissue engineering because of their properties such as biocompatibility and biodegradability. In addition, polymers have a wide range of applications in tissue regeneration, drug delivery, and wound healing. Polymers have varying structural properties based on their backbone structure, molecular weight, and crystallinity. For this cause, a great deal of study in the medicine has been based on this category of materials. This workfocuses on the importance of polymers in the medicine, 3D printed polymer composites and Fourier transform infrared, and Raman spectroscopic investigations of polymeric structures.
  • PublicationOpen Access
    Phenylpropiolic Acid Isolated in Cryogenic Nitrogen and Xenon Matrices: NIR and UV-Induced Study
    (AIP Publishing, 2023) Lopes S.; Nikitin T.; FAUSTO, RUI
    Phenylpropiolic acid (C6H5C≡CCOOH, PPA) isolated in nitrogen and xenon cryogenic matrices was studied by infrared spectroscopy. The experimental studies were complemented by a series of quantum chemical calculations carried out at the density functional theory (B3LYP) and MP2 levels of theory (with different basis sets). The calculations predicted the existence of two planar PPA conformers, differing in the arrangement of the carboxylic group. The higher-energy trans-PPA conformer has a negligible population in the gas phase at room temperature and was prepared in situ in the N2 cryomatrix through vibrationally-induced rotamerization of the lower-energy cis-PPA conformer, achieved using selective narrowband infrared excitation of the OH stretching coordinate of the latter species. Broadband UV (λ > 235 nm) irradiation of matrix-isolated cis-PPA was also undertaken, leading to the observation of cis-PPA → trans-PPA isomerization. No other UV-induced photoreactions were observed. The in situ generated trans-PPA conformer was found to decay back to cis-PPA in the dark by tunneling, and its lifetimes under different experimental conditions were determined. The assignment of the infrared spectra of both conformers is presented, considerably extending the vibrational information available on this molecule.
  • PublicationOpen Access
    Sandwich-Type Double-Layer Piezoelectric Nanogenerators Based on One- and Two-Dimensional ZnO Nanostructures With Improved Output Performance
    (Nature Research, 2023) Fakhri, Parisa; Eaianli, Naeimeh; Bagherzadeh, Roohollah; Jaleh, Babak; Kashfi, Mohammad; FAUSTO, RUI
    Piezoelectric nanogenerators (PENGs) have attracted great interest owing to their broad range application in environmental mechanical energy harvesting to power small electronic devices. In this study, novel flexible and high-performance double-layer sandwich-type PENGs based on one-dimensional (1-D) and two-dimensional (2-D) zinc oxide (ZnO) nanostructures and Ni foam as the middle layer have been developed. The morphology and structure of 1- and 2-D ZnO nanostructures have been studied by scanning electron microscopy (SEM) and X-ray diffraction (XRD). To investigate the effect of structural design on the piezoelectric performance, single-layer PENGs were also fabricated. The piezoelectric output of all prepared PENGs were evaluated under different human impacts at various forces and frequencies. The double-layer designed PENGs showed a two times larger voltage output compared to the single-layer PENGs, and the use of Ni foam as middle-layer and of 2-D ZnO nanosheets (compared to 1-D nanorods) was also found to increase the performance of the designed PENGs. The working mechanism of the prepared PENGs is also discussed. The design of nanogenerators as double-layer sandwich structures instead of two integrated single-layer devices reduces the overall preparation time and processing steps and enhances their output performance, thus opening the gate for widening their practical applications.
  • PublicationRestricted
    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, RUI
    A 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+.
  • PublicationOpen Access
    Nanoscale Study of the Polar and Electronic Properties of a Molecular Erbium(III) Complex Observed via Scanning Probe Microscopy
    (MDPI, 2023) Ivanov, Maxim; Grempka, Arkadiusz; Buryakov, Arseniy; Nikitin, Timur; Justino, Licinia L. G.; FAUSTO, RUI; Vilarinho, Paula M.; Paixao, Jose A.
    We successfully synthesized millimeter-sized single crystals of the molecular erbium(III) complex Er(acac)(3)(cphen), where acac = acetylacetonate and cphen = 5-chloro-1,10-phenanthroline. The novelty of this work stems from the exhaustive examination of the polar and electronic properties of the obtained samples at the macro-, micro-, and nanoscale levels. The single crystal X-ray diffraction method demonstrates the monoclinic (noncentrosymmetric space group P2(1)) crystallographic structure of the synthesized samples and scanning electron microscopy exhibits the terrace-ledge morphology of the surface in erbium(III) crystals. By using the piezoelectric force microscopy mode, the origin of the polar properties and the hyperpolarizability in the synthesized samples were assigned to the internal domain structure framed by the characteristic terrace-ledge topography. The direct piezoelectric coefficient (similar to d33) was found to be intensely dependent on the local area and was measured in the range of 4-8 pm/V. A nanoscale study using the kelvin probe force and capacitance force (dC/dz) microscopy modes exposed the effect of the Er ions clustering in the erbium(III) complex. The PFM method applied solely to the Er ion revealed the corresponding direct piezoelectric coefficient (similar to d33) of about 4 pm/V. Given the maximum piezoelectric coefficient in the erbium(III) complex at 8 pm/V, we highlight the significant importance of the spatial coordination between the lanthanide ion and the ligands. The polar coordination between the lanthanide ion and the nitrogen and oxygen atoms was also corroborated by Raman spectroscopy supported by the density functional theory calculations. The obtained results can be of paramount importance for the application of molecular erbium(III) complex crystals in low-magnitude magnetic or electric field devices, which would reduce the energy consumption and speed up the processing switching in nonvolatile memory devices.
  • PublicationRestricted
    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.
  • PublicationOpen Access
    Crystallization Kinetics: Relationship Between Crystal Morphology and the Cooling Rate-Applications for Different Geological Materials
    (MDPI, 2023-01-24) Aysal, Namık; Kurt, Yiğit; ILDIZ, GÜLCE ÖĞRÜÇ; Öztürk, Hüseyin; Yeşiltaş, Mehmet; Laçin, Davut; Öngen, Sinan; Nikitin, Timur; FAUSTO, RUI
    Crystal morphology is controlled by several physicochemical parameters such as the temperature, pressure, cooling rate, nucleation, diffusion, volatile composition, and viscosity. The development of different crystal morphologies is observed as a function of the cooling rate in many different rock types (i.e., glassy volcanic rocks, and archeometallurgical slags). Crystallization is a two-stage kinetic process that begins with the formation of a nucleus and then continues with the accumulation of ions on it. The shapes of the crystals depend on the degree of undercooling (& UDelta;T), and euhedral crystals, having characteristic forms that reflect their crystallographic internal structure, that grow just below their liquidus temperature. In this study, crystal morphologies in different minerals (e.g., quartz, sanidine, olivine, pyroxene, magnetite, etc.) that had developed in silicic volcanic rocks (spherulites) and slags from ancient mining were investigated and characterized using optical microscopy, X-ray diffraction, and Fourier-transform infrared (FTIR), Raman, and scanning electron microscope-energy dispersive X-ray fluorescence (SEM-EDX) spectroscopic techniques. Depending on the increase in the cooling rate, quartz, feldspar, olivine, pyroxene, and magnetite minerals were found to crystallize in subhedral, skeletal, dendritic, spherical, bow-tie and fibrous forms in glassy volcanic rocks and archeometallurgical slags.
  • PublicationRestricted
    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[,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.
  • PublicationRestricted
    Effects of Enol-Imine/Keto-Amine Tautomerism and Conformational Changes on the Electronic Spectra of a Novel 1,2,4-Triazole Ortho-Hydroxyaryl Schiff Base in Different Solvents
    (Elsevier, 2023) Sıdır, İsa; Sıdır, Yadigar Gülseven; Berber, Halil; FAUSTO, RUI
    In this study, a novel o-hydroxyaryl Schiff base bearing the 1,2,4-triazole heterocyclic core, (E)-2-(((4H-1,2,4-triazol-4-yl)imino)methyl)-6-methoxyphenol, was synthesized and structurally characterized by NMR (1H-and 13C-) and IR spectroscopies as well as by Density Functional Theory (DFT) electronic structure calculations. The compound was then investigated by UV-Vis absorbance and fluorescence emission spectroscopies in different solvents. The wavelength shifts observed in the band corresponding to the lowest energy transition in the absorbance spectra upon changing the solvent, as well as in the emission bands observed in the fluorescence spectra (upon excitation at 310 nm) were explained considering the effects of solvent-induced conformational changes and photoinduced enol-imine/keto-amine tautomerism. The interpretation of the experimental results was supported by structural data calculated for the different isomeric forms of the compound and of their electronic spectra in the gas phase and in solvents of different polarity. Solvent effects were also evaluated at the light of the Kamlet-Taft and Catal & PRIME;an solvatochromic models.
  • PublicationRestricted
    The Meta and Para OH Substitution Effect on C-Phenyl-Nitrilimine Bond-Shift Isomers
    (Wiley-VCH Verlag GmbH, 2023) Ferreira, Gil A.; Nunes, Claudio M.; Jesus, A. J. Lopes; FAUSTO, RUI
    The geometric and electronic structure of 1,3-dipolar species, in particular of nitrile imines, can be surprisingly intricate. A particular example is the C-phenyl-nitrilimine, which exists as two energy minima that constitute bond-shift isomers. To examine the effect of substituents in the phenyl ring, here we investigate the meta and para OH substituted derivatives. These two nitrile imines were generated in an argon matrix by UV-irradiation of 2H-tetrazole precursors and found to photoisomerize to carbodiimides via 1H-diazirines. The different effects of the OH substitution in meta and para positions on the bond-shift isomerism are rationalized with the support of Natural Resonance Theory and Hirshfeld atomic charges. The understanding of how substitution affects the structural characteristics of C-phenyl-nitrilimines, opens a door to modulate the chemistry of those compounds (e. g. in cycloaddition reactions) by appropriate tuning of their substitution (substituent type and position).
  • PublicationOpen 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, Rui
    6-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.
  • PublicationRestricted
    Structure, Conformational Landscape and UV-Induced Selective Rotamerization of 2-Aminoacetanilide
    (Elsevier Science SA, 2023) Brito, Anna Luiza B.; Justino, Licinia L. G.; Çatıkkaş, Berna; Lopes, Susy; ILDIZ, GÜLCE ÖĞRÜÇ; Fausto, Rui
    The molecular structure, conformational space and UV-induced rotamerization and decarbonylation of 2-aminoacetanilide (2AA) were investigated by matrix isolation infrared spectroscopy and quantum chemical electronic structure calculations. The compound was isolated in a cryogenic (15 K) argon matrix, and four conformers were spectroscopically identified: two trans-amide (O--C-N-H dihedral - 180 degrees) conformers (trans-I and trans-II), and two higher-energy cis-amide (O--C-N-H dihedral - 0 degrees) conformers (cis-I and cis-II). These four conformers were found to be present in the as-deposited matrix of 2AA in a population ratio matching well that predicted by the calculations for the gas-phase equilibrium at the temperature of the vapor of the compound before deposition (60 degrees C = 333.15 K). The calculations predicted also the existence of an additional higherenergy trans-amide conformer (trans-III) which was not observed experimentally. In situ broadband UV irradiation (lambda > 235 nm) of the matrix-isolated compound was found to induce selective conversion of conformer trans-I into conformer trans-II, in a few minutes (55 % after 2 min. of irradiation; 70 % after 10 min.), while the populations of the cis-amide conformers did not change. Prolonged UV irradiation was found to result in decomposition of the compound, leading to generation of carbon monoxide and 2-amine-N-methylaniline. The infrared spectra of the experimentally relevant conformers of 2AA were interpreted and assigned with help of normal coordinate analysis, and the different behavior of the conformers of 2AA upon UV-irradiation of the argon matrix was explained with help of time-dependent DFT (TD-DFT) calculations.
  • PublicationRestricted
    Shedding Light Into the Biological Activity of Aminopterin, Via Molecular Structural, Docking, and Molecular Dynamics Analyses
    (Taylor & Francis Inc., 2023) Çelik, Sefa; YILMAZ, GÖZDE; AKYÜZ, SEVİM; Özel, Ayşen E.
    In this study, the structural and anticancer properties of aminopterin, as well as its antiviral characteristics, were elucidated. The preferred conformations of the title molecule were investigated with semiempirical AM1 method, and the obtained the lowest energy conformer was then optimized by using density functional (DFT/B3LYP) method with 6-311++G(d,p) as basis set. The vibrational frequencies of the optimized structure were calculated by the same level of theory and were compared with the experimental values. The vibrational assignments were performed based on the computed potential energy distribution (PED) of the vibrational modes. The molecular electrostatic potential (MEP) and frontier molecular orbitals (HOMO, LUMO) analyses were carried out for the optimized structure and the chemical reactivity has been scrutinized. To enlighten the biological activity of aminopterin as anticancer and anti-COVID-19 agents, aminopterin was docked into DNA, & alpha;(IIB)& beta;(3) and & alpha;(5)& beta;(1)integrins, human dihydrofolate reductase, main protease (M-pro) of SARS-CoV-2 and SARS-CoV-2/ACE2 complex receptor. The binding mechanisms of aminopterin with the receptors were clarified. The molecular docking results revealed the strong interaction of the aminopterin with DNA (-8.2 kcal/mol), & alpha;(IIB)& beta;(3) and & alpha;(5)& beta;(1) integrins (-9.0 and -10.8 kcal/mol, respectively), human dihydrofolate reductase (-9.7 kcal/mol), M-pro of SARS-CoV-2 (-6.7 kcal/mol), and SARS-CoV-2/ACE2 complex receptor (-8.1 kcal/mol). Moreover, after molecular docking calculations, top-scoring ligand-receptor complexes of the aminopterin with SARS-CoV-2 enzymes (6M03 and 6M0J) were subjected to 50 ns all-atom MD simulations to investigate the ligand-receptor interactions in more detail, and to determine the binding free energies accurately. The predicted results indicate that the aminopterin may significantly inhibit SARS-CoV-2 infection. Thus, in this study, as both anticancer and anti-COVID-19 agents, the versatility of the biological activity of aminopterin was shown.
  • PublicationOpen Access
    UV-induced-OCH3 Rotamerization in a Matrix-Isolated Methoxy-Substituted Ortho-Hydroxyaryl Schiff Base
    (Springernature, 2022) Sıdır, İsa; Sıdır, Yadigar Gülseven; Gobi, Sandor; Berber, Halil; ILDIZ, GÜLCE ÖĞRÜÇ; Fausto, Rui
    A new methoxy-substituted ortho-hydroxyaryl Schiff base, 4-(3-methoxy-2-hydroxybenzylidene-amino) phenol was synthesized from 4-aminophenol and 2-hydroxy-3-methoxybenzaldehyde in methanol solution and characterized by H-1-NMR, C-13-NMR and infrared spectroscopies and elemental analysis. The compound was isolated in a cryogenic (10 K) argon matrix, and the analysis of the infrared spectrum of the matrix-isolated compound revealed that it corresponds to the E-enol-imine isomeric form, with 3 different conformers being present in the matrix. These conformers share as common structural features the conformation of the free hydroxyl group (trans relatively to the para-substituent of the ring) and the presence of an OH center dot center dot center dot N intramolecular H-bond involving the methoxy-substituted phenol ring and the azomethine bridge, while they differ in the orientation of the methoxy-substituent group. The structures and relative energies of the conformers of the molecule, and relevant barriers for their interconversion were obtained through quantum chemical calculations, which were also used to calculate the infrared spectra of the different forms. Calculations were also carried out for the higher-energy Z-enol-imine and keto-amine forms of the compound. Upon UV (230 nm) irradiation, -OCH3 rotamerization was observed, leading to conversion of the lowest energy conformer, where the methoxy group is aligned with the plane of the ring, into the other two conformers initially present in the matrix, in which the OCH3 group is out-of-the-plane of the ring. As for other phenolic compounds previously studied, spontaneous quantum mechanical tunneling conversion of the cis-OH conformers present in the gas-phase into the three observed conformers was found to take place during matrix deposition.
  • PublicationRestricted
    A New Tetramine Bis(2-Naphthol)-Derivative Fluorescent Chemosensor for Aluminum Ion (Al3+)
    (Elsevier, 2022) Golbedaghi, Reza; ILDIZ, GÜLCE ÖĞRÜÇ; Azadbakht, Reza; Fausto, Rui
    A new tetramine bis(2-naphthol)-derivative was synthesized and its structure investigated by H-1- and C-13 NMR, UV-Vis absorption and fluorescence spectroscopies, as well as through density functional theory calculations (including time-dependent DFT). The effect of a series of metal ions (Ag+, Al3+, Ba2+, Ca2+, Cd2+, Co2+, Cs (+), Cu2+, Fe2+, Fe3+, K+, Mg2+, Mn2+, Ni2+, Pb2+ and Zn2+) on the fluorescence spectra of the synthesized compound was then investigated and it was observed that the presence of Al3+ ion causes a strong increase in the fluorescence emission of the ligand, by about 70 times. This exceptional intensification is specific for Al3+ within the whole series of ions investigated, together with the selectivity found for many of the remaining ions (in particular the ions of Groups I and II of the Periodic Table and Mn2+), makes the compound a promising candidate to act as chemosensor for Al3+. Possible structures for the ligand:Al3+ complex are suggested based on DFT results. TD-DFT calculations performed on these structures suggest that the fluorescence enhancement upon binding of Al3+ to the ligand results most probably from metal-to-ligand charge transfer where the acceptor groups of the ligand are the naphthol moieties. (C) 2021 Elsevier B.V. All rights reserved.
  • PublicationRestricted
    Synthesis, Vibrational Spectroscopic Investigation, Molecular Docking, Antibacterial and Antimicrobial Studies of a New Anthraquinone Derivative Compound
    (Taylor & Francis Inc., 2022) Çelik, Sefa; Vagifli, Fidan; AKYÜZ, SEVİM; Özkök, Funda; Özel, Ayşen E.; Dosler, Sibel; Onur, Nihal
    A new anthraquinone derivative, 1-(2,5-dimethylpiperazin-1-yl)anthracene-9,10-dione, was synthesized and characterized by Fourier Transform-Infrared, Raman and nuclear magnetic resonance analysis. The optimized molecular geometry was obtained using Density Functional Theory, B3LYP method with a 6-311++G(d,p) basis set. The fundamental vibrational wavenumbers, IR and Raman intensities were calculated for the optimized structure and simulated spectra were compared with the experimental vibrational spectra. The calculated highest occupied molecular orbital and lowest occupied molecular orbital energies indicated the presence of charge transfer within the molecule. The antibacterial activities of the new amino anthraquinone derivate against gram-positive and gram-negative bacteria were determined. Molecular docking simulations were performed with the new anthraquinone derivative and DNA to reveal its anticancer property. It was found that the anthraquinone derivate was bound to DNA with a high binding affinity (Delta G = -31.8 kJ/mol) and interacted with the DG10, DC11 and DG16 residues via the intermolecular hydrogen bonds. Moreover, to investigate the antiviral activity of the compound and to expose its action mechanism as an antiCOVID-19 agent, in silico molecular docking studies were performed on the Angiotensin-Converting Enzyme-2, and SARS-CoV-2 targets (holo and apo forms of main proteases M-pro and spike glycoprotein).
  • PublicationRestricted
    Investigation of Menopause-Induced Changes on Hair by Raman Spectroscopy and Chemometrics
    (Pergamon-Elsevier Science Ltd., 2022) Brito, Anna Luiza B.; Brueggen, Carlotta; ILDIZ, GÜLCE ÖĞRÜÇ; Fausto, Rui
    The ending of estrogen production in the ovaries after menopause results in a series of important physiologic changes, including hair texture and growth. In this study we demonstrate that Raman spectroscopy can be used successfully as a tool to probe menopause-induced changes on hair, in particular when coupled with suitable chemometrics approaches. The detailed analysis of the average Raman spectra (in particular of the Amide I and vS-S stretching spectral regions) of the hair samples of women pre- and post-menopause allowed to estimate that absence of estrogen in post-menopause women leads to an average reduction of similar to 12% in the thickness of the hair cuticle, compared to that of pre-menopause women, and revealed the strong prevalence of disulphide bonds in the most stable gauche-gauche-gauche conformation in the hair cuticle. From the analysis of the vS-S stretching spectral region it could also be concluded that the amount of alpha-helix keratin is slightly higher for post-menopause than for pre-menopause women. A series of statistical models were developed in order to classify the hair samples. Outperforming the traditional PCA-LDA (principal component analysis - linear discriminant analysis) approach, in the present study a GA-LDA (genetic algorithm - linear discriminant analysis) strategy was used for variable reduction/selection and samples' classification. This strategy allowed to develop of a statistical model (L16), which has exceptional prediction capability (total accuracy of 96.6%, with excellent sensitivity and selectivity) and can be used as an efficient instrument for the hair samples' classification. In addition, a new chemometrics approach is here presented, which allows to overcome the intrinsic limitations of the GA algorithm and that can be used to develop statistical models that use GA as the variable reduction/selection method, but superseding its stochastic nature. Three suitable models for classification of the hair samples according to the menopause status of the women were developed using this novel approach (LV17, BLV20 and PLS7 models), which are based on the Fisher's and Bayers' LDA approaches and the PLS-DA method. The followed new chemometrics approach uses the results of a large set of GA-LDA runs over the full data matrix for the selection of the reduced data matrices. The criterion for the selection of the variables is their statistical significance in terms of number of occurrences as solutions of the whole set of GA-LDA runs. (C) 2022 Elsevier B.V. All rights reserved.
  • PublicationOpen Access
    Micro-Raman Spectroscopy and X-ray Diffraction Analyses of the Core and Shell Compartments of an Iron-Rich Fulgurite
    (MDPI, 2022) KARADAĞ, AHMET; Kaygısız, Ersin; Nikitin, Timur; Öngen, Sinan; ILDIZ, GÜLCE ÖĞRÜÇ; Aysal, Namık; Yılmaz, Ayberk; Fausto, Rui
    Fulgurites are naturally occurring structures that are formed when lightning discharges reach the ground. In this investigation, the mineralogical compositions of core and shell compartments of a rare, iron-rich fulgurite from the Mongolian Gobi Desert were investigated by X-ray diffraction and micro-Raman spectroscopy. The interpretation of the Raman data was helped by chemometric analysis, using both multivariate curve resolution (MCR) and principal component analysis (PCA), which allowed for the fast identification of the minerals present in each region of the fulgurite. In the core of the fulgurite, quartz, microcline, albite, hematite, and barite were first identified based on the Raman spectroscopy and chemometrics analyses. In contrast, in the shell compartment of the fulgurite, the detected minerals were quartz, a mixture of the K-feldspars orthoclase and microcline, albite, hematite, and goethite. The Raman spectroscopy results were confirmed by X-ray diffraction analysis of powdered samples of the two fulgurite regions, and are consistent with infrared spectroscopy data, being also in agreement with the petrographic analysis of the fulgurite, including scanning electron microscopy with backscattering electrons (SEM-BSE) and scanning electron microscopy with energy dispersive X-ray (SEM-EDX) data. The observed differences in the mineralogical composition of the core and shell regions of the studied fulgurite can be explained by taking into account the effects of both the diffusion of the melted material to the periphery of the fulgurite following the lightning and the faster cooling at the external shell region, together with the differential properties of the various minerals. The heavier materials diffused slower, leading to the concentration in the core of the fulgurite of the iron and barium containing minerals, hematite, and barite. They first underwent subsequent partial transformation into goethite due to meteoric water within the shell of the fulgurite. The faster cooling of the shell region kinetically trapped orthoclase, while the slower cooling in the core area allowed for the extensive formation of microcline, a lower temperature polymorph of orthoclase, thus justifying the prevalence of microcline in the core and a mixture of the two polymorphs in the shell. The total amount of the K-feldspars decreases only slightly in the shell, while quartz and albite appeared in somewhat larger amounts in this compartment of the fulgurite. On the other hand, at the surface of the fulgurite, barite could not be stabilized due to sulfate lost (in the form of SO2 plus O-2 gaseous products). The conjugation of the performed Raman spectroscopy experiments with the chemometrics analysis (PCA and, in particular, MCR analyses) was shown to allow for the fast identification of the minerals present in the two compartments (shell and core) of the sample. This way, the XRD experiments could be done while knowing in advance the minerals that were present in the samples, strongly facilitating the data analysis, which for compositionally complex samples, such as that studied in the present investigation, would have been very much challenging, if possible.
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    Raman Spectroscopic Investigation of the Wear Effect on the Titanium Carbonitride/Aluminum Oxide/Titanium Nitride Coated Cutting Tool
    (Taylor & Francis Inc., 2022) Çelik, Sefa; Üllen, Nuray Bekoz; AKYÜZ, SEVİM; Özel, Ayşen E.
    In this study, micro-Raman spectroscopy technique in combination with multivariate statistical analysis was carried out to investigate the worn surfaces and metallurgical changes in the wear land of chemical vapor deposition-applied titanium carbonitride/aluminum oxide/titanium nitride-coated cutting inserts. To understand the wear process, detailed scanning electron microscopy analysis was also performed. The structural change at the molecular level of the coating due to the wear of the cutting-edge layers was investigated. Tool life was determined at 0.5 mm flank wear of the cutting tool. Thirty-four Raman spectra recorded from the different points of the worn parts of nine cutting inserts were investigated in comparison with the seven spectra of the different points of three unused cutting inserts. The principal component analysis followed by linear discriminant analysis performed on 41 Raman spectral data, clearly separated the samples as worn and unworn cutting inserts, and showed the wear effects. The comparison of the mean Raman spectrum of worn and unworn (unused) cutting inserts showed that the intensities of the aluminum oxide and titanium nitride bands were decreased, whereas the titanium carbide band at 672 cm(-1) was increased, as a result of the wear effect. Moreover, the relative intensity of disordered carbon (D band) band to the graphitic sp(2) bonded carbon (G band) band was found to increase, due to wear.
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    Structural and Vibrational Investigations and Molecular Docking Studies of a Vinca Alkoloid, Vinorelbine
    (Taylor & Francis Inc., 2022) Çelik, Sefa; AKYÜZ, SEVİM; Özel, Ayşen E.
    Vinorelbine, a vinca alkaloid, is an antimitotic drug that inhibits polymerisation process of tubulins to microtubules, and is widely used in cancer chemotherapy. Due to the importance of the structure-activity relationship, in this work the conformational preferences of the vinorelbine molecule were surched by PM3 method. The obtained lowest energy conformer was then optimized at DFT/B3LYP/6-31G(d,p) level of theory and the structural characteristics were determined. Frontier orbital (HOMO, LUMO) and molecular electrostatic potential (MEP) analyses were performed for the optimized structure. The experimental FT-IR, Raman and UV-VIS spectral data of vinorelbine along with the theoretical DFT/B3LYP/6-31G(d,p) calculations were investigated in detail. The vibrational wavenumbers were assigned based on the calculated potential energy distribution (PED) of the vibrational modes. To shed light into the anticancer property of vinorelbine as microtubule destabilizer, the most favourable binding mode and the interaction details between vinorelbine and tubulin were revealed by molecular docking studies of vinorelbine into the alpha,beta-tubulin (PDB IDs: 4O2B; 1SA0; 7CNN) and binding free energies were calculated by the combination of Molecular Mechanics/Generalized Born Surface Area (MMGBSA) and Molecular Mechanics/Poisson-Boltzmann Surface Area (MM-PBSA) methods {MM/PB(GB)SA}. The calculated vinorelbine-7CNN binding free energy, using by MM/PB(GB)SA approach, was found to be the best (-50.39 kcal/mol), and followed by vinorelbine-4O2B (-28.5 kcal/mol) and vinorelbine-1SA0 (-17.59 kcal/mol) systems. Moreover, the interaction of vinorelbine with the cytochrome P450 enzymes (CYP), which are known to help in the metabolism of many drugs in the body, was investigated by docking studies against CYP2D6 and CYP3A4 targets. Communicated by Ramaswamy H. Sarma