Fizik Bölümü / Department of Physics
Permanent URI for this collectionhttps://hdl.handle.net/11413/6785
Browse
Browsing Fizik Bölümü / Department of Physics by Rights "info:eu-repo/semantics/closedAccess"
Now showing 1 - 6 of 6
- Results Per Page
- Sort Options
Publication Blood Serum-Infrared Spectra-Based Chemometric Models for Auxiliary Diagnosis of Autism Spectrum Disorder(Elsevier, 2021) ILDIZ, GÜLCE ÖĞRÜÇ; Bayarı, Sevgi; Yorguner, Neşe; Fausto, RuiThis chapter focuses on the use of chemometric models developed from infrared (IR) spectroscopic data of blood serum as an auxiliary tool for autism spectrum disorder (ASD) diagnosis. In the introductory sections the fundamentals of IR spectroscopy are shortly reviewed and brief descriptions of the different chemometric methods used in the case study described in the last section of the chapter are presented. The last section deals with the application of the described strategy to the diagnosis of ASD in children and adolescents. © 2021 Elsevier Inc. All rights reserved.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.Publication Polymorphism in 1-Methylhydantoin: Investigation by Periodic DFT Calculations and Characterization of the Third Polymorph(Royal Society of Chemistry, 2020) Nogueira, Bernardo A.; Milani, Alberto; ILDIZ, GÜLCE ÖĞRÜÇ; Paixão, José A.; Castiglioni, Chiara; Fausto, RuiIn previous studies [Puszyńska-Tuszkanow et al. Polyhedron, 2011, 30(12), 2016; Nogueira et al. J. Phys. Chem. A, 2014, 118(31), 5994; Nogueira et al., J. Mol. Struct., 2017, 1148, 111], two different polymorphs of 1-methylhydantoin (1-MH, C4H6N2O2) were identified (forms I and II) and characterized using infrared and Raman spectroscopies, as well as by X-ray diffraction. In this work, a new polymorph of the compound (form III) is described. The new polymorph was characterized spectroscopically and its structure was determined for the first time by single crystal X-ray diffraction. Very interestingly, the crystal of polymorph III was found to exhibit a high-Z′ (Z′ = 3) asymmetric unit and 12 molecules in the unit cell (Z = 12), which contrasts with the simpler crystal structures found previously for forms I and II (Z = 4; Z′ = 1). Besides, a thorough study of the polymorphism of 1-MH was performed with the help of state-of-the-art first principles fully periodic calculations of the structure, as well as infrared and Raman spectra of the different polymorphs of the compound. Marker-bands in the infrared and Raman spectra of the polymorphs are proposed for fast spectroscopic identification of the polymorphs.Publication 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 Unveiling the Red and Brownish-Green Polymorphs of a Novel ROY Derivative: 2-(4-((3-Cyanothiophen-2-yl)amino)-3-nitrophenyl)Acetic Acid(American Chemical Society, 2024) Nogueira, Bernardo A.; Lopes, Susana M. M.; Rodrigues, Ana Clara B.; Eusebio, M. Ermelinda S.; Andre, Vania; Duarte, Teresa; Paixao, J. A.; Melo, Teresa M. V. D. Pinho e; FAUSTO, RUIPolymorphism has been the subject of many studies in the last decades, including a particular type of polymorphism where the colors exhibited by the polymorphs differ. However, only relatively limited or narrow differences in color were observed in color polymorphs of the same compound. Indeed, to this date, almost all compounds known to show color polymorphism exhibit red, orange, or yellow tones, as is the case of the notable ROY molecule (5-methyl-2-[(2-nitrophenyl)-amino]-3-thiophenecarbonitrile), which is the compound with more polymorphs reported and structurally characterized hitherto. In this work, we report a new color polymorphic material derived from ROY, (2-(4-((3-cyanothiophen-2-yl)-amino)-3-nitrophenyl)-acetic acid; or ROY-CAM), synthesized for the first time by nucleophilic aromatic substitution reaction between 2-(4-fluoro-3-nitrophenyl)-acetic acid and 2-aminothiophene-3-carbonitrile, which exhibits a red (P21/n, m.p.: 184 C-degrees and theta = -4.4(degrees) and 3.0(degrees)) and a brownish-green polymorph (P1, m.p.: 190 C-degrees and theta = -66.1(degrees)). This is the first time a member of the ROY family of compounds was observed to exhibit a brownish-green polymorph and, more importantly, the first time that a molecular compound exhibits a red and a greenish polymorphs, i.e., this is the first example of an organic molecule that originates polymorphs covering such a wide range of color. The isolated molecule of ROY-CAM has 11 low-energy conformers, which were accessed by DFT calculations, with two of these conformers being identified in the observed polymorphs of the compound: in the brownish-green polymorph, the most stable conformer exists, while the red polymorph is composed of molecules assuming a conformation similar to that of the third most stable conformer. In the latter polymorph, the intramolecularly disfavored conformation assumed by the molecules is stabilized in the crystal lattice through interactions between carboxylic acid groups of neighboring molecules, resulting in dimeric units formed between pairs of the two distinct molecules that constitute the asymmetric unit of the crystal. The two identified polymorphs were characterized vibrationally (by both IR and Raman spectroscopies), and a thermal study is also presented (based on DSC, PLTM, and TGA measurements). Furthermore, the brownish-green and red colors exhibited by the polymorphs of ROY-CAM are explained based on the differences in the structures of the molecules that are present in these crystals.Publication Using Raman Spectroscopy to Investigate the Molecular Level Characteristics of Endometriosis(Pleiades Publishing Inc., 2020) AKYÜZ, SEVİM; Çelik, Sefa; Usta, Abdullah Taner; Özel, Ayşen E.; Yılmaz, Salih; YILMAZ, GÖZDEEndometriosis is a benign gynecologic disorder. It is particularly common among young women and may make pregnancy difficult. In this study molecular level characterization of endometriosis tissues were performed using Raman spectroscopy in combination with multivariate statistical analysis. Three hundred sixty six Raman spectra recorded from different points of seventy two tissue samples, taken from the cyst walls of twelve patients were examined. Principle component analysis (PCA) followed by linear discriminant analysis (LDA) were performed on the Raman data, and the samples were then classified into three groups: severe, moderate, and weak endometriosis. In the severe endometriosis group, the relative band intensities of DNA were increased. Moreover, increase in pyrrole moieties and kynurenine were seen. The results show that endometriosis severity correlates to increase in DNA concentration, and degradation of tryptophan due to increased indoleamine-pyrrole 2,3-dioxygenase (IDO) activity, and an increase in kynurenine concentration and pyrrole intermediate. It is concluded that Raman spectroscopy is capable of providing a quick diagnosis, ahead of the pathology result being reported.