Fen Edebiyat Fakültesi / Faculty of Letters and Sciences
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Browsing Fen Edebiyat Fakültesi / Faculty of Letters and Sciences by Type "Article Early Access"
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Publication Assessment of Psychometric Characteristics of the Coronavirus Anxiety Scale in Patients with Preexisting Psychiatric Disorders(Taylor & Francis, 2022) Karahamet, Elif; Angın, Ülkem; Yılmaz, Onat; DENİZ, DERYA; Konuk, NumanThis study aimed to evaluate the psychometric characteristics of the Turkish version of the CAS in a Turkish psychiatric outpatient setting. A total of 198 patients with a preexisting psychiatric disorder completed the CAS scale. The scale's validity and reliability were evaluated using convergent and concurrent validity, internal consistency, exploratory and confirmatory factor analyses, and ROC analysis. The Turkish version of CAS might help physicians assess the COVID-19 associated anxiety in patients with psychiatric comorbidities.Publication An Exploration of the Subtypes of Male Youth Adjudicated for Sex Offenses: A Latent Class Analysis Based on Personal, Offense, and Victim Characteristics(Sage Publications Inc., 2022) Büker, Hasan; Cohen, Achraf; ERBAY, AYHANThis study intended to explore possible variations among youth adjudicated for sexual offenses based on personal criminogenic factors, offense, and victim characteristics. Utilizing a data set collected from the juvenile court files in Turkey (n = 460), the Latent Class Analysis revealed that the study sample included three different subgroups with distinct features: "non-delinquent, peer victim-targeting," "non-delinquent, younger victim-targeting," and "delinquent, versatile" youth adjudicated for sex offenses. The first two of these groups were similar in terms of having low levels of delinquency, while the third group included the lowest number of youth with significantly broad delinquent activity patterns. These findings were in line with the results of previous studies, and the implications were discussed for future research and policy development.Publication Graphene-Assisted Chemical Stabilization of Liquid Metal Nano Droplets for Liquid Metal Based Energy Storage(Wiley, 2024) Sanati, Afsaneh L.; Nikitin, Timur; FAUSTO, RUI; Majidi, Carmel; Tavakoli, MahmoudEnergy storage devices with liquid-metal electrodes have attracted interest in recent years due to their potential for mechanical resilience, self-healing, dendrite-free operation, and fast reaction kinetics. Gallium alloys like Eutectic Gallium Indium (EGaIn) are appealing due to their low melting point and high theoretical specific capacity. However, EGaIn electrodes are unstable in highly alkaline electrolytes due to Gallium oxide dissolution. In this letter, this bottleneck is addressed by introducing chemically stable films in which nanoscale droplets of EGaIn are coated with trace amounts of graphene oxide (GO). It is demonstrated that a GO to EGaIn weight ratio as low as 0.01 provides enough protection for a thin film formed by GO@EGaIn nanocomposite against significantly acidic or alkaline environments (pH 1-14). It is shown that GO coating significantly enhances the surface stability in such environments, thus improving the energy storage capacity by over 10x. Microstructural analysis confirms GO@EGaIn composite stability and enhanced electrochemical performance. Utilizing this, a thin-film supercapacitor is fabricated. Results indicate that when coating the EGaIn with GO to EGaIn ratio of 0.001, the areal capacitance improves by 10 times, reaching 20.02 mF cm(-2). This breakthrough paves the way for advanced liquid metal-based thin-film electrodes, promising significant improvements in energy storage applications.Publication Hydrogen Tunneling Exhibiting Unexpectedly Small Primary Kinetic Isotope Effects(Wiley - VCH Verlag GmbH, 2024) Roque, Jose P. L.; Nunes, Claudio M.; Schreiner, Peter R.; FAUSTO, RUIProbing quantum mechanical tunneling (QMT) in chemical reactions is crucial to understanding and developing new transformations. Primary H/D kinetic isotopic effects (KIEs) beyond the semiclassical maximum values of 7–10 (room temperature) are commonly used to assess substantial QMT contributions in one-step hydrogen transfer reactions, because of the much greater QMT probability of protium vs. deuterium. Nevertheless, we report here the discovery of a reaction model occurring exclusively by H-atom QMT with residual primary H/D KIEs. 2-Hydroxyphenylnitrene, generated in N2 matrix, was found to isomerize to an imino-ketone via sequential (domino) QMT involving anti to syn OH-rotamerization (rate determining step) and [1,4]-H shift reactions. These sequential QMT transformations were also observed in the OD-deuterated sample, and unexpected primary H/D KIEs between 3 and 4 were measured at 3 to 20 K. Analogous residual primary H/D KIEs were found in the anti to syn OH-rotamerization QMT of 2-cyanophenol in a N2 matrix. Evidence strongly indicates that these intriguing isotope-insensitive QMT reactivities arise due to the solvation effects of the N2 matrix medium, putatively through coupling with the moving H/D tunneling particle. Should a similar scenario be extrapolated to conventional solution conditions, then QMT may have been overlooked in many chemical reactions.Publication Investigation of Tos17 LTR Retrotransposon Movements in Rice (Oryza sativa L.) Under Nickel and Boron Stress(Springer Heidelberg, 2024) MERİÇ, SİNAN; AYAN, ALP; GÜNDÜZ, BURCU; ÖZPİRİNÇCİ, CAN; ÇELİK, ÖZGE; ATAK, ÇİMENHeavy metal and metalloid pollution caused by the industrialization became a leading stress factors for agricultural plants. The increase in the amount of nickel and boron in agricultural areas due to mining and increasing industrial activity is an important agricultural constraint. The difference between deficiency and toxicity levels of these heavy metal and metalloid is extremely critical. Nickel and boron are important micronutrients for plant growth, while they become toxic at critical densities. Plants exhibit different responses to these pollutants. It is essential to find specific biomarkers to discriminate the tolerant varieties to develop elite varieties. Transposable elements are known to have an efficient role against environmental stress factors. In this research, we evaluated the potential use of Tos17 retrotransposon movement as a molecular marker to identify the stress tolerances of two Oryza sativa L. varieties against nickel and boron pollutants.Publication 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.Publication Molecular Docking of the Pentapeptide Derived From Rice Bran Protein as Anticancer Agent Inhibiting Both Receptor and Non-Receptor Tyrosine Kinases(Taylor & Francis Inc., 2022) Gasymov, Oktay K; Keçel-Gündüz, Serda; Çelik, Sefa; AKYÜZ, SEVİM; Özel, Ayşen E.; Ağaeva, Gülşen; Süleymanova, Leman M.; Ağaeva, Ülker; Bakhishova, Matanat; Aliyev, JAThe cationic pentapeptide Glu-Gln-Arg-Pro-Arg (EQRPR) belongs to the family of anti-cancer peptides with significant anti-cancer activity. However, the mechanism by which the peptide performs this activity is unknown. In this study, we explored the pharmaceutical profile of Glu-Gln-Arg-Pro-Arg pentapeptide and revealed its anticancer properties by in silico docking studies. Moreover, the effect of EQRPR behavior of the DPPC membrane was investigated by means of Langmuir monolayer technique and the results were discussed in terms of mutual interactions. To evaluate the binding mechanisms, the pentapeptide and its various D-amino acid substituted analogs were docked to both epidermal growth factor receptor (EGFR) tyrosine kinase and proto-oncogene tyrosine-protein kinase, Fyn. Simultaneous binding of the pentapeptides to both EGFR and Fyn proteins, which are receptor- and non-receptor-kinases, respectively, suggest that these peptides can be an effective agent for cancer treatment. Moreover, to show the potential of the investigated pentapeptides to overcome the generated mutation-related drug resistance to EGFR targeted therapies, molecular docking investigations of EQRPR and all its D-analogs were performed against the prospective targets: Wild type EGFR(WT) and mutant EGFR(T790M). Erlotinib and TAK-285 were used as reference molecules. The strong interaction of the peptide with EGFR(WT) (from -9.24 to -9.75 kcal/mol) and the secondary mutant EGFR(T790M) (from -9.28 to -9.64 kcal/mol) observed in most cancer recurrence cases indicates its good potential to overcome drug resistance in cancer therapy. In addition, the pharmacological properties of the investigated pentapeptides were revealed by in silico ADME (Absorption, Distribution, Metabolism, Excretion) and toxicity analysis. Communicated by Ramaswamy H. SarmaPublication Molecular Modeling, DFT Quantum Chemical Analysis, and Molecular Docking on Edotecarin, an Indolocarbazole Anticancer Agent(Taylor & Francis Ltd., 2022) Çelik, Sefa; AKYÜZ, SEVİM; Özel, Ayşen E.Edotecarin is an indolocarbazole class antitumor agent that has significant anticancer effects against various types of cancer, especially lung, breast, and stomach cancer.The conformation analysis of the edotecarin was performed using the PM3 method and six stable conformations were obtained.Afterwards the obtained lowest energy conformation was optimized at the DFT/B3LYP/6-31++G(d,p) level of theory. The vibrational wavenumbers, the highest occupied molecular orbital, the lowest unoccupied molecular orbital and molecular electrostatic potential of the most stable conformer of edotecarin were calculated at the DFT/B3LYP/6-31++G(d,p) level of theory.The molecular docking of the edotecarin molecule against DNA, Topoisomerase I, DNA-Topoisomerase I complex,alpha(5)beta(1) and alpha(IIb)beta(3) integrins were performed to reveal its binding modes and binding affinities.Publication A New Viewpoint to Schema Modes and Mode Domains Through Polyvagal Theory: Could Schema Modes Be Just a Way of Coping?(Springer, 2022) Karaosmanoğlu, Hasan Alp; ATEŞ, NİDA; Köse Karaca, Bahar; Aytaç, MertThe aim of this study is to investigate how the schema modes defined in Schema Theory group together and accordingly question the conceptualization of schema modes considering the theories combining evolutionary, neuroscientific, and psychological point of views in psychology literature. It was hypothesized that there would be differences in the categorization and conceptualization of schema modes conceptualized by Schema Theory based on Polyvagal Theory. The sample of the study consists of 2032 participants aged between 18 and 71 years old (M = 36.00, SD = 14.312) who applied to a psychotherapy center in Istanbul working with the approach of Schema Therapy. Short Schema Mode Inventory was applied to the participants. According to the results of the second-order factor analysis, compliant surrenderer, healthy adult, punitive parent, happy child, and detached protector modes were clustered in the first factor. Impulsive child, enraged child, condescending, and easily bored child modes were loaded under the second factor while demanding parent, detached self-soother, and status-seeking modes were loaded under the third factor. When the results were evaluated with respect to Polyvagal Theory, it was determined that the first factor represented the parasympathetic nervous system activation and consisted of schema modes that include surrender, freezing, and socialization responses while the second factor consisting of schema modes related to flight or fight responses represented the sympathetic nervous system activation. Moreover, the third factor consisted of the schema modes of the sympathetic nervous system, which included flight or fight responses with parasympathetic inhibition (vagal brake). The results were discussed in line with the literature.Publication Reduced False Memory in the Second Language of Turkish-English Bilinguals(Routledge Journals, Taylor & Francis Ltd., 2024) Sıtkı, Merve; Ikier, Simay; ŞENER, NİLÜFERIn the Deese-Roediger-McDermott (DRM) paradigm, studying a list of semantically related words leads to false memory for the critical non-studied word that is related to all the words in the study list. Previous studies questioning whether bilinguals are more prone to false memory in their first language (L1) or second language (L2) in the DRM paradigm revealed mixed results. The present study investigated the same question with Turkish-English bilinguals. The revised hierarchical model proposes that the link between the lexicon and the semantic system is weaker in L2 than in L1, suggesting that false memory in the DRM paradigm that relies on semantic relatedness would be higher in L1 than in L2. Furthermore, previous studies showed that L2 is more resistant to errors in decision-making when the two languages are dissimilar, but not when they are similar, and Turkish and English are historically distant and typologically dissimilar languages. We tested Turkish-English bilingual participants whose L1 is Turkish with Turkish and English DRM word lists that had similar prior norms for generating false recognition. In the recognition test, some of the studied items and the critical non-studied items were presented and participants identified the studied items. False recognition for the critical non-studied items was lower and correct recognition for studied items was higher in L2 than in L1. The results suggest that L2 is more resistant to false memory due to its weaker lexicon and semantic system associations, at least when the two languages spoken by the bilingual are dissimilar.Publication 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.Publication 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. SarmaPublication Synthesis, Antimicrobial Activity, Molecular Docking and ADMET Study of a Caprolactam-Glycine Cluster(Taylor & Francis Inc., 2021) Çelik, Sefa; Albayrak, Ali Tuğrul; AKYÜZ, SEVİM; Özel, Ayşen E.; Sığırcı, Belgi DirenDensity functional theory calculations were performed with DFT method using both b3lyp/6-311++G(d,p) and wb97xd/6-311++G(d,p) levels of theory to predict the molecular geometry, to evaluate the molecular electrostatic potential and frontier molecular orbitals of synthesized a new compound: caprolactam-glysine cluster (CL-Gly). Molecular docking study of the CL-Gly was carried out to clarify the interaction and the probable binding modes, between the title compound and DNA. The antibacterial activities of CL-Gly cluster against Gram-positive and Gram-negative bacteria was determined. In silico ADMET study was also performed for predicting pharmacokinetic and toxicity profile of the synthesized cluster which expressed good drug-like behavior and non-toxic nature. It was revealed that the compound has importance in drug discovery process. Communicated by Ramaswamy H. Sarm