Chemistry / Kimya
Permanent URI for this collectionhttps://hdl.handle.net/11147/4072
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Article Citation - WoS: 3Citation - Scopus: 41,2-Diboranes With Strong Donor Substitutes: Synthesis, Ovicidal and Larvicidal Effect on Important Vector Species(Elsevier, 2024) Bursali, Fatma; Sahin, Yueksel; Aygun, Muhittin; Sevincek, Resul; Biyik, H. Halil; Özgener, Hüseyin; Gurbuz, BurcinNovel control products are needed in the control of important insects like mosquitoes which are developing resistance to insecticides and larvicides currently in the market. Boron compounds have been demonstrated to exhibit antibacterial and anticancer effects. 1,2-diboranes with a long history and importance in boron chemistry have been described. These compounds are synthesized from reactions of 1,2-dichlordiborane derivatives with lidium amides (ArNHLi/Et2NLi, etc.). In addition to the three previously synthesized diborane compounds, five novel 1,2-diborane compounds were synthesized in good yield using the same method for the first time. The structures of the novel derivatives were characterized by nuclear magnetic resonance spectroscopy, and the molecular structure of one of them (2a) was also demonstrated using single crystal X-ray diffraction. In this preliminary study, the ovicidal and larvicidal effects of new 1,2-diamino-1,2-diborane derivatives against Aedes aegypti and Aedes albopictus eggs and larvae were investigated for the first time. Of these, 2a and 2e showed the highest ovicidal activity against both species, while 7, 4 and 2d showed particularly high larvicidal activity. Some 1,2-diborane derivatives were found to be significantly toxic, with LC50 values ranging from 14,930 to 27,975 mu g/mL. Some derivatives (6, 2a, 2c) were less effective against mosquito larvae. 1,2-Diborane derivatives have high ovicidal and larvicidal effects on mosquitoes and are therefore potential candidates for the development of new larvicides. Further studies are needed to evaluate its mode of action and safety. Understanding their mode of action against mosquito development is crucial to optimizing their use and reducing the potential development of resistance. Their potential effects on other mosquito species and non -target organisms need to be investigated.Article Citation - Scopus: 3Development of Chrono-Spectral Gold Nanoparticle Growth Based Plasmonic Biosensor Platform(Elsevier, 2024) Sözmen, Alper Baran; Elveren, Beste; Erdoğan, Duygu; Mezgil, Bahadır; Baştanlar, Yalın; Yıldız, Ümit Hakan; Arslan Yıldız, AhuPlasmonic sensor platforms are designed for rapid, label-free, and real-time detection and they excel as the next generation biosensors. However, current methods such as Surface Plasmon Resonance require expertise and well-equipped laboratory facilities. Simpler methods such as Localized Surface Plasmon Resonance (LSPR) overcome those limitations, though they lack sensitivity. Hence, sensitivity enhancement plays a crucial role in the future of plasmonic sensor platforms. Herein, a refractive index (RI) sensitivity enhancement methodology is reported utilizing growth of gold nanoparticles (GNPs) on solid support and it is backed up with artificial neural network (ANN) analysis. Sensor platform fabrication was initiated with GNP immobilization onto solid support; immobilized GNPs were then used as seeds for chrono-spectral growth, which was carried out using NH2OH at varied incubation times. The response to RI change of the platform was investigated with varied concentrations of sucrose and ethanol. The detection of bacteria E.coli BL21 was carried out for validation as a model microorganism and results showed that detection was possible at 102 CFU/ml. The data acquired by spectrophotometric measurements were analyzed by ANN and bacteria classification with percentage error rates near 0% was achieved. The proposed LSPR-based, label-free sensor application proved that the developed methodology promises utile sensitivity enhancement potential for similar sensor platforms. © 2024 The Author(s)Article Citation - WoS: 1Citation - Scopus: 1The Soft Nanodots as Fluorescent Probes for Cell Imaging: Analysis of Cell and Spheroid Penetration Behavior of Single Chain Polymer Dots(Wiley, 2024) Yücel, Müge; Onbaş, Rabia; Arslan Yıldız, Ahu; Yıldız, Ümit HakanThis study describes the formation, size control, and penetration behavior of polymer nanodots (Pdots) consisting of single or few chain polythiophene-based conjugated polyelectrolytes (CPEs) via nanophase separation between good solvent and poor solvent of CPE. Though the chain singularity may be associated with dilution nanophase separation suggests that molecules of a good solvent create a thermodynamically driven solvation layer surrounding the CPEs and thereby separating the single chains even in their poor solvents. This statement is therefore corroborated with emission intensity/lifetime, particle size, and scattering intensity of polyelectrolyte in good and poor solvents. Regarding the augmented features, Pdots are implemented into cell imaging studies to understand the nuclear penetration and to differentiate the invasive characteristics of breast cancer cells. The python based red, green, blue (RGB) color analysis depicts that Pdots have more nuclear penetration ability in triple negative breast cancer cells due to the different nuclear morphology in shape and composition and Pdots have penetrated cell membrane as well as extracellular matrix in spheroid models. The current Pdot protocol and its utilization in cancer cell imaging are holding great promise for gene/drug delivery to target cancer cells by explicitly achieving the very first priority of nuclear intake. The penetration capability of cationic soft nanodots in to tumor models of breast cancer is demonstrated. The image analysis based on fluorescence intensity variation reveals the characteristics of translocation of nanodots in dense mediums such as tumor models.imageArticle Citation - WoS: 13Citation - Scopus: 13Design, Fabrication, and Application of Micro-Structured Surfaces for Laser-Induced Breakdown Spectroscopic Analysis of Liquids: a Sample-Loading Target Development Studies(Elsevier, 2024) Kaplan, Dilara; Aras, Nadir; Yalcin, SerifeIn this paper, design, fabrication, and application studies of a sample loading target patterned with periodical micro-structures were presented. Two different geometrical shapes; triangular prisms and cylinders of two different feature sizes; 5-mu m, and 20-mu m, were photo-lithographically patterned on Si-wafer substrates, and dry etched to 10 mu m height. Followed by a 1-mu m thick silicon nitride film coating over micro-patterned substrates, final products were obtained after dicing into one-inch size squares, each containing 36 patterned sample loading areas. Among the three different patterns studied; a geometric design with 20-mu m diameter cylinders exhibited a more effective task in increasing the LIBS signal strength, compared to the other two patterns. The characterization of the surface morphology and the size-shape distribution of the micro-patterns were carried out through optical and scanning electron microscopic measurements. SEM images proved a more effective ablation occur-ring on triangular prism micro-structured surfaces that can be associated with an increased path length and enhanced absorption of the laser beam on the flat surfaces of triangular prism via multiple reflections. The results of structured surfaces were also compared with the ones from non-structured surfaces of 300 nm and 1000 nm thicknesses of silicon nitride-coating. The applications of micro-structured surfaces for heavy metals analysis were performed with Cr and Pb solutions via dried-droplet LIBS methodology. The enhancement factor of 4 for Pb(I) 405.8 nm, and 8 for Cr(I) 428.9 nm were observed from the 20-mu m diameter cylinder, CYL-20, surfaces compared to 300 nm thick Si3N4 surfaces, respectively. This study of micro-structuring substrate surfaces with an emphasis on the signal enhancement effect is promising in terms of improving the capacity and limitations of the dried-droplet methodology by LIBS.Article Citation - Scopus: 1A Perspective on the State-Of Functionalized 2d Materials(American Institute of Physics, 2023) Duran, Tuna; Yayak, Yankı Öncü; Aydın, Hasan; Peeters, François M.; Yağmurcukardeş, MehmetTwo-dimensional (2D) ultra-thin materials are more crucial than their bulk counterparts for the covalent functionalization of their surface owing to atomic thinness, large surface-to-volume ratio, and high reactivity of surface atoms having unoccupied orbitals. Since the surface of a 2D material is composed of atoms having unoccupied orbitals, covalent functionalization enables one to improve or precisely modify the properties of the ultra-thin materials. Chemical functionalization of 2D materials not only modifies their intrinsic properties but also makes them adapted for nanotechnology applications. Such engineered materials have been used in many different applications with their improved properties. In the present Perspective, we begin with a brief history of functionalization followed by the introduction of functionalized 2D materials. Our Perspective is composed of the following sections: the applications areas of 2D graphene and graphene oxide crystals, transition metal dichalcogenides, and in-plane anisotropic black phosphorus, all of which have been widely used in different nanotechnology applications. Finally, our Perspectives on the future directions of applications of functionalized 2D materials are given. The present Perspective sheds light on the current progress in nanotechnological applications of engineered 2D materials through surface functionalization. © 2023 Author(s).Editorial Citation - WoS: 1Citation - Scopus: 1Editorial: Biomaterial Applications in Soft Tissue Engineering and Replacement(Frontiers Media S.A., 2023) Hornyak, Istvan; Jedlovszky-Hajdu, Angela; Kehr, SedaThe research related to the application of biomaterials encompasses a large area within the field of tissue engineering and regenerative medicine (TERM), and this Research Topic was dedicated to the versatile possibilities in the use of biomaterials. The sum of 10 manuscripts were submitted to this Research Topic and six were selected for this Research Topic with the contribution of 35 authors, Four of the accepted manuscripts were original research articles and two were review articlesArticle Citation - WoS: 9Citation - Scopus: 8Quantitative Determination of Phenolic Compounds in Propolis Samples From the Black Sea Region (türkiye) Based on Hptlc Images Using Partial Least Squares and Genetic Inverse Least Squares Methods(Elsevier, 2023) Güzelmeriç, Etil; Özdemir, Durmuş; Şen, Nisa Beril; Çelik, Cansel; Yeşilada, ErdemThe complex chemical composition of propolis is related to the plant source to be used by honeybees. Propolis type is defined based on the plant source with the highest proportion in its composition, which is determined by chromatographic techniques as high-performance thin-layer chromatography (HPTLC). In addition to marker component identification to specify the propolis type, quantification of its proportion is also significant for prediction and reproducible pharmacological activity. One drawback for propolis marker component quantita-tion is that during the chromatographical analysis, not the main but the other plant sources with less proportion may cause interferences during the chemical analysis. In this study, the amounts of marker components were compared with the reference analysis data obtained by high-performance liquid chromatography (HPLC) and from HPTLC images using Partial Least Squares (PLS) and Genetic Inverse Least Squares (GILS) regression methods. Firstly, HPTLC images of propolis samples were processed by an image algorithm (developed in MATLAB) where the bands of each standard and the samples were cut same dimensional pieces as 351 x 26 pixels in height and width, respectively. Simultaneously, reference analysis of the marker components in propolis samples was performed with a validated HPLC method. Consequently, the reference values obtained from HPLC versus PLS, and GILS predicted values of the eight compounds based on the digitized HPTLC images of the chromatograms were found to be matched successfully. The results of the multivariate calibration models demonstrated that HPTLC images could be used quantitatively for quality control of propolis used as a food supplement.Article Molecular Dynamics Simulation of Ssdna and Cationic Polythiophene(Elsevier, 2023) Nalıncı Bardak, Nehir; Kıbrıs, Erman; Demirci, Fethi Can; Elmacı Irmak, NuranIn this work, molecular dynamics simulations of complexes composed of single strand DNA (ssDNA) sequences and cationic oligothiophenes are performed to understand experimental findings and the sensing ability of polythiophene electrolytes toward ssDNA. The simulation results exhibit no significant structural effect for replacing the cationic amine moiety with imidazole derivative on the side group of the oligomer. Adding a homopurine strand elongates the oligomer backbone; on the contrary, mixing up the homopyrimidine strand causes compression. On the other hand, these ssDNAs do not notably affect the compactness of the oligomer backbones. The anion-cation interactions play an essential role in the structural and spectroscopic change of cationic polythiophenes (CPTs) upon complexation with ssDNAs. The red shift of CPTs in the UV-VIS spectra with the addition of homopurine strands might be explained by the strong anion-cation, weak pi -cation interactions, and high binding affinities. Nonpolar interactions (vdW and SA) and complex solvation energies dominate binding free energies. Hydrogen interaction analyses show that oligomers most likely approach the ssDNAs from their backbone upon complexation except for the duplex containing homopyrimidine strand and oligothiophene possessing imidazole derivative side chain.Article Citation - WoS: 2Citation - Scopus: 4Identification of Turkish Extra Virgin Olive Oils Produced in Different Regions by Using Nmr (h-1 and C-13) and Irms (c-13/C-12)(Wiley, 2023) Sevim, Didar; Köseoğlu, Oya; Ertaş, Hasan; Özdemir, Durmuş; Ulaş, Mehmet; Günnaz, Salih; Çelenk, Veysel UmutIsotope ratio mass spectroscopy (IRMS) and nuclear magnetic resonance (NMR) spectroscopy techniques are two of the analytical methods that are used to characterize food products. The aim of this study is to classify extra virgin olive oil (EVOO) samples collected from different regions of Turkey based on H-1 and C-13 NMR spectra along with IRMS d(13)C carbon isotope ratio data by using chemometrics multivariate data analysis methods. A total of 175 EVOO samples were analyzed in 2014/15 and 2015/16 harvest seasons. Multivariate classification and clustering models were used to identify geographical and botanical origins of the EVOOs. IRMS results showed that there was no significant difference in terms of d(13)C values between the years in terms of harvest year (p > 0.05), only extraction phase and variety were statistically significant factors (p < 0.05). The interactions of the factors showed that the harvest year x variety interaction is important. The outcomes of this research clearly indicated that considering the partial least squares discriminant analysis result with NMR spectra, the percent success of the model in the South Marmara, North Aegean, and South Aegean region samples were 95%, 95.7%, and 96.4% in the model set, respectively. The results showed that by using classification and clustering models, geographic marking and labeling of these oils can be carried out regardless of differences in year and production systems (2 and 3 phase extraction system) according the NMR analysis.Article Citation - WoS: 21Citation - Scopus: 23Engineering of Xylanases for the Development of Biotechnologically Important Characteristics(Wiley, 2023) Sürmeli, Yusuf; Şanlı Mohamed, GülşahXylanases are the main biocatalysts used for the reduction of the xylan backbone from hemicellulose, randomly splitting off β-1,4-glycosidic linkages between xylopyranosyl residues. Xylanase market has been annually estimated at 500 million US Dollars and they are potentially used in broad industrial process ranges such as paper pulp biobleaching, xylo-oligosaccharide production, and biofuel manufacture from lignocellulose. The highly stable xylanases are preferred in the downstream procedure of industrial processes because they can tolerate severe conditions. Almost all native xylanases can not endure adverse conditions thus they are industrially not proper to be utilized. Protein engineering is a powerful technology for developing xylanases, which can effectively work in adverse conditions and can meet requirements for industrial processes. This study considered state-of-the-art strategies of protein engineering for creating the xylanase gene diversity, high-throughput screening systems toward upgraded traits of the xylanases, and the prediction and comprehensive analysis of the target mutations in xylanases by in silico methods. Also, key molecular factors have been elucidated for industrial characteristics (alkaliphilic enhancement, thermal stability, and catalytic performance) of GH11 family xylanases. The present review explores industrial characteristics improved by directed evolution, rational design, and semi-rational design as protein engineering approaches for pulp bleaching process, xylooligosaccharides production, and biorefinery & bioenergy production.