Chemistry / Kimya
Permanent URI for this collectionhttps://hdl.handle.net/11147/4072
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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: 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.Article Citation - WoS: 49Citation - Scopus: 54Highly Porous Poly(o-Phenylenediamine) Loaded Magnetic Carboxymethyl Cellulose Hybrid Beads for Removal of Two Model Textile Dyes(Springer, 2022) Arıca, Tuğçe Aybüke; Balcı, Fadime Mert; Balcı, Sinan; Arıca, Mehmet YakupEnsuring the removal of complex dyes from wastewater is a topic of great interest as it is vital for the environment. The present study reports a facile preparation method for poly(o-phenylenediamine) [p(o-PDA)] micro-particles loaded to magnetic carboxymethyl cellulose (CMC) hydrogel beads as adsorbents. The prepared products were characterized by FTIR, TGA, VSM, SEM, BET, and zeta sizer. The Fe3O4@p(o-PDA)@CMC beads were used for the removal of Reactive Blue 4 (RB-4) and Congo Red (CR) textile dyes from an aqueous medium. Different factors, such as adsorbent dose, initial pH, ionic strength, contact time, temperatures, and initial RB-4 and CR concentrations were examined. The maximum adsorption capacities of the RB-4 dye and CR at optimum pH 5 reached 398.7 and 524.6 mg/g in 120 min, respectively. The adsorption of RB-4 and CR on the hybrid magnetic beads can be due to the electrostatic, hydrogen bonding, and π-π interactions. Moreover, the magnetic hybrid beads showed easy regeneration ability and good reusability. The adsorbent can be a very good candidate for the efficient removal of micro-pollutant from wastewater.Article Citation - WoS: 4Citation - Scopus: 4Identification of a Magnetic Phase Via a Raman Spectrum in Single-Layer Mnse: an Ab Initio Study(Elsevier, 2022) Yayak, Yankı Öncü; Şahin, Hasan; Yağmurcukardeş, MehmetMotivated by the recent experimental realization of single-layer two-dimensional MnSe [ACS Nano2021, 15, 13794-13802], structural, magnetic, elastic, vibrational, and electronic properties of single-layer MnSe are investigated by using density functional theory-based calculations. Among four different magnetic phases, namely, ferromagnetic (FM) and Nẽel-, zigzag-, and stripy-antiferromagnetic (AFM) phases, the Nẽel-AFM structure is found to be the energetically most favorable phase. Structural optimizations show the formation of in-plane anisotropy within the structures of zigzag- and stripy-AFM phases in single-layer MnSe. For the dynamically stable four magnetic phases, predicted Raman spectra reveal that each phase exhibits distinctive vibrational features and can be distinguished from each other. In addition, the elastic constants indicate the mechanical stability of each magnetic phase in single-layer MnSe and reveal the soft nature of each phase. Moreover, electronic band dispersion calculations show the indirect band gap semiconducting nature with varying electronic band gap energies for all magnetic phases. Furthermore, the atomic orbital-based density of states reveals the existence of out-of-plane orbitals dominating the top valence states in zigzag- and stripy-AFM phases, giving rise to the localized states. The stability of different magnetic phases and their distinct vibrational and electronic properties make single-layer MnSe a promising candidate for nanoelectronic and spintronic applications.Article Citation - WoS: 5Citation - Scopus: 5Structural Analysis of Hyperbranched Polyhydrocarbon Synthesized by Electrochemical Polymerization(Royal Society of Chemistry, 2022) Jiang, Yi; Kim, Minhyeok; Nam, Hyunju; Kwak, Sang Kyu; Ruoff, Rodney S.; Lee, Sun Hwa; Seo, Jae Hong; Shin, Eunhye; Joo, Se Hun; Büyükçakır, OnurWe describe a structural analysis method for a hyperbranched polyhydrocarbon (PHC) produced by electrochemical polymerization. Nuclear magnetic resonance (NMR) techniques including 1H-NMR, quantitative 13C-NMR, DEPT 13C-NMR, and 1H-13C HSQC 2D NMR along with elemental analysis and FTIR were used to experimentally assess the likely structure of this complex polymer with random branching. The polymer structure was modeled based on the NMR results. Room temperature density, refractive index, melting temperature, and IR spectrum were good matches to the values, and spectrum, calculated using the simulated structure. Calculated Hildebrand solubility parameters for the simulated structure rationalize the room temperature solubility measured in a range of solvents. The experimental and modeling methods are likely to be applicable to any type of highly branched random branching polymer. To the best of our knowledge, this is the first comprehensive elucidation of the structure of an unknown and randomly hyperbranched polymer by combining experimental results and theoretical simulation, and the methods described should find broad use in the future.Article Citation - WoS: 13Citation - Scopus: 15Effect of Silicon Nitride Coating Thickness on Silicon Wafer Substrates for Signal Enhancement in Laser-Induced Breakdown Spectroscopic Analysis of Liquids(Elsevier, 2022) Kaplan, Dilara; Yalçın, Şerife HanımIt has been shown by previous studies of our group that the use of nitride-coated silicon wafer surfaces as a sample loading substrate in dried-droplet LIBS analysis provided enhancement in plasma emission signal and better detection limits compared to uncoated or oxide-coated silicon wafer surfaces. To further investigate the effect of coating thickness for enhanced sensitivity in dried nano-droplet analysis of liquids, silicon-wafer substrates of different nitride coating thicknesses; 75, 300, 450, and 1000 nm, were comparatively studied. With 75 nm silicon nitride coating, the thin-film effect due to the anti-reflective behavior of the silicon nitride film is observed, and plasma emission signal is enhanced up to three times compared to 300 nm coated substrates. With coating thicknesses of 450 nm and 1000 nm, on the other hand, thermophysical and mechanical properties of the silicon nitride material, like thermal conductivity and hardness, become more dominant factors, leading to higher emission signals for all the elements studied. With 1000 nm coating thickness, enhancement factors of 4.8, 6.4, and 3.7 were obtained for the elements of Pb, Cu, and Cr, respectively. Optimization of the experimental LIBS parameters was conducted, calibration curves were constructed, and analytical figures of merits were determined. Sub-picogram amounts absolute detection limits; 0.7 pg Pb, 0.6 pg Cr, and 0.4 pg Cu, in 500 nanoliter droplets were obtained from the slopes of the calibration curves. The nitride-coated substrates' analytical performance was tested using certified reference solutions, standard water, and real water samples. The materials and the methodology developed can be used for waste-water monitoring of environmental samples by LIBS.Article Citation - WoS: 14Citation - Scopus: 19Influence of Carbon Nanotube Inclusions To Electrical, Thermal, Physical and Mechanical Behaviors of Carbon-Fiber Abs Composites(Springer, 2022) Akar, Alinda Öykü; Yıldız, Ümit Hakan; Tirkeş, Seha; Tayfun, Ümit; Hacıvelioğlu, FerdaAcrylonitrile–butadiene–styrene (ABS) terpolymer was compounded with short carbon fiber (CF) and carbon nanotube (CNT) using a micro-extruder followed by the injection molding process. Composite samples were fabricated with loading ratios of 20 wt.% CF and 0.1, 0.5 and 1.0 wt.% of CNT. Mechanical, electrical, thermo-mechanical, thermal, melt-flow, and structural investigations of ABS-based composites were conducted by performing tensile, impact, hardness, and wear tests, conductive atomic force microscopy (AFM), dynamic mechanical analysis (DMA), thermal gravimetric analysis (TGA), melt flow rate test (MFR), scanning electron microscopy (SEM) characterization techniques, respectively. According to mechanical test data of resultant composites including tensile and impact test findings, CNT additions led to the remarkable increase in tensile strength and impact resistance for CF reinforced ABS composites. The formation of synergy between CNT nanoparticles and CF was confirmed by electrical conduction results. The conductive path in ABS/CF composite system was achieved by the incorporation of CNT with different loading levels. SEM micrographs of composites proved that CNT nanoparticles exhibited homogeneous dispersion into ABS matrix for lower loadings. Graphical abstract: [Figure not available: see fulltext.].Article Citation - WoS: 4Citation - Scopus: 3Hg(ii)-Mediated Intramolecular Cyclization of Alkynyl Hydrazones: Towards a New Reaction-Based Sensing Approach for Hg(ii) Ions(Wiley, 2022) Tütüncü, Büşra Buse; Cebeci, Miray; Emrullahoğlu, MustafaDrawing upon an intramolecular cyclization/annulation reaction sequence mediated by Hg2+ ions, a BODIPY-based fluorescent probe decorated with an alkynyl hydrazone motif responds rapidly and selectively to Hg2+ ions, with a detection limit of 29 nM and a fluorescence turn-on ratio of 15-fold. With the addition of Hg2+ ions, the BODIPY-based alkynyl hydrazone transforms into a pyrazole ring to mediate a turn-on emission response clearly observable to the naked eye under visible light excitation.Article Citation - WoS: 3Citation - Scopus: 5Physically Unclonable Security Patterns Created by Electrospinning, and Authenticated by Two-Step Validation Method(IOP Publishing, 2022) Taşcıoğlu, Didem; Atçı, Arda; Sevim Ünlütürk, Seçil; Özçelik, SerdarCounterfeiting is a growing economic and social problem. For anticounterfeiting, random and inimitable droplet/fiber patterns were created by the electrospinning method as security tags that are detectable under UV light but invisible in daylight. To check the authenticity of the original security patterns created; images were collected with a simple smartphone microscope and a database of the recorded original patterns was created. The originality of the random patterns was checked by comparing them with the patterns recorded in the database. In addition, the spectral signature of the patterns in the droplet/fiber network was obtained with a simple and hand-held spectrometer. Thus, by reading the spectral signature from the pattern, the spectral information of the photoluminescent nanoparticles was verified and thus a second-step verification was established. In this way, anticounterfeiting technology that combines ink formula, unclonable security pattern creation and two-level verification is developed.Article Citation - WoS: 8Citation - Scopus: 11The Effect of Protein Bsa on the Stability of Lipophilic Drug (docetaxel)-Loaded Polymeric Micelles(Elsevier, 2021) Polat, Hürriyet; Çevik Eren, Merve; Polat, MehmetPolymeric micelles are promising delivery vehicles for improving the efficacy of anticancer drugs and reducing their side effects. However, considering the binding ability of serum albumin, the possible interaction of micelles with the native plasma components in the bloodstream raises serious questions on micellar stability. The stability of barren or drug-loaded copolymeric micelles was investigated systematically in distilled water (DW) and simulated body fluid (SBF) solutions in the presence of a model protein. The copolymer was a Pluronic® series triblock copolymer (P-123), the drug was strongly lipophilic docetaxel (DOC) and the protein was Bovine Serum Albumin (BSA). The effect of such factors as BSA and DOC concentrations and the aging of the micellar solutions was studied. Both the barren and drug-loaded micelles were quite stable in blank DW and SBF solutions for long times up to 10 days. They lost integrity and showed no inclination to re-assemble when the BSA concentration reached a critical value, which was very close to the plasma Human Serum Albumin (HSA) concentration. The presence of DOC in the micellar cores could not prevent disintegration. The results illustrate clearly that ensuring the stability of polymeric micelles in blood plasma should be an important design factor in their use as drug carriers.