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: 2Citation - Scopus: 2Tuning the Solid Phase Fluorescence Emission From Long Wavelength Visible To Near-Infrared in Oxazol-5 Derivatives: Structure–property Relationship, Theoretical and Experimental Studies(Springer, 2023) Nazlı, İbrahim Hanif; Yakalı, Gül; Topkaya, Derya; İzmirli, Merve; Uzun, Sema Demirci; Alp, SerapMost of the fluorescent molecules among organic π-conjugated materials show blue or green emission in the solid phase but few of them emit red-shifted visible and near-infrared light in the material science. To create molecules emitting for this feature, two π-conjugated oxazol-5-one derivatives containing donor (OCH3) and acceptor groups (NO2) were synthesized. Their optical and charge-transport properties were investigated through experimental and theoretical methods including the single crystal X-ray crystallography, Hirshfeld Surface Analysis, photophysical studies and Density Functional Theory (DFT), respectively. In addition, FT-IR, 1H-NMR, 13C-NMR spectroscopy, cyclic voltammetry (CV) measurements were performed. According to our results, both molecules may provide the significant pathway of development of long wavelength visible and red emissive features in solid phase with the aggregation induced enhanced emission (AIEE) properties particularly in the fields of OLEDs, optical communication, defence and bioimaging.Article Characterization of Yellow Patina on Stone Surfaces by Instrumental Analysis Including Libs(Taylor & Francis, 2022) Badur, Fulya; Aras, Nadir; Yalçın, Şerife; Böke, HasanYellow patina formed on the stone surfaces of historical buildings, monuments, and archaeological structures due to weathering is considered a value of the building in the conservation of cultural heritage studies. Although yellow patina layers can be easily distinguished on white marble surfaces, it is not possible to distinguish them on the yellow travertine surfaces with the naked eye. It should be taken into account in yellow travertines as well as marble surfaces before conservation treatments of the stone. In this study, mineralogical and chemical compositions and the thicknesses of yellow patina layers formed on yellow travertine and marble surfaces in Aizanoi, Aphrodisias, and Hierapolis archaeological sites in Turkey were analyzed in order to constitute a conservation approach in the archaeological sites. In this respect, XRD, FT-IR, SEM-EDX, and LIBS were used in the determination of compositions and thicknesses of yellow patina. Although LIBS analysis is a more convenient method to investigate patina layers on stone surfaces, this technique is not as well known as the others. Yellow patina layers contained calcium oxalate in the form of whewellite (CaC2O4.H2O). Their thicknesses were between 15 and 100 μm and should be protective against weathering on travertine and marble surfaces. Highlights LIBS analysis seems to be the most convenient micro-destructive method to estimate the thickness of the yellow patina layers on the marble and yellow travertine surfaces. The determination of the thickness of the yellow patina is critical to keep irreversible cleaning interventions, especially for the yellow travertines due to their similar colors. Yellow patina is mainly composed of calcium oxalate with clay minerals and organic compounds.Article Citation - WoS: 3Citation - Scopus: 3Structural and Functional Analyses of Gh51 Alpha-L of Geobacillus Vulcani Gs90 Reveal Crucial Residues for Catalytic Activity and Thermostability(Wiley, 2022) Sürmeli, Yusuf; Şanlı Mohamed, GülşahAlpha-L-arabinofuranosidase (Abf) is of big interest in various industrial areas. Directed evolution is a powerful strategy to identify significant residues underlying Abf properties. Here, six active variants from GH51 Abf of Geobacillus vulcani GS90 (GvAbf) by directed evolution were overproduced, extracted, and analyzed at biochemical and structural levels. According to the activity and thermostability results, the most-active and the least-active variants were found as GvAbf51 and GvAbf52, respectively. GvAbf63 variant was more active than parent GvAbf by 20% and less active than GvAbf51. Also, the highest thermostability belonged to GvAbf52 with 80% residual activity after 1 h. Comparative sequence and structure analyses revealed that GvAbf51 possessed L307S displacement. Thus, this study suggested that L307 residue may be critical for GvAbf activity. GvAbf63 had H30D, Q90H, and L307S displacements, and H30 was covalently bound to E29 catalytic residue. Thus, H30D may decrease the positive effect of L307S on GvAbf63 activity, preventing E29 action. Besides, GvAbf52 possessed S215N, L307S, H473P, and G476C substitutions and S215 was close to E175 (acid–base residue). S215N may partially disrupt E175 action. Overall effect of all substitutions in GvAbf52 may result in the formation of the C–C bond between C171 and C213 by becoming closer to each other.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: 35Citation - Scopus: 44Current Trends and Challenges in Point-Of Urinalysis of Biomarkers in Trace Amounts(Elsevier, 2022) Yeasmin, Sanjida; Ammanath, Gopal; Önder, Ahmet; Yan, Evelias; Yıldız, Ümit Hakan; Palaniappan, Alagappan; Liedberg, BoUrinalysis enables non-invasive point-of-care (POC) testing of numerous biomarkers at their physiological and elevated levels, obviating the need for sophisticated equipment or trained personnel. POC urinalysis is used to identify biomarkers that are rich in urine (greater than 1 μM), such as lactate, uric acid, glucose, ions, and adenosine. Urine also contains biomarkers such as small molecules, nucleic acids, neurotransmitters, and drugs in trace amounts (less than 1 μM). These biomarkers are of significant importance for health care monitoring, diagnosis of various disorders (cancer, metabolic diseases, etc.) and illicit drug control (cocaine, steroids, etc.). While POC detection of urinary biomarkers at higher concentration (μM to mM) levels is feasible, direct assaying of biomarkers in nM to fM levels is challenging, as assay responses are typically masked by interferences from the urine sample matrix. This report is a consolidated review of emerging trends and challenges in the POC urinalysis for detecting biomarkers that are less abundant in urine. The sensing mechanisms, analytical device fabrication, discrete and integrated sample pre-treatment procedures for POC assaying of urinary markers in trace amounts are elaborated. Subsequently, the utilization of smart data analytics for facilitating personalized urinalysis is presented. A comprehensive outlook on associated challenges in POC urinalysis of biomarkers in trace amounts is further provided, which would facilitate the advancement of POC urinalysis for a wide range of healthcare applications.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.
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