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: 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: 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.Article Citation - WoS: 7Citation - Scopus: 7Regio- and Stereo-Chemical Ring-Opening Reactions of the 2,3-Epoxy Alcohol Derivative With Nucleophiles: Explanation of the Structures and C-2 Selectivity Supported by Theoretical Computations(Elsevier, 2022) Gündoğdu, Özlem; Atalay, Abdurrahman; Çelebioğlu, Neslihan; Anıl, Barış; Şahin, Ertan; Şanlı Mohamed, Gülşah; Bozkaya, Uğur; Kara, YunusThe ring-opening reactions of (1aS,2S,6bR)-5-ethyl-2-hydroxyhexahydro-4H-oxireno[2,3-e]isoindole-4,6(5H)-dione were investigated under very mild and nonchelated conditions. C-2 selective ring-opening products were obtained with nucleophilic additions such as Cl−, Br− and N3−. The exact configuration of (3aS,4R,5R,6S,7aS)-5-chloro-2-ethyl-4,6-dihydroxyhexahydro-1H-isoindole-1,3(2H)-dione was determined by X-Ray diffraction analysis which was obtained from the reaction of epoxy alcohol with HCl. On the other hand, theoretical computations were carried out to explain the regioselectivity in the ring opening reaction of epoxy alcohols. The results showed that the ring-opening reaction of both epoxy alcohols proceeds in a kinetically controlled manner and regioselectivity occurs depending on the transition state.Article Citation - WoS: 3Citation - Scopus: 6Hybrid Photonic-Plasmonic Mode-Coupling Induced Enhancement of the Spontaneous Emission Rate of Cds/Cdse Quantum Emitters(Elsevier, 2022) Gökbulut, Belkıs; İnanç, Arda; Topçu, Gökhan; Özçelik, Serdar; Demir, Mustafa Muammern this paper, a hybrid photonic-plasmonic resonator, which comprises an electrospun polymer fiber with a micrometer diameter and a core/shell nanostructure with a gold nanoparticle core, is constructed to investigate the dynamics of the coupled spontaneous emission of CdS/CdSe quantum dots (QDs). The gold nanoparticle core; covered with a silica shell, anchored with individual CdS/CdSe QDs, is placed inside a hollow cylindrical nanocavity formed on the surface of the microfiber to enable integration of the optical mode with the plasmonic effect, which is induced by the localized surface plasmons of the metal nanoparticle being present in the vicinity of the dipoles. The spontaneous emission rate of the QDs, coupled into the hybrid photonic-plasmonic mode, is measured to enhance by a factor of 23 via a time-resolved experimental technique. This result suggests that the regeneration of the optical mode-field inside the photonic-plasmonic resonator through the interaction of the dipoles with the localized surface plasmons of a metal nanoparticle strongly enhances the density of the electromagnetic states of the quantum emitters to facilitate an enhanced spontaneous emission within the host medium of the proposed polymer based-photonic structure.Article Citation - WoS: 4Citation - Scopus: 5Cytotoxic and Apoptotic Effects of 1,2-Diborolanes With Strong Donor Substitutes on Human Cancer Cells(Elsevier, 2021) Şahin, Yüksel; Aslantürk, Özlem Sultan; Çelik, Tülay; Sevinçek, Resul; Aygün, Muhittin; Metin, Kubilay; Fırıncı, Erkan; Özgener, HüseyinIn recent years, boron compounds have become more common as chemotherapy agents against certain types of cancers. Along with the development of boron-based therapeutic agents have come investigations into the various cancers and biochemical and molecular mechanisms affected by boron compounds and the relationships between boron compounds and chemical protection against cancer. In this preliminary study, the effects of new 1,2-N-substituted-1,2-diborolane derivatives on types of breast and liver cancers were examined for the first time. Four were found to significantly affect the cell viabilities and mitochondrial membrane potential changes in MCF-7, HepG2 and Hep3B cancer cells. Each was prepared in n-hexane at various concentrations (5, 10, 25, 50, 75 and 100 µg/mL). Human peripheral blood lymphocytes were used as control cells. Compounds 1, 2, 3a, and 3b 1,2-diborolane derivatives selectively killed cancer cells, but compound 1 was cytotoxic in a concentration-dependent manner on HepG2 and Hep3B and only at concentrations of at least 75 µg/mL on MCF-7 cells. Compound 3a exhibited cytotoxic effect on lymphocytes at 75 and 100 µgmL-1 concentrations, but compounds 1, 2 and 3b, 3c and 3d have not possessed significant cytotoxic effect on lymphocytes. Compounds 3c and 3d have not possessed significant cytotoxic effects. Mitochondrial membrane potential assay results supported these findings. Our results reveal that 1,2-diborolane derivates have high cytotoxic and apoptotic activities on human hepatocarcinoma cells and are therefore potential candidates in the development of new drugs against liver cancer.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.