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Öğe Biosorption of Rhodamine B dye from aqueous solution by Rhus coriaria L. plant: Equilibrium, kinetic, thermodynamic and DFT calculations(Elsevier, 2023) Çelik, Muhammed Safa; Akkuş Çetinus, Şenay; Yenidünya, Ali Fazıl; Çetinkaya, Serap; Tüzün, BurakWater-soluble basic rhodamine B (RhB) was adsorbed onto fruit powders of Rhus coriaria L. (Anacar- diaceae), sumac in batch reactions. Adsorption was optimized by employing concentration, pH, and time parameters. Experimental data were in accordance with the Freundlich isotherm, adsorption obeyed the pseudo-second-order kinetics, and thermodynamic parameters indicated that adsorption was exothermic, spontaneous, and chemical. Results were also evaluated by theoretical means: lowest Unoccupied Molec- ular Orbitals (LUMO), and the Highest Occupied Molecular Orbitals (HOMO). The HOMO energy values of the rhodamine B molecule had the highest activity with -3.3729 at the B3LYP level, -6.0361 at the HF level, and -4.3299 at the M062X level. In the calculations made, it was seen that the rhodamine B molecule has more electron density on the oxygen molecules. Taken together, the findings suggested that the dried fruit of the Rhus coriaria L. could be a useful biosorbent for the removal of dyes from aqueous media.Öğe Polymeric nanoparticles and their composites in corrosion inhibition(De Gruyter, 2023) Çelik, Muhammed Safa; Çetinkaya, Hüseyin Fatih; Çetinkaya, Serap; Tüzün, Gamze; Tüzün, BurakMetal hardware is inherently prone to corrosion. Substantial research has been undertaken to explore to supersede this challenge. Initially, paints, pigments and organic coatings were utilized to circumvent metal corrosion. Lately, polymer composites and nanocomposites have become favored anticorrosion agents, especially epoxy, polyethylene glycol, polyaniline and polystyrene. The future research on poly- mer nanocomposites has the potential to address the current challenges of metal corrosion.Öğe Prunus mahleb ağacının kök florasından izole edilen bacillus subtilis glukoamilazının saflaştırılması, LC-MS/MS analizi, karakterizasyonu ve sitotoksik değerlendirilmesi(Sivas Cumhuriyet Üniversitesi, 2024) Çelik, Muhammed Safa; Çetinkaya, Serap; Kapancık, SerkanBacillus subtilis'ten izole edilen ve amiloglukosidaz olarak da bilinen glukoamilaz enzimi, nişasta işlenmesinde önemli bir rol oynar. Bu enzim, amonyum sülfat çöktürmesi kullanılarak saflaştırıldı ve moleküler kütlesinin, SDS-PAGE yoluyla yaklaşık 65,2 kDa olduğu belirlendi. Saflaştırılmış numunede aktif glukoamilazın varlığı, zimogram analizi kullanılarak doğrulandı. Nano-Sıvı Kromatografi Kütle Spektrometrisi (nLC-MS/MS) analizi, glukoamilaz protein dizisinin %46'sını kapsayan peptidleri tanımladı; bu, enzimin kısmi karakterizasyonunu gösterir. Glukoamilaz aktivitesi için optimum pH ve sıcaklığın sırasıyla 6,0 ve 37°C olduğu bulundu. Substrat olarak çözünür nişasta kullanılarak kinetik parametreler hesaplandı: Km (yarı maksimum hızdaki substrat konsantrasyonu) 30,21 μM ve Vmax (maksimum reaksiyon hızı) 35,59 µmol mg protein⁻¹ min⁻¹ idi. Enzim, çözünebilir nişasta ile optimal aktivite göstererek nişasta hidrolizi konusundaki spesifikliğini vurguladı. Ek olarak, CaCl2 varlığında enzimatik aktivitenin arttığı, bu da kalsiyum iyonlarının olumlu bir etkisine işaret etmektedir. Saflaştırılmış glukoamilaz, nişasta işlemedeki geleneksel rolünün ötesinde potansiyel antikanser aktivitesi sergiledi. Bu, MCF-7 ve A549 hücre hatları üzerinde MTT yöntemi kullanılarak araştırıldı ve oldukça etkili biyoaktivite gösterdi.Öğe Purification and characterization of glucoamylase from Bacillus sp. isolated from root flora of Prunus mahaleb tree by LC-MS/MS analysis(Elsevier B.V., 2025) Çelik, Muhammed Safa; Kapancık, Serkan; Seyran, Esra; Çetinkaya, SerapGlucoamylases are enzymes that release free glucose by hydrolyzing consecutive α-1,4 bonds at the non-reducing ends of starch molecules. This enzyme was purified using ammonium sulfate precipitation, and its molecular mass was determined to be approximately 65.2 kDa via SDS-PAGE. Using zymogram analysis, the purified sample's active glucoamylase content was verified. Nano-Liquid Chromatography Mass Spectrometry (nLC-MS/MS) characterization identified peptides covering 46 % of the glucoamylase protein sequence, indicating partial characterization of the enzyme. It was found that the ideal pH and temperature for glucoamylase activity were 6.0 and 37 °C, respectively. Using soluble starch as a substrate, the kinetic parameters were calculated: the Km (substrate concentration at half-maximal velocity) was 30.21 μM, and the Vmax (maximum reaction velocity) was 35.59 μmol mg protein−1 min−1. The enzyme demonstrated optimal activity with soluble starch, highlighting its specificity for starch hydrolysis. Additionally, the enzymatic activity was enhanced in the presence of CaCl2, indicating a positive effect of calcium ions. Its optimal conditions and kinetic parameters provide valuable insights for its industrial and biomedical use. © 2025 Elsevier B.V.Öğe Removal of safranin O from wastewater using Streptomyces griseobrunneus dead biomass and in silico calculations(Springer, 2.07.2023) Çelik, Muhammed Safa; Kütük, Nurşah; Yenidünya, Ali Fazıl; Çetinkaya, Serap; Tüzün, BurakEnvironmental pollution with the dye produced by the textile industry causes a serious problem worldwide. The aim of the study is to use the environmentally friendly and low-cost Streptomyces griseobrunneus (S. griseus S15) dead cells for the adsorption of safranin O from aqueous milieu. Optimum retention was achieved with 200 mg/L safranin O and 25 g/L adsorbent at pH 9. Biosorption was found to better fit the Langmuir isotherm and PSO kinetics. The maximum biosorption (qmax) was 188.67 mg/g. The reaction between S. griseus S15 and safranin O was chemical, exothermic, and spontaneous. S. griseus S15 biomass was reusable. Molecules supposed to be involved in the process were investigated by using a Gauss- ian software program, calculations B3LYP, HF, and M06-2X, 6-31G, 6-31++G, and 6-31++G**. For molecular docking calculations, the affinity of safranin O molecule to various proteins was investigated. Finally, ADME/T was applied to gain an insight into the possible effects of safranin O on human health.Öğe Studies on pyrimidine derivatives(Nova Science Publishers, Inc., 2024) Çetinkaya, Hüseyin Fatih; Çelik, Muhammed Safa; Abbaszada, Nübar; Çetinkaya, Serap; Tüzün, BurakPyrimidine is a nitrogen-containing heterocyclic aromatic compound. Together with its derivatives it plays an expansive role in drug discovery studies. In the chemistry of biological systems, pyrimidine derivatives have engrossed interests as they formed the bases of therapeutic natural products. They are the building blocks of many natural compounds: antibiotics, liposaccharides, and vitamins, to name a few. Pyrimidine is used in heterocyclic drugs with antimicrobial, anti-inflammatory, antidiabetic, antiviral, anticancer, and antifungal activities. Hence, it also serves as a versatile tool in the theoretical development of heterocyclic chemistry and organic synthesis. This study attempted to cover various pyrimidine derivatives with powerful biological and pharmacological applications. © 2024 Nova Science Publishers, Inc. All rights reserved.
