Chemistry / Kimya
Permanent URI for this collectionhttps://hdl.handle.net/11147/4072
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Article Citation - WoS: 2Citation - Scopus: 2Transition-Metal Direct C-H Arylation of Thiophene in Aqueous Media Via Potassium Peroxymonosulfate(John Wiley and Sons Inc., 2019) Özenler, Sezer; Kaya, Hakan; Elmacı, Nuran; Yıldız, Ümit HakanThis study covers the use of potassium peroxymonosulfate (PPS) which, is a mild and inexpensive catalyst, for direct coupling of C-H/C-H for water soluble thiophene. The 3-(4-methyl-3 '- thienyloxy)propyltriethylammonium bromide (M1) has been selected as model monomer that reacted PPS in 2.0, 0.20 and 0.020 monomer to PPS ratio. The reaction has been monitored via NMR spectroscopy revealing the monomer consumption and formation of dimers to tetramers as well as completion of reaction within 15 minutes. Resultant product is easily collected without tedious work up steps. The computational calculation has optimized the regularity of the coupling as head to tail, tail to tail, head to tail (HT-TT-HT) for tetramer. The regularity of tetramer which is further satisfied via NMR analysis showing emergence of new peaks at 3.56 and 4.48. The shifts in the UV maximum of reactive species have been monitored by absorbance spectroscopy showing time dependent red shift corresponds to growing from monomer to tetramers. The reaction has self-stopped due to low solubility of moderate condensates (higher than trimer), however further experiments have performed in water-organic mixtures showed great promises to obtain higher condensates.Article Citation - WoS: 15Citation - Scopus: 17Improved Activity of Alpha-L From Geobacillus Vulcani Gs90 by Directed Evolution: Investigation on Thermal and Alkaline Stability(John Wiley and Sons Inc., 2019) Sürmeli, Yusuf; İlgü, Hüseyin; Şanlı Mohamed, Gülşahalpha-L-Arabinofuranosidase (Abf) is a potential enzyme because of its synergistic effect with other hemicellulases in agro-industrial field. In this study, directed evolution was applied to Abf from Geobacillus vulcani GS90 (GvAbf) using one round error-prone PCR and constructed a library of 73 enzyme variants of GvAbf. The activity screening of the enzyme variants was performed on soluble protein extracts using p-nitrophenyl alpha-L-arabinofuranoside as substrate. Two high activity displaying variants (GvAbf L307S and GvAbf Q90H/L307S) were selected, purified, partially characterized, and structurally analyzed. The specific activities of both variants were almost 2.5-fold more than that of GvAbf. Both GvAbf variants also exhibited higher thermal stability but lower alkaline stability in reference to GvAbf. The structural analysis of GvAbf model indicated that two mutation sites Q90H and L307S in both GvAbf variants are located in TIM barrel domain, responsible for catalytic action in many Glycoside Hydrolase Families including GH51. The structure of GvAbf model displayed that the position of L307S mutation is closer to the catalytic residues of GvAbf compared with Q90H mutation and also L307S mutation is conserved in both variants of GvAbf. Therefore, it was hypothesized that L307S amino acid substitution may play a critical role in catalytic activity of GvAbf. (C) 2018 International Union of Biochemistry and Molecular Biology, Inc.Article Citation - WoS: 56Citation - Scopus: 55A Bodipy-Based Fluorescent Probe To Visually Detect Phosgene: Toward the Development of a Handheld Phosgene Detector(John Wiley and Sons Inc., 2018) Sayar, Melike; Karakuş, Erman; Güner, Tuğrul; Yıldız, Büşra; Yıldız, Ümit Hakan; Emrullahoğlu, MustafaA boron-dipyrromethene (BODIPY)-based fluorescent probe with a phosgene-specific reactive motif shows remarkable selectivity toward phosgene, in the presence of which the nonfluorescent dye rapidly transforms into a new structure and induces a fluorescent response clearly observable to the naked eye under ultraviolet light. Given that dynamic, a prototypical handheld phosgene detector with a promising sensing capability that expedites the detection of gaseous phosgene without sophisticated instrumentation was developed. The proposed method using the handheld detector involves a rapid response period suitable for issuing early warnings during emergency situations.Conference Object Determination of Aluminum Rolling Oil and Machinery Oil Residues on Finished Aluminum Sheet and Foil Using Elemental Analysis and Fourier Transform Infrared Spectroscopy Coupled With Multivariate Calibration(John Wiley and Sons Inc., 2014) İnanç Uçar, Özlem; Mollaoğlu Altuner, Hatice; Günyüz, Mert; Dündar, Mustafa Murat; Özdemir, DurmuşThe surface characteristics of rolled aluminum products such as sheets and foils are strongly affected by the particular rolling process and the type of aluminum rolling oil compositions. After the rolling process, coiled aluminum sheets and foils undergoes annealing to form desired crystal structure and remove the rolling oil residues. Depending on the time and the temperature that rolled aluminum exposed for annealing, rolling oil residues are mostly removed from the coiled aluminum products but if there is any contamination in rolling oil due to hydraulic and gearing parts of the rolling systems these heavier oils are not easily evaporates from the aluminum surfaces especially inner parts of the coiled aluminum sheets and foils. These rolling oil contaminants create serious problems for the some specific applications of these aluminum products in certain industries such as automotive and coating as remaining thin oil layer prevents proper painting and coating. Therefore, it is very crucial for the rolling industry to be able to monitor the heavy oil contamination on the rolled products and determine the source of these contaminants .In this study, it was aimed to develop a nondestructive infrared spectroscopic method combined with chemometric multivariate calibration techniques for the quantitative determination of rolling oil residues and contaminants on the rolled aluminum products. To be able to generate multivariate calibration methods, an industrial elemental analysis system was adopted for the quantitative determination of heavy oil contaminants on the rolled aluminum products and these were used as reference values for infrared analysis of the same samples. In addition, apart from conventional use of elemental analysis systems for the total organic analysis, the raw data (raw chromatogram) obtained from elemental analysis was used to directly generate multivariate calibration models for each contaminant by using synthetically contaminated surfaces as the calibration samples. The results promised that elemental analysis can be used not just for the total organic content but also specifically to determine amount of each contaminant on the aluminum surfaces, it is also, expected that infrared spectroscopy with grazing angle spectra collection accessories can be used for nondestructive analysis of these contaminants.s.Book Part Citation - Scopus: 1Mass Spectroscopy in Polymer Research(John Wiley and Sons Inc., 2012) Hacaloğlu, Jale; Yalçın, TalatMass spectrometers are currently available in numerous confi gurations with various ionization techniques and mass analyzers. For a specifi c polymer sample, an optimal choice should be done depending on the information sought. In practice, no single mass spectrometric technique can provide all necessary information for structural, compositional, and thermal and oxidative degradation characteristics of polymeric samples. The analyzer used determines the limits of the sensitivity and resolution and the mass range, whereas the type of ionization source specifi es the information that can be gained.Article Citation - WoS: 6Citation - Scopus: 7Utilization of Electrospun Polystyrene Membranes as a Preliminary Step for Rapid Diagnosis(John Wiley and Sons Inc., 2016) Işık, Tuğba; Horzum, Nesrin; Yıldız, Ümit Hakan; Liedberg, Bo; Demir, Mustafa MuammerRecent advances in clinical practice drive deoxyribonucleic acid (DNA) as an important class of biomarker. Monitoring the change in their concentration suggests the initiation and/or progression of various disorders. However, low quantity of DNA biomarkers in body fluids requires a delicate isolation methodology that provides efficient separation and easy handling. This study describes a newer-generation separation technology relying on electrospun fibers of sub-micrometer diameter of a commodity polymer for DNA biomarkers in simulative serum. Fibrous polystyrene membranes are prepared by electrospinning and they are subjected to post-modification with Au. The composite membranes may provide a convenient environment for the removal of bovine serum albumin (BSA) from BSA and DNA mixtures. The eluent can be used as an efficient tool for detection of DNA biomarkers associated with diagnosis of numerous life-threatening diseases.Article Citation - WoS: 24Citation - Scopus: 24A Ratiometric Fluorescent Probe for Gold and Mercury Ions(John Wiley and Sons Inc., 2015) Üçüncü, Muhammed; Karakuş, Erman; Emrullahoğlu, MustafaA fluorescent probe that displays a ratiometric fluorescence response towards gold and mercury ions has been devised. Emitting at a relatively longer wavelength, the conjugated form of the fluorescent dye transforms in the presence of the gold or mercury ions into a new dye, the molecular structure of which lacks the conjugation and consequently emits at a distinctly shorter wavelength. A fluorescent probe that displays a ratiometric fluorescence response towards gold and mercury ions has been devised. Emitting at a relatively longer wavelength, the conjugated form of the fluorescent dye transforms in the presence of the gold or mercury ions into a new dye (see figure).Article Citation - WoS: 47Citation - Scopus: 49Simultaneous Identification of Spectral Properties and Sizes of Multiple Particles in Solution With Subnanometer Resolution(John Wiley and Sons Inc., 2016) Karabudak, Engin; Brookes, Emre; Lesnyak, Vladimir; Gaponik, Nikolai; Eychmüller, Alexander; Walter, Johannes; Segets, Doris; Peukert, Wolfgang; Wohlleben, Wendel; Demeler, Borries; Cölfen, HelmutWe report an unsurpassed solution characterization technique based on analytical ultracentrifugation, which demonstrates exceptional potential for resolving particle sizes in solution with sub-nm resolution. We achieve this improvement in resolution by simultaneously measuring UV/Vis spectra while hydrodynamically separating individual components in the mixture. By equipping an analytical ultracentrifuge with a novel multi-wavelength detector, we are adding a new spectral discovery dimension to traditional hydrodynamic characterization, and amplify the information obtained by orders of magnitude. We demonstrate the power of this technique by characterizing unpurified CdTe nanoparticle samples, avoiding tedious and often impossible purification and fractionation of nanoparticles into apparently monodisperse fractions. With this approach, we have for the first time identified the pure spectral properties and band-gap positions of discrete species present in the CdTe mixture.Article Citation - WoS: 1Citation - Scopus: 1Specific Rearrangement Reactions of Acetylated Lysine Containing Peptide Bn (n=4-7) Ion Series(John Wiley and Sons Inc., 2014) Atik, Ahmet Emin; Hernandez, Oscar; Maitre, Philippe; Yalçın, TalatCharacterization of ε-N-acetylated lysine containing peptides, one of the most prominent post-translational modifications of proteins, is an important goal for tandem mass spectrometry experiments. A systematic study for the fragmentation reactions of b ions derived from ε-N-acetyllysine containing model octapeptides (KAcYAGFLVG and YAKAcGFLVG) has been examined in detail. Collision-induced dissociation (CID) mass spectra of bn (n=4-7) fragments of ε-N-acetylated lysine containing peptides are compared with those of N-terminal acetylated and doubly acetylated (both ε-N and N-terminal) peptides, as well as acetyl-free peptides. Both direct and nondirect fragments are observed for acetyl-free and singly acetylated (ε-N or N-terminal) peptides. In the case of ε-N-acetylated lysine containing peptides, however, specific fragment ions (m/z 309, 456, 569 and 668) are observed in CID mass spectra of bn (n=4-7) ions. The CID mass spectra of these four ions are shown to be identical to those of selected protonated C-terminal amidated peptides. On this basis, a new type of rearrangement chemistry is proposed to account for the formation of these fragment ions,which are specific for ε-N-acetylated lysine containing peptides. Consistent with the observation of nondirect fragments, it is proposed that the b ions undergo head-to-tail macrocyclization followed by ring opening. The proposed reaction pathway assumes that bn (n=4-7) of ε-N-acetylated lysine containing peptides has a tendency to place the KAc residue at the C-terminal position after macrocyclization/reopening mechanism. Then, following the loss of CO, it is proposed that the marker ions are the result of the loss of an acetyllysine imine as a neutral fragment.Article Citation - WoS: 13Citation - Scopus: 15In Vitro Evaluation of Doxorubicin-Incorporated Magnetic Albumin Nanospheres(John Wiley and Sons Inc., 2014) Zeybek, Ayça; Şanlı Mohamed, Gülşah; Ak, Güliz; Yılmaz, Habibe; Şanlıer, Şenay H.Magnetic albumin nanospheres that incorporate doxorubicin (M-DOX-BSA-NPs) were prepared previously by our research group to develop magnetically responsive drug carrier system. This nanocarrier was synthesized as a drug delivery system for targeted chemotherapy. In this work, cytotoxic effects of doxorubicin (DOX)-loaded/unloaded or magnetic/non-magnetic nanoparticles and free DOX against PC-3 cells and A549 cells were determined with the MTT test and the results were compared with each other. DOX-loaded magnetic albumin nanospheres (M-DOX-BSA-NPs) were found more cytotoxic than other formulations. The quantitative data obtained from flow cytometry analysis further verified the higher targeting and killing ability of M-DOX-BSA-NPs than free DOX on both of the cancer cell lines. Additionally, the results of cell cycle analysis have showed that M-DOX-BSA-NPs affected G1 and G2 phases. Finally, cell images were obtained using spin-disk confocal microscopy, and cellular uptake of M-DOX-BSA-NPs was visualized. The findings of this study suggest that M-DOX-BSA-NPs represent a potential doxorubicin delivery system for targeted drug transport into prostate and lung cancer cells. In this study, we found that M-DOX-BSA-NPs provide many advantages as targeted drug delivery, enhanced drug killing ability and bioavailability based on cytotoxicity, flow cytometry, and confocal microscopy image results.
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