Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7148
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Article Host Isotope Effects on the Oxygen Local Vibrations in Cdte(IOP Publishing Ltd, 2023) Tarhan, Enver; Ramdas, Anant K.Strong absorption peak observed near 350 cm-1 in the infrared spectrum of CdTe is assigned to a localized vibrational mode of 16O impurity atoms at tellurium sites. In this work, we studied the nature of these vibrations in terms of the effect of isotopic mass variations in the nearest neighbor Cd atoms. We showed that Cd atoms with 8 stable natural isotopes of varying abundances cause the observed line shape in the observed localized vibrational absorption peak. To calculate the effect of isotopic mass variations, we used the XY4 molecular model, X being the impurity atom at a host Te atom site and Y's are various isotopes of the host Cd atoms. Corresponding frequencies of local modes were calculated for each possible combinations of neighboring Cd atoms. For an XY4 molecule with Td symmetry, only the triply degenerate Gamma 5 mode is infrared active. The energies of this mode are higher than those of the others. This mode is possible only when all neigboring Cd atoms are the same isotope. To simulate the absorption data, we used a dynamical matrix approach where a force constant is given for each of the bending and stretching potential energy terms. By diagonalization of the dynamical matrix we were able to fit the calculated spectrum to the data with a proper choice of the bending and stretching force constants. A good agreement with the experiment as well as reported force constants for other impurities in CdTe is obtained.Article Citation - WoS: 5Citation - Scopus: 5Non-Direct Sequence Ions in the Tandem Mass Spectrometry of Protonated Peptide Amides - an Energy-Resolved Study(American Chemical Society, 2013) Harrison, Alex G.; Taşoğlu, Çağdaş; Yalçın, TalatThe fragmentation reactions of the MH+ ions of Leu-enkephalin amide and a variety of heptapeptide amides have been studied in detail as a function of collision energy using a QqToF beam type mass spectrometer. The initial fragmentation of the protonated amides involves primarily formation of bn ions, including significant loss of NH3 from the MH+ ions. Further fragmentation of these bn ions occurs following macrocyclization/ring opening leading in many cases to bn ions with permuted sequences and, thus, to formation of non-direct sequence ions. The importance of these non-direct sequence ions increases markedly with increasing collision energy, making peptide sequence determination difficult, if not impossible, at higher collision energies. [Figure not available: see fulltext.]Article Citation - WoS: 1Citation - Scopus: 1Protonated Dipeptide Losses From B 5 and B 4 Ions of Side Chain Hydroxyl Group Containing Pentapeptides(American Chemical Society, 2013) Atik, Ahmet Emin; Yalçın, TalatIn this study, C-terminal protonated dipeptide eliminations were reported for both b 5 and b 4 ions of side chain hydroxyl group (-OH) containing pentapeptides. The study utilized the model C-terminal amidated pentapeptides having sequences of XGGFL and AXVYI, where X represents serine (S), threonine (T), glutamic acid (E), aspartic acid (D), or tyrosine (Y) residue. Upon low-energy collision-induced dissociation (CID) of XGGFL (where X = S, T, E, D, and Y) model peptide series, the ions at m/z 279 and 223 were observed as common fragments in all b 5 and b 4 ion (except b 4 ion of YGGFL) mass spectra, respectively. By contrast, peptides, namely SMeGGFL-NH2 and EOMeGGFL- NH2, did not show either the ion at m/z 279 or the ion at m/z 223. It is shown that the side chain hydroxyl group is required for the possible mechanism to take place that furnishes the protonated dipeptide loss from b 5 and b 4 ions. In addition, the ions at m/z 295 and 281 were detected as common fragments in all b 5 and b 4 ion (except b 4 ion of AYVYI) mass spectra, respectively, for AXVYI model peptide series. The MS4 experiments exhibited that the fragment ions at m/z 279, 223, 295, and 281 entirely reflect the same fragmentation behavior of [M + H]+ ion generated from commercial dipeptides FL-OH, GF-OH, YI-OH, and VY-OH. These novel eliminations reported here for b 5 and b 4 ions can be useful in assigning the correct and reliable peptide sequences for high-throughput proteomic studies. [Figure not available: see fulltext.]Article Citation - WoS: 119Citation - Scopus: 151Batch Removal of Aqueous Cu2+ Ions Using Nanoparticles of Zero-Valent Iron: a Study of the Capacity and Mechanism of Uptake(American Chemical Society, 2008) Karabelli, Duygu; Üzüm, Çağrı; Shahwan, Talal; Eroğlu, Ahmet Emin; Scott, Tom B.; Hallam, Keith R.; Lieberwirth, IngoIn this study, nZVI prepared by borohydride reduction was applied for the removal of Cu2+ ions under a variety of experimental conditions. The uptake experiments investigated the effects of initial concentration, contact time, pH, and repetitive loading on the extent of retardation of Cu2+ ions. Within the applied conditions, the sorbent demonstrated fast uptake kinetics and outstanding fixation abilities up to an initial Cu2+ concentration of 200.0 mg/L. Partitioning of Cu2+ ions between liquid and solid phases demonstrated an isotherm of L-type. Within the studied conditions, the capacity of uptake was found to be 250 mg of Cu2+ per g of nZVI. According to X-ray photoelectron spectroscopy (XPS) and X-ray diffraction (XRD) results, Cu2+ ions were sorbed primarily via a redox mechanism that resulted in the formation of Cu2O and Cu0. The contact of iron nanoparticles with aqueous media caused extensive formation of iron oxide. However, the material did not completely lose its removal capacity and was repeatedly applied at low concentrations for further uptake trials.