Chemistry / Kimya

Permanent URI for this collectionhttps://hdl.handle.net/11147/4072

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  • Article
    Citation - WoS: 5
    Citation - Scopus: 5
    Non-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, Talat
    The 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: 1
    Citation - Scopus: 1
    Protonated Dipeptide Losses From B 5 and B 4 Ions of Side Chain Hydroxyl Group Containing Pentapeptides
    (American Chemical Society, 2013) Atik, Ahmet Emin; Yalçın, Talat
    In 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: 119
    Citation - Scopus: 151
    Batch 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, Ingo
    In 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.