Master Degree / Yüksek Lisans Tezleri
Permanent URI for this collectionhttps://hdl.handle.net/11147/3008
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Master Thesis A Computational Chemistry Study on the Interactions Between Hydrogenated Borophene and Amino Acids(Izmir Institute of Technology, 2022) Bozkurt, Yağmur; Elmacı Irmak, NuranIn this work, the adsorption behavior of hydrogenated borophene to amino acids was examined to provide its geometric and electronic structures information and to check whether hydrogenated borophenes’ potential can be used in new biosensor devices for amino acids or not. In the aspect of this thesis adsorption of 4 amino acids from different types of amino acid classes (acidic, basic, nonpolar, and polar) on hydrogenated borophene surfaces has been studied by computational chemistry methods. Electronic and geometric structures of B36H6 and its complexes with glycine, tyrosine, aspartic acid, and histidine were obtained by DFT calculations at B3LYP-D2 / 6-311G** level of theory. In the energetically most favorable configurations of complexes, amino acids approaching from the bottom of the B36H6 surface with a horizontal orientation (exception for histidine complexes) of amino acid was observed. The most reactive parts of the B36 structure (edges) have been stabilized with hydrogenation, the whole boron cluster became more stable and adsorption ability has fallen. It was found that hydrogenated borophene has indistinguishable electronic responses for each the amino acids studied in this thesis since the complexes exhibited nearly the same band gap. Thus, hydrogenated borophene shows no sensor ability to GLY, TYR, ASP, and HIS.Master Thesis Interactions Between Metal Surfaces and Sulfur-Containing Amino Acids(01. Izmir Institute of Technology, 2022) Çevlikli, Mustafa; Ataman, EvrenWith Covid-19 pandemic, the scientific studies over viruses gained a big acceleration. Some of these studies show that SARS-CoV-2 can infect through direct ways from a patient. Besides that, surfaces that are contaminated from adsorption of the virus can indirectly infect a person. Because of this, the studies on the interaction between viruses and environment is an important field on virus studies. Spike proteins which project out from protective structure called lipid bilayer and they are outmost elements of SARS-CoV-2 viruses. Spike proteins play a vital role on functions like viral entry to the host cell and attachment to the surfaces. Purpose of this study is to contribute to the existing knowledge about surface interaction of these proteins which have an important role on virus-surface interactions. Because of the complicated physical and chemical form of proteins, in this study, the interaction of amino acids, which are building block of proteins, with metal surfaces are investigated. 0.01M, 0.02M and 0.05M L-cysteine and L-methionine aqueous solution was dropped to the metals frequently used in daily life, chrome (Cr) and iron (Fe) polycrystalline substrates and left to dry out at room temperature and under atmospheric conditions. Since the water solubility of L-cystine is low, only a saturated solution of Lcystine was prepared and same process was applied. After, dried out samples were analyzed with x-ray photoelectron spectroscopy (XPS). Functional sulfur groups on L-cysteine/Cr, L-methionine/Cr and L-Methionine/Fe system stayed intact. On the other hand, sulfur atoms on L-Cysteine/Fe system oxidized and formed --SO x species. While all other systems behaved oppositely, the amount of protonated functional amino species ( ) on L-methionine/Fe system decreased relative to functional amino group () with increase in coverage. Due to surface amino acid interaction of L-methionine in different substrates, binding energy of sulfur on iron was measured 1 eV lower than on chromium. In L-cystine/Cr system, while disulfide bonds stayed intact, and functional groups were observed on the surface together.Master Thesis Investigation of Gas Phase Fragmentation Mechanism of Doubly Charged a Ions by Mass Spectrometry(Izmir Institute of Technology, 2019) Kızılkoca, Doğacan; Yalçın, Talat; Arslanoğlu, AlperThis dissertation presents studies of gas-phase fragmentation mechanism of doubly-charged a7 ions from basic amino acid containing model peptides under low-energy collision-induced dissociation (CID). The study includes three sets of C-terminal amidated model peptides which are alanine series containing basic amino acids (His – Arg – Lys). Position of His, Arg and Lys residue is varied from N-to-C terminal. Both positional effect and peptide sequence effect were examined for the fragmentation reactions of doubly-protonated a7 ions for these heptapeptides. The CID-MS4 mass spectra of doubly-protonated a7 ions have internal amino acid losses which provide an evidence for macrocyclization reaction. The proposed reaction mechanism involves production of doubly-charge a ions and charge-separation reaction of doubly-protonated a ions in the gas-phase which generates a protonated direct and non-direct a ion. All model peptides were also studied to understand behavior of doubly-protonated a ions better. Direct and non-direct sequence fragmentations which are singly or doubly protonated were observed for all studies. The reactions mechanisms were adjusted according to the results. In conclusions, the results presented in this dissertation can be used to elucidate the correct and reliable peptide sequences, and this improve protein identification strategies which is required for high-throughput proteomic studies.Master Thesis A Computational Study on the Structures and Proton Affinities of B3+ Ions; Peptide Mass Fragment Product(Izmir Institute of Technology, 2015) Boz, Seçkin; Elmacı Irmak, NuranMass spectrometry is the tool of choice during most of the proteomics studies to get amino acid sequence. However, unambiguously identifying amino acid sequence from mass spectra is not easy and straight forward task. Deeper understanding is needed to support both existing knowledge and develop newer models on dissociation patterns of protonated peptides and it will help to improve efficiency of current algorithms used in peptide identification. In this study, the structures of b3+ ions and their neutral forms were investigated by using computational methods. First, potential energy surface of b ions are scanned using molecular dynamics simulations and conformer samples are collected. Then, in order to reduce number of conformers, principal coordinate analysis was applied to find and select different structures within the sample. Selected conformers were optimized using density functional theory calculations. Proton affinities of b ions are determined by the energy difference between most stable conformers of the positively charged and neutral peptide fragments. Different amino acids were used to understand the role of side chain of amino acids on both structures and proton affinities of b3+ ions; XA2+ where X=N, H, C, Y, D, L and F. The results showed that, b3+ ions prefer to have linear oxazolone structure. However, in their neutral states, cyclic structures are relatively far more stable than linear isomers. Histidine display different behavior than other amino acids. Side chain of histidine holds protons and forms stable structures. The energies of cyclic and linear isomers of Histidine containing b ions are close to each other. Histidine containing peptide fragments have larger proton affinity comparing to others. Difference of proton affinities between linear and cyclic conformers varies based on amino acid used. This difference is lower than 10kcal/mol in histidine, asparagine and aspartic acid containing peptide fragments. There is no dramatic position preference of the X-amino acid for the N- or C- terminals or middle position with the exception of Asn and Asp (unlike the center) and Histidine which likes to be at C-terminal.