Master Degree / Yüksek Lisans Tezleri

Permanent URI for this collectionhttps://hdl.handle.net/11147/3008

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Access Right: Open AccessSubject: search.filters.subject.Density functional theory

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  • Master Thesis
    Synthesis and Nitrogen Doping of Graphene by Chemical Vapor Deposition
    (Izmir Institute of Technology, 2017) Yanılmaz, Alper; Çelebi, Cem; Adem, Umut
    Controllable carrier transport due to charged impurities in the graphene lattice is still lacking. Doping of graphene by foreign atoms leads to modify its band structure and electro chemical properties. Among numerous potential dopants, nitrogen (N2) is considered to be an excellent candidate to form strong valence bonds with carbon atoms, which would provide n or p-doping according to bonding character of charged-impurity atom. Exposure of graphene lattice to nitrogen gas leads to a change in the carrier concentration and opens a bandgap due to symmetry breaking. Furthermore, this seems to be an effective way to customize the properties of graphene and exploit its potential for various applications. This thesis focuses on the growth of graphene by low pressure chemical vapor deposition (LPCVD) and doping it with N2 by using N2 plasma treatment. Here, copper foil was used as the catalytic substrate to grow large area graphene at LPCVD system. The grown graphene was transferred onto SiO2, Au (111) and Sapphire substrates. The effect of different plasma time and power on doping process was investigated while keeping the N2 flow rates constant by using N2 plasma. The nitrogen doped graphene (N-graphene) was characterized via Raman Spectroscopy, X-ray photoelectron spectroscopy (XPS), scanning tunneling microscopy/spectroscopy (STM/STS), Kelvin probe force microscopy (KPFM). Raman mapping of N-graphene was also conducted to show the homogeneity of N2 incorporation into graphitic lattice. STM results were theoretically modelled by using density functional theory (DFT). Our results provide the opportunity to produce N-graphene with homogenous and effective doping which would be valuable in electronic and optoelectronic applications.
  • 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, Nuran
    Mass 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.