Phd Degree / Doktora

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  • Doctoral Thesis
    Molecular Modeling of Polyelectrolytes - Nucleotides / Nucleic Acids Interaction
    (01. Izmir Institute of Technology, 2022) Kıbrıs, Erman; Elmacı Irmak, Nuran
    In this thesis, poly- N, N, N-trimethyl-3-(4-methylthiophen-3-yl) oxy) propan-1-aminium force field parameters were generated via ffTK and CHARMM program to perform MD simulations. NBFIX parameters for the interactions of adenosine nucleotides and oligomer were also produced to improve simulations. The parameters were verified by comparing MM vs QM calculations, and simulated vs experimental UV/Vis spectra. Our results revealed that force field parameters obtained by CHARMM program can be applied successfully for the MD simulations of CPTs with different types of adenosine nucleotides (AMP, ADP, and ATP). Poly-(3-(2-((4-methylthiophen-3-yl) oxy) ethyl)-1-ethyl-4H-1λ4-imidazol-3-ium) and poly- N,N,N-trimethyl-6-((4-methylthiophen-3-yl) oxy) hexan-1-aminium are used for optical sensors, therefore parametrization and MD simulations for these compounds were performed to see the effect of nucleotides on the backbone structures of oligomers. Generally, increasing the phosphate group on nucleotides stretched out the backbone of structures, but the largest response was observed in the presence of ATP. The salt effect and temperature effect were also investigated on oligomer – nucleotide complexes. The increasing temperature shortened the backbone of the compounds, but not significant as experimentally. Addition of the monovalent or divalent cations do not affect linearity of oligomer structure in ATP medium for O3. However, O1 and O2 have a great respond to ATP with Mg2+, K+ and Ca2+ (most sensed) ions, O2 has almost no respond to ATP without these ions. Ca2+ is a key ion which regulates ATP production by mitochondria. O2 may take a part of a biosensor design to recognize ATP in the presence of Ca+2.