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Browsing Kimya by Author "Akın, Fatma Ahu."
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Item A computational approach to evaluate the pKa's of quinazoline derivatives(Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2022., 2022) Kıran, Melisa.; Akın, Fatma Ahu.; Aviyente, Viktorya.One of the most important constants in chemistry is the ionization (dissociation) constant (pKa). Estimating the pKa value(s) for a potential drug is critical, especially since computations are considerably less expensive than obtaining pKa values experi mentally. Nearly 68 % of ionized medicines are said to have weak bases [1]. As a first step in developing an efficient estimation methodology for the pKa of quinazoline and derivatives we studied three protocols. First one is based on the linear relationship between computed atomic charges of quinazoline and derivatives and the experimental pKa. Based on our observations, the optimum method for reproducing observed pKa’s is to compute NPA (Natural Population Analysis) atomic charge using the CPCM (Conductor Like Polarizable Continuum Model) at the M06L/6-311++G** level (R2 = 0.93). The experimental pKa of a collection of quinazoline and derivatives were compared to several Conceptual Density Functional Theory descriptors computed. The highest approximations were observed when employing the M06L/6-311++G** with the CPCM solvation model using water as a solvent. In the final part of our study, M06L/6-311++G** have been used, in combination with CPCM continuum solvent model, to calculate the aqueous pKa values of quinazoline derivatives by using an isodesmic reaction. Possible improvements to current methodology are suggested.Item Modelling of the binding of TRPV1 receptor to capsaicin, capsazepine and related agonists and antagonists(Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2019., 2019.) İnce, Büşra.; Akın, Fatma Ahu.Capsaicin is a natural compound found in hot pepper and is an agonist of the receptor protein TRPV1 (Transient Receptor Potential Vanilloid) in dorsal root ganglia. TRPV1 is responsible for pain and heat perception. Capsazepine is a synthetic compound and is the first known antagonist of TRPV1; it interferes with the binding of capsaicin to TRPV1 in order to prevent protein activation and the resulting pain sensation. In this study, multiple conformations of capsaicin and capsazepine are docked to the active site of TRPV1 protein with rigid docking by Autodock4 to find which conformations give the lowest binding energy. We also observe analog molecule results in similar conformation conditions. The consistency of the results is checked by comparison with analog molecule binding. Agonists like resiniferatoxin, gingerol, nonivamide, nordihydrocapsaicin, and 6-shogaol and antagonist; sb-366791 is chosen as the analog molecules. The docking results of gingerol, shogaol, dihydrocapsaicin, nonivamide, and sb366791 had similar binding energies. Nordihydrocapsaicin and resiniferatoxin gave better binding energies in their capsaicin-like conformations. In general, all analog molecules are observed to make more hydrogen bonds with the protein.Item The energy and effect of ionization on cluster formation and post ionization dynamics of energetic materials : a density functional study on (C3H6N6O6)2(Thesis (M.S.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2011., 2011.) Kıyak, Güven.; Akın, Fatma Ahu.In this work, structures and energetics of (C3H6N6O6)2 and [(C3H6N6O6)2]+ molecules have been investigated via computational chemistry methods. Using Density Functional Theory, the neutral and positively charged dimer structures of C3H6N6O6 have been calculated. The adiabatic and vertical ionization energies have been bracketed between 8 and 10 eV. The dominant dissociation pathways have been identified. Possibilities for further clustering have been investigated. A sum of 33 neutrals and 27 cations have been found. These structures coexist within an energy range of 30 kJ/mol. Cations are encountered in the form of charge-dipole complexes and proton-transfer complexes while the neutrals are brought together by long range dispersion forces.