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  • Küçük Resim
    Öğe
    Experimental and computational study of various chemical processes
    (2017) Özhan Kocakaya, Şafak; Pirinççioğlu, Necmettin
    Studying chemical processes are a very important but very difficult task, mainly those occurring in organisms. Understanding these processes at atomic level will assist scientists recognize and compact many major diseases. Computational modeling is one of the current tools employed in understanding of chemical rates, equilibria and molecular interactions. The aim of the thesis is to use experimental and computational techniques in investigation of some chemical processes, which may be relevant to biological interests. The first chapter of this thesis gives a brief introduction to computational techniques and methodologies applied in chemistry and biochemistry. The second chapter describes comparison of DFT and MP2 calculations in the study of effects of polar substitution on the activation barriers for internal rotation around the C-N bond in p-substituted nitrosobenzenes. The activation barriers for internal rotation were calculated using the density functional theory (DFT) and second-order Møller-Plesset (MP2) methods with 6-31+g(d) basis set. The activation barriers were well-correlated with Hammett sigma values and MP2 method produces better and comparable results with few available experimental values. In the third chapter a detail mechanistic study of polar substituted effects on the alkaline hydrolysis of substituted methyl benzoates using B3LYP/6-31+g(d) computational method in PCM solvents (water, methanol and acetonitril) is given. The results indicate that activation free energies and bond lengthes going from ground state to transition state for alkaline hydrolysis of methyl substituted benzoic acids are well-correlated with polar Hammett sigma constants and pKa?s of substituted benzoic acids. It was found that the PCM solvents did not have any significant effect on the free energy relationship. The fourth chapter examines the nonmode of complexation of an octacarboxylatedmethlresorcincalix[4]arene with acetate, benzoic hegzagonate, N-methylnikotinate and methyl isonicotinate. The binding free energies respectively, (?Ebind = -26.47, -27.82, -40.12, -363.76, -370.95, calculated by MM/PBSA and (?Ebind = -2.17, -7.22, -10.27, -15.15, -18.47, kcal/mol calculated by ONIOM (B3LYP/6-31+G*) methods. The results showed the host binds to charged guests via electrostatic interactions while it binds to neutral guests via van der Waals interactions. The calculated binding constants are consistent with previously found experimental results by kinetic method. In the fifth chapter experimental description is detailed for the mechanisms of aqueous bromine addition to disodium salts of citraconic and mesaconic acids. Product analysis by NMR and x-ray reveals that citraconate generates erythro ß-lactone and erythro bromohydrin with expected stereo with overall syn addition and regiochemistry forming CMe-Nu bond rather CH-Nu bond. Surprisingly, it also generates threo ß-lactone, which is the major product of the addition reaction of mesaconate with overall anti addition, a traceable amount of 2,3-dibromo acids with overall anti addition. However, the addition reaction of mesaconate yields the expected threo ß-lactone and threo bromohydrin with overall syn addition but also eryhtro bromohydrin with overall anti addition. It was found that the addition reactions of both free acids produce similar product composition. A rational mechanistic detail was proposed for the reactions. The final chapter gives insight at atomic level concerning the molecular recognition and discrimination properties of a chiral aza-15-crown-5 with methyl esters of alanine and valine hydrochloride salts. Enantiomeric discrimination of the host against salts was studied by 1H NMR titration. The binding free energies are calculated as -(?Ebind = 3.32, -3.53, -2.83,ve -2.89, experimental results; 260, 372, 116, 129 M- 1. The results indicated that the host binds and discriminates alanine salts better than valine salts. Enantiomeric discrimination factors are calculated as 17.36 ve 5.22 for alanin and valine salt pair, respectively. The molecular dynamics, MM/PBSA and ONIOM (B3LYP/6-31+G*) calculations are consistent with 1H NMR results.