Date

2022-8-26

Author

Göçer, Ayşe

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Estimating pKa of molecules with accurate, general, and efficient protocols is essen- tial for many applications, notably for proteins modelling. For example, although individual amino acids pKa is known in aqueous solutions, it might be changed in the protein environment and in general in a different environment. Desolvation, hydro- gen bonding, or charge charge interactions can cause such pKa shift, and it is often crucial to explain the bonding preferences of molecules during the chemical reaction. There are various ways to predict pKa values with approaches such as QM based, MM based, continuum based, and knowledge based methods. These approaches, however, tend to lack generality and are usually tailored to predict the pKa of certain classes of molecules only. Our aim is to identify a general electronic descriptor that would grasp the essence of what makes proton affinity vary from one molecule to another, and from one environment to another. Our protocol is based on descriptors initially designed to characterize topological changes in molecular electron density upon elec- tronic excitation. By repurposing these tools, we aim at exploring the reorganization of the electron density upon de-protonation to eventually rationalize the concept of pKa with clear-cut electronic descriptors that can be transferred to various molecular environments, i.e., from the gas phase to a protein interior.

Subject Keywords

pKa, quantum chemistry, ab-initio, acidity

URI

https://hdl.handle.net/11511/98674

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Graduate School of Natural and Applied Sciences, Thesis