Computational elucidation of chemical transformations in biochemically active molecules: from NMR chemical shifts to reaction pathways

Szántó, Judit Katalin (2026): Computational elucidation of chemical transformations in biochemically active molecules: from NMR chemical shifts to reaction pathways. Dissertation, LMU München: Faculty of Chemistry and Pharmacy

Abstract

Conformational changes play a central role in biochemistry by enabling molecules to adopt structures required for their biological function. This thesis focuses on two particular cases in which conformational changes are crucial: enzymatic catalysis and azobenzenes as potential drug candidates. Enzymatic adenosine triphosphate (ATP) hydrolysis serves as a prime example of catalytic efficiency, as phosphate esters are chemically inert compounds characterized by a high kinetic barrier for hydrolysis. This high energy barrier ensures that molecules such as ATP can be transported throughout the cellular environment without undergoing spontaneous degradation, a property that makes ATP the energy currency of the human cell. Although biologically fundamental, the hydrolysis of ATP to yield adenosine diphosphate (ADP) and inorganic phosphate (Pi ) is mechanistically complex and can proceed through various pathways. In this thesis, ATP hydrolysis in the human p97 protein is investigated for the first time through molecular simulations that employ the wide methodological toolbox of theoretical chemistry. The first part of this thesis is methodology-focused and a computational framework is presented that links electronic structure to NMR observables predicted at distinct stages of the ATP hydrolysis reaction. While experimental chemists use NMR chemical shifts to obtain structural information, computational approaches follow the reverse route: the structure is the starting point and the chemical shift, which is highly sensitive to the electronic structure, is the result. Reliable chemical shift predictions therefore require a combination of methods that account for conformational diversity and solvent effects through molecular dynamics (MD) simulations together with accurate electronic structure methods. By validating the simulations against experimental data, structural features are identified that influence NMR chemical shifts, highlighting the importance of quantum mechanical (QM) methods in structural refinement. In the second part, an in-depth mechanistic study of ATP hydrolysis in p97 is presented. The link between electronic structure and catalytic function is explored, with the aim of identifying the amino acids involved in the process. It is shown that the “protagonist” of the reaction is a buried water molecule that is positioned by an asparagine residue optimally for the attack, while a glutamate acts as a base and accepts the proton. The findings reveal that the nucleophilic attack is the rate-limiting step of the reaction, and the proton transfer occurs with a negligible barrier. These results provide a structural explanation for existing mutational data, clarifying the catalytic strategy of p97. Finally, in a separate study, contributions to the design of new molecular photoswitches based on azobenzene scaffolds are presented. A comprehensive quantum chemical investigation combined with structure–property relationship analysis reveals how distinct substitution patterns influence the electronic and photophysical properties. These insights provide guidance for the design of red-shifted azobenzene-based photoswitches with characteristics tailored to specific applications. Overall, this thesis demonstrates that the complexities of enzymatic catalysis and molecular design can only be resolved through careful computational studies that both reproduce and rationalize experimental observables.

• Item Type: Theses (Dissertation, LMU Munich)
• Keywords: ATP hydrolysis, p97, AAA proteins, computational enzymology, NMR chemical shifts, QM/MM, reaction mechanism, azoswitches
• Subjects: 500 Natural sciences and mathematics; 500 Natural sciences and mathematics > 540 Chemistry and allied sciences
• Faculties: Faculty of Chemistry and Pharmacy
• Language: English
• Date of oral examination: 14. July 2026
• 1. Referee: Ochsenfeld, Christian
• Signature of the printed copy: 0001/UMC 32248