Primordia : software para cálculos de reatividade e análise de estrutura eletrônica para biomoléculas

Abstract

Interactions at the molecular level are fundamental in biological processes. Understanding the correct role played by these involves the most appropriate theoretical treatment, which takes place through quantum chemistry methods. The central hypothesis of this thesis is about the ability to recover important molecular information from biological processes through the calculation of chemical-quantum molecular descriptors of biomolecules. For this, the PRIMoRDiA software was developed, with specific tools to deal with the particularities of the electronic structure of these molecular systems with many atoms, generation of scripts for the automation of statistical analyzes and visualization of these theoretical quantities, as well as an efficient implementation of code to handle the large volume of data produced by quantum chemistry packages. As an usability test of the modified descriptors, the reactivity roles of residues from the active sites of enzyme complexes were studied with PRIMoRDiA. As an application, the descriptors were successful in the theoretical characterization of enzymatic reaction paths, where the results and their interpretations are explored in this thesis. It was possible to observe that quantum descriptors can recover important information from simulations in biological processes from electronic structure methods with less computational demand, such as semiempirical ones. In addition, the program has already contributed and has been useful in several works, in which it was applied to studies of protein-ligand interaction and for analysis of the dependence of reactivity with different conformations of the Main Protease (MPro) of the SARS-CoV-2 virus.