Simulação por dinâmica molecular de um modelo de DNA em meio aquoso

Abstract

Molecular Dynamics (MD) is a computational technique used to study chemical and biological systems at the atomic level. This work aimed to validate the physicochemical foundations of MD by evaluating how classical statistical mechanics represents the physiological environment. To this end, a simulation of a B-DNA dodecamer, the natural form of DNA in a physiological medium, for the d(CGCGATATCGCG) strand in aqueous solution was performed using the GROMACS software. The system was modeled with the AMBER99SB-ILDN force field and TIP3P explicit solvent. The simulation involved energy minimization, thermodynamic equilibration in the NVT and NPT ensembles, and trajectory acquisition. Solvent parameters agree with the literature for biological systems, although the solvent exhibits a high diffusion coefficient. The Root Mean Square Deviation (RMSD) indicated the stability of the double helix over time, without denaturation of the macromolecule. Additionally, the Radial Distribution Function (RDF) showed that Mg²⁺ ions concentrate around the phosphate groups of the nucleic acids at the center of the DNA, with an average distance of 0.38 nm. These values corroborate crystallographic data and quantum-mechanical calculations described in the literature. It is concluded that the adopted methodology validates the fundamental parameters of MD, reproduces the thermodynamic and ionic interactions of the cellular environment, and opens avenues for future hybrid Quantum Mechanics/Molecular Mechanics (QM/MM) studies.