Hydroxylic, sulfur-containing and amidic amino acids in water solution: atomic charges parameters for computational modeling using molecular dynamics simulation and DFT calculations

Abstract

In the present paper, we investigated the polarization effects on different amino acids (AAs) structures, i.e., Serine, Threonine, Cysteine, Methionine, Asparagine, and Glutamine. Initially, the AAs were modeled with CHARMM36 force field parameters and water molecules with TIP3P. Next, a polarization process was obtained from quantum calculations (using Density Functional Theory) of structures previously produced by simulations of Molecular Dynamics (MD) giving us improved values of the mean dipole moment and the new average atomic charges. Indeed, with these new values of the atomic charges we replace those ones used in previous MD-simulations and new MD-simulations stages are performed for each one of the structures under consideration. This process is repeated until the dipole moment and atomic charges presents a convergence. Finally, we analyze the hydrogen bonds, Coulombic and Lennard-Jones interaction energies, the mobility of AAs through the Einstein diffusion coefficient, nuclear magnetic resonance as well as the absorption spectrum. The results obtained for the improved (polarized) model are in full agreement with experimental results, which reinforces the feasibility of the present methodology.