Free energy gradient for understanding the stability and properties of neutral and charged L-alanine molecule in water

Abstract

Amino acids exhibit their most important properties in aqueous environment in physiological conditions. These properties are related to their structural changes in water. Although several studies have been performed earlier for obtaining the structure of alanine in a solvent environment, an explicit consideration of the solvent molecular system is still in need. This work uses a Free Energy Gradient method to obtain the structures of alanine with an explicit consideration of the water environment. This is combined with a QM/MM method. Next, the electronic and vibrational properties of L-Alanine in water solution at different pH scales are obtained. The equilibrium structures of L-alanine are obtained in its neutral, anionic and cationic form. A systematic study of the solute-solvent hydrogen bonds was performed to predict the stability of neutral and charged L-alanine molecules. Quantum mechanical calculations were also performed to obtain the infrared spectrum, pH induced changes and to predict NMR parameters such as chemical shifts, magnetic shieldings and spin-spin coupling constants.