Computational prediction of the protonation sites of Ac-Lys-(Ala)n-Lys-NH2 peptides through conceptual DFT descriptors

Abstract

Six density functionals (M11, M11L, MN12L, MN12SX, N12, and N12SX) in connection with the Def2TZVP basis set and the SMD solvation model (water as a solvent) have been assessed for the calculation of the molecular structure and properties of several peptides with the general formula Ac-Lys-(Ala)n-Lys-NH2, with n = 0 to 5. The chemical reactivity descriptors for these systems have been calculated through Conceptual density functional theory (DFT). The active sites for nucleophilic and electrophilic attacks have been chosen by relating them to the Fukui function indices, the condensed dual descriptor Df(r), and the electrophilic Parr functions. The results allowed the prediction of the protonation sites of the peptides and rendered a qualitative explanation of the difference in pKa of the two Lys groups.