Abstract: In this study, the aqueous pKa for cationic amino acid of lysine in a peptide chain which composed of eight glycine molecule have been calculated. HF and B3LYP methods using the 6-31G(d) combined with solvation energies that were computed by the SCRF-(CPCM/UFF) continuum models as implemented in Gaussian 09 computational package. pKas were further calculated using two thermodynamic schemes, namely the direct method and the proton exchange method with the inclusion of solvent water molecule. The results of this research verify that the direct method is not suitable for computing pKa of the amino acids in a peptide chain, while the other scheme in the presence of water molecule significantly improved the pka in comparison to the experimental data. The combination of the proton exchange scheme and CPCM-UFF model performed. Because of the convergence problems, the inclusion of large numbers of water molecule, the computation procedure in the solvated model produces failed. Comparison between the pKa alpha-helix (α), beta-sheet (β) and random (R) structures of the studied proteins reveals that the strongest acidic character belongs to α, β and R, respectively at the HF and B3LYP levels of the theory which can be described according to natural bond orbital (NBO) and atom in molecule (AIM) analysis.

Keywords