An efficient method for calculating atomic charges of peptides and proteins from electronic populations

An efficient method is presented to calculate atomic charges of peptides and proteins derived from Mulliken electronic populations for terminally blocked amino acids (Ac-X-NHMe, X = any neutral or charged residue) calculated at the B3LYP/6-31G(d,p)//HF/6-31G(d,p) level of theory. This electronic population-derived atomic charges (EPAC) method is based on the geometry-dependent atomic charge (GDAC) method proposed by Cho et al. (J. Phys. Chem. B 2001, 105, 3624), in which atomic charges are calculated by using the partial equalization of atomic electronegativities with electronegativity parameters and damping factors given by interatomic distances between covalently bonded atoms in a molecule. The overall mean absolute difference (mad) and root-mean-square deviation (rmsd) between dipole moments micro(EPAC) and micro(B3LYP), obtained from EPAC charges and from B3LYP/6-31G(d,p) level calculations, respectively, for Ac-X-NHMe are estimated to be 0.38 and 0.59 D, respectively, for 26 representative conformations in the training set, and 0.54 and 0.79 D, respectively, for 172 representative conformations not used for parametrization. For Ac-(Ala)(n)-NHMe (n = 2-6), the EPAC method reasonably predicts the increase of the dipole moment with increase of the chain length, although the deviations from the micro(B3LYP) values are somewhat larger. For Ac-Ala-NHMe and Ac-(Ala)(3)-NHMe, the EPAC charge for a specific type of atom does not depend on its position in the sequence or on the length of the sequence. In addition, charge neutrality holds for any Ala residue of these two peptides. Thus, these results suggest that the EPAC charges derived from B3LYP/6-31G(d,p) Mulliken populations can be used reliably for conformational analysis of peptides and proteins.