Density functional theory and biomolecules: A study of glycine, alanine, and their oligopeptides

We present density functional (DF) calculations, using a pseudopotential scheme and plane waves as basis functions, for isolated molecules of the amino acids glycine and alanine, for small oligopeptides composed of glycine and alanine, and for periodic (infinite) polyalanine helices. We calculate relative energies and geometries for the low-lying isomers of glycine and alanine and for a variety of oligopeptide geometries using various DF formulations for electron exchange and correlation (LDA, PBE, BLYP, BP). Comparison is made with other theories and experiment where possible. The free molecule equilibrium geometries agree well with the limited experimental data and with post-Hartree-Fock (post-HF) calculations. The inclusion of gradient-corrected (nonlocal) functionals is essential when hydrogen bonds play a role in determining relative energies. This is especially true for hydrogen bonds of the type N ... H-O, which appear in two isomers of glycine and alanine. We obtain the most reliable results with BLYP, but the best compromise, with a considerably smaller cutoff energy, is PBE. For the polypeptides we find that the peptide bonds in the equilibrium,geometries are planar to high accuracy, with dihedral angles deviating from planarity by up to 15 degrees. The relative energies of the low-lying isomers of alanine dipeptide agree very well with post-HF calculations. The equilibrium structure of the polyalanine a helix is very well reproduced by our calculations.