Molecular orbital calculations on the protonation of hydrogen-bonded formamide chains. Implications for peptides

We report density functional studies of the protonation of H-bonded formamide chains containing up to 10 monomeric units. These chains contain H bonds that are similar to those in peptides and proteins. All structures considered were completely geometrically optimized at the B3LYP/D95** level of calculation. The proton affinities of the chains are greatest at the terminal C=O oxygen atoms. They increase significantly with the length of the formamide chain from two to five formamides. Protonation of the terminal C=O of chains containing five or more formamides results in the transfer of the N-H proton of the terminal (protonated) monomer across the H bond to the adjacent formamide. Protonations at the NH2 termini of the formamide chains are generally unfavorable as they result in the rupture of the proximate H bond. The proton affinities at the C=O's of formamide chains containing three or more monomers exceed that of the amino group of glycine, implying that peptides that contain such H-bonding chains might be preferentially protonated on a C=O rather than a terminal amino group, in contrast to small oligopeptides where H-bonding chains do not form. The quasi-linear relationship between H-bond strength and length clearly does not hold for the protonated chains. The implications for studies on peptides are discussed.