A theoretical study of the structure and electron density of the peptide bond

Abstract

We present a systematic study of the geometries and bond critical point electron densities of each of the 400 possible dipeptide structures. Equilibrium conformations for each of the dipeptides were located using the MMFF94 force field and the resultant geometries were further optimized using the B3LYP/6-311+G (d,p) method in the gas phase. We find that intramolecular hydrogen bonding is generally responsible for the observed conformations and that the peptide plane is significantly distorted in 15% of the compounds. The steric bulk of the amino acid side chains does not appear to be a significant contributor to the geometry about the peptide bond but rather the potential for hydrogen bonding determines the conformational preference. We also find that the electron density at the bond critical point ( ρ c ) of the peptide bond strongly correlates to the equilibrium bond length ( r e ) and that this relationship compares well with others reported for similar bond types. Using a power law relationship between ρ c and r e (i.e. ρ c = α r e - β ), we show that the regression coefficients ( α, β) for heteronuclear bonds may be estimated from those of homonuclear bonds.