[Electronic and spatial parameters of antiparallel and parallel double-stranded beta-structure of a protein and its...

Calculations of valerolactam and N-methylacetamide dimers by the method of molecular orbitals in CNDO/2H, MINDO/3, MINDO/3H, MNDO, MNDO/H, AM1, and PM3 approximations showed that the PM3 was the most suitable method for the description of geometrical and thermodynamic characteristics of hydrogen bonds between their amide groups. The calculation of the H-bound dimers of N-acetylalanine methylamide, which mimicked the beta structure of protein macromolecule, showed that the antiparallel conformation of the dimer is by 2.85 kcal/mol more stable than the parallel conformation. According to the data obtained by using the AM1 approximation, the parallel type dimer has the enhanced ability to transmit the electron disturbance along the chain of amide-amide hydrogen bonds. The formation of the complexes of the antiparallel and the parallel types lead to the increase of the H-bonding ability of the outer oxygen atom of the amide group in comparison with the monomer.