Molecular orbital analysis of the effect of d- and l-alanyl residues on the glycine chirality within the tripeptide N-Ac-Ala-Gly[β]-Ala-NH-Me. An ab initio and DFT study

A conformational analysis of the tripeptide models, N-Ac-d-Ala-Gly[β]-l-Ala-NH-Me and N-Ac-l-Ala-Gly[β]-l-Ala-NH-Me, was carried out using ab initio Molecular Orbital (MO) computations at the RHF/6-31G(d) and B3LYP/6-31G(d) levels of theory. At both levels of theory, global and local minima on the Ramachandran potential energy surfaces (PES), E=f(φ1,ψ1) and E=f(φ3,ψ3), of the two systems associated with the possible 18 backbone orientations were geometries optimized. When a glycyl residue was sandwiched between two chiral amino acids such as alanyl residues, its Cα–HR and Cα–HS bond lengths were no longer equal but instead perturbed slightly; inducing a chirality on the glycyl residue. Depending on the respective conformations of the adjacent alanyl residues, the magnitude of the conformational impact was investigated in this article.