Abstract
It is extremely important to elucidate the formation mechanism of the secondary structure in polypeptides and proteins. This enables the stability of the three-dimensional structure of proteins to be predicted theoretically. For this purpose, the development of a precise structural calculation is indispensable. We computed the optimized structure of a poly( l-alanine) (PLA) molecule, H Ala 18 OH (C 54H 92N 18O 19), adopting a right-handed α-helix (α R-helix) conformation based on the molecular orbital calculation with density functional theory (DFT/6-31G(d)). As a result, we confirmed highly accurate conformational parameters characteristic to the “most acceptable α R-helix PLA” as follows; intrinsic dihedral angles ( ϕ, ψ, ω) = (−62°, −43°, 178°); hydrogen-bond distances R O…H = 0.205 nm and R O…N = 0.303 nm; hydrogen-bond angles ∠C O…H = 149°and ∠N H…O = 160°. Furthermore, we calculated the 1H, 13C, 15N and 17O nuclear shieldings of the optimized α R-helical H Ala 18 OH with the base set of DFT/6-311G(d,p), and demonstrated that the calculated isotropic 13C and 1H chemical shifts were identical with those measured by high-resolution solid-state NMR.
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