Hierarchy of the non-covalent interactions in the alanine-based secondary structures. DFT study of the frequency shifts and electron-density features

摘要

The alanine (Ala)-based cluster models of C5, C7, and C10 H-bonds are studied at the DFT/B3LYP level. CPMD/BLYP simulations of the infinite polyalanine alpha-helix (C13 H-bond) and the two-stranded beta-sheets are performed. Combined use of frequency shifts and electron-density features enable us to detect and describe quantitatively the non-covalent interactions (H-bonds) defining the intrinsic properties of Ala-based secondary structures. The energies of the primary N-H center dot center dot center dot O H-bonds are decreasing in the following way: C13 > C5 >= C7 > C10. The energies of the secondary N-H center dot center dot center dot O, N-H center dot center dot center dot N, and H center dot center dot center dot H interactions are comparable to those of the primary H-bonds (similar to 4.5 kcal/mol). Side chain-backbone C-H... 0 interaction is found to be the weakest non-covalent interaction in the considered species. Its energy is similar to 0.5 kcal/mol in the infinite polyalanine alpha-helix. Quantum-topological electron-density analysis is found to be a powerful tool for the detection of secondary non-covalent interactions (C=O center dot center dot center dot H-C and H center dot center dot center dot H) and bifurcated H-bonds, while the frequency shift study is useful for the identification and characterization of primary or secondary H-bonds of the N-H center dot center dot center dot O type. Copyright (C) 2008 John Wiley & Sons, Ltd.