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

Abstract

The alanine (Ala)-based cluster models of C5, C7, and CIO H-bonds are studied at the DFT/B3LYP level. CPMD/BLYP simulations of the infinite polyalanine a-helix (C13 H-bond) and the two-stranded β-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... O H-bonds are decreasing in the following way: C I3 > C5 >C7 > C IO. The energies of the secondary N-H O, N-H N, and H H interactions are comparable to those of the primary H-bonds ( 4.5 kcal/mol). Side chain- backbone C-H ■ O interaction is found to be the weakest non-covalent interaction in the considered species. Its energy is 0.5 kcal/mol in the infinite polyalanine a-helix. Quantum-topological electron-density analysis is found to be a powerful tool for the detection of secondary non-covalent interactions (C=0 H-C and H 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 O type. Copyright © 2008 John Wiley & Sons, Ltd.