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Hierarchy of the non‐covalent interactions in the alanine‐based secondary structures. DFT study of the frequency shifts and electron‐density features
Author(s) -
Vener M. V.,
Egorova A. N.,
Fomin D. P.,
Tsirelson V. G.
Publication year - 2009
Publication title -
journal of physical organic chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.325
H-Index - 66
eISSN - 1099-1395
pISSN - 0894-3230
DOI - 10.1002/poc.1445
Subject(s) - covalent bond , chemistry , crystallography , electron density , density functional theory , alanine , computational chemistry , protein secondary structure , cluster (spacecraft) , stereochemistry , electron , amino acid , organic chemistry , physics , biochemistry , quantum mechanics , computer science , programming language
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 α ‐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 NH $\cdots $ O H‐bonds are decreasing in the following way: C13 > C5 ≥ C7 > C10. The energies of the secondary NH $\cdots $ O, N−H $\cdots $ N, and H $\cdots $ H interactions are comparable to those of the primary H‐bonds (∼4.5 kcal/mol). Side chain–backbone CH $\cdots $ 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 α ‐helix. Quantum‐topological electron‐density analysis is found to be a powerful tool for the detection of secondary non‐covalent interactions (CO $\cdots $ HC and H $\cdots $ 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 NH $\cdots $ O type. Copyright © 2008 John Wiley & Sons, Ltd.