Chiral effects on helicity studied via the energy landscape of short (D, L)-alanine peptides

The homochirality of natural amino acids facilitates the formation of regular secondary structures such as alpha-helices and beta-sheets. Here, we study the relationship between chirality and backbone structure for the example of hexa-alanine. The most stable stereoisomers are identified through global optimisation. Further, the energy landscape, a database of connected low-energy local minima and transition points, is constructed for various neutral and zwitterionic stereoisomers of hexa-alanine. Three order parameters for partial helicity are applied and metric disconnectivity graphs are presented with partial helicity as a metric. We also apply the Zimm-Bragg model to derive average partial helicities for Ace-(L-Ala)(6)-NHMe, Ace-(D-Ala-L-Ala)(3)-NHMe, and Ace-(L-Ala)(3)-(D-Ala)(3)-NHMe from the database of local minima and compare with previous studies. (C) 2015 AIP Publishing LLC.