Eur. Phys. J. D (2017) 71: 203
https://doi.org/10.1140/epjd/e2017-80187-5

Regular Article

Conformational landscape of isolated capped amino acids: on the nature of non-covalent interactions^*,**

¹ Departamento de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco-UPV/EHU, Barrio Sarriena s/n, 48940 Leioa, Spain
² Departamento de Química, Facultad de Ciencia y Tecnología, Universidad de La Rioja, Madre de Dios, 53, 26006 Logroño, Spain

^a e-mail: judith.millan@unirioja.es

Received: 17 March 2017
Received in final form: 19 May 2017
Published online: 3 August 2017

Abstract

The intramolecular interactions for isolated capped amino acids were investigated computationally by characterizing the conformers for selected amino acids with charged (arginine), polar (asparagine and glutamine), non-polar (alanine, valine and isoleucine), and aromatic (phenylalanine, tryptophan and tyrosine) side chains. The computational method applied combined a molecular mechanics conformational search (with an MMFFs forced field) followed by structural and vibrational density-functional calculations (M06-2X with a triple-ζ Pople’s basis set). The intramolecular forces in each amino acid were analyzed with the Non-Covalent Interactions (NCI) analysis. The results for the 15 most stable conformers studied showed that the structure of isolated capped amino acids resembles those found in proteins. In particular, the two most stable conformers of the nine amino acids investigated exhibit γ_L and β_L conformations with 7- and 5-membered rings, respectively, as a result of the balance between non-covalent interactions (hydrogen bonds and van der Waals).