Infrared spectroscopy of the alanine dipeptide analog in liquid water with DFT-MD. Direct evidence for P(II)/beta conformations.
Following our previous work [J. Phys. Chem. B. Lett., 2009, 113, 10059], DFT-based molecular dynamics (DFTMD) simulations of 2-Ala peptide (i.e. Ac-Ala-NHMe dialanine peptide analog with methyl group caps at the extremities) immersed in liquid water at room temperature are reported. Our goal here is the theoretical calculation of the infrared spectrum of aqueous 2-Ala, in order to provide a definitive understanding of the average conformation adopted by this peptide in the liquid phase, taking into account solute and solvent at the same theoretical level of representation. We find that the experimental Amide I-II band predominantly results from a mixture of partially unfolded P(II) and unfolded beta conformational equilibrium of aqueous 2-Ala at room temperature.
Gaigeot
Marie-Pierre
MP
Université d'Evry val d'Essonne, LAMBE UMR8587 Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, Blvd F. Mitterrand, Bât. Maupertuis, 91025 Evry, France. mgaigeot@univ-evry.fr
D000577:Amides / Q000737:chemistry; D004151:Dipeptides / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D009068:Movement; D017433:Protein Structure, Secondary; D058767:Protein Unfolding; D011789:Quantum Theory; D013055:Spectrophotometry, Infrared; D013696:Temperature; D014867:Water / Q000737:chemistry*
D000577:Amides; D004151:Dipeptides; D014867:Water; C002956:alanylalanine