Issue 35, 2010

Infrared spectroscopy of the alanine dipeptide analog in liquid water with DFT-MD. Direct evidence for PII/β conformations

Abstract

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 PII and unfolded β conformational equilibrium of aqueous 2-Ala at room temperature.

Graphical abstract: Infrared spectroscopy of the alanine dipeptide analog in liquid water with DFT-MD. Direct evidence for PII/β conformations

Article information

Article type
Paper
Submitted
23 Feb 2010
Accepted
14 Apr 2010
First published
10 Jun 2010

Phys. Chem. Chem. Phys., 2010,12, 10198-10209

Infrared spectroscopy of the alanine dipeptide analog in liquid water with DFT-MD. Direct evidence for PII/β conformations

M. Gaigeot, Phys. Chem. Chem. Phys., 2010, 12, 10198 DOI: 10.1039/C003485A

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