Relating circular dichroism to atomic structure by means of MD simulations and computed CD spectra with α-peptoids as an example

Abstract

Classical molecular dynamics simulations have been combined with quantum calculations of CD spectra in order to fruitfully relate the experimental CD spectra, not only to the overall conformation of chiral α-peptoids, but also to their structure at the atomic scale, including the dihedral feature of the backbone (ψ,φ) and the orientation of the chiral side-chain (χ1). These simulations have been performed up to the hexamer Ac-(stbe)₆-CO₂tBu. We have shown that the number of states has a significant impact on the shape of the spectrum below 215 nm. The number of states computed is also critical to simulate the spectra of long oligomers. While 10 to 20 states are sufficient to simulate the CD spectra of short oligomers, 100 states or more are mandatory to converge the CD spectral shape for longer oligomers. The conformational sampling and the analysis of the intramolecular interactions responsible for the specific folding of the objects have been jointly explored by means of Replica Exchange MD and DFT calculations.