The influence of flexibility on the spectroscopic properties for organic molecules in solution: a theoretical study applied to A3R polypeptide

Abstract

Here we reported the impact of flexibility of solvent effects on the optical absorption, nuclear magnetic resonance (NMR) and electrical properties of A3R, a tetrapeptide compound derived from peptide bonds in the α-helix form of 3-alanines and one arginine, in aqueous environment. The in-water A3R configurations were generated by S-MM/QM and MD procedures and also using the PCM model. We have used the ASEC approach with 100 uncorrelated settings obtained from Monte Carlo simulation to achieve the convergence of the dipole moment for each in-water geometry in all steps between MC and QM calculations. The converged values of μ for A3R-MD geometries present increments between 69 and 392% in comparison with the gas phase value. Our results for optical absorption demonstrate the possibility of absorption in large range, with strong dependence of the geometric conformation of the A3R molecule. Our findings corroborate both the importance of the solute polarization and the geometric flexibility in the analyzed properties. Spectroscopic results obtained experimentally for the σ(13C) indicates that our A3R-MD geometry calculations are consistent with the adopted model.