2025/10/30 by Aydin, Sena, Andreichev, Valerii, Maragkoudakis, Pantelis +1
#Biological Physics (physics.bio-ph) #Chemical Physics (physics.chem-ph) #FOS: Physical sciences
paper · doi:10.48550/arxiv.2510.26145
Molecular dynamics simulations for tripeptides in the gas phase and in solution using empirical and machine-learned energy functions are presented. For cationic AAA a machine-learned potential energy surface (ML-PES) trained on MP2 reference data yields quantitative agreement with measured splittings of the amide-I vibrations. Experimental spectroscopy in solution reports a splitting of 25 cm-1 which compares with 20 cm-1 from ML/MM-MD simulations of AAA in explicit solvent. For the AMA tripeptide a ML-PES describing both, the zwitterionic and neutral form is trained and used to map out the accessible conformational space. Due to cyclization and H-bonding between the termini in neutral AMA the NH- and OH-stretch spectra are strongly red-shifted below 3000 cm-1. The present work demonstrates that meaningful MD simulations on the nanosecond time scale are feasible and provides insight into experiments.