Computational investigation of uracil dimers in water and the role of classical potentials

Abstract

Nucleobases possess a marked tendency to establish hydrogen bonds – a structural trait at the base of the storage of biological information. It is crucial to understand what is the impact on this intermolecular interaction when free nucleobases are moved to aqueous media. In this work, we present a systematic investigation of the thermodynamics of uracil dimers in explicit water solvent. We employ well-tempered metadynamics simulations to generate a reliable free energy surface and classify all low-energy states. We perform detailed structural analysis of the relevant dimer configurations. The results obtained with different force fields are compared and a methodological assessment of the force fields accuracies are presented.