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Accurate hydrogen placement in molecular modeling is crucial for studying the interactions and dynamics of biomolecular systems. The carboxyl functional group is a prototypical example of a functional group that requires protonation during structure preparation. To our knowledge, when in their neutral form, carboxylic acids are typically protonated in the syn conformation by default in classical molecular modeling packages, with no consideration of alternative conformations, though we are not aware of any careful examination of this topic. Here, we investigate the general belief that carboxylic acids should always be protonated in the syn conformation. We calculate and compare the relative energetic stabilities of syn and anti acetic acid using ab initio quantum mechanical calculations and atomistic molecular dynamics simulations. We focus on the carboxyl torsional potential and configurations of microhydrated acetic acid from molecular dynamics simulations, probing the effects of solvent, force field (GAFF vs GAFF2), and partial charge assignment of acetic acid. We show that while the syn conformation is the preferred state, the anti state may in some cases also be present under normal NPT conditions in solution.

Assessing the Conformational Equilibrium of Carboxylic Acid via Quantum Mechanical and Molecular Dynamics Studies on Acetic Acid