Accurate hydrogen placement in molecular modeling is crucial for studying the interactions and dynamics of biomolecular systems. It is difficult to locate hydrogen atoms from many experimental structural characterization approaches, such as due to the weak scattering of x-ray radiation. Hydrogen atoms are usually added and positioned <i>in silico</i> when preparing experimental structures for modeling and simulation. The carboxyl functional group is a prototypical example of a functional group

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... hat requires protonation during structure preparation. To our knowledge, when in their neutral form, carboxylic acids are typically protonated in the <i>syn</i> 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 <i>syn</i> conformation. We calculate and compare the relative energetic stabilities of <i>syn</i> and <i>anti</i> acetic acid using <i>ab initio</i> quantum mechanical calculations and atomistic molecular dynamics simulations. We show that while the <i>syn</i> conformation is the preferred state, the <i>anti</i> state may in some cases also be present under normal NPT conditions in solution.