The gas-phase sodium binding energies for four small aromatic molecules, which are used as matrices in matrix-assisted laser desorption/ionization (MALDI) mass spectrometry, were calculated using the B3LYP hybrid density functional theory at the 6-31+G* level. The gas-phase sodium binding free energies were compared with recently reported experimental results obtained by the ligand-exchange equilibrium method. The compounds investigated in this work are 2,5-dihydroxybenzoic acid, para-nitroaniline, 2,4,6-trihydroxy-acetophenone, and 3-hydroxypicolinic acid. In general, good agreement was found between the experimental gas-phase sodium binding free energies and the theoretical results. Detailed geometrical information and vibrational frequencies for both neutral molecules and sodium complexes are shown. The theoretical results give insight into the gas-phase sodium ion transfer reaction mechanism.