Malic acid (MA) (C4H6O5) is one of the most important organic constituents of fruits that is widely used in food and beverage industries. It is also detected in the atmospheric aerosol samples collected in different parts of the world. Considering the fact that secondary organic aerosols have adverse impacts on the global atmosphere and climate and a molecular-level understanding of the compositions and formation mechanism of secondary organic aerosols is necessary, we have performed systematic density functional electronic structure calculations to investigate the hydrogen-bonding interactions between MA and several naturally occurring nitrogen-containing atmospheric bases such as ammonia and amines that are derived from ammonia by the substitution of hydrogens by a methyl group. The base molecules were allowed to interact with the carboxylic COOH and the hydroxyl-OH group of the MA separately. While at both sites, MA produces energetically stable binary complexes with bases with large negative values of binding energy, the thermodynamical stability, at an ambient temperature and pressure of 298.15 K and 1 atm, respectively, is favored only for the clusters formed at the COOH site. A much larger red shift of the carboxylic-OH stretch than that of the hydroxyl-OH reinforces the preference of this site for cluster formation. Both the binding electronic energy and binding free energy of MA–ammonia complexes are lower than those of MA–amine complexes, although the amines are derivatives of NH3. The large increase in the Rayleigh activities upon cluster formation indicates that the MA-atmospheric base cluster may interact strongly with solar radiation. The detailed analysis of the structural, energetic, electrical, and spectroscopic properties of the binary complexes formed by MA with atmospheric bases shows that MA could participate in the atmospheric nucleation processes and subsequently contribute effectively to new particle formation in the atmosphere.