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In the atmosphere, water in all phases is ubiquitous and plays important roles in catalyzing atmospheric chemical reactions, participating in cluster formation and affecting the composition of aerosol particles. Direct measurements of water-containing clusters are limited because water is likely to evaporate before detection, and therefore, theoretical tools are needed to study hydration in the atmosphere. We have studied thermodynamics and population dynamics of the hydration of different atmospherically relevant base monomers as well as sulfuric acid–base pairs. The hydration ability of a base seems to follow in the order of gas-phase base strength whereas hydration ability of acid–base pairs, and thus clusters, is related to the number of hydrogen binding sites. Proton transfer reactions at water–air interfaces are important in many environmental and biological systems, but a deeper understanding of their mechanisms remain elusive. By studying thermodynamics of proton transfer reactions in clusters containing up to 20 water molecules and a base molecule, we found that that the ability of a base to accept a proton in a water cluster is related to the aqueous-phase basicity. We also studied the second deprotonation reaction of a sulfuric acid in hydrated acid–base clusters and found that sulfate formation is most favorable in the presence of dimethylamine. Molecular properties related to the proton transfer ability in water clusters are discussed.