Ionization of 2-nonanone, cyclopentanone, acetophenone, pyridine, and di-tert-butylpyridine (DTBP) in a corona discharge (CD) atmospheric pressure chemical ionization (APCI) ion source was studied using ion mobility (IMS) and time-of-flight mass spectrometry (TOF-MS). The IMS and MS spectra were recorded in the absence and presence of ammonia dopant. Without NH3 dopant, the reactant ion (RI) was H+(H2O)(n), n = 3,4, and the MH+(H2O)(x) clusters were produced as product ions. Modeling of hydration shows that the amount of hydration (x) depends on basicity of M, temperature and water concentration of drift tube. In the presence of ammonia (NH4+(H2O)(n) as RI) two kinds of product ions, MH+(H2O)(x) and MNH4+(H2O)(x), were produced, depending on the basicity of M. With NH4+(H2O)(n) as RI, the product ions of pyridine and DTBP with higher basicity were MH+(H2O)(x) while cyclopentanone, 2-nonanone, and acetophenone with lower basicity produce MNH4+(H2O)(x). To interpret the formation of product ions, the interaction energies of M-H+, H+-NH3, and H+-OH2 in the M-H+-NH3 and M-H+-OH2 and M-H+-M complexes were computed by B3LYP/6-311++G(d,p) method. It was found that for a molecule M with high basicity, the M-H+ interaction is strong leading in weakening of the H+-NH3, and H+-OH2 interactions in the M-H+-NH3 and M-H+-OH2 complexes.