The present article is the second part of a general overview of the gas‐phase protonation thermochemistry of polyfunctional molecules. The first part of the review (Mass Spectrom. Rev., 2007, 26:775–835) was devoted to the description of the physico‐chemical concepts and of the methods of determination, both experimental and theoretical, of gas‐phase basicity. Several clues concerning the structural and energetic aspects of the protonation of isolated species have been emphasized. In the present article, specific examples are examined. The field of investigation is limited to molecules containing a “saturated” basic site, that is, nitrogen or oxygen atoms engaged in simple σ bonds with their neighboring. Aliphatic, cyclic and aromatic poly‐amines, aminoalcohols, alcohols, ethers, and hydroxyl‐ethers, are successively presented.