The complex of Na+ with phenylalanine (Phe) is a prototype for the participation of cation-pi interactions in metal-ion binding to biological molecules. A recent comparison of this complex with the Na+/alanine (Na+/Ala) counterpart suggested only a small contribution of the phenyl ring interaction to binding, casting doubt on the extent of the cation-pi effect. The present work reexamines this thermochemistry using ligand-exchange equilibrium measurements in the Fourier transform ion cyclotron resonance (FT-ICR) ion trapping mass spectrometer. An increment of 7 +/- 2 kcal mol(-1) was found in the Ala/Phe comparison of binding enthalpies, confirming the importance of cation-pi binding enhancement in the Phe case. Absolute Na+ binding enthalpies of 38 +/- 2 and 45 +/- 2 kcal mol(-1) were assigned for Ala and Phe, respectively, using pyridine as the thermochemical reference ligand. All of these results were supported by quantum calculations using both density functional and Hartree-Fock/MP2 methods, improved in several respects over previous calculations. Alanine methyl ester (AlaMe) was also observed, and found to have an Na+ ion affinity larger by 2.3 kcal mol(-1) than Ala. New, lower energy conformations of neutral Phe were discovered in the computations.