Some α-amino acids, especially arginine, form protonated clusters when examined by electrospray ionization in an ion trap mass spectrometer. Singly-, doubly-, triply- and quadruply-protonated arginine clusters [(Arg)_n + H]⁺, [(Arg)_m + 2H]⁺², [(Arg)_l + 3H]⁺³ and [(Arg)_k + 4H]⁺⁴, were further studied by collision-induced dissociation (CID). The singly-protonated cluster n = 4 displayed enhanced stability and CID of larger clusters (n > 4) showed fragmentation leading to the preferential formation of n=4 product ions. The n = 4 stable cluster is proposed to bear a formal resemblance to the simple salt cluster [(NaCl)₄ + Na]⁺, a 3 x 3 x 1 micro-crystallite. This leads to the suggestion that [(Arg)₄ + H]⁺ is planar, with bonding primarily due to the electrostatic interactions between four zwitterionic arginine molecules. In the doubly-charged ion series, clusters of m = 12–15 have enhanced stability relative to those of immediately smaller size. Drawing on the analogous salt structures, the dication, [(Arg)₁₂ + 2H]⁺² might have a structure consisting of three layers of tetramers, two of which are protonated. This structure is analogous to that of the magic number doubly-charged ionic cluster [(NaCl)₁₂ + 2Na]⁺² which is a 3 x 3 x 3 micro-crystallite with an internal anion defect.

Keywords: arginine, amino acid clusters, ion trap, electrospray ionization, tandem mass spectrometry, collision-induced dissociation, non-covalent interactions, magic numbers, cluster ions