Charge matters! The charge state significantly influences the conformation and the binding energy between vancomycin antibiotic and bacterial cell-wall analogue peptides (see figure). Surface-induced dissociation (SID) studies provide a quantitative comparison between the stabilities of different charge states of the complex.In this study we examined the effect of the charge state on the energetics and dynamics of dissociation of the noncovalent complex between the vancomycin and the cell-wall peptide analogue N(alpha),N(epsilon)-diacetyl-L-Lys-D-Ala-D-Ala (V-Ac(2)LKdAdA). The binding energies between the vancomycin and the peptide were obtained from the RRKM (Rice, Ramsperger, Kassel, Marcus) modeling of the time- and energy-resolved surface-induced dissociation (SID) experiments. Our results demonstrate that the stability of the complex towards fragmentation increases in the order: doubly protonated<singly protonated<deprotonated. Dissociation of the singly protonated and singly deprotonated complex is characterized by very large entropy effects, which indicate a substantial increase in the conformational flexibility of the resulting products. The experimental threshold energies of (1.75+/-0.08) eV ((40.3+/-1.8) kcal mol(-1)) and (1.34+/-0.08) eV ((30.9+/-1.8) kcal mol(-1)) obtained for the deprotonated and singly protonated complexes, respectively, are in excellent agreement with the results of density functional theory calculations. The increased stability of the deprotonated complex observed experimentally is attributed to the presence of three charged sites in the deprotonated complex, as compared with only one charged site in the singly protonated complex. The low binding energy of (0.93+/-0.04) eV ((21.4+/-0.9) kcal mol(-1)) obtained for the doubly protonated complex suggests that this ion is destabilized by Coulomb repulsion between the singly protonated vancomycin and the singly protonated peptide comprising the complex.