Structures of protonated dipeptides: the role of arginine in stabilizing salt bridges.

Structures of protonated dipeptides containing N-terminal Gly, Val, Pro, Lys, His, or Arg and C-terminal Arg are investigated with infrared multiple photon dissociation (IRMPD) spectroscopy between 900 and 1850 cm(-1) and theory. The IRMPD spectra clearly indicate that, when Gly, Val, Pro, Lys, or His are N-terminal to Arg, these protonated dipeptides adopt gas-phase structures with a single formal charge site (SCS), whereas ArgArg x H(+) has a salt-bridge (SB) structure in which the C-terminus is deprotonated and two basic sites are protonated. There are only subtle differences in the IRMPD spectra for dipeptides containing Gly, Val, Pro, and Lys. A sharp, intense peak at 1080 cm(-1) is observed for HisArg x H(+) that is attributed to the neutral histidine side chain, an assignment that is confirmed by comparison to the IRMPD spectrum of (HisArg x H(2))(2+). Lowest-energy B3LYP/6-31+G(d,p) structures and energies for the SCS and SB forms of these protonated dipeptides indicate that stability of the SB form relative to the SCS form generally increases with increasing gas-phase basicity of the N-terminal amino acid, but only ArgArg x H(+) is calculated to have a SB ground state at 298 K, in agreement with the results from IRMPD spectroscopy. This is the first direct experimental evidence for a salt-bridge structure in a gaseous protonated peptide, and ArgArg x H(+) is the smallest protonated peptide for which a SB structure has been reported. These results suggest that SB structures should be common for protonated peptides containing at least two arginine residues and may also occur for large protonated peptides or proteins with at least one arginine residue and other basic residues, such as lysine or histidine.