Development of non-standard arginine residue parameters for use with the AMBER force fields

Amino acid radicals are often involved as intermediates in biological processes, but are difficult to capture by experiment. Computational modeling can be employed to study the features of the species involved. The neutral arginyl radical has previously been detected experimentally using ECD and ETD spectroscopy. Protonation of the radical can occur on the guanidinium carbon, depending on the peptide structure and protein environment. Accurate force fields are essential for reproducing the conformational and dynamic behavior of these intermediates. New AMBER ff99 parameters for the arginyl radical and hydrogenated arginyl side chains are presented based on ab initio quantum chemical calculations.