How Good Are Force Fields for Gas-Phase Protonated Peptides?
Christopher Kinsinger, Karl K. Irikura
With the increase in mass-spectrometry-based proteomics, many research projects depend on the chemistry of peptide fragmentation. Elucidating fragmentation mechanisms requires a thorough exploration of the potential energy surface. Conformational searching tools have not yet been tested for gas-phase, protonated peptides. Herein we present and validate a method for identifying low-energy conformations and calculating reliable energetic data. This method uses a molecular mechanics force field for conformational searching and then optimizes low-energy structures with a quantum mechanical method. When compared to grid-based conformational searches by the same quantum mechanical method, the method combining molecular and quantum mechanical calculations is more efficient and locates the same global minimum.