Paper Citing NAMD - Abstract
Moss, Christopher L.; Liang, Wenkel; Li, Xiaosong; Turecek, Frantisek
The Early Life of a Peptide Cation-Radical. Ground and Excited-State Trajectories of Electron-Based Peptide Dissociations During the First 330 Femtoseconds
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY, 23:446-459, MAR 2012
We report a new approach to investigating the mechanisms of fast peptide cation-radical dissociations based on an analysis of time-resolved reaction progress by Ehrenfest dynamics, as applied to an Ala-Arg cation-radical model system. Calculations of stationary points on the ground electronic state that were carried out with effective CCSD(T)/6-311++ G(3df,2p) could not explain the experimental branching ratios for loss of a hydrogen atom, ammonia, and N-C-alpha bond dissociation in (AR + 2H)(+center dot) The Ehrenfest dynamics results indicate that the ground and low-lying excited electronic states of (AR + 2H)(+center dot). follow different reaction courses in the first 330 femtoseconds after electron attachment. The ground (X) state undergoes competing loss of N-terminal ammonia and isomerization to an aminoketyl radical intermediate that depend on the vibrational energy of the charge-reduced ion. The A and B excited states involve electron capture in the Arg guanidine and carboxyl groups and are non-reactive on the short time scale. The C state is dissociative and progresses to a fast loss of an H atom from the Arg guanidine group. Analogous results were obtained by using the B3LYP and CAM-B3LYP density functionals for the excited state dynamics and including the universal M06-2X functional for ground electronic state calculations. The results of this Ehrenfest dynamics study indicate that reaction pathway branching into the various dissociation channels occurs in the early stages of electron attachment and is primarily determined by the electronic states being accessed. This represents a new paradigm for the discussion of peptide dissociations in electron based methods of mass spectrometry.
