Paper Citing NAMD - Abstract
Turecek, Frantisek; Moss, Christopher L.; Pikalov, Ioannis; Pepin, Robert; Gulyuz, Kerim; Polfer, Nicolas C.; Bush, Matthew F.; Brown, Jeffery; Williams, Jonathan; Richardson, Keith
Gas-phase structures of phosphopeptide ions: A difficult case
INTERNATIONAL JOURNAL OF MASS SPECTROMETRY, 354:249-256, NOV 15 2013
The goal of this paper was to investigate gas-phase structures of conformers of doubly charged phosphopeptide ions (ApSAAR + 2H)(2+) and (AApSAR + 2H)(2+) using traveling-wave and drift-tube ion mobility and IR action spectroscopy measurements in combination with molecular dynamics and electronic structure calculations. Lowest free-energy conformers were identified by extensive search of the conformational space with combined molecular dynamics, semi-empirical, density functional theory and perturbational Moller-Plesset ab initio calculations. The low-energy conformers had collisional cross sections that were compatible with the experimental data but did not allow the conformers to be distinguished. IR absorption spectra that were calculated by density functional theory for harmonic normal modes showed several intense bands that were absent in the experimental action spectrum. Agreement with experiment was improved upon implementing second-order anharmonic corrections to the calculated vibrational frequencies. Several factors affecting the action spectra are discussed such as effects of mode anharmonicity on the absorption band intensities, the magnitude of frequency shifts in anharmonic corrections, as well as non-linear effects in multiple-photon absorption that may suppress the detection of strongly H-bonded modes in these measurements. (C) 2013 Elsevier B.V. All rights reserved.
