On the structure elucidation using ion mobility spectrometry and molecular dynamics. Academic Article uri icon

abstract

  • A new approach is described for the elucidation of gas-phase peptide ion structures combining ion mobility spectrometry (IMS) data and molecular dynamics (MD)-cluster analysis (CA) prediction. The new approach is based on the determination of the gas-phase ion structure identity vectors (e.g., structure and population vectors) that generate the total conformational space of the gas-phase ion as a function of the IMS experimental conditions (e.g., field strength, pressure, bath gas temperature, and IM cell geometry). Two methods to efficiently sample the gas-phase conformational space of molecular ions as a function of the effective ion temperature characteristic of the IMS experiments are described: (i) a simulated annealing MD-CA-constant temperature MD-CA, and (ii) a generalized non-Boltzmann sampling MD-free energy analysis-CA. The new theoretical method has been successfully applied to two model peptide ions (Bradykinin fragments 1-5 and 1-8, RPPGF and RPPGFSPF, respectively) for which multiple conformations sensitive to the effective ion temperature have been suggested in previous studies.

published proceedings

  • J Phys Chem A

altmetric score

  • 3

author list (cited authors)

  • Fernandez-Lima, F. A., Wei, H., Gao, Y. Q., & Russell, D. H.

citation count

  • 49

complete list of authors

  • Fernandez-Lima, FA||Wei, H||Gao, YQ||Russell, DH

publication date

  • July 2009