title: Does Thermal Breathing Affect Collision Cross Sections of Gas-Phase Peptide Ions? An Ab Initio Molecular Dynamics Study.
abstract: Ab initio molecular dynamics (AIMD) with density functional theory (DFT) was applied to explore conformational motions and collision cross sections (Ω) of folded (2) and extended (7) conformers of doubly charged peptide ions, (Ala-Ala-Leu-Arg + 2H)(2+), in the gas phase at 300 and 473 K. The experimental Ω of (Ala-Ala-Leu-Arg +2H)(2+) was measured as 149 ± 1.2 Å(2) at 298 K. Thermally distributed mean values of Ω for 2 and 7 at 300 and 473 K were only 0.8-1.1% larger than for the equilibrium 0 K structures. Long (>10 ps) trajectory calculations indicated entropy-driven conformational change of 2 to 7 that occurred at random within a ∼ 4 ps time window. The experimental Ω was found to fit the calculated population averaged values for 2 and 7, indicating a rapid conformer interconversion. Overall, thermal breathing had only a minor effect on the peptide ion collision cross sections.
authors.affiliation: Department of Chemistry, University of Washington , Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States.
authors.forename: Robert
authors.initials: R
authors.lastname: Pepin
authors.affiliation: Department of Chemistry, University of Washington , Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States.
authors.forename: Alessio
authors.initials: A
authors.lastname: Petrone
authors.affiliation: Department of Chemistry, University of Washington , Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States.
authors.forename: Kenneth J
authors.initials: KJ
authors.lastname: Laszlo
authors.affiliation: Department of Chemistry, University of Washington , Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States.
authors.forename: Matthew F
authors.initials: MF
authors.lastname: Bush
authors.affiliation: Department of Chemistry, University of Washington , Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States.
authors.forename: Xiaosong
authors.initials: X
authors.lastname: Li
authors.affiliation: Department of Chemistry, University of Washington , Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States.
authors.forename: František
authors.initials: F
authors.lastname: Tureček