Statistical analysis of ion mobility spectrometry. II. Adaptively biased methods and shape correlations.

Journal of the American Society for Mass Spectrometry
Florent CalvoPhilippe Dugourd

Abstract

Following a recent effort [J. Am. Soc. Mass Spectrom. 23, 386-396 (2012)], we continue to explore computational methodologies for generating molecular conformations to support collisional cross sections suggested by ion mobility measurements. Here, adaptively biased molecular dynamics (ABMD) simulations are used to sample the configuration space and to achieve flat-histogram sampling along the reaction coordinates of the first two moments of the gyration tensor. The method is tested and compared with replica-exchange simulations on triply-protonated bradykinin and on a larger 25-residue peptide. It is found to have a much higher efficiency for producing large sets of conformations in a broad range of diffusion cross-sections, whereas it does not compete with conventional replica-exchange molecular dynamics in locating the lowest-energy structure. Nevertheless, the broad sampling obtained from the ABMD method allows to quantitatively correlate the diffusion cross-section Ω with other geometric order parameters that have simpler interpretation. The strong correlations found between the diffusion cross-section and the radius of gyration, the surface area and the volume of the convex hull suggest an optimal template for accurately ...Continue Reading

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Citations

Feb 5, 2013·Journal of the American Chemical Society·Nicholas A PiersonDavid E Clemmer
Oct 18, 2013·International Journal of Molecular Sciences·Jaewoo Pi, Lee Sael
Aug 12, 2015·Journal of Mass Spectrometry : JMS·Valentina D'AtriValérie Gabelica
Jun 22, 2016·Journal of Pharmaceutical and Biomedical Analysis·Maria Kristina ParrHouda Montacir
Mar 15, 2016·Physical Chemistry Chemical Physics : PCCP·Alexander KuleszaPhilippe Dugourd
Jun 10, 2018·Rapid Communications in Mass Spectrometry : RCM·Chang Min ChoiFabien Chirot
Oct 13, 2017·Journal of Separation Science·Valentina D'AtriDavy Guillarme
Feb 25, 2021·Analytical Chemistry·Aurélien Le FèvreFabien Chirot

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