Optimization of parameters used in algorithms of ion-mobility calculation for conformational analyses.

Structural information of gaseous ions can be obtained by comparing their collision cross sections as determined by ion-mobility experiments with those by theoretical modeling. Three theoretical models, the projection approximation (PA), the exact hard-sphere scattering (EHSS), and the trajectory (TJ) models, have been employed to determine the theoretical cross sections of candidate geometries. The accuracy of these models is largely dependent on the empirical parameters used for ion-buffer gas interactions. Optimal empirical parameters for each model have been determined by comparing the experimental cross sections of 20 calibrant ions with their theoretical cross sections obtained by using geometries sampled by density-functional-theory-based molecular dynamics simulations. The maximum absolute deviations of the cross sections of 15.5% (PA), 20.7% (EHSS), and 11.7% (TJ) obtained from the original parameters are reduced to 5.6% (PA), 4.6% (EHSS), and 3.4% (TJ) obtained from the new optimized parameters. The root-mean-square deviations of the predicted cross sections using the new parameters from the experimental values are also drastically reduced to 2.1% (PA), 1.9% (EHSS), and 1.6% (TJ). The new parameters are verified on protonated triglycine, protonated trialanine, and doubly protonated bradykinin.