A parallelized molecular collision cross section package with optimized accuracy and efficiency

Abstract

A new parallelized calculation package predicts collision cross sections with high accuracy and efficiency.

Unravelling the factors that drive separation in differential mobility spectrometry: A case study of regioisomeric phosphatidylcholine adducts

“…All isomers were carried forward to obtain theoretical CCSs in N2 using the MobCal-MPI package. [48] Molecular graphics were generated using the UCSF Chimera package. Chimera is developed by the Resource for Biocomputing, Visualization, and Informatics at the University of California, San Francisco (supported by NIGMS P41-GM103311).…”

“…[50] Calculations were conducted using MobCal-MPI, a parallelized CCS calculation package developed by our group. [48] Briefly, MobCal-MPI describes van der Waals (vdW) potentials using parameterized sets from molecular mechanics forcefields, namely MMFF94, enabling distinction of unique atom types (e.g., H bonded to O versus C). Since Ag + is not included in MMFF94, and there is an insufficient literature precedent of ion mobility studies of silver cationized species to parameterize vdW interactions for Ag + , the Cu + vdW parameters were used in its place with the mass of 107 Ag.…”

Augmenting Basin-Hopping With Techniques From Unsupervised Machine Learning: Applications in Spectroscopy and Ion Mobility

“…This is plotted for [AAA + H] + in Figure 10. It is worth noting that the experimentally-measured T ≈ 293 K value of Ω ave (N 2 ) = 151 Å 2 (Bush et al, 2012) is well-modeled by the T = 300 K Boltzmann-weighted sum of the various isomer CCSs as calculated using the MobCal-MPI code (https://uwaterloo.ca/hopkins-lab/mobcal-mpi), Ω Boltzmann (N 2 ) = 151.3 Å 2 (Ieritano et al, 2019b). In comparison, the calculated CCS for the static global minimum structure is Ω Boltzmann (N 2 ) = 148.7 Å 2 .…”

“…The success of IMS in determining analyte structure relies on accurate modeling of ion structure and subsequent calculation of CCSs for comparison with those determined experimentally. Experimental CCSs are obtained by relating the ion mobility, K, to CCS via the Mason-Schamp Equation (Mason and Mcdaniel, 1988; Ieritano et al, 2019b):…”

Plate‐height model of ion mobility‐mass spectrometry: Part 2—Peak‐to‐peak resolution and peak capacity

“…Second, two-body interactions governing separation in IMS are much more amenable to computational treatment than many-body encounters determining retention in chromatography [49]. If the aforementioned suitable ion structures are available, Ω and K can be calculated in a variety of buffer gases with satisfying accuracy [50][51][52][53][54][55]. Thus, with increasing computational power and further progress of theoretical methods, the prospect of predicting selectivity in DTIMS entirely computationally, at least for simpler systems, does not seem far fetched.…”