CoSIMS: An Optimized Trajectory-Based Collision Simulator for Ion Mobility Spectrometry

Abstract

A new, multi-threaded, trajectory method based software platform, CoSIMS, is revealed and compared to reference MOBCAL collision cross sections (CCS). CoSIMS employs various molecular mechanics algorithms to lessen the computational resources required to simulate thousands of buffer gas-ion collisions, including the neglect of London dispersion interactions at long distances and the removal of trajectories that insignificantly contribute to the total CCS via an ellipsoidal projection approximation. The showcased program is used to calculate the collision cross sections of carbon fullerenes, proteins, and DNA strands of various lengths, sizes, and molecular weights, and compared against the the CCSs calculated by MOBCAL. Through this analysis, it is shown that the application the aforementioned algorithms enables for both faster and more reasonable CCS calculations than MOBCAL for highly elongated molecules such as nucleic acids; for all other molecules, CoSIMS is able to reproduce the CCSs generated by MOBCAL's trajectory method within a few percent. Overall, CoSIMS is able to calculate nearly identical CCSs as MOBCAL in nearly two orders of magnitude less CPU time due to the various numerical methods implemented into the software, even when run on a single CPU core.

Cyclosporin A: Conformational Complexity and Chameleonicity

“…This conformation corresponds to the position at (PC-1, PC-2) = (0.5, 0.45), where only AMBER12:EHT exhibited PMF ≈ 1.7 kcal/mol and the other force fields have PMF > 2.5 kcal/mol using our bulk solvent simulations (Figure a and Figure S3), which is completely different from the one we found at (PC-1, PC-2) = (1.4, 0.0) that contains the same two cis isomers. Here, the CCSs were also calculated by the CoSIMS program for the ensembles at T = 300 K, although we could not obtain CCS = 271 Å 2 that corresponds to the bent conformation reported by Gray et al Rather, a bent-twisted conformer comprising only 9–10 cis ( C in Figure b) might be a candidate for a minor conformation employing the McMD simulations, as discussed above. Another CCS study by Hyung et al revealed the bimodal distributions at 272 and 278 Å 2 via solvent-free replica exchange MD, whereas the three modal distributions at 283, 295, and 315 Å 2 were determined by our simulation in CHCl 3 using ff03 (see Figure S10a).…”

Efficient modeling of liquid phase photoemission spectra and reorganization energies: Difficult case of multiply charged anions

“…One possibility is to combine the PES with additional experimental techniques, such as Raman spectroscopies to identify the vibrational modes responsible for the reorganization. [82] We propose that useful information can be reached even without additional experiments assuming that the water solvent response is dominated by librational motion.…”

Molecular Dynamics-Assisted Interpretation of Experimentally Determined Intrinsically Disordered Protein Conformational Components: The Case of Human α-Synuclein

“…The collisional cross-section values were computed using the CoSIMS code . The smFRET efficiency (FE), defined as (where Ro is the Förster distance and r the Cα-Cα distance), was computed using the ISDB module within the PLUMED driver .…”

“…The collisional cross-section values were computed using the CoSIMS code. 31 The smFRET efficiency (FE), defined as…”