Dataset Information

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

ABSTRACT: A new, multithreaded, 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 these are compared against the CCSs calculated by MOBCAL. Through this analysis, it is shown that the application of the aforementioned algorithms enables 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 2 orders of magnitude less CPU time due to the various numerical methods implemented into the software, even when run on a single CPU core.

SUBMITTER: Myers CA

PROVIDER: S-EPMC6958516 | biostudies-literature | 2019 May

REPOSITORIES: biostudies-literature

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

Myers Christopher A CA D'Esposito Rebecca J RJ Fabris Daniele D Ranganathan Srivathsan V SV Chen Alan A AA

The journal of physical chemistry. B 20190510 20

A new, multithreaded, 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 approximatio ...[more]

PMID: 31042389

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Project description:RationaleCoordinatively driven self-assembly of transition metal ions and bidentate ligands gives rise to organometallic complexes that usually contain superimposed isobars, isomers, and conformers. In this study, the double dispersion ability of ion mobility mass spectrometry (IM-MS) was used to provide a comprehensive structural characterization of the self-assembled supramolecular complexes by their mass and charge, revealed by the MS event, and their shape and collision cross-section (Ω), revealed by the IM event.MethodsSelf-assembled complexes were synthesized by reacting a bis(terpyridine) ligand exhibiting a 60o dihedral angle between the two ligating terpyridine sites (T) with divalent Zn, Ni, Cd, or Fe. The products were isolated as (Metal2+ [T])n (PF6 )2n salts and analyzed using IM-MS after electrospray ionization (ESI) which produced several charge states from each n-mer, depending on the number of PF6 - anions lost upon ESI. Experimental Ω data, derived using IM-MS, and computational Ω predictions were used to elucidate the size and architecture of the complexes.ResultsOnly macrocyclic dimers, trimers, and tetramers were observed with Cd2+ , whereas Zn2+ formed the same plus hexameric complexes. These two metals led to the simplest product distributions and no linear isomers. In sharp contrast, Ni2+ and Fe2+ formed all possible ring sizes from dimer to hexamer as well as various linear isomers. The experimental and theoretical Ω data indicated rather planar macrocyclic geometries for the dimers and trimers, twisted 3D architectures for the larger rings, and substantially larger sizes with spiral conformation for the linear congeners. Adding PF6 - to the same complex was found to mainly cause size contraction due to new stabilizing anion-cation interactions.ConclusionsComplete structural identification could be accomplished using ESI-IM-MS. Our results affirm that self-assembly with Cd2+ and Zn2+ proceeds through reversible equilibria that generate the thermodynamically most stable structures, encompassing exclusively macrocyclic architectures that readily accommodate the 60o ligand used. In contrast, complexation with Ni2+ and Fe2+ , which form stronger coordinative bonds, proceeds through kinetic control, leading to more complex mixtures and kinetically trapped less stable architectures, such as macrocyclic pentamers and linear isomers.

Dataset Information

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

Publications

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

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