CoSIMS

CoSIMS simulates ion–buffer gas collisions to calculate collision cross sections (CCS) for ion mobility spectrometry using optimized trajectory-based molecular mechanics and multithreading to improve computational efficiency.

Key Features:

• Multithreaded molecular mechanics: Implements multithreaded, optimized molecular mechanics algorithms to simulate thousands of buffer gas–ion collisions.
• Trajectory-based simulation: Employs a trajectory method to model ion–buffer gas interactions and determine CCS values.
• Neglect of London dispersion interactions: Omits London dispersion interactions at long range to reduce computational cost.
• Ellipsoidal projection approximation: Uses an ellipsoidal projection approximation to remove trajectories that contribute negligibly to total CCS.
• Performance efficiency: Reduces CPU time by up to two orders of magnitude compared to traditional methods such as MOBCAL while producing nearly identical CCS calculations.
• Comparative accuracy with MOBCAL: Reproduces CCS values within a few percent of MOBCAL's trajectory method for many molecular types.
• Advantage for elongated molecules: Provides faster and more reasonable CCS calculations than MOBCAL for highly elongated molecules such as nucleic acids.

Scientific Applications:

• Carbon fullerenes: Calculation of CCS for fullerenes relevant to materials science and nanotechnology.
• Proteins: CCS determination for proteins to inform studies of protein structure and dynamics.
• DNA strands: CCS evaluation for DNA and nucleic acids relevant to genomics and molecular biology research.

Methodology:

Trajectory-based simulation of thousands of buffer gas–ion collisions using optimized molecular mechanics; omission of long-range London dispersion interactions; ellipsoidal projection approximation to discard low-contribution trajectories; and multithreading.