A novel projection approximation algorithm for the fast and accurate computation of molecular collision cross sections (III): Application to supramolecular coordination-driven assemblies with complex shapes

Abstract The temperature dependence of the cross sections of rectangular, cyclobis[(2,9-bis[ trans -Pt(PEt 3 ) 2 (PF 6 )]anthracene)(4,4′-dipyridyl)] and triangular cyclotris[(2,9-bis[ trans -Pt(PEt 3 ) 2 (PF 6 )]phenanthrene)(4,4′-dipyridyl)] supramolecular assemblies has been investigated by ion mobility mass spectrometry. Molecular dynamics simulations starting with published X-ray structures of both the rectangle and triangle are used to generate model structures. These model structures are used to generate cross sections for comparison with experiment using the simple projection approximation, the computer intensive trajectory method and the new projected superposition approximation (PSA). It is shown that the PSA method provides the best comparison with experiment for these molecules with unusual topographies but the shape factor needs to use a finer mesh in its calculation than for molecules with more regular shapes like folded proteins. Even so the PSA is nearly a factor of 10 faster than the trajectory method for a “small” system like the triangle with 410 atoms.