From QCEIMS to QCxMS: A Tool to Routinely Calculate CID Mass Spectra Using Molecular Dynamics

Mass spectrometry
(MS) is a powerful tool in chemical research
and substance identification. For the computational modeling of electron
ionization MS, we have developed the quantum-chemical electron ionization
mass spectra (QCEIMS) program. Here, we present an extension of QCEIMS
to calculate collision-induced dissociation (CID) spectra. The more
general applicability is accounted for by the new name QCxMS, where
“x” refers to EI or CID. To this end, fragmentation
and rearrangement reactions are computed “on-the-fly”
in Born–Oppenheimer molecular dynamics (MD) simulations with
the semiempirical GFN2-xTB Hamiltonian, which provides an efficient
quantum mechanical description of all elements up to Z = 86 (Rn). Through the explicit modeling of multicollision processes
between precursor ions and neutral gas atoms as well as temperature-induced
decomposition reactions, QCxMS provides detailed insight into the
collision kinetics and fragmentation pathways. In combination with
the CREST program to determine the preferential protonation sites,
QCxMS becomes the first standalone MD-based program that can predict
mass spectra based solely on molecular structures as input. We demonstrate
this for six organic molecules with masses ranging from 159 to 296
Da, for which QCxMS yields CID spectra in reasonable agreement with
experiments.