From QCEIMS to QCxMS: A Tool to Routinely Calculate CID Mass Spectra Using Molecular Dynamics
Abstract
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.
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“Lastly, quantum chemistry-based simulations using Koopman and Grimme’s method [30] (see Data S1) supported the plausibility of the corresponding biotransformation reaction for both substances.”
- Authors
- Koopman, J., & Grimme, S.
- Affiliations
- University of Bonn (DE)
- Corresponding author
- Grimme, Stefan
- Venue
- Journal of the American Society for Mass Spectrometry
- Publisher
- American Chemical Society (ACS)
- Published
- 2021-06-03
- Volume
- 32
- Issue
- 7
- Pages
- 1735-1751
- ISSN
- 1044-0305 (ISSN-L)
- 1879-1123
- OpenAlex
- W3164251820
- Cited by
- 80
- References
- 110
- Citations by year
- 2026: 14 · 2025: 18 · 2024: 18 · 2023: 13 · 2022: 13 · 2021: 4
- FWCI
- 4.38
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- Locations
- Journal of the American Society for Mass Spectrometry (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Deutsche Forschungsgemeinschaft (1927/10-1)
- Topics
- Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
- Physical Sciences › Physics and Astronomy › Atomic and Molecular Physics, and Optics › Advanced Chemical Physics Studies
- Physical Sciences › Physics and Astronomy › Atomic and Molecular Physics, and Optics › Atomic and Molecular Physics
- Keywords
- collision-induced dissociation, electron ionization mass spectra, mass spectrum prediction, molecular dynamics, Born-Oppenheimer molecular dynamics, GFN2-xTB, fragmentation pathways, protonation sites, CREST
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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