Koopman, Jeroen Gertjan: Computation of Mass Spectra Using Quantum Chemical Methods. - Bonn, 2022. - Dissertation, Rheinische Friedrich-Wilhelms-Universität Bonn.
Online-Ausgabe in bonndoc: https://nbn-resolving.org/urn:nbn:de:hbz:5-68759
urn: https://nbn-resolving.org/urn:nbn:de:hbz:5-68759,
author = {{Jeroen Gertjan Koopman}},
title = {Computation of Mass Spectra Using Quantum Chemical Methods},
school = {Rheinische Friedrich-Wilhelms-Universität Bonn},
year = 2022,
month = nov,

note = {Mass spectrometry (MS) is widely used for the structural elucidation of compounds in a vast variety of scientific research. Unfortunately, many methods that aim to predict mass spectra cannot often elucidate the complete fragmentation pathways of unknown compounds. For this reason, the QCEIMS program was developed in 2013, which combines quantum chemical (QC) methods with statistical models to calculate standard 70 eV Electron Ionization (EI) mass spectra. In this thesis, this software was improved to compute more reliable EI spectra and extended to enable calculations of collision-induced dissociation (CID) processes. This development led to the renaming of the program to QCxMS (x = EI, CID), reflecting the greater general applicability of the software. For a perspective overview of the subject, the introduction to this thesis provides an outline of the operating principles of mass spectrometry and highlights the differences between the EI and CID methods.
Since the software is based on calculating a statistically relevant number of dissociation processes through massively parallel molecular dynamics (MD) simulations, the use of fast and reliable QC methods is mandatory. In particular, semiempirical quantum mechanical (SQM) methods are well suited for this purpose, making the GFNn-xTB (n = 1, 2) methods essential in this context. Their implementation into QCxMS and the calculation of EI mass spectra are evaluated for various compounds consisting of organic, inorganic main-group, and transition metal elements.
To enable the simulation of CID mass spectra, collision-based activation is implemented into the software in the form of different run types, allowing the calculation of slow heating and collision processes between ions and neutral gas atoms. The effectiveness of the method is shown by testing various benchmark structures. Furthermore, the unknown fragmentation pathways of the two large molecules nateglinide and zopiclone are fully elucidated for the first time, by combining generic rules and calculated MD trajectories. Unusual decompositions and unintuitive protonation sites are found and discussed.
Developments for the CID module are concluded by removing the charge constraints on the molecular ion when calculating mass spectra. Negatively charged spectra of deprotonated organic compounds are calculated, and the influence of the deprotonation sites on the computed spectrum is analyzed. In addition, mass spectra of multiply charged compounds are calculated fully automatically, which was not possible by other methods so far.},

url = {https://hdl.handle.net/20.500.11811/10459}

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