Quantum Chemistry‐based Molecular Dynamics Simulations as a Tool for the Assignment of ESI‐MS/MS Spectra of Drug Molecules

Abstract

In organic mass spectrometry, fragment ions provide important information on the analyte as a central part of its structure elucidation. With increasing molecular size and possible protonation sites, the potential energy surface (PES) of the analyte can become very complex, which results in a large number of possible fragmentation patterns. Quantum chemical (QC) calculations can help here, enabling the fast calculation of the PES and thus enhancing the mass spectrometry-based structure elucidation processes. In this work, the previously unknown fragmentation pathways of the two drug molecules Nateglinide (45 atoms) and Zopiclone (51 atoms) were investigated using a combination of generic formalisms and calculations conducted with the Quantum Chemical Mass Spectrometry (QCxMS) program. The computations of the de novo fragment spectra were conducted with the semi-empirical GFNn-xTB (n = 1, 2) methods and com-pared against Orbitrap measured electrospray ionization (ESI) spectra in positive ion mode. It was found that the unbiased QC calculations are particularly suitable to predict nonevident fragment ion structures, sometimes contrasting the accepted generic formulation of fragment ion structures from electron migration rules, where the "true" ion fragment structures are approximated. For the first time, all fragment and intermediate structures of these large-sized molecules could be elucidated completely and routinely using this merger of methods, finding new undocumented mechanisms, that are not considered in common rules published so far. Given the importance of ESI for medicinal chemistry, pharmacokinetics, and metabolomics, this approach can significantly enhance the mass spectrometry-based structure elucidation processes and contribute to the understanding of previously unknown fragmentation pathways.

Calculation of Mass Spectra with the QCxMS Method for Negatively and Multiply Charged Molecules

“…The various reasons for observed differences between experimental and calculated spectra were discussed in detail in earlier work. , In experiments, the “hardness” of the ionization process influences the degree of fragmentation. , The conditions in the collision cells are device-specific and cannot exactly be reproduced by the simulation . Thus, collision cell settings used in QCxMS are determined empirically and do not necessarily reflect the instrumental specifics.…”

“…Based on these ideas, the Quantum Chemical Mass Spectrometry program (QCxMS) was developed, which can operate in x = electron ionization (EI), dissociative electron attachment (DEA) and collision-induced dissociation (CID) run modes. The effectiveness of QCxMS to successfully generate in silico spectra in its EI mode is well documented − and has been demonstrated recently by its use for extension of mass spectra databases. − Detailed fragmentation pattern analysis using the EI, DEA, and positive ion CID modes have successfully been conducted earlier. ,− In this work, an extension of the CID run mode is presented, in which the charge state of the molecular ion is no longer restricted to single positive values so that computations of negatively and multiply charged molecular ions are now possible. This improvement is important because common experimental ionization techniques used in tandem with CID − can produce ions with multiple positive or negative charges. , The new charge unrestricted CID mode was tested on a benchmark set of molecules, for which the most apparent fragmentation pathways are discussed in detail.…”

Calculation of mass spectra with the QCxMS method for negatively and multiply charged molecules

“…The various reasons for observed differences between experimental and calculated spectra were discussed in detail in ear-lier work. [18,28] In experiments, the 'hardness' of the ionization process influences the degree of fragmentation. [96,97] The conditions in the collision cells are device-specific and cannot exactly be reproduced by the simulation.…”

“…Detailed fragmentation pattern analysis using the EI, DEA, and positive ion CID modes have successfully been conducted earlier. [17,[26][27][28] In this work, an extension of the CID run mode is presented, in which the charge state of the molecular ion is no longer restricted to single positive values so that computations of negatively and multiply charged molecular ions are now possible. This improvement is important because common experimental ionization techniques used in tandem with CID [29][30][31][32] can produce ions with multiple positive or negative charges.…”

Towards determining molecular structure with ESI-MS backed by computational methods: structures of subnanoclusters of Pd and Cu chlorides, ion dynamics in vacuum, and challenges to the methodology

“…Established integrations of quantum chemical modeling and MS are mostly related to tandem MS, see notable examples in ref. 38,39,82.…”