Synthesis, experimental, and molecular dynamics simulation of the ESI-CID spectrum of the nerve agent Novichok analog O-2-methoxyethyl N-[bis(dimethylamino)methylidene]-P-methylphosphonamidate

02 March 2023, Version 1
This content is a preprint and has not undergone peer review at the time of posting.


The comprehensive and accurate analysis of mass spectral data is critical for the unequivocal identification of environmental samples containing compounds short-listed by the Chemical Weapons Convention (CWC). In particular, experiments with nerve agents are limited by the high risks involved in their handling. Therefore, the possibility of studying fragmentation pathways by a theoretical approach is especially welcome. In this work, for the first time, O-2-methoxyethyl N-[bis(dimethylamino)methylidene]-P-methylphosphonamidate, an analog of the Novichok nerve agent A-242, was synthesized employing a one-pot microscale synthesis. Electron ionization (EI) and electrospray ionization (ESI) mass spectrometry (MS) spectra were measured to produce data for CWC verification purposes. Considering that ESI-MS/MS is a powerful method for analyzing non-volatile, highly polar, and very water-soluble compounds, such as degradation products of nerve agents, we extensively investigated for the first time the ESI-(collision-induced dissociation) CID fragmentation pathways of the selected molecule. For this purpose, molecular dynamics simulations using the Quantum Chemical Mass Spectrometry (QCxMS) method employing the semiempirical electronic structure method GFN2-xTB were compared with Triple Quadrupole electrospray ionization (ESI) experimental spectra in positive ion mode. The base peak of the EI spectrum for this molecule was found to be m/z 151, which strongly suggests a McLafferty +1 rearrangement involving the 2-methoxyethyl moiety. According to the simulations, the formation of the m/z 106 ion in the ESI-CID spectrum results from the rearrangement involving a transfer of one dimethylamino group to the phosphorus atom. This mechanism would be difficult to identify without employing theoretical methods.


fragmentation pathways
mass spectrometry
molecular dynamics

Supplementary materials

MP4 movies of relevant trajectories
The movies can be obtained upon request from the corresponding author .


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