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qcxms / QCxMS

Quantum mechanic mass spectrometry calculation program
https://xtb-docs.readthedocs.io/en/latest/qcxms_doc/qcxms.html
GNU Lesser General Public License v3.0
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Allow nitrogen to react with ion #36

Open tobigithub opened 3 years ago

tobigithub commented 3 years ago

Hi, this is for version plotms 5.2.

Noble gases that we use as collision gases can sometimes form adducts. While rare it could be a possibility and has been observed before.

References: https://scholar.google.com/scholar?hl=en&as_sdt=0%2C5&q=%22argon+adducts%22&btnG= Tobias

JayTheDog commented 3 years ago

Interesting and probably something to consider. The noble gases are ignored after each step in QCxMS, so adding these under certain conditions has to be checked inside the QCxMS program, not within PlotMS I guess.

tobigithub commented 3 years ago

Actually even more prevalent for nitrogen, which is used for Orbitraps as collision gas, but I think that is already covered.

Reaction of arylium ions with the collision gas N2 in electrospray ionization mass spectrometry https://tsapps.nist.gov/publication/get_pdf.cfm?pub_id=917566

JayTheDog commented 3 years ago

Interestingly I have witnessed this before, but thought it is a wrong behavior of GFN-xTB. Implementing this requires flexible allocation of the number of nuclei, which has to be done very carefully. I will take a look into this,

tobigithub commented 3 years ago

I know for sure that many semiempirical approaches (MNDO, AM1, PM6, RM1) model this behavior. Not sure about DFT, but its also observed experimentally, just people sweep this under the carpet, because they can not explain it. I have observed this and it leads also to different product ions and precursor ions [M+N2]+ because of the included N2 or other collision gases. Especially large molecules such as HEME (https://pubchem.ncbi.nlm.nih.gov/compound/Heme) can capture nitrogen as collision gas and N2 is just absorbed at lower velocities, similar to a dragnet, into the molecule.