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I have looked virtually everywhere for an explanation of why alcohols EI GC-MS always have a more prominent M-1 signal over a Parent chain signal--sometimes no parent signal at all.

One site says http://people.whitman.edu/~dunnivfm/C_MS_Ebook/CH6/6_10.html that primary alcohol chains line 1-pentanol lose a hydrogen from the alpha carbon but there is no explanation or mention of a suggested mechanism.

I have tried writing out potential mechanisms and have come to the conclusion that the Hydrogen lost during ionization leaves as a hydrogen radical thus leaving an overall cation like ion, (which seems very unlikely since C and O in the compound are more E.N. so I imagine the electrons would be more likely to remain with them).

Additionally, I came to the conclusion that Zwitterions can perhaps still be detected as long as there is a cation or radical cation present somewhere in the compound? Even if the compound also now has a negative charge on it where it lost the H+ at the alpha carbon or the Oxygen. (this seems likely since I believe we can measure amino acids via MS correct?)

Any insight on this would be greatly appreciated

Here is some of the MS spectra's available online I have been referencing: https://webbook.nist.gov/cgi/cbook.cgi?ID=C71410&Mask=200 on the NIST website it says these spectra's are made using the GC-MS method, Electron impact is noted but not explicitly stated, (but to my knowledge GC-MS uses electron impact usually).

Thank you,

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  • $\begingroup$ Welcome! Any discussion of mass spectrometry without the corresponding ionization method (electron impact, electrospray etc.) is a futile exercise. Also, it is better to provide links rather than saying "one site says...." $\endgroup$
    – ACR
    Commented May 25 at 3:02
  • $\begingroup$ Thanks for the advice, I updated the question $\endgroup$
    – James Perrin
    Commented May 25 at 3:40

1 Answer 1

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One possibility (R = alkyl or hydrogen):

$\ce{RCH2 –OH -> RCH=\overset{+}{O}H + H• + e^-},$

where the cation shown is stabilized by the oxygen donating an otherwise nonbonding electron pair to what would be the carbocation center. In effect you have a protonated aldehyde.

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  • $\begingroup$ Incredible! So radical hydrogen is produced routinely in EI GC-MS? Also am I understanding correctly that we are losing an electron from the oxygen during electron impact as well as simultaneously/subsequently losing a radical hydrogen from the alpha carbon via homolytic cleavage? $\endgroup$
    – James Perrin
    Commented May 25 at 23:54
  • $\begingroup$ Hydrogen atoms have an ionization energy of 13.6 eV, which is fairly high (it beats methane and ethane), so some hydrogen is likely in radical form in MS. The measurement methodology simply does not reveal it. $\endgroup$
    – Oscar Lanzi
    Commented May 26 at 0:03
  • $\begingroup$ Meanwhile the oxygen does not ionize any electrons off itself. It gains a positive formal charge through sharing an extra electron pair with electron-deficient carbon. $\endgroup$
    – Oscar Lanzi
    Commented May 26 at 0:05
  • $\begingroup$ Amazing, thank you so much, do you have any literature recommendations on similar GC-MS topics I might run into? $\endgroup$
    – James Perrin
    Commented May 26 at 19:37
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    $\begingroup$ @James Perrin: well the standard McLafferty Interpretation of Mass Spectra (books.google.fr/books/about/Interpretation_Of_Mass_Spectra.html) would be an excellent starting point. $\endgroup$
    – PLD
    Commented May 27 at 8:34

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