[lohjxMARCUS]

I have a question on MS. Why isn't the molecular ion (parent ion) sometimes not observed in the mass spectrum? Does it have anything to do with the isotopes?

[Irlanur]

not really, it might just be too unstable.

[lohjxMARCUS]

not really, it might just be too unstable.

Too unstable? could you explain it more or is there more to it this question?

[Arkcon]

Well, what exactly happens inside the mass spec to form the parent ion.  It depends on the instrument, and its settings as much as it does on the molecule in question.  And yes, for very large molecules, or molecules with certain atoms, the isotopes do affect the appearance of what we'd expect was the molecular ion.

[lohjxMARCUS]

Or would it be because MS is a destructive process and thus the molecular ion gets fragmented into pieces, thus destroyed?

[Arkcon]

No, a small enough molecule, with a soft enough ionization source, will persist to the detector.

[Furanone]

My understanding was with electronic ionization an electron beam fragments the incoming molecules and then the quadrapole or ion trap separates the fragments based on their m/z ratio over time sending to the electron multiplier (detector) for a signal.

Typically 70 eV (electron volts) is used since it was found that this was where the best differentiation between molecules was found since at higher eV a mess of too many fragments was created (too much noise) and lower eV caused less fragmentation (less signal and less information). Now, mostly all of the mass spectral libraries are based on fragmentation at 70 eV. For some molecules that fragment easier the parent ion will be incredibly small or not visible. For soft ionization techniques such as chemical ionization, then the molecular ion is actually higher than the original MW since it forms an adduct with the chemical ionizing gas (ie methane)

[MOTOBALL]

"For soft ionization techniques such as chemical ionization, then the molecular ion is actually higher than the original MW since it forms an adduct with the chemical ionizing gas (ie methane)"

I'm afraid that this is just not true.  In the case of CH4 CI, an [M+CH5]+ adduct is certainly formed, as is an [M+C2H5]+ adduct and sometimes an [M+C3H5]+ adduct is also observed.
However, [M+H]+ is always* at greater intensity than the other adducts, typically of the order 100:10:1.
In NH3 CI, the analyte may or may not be sufficiently basic (in the gas phase) to abstract H+ from the ionizing species, NH4+; the relative intensities of [M+H]+ and [M+NH4]+ are therefore more variable across classes of compounds.

Incidentally, although we refer casually to the "molecular ion", that strictly refers only to the
[M]+. radical cation (+ve ion mode) or [M]- (-ve ion mode); [M+H]+ is a protonated molecule-ion (if I remember my definitions correctly).

*Since I haven't seen the CH4 CI spectra for the 20 million odd organic compounds, maybe I should state...."usually"...

[rwiew]

I feel there's a bit of confusion in this topic, as lohjxMARCUS never said what type of MS they're talking about - electron impact / electrospray / MALDI / whatever else?

[MOTOBALL]

I have a question on MS. Why isn't the molecular ion (parent ion) sometimes not observed in the mass spectrum? Does it have anything to do with the isotopes?

To try to dispel any confusion,

the ionization technique is not relevant---the "molecular ion" will not be observed if the amount of energy deposited in the molecule is sufficiently high.  With electron impact (EI), electrons at 70eV are typically used; this is well above the typical ~10 eV ionization potential of the average organic compound, and the ion then fragments to give the standard (EI) spectrum seen in MS data system libraries.  On older EI systems in the 1980's there was the option to manually adjust downwards the eV, which I sometimes dropped to 20-30 eV to observe the molecular ion.  Even the so-called "soft" ionization techniques (CI, ESI, FAB, MALDI etc), which deposit much less energy, can produce losses of small neutrals (H2O, NH3, HCl etc) or loss of large chunks if the energetics are right.  Large molecules have more degrees of freedom over which to distribute the excess energy, and their mol. ions are generally more stable.

The presence of isotopes (13C, 2H, 15N, 37Cl etc) has absolutely NO bearing on the above discussion.