Molecular Ion

[chrom]

In our lab we are having perkinelmer GCMS, observation Molecular ion in most of our analysis is difficult. Although the EI technique is hard ionization, positive ion formed may undergo fragmentation. But is there any instrument parameter is there to get the molecular ion peak.

Thanks in advance.

[lmh]

do you have the possibility of using CI instead of EI?

[Don_Hilton]

Fragmentation in an EI ion source is a function of energy transferred to the molecule. This comes from the energy of the electron beam and the temperature of the ion source. Dropping the ion source temperature may have a small effect on fragmentation - but don't expect much. And, dropping ion source temperature in some instruments results in more rapid fouling of the ion source. I have dropped the electron energy in two different types of instruments. In one I did see what looked like soft ionization -- as my signal dropped into the noise. On the other the signal only went away. (In short, not a productive method of finding a molecuar ion.)

There is a researcher who uses supersonic cooling of the molecuar beam coming off the column to avoid fragmentation. This looks like a really nice technique to acchieve what you want to do - but it would require changing some hardware.

Is there a particular reason you are looking for the molecuar ion? The molecuar ion is very helpful when you are attempting to solve a structure - but there are even molecules that do not show a significant moleucar ion in CI. So with a bit more information about what you are trying to do, perhaps someone may be able to direct you to a different - and better solution.

[chrom]

1. We have only EI.

2. For identification of Unknown impurity, if probable route cause not known it will be helpful.

Thanks for your valuable sharing of supersonic cooling.

[Peter Apps]

Unless you have strong expectations of what the unknown is likely to be you will not be able to identify from a low resolution mass spectrum even if you have the molecular ion.

This might be a job for a contract lab that can do high res MS, perhaps MS-MS, or ideally NMR if you can accumualte enough of the mystery compound.

I toyed briefly with the idea of getting supersonic cooling, if I remember correctly the add-on hardware and software cost more than the benchtop MS !

Peter

[Loekie]

decreasing the electron enegry can give you a better molecular ion/ less fragmentation but it probably will cost you some sensitivety. I don't know if you have that capability on your system.

[chrom]

I will try to do the same.

Analysis of sample in direct insertion probe vs passing through GC column may affect the observation of molecular ion ?

When analyzing in DIP mode, sample has to be kept in probe and it immediately heated then formation of ions, is it favour the molecular ion presence. I know that the detection is based on mass analyzer.

[lmh]

I am so happy to hear someone of the experience of Peter Apps saying it's tricky to identify something with only low-res MS data to go on! I find it really hard, but thought it was just me being a bit dumb.

[Peter Apps]

Hi lmh

Interpreting integer resolution mass spectra back to stuctures is a straightforward matter of organic chemistry mechanisms - or so I've been told by those who can do it !

The problem is that a given spectrum is very nearly always compatible with several different structures, and to tell which of those is the correct one needs other information - at the very minimum a high res MS value for the molecular weight to be compared against the calculated value for that stucture. And even with that you still cannot tell isomers apart.

Peter