Chromatography Forum

Dear All,
I am not familiar enough with GC-MS but I have to operate it for my colleagues . Most of my colleagues are organic synthesis chemists. They bring me their synthesized compounds (mostly solids) and ask for the mass spectra and molecular weight. We have a Varian Ion Trap GC-MS system.

My question is:

Are there rules to help in deciding what samples are suitable for injection in such a GC-MS system?


Many thanks in advance for any contribution.

One simple one is that any compound that has a significant vapour pressure below 400C can usually be determined by GC. No vapour pressure no chance.

any compound that has a significant vapour pressure

Thanks for the rule, but how to define "significant" for a beginner like me?

One way to gauge it is to know other molecules that can make it through a GC. Cholesterol and Vitamin E chromatograph nicely as do hydrocarbons in petroleum up to at least C40. As you add polarity the size of the molecule that will make it through a GC column will decrease. So, if you do not have a reference of something that will or will not go through a column, you can look for molecules with similar formula and see if they have been separated by GC.

And a caution on being given a compound by the synthetic organic group: Be sure you know what else can be present in teh event the compund is not pure. If you have strong acids, bases, or other reactive compounds (include catalysts), they may go into solution with the compound of interest. These can do some chemistry in the inlet and are often retained in the inlet or on the head of the column where they can react with compounds in the next injection.

Many thanks for all of you.
Can we get any benefit of knowing the melting point? Boiling point? expected molecular weight?

hplc-chem
If your sample compound has a boiling point below 500C it is a stable compound that can be analyzed by GC-MS. If it has a high melting point chances are increased that you can analyze it by GC-MS. Non-polar compounds up to about 600 amu (C42) can be analyzed by GC-MS while as the compound becomes more polar the upper molecular weight that can be analyzed decreases and for semi-polar compounds the upper molecular weight is about 300-350 amu while very polar compounds can not be analyzed by GC-MS. Note that not all GC-MS systems are the same and single quad GC-MS can analyze bigger compounds than internal ionization based ion traps such as the Varian 2000 or 220 due to the closed structure of the ion trap. GC-MS with Cold EI has the biggest range of compounds amenable for analysis as it can use short columns with high columns flow rates and it has a fly-through ion source (~doubled size). Note that GC-MS has an important advantage over LC-MS in the analysis of new synthetic compounds which is the fact that unlike with ESI its electron ionization yield is relatively uniform and thus one can determine chemical reaction yields with GC-MS up to the onset of ion source peak tailing (if you can trust that the explored compounds have molecular ions). A paper on the use of GC-MS with Cold EI for the analysis of chemical reaction mixtures is available upon request at my Email below.
Amirav
amirav@tau.ac.il

Thanks for all.

In order to do GC one needs to be able to make the anayte a gas in the range of the instrument (up to 325 for normal nonpolar columns)
In order to maks something a gas the intermolecular forces must be broken. The more polar groups the stronger the forces are. Also being smaller and having more C=C bonds gives a lower boiling point.


Ionic bonds very strong hard to breake therefore most charged molecules can't be GC'd
H-bonds strong if there are many H-bonding groups it is likely too nonvolatile for GC especially as the size of the molecule increaes
Polar groups same C=0 not as strong as C-OH
Lond disp/induced dipole weak and are the only forces found on nonpolar analytes like alkanes.

dissolve 1mg of that solid in 10ml Methanol, centrifuge if required and inject 2 micro in you gc

A note regarding the previous comment. For many of us, methanol is not the first choice of solvent. It does not provide solvent focusing on non-polar GC columns and it is not a good solvent for non-polar compunds.

dissolve 1mg of that solid in 10ml Methanol, centrifuge if required and inject 2 micro in you gc

Bad plan - methanol dissolves a whole range of substances; salts, sugars and urea among them that will crud up the inlet and destroy your column. As a solvent for GC it ranks only slightly better than water - the last resort when nothing else works and you have a well understood problem for which these intractable solvents offer a specific solution.

Happy New Year.

Peter

You will need to use the methanol (or ethanol to be more safely) to get every organic compounds in the sample.
What is the problem of injecting urea in the gc-ms it could be the analyte?!!

You will need to use the methanol (or ethanol to be more safely) to get every organic compounds in the sample.
What is the problem of injecting urea in the gc-ms it could be the analyte?!!

The problem with urea is that it polymerises in the gas phase at GC temperatures to produce cyanuric acid, which generates an unstable baseline and serious baseline drift. Urea itself can get through a GC, but unless the deactivation is more or less perfect it produces an ugly hump on non-polar phases. The peak on polar phases is front-tailed.

Have you ever run samples containing urea on GC-MS ? I have.

Many, perhaps most, of the compounds that will dissolve only in methanol or water are very poor candidates for GC anyway, because they are highly polar and/or non-volatile or unstable in the gas phase.

Peter

You will need to use the methanol (or ethanol to be more safely) to get every organic compounds in the sample.
What is the problem of injecting urea in the gc-ms it could be the analyte?!!

An important thing for any analytical technique: There are some things you do not want to introduce into any particular instrument. Thus, with GC we try to separate our compounds of interest from salts and other compounds that will only foul the inlet and column. We also do not want try to analyze a compound that will be changed in such a way that we will be misled by the results. And we want to avoid damaging or fouling the instrument unnecessarily.

On what might be the analyte: it is best to have some kind of an idea of the nature of the sample before accepting a sample to be run on an instrument.

If someone hands me a unknown sample that happens to be sucrose, I can dissolve it in methanol. I can inject the solution into a GC. I will probably see peaks. None of them will be sucrose, but rather decomposition products. By blindly putting a sample into the wrong instrument, I will not give the correct answer. Not what I want to do...

My favorite broad solubility solvent is acetone.