I'm not detecting ammonia in my samples while using a NOESY pulse program for a 1H-NMR experiment.
Is it possible for ammonia to be detected by a 1D-1H-NOESY experiment?
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In the 1H,1H-NOESY experiment you are using the nuclear Overhauser effect to transfer magnetization from one proton to another proton in close proximity (< 5 Å). This only works within a single molecule, unless you have a reasonably stable complex you can't observe signals in the NOESY between protons of different molecules in your solution.
Ammonia has three protons which are at least chemically equivalent, their signals will appear at the same chemical shift. In a 1D NOESY you irradiate at the frequency of a specific proton and then observe the transferred magnetization at other frequencies. You can't observe magnetization transfer between protons at the same frequency that way, as your irradiation will destroy any signal at this specific frequency.
You can ignore the explanation above, as the NOESY experiment you are using is different. In metabolomics the NOESY 1D is used for water suppression, this is a different experiment than the 1D NOESY I explained above.
The common variant of this I found also uses presaturation to suppress water. This presaturation will also affect all signals that exchange quickly with the solvent, and the protons of ammonia are exchanging with water. So I would expect the ammonia signal to be far weaker or even not visible in such an experiment.
If you want to observe ammonia, you have to use a water suppression method that doesn't affect exchanging protons.
First off, NOESY is a tool that gives information more useful for structure determination and confirmation (as Mad Scientist has explained). A simple and quick 1H NMR experiment should be enough to quantify your compounds assuming you have sufficient peak resolution (often a problem with multiple compound quantification).
How do you know that you cannot detect the ammonia? Where do you expect to find its peak (I believe it is a triplet found around 0 ppm, depending on solvent/conditions)?. Remember that the chemical shift may be affected by temperature, concentration, or hydrogen bonding, so it may not be where you expect to find it.
I suspect your problem could also be with the deuterated solvent you use to prepare samples. For example, if you are using D2O, you will not see any OH, NH (ammonia), or SH protons as they will rapidly exchange with deuterium from the solvent, effectively making your ammonia "invisible". You may try to dissolve your compounds in deuterated solvents that do not exchange as readily (CDCl3, DMSO-d6).
Another possibility which I already mentioned is your peak resolution. If you have multiple compounds in this sample at various concentrations then you will likely have many peaks where the ammonia signal could "hide" under, so be careful there as well.
I have found by experience that when trying to quantify mixtures in 1H NMR (especially as part of a routine) it is extremely valuable to first collect a reference spectrum of each individual compound (when possible) using identical preparation techniques and experimental conditions in order to make peak identification and quantification of mixtures a breeze.
Hope this helps you sort out your problem!