# Why are isomers difficult to separate?

I recently learned that attempts to compare the spectra of two isomers of $\ce{C_3H_3^+}$ were frustrated by the difficulty of separating the two species.

What makes these isomers difficult to separate?

• I'm not even sure how one would try to separate them. Could you provide some more detail that would help someone answer the question? What kind of spectroscopy and what kind of separation were discussed? – Ben Norris Oct 6 '12 at 0:00

It would be important to know what kind of "separation" you are talking about -- spectral separation, which would just mean suppression on the spectroscopic response from undesired species, or physical separation, where you actually remove those species from your sample?

The problem is that not only may your sample contain different isomers, but these may actually interconvert through rearrangement reactions after ionization. This is a very common phenomenon in mass spectrometry, for example. If you want to single out the spectral signals of a certain isomer in a bulk sample, the simplest method would be to take the spectra of all unwanted components (from the literature or, preferably, separate measurements) and subtract them from your "mixed" spectrum. You would need information about the composition of your sample, though, or at least some indicator which tells you how much and what you have to subtract. Physically separating isomers may also be possible, e.g. if one of the isomers can be selectively ionized by laser irradiation, then separated from the remaining non-ionized sample. Such techniques are actually somewhat common in physical chemistry (not so much in everyday analytics, I think), although their applicability does depend heavily on the compounds and isomers under investigation. And there certainly are cases where different isomers are just too difficult to separate, or interconvert so readily that one structure virtually don't exist without the other.

Molecules which are made up of exactly the same elements but differ in atomic arrangement are called isomers.

Since the two isomers have the same mass and charge, any seperation techniques which rely on a difference in mass and/or density would be very difficult.

Mass spectrometry is an analytical technique in which components of different mass are separated and detected, typically by ionizing (charging), accelerating through an electric field to a given velocity and finally, 'bending' through a magnetic field. The final position of the is detected as a function of its charge-to-mass ratio.

Any two isomers of $\small\ce{(C3H3)^+}$ have the same charge-to-mass ratio and therefore would be very difficult to separate and detect with mass spectrometry.

• So it's just that isomers in general are difficult to separate, not something special about this particular configuration? – Dan Oct 6 '12 at 3:13
• Isomers can be identified by techniques other than mass spectrometry. For example, since each monomer would have different electron configurations and bond lengths, it is possible to detecting the energies associated with molecular orbitals using infra-red spectrometry. Each isomer can also be modified and separated by some chemical means by forming ligands within in a complex. – theo Oct 6 '12 at 9:49

Firstly, the reasons above—identical density and molar mass—are very true.

I also know that at least for some enantiomers they racemize, or readily and spontaneously convert between both forms. This means that even if you start with a pure sample of one form, you will eventually end up with both. A famous example of this is with the banned drug Thalidomide, made in the 50s to treat the morning sickness of pregnant women. The R-form worked fine. Unfortunately, its S-form caused severe birth defects. If someone could figure out how to separate the two without it racemizing (there is some work on similarly structured molecules, I'm sure), they would have done so.