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When we perform column chromatography with silica to purify the reaction crude product, we sometimes need to change the solvent system to better extract our target product.

For example, changing from pure hexane to 1:4 hexane:DCM. However, if the polarity is not change gradually, it often leads to column cracking, which means there are air bubbles (or is it solvent bubbles?) in the column, and it will affect elution the pattern.

Why might changing solvent polarity crack the column? And where is the air coming from? I do not see how the air is getting into the column when there are solvents sitting above it.

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    $\begingroup$ Based on both answers, when the run is finished it may be best to run a gradual gradient back to non-polar solvent (hexane) as well. $\endgroup$ Commented Feb 25, 2023 at 12:31
  • $\begingroup$ @PeterMortensen Why a silica gel and why not a link for that one? This is some English that I, a non-native, don't understand. Can you provide more context for that, please. Are the links to such common chemicals as hexane and DCM really necessary? $\endgroup$ Commented Feb 25, 2023 at 16:20

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The fundamental reason for cracks in packed beds is that all chromatography columns (used in organic labs or even HPLC) do not have particles packed in a regular crystalline manner. This means that the bed density is neither radially nor axially uniform. At best we have random closed packing in HPLC columns, which are typically packed at 10,000 to 30,000 psi (!!) but the "home-made" organic lab column has a loose-packed structure. This means that there are large gaps in this structure. As an analogy consider a heap of quasi-stable grape bunches (randomly arranged spheres). Grape columns can collapse when a few bunches of grapes are moved.

Now there are two types of solvents (i) aggregating and (ii) dispersive if we classify them on the basis of their suspension properties. You can readily check a suspension of silica in those solvents under an optical microscope. When you change solvents, you actually change how those loose particles stick to each other. If a bed is loosely packed, and suddenly a solvent is added which is strongly aggregating, cracks may develop in the bed.

P.S.: The solubility of gases may cause air bubbles to form at the interface of two different solvents. Helium sparging has become almost obsolete because it is becoming expensive and there is a predicted shortage of this element in the future. If you are concerned, vacuum degassing under an ultrasonic bath is a routine procedure these days.

Regardless, the punch line is that an ordinary silica bed is loosely packed. If the particles were arranged in a perfectly crystalline manner, cracks would never appear regardless of the solvent used. We can only dream about discovering a magical way to arrange silica particles in crystalline form.

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  • $\begingroup$ Helium sparging is obsolete? I think the "punch line" is not to change the ratio of polar and non-polar so quickly. Any movement of column material will be a result of permeating and swelling of silica by the polar solvent. $\endgroup$ Commented Feb 25, 2023 at 10:50
  • $\begingroup$ In this case, hexane is the "aggregating solvent". But this is "normal phase" chromatography. That's what you start with. The more polar mobile phase is used to elute the components that are more attracted to the silica. $\endgroup$ Commented Feb 25, 2023 at 10:53
  • $\begingroup$ It's the polar mobile phase that's going to change the column if it is added in too abruptly. Check the packing/storage solvent. I would not give up on a "cracked" column without washing it for a few hours. $\endgroup$ Commented Feb 25, 2023 at 10:57
  • $\begingroup$ "When you change solvents (mobile phases), you actually change how those loose particles stick together". This can "crack" even a highly compressed silica mass. The polar solvent will swell a mass of silica. Then add hexane, what happens? But I would agree a more consistant particle size, shape, and method of packing would be contributing factors. $\endgroup$ Commented Feb 25, 2023 at 11:01
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The model of liquid chromatography with a stationary phase (silica, alumina, ...) and a mobile phase (your eluent / eluent mixture) is a simplification. If your liquid chromatography is not based on size exclusion, then recurrent adsorption of molecules to, and desorption of molecules from the stationary phase are detrimental to the success of your intended purification.

Note, this back and forth isn't only about the molecules you want to separate. It equally happens to the molecules of your eluent (which itself can be a mixture), which are of much higher concentration. Hence, the dissipation of heat of adsorption can become an issue, especially for a sudden substitution of one eluent (mixture) by one other, or if the gradient to change the eluent's composition is too steep: The temperature can rise this much that outer walls of the (preparative) column feels warmer, and that solvents of lower boiling point pass this threshold. A preparative column filled by gravity / settlement of a suspension then can break. Perhaps someone else can back my impression with experimental data, the larger the ratio of diameter to enclosed volume of a preparative column, the more likely this is to happen.

(A rise of temperature equally can be observed preparing the silica suspension if solvent is added to still dry silica.)

VWR / Ace glass offers jacketed chromatography columns with dimensions suitable for preparative scale; in principle, their connection with a thermostat could attenuate the problem. So far, I didn't use them; their threads suggests they might anyway be designed for automated use with a fraction collector, or a MPLC:

enter image description here

(picture credit VWR)

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Silica gel is polar. Hexane is non-polar. DCM (dichloromethane) is polar.

Adding polar solvent to the column too quickly could cause uneven permeation into the column packing.

But the main concern is solubility of gasses in DCM vs hexane. When the DCM mixes in with hexane in the column, outgassing may occur.

Sparging mobile phases with helium is known to reduce outgassing and might help if running a strong gradient.

If possible, ease off on the rate of gradient change as well, and let the best column storage solvent elute through for a while at the end of each run.

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