8 years ago, when I was a lab technician in organic synthesis, thin layer chromatography(TLC) and Column Chromatography(CC) was a daily task I had to do. And Column Chromatography(CC) was a basic skill that nobody did not know.

CC is a very time-consuming and labor-intensive task. A column commonly takes several hours or even longer to finish.

Sometimes, our lab does some reactions with particularly small amounts, it maybe takes at least a morning to complete a column for just a few hundred mg. For more complex separations of natural extracts, it is very common to finish a column for several days.

At that time, my leader often told me, “Never let the stationary phase get dry during the chromatography column? You need to keep an eye on it all the time.”

Why is it terrible when the Column Chromatography(CC) runs dry?

The reason is that when the Column Chromatography(CC) runs dry, there may be a lot of bubbles in the silica gel, which will make it difficult to separate the product out. Especially in the projects that require the strict calculation of product yield, the yield may be directly dropped by ten points, even halved if the column dries out or stops in the middle of the run. This kind of blow is very fatal, and in many cases, it may be reworked from scratch.

However, if you just want to get the product and don’t need to consider more about the reaction yield, it is not a big problem when the column dries out in the late stage.

For example, to make small molecule functional materials, only need to get enough amount which is enough to test its performance, and the yield is not the primary factor to consider. In this case, then don’t need to worry about the dry-out situation.

What is Column Chromatography(CC)?

Chromatographic columns are the most basic means of separation in organic laboratories.

Unlike inorganic chemical reactions that generate gases or precipitates, organic synthesis reactions are homogeneous in most cases. That means the product we need is mixed and dissolved in the solvent.

And there may be other substances such as the substrate that has not reacted completely, by-products of the reaction, catalysts, etc.

In order to get what we need, we should consider separating these mixed substances, and the column is the most widely used and most adaptable method of separating these things.

The principles of chromatography use the “speed” of different substances on the stationary phase to separate different substances under the mobile phase flushing.

Actually, it is based on the distribution ratio of the substance in the stationary phase/mobile phase or fixed relative to the difference of the “retention capacity” of different substances.

How to choose the right column?

Nowadays, the most common column in the organic laboratory is the silica gel column, which uses silica gel as the stationary phase. Substances with lower polarity on the forward silica column climb faster, and substances with greater polarity on the reverse silica column climb faster.

So what kind of silica gel to use depends on the product mixture. In most cases, the separation of small molecule compounds can be solved by using a forward silica column. If the product has a particularly much center of positive charge, it may be easier to invert the phase column.

There is also an alumina column. The basic alumina column can be used to deal with the production system that needs to be separated in a high pH environment.

Neutral alumina columns tend to retain some electron-rich compounds. The acidic alumina column can separate some strongly acidic substances.

The absorptivity of the alumina column is weaker than silica gel, so if the product is extremely polar and cannot be washed off on silica gel, you can try the alumina column, maybe it will work well.

As for the gel column, it is high-tech compared to the silica gel column and alumina column. It is mainly aimed at the separation of high molecular products, which can quickly separate high molecular products and small molecular compounds.

The principle of the gel column is equivalent to that the stationary phase as an “anti-sieve”, it is because the larger molecules cannot enter the gel, they go through the gaps between the gels, so they run faster.

And the smaller-sized molecules will enter the micropores in the gel and will not be washed down too quickly. In this way, the mixture can be separated according to the size of the molecule.


It’s very tiring and boring to run a column, but it is what it is, no one can avoid that in most organic synthesis fields. Because the application of preparative chromatography is limited and considers the factor of cost, manual columns can’t be completely replaced.

Although a little bit boring to install the column, I feel it’s a sense of accomplishment when the product was finally released.

How do you think when you are doing the same thing?

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