Organic chemistry syntheses often use polar, high boiling point solvents to facilitate high temperature reactions. However, these solvents also can complicate down-stream compound purification, either by evaporation, crystallization, or even flash chromatography.

As chemists, our job is to make new molecules. If our synthetic design works as planned, we will have success and the target product made. As we all know, along with our desired compound, by-products are often created as well. To remove the by-products, the reaction mixture requires purification, typically with flash chromatography.

Synthetic chemists continually seek ways to create novel compounds. Along the way they evaluate reagents, solvents, and reaction conditions giving rise to various reaction products and by-products.

As synthetic chemistry has evolved, so has flash chromatography. Target molecule synthesis is becoming more complicated and the synthetic products more polar. This shift in compound polarity has changed purification strategy from almost entirely normal-phase flash chromatography using silica to a significant percentage of flash chromatography now being reversed-phase during the past 9 or so years.

Most chemical reactions take place in liquid form since compounds in solution are more likely to interact with each other, especially when heated. Reaction solvent choice varies based on reagent solubility and reaction temperature requirements. Because many reactions today require high temperatures, solvents such as dimethylformamide (DMF) and dimethylsulfoxide (DMSO) are frequently used. However, just because a reaction solvent has the proper reagent solubility and/ or a high boiling point does not mean it should be used. Why? Well, as we will show in this post, the solvent itself can alter synthetic efficiency by changing reaction kinetics as well as the number and type of by-products.

In drug discovery, microwaves are common tools for heating reactions to high temperatures and pressures so that it is possible to synthesize compounds in minutes that might otherwise take hours by conventional heating. However, another environment where this is a considerable advantage is in the teaching laboratory. By greatly speeding reaction rates, students can try multi-step synthesis is a single day, and look at the effect of altering reaction conditions on products and yields.

Flash chromatography is a standard part of an organic chemist’s workflow. It is utilized after most reaction steps in order to remove most of the generated by-products and excess reagents.

Scaling up reversed-phase flash chromatography methods is often necessary as reaction scale increases. This is especially true when other non-chromatographic purification techniques do not work or meet purity and/or yield needs.

Sometimes we find ourselves having to make decisions fast, and act even faster - especially in situations like the one we live in today, where there is a high degree of uncertainty.  In this kind of situation it is ideal to find a partner that is willing to share the risk with us, so that the long-term consequences of a decision made in times of uncertainty are not going to make us regret our choice when things get back to normal.

The bane of organic synthesis for most chemists is purification rather than synthesis. Synthetic reaction mixtures are rarely devoid of impurities so some type of purification is necessary.  Most often flash chromatography is used but for many chemists, it is less well understood than their chemical reaction and provides some level of anxiety.

In this post, I will summarize the five most important steps to creating a successful flash chromatography method and thus the anxiety associated with it.

This is an interesting question that I am asked from time to time. There does seem to be two camps in which chemists reside – one believing longer and thinner columns provide better separations and the other preferring shorter and fatter columns to do the same chromatography.

Which is right? That is a question I will try to answer based on my own data.

The Biotage® Selekt Flash purification system is designed for the rapid and simple isolation of target molecules from complex mixtures. Typically, this is seen in the area of drug discovery, where large numbers of molecules are synthesized in order to find active pharmaceutical ingredients for future pharmaceutical use. However, flash purifications can be employed in any work that involves the requirement to purify compounds, which is most branches of chemistry.

Recently, I posted an article explaining why high performance TLC plates are not needed for method development for high-performance flash chromatography.  Based on some excellent feedback, I see a need to discuss silica chemistry and its impact on chromatography.

For many chemists using generic linear gradients and even gradients based on TLC the purification results often are not selective enough to separate all of the compounds in their mix.  This is especially true if your target has a closely eluting impurity. One method used to try and increase resolution is the use of an isocratic hold or gradient pause during purification.

In this post I examine the use of the isocratic hold to determine how well it works and when/if it should be inserted into a gradient method.

Have you ever run flash column chromatography with mass detection (Flash-MS) and observed the total ion current or TIC increase during the purification only to find that there was no discernible compound contributing to the effect?

In this post I discuss how I came across this issue and the solution I found to work.

Chromatography is a common tool of the chemistry laboratory, and most chemists involved in synthesis have a good idea how automated flash purification system work on the lab bench. However, knowing how to take purifications from the laboratory to a manufacturing environment is a different question altogether.