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.

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.

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.

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.

The products of organic synthesis are designed with specific functional groups in order to possess desired properties. Depending on the compound’s functionality, it can be neutral, acidic, or basic as determined by a compound measurement called pKa or acid dissociation constant. Compounds with low pKa are typically acidic while those with high pKa tend to be basic. Compounds with a pKa near 7 are deemed neutral.

For medicinal chemists, maximizing the synthetic yield of their newly created intermediate compound is their priority. More times than not, flash chromatography is used to purify these intermediate compounds to at least 80% purity. Final compounds, however, not only require high yield but maximum attainable purity, typically in excess of 95%. For this purity level, chemists will either send the reaction mixture to an in-house prep HPLC lab or perform their own preparative HPLC compound purification, if it is available in the lab.

In my previous post, I talked about the "Chemistry Behind Normal-phase Flash Chromatography", the most common form of liquid-solid chromatography. In this post, I focus on reversed-phase flash chromatography and how it differs from normal-phase.

Our clientele at Biotage have interesting and diverse backgrounds from highly skilled synthetic chemists, to experts in natural product chemistry, to those who are just beginning they journey with chemistry. What I have learned over my 40+ year career in the “art” of chromatography is that for many of these fine folks there is a lack of understanding about chromatographic principles. This lack of understanding, I believe, is only due to their core study curriculum where separation science is used as a tool during lab work but the principles behind why a mixture’s components separate (or do not separate) perhaps are not effectively explained, understood, or studied.