Though this is a purification blog I do, from time to time, like to address synthetic chemistry experimentation findings in the desire to assist you with your reactions, as this is the front-end of your synthesis workflow. So, in this post, I report on some findings of the effect of reaction temperature on the synthesis of an amide, 2-amino-N-benzylbenzamide, a potential antibacterial compound.
This is a question I asked myself while I have been studying synthesis variables to see what, if any, impact each variable has on reaction product yield and purity. For this post, I evaluated the order in which I added reactants and solvent.
Chemical reactions gone wrong, I’m sure we all have experienced this issue, I know I have. You add your reagents in the proper amounts with a suitable solvent and perform your reaction only to find your by-product yield was greater than your product; by a lot. So, what do you do to isolate what little product you created with maximum yield and purity without breaking the proverbial bank on a big flash column and the solvent required for the purification?
Think of orthogonal flash chromatography as 2D-chromatography where a reaction mixture or natural product extract is purified first with one methodology or solvent gradient then re-purified with a different method or solvent pair in order to remove co-eluting impurities. This is a technique practiced in medicinal chemistry, especially for final compound purification, when the final product is purified first with normal-phase flash followed by reversed-phase prep HPLC.
There are two general flash chromatography techniques...
For most chemists purifying organic reaction mixtures, normal-phase flash chromatography is the go-to technique. Why not, it is quick, relatively efficient, and can provide relatively high loading capacities if the separation is properly optimized. However, most of these same chemists rely on only two sets of solvents to perform these purifications…
Chromatography is as much an art as it is a science. Between synthetic reaction products and natural products, the range of compounds requiring separation, purification, and isolation is broad and diverse creating challenges from time to time. Because of this diversity, not all chromatographic separations can be performed with a “neutral” solvent system – one without added pH modifiers or buffers.
Automated flash chromatography systems have helped synthetic chemists speed up their synthetic research. One major advancement with these systems over the past 15 or so years has been the addition of photo-diode array ultraviolet (PDA-UV) UV detectors with which chemists can detect and fractionate using one, two, or multiple wavelengths. Enabling detection and fractionation with multiple wavelengths increases the likelihood that target and by-product compounds will be isolated with increased purity.
Flash chromatography is a purification technique used by chemists to isolate their targeted compound from by-products and impurities. Because the reaction mixture (or natural product extract) may have its best solubility in a solvent that is chromatographically “stronger” than the mobile phase, liquid sample loading can be problematic causing early eluting and/or broad peaks with poor purity. In those cases, a technique called dry loading is frequently used.
Flash chromatography is a purification technique used by chemists to isolate their targeted compound from by-products and impurities. Because the reaction mixture (or natural product extract) may have its best solubility in a solvent that is chromatographically “stronger” than the mobile phase, liquid sample loading can be problematic causing early-eluting, broad peaks which can reduce purification efficacy and product purity. In those cases, a technique called dry loading is a better alternative.
With all forms of chromatography there are limitations relating to sample load – both mass and volume. These are independent variables which, for the best results, should be investigated separately. In this post, I will address the impact of increasing solvent volume on flash chromatographic separations.
A good question I get asked frequently to which there is no specific value. When asked this question I answer, “it depends on your sample and how good your separation is”; not a satisfying response, but it is the truth.
Chemists using silica columns for normal-phase flash chromatography typically equilibrate their columns prior to loading their samples. Companies manufacturing automated flash purification systems often have the equilibration volume and flow rate pre-programmed and tied to a column size. Some of these flash system companies allow equilibration volume to be edited while others have the volume fixed. Is one of these options better than the others? In this post I discuss how equilibration volume impacts flash chromatography results.
Have you ever been faced with the challenge of evaporating solvent from a reaction mixture where the target compound and perhaps some by-products are temperature sensitive and degrade or decompose with elevated heat? How do you efficiently accomplish this evaporation challenge?
For chemists isolating their synthesized product in maximum yield and purity is a primary goal. Sometimes the crude reaction mixture stays in solution, sometimes it does not. In these cases, is it better to just redissolve in a strong solvent, say DMSO, or to filter, wash, and then purify? After all, the precipitating material may be unreacted starting material and could potentially complicate the subsequent flash purification step. On the other hand, it may be product crystallizing on its own and worthy of your attempt to isolate it without further work-up other than filtration.
Purifying your synthetic product efficiently in high yield with minimal impurities is every chemist’s goal. At discovery-scale, flash chromatography is the go-to purification technique as it is relatively simple and effective.