How to minimize particulate build-up in flash chromatography systems

In order to perform flash chromatography consistently, the equipment you use must be properly maintained by following some “best practices”. These best practices include using clean solvents (I typically use ACS grade), volatile organic modifiers, and quality columns.

Only miscible solvents should be used when building methods (e.g. hexane with ethyl acetate but not hexane with methanol). Mobile phase modifiers, acids, bases, buffers, must be fully organic (no phosphate, sulfates, etc.), fully soluble in all method solvents, volatile, used sparingly (1% or less), and used within the appropriate pH range for the column’s media (between pH 2 and 7 for silica, pH 2-12 for most reversed-phase media). Why should these modifiers be organic, volatile, and under at the appropriate pH? Well, after flash purification, you probably do not want to perform another step to remove inorganic salts and/or silica, for example, from your product (silica dissolves at pH <2 and above pH 7, C18 hydrolyzes at pH <2, >12).

There is another, potentially worse problem from not using compatible volatile organic modifiers - salt build-up in your flash system. This happens over time from inorganic salt and/or silica precipitation in the system's fluidics (pump, valves, tubing), both in normal- and reversed-phase environments, especially when used at high concentration. Particulate build-up will cause system over-pressurization and damage pumps.

Another potential particulate source is your column. Columns made using lower grade components (filter frits, silica) can allow particulates into the flash system fluidics plugging tubing and valves. Columns can liberate particles when they are re-used or re-filled or if the mobile phase pH is outside the range of 2 - 7. Also, continual exposure to organic solvents swells the column body and bottom frit’s pores allowing small media particles to pass out of the column (a good reason not to re-use normal-phase flash columns).

Even new, commercially available columns can shed particles. In research I conducted a few years ago determining silica’s solubility in methanol, I found that commercially available columns packed with granular (e.g. irregular) silica generate particulates while columns packed with spherical silica do not (one of the reasons Biotage developed Sfär™ columns filled with spherical silica). The reason for this is physical instability of the granular/irregular silica under certain conditions (DCM/MeOH), an issue not observed with spherical silica.

So, how do you avoid these pitfalls and potentially expensive repairs? Well, be smart about flash chromatography.

Do use

• -ACS grade (or better) solvents
• -Volatile organic acids, bases, buffers (acetates, formats, carbonates) at appropriate pH for the media (typically 2-7 for silica)
• -Keep acid, base, and buffer concentrations as low as possible (no more than 1% or 0.1M)
• -New, quality columns packed with spherical silica

Do not use

• -Previously used silica or silica-packed columns (reversed-phase (e.g. C18) are re-usable)
• -Previously used filter frits
• -Irregular/granular silica
• -Inorganic, non-volatile acids, bases, buffers (no phosphates, NaOH, KOH, sulfuric acid, nitric acid, etc.)
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