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Capillary GC Column Killers – Part 2

21 May 2012

For my second installment of Capillary GC Column Killers, I am going to discuss derivatization reagents.  If you haven’t already read my first installment which covered the topic of a “safe” pH range, I encourage you to do so.

Capillary GC Column Killers – Part 1

Derivatization Reagents

Derivatization reagents are commonly used in gas chromatography to convert non-volatile compounds into volatile compounds by replacing certain functional groups with others.  Derivatization may also be used for increased compound thermal stability and/or increased detector response.


However, before you begin your next project, I would like you to keep something in mind.  Excess derivatization reagent in sample extracts may cause irreparable damage to the GC column’s stationary phase. For this reason, many methods specify that the derivatized sample extract be evaporated to dryness to remove excess reagent. After evaporation, the sample residue can be diluted in a pure solvent prior to analysis.

Several of the most damaging derivatization reagents are the perfluoro acid anhydride acylation reagents (such as trifluoroacetic anhydride – TFAA, pentafluoropropionic anhydride – PFPA, and heptafluorobutyric anhydride - HFBA).  These reagents form acid by-products, which will likely attack the column’s stationary phase. Silyl reagents trifluoroacetic acid (TFA) and dimethyldichlorosilane (DMDCS) are especially damaging to polyethene glycol (Carbowax) stationary phases, but are much less damaging to polysiloxane stationary phases.  Just like many silylating agents, TMS derivatives react with active hydrogen atoms; therefore, using polyethene glycol (Carbowax) stationary phase columns should be avoided when analyzing these sample extracts.

While it is best to assume that most derivatizing reagents will damage a column, there are a few exceptions that present little chance of damaging any capillary column stationary phase, including acylation reagents N-methylbis trifluoroacetamide (MBTFA) and the perfluoroacylimidazoles (trifluoroacetylimidazole – TFAI, pentafluoropropanylimidazole – PFPI, and heptafluorobutyrylimidazole – HFBI).  One thing to keep in mind, as pointed out by one of my co-workers, Kristi Sellers, is that even though these reagents may not damage a column, they still may cause contamination in the inlet, which could lead to ghost peaks.

Since there is no complete list of “safe” or “damaging” derivatizing reagents, we recommend using caution when analyzing samples that have been treated with any derivatizing reagent. If you notice any degradation in chromatography while analyzing derivatized samples, you may need to choose another derivatizing reagent.