Would anyone care to comment on their experiences with stationary phases containing amide linkages? I'm aware that amides are susceptible to hydrolysis but are there any limitations on these columns regarding pH and additives that differ from the traditional C8 or C18 columns? I was woking with a Supelco RP-Amide column and noticed the chromatography was completely different after flushing and storing the column with ACN. Supeclo concluded that the problem was due to the sample diluent which was 0.1M HCl. Any other observations/suggestions and/or cautionary notes would be greatly appreciated.

The polar embedded group does shield the silica surface and makes the packing more suitable for basic analytes at neutral pH and stable in high aqueous environments. However it is still an amide and can be affected by pH, which will allter the selectivity over time. One look at acidic analytes on the amide columns and you'll see they tail much more than standard C18 phases. This indicates that the amide adds a type anion exchange function to the separation. So by switching between pH's in your mobile phase you may protonate or deprotonate the amide group and thus change selectivity and/or capacity. This is most likely what you are experiencing.

I noticed Alltech has a new select C18 phase which looks like it might be good for basic compounds it may be worth evaluating one of those.

I don't know about this. The tail under acidic conditions on most amode columns stems from a two-step synthesis, which leaves amine on the surface, and not from a hydrolysis of the amide.
Anyway, there are phases with embedded polar groups that do not have this problem. Carbamate phases are synthesized in a single step. Even if they fall apart, they do not result in amine on the surface.

I have noticed that acids are worse on amide columns vs. carbamate columns for the reasons that Uwe pointed out above. I also observed that the type of acid used to pH a buffer greatly affects the retention of ionic compounds on amide columns. For example, we observed a decrease in retention with decreasing buffer concentration for an amine type compound. We used HCl to titrate to the desired pH. However, using the same concentration and pH but instead titrating to the desired pH with H3PO4, decreased the retention of the amine compound by about 1 minute. Would someone mind explaining this?