I thought about removing the DMF through extraction, which I have done but my students have not. Do you include LiCl in the aqueous rinses? I seem to recall seeing that in one recipe, but I could be mistaken. I was a little worried about how our product would partition in multiple rinses, and given our modest yield after the silica column (I will ask my students to calculate it today, but my guess is 30%), possibly my concerns were not wrong. Just to clarify, we used a more polar solvent in the silica column than we had thought we would, based on the time points.
I only saw one product by TLC; therefore, the low yield cannot easily be explained by forming a side product. We did make sufficient material to test. If I had this synthesis to do over again, I would have tried THF before trying DMF. One of the reasons that I attempted to remove (most of?) the DMF by rotary evaporation after the reaction was to minimize its presence in chromatography. I was worried that it would drive the product through the column too quickly. What, specifically, was the reason you think DMF is bad in chromatography? We used a model of Welch DryFast pump that was advertised as being able to pull a slightly higher vacuum than their base model.
My students tend to use a small portion of chloroform reflexively when they dissolve their crude product, and I wonder that it might have a negative effect on chromatography in some situations. The dry load technique is one that we need to put more regularly into our bag of tricks. Any tips on avoiding silica dust flying about in the rotary evaporator?