How to determine polarity of components in TLC Estimate how a TLC-analysis would look like for the following reaction when you take a TLC at: a) the start of the reaction, b) after 65% conversion and c) after full conversion of A. (You may assume that A-C separate on the TLC-plate)


I am having a very difficult time understand how you can determine which compound is more polar by just looking at the structure. I don't know what to look at or what to prioritize.
When attempting to answer this question I assumed that B would be more polar (why: because it contains a nitrogen which is more electronegative than oxygen). So B should be closest to the baseline and A should be further away. What I then thought was that C should be in between A and B because the reaction reacts something polar and something less polar. This was not correct. Our professor drew the TLC-analysis like this:

And I don't really understand how I can determine that the product is more polar than both of the reactants. Is it because it contains both an oxygen and a nitrogen?
I would truly appreciate it if someone could give me some general rules or steps to follow to easily determine the polarity of different compounds.
I am assuming this is TLC run on silica. Silica is a mildly acidic surface so basic compounds such as amines do not come off the baseline unless you use a very polar eluent with added base (e.g. ammonia/triethylamine). Starting material B is a basic amine. Starting material A is an epoxide and fairly non-polar (kinda similar to an ether) and will run high in most systems, certainly any system where B comes off the baseline. Your product C is more basic (tertiary v secondary), this is the strongest effect. The second non-polar aromatic group raises the likelihood that it will run above B, but this is a weak effect. The alcohol is a polar group and will also pull it down thus the sum of these effects is that it runs lower 

This missing information is the eluent. From what what is given in the question it is clear that the eluent is something like DCM/MeOH/NH3 (that would be my first attempt to separate such basic components). As B is in excess what you are really looking for is loss of A. When you can no longer see any A by TLC, the reaction can be worked up.

The groups that make for low running are those that interact strongly with the silica surface: basic amines, acids, alcohols. This is a general rule of thumb, but in my experience trying to guess where a multi-functioned molecule is going to run is quite a lottery. I do not believe that it is a safe assumption that a product similar to C would always run below a SM similar to B.