[RaInBowDaSh1488]

I have recently synthesized 5,6-diethoxybenzimidazole (confirmed by NMR). This was done from the corresponding o-phenylenediamine using formic acid/4M HCl. My first question is in regard to some strange coloration during the reaction. The diamine is very air sensitive and I use it immediately after synthesizing it. The base is a white crystalline solid, but on contact with any acid, it immediately turns purple black. This black color stains the aqueous solution and makes the work up tough. I've not synthesized benzimidazole's before, but I can't find any reference of this kind of behavior. My best guess was the color was given by the diamine's salts being formed in the acid solution, but the reaction goes to completion and the color remains. Does anyone know if this is common behavior in benzimidazole synthesis? I've done the reaction with an orthoformate and catalytic DBDMH and had similar results, albeit the color was less strong. 

I am also curious about the acid base behavior of this kind of heterocycle. At low pH, my product precipitates from water. At high pH, it seems to form an insoluble oil as expected. I've tried both collecting the HCl salt through filtration and the base through extraction; neither have given acceptable yields. I am a bit confused as to why salt is precipitating, I sort of expected it to be soluble.

Any advice on the workup for this kind of compound would be much appreciated. I just seem to have a hard time getting it out of the solvent. Should I maybe try making it extremely basic or acidic? If so which one should I try first?

[TheUnassuming]

So remember first that a little color goes a long way.  In other words, if the compound is highly active it takes very little to give drastic color changes to the solution.  In this case I'm guessing you have a side reaction that takes place which gives you the color.  This would explain why it doesn't go away once your starting material is gone.  How are you monitoring the reaction? 
What solvents have you tried for extraction?

[Eloquentia]

Aromatic amines are known to be sensitive to oxidation by air. In your case, it is a diamine, which is also very electron rich due to the electron donating ethoxy groups. I have observed dark color and sometimes formation of dark colored tar-like byproducts due to oxidation both during a reaction or due to prolonged storage (have you ever seen a very old aniline bottle?). IMHO you have oxidation byproducts and maybe acid catalyzes the oxidation process. I would bubble my reaction mixture with argon before it comes in contact with the diamine. Water dissolves quite high amounts of oxygen at RT (I guessed you use water). Also consider this classic procedure from "Organic Syntheses" http://www.orgsyn.org/Result.aspx?ga=na. They do not use HCl, maybe you shouldn't either. Hope your yields get better.