[Kilgore Trout]

Greetings everybody, I am an senior biochemistry undergraduate working on a project which consists of protecting uridine at the 5 prime position with TBDMS-Cl. I have resulted in low yields so far (55%) even though the literature reports 97%. Any advice you all can offer would be greatly appreciated.

1. 100 mg's of uridine was co-evaporated twice with pyridine and then once with toluene (strangely, even though I use toluene, the pyridine odor is still there)
2. To a solution of uridine (100 mg, 0.410 mmol) dissolved in 2 mL of anhydrous pyridine, there was added 4 equiv. of imidazole (111.6 mg,
1.64 mmol) and 2 equiv's of TBDMS-Cl (123.59 mg, 0.820 mmol) at 0 °C under Ar atmosphere. The reaction mixture was stirred
at room temperature over night then treated with methanol (100 microliters). After stirring at room temperature for 1 hour, the solvent was removed under reduced pressure. The residue was purified by silica gel column chromatography (DCM/MeOH).

TLC shows that there is still a lot of starting material left over (uridine). I even collect three test tubes full of this stuff after c.c and I get anywhere from 50-55% yield of my product. Could it be possible that the TBDMS-Cl has been hydrolyzed?

[Kilgore Trout]

Or I'm thinking maybe I'm doing the co-evaporation wrong.

NMR shows a clean product, btw.

Forgot to mention more abotu the TLC (wish I had a picture: I get one spot on the bottom (uridine) and one right above it which is my product. Done with 5% MeOH in DCM.

[discodermolide]

Why are you co-evaporating with pyridine? Toluene should be sufficient.
Anyway you got it now so it does not really matter.

[Babcock_Hall]

What is the purpose of adding 100 µL of methanol?

[OC pro]

Try TBSOTf (same conditions but keep at 0°C!). TBSCl seems to be the wrong reagent here.

[zuriel]

What is the purpose of adding 100 µL of methanol?

I'm guessing that's to quench the TBSCl

[Babcock_Hall]

It is early, and the coffee has not kicked in yet, but the methanol seems to be in large excess over the other reagents (2.5 mmol?).  Is there any possibility that the desired product is transferring some of the tert-butyldimethylsilyl groups to the methanol, lowering the yield?

[Dan]

Is there any possibility that the desired product is transferring some of the tert-butyldimethylsilyl groups to the methanol, lowering the yield?

I'd say this is unlikely under the conditions reported. I think this is a lit prep, e.g. Org. Lett. 2012, 14, 2488 (there are many other similar protocols reported). My bet is either it's the quality of the TBSCl (check NMR) or the "dry" pyridine is not so dry - I have had issues with these reagents in the past when the bottles were old and/or improperly stored. I would also suggest DMF as the solvent instead of pyridine as I have observed faster silylation rates in DMF compared to pyridine in the past with similar substrates. Stirring the reaction mixture with flame dried, powdered molecular sieves prior to introduction of TBSCl has also helped me in the past.

[Kilgore Trout]

The nmr of tbdms-cl looks fine. My bet is that people are not flushing with argon after usage.
 
Our suspicion is exactly what you said, our anydrous pyridine is probably not good anymore. We're currently revising our procedure and taking a look at the literature. We have our eye on anydrous THF at the moment and are aiming at silylating at the 2 prime and 5 prime position in one pot. Thanks for the advise gentlemen. 

[appler]

Anhydrous condition was not controlled well. Silylation in Py was much slower than in DMF. Maybe it needed longer time. TBSOTf is bad choice. Because its reactivity is so strong that no regioselectivity will be observed.