Blog Profile / Org Prep Daily

Blood curdles if you don’t stir it

Trityl group on sulfur is unstable to LiAlH4 reduction. It falls off as triphenylmethyl anion – that’s where the gorgeous red color is coming from. (Unlike trityl cation, which is canary yellow). I did not know about this S-trityl instability – my Greene book (3rd edition) for example mentions only the electrochemical reduction at highly [...]

It curdles if you don’t stir it

Uroboros

I have been making water-soluble polymers with biomedical applications for the last 16 months and it is quite satisfying: Our macromolecules are usually well behaved – they extract into organic phase. They precipitate as a snow-white fluffy crystalline solid, on a kilo scale. They even have beautiful NMR spectra. Unfortunately, such was not the case [...]

Shake and pray

There is a pop-chem procedure on YouTube that I find astonishing – it beats the Diet Coke and Mentos trick hands down: A guy loads NaOH dry solid pellets, about 1 inch high, into a plastic bottle, and adds about 2-3 inch thick layer of dry ammonium nitrate granules. Then he fills the bottle with [...]

Uroboros

. So I have been making water-soluble polymers with biomedical applications for the last 16 months and its quite satisfying. Some macromolecules are nicely behaved – they extract into organic phase if you want them to and they even precipitate as a snow-white crystalline solid, on a pound scale. Unfortunately the frothy solution in the [...]

S-tritylthioacetic acid

Neat mercaptoacetic acid 24.0g (260 mmol, about 18 mL) was added in one portion to a solution of trityl chloride 58.0g (208.0 mmol) in benzene 200mL (non-anhydrous, ACS grade). The flask was equipped with a gas outlet Drierite tube and the mixture was stirred for 17 hours: The HCl gas evolution ceased at this point [...]

Shake and pray

There is a popular synthetic organic chemistry procedure on YouTube that I find absolutely astonishing. It beats the Diet Coke and Mentos trick hands down. It goes like this: A masked dude – or a gal – takes an empty plastic bottle with a cap (preferably a wide mouth bottle – i.e. from a large [...]

Potassium hydride self-ignition

I had a rather bad fire last Friday. I was washing a large jacketed glass reaction vessel used for polymer scale-ups, after pouring the reaction mixture out, and a tiny particle of potassium hydride (from this poorly quenched reaction) that was adhering to the bottom of the reaction flask ignited just as I was giving [...]

Potassium hydride self-ignition

I had a rather bad fire last Friday, probably the most serious lab mishap in 15+ years. As I was washing a large jacketed glass reaction vessel used for polymer scale-ups, a tiny particle of potassium hydride from a poorly quenched reaction – a particle that was adhering to the bottom of an empty flask [...]

Replacement process solvents

A recent Organic Process R&D editorial (thanks Chemjobber for pointing it out) publicizes Pfizer Process green solvent replacement chart that discourages chemists from using solvents that are either known to be toxic or are expensive to dispose as waste. OPR&D makes it now a submission policy too, and if you submit a paper that uses a [...]

Fighting Pd colloids with salt

I have been running some debenzylations of a macromolecule with the Pearlman catalyst  in water. The hydrogenation often results in reaction mixtures with persistant dark colloids. I have seen this kind of problem before, with small molecule-hydrogenations on Pd/C though it was never quite as bad. I suppose this polymer loves to stabilize Pd nanoparticles [...]

Medchem Immigrant in the Polymer Republic

Five months on – and there is no looking back. With potassium metal freshly cut, with the glassware, solvent and monomer lines pumped down overnight to 20 mTorr, ready or not, macromolecules, here I come.

Vaclav Havel, RIP

Removing Pd colloids with salt

I have been running hydrogenolytic N-debenzylations of a large molecule substrate with Pearlman catalyst lately. In this particular case the hydrogenation is done in water, followed by product extraction into organics. UnfortunatelyShow More Summary

Trehalose!

A remarkable molecule:  Hygroscopic, edible, stable and pleasantly-tasting natural sugar. While keeping foodstuff moist and producing a desirable mouth-feel, trehalose also masks greasy rancid off-flavors like no other food additive....Show More Summary

A scent of fresh soil

Our lab has been smelling a lot like disturbed soil lately, due to my work with 2-ethylfenchol. The flavor and fragrance division of Aldrich is a good place to start when you need highly hindered tertiary alcohols. While many of the low-molecular weight tertiary alcohols are minty and camphor-like, Et-fenchol smells like dirt. Actually in [...]

A taste of their own medicine

 Credit: Jirí Slíva I got an e-mail from a patent litigation attorney representing a major pharma company, a company that puts beautiful ads on TV almost every night and whose name rhymes with “Mergers and Massacres”. Turns out, they have a problem with one of their drugs: the drug is selling just over a billion a [...]

Expanding liquids break closed vessels

I had a dumb mishap today: A 100mL Schlenk storage flask with 1,5-cyclooctadiene shattered. When I distilled my COD by vacuum transfer this morning I filled the storage flask all the way to the top and then turned the teflon stopcock shut. There was no head space left in the flask; as the liquid warmed from [...]

Neglected lab solvents

Trifluoroethanol as a solvent dramatically accelerates epoxide opening with amines and also conjugate addition of amines to enones and acrylates. Thermal Diels-Alder is another good reaction to try in TFE. 1-methoxy-2-propanol behaves as a higher-boiling version of iPrOH. It has a reasonable volatility and it is miscible with water (so it could be pulled off on [...]

Life of an Immigrant in the Polymer Republic

Five months on, and there is no looking back now. With potassium metal freshly cut, with the glassware, solvent and monomer lines pumped down overnight  to 20 mTorr, ready or nor, macromolecules, here I come.