Blog Profile / Org Prep Daily

Filed Under:Academics / Chemistry
Posts on Regator:55
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Archived Since:July 23, 2009

Blog Post Archive


There is a darkly funny story behind this post, stay tuned. I guess you have seen this one before: “Experienced MS level chemist with a track record of research accomplishment is looking for a process development or medicinal chemistry position in the industry…”

Drying sieves

I was going to expound on advantages of using high-temperature dry bath made of graphite flakes (cheap, good thermal conductivity, easy to clean, soft-and shiny, does not scratch the glassware) and so I took this picture of half kilo sieves being baked at 380 C under vacuum, on a heating mantle filled with graphite flakes. […]

In which I destroy 18 teflon Schlenk stopcocks

A year-long process project with many gallons of boiling conc. HCl came to end. The fume hood wasn’t pretty anymore – metal surface covered with a furry crust, dark ooziness dripping and pooling in the back; I was eager to pull the equipment from that hood and scrub and repair everything. The vacuum manifold glass […]

The End of Affair

We first met just over a year ago. I was incredibly fortunate to have you for twelve more months – much longer than they were giving us in the beginning. I will always remember our time together: the stunning saffron, cinnamon and maroon colors of your intermediates, the lustrous flakes when you precipitate. I held […]

The power of blunder – based optimization

I have been trying to optimize a difficult reaction; I thought a presence of zinc chloride might help so I gave this a try and there was an improvement: The results were getting better, week after week. Some time later – by now with improved product purity and filtrability – I begun to wonder if […]

How to leave a strong impression as a summer intern

I would like to describe my brief high school summer internship in a natural product lab. The group was doing a medicinal chemistry research on cardioglycosides. I didn’t realize the PI really did not want me but agreed just to please his boss. On my first day, I was dispatched to the institute’s library, where […]

Pleasures of Process Development

Refluxed in 12 molar HCl Carefully watched for a frothing Painstakingly drained from the reactor To strip down and scrub off that gross thing My bosses, I tried please believe me I’m doing my best as you insist I’m ashamed of the material I burned through I’m ashamed of the deadlines I missed But if […]

Pleasures of Process Development

I refluxed six liters of HCl, 12M And fought a terrible foaming Now I can filter that mud, Then take the reactor apart To clean the whole damn thing

A kilo-scale hydrogenation reactor?

I have been running some kilo-scale hydrogenations of our polymers, at atmospheric pressure, under balloons, and it is a bit of a chore. It would be nice to have something akin to a giant-sized Parr shaker and run the hydrogenation at few bars, to reduce the catalyst loading and shorten the reaction time. I wanted […]

O-acetyl L-tyrosine

1. HTyr(Ac)OH.MsOH: In a 2L round flask with a wide 29/42 joint and a large egg-shaped stir bar, neat methanesulfonic acid 80mL (1.2 mol) was added to a slurry of L-tyrosine 181.2g (1.0 mol) in acetic acid 0.5L and the resulting warm mixture was stirred vigorously without cooling until complete tyrosine dissolution. The flask walls […]

nitrilotriacetic acid anhydride; 4-(carboxymethyl)-morpholine-2,6-dione

30 mL of acetanhydride (317 mmol) was added to a slurry of nitrilotriacetic acid N(CH2CO2H)3 50.0g (261.5 mmol) in DMF 100mL. N-methylimidazole 0.21mL (1 mol%) was added and the mixture was stirred and heated on a 60 C oil bath for 6 hours under Ar – the mixture gradually became homogenous. Neat allyl bromide 0.5mL […]

Happy 4th!

                                              Credit: Jiri Sliva

Oil pump desanguination – brilliant!

I just had the fastest pump oil change of my career, thanks to invention of my colleague. We use giant Welsh belt-driven pumps installed in steel cabinets under the hoods and these beasts are reliable – but so heavy: they take just over 3 liters of oil to fill, and the whole thing weights about […]

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 [...]


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 [...]


. 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 [...]

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