Org Prep Daily

June 10, 2015

The power of blunder – based optimization

Filed under: industry life, procedures — milkshake @ 8:46 pm

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 the zinc chloride effect was real, or maybe something else was going on, so I finally got around to run a control. And sure enough, the reaction worked even better without zinc chloride. So, after many tries with quantities of reagents and additives, I arrived at optimized procedure which looked almost exactly like the one that I started with, except few minor details – the little changes that were incidentally co-introduced because of the ZnCl2 addition – few small changes that make a difference… I would have never tried these changes without it. And I would have given up if I had run the control experiments earlier and found out it does nothing.

It is delightful to read methodology papers, the observations and explanations arranged neatly, flowing like a good detective story, with a chain of clear logical reasoning based on the experimental evidence. But I suspect it is mostly fictional (There is no good place in a process paper to explain that after very slow reagent addition because of a clogged valve that no-one cared to inspect before the pilot run, the impurity profile improved and the troublesome sideproduct from the second step no longer buggers up the recrystallization). I worry that reading published accounts of process research can give the management a very unrealistic impression what a normal project should look like.

May 22, 2014

A kilo-scale hydrogenation reactor?

Filed under: procedures — milkshake @ 8:22 pm

I have been running some hydrogenations of our polymers on kilo scale, at atmospheric pressure under balloons, and it is a bit of a chore. It would be nice to have something akin to a beer keg-sized Parr shaker and run the hydrogenation under few bars of H2, to reduce the catalyst loading and shorten the reaction time.

I wanted to ask the readers from process groups if they worked with a low-pressure batch stirred hydrogenation reactor that they liked and could recommend – for us to buy. Specifically,  we would need a hydrogenator that can accommodate 8-10 liters of a reaction mixture that has tendency to initially foam under reduced pressure (this means that the total available volume should be about 15-20 liters). Maximum operating pressure 3 bar would be enough, no heating or cooling is required and the typical solvent is water. I am not really interested in flow hydrogenation systems because they would be unsuitable to our particular case. A glass vessel or at least a glass window on the top would be nice to have, because of the foaming problem during evacuation.  Thank you for your suggestions!


September 24, 2013

O-selective acetylation of tyrosine

Filed under: procedures — milkshake @ 7:30 pm

1. HTyr(Ac)OH.MsOH:

Methanesulfonic acid 80mL (1.2 mol) solution in acetic acid 0.5L was added to L-tyrosine 181.2g (1.0 mol, Aldrich 97%+) in a 5L 29/42 joint flask and the mixture was stirred vigorously without cooling until complete tyrosine dissolution (about 2 hours). The flask was placed in +10C water bath and the mixture was stirred till the internal temperature was about 15C. Neat acetanhydride 105mL (1.1 mol) was added dropwise over a 30 min period with a vigorous stirring and cooling on cold water bath, then continued at 15-20C for additional 90 min, at which time a voluminous precipitate solidified the reaction mixture. Peroxide-free THF 1L was added to the crystalline mass, the mixture was mashed up with a large spatula to break the lumps and then stirred vigorously for 20 min. The precipitate was collected by filtration, washed thoroughly with THF, the product was dried by suction under N2 blanket and then in vacuo until only a faint smell of AcOH remained with the product (10 Torr, 1 day). Y=259.8g of white solid (84% th)
1H(d6-DMSO, 400MHz): 8.28(br s, 3H), 7.29(app d, 8.6Hz, 2H), 7.10(app d, 8.6Hz, 2H), 4.20(br t, 6.4Hz, 1H), 3.10(br d, 6.4Hz, 2H), 2.33(s, 3H), 2.26(s, 3H)

2. HTyr(Ac)OH:

The O-acetyl tyrosine mesylate salt from the first step was dissolved in D.I. water 0.5L in a 4L large beaker, a solution of triethylamine 118mL (0.84 mol; 1 eq.) in ethanol 0.5L was added rapidly with stirring, the crystallized mixture was combined with additional ethanol 1L and agitated with a large spatula, then stirred for 30 min and finally placed into a refrigerator (+ 4C) overnight. The precipitated product was collected by filtration, rinsed thoroughly with chilled 200-proof ethanol (0.5L, +4C) and then with few small portions of ambient ethanol (4x20mL), dried by suction under N2 blanket and then thoroughly dried in vacuo. Y=168.4g (79.5% overall) of a white fluffy solid.
1H(D2O 0.7mL/10mg, 400MHz): 7.36(app d, 8.4Hz, 2H), 7.14(app d, 8.4Hz, 2H), 4.79(s, 3H; HOD), 3.98(dd, 8.0Hz, 5.5Hz, 1H), 3.29(dd-ABX, 14.7Hz, 5.3Hz, 1H), 3.14(dd-ABX, 14.7Hz, 7.8Hz, 1H), 2.34(s, 3H)

Note:  Effective stirring and cooling during the Ac2O addition is important for achieving good results. Using a cheap grade of tyrosine (a yellowish muddy powder, with some impurities detectable on NMR in aromatic region) is tolerable – and MsOH from an old bottle that was already a bit dark worked fine in this procedure – but the used THF should be aldehyde+peroxide free.

September 4, 2013

nitrilotriacetic acid anhydride

Filed under: procedures — milkshake @ 1:48 pm


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 (2.2 mol%) was then added and the heating was continued for additional 30 min, to inactivate the catalyst. The flask was finally equipped with a shortpath distillation adapter and the mixture was concentrated by vacuum distillation from a 60 C oil bath (1 to 0.1 Torr; the receiving flask was chilled with liquid nitrogen). With most volatiles removed and the distillation residue solidifying, the distillation was terminated and the distillation flask was cooled to ambient temperature under Ar. The residue was dissolved in acetone 300mL (15 min stirring at ambient temperature. Fisher histology grade acetone was used straight from the can). The obtained cloudy solution was diluted with 1,2-dichloroethane 200mL and filtered through a fine-porosity Buchner funnel. The filtrates were slowly concentrated on rotovap from an ambient water bath down to about 150mL total volume. The precipitated crude product (35g) was collected by filtration, washed with dichloroethane and dried in vacuo. The crude product was dissolved in acetone 250mL, the solution was diluted with dichloroethane 250mL and then slowly concentrated on rotovap from ambient water bath, down to about 200mL total volume. The precipitated purified product was collected by filtration, rinsed with dichloroethane and dried in vacuo. Y=31.81g (70% theory) of a light-pink colored crystalline solid that gradually turns white on storage.

1H(d6-acetone, 400 MHz): 3.920(s, 4H), 3.620(s, 2H); 13C(d6-acetone, 100 MHz): 171.18, 165.51(2C), 54.79, 52.54(2C)

Note: The crude product from reaction mixture evaporation residue contains another anhydride species, up to 15% by NMR (similar spectra but shifted downfield), which “disappears” during the workup. It is probably a dimeric bis-anhydride because it gets hydrolyzed by traces of moisture during the workup whereas the desired product is reasonably stable in non-dried acetone (in the absence of N-methylimidazole). The starting material N(CH2CO2H)3 is insoluble in acetone, so it is removed by filtration

May 24, 2013

Oil pump desanguination – brilliant!

Filed under: procedures — milkshake @ 3:38 pm

I just had the fastest and most enjoyable pump oil change of my career, thanks to a colleague. We use large Welsh DuoSeal belt-driven pumps installed in metal cabinets under the hoods and these beasts are rugged, dependable – but so heavy: They take over 3 liters of oil to fill and the whole damned thing weights about 50 kilos. The oil drain valve is inconveniently located right near the bottom so the pump cannot be easily drained inside the cabinet. The normal oil change procedure requires disconnecting the vacuum hose and dragging the pump out. I would prop the pump on an empty solvent barrel, put oil collection bucket beneath the drain valve and keep draining, tilting, flushing, draining, filling, cursing. Lifting the pump requires two pairs of hands, the oil drips everywhere, and given the large and awkward shape of the (very heavy) re-filled pump that has to be finally coaxed back in and over the cabinet lip, the vacuum hose reattached and the inadvertent vacuum leaks fixed, it is a pretty unpopular job – a job that keeps getting postponed for as long as is possible, while pumps are left sloshing with tired crud that has the look and smell of burnt molasses. But not much longer!

Prodded by his injured back and by desperation, my colleague conceived a brilliant apparatus –  he took a large (4L) Erlenmeyer filtration flask closed with a stopper with a tube through it. To the tube he attached a cheap vinyl transparent tubing (like you would use for water in reflux condensers) and connected it to the oil drain valve at the bottom of the pump so that he can aspirate the spent oil by vacuum. Turns out, if the oil is warm (from a pump that has been run, so it is less viscous), it can by sucked out through the drain valve into the Erlenmeyer filtration flask under house vacuum in few minutes. After one fill with flushing oil, 2 min pump run and another suction-assisted drain and final re-fill, the entire oil changing operation can be completed in less than 15 minutes. No mess, no need to take the pump out, no need to disconnect the vacuum hose from the pump.

Our biologists of course claimed credit for the pump oil change idea, for having used this kind of setup previously when sucking off liquor from cells in multi-well plates. But I am afraid the true origin of this oil change breakthrough is rather more disturbing. You see, my colleague is leaving for medical school in few weeks and in preparation, he has already taken the anatomy labs. As I was sucking out gallon of alarmingly dark rotten muck from my pump with his gadget, he calmly observed that the really good, top-of-the-line embalming machines can aspirate blood while at the same time pumping formaldehyde solution back into the empty veins: The happy operator just needs to correctly insert the inlet and outlet tubes into the still body, turn on the flush routine and wait until the aspirate finally starts coming out clear…

August 2, 2012

Shake and pray

Filed under: lab destruction, procedures — milkshake @ 6:16 pm

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 ethyl ether and adds a good chunk of lithium metal foil. He screws the cap on and swirls the mix around. God have mercy.

This man is not building a home-made ANFO for roadside bombing. It is not going to be a Molotov cocktail enhanced with a metal/oxidizer, or perhaps a crude rocket. He is making a batch of meth by the Shake and Bake method. As he ads a pack of ground pseudoephedrine pills, he squirts in a small amount of water, caps the bottle and starts shaking real fast. The water initiates a vigorous and pretty much uncontrollable reaction of the lithium metal with ammonium nitrate. The solids in ether gradually liquify and become a bottom layer sludge – this all is accompanied by evolution of  copious amounts of ammonia and hydrogen. So he shakes this thing by hand and he periodically vents the ammonia by loosening the cap  when the plastic bottle bulges up too much. Eventually the reaction slows down, the majority of lithium metal gets dissolved and the leftover lithium pieces floating on top of ether attain a bronze/copper hue, this marks the completion of the reduction. The ether layer is decanted into a small plastic bag, saturated with HCl gas (evolved from another soda bottle with sulfuric acid and NaCl) and the hydrochloride salt crashes out and is collected on coffee filter and dried. The yield is about 1-2 grams of a hilbilly-grade crank in form of a white powder, from one large pack of pseudoephedrine pills, about 2 hours start to finish. No glassware anywhere.

The method does not scale – attempts at running bigger batches end in self-immolation. A common error is adding too much water at the beginning, which leads to uncontrollable takeoff:  the whole ether/ammonia/NaOH/NH4NO3/Li brew squirts out. One can try and keep the lid on an a bulging soda bottle by a sheer force but as the Li metal floats on top and fast reaction makes the chunks of lithium pretty hot,  they tend to burrow through the plastic wall and an impressive stream of flaming goodness rushes out with them, delivering bright red and yellow-colored ether flames accelerated by ammonium nitrate and lithium metal all over the place. As one skin graft patient observed “I haven’t seen stuff burning this fast before”.

The Shake and Bake meth is a twist on the classic method using Li metal with anhydrous liquid ammonia/ether. The outdoor storage ammonia tanks are now getting watched and additives are introduced into agriculture-grade NH3(l) so as to ruin its usefulness for dissolved metal reduction. Hence the soda bottle modification for ammonia generation in situ. No need to go to fields, now you can cook in the safety of your home…

Note: It would be easy for a manufacturer to add some organic soluble iron compound like Fe(acac)3 or ferrocene to the ether-based starter fluid  and likewise a small pinch of FeSO4 to the ammonium nitrate in cold packs and lye/drain opener. A finely divided iron promptly decomposes Li metal solution in ammonia to lithium amide and so it would make these materials useless for home brewing.

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