Org Prep Daily

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 upon 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

July 4, 2013

Happy 4th

Filed under: Uncategorized — milkshake @ 3:22 am
“The difference between theory and practice is much bigger in practice than in theory”

The difference between theory and practice is far greater in practice than in theory


















Credit: Jiri Sliva


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…

April 1, 2013

It curdles if you don’t stir it

Filed under: mechanisms — milkshake @ 5:07 pm


Trityl group on sulfur is unstable to LiAlH4 reduction. It falls off as triphenylmethyl anion – that’s where the gorgeous blood-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 negative potentials – and so I presume it is not as widely known.

In my hands, sulfur de-tritylation with LAH happens both with primary and secondary thiols protected as trityl thioethers. The rate of trityl loss seems structure-dependent: metal coordinating groups (such as OH, amino) in the vicinity of sulfur accelerate the LAH-promoted de-tritylation to a point that it cannot be avoided even under mild reaction conditions. In such cases all that remains to be done is completing the de-tritylation by overnight reflux and isolating the free-thiol product from the Al basic salt cake after the usual Fieser workup. The thiol actually ends up stuck within the salt cake as a thiolate; the filtrates contain only triphenylmethane.

Trityl-S group seems to be reasonably stable to borane-THF at room temperature.

October 29, 2012


Filed under: industry life — milkshake @ 6:56 am

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 with the frothy mixture in the picture. I had to isolate the material from a solution in concentrated HCl (0.3L), with extra sludge of inorganic salts and assorted gunk that included gram quantity of dimethyl sulfide.

The usual process would be: dilute, filtrer, dialyze. But dialysis is a slow and rather frustrating business and we don’t even have bags giant enough for removing few mols of salts and HCl. So I was delighted to learn that ultrafiltration is a turbo-alternative to a dialysis – instead of steeping a swollen dialysis sausage bag (that can burst overnight) for days and waiting for the diffusion to run its course, an ultrafiltration setup visibly labors for you: the pump pushes the mixture against a semi-permeable membrane, water and other small molecular weight material leak out, the macromolecular fraction stays in. The purification is done in few hours.

The peristaltic pump in the picture circulates the crude mixture at moderate pressure and high flow rate (20 psi, 1.7 L/min) from the beaker to bottom of the column; the stuff that flows out at the top is fed back into the beaker in a closed loop. The column consist of a bunch of spaghettini-like capillaries that are coated with a semipermeable membrane. The spaghettini are housed in a plastic pipe casing. It is inside these capillaries that the mixture rushes through at high speed over and over again – water and small molecule material that leaks out through the walls of the capillaries collect in the casing and flow into waste (the sidearm and the transparent bottle). One has to keep adding water into the beaker quite often because with a good column + pumping rate/pressure the mixture gets concentrated rather quickly.

The time to end the purification is when chromatography (GPC) can no longer detect small-molecular weight impurities. Of course with a whopping excess of HCl at the beginning, one doesn’t need to run GPC to confirm that all low-molecular weight material is gone – a pH paper will tell you that. (A sniff test for dimethylsulfide presence is also fast … and revolting…)

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