Org Prep Daily

September 27, 2006

TLC Staining solutions

Filed under: procedures — milkshake @ 2:28 am

General Staining:

Cerium-ammonium-molybdate, CAM

40g of ammonium pentamolybdate + 1.6g of cerium(IV) sulfate + 800mL of diluted sulfuric acid (1:9, with water, v/v). On heating, blue-black spots on light background. Slowly fades over several days. Quite universal, often very sensitive. Some amines, amides and oxidation-resistant aromatics do not detect well.

Basic KMnO4

40g of K2CO3 + 6g of KMnO4 in 600mL of water, then 5mL of 10% NaOH added. (KMnO4 takes some time to dissolve completely. Lazy people like me substitute it with NaMnO4 concentrated aq. solution from Aldrich). No heating. Brown spots on pink background. Often very sensitive but staining very disproportionate to quantity, depending on the compound. Fades within hours. Oxidizes anything with diol, C=C, reactive methylene, phenol, thiol, phosphine etc. Particularly useful for detection of tertiary amines.

Phosphomolybdic acid

30-40g of phosphomolybdic acid in 100mL of ethanol (preferably non-denaturated). Good grade of phosphomolybdic acid should provide clear, bright yellow solution. (If there is cloudiness, let it settle and decant.) Light sensitive. On heating, blue-black spots on yellow-green. Good for lipids. Do not overheat or the background goes dark. Usefull for spraying but expensive as dipping-jar solution. (I stopped using PMA, in favor of CAM. One advantage of PMA is that it is compatible with aluminium-backed TLC places whereas most other universal stains containing diluted sulfuric acid, like CAM or anisaldehyde, are not and must be used with glass TLC plates.


40mL of conc. H2SO4 is added (slowly!) into ethanol 800mL, followed by acetic acid 12mL and anisaldehyde 16mL. Light and oxidation sensitive. On heating, colorfull spots on pink background. Color varies on the compound. Good for all things with active methylene, and for distinguishing closely-spaced spots on TLC by their color difference.


Iodine vapor chamber is made from a TLC jar with a good-sealing lid, by adding a dry mix of iodine crystals  (a small spoon) covered with silicagel for chromatography, about a half-inch layer. Put dry TLC in the chamber onto the silica layer face down and watch the brown spots developing. Works on variety compounds but often it is only moderately sensitive. Iodine stained TLC can be developed subsequently with other stains.

Functional group-selective stains


20g of ninhydrin in 600mL of ethanol. (Don’t spill ninhydrin onto your fingers – they would go blue.) Primary amines produce blue spots at R.T., very sensitive detection. Boc-protected primary amines produce spots on heating (as the Boc falls off). Secondary amines sometimes detect but the stain is weak.


3g of dinitrophenylhydrazine in 750mL of 2M HCl. (If htere is some insoluble portion, decant it off.) Aldehydes and ketones produce yellow-orange spots at R.T., quite selective.

Stain dip station: 4 or 6 wide-mouth jars covered with aluminum foil (secured by tape) to protect from light, placed within a tray (to guard against spill).

Spray station: Hand-operated rubber-baloon/glass top sprayers are wonderful but antiquity now – they are hard to get by nowadays. Compressed gas sprayers are much harder to control. Spray advantage: economical on stain solution, the TLC spots do not move as with dipping. Disadvantage: big mess in the hood, a receiver for spraying has to be built (i.e. from a cardboard box). I used to be very partial to spray-staining but was won over by the dip jar convenience.

Update: A procedure for improved Dragendorff stain that keeps well in refrigerator (+4C). This stain is particularly useful for detection of lipophilic amines, basic heterocycles like pyridines but also aryl phosphines, crown ethers and polyethylene glycol polymers. Brown spots on yellow background develop almost instantly at R.T.

A solution of L(+)-tartaric acid 20g in D.I. water 80 mL was added to BiO(NO3) 1.7g and the mixture was sonicated on ultrasonic bath for 15 minutes. A solution of KI 32g in D.I. water 80 mL was added into the mix. Finally, a solution of tartaric acid 175g in D.I. water 950mL was added. The resulting bright orange mixture was stirred for 15 minutes and then placed into a fridge overnight. The solution was decanted off from precipitated crystalline solids (probably K-tartarate), transferred into a wide-mouth dip jar and kept in fridge when not in use. (This Dragendorff reagent gradually darkens over time but the aged reagent still performs quite well even after several months in the fridge.)

September 26, 2006


Filed under: procedures — milkshake @ 9:38 pm

A sulfuric acid solution obtained by combining 95.5% sulfuric acid 12.60g (122.7mmol) with ice 12g was gradualy added to a mixture of L-Prolinol 12.50g (123.5mmol) and ice 12g with cooling on ice bath (exothermic). The obtained solution was concentrated on rotavap (R.T. to 80C at 8 Torr). The obtained oily residue was heated and rotated on Kugelrohr air bath at 5-8 Torr at 110C for 10 min, the air bath temperature was then increased 130C and, after additional 15 min, to 150C. The heating at 150C was continued for 30 min. The obtained solid material was cooled to R.T.,  dissolved in a mix of water 20mL and ethanol 10mL at reflux, additional ethanol 20mL was added and the mixture was allowed to crystallize at R.T. for 5 hours. The crystallized product was collected by filtration, washed with ethanol 30mL and dried on highvac. (17.129g of crystalline solid) A second crop was obtained by diluting the supernatants with ether 60mL, shaking vigorously for 5 min, collecting the precipitate by filtration and washing with ethanol (Second crop: 2.214g of crystalline solid). Combined Y= 19.343g (86.5%) of L-prolinol-O-sulfate as a white crystalline solid.

1H(d6-DMSO, 400MHz): 8.990(br s, 1H), 8.464(br s, 1H), 3.997(dd, 12.1Hz, 3.9Hz, 1H), 3.843(dd, 11.7Hz, 8.2Hz, 1H), 3.701(m, 1H), 3.114(m, 2H), 1.981(m, 1H), 1.831(m, 2H), 1.578(m, 1H); 13C(d6-DMSO, 100MHz): 65.54, 59.57, 46.02, 26.78, 24.00

L-prolinol-O-sulfate 18.970g (104.7mmol) solution in water 150mL was gradualy added into a vigorously-distilling 20% NaOH (310mL) in a distillation apparatus with ice-cooled receiver over 15 minutes. The distillation was continued until distilates were no longer fishy-smelling. The distillates were cooled on ice, saturated with solid KOH , extracted with ether 250mL and re-extracted twice with additional ether (2x100mL). The combined extracts were dried with Na2CO3 and carefully concentrated, the residue was distilled at atmospheric pressure through a short (2in) Vigreaux column. A pure product fraction distilled at 105-110C. Y=4.179g (48%) of a colorless liquid with an intense irritant fishy odor.

1H(D2O, 400MHz): 2.687(dd, 11.7Hz, 8.6Hz, 1H), 2.550(m, 1H), 2.146(m, 1H), 1.827(dd, 12.9Hz, 8.2Hz, 1H), 1.620(m, 1H), 1.397(m, 1H), 1.309(d, 5.4Hz, 1H), 1.246(m, 1H), 1.139(d, 3.9Hz, 1H); 13C(D2O, 100MHz): 51.00, 39.42, 25.96, 25.14, 19.08

JOC 32, 2388-91 (Gassman et al)


Filed under: procedures — milkshake @ 2:13 pm

4-Fluoro-2-methylaniline 6.258g (50 mmol) was dissolved in anhydrous acetic acid 20mL and acetic anhydride 5.00mL (53 mmol) was added without cooling (exothermic reaction). After 10 minutes, the mixture was heated to 90 C on oil bath and a solution of tBuOCl 9.0mL (81.8mmol) in acetic acid 60mL was slowly added (using an addition funnel) over a 3 hour period and the reaction was then  continued for additional 1 hour at 90C. The mixture was cooled and evaporated to dryness. The solid residue was re-crystallized from a mixture of ethanol 20mL and water 20mL (5 hours at ambient temperature). The precipitated product (6.305g) was collected by filtration, dried on highvac and re-crystallized from benzene (100mL, overnight), to obtain 5.484g of the chloroacetanilide intermediate as a white crystalline solid (96% pure by HPLC). 1H(d6-DMSO, 400MHz): 9.476 (br s, 1H), 7.316(dd, 8.4Hz, 2.9Hz, 1H), 7.158(dd, 9.3Hz, 2.8Hz, 1H), 2.174(s, 3H), 2.042(s, 3H).

The chloroacetanilide 5.484g was dissolved in conc. HCl 120mL. Water 120mL was added and the resulting slurry was refluxed for 3 hours (oil bath 130-140C). The resulting homogenous mixture was evaporated to dryness, the residue was dissolved in water 100mL, the solution was made basic with concentrated ammonia (pH approx 9.5 to 10) and the mixture was extracted with dichloromethane (2x100mL). The combined extracts were dried (MgSO4) and evaporated. The residue was dried on higvac with cooling on ice bath. Y=4.259g (53.5% overall) of a light-tan liquid that solidifies upon cooling to 0C.

1H(d6-DMSO, 400MHz): 7.022(dd, 8.5Hz, 2.9Hz, 1H), 6.866(dd, 9.3Hz, 2.8Hz, 1H), 4.880(br s, 2H), 2.139(s, 3H); 19F(d6-DMSO, 376.5MHz): -128.10(m, 1F)

September 25, 2006

N,N,N’,N’ -tetramethylguanidinium azide

Filed under: procedures — milkshake @ 8:54 pm


Neat azidotrimethylsilane 13.30mL (100mmol) was added to a solution of N,N,N’N’-tetramethylguanidine 12.55mL (100mmol) in cyclohexane 100mL. Methanol 5mL (125mmol) was added dropwise with cooling on ambient water bath (exothermic) and the mixture was stirred for additional 1 hour. The precipitated product was quickly transferred into a funnel for positive pressure filtration (or a fritted short chromatographic column), the supernatants were expelled under positive pressure of  dry nitrogen, the solids were washed with cyclohexane and hexane, then dried under stream of dry nitrogen. Y=15.98g (100%) of a white extremely hygroscopic solid.

This is an organic-soluble azide that that works wonderfully for substituting halides, sulfonate esters with azide in anhydrous acetonitrile. Please do not use heavy metal salts or chlorinated solvents in combination with azides if you want to live. Evans group originally reported use of this azide in refluxing DCM (which worked for their reactive substrates on small scale) but in Hruby lab there were several serious detonations caused by diazidomethane accumulation on rotavap when evaporating react. mixtures from large-scale experiments performed in DCM. Always use acetonitrile, DMF, etc. but not chlorinated solvents. Azide is a powerful nucleophile and will displace “unreactive” chlorine. 

TMS-azide has lower volatility than HN3 (and is also non-explosive) but is almost as toxic upon inhalation and skin contact because of its facile hydrolysis. Use gloves with TMSN3. Azide acute poisoning produces excruciating headaches and vertigo – old-time peptide chemists (doing azide couplings) swore that orally-administered ethanol (40-50%) in large volume was a quick antidote to hydrazoic acid. There is also a story about chemist who was trying to wipe a TMSN3 spill in glovebox and he was found unconcious – still hanging from the glovebox sleeves because TMSN3 soaked through the rubber sleeves. 

Update: TMG azide can be also generated in situ and used as a solution, see Org Prep Daily, August 27, 2008


Filed under: procedures — milkshake @ 7:39 pm

2,2-Bis-(bromomethyl)-1,3-propanediol 131.0g (500mmol) and sodium methoxide 27.0g (500mmol) slurry in anhydrous ethanol 0.4L was stirred at 60C for 8 hours (overnight). The mixture was cooled, filtered (the salts were washed with ethanol) and the filtrates were concentrated on rotavap. The residue was distilled on Kugelrohr apparatus at 1 Torr (the air bath temperature was gradually increased from R.T. to 160C) to provide crude 3-bromomethyloxetane-3-methanol 69.0g (76.5%) as a colorless syrupy liquid.

This intermediate bromide was mixed with neat morpholine 130mL (1.5 mol) and the mixture was stirred at 60C for 20 hours. The mixture was cooled, diluted with TBME 100mL, the salts were removed by filtration (washed with additional TBME) and the filtrates were concentrated on rotavap. The residue was distilled on highvac using a shortpath distillation head. The pure product distilled at 125-135C/0.5Torr. Y=61.12g (85% from monobromide, 65% overall) of a colorless syrup.

1H(CDCl3, 400MHz): 4.976(br s, 1H), 4.480(d, 6.3Hz, 2H), 4.388(d, 6.3Hz, 2H), 4.055(s, 2H), 3.666(app br t, 4.7Hz, 4H), 2.819(s, 2H), 2.433(app br t, 4.7Hz, 4H); 13C(CDCl3, 100MHz): 78.01(2C), 69.08, 66.47(2C), 65.46, 54.16(2C), 42.23

Mosher Pfp ester

Filed under: procedures — milkshake @ 12:26 pm




R(+) Mosher acid 1.856g (99%ee, Aldrich, 7.926mmol) and pentafluorophenol 2.188g (11.89mmol, 1.5eq.) solution in anh. acetonitrile 12mL was cooled on ice bath. Solid DCC 1.635g (7.926mmol) was added in one portion and the mixture was stirred at 0C for 1h, the cooling bath was removed and continued at ambient temperature for 14 hours (overnight). The precipitated dicyclohexyl urea was removed by flitration, washed with acetonitrile and discarded. The combined filtrates were evaporated and the obtained semi-solid residue was dried on highvac for 6 hours to remove excess of pentafluorophenol. The crude product was dissolved in hexane 10mL, the cloudy solution was filtered through a 2g-plug of silica, the silica plug was washed with cyclohexane 30mL. The combined filtrates were evaporated and the residue was dried on highvac (for 1 hour). The residue was dissolved in hexane 15mL, allowed to crystallize in freezer for 10 hours (-20C overnight). The supernatants were decanted, the crystalline product quickly rinsed with freezer-cooled hexane (2x5mL) and dried on highvac while cold. Y=2.601g (82%) of large white crystals 

The Pfp-ester of Mosher acid is a non-hygroscopic solid that can be stored at room temperature. It is used as an inexpensive and stable alternative to Mosher acid chloride. The OH acylation with the Pfp ester is typically done in a concentrated DMF solution, with DMAP as a base. This protocol is suitable for derivatization without purification – just the DMF is evaporated by stream of nitrogen before the NMR analysis. The pentafluorophenyl signals in the 19-F spectra are far to the left so they do not interfere with the Mosher CF3 group signals. Unreacted Mosher acid Pfp ester signals can be used as internal standard. 

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