Laboratoire Organique: The Notebook

Do you remember that, back in June, I proposed to sell copies of my organic chem lab notebook? Well, following the advice of a reader, I’ve decided to give it for free, for the benefit of all mankind!

Hmm… So, ladies and gentlemen, click here to download the ultimate version of Laboratoire Organique The NoteBook, which, as you’ll notice, is a little bit more formal than the posts but there’s a good reason for this as it’s the very edition I handed over to my professor once the lab course was over.

Enjoy yourself!


Laboratoire Organique: Reloaded

Laboratoire Organique: Reloaded

This is it: the end of Laboratoire Organique, which also coincides with the last post which deals with organic chemistry on this blog. Actually this is not completely true, since I'll keep talking about pharmaceutical chemistrysyntheses of drugs and other things which have undoubtedly something to do with organic chemistry.

This post also doubles as the first one of the Camptothecin Week, a series of articles about this drug and its properties. On this occasion, molecular biology will appear for the first time: oddly, I've covered a lot of different subjects, but never spent a word on what's likely to be centre of my entire life, as I said a few months ago.

To kick off the Camptothecin Week and give a proper send off to organic chemistry, it's time to put on your black, leather coat and dark sunglasses. Oh, and don't forget to take that pill (no, I don't mean Viagra: I was just trying to mock the film!). It's time to tackle the mind-blowing, outrageously long, total synthesis of camptothecin!

Ready for the Massive Total Synthesis

Our first reagent is a derivative of furan, which will provide the base for two of the five rings this molecule is composed of (namely, D and E). This procedure, though, requires the use of several protecting groups: right after the esterification of a carboxyl (where triethylamine is needed to neutralize the HCl the reaction produces), the other acidic function is reduced to alcohol (using borane in THF) and protected by dihydropyran. This step takes place in the presence of a very weak acid (p-toluenesulfonic acid), so that neither the already formed protecting groups nor the esters are altered at all.

Part One

The ester is finally reduced as well and subsequently oxidized to ketone: this is a perfect target for a Grignard which introduces a precious ethyl group. Then the ketone is synthesized again, this time utilizing Collins reagent.

Molecules with terribly complicated names (but, fortunately, clear structures) appear as the ketone is turned into a pretty weird compound, a cyano silyl ether, which is chromatographically isolated and treated in such a way that an amide is obtained. Apparently, quenching has to be performed as soon as the hydrolysis is over: this is, in my opinion, the sole step in the whole preparation where you have to be quick. The rest of the time, you generally wait days before you could go on.

Part Two
Part Two
A couple of time-consuming steps lead to an unprotected, chiral derivative of furan: this mixture has to be resolved through (3) fractional crystallization(s) (benzene:heptane 1:1) using 5 equivalents of natural quinine (very environmentally friendly, eh?).

A lactone is yielded adding a lot of either triethylamine and methyl chloroformate. Quinine is removed and the product purified. A photooxidation of the lactone, in the presence of eosin, with 2,6-lutidine results in a mixture of products: both undergo halogenation of their newly synthesized hydroxyl with thionyl chloride and Vilsmeier reagent (which, if you remember, appeared in one of the best Saturday Night Synthesis I've ever posted). That hydroxyl, in fact, doesn't look like the easiest to be substituted, does it?

To complete the synthesis, you now need to synthesize the remaining three cycles: acridine nicely provide them, by simply getting its ozonide, reducing it with sodium borohydride and, finally, converting it to a secondary tricyclic diamine.

Part Three

Both pseudo-acid chlorides react with the amine yielding, after a worryingly long series of chromatographic separations, a close derivative of camptothecin.

Part Four

The final product is obtained by adding lithium mercaptide in a polar solvent such as HMPA, resulting in an impressive 90% yield.

Sadly, this synthesis used to be performed by (undergraduate) students of industrial pharmacy, many years ago, but, nowadays, as either the number of students and exams (hence, lectures) increased, we simply study it. As a result I can't report the many incidents that might have occurred during such a complex synthesis.

This job is supposed to be done by those who opt for a career as organic chemist, but, as I told you, I chose something rather different. And that means it's time to say goodbye (not farewell) to organic chemistry.

Stay tuned, pharmacologists, because our time has come again, at last!


TLC-ism

When I launched Laboratoire Organique I said I aimed to display organic synthesis in a rather stylish way, although I admitted I had no idea on how to fulfill such an ambitious purpose.

I wasn't helped by those who actually chose our experiment: unlike ψ*ψ, we weren't given the opportunity to work with outrageously glossy materials or, since this was meant to serve as an introduction or an outlook on organic chemistry lab work, none of our syntheses was either complicated or new.

Nevertheless, I think sometimes I managed to garnish my posts with some good stuff: old-fashioned pictures of plants embellish a couple of extractions of natural product; unprecedented in the blogosphere, world-famous actress Monica Bellucci has been seen filling a separatory funnel while I was pimping amino acids (please, don't make confusion: I reject any allegation of me trying to pimp any Monica-Belluci-look-alike girl); a rather psychedelic Georg Wittig dropped in one of my first posts, to salute the beginning of our lab course.

Now, theoretically, the brightest pictures could (and should) have been the TLCs. However, we didn't have the equipment you need to properly keep a (full-colour) record of your layers. And, above all, once we were told it was sufficient to photocopy the layers (wrapped in cellophane), I stopped worrying.

For the second special episode of Laboratoire Organique, however, I'd like to present (before you see it at the Biennale or at the Moma), the latest artistic trend: TLCism.

Here I propose, once again, all the TLCs I've posted and some new ones you haven't seen (do you remember the many coming soon's?). I'd like to know your favourite one (although I am looking forward to reading your comments on my previous post more than on this).

We begin with 9-styrylanthracene: mobile phase is n-hexane.ethyl acetate (5:1); UV light at 254 nm.

9-styrylanthracene

Nifedipine: n-hexane.ethyl acetate (1.5:1); UV light at 254 nm.

Nifedipine

Nicotine: dichloromethane:methanol:ammonia (60:10:1); UV light at 254 nm.

Nicotine

S-Methyl-3-Hydroxybutanoate: dichloromethane:methanol (98:2); revelation: potassium permanganate at basic pH.

S-Methyl-3-Hydroxybutanoate

p-Nitroacetanilide: toluene:ethyl acetate (4:1); UV light at 254 nm...

p-Nitroacetanilide

...and after Flash Chromatography, using the same mobile phase (please, notice the nasty traces of reagent, acetanilide, above the highlighted product).

Flash Chromatography of p-Nitroacetanilide

Xanthines: dichloromethane:methanol (9:1); UV light at 254 nm.

Xanthines

Chamomile (essential oils): toluene:ethyl acetate (93:7); sulphuric acid (5% in ethanol) and vanillin (1% in ethanol) in the stove.

Terpenes

Chamomile (flavonoids): ethyl acetate:acetic acid:water (100:22:27); Natural Probe (1% in ethanol) and PEG.

Flavonoids

Tacrine hydrochloride: dichloromethane:methanol:ammonia (9:1:0.1); UV light at 254 nm.

Tacrine

So, after this summary of part of the experiments there is time only for one, last thing...


Coo coo ca-choo, Mrs. Fieser

If you remember, three months ago I asked you to help me to fill my MP3 player with whatever song or album you reckoned as the most appropriate for a chemist's iPod.

Today, for the first special episode of Laboratoire Organique, I'm going to try something which has never been done in the scientific blogosphere. This time I give you the chance to tell me how to do part of one of my forthcoming, organic chem exam!

Let me explain. This is one of the latest editions of the famous "Fiesers' Reagents for Organic Synthesis", created by Mr. napalm Louis Fieser and his wife and assistant Mary.

Massive Book

The lab course I've described was completed by a series of lectures, covering the general themes, linked to the practical work in an organic chemistry lab.  All this amount of information provides the basis for what will be my very last organic chemistry exam.

However, there is something lectures didn't cover, but we are supposed to brilliantly master: in a nutshell, our professor said any chemist must have at least know how Mr. and Mrs. Fieser's book looks like and how to fully utilize it, whenever needed.

Courtesy of ChemBark

So, we were told to learn by heart the five monographs (only acids and/or bases, though: the number is paramount) that we liked the most and discuss them during the exam, giving examples of the use of that reagent through the syntheses described on the book. However, because I can't make my mind about which acids or bases are the coolest ones, I now ask you to tell me what I should choose: you don't have to give any explaination, just a list of your five, favourite reagents.

Mrs. Fieser...!


I'm looking forward to your replies.
 


The stupidly dangerous grand finale of Laboratoire Organique

Yes, my dear organic chemists, all the beautiful things have to finish and, what I'm going to describe today is the last of the experiments we performed during our lab course. However, while non-organic chemists may be jumping happily, in the knowledge that, from last week, I'll be back to the "normal service", I must point out this is not the end of the "Laboratoire Organique" series: I'm preparing not one, not two but (ready for this!?) THREE special episodes which will certainly entertain you like nothing else before!

Em, well, I should calm myself now, shouldn't I?

OK, the last experience I present what was described to us as the (only) dangerous experiment, because involved the most toxic substances we had handled so far. And, in fact, although so dramatically warned, there was a incident, but you'll have to read the whole story to know what happened. Ah, ah, ah, ah, ah!

Today, ladies and gentlemen, we synthesize p-Nitroacetanilide from Acetanilide.

From acetanilide to its nitro derivative

I know, as usual, the reaction is not that difficult: you just nitrate acetanilide (which we, due to our endemic lack of time, hadn't synthesized but, annoyingly, bought). The main purpose, though, wasn't the synthesis per se: what our professor(s) wanted us to learn was how to purify the final product through Flash Chromatography.

We began by dissolving 5.0084 g of acetanilide, in a 250 mL beaker, with 5 mL of concentrated acetic acid. However, this is almost impossible, given the poor solubility of acetanilde in that solvent, so, having stirred this mixture for a long time, we ended up with a dense amalgam which, to be honest, looked more like honey rather than a liquid.

The beaker was placed on ice and we added (drop by drop) 10 mL of concentrated sulphuric acid. Keeping the reagents cool we tried to avoid not only the nasty effects of the exothermic nitration, but also the hydrolysis of the amide which, as it turned out, led to a considerable amount of byproducts (namely, derivatives of aniline, bearing a nitro group).

Aniline derivatives

But there's more. While my colleague was carefully adding the acid, I set to prepare the nitration mixture: in a nutshell, 2.2 mL of concentrated nitric plus 1.4 mL of concentrated sulphuric acid.

This reagent was in a test tube I placed on ice too. To prevent us from inhaling an awful lot of toxic nitrogen dioxide, we were told to be extra careful not to add it too quickly, but gently dropwise.

Finally, the beaker was left on the bench, at room temperature, to allow nitration to occur. During our 40 minutes wait, we stirred the solution every so often.

Synthesis of p-nitroacetanilide

To quench the reaction, 50 mL of water were used and, subsequently, we waited for 15 minutes before filtering it with a Büchner funnel.

We kept the filtered solution and then washed, thrice, the yellow precipitate with three aliquots of 50 mL of water. each time verifying whether the pH of the wash waters was neutral. These three aqueous solutions were, in the end, discarded.

We raised the pH of the first, yellow, filtered solution with NaOH (10%) and performed a liquid-liquid extraction in a sep funnel with 10 mL of dichloromethane. Because the aqueous phase contained a lot of aniline derivatives, dichloromethane became bright yellow, which made the separation pretty easy.
The organic phase was first dried with sodium sulphate and then concentrated to 2 mL. We labelled it solution A.

We weighed our crude product and, predictably, our yield was a mind-blowing 133% (8.9056 g), which was obviously a result of the percentage of water still present.
However, we put a bit of this highly impure product in a test tube where 3 mL of dichloromethane dissolved it. We dried this solution as well and named it solution B.

For our solution C, we recrystallized a tip of a narrow microspatula of p-nitroacetanilide (and other byproducts) with ethanol. In the beginning, we yielded a yellowish suspension, but, placing the test tube in a hot bath and then allowing the solution to cool to room temperature, we obtained our crystals.

This solution was filtered, this time a Hirsch funnel was enough, and labelled solution C. Our last solution, D, was yielded dissolving a small quantity of the pure crystals in dichloromethane and removing any trace of water with sodium sulphate.

We completed our synthesis with a TLC (mobile phase: toluene/ethyl acetate 4/1), which proved how beautifully pure our p-nitroacetanilide crystals were.

First TLC

 

Moreover, we determined the melting point of these purified product (212°C), which nicely matched that found in literature (215°C). By the way, this assay wanted to make sure we hadn't got everything wrong: o-nitroacetanilide has, in fact, a completely different melting point (92-94°C).

 

Nitroacetalinide(s)
For the grand finale, however, we had to try to purify our crude product through flash chromatography. Now, although we were more than just guided by our professors (who actually prepared everything and witnessed the whole thing, while we solely had to manually collect the samples and staining the TLC layers), I can at least describe the procedure.

First of all, however, this being a lab course, there was just one column for each of the two labs, we were divided in groups of 4 couples each and queued: anyhow, every couple gave 1.5 g of crude product, which were placed in a 250 mL round-bottom flask, dissolved with 80 mL of dichloromethane (plus 5 mL of extra ethanol), dried with sodium sulphate and transferred in another round-bottom flask (through a funnel with some cotton in the middle).

In the flask we also put 8 g of silica gel for flash chromatography (40-63 µm; mesh: 230-400) and concentrated the whole mixture: we begin setting the temperature at 40°C and then raised it to 60°C, until the only thing in the flask was a powder.

The column was packed with a bit of cotton right over the bottom valve and a volume of silica gel to fill two thirds of the column. A layer of sand was then placed on top of the gel and the mobile phase (the same toluene/ethyl acetate 4/1 solution used for the first TLC and for those carried out during the flash chromatography) was poured in the column.

The flow controller was placed on top of the column and connected to a small compressor: the mobile phase went through the stationary phase as the professor closed the bleed port with a finger. With some mobile phase still covering the sand layer, we loaded the system: someone (don't blame me, I was having a cup of tea: it was 5 o'clock) removed the dry powder from the inner surface of the round-bottom flask, placed it on a piece of weighing paper and put it on top of the stationary phase.

So, we were ready to start the chromatography: sticking to what described in the original paper (and due to dire financial crisis of our university) we manually collected the samples in 25 mL test tubes placed in a rack.

While some of us looked after the column, a series of TLCs were carried out to assay the quality of our purification: please notice that sample #1 is the dead volume of the system.

Massive TLC

Now, there's a distinct possibility the sole reason you have read the post is because you want to know about the incident. Well, towards the end of the first day (this experiment covered two days), we heard the noise of glassware exploding coming from the other lab: their flash chromatography column.

Eyewitnesses reported that a lab assistant had just checked the compressor, which wasn't working well, when, as a student opened the flow controller, the solvent reservoir in between the controller and the column suddenly exploded. Other people who were working there claim the upper part of the column actually burst.
Fortunately, the column was behind a hood, so, nobody got hurt.

So, here we are. This concludes our syntheses: I hope the organic chemists, who have begun reading this blog, thanks to these syntheses, will go on visiting this site.
Moreover, don't miss the three, forthcoming, ass-kicking specials that, I hope, will provide a proper sent-off to "pure" organic chemistry on this pages.

Stay tuned!

 


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