general chemistry

Life in Chemical Development, Part 2.

In the first part of this little series I recounted my experience with two steps of a four-step sequence, now I would like to move on to the last two steps: The preparation of a benzyl chloride and it’s conversion to a benzyl azide.

If you remember I had to convert 7098 kg of the benzyl alcohol ultimately to the azide. According to the plan:

Now benzyl halides are well known for their lachrymatory properties and this one made me cry just thinking about it. All that was required was to walk past the building, where it was being produced, to burst into tears and I had to run 46 batches (1.02 kMol) to make this stuff plus 9 for use tests. In fact we made the chloride then almost immediately concerted it to the azide.

As part of the safety checks in the pre-reaction control of the equipment the conductance of the enamelled stainless steel reactor was checked to make sure there were no cracks in the enamelling, it was deemed to be ok so we carried on. The alcohol was placed in a 630 L reactor and 312.8 kg of 37% hydrochloric acid was pumped in. The solution was heated slowly to an internal temperature of 90-93°C ( to avoid loosing too much HCl) and held there for 5 hours. During the reaction a two-phase system formed and we all cried. The product was on the bottom and it was separated from the acid after cooling to 40°- 45°C because the compound solidified at 37°C. It was then filtered and the pH adjusted to 9-12 with 30% NaOH solution and stored at 40°C as a two-phase system with water with minimal stirring and constant pH adjustment maintaining the 9-12 range. In the meantime we got things going for the conversion to the benzyl azide, more about that later.

When we examined the filter from the very last reaction we observed bits of blue glass. I hear you say “not again”. I don’t seen to have much luck with enamelled reactors. Well this time we were really lucky, and I mean really. Have a look at these two pictures.

The hole was a hairline crack in the enamel. Now this did not show up in the conductivity tests as it was right up at the top of the reactor where the stirrer joined together with the motor and could not be reached with the equipment we had, a pathetic excuse really. Maybe we should have used, you know that beer that reaches places that other beers can’t.  Remember under the enamel is stainless steel and we were using almost boiling 37% hydrochloric acid. So the acid seeped through during the course of the 46 batches and started munching away at the steel. The metal was so thin that if you pinched it between thumb and forefinger you could move the bottom part back and forward. I would say that one more reaction and the stirrer would have broken off at 100 rpm making God only knows what kind of mess. Furthermore it is well known that the presence of iron (rust) benzyl halides decompose exothermically at quite low temperatures. I can’t remember the exact temperatures but it moves the decomposition point (where the exotherm begins in DSC measurements) down about 50 or so degrees and increases the size of the exotherm markedly. So I guess we were lucky on two points, we stopped just in time and we were using steel with a very low iron content. After I saw this and realised the implications I my knees started knocking together and I staggered across the road to a pub and had a few stiff drinks and went home where I continued the treatment.

Back to the chemistry: Working with azides is particularly dangerous because of potential explosion and health hazards. Sodium azide is a very nasty compound. It is a CNS depressant and breathing the dust causes almost immediate breathing problems amongst others, see this page for more information, azides. Furthermore it also contains traces of hydrogen azide, which has similar biological behaviour to sodium azide but has the pleasant habit of being shock sensitive and hence explosive. The stirrer episode was bad enough; and we were using 70 kg of sodium azide per batch, my poor knees (never mind the liver). Even at pH 9 or above one can still detect HN3 in the gas phase. For the reaction we had an extensive gas washing system with 4 washers filled with 30% sodium hydroxide solution through which the exhaust went. At the end of this chain we periodically monitored for the presence of HN3 using ferric chloride spot tests, which are very sensitive for this compound. I’m happy to say that at the end of the chain we never detected any HN3. The reactor was specially made out of high quality tantalum steel, where the heavy metal content was minimised so we hopefully avoided the formation of heavy metal azides, I do not know if tantalum azide exists (perhaps someone who reads this may know) and heated glass tubing was employed for the transfers.

We threw the following into a 630 L reactor; 200 kg water, 2.6 mL of 30%NaOH solution, 700g tetra-n-butylammonium bromide, 70 kg sodium azide and a pH electrode. After heating this mixture to 90-95°C internal temperature and added the alkaline mixture of the benzyl chloride to it within 60 minutes. The pH drifted during this reaction and it was constantly monitored and kept between 9 and 12. The reaction is exothermic and the temperature control was also monitored closely during the 2 hour stirring at 90-95°C.

We then cooled to room temperature and filtered the lower organic phase (this time no glass was observed!) and removed the aqueous layer. This time everything went ok and from 55 batches we obtained a total of 9284.64 kg with an average purity of 94% and an average yield of 97.9%. All of the batches were released for the next step by QA. At last I was almost finished, I still had to dispose of all the azide containing waste from all the gas washers and all the water layers and reactor cleaning! This was really funny. We disposed of it by treatment of the waste with 37% hydrochloric acid and sodium nitrite, generating nitrogen, laughing gas and various other oxides or nitrogen that were washed out by the exhaust treatment. This was another foaming reaction, but by this time I was immune to foaming, didn’t worry me anymore. The aqueous phases went down to the water treatment plant.

There it was finished at last, with enough material for my colleague to play with. There is still more to tell about this chemistry but that will be part 3.

I hope you enjoyed my ramblings and look forward to many comments!

The Wonderful Life of Elements

The Wonderful Life of Elements may just be the most beautiful chemistry book I’ve read in, well, ever.

For anyone with even a sniff of an interest in chemistry Bunpei Yorifuji has created a book of pure joy. And for those who have only ever held a chemistry text  by accident this book may just grab their attention long enough to show them what the rest of us see in the subject.

First up you are treated to a lovely introduction to chemistry and its relevance, including illustrations of the elemental composition of the Universe, the Sun, the Earth and your living room. But this is just the B-movie, because the main event is the wonderful personifications of the elements. 

Each of the 118 elements are beautifully drawn with features that relate to their characteristics: Gases are wispy and ghost like, the liquids’ legs are flowing away and solids are bipeds. Whilst the newly discovered elements are depicted as babies and those with a longer history are old and bearded.

Each element has a page or two of additional cartoons that describe it  uses and other characteristics. All of which make for a fascinating collection of drawings.

Then to cap it all off there’s a equally lovely poster of the periodic table.

The Wonderful Life of Elements is available from Amazon, but I’d urge you to pay a little more and get it directly from the publisher, No Starch , that way you get an electronic copy in your email box whilst you wait for the hardcopy to arrive.

By September 23, 2012 2 comments chemical education, general chemistry

From Natural Product to Pharmaceutical.

In a recent discussion (Nicolau), about the suggested move of Prof. NicoIau from Scripps, the issue of the practicality of natural product total synthesis was raised. Here is a wonderful example of just that very usefulness, a wonderful piece of science extending over many years. It concerns the journey from Halichondrin B to Eribulin (E7389) a novel anti-cancer drug. The two compounds have the following structures:


I think you can see the relationship and as a development chemist I am glad they managed to simplify things (a bit).

Both compounds have an enormous number of possible isomers: Halichondrin B, with 32 stereocenters has 232 possible isomers; Eribulin has 19 with 219 isomers (if I have counted correctly, it does not really matter, there are lots of isomers). Remarkable is the fact that only one of these isomers is active in the given area of anti-cancer agents.

An excellent review of the biology and chemistry of these compounds has been published by Phillips etal1. This review is an excellent read and is to be commended. Another one written by Kishi2, is also full of information about the discovery of E7389 and I hope you will all get a chance to read this chapter.

The history of Halichondrin B goes back to 1987 when Blunt2-5 isolated it with other similar compounds from extraction of 200Kg of a sponge. Independently Pettit isolated the same compound from a different species4. The appearance of this compound in different species of sponge may indicate that it is produced by a symbiote.

The biological activity of Halichondrin B is amazing. When evaluated against B-16 melanoma cells it was found to have an IC50 of 0.093ng/mL. Against various cancers, generated in mice, it was shown to be affective at a daily dose of 5ug/kg, which resulted in a doubling of the survival rate. It has also been demonstrated that Halichondrin acts as a microtubule destabiliser and mitoitic spindle poison. It was proven that it is has tremendous in vivo activity against a variety of drug resistant cancers, lung, colon, breast, ovarian to mention a few. Consequently the National Cancer Institute selected it for pre-clinical trials and it’s here that the problems began. According to reference 1 the entire clinical development would require some 10g, and if successful the annual production amount would be between 1-5 kg. Blunt and co-workers managed to isolate 310mg from 1000kg-harvested sponge therefore, the only way to obtain the amounts required is total chemical synthesis. But synthesising 1-5 kg of such a compound would indeed be a mammoth task.

Kishi synthesised this compound7 in 1992 starting from carbohydrate precursors employing the Nozaki-Hiyama-Kishi Ni/Cr reaction, several times, in the long synthetic sequence8, 9. Now as an aside I have used this reaction on scale several times and although it works well its success is very dependant upon the quality of the chromium source and also the presence of other trace transition metals.

In collaboration with Eisai work on the SAR of Halichondrin began. They had a good start: Thanks to the total syntheses of Kishi several advanced intermediates were available for biological screening and one popped out of the screen as being very active:


 The first active lead compound

As one can see the complete left hand side of Halichondrin has gone! However, this compound was not active in vivo. Many derivatives and analogues of this compound were prepared: furans, diols, ketones and so on and a lead emerged from this complex SAR study, ER-076349. The vicinal diol was used as a handle for further refinement and lead ultimately to E7389, the clinical candidate.

It can be synthesised in around 35 steps from simple starting materials.

Going through all this work in a few sentences really belittles the tremendous amount of effort that went into discovery and development of this compound and the people involved are to be applauded for their dedication.

Kishi continues to optimise the synthesis of Eribulin as judged by a recent publication10. Where he describes an approach to the amino-alcohol-tetrahydrofuran part of Eribulin (top left fragment, compound 1 below). The retro-synthetic analysis is shown below. The numbering corresponds to that of Eribulin.

The first generation synthesis consisted of 20 steps and delivered compound 1 about 5% yield, the second-generation route was completed in 12 steps with a yield of 48%. One of the highlights includes a remarkable asymmetric hydrogenation11 with Crabtree’s catalyst12:


This selectivity was not just luck; it seems to quite general, at least in this system. I always wonder how long it took them to stumble across this catalyst, but then I suppose that Eisai like most of the large pharma. companies has a hydrogenation group that probably indulges in catalyst screening.

The C34-C35 diol was obtained by a Sharpless asymmetric hydroxylation, here the diastereoisomeric ratio was not very high, only about 3:1 in favour of the desired isomer. Fortunately the undesired isomer could be removed completely by crystallisation.

This is a remarkable story and references 1 and 2 are worth reading to obtain the complete picture and learn lots of new chemistry as well. Eisai filed a NDA and the FDA approved the compound in 2010 for the treatment of metastatic breast cancer.


  1. Jackson, K. L., Henderson, J. A., Phillips, A. J., Chem. Rev., 2009, 109, 3044-3079.
  2. Yu, M. J. Kishi, Y., Littlefield, B. A., in Anticancer Agents from Natural Products, page 241; Editors Cragg, G. M., Kingston, D. G. I., and Newmann, D. J. Published by CRC press, Taylor and Francis group, Boca Raton, 2005. ISBM 10:0-8493-1863-7.
  3. Lake, R. J. Internal Report, University of Canterbury, February 26, 1988.
  4. Litaudon, M.; Hart, J. B.; Blunt, J. W.; Lake, R. J.; Munro, M. H. G. Tetrahedron Lett. 1994, 35, 9435.
  5. Litaudon, M.; Hickford, S. J. H.; Lill, R. E.; Lake, R. J.; Blunt,J. W.; Munro, M. H. G. J. Org. Chem. 1997, 62, 1868.
  6. Pettit, G. R.; Herald, C. L.; Boyd, M. R.; Leet, J. E.; Dufresne, C.; Doubek, D. L.; Schmidt, J. M.; Cerny, R. L.; Hooper, J. N. A.; Rutzler, K. C. J. Med. Chem. 1991, 34, 3339.
  7. Aicher, T. D.; Buszek, K. R.; Fang, F. G.; Forsyth, C. J.; Jung, S. H.; Kishi, Y.; Matelich, M. C.; Scola, P. M.; Spero, D. M.; Yoon, S. K. J. Am. Chem. Soc. 1992, 114, 3162.
  8. Takai, K.; Kimura, K.; Kuroda, T.; Hiyama, T.; Nozaki, H. Tetrahedron Lett. 1983, 24, 5281.
  9. (a) Jin, H.; Uenishi, J.; Christ, W. J.; Kishi, Y. J. Am. Chem. Soc. 1986, 108, 5644. (b) Kishi, Y. Pure Appl. Chem. 1992, 64, 343.
  10. Yang, Yu-Rong, Kim Dae-Shik and Kishi Yoshito, Org. Lett., 2009, 11 (20), 4516–4519.
  11. Stork, G.; Kahne, D. E. J. Am. Chem. Soc. 1983, 105, 1072.
  12. Crabtree, R. H.; Felkin, H.; Fellebeen-Khan, T.; Morris, G. E. J. Organomet. Chem. 1979, 168, 183.
By September 15, 2012 9 comments general chemistry, synthetic chemistry

Life in Chemical Development Part 1.

After spending some years in medicinal chemistry (CNS) I moved to chemical development. Now this change I can recommend to everyone. In med. chem. you are just another tool for the biologists churning out compounds (methyl, ethyl, futile). I think this says it all, one of my biological colleagues asked me for more of a particular compound and added “make it more soluble the next time.”

You don’t get a real chance to use your chemical knowledge and training, you know all that stuff you learnt at university, some of which may have gone into a thesis. Now, in chemical development that is completely different. There you can actually apply your knowledge to scores of problems, even using physical organic chemistry! For me it was like a breath of fresh air and it re-vitalised my organic chemistry tick. At that time we were responsible for everything, reservation of the pilot plant equipment, ordering the starting materials, carrying out use tests of material from new suppliers1, organisation of all the analytics, all the lab work to produce a lab procedure, all the pilot plant supervision including writing a pilot plant procedure, all the safety studies, proposing and carrying out alternative routes, when required, in fact, everything one can think of we were responsible for. It all boiled down to quality, quantity and delivery (on time).

In a previous post here I recalled some of my experiences my first project, now I recount the second. This compound could loosely be called a dinosaur, it had been in development for more than a decade or so and the chemistry, as we will see, had some bite to it. It was a 9-step synthesis of which I had the first 4 steps. The steps under my supervision were; 1) an acid catalysed esterification of a benzoic acid to its methyl ester, 2) reduction with sodium borohydride, 3) conversion of the benzyl alcohol to the benzyl chloride, 4) conversion of the benzyl chloride to the benzyl azide.

A good friend and colleague, not to mention an excellent chemist, had largely completed the chemical development; there were just a few more things to look at in the lab. My role was to produce quantities in the pilot plant to maintain the clinical supply and for the formulation validation. This, of course, meant lots of material had to be produced. We had to obtain around 7000 kg’s of drug substance by a date given by the start of the clinical trials (I don’t remember which ones it was, Phase II Z perhaps?). Calculated was 1 month for release of the drug product by QA, which meant for me I had to start in January and deliver my last step by the end of September. Here is the plan I generated at that time.


The esterification was easy: it was done in a 2-phase system, hexane/methanol and catalysed by conc. sulphuric acid (extractive esterification). We did 16 batches of 528 kg of the benzoic acid using 238 kg 98% conc. sulphuric acid per batch. After a bicarbonate neutralisation, phase separation and distillation of solvent I got 614 kg of the ester. I did it 16 times, the average yield was 95.75%, and 9145 kg was prepared and used in the next step. It had some residual hexane in it,, about 10% per batch, but this was not a problem for the reduction. The hexane distillate was re-used each batch, just being replenished with fresh material to make up the losses.

Dimethyl ether formation was not a problem. It maximised at a production rate of 500 mg/minute after 1 hour then dropped away to <50 mg/minute after the regular reaction time was over. Not bad for a 528 kg batch and certainly not a hazard.

In contrast to med. chem. at least you can see what you get from your reaction, 16×1 cubic meter containers were used to store the stuff until we started the next step. Remember the plan, it was overlapping so we started step 2 about halfway through the step 1 campaign so thing were getting more complicated.

The borohydride reduction was a bit trickier. I did 42 batches of 200kg of the ester as a 90% solution in hexane corresponding to around 1 kMol of starting material plus 8 more batches as “use tests”. Everything was tossed into a 1000 L reactor, warmed to 55-57°C and methanol added via a membrane pump over an 8 hour period.

There is still not a good system for the introduction of such solids as sodium borohydride to a reactor. Borohydride is very hydroscopic and it blocks up the machine. We tried pellets, and these bags that dissolve and release the reagent, but then you just get mushy plastic bag in your product. Neither was as good as the powdered stuff. So in the end we just quickly shovelled it in through the manhole. The hydrogen liberated was vented with a nitrogen flow via a cold (-30°C condenser to trap THF) to the roof via a specially designed pipe with a non-return valve built in so no flames could return and cause a nasty experience.

We set up the first reaction and got it going, then the operator turned to me and said “I’m off for my coffee break now, if anything happens press the red button.” And with that left me standing there praying nothing would happen. Of course he was joking, I hoped, sure enough another operator arrived laughing at my obvious relief. Just as well he came. I looked in the reactor to see a wall of foam coming up to meet me, alarms started to go off as we had about 0.5 Bar overpressure in the reactor which was rapidly increasing. The hydrogen-venting pipe was blocked. So everything was shut down (except the stirrer) and fortunately the foam was contained. Now, it turned out that this pipe had not been used for some months. We went up on the roof and blew a terrific pressure of nitrogen through it from below, and saw several dead birds and various other bits of detritus shooting out of it. Thank God for the non-return valve. The blockage problem solved they placed a steel net over the top to prevent this happening again although why this had not been done before I don’t know. Anyway I went off to change my underclothes and when I got back we started the thing up again and it seemed to be ok this time.

The safety department recommended that, if the reaction got out of control, we should dilute the reaction rapidly mixture by pumping in THF, so a 500 L container under 1 Bar pressure was connected at all times during the reaction, fortunately we never had to use it. This was a safety measure because during DSC experiments we observed a long flat exothermic decomposition between 75°C – 500°C. Our requirements said the reaction must be carried out 20°C below the start of the decomposition temperature which is why we did it at 55-56°C. In any case it would not have been critical, as the maximum temperature of the synthetic reaction (132°C) would not have been reached even if all the THF had evaporated in the case of a condenser problem, the evaporation of the THF would cool the system down. The total energy under that curve from 75° – 500°C was around 700 kJ/kg. Note here the time to maximum rate of the decomposition reaction was estimated at >24 hours, which was fine and meant we would just about survive and the blast proof windows would live another day.

The work-up was interesting; it involved a solvent change to toluene followed by aqueous extraction. So off we went and distilled off the THF/MeOH down to a predetermined volume in the reactor. Note if you applied the vacuum too hard you obtained another foamy mixture advancing its way up and out of the reactor. This was fascinating to watch but I was used to foam by now I knew it would stop which it did, just in time before it reached the condensers. Toluene went in, toluene/THF/MeOH came out and more toluene went in and toluene/THF/MeOH came out, more toluene went in this time followed by water. Now if you did not stir for long enough (2 hours) the aqueous layer was on the top! But I didn’t fall for this one, after the required time the phases swapped over and I obtained a normal water/toluene/product mixture. Off came the water, which was re-extracted and the combined toluene layers evaporated to dryness. All the toluene from the extractions was re-cycled, and used in the next operation for the extraction after checking to make sure there was no accumulation of any side products (which, of course, there was not). Filtration of the distillation residue to remove floating white solids provided the product.

So, after nearly 5 months we ended up with the benzyl alcohol. The mean yield was 96.88% corrected for the concentration of the product (as about 3% toluene remained) and we produced 7098 kg. With this we were ready for the two most critical steps in the sequence, the formation of the benzyl chloride and finally the benzyl azide. That will be the topic of the next missive in this small series.


  1. A use test is employed in order to investigate material from potential starting material suppliers: The compound must meet the given specifications and perform in the series of reactions to deliver the desired product according to its specifications.
By September 12, 2012 9 comments general chemistry, synthetic chemistry