Org Prep Daily

February 27, 2007

Studying from textbooks

Filed under: Uncategorized — milkshake @ 12:37 am

sliva5.jpg Credit: Jiri Sliva 

Trying to study from organic chemistry textbook can induce anxiety and overload. One should focus on things he enjoys rather than trying to memorize everything or he will end up fogged out and worried about being inadequate for the job. Chemistry is supposed to be a fun thing to do, not a drudgery – when reading the organic chemistry textbook for your own curiosity (rather than for the exam)  it is best to flip through the chapters while trying to find the interesting bits. It helps to have your mind focused on a particular problem – for example, “what would be the best set of reactions that one can use to synthesize Ecstasy from safrol or piperonal?” or “Can I put together a short retro-synthetic analysis of morphine?”

I would encourage any organic chemistry student to get a manual for organic synthesis labs- something that has procedures much like OrgSyn – and after reading those experimental procedures to close the eyes and dream about doing the experiments. I had a translation of an old German book “Organikum”. It was a very dated book even 25 years ago – but for me it was more helpful than the regular introductory textbook. It had chapters named “Friedel-Crafts”, “Diels-Alder” etc. Each chapter started with mechanism and general description intro that was followed by the experimental procedure (usually in two or three versions, to be used depending on reactivity and sensitivity of the starting material) and tables and tables of molecules that were actually made with these procedures, the yields, the melting and boiling points. It was great fun to learn not only about reaction mechanisms – but also about how the stuff is done and what practical complications can happen during the synthesis 

Any book or journal or chemical catalog that produces interest is helpful. It is possible to cram lots of information from a textbook to pass the exam. But if the information is not anchored in true interest, about something dear to you – if it remains isolated or does not get used for anything that you enjoy – then you will forget it all rather quickly.

Also, one should not get too religious about what he is learning in chemistry even if the reactions in the book can look arcane or threateningly complicated. It takes no genius to do chemistry – it was put together by regular blokes. Sure, some of them were very smart but many of them were quite normal types that were sufficiently organized and persistant and eventually got good results – but all of them were doing chemistry for years, so gradually they got good at it.


About not studying from textbooks: A friend of mine (a tiny quiet and unassuming type) was taking engineering classes. She was born into a family of engineers – her dad was designing engines for military planes and her mom was also a technical type. At the end of the second semester they had a big oral exam that everybody was very afraid of. My friend was worried about it too – but luckily for her the exam question she got was about turbines. Turbines were a friendly territory to her and she did not hesitate – she outlined the turbine general principles and progressed naturally into their application in turboprop engines and from turboprops she went onto the jet engines. With the ease of someone describing her CD collection she was explaining the merits and problems of various designs and then went also into the choice of alloys, methods used for machining and finishing the engine parts and the problems related to maintenance and repair. The professor’s jaw was slowly dropping lower and lower as his eyes were bugging out (the aircraft turbine lecture went on for quite some time).  At the end of it the professor said: “Uh, I must ask you – because we have some faculty members here that should, uh, like to use your sources in their classes – please where did you get this all from??” She replied shyly: “When I was a little girl, my dad used to tell me bedside stories, about aircraft engines…”

February 26, 2007

4,6-dimethylpyrimidine-5-carboxylic acid ethyl ester

Filed under: procedures — milkshake @ 6:25 am


Ethyl diacetoacetate 12.50g (72.6 mmol) was added to a stirred slurry of caesium carbonate 50.5g (155mmol) in anhydrous acetonitrile (300mL) in a 1L flask. A white voluminous precipitate formed. The mixture was stirred for 30 min at RT, then cooled to 0C. Neat methyl triflate 9.5mL (86mmol, DANGER) was carefully added, dropwise over 10 min and the mixture was stirred under Ar on a melting ice bath (0 to 20C) for 1 hour, then at ambient temperature for 11 hours (overnight). The entire slurry was concentrated to a small volume on rotavap. Solid formamidinium acetate 31.2g (300mmol) was added to the residue followed by a solution of sodium ethoxide, made freshly by dissolving sodium metal 5.05g (220 mmol) in 0.5L of anhydrous non-denatured ethanol. The mixture was refluxed on oil bath under blanket of Ar for 4 hours. (Some ammonium carbonate sublimate deposited in the reflux condenser). The reaction mixture was cooled, filtered and the filtrates evaporated. The residue was portioned between dichloromethane 0.4L and sat. bicarbonate solution 0.5L with some additional water (100mL). The aqueous phase was re-extracted three times with dichloromethane (3x250mL). The combined organic extracts were filtered to break the emulsion, washed with sat. bicarbonate 0.5L, dried (MgSO4) and evaporated. The residue was purified on a column of silica 250g in hexane-EtOAc 3:2 mixture. The purified product (7.5g of a pale-yellow oil) was re-distilled at reduced pressure , b.p. 105-110C/20 Torr. Y=6.307g (48%) of a colorless liquid.

1H(CD3CN, 400MHz): 8.902(s, 1H), 4.409(q, 7.1Hz, 2H), 2.482(s, 6H), 1.364(t, 7.1Hz, 3H)

Note: On cannot be careful enough when working with methyl triflate. The vapor inhalation can cause lethal lung edema, skin absorption will cause painful blisters and the long-term effect is genotoxicity and cancer. Be careful when opening the MeOTf ampule, work with the stuff only in the hood. Evaporating some concentrated ammonia can be used to decontaminate the rotavap after the methylation step. Leave the MeOTf syringe to dry up in the back of the hood. Use double gloves. Do not try to clean a MeOTf spill – evacuate.

February 23, 2007

The visitors from Hell

Filed under: industry life — milkshake @ 7:26 pm


I have great respect for safety officers – the job is thankless and the burden great if things go wrong. It takes foresight to protect people from getting hurt and the company from getting fined and sued. Respect has to go both ways though. The purpose of the safety office is to be helpful – guiding people to work better. Unfortunately many safety officers worry first about their alibi. Safety officers from the unhelpful category also like to throw their weight around – threatening people with disciplinary action or punitive “re-education” classes. I am fortunate to be at institute that doesn’t have trolls running the EH&S office. But I got some exposure in the past.

The problem is much like with the traffic cops – the authority of the safety office gives means to a bully. A bad safety officer can make the safety compliance hard, by promulgating rules like”maximum 3L of highly flammable materials can be stored in the lab”. Trolls are stubborn – they like to insist “no, you can’t” and “yes, you will have to” (to make their arbitrary position sound impartial and prudent, it gets usualy dressed up like …”it is our written safety policy”… or …”not permissible according to the state regulations”). A safety troll will write you citations for “unsheathed needles left in the open, unattended” for a Hamilton syringe on the bench, or “unsafely-stored chemicals” for a plastic bottle of bicarbonate solution kept on the window-still.  

There is a huge amount of government chemistry-related safety regulations that would, if taken to extreme, prevent all accidents from occuring in the lab – simply because people would be unable to do any lab work while observing these rules. A good safety officer should know about the work done in the labs so that he could decide for himself what is required, what is possible, and what is reasonable. One has to first understand the work that one is trying to make safer and use common sense to see what rules are applicable. To learn which procedures and equipment pose a particular hazard and to find out which chemicals are nasty. The way to identify and solve real safety problems (rather than imagined ones) is to encourage the lab researchers to propose the ways to go about minimising risks. They tend to have a more detailed knowledge about the problem and voluntary arrangements work better in the long run than half-baked safety policies imposed with heavy hand. 

But if the safety officer is a pompous troll that knows everything best and enjoys pushing others around, he will have no knowledge about the lab and he will remain isolated and despised. So, he will resort to writing down (and sending up) his thoughts on the bicarbonate bottle and syringe on the bench – and maybe also about that yellow floor-stain in the corner that he noticed on his inspection. These “problems” are not called by their true names in the safety violation report though – alarming but vague language can give an appearance of solidity to pure wind.


The most absurd lab safety system that I heard of was at Hoechst medicinal chemistry institute in Frankfurt in 90s. The medchem building was located within an industrial area – a major plant making commodity chemicals. The chemical plant had serious accidents over the years, chemicals spilled into the river too often, the company was fined repeatedly and the bad press was getting out of hand. So the management decided to implement a new safety oversight and the safety office got free run of the place, including the medchem labs at the location. The main outcome was a relentless scrutiny of the medchem labs.  The hoods and chemical cabinets and analytical instrument rooms seemed infinitely more interesting than reactors full of cresol and more pleasant to inspect. So many different little things in these labs could be regulated and the safety officers found out that they could demonstrate their newly-mandated proactiveness by issuing repeated citations to medicinal chemists. (The plant processes workers were cited less because they knew how to fight back and dispute the accuracy of the safety violation reports with their process manuals and operating parameter logs; it was just taking too much work for the safety people to go after them)… This affair progressed into a serious medicinal chemistry harassment – the repeated citations, including minor ones were referred to HR and carried pay-cut penalties and even a possibility of a dismissal.

The pinnacle of the Frankfurt rules (a typical one: “no benzene allowed in the lab, including C6D6 for NMR”) was that the medicinal chemists were required to turn off all instruments including the stirplates at the end of the day. The power to the labs was always cut at 7pm and the fume hoods were turned off at 8pm. (The labs reeked every morning) A reaction that required a one-day reflux took three workdays in Frankfurt.

My friend, a boss of a small group there got so worried about the inspections and possible fines and summons to HR “to deal with the repeated safety violations” that he asked his colleagues to organize and clean up everything, even to climb and reach deep into the hoods to remove all the accumulated dust and grime from inside. Unfortunately he forgot about the newly-installed smoke detectors in the hoods. A shot of freon gas from a can dust-blower was enough to set the detectors off. The fire alarm triggered a massive response – the city had a heavy-duty firefighter squad located right outside the plant gates. Afterwards, the group members held a lovely discussion with the management about who is going to pay the 20 000 Deutchmark bill for all the fire trucks and people in bunny suits on the scene…


Filed under: procedures — milkshake @ 12:37 am


2-Bromothiazole-5-carboxylic acid ethyl ester 17.75g (75.18mmol) was dissolved in THF 300mL and a solution of NaOH 8.6g in water 150mL was added, followed by additional water 150mL. The mixture was stirred vigorously for 45min (the hydrolysis was complete in 15 min) and the obtained homogeneous mixture was concentrated on rotavap to remove THF. The concentrated mixture was acidified with conc. HCl 20mL, the produced acid was allowed to precipitate on ice bath for 1 hour. The precipitate was collected by filtration, washed with ice-cold water, partially dried by suction. The wet paste of the acid was transferred out from the Buchner funnel, into a small beaker and the material was dried thoroughly on highvac for 1 day. Y=15.045g (96%) of the 2-bromothiazole-5-carboxylic acid as a white solid.

2-bromothiazole-5-carboxylic acid 3.78g (18.17mmol) and 3 drops of DMF was suspended in anhydrous chloroform 40mL. Oxalyl bromide 1.85mL (19.68mmol) was added and the mixture was refluxed on oil bath (85C) under a Drierite-filled tube as a gas outlet for 6 hours. The reaction mixture was cooled, diluted with anhydrous toluene 20mL and evaporated to dryness. The residue was dissolved in anhydrous toluene 40mL. TMS-N3 2.90mL (22 mmol) was added (gas evolution) and the mixture was stirred at 70C under Ar for 2 hours. The reaction mixture was cooled to RT, 2,6-lutidine 3.5mL and isobutyl alcohol (anh, 40mL) was added. The mixture was refluxed under Ar on oil bath (120C) for 1 day. The reaction mixture was evaporated . The residue was portioned between ether 150mL and 1M citric acid 150mL, the aqueous phase was re-extracted with ether 150mL. The organic extracts were washed with water 150mL and then with sat. bicarbonate 150mL. The combined extracts were dried (MgSO4) and evaporated. The residue was purified on a column of silica 80g in a EtOAc gradient in hexane, 0 to 50% EtOAc. Y=3.987g of a light yellow oil that gradualy solidified into a white crystalline mass. (78.5% yield from the acid, 75% from the ester).

1H(d6-DMSO, 400MHz): 11.187(br s, 1H), 7.153(s, 1H), 3.926(d, 6.6Hz, 2H), 1.916(app sept, 6.6Hz, 1H), 0.913(d, 6.7Hz, 6H)

The wet paste of 2-bromothiazole-5-carboxylic acid tends to dry into hard chunks; it is a good idea to transfer the wet product before drying it on highvac – the dried acid is difficult to scrape out of a Buchner funnel. The dried and powdered acid is quite static, crushing the chunks of the dried acid is best done with a spatula in a wide-mouth storage bottle.

Oxalyl bromide was used to avoid a halogen scrambling on the thiazole (chlorothiazole acyl chloride is the main product with oxalyl chloride).  

Note: TMS-azide is volatile, latex-permeable and absorbed by skin. Quite a small quantity of TMSN3 can make you very sick very fast. Use double gloves and work with TMSN3 only in the hood, don’t spill it. Don’t try to clean up the spill, just evacuate quickly if it happens. Drinking few shots of vodka can relieve symptoms of moderate azide poisoning, i.e. the azide-induced head-splitting migraine. 

February 19, 2007

Ethanolamine can save your skin

Filed under: procedures — milkshake @ 12:37 am


I did many terrible things in the lab over the years. One of the earliest mishaps involved a beaker filled with thionyl chloride – about 250mL of it – that I spilled on myself. My advisor was standing next to me as this was happening – and in one instant motion he grabbed a 1 liter bottle of ethanolamine and poured it on me. A cloud of white smoke rose up, I ripped my clothes off and run for the shower. I suffered no burns from the incident.

From that time on, a friendly ethanolamine bottle has been sitting on the shelf in my lab. I later worked at a combichem company and accidental TFA splashes were a frequent occurrence there. Ethanolamine proved to be enormously useful in preventing TFA burns. 

There are many corosive liquids that soak into skin and cause painful burns: acyl chlorides, alkylating agents, bromine, strong acids like HCl in dioxane. The problem is that water, bicarbonate and acetone washing has limited utility if the agent is allowed to soak in – the burn develops from within. But if one applies ethanolamine onto the affected area the amine soaks into skin and neutralizes the corrosive agent there without causing much additional damage. Unlike many amines, ethanolamine is non toxic – it is actually a building block of some phospholipids within cell membranes.

Ethanolamine is applied on the skin in undiluted form for about half a minute and is washed off with water. Afterwards it helps to put a lotion or ointment on the affected area because skin tends to get de-greased and reddened from ethanolamine. A sterile bandage is probably a good idea. Ethanolamine must not be used in or around the eyes.  For HF burns, calcium gluconate in glycerin is more efficient since Ca(2+) can neutralise the toxic effects of fluoride. 

February 15, 2007

Biotech management and its casualties

Filed under: industry life — milkshake @ 2:59 pm

sand_sculpture.jpg Credit: Harry van Reeken

There are too many PIs in academia eager to start their own company – without understanding basic things like the drug PK optimization stage. There are naive investors ready to pour their money into any start-up that it is presented to them as an exciting investment opportunity. And then there is an industry-wide problem with business-people that have great confidence in their own management qualities but little knowledge about how the research that they are directing is actually done. I will add some comments about the management part.

People with business background like business models, charts, decision-making diagrams. They hope that it is possible to succeed in a research-based business according to some management formula. They like to impose methods of dynamic management on drug discovery, assuming that the modern management theories actually work in real life and that they are applicable to any business activity (like organizing those fuzzy wuzzies in the labs, to make them more efficient). But they don’t realize that drawing out detailed research progress flowcharts won’t increase rate of real research progress; only the number of meetings will increase. Identifying the “Go/no-go” checkpoints on he diagram is no substitute for the common sense.

Business-people also don’t appreciate the enormous personality factor in research, something obvious to anybody who has worked in the lab. Research is not some kind of franchise. The research people are not a comodity – or a concrete sludge poured into free slots of a well-laid organization structure. The actual choice in hiring research individuals is more important than anything that can be done later about managing them. One pushy or dishonest person can ruin the motivation of the entire lab.


The other thing that always bothered me is that the proprietary core technology/research results get so over-hyped by startups, to please their investors.

Salesmanship used on investors is not illegal – but the dishonesty bites back. If one begins with unrealistic projections and then makes too many promises, the moment will come when it becomes hard to make good on these promises. More often than not some kind of wishful thinking sets in during this process of sustained exaggeration, and the baloney corrodes the management and research alike. Disagreeable information are not acted on but are suppressed. Eventually a culture develops when CEO keeps saying “we will have two clinical candidates next year” while the entire research staff grumbles “not a prayer” and the lower management is already preparing evasive manoeuvres so that they wouldn’t be blamed when the reality sets in.

The investors encourage the deceit – by allowing the management to award themselves ridiculous quantities of stock options. To inflate the stock price until the stock options are cashed, clinical trials of troubled drug candidates are not cancelled in favor of improved backup candidates but are dragged out into late-stage trials, only to fail two years later at incredible expense.

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