Chemistry Heartbreak

…With emphasis on the break.

I’ve not posted recently for a variety of reasons. This prompted me to break that silence:


What you see here is the 1 liter erlenmeyer flask that contained my reaction from yesterday, which I was about to pour. Pick up, slip and, it being quite full, crash.

On the plus side, it is the first step and the starting materials are readily available. It is still one of the worst feelings, to see your work smashed on the hood floor.

Working a Saturday

At this point in my career, working on the weekend is generally not what is done. But needs must when the devil drives and all that, a compound is needed for a study and it is needed soon. For that to work, sometimes you just have to put in a weekend shift to make it. Plus I figure that if I am having to work on a Saturday, at least I can get a blog post out of it.

There is an occasional Twitter topic called #realtimechem, so I will do something like that in considerably more than 140 characters.

So setting the scene: we have a compound that went into a study. They asked for some more and we took what intermediates we had to try and get the required amount. It looked like we would be short, but then they said they could finish the study with a lesser amount. Here I was guilty of too much optimism for I said that we might make that with what we have and it turned out I was wrong.

But wheels were set in motion and the deadline was set. We had more starting material in hand but in order to make it in time would need dedication, hard work and to not waste the weekend on trivial things like lazing about the house and telling off the kids for playing too loudly.

So Saturday morning dawns. First things first: check on the reaction I set up Friday evening. An alkylation of a phenol, often done with potassium carbonate as the base, here I found that to give me poor yields and cesium carbonate to be more effective. So I run the TLC to check the reaction is complete. I take a small sample out, add it to a mixture of ethyl acetate and water to take my TLC from the organic layer. The solvent is dimethylformamide which tends to mess up the TLC analysis, so I often do a mini work-up of the reaction to clarify matters.

The reaction is complete, so the reaction is cooled and I turn that mini work-up I just did into a maxi work-up in the big separatory funnel. A bit of an emulsion is dealt with by addition of some sodium chloride solution. The solution of my product and assorted impurities is then absorbed on Celite for solid phase loading onto the chromatography apparatus.

Back in the old days, all the purification was done by hand in mind numbing tedium. Nowadays it is all automated with disposable silica cartridges and pumping automatically altering the solvent mixtures for optimal separation. Well, that is the theory anyway. It is considerably less mind-numbing but not always smooth sailing.

Today my column set up well, but when you need it to behave it always wants to be a little mischievous. I set it going and from having done it before I knew when to expect the compound to elute (and you see a nice UV trace on the screen to reassure you of that fact). Well a little peak comes out and it is not at all what I am expecting, for I put a good amount of there and I want a BIG peak. I frown at the screen, concerned. Another peak comes out – perhaps this is the one? But no, again it is but a tiny hillock when I am looking for a mighty mountain.

Then I notice that the test tube fractions collected are coming out half filled. The pump for the polar solvent is misbehaving.

I comfort myself with the fact that the more polar solvent is already at 100%, so the misbehaving pump shouldn’t affect the column from here on out, though it probably made the gradient less steep than was planned, delaying elution. But then a big peak starts coming out and all is right with the world again. Peak shape is a little ugly. But I can live with that. Then as the peak is coming off, another big peak starts to elute.

This was not according to the scheduled program. The TLC had shown no starting material and only faint spots of any other type. What was this monstrosity?

Well, TLC soon told me that the peak shape was so ugly that it had split into a double headed peak. It was all my compound. So just need to strip it down to dryness for a quick NMR analysis before setting up the next step.

There are two possible states for the NMR machine on a Saturday afternoon. The first is that it sits idle and no one has touched it for hours. But because no one much uses it over the weekend, it is a good time for setting up long carbon-13 experiments and once in a while a couple of those will get queued up and black out any possible NMR time until Sunday night. So it is with some trepidation that I take my NMR tube of compound and deuterated chloroform to the room. And a sigh of relief as I find it all sitting idle.

The analysis confirms what I really knew already, as the white solid on the inside of the flask was clearly (by retinal analysis) the purest and best. So into the next step we go.

I keep some back, as this next reaction can be capricious. It is a cyclization reaction and depending on substituents on the parent molecule, gives different yields, but also is variable in the recovery from batch to batch. I’m putting nice material in, so I am giving it the best chance, though one of the substituents is slightly unfavorable.

In true #realtimechem fashion, I was running the TLC as I typed that. And now I have checked it and the reaction is complete.

My Saturday is about done.

How to Make the Perfect Snowball

It is that time of year when the hand of Winter is felt upon the land and we turn our thoughts to such pursuits as skiing, hot chocolate and, of course, making snowballs. But this is an art not to be undertaken lightly, for there are arcane and obscure techniques to be used. I shall reveal one for you here today and you will never add a snowflake, nor even a drop of water to make it.

First, you require a Dewar. Use it for a while as a vacuum trap, with plenty of dry ice and a little isopropanol. Keeping topping it up with dry ice regularly. Do this for a while, until your extensive experience tells you it is time to move to the next phase. A sign that it is ready is when you have trouble getting the trap out of the Dewar when you want to empty it. This is an art that requires great patience.

Next you let the trap thaw and remove the trap, preferably without breaking it (if you can). The dry ice has gone, but a large block of ice is within, ready to form your perfect snowball.

Now you add some acetone, as the snowball won’t come out without some help. I don’t recommend breaking the Dewar. Let that sit for a short while then drain out the acetone (save it for making cold baths later).

If you have done it right, the snowball shall emerge, perfectly smooth and rounded. Is it not both beautiful and awe-inspiring?



Perfect Separation

They don’t just occur in chemistry catalogs, they can be something in real life too (though the :

My Separatory Funnel

My Separatory Funnel

I will contrast this with the same reaction when I first did it, wherein the layers were darker, murkier and had more insoluble muck in them. The reaction conditions have been slightly tweaked, but broadly the chemicals in the flask are the same, so it is as much about the hands that do the chemistry getting better at it as it is the reaction going on in the flask. Though I did learn some things about the accuracy of the thermocouple of my heating/stirring plate at higher temperatures – this reaction was run at a high enough temperature that the cooling from the air in the hood was enough to prevent the oil bath reaching the desired temperature and the oil temperature measured by thermometer was a little lower than the reading on the dial as well.

Anyway, I thought it was a nice shot to share.

It Shipped Today!

I ordered a chemical a couple of weeks ago. It was fairly obscure and I was happy to get it for a reasonable price and from a company I trust too. Order placed, I got back on with other things.

A week or so later, I started wondering where it had gotten to. I don’t recall any back-order notifications. Other chemicals our group had ordered at the same time had arrived. Plus it was not the highest priority, so I merely shrugged and assumed that it was on its way. Any day now.

With a full 3 weeks elapsed since time of order, I finally get on the phone to our purchasing department. The lady there looks into it and I get the call back. It just shipped! I got it the very next day.

Now call me cynical if you will, but I never believe the line that “we just the minute got your order ready and we’re just putting it on the truck”. I mean, it could happen, but it just seems so unlikely that exactly on the day 21 days (not 20 days and not 22 days) after we placed our order, on the very day we call and ask, that they just this minute got it in the box for shipping. How uncanny that as you were pouring in the packing peanuts, the phone rang. That is quite the coincidence. It is like you were reading my thoughts that I must have broadcast telepathically. Astounding. Are you sure you didn’t just forget to send it?

Well, at least they did send it eventually.

Not Quite What it Says on the Bottle

A few weeks back there was a lot of discussion over the bad bosutinib which had come from the wrong aniline being used in its synthesis – fortunately none in the clinical trials, but making a mess of the other research work being done using it.

I will guess that most folks working in a lab have had some sort of “bad bosutinib” story, though obviously not quite so important and more easily caught. Many wise heads shake when a bright young chemist offers up his bought LDA solution – better make it yourself, I was always told. I’ve had another couple of stories recently that I will share today.

The first was a bought chemical – ethyl bromoisovalerate. I was interested in that isopropyl group being added to my molecule and ran my chemistry as usual. But when I got my NMR of my product, the distinctive isopropyl was nowhere to be found. Turned out to be ethyl bromovalerate – the straight chain version. A shame, as I had already bought that one.

This one was easily caught because I knew what I was looking for. The other was not so easy for me for the exact opposite reason – I did not know what was wrong.

This one was some HPLC vials. I had used screw cap ones all my career to date, but my colleague that was in charge of the HPLC (and whose stock of vials I was raiding) used push on caps. Well, no problem, except they wouldn’t stay on. Not just one or two either, but half the vials had the caps slowly rising up off the vial again – a major concern when you are doing automatic injections. The needle will not like that. I complained to my colleague about the caps and how terrible they were and she told me that she’d never had a problem with them before. Then we really looked at them – they weren’t quite right. There was no little groove on the vial lip for the cap to clip onto (see my poorly taken photo).

As soon as I changed the vials for a fresh box that weren’t all faulty, the problem went away. I didn’t realize straight away because I wasn’t familiar with these kinds of caps and how they worked. Sometimes you just have to say to yourself “they wouldn’t deliberately make them so difficult to use.”

Would they?

Running Reactions: The Journey and the Destination

I was running a Curtius rearrangement last week and it struck me that this was exactly the kind of reaction I like to run, one with several steps, the kind of reaction that you have to base your entire day around.

For those who don’t know it, the Curtius involves forming an acyl azide, which rearranges to an isocyanate (releasing nitrogen in the process), which can then be either hydrolyzed to an amine or condensed with an alcohol (to form a carbamate) or an amine (to form a urea). It is a very neat way of changing an acid into an amine. But more to the point of my post, there are several stages in the procedure: formation of the acyl azide, which is usually accomplished by careful addition of diphenyl phosphoryl azide to a solution of your acid, then inducing the rearrangement by heating, then I cooled it back down to add an amine (I was making a urea), before heating it up again to push the condensation reaction to completion.

Thinking more about it, this kind of reaction is a luxury. Most of the lab work goes into purifying and analyzing compounds, not the reaction itself. So to take time to run the reaction, to enjoy the journey as it were, is something that the average busy laboratory chemist doesn’t get the chance to do a lot. Or when they do, it is artistically arranged around group meetings, seminars and any other work you’ve got going on. In short, enjoying the journey can make life a lot more stressful.

Which is of course why the medicinal chemist’s stock-in-trade reactions are amide couplings, Suzuki reactions and reductive aminations. Reactions for which the procedure reads “put everything in the flask and mix it up”. For these reactions, the destination is the thing and the hustle and bustle of the journey is avoided as much as possible. You set it up, get on with other stuff, then come back and it is done. The perfect reaction to set up late in the afternoon, then you come back next morning to complete reactions, spot-to-spot conversions with hardly any need for purification. Or, more usually, it flows into a morning of work-ups and purification, which is the usual way we spend our day.

Maybe it is a change on time – or the stage of my own career. When making a ketone or aldehyde, the way I always did it in graduate school was via a Swern oxidation. It had the advantage of high yields, clean reaction and also a satisfyingly involved reaction procedure. Plus it was a mechanism that came up practically every week in group meetings. There was that little problem with the smell of the dimethyl sulfide by-product. But nothing is perfect.

I can’t actually recall the last time I did an oxidation that way. Dess-Martin periodinane, sure. Even a manganese dioxide oxidation. But the Swern seems to be too much of a luxury when easier and more straightforward methods are available.

But sometimes it is worthwhile to slow down and enjoy the process of running a reaction, enjoying the color changes that tell you everything is working and the satisfaction at the end of a product you worked, really worked, to obtain.

Cleaning up the Hood

We had one of those sporadic lab clean ups this week. More specifically, I had a really good clean up of my hood.

I am far from the tidiest person in the world, but I do try to keep things pretty respectable. I do know people who have hoods you could serve dinner in and I marvel at their obsessive-compulsive cleanliness. So I’ll say that before this clean-up, I’d have said my hood was OK. It helped that I spilled some sand and had to clean that up, which helped the general vicinity of that end of the hood get a bit better.

However it is also true that I am also not the first resident of my hood and the untold stories of the various splashes and stains that adorn the walls attest to that in numerous little ways. So while I might have said my hood was “OK”, I would also acknowledge that there was room for improvement.

We went all out. Everything out of the hood, the walls washed down. All kinds of yucky lint washed off the baffles and joints. All kinds of good reasons you don’t make such things white. We did our best to get back to white, at least.

Then there was the grill at the back at the bottom of the hood. It has a rough edge to it, so wiping it down tears the paper towel, leaving bits of paper stuck on it. It is an important place for the air flow inside the hood too, so it was unsurprising to find more bits of paper towel back there. The quantity was perhaps a bit more of a surprise. And all sorts of little bits of kit – pipette bulbs, some TLC spotters, that kind of thing, all crowned with black lint.

It was hard work but oddly satisfying. As I returned my stirrers and other equipment back in their places, I reflected that it was going to be hard to mess up the temporarily perfect hood with chemistry again. For a little while, every spill is pounced on and I keep noticing more bits of paper towel hanging from the grill at the back.

But another thing I noticed: the air flow in my hood is definitely improved. Before, when I was working in it, it would sometimes give the low flow alarm, if I had the doors open too far. Now, with the baffles cleared of the assorted detritus of the years, that is a lot less frequent. I had to work at it to make it go off today.

Diphenyl Ether

A quick post to share my experience with this reagent, as it was really a joy to work with.

Firstly, diphenyl ether is a solid at room temperature, melting at 25-26 C. I was using it as a solvent for a high temperature reaction – it seems like a primary use for it is to enable quite high temperature reactions, as its reflux is 258 C. It also demonstrated that I need a thermometer that goes over 250 C. Let me also add that this is notably higher than I like to work at, but when the procedure calls for it, I stand ready.

Anyway, this was supposed to be the solvent but fortunately you can get essentially the same thing as Dowtherm A and that is actually a pourable liquid.

The procedure was one in which a solid was added to the heated Dowtherm A then heated at reflux to give a cyclization reaction. Adding solid to a reaction vessel at above 200 C is not among my favorite procedure methods.

Getting rid of such a high boiling solvent was, surprisingly, not so bad as my product was a solid and it was just a matter of washing the pad with a more friendly solvent. However, getting rid of it off the glassware was somehow more tricky and all the more annoying because of its peculiar smell, which seems to linger for quite some time on anything it is spilled on.

The best part was how I got to do it again as it worked so well. And how I am penciled it to run it when we ever need some more of that material.

An Important Message About Sharpies

A colleague walks into the lab and says, very casually, “Your sharpies are upside down.”

The Sharpie is very common in the laboratory for the obvious reason that we use it to label things (on the glass directly mostly) and then it can be removed with a little acetone once we are done. So imagine my surprise when I found out yesterday that I had been storing them wrong. If you want maximum performance from your writing implement then you need the ink at the business end and that means keeping them point down. I didn’t want to just take my colleague’s word for it, so I asked the smart word box and the font of all some wisdom, Yahoo Answers, confirmed the story.

Cleverly, the company sells them with a clip on the cap so you can hook them in a top pocket. This is convenient and also brilliant, as the ink runs away from the tip and makes the pen run out quicker, thus making you get a new Sharpie sooner. Fiendish.

They might claim it is so they don’t leak all over your shirt, but we are onto them now.