Blog Comments Back On Line

I was wondering why no one ever seems to comment on the blog posts anymore and just discovered that I no longer get notified when someone submits a comment. ARghhh. I am really sorry about this. I have been through the long list of comments (and spam) and have posted stuff from the last couple of years just now. In the future I will see them as they come in and post them straight away. As I have done in the past I will answer any (meaningful) questions that come in.

Happy Holidays to all Curly Arrow supporters. D!

Transfer of nasty stuff with a syringe and needle

Synthetic organic chemists often have to transfer something pyrophoric, toxic, volatile, smelly etc. from a commercially acquired sealed bottle such as a Sigma-Aldrich Sure/Seal bottle using a needle and syringe. Even with great care it has a tendency to drip from the needle tip, which is the last thing you are interested in. Now a Danish team has published a simple DIY solution that should be adapted broadly since it solves the problem and increases lab safety.

Basically they have developed a 3D printed mount for the sealed bottle that makes is easy and safe to remove what you need (using both hands) and the needle tip is contained inside a small airlock during transport to the reaction vessel. I have taken the liberty of inserting a figure from the paper above that describes the set-up nicely. If you use this set-up and remember to always employ Luer locked syringes I believe that most accidents can be eliminated and that we can avoid another Sheri Sangji incident in the future. D! 

How to make dry HCl gas

Dry HCl gas is essential for certain reaction types and can come in handy for making various saturated HCl solutions. The easy solution to this problem is to have an HCl cylinder handy. However, I’m sure that some of you have experienced (or have heard of) the horrors of the corroded gas regulator on an HCl cylinder. Regulators on HCl cylinders have a very bad habit off snapping off! One of my good friends had a very close call with a big HCl cylinder. Luckily he was standing right next to the door so the only thing that needed to be replaced was that particular lab. If you must have an HCl cylinder standing around I’d recommend a lecture bottle (see photo). These are (in theory) less likely to go off since they have a relatively short life time and if they go off they are likely to kill fewer chemists. Nonetheless, this particular HCl lecture bottle in my current lab has decided to corrode/fuse. A tech-guy has been by three times over the last 6 months trying to get the regulator off. I just wish he would take the damn thing with him and not store it in the hood next to me. A safer, relatively simple, cheap and convenient way to get hold of some dry HCl gas is to make it yourself. The standard approach that I’m guessing most chemists still use is to add conc. sulfuric acid to sodium chloride or conc. HCl. However, avoiding the use of conc. sulfuric is desirable because it’s nasty and you’ll have to clean up afterwards. So in the interest of safety I would recommend the addition of conc. HCl to calcium chlorid. It’s cheap, the HCl gas that you generate is completely dry, it’s relatively easy to clean things up and the reaction is very easy to control. Here’s the original reference:

A Convenient Way to Generate Hydrogen Chloride in the Freshman Lab, Francisco J. Arnáiz, Journal of Chemical Education, 1995, 72 (16), 1139.

On the photo you can see one of my recent set-ups. Here I am adding conc. HCl to calcium chloride with a pressure equalising addition funnel and bubbling the HCl directly into my reaction flask. Please note the use of a Pasteur pipette for bubbling the gas into the reaction flask. Do not get tempted to use a metal needle. Also I often add a wash bottle between the reaction flask and the gas source in case of unexpected suck backs. D!

Evil Molecules Part 1 - Explosive Azides, Diazidomethane

Say hello to diazidomethane. Is it time for a change of underwear yet? I work with azides on a daily basis and I even determine the melting point of my azides. My azides are nice a stable because they all adhere to the 6 heavy atoms (carbon or heavier) per azido-group rule of thumb. However, if you stray from the 6 heavy atom path you are looking for trouble and if you decide to do 1/2 a carbon per azide as we have in this case you will be looking for a new chemistry department.

In this really interesting paper from Alcon Research Ltd. they unintentionally made a fair bit of diazidomethane when performing the synthetic sequence shown in the scheme below. To remove residual dichloromethan after the first step the chemists at Alcon redissolved the crude product in DMF and concentrated it to dryness. To my (and theirs I'm sure) surprise this doesn't remove all dichloromethane despite a huge difference in boiling point. After performing the second step, they worked the reaction up and concentrated it on a rotary evaporator.

 This is what they observed when they came back the next morning:

“... it was noted that about 30 mL of a twophase liquid had collected in the glass crosspiece at the bottom of the condenser assembly.”

When they attempted draining the stuff it decided to go nuts. All I’ll say is that nobody died but you’ll have to dig the paper out yourself if you want the full story.

Remember, halogenated solvents (dichoromethan, chloroform, 1,2-dichloroethane...) and azide ions are bad news. Don’t do it!

Diazidomethane explosion, R. E. Conrow and W. D. Dean, Org. Proc. Res. Dev., 2008, 12 (6), pp. 1285-1286. D!

Catalytic Hydrogenation - now fire free

In my experience you should not do synthetic organic chemistry if:

-

(A) You are drunk (or the following day when you have a hang over)

and/or

(B) You are in a hurry

-

Recently, I violated Commandment B and decided to put a large scale catalytic hydrogenation on really, really fast. Bad idea!

-

Now hopefully most of you realise that the addition of palladium on charcoal (or charcoal alone) to organic solvents can result in instant bonfire. Unfortunately the chemists hand is often right above the flask as the catalyst gets added and some very nasty burns can result. Even worse the whole thing may take off and you'll frantically be looking for a fire extinguisher (Always know where the fire extinguisher is. You will need it one day).

-

There is an easy way to avoid this problem. If you first remove all atmospheric air inside your flask there will be no fire. In other words what you have to do is flush the flask with nitrogen or argon. I normally hook my flask up in such a way that I can evacuate it with a pump and fill it with nitrogen. I've shown one of my recent setups on the picture. You can obviously connect things in many different ways depending on what equipment you have available.

I normally evacuate the flask and fill it with nitrogen at least three times. Only then do I proceed to add my catalyst. After addition I repeat the evacuate the flask procedure but this time I flush the flask with hydrogen and at the end I attach a big fat balloon with hydrogen gas and stir the reaction mixture vigorously.

-

The other day when I was in a big hurry I decided to skip the flushing with nitrogen step (for the first time ever) and as a consequence I had my first Pd on charcoal fire. I was very lucky and didn't burn myself because the weighing paper was shielding my hand. The drama was quickly over as I had my lab book handy and sealed the flask with it. The hydrogenation worked fine and I made it in time to the pub. However, next time I think I'll skip the first pint with the boys and flush that flask as I normally do. D!

Revenge of the NMR tube

Well I guess it had to happen to someone sooner or later. It appears that I applied slightly too much pressure when I was sticking the lid on my NMR tube the other night. As a result the tube snapped and proceeded to go straight through my glove and into my finger. Now that's obviously annoying but can be fixed with band aid. However, when the tube had finally embedded itself in my finger it decided to snap for the second time. In other words I had a piece of NMR tube thoroughly buried in my finger. This is not the sort shit you want to happen to you at 11 pm on a Monday. Trying to fish the glass out myself only resulted in pain and blood everywhere so off to the hospital. Fortunately, the hospital is only a short walk from the Chemistry Department. After waiting for an hour amongst screaming people on various drugs and/or totally shit faced with blood coming out of various openings I was attended by a very nice Doctor. She told me straight away that X-ray was no good for glass so she would have to dig around for the glass bits. At this point I would like to say thank you to whoever it was that came up with anesthetics. Anyway, after some serious digging and cutting a big chunk of NMR tube was extracted. This is what my finger looked like at 1.30 am when I was finally out of the Emergency room.
No my fingers weren't really blue. I have no idea why it keeps uploading the picture like this but it looks kind off cool and scientific. Anyway, it really wasn't particularly dramatic and if it wasn't for the glass I would never have gone to the Emergency Room. I have always heard that impaling yourself with an NMR tube is a particularly common accident amongst chemists. Nevertheless, I'm the first casualty that I know off. Does anyone else know of similar incidents? Finally, I have to say that there wasn't really anything I could have done to prevent this from happening. I used a brand new tube and applied a minimum amount of pressure when putting the lid on........just got unlucky I guess. And by the way what are people thinking off getting drunk and on drugs on a Monday. Save it for the weekend people. D!