The Antistatic Portal

For a change I had to leave the office, put on a lab coat and go to the lab to weigh out some compound. I had a nice fluffy freeze dried substance that had to be transferred from one vial to another. I was faced with usual static electricity problem. The easy solution is to take your plastic gloves off and hope that your compound doesn't fly around the hood when you try to transfer it. However, as often as not this will not do the trick. For the same reason the antistatic gun has been developed (see picture).

If you "shoot" your vials a couple of times this will help, sometimes, maybe. I find it a bit of a lottery whether this works even without gloves on. Which brings me to the point of this post, the Mettler Toledo™ U-shaped Ionizer Antistatic System or as I call it "The Antistatic Portal". It reminds me of the movie Stargate as it's standing there next to your balance humming with electricity (see picture below). Basically the idea is that you just move the stuff that is being weighed through the portal and voila the problem is solved without travelling to distant planets and fighting Egyptian Gods.

Pretty neat and the damn thing actually works with plastic gloves and all so I can recommend this addtion to your lab (if you can afford it). D!

The Disconnection Approach - Automated!

In my time as a synthetic organic chemist the most important advance in the field was definitely the introduction of searchable databases such as SciFinder and Reaxys. Life before these involved spending days on end in the library flipping though dusty tomes of chemical abstracts and Beilstein. And at the end you weren't even sure if you missed something of critical importance. The introduction of open access LC-MS and high field NMR has also had a big impact for me by speeding things up considerably. However, besides these milestones I think that I have pretty much been doing chemistry the same way >25 years. Anyway, what I am getting at is "what will the next BIG thing be?" It's been a considerable time since we had a major technical breakthrough for the synthetic organic chemist. My colleagues and I have been discussing this for more than a decade and now I think I am spotting the next big thing - Chematica! Chematica was developed by Polish scientist Grzybowski and has been around for quite a while. Basically it is a computer programme that disconnects your molecule and suggests ways for you to synthesise it. What's changed since I first heard mention of Chematica ~5 years ago is that apparently now it works the way you would like it to. Recently Grzybowski and co-workers published an impressive paper where they synthesise 8 very different and rather challenging molecules. The abstract from the paper nicely summarises the achievement:

"Multistep synthetic routes to eight structurally diverse and medicinally relevant targets were planned autonomously by the Chematica computer program, which combines expert chemical knowledge with network-search and artificial intelligence algorithms. All of the proposed syntheses were successfully executed in the laboratory and offer substantial yield improvements and cost savings over previous approaches or provide the first documented route to a given target. These results provide the long-awaited validation of a computer program in practically relevant synthetic design."

You really should read this paper. These are not simple syntheses and would have taken quite some time to come up with if at all. Now it is still early days and Chematica is only for those with deep pockets. I am personally waiting for a quote right now and am very curious to see exactly how deep my pockets need to be. BUT it has started and I believe that now it's just a question of time (I'm guessing  less than 10 years) before you simply hit the disconnect button in ChemDraw, look through the suggestions that appear on your screen and pick the one that you like best.

And there is more. Another game changer is already here and everyone with a PC can do this: Machine Learning. My next post will be on this topic that we are already using to great effect at my work place. 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! 

Dry Column Vacuum Chromatography (DCVC) - The Movie!

I have on several occasions been asked to make a DCVC video tutorial and quite liked the idea of doing so. Thus, I have started my acting career as you can see in the video below. I think the video will be a useful guide for first time DCVCers. For more info you should consult this and this blog post on DCVC. Many thanks to the University of Copenhagen's Communication Department, in particular Jacob Lejbach Sørensen, for investing some time in making this possible. D!

Diazomethane and the Arndt-Eistert Homologation

For the past year we have been starting peptidomimetic chemistry up as a new research area in our group. Many chemists believe that peptide chemistry is easy and that peptide chemists aren't "real chemists". However, let me tell you from personal experience that there is absolutely nothing trivial about peptide chemistry. Even short sequences with normal alpha amino acids can be a nightmare to make, troubleshooting is complicated, purification can be a major pain and yields that a small molecule chemist would consider a total fail is generally acceptable in this area of research. Some years ago I was working with a Post Doc that came from Dieter Seebach's lab at ETH. He introduced me to beta amino acids and ever since I have been fascinated by the use of these building blocks in peptidomimetic research. Inspired by the work of Samuel Gellman we are focusing on the use of beta-3 amino acids in combination with alpha amino acids. Consequently, we synthesise beta-3 amino acids to incorporate these in our peptides.

There is a number of ways to make beta-3 amino acids but from personal experience one method stands out as the best route to these molecules: the Arndt-Eistert homologation. In this classic approach an alpha amino acid is converted to a diazoketone followed by the Wolff rearrangement to provide beta-3 amino acids. The Arndt-Eistert homologation basically homologates a carboxylic acid with one methylene group as shown in the scheme below.

The last step, the Wolff rearrangement, is carried out by sonicating the diazoketone in the presence of a silver catalyst (in the dark). Because nitrogen is evolved during the course of the reaction we normally have an empty balloon fitted on the flask to avoid pressure build up. I rather like the feature that the balloon slowly gets inflated during the course of the reaction as shown in the picture below.

Silver catalysed Wolff rearragement in a sonicator. Left t = 0 hr; Right t = 2 hr.

However, as you may have noticed there is a down side to the Arndt-Eistert homologation: diazomethane! The reagent has a fearsome reputation and I have heard of a couple of guys who have managed to blow themselves up and gone deaf in the process. Allegedly, one chemist at our department even managed to set fire to himself! This was a long time a go when less attention was being paid to laboratory safety and the accidents were due to sloppiness and improper handling of diazomethane. If you are careful and use the correct glassware (with clear seal joints) there is (almost) nothing to worry about. We have purchased the setup shown on the picture below. This is a very nice diazomethane still consisting of only three pieces that will produce up to 40 mmol of diazomethane in approximately one hour. We only use hot water as the heating source and keep everything behind a blast shield just in case. Diazomethan is generated from Diazald  as shown in the scheme below and used immediately. The procedure it quite simple. In the separatory funnel you place a solution of Diazald in ether this is added dropwise to a heated mixture of aqueous potassium hydroxide, ether and a high boiling alcohol [commonly 2-(2-ethoxy-ethoxy)ethanol]. Diazald reacts with the base to produce diazomethane that is distilled with ether to the receiving flask.

Notice that diazomethane is always handled in solution. The neat stuff is known to explode unpredictably so don't even think about doing that. Because of the way that diazomethane is produced it is hard to add an exact number of equivalents to a reaction. For the synthesis of diazoketones we simply go for an excess of diazomethane (approximately 2-3 equivalents based on a 70% yield of diazomethane). We commonly distill the diazomethan directly into the reaction flask to minimise handling. For the synthesis of beta-3 amino acids the alpha amino acid is first transformed into a mixed anhydride which is exposed directly to an excess of diazomethane.

Diazoinsane clear seal distillation kit purchased from Sigma-Aldrich.

Unlike diazomethane, Diazald is reasonably stable and easy to handle yellow solid. Unfortunately, Diazald has obtained a rather bad reputation despite being relatively safe to deal with as long as you don't eat it, set fire to it, beat it with a hammer or something similarly stupid. Consequently, it can be rather hard to get hold of. When I worked in Australia it was particularly problematic as it can only be shipped by road and isn't produced in the country! Here in Denmark we get it from Germany but it does take a while because they don't send it with the regular shipments so you have to plan a bit ahead.

If you think that playing around with beta-3 amino acids could be fun I can recommend the company Anand Chem based in Slovakia. They produce almost all beta-3 amino acids with the proteinogenic side chains of excellent quality at a highly competitive price. Depending on what they have in stock you may have to wait a couple of weeks for the stuff but it is worth the wait considering the quality and the price. D!

The Sand Bath - An Alternative to the Oil Bath

Yes, I am still alive! I have been out of the lab for a loooong time so the inspiration hasn't been there. However, I am now finding myself in the lab again and it appears that I will get to stay there for a while. And today inspiration struck.

Let's talk about oil baths. Good way to heat stuff up in a controlled way, BUT, what a bloody mess they are. The oil becomes disgusting after a while, the glassware gets nasty, ocassionally oil baths break and make the mess from hell....
So whenever possible I use an aluminium heating block. However, we have a limited number of these in a limited number of shapes and sizes. When a heating block isn't available my next choice is a sand bath. These are traditionally used when you have to heat something to a ridiculous temperature that oil can't handle. However, I use them for any reflux (see picture). The problem with these things is that heat transfer isn't particularly effective so it's only really good for reflux and not for heating something at a well defined temperature below the boiling point. Also it can be quite tricky for the sand bath to heat up in a well ventilated fume hood so it is generally a good idea to wrap a bit of aluminium foil around the bath to get the heating going. D!

Anhydrous Solvents Part 3: Acetone and Molecular Sieves - Bad idea!

I have discussed anhydrous solvents a couple of times and have been advertising the use of molecular sieves (MS) quite strongly. During my MS crusade I have pointed out that MS are no good for drying THF but that pretty much all other standard solvents work well with sieves. As it turns out this is incorrect and I have received a terrible punishment from the MS God. It's all rather embarrassing as a PhD student in the lab was fully aware of the particular problem I'm getting to shortly. The deal with MS is that they are weakly basic. I take advantage of this by always adding some MS to my CDCl3 which keeps it dry and mops up any HCl formed by the slow decomposition of CDCl3. The other day I was running some of 1H NMR and to my great pleasure I had finally (after months of struggling) made a very important target molecule. I had split the fractions from a column up in three batches to be on the safe side. All three 1H NMR spectra were great so I decided to combine them in one flask. I was running NMR in acetone-d6 and decided to use some acetone for the transfer. I couldn't find the HPLC acetone we normally have standing around and was getting a bit frustrated when I remembered that about a year ago I had made a bottle of acetone over MS (This is were all the alarm bells go of with the experienced chemist). I managed to find the bottle and proceeded to transfer all my stuff into a new flask. However to my utter surprise I was unable to remove the solvent on the rotary evaporator. On the high vacuum pump with a fair bit of heating most of it came off but by TLC there was a new UV acitve (and quite polar) compound. I had to re-column my product but it still wasn't pure! Currently I am attempting to crystallise it from the impurities. A fair bit of yelling and acussing people of sabotage took place. Fortunately it was late and there was only one other person in the lab.

Before I proceeded to clean up my compound I decided to figure out what the source of the problem was and I quickly discovered that the acetone smelt funny. Initially, I thought it was contaminated with benzaldehyde but when more dilute it had a floral/perfume scent that reminded me of ketones/esters. At some point the PhD student in the lab realised that I had been adding MS to acetone and mentioned that as far as he knew that was a no go because it goes Aldol in the presence of the weakly basic MS. I cannot believe that this hadn't occurred to me. As it turns out it is well known that ketones go Aldol when exposed to MS and many different compounds are formed. A selection of possible products from acetone are shown in the Scheme above. The polar compound I removed by chromatography is the acetone trimer with one hydroxy group.
In my defence I'll say that acetone can be dried with MS provided you use the acetone within a few days. I successfully used the anhydrous acetone during a week of experiments back in July 2009. The take home message is to bin it after a week and not use it a year later as I did. In fact just don't add MS to acetone but instead dry it with MgSO4 as described here. D!

Catalytic Hydrogenation Part III - More Tips and Tricks

I do apologies for the very infrequent posting. I seem to have developed a life with other areas of interest than chemistry. However, due to the many old posts that people find useful the blog gets around 150 unique visitors every day (Including Nobel Laureates!!! Can you guess who?) so I'll keep Curly Arrow running at a gentle simmer.

---
Returning to catalytic hydrogenation, as promised:
Mechanistic considerations: What is the mechanism for catalytic hydrogenation. I am really not up to date on what people have figured out but about 15 years ago no one was really sure. There is good evidence that the reaction proceeds by a stepwise radical mechanism. So if you are reducing a double bond you add a H-dot and end up with an adjacent radical. This can be helpful since the dot could be ending up at a carbon where it is "stabilised". As a result you may have rotation around bonds before the next H-dot makes an appearance. Also you could end up with selectivity issues that are worth considering. For example, when I try to peel a benzyl group of an alcohol will it come off as toluene (good) or benzyl alcohol (bad)?
I recently, suppressed an unwanted side reaction by selecting hydrogenation condition that would suppress formation of an unwanted radical and promote the debenzylation of an alcohol that I was interested in so these things are (of course) worth thinking about.
---
How do I work a catalytic hydrogenation up?
Activated charcoal sticks to all surfaces. Your stir bar is a mess, the flask is a mess etc. To minimise the problem tip some Celite into the reaction and leave it to stir. This rather effectively mops up almost all the catalyst. Meanwhile pack a sintered funnel with a firm pad of Celite. Put a filter paper on top and suck some solvent through to check that it is packed properly. You do not want catalyst in your sinter! It will go black and nasty and stay that way. Pour the reaction mixture on top of the celite pad and suck the solvent through the Celite. Wash a couple of times with a polar solvent (and ideally hot). Compounds tend to stick to the catalyst so this is an attempt at getting it all off.
Concentrate your solvent in vacuo and check how much you have before binning the catalyst. I have done fairly large scale reductions and ended up with nothing after filtering because my product wouldn't let go of the catalyst. In one case I had to reflux the catalyst in DMF and filter the boiling solution to get my compound.
Finally, when you do have your product don't just throw the catalyst waste in the bin. The stuff tends to get really hot and catch fire. In the perfect lab you have a plastic bin only for your used hydrogenation catalyst where you keep all the waste nicely soaked in water to prevent it going off.
---
A note on Celite. As some of you may have noticed Celite comes in many, many different varieties. Catalytic hydrogenation is potentially an extremely clean process. I have used this as the very last step in the synthesis of unnatural amino acids and after filtration the product really is completely pure as it is. This is handy since it is incredibly polar at this stage and I really don't enjoy preparative RP HPLC. However, be careful with Celite. Make sure you get some good quality stuff that doesn't partly dissolve in organic solvents. I used some stuff in Australia that was slightly soluble in methanol. Moreover, I recently discovered that Aldrich Celite 545 is weakly basic and will dissolve in acetic acid giving you a ridiculous crude yield after filtering and concentrating. A student of mine even managed to isolate a metal salt of her carboxylic acid product because she concentrated it on Celite 545 prior to running a column. So check the specs for your Celite before you tip it into your valuable product.
---
Catalysts - what is available and what should I use? Books have been written about this so I regret promising to comment on the topic. However, it is worth remembering that a huge variety of catalysts are available that may save the day. Poisoned catalyst are worthy of mention. For example, you can get sulfided Pd-black. This stuff is sometimes useful when working with sulfur containing compounds that poison the regular of the shelf catalysts. Also there is classic stuff such as Lindlar's catalyst. Lindlar's catalyst is Pd poisoned with lead, for example, allowing the reduction of alkynes to cis-alkenes.
---
Deuterium! Finally, I should remind you that you can get deuterium (and tritium) gas. Deuterium of high purity is reasonably affordable giving you a simple way to isotope label compounds often using exactly the same reaction conditions as employed for hydrogenation. However, where possible I would recommend using aprotic solvents. We have observed some hydrogen-scrambling when performing deuteration in methanol and ethanol. D!

Catalytic Hydrogenation Part II - Tips and Tricks

Well since I appear to be suffering from insomnia I may as well blog a bit. It's about time anyway.
All synthetic organic chemists will eventually be facing a catalytic hydrogenation. Catalytic hydrogenations are great because they are easy to perform, generally work well and it allows you to do a fair bit of rather useful chemistry. But remember not to set them on fire.
I have helped many chemists trouble shoot their hydrogenations so a post on the subject seems appropriate. I am by all means not an expert on this stuff but here are some things you may find useful.
---
Which and how much catalyst should I use, what solvent is good?
For your basic reduction, e.g. debenzylation or reducing an olefin Pd on activated charcoal should be your first stop. Polar solvents such as methanol and ethanol are good. Even water is fine if your compound dissolves. But in reality anything that doesn't kill off your catalyst will work. I can recall using MeOH, EtOH, EtOAc, acetone, THF, DMF, AcOH. Sometimes I've even used mixtures for solubility reasons. I generally aim for a 10% (w/w) catalyst loading to start with.
Remember to have a large solvent surface area in your flask and stir it vigorously to allow the H2-atmosphere to get in there.
---
What do I do when the standard condition don't work?
This is the tricky bit. There can be many reasons why it isn't going.

• Your catalyst could be old and inactive. Try a fresh pot.
• If your are trying to remove a protection group such as benzyl or Cbz from an alcohol or an amine try using acetic acid as the solvent. Protonating the heteroatom facilitates the reaction.
• Try using Pearlmann's catalyst Pd(OH)2 on activated charcoal which in my experience is a more active catalyst.
• Try heating the reaction.
• Try combinations of the above. E.g. heat the sucker using Pearlmann's catalyst in acetic acid.
• Your product or an impurity in your product may be poisoning the catalyst. This could mean that it just isn't going to work unless you remove the impurities that are giving you trouble or alternatively use a hydrogenator that allows high pressure and temperature. The classic piece of kit for this is the Parr shaker (see picture above) which looks like a steam train and makes the entire floor vibrate. Alternatively a more modern alternative such as a Parr series 5500 model could be used.
  

However, sometimes regardless of what you do the stuff just cannot be reduced. I personally tried this once and believe me I tried a lot of conditions. I could just about break any bond in my molecule except the one I wanted to get rid off. In the end I had to start over introducing a different protection group. The problem in this case was probably the positioning of a sulfur atom right next to the benzyl group I was trying to remove. In the final paper weeks of debenzylation attempts were summed up in one sentence, depressing. Some of the stuff I tried can be seen in the scheme. Four slightly different starting materials were tested. The most exciting result was decomposition.
In the next post we'll have a look at how to work the reaction up and have a quick glance at different catalyst systems and touch upon the mechanism. D

Lithium Aluminium Hydride Reductions - Rochelle's Salt

Haha I'm still (barely) alive. Thanks for sticking around. Been busier than usual sorting my private and professional life out. Wrote a ton of grant proposals, published some papers (here, here, here and here), writing a book chapter, trying to be productive in the lab (fat chance) as well as having a life after work and some time off. So Curly Arrow got down prioritised for a while. Hopefully that is changing now.

---

Last week I did a lithium aluminium hydride reduction on large scale (see picture). This reminded me of the first time I had to work a reaction of this type up. My first experience (sometime last century) was a DIBAL reduction and if you haven't tried this stuff yet I can tell you that all these aluminium hydride reagents end up forming massive aluminium emulsions that are impossible to work with. The first time round I ended up making an utter mess and getting a very low yield. Realising that I couldn't possibly be the first chemist to encounter this problem I looked into things. The trick is obviously to break the emulsion up. There is a number of ways to do this. My favourite method is to use a saturated aqueous solution of Rochelle's salt (sodium potassium tartrate). Rochelle's salt is an excellent ligand for aluminium and breaks the aluminium emulsion. The procedure is simple. Cool your finished reduction down to 0 degrees C, or lower depending on the situation (For my large scale reduction I cooled it with acetone/dry ice) and quench excess reducing agent with something non-protic. For example ethyl acetate or acetone works well. Just remember to use something you can easily evaporate off when things are done. Don't be impatient and add it dropwise with vigorous stirring. Use a addition funnel for larger scale reactions. When the quench is complete remove the cooling bath.

I find it convenient to have a saturated aqueous solution of Rochelle's salt standing around. Please note that Rochelle's salt has a ridiculously high solubility in water so when preparing the aqueous solution go easy on the water and pick a small flask. When my reaction is quenched and everything looks like jelly I add some Rochelle's salt solution. Often I'll add it as a half saturated (or even more dilute) solution (a larger aqueous layer sometimes makes separation of the phases at the end easier). After pouring Rochelle's into your flask get the mixture stirring vigorously, have a cup of coffee and check your email. The better stirring and the more Rochelle's you use the faster it'll break up the emulsion. Ultimately you end up with two nice and clear phases that are simple to separate in a separatory funnel. 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!

Whatman Phase Separators

I hope everyone had a merry Christmas and I wish you all a happy and prosperous New Year. Time for the first post of 2009.
-
A former colleague of mine introduced me to the ingenious invention: Phase Separators. This is a big help in the lab and really saves me a lot of time, particularly with qualitative work. A Phase Separator is essentially a piece of filter paper that has been treated with silicone. If you fold it up and stick it in a funnel and pour a mix of organic solvent and water on it it will only let the organic solvent pour through. It only works well with solvents more dense than water, typically dichloromethane or chloroform. They are best employed for qualitative work where all that's required is a quick NMR to determine a ratio between isomers, whether a reaction is finished etc. For this type of work I basically transfer my reaction to a separation funnel with dichloromethane and wash it with appropriate aqueous phases. After the final wash the whole thing is poured directly into a Phase Separator, the organic phase is collected in a round bottom flask and concentrated in vacuo. I never observe any residual water in my NMR spectra so drying the organic solvent is unnecessary. D!

Vacuum Control - updated!

It took 88 cardboard boxes and 1.5 km of packing tape to get my belongings packed up and on its way in a container destined for Denmark. Hopefully, I'll see it all at the other end in 2 months time. So with that stage of the move over and done I believe it's time for a post.

Rotary evaporators are great and we use them all the time but solvents have a bad tendency to bump and splash resulting in a mess. One way to partly control the mess is the use of a splash guard but it is still a pain. Chemists in industry generally don't have these bumping issues because they can afford a vacuum controller. These are great little gadgets where you punch the vacuum you would like to achieve in and hit go. On the more fancy systems even this is unnecessary as a clever little vapour pressure sensing device regulates the pressure ensuring the perfect distillation. However, these things are expensive and high maintenance so universities don't normally have them. Recently, a good friend that works at one of Australia's top institutions introduced me to a simple piece of glassware that essentially replaces the fancy vacuum controller at a very low cost (see picture left). The principle is very simple. The tap has two setting one allows passage through a wide glass tube and the other through a capillary tube. When you start the rotary evaporator you have the wide tube open and when the distillation starts you switch to the capillary tube. The capillary tube basically ensures that the current vacuum is maintained and stops it from going further down. Too easy! In addition the solvent recovery is dramatically improve saving the planet and importantly also your pump. All specifications for the gadget can be found in this paper:
Prevent the Loss of Volatile Solvents in Rotary Evaporators with a Simple Device, Daan van Leusen, Journal of Chemical Education, 1994, 71 (1), pp. 54-55. D!
One of the regular readers just emailed me a picture with a similar set-up to mine that does the same trick (See comments and picture right). The main difference is that this alternative set-up doesn't allow you to turn the vacuum off by turning the tap. Were I work we have a house vacuum system that requires a lot of tap turning so the set-up above is nice as this simplifies turning the vacuum off. However, if you are using a diaphragm pump this alternative is perfect and presumably also significantly cheaper to produce. D!

The Invisible Phase Boundary

All organic chemists have experienced it. Your reaction is done and your transfer it to a separatory funnel with an aqueous and an organic phase. You do your shaky, shaky bit and the phases separate but it is impossible to tell where the phase boundary is. The problem is most commonly encountered when very dark phases are obtained but it can also occur with perfectly clear phases (see picture). The solution to this problem is very simple. Simply tip a clean NMR tube cap into the separatory funnel and observe as it settles on top of the bottom phase. Problem solved. 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!

Recycling Silica Gel

Insert usual excuse for infrequent posting here: .....

-

I recently received the following email regarding recycling of silica gel:

-

"In the past we used to regenerate SiGel with fuming nitric acid, much as you do here (refers to previous post - D!) .Place the coloured, used SiGel (which of course must be uncoated and completely dry) in a large beaker. Approximately a third full. Place it inthe fume cupboard and pour in the nitric acid so the SiGel is completely moistened. If necessary, stir it. After a possible initial fuming has stopped, heat it on a steam bath for 10 minutes - leave it overnight. Next day, fill up with water, stir and let it settle. Wash 3 more times. At this point, it should be colourless, if not, repeat with more nitric acid. Then wash with satd. sodium bicarbonate until neutral and filter on a Buchner funnel. Wash with water, methanol and acetone and let it suck completely dry. Finally, activate by heating it in an oven overnight at 100-120 C.This way, it is as good as new for most purposes."

-

This may be of use to some chemists working at institutions where money is very scarce. However, considering the amount of time and large volumes of solvent required to do this I think it can be classified as historically interesting but not practically useful to most of us.

-

Nevertheless thank you for the email. I have wondered exactly how you would go about recycling your silica gel.

-

Speaking of silica gel and techniques that are disappearing from the chemists hood check one of the most recent posts at In the Pipeline out. Derek seems to think that TLCs are on their way out as LC-MS is becoming more and more common. I believe that it will take several decades before Derek's predictions come true (especially in academia) but he does have some very good points. D!

How to clean your sintered funnel

Lately when I have been cleaning my sintered funnels people have stopped and asked me what I was doing. To my surprise many chemists don't seem to know how to take a nasty, dirty sintered funnel and making it nice, white and shining again in about 15 minutes.
These days I'm doing lots of old school chemistry that involves heating the crap out of the components using for example conc. sulfuric acid as the solvent. Needless to say things are polymerising and decomposing left, right and centre and when you filter it through your nice white sinter it ends up looking nasty (see picture above). The stuff doesn't go anywhere with acetone, water, 2M sodium hydroxide or hydrochloric acid etc. so what should you do? Before I proceed please note that if you attempt any of the following you must:

(1) Wear a closed lab coat, safety glasses and plastic gloves

(2) Conduct the cleaning in a fume hood with the sash down at all times
(3) Ensure that all the glassware is clean and doesn't contain residual organic material such as acetone
-
Please take the above advice seriously. People have had nasty accidents doing the following because they weren't careful.
-
There are two common ways to get your sinter clean:
(1) Conc. nitric acid, or
(2) Conc. sulfuric acid and hydrogen peroxide
-
Nitric acid is the easy solution and more often than not it does the trick. However, occasionally it is necessary to use more vigorous conditions. I have never had a sinter that didn't become white after treatment with conc. sulfuric acid and hydrogen peroxide and this is generally the method that I use because I know it works every time.
-
Procedure:
(1) Fit the funnel to a Büchner flask attached to a vacuum that you can control easily
(2) Add a small amount of conc. sulfuric acid so that it covers the surface of the sinter
(3) Add a dash of hydrogen peroxide and stand back. Things get pretty hot, bubbly and exciting at this point (See picture above).

-
(4) When the ingredients have been cooking away for a minute or so apply a very gentle vacuum briefly. This should be sufficient to suck the sinter dry (See picture above),
(5) Allow the cocktail to settle down and cool off and clean all the equipment with lots of water taking care not to pour the contents all over yourself. Your sinter will now look like this.
-

Too easy but please do be careful guys. D!

Let's talk about TLCs Part 2 - Hanessian's Stain

Don't you just love that feeling when you are checking your reaction mixture by TLC and no matter which stain you use nothing appears on the plate. If your compound also isn't UV active you've got a real problem. Well the good news is that there is one stain that will do the job for you - Hanessian's Stain! Hanessian's stain is an excellent multi-purpose stain that when used the right way usually gives blue spots (TLC plate A). Since it is a water based stain it requires vigorous heating for development. However, if you overdo it the entire plate goes dark blue (TLC plate B).

Hanessian's Stain Recipe 1

100 ml container
90 ml Water
5 g Ammonium molybdate, (NH4)6Mo7O24-4H20
1 g Cerium sulfate, Ce(SO4)2
10 ml Concentrated sulfuric acid

-

Hanessian's Stain Recipe 2

100 ml container

90 ml Water

2.5 g Ammonium molybdate, (NH4)6Mo7O24-4H20

1 g Cerium ammonium sulfate, Ce(NH4)4(SO4)4-2H2O

10 ml Concentrated sulfuric acid

-

Dissolve ammonium molybdate and cerium sulfate in water (with heating if required) followed by careful addition of concentrated sulfuric acid. Sometimes an insoluble residue is observed. If that happens remove it by filtration. Cerium sulfate can be replaced with Cerium ammonium sulfate which is significantly cheaper (Recipe 2). Hanessian's stain is used just as previously described for the Vanillin Stain although it requires more vigorous heating. Because rather harsh heating is required this stain may prove inefficient with volatile compounds. Also keep in mind that this a very sensitive stain so even trace impurities can appear as significant spots on your TLC plate. D!

Anhydrous solvents

Most organic chemists need dry solvents from time to time and almost every single day you bump into someone who's looking for dry DMF, ether, acetonitrile, THF etc. When I was working in Cambridge this was never a problem. They simply have a still for every single solvent you could imagine. Above there's a picture from the still room in Cambridge. Pretty nice innit? A massive fire hazard but quite handy as long as it doesn't blow up. Now I've moved on and where I work now we've just been inspected by OH&S (Occupational Health & Safety) and they don't like stills because of the fire hazard etc. and I have to say I completely agree with them. Nice as they may be they are dangerous and more or less completely redundant. The solvents you can buy nowadays are of super high quality and do not require distilling so it's basically only distilled in an effort to dry it. Now I will concede that there are stabilisers in many solvents, in particular ethers, but it is very rarely something that will affect your chemistry. So what should you do? The perfect setup that will provide guaranteed anhydrous solvents every day consists of good quality super activated molecular sieves (MS) and a Karl Fischer (KF) apparatus. MS are expensive but you can reduce the cost significantly by buying bulk quantities. We used to get ours from Grace Davison in big drums and they were very very good. The Karl Fischer apparatus (see picture below) can be purchased from Metrohm. All you have to do when you have this set up is add some 3 or 4 Å MS (depending on the solvent) to your solvent close the flask tightly and when you come back the next day take a small quantity out with a syringe and needle and squirt it into you KF apparatus. The display will now show you how many ppm's of water there was in the volume you just added. Everyone doing anhydrous chemistry should have this set up. It's safe, you are always confident about whether your solvent is dry or not and it requires close to no maintenance. Unfortunately, molecular sieves will not dry everybody's favourite solvent THF so you have to hold on to one still. Also you cannot add anything with acidic protons to a KF apparatus successfully. It will think it's all water. So for example acetone or methanol wouldn't work. Regarding MS I believe that you should never attempt to dry them yourself and never recycle them unless they are going into exactly the same solvent (just bin them when they are dead). Many chemists think they are saving money when they reactivate MS. However, I seriously doubt that is the case with the amount of energy not to mention time required to do so. So in other words buy good ones and bin them when they stop working. If you aren't sure whether the MS you've got are any good put a couple in the palm of your hand and add one drop of water. If they get really really hot they a very good and if they only warm up a little bit they are rubbish. If you are in a situation where you can't get good MS I guess you will have to dry them. Apparently one way of doing this is to throw them in a microwave and nuke them on max power until they start glowing. At this point you have to stop immediately unless you want the entire microwave to melt and transfer the MS to a desiccator that you stick on a high vacuum pump (I haven't tried this myself so no guarantees). If you don't feel like burning your department to the ground there is always the good old vacuum oven that most departments have. Just heat them under vacuum for a couple of days and then stick them in a desiccator attached to a high vacuum line. Drying solvents overnight using good 4 Å MS should get acetonitrile, DMF, DMSO, dichloromethane, toluene, ether, 1,2-dichloroethane, chloroform and hexane down to a water content of 10 ppm or less. If you check your freshly distilled THF on the KF it should be around 15 ppm. So for successful living convince your boss or department to get one of these babies and shut down all those damn stills for good. D!

Let's talk about TLCs Part 1 - Vanillin Stain

I've lost count of the number of times I've searched the web for TLC stain information long ago. I have a feeling that this is a reoccurring issue for many synthetic organic chemists so we've decided to start a "Let's talk about TLCs"-series on Curly Arrow. With time this site will hopefully be the only place you'll ever have to visit for information on TLC stains and related stuff. Not only will we present the recipe for any particular stain but there will also be some comments regarding what it's good for detecting and some pretty pictures so you can see what it looks like after the stain treatment. Let's start the series with a classic: The Vanillin Stain. This is my favourite all purpose stain and after a quick look under the UV lamp this is my next stop. It virtually always works well to give spots in a wide variety of colours which can be handy for spotting what your after when you have multiple spots.

Vanillin Stain Recipe:
100 ml container
6 g Vanillin

1.5 ml Conc. sulfuric acid
95 ml 96% Ethanol

Add the vanillin to your container followed by ethanol to give a clear solution. Carefully add the sulfuric acid. The final product is a clear colourless solution. However, after some dipping of plates it will quickly become a clear yellow solution (see picture above).

How to use the vanillin stain: Run your TLC and let it dry. If you want to check for UV activity you should do so now and not later. Dip the TLC plate in your vanillin stain and heat it using a heat gun (gently at first so that you don't spray the stuff all over your hood) until coloured spots appear. Remember to put the lid back on tightly otherwise it'll dry out.

To the left there's a picture of a TLC plate that I developed today using the vanillin stain.

Alternatively, you can use an atomiser and spray the TLC plate with the stain. This prevents the stain from turning yellow and makes it last a lot longer since you are using much less per treatment. D!